From mikael.k.eriksson at philips.com Mon Sep 1 02:11:54 2014 From: mikael.k.eriksson at philips.com (Eriksson, Mikael) Date: Mon, 1 Sep 2014 06:11:54 +0000 Subject: [ITK] Registration of multislice images Message-ID: <2D9DC0609429E24BA87612C012C580C318A75ED3@AMSPRD9002MB028.MGDPHG.emi.philips.com> Hello, I have obtained multislice image data for trying to do real-time registration for motion correction purposes. Specifically, every 0.x seconds, one coronal, one sagittal and one axial slice is obtained during the imaging, and I would like to register pairs of such sets with each other, e.g. each set after the first set at time zero should be registered to this time zero set. The slices cover the entire body in the axial plane, and the upper body from the hips to the neck in the sagittal and coronal planes with a size of 336 x 336 and pixel spacing of 1.19 x 1.19. I have searched for possible implementations in ITK and haven't found anything. An interesting article on the subject which describes what I want to do can be found here: http://www.researchgate.net/publication/221623301_Intersection_based_registration_of_slice_stacks_to_form_3D_images_of_the_human_fetal_brain Essentially, what they did was to optimize the (rigid) transform the slices in the moving set until their intensity profiles along the intersections with orthogonal slices match the intensity profiles at the corresponding intersections in the fixed set, within a certain tolerance. Now, this is one way that I would be more than happy to try out on my data, but likewise, if there are other methods already implemented in ITK I'll try them out as well. If there isn't anything already implemented, could someone please give me some hints as for how to write a program which does something along the lines of what I described above (and is described in more detail in the link)? Oh, and just knowing whether anything like this already exists and can be used in ITK will be a huge help, since it would allow me to plan my work. Best regards, Mikael ....................................................................................................... Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies mikael.k.eriksson at philips.com ....................................................................................................... ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuetian926 at 163.com Mon Sep 1 02:32:05 2014 From: yuetian926 at 163.com (Yuetian Liu) Date: Mon, 1 Sep 2014 14:32:05 +0800 (CST) Subject: [ITK] [ITK-users] How to fusion the MR volume to the CT volume Message-ID: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> Hi itkusers, Recently I want to fuse the MR volume to the CT volume, but I search the itk mailist. I haven;t known how to realise it. And there isn't example in the InsightSoftwareGuide-4.5.0.pdf and InsightSphinxExamplesPDF-4.5.0.pdf. So I want to ask how to fuse the MR volume to the CT volume by itk. Thank you for helping me! Best Yuetian -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michael.meuli at gmail.com Mon Sep 1 09:38:40 2014 From: michael.meuli at gmail.com (Michael Meuli) Date: Mon, 1 Sep 2014 15:38:40 +0200 Subject: [ITK] Distances of objects in LabelMap Message-ID: I have objects in a LabelMap (having used BinaryImageToLabelMapFilter). How do I best get the distance to the closest neighbouring object for each of these objects? (As I would like to exclude objects if they are too close to each other.) Best regards and many thanks Michael From indianzeppelin at gmail.com Mon Sep 1 09:59:13 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Mon, 1 Sep 2014 14:59:13 +0100 Subject: [ITK] Distances of objects in LabelMap In-Reply-To: References: Message-ID: Did you look into LabelGeometryImageFilter? You could get the centroids of the objects using that, and then use some nearest-neighbor searching algorithm for each centroid. On Mon, Sep 1, 2014 at 2:38 PM, Michael Meuli wrote: > I have objects in a LabelMap (having used BinaryImageToLabelMapFilter). > How do I best get the distance to the closest neighbouring object for > each of these objects? > (As I would like to exclude objects if they are too close to each other.) > > Best regards and many thanks > Michael > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From lasso at queensu.ca Mon Sep 1 10:40:38 2014 From: lasso at queensu.ca (Andras Lasso) Date: Mon, 1 Sep 2014 14:40:38 +0000 Subject: [ITK] Registration of multislice images In-Reply-To: <2D9DC0609429E24BA87612C012C580C318A75ED3@AMSPRD9002MB028.MGDPHG.emi.philips.com> References: <2D9DC0609429E24BA87612C012C580C318A75ED3@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: Hi Mikael, You can copy the voxels from each slice into a volume and use that as fixed image, use a mask that has non-zero values only at valid pixels (usually you can use the constructed image itself as a mask), then do a usual volumetric registration. This works quite well, if you have orthogonal images and their resolution is similar (see for example http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5975205). You can use ITK as is, no modifications are needed. Alternatively, you can modify a similarity metric to accept multiple images and compute the metric value as sum of the metric value of each image (this is necessary when the image slices are not orthogonal). An IJCARS paper is in press, a high-level overview is given in this abstract: http://perk.cs.queensu.ca/contents/target-localization-mriguided-transperineal-prostate-biopsy-using-multislicetovolume-regist . Andras From: Eriksson, Mikael Sent: ?Monday?, ?September? ?1?, ?2014 ?1?:?26? ?AM To: community at itk.org Hello, I have obtained multislice image data for trying to do real-time registration for motion correction purposes. Specifically, every 0.x seconds, one coronal, one sagittal and one axial slice is obtained during the imaging, and I would like to register pairs of such sets with each other, e.g. each set after the first set at time zero should be registered to this time zero set. The slices cover the entire body in the axial plane, and the upper body from the hips to the neck in the sagittal and coronal planes with a size of 336 x 336 and pixel spacing of 1.19 x 1.19. I have searched for possible implementations in ITK and haven?t found anything. An interesting article on the subject which describes what I want to do can be found here: http://www.researchgate.net/publication/221623301_Intersection_based_registration_of_slice_stacks_to_form_3D_images_of_the_human_fetal_brain Essentially, what they did was to optimize the (rigid) transform the slices in the moving set until their intensity profiles along the intersections with orthogonal slices match the intensity profiles at the corresponding intersections in the fixed set, within a certain tolerance. Now, this is one way that I would be more than happy to try out on my data, but likewise, if there are other methods already implemented in ITK I?ll try them out as well. If there isn?t anything already implemented, could someone please give me some hints as for how to write a program which does something along the lines of what I described above (and is described in more detail in the link)? Oh, and just knowing whether anything like this already exists and can be used in ITK will be a huge help, since it would allow me to plan my work. Best regards, Mikael ??????????????????????????????????. Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies mikael.k.eriksson at philips.com ??????????????????????????????????. ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 1 15:09:38 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Sep 2014 15:09:38 -0400 Subject: [ITK] [ITK-dev] [ITK-users] How to fusion the MR volume to the CT volume In-Reply-To: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> References: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> Message-ID: Hi Yeutian, Try a registration algorithm using a mutual information based metric. See also the Slicer Registration Case Library [1], which uses ITK under the hood, for examples. HTH, Matt [1] http://www.na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory On Mon, Sep 1, 2014 at 2:32 AM, Yuetian Liu wrote: > > Hi itkusers, > > Recently I want to fuse the MR volume to the CT volume, but I search the itk > mailist. > I haven;t known how to realise it. And there isn't example in the > InsightSoftwareGuide-4.5.0.pdf > and InsightSphinxExamplesPDF-4.5.0.pdf. > So I want to ask how to fuse the MR volume to the CT volume by itk. > > Thank you for helping me! > > Best > Yuetian > > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Sep 1 15:09:38 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Sep 2014 15:09:38 -0400 Subject: [ITK] [ITK-users] How to fusion the MR volume to the CT volume In-Reply-To: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> References: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> Message-ID: Hi Yeutian, Try a registration algorithm using a mutual information based metric. See also the Slicer Registration Case Library [1], which uses ITK under the hood, for examples. HTH, Matt [1] http://www.na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory On Mon, Sep 1, 2014 at 2:32 AM, Yuetian Liu wrote: > > Hi itkusers, > > Recently I want to fuse the MR volume to the CT volume, but I search the itk > mailist. > I haven;t known how to realise it. And there isn't example in the > InsightSoftwareGuide-4.5.0.pdf > and InsightSphinxExamplesPDF-4.5.0.pdf. > So I want to ask how to fuse the MR volume to the CT volume by itk. > > Thank you for helping me! > > Best > Yuetian > > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From mikael.k.eriksson at philips.com Tue Sep 2 01:04:53 2014 From: mikael.k.eriksson at philips.com (Eriksson, Mikael) Date: Tue, 2 Sep 2014 05:04:53 +0000 Subject: [ITK] Registration of multislice images In-Reply-To: References: <2D9DC0609429E24BA87612C012C580C318A75ED3@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: <2D9DC0609429E24BA87612C012C580C318A7607F@AMSPRD9002MB028.MGDPHG.emi.philips.com> Thank you Andras, this helps a lot! Glad to see that the solutions are simple and elegant. Best regards, Mikael ??????????????????????????????????. Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies +358 40 631 8500 mikael.k.eriksson at philips.com ??????????????????????????????????. From: Andras Lasso [mailto:lasso at queensu.ca] Sent: 1. syyskuuta 2014 17:41 To: Eriksson, Mikael; community at itk.org Subject: Re: [ITK] Registration of multislice images Hi Mikael, You can copy the voxels from each slice into a volume and use that as fixed image, use a mask that has non-zero values only at valid pixels (usually you can use the constructed image itself as a mask), then do a usual volumetric registration. This works quite well, if you have orthogonal images and their resolution is similar (see for example http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5975205). You can use ITK as is, no modifications are needed. Alternatively, you can modify a similarity metric to accept multiple images and compute the metric value as sum of the metric value of each image (this is necessary when the image slices are not orthogonal). An IJCARS paper is in press, a high-level overview is given in this abstract: http://perk.cs.queensu.ca/contents/target-localization-mriguided-transperineal-prostate-biopsy-using-multislicetovolume-regist . Andras From: Eriksson, Mikael Sent: ?Monday?, ?September? ?1?, ?2014 ?1?:?26? ?AM To: community at itk.org Hello, I have obtained multislice image data for trying to do real-time registration for motion correction purposes. Specifically, every 0.x seconds, one coronal, one sagittal and one axial slice is obtained during the imaging, and I would like to register pairs of such sets with each other, e.g. each set after the first set at time zero should be registered to this time zero set. The slices cover the entire body in the axial plane, and the upper body from the hips to the neck in the sagittal and coronal planes with a size of 336 x 336 and pixel spacing of 1.19 x 1.19. I have searched for possible implementations in ITK and haven?t found anything. An interesting article on the subject which describes what I want to do can be found here: http://www.researchgate.net/publication/221623301_Intersection_based_registration_of_slice_stacks_to_form_3D_images_of_the_human_fetal_brain Essentially, what they did was to optimize the (rigid) transform the slices in the moving set until their intensity profiles along the intersections with orthogonal slices match the intensity profiles at the corresponding intersections in the fixed set, within a certain tolerance. Now, this is one way that I would be more than happy to try out on my data, but likewise, if there are other methods already implemented in ITK I?ll try them out as well. If there isn?t anything already implemented, could someone please give me some hints as for how to write a program which does something along the lines of what I described above (and is described in more detail in the link)? Oh, and just knowing whether anything like this already exists and can be used in ITK will be a huge help, since it would allow me to plan my work. Best regards, Mikael ??????????????????????????????????. Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies mikael.k.eriksson at philips.com ??????????????????????????????????. ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Sep 2 09:18:47 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Sep 2014 09:18:47 -0400 Subject: [ITK] [ITK-dev] issues.itk.org maintenance In-Reply-To: References: Message-ID: Thanks again for running the server! Brad On Aug 28, 2014, at 2:37 PM, Johnson, Hans J wrote: > The ITK bug tracker will be down for approximately 30 minutes at 4:30CST today for routine maintenance. > > Hans > > > > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 2 11:52:03 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 2 Sep 2014 11:52:03 -0400 Subject: [ITK] [ITK-users] ResampleDICOM example and DCMTK In-Reply-To: References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com> Message-ID: Hi Nick, The DCMTKImageIO class does not yet populate and extract tag information to / from the an Image's MetaDataDictionary. This will have to be implemented for this to work. HTH, Matt On Sun, Aug 31, 2014 at 5:38 PM, Matt McCormick wrote: > Hi Nick, > > Nothing stands out from inspecting the code. Could you please send an > example dataset? > > Thanks, > Matt > > On Sun, Aug 31, 2014 at 4:06 PM, NPatterson wrote: >> Hi, I wondered if anyone could test the code attached in the thread header >> "ResampleDICOM example and DCMTK" regarding the use of DCMTK for DICOM >> reading writing in ITK. I adapted the ResampleDICOM example to work with >> DCMTK instead of GDCM, and although I get no errors, I also do not get any >> output dicom images. If someone has the time to test this code to see if >> they observe the same behaviour/or can suggest a fix, I would be very >> appreciative. >> >> Regards, Nick. >> >> >> >> -- >> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-ResampleDICOM-example-and-DCMTK-tp7586131p7586158.html >> Sent from the ITK Insight Users mailing list archive at Nabble.com. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From tejasl2603 at gmail.com Tue Sep 2 16:07:25 2014 From: tejasl2603 at gmail.com (tejas lunawat) Date: Wed, 3 Sep 2014 01:37:25 +0530 Subject: [ITK] Error while building ITK Message-ID: Hey... I am an engineering student, working on a project, based on ITK libraries. I am new to ITK. I have encounter an error while building 'itkhdf5.sln' file. Details of the error are as follows: Error 1 error MSB6006: "cmd.exe" exited with code 216. Error 2 error LNK1104: cannot open file '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' I have searched for the solution of this error, but I didn't found it. Is their any possible way to solve this error Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Sep 2 16:30:17 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 2 Sep 2014 20:30:17 +0000 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: You are building a Debug program. Check that you have Debug ITK libraries installed. If not change the build selection in Visual Studio to Release. ________________________________ From: Community [community-bounces at itk.org] on behalf of tejas lunawat [tejasl2603 at gmail.com] Sent: Wednesday, 3 September 2014 8:07 a.m. To: community at itk.org Subject: [ITK] Error while building ITK Hey... I am an engineering student, working on a project, based on ITK libraries. I am new to ITK. I have encounter an error while building 'itkhdf5.sln' file. Details of the error are as follows: Error 1 error MSB6006: "cmd.exe" exited with code 216. Error 2 error LNK1104: cannot open file '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' I have searched for the solution of this error, but I didn't found it. Is their any possible way to solve this error Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: From tejasl2603 at gmail.com Wed Sep 3 01:59:39 2014 From: tejasl2603 at gmail.com (tejas lunawat) Date: Wed, 3 Sep 2014 11:29:39 +0530 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: ?? Even after changing the build selection in Visual Studio to Release, same error still persisits. On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle wrote: > You are building a Debug program. Check that you have Debug ITK > libraries installed. If not change the build selection in Visual Studio to > Release. > ------------------------------ > *From:* Community [community-bounces at itk.org] on behalf of tejas lunawat [ > tejasl2603 at gmail.com] > *Sent:* Wednesday, 3 September 2014 8:07 a.m. > *To:* community at itk.org > *Subject:* [ITK] Error while building ITK > > Hey... > > I am an engineering student, working on a project, based on ITK libraries. > I am new to ITK. I have encounter an error while building 'itkhdf5.sln' > file. Details of the error are as follows: > > Error 1 error MSB6006: "cmd.exe" exited with code 216. > Error 2 error LNK1104: cannot open file > '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' > > I have searched for the solution of this error, but I didn't found it. > Is their any possible way to solve this error Thank you > -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 3 02:36:55 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 3 Sep 2014 06:36:55 +0000 Subject: [ITK] Error while building ITK In-Reply-To: References: , Message-ID: Are you using a CMakeLists.txt file and cmake to create your project files? ________________________________ From: tejas lunawat [tejasl2603 at gmail.com] Sent: Wednesday, 3 September 2014 5:59 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] Error while building ITK ?? Even after changing the build selection in Visual Studio to Release, same error still persisits. On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle > wrote: You are building a Debug program. Check that you have Debug ITK libraries installed. If not change the build selection in Visual Studio to Release. ________________________________ From: Community [community-bounces at itk.org] on behalf of tejas lunawat [tejasl2603 at gmail.com] Sent: Wednesday, 3 September 2014 8:07 a.m. To: community at itk.org Subject: [ITK] Error while building ITK Hey... I am an engineering student, working on a project, based on ITK libraries. I am new to ITK. I have encounter an error while building 'itkhdf5.sln' file. Details of the error are as follows: Error 1 error MSB6006: "cmd.exe" exited with code 216. Error 2 error LNK1104: cannot open file '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' I have searched for the solution of this error, but I didn't found it. Is their any possible way to solve this error Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Wed Sep 3 05:16:48 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Wed, 3 Sep 2014 10:16:48 +0100 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: 1) From your question, I understand that you are having a problem building the ITK library itself and not a project which uses the library. Is that correct? 2) If so, I assume you have used CMake for configuring and generating the .sln files from the ITK source files on your computer. Specifically, did you follow the steps described here - http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? 3) Are you trying to build only "ITKHDF5.sln" (located at "your_ITK_build_folder\Modules\ThirdParty\HDF5)? On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle wrote: > Are you using a CMakeLists.txt file and cmake to create your project > files? > ------------------------------ > *From:* tejas lunawat [tejasl2603 at gmail.com] > *Sent:* Wednesday, 3 September 2014 5:59 p.m. > *To:* Gib Bogle > *Cc:* community at itk.org > *Subject:* Re: [ITK] Error while building ITK > > ?? > Even after changing the build selection in Visual Studio to Release, > same error still persisits. > > > On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle wrote: > >> You are building a Debug program. Check that you have Debug ITK >> libraries installed. If not change the build selection in Visual Studio to >> Release. >> ------------------------------ >> *From:* Community [community-bounces at itk.org] on behalf of tejas lunawat >> [tejasl2603 at gmail.com] >> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >> *To:* community at itk.org >> *Subject:* [ITK] Error while building ITK >> >> Hey... >> >> I am an engineering student, working on a project, based on ITK libraries. >> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >> file. Details of the error are as follows: >> >> Error 1 error MSB6006: "cmd.exe" exited with code 216. >> Error 2 error LNK1104: cannot open file >> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >> >> I have searched for the solution of this error, but I didn't found it. >> Is their any possible way to solve this error Thank you >> > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From tejasl2603 at gmail.com Wed Sep 3 06:18:28 2014 From: tejasl2603 at gmail.com (tejas lunawat) Date: Wed, 3 Sep 2014 15:48:28 +0530 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Yes, You are right. I am having a problem in building the ITK library itself. I followed all the steps described in this link http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio I have used CMake for configuring and generating the .sln files from the ITK source file. And then I am building the libraries by using itk.sln. On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < indianzeppelin at gmail.com> wrote: > 1) From your question, I understand that you are having a problem building > the ITK library itself and not a project which uses the library. Is that > correct? > > 2) If so, I assume you have used CMake for configuring and generating the > .sln files from the ITK source files on your computer. Specifically, did > you follow the steps described here - > http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? > > 3) Are you trying to build only "ITKHDF5.sln" (located at > "your_ITK_build_folder\Modules\ThirdParty\HDF5)? > > > On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle wrote: > >> Are you using a CMakeLists.txt file and cmake to create your project >> files? >> ------------------------------ >> *From:* tejas lunawat [tejasl2603 at gmail.com] >> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >> *To:* Gib Bogle >> *Cc:* community at itk.org >> *Subject:* Re: [ITK] Error while building ITK >> >> ?? >> Even after changing the build selection in Visual Studio to Release, >> same error still persisits. >> >> >> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle wrote: >> >>> You are building a Debug program. Check that you have Debug ITK >>> libraries installed. If not change the build selection in Visual Studio to >>> Release. >>> ------------------------------ >>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>> lunawat [tejasl2603 at gmail.com] >>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>> *To:* community at itk.org >>> *Subject:* [ITK] Error while building ITK >>> >>> Hey... >>> >>> I am an engineering student, working on a project, based on ITK libraries. >>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>> file. Details of the error are as follows: >>> >>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>> Error 2 error LNK1104: cannot open file >>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>> >>> I have searched for the solution of this error, but I didn't found it. >>> Is their any possible way to solve this error Thank you >>> >> >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Wed Sep 3 06:23:16 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Wed, 3 Sep 2014 11:23:16 +0100 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Ok. So, when you build "ITK.sln", do all the projects in it build fine with only "itkhdf5" failing? On Wed, Sep 3, 2014 at 11:18 AM, tejas lunawat wrote: > Yes, You are right. > I am having a problem in building the ITK library itself. > I followed all the steps described in this link > http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio > I have used CMake for configuring and generating the .sln files from the > ITK source file. > And then I am building the libraries by using itk.sln. > > > > On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < > indianzeppelin at gmail.com> wrote: > >> 1) From your question, I understand that you are having a problem >> building the ITK library itself and not a project which uses the library. >> Is that correct? >> >> 2) If so, I assume you have used CMake for configuring and generating the >> .sln files from the ITK source files on your computer. Specifically, did >> you follow the steps described here - >> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? >> >> 3) Are you trying to build only "ITKHDF5.sln" (located at >> "your_ITK_build_folder\Modules\ThirdParty\HDF5)? >> >> >> On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle wrote: >> >>> Are you using a CMakeLists.txt file and cmake to create your project >>> files? >>> ------------------------------ >>> *From:* tejas lunawat [tejasl2603 at gmail.com] >>> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >>> *To:* Gib Bogle >>> *Cc:* community at itk.org >>> *Subject:* Re: [ITK] Error while building ITK >>> >>> ?? >>> Even after changing the build selection in Visual Studio to Release, >>> same error still persisits. >>> >>> >>> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle >>> wrote: >>> >>>> You are building a Debug program. Check that you have Debug ITK >>>> libraries installed. If not change the build selection in Visual Studio to >>>> Release. >>>> ------------------------------ >>>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>>> lunawat [tejasl2603 at gmail.com] >>>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>>> *To:* community at itk.org >>>> *Subject:* [ITK] Error while building ITK >>>> >>>> Hey... >>>> >>>> I am an engineering student, working on a project, based on ITK libraries. >>>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>>> file. Details of the error are as follows: >>>> >>>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>>> Error 2 error LNK1104: cannot open file >>>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>>> >>>> I have searched for the solution of this error, but I didn't found >>>> it. Is their any possible way to solve this error Thank you >>>> >>> >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >> >> >> -- >> Regards, >> Girish >> > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Wed Sep 3 10:04:03 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Wed, 3 Sep 2014 15:04:03 +0100 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Strange. Have you tried opening and building the solution "ITKHDF5.sln" alone (located in "your_ITK_Build_folder\Modules\ThirdParty\HDF5")? If not, please try it and paste the contents of the output window (not just the error list). PS: Please keep the discussion on the mailing list (by cc'ing the community or replying to all)...:) On Wed, Sep 3, 2014 at 11:34 AM, tejas lunawat wrote: > yes, the problem is with "itkhdf5" and all others which are dependent on > it. As error are: > > Error 1 error MSB6006: "cmd.exe" exited with code 216. > Error 2 error LNK1104: cannot open file > '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' > > > On Wed, Sep 3, 2014 at 3:53 PM, Girish Mallya Udupi < > indianzeppelin at gmail.com> wrote: > >> Ok. So, when you build "ITK.sln", do all the projects in it build fine >> with only "itkhdf5" failing? >> >> >> On Wed, Sep 3, 2014 at 11:18 AM, tejas lunawat >> wrote: >> >>> Yes, You are right. >>> I am having a problem in building the ITK library itself. >>> I followed all the steps described in this link >>> >>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio >>> I have used CMake for configuring and generating the .sln files from >>> the ITK source file. >>> And then I am building the libraries by using itk.sln. >>> >>> >>> >>> On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < >>> indianzeppelin at gmail.com> wrote: >>> >>>> 1) From your question, I understand that you are having a problem >>>> building the ITK library itself and not a project which uses the library. >>>> Is that correct? >>>> >>>> 2) If so, I assume you have used CMake for configuring and generating >>>> the .sln files from the ITK source files on your computer. Specifically, >>>> did you follow the steps described here - >>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? >>>> >>>> 3) Are you trying to build only "ITKHDF5.sln" (located at >>>> "your_ITK_build_folder\Modules\ThirdParty\HDF5)? >>>> >>>> >>>> On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle >>>> wrote: >>>> >>>>> Are you using a CMakeLists.txt file and cmake to create your project >>>>> files? >>>>> ------------------------------ >>>>> *From:* tejas lunawat [tejasl2603 at gmail.com] >>>>> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >>>>> *To:* Gib Bogle >>>>> *Cc:* community at itk.org >>>>> *Subject:* Re: [ITK] Error while building ITK >>>>> >>>>> ?? >>>>> Even after changing the build selection in Visual Studio to Release, >>>>> same error still persisits. >>>>> >>>>> >>>>> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle >>>>> wrote: >>>>> >>>>>> You are building a Debug program. Check that you have Debug ITK >>>>>> libraries installed. If not change the build selection in Visual Studio to >>>>>> Release. >>>>>> ------------------------------ >>>>>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>>>>> lunawat [tejasl2603 at gmail.com] >>>>>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>>>>> *To:* community at itk.org >>>>>> *Subject:* [ITK] Error while building ITK >>>>>> >>>>>> Hey... >>>>>> >>>>>> I am an engineering student, working on a project, based on ITK libraries. >>>>>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>>>>> file. Details of the error are as follows: >>>>>> >>>>>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>>>>> Error 2 error LNK1104: cannot open file >>>>>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>>>>> >>>>>> I have searched for the solution of this error, but I didn't found >>>>>> it. Is their any possible way to solve this error Thank you >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>>>> >>>> >>>> >>>> -- >>>> Regards, >>>> Girish >>>> >>> >>> >> >> >> -- >> Regards, >> Girish >> > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From tejasl2603 at gmail.com Wed Sep 3 10:17:47 2014 From: tejasl2603 at gmail.com (tejas lunawat) Date: Wed, 3 Sep 2014 19:47:47 +0530 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Output in build selection as Debug 1>------ Build started: Project: ZERO_CHECK, Configuration: Debug x64 ------ 1>Build started 9/3/2014 7:43:45 PM. 1>InitializeBuildStatus: 1> Creating "x64\Debug\ZERO_CHECK\ZERO_CHECK.tlog\unsuccessfulbuild" because "AlwaysCreate" was specified. 1>CustomBuild: 1> Checking Build System 1> CMake does not need to re-run because E:/mtp win/ITK-build/CMakeFiles/generate.stamp is up-to-date. 1> CMake does not need to re-run because E:/mtp win/ITK-build/Modules/Remote/CMakeFiles/generate.stamp is up-to-date. 1> CMake does not need to re-run because E:/mtp win/ITK-build/Modules/ThirdParty/DoubleConversion/CMakeFiles/generate.stamp is up-to-date. 1> CMake does not need to re-run because E:/mtp 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Configuration: Debug x64 ------ 3>------ Build started: Project: H5make_libsettings, Configuration: Debug x64 ------ 4>------ Build started: Project: itkzlib, Configuration: Debug x64 ------ 2>Build started 9/3/2014 7:44:00 PM. 2>InitializeBuildStatus: 2> Creating "H5detect.dir\Debug\H5detect.tlog\unsuccessfulbuild" because "AlwaysCreate" was specified. 2>CustomBuild: 2> All outputs are up-to-date. 3>Build started 9/3/2014 7:44:01 PM. 2>ClCompile: 2> All outputs are up-to-date. 4>Build started 9/3/2014 7:44:01 PM. 2>Link: 2> All outputs are up-to-date. 2> H5detect.vcxproj -> E:\mtp win\ITK-build\bin\Debug\H5detect.exe 2>FinalizeBuildStatus: 2> Deleting file "H5detect.dir\Debug\H5detect.tlog\unsuccessfulbuild". 2> Touching "H5detect.dir\Debug\H5detect.tlog\H5detect.lastbuildstate". 2> 2>Build succeeded. 2> 2>Time Elapsed 00:00:00.67 3>InitializeBuildStatus: 3> Creating "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\unsuccessfulbuild" because "AlwaysCreate" was specified. 3>CustomBuild: 3> All outputs are up-to-date. 4>InitializeBuildStatus: 4> Creating "itkzlib.dir\Debug\itkzlib.tlog\unsuccessfulbuild" because "AlwaysCreate" was specified. 4>CustomBuild: 4> All outputs are up-to-date. 3>ClCompile: 3> All outputs are up-to-date. 3>Link: 3> All outputs are up-to-date. 3> H5make_libsettings.vcxproj -> E:\mtp win\ITK-build\bin\Debug\H5make_libsettings.exe 3>FinalizeBuildStatus: 3> Deleting file "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\unsuccessfulbuild". 3> Touching "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\H5make_libsettings.lastbuildstate". 3> 3>Build succeeded. 3> 3>Time Elapsed 00:00:00.79 4>ClCompile: 4> All outputs are up-to-date. 4>Lib: 4> All outputs are up-to-date. 4> itkzlib.vcxproj -> E:\mtp win\ITK-build\lib\Debug\itkzlib-4.6.lib 4>FinalizeBuildStatus: 4> Deleting file "itkzlib.dir\Debug\itkzlib.tlog\unsuccessfulbuild". 4> Touching "itkzlib.dir\Debug\itkzlib.tlog\itkzlib.lastbuildstate". 4> 4>Build succeeded. 4> 4>Time Elapsed 00:00:00.78 5>------ Build started: Project: itkhdf5, Configuration: Debug x64 ------ 5>Build started 9/3/2014 7:44:02 PM. 5>InitializeBuildStatus: 5> Touching "itkhdf5.dir\Debug\itkhdf5.tlog\unsuccessfulbuild". 5>CustomBuild: 5> Building Custom Rule E:/mtp win/ITK/InsightToolkit-4.6.0/Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeLists.txt 5> CMake does not need to re-run because E:\mtp win\ITK-build\Modules\ThirdParty\HDF5\src\itkhdf5\src\CMakeFiles\generate.stamp is up-to-date. 5> Generating ../H5Tinit.c 5> This version of E:\mtp win\ITK-build\bin\Debug\H5detect.exe is not compatible with the version of Windows you're running. Check your computer's system information to see whether you need a x86 (32-bit) or x64 (64-bit) version of the program, and then contact the software publisher. 5>C:\Program Files\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(170,5): error MSB6006: "cmd.exe" exited with code 216. 5> 5>Build FAILED. 5> 5>Time Elapsed 00:00:01.87 ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped ========== On Wed, Sep 3, 2014 at 7:34 PM, Girish Mallya Udupi < indianzeppelin at gmail.com> wrote: > Strange. Have you tried opening and building the solution "ITKHDF5.sln" > alone (located in "your_ITK_Build_folder\Modules\ThirdParty\HDF5")? If not, > please try it and paste the contents of the output window (not just the > error list). > > PS: Please keep the discussion on the mailing list (by cc'ing the > community or replying to all)...:) > > > > On Wed, Sep 3, 2014 at 11:34 AM, tejas lunawat > wrote: > >> yes, the problem is with "itkhdf5" and all others which are dependent on >> it. As error are: >> >> Error 1 error MSB6006: "cmd.exe" exited with code 216. >> Error 2 error LNK1104: cannot open file >> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >> >> >> On Wed, Sep 3, 2014 at 3:53 PM, Girish Mallya Udupi < >> indianzeppelin at gmail.com> wrote: >> >>> Ok. So, when you build "ITK.sln", do all the projects in it build fine >>> with only "itkhdf5" failing? >>> >>> >>> On Wed, Sep 3, 2014 at 11:18 AM, tejas lunawat >>> wrote: >>> >>>> Yes, You are right. >>>> I am having a problem in building the ITK library itself. >>>> I followed all the steps described in this link >>>> >>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio >>>> I have used CMake for configuring and generating the .sln files from >>>> the ITK source file. >>>> And then I am building the libraries by using itk.sln. >>>> >>>> >>>> >>>> On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < >>>> indianzeppelin at gmail.com> wrote: >>>> >>>>> 1) From your question, I understand that you are having a problem >>>>> building the ITK library itself and not a project which uses the library. >>>>> Is that correct? >>>>> >>>>> 2) If so, I assume you have used CMake for configuring and generating >>>>> the .sln files from the ITK source files on your computer. Specifically, >>>>> did you follow the steps described here - >>>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? >>>>> >>>>> 3) Are you trying to build only "ITKHDF5.sln" (located at >>>>> "your_ITK_build_folder\Modules\ThirdParty\HDF5)? >>>>> >>>>> >>>>> On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle >>>>> wrote: >>>>> >>>>>> Are you using a CMakeLists.txt file and cmake to create your >>>>>> project files? >>>>>> ------------------------------ >>>>>> *From:* tejas lunawat [tejasl2603 at gmail.com] >>>>>> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >>>>>> *To:* Gib Bogle >>>>>> *Cc:* community at itk.org >>>>>> *Subject:* Re: [ITK] Error while building ITK >>>>>> >>>>>> ?? >>>>>> Even after changing the build selection in Visual Studio to >>>>>> Release, same error still persisits. >>>>>> >>>>>> >>>>>> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle >>>>>> wrote: >>>>>> >>>>>>> You are building a Debug program. Check that you have Debug ITK >>>>>>> libraries installed. If not change the build selection in Visual Studio to >>>>>>> Release. >>>>>>> ------------------------------ >>>>>>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>>>>>> lunawat [tejasl2603 at gmail.com] >>>>>>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>>>>>> *To:* community at itk.org >>>>>>> *Subject:* [ITK] Error while building ITK >>>>>>> >>>>>>> Hey... >>>>>>> >>>>>>> I am an engineering student, working on a project, based on ITK libraries. >>>>>>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>>>>>> file. Details of the error are as follows: >>>>>>> >>>>>>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>>>>>> Error 2 error LNK1104: cannot open file >>>>>>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>>>>>> >>>>>>> I have searched for the solution of this error, but I didn't found >>>>>>> it. Is their any possible way to solve this error Thank you >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Community mailing list >>>>>> Community at itk.org >>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Regards, >>>>> Girish >>>>> >>>> >>>> >>> >>> >>> -- >>> Regards, >>> Girish >>> >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pattersonnp.work at gmail.com Wed Sep 3 11:10:02 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 3 Sep 2014 16:10:02 +0100 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) Message-ID: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Hi, This is a problem that I have had before and have reported it as a ticket on the GDCM Git page. I have written some code which is heavily dependent on being able to read in a series of DICOM images, in this case they are of PET/NM modality. When a series of images are provided, which have "non-integer" rescale slope, the following error is returned at the final stage when SeriesWriter->Update() is invoked. Assertion failed: (slope == (int)slope), function InverseRescaleFunction, file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, line 67. Abort trap: 6 I cannot provide my own code here, as it may make the problem less clear. However, the problem is directly recreated using the ResampleDICOM.cxx example from the ITK examples page. If a series of PT/NM images are run through the code the above problem occurs. This is particularly problematic since NM/PT modality images do often have non-integer rescale slopes and currently I am not able to deal with images of this modality. There are 2 things to note:- 1) I have reported this error with GDCM developer and this problem appeared to have been resolved. I have previously been resampling NM/PT DICOM images using the ResampleDICOM.cxx example in the past without issue. If I recall correctly, ITK 4.5.2 worked with the latest GDCM release. 2) CT images (where the slope/intercepts are integer) work fine. I shall re-log this on the GDCM pages, but since I am unsure that something didn?t change in latest versions of ITK I wanted to report it here too. I would be much obliged if anyone would be able to test the ResampleDICOM.cxx example with DICOM images which have a rescale slope which is not-integer - and see if the problem can be recreated. I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from Git Repo yesterday. Regards, Nick. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From pattersonnp.work at gmail.com Wed Sep 3 11:51:14 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 3 Sep 2014 16:51:14 +0100 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) In-Reply-To: References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Message-ID: Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the time being. It seems to reappear in any version after 4.6. Nick. >> Hi Nick, >> >> This issue may be coming up now because a bug was fixed before ITK 4.6 >> which makes sure the rescale slope is applied when using GDCMImageIO >> for writing [1]. >> >> HTH, >> Matt >> >> >> [1] http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c0677793aa23a1e >> >> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson >> wrote: >>> Hi, >>> >>> This is a problem that I have had before and have reported it as a ticket >>> on the GDCM Git page. I have written some code which is heavily dependent on >>> being able to read in a series of DICOM images, in this case they are of >>> PET/NM modality. >>> >>> When a series of images are provided, which have "non-integer" rescale >>> slope, the following error is returned at the final stage when >>> SeriesWriter->Update() is invoked. >>> >>> Assertion failed: (slope == (int)slope), function InverseRescaleFunction, >>> file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, >>> line 67. >>> Abort trap: 6 >>> >>> >>> I cannot provide my own code here, as it may make the problem less clear. >>> However, the problem is directly recreated using the ResampleDICOM.cxx >>> example from the ITK examples page. If a series of PT/NM images are run >>> through the code the above problem occurs. This is particularly problematic >>> since NM/PT modality images do often have non-integer rescale slopes and >>> currently I am not able to deal with images of this modality. >>> >>> There are 2 things to note:- >>> 1) I have reported this error with GDCM developer and this problem appeared >>> to have been resolved. I have previously been resampling NM/PT DICOM images >>> using the ResampleDICOM.cxx example in the past without issue. If I recall >>> correctly, ITK 4.5.2 worked with the latest GDCM release. >>> >>> 2) CT images (where the slope/intercepts are integer) work fine. >>> >>> >>> I shall re-log this on the GDCM pages, but since I am unsure that something >>> didn?t change in latest versions of ITK I wanted to report it here too. >>> >>> I would be much obliged if anyone would be able to test the >>> ResampleDICOM.cxx example with DICOM images which have a rescale slope which >>> is not-integer - and see if the problem can be recreated. >>> >>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from >>> Git Repo yesterday. >>> >>> >>> Regards, Nick. >>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Wed Sep 3 12:10:02 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Wed, 3 Sep 2014 16:10:02 +0000 Subject: [ITK] [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent topics OK now? Message-ID: I?ve been trying to help out with changes related to the HDF5ImageIO, and there?s a string of 4 different patches: http://review.source.kitware.com/#/c/16579 http://review.source.kitware.com/#/c/16578 http://review.source.kitware.com/#/c/16577 http://review.source.kitware.com/#/c/16576 Incredibly, 16578 and 16579 seem to be circularly dependent. I?ve just pushed a new version of 16576 which addresses the comments Matt made. Should those others be abandoned and one free-standing patch be made of the actually substantive changes? ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Sep 3 12:26:23 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 12:26:23 -0400 Subject: [ITK] [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent topics OK now? In-Reply-To: References: Message-ID: Hi Kent, Thanks for taking a look at these. We had a good discussion about them this morning at the Google Hangout [1]. New versions are likely coming soon. Thanks, Matt [1] https://plus.google.com/events/c04l669q5omm7oo5p2ov1dp7kb4?authkey=CIH2womZ7I_9Fw On Wed, Sep 3, 2014 at 12:10 PM, Williams, Norman K wrote: > I?ve been trying to help out with changes related to the HDF5ImageIO, and > there?s a string of 4 different patches: > > http://review.source.kitware.com/#/c/16579 > http://review.source.kitware.com/#/c/16578 > http://review.source.kitware.com/#/c/16577 > http://review.source.kitware.com/#/c/16576 > > Incredibly, 16578 and 16579 seem to be circularly dependent. > > I?ve just pushed a new version of 16576 which addresses the comments Matt > made. Should those others be abandoned and one free-standing patch be made > of the actually substantive changes? > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Sep 3 12:30:25 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 12:30:25 -0400 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) In-Reply-To: References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Message-ID: Hi Nick, A reasonable way move forward; 1) A patch could be made to ITK's internal GDCM to support non-integer slope's. 2) This patch could then be submitted to upstream GDCM. Thanks, Matt On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson wrote: > Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the time being. It seems to reappear in any version after 4.6. > > Nick. > > >>> Hi Nick, >>> >>> This issue may be coming up now because a bug was fixed before ITK 4.6 >>> which makes sure the rescale slope is applied when using GDCMImageIO >>> for writing [1]. >>> >>> HTH, >>> Matt >>> >>> >>> [1] http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson >>> wrote: >>>> Hi, >>>> >>>> This is a problem that I have had before and have reported it as a ticket >>>> on the GDCM Git page. I have written some code which is heavily dependent on >>>> being able to read in a series of DICOM images, in this case they are of >>>> PET/NM modality. >>>> >>>> When a series of images are provided, which have "non-integer" rescale >>>> slope, the following error is returned at the final stage when >>>> SeriesWriter->Update() is invoked. >>>> >>>> Assertion failed: (slope == (int)slope), function InverseRescaleFunction, >>>> file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, >>>> line 67. >>>> Abort trap: 6 >>>> >>>> >>>> I cannot provide my own code here, as it may make the problem less clear. >>>> However, the problem is directly recreated using the ResampleDICOM.cxx >>>> example from the ITK examples page. If a series of PT/NM images are run >>>> through the code the above problem occurs. This is particularly problematic >>>> since NM/PT modality images do often have non-integer rescale slopes and >>>> currently I am not able to deal with images of this modality. >>>> >>>> There are 2 things to note:- >>>> 1) I have reported this error with GDCM developer and this problem appeared >>>> to have been resolved. I have previously been resampling NM/PT DICOM images >>>> using the ResampleDICOM.cxx example in the past without issue. If I recall >>>> correctly, ITK 4.5.2 worked with the latest GDCM release. >>>> >>>> 2) CT images (where the slope/intercepts are integer) work fine. >>>> >>>> >>>> I shall re-log this on the GDCM pages, but since I am unsure that something >>>> didn?t change in latest versions of ITK I wanted to report it here too. >>>> >>>> I would be much obliged if anyone would be able to test the >>>> ResampleDICOM.cxx example with DICOM images which have a rescale slope which >>>> is not-integer - and see if the problem can be recreated. >>>> >>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from >>>> Git Repo yesterday. >>>> >>>> >>>> Regards, Nick. >>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Wed Sep 3 12:38:26 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Wed, 3 Sep 2014 16:38:26 +0000 Subject: [ITK] [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent topics OK now? In-Reply-To: References: Message-ID: Watch out for my new version of 16576 ;-) On 9/3/14, 11:26 AM, "Matt McCormick" wrote: >Hi Kent, > >Thanks for taking a look at these. > >We had a good discussion about them this morning at the Google Hangout >[1]. New versions are likely coming soon. > >Thanks, >Matt > > >[1] >https://plus.google.com/events/c04l669q5omm7oo5p2ov1dp7kb4?authkey=CIH2wom >Z7I_9Fw > >On Wed, Sep 3, 2014 at 12:10 PM, Williams, Norman K > wrote: >> I?ve been trying to help out with changes related to the HDF5ImageIO, >>and >> there?s a string of 4 different patches: >> >> http://review.source.kitware.com/#/c/16579 >> http://review.source.kitware.com/#/c/16578 >> http://review.source.kitware.com/#/c/16577 >> http://review.source.kitware.com/#/c/16576 >> >> Incredibly, 16578 and 16579 seem to be circularly dependent. >> >> I?ve just pushed a new version of 16576 which addresses the comments >>Matt >> made. Should those others be abandoned and one free-standing patch be >>made >> of the actually substantive changes? >> >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered >>by the >> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >>confidential >> and may be legally privileged. If you are not the intended recipient, >>you >> are hereby notified that any retention, dissemination, distribution, or >> copying of this communication is strictly prohibited. Please reply to >>the >> sender that you have received the message in error, then delete it. >>Thank >> you. >> ________________________________ >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From hans-johnson at uiowa.edu Wed Sep 3 13:58:53 2014 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Wed, 3 Sep 2014 17:58:53 +0000 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) In-Reply-To: References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Message-ID: Matt, Can you comment on the efforts to update GDCM to a newer version? The version of GDCM in ITK is very much out of date. Hans -----Original Message----- From: Matt McCormick Date: Wednesday, September 3, 2014 at 11:30 AM To: Nick Patterson Cc: "insight-users at itk.org" Subject: Re: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope == (int)slope) Hi Nick, A reasonable way move forward; 1) A patch could be made to ITK's internal GDCM to support non-integer slope's. 2) This patch could then be submitted to upstream GDCM. Thanks, Matt On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson wrote: > Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the >time being. It seems to reappear in any version after 4.6. > > Nick. > > >>> Hi Nick, >>> >>> This issue may be coming up now because a bug was fixed before ITK 4.6 >>> which makes sure the rescale slope is applied when using GDCMImageIO >>> for writing [1]. >>> >>> HTH, >>> Matt >>> >>> >>> [1] >>>http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c067 >>>7793aa23a1e >>> >>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson >>> wrote: >>>> Hi, >>>> >>>> This is a problem that I have had before and have reported it as a >>>>ticket >>>> on the GDCM Git page. I have written some code which is heavily >>>>dependent on >>>> being able to read in a series of DICOM images, in this case they are >>>>of >>>> PET/NM modality. >>>> >>>> When a series of images are provided, which have "non-integer" rescale >>>> slope, the following error is returned at the final stage when >>>> SeriesWriter->Update() is invoked. >>>> >>>> Assertion failed: (slope == (int)slope), function >>>>InverseRescaleFunction, >>>> file >>>>/opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, >>>> line 67. >>>> Abort trap: 6 >>>> >>>> >>>> I cannot provide my own code here, as it may make the problem less >>>>clear. >>>> However, the problem is directly recreated using the ResampleDICOM.cxx >>>> example from the ITK examples page. If a series of PT/NM images are >>>>run >>>> through the code the above problem occurs. This is particularly >>>>problematic >>>> since NM/PT modality images do often have non-integer rescale slopes >>>>and >>>> currently I am not able to deal with images of this modality. >>>> >>>> There are 2 things to note:- >>>> 1) I have reported this error with GDCM developer and this problem >>>>appeared >>>> to have been resolved. I have previously been resampling NM/PT DICOM >>>>images >>>> using the ResampleDICOM.cxx example in the past without issue. If I >>>>recall >>>> correctly, ITK 4.5.2 worked with the latest GDCM release. >>>> >>>> 2) CT images (where the slope/intercepts are integer) work fine. >>>> >>>> >>>> I shall re-log this on the GDCM pages, but since I am unsure that >>>>something >>>> didn?t change in latest versions of ITK I wanted to report it here >>>>too. >>>> >>>> I would be much obliged if anyone would be able to test the >>>> ResampleDICOM.cxx example with DICOM images which have a rescale >>>>slope which >>>> is not-integer - and see if the problem can be recreated. >>>> >>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM >>>>from >>>> Git Repo yesterday. >>>> >>>> >>>> Regards, Nick. >>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 3 14:28:19 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 14:28:19 -0400 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) In-Reply-To: References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Message-ID: Hi Hans, Brian did work on it, but those efforts stalled. I will not have resources to put on it until sometime after the 4.7 release. Thanks, Matt On Wed, Sep 3, 2014 at 1:58 PM, Johnson, Hans J wrote: > Matt, > > Can you comment on the efforts to update GDCM to a newer version? The > version of GDCM in ITK is very much out of date. > > Hans > > > -----Original Message----- > From: Matt McCormick > Date: Wednesday, September 3, 2014 at 11:30 AM > To: Nick Patterson > Cc: "insight-users at itk.org" > Subject: Re: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope > == (int)slope) > > Hi Nick, > > A reasonable way move forward; > > 1) A patch could be made to ITK's internal GDCM to support non-integer > slope's. > 2) This patch could then be submitted to upstream GDCM. > > Thanks, > Matt > > On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson > wrote: >> Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the >>time being. It seems to reappear in any version after 4.6. >> >> Nick. >> >> >>>> Hi Nick, >>>> >>>> This issue may be coming up now because a bug was fixed before ITK 4.6 >>>> which makes sure the rescale slope is applied when using GDCMImageIO >>>> for writing [1]. >>>> >>>> HTH, >>>> Matt >>>> >>>> >>>> [1] >>>>http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c067 >>>>7793aa23a1e >>>> >>>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson >>>> wrote: >>>>> Hi, >>>>> >>>>> This is a problem that I have had before and have reported it as a >>>>>ticket >>>>> on the GDCM Git page. I have written some code which is heavily >>>>>dependent on >>>>> being able to read in a series of DICOM images, in this case they are >>>>>of >>>>> PET/NM modality. >>>>> >>>>> When a series of images are provided, which have "non-integer" rescale >>>>> slope, the following error is returned at the final stage when >>>>> SeriesWriter->Update() is invoked. >>>>> >>>>> Assertion failed: (slope == (int)slope), function >>>>>InverseRescaleFunction, >>>>> file >>>>>/opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, >>>>> line 67. >>>>> Abort trap: 6 >>>>> >>>>> >>>>> I cannot provide my own code here, as it may make the problem less >>>>>clear. >>>>> However, the problem is directly recreated using the ResampleDICOM.cxx >>>>> example from the ITK examples page. If a series of PT/NM images are >>>>>run >>>>> through the code the above problem occurs. This is particularly >>>>>problematic >>>>> since NM/PT modality images do often have non-integer rescale slopes >>>>>and >>>>> currently I am not able to deal with images of this modality. >>>>> >>>>> There are 2 things to note:- >>>>> 1) I have reported this error with GDCM developer and this problem >>>>>appeared >>>>> to have been resolved. I have previously been resampling NM/PT DICOM >>>>>images >>>>> using the ResampleDICOM.cxx example in the past without issue. If I >>>>>recall >>>>> correctly, ITK 4.5.2 worked with the latest GDCM release. >>>>> >>>>> 2) CT images (where the slope/intercepts are integer) work fine. >>>>> >>>>> >>>>> I shall re-log this on the GDCM pages, but since I am unsure that >>>>>something >>>>> didn?t change in latest versions of ITK I wanted to report it here >>>>>too. >>>>> >>>>> I would be much obliged if anyone would be able to test the >>>>> ResampleDICOM.cxx example with DICOM images which have a rescale >>>>>slope which >>>>> is not-integer - and see if the problem can be recreated. >>>>> >>>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM >>>>>from >>>>> Git Repo yesterday. >>>>> >>>>> >>>>> Regards, Nick. >>>>> >>>>> >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > ________________________________ _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 3 14:34:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 14:34:21 -0400 Subject: [ITK] ITK Software Guide Development Environment Message-ID: Hi Katie, Please review the instructions in this patch [1] on how to get an ITK Software Guide build environment. Thanks, Matt [1] http://review.source.kitware.com/#/c/16881/ From blowekamp at mail.nih.gov Wed Sep 3 14:38:29 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 3 Sep 2014 14:38:29 -0400 Subject: [ITK] [ITK-dev] CMake test macro for standard streaming behavior Message-ID: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov> Hello, In ITK 3.20 there was a macro to test the expected behavior of ImageIOs when streaming. It was defined here: https://github.com/InsightSoftwareConsortium/ITK/blob/v3.20.1/Testing/Code/IO/CMakeLists.txt#L406-L470 The intention of this code block was to reuse this sequence for tests for different file formats. ( I thought it was working for VTK and MRC file formats too, but I think that didn't happen when integrating from the IJ ). I wish to create a new and improved version of this macro ( or function ) to help test the HDF5 streaming contributions to ensure it's behavior matches that of the other ImageIOs. The issues are: 1) Where can "common" cmake testing code go so that other modules can use it? 2) Dependencies with modules and test drivers. It appears that I can call the ImageIOBaseTestDriver from other modules i.e. mha and HDF5. Any problem with this? 3) ImageIO registration - Currently I can just add additional dependencies to the TestingKernel to ensure that the HDF5 imageIO is registered everywhere. Is there any other better alternative? Thanks, Brad p.s. Alternatively, the test could be refactored to include the different states internally, as opposed to defined in cmake code. But I don't think it should be hard to get the cmake stuff working... _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Sep 3 15:01:16 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 15:01:16 -0400 Subject: [ITK] [ITK-dev] CMake test macro for standard streaming behavior In-Reply-To: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov> References: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov> Message-ID: Hi Brad, > 1) Where can "common" cmake testing code go so that other modules can use it? This can be added in the CMakeLists.txt for module that other modules will depend on. See "include(CreateTestDriver.cmake)" in Modules/Core/TestKernal/CMakeLists.txt. > 2) Dependencies with modules and test drivers. It appears that I can call the ImageIOBaseTestDriver from other modules i.e. mha and HDF5. Any problem with this? I don't think so, as long as all the other modules TEST_DEPEND ITKImageIOBase. > 3) ImageIO registration - Currently I can just add additional dependencies to the TestingKernel to ensure that the HDF5 imageIO is registered everywhere. Is there any other better alternative? Hopefully this can be avoided -- cross-compiling HDF5 is a pain. Thanks, Matt _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From arman.eshaghi at gmail.com Thu Sep 4 03:39:52 2014 From: arman.eshaghi at gmail.com (Arman Eshaghi) Date: Thu, 4 Sep 2014 12:09:52 +0430 Subject: [ITK] [ITK-users] Update on integration with R Message-ID: Hi, I'm wondering whether this proposal below from 2009 had any progresses regarding the integration of R statistics with ITK? http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages Thanks Arman -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Sep 4 08:44:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 4 Sep 2014 08:44:21 -0400 Subject: [ITK] [ITK-users] Update on integration with R In-Reply-To: References: Message-ID: Hi Arman, Since WrapITK uses SWIG, generating an R interface should be possible, but I do not know anyone who has tried it recently. SimpleITK uses SWIG and the R interface is enabled [1]. HTH, Matt [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi wrote: > Hi, > > I'm wondering whether this proposal below from 2009 had any progresses > regarding the integration of R statistics with ITK? > > http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages > > Thanks > Arman > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 4 08:58:40 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 4 Sep 2014 08:58:40 -0400 Subject: [ITK] [ITK-users] Update on integration with R In-Reply-To: References: Message-ID: Hello, What are you looking to do with R and ITK? The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version and is tested on linux and OSX. There are some issue with building R on windows that have not been addressed. Please let us know if you have further questions about getting this built. Good luck, Brad On Sep 4, 2014, at 8:44 AM, Matt McCormick wrote: > Hi Arman, > > Since WrapITK uses SWIG, generating an R interface should be possible, > but I do not know anyone who has tried it recently. > > SimpleITK uses SWIG and the R interface is enabled [1]. > > HTH, > Matt > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation > > On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi wrote: >> Hi, >> >> I'm wondering whether this proposal below from 2009 had any progresses >> regarding the integration of R statistics with ITK? >> >> http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages >> >> Thanks >> Arman >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arman.eshaghi at gmail.com Thu Sep 4 09:09:57 2014 From: arman.eshaghi at gmail.com (Arman Eshaghi) Date: Thu, 4 Sep 2014 17:39:57 +0430 Subject: [ITK] [ITK-users] Update on integration with R In-Reply-To: References: Message-ID: Thanks Brad and Matt, just wanted to read and write files with ITK in R. SITK works fine on Linux. All the best, Arman ps Just found another package (Rcpp) that may be useful for this as well On Thu, Sep 4, 2014 at 5:28 PM, Bradley Lowekamp wrote: > Hello, > > What are you looking to do with R and ITK? > > The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version > and is tested on linux and OSX. There are some issue with building R on > windows that have not been addressed. Please let us know if you have > further questions about getting this built. > > Good luck, > Brad > > On Sep 4, 2014, at 8:44 AM, Matt McCormick > wrote: > > > Hi Arman, > > > > Since WrapITK uses SWIG, generating an R interface should be possible, > > but I do not know anyone who has tried it recently. > > > > SimpleITK uses SWIG and the R interface is enabled [1]. > > > > HTH, > > Matt > > > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation > > > > On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi > wrote: > >> Hi, > >> > >> I'm wondering whether this proposal below from 2009 had any progresses > >> regarding the integration of R statistics with ITK? > >> > >> > http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages > >> > >> Thanks > >> Arman > >> > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-users > >> > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From stnava at gmail.com Thu Sep 4 09:33:44 2014 From: stnava at gmail.com (brian avants) Date: Thu, 4 Sep 2014 09:33:44 -0400 Subject: [ITK] [ITK-users] Update on integration with R In-Reply-To: References: Message-ID: you can also do ( in R ) install.packages("devtools") library(devtools) install_github("stnava/ANTsR") library(ANTsR) img<-antsImageRead("image.nii.gz",3) antsImageWrite(img,'temp.nii.gz') it's itk underneath brian On Thu, Sep 4, 2014 at 9:09 AM, Arman Eshaghi wrote: > Thanks Brad and Matt, just wanted to read and write files with ITK in R. > SITK works fine on Linux. > > All the best, > Arman > > ps Just found another package (Rcpp) that may be useful for this as well > > > On Thu, Sep 4, 2014 at 5:28 PM, Bradley Lowekamp > wrote: > >> Hello, >> >> What are you looking to do with R and ITK? >> >> The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version >> and is tested on linux and OSX. There are some issue with building R on >> windows that have not been addressed. Please let us know if you have >> further questions about getting this built. >> >> Good luck, >> Brad >> >> On Sep 4, 2014, at 8:44 AM, Matt McCormick >> wrote: >> >> > Hi Arman, >> > >> > Since WrapITK uses SWIG, generating an R interface should be possible, >> > but I do not know anyone who has tried it recently. >> > >> > SimpleITK uses SWIG and the R interface is enabled [1]. >> > >> > HTH, >> > Matt >> > >> > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation >> > >> > On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi >> wrote: >> >> Hi, >> >> >> >> I'm wondering whether this proposal below from 2009 had any progresses >> >> regarding the integration of R statistics with ITK? >> >> >> >> >> http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages >> >> >> >> Thanks >> >> Arman >> >> >> >> _____________________________________ >> >> Powered by www.kitware.com >> >> >> >> Visit other Kitware open-source projects at >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> http://www.kitware.com/products/protraining.php >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Thu Sep 4 10:06:44 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 4 Sep 2014 15:06:44 +0100 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Okay, looks like the problem occurs while executing H5detect.exe (generated by the project "H5detect"). This exe is executed to generate H5Tinit.c which is a source file required by the "itkhdf5" project. For some reason (and this is probably something to do with VS), it is not able to execute the exe. Have you tried to do a 32-bit build of ITK (by choosing the 32-bit version of VS during CMake configure)? Also, what versions of VS and Windows are you using? On Wed, Sep 3, 2014 at 3:17 PM, tejas lunawat wrote: > Output in build selection as Debug > > 1>------ Build started: Project: ZERO_CHECK, Configuration: Debug x64 > ------ > 1>Build started 9/3/2014 7:43:45 PM. > 1>InitializeBuildStatus: > 1> Creating "x64\Debug\ZERO_CHECK\ZERO_CHECK.tlog\unsuccessfulbuild" > because "AlwaysCreate" was specified. > 1>CustomBuild: > 1> Checking Build System > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/Remote/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/DoubleConversion/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/DoubleConversion/src/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > 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win/ITK-build/Examples/Numerics/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Segmentation/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Segmentation/test/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/SpatialObjects/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Statistics/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Statistics/test/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/RegistrationITKv4/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/RegistrationITKv4/test/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Utilities/Doxygen/CMakeFiles/generate.stamp is up-to-date. > 1>FinalizeBuildStatus: > 1> Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.tlog\unsuccessfulbuild". > 1> Touching > "x64\Debug\ZERO_CHECK\ZERO_CHECK.tlog\ZERO_CHECK.lastbuildstate". > 1> > 1>Build succeeded. > 1> > 1>Time Elapsed 00:00:15.42 > 2>------ Build started: Project: H5detect, Configuration: Debug x64 ------ > 3>------ Build started: Project: H5make_libsettings, Configuration: Debug > x64 ------ > 4>------ Build started: Project: itkzlib, Configuration: Debug x64 ------ > 2>Build started 9/3/2014 7:44:00 PM. > 2>InitializeBuildStatus: > 2> Creating "H5detect.dir\Debug\H5detect.tlog\unsuccessfulbuild" because > "AlwaysCreate" was specified. > 2>CustomBuild: > 2> All outputs are up-to-date. > 3>Build started 9/3/2014 7:44:01 PM. > 2>ClCompile: > 2> All outputs are up-to-date. > 4>Build started 9/3/2014 7:44:01 PM. > 2>Link: > 2> All outputs are up-to-date. > 2> H5detect.vcxproj -> E:\mtp win\ITK-build\bin\Debug\H5detect.exe > 2>FinalizeBuildStatus: > 2> Deleting file "H5detect.dir\Debug\H5detect.tlog\unsuccessfulbuild". > 2> Touching "H5detect.dir\Debug\H5detect.tlog\H5detect.lastbuildstate". > 2> > 2>Build succeeded. > 2> > 2>Time Elapsed 00:00:00.67 > 3>InitializeBuildStatus: > 3> Creating > "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\unsuccessfulbuild" > because "AlwaysCreate" was specified. > 3>CustomBuild: > 3> All outputs are up-to-date. > 4>InitializeBuildStatus: > 4> Creating "itkzlib.dir\Debug\itkzlib.tlog\unsuccessfulbuild" because > "AlwaysCreate" was specified. > 4>CustomBuild: > 4> All outputs are up-to-date. > 3>ClCompile: > 3> All outputs are up-to-date. > 3>Link: > 3> All outputs are up-to-date. > 3> H5make_libsettings.vcxproj -> E:\mtp > win\ITK-build\bin\Debug\H5make_libsettings.exe > 3>FinalizeBuildStatus: > 3> Deleting file > "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\unsuccessfulbuild". > 3> Touching > "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\H5make_libsettings.lastbuildstate". > 3> > 3>Build succeeded. > 3> > 3>Time Elapsed 00:00:00.79 > 4>ClCompile: > 4> All outputs are up-to-date. > 4>Lib: > 4> All outputs are up-to-date. > 4> itkzlib.vcxproj -> E:\mtp win\ITK-build\lib\Debug\itkzlib-4.6.lib > 4>FinalizeBuildStatus: > 4> Deleting file "itkzlib.dir\Debug\itkzlib.tlog\unsuccessfulbuild". > 4> Touching "itkzlib.dir\Debug\itkzlib.tlog\itkzlib.lastbuildstate". > 4> > 4>Build succeeded. > 4> > 4>Time Elapsed 00:00:00.78 > 5>------ Build started: Project: itkhdf5, Configuration: Debug x64 ------ > 5>Build started 9/3/2014 7:44:02 PM. > 5>InitializeBuildStatus: > 5> Touching "itkhdf5.dir\Debug\itkhdf5.tlog\unsuccessfulbuild". > 5>CustomBuild: > 5> Building Custom Rule E:/mtp > win/ITK/InsightToolkit-4.6.0/Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeLists.txt > 5> CMake does not need to re-run because E:\mtp > win\ITK-build\Modules\ThirdParty\HDF5\src\itkhdf5\src\CMakeFiles\generate.stamp > is up-to-date. > 5> Generating ../H5Tinit.c > 5> This version of E:\mtp win\ITK-build\bin\Debug\H5detect.exe is not > compatible with the version of Windows you're running. Check your > computer's system information to see whether you need a x86 (32-bit) or x64 > (64-bit) version of the program, and then contact the software publisher. > 5>C:\Program > Files\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(170,5): > error MSB6006: "cmd.exe" exited with code 216. > 5> > 5>Build FAILED. > 5> > 5>Time Elapsed 00:00:01.87 > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped ========== > > > > On Wed, Sep 3, 2014 at 7:34 PM, Girish Mallya Udupi < > indianzeppelin at gmail.com> wrote: > >> Strange. Have you tried opening and building the solution "ITKHDF5.sln" >> alone (located in "your_ITK_Build_folder\Modules\ThirdParty\HDF5")? If not, >> please try it and paste the contents of the output window (not just the >> error list). >> >> PS: Please keep the discussion on the mailing list (by cc'ing the >> community or replying to all)...:) >> >> >> >> On Wed, Sep 3, 2014 at 11:34 AM, tejas lunawat >> wrote: >> >>> yes, the problem is with "itkhdf5" and all others which are dependent on >>> it. As error are: >>> >>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>> Error 2 error LNK1104: cannot open file >>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>> >>> >>> On Wed, Sep 3, 2014 at 3:53 PM, Girish Mallya Udupi < >>> indianzeppelin at gmail.com> wrote: >>> >>>> Ok. So, when you build "ITK.sln", do all the projects in it build fine >>>> with only "itkhdf5" failing? >>>> >>>> >>>> On Wed, Sep 3, 2014 at 11:18 AM, tejas lunawat >>>> wrote: >>>> >>>>> Yes, You are right. >>>>> I am having a problem in building the ITK library itself. >>>>> I followed all the steps described in this link >>>>> >>>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio >>>>> I have used CMake for configuring and generating the .sln files from >>>>> the ITK source file. >>>>> And then I am building the libraries by using itk.sln. >>>>> >>>>> >>>>> >>>>> On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < >>>>> indianzeppelin at gmail.com> wrote: >>>>> >>>>>> 1) From your question, I understand that you are having a problem >>>>>> building the ITK library itself and not a project which uses the library. >>>>>> Is that correct? >>>>>> >>>>>> 2) If so, I assume you have used CMake for configuring and generating >>>>>> the .sln files from the ITK source files on your computer. Specifically, >>>>>> did you follow the steps described here - >>>>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? >>>>>> >>>>>> 3) Are you trying to build only "ITKHDF5.sln" (located at >>>>>> "your_ITK_build_folder\Modules\ThirdParty\HDF5)? >>>>>> >>>>>> >>>>>> On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle >>>>>> wrote: >>>>>> >>>>>>> Are you using a CMakeLists.txt file and cmake to create your >>>>>>> project files? >>>>>>> ------------------------------ >>>>>>> *From:* tejas lunawat [tejasl2603 at gmail.com] >>>>>>> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >>>>>>> *To:* Gib Bogle >>>>>>> *Cc:* community at itk.org >>>>>>> *Subject:* Re: [ITK] Error while building ITK >>>>>>> >>>>>>> ?? >>>>>>> Even after changing the build selection in Visual Studio to >>>>>>> Release, same error still persisits. >>>>>>> >>>>>>> >>>>>>> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle >>>>>>> wrote: >>>>>>> >>>>>>>> You are building a Debug program. Check that you have Debug ITK >>>>>>>> libraries installed. If not change the build selection in Visual Studio to >>>>>>>> Release. >>>>>>>> ------------------------------ >>>>>>>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>>>>>>> lunawat [tejasl2603 at gmail.com] >>>>>>>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>>>>>>> *To:* community at itk.org >>>>>>>> *Subject:* [ITK] Error while building ITK >>>>>>>> >>>>>>>> Hey... >>>>>>>> >>>>>>>> I am an engineering student, working on a project, based on ITK libraries. >>>>>>>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>>>>>>> file. Details of the error are as follows: >>>>>>>> >>>>>>>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>>>>>>> Error 2 error LNK1104: cannot open file >>>>>>>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>>>>>>> >>>>>>>> I have searched for the solution of this error, but I didn't >>>>>>>> found it. Is their any possible way to solve this error Thank you >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Community mailing list >>>>>>> Community at itk.org >>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Regards, >>>>>> Girish >>>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Regards, >>>> Girish >>>> >>> >>> >> >> >> -- >> Regards, >> Girish >> > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Thu Sep 4 11:29:42 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 4 Sep 2014 16:29:42 +0100 Subject: [ITK] [ITK-dev] New to the Gerrit review process Message-ID: Hello, I have a couple of questions about the Gerrit review process - 1) Is the creator of a topic automatically added as a reviewer on subsequent patches in the topic? 2) As a reviewer, if I am unable to understand the changes made to the code (simply because I am not an advanced programmer), should I leave the patch unscored? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Sep 4 11:34:47 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 4 Sep 2014 11:34:47 -0400 Subject: [ITK] [ITK-dev] New to the Gerrit review process In-Reply-To: References: Message-ID: Hi Girish, Thanks for participating on Gerrit. > 1) Is the creator of a topic automatically added as a reviewer on subsequent > patches in the topic? No, they have to be manually added at the moment. > 2) As a reviewer, if I am unable to understand the changes made to the code > (simply because I am not an advanced programmer), should I leave the patch > unscored? An feedback is welcome. If you do not feel very knowledgeable about a patch, give it a "+1" as opposed to a "+2". Some more information can be found here [1]. Thanks, Matt [1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/PerformAGerritReview/index.html _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Thu Sep 4 11:43:14 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 4 Sep 2014 11:43:14 -0400 Subject: [ITK] [ITK-dev] New to the Gerrit review process In-Reply-To: References: Message-ID: Hello Girish, I assume you are talking about this patch: http://review.source.kitware.com/#/c/16868/ Thanks again for contributing the patch which demonstrated the bug you encountered. For this particular case I would encourage you to download, checkout, and compile the patch and verify that is resolves the issue you initially encountered. Then report back if it fixes the problem. Brad On Sep 4, 2014, at 11:29 AM, Girish Mallya Udupi wrote: > Hello, > > I have a couple of questions about the Gerrit review process - > > 1) Is the creator of a topic automatically added as a reviewer on subsequent patches in the topic? > > 2) As a reviewer, if I am unable to understand the changes made to the code (simply because I am not an advanced programmer), should I leave the patch unscored? > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Sep 4 11:50:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 4 Sep 2014 11:50:13 -0400 Subject: [ITK] Opportunity to share, discuss, design, and learn with other ITK community members Message-ID: There is an opportunity to share, discuss, design, and learn with your fellow ITK community members. On Friday, 11 AM Eastern USA time, join us as we discuss ITK development. We will use the Hangout link for the Event. https://plus.google.com/events/c4np6cgd8oosd5je818d9r1n3j8 For those that cannot join via Hangout, telephone call-in is also possible. Dial: +1-585-632-6296 Enter pin: 31423? All are welcome. Hope to talk to you then! From indianzeppelin at gmail.com Thu Sep 4 11:58:19 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 4 Sep 2014 16:58:19 +0100 Subject: [ITK] [ITK-dev] New to the Gerrit review process In-Reply-To: References: Message-ID: Hi Brad, Yes, that one (and its parent). I did in fact pull the patch and compile it without any issues. I ran the related tests too, which passed. But it seemed to me that I couldn't give a "Verify" score alone and had to give a "Code Review" score as well. Matt's reply has made it clearer now. Thanks! On Thu, Sep 4, 2014 at 4:43 PM, Bradley Lowekamp wrote: > Hello Girish, > > I assume you are talking about this patch: > http://review.source.kitware.com/#/c/16868/ > > Thanks again for contributing the patch which demonstrated the bug you > encountered. > > For this particular case I would encourage you to download, checkout, and > compile the patch and verify that is resolves the issue you initially > encountered. Then report back if it fixes the problem. > > Brad > > On Sep 4, 2014, at 11:29 AM, Girish Mallya Udupi > wrote: > > > Hello, > > > > I have a couple of questions about the Gerrit review process - > > > > 1) Is the creator of a topic automatically added as a reviewer on > subsequent patches in the topic? > > > > 2) As a reviewer, if I am unable to understand the changes made to the > code (simply because I am not an advanced programmer), should I leave the > patch unscored? > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From marcus.hanwell at kitware.com Fri Sep 5 11:31:30 2014 From: marcus.hanwell at kitware.com (Marcus D. Hanwell) Date: Fri, 5 Sep 2014 11:31:30 -0400 Subject: [ITK] [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent topics OK now? In-Reply-To: <8D195ACD03190B6-15CC-C133@webmail-m269.sysops.aol.com> References: <8D195ACD03190B6-15CC-C133@webmail-m269.sysops.aol.com> Message-ID: On Wed, Sep 3, 2014 at 12:39 PM, David Cole via Insight-developers wrote: >> http://review.source.kitware.com/#/c/16579 >> http://review.source.kitware.com/#/c/16578 >> Incredibly, 16578 and 16579 seem to be circularly dependent. > > > Why do you say they're circularly dependent? It looks to me like 79 is > based on 78... I'm not seeing the circularity. > If you managed a circular dependency I would love to see it - is that even possible in git? _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Fri Sep 5 13:23:22 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 5 Sep 2014 13:23:22 -0400 Subject: [ITK] [ITK-dev] Using ITK with optional components Message-ID: <1C470533-952F-4836-81C1-1DA697FA8213@mail.nih.gov> Hello, I was wondering if anyone had looked into adding support for CMake's find_package OPTIONAL_COMPONENTS option? This would be quite convenient in some situations. Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From zeinsalah at gmail.com Mon Sep 8 04:18:10 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 8 Sep 2014 10:18:10 +0200 Subject: [ITK] [ITK-users] Background / Foreground separation Message-ID: Hello, I want to reliably define the main object in CT/MRI image from the background. I.e. I want to do some kind of defining the boundary (skin) of the patient. Are there filters in ITK dedicated for this? or should I adapt filters like the Otsu? Thanks, Zein Sorry! I have not been using ITK since Release 3.20 :). -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From zeinsalah at gmail.com Mon Sep 8 10:10:49 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 8 Sep 2014 16:10:49 +0200 Subject: [ITK] ITK mailing list Message-ID: Hi, I have not been using ITK in the last 2 years. Has anything been changed since then regarding the mailing list email address? used to write my questions to isight-users at itk.org. Is this still valid? Thanks, Zein -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Mon Sep 8 10:17:17 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Mon, 8 Sep 2014 15:17:17 +0100 Subject: [ITK] ITK mailing list In-Reply-To: References: Message-ID: Yes, it is (assuming there's a typo in your question and you actually meant insight-users at itk.org). On Mon, Sep 8, 2014 at 3:10 PM, Zein Salah wrote: > Hi, > > I have not been using ITK in the last 2 years. Has anything been changed > since then regarding the mailing list email address? used to write my > questions to isight-users at itk.org. Is this still valid? > > Thanks, > Zein > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 8 10:41:40 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Sep 2014 10:41:40 -0400 Subject: [ITK] ITK mailing list In-Reply-To: References: Message-ID: Hi, While insight-user at itk.org will still work, community at itk.org [1] is recommended. Subscribing to this list will receive mails from both insight-user at itk.org and insight-developers at itk.org. Thanks, Matt [1] http://www.itk.org/mailman/listinfo/community On Mon, Sep 8, 2014 at 10:17 AM, Girish Mallya Udupi wrote: > Yes, it is (assuming there's a typo in your question and you actually meant > insight-users at itk.org). > > On Mon, Sep 8, 2014 at 3:10 PM, Zein Salah wrote: >> >> Hi, >> >> I have not been using ITK in the last 2 years. Has anything been changed >> since then regarding the mailing list email address? used to write my >> questions to isight-users at itk.org. Is this still valid? >> >> Thanks, >> Zein >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > > > > -- > Regards, > Girish > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Mon Sep 8 10:52:54 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Sep 2014 10:52:54 -0400 Subject: [ITK] [ITK-users] Background / Foreground separation In-Reply-To: References: Message-ID: Hi Zein, Welcome back! :-) One possible sequence of filters to obtain the "skin": OtsuThresholdImageFilter [1] BinaryShapeKeepNObjectImageFilter (keep only the largest object) [2] BinaryClosingByReconstructionImageFilter or BinaryFillholeImageFilter [3][4] BinaryContourImageFilter [5] HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1OtsuThresholdImageFilter.html [2] http://www.itk.org/Doxygen/html/classitk_1_1BinaryShapeKeepNObjectsImageFilter.html [3] http://www.itk.org/Doxygen/html/classitk_1_1BinaryClosingByReconstructionImageFilter.html [4] http://www.itk.org/Doxygen/html/classitk_1_1BinaryFillholeImageFilter.html [5] http://www.itk.org/Doxygen/html/classitk_1_1BinaryContourImageFilter.html On Mon, Sep 8, 2014 at 4:18 AM, Zein Salah wrote: > Hello, > > I want to reliably define the main object in CT/MRI image from the > background. I.e. I want to do some kind of defining the boundary (skin) of > the patient. Are there filters in ITK dedicated for this? or should I adapt > filters like the Otsu? > > Thanks, > Zein > > Sorry! I have not been using ITK since Release 3.20 :). > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From zeinsalah at gmail.com Mon Sep 8 11:14:06 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 8 Sep 2014 17:14:06 +0200 Subject: [ITK] OtsuMultipleThresholdsCalculator Message-ID: Hi, I was trying to use the OtsuMultipleThresholdsCalculator. Bellow is the corresponding code from my program. The compiler reports an error that Compute() is not a member of itk::OtsuMultipleThresholdsCalculator. I can't figure out what the actual error is!! BTW, due to compatibly reasons within our working team, I have to use ITK3.14 and and not a newer release. Does this have to do with the error?? Much thanks, Z. typedef itk::Statistics::ScalarImageToHistogramGenerator< InputImageType > ScalarImageToHistogramGeneratorType; typedef ScalarImageToHistogramGeneratorType::HistogramType HistogramType; typedef itk::OtsuMultipleThresholdsCalculator< HistogramType > CalculatorType; ScalarImageToHistogramGeneratorType::Pointer scalarImageToHistogramGenerator = ScalarImageToHistogramGeneratorType::New(); CalculatorType::Pointer calculator = CalculatorType::New(); scalarImageToHistogramGenerator->SetNumberOfBins( 128 ); scalarImageToHistogramGenerator->SetInput( m_ShiftedImage ); scalarImageToHistogramGenerator->Compute(); calculator->SetNumberOfThresholds( 3 ); calculator->SetInputHistogram(scalarImageToHistogramGenerator->GetOutput()); calculator->Compute(); -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 8 11:22:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Sep 2014 11:22:24 -0400 Subject: [ITK] OtsuMultipleThresholdsCalculator In-Reply-To: References: Message-ID: Hi Zein, If looking at Doxygen, the documentation for ITK 3.14 will need to be used [1]. The documentation suggests that Update() should be called [2]. HTH, Matt [1] http://itk.org/Doxygen314/html/ [2] http://itk.org/Doxygen314/html/classitk_1_1OtsuMultipleThresholdsCalculator.html On Mon, Sep 8, 2014 at 11:14 AM, Zein Salah wrote: > Hi, > > I was trying to use the OtsuMultipleThresholdsCalculator. Bellow is the > corresponding > code from my program. The compiler reports an error that Compute() is not a > member > of itk::OtsuMultipleThresholdsCalculator. I can't figure out what the actual > error is!! > BTW, due to compatibly reasons within our working team, I have to use > ITK3.14 and > and not a newer release. Does this have to do with the error?? > > Much thanks, > Z. > > > typedef itk::Statistics::ScalarImageToHistogramGenerator< InputImageType > > ScalarImageToHistogramGeneratorType; > typedef ScalarImageToHistogramGeneratorType::HistogramType > HistogramType; > typedef itk::OtsuMultipleThresholdsCalculator< HistogramType > > CalculatorType; > > ScalarImageToHistogramGeneratorType::Pointer > scalarImageToHistogramGenerator = > ScalarImageToHistogramGeneratorType::New(); > CalculatorType::Pointer calculator = CalculatorType::New(); > > scalarImageToHistogramGenerator->SetNumberOfBins( 128 ); > scalarImageToHistogramGenerator->SetInput( m_ShiftedImage ); > scalarImageToHistogramGenerator->Compute(); > > calculator->SetNumberOfThresholds( 3 ); > > calculator->SetInputHistogram(scalarImageToHistogramGenerator->GetOutput()); > calculator->Compute(); > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From elena.bresciani87 at gmail.com Tue Sep 9 11:50:31 2014 From: elena.bresciani87 at gmail.com (elena bresciani) Date: Tue, 9 Sep 2014 17:50:31 +0200 Subject: [ITK] [ITK-users] Pipeline update problem (I suppose) Message-ID: Hello guys, I'm writing an ITK script using C++ functions in order to reduce the number of operations repetition. What I need to do is: given a scan with 4 objects I need to separate them in 4 images and, if vertically oriented, rotate them 90 degrees in order to have them horizontal. I already have successfully compiled the code necessary to crop ROIs and the rotation step separately, everything works well, but when I try to unify all in a single script I don't get the desired output. I suppose that the problem could be in a missing Update() or something but I can't identify it. Attached you can find a concise version of the code; whilst SegmentedImage1..4 are as attended OutputImage1..4 have right size but are all filled with gray level 100. As I said before, I can't understand the problem because the same code used alone (attachment rotation.cxx), works well. Any guess? Thanks Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: code Type: application/octet-stream Size: 6155 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rotation.cxx Type: application/octet-stream Size: 3565 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dagarshali at gmail.com Tue Sep 9 22:33:46 2014 From: dagarshali at gmail.com (dagarshali) Date: Tue, 9 Sep 2014 19:33:46 -0700 (PDT) Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution Message-ID: <1410316426142-7586179.post@n2.nabble.com> I downloaded the source code for simple itk and complied it as instructed. In the cmake configuration, I changed the python paths according to using the python distribution of anaconda. I was able to compile it. I have attached a snapshot of the cmake configuration I am not sure what to do after the compiling.. If I enter import SimpleITK as sitk, I get a fatal python error. Can anybody please suggest how to overcome this problem?Thanks in advance.dagarshali -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Sep 9 22:41:57 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 9 Sep 2014 22:41:57 -0400 Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution In-Reply-To: <1410316426142-7586179.post@n2.nabble.com> References: <1410316426142-7586179.post@n2.nabble.com> Message-ID: Hi dagarshall, There is a SimpleITK recipe for conda [1]. To install it from a manual build, use the same commands at the end of build.sh: cd ${BUILD_DIR}/SimpleITK-build/Wrapping ${PYTHON} PythonPackage/setup.py install HTH, Matt [1] https://github.com/conda/conda-recipes/tree/master/simpleitk On Tue, Sep 9, 2014 at 10:33 PM, dagarshali wrote: > I downloaded the source code for simple itk and complied it as instructed. In > the cmake configuration, I changed the python paths according to using the > python distribution of anaconda. I was able to compile it. I have attached a > snapshot of the cmake configuration > > I am not sure what to do after the compiling.. If I enter import SimpleITK > as sitk, I get a fatal python error. Can anybody please suggest how to > overcome this problem?Thanks in advance.dagarshali > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From 88172828 at qq.com Wed Sep 10 07:42:59 2014 From: 88172828 at qq.com (Eping Wang) Date: Wed, 10 Sep 2014 04:42:59 -0700 (MST) Subject: [ITK] =?utf-8?q?=5BITK-users=5D_itk=3A_=3AImageFileReader_to_igst?= =?utf-8?q?k=3A_=3AImageSpatialObject=E2=80=8F?= In-Reply-To: <1403279378508-34126.post@n7.nabble.com> References: <1403279378508-34126.post@n7.nabble.com> Message-ID: <1410349379582-34523.post@n7.nabble.com> Hi SeanLee, Try this: igstk::Friends::ImageReaderToImageSpatialObject::ConnectImage(&m_MhdImageReader,&m_ImageSpatialObject.GetPointer()); It worked in my project. -- View this message in context: http://itk-users.7.n7.nabble.com/itk-ImageFileReader-to-igstk-ImageSpatialObject-tp34126p34523.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 10 08:22:44 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 10 Sep 2014 08:22:44 -0400 Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> Message-ID: Hi, I think the best route is to use their package build system so the build environment is set up correctly. However, the SimpleITK package may need some tweaks. HTH, Matt On Wed, Sep 10, 2014 at 2:27 AM, Vishwa wrote: > I tried installing again. Get the same error. Any ideas as to why this might > be happening? or how to even debug the issue? > > Vishwa > > On Tue, Sep 9, 2014 at 10:44 PM, Matt McCormick > wrote: >> >> Instructions to build the recipe are here [1], although there is >> currently a bug in the clone url [2]. >> >> The error you get is usually from using incompatible versions of >> Python in the CMake configuration. Your screenshot in the first >> message look good, but conda may be doing some funny business. >> >> HTH, >> Matt >> >> [1] http://conda.pydata.org/docs/build_tutorials/pkgs.html >> >> [2] https://github.com/conda/conda-recipes/pull/176 >> >> On Tue, Sep 9, 2014 at 10:55 PM, Vishwa >> wrote: >> > Thanks for getting back to me.. I am not sure how to use the build.sh. >> > Am i >> > to create those variables mentioned in that file? >> > >> > In the previous mail, I forgot to mention after I compiled, I tried what >> > you >> > suggest here >> > >> > cd ${BUILD_DIR}/SimpleITK-build/Wrapping >> > ${PYTHON} PythonPackage/setup.py install >> > >> > The last few lines of the output is shown below >> > >> > Installed >> > >> > /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev584-py2.7-macosx-10.5-x86_64.egg >> > >> > Processing dependencies for SimpleITK==0.9.0.dev584 >> > >> > Finished processing dependencies for SimpleITK==0.9.0.dev584 >> > >> > However, when i import simple itk in python, >> > >> > import SimpleITK as sitk >> > >> > Fatal Python error: PyThreadState_Get: no current thread >> > >> > Abort trap: 6 >> > >> > >> > On Tue, Sep 9, 2014 at 9:41 PM, Matt McCormick >> > >> > wrote: >> >> >> >> Hi dagarshall, >> >> >> >> There is a SimpleITK recipe for conda [1]. To install it from a >> >> manual build, use the same commands at the end of build.sh: >> >> >> >> cd ${BUILD_DIR}/SimpleITK-build/Wrapping >> >> ${PYTHON} PythonPackage/setup.py install >> >> >> >> HTH, >> >> Matt >> >> >> >> [1] https://github.com/conda/conda-recipes/tree/master/simpleitk >> >> >> >> On Tue, Sep 9, 2014 at 10:33 PM, dagarshali >> >> wrote: >> >> > I downloaded the source code for simple itk and complied it as >> >> > instructed. In >> >> > the cmake configuration, I changed the python paths according to >> >> > using >> >> > the >> >> > python distribution of anaconda. I was able to compile it. I have >> >> > attached a >> >> > snapshot of the cmake configuration >> >> > >> >> > >> >> > >> >> > I am not sure what to do after the compiling.. If I enter import >> >> > SimpleITK >> >> > as sitk, I get a fatal python error. Can anybody please suggest how >> >> > to >> >> > overcome this problem?Thanks in advance.dagarshali >> >> > >> >> > >> >> > >> >> > -- >> >> > View this message in context: >> >> > >> >> > http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html >> >> > Sent from the ITK Insight Users mailing list archive at Nabble.com. >> >> > _____________________________________ >> >> > Powered by www.kitware.com >> >> > >> >> > Visit other Kitware open-source projects at >> >> > http://www.kitware.com/opensource/opensource.html >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > http://www.kitware.com/products/protraining.php >> >> > >> >> > Please keep messages on-topic and check the ITK FAQ at: >> >> > http://www.itk.org/Wiki/ITK_FAQ >> >> > >> >> > Follow this link to subscribe/unsubscribe: >> >> > http://public.kitware.com/mailman/listinfo/insight-users >> > >> > >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Wed Sep 10 10:13:10 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 10 Sep 2014 10:13:10 -0400 Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> Message-ID: <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> Hello, This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment. I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct. You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker. Also you can inspect the runtime libraries: otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0) [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme Hope this helps, Brad On Sep 9, 2014, at 10:55 PM, Vishwa wrote: > import SimpleITK as sitk > > Fatal Python error: PyThreadState_Get: no current thread > > > Abort trap: 6 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Wed Sep 10 11:10:37 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 10 Sep 2014 11:10:37 -0400 Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> Message-ID: <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> Hello, You need to use the conda build environment. Look at the readme in this repo[1]. Basically you'll need to do the following: $ conda install conda-build $ cd src $ git clone https://github.com/thewtex/conda-recipes.git $ git checkout simpleitk-clone-url $ conda build simpleitk [1] https://github.com/conda/conda-recipes On Sep 10, 2014, at 11:01 AM, Vishwa wrote: > Thanks very much for the information. I looked at the conda recipe. There are three files. > One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile.. > > There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. > > Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. > > Best regards, > Vishwa > > > > On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp wrote: > Hello, > > This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment. > > I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct. > > You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker. > > Also you can inspect the runtime libraries: > > otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so > /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: > @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0) > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1) > /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0) > /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0) > > [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme > > Hope this helps, > Brad > > On Sep 9, 2014, at 10:55 PM, Vishwa wrote: > >> import SimpleITK as sitk >> >> Fatal Python error: PyThreadState_Get: no current thread >> >> >> Abort trap: 6 >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From smrolfe at u.washington.edu Wed Sep 10 17:25:57 2014 From: smrolfe at u.washington.edu (smrolfe at u.washington.edu) Date: Wed, 10 Sep 2014 14:25:57 -0700 (PDT) Subject: [ITK] Image bounds question Message-ID: Hello, I've been using a program for adding a constant padding to an image. This has worked to pad each edge, resulting in negative bounds. Now I've added the code as a subroutine and the behavior has changed. The padding now appears on only the positive side of the bounds, so the bounds still start at 0, 0, 0. It appears that writing the image changes the behavior of the bounds? Does this have to do with the position of the origin? I'd like to understand this better. My subroutine is below. InternalImageType::Pointer PadImage(InternalImageType::Pointer origIm, double padFactor ) { typedef itk::ConstantPadImageFilter ConstantPadImageFilterType; InternalImageType::SizeType lowerExtendRegion; lowerExtendRegion[0] = padFactor ; lowerExtendRegion[1] = padFactor ; lowerExtendRegion[2] = padFactor ; InternalImageType::SizeType upperExtendRegion; upperExtendRegion[0] = padFactor ; upperExtendRegion[1] = padFactor ; upperExtendRegion[2] = padFactor ; InternalImageType::PixelType constantPixel = 0; ConstantPadImageFilterType::Pointer padFilter = ConstantPadImageFilterType::New(); padFilter->SetInput(origIm); padFilter->SetPadLowerBound(lowerExtendRegion); padFilter->SetPadUpperBound(upperExtendRegion); padFilter->SetConstant(0); padFilter->Update(); return padFilter->GetOutput(); } Thanks, Sara From biradarsumangala at gmail.com Wed Sep 10 18:06:29 2014 From: biradarsumangala at gmail.com (biradarsumangala at gmail.com) Date: Wed, 10 Sep 2014 17:06:29 -0500 Subject: [ITK] [ITK-users] biradarsumangala@gmail.com has indicated you're a friend. Accept? 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URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From gabrielgimenez85 at gmail.com Wed Sep 10 21:55:56 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Wed, 10 Sep 2014 18:55:56 -0700 (PDT) Subject: [ITK] [ITK-users] itkParticleSwarmOptimizer - Example Message-ID: <1410400556611-7586188.post@n2.nabble.com> Hello everyone, is there an example of using the ParticleSwarmOptimizer in ITK? I tried using it but it throws the following error: *itkParticleSwarmOptimizerBase.cxx Line: 360 Description: itk::ERROR: ParticleSwarmOptimizer(0xa2a19d8): cost function and parameter bounds dimensions mismatch* I found no information about the error nor the optimizer. Thank you very much. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/itkParticleSwarmOptimizer-Example-tp7586188.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 11 09:05:28 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 11 Sep 2014 09:05:28 -0400 Subject: [ITK] [ITK-users] Fwd: using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> Message-ID: <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov> Hello, First I would look at the output of the conda build. What that OK? Did it give a successful output? Next I would look into the site packages directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages) for the SimpleITK directory. Brad On Sep 11, 2014, at 12:43 AM, Vishwa wrote: > > > I did install anaconda again and ran the conda build like you suggest. It ran without and problem. However, when I import simpleitk, it gives a error saying no module found. > > Any ideas? > > Vishwa > > On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] wrote: > Hello, > > You need to use the conda build environment. Look at the readme in this repo[1]. > > Basically you'll need to do the following: > > $ conda install conda-build > $ cd src > $ git clone https://github.com/thewtex/conda-recipes.git > $ git checkout simpleitk-clone-url > $ conda build simpleitk > > > > [1] https://github.com/conda/conda-recipes > > On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]> wrote: > >> Thanks very much for the information. I looked at the conda recipe. There are three files. >> One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile.. >> >> There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. >> >> Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. >> >> Best regards, >> Vishwa >> >> >> >> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]> wrote: >> Hello, >> >> This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment. >> >> I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct. >> >> You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker. >> >> Also you can inspect the runtime libraries: >> >> otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so >> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: >> @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0) >> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0) >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1) >> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0) >> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0) >> >> [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme >> >> Hope this helps, >> Brad >> >> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]> wrote: >> >>> import SimpleITK as sitk >>> >>> Fatal Python error: PyThreadState_Get: no current thread >>> >>> >>> Abort trap: 6 >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > If you reply to this email, your message will be added to the discussion below: > http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179p7586186.html > To unsubscribe from using simpleITK with anaconda python distribution, click here. > NAML > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 11 20:36:50 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 11 Sep 2014 20:36:50 -0400 Subject: [ITK] [ITK-users] Fwd: using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov> Message-ID: <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov> From [1] did you try: conda install --use-local simpleitk Brad [1] http://conda.pydata.org/docs/build_tutorials/pkgs.html On Sep 11, 2014, at 1:06 PM, Vishwa wrote: > Hi All, > I think python PythonPackage/setup.py installed wasn't in the location that the recipe calls for. I manually went to the location and ran the command. It was in the following folder > > /Users/dagarshali/anaconda/conda-bld/work/build/SimpleITK-build/Wrapping > > After that when I checked for simpleITK in /Users/dagarshali/anaconda/lib/python2.7/site-packages, I found > > > /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK > > Now, when I try to import simpleitk, i get an error which is shown below. > > >>> import SimpleITK as sitk > > Traceback (most recent call last): > > File "", line 1, in > > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in > > from .SimpleITK import * > > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in > > _SimpleITK = swig_import_helper() > > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > > ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libjpeg.8.dylib > > Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so > > Reason: image not found > > > > I am guessing that's a progress from where I was. Any ideas to fix this one? > > > > Vishwa > > > On Thu, Sep 11, 2014 at 11:18 AM, Vishwa wrote: > Hi, > I looked in ~/anaconda//lib/python2.7/site-packages and couldn't find the simpleitk directory. I ran the conda build again and saved the log file. I am attaching here for your reference. Hopefully, that should tell us something. > > Vishwa > > On Thu, Sep 11, 2014 at 8:05 AM, Bradley Lowekamp wrote: > Hello, > > First I would look at the output of the conda build. What that OK? Did it give a successful output? Next I would look into the site packages directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages) for the SimpleITK directory. > > Brad > On Sep 11, 2014, at 12:43 AM, Vishwa wrote: > >> >> >> I did install anaconda again and ran the conda build like you suggest. It ran without and problem. However, when I import simpleitk, it gives a error saying no module found. >> >> Any ideas? >> >> Vishwa >> >> On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] wrote: >> Hello, >> >> You need to use the conda build environment. Look at the readme in this repo[1]. >> >> Basically you'll need to do the following: >> >> $ conda install conda-build >> $ cd src >> $ git clone https://github.com/thewtex/conda-recipes.git >> $ git checkout simpleitk-clone-url >> $ conda build simpleitk >> >> >> >> [1] https://github.com/conda/conda-recipes >> >> On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]> wrote: >> >>> Thanks very much for the information. I looked at the conda recipe. There are three files. >>> One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile.. >>> >>> There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. >>> >>> Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. >>> >>> Best regards, >>> Vishwa >>> >>> >>> >>> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]> wrote: >>> Hello, >>> >>> This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment. >>> >>> I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct. >>> >>> You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker. >>> >>> Also you can inspect the runtime libraries: >>> >>> otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so >>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: >>> @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0) >>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0) >>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1) >>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0) >>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0) >>> >>> [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme >>> >>> Hope this helps, >>> Brad >>> >>> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]> wrote: >>> >>>> import SimpleITK as sitk >>>> >>>> Fatal Python error: PyThreadState_Get: no current thread >>>> >>>> >>>> Abort trap: 6 >>>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> If you reply to this email, your message will be added to the discussion below: >> http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179p7586186.html >> To unsubscribe from using simpleITK with anaconda python distribution, click here. >> NAML >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Fri Sep 12 02:02:22 2014 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Fri, 12 Sep 2014 02:02:22 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: DICOM Spatial Transform IO in the Insight Toolkit Message-ID: <20140912060222.BDC953D6C18C@insightsoftwareconsortium.org> Hello, A new submission has been added to the Insight Journal. Title: DICOM Spatial Transform IO in the Insight Toolkit Authors: McCormick M., Wang K., Lasso A., Sharp G., Pieper S. Abstract: This document describes a module that extends the Insight Toolkit, ITK, which reads DICOM Spatial Rogistration Object files in itk::Transform's. Currently, DICOM files are read by applying the DCMTK library as a backend. An itk::DCMTKTransformIO class can be registration with the IO factory mechanism so itk::TransformFileReadertemplate will recognize and read these files. This paper is accompanied with the source code, input data, parameters and output data that the authors used for validating the algorithm described in this paper. This adhere to the fundamental principle that scientific publications must facilitate reproducibility of the reported results. Download and review this publication at: http://hdl.handle.net/10380/3468 Generated by the Insight Journal You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://insight-journal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jean-charles.quillet at alyotech.fr Fri Sep 12 03:59:22 2014 From: jean-charles.quillet at alyotech.fr (QUILLET Jean-Charles) Date: Fri, 12 Sep 2014 09:59:22 +0200 Subject: [ITK] Hyperspectral images resampling Message-ID: <06A7AD4E92172446ADDEB44F8A5D5C1032802DC904@ARE01.alyotech.fr> Hello, I need to resample hyperspectral images along the third dimension. I mean, let's say I have an image with 200 bands. Can I resample the image to have 100 bands ? I'm pretty sure it is possible to do it with Itk. Can you confirm me this ? Can someone point me to the right direction (documentation, example) ? Thanks, Jean-Charles -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilian_oliver.mordig at roche.com Fri Sep 12 07:10:51 2014 From: maximilian_oliver.mordig at roche.com (maximilian) Date: Fri, 12 Sep 2014 04:10:51 -0700 (PDT) Subject: [ITK] [ITK-users] Integrate SCIFIO into ITK Message-ID: <1410520251887-7586194.post@n2.nabble.com> Dear All, I have problems including the image IO that comes with SCIFIO. I rebuilt ITK with the MODULE_SCIFIO flag activated. Then, I created a new project with the same content as "itkSCIFIOImageIOTest.cxx" that comes with the SCIFIO plugin. ITK can't find the itkSCIFIOImageIO.h header. The error is: fatal error C1083: Cannot open include file: 'itkSCIFIOImageIO.h': No such file or directory What do I have to add in my CMake file? My current CMakeLists.txt is: cmake_minimum_required(VERSION 2.8) project( ReadFlex ) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) add_executable(ReadFlex ReadFlex.cxx) target_link_libraries( ReadFlex ${ITK_LIBRARIES} ) Thanks in advance -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Integrate-SCIFIO-into-ITK-tp7586194.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From mikael.k.eriksson at philips.com Fri Sep 12 08:48:04 2014 From: mikael.k.eriksson at philips.com (Eriksson, Mikael) Date: Fri, 12 Sep 2014 12:48:04 +0000 Subject: [ITK] Multiple ITK-builds and CMake Message-ID: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> Hello, I'm experiencing some problems trying to build BRAINSTools (https://github.com/BRAINSia/BRAINSTools), from where I wanted to run the registration algorithms implemented in the 3DSlicer gui from the command line. The initial situation was: I had ITK (4.5) and VTK built from downloaded files in debug mode on my computer. I managed to build the modules that I wanted from BRAINSTools (BRAINSFit and BRAINSDemonWarp and their dependencies) in debug mode. Everything was fine until I tried running a registration - I hadn't realized until then that debug mode would make the registrations run really slowly. So, since I now have git on my computer, I cloned fresh versions of ITK and VTK to new source folders at the same levels as the old source folders, and built one debug version and one release version for both ITK and VTK, into separate folders. So my directory structure looked like this. C:/ - ITK/ - srcOld (ITK 4.5, from files) binOld (debug) srcNewDebug (ITK 4.7, from source) srcNewRelease (ITK 4.7, from source) binNewDebug binNewRelease C:/ - VTK/ - corresponding... I probably have an unnecessary amount of builds and folders, but I was afraid to ruin any previous work. Now I tried to build BRAINSTools again with CMake. The problem here is that there is no option to specify ITK_DIR in the CMakeGUI, as there is in other programs. So I'm not sure how CMake finds and chooses an ITK-build, but I think it fails, because when compiling the BRAINSTools solution in Visual Studio 2010 as usual, using release mode this time, I got linking errors saying that some ITK-libraries couldn't be found: error LNK1181: cannot open input file '..\..\lib\Release\ITKCommon-4.7.lib' I changed my environment variables ITK_DIR to C:/ITK/binNewRelease and changed the old ITK and VTK entries in the PATH variables to the new ones (changed C:\ITK\binOld\bin\debug to C:\ITK\binNewRelease\bin\Release and same for VTK). The same problem persisted however. Can anybody, give any suggestions for how to solve this particular problem? Also, I would be very happy for an explanation or a good link for how CMake and ITK interconnect, and especially, how CMake chooses an ITK build. I looked at the findITK.CMake files, and the ITKConfig.cmake and useITK.cmake files and read the documentation for the find_package function, but it's still not clear to me how it works. Best regards, Mikael ....................................................................................................... Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies mikael.k.eriksson at philips.com ....................................................................................................... ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Sep 12 09:37:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 12 Sep 2014 09:37:24 -0400 Subject: [ITK] Hyperspectral images resampling In-Reply-To: <06A7AD4E92172446ADDEB44F8A5D5C1032802DC904@ARE01.alyotech.fr> References: <06A7AD4E92172446ADDEB44F8A5D5C1032802DC904@ARE01.alyotech.fr> Message-ID: Hi Jean-Charles, If the spectral components are treated as the third dimension, then the image can be resampled with the ResampleImageFilter with a low-pass filter to prevent aliasing [1] or with the BinShrinkFilter [2]. Hope this helps, Matt [1] http://www.itk.org/Doxygen/html/Filtering_2SubsampleVolume_8cxx-example.html [2] http://www.itk.org/Doxygen/html/classitk_1_1BinShrinkImageFilter.html On Fri, Sep 12, 2014 at 3:59 AM, QUILLET Jean-Charles wrote: > Hello, > > > > I need to resample hyperspectral images along the third dimension. I mean, > let's say I have an image with 200 bands. Can I resample the image to have > 100 bands ? > > > > I'm pretty sure it is possible to do it with Itk. Can you confirm me this ? > Can someone point me to the right direction (documentation, example) ? > > Thanks, > > > > Jean-Charles > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Fri Sep 12 09:54:31 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 12 Sep 2014 09:54:31 -0400 Subject: [ITK] Multiple ITK-builds and CMake In-Reply-To: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> References: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: Hi Mikael, A few pointers: - Only a single source per project directory is needed. - Set ITK_DIR in the cmake-gui explicitly for each configuration -- don't try to use environmental variables, etc. More details on how find_package works can be found here [1] and here [2]. Hope this helps, Matt [1] http://www.cmake.org/cmake/help/v3.0/command/find_package.html#command:find_package [2] http://www.cmake.org/cmake/help/v3.0/manual/cmake-packages.7.html On Fri, Sep 12, 2014 at 8:48 AM, Eriksson, Mikael wrote: > Hello, > > > > I?m experiencing some problems trying to build BRAINSTools > (https://github.com/BRAINSia/BRAINSTools), from where I wanted to run the > registration algorithms implemented in the 3DSlicer gui from the command > line. The initial situation was: I had ITK (4.5) and VTK built from > downloaded files in debug mode on my computer. I managed to build the > modules that I wanted from BRAINSTools (BRAINSFit and BRAINSDemonWarp and > their dependencies) in debug mode. Everything was fine until I tried running > a registration ? I hadn?t realized until then that debug mode would make the > registrations run really slowly. > > > > So, since I now have git on my computer, I cloned fresh versions of ITK and > VTK to new source folders at the same levels as the old source folders, and > built one debug version and one release version for both ITK and VTK, into > separate folders. So my directory structure looked like this. > > > > C:/ - ITK/ - srcOld (ITK 4.5, from > files) > > binOld > (debug) > > srcNewDebug (ITK 4.7, from source) > > srcNewRelease (ITK 4.7, from source) > > binNewDebug > > binNewRelease > > > > C:/ - VTK/ - corresponding? > > > > I probably have an unnecessary amount of builds and folders, but I was > afraid to ruin any previous work. > > > > Now I tried to build BRAINSTools again with CMake. The problem here is that > there is no option to specify ITK_DIR in the CMakeGUI, as there is in other > programs. So I?m not sure how CMake finds and chooses an ITK-build, but I > think it fails, because when compiling the BRAINSTools solution in Visual > Studio 2010 as usual, using release mode this time, I got linking errors > saying that some ITK-libraries couldn?t be found: > > > > error LNK1181: cannot open input file '..\..\lib\Release\ITKCommon-4.7.lib' > > > > I changed my environment variables ITK_DIR to C:/ITK/binNewRelease and > changed the old ITK and VTK entries in the PATH variables to the new ones > (changed C:\ITK\binOld\bin\debug to C:\ITK\binNewRelease\bin\Release and > same for VTK). The same problem persisted however. Can anybody, give any > suggestions for how to solve this particular problem? Also, I would be very > happy for an explanation or a good link for how CMake and ITK interconnect, > and especially, how CMake chooses an ITK build. I looked at the > findITK.CMake files, and the ITKConfig.cmake and useITK.cmake files and read > the documentation for the find_package function, but it?s still not clear to > me how it works. > > > > Best regards, > > Mikael > > > > ??????????????????????????????????. > > Mikael Eriksson > > R&D Physicist Trainee > > Philips Medical Systems MR Finland, Feasibility studies > > mikael.k.eriksson at philips.com > > ??????????????????????????????????. > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From HIROTATSU.ARMSTRONG at UCDENVER.EDU Fri Sep 12 14:05:52 2014 From: HIROTATSU.ARMSTRONG at UCDENVER.EDU (Armstrong, Hirotatsu) Date: Fri, 12 Sep 2014 18:05:52 +0000 Subject: [ITK] VTK Deplacement Field Format Message-ID: <6a5c51da2497473e9b17bc41ba196482@CO1PR05MB411.namprd05.prod.outlook.com> Hello, I am having some trouble understanding the format of a .vtk file. I am deformably registering 2 CT images and saving the displacement field in a .vtk file. According to a pdf I found (for VTK v4.2), when written in ASCII format, vector data should have 3 values on each line corresponding to the x,y,z components for each vector. When I write my .vtk file, I get this, # vtk DataFile Version 3.0 VTK File Generated by Insight Segmentation and Registration Toolkit (ITK) ASCII DATASET STRUCTURED_POINTS DIMENSIONS 512 512 88 SPACING 9.7656250000000000e-001 9.7656250000000000e-001 3.0000000000000000e+000 ORIGIN -2.5000000000000000e+002 -1.0900000000000000e+002 -1.5900000000000000e+002 POINT_DATA 23068672 VECTORS vectors float -0.0644559 -0.0859412 0 0.231144 -0.231144 0 0.242202 -0.201835 0 -0.211765 0 0 0.164835 -0.362637 0 0.159204 -0.437811 0 0.108108 -0.0405405 0 0.395062 -0.0493827 0 -0.0987654 0.00493827 0 0.447702 -0.127915 0 -0.167866 0.167866 0 -0.359551 -0.134831 0 . . . Which is giving 6 values on each line. I looked for some documentation but couldn't find anything other than the pdf. Could someone please point me to the latest documentation for the .vtk file format? Also, I originally wrote the files in binary format, but was having some issue with that as well, which is why I switched to ASCII so I can actually visualize the data. The documentation is not clear if there are newline characters included or not when binary data is written. I would assume not, but could this be clarified as well? Thanks James Armstrong, Ph.D. PostDoctoral Fellow, Physics Department of Radiation Oncology University of Colorado School of Medicine 1665 Aurora Ct, MS F706 Aurora, CO 80045 720-848-0257 -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Sep 12 14:44:50 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 12 Sep 2014 14:44:50 -0400 Subject: [ITK] VTK Deplacement Field Format In-Reply-To: <6a5c51da2497473e9b17bc41ba196482@CO1PR05MB411.namprd05.prod.outlook.com> References: <6a5c51da2497473e9b17bc41ba196482@CO1PR05MB411.namprd05.prod.outlook.com> Message-ID: Hi James, Yes, it looks like ITK's .vtk files writer is not following the standard very well, and it is printing six values per line [1]. The binary version will not have any newlines. Hope this helps, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/src/itkImageIOBase.cxx;h=ae10e65dee1ecff0579d9ba43db9118c4466eec7;hb=HEAD#l656 On Fri, Sep 12, 2014 at 2:05 PM, Armstrong, Hirotatsu wrote: > Hello, > > > > I am having some trouble understanding the format of a .vtk file. I am > deformably registering 2 CT images and saving the displacement field in a > .vtk file. According to a pdf I found (for VTK v4.2), when written in ASCII > format, vector data should have 3 values on each line corresponding to the > x,y,z components for each vector. When I write my .vtk file, I get this, > > > > > > # vtk DataFile Version 3.0 > > VTK File Generated by Insight Segmentation and Registration Toolkit (ITK) > > ASCII > > DATASET STRUCTURED_POINTS > > DIMENSIONS 512 512 88 > > SPACING 9.7656250000000000e-001 9.7656250000000000e-001 > 3.0000000000000000e+000 > > ORIGIN -2.5000000000000000e+002 -1.0900000000000000e+002 > -1.5900000000000000e+002 > > POINT_DATA 23068672 > > VECTORS vectors float > > -0.0644559 -0.0859412 0 0.231144 -0.231144 0 > > 0.242202 -0.201835 0 -0.211765 0 0 > > 0.164835 -0.362637 0 0.159204 -0.437811 0 > > 0.108108 -0.0405405 0 0.395062 -0.0493827 0 > > -0.0987654 0.00493827 0 0.447702 -0.127915 0 > > -0.167866 0.167866 0 -0.359551 -0.134831 0 > > . > > . > > . > > > > > > Which is giving 6 values on each line. I looked for some documentation but > couldn?t find anything other than the pdf. Could someone please point me to > the latest documentation for the .vtk file format? Also, I originally wrote > the files in binary format, but was having some issue with that as well, > which is why I switched to ASCII so I can actually visualize the data. The > documentation is not clear if there are newline characters included or not > when binary data is written. I would assume not, but could this be > clarified as well? > > > > Thanks > > > > James Armstrong, Ph.D. > > PostDoctoral Fellow, Physics > > Department of Radiation Oncology > > University of Colorado School of Medicine > > 1665 Aurora Ct, MS F706 > > Aurora, CO 80045 > > 720-848-0257 > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From lasso at queensu.ca Fri Sep 12 15:08:11 2014 From: lasso at queensu.ca (Andras Lasso) Date: Fri, 12 Sep 2014 19:08:11 +0000 Subject: [ITK] VTK Deplacement Field Format In-Reply-To: References: <6a5c51da2497473e9b17bc41ba196482@CO1PR05MB411.namprd05.prod.outlook.com> Message-ID: .vtk is the old generic VTK file format, replaced by the XML-based file formats (.vti, .vtp, ...). I would not recommend using .vtk file format for image storage, especially the ASCII version (because it's big and floating-point numbers are not represented accurately). You can use MetaIO (.mha, .mhd) or NRRD (.nrrd, .nhdr) formats instead. They are both widely supported (ITK, VTK, 3D Slicer, ParaView, Matlab, etc.), well documented, and simple and efficient to parse. Andras -----Original Message----- From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt McCormick Sent: Friday, September 12, 2014 2:45 PM To: Armstrong, Hirotatsu Cc: community at itk.org Subject: Re: [ITK] VTK Deplacement Field Format Hi James, Yes, it looks like ITK's .vtk files writer is not following the standard very well, and it is printing six values per line [1]. The binary version will not have any newlines. Hope this helps, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/src/itkImageIOBase.cxx;h=ae10e65dee1ecff0579d9ba43db9118c4466eec7;hb=HEAD#l656 On Fri, Sep 12, 2014 at 2:05 PM, Armstrong, Hirotatsu wrote: > Hello, > > > > I am having some trouble understanding the format of a .vtk file. I > am deformably registering 2 CT images and saving the displacement > field in a .vtk file. According to a pdf I found (for VTK v4.2), when > written in ASCII format, vector data should have 3 values on each line > corresponding to the x,y,z components for each vector. When I write > my .vtk file, I get this, > > > > > > # vtk DataFile Version 3.0 > > VTK File Generated by Insight Segmentation and Registration Toolkit > (ITK) > > ASCII > > DATASET STRUCTURED_POINTS > > DIMENSIONS 512 512 88 > > SPACING 9.7656250000000000e-001 9.7656250000000000e-001 > 3.0000000000000000e+000 > > ORIGIN -2.5000000000000000e+002 -1.0900000000000000e+002 > -1.5900000000000000e+002 > > POINT_DATA 23068672 > > VECTORS vectors float > > -0.0644559 -0.0859412 0 0.231144 -0.231144 0 > > 0.242202 -0.201835 0 -0.211765 0 0 > > 0.164835 -0.362637 0 0.159204 -0.437811 0 > > 0.108108 -0.0405405 0 0.395062 -0.0493827 0 > > -0.0987654 0.00493827 0 0.447702 -0.127915 0 > > -0.167866 0.167866 0 -0.359551 -0.134831 0 > > . > > . > > . > > > > > > Which is giving 6 values on each line. I looked for some > documentation but couldn?t find anything other than the pdf. Could > someone please point me to the latest documentation for the .vtk file > format? Also, I originally wrote the files in binary format, but was > having some issue with that as well, which is why I switched to ASCII > so I can actually visualize the data. The documentation is not clear > if there are newline characters included or not when binary data is > written. I would assume not, but could this be clarified as well? > > > > Thanks > > > > James Armstrong, Ph.D. > > PostDoctoral Fellow, Physics > > Department of Radiation Oncology > > University of Colorado School of Medicine > > 1665 Aurora Ct, MS F706 > > Aurora, CO 80045 > > 720-848-0257 > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From vijayarani.shanmugavadivu at appasamy.com Sat Sep 13 08:34:42 2014 From: vijayarani.shanmugavadivu at appasamy.com (vijayarani) Date: Sat, 13 Sep 2014 05:34:42 -0700 (PDT) Subject: [ITK] [ITK-users] Resampling a mha image and finding histogram Message-ID: <1410611682783-7586198.post@n2.nabble.com> Hi I have a mha image which is very large.How to subsample it and find histogram of the image? Thanks Vijaya Rani S -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Resampling-a-mha-image-and-finding-histogram-tp7586198.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From vijayarani.shanmugavadivu at appasamy.com Sat Sep 13 08:39:28 2014 From: vijayarani.shanmugavadivu at appasamy.com (vijayarani) Date: Sat, 13 Sep 2014 18:09:28 +0530 Subject: [ITK] [ITK-users] Subsampling a mha image and finding histogram Message-ID: <54143B00.1070906@appasamy.com> Hi I have a mha image which is very large in size.How to subsample it and find histogram? Thanks Vijaya Rani S _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Sat Sep 13 13:00:50 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Sat, 13 Sep 2014 13:00:50 -0400 Subject: [ITK] [ITK-users] Fwd: using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov> <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov> Message-ID: <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov> Did you remove the installed SimpleITK from the setup.py script before running "const install --use-local simpleitk". I am guessing conda didn't install simpleitk correctly because of the old version manually installed. Brad On Sep 12, 2014, at 10:52 PM, Vishwa wrote: > Hi Brad, > Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter.. > > Here is the thing that I noticed.. > > If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error. > > >>import SimpleITK as sitk > Traceback (most recent call last): > File "", line 1, in > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in > from .SimpleITK import * > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in > _SimpleITK = swig_import_helper() > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib > Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so > Reason: image not found > > Any suggestions? > > > On Fri, Sep 12, 2014 at 6:59 PM, Vishwa wrote: > Hi Brad, > Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter.. > > Here is the thing that I noticed.. > > If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error. > > >>import SimpleITK as sitk > Traceback (most recent call last): > File "", line 1, in > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in > from .SimpleITK import * > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in > _SimpleITK = swig_import_helper() > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib > Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so > Reason: image not found > > Any suggestions? > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From brad at lowekamp.net Sat Sep 13 21:51:48 2014 From: brad at lowekamp.net (Bradley Lowekamp) Date: Sat, 13 Sep 2014 21:51:48 -0400 Subject: [ITK] [ITK-users] Fwd: using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov> <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov> <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov> Message-ID: <358E123A-966E-4C49-B2ED-9EC69B663C37@mail.nih.gov> Great to hear you got it working!!! I'll add a FAQ with specific instruction and some of the lessons learned here. Brad > On Sep 13, 2014, at 8:20 PM, Vishwa wrote: > > It finally worked with the conda install --use-local simpleitk command. > > Thanks everyone > > Regards, > vishwa > >> On Sat, Sep 13, 2014 at 2:36 PM, Vishwa wrote: >> I didn't remove it. How exactly do I do that? Also, from which folder should i run the conda install --use-local simpleitk command. >> >> I changed to conda recipes folder and issued the command. I got an error >> >> conda install --use-local simpleitk >> Fetching package metadata: ...Error: Could not find URL: file:///Users/dagarshali/anaconda/conda-bld/osx-64/ >> >> >>> On Sat, Sep 13, 2014 at 12:00 PM, Bradley Lowekamp wrote: >>> Did you remove the installed SimpleITK from the setup.py script before running "const install --use-local simpleitk". I am guessing conda didn't install simpleitk correctly because of the old version manually installed. >>> >>> Brad >>> >>>> On Sep 12, 2014, at 10:52 PM, Vishwa wrote: >>>> >>>> Hi Brad, >>>> Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter.. >>>> >>>> Here is the thing that I noticed.. >>>> >>>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error. >>>> >>>> >>import SimpleITK as sitk >>>> Traceback (most recent call last): >>>> File "", line 1, in >>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in >>>> from .SimpleITK import * >>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in >>>> _SimpleITK = swig_import_helper() >>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >>>> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >>>> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib >>>> Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so >>>> Reason: image not found >>>> >>>> Any suggestions? >>>> >>>> >>>>> On Fri, Sep 12, 2014 at 6:59 PM, Vishwa wrote: >>>>> Hi Brad, >>>>> Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter.. >>>>> >>>>> Here is the thing that I noticed.. >>>>> >>>>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error. >>>>> >>>>> >>import SimpleITK as sitk >>>>> Traceback (most recent call last): >>>>> File "", line 1, in >>>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in >>>>> from .SimpleITK import * >>>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in >>>>> _SimpleITK = swig_import_helper() >>>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >>>>> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >>>>> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib >>>>> Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so >>>>> Reason: image not found >>>>> >>>>> Any suggestions? > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Sun Sep 14 13:26:09 2014 From: llliu at umich.edu (Lianli Liu) Date: Sun, 14 Sep 2014 13:26:09 -0400 Subject: [ITK] [ITK-users] how to modify existing algorithm in ITK Message-ID: Hi all, I am brand new to ITK and I want to modify some ITK registration functions for specific use. But I am not clear about how to do this. After installation, it seems that I cannot find source code in the ITK-build folder. I just wonder if I want to redefine some functions, do I need to download the source code again? Or is there a tutorial giving example on how to modify existing algorithms in ITK? Thanks a lot! Regards, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Sun Sep 14 18:28:32 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sun, 14 Sep 2014 22:28:32 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff Message-ID: Hi all, I have run into an issue with 4.6, triggered by a problem with Slicer (another story - unable to load big tiffs). I have built Slicer, which includes ITK-4.6, on Windows 7. In my efforts to track down the problem Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 installation that I now have (I have previously been using 4.0). In principle the failure to load a big tiff should be a problem with ITK, not with Slicer. When I run cmake to set up the Visual Studio 10 project files for my simple test program (which works with 4.0), I get errors concerning DCMTK: D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 (message): Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR DCMTK_dcmimgle_LIBRARY) Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 (find_package_handle_standard_args) C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 (find_package) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 (itk_module_load) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 (_itk_module_config_recurse) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 (itk_module_config) C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 (find_package) CMakeLists.txt:4 (FIND_PACKAGE) Here is the stock-standard CMakeLists.txt: cmake_minimum_required(VERSION 2.8) PROJECT(makebig) FIND_PACKAGE(ITK) IF(ITK_FOUND) INCLUDE(${ITK_USE_FILE}) ELSE(ITK_FOUND) MESSAGE(FATAL_ERROR "ITK not found. Please set ITK_DIR.") ENDIF(ITK_FOUND) MESSAGE (${ITK_USE_FILE}) MESSAGE (${ITK_INCLUDE_DIRS}) set(PROJECTNAME "makebig") ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the error messages did not change. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Sun Sep 14 18:34:02 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sun, 14 Sep 2014 22:34:02 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: cmake-3.0.2 ________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 15 September 2014 10:28 a.m. To: community at itk.org Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi all, I have run into an issue with 4.6, triggered by a problem with Slicer (another story - unable to load big tiffs). I have built Slicer, which includes ITK-4.6, on Windows 7. In my efforts to track down the problem Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 installation that I now have (I have previously been using 4.0). In principle the failure to load a big tiff should be a problem with ITK, not with Slicer. When I run cmake to set up the Visual Studio 10 project files for my simple test program (which works with 4.0), I get errors concerning DCMTK: D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 (message): Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR DCMTK_dcmimgle_LIBRARY) Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 (find_package_handle_standard_args) C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 (find_package) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 (itk_module_load) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 (_itk_module_config_recurse) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 (itk_module_config) C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 (find_package) CMakeLists.txt:4 (FIND_PACKAGE) Here is the stock-standard CMakeLists.txt: cmake_minimum_required(VERSION 2.8) PROJECT(makebig) FIND_PACKAGE(ITK) IF(ITK_FOUND) INCLUDE(${ITK_USE_FILE}) ELSE(ITK_FOUND) MESSAGE(FATAL_ERROR "ITK not found. Please set ITK_DIR.") ENDIF(ITK_FOUND) MESSAGE (${ITK_USE_FILE}) MESSAGE (${ITK_INCLUDE_DIRS}) set(PROJECTNAME "makebig") ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the error messages did not change. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Sun Sep 14 20:12:48 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 14 Sep 2014 20:12:48 -0400 Subject: [ITK] [ITK-users] how to modify existing algorithm in ITK In-Reply-To: References: Message-ID: Hi Lianli, Welcome to ITK! ITK separates source from build artifacts. Usually, all source code is kept in the source tree, and all build artifacts are kept in the build tree. An install tree will install header files from the source tree and libraries from the build tree, and it will leave out the .cxx sources and .o object files. You can extend ITK by writing your own classes in a module as described here [1]. For investigating registration, some tools built on ITK like elastix [2] can be useful. As always, The ITK Software Guide is a great resource [3]. Hope this helps, Matt [1] http://www.kitware.com/blog/home/post/557 [2] http://elastix.isi.uu.nl/ [3] http://itk.org/ITK/resources/software.html On Sun, Sep 14, 2014 at 1:26 PM, Lianli Liu wrote: > Hi all, > > I am brand new to ITK and I want to modify some ITK registration functions > for specific use. But I am not clear about how to do this. After > installation, it seems that I cannot find source code in the ITK-build > folder. I just wonder if I want to redefine some functions, do I need to > download the source code again? Or is there a tutorial giving example on how > to modify existing algorithms in ITK? Thanks a lot! > > Regards, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sun Sep 14 22:51:04 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 14 Sep 2014 22:51:04 -0400 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: Hi Gib, Which version of DCMTK was built? Was it installed? Thanks, Matt On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: > cmake-3.0.2 > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 15 September 2014 10:28 a.m. > To: community at itk.org > Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi all, > > I have run into an issue with 4.6, triggered by a problem with Slicer > (another story - unable to load big tiffs). I have built Slicer, which > includes ITK-4.6, on Windows 7. In my efforts to track down the problem > Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 > installation that I now have (I have previously been using 4.0). In > principle the failure to load a big tiff should be a problem with ITK, not > with Slicer. > > When I run cmake to set up the Visual Studio 10 project files for my simple > test program (which works with 4.0), I get errors concerning DCMTK: > > D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" > -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ > CMake Error at C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 > (message): > Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY > DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR > DCMTK_dcmimgle_LIBRARY) > Call Stack (most recent call first): > C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard > Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 > (find_package_handle_standard_args) > C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 > (find_package) > > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 > (itk_module_load) > > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 > (_itk_module_config_recurse) > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 > (itk_module_config) > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 > (find_package) > CMakeLists.txt:4 (FIND_PACKAGE) > > Here is the stock-standard CMakeLists.txt: > > cmake_minimum_required(VERSION 2.8) > > PROJECT(makebig) > FIND_PACKAGE(ITK) > IF(ITK_FOUND) > INCLUDE(${ITK_USE_FILE}) > ELSE(ITK_FOUND) > MESSAGE(FATAL_ERROR > "ITK not found. Please set ITK_DIR.") > ENDIF(ITK_FOUND) > MESSAGE (${ITK_USE_FILE}) > MESSAGE (${ITK_INCLUDE_DIRS}) > set(PROJECTNAME "makebig") > ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) > TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) > > I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the > error messages did not change. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From g.bogle at auckland.ac.nz Sun Sep 14 22:56:30 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 15 Sep 2014 02:56:30 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: , Message-ID: Hi Matt, Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. Cheers Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Monday, 15 September 2014 2:51 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi Gib, Which version of DCMTK was built? Was it installed? Thanks, Matt On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: > cmake-3.0.2 > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 15 September 2014 10:28 a.m. > To: community at itk.org > Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi all, > > I have run into an issue with 4.6, triggered by a problem with Slicer > (another story - unable to load big tiffs). I have built Slicer, which > includes ITK-4.6, on Windows 7. In my efforts to track down the problem > Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 > installation that I now have (I have previously been using 4.0). In > principle the failure to load a big tiff should be a problem with ITK, not > with Slicer. > > When I run cmake to set up the Visual Studio 10 project files for my simple > test program (which works with 4.0), I get errors concerning DCMTK: > > D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" > -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ > CMake Error at C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 > (message): > Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY > DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR > DCMTK_dcmimgle_LIBRARY) > Call Stack (most recent call first): > C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard > Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 > (find_package_handle_standard_args) > C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 > (find_package) > > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 > (itk_module_load) > > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 > (_itk_module_config_recurse) > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 > (itk_module_config) > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 > (find_package) > CMakeLists.txt:4 (FIND_PACKAGE) > > Here is the stock-standard CMakeLists.txt: > > cmake_minimum_required(VERSION 2.8) > > PROJECT(makebig) > FIND_PACKAGE(ITK) > IF(ITK_FOUND) > INCLUDE(${ITK_USE_FILE}) > ELSE(ITK_FOUND) > MESSAGE(FATAL_ERROR > "ITK not found. Please set ITK_DIR.") > ENDIF(ITK_FOUND) > MESSAGE (${ITK_USE_FILE}) > MESSAGE (${ITK_INCLUDE_DIRS}) > set(PROJECTNAME "makebig") > ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) > TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) > > I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the > error messages did not change. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Sun Sep 14 23:05:46 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 14 Sep 2014 23:05:46 -0400 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: Hi Gib, Thanks for the information. What happens if DCMTK_DIR is pointed to the DCMTK build directory in the Slicer build tree? Thanks, Matt On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: > Hi Matt, > > Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. > > Cheers > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 2:51 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Which version of DCMTK was built? Was it installed? > > Thanks, > Matt > > On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >> cmake-3.0.2 >> ________________________________ >> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >> [g.bogle at auckland.ac.nz] >> Sent: Monday, 15 September 2014 10:28 a.m. >> To: community at itk.org >> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi all, >> >> I have run into an issue with 4.6, triggered by a problem with Slicer >> (another story - unable to load big tiffs). I have built Slicer, which >> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >> installation that I now have (I have previously been using 4.0). In >> principle the failure to load a big tiff should be a problem with ITK, not >> with Slicer. >> >> When I run cmake to set up the Visual Studio 10 project files for my simple >> test program (which works with 4.0), I get errors concerning DCMTK: >> >> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >> CMake Error at C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >> (message): >> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >> DCMTK_dcmimgle_LIBRARY) >> Call Stack (most recent call first): >> C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >> (find_package_handle_standard_args) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >> (find_package) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >> (itk_module_load) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >> (_itk_module_config_recurse) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >> (itk_module_config) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >> (find_package) >> CMakeLists.txt:4 (FIND_PACKAGE) >> >> Here is the stock-standard CMakeLists.txt: >> >> cmake_minimum_required(VERSION 2.8) >> >> PROJECT(makebig) >> FIND_PACKAGE(ITK) >> IF(ITK_FOUND) >> INCLUDE(${ITK_USE_FILE}) >> ELSE(ITK_FOUND) >> MESSAGE(FATAL_ERROR >> "ITK not found. Please set ITK_DIR.") >> ENDIF(ITK_FOUND) >> MESSAGE (${ITK_USE_FILE}) >> MESSAGE (${ITK_INCLUDE_DIRS}) >> set(PROJECTNAME "makebig") >> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >> >> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >> error messages did not change. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> From g.bogle at auckland.ac.nz Sun Sep 14 23:09:33 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 15 Sep 2014 03:09:33 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: , Message-ID: The same result. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Monday, 15 September 2014 3:05 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi Gib, Thanks for the information. What happens if DCMTK_DIR is pointed to the DCMTK build directory in the Slicer build tree? Thanks, Matt On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: > Hi Matt, > > Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. > > Cheers > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 2:51 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Which version of DCMTK was built? Was it installed? > > Thanks, > Matt > > On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >> cmake-3.0.2 >> ________________________________ >> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >> [g.bogle at auckland.ac.nz] >> Sent: Monday, 15 September 2014 10:28 a.m. >> To: community at itk.org >> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi all, >> >> I have run into an issue with 4.6, triggered by a problem with Slicer >> (another story - unable to load big tiffs). I have built Slicer, which >> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >> installation that I now have (I have previously been using 4.0). In >> principle the failure to load a big tiff should be a problem with ITK, not >> with Slicer. >> >> When I run cmake to set up the Visual Studio 10 project files for my simple >> test program (which works with 4.0), I get errors concerning DCMTK: >> >> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >> CMake Error at C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >> (message): >> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >> DCMTK_dcmimgle_LIBRARY) >> Call Stack (most recent call first): >> C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >> (find_package_handle_standard_args) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >> (find_package) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >> (itk_module_load) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >> (_itk_module_config_recurse) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >> (itk_module_config) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >> (find_package) >> CMakeLists.txt:4 (FIND_PACKAGE) >> >> Here is the stock-standard CMakeLists.txt: >> >> cmake_minimum_required(VERSION 2.8) >> >> PROJECT(makebig) >> FIND_PACKAGE(ITK) >> IF(ITK_FOUND) >> INCLUDE(${ITK_USE_FILE}) >> ELSE(ITK_FOUND) >> MESSAGE(FATAL_ERROR >> "ITK not found. Please set ITK_DIR.") >> ENDIF(ITK_FOUND) >> MESSAGE (${ITK_USE_FILE}) >> MESSAGE (${ITK_INCLUDE_DIRS}) >> set(PROJECTNAME "makebig") >> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >> >> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >> error messages did not change. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> From g.bogle at auckland.ac.nz Sun Sep 14 23:45:24 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 15 Sep 2014 03:45:24 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: , , Message-ID: Slicer built OK before I added DCMTK_DIR. ________________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 15 September 2014 3:09 p.m. To: Matt McCormick Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff The same result. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Monday, 15 September 2014 3:05 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi Gib, Thanks for the information. What happens if DCMTK_DIR is pointed to the DCMTK build directory in the Slicer build tree? Thanks, Matt On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: > Hi Matt, > > Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. > > Cheers > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 2:51 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Which version of DCMTK was built? Was it installed? > > Thanks, > Matt > > On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >> cmake-3.0.2 >> ________________________________ >> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >> [g.bogle at auckland.ac.nz] >> Sent: Monday, 15 September 2014 10:28 a.m. >> To: community at itk.org >> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi all, >> >> I have run into an issue with 4.6, triggered by a problem with Slicer >> (another story - unable to load big tiffs). I have built Slicer, which >> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >> installation that I now have (I have previously been using 4.0). In >> principle the failure to load a big tiff should be a problem with ITK, not >> with Slicer. >> >> When I run cmake to set up the Visual Studio 10 project files for my simple >> test program (which works with 4.0), I get errors concerning DCMTK: >> >> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >> CMake Error at C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >> (message): >> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >> DCMTK_dcmimgle_LIBRARY) >> Call Stack (most recent call first): >> C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >> (find_package_handle_standard_args) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >> (find_package) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >> (itk_module_load) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >> (_itk_module_config_recurse) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >> (itk_module_config) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >> (find_package) >> CMakeLists.txt:4 (FIND_PACKAGE) >> >> Here is the stock-standard CMakeLists.txt: >> >> cmake_minimum_required(VERSION 2.8) >> >> PROJECT(makebig) >> FIND_PACKAGE(ITK) >> IF(ITK_FOUND) >> INCLUDE(${ITK_USE_FILE}) >> ELSE(ITK_FOUND) >> MESSAGE(FATAL_ERROR >> "ITK not found. Please set ITK_DIR.") >> ENDIF(ITK_FOUND) >> MESSAGE (${ITK_USE_FILE}) >> MESSAGE (${ITK_INCLUDE_DIRS}) >> set(PROJECTNAME "makebig") >> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >> >> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >> error messages did not change. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From mikael.k.eriksson at philips.com Mon Sep 15 01:40:41 2014 From: mikael.k.eriksson at philips.com (Eriksson, Mikael) Date: Mon, 15 Sep 2014 05:40:41 +0000 Subject: [ITK] Multiple ITK-builds and CMake In-Reply-To: References: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: <2D9DC0609429E24BA87612C012C580C318A76AB7@AMSPRD9002MB028.MGDPHG.emi.philips.com> Hi Matt and community, - Got it! - That is the problem here, the CMake-gui for this application has no ITK_DIR entry so that I can explicitly specify which one to use. Any suggestions for how to get around this? Best, Mikael ??????????????????????????????????. Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies +358 40 631 8500 mikael.k.eriksson at philips.com ??????????????????????????????????. -----Original Message----- From: Matt McCormick [mailto:matt.mccormick at kitware.com] Sent: 12. syyskuuta 2014 16:55 To: Eriksson, Mikael Cc: community at itk.org Subject: Re: [ITK] Multiple ITK-builds and CMake Hi Mikael, A few pointers: - Only a single source per project directory is needed. - Set ITK_DIR in the cmake-gui explicitly for each configuration -- don't try to use environmental variables, etc. More details on how find_package works can be found here [1] and here [2]. Hope this helps, Matt [1] http://www.cmake.org/cmake/help/v3.0/command/find_package.html#command:find_package [2] http://www.cmake.org/cmake/help/v3.0/manual/cmake-packages.7.html On Fri, Sep 12, 2014 at 8:48 AM, Eriksson, Mikael wrote: > Hello, > > > > I?m experiencing some problems trying to build BRAINSTools > (https://github.com/BRAINSia/BRAINSTools), from where I wanted to run > the registration algorithms implemented in the 3DSlicer gui from the > command line. The initial situation was: I had ITK (4.5) and VTK built > from downloaded files in debug mode on my computer. I managed to build > the modules that I wanted from BRAINSTools (BRAINSFit and > BRAINSDemonWarp and their dependencies) in debug mode. Everything was > fine until I tried running a registration ? I hadn?t realized until > then that debug mode would make the registrations run really slowly. > > > > So, since I now have git on my computer, I cloned fresh versions of > ITK and VTK to new source folders at the same levels as the old source > folders, and built one debug version and one release version for both > ITK and VTK, into separate folders. So my directory structure looked like this. > > > > C:/ - ITK/ - srcOld (ITK 4.5, from > files) > > binOld > (debug) > > srcNewDebug (ITK 4.7, from source) > > srcNewRelease (ITK 4.7, from source) > > binNewDebug > > binNewRelease > > > > C:/ - VTK/ - corresponding? > > > > I probably have an unnecessary amount of builds and folders, but I was > afraid to ruin any previous work. > > > > Now I tried to build BRAINSTools again with CMake. The problem here is > that there is no option to specify ITK_DIR in the CMakeGUI, as there > is in other programs. So I?m not sure how CMake finds and chooses an > ITK-build, but I think it fails, because when compiling the > BRAINSTools solution in Visual Studio 2010 as usual, using release > mode this time, I got linking errors saying that some ITK-libraries couldn?t be found: > > > > error LNK1181: cannot open input file '..\..\lib\Release\ITKCommon-4.7.lib' > > > > I changed my environment variables ITK_DIR to C:/ITK/binNewRelease and > changed the old ITK and VTK entries in the PATH variables to the new > ones (changed C:\ITK\binOld\bin\debug to > C:\ITK\binNewRelease\bin\Release and same for VTK). The same problem > persisted however. Can anybody, give any suggestions for how to solve > this particular problem? Also, I would be very happy for an > explanation or a good link for how CMake and ITK interconnect, and > especially, how CMake chooses an ITK build. I looked at the > findITK.CMake files, and the ITKConfig.cmake and useITK.cmake files > and read the documentation for the find_package function, but it?s still not clear to me how it works. > > > > Best regards, > > Mikael > > > > ??????????????????????????????????. > > Mikael Eriksson > > R&D Physicist Trainee > > Philips Medical Systems MR Finland, Feasibility studies > > mikael.k.eriksson at philips.com > > ??????????????????????????????????. > > > > > ________________________________ > The information contained in this message may be confidential and > legally protected under applicable law. The message is intended solely > for the addressee(s). If you are not the intended recipient, you are > hereby notified that any use, forwarding, dissemination, or > reproduction of this message is strictly prohibited and may be > unlawful. If you are not the intended recipient, please contact the > sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From arnaudgelas at gmail.com Mon Sep 15 06:05:02 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Mon, 15 Sep 2014 12:05:02 +0200 Subject: [ITK] [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData Message-ID: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com> Hi guys, I have been looking at GDCMImageIO this morning and I thought it would be great if it was possible to iterate directly on the Dictionary and do not use ExposeMetaData cause internally there are 2 finds (HasKeys and [] ) per iterator (in which we already know both keys and values). https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L700 https://github.com/Kitware/ITK/blob/master/Modules/Core/Common/include/itkMetaDataObject.h#L171-L189 I have tried to create a new function which would take an iterator as parameter, I have compilation error or a failing dynamic_cast? I guess I am missing something obvious? I have been testing something like that: http://review.source.kitware.com/#/c/17026/ Any idea on how to fix the code ( both compilation & dynamic_cast ), please? Thanks, Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Sep 15 11:36:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 11:36:11 -0400 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: Hi Gib, Please try building DCMTK by pointing a clean build directory to this directory [1]. Then, start a clean build of ITK with DCMTK_DIR pointing to that directory. Please let us know if this works. Thanks, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/DCMTK/WindowsBuild/CMakeLists.txt;h=70c5ef6cfc25895ed54755818d7aa49299869fe6;hb=HEAD On Sun, Sep 14, 2014 at 11:45 PM, Gib Bogle wrote: > Slicer built OK before I added DCMTK_DIR. > ________________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] > Sent: Monday, 15 September 2014 3:09 p.m. > To: Matt McCormick > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > The same result. > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 3:05 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Thanks for the information. > > What happens if DCMTK_DIR is pointed to the DCMTK build directory in > the Slicer build tree? > > Thanks, > Matt > > > On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: >> Hi Matt, >> >> Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. >> >> Cheers >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Monday, 15 September 2014 2:51 p.m. >> To: Gib Bogle >> Cc: community at itk.org >> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi Gib, >> >> Which version of DCMTK was built? Was it installed? >> >> Thanks, >> Matt >> >> On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >>> cmake-3.0.2 >>> ________________________________ >>> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >>> [g.bogle at auckland.ac.nz] >>> Sent: Monday, 15 September 2014 10:28 a.m. >>> To: community at itk.org >>> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >>> >>> Hi all, >>> >>> I have run into an issue with 4.6, triggered by a problem with Slicer >>> (another story - unable to load big tiffs). I have built Slicer, which >>> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >>> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >>> installation that I now have (I have previously been using 4.0). In >>> principle the failure to load a big tiff should be a problem with ITK, not >>> with Slicer. >>> >>> When I run cmake to set up the Visual Studio 10 project files for my simple >>> test program (which works with 4.0), I get errors concerning DCMTK: >>> >>> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >>> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >>> CMake Error at C:/Program Files >>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >>> (message): >>> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >>> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >>> DCMTK_dcmimgle_LIBRARY) >>> Call Stack (most recent call first): >>> C:/Program Files >>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >>> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >>> (find_package_handle_standard_args) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >>> (find_package) >>> >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >>> (itk_module_load) >>> >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >>> (_itk_module_config_recurse) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >>> (itk_module_config) >>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >>> (find_package) >>> CMakeLists.txt:4 (FIND_PACKAGE) >>> >>> Here is the stock-standard CMakeLists.txt: >>> >>> cmake_minimum_required(VERSION 2.8) >>> >>> PROJECT(makebig) >>> FIND_PACKAGE(ITK) >>> IF(ITK_FOUND) >>> INCLUDE(${ITK_USE_FILE}) >>> ELSE(ITK_FOUND) >>> MESSAGE(FATAL_ERROR >>> "ITK not found. Please set ITK_DIR.") >>> ENDIF(ITK_FOUND) >>> MESSAGE (${ITK_USE_FILE}) >>> MESSAGE (${ITK_INCLUDE_DIRS}) >>> set(PROJECTNAME "makebig") >>> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >>> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >>> >>> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >>> error messages did not change. >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Mon Sep 15 11:41:37 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 11:41:37 -0400 Subject: [ITK] Multiple ITK-builds and CMake In-Reply-To: <2D9DC0609429E24BA87612C012C580C318A76AB7@AMSPRD9002MB028.MGDPHG.emi.philips.com> References: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> <2D9DC0609429E24BA87612C012C580C318A76AB7@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: Hi Mikael, Since BRAINSTools is a "superbuild", i.e. it will build its own ITK/VTK by default, you will need to tell the the build system to first not build its own, so that you can specify your manually built version. HTH, Matt On Mon, Sep 15, 2014 at 1:40 AM, Eriksson, Mikael wrote: > Hi Matt and community, > > - Got it! > - That is the problem here, the CMake-gui for this application has no ITK_DIR entry so that I can explicitly specify which one to use. Any suggestions for how to get around this? > > Best, > Mikael > > ??????????????????????????????????. > Mikael Eriksson > R&D Physicist Trainee > Philips Medical Systems MR Finland, Feasibility studies > > +358 40 631 8500 > mikael.k.eriksson at philips.com > ??????????????????????????????????. > > -----Original Message----- > From: Matt McCormick [mailto:matt.mccormick at kitware.com] > Sent: 12. syyskuuta 2014 16:55 > To: Eriksson, Mikael > Cc: community at itk.org > Subject: Re: [ITK] Multiple ITK-builds and CMake > > Hi Mikael, > > A few pointers: > > - Only a single source per project directory is needed. > - Set ITK_DIR in the cmake-gui explicitly for each configuration -- don't try to use environmental variables, etc. > > More details on how find_package works can be found here [1] and here [2]. > > Hope this helps, > Matt > > [1] http://www.cmake.org/cmake/help/v3.0/command/find_package.html#command:find_package > > [2] http://www.cmake.org/cmake/help/v3.0/manual/cmake-packages.7.html > > On Fri, Sep 12, 2014 at 8:48 AM, Eriksson, Mikael wrote: >> Hello, >> >> >> >> I?m experiencing some problems trying to build BRAINSTools >> (https://github.com/BRAINSia/BRAINSTools), from where I wanted to run >> the registration algorithms implemented in the 3DSlicer gui from the >> command line. The initial situation was: I had ITK (4.5) and VTK built >> from downloaded files in debug mode on my computer. I managed to build >> the modules that I wanted from BRAINSTools (BRAINSFit and >> BRAINSDemonWarp and their dependencies) in debug mode. Everything was >> fine until I tried running a registration ? I hadn?t realized until >> then that debug mode would make the registrations run really slowly. >> >> >> >> So, since I now have git on my computer, I cloned fresh versions of >> ITK and VTK to new source folders at the same levels as the old source >> folders, and built one debug version and one release version for both >> ITK and VTK, into separate folders. So my directory structure looked like this. >> >> >> >> C:/ - ITK/ - srcOld (ITK 4.5, from >> files) >> >> binOld >> (debug) >> >> srcNewDebug (ITK 4.7, from source) >> >> srcNewRelease (ITK 4.7, from source) >> >> binNewDebug >> >> binNewRelease >> >> >> >> C:/ - VTK/ - corresponding? >> >> >> >> I probably have an unnecessary amount of builds and folders, but I was >> afraid to ruin any previous work. >> >> >> >> Now I tried to build BRAINSTools again with CMake. The problem here is >> that there is no option to specify ITK_DIR in the CMakeGUI, as there >> is in other programs. So I?m not sure how CMake finds and chooses an >> ITK-build, but I think it fails, because when compiling the >> BRAINSTools solution in Visual Studio 2010 as usual, using release >> mode this time, I got linking errors saying that some ITK-libraries couldn?t be found: >> >> >> >> error LNK1181: cannot open input file '..\..\lib\Release\ITKCommon-4.7.lib' >> >> >> >> I changed my environment variables ITK_DIR to C:/ITK/binNewRelease and >> changed the old ITK and VTK entries in the PATH variables to the new >> ones (changed C:\ITK\binOld\bin\debug to >> C:\ITK\binNewRelease\bin\Release and same for VTK). The same problem >> persisted however. Can anybody, give any suggestions for how to solve >> this particular problem? Also, I would be very happy for an >> explanation or a good link for how CMake and ITK interconnect, and >> especially, how CMake chooses an ITK build. I looked at the >> findITK.CMake files, and the ITKConfig.cmake and useITK.cmake files >> and read the documentation for the find_package function, but it?s still not clear to me how it works. >> >> >> >> Best regards, >> >> Mikael >> >> >> >> ??????????????????????????????????. >> >> Mikael Eriksson >> >> R&D Physicist Trainee >> >> Philips Medical Systems MR Finland, Feasibility studies >> >> mikael.k.eriksson at philips.com >> >> ??????????????????????????????????. >> >> >> >> >> ________________________________ >> The information contained in this message may be confidential and >> legally protected under applicable law. The message is intended solely >> for the addressee(s). If you are not the intended recipient, you are >> hereby notified that any use, forwarding, dissemination, or >> reproduction of this message is strictly prohibited and may be >> unlawful. If you are not the intended recipient, please contact the >> sender by return e-mail and destroy all copies of the original message. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From bilgincc at gmail.com Mon Sep 15 11:50:51 2014 From: bilgincc at gmail.com (Cagatay Bilgin) Date: Mon, 15 Sep 2014 08:50:51 -0700 Subject: [ITK] [ITK-users] Motion under Mean Curvature with LevelSetv4 Framework In-Reply-To: References: Message-ID: Hi Arnaud, Sorry for the late response, I somehow missed this email. I have not done the same experiment in the old framework to compare against. I can giving it a shot but the old framework is more mysterious to me. Best, Cagatay Bilgin On Fri, Aug 8, 2014 at 1:44 AM, Arnaud Gelas wrote: > Hi Cagatay, > > I just came back from vacation... Have you solved this problem? > It would be great if we could make the equivalent code in the old > framework to compare and fix what could be wrong. Have you done something > like this? > > I'll start looking at it... > > Best, > Arnaud > > > On Tue, Jul 22, 2014 at 9:58 AM, Cagatay Bilgin > wrote: > >> Dear ITK Community, >> >> I am trying to familiarize myself with the new level set classes. My goal >> is to simulate motion under mean curvature using the new design. >> >> I have put together the following, looking at the examples and tests. >> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872740/ is a great source >> to understand the design and tests in source directory are very helpful, >> thank you for the resources! >> >> The test scenario I have is a L shaped object. I would expect the object >> to become somewhat ellipse and then disappear at the end of the evolution. >> However I get the following results attached to the email. I don't quite >> follow these results. Am I missing something obvious? >> >> Here is the code and CMakeLists.txt. I ran the program with ./Motion 100 >> 0 0 0.05 >> >> #include "itkBinaryImageToLevelSetImageAdaptor.h" >> #include "itkImageFileReader.h" >> #include "itkLevelSetContainer.h" >> #include "itkLevelSetEquationPropagationTerm.h" >> #include "itkLevelSetEquationAdvectionTerm2.h" >> #include "itkLevelSetEquationContainer.h" >> #include "itkLevelSetEquationTermContainer.h" >> #include "itkLevelSetEvolution.h" >> #include "itkLevelSetEvolutionNumberOfIterationsStoppingCriterion.h" >> #include "itkLevelSetDenseImage.h" >> #include "itkVTKVisualizeImageLevelSetIsoValues.h" >> #include "itkSinRegularizedHeavisideStepFunction.h" >> #include "itkLevelSetIterationUpdateCommand.h" >> #include "itkLevelSetEquationCurvatureTerm.h" >> #include "itkCastImageFilter.h" >> #include "itkWhitakerSparseLevelSetImage.h" >> #include "itkSpatialObjectToImageFilter.h" >> #include "itkEllipseSpatialObject.h" >> >> typedef itk::Image< float, 2 > FIT; >> >> /* >> * L Shape >> */ >> void CreateSquareImage(FIT::Pointer image) >> { >> FIT::RegionType region; >> FIT::IndexType start; >> start[0] = 0; >> start[1] = 0; >> >> FIT::SizeType size; >> size[0] = 200; >> size[1] = 300; >> >> region.SetSize(size); >> region.SetIndex(start); >> >> image->SetRegions(region); >> image->Allocate(); >> >> // Set pixels in a square to one value >> for(unsigned int r = 20; r < 160; r++) >> { >> for(unsigned int c = 30; c < 100; c++) >> { >> FIT::IndexType pixelIndex; >> pixelIndex[0] = r; >> pixelIndex[1] = c; >> >> image->SetPixel(pixelIndex, 255); >> } >> } >> >> for(unsigned int r = 20; r < 80; r++) >> { >> for(unsigned int c = 100; c < 200; c++) >> { >> FIT::IndexType pixelIndex; >> pixelIndex[0] = r; >> pixelIndex[1] = c; >> >> image->SetPixel(pixelIndex, 255); >> } >> } >> } >> >> >> /* >> */ >> int main( int argc, char* argv[] ) >> { >> if( argc != 5) >> { >> std::cerr << "Missing Arguments" << std::endl; >> std::cerr << argv[0] << std::endl; >> std::cerr << "1- Number of Iterations" << std::endl; >> std::cerr << "2- Propagation Term" << std::endl; >> std::cerr << "3- Advection Term" << std::endl; >> std::cerr << "4- Curvature Term" << std::endl; >> return EXIT_FAILURE; >> } >> >> // Image Dimension >> const unsigned int Dimension = 2; >> >> typedef unsigned char InputPixelType; >> typedef itk::Image< InputPixelType, Dimension > IIT; >> typedef itk::Image< float, 2 > FIT; >> >> FIT::Pointer input = FIT::New(); >> CreateSquareImage(input); >> >> int numberOfIterations = atoi( argv[1]); >> >> typedef float >> LevelSetPixelType; >> typedef itk::Image< LevelSetPixelType, Dimension > LSIT; >> typedef itk::LevelSetDenseImage< LSIT > LST; >> //typedef itk::WhitakerSparseLevelSetImage< LevelSetPixelType, 2 > >> LST; >> >> typedef LST::OutputType LevelSetOutputType; >> typedef LST::OutputRealType LevelSetRealType; >> >> // convert a binary mask to a level-set function >> typedef itk::BinaryImageToLevelSetImageAdaptor BI2LST; >> BI2LST::Pointer adaptor = BI2LST::New(); >> adaptor->SetInputImage( input ); >> adaptor->Initialize(); >> LST::Pointer levelSet = adaptor->GetLevelSet(); >> >> // The Heaviside function >> typedef itk::SinRegularizedHeavisideStepFunction< LevelSetRealType, >> LevelSetRealType > HeavisideFunctionType; >> HeavisideFunctionType::Pointer heaviside = >> HeavisideFunctionType::New(); >> heaviside->SetEpsilon( 1 ); >> >> // Create the level set container >> typedef itk::LevelSetContainer< itk::IdentifierType, LST > >> LSContainerT; >> LSContainerT::Pointer levelSetContainer = LSContainerT::New(); >> levelSetContainer->SetHeaviside( heaviside ); >> levelSetContainer->AddLevelSet( 0, levelSet ); >> >> // Create the terms. >> typedef itk::LevelSetEquationPropagationTerm >> PropagationTermType; >> PropagationTermType::Pointer propagationTerm = >> PropagationTermType::New(); >> propagationTerm->SetInput(input); >> propagationTerm->SetCoefficient(atof(argv[2])); >> >> typedef itk::LevelSetEquationAdvectionTerm2 >> AdvectionTermType; >> AdvectionTermType::Pointer advectionTerm = AdvectionTermType::New(); >> advectionTerm->SetInput(input); >> advectionTerm->SetCoefficient(atof(argv[3])); >> >> typedef itk::LevelSetEquationCurvatureTerm >> CurvatureTermType; >> CurvatureTermType::Pointer curvatureTerm = CurvatureTermType::New(); >> //curvatureTerm->SetInput(input); >> curvatureTerm->SetCoefficient(atof(argv[4])); >> >> >> // Create term container (equation rhs) >> typedef itk::LevelSetEquationTermContainer< FIT, LSContainerT > >> TermContainerType; >> TermContainerType::Pointer termContainer = TermContainerType::New(); >> termContainer->SetLevelSetContainer( levelSetContainer ); >> termContainer->SetInput( input ); >> //termContainer->AddTerm( 0, propagationTerm ); >> //termContainer->AddTerm( 1, advectionTerm ); >> termContainer->AddTerm( 0, curvatureTerm ); >> >> // Create equation container >> typedef itk::LevelSetEquationContainer< TermContainerType > >> EquationContainerType; >> EquationContainerType::Pointer equationContainer = >> EquationContainerType::New(); >> equationContainer->SetLevelSetContainer( levelSetContainer ); >> equationContainer->AddEquation( 0, termContainer ); >> >> // Create stopping criteria >> typedef itk::LevelSetEvolutionNumberOfIterationsStoppingCriterion< >> LSContainerT > StoppingCriterionType; >> StoppingCriterionType::Pointer criterion = >> StoppingCriterionType::New(); >> criterion->SetNumberOfIterations( numberOfIterations ); >> >> // Create the visualizer >> typedef itk::VTKVisualizeImageLevelSetIsoValues< FIT, LST > >> VisualizationType; >> VisualizationType::Pointer visualizer = VisualizationType::New(); >> visualizer->SetInputImage( input ); >> visualizer->SetLevelSet( levelSet ); >> visualizer->SetScreenCapture( true ); >> >> // Create evolution class >> typedef itk::LevelSetEvolution< EquationContainerType, LST > >> LevelSetEvolutionType; >> LevelSetEvolutionType::Pointer evolution = >> LevelSetEvolutionType::New(); >> evolution->SetEquationContainer( equationContainer ); >> evolution->SetStoppingCriterion( criterion ); >> evolution->SetLevelSetContainer( levelSetContainer ); >> >> typedef itk::LevelSetIterationUpdateCommand< LevelSetEvolutionType, >> VisualizationType > IterationUpdateCommandType; >> IterationUpdateCommandType::Pointer iterationUpdateCommand = >> IterationUpdateCommandType::New(); >> iterationUpdateCommand->SetFilterToUpdate( visualizer ); >> iterationUpdateCommand->SetUpdatePeriod( 1 ); >> >> evolution->AddObserver( itk::IterationEvent(), iterationUpdateCommand >> ); >> >> evolution->Update(); >> >> return EXIT_SUCCESS; >> } >> >> >> >> cmake_minimum_required(VERSION 2.8) >> >> project(CurvatureMotion) >> >> find_package(ITK REQUIRED) >> include(${ITK_USE_FILE}) >> >> find_package(VTK REQUIRED) >> include(${VTK_USE_FILE}) >> >> add_executable(Motion main.cpp) >> target_link_libraries(Motion ${ITK_LIBRARIES} ${VTK_LIBRARIES}) >> >> [image: Inline image 4][image: Inline image 3] >> -- >> Cemal Cagatay Bilgin, PhD >> Life Sciences Division >> Lawrence Berkeley National Lab >> MS977, One Cyclotron Road >> Berkeley, CA 94720, USA >> Email: ccbilgin at lbl.gov >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -- Cemal Cagatay Bilgin, PhD Life Sciences Division Lawrence Berkeley National Lab MS977, One Cyclotron Road Berkeley, CA 94720, USA Email: ccbilgin at lbl.gov -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: levelset_000.png Type: image/png Size: 2652 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: levelset_040.png Type: image/png Size: 3421 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bilgincc at gmail.com Mon Sep 15 11:53:06 2014 From: bilgincc at gmail.com (Cagatay Bilgin) Date: Mon, 15 Sep 2014 08:53:06 -0700 Subject: [ITK] [ITK-users] Different output with dense and sparse level set representations In-Reply-To: References: Message-ID: Arnaud, should I also try this with the old framework? This really looks like a bug to me regardless of the framework used. Best, Cagatay Bilgin On Thu, Aug 21, 2014 at 10:33 AM, Cagatay Bilgin wrote: > Hello everybody, > > I continue with my exploration of the new level set framework. I have > modified one of the examples and have an advection field in the positive x > direction. I would expect the initial contour to move in that direction and > that's the case with the sparse representation. Using the dense > representation however, only half of the contour moves to my surprise. Is > this a bug or I am missing something here. Here is the code and the cmake > file and snapshots of the movements. > > [image: Inline image 2][image: Inline image 1] > > > #include "itkBinaryImageToLevelSetImageAdaptor.h" > #include "itkLevelSetContainer.h" > #include "itkLevelSetEquationPropagationTerm.h" > #include "itkLevelSetEquationAdvectionTerm.h" > #include "itkLevelSetEquationContainer.h" > #include "itkLevelSetEquationTermContainer.h" > #include "itkLevelSetEvolution.h" > #include "itkLevelSetEvolutionNumberOfIterationsStoppingCriterion.h" > #include "itkLevelSetDenseImage.h" > #include "itkVTKVisualizeImageLevelSetIsoValues.h" > #include "itkSinRegularizedHeavisideStepFunction.h" > #include "itkLevelSetIterationUpdateCommand.h" > #include "itkLevelSetEquationCurvatureTerm.h" > #include "itkWhitakerSparseLevelSetImage.h" > #include "itkLevelSetSparseImage.h" > > typedef itk::Image< float, 2 > FIT; > > void CreateSquareImage(FIT::Pointer image, FIT::Pointer prop, FIT::Pointer > advec) > { > FIT::RegionType region; > FIT::IndexType start; > start[0] = 0; > start[1] = 0; > > FIT::SizeType size; > size[0] = 100; > size[1] = 100; > > region.SetSize(size); > region.SetIndex(start); > > image->SetRegions(region); > image->Allocate(); > image->FillBuffer(0); > > //constant grow in all directions > prop->SetRegions(image->GetLargestPossibleRegion()); > prop->Allocate(); > prop->FillBuffer(1); > > //advec will increase in positive x direction > advec->SetRegions(image->GetLargestPossibleRegion()); > advec->Allocate(); > advec->FillBuffer(0); > > // Set pixels in a square to one value > for(unsigned int x = 35; x < 65; x++){ > for(unsigned int y = 35; y < 65; y++){ > FIT::IndexType pixelIndex; > pixelIndex[0] = x; > pixelIndex[1] = y; > > image->SetPixel(pixelIndex, 255); > } > } > > //advection in positive x direction > for(unsigned int x = 0; x < 100; x++){ > for(unsigned int y = 0; y < 100; y++){ > FIT::IndexType pixelIndex; > pixelIndex[0] = x; > pixelIndex[1] = y; > > advec->SetPixel(pixelIndex, x); > } > } > } > > > /* > */ > int main(int argc, char* argv[] ) > { > using namespace itk; > if(argc != 5) > { > std::cerr << "Missing Arguments" << std::endl; > std::cerr << argv[0] << std::endl; > std::cerr << "1- Number of Iterations" << std::endl; > std::cerr << "2- Propagation Term" << std::endl; > std::cerr << "3- Advection Term" << std::endl; > std::cerr << "4- Curvature Term" << std::endl; > return EXIT_FAILURE; > } > > FIT::Pointer input = FIT::New(); > FIT::Pointer prop = FIT::New(); > FIT::Pointer advec = FIT::New(); > > CreateSquareImage(input, prop, advec); > > int numberOfIterations = atoi(argv[1]); > > typedef float LSPT; > typedef Image< LSPT, 2 > LSIT; > typedef LevelSetDenseImage< LSIT > LST; > //typedef WhitakerSparseLevelSetImage< LSPT, 2 > LST; > > typedef LST::OutputRealType LSOutputT; > > // convert a binary mask to a level-set function > typedef BinaryImageToLevelSetImageAdaptor BI2LST; > BI2LST::Pointer adaptor = BI2LST::New(); > adaptor->SetInputImage(input ); > adaptor->Initialize(); > LST::Pointer levelSet = adaptor->GetLevelSet(); > > // The Heaviside function > typedef SinRegularizedHeavisideStepFunction > HeavisideFunctionType; > HeavisideFunctionType::Pointer heaviside = > HeavisideFunctionType::New(); > heaviside->SetEpsilon(1 ); > > // Create the level set container > typedef LevelSetContainer< IdentifierType, LST > LSContainerT; > LSContainerT::Pointer levelSetContainer = LSContainerT::New(); > levelSetContainer->SetHeaviside(heaviside ); > levelSetContainer->AddLevelSet(0, levelSet ); > > // Create the terms. > typedef LevelSetEquationPropagationTerm PropT; > PropT::Pointer propagationTerm = PropT::New(); > propagationTerm->SetInput(prop); > propagationTerm->SetCoefficient(atof(argv[2])); > > typedef LevelSetEquationAdvectionTerm AdvecT; > AdvecT::Pointer advectionTerm = AdvecT::New(); > advectionTerm->SetInput(advec); > advectionTerm->SetCoefficient(atof(argv[3])); > > typedef LevelSetEquationCurvatureTerm CurvT; > CurvT::Pointer curvatureTerm = CurvT::New(); > curvatureTerm->SetCoefficient(atof(argv[4])); > > // Create term container (equation rhs) > typedef LevelSetEquationTermContainer< FIT, LSContainerT > > TermContainerT; > TermContainerT::Pointer termContainer = TermContainerT::New(); > termContainer->SetLevelSetContainer(levelSetContainer ); > termContainer->SetInput(input ); > termContainer->AddTerm(0, curvatureTerm ); > termContainer->AddTerm(1, advectionTerm ); > termContainer->AddTerm(2, propagationTerm ); > > // Create equation container > typedef LevelSetEquationContainer< TermContainerT > > EquationContainerType; > EquationContainerType::Pointer equationContainer = > EquationContainerType::New(); > equationContainer->SetLevelSetContainer(levelSetContainer ); > equationContainer->AddEquation(0, termContainer ); > > // Create stopping criteria > typedef LevelSetEvolutionNumberOfIterationsStoppingCriterion< > LSContainerT > StoppingCriterionType; > StoppingCriterionType::Pointer criterion = > StoppingCriterionType::New(); > criterion->SetNumberOfIterations(numberOfIterations ); > > // Create the visualizer > typedef VTKVisualizeImageLevelSetIsoValues< FIT, LST > VisT; > VisT::Pointer visualizer = VisT::New(); > visualizer->SetInputImage(input ); > visualizer->SetLevelSet(levelSet ); > visualizer->SetScreenCapture(true ); > > // Create evolution class > typedef LevelSetEvolution< EquationContainerType, LST > LSEvolT; > LSEvolT::Pointer evolution = LSEvolT::New(); > evolution->SetEquationContainer(equationContainer ); > evolution->SetStoppingCriterion(criterion ); > evolution->SetLevelSetContainer(levelSetContainer ); > > typedef LevelSetIterationUpdateCommand< LSEvolT, VisT > > IterationUpdateCommandType; > IterationUpdateCommandType::Pointer iterationUpdateCommand = > IterationUpdateCommandType::New(); > iterationUpdateCommand->SetFilterToUpdate(visualizer ); > iterationUpdateCommand->SetUpdatePeriod(1 ); > > evolution->AddObserver(IterationEvent(), iterationUpdateCommand ); > evolution->Update(); > > return EXIT_SUCCESS; > } > > > cmake_minimum_required(VERSION 2.8) > project(Motion) > > find_package(ITK REQUIRED) > include(${ITK_USE_FILE}) > > find_package(VTK REQUIRED) > include(${VTK_USE_FILE}) > > add_executable(Motion main.cpp) > target_link_libraries(Motion ${ITK_LIBRARIES} ${VTK_LIBRARIES}) > > Params used for the experiment: > Ran sparse representation with > ./Motion 15 0 1 1 > > Ran dense representation with > ./Motion 15 0 1 0 > > > Cemal Cagatay Bilgin, PhD > Life Sciences Division > Lawrence Berkeley National Lab > MS977, One Cyclotron Road > Berkeley, CA 94720, USA > Email: ccbilgin at lbl.gov > -- Cemal Cagatay Bilgin, PhD Life Sciences Division Lawrence Berkeley National Lab MS977, One Cyclotron Road Berkeley, CA 94720, USA Email: ccbilgin at lbl.gov -------------- next part -------------- An HTML attachment was scrubbed... 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Name: dense_00010.png Type: image/png Size: 2737 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From gowithking at googlemail.com Mon Sep 15 13:04:36 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 19:04:36 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK Message-ID: Hi, my Itk friends, I am using python warped ITK to write my first itk process to analysis series of mhd images, I test my procedure in slicer4 first to make sure it works well. Then I start the programming. However, two problem block me for a whole day. - The imagetype of itk.Image.UC3 should be used for 16 bit image in all the itk instructions. But in my case it only has a range of 0-255. Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I read it proprietorially? - I need to get a label map with simply threshold method, and then make few statistics with LabelStatisticsImageFilter. So the BinaryImageToLabelMapFilter is taken. but then the key error occurs: LabelFilter = itk.BinaryImageToLabelMapFilter[IUC3].New() File "/usr/local/lib/ITK-4.7/Python/itkTemplate.py", line 263, in __getitem__ (str(parameters), self.__name__)) KeyError: "itkTemplate : No template [] for the itk::BinaryImageToLabelMapFilter class" What should I do to achieve the LabelStatisticsImageFilter ? Thank you in advance[?] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From blowekamp at mail.nih.gov Mon Sep 15 13:09:11 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 15 Sep 2014 13:09:11 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: <90BD17AA-DADF-4EAA-94A5-2863F7DAF4CF@mail.nih.gov> Hello, 2) I believe that is the error message when the the filter hasn't been instantiated with that template argument. Poke around itk.BinaryImageToLabelMapFilter's dict interface, some method along the lines 'keys()' should give you a list of the types that have been compiled and can be created. hope this helps, Brad On Sep 15, 2014, at 1:04 PM, gowith king wrote: > Hi, my Itk friends, > I am using python warped ITK to write my first itk process to analysis series of mhd images, I test my procedure in slicer4 first to make sure it works well. Then I start the programming. However, two problem block me for a whole day. > The imagetype of itk.Image.UC3 should be used for 16 bit image in all the itk instructions. But in my case it only has a range of 0-255. Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I read it proprietorially? > > > I need to get a label map with simply threshold method, and then make few statistics with LabelStatisticsImageFilter. So the BinaryImageToLabelMapFilter is taken. but then the key error occurs: > LabelFilter = itk.BinaryImageToLabelMapFilter[IUC3].New() > File "/usr/local/lib/ITK-4.7/Python/itkTemplate.py", line 263, in __getitem__ > (str(parameters), self.__name__)) > KeyError: "itkTemplate : No template [] for the itk::BinaryImageToLabelMapFilter class" > > > What should I do to achieve the LabelStatisticsImageFilter ? > Thank you in advance<330.gif> > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 15 13:54:09 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 13:54:09 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: > > Hi, > > > - The imagetype of itk.Image.UC3 should be used for 16 bit image > in all the itk instructions. But in my case it only has a range of 0-255. > Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 > 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I > read it proprietorially? > > itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) and with three dimension. For the correspondence between mangled names and basic types see [1]. For a 16 bit image use 'US' or 'SS'. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From gowithking at googlemail.com Mon Sep 15 13:49:27 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 19:49:27 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: <90BD17AA-DADF-4EAA-94A5-2863F7DAF4CF@mail.nih.gov> References: <90BD17AA-DADF-4EAA-94A5-2863F7DAF4CF@mail.nih.gov> Message-ID: Hi Lowekamp I think I may get your meaning: I have to define something before I can use this filter in python? I so glad to get your reply, but could not figure out how to achieve your suggestion: Poke around itk.BinaryImageToLabelMapFilter's dict interface, some method along the lines 'keys()' should give you a list of the types that have been compiled and can be created. [?] On Mon, Sep 15, 2014 at 7:09 PM, Bradley Lowekamp wrote: > Hello, > > 2) I believe that is the error message when the the filter hasn't been > instantiated with that template argument. Poke around > itk.BinaryImageToLabelMapFilter's dict interface, some method along the > lines 'keys()' should give you a list of the types that have been compiled > and can be created. > > hope this helps, > Brad > > On Sep 15, 2014, at 1:04 PM, gowith king > wrote: > > Hi, my Itk friends, > I am using python warped ITK to write my first itk process to > analysis series of mhd images, I test my procedure in slicer4 first to > make sure it works well. Then I start the programming. However, two problem > block me for a whole day. > > - The imagetype of itk.Image.UC3 should be used for 16 bit image > in all the itk instructions. But in my case it only has a range of 0-255. > Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 > 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I > read it proprietorially? > > > > - I need to get a label map with simply threshold method, and > then make few statistics with LabelStatisticsImageFilter. So the > BinaryImageToLabelMapFilter is taken. but then the key error occurs: > > LabelFilter = itk.BinaryImageToLabelMapFilter[IUC3].New() > File "/usr/local/lib/ITK-4.7/Python/itkTemplate.py", line 263, in > __getitem__ > (str(parameters), self.__name__)) > KeyError: "itkTemplate : No template [ 'itkImagePython.itkImageUC3'>] for the itk::BinaryImageToLabelMapFilter > class" > > > What should I do to achieve the LabelStatisticsImageFilter ? > Thank you in advance<330.gif> > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1C4.gif Type: image/gif Size: 667 bytes Desc: not available URL: From gowithking at googlemail.com Mon Sep 15 14:11:47 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 20:11:47 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi McCormick Thank you so much for your suggestion, when I use US it pops out a keyerror , not template for the us3 [?]. But then I change to SS it works well for now. any suggestion for the second issue ? I dig for really long time for this keyerror problem , but have no clue at all On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick wrote: > Hi, >> > > >> >> - The imagetype of itk.Image.UC3 should be used for 16 bit image >> in all the itk instructions. But in my case it only has a range of 0-255. >> Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 >> 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I >> read it proprietorially? >> >> itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) > and with three dimension. For the correspondence between mangled names and > basic types see [1]. For a 16 bit image use 'US' or 'SS'. > > HTH, > Matt > > [1] > http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: From gowithking at googlemail.com Mon Sep 15 14:19:56 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 20:19:56 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi McCormick I think you give me a hint for the key error problem: I tried few other types in my python such as US , UI, SI ... most of them could not work well . another keyerror pops out for the template lose: when I try itk.Image[itk.SI, 3] KeyError: 'itkTemplate : No template (, 3) for the itk::Image class' On Mon, Sep 15, 2014 at 8:11 PM, gowith king wrote: > Hi McCormick > Thank you so much for your suggestion, when I use US it pops out a > keyerror , not template for the us3 [?]. But then I change to SS it works > well for now. > any suggestion for the second issue ? > I dig for really long time for this keyerror problem , but have no > clue at all > > > On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi, >>> >> >> >>> >>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>> image in all the itk instructions. But in my case it only has a range of >>> 0-255. Then I take itk.Image.F3, then it get a range of >>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>> 0-9000 . How could I read it proprietorially? >>> >>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) >> and with three dimension. For the correspondence between mangled names and >> basic types see [1]. For a 16 bit image use 'US' or 'SS'. >> >> HTH, >> Matt >> >> [1] >> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: From matt.mccormick at kitware.com Mon Sep 15 16:12:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 16:12:56 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi gowith, To see the available types for itk.Image, run dir(itk.Image) If a type is not available that is desired, enable the option in CMake for that pixel type. For unsigned short, set ITK_WRAP_unsigned_short to ON. Hope this helps, Matt On Mon, Sep 15, 2014 at 2:19 PM, gowith king wrote: > Hi McCormick > I think you give me a hint for the key error problem: I tried few > other types in my python such as US , UI, SI ... most of them could not > work well . another keyerror pops out for the template lose: when I try > itk.Image[itk.SI, 3] > KeyError: 'itkTemplate : No template (, 3) for the > itk::Image class' > > > > On Mon, Sep 15, 2014 at 8:11 PM, gowith king > wrote: > >> Hi McCormick >> Thank you so much for your suggestion, when I use US it pops out a >> keyerror , not template for the us3 [?]. But then I change to SS it works >> well for now. >> any suggestion for the second issue ? >> I dig for really long time for this keyerror problem , but have no >> clue at all >> >> >> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >> matt.mccormick at kitware.com> wrote: >> >>> Hi, >>>> >>> >>> >>>> >>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>> image in all the itk instructions. But in my case it only has a range of >>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>> 0-9000 . How could I read it proprietorially? >>>> >>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) >>> and with three dimension. For the correspondence between mangled names and >>> basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>> >>> HTH, >>> Matt >>> >>> [1] >>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>> >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: From gowithking at googlemail.com Mon Sep 15 17:31:14 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 23:31:14 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Thanks McCormick , I use the dir(itk,Image) and dir(itk.LabelMap) and dir(to get some information : UC3 is included in itk.image then it is good. Then I tried all the other dir() for each of my filter , made lots of correction , now the pepline works perfect [?] Thank you again . But I still could not get my result ... because of the filters I may not really understand. I have three filters BinaryThresholdImageFilter # to get a binary image for now I get only two values 1 and 100 it works well. I what the labelmap contains both two parts of them BinaryImageToLabelMapFilter #I have no idea if it works well or not LabelMapToLabelImageFilter # returns a empty image Do you have any idea about this ? On Mon, Sep 15, 2014 at 10:12 PM, Matt McCormick wrote: > Hi gowith, > > To see the available types for itk.Image, run > > dir(itk.Image) > > If a type is not available that is desired, enable the option in CMake for > that pixel type. For unsigned short, set > > ITK_WRAP_unsigned_short > > to ON. > > Hope this helps, > Matt > > On Mon, Sep 15, 2014 at 2:19 PM, gowith king > wrote: > >> Hi McCormick >> I think you give me a hint for the key error problem: I tried few >> other types in my python such as US , UI, SI ... most of them could not >> work well . another keyerror pops out for the template lose: when I try >> itk.Image[itk.SI, 3] >> KeyError: 'itkTemplate : No template (, 3) for the >> itk::Image class' >> >> >> >> On Mon, Sep 15, 2014 at 8:11 PM, gowith king >> wrote: >> >>> Hi McCormick >>> Thank you so much for your suggestion, when I use US it pops out a >>> keyerror , not template for the us3 [?]. But then I change to SS it >>> works well for now. >>> any suggestion for the second issue ? >>> I dig for really long time for this keyerror problem , but have no >>> clue at all >>> >>> >>> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >>> matt.mccormick at kitware.com> wrote: >>> >>>> Hi, >>>>> >>>> >>>> >>>>> >>>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>>> image in all the itk instructions. But in my case it only has a range of >>>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>>> 0-9000 . How could I read it proprietorially? >>>>> >>>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) >>>> and with three dimension. For the correspondence between mangled names and >>>> basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>>> >>>> HTH, >>>> Matt >>>> >>>> [1] >>>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>>> >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From gowithking at googlemail.com Mon Sep 15 17:48:50 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 23:48:50 +0200 Subject: [ITK] How to binary image to label image correctly Message-ID: Hi. My lovely ITK friends I got so much help from here today , However I still could not achieve my goal correctly. The main issue of me is the understanding of binary to labelimage process: from binary to label image and then labelstatistic since I get a binary image which means I have only two values in the image as I set itk.BinaryThresholdImageFilter.ISS3IUC3 itk.BinaryImageToLabelMapFilter.IUC3LM3 itk.LabelMapToLabelImageFilter.LM3IUC3 itk.LabelStatisticsImageFilter.ISS3IUC3 However I got nothing for the outcome of : GetValidLabelValues() Then I checked the pepline: binary image works well it only contains 1 and 100 as I set. But the Labelimage is empty anyong have any idea about it ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 15 17:58:36 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 17:58:36 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: On Mon, Sep 15, 2014 at 5:31 PM, gowith king wrote: > Thanks McCormick , I use the dir(itk,Image) and dir(itk.LabelMap) and > dir(to get some information : UC3 is included in itk.image then it is good. > Then I tried all the other dir() for each of my filter , made lots of > correction , now the pepline works perfect [?] Thank you again . > > But I still could not get my result ... > because of the filters I may not really understand. > > I have three filters > BinaryThresholdImageFilter # to get a binary image for now I get only two > values 1 and 100 it works well. I what the labelmap contains both two parts > of them > BinaryImageToLabelMapFilter #I have no idea if it works well or not > LabelMapToLabelImageFilter # returns a empty image > > Do you have any idea about this ? > Perhaps SetInputForegroundValue [1] needs to be set? HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToLabelMapFilter.html#a5c56958ec0ae8d3a9bf7ae759c680c4a > > On Mon, Sep 15, 2014 at 10:12 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi gowith, >> >> To see the available types for itk.Image, run >> >> dir(itk.Image) >> >> If a type is not available that is desired, enable the option in CMake >> for that pixel type. For unsigned short, set >> >> ITK_WRAP_unsigned_short >> >> to ON. >> >> Hope this helps, >> Matt >> >> On Mon, Sep 15, 2014 at 2:19 PM, gowith king >> wrote: >> >>> Hi McCormick >>> I think you give me a hint for the key error problem: I tried few >>> other types in my python such as US , UI, SI ... most of them could not >>> work well . another keyerror pops out for the template lose: when I try >>> itk.Image[itk.SI, 3] >>> KeyError: 'itkTemplate : No template (, 3) for the >>> itk::Image class' >>> >>> >>> >>> On Mon, Sep 15, 2014 at 8:11 PM, gowith king >>> wrote: >>> >>>> Hi McCormick >>>> Thank you so much for your suggestion, when I use US it pops out a >>>> keyerror , not template for the us3 [?]. But then I change to SS it >>>> works well for now. >>>> any suggestion for the second issue ? >>>> I dig for really long time for this keyerror problem , but have no >>>> clue at all >>>> >>>> >>>> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >>>> matt.mccormick at kitware.com> wrote: >>>> >>>>> Hi, >>>>>> >>>>> >>>>> >>>>>> >>>>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>>>> image in all the itk instructions. But in my case it only has a range of >>>>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>>>> 0-9000 . How could I read it proprietorially? >>>>>> >>>>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range >>>>> 0-255) and with three dimension. For the correspondence between mangled >>>>> names and basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>>>> >>>>> HTH, >>>>> Matt >>>>> >>>>> [1] >>>>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>>>> >>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From g.bogle at auckland.ac.nz Mon Sep 15 17:59:51 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 15 Sep 2014 21:59:51 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: , Message-ID: I'm sorry, Matt, but I'm not sure what you mean by "pointing a clean build directory to this directory [1]." I tried copying the DCMTK-build tree somewhere else, deleting CMakeCache.txt then running cmake with the CMakeLists.txt you provided (downloaded), but it wants DCMTKGitTag.cmake: D:\testing\DCMTK-build>cmake -G "Visual Studio 10 Win64" -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ CMake Error at CMakeLists.txt:6 (include): include could not find load file: D:/testing/DCMTK-build/../DCMTKGitTag.cmake CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message): error: no download info for 'DCMTK' -- please specify existing/non-empty SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY, GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command) CMakeLists.txt:17 (ExternalProject_add) -- Configuring incomplete, errors occurred! See also "D:/testing/DCMTK-build/CMakeFiles/CMakeOutput.log". See also "D:/testing/DCMTK-build/CMakeFiles/CMakeError.log". Please tell me in more detail what I need to do. Thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Tuesday, 16 September 2014 3:36 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi Gib, Please try building DCMTK by pointing a clean build directory to this directory [1]. Then, start a clean build of ITK with DCMTK_DIR pointing to that directory. Please let us know if this works. Thanks, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/DCMTK/WindowsBuild/CMakeLists.txt;h=70c5ef6cfc25895ed54755818d7aa49299869fe6;hb=HEAD On Sun, Sep 14, 2014 at 11:45 PM, Gib Bogle wrote: > Slicer built OK before I added DCMTK_DIR. > ________________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] > Sent: Monday, 15 September 2014 3:09 p.m. > To: Matt McCormick > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > The same result. > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 3:05 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Thanks for the information. > > What happens if DCMTK_DIR is pointed to the DCMTK build directory in > the Slicer build tree? > > Thanks, > Matt > > > On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: >> Hi Matt, >> >> Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. >> >> Cheers >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Monday, 15 September 2014 2:51 p.m. >> To: Gib Bogle >> Cc: community at itk.org >> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi Gib, >> >> Which version of DCMTK was built? Was it installed? >> >> Thanks, >> Matt >> >> On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >>> cmake-3.0.2 >>> ________________________________ >>> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >>> [g.bogle at auckland.ac.nz] >>> Sent: Monday, 15 September 2014 10:28 a.m. >>> To: community at itk.org >>> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >>> >>> Hi all, >>> >>> I have run into an issue with 4.6, triggered by a problem with Slicer >>> (another story - unable to load big tiffs). I have built Slicer, which >>> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >>> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >>> installation that I now have (I have previously been using 4.0). In >>> principle the failure to load a big tiff should be a problem with ITK, not >>> with Slicer. >>> >>> When I run cmake to set up the Visual Studio 10 project files for my simple >>> test program (which works with 4.0), I get errors concerning DCMTK: >>> >>> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >>> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >>> CMake Error at C:/Program Files >>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >>> (message): >>> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >>> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >>> DCMTK_dcmimgle_LIBRARY) >>> Call Stack (most recent call first): >>> C:/Program Files >>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >>> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >>> (find_package_handle_standard_args) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >>> (find_package) >>> >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >>> (itk_module_load) >>> >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >>> (_itk_module_config_recurse) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >>> (itk_module_config) >>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >>> (find_package) >>> CMakeLists.txt:4 (FIND_PACKAGE) >>> >>> Here is the stock-standard CMakeLists.txt: >>> >>> cmake_minimum_required(VERSION 2.8) >>> >>> PROJECT(makebig) >>> FIND_PACKAGE(ITK) >>> IF(ITK_FOUND) >>> INCLUDE(${ITK_USE_FILE}) >>> ELSE(ITK_FOUND) >>> MESSAGE(FATAL_ERROR >>> "ITK not found. Please set ITK_DIR.") >>> ENDIF(ITK_FOUND) >>> MESSAGE (${ITK_USE_FILE}) >>> MESSAGE (${ITK_INCLUDE_DIRS}) >>> set(PROJECTNAME "makebig") >>> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >>> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >>> >>> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >>> error messages did not change. >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Mon Sep 15 18:08:37 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 18:08:37 -0400 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: Hi Gib, Sorry for the insufficient detail. - Delete everything in D:\testing\DCMTK-build - Run D:\testing\DCMTK-build>cmake -G "Visual Studio 10 Win64" D:\testing\ITK-source\Modules\ThirdParty\DCMTK\WindowsBuild Assuming that ITK sources are in ITK-source. - Build the resulting project, which should build DCMTK. - In a clean ITK-build, set DCMTK_DIR to D:\testing\DCMTK-build Please let me know if anything is unclear. Thanks, Matt On Mon, Sep 15, 2014 at 5:59 PM, Gib Bogle wrote: > I'm sorry, Matt, but I'm not sure what you mean by "pointing a clean build directory to this directory [1]." I tried copying the DCMTK-build tree somewhere else, deleting CMakeCache.txt then running cmake with the CMakeLists.txt you provided (downloaded), but it wants DCMTKGitTag.cmake: > > D:\testing\DCMTK-build>cmake -G "Visual Studio 10 Win64" > -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ > CMake Error at CMakeLists.txt:6 (include): > include could not find load file: > D:/testing/DCMTK-build/../DCMTKGitTag.cmake > > CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message): > error: no download info for 'DCMTK' -- please specify existing/non-empty > SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY, > GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND > Call Stack (most recent call first): > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command) > CMakeLists.txt:17 (ExternalProject_add) > > -- Configuring incomplete, errors occurred! > See also "D:/testing/DCMTK-build/CMakeFiles/CMakeOutput.log". > See also "D:/testing/DCMTK-build/CMakeFiles/CMakeError.log". > > Please tell me in more detail what I need to do. > > Thanks > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Tuesday, 16 September 2014 3:36 a.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Please try building DCMTK by pointing a clean build directory to this > directory [1]. Then, start a clean build of ITK with DCMTK_DIR > pointing to that directory. Please let us know if this works. > > Thanks, > Matt > > [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/DCMTK/WindowsBuild/CMakeLists.txt;h=70c5ef6cfc25895ed54755818d7aa49299869fe6;hb=HEAD > > On Sun, Sep 14, 2014 at 11:45 PM, Gib Bogle wrote: >> Slicer built OK before I added DCMTK_DIR. >> ________________________________________ >> From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] >> Sent: Monday, 15 September 2014 3:09 p.m. >> To: Matt McCormick >> Cc: community at itk.org >> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> The same result. >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Monday, 15 September 2014 3:05 p.m. >> To: Gib Bogle >> Cc: community at itk.org >> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi Gib, >> >> Thanks for the information. >> >> What happens if DCMTK_DIR is pointed to the DCMTK build directory in >> the Slicer build tree? >> >> Thanks, >> Matt >> >> >> On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: >>> Hi Matt, >>> >>> Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. >>> >>> Cheers >>> Gib >>> ________________________________________ >>> From: Matt McCormick [matt.mccormick at kitware.com] >>> Sent: Monday, 15 September 2014 2:51 p.m. >>> To: Gib Bogle >>> Cc: community at itk.org >>> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >>> >>> Hi Gib, >>> >>> Which version of DCMTK was built? Was it installed? >>> >>> Thanks, >>> Matt >>> >>> On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >>>> cmake-3.0.2 >>>> ________________________________ >>>> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >>>> [g.bogle at auckland.ac.nz] >>>> Sent: Monday, 15 September 2014 10:28 a.m. >>>> To: community at itk.org >>>> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >>>> >>>> Hi all, >>>> >>>> I have run into an issue with 4.6, triggered by a problem with Slicer >>>> (another story - unable to load big tiffs). I have built Slicer, which >>>> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >>>> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >>>> installation that I now have (I have previously been using 4.0). In >>>> principle the failure to load a big tiff should be a problem with ITK, not >>>> with Slicer. >>>> >>>> When I run cmake to set up the Visual Studio 10 project files for my simple >>>> test program (which works with 4.0), I get errors concerning DCMTK: >>>> >>>> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >>>> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >>>> CMake Error at C:/Program Files >>>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >>>> (message): >>>> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >>>> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >>>> DCMTK_dcmimgle_LIBRARY) >>>> Call Stack (most recent call first): >>>> C:/Program Files >>>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >>>> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >>>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >>>> (find_package_handle_standard_args) >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >>>> (find_package) >>>> >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >>>> (itk_module_load) >>>> >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >>>> (_itk_module_config_recurse) >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >>>> (itk_module_config) >>>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >>>> (find_package) >>>> CMakeLists.txt:4 (FIND_PACKAGE) >>>> >>>> Here is the stock-standard CMakeLists.txt: >>>> >>>> cmake_minimum_required(VERSION 2.8) >>>> >>>> PROJECT(makebig) >>>> FIND_PACKAGE(ITK) >>>> IF(ITK_FOUND) >>>> INCLUDE(${ITK_USE_FILE}) >>>> ELSE(ITK_FOUND) >>>> MESSAGE(FATAL_ERROR >>>> "ITK not found. Please set ITK_DIR.") >>>> ENDIF(ITK_FOUND) >>>> MESSAGE (${ITK_USE_FILE}) >>>> MESSAGE (${ITK_INCLUDE_DIRS}) >>>> set(PROJECTNAME "makebig") >>>> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >>>> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >>>> >>>> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >>>> error messages did not change. >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community From g.bogle at auckland.ac.nz Tue Sep 16 01:15:09 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 16 Sep 2014 05:15:09 +0000 Subject: [ITK] ITK-4.6 problem Message-ID: Hi all, There definitely seems to be a problem with ITK-4.6, at least with the code that got installed while building Slicer. This was carried out with ITKV3_COMPATIBILITY off. I am doing some testing with this installation to try to understand why Slicer cannot handle big tiffs (on my Windows 7 system). There is something a bit funny about the installed ITK-4.6, in that the compiler complained about some missing include files, vnl_*.h and others, which are in my ITK-4.0 installation but not in 4.6. I just copied them across - I hope this is not a problem. Anyway, I now find that my very simple program that uses ITK to create a tiff file now crashes when built with 4.6. What is a big clue is that it fails while creating the image, i.e. writing to the buffer, on page 73 - it's surely more than a coincidence that Slicer fails when reading page 72 of a 4 GB tiff. In this case only 73 bytes have been written to buffer when it fails. The whole program is below. It fails having written x=0, y=0, z=0...73 to the console. Unless my code (which was fine with 4.0) is no longer OK with 4.6, this is a very basic bug, since all I do is set the image size, allocate memory, get a pointer to the buffer and start writing to it. The program is short enough to paste in its entirety, but the relevant section is just a few lines. #include #include #include #include #include #include #include #include #include #include "itkImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkSize.h" typedef itk::Image ImageType; ImageType::Pointer im; unsigned char *p; #define V(a,b,c) p[(c)*xysize+(b)*width+(a)] int main(int argc, char**argv) { int x1, x2, y1, y2, z1, z2; int x0, y0, z0, dx, dy, dz; int x, y, z, xx, yy, zz, n, comp_flag; long long width, height, depth, xysize; int R, R2; bool use_compression; bool use_sphere = false; if (argc != 4) { printf("Usage: makebig tiff_file N compress\n"); printf(" the image will be NxNxN\n"); printf(" set compress=1 to use compression, =0 otherwise\n"); return 1; } printf("Output image file: %s\n",argv[1]); sscanf(argv[2],"%d",&n); sscanf(argv[3],"%d",&comp_flag); use_compression = (comp_flag == 1); x0 = n/2; y0 = n/2; z0 = n/2; R = 5; R2 = R*R; width = n; height = n; depth = n; xysize = width*height; printf("Desired image dimensions: width, height, depth: %d %d %d\n",width,height,depth); ImageType::Pointer im = ImageType::New(); ImageType::SizeType imsize; imsize[0] = width; imsize[1] = height; imsize[2] = depth; ImageType::IndexType imstart; imstart[0] = 0; imstart[1] = 0; imstart[2] = 0; ImageType::RegionType imregion; imregion.SetSize(imsize); imregion.SetIndex(imstart); im->SetRegions(imregion); im->Allocate(); p = (unsigned char *)(im->GetBufferPointer()); width = im->GetLargestPossibleRegion().GetSize()[0]; height = im->GetLargestPossibleRegion().GetSize()[1]; depth = im->GetLargestPossibleRegion().GetSize()[2]; printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); for (x=0; x x0+R) { V(x,y,z) = 0; } else { V(x,y,z) = 255; } } } } } typedef itk::ImageFileWriter FileWriterType; FileWriterType::Pointer writer = FileWriterType::New(); writer->SetFileName(argv[1]); writer->SetInput(im); if (use_compression) { writer->UseCompressionOn(); } printf("Writing tiff file\n"); try { writer->Update(); } catch (itk::ExceptionObject &e) { std::cout << e << std::endl; return 4; } if (use_compression) { printf("Created compressed image file: %s\n",argv[1]); } else { printf("Created uncompressed image file: %s\n",argv[1]); } return 0; } -------------- next part -------------- An HTML attachment was scrubbed... URL: From gowithking at googlemail.com Tue Sep 16 04:27:49 2014 From: gowithking at googlemail.com (gowith king) Date: Tue, 16 Sep 2014 10:27:49 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi , Matt I tried it , it does not work as well. the print LabelFilter0.GetNumberOfObjects() always returns 0, what i want to do it every nasty: sign 1 to label 1, 100 to label 2 ,and there is no background at all. My images all like the attached image but in 3D , the 3D version will be attached later ,thank you for your attention On Mon, Sep 15, 2014 at 11:58 PM, Matt McCormick wrote: > > > On Mon, Sep 15, 2014 at 5:31 PM, gowith king > wrote: > >> Thanks McCormick , I use the dir(itk,Image) and dir(itk.LabelMap) and >> dir(to get some information : UC3 is included in itk.image then it is good. >> Then I tried all the other dir() for each of my filter , made lots of >> correction , now the pepline works perfect [?] Thank you again . >> >> But I still could not get my result ... >> because of the filters I may not really understand. >> >> I have three filters >> BinaryThresholdImageFilter # to get a binary image for now I get only two >> values 1 and 100 it works well. I what the labelmap contains both two parts >> of them >> BinaryImageToLabelMapFilter #I have no idea if it works well or not >> LabelMapToLabelImageFilter # returns a empty image >> >> Do you have any idea about this ? >> > > Perhaps SetInputForegroundValue [1] needs to be set? > > HTH, > Matt > > [1] > http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToLabelMapFilter.html#a5c56958ec0ae8d3a9bf7ae759c680c4a > > > >> >> On Mon, Sep 15, 2014 at 10:12 PM, Matt McCormick < >> matt.mccormick at kitware.com> wrote: >> >>> Hi gowith, >>> >>> To see the available types for itk.Image, run >>> >>> dir(itk.Image) >>> >>> If a type is not available that is desired, enable the option in CMake >>> for that pixel type. For unsigned short, set >>> >>> ITK_WRAP_unsigned_short >>> >>> to ON. >>> >>> Hope this helps, >>> Matt >>> >>> On Mon, Sep 15, 2014 at 2:19 PM, gowith king >>> wrote: >>> >>>> Hi McCormick >>>> I think you give me a hint for the key error problem: I tried few >>>> other types in my python such as US , UI, SI ... most of them could not >>>> work well . another keyerror pops out for the template lose: when I try >>>> itk.Image[itk.SI, 3] >>>> KeyError: 'itkTemplate : No template (, 3) for the >>>> itk::Image class' >>>> >>>> >>>> >>>> On Mon, Sep 15, 2014 at 8:11 PM, gowith king >>> > wrote: >>>> >>>>> Hi McCormick >>>>> Thank you so much for your suggestion, when I use US it pops out >>>>> a keyerror , not template for the us3 [?]. But then I change to SS it >>>>> works well for now. >>>>> any suggestion for the second issue ? >>>>> I dig for really long time for this keyerror problem , but have >>>>> no clue at all >>>>> >>>>> >>>>> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >>>>> matt.mccormick at kitware.com> wrote: >>>>> >>>>>> Hi, >>>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>>>>> image in all the itk instructions. But in my case it only has a range of >>>>>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>>>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>>>>> 0-9000 . How could I read it proprietorially? >>>>>>> >>>>>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range >>>>>> 0-255) and with three dimension. For the correspondence between mangled >>>>>> names and basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>>>>> >>>>>> HTH, >>>>>> Matt >>>>>> >>>>>> [1] >>>>>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Selection_001.png Type: image/png Size: 23881 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From gowithking at googlemail.com Tue Sep 16 05:32:16 2014 From: gowithking at googlemail.com (gowith king) Date: Tue, 16 Sep 2014 11:32:16 +0200 Subject: [ITK] Fwd: How to label this binary image into two labels In-Reply-To: References: Message-ID: Hi, I tried to label this image into two labels since yesterday , However it always give no label for result. Here is my code: LabelFilter0 = itk.BinaryImageToLabelMapFilter.IUC3LM3.New() LabelFilter0.SetInput(BinaryFilter.GetOutput()) LabelFilter0.SetInputForegroundValue(100) LabelFilter0.SetFullyConnected(False) print LabelFilter0.GetNumberOfObjects() LabelImage0 = itk.LabelMapToLabelImageFilter.LM3IUC3.New() LabelImage0.SetInput(LabelFilter0.GetOutput()) Sta0Filter = itk.LabelStatisticsImageFilter.ISS3IUC3.New() Sta0Filter.SetLabelInput(LabelImage0.GetOutput()) Sta0Filter.SetInput(reader0.GetOutput()) ?here is the mhd file : https://drive.google.com/file/d/0B6iiB8fojky9NXhOZXFVWTNIbHlLc01jdmFyT2FkdDVmdXFB/edit?usp=sharing https://drive.google.com/file/d/0B6iiB8fojky9dnlSSmNqOHk4NDM1WHRBLVRhWWpHLUxGZ1JF/edit?usp=sharing -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Selection_001.png Type: image/png Size: 23881 bytes Desc: not available URL: From matt.mccormick at kitware.com Tue Sep 16 09:48:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Sep 2014 09:48:17 -0400 Subject: [ITK] ITK-4.6 problem In-Reply-To: References: Message-ID: Hi Gib, > > There is something a bit funny about the installed ITK-4.6, in that the > compiler complained about some missing include files, vnl_*.h and others, > which are in my ITK-4.0 installation but not in 4.6. I just copied them > across - I hope this is not a problem. > This is probably a problem. Did the ITK 4.6 build complete successfully and the install complete successfully? Thanks, Matt From joel.schaerer at laposte.net Tue Sep 16 10:27:01 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Tue, 16 Sep 2014 16:27:01 +0200 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty Message-ID: <541848B5.9060901@laposte.net> Hi all, The template for Insight Journal submissions that is available on GitHub and recommended on the Insight Journal website (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) does not build with ITK4. I can try to fix it, but before I do I would like to make sure it is still the current version? Thanks! Jo?l _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Tue Sep 16 10:46:05 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 16 Sep 2014 14:46:05 +0000 Subject: [ITK] [ITK-dev] Coverity 'Uncaught Exception' errors Message-ID: Hans asked me to look at a couple of ITK Coverity defects, as they were in code written in our lab. A couple of them are understandable but problematic. Basically there?s an exception thrown at itkObjectFactoryBase.cxx at line 533: 531 if ( ObjectFactoryBase::m_StrictVersionChecking ) 532 { 1. exception_thrown: An exception of type "itk::ExceptionObject" is thrown. 533 itkGenericExceptionMacro(<< "Incompatible factory version load attempt:" 534 << "\nRunning itk version :\n" << Version::GetITKSourceVersion() 535 << "\nAttempted loading factory version:\n" << factory->GetITKSourceVersion() 536 << "\nAttempted factory:\n" << factory->m_LibraryPath << "\n"); 537 } 538 else 539 { 540 itkGenericOutputMacro(<< "Possible incompatible factory load:" 541 << "\nRunning itk version :\n" << Version::GetITKSourceVersion() 542 << "\nLoaded factory version:\n" << factory->GetITKSourceVersion() 543 << "\nLoading factory:\n" << factory->m_LibraryPath << "\n"); 544 } 545 } There are 4 Coverity defects reported that all point to this code. Given where the exceptions are thrown, it looks like every call to itk::::New() should be bracketed by a try/catch pair. But in fact Coverity only reports 4 instances of this being a problem. I can fix the reported defects for completeness? sake, but I find it mysterious that more defects caused by this occur. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From yxp233 at postech.ac.kr Tue Sep 16 10:37:18 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Tue, 16 Sep 2014 23:37:18 +0900 Subject: [ITK] [ITK-users] Compiling ITK 4.6.0 error In-Reply-To: <1410796270474129.115529.ptmail04@ptmail04> References: <1410796270474129.115529.ptmail04@ptmail04> Message-ID: <024f01cfd1bb$b7c4a0c0$274de240$@ac.kr> Dear Users, I was trying to compile ITK 4.6.0 with MSVS 2010 with GPU enabled, but I got the following error: Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): Syntax error in cmake code at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 when parsing string D:\Toolbox\ITK-4.6.0 Invalid escape sequence \T Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set) CMake/ITKModuleEnablement.cmake:171 (include) CMakeLists.txt:322 (include) Configuring incomplete, errors occurred! See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". Could anyone tell me what caused this error? Thank you. Best regards, Xiaopeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Tue Sep 16 10:53:10 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 16 Sep 2014 10:53:10 -0400 Subject: [ITK] [ITK-dev] Coverity 'Uncaught Exception' errors In-Reply-To: References: Message-ID: I think we ignored a number of those. On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K wrote: > Hans asked me to look at a couple of ITK Coverity defects, as they were in > code written in our lab. > > A couple of them are understandable but problematic. Basically there?s an > exception thrown at itkObjectFactoryBase.cxx at line 533: > > 531 if ( ObjectFactoryBase::m_StrictVersionChecking ) > 532 { > 1. exception_thrown: An exception of type "itk::ExceptionObject" is > thrown. > 533 itkGenericExceptionMacro(<< "Incompatible factory version load > attempt:" > 534 << "\nRunning itk version :\n" << > Version::GetITKSourceVersion() > 535 << "\nAttempted loading factory version:\n" > << factory->GetITKSourceVersion() > 536 << "\nAttempted factory:\n" << > factory->m_LibraryPath << "\n"); > 537 } > 538 else > 539 { > 540 itkGenericOutputMacro(<< "Possible incompatible factory load:" > 541 << "\nRunning itk version :\n" << > Version::GetITKSourceVersion() > 542 << "\nLoaded factory version:\n" << > factory->GetITKSourceVersion() > 543 << "\nLoading factory:\n" << > factory->m_LibraryPath << "\n"); > 544 } > 545 } > > There are 4 Coverity defects reported that all point to this code. Given > where the exceptions are thrown, it looks like every call to > itk::::New() should be bracketed by a try/catch pair. > > But in fact Coverity only reports 4 instances of this being a problem. > > I can fix the reported defects for completeness? sake, but I find it > mysterious that more defects caused by this occur. > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From norman-k-williams at uiowa.edu Tue Sep 16 12:25:02 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 16 Sep 2014 16:25:02 +0000 Subject: [ITK] [ITK-dev] Coverity 'Uncaught Exception' errors In-Reply-To: References: Message-ID: You mean we told Coverity to ignore them? I guess that makes sense. On 9/16/14, 9:53 AM, "Bill Lorensen" wrote: >I think we ignored a number of those. > > >On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K > wrote: >> Hans asked me to look at a couple of ITK Coverity defects, as they were >>in >> code written in our lab. >> >> A couple of them are understandable but problematic. Basically there?s >>an >> exception thrown at itkObjectFactoryBase.cxx at line 533: >> >> 531 if ( ObjectFactoryBase::m_StrictVersionChecking ) >> 532 { >> 1. exception_thrown: An exception of type "itk::ExceptionObject" is >> thrown. >> 533 itkGenericExceptionMacro(<< "Incompatible factory version load >> attempt:" >> 534 << "\nRunning itk version :\n" << >> Version::GetITKSourceVersion() >> 535 << "\nAttempted loading factory >>version:\n" >> << factory->GetITKSourceVersion() >> 536 << "\nAttempted factory:\n" << >> factory->m_LibraryPath << "\n"); >> 537 } >> 538 else >> 539 { >> 540 itkGenericOutputMacro(<< "Possible incompatible factory load:" >> 541 << "\nRunning itk version :\n" << >> Version::GetITKSourceVersion() >> 542 << "\nLoaded factory version:\n" << >> factory->GetITKSourceVersion() >> 543 << "\nLoading factory:\n" << >> factory->m_LibraryPath << "\n"); >> 544 } >> 545 } >> >> There are 4 Coverity defects reported that all point to this code. >>Given >> where the exceptions are thrown, it looks like every call to >> itk::::New() should be bracketed by a try/catch pair. >> >> But in fact Coverity only reports 4 instances of this being a problem. >> >> I can fix the reported defects for completeness? sake, but I find it >> mysterious that more defects caused by this occur. >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered >>by the >> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >>confidential >> and may be legally privileged. If you are not the intended recipient, >>you >> are hereby notified that any retention, dissemination, distribution, or >> copying of this communication is strictly prohibited. Please reply to >>the >> sender that you have received the message in error, then delete it. >>Thank >> you. >> ________________________________ >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > > > >-- >Unpaid intern in BillsBasement at noware dot com ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From norman-k-williams at uiowa.edu Tue Sep 16 12:50:39 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 16 Sep 2014 16:50:39 +0000 Subject: [ITK] [ITK-dev] Review.source.kitware.com down? Message-ID: Is it just me or is ITK Gerrit inaccessible? ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 16 13:02:06 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Sep 2014 13:02:06 -0400 Subject: [ITK] [ITK-dev] Review.source.kitware.com down? In-Reply-To: References: Message-ID: It's not just you. I will find the status. Thanks, Matt On Tue, Sep 16, 2014 at 12:50 PM, Williams, Norman K wrote: > Is it just me or is ITK Gerrit inaccessible? > > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From norman-k-williams at uiowa.edu Tue Sep 16 13:15:48 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 16 Sep 2014 17:15:48 +0000 Subject: [ITK] [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData In-Reply-To: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com> References: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com> Message-ID: I?ll have a look when review.source.kitware.com comes back up. It would be OK to replaces the [] operator with using the iterator directly. The only reason I can think of not to is that even with a DICOM file, the time spent in writing and reading the MetaDataDictionary is not going to have a significant computational cost, since it only happens when you read or write a DICOM file. It?s not something done in the inner loop of a big computation. From: Arnaud Gelas > Date: Monday, September 15, 2014 at 5:05 AM To: ITK > Subject: [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData Hi guys, I have been looking at GDCMImageIO this morning and I thought it would be great if it was possible to iterate directly on the Dictionary and do not use ExposeMetaData cause internally there are 2 finds (HasKeys and [] ) per iterator (in which we already know both keys and values). https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L700 https://github.com/Kitware/ITK/blob/master/Modules/Core/Common/include/itkMetaDataObject.h#L171-L189 I have tried to create a new function which would take an iterator as parameter, I have compilation error or a failing dynamic_cast? I guess I am missing something obvious? I have been testing something like that: http://review.source.kitware.com/#/c/17026/ Any idea on how to fix the code ( both compilation & dynamic_cast ), please? Thanks, Arnaud ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 16 13:26:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Sep 2014 13:26:17 -0400 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: <541848B5.9060901@laposte.net> References: <541848B5.9060901@laposte.net> Message-ID: Hi Jo?l, Yes, that the current best repository, and fixes are welcome! Please add a pull request on the repository and ping the mailing list if it is not merged after a few days. Thanks, Matt On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer wrote: > Hi all, > > The template for Insight Journal submissions that is available on GitHub and > recommended on the Insight Journal website > (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) does > not build with ITK4. > > I can try to fix it, but before I do I would like to make sure it is still > the current version? > > Thanks! > > Jo?l > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Sep 16 13:29:31 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Sep 2014 13:29:31 -0400 Subject: [ITK] [ITK-dev] Review.source.kitware.com down? In-Reply-To: References: Message-ID: And we're back :-) On Tue, Sep 16, 2014 at 1:02 PM, Matt McCormick wrote: > It's not just you. I will find the status. > > Thanks, > Matt > > On Tue, Sep 16, 2014 at 12:50 PM, Williams, Norman K > wrote: >> Is it just me or is ITK Gerrit inaccessible? >> >> >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered by the >> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential >> and may be legally privileged. If you are not the intended recipient, you >> are hereby notified that any retention, dissemination, distribution, or >> copying of this communication is strictly prohibited. Please reply to the >> sender that you have received the message in error, then delete it. Thank >> you. >> ________________________________ >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Sep 16 13:28:20 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 16 Sep 2014 13:28:20 -0400 Subject: [ITK] [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData In-Reply-To: References: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com> Message-ID: <6367ECBA-9742-4DCD-A0F7-387C11195CF7@mail.nih.gov> Kent, A long time ago, when I was working on IO streaming, I had modified the ImageSeries reader to populate the metadata dictionary on the GenerateOutputInformation phase of the pipeline. This ended up getting called 2 or 3 times, and it caused a significant performance penalty with the GDCM meta-data that the Slicer folks loudly complained and it was fixed [ likely here 1]. I have doubts about your assumption that there are not significant computation expenses with metadata IO. However I am not quite certain if my experience is relavent to this issue. just an FYI, Brad [1] https://github.com/InsightSoftwareConsortium/ITK/commit/e92d78ee3b26069d3aeb6aa9f6460a46f20ec2de On Sep 16, 2014, at 1:15 PM, Williams, Norman K wrote: > the time spent in writing and reading the MetaDataDictionary is not going to have a significant computational cost, since it only happens when you read or write a DICOM file. It?s not something done in the inner loop of a big computation. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From daviddoria at gmail.com Tue Sep 16 14:01:46 2014 From: daviddoria at gmail.com (David Doria) Date: Tue, 16 Sep 2014 14:01:46 -0400 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: References: <541848B5.9060901@laposte.net> Message-ID: On Tue, Sep 16, 2014 at 1:26 PM, Matt McCormick wrote: > Hi Jo?l, > > Yes, that the current best repository, and fixes are welcome! Please > add a pull request on the repository and ping the mailing list if it > is not merged after a few days. > > Thanks, > Matt > I found an email from Hans from almost 2 years ago where it looks like he fixed the compatibility problems here: https://github.com/BRAINSia/LogSymmetricDemons I had fixed a few things in the same thread as well: http://public.kitware.com/pipermail/insight-developers/2012-December/022304.html Both might be worth a look. David -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From huanhehot at gmail.com Tue Sep 16 17:07:35 2014 From: huanhehot at gmail.com (=?UTF-8?B?5L2V5qyi?=) Date: Tue, 16 Sep 2014 17:07:35 -0400 Subject: [ITK] 3d volume construction with itk/vtk Message-ID: Hello, I'm a new user to ITK and a beginner to medical image processing. I'm working on a task of constructing a 3d volume from a series of micro-CT brain slices, the volume will be used for registration in later stage. What preparations do I make on those 2-d images? noise reduction? Do I have to segment tissue? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Sep 16 18:39:47 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 16 Sep 2014 22:39:47 +0000 Subject: [ITK] ITK-4.6 problem In-Reply-To: References: , Message-ID: Update on the bug in the version of ITK-4.6 installed by Slicer: What can we make of this: ImageType::Pointer im = ImageType::New(); ImageType::SizeType imsize; imsize[0] = width; imsize[1] = height; imsize[2] = depth; ImageType::IndexType imstart; imstart[0] = 0; imstart[1] = 0; imstart[2] = 0; ImageType::RegionType imregion; imregion.SetSize(imsize); imregion.SetIndex(imstart); im->SetRegions(imregion); im->Allocate(); p = (unsigned char *)(im->GetBufferPointer()); width = im->GetLargestPossibleRegion().GetSize()[0]; height = im->GetLargestPossibleRegion().GetSize()[1]; depth = im->GetLargestPossibleRegion().GetSize()[2]; printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); printf("imregion size(0): %d\n",imregion.GetSize(0)); printf("imregion size(1): %d\n",imregion.GetSize(1)); printf("imregion size(2): %d\n",imregion.GetSize(2)); int i = 195000000; for (int i=197160890; i<200000000;i++) { printf("offset: %d\n",i); p[i] = 0; } yields (reproducibly): D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 ... Requested image dimensions: width, height, depth: 1650 1650 1650 imregion size(0): 1650 imregion size(1): 1650 imregion size(2): 1650 offset: 197160890 offset: 197160891 offset: 197160892 offset: 197160893 offset: 197160894 offset: 197160895 offset: 197160896 (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? I'd appreciate some pointers. Thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Wednesday, 17 September 2014 1:48 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] ITK-4.6 problem Hi Gib, > > There is something a bit funny about the installed ITK-4.6, in that the > compiler complained about some missing include files, vnl_*.h and others, > which are in my ITK-4.0 installation but not in 4.6. I just copied them > across - I hope this is not a problem. > This is probably a problem. Did the ITK 4.6 build complete successfully and the install complete successfully? Thanks, Matt From bill.lorensen at gmail.com Tue Sep 16 18:59:59 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 16 Sep 2014 18:59:59 -0400 Subject: [ITK] [ITK-dev] Coverity 'Uncaught Exception' errors In-Reply-To: References: Message-ID: Yes On Sep 16, 2014 12:25 PM, "Williams, Norman K" wrote: > You mean we told Coverity to ignore them? > > I guess that makes sense. > > On 9/16/14, 9:53 AM, "Bill Lorensen" wrote: > > >I think we ignored a number of those. > > > > > >On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K > > wrote: > >> Hans asked me to look at a couple of ITK Coverity defects, as they were > >>in > >> code written in our lab. > >> > >> A couple of them are understandable but problematic. Basically there?s > >>an > >> exception thrown at itkObjectFactoryBase.cxx at line 533: > >> > >> 531 if ( ObjectFactoryBase::m_StrictVersionChecking ) > >> 532 { > >> 1. exception_thrown: An exception of type "itk::ExceptionObject" is > >> thrown. > >> 533 itkGenericExceptionMacro(<< "Incompatible factory version load > >> attempt:" > >> 534 << "\nRunning itk version :\n" << > >> Version::GetITKSourceVersion() > >> 535 << "\nAttempted loading factory > >>version:\n" > >> << factory->GetITKSourceVersion() > >> 536 << "\nAttempted factory:\n" << > >> factory->m_LibraryPath << "\n"); > >> 537 } > >> 538 else > >> 539 { > >> 540 itkGenericOutputMacro(<< "Possible incompatible factory load:" > >> 541 << "\nRunning itk version :\n" << > >> Version::GetITKSourceVersion() > >> 542 << "\nLoaded factory version:\n" << > >> factory->GetITKSourceVersion() > >> 543 << "\nLoading factory:\n" << > >> factory->m_LibraryPath << "\n"); > >> 544 } > >> 545 } > >> > >> There are 4 Coverity defects reported that all point to this code. > >>Given > >> where the exceptions are thrown, it looks like every call to > >> itk::::New() should be bracketed by a try/catch pair. > >> > >> But in fact Coverity only reports 4 instances of this being a problem. > >> > >> I can fix the reported defects for completeness? sake, but I find it > >> mysterious that more defects caused by this occur. > >> > >> > >> ________________________________ > >> Notice: This UI Health Care e-mail (including attachments) is covered > >>by the > >> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is > >>confidential > >> and may be legally privileged. If you are not the intended recipient, > >>you > >> are hereby notified that any retention, dissemination, distribution, or > >> copying of this communication is strictly prohibited. Please reply to > >>the > >> sender that you have received the message in error, then delete it. > >>Thank > >> you. > >> ________________________________ > >> > >> _______________________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-developers > >> > >> _______________________________________________ > >> Community mailing list > >> Community at itk.org > >> http://public.kitware.com/mailman/listinfo/community > >> > > > > > > > >-- > >Unpaid intern in BillsBasement at noware dot com > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by > the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is > confidential and may be legally privileged. If you are not the intended > recipient, you are hereby notified that any retention, dissemination, > distribution, or copying of this communication is strictly prohibited. > Please reply to the sender that you have received the message in error, > then delete it. Thank you. > ________________________________ > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From gowithking at googlemail.com Tue Sep 16 19:53:39 2014 From: gowithking at googlemail.com (gowith king) Date: Wed, 17 Sep 2014 01:53:39 +0200 Subject: [ITK] Bug in StatisticsImageFilter? Message-ID: I was trying to use itk.StatisticsImageFilter to check the outcome of my image reader. but all the results are wrong. reader1 = itk.ImageFileReader.IUC3.New() reader1.SetFileName(inputImagetest) rangetest=itk.StatisticsImageFilter.IUC3.New() rangetest.SetInput(reader1) print 'range: ', str(rangetest.GetMinimum()) result: range: 255 obviously this is not true for my image : it is a binary image and has only 1 and 100 two values. I am working on a python 2.7 wrapped ITK4 . if the python2 is incompatible with itk? -------------- next part -------------- An HTML attachment was scrubbed... URL: From yxp233 at postech.ac.kr Tue Sep 16 20:19:21 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Wed, 17 Sep 2014 09:19:21 +0900 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support In-Reply-To: <1410878838500935.032749.ptmail04@ptmail04> References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> Message-ID: <02a501cfd20d$079448c0$16bcda40$@ac.kr> Hello, Is there any detailed instructions of how to compile ITK with GPU module on? I had a hard time to get it work properly. Any information or help is appreciated. Thanks, Xiaopeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Tue Sep 16 21:12:37 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 01:12:37 +0000 Subject: [ITK] ITK-4.6 problem - OffsetValueType Message-ID: Hi, I've been digging into the code, and trying to track down where the memory access problem occurs. By putting some printf statements in itkImage.hxx and itkImageBase.h I think I've got close to the source. As I suspected it is in the Image::Allocate() function. As the program output below shows, with N=1625 GetOffsetTable() returns the correct size of the image, but with N=1626 it returns 1626^3 - 2^32. The problem is that OffsetValueType is only 4 bytes. I'm reluctant to go further with this because I don't want to risk breaking something, but somebody should know why OffsetValueType has this size and how to increase it to 8 bytes in the case of ITK_USE_64BITS_IDS on. itkImage.hxx: void Image< TPixel, VImageDimension > ::Allocate(bool initializePixels) { SizeValueType num; this->ComputeOffsetTable(); num = static_cast(this->GetOffsetTable()[VImageDimension]); printf("Image::Allocate: GetOffsetTable(): %lld\n",this->GetOffsetTable()[VImageDimension]); //Gib printf("Image::Allocate: num: %lld\n",num); //Gib m_Buffer->Reserve(num, initializePixels); } itkImageBase.h: const OffsetValueType * GetOffsetTable() const { printf("Image::Allocate: sizeof(OffsetValueType): %d\n",sizeof(OffsetValueType)); //Gib return m_OffsetTable; } D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1625 1 Output image file: zzz-4.6.tif Desired image dimensions: width, height, depth: 1625 1625 1625 Image::Allocate: sizeof(OffsetValueType): 4 Image::Allocate: sizeof(OffsetValueType): 4 Image::Allocate: GetOffsetTable(): 4291015625 Image::Allocate: num: 4291015625 Requested image dimensions: width, height, depth: 1625 1625 1625 imregion size(0): 1625 imregion size(1): 1625 imregion size(2): 1625 Image::FillBuffer: numberOfPixels: 4291015625 D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1626 1 Output image file: zzz-4.6.tif Desired image dimensions: width, height, depth: 1626 1626 1626 Image::Allocate: sizeof(OffsetValueType): 4 Image::Allocate: sizeof(OffsetValueType): 4 Image::Allocate: GetOffsetTable(): 3975080 Image::Allocate: num: 3975080 Requested image dimensions: width, height, depth: 1626 1626 1626 imregion size(0): 1626 imregion size(1): 1626 imregion size(2): 1626 Image::FillBuffer: numberOfPixels: 3975080 ________________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, 17 September 2014 10:39 a.m. To: Matt McCormick Cc: community at itk.org Subject: Re: [ITK] ITK-4.6 problem Update on the bug in the version of ITK-4.6 installed by Slicer: What can we make of this: ImageType::Pointer im = ImageType::New(); ImageType::SizeType imsize; imsize[0] = width; imsize[1] = height; imsize[2] = depth; ImageType::IndexType imstart; imstart[0] = 0; imstart[1] = 0; imstart[2] = 0; ImageType::RegionType imregion; imregion.SetSize(imsize); imregion.SetIndex(imstart); im->SetRegions(imregion); im->Allocate(); p = (unsigned char *)(im->GetBufferPointer()); width = im->GetLargestPossibleRegion().GetSize()[0]; height = im->GetLargestPossibleRegion().GetSize()[1]; depth = im->GetLargestPossibleRegion().GetSize()[2]; printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); printf("imregion size(0): %d\n",imregion.GetSize(0)); printf("imregion size(1): %d\n",imregion.GetSize(1)); printf("imregion size(2): %d\n",imregion.GetSize(2)); int i = 195000000; for (int i=197160890; i<200000000;i++) { printf("offset: %d\n",i); p[i] = 0; } yields (reproducibly): D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 ... Requested image dimensions: width, height, depth: 1650 1650 1650 imregion size(0): 1650 imregion size(1): 1650 imregion size(2): 1650 offset: 197160890 offset: 197160891 offset: 197160892 offset: 197160893 offset: 197160894 offset: 197160895 offset: 197160896 (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? I'd appreciate some pointers. Thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Wednesday, 17 September 2014 1:48 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] ITK-4.6 problem Hi Gib, > > There is something a bit funny about the installed ITK-4.6, in that the > compiler complained about some missing include files, vnl_*.h and others, > which are in my ITK-4.0 installation but not in 4.6. I just copied them > across - I hope this is not a problem. > This is probably a problem. Did the ITK 4.6 build complete successfully and the install complete successfully? Thanks, Matt _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From g.bogle at auckland.ac.nz Wed Sep 17 03:35:18 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 07:35:18 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> References: , <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Hi Bradley, Matt and Steve, Now for the embarrassing confession. In External_ITK4.cmake I turned ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I finally checked what the code that is being built was using (with #if defined ...) I discovered that both ITKV3_COMPATIBILITY and ITK_USE_64BITS_IDS were off. How can this be? It's easy, all it takes is a typo: -DITK_USE_64_BITS_IDS:BOOL=ON That typo has cost me a couple of days, and caused annoyance to a few people, I suspect. Unfortunately... now Slicer's vtkITK does not build. There are very many errors like this: 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ 3>Build started 17/09/2014 7:25:52 p.m.. 3>InitializeBuildStatus: 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". 3>CustomBuild: 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt 3> CMake does not need to re-run because C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. 3>ClCompile: 3> vtkITKNumericTraits.cxx 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx 3> vtkITKArchetypeImageSeriesReader.cxx 3> vtkITKArchetypeImageSeriesScalarReader.cxx 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx 3> vtkITKImageWriter.cxx 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx 3> vtkITKDistanceTransform.cxx 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): error C2679: binary '=' : no operator found which takes a right-hand operand of type 'itk::ImportImageContainer *' (or there is no acceptable conversion) 3> with 3> [ 3> TElementIdentifier=unsigned __int64, 3> TElement=double 3> ] 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): could be 'itk::SmartPointer &itk::SmartPointer::operator =(const itk::SmartPointer &)' 3> with 3> [ 3> TObjectType=itk::ImportImageContainer 3> ] 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): or 'itk::SmartPointer &itk::SmartPointer::operator =(itk::ImportImageContainer *)' 3> with 3> [ 3> TObjectType=itk::ImportImageContainer, 3> TElementIdentifier=unsigned long, 3> TElement=double 3> ] 3> while trying to match the argument list '(itk::SmartPointer, itk::ImportImageContainer *)' 3> with 3> [ 3> TObjectType=itk::ImportImageContainer 3> ] 3> and 3> [ 3> TElementIdentifier=unsigned __int64, 3> TElement=double 3> ] I presume these are related to the use of 64-bit integers. Over to you guys :) Gib ________________________________ From: Bradley Lowekamp [blowekamp at mail.nih.gov] Sent: Tuesday, 16 September 2014 12:45 a.m. To: Steve Pieper Cc: Gib Bogle; slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hello, For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 To test for ITK big tiff compatibility, I'd recommend getting python 2.7 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to read and write files like these there. More information about getting started is here[1]. You should be a able to generate a image with: import SimpleITK as sitk img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) img += 10 stats = sitk.StatisticsImageFilter() stats.Execute(img) print stats This should give you basic access to ITK in python to interactively experiment with options with these large images. I have been able to load large images with the binaries of SimpleITK on windows 64-bits. I don't know if I have tried big tiff though. A simular test could be done with C++ and ITK directly, but I think SimpleITK in python may be quicker for experimentation. Brad [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted [2] http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: Hi Gib - Are you testing only on windows? What we would often try to do for this kind of debugging is to create a small example that other people can test on their configurations. Slicer has a mechanism called a Self Test [1] to allow easy replication and debugging across multiple platforms. It's ideal if we can hone it down to something like what is described as a 'sscce' [2]. The self tests will typically download some data from a public web site, run some operations, and then print something out saying if it passed or failed (or it may crash). Since it's possible to make a small data file that expands into a giant tiff image it should be pretty tractable to pose this issue in the form of a self test. Best, Steve [1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule [2] http://sscce.org/ On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: Hi J-C, Some more info about Slicer with big tiff files. 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page 72) All suggestions will be gratefully received. Cheers Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Sunday, 14 September 2014 8:32 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Gib, What do you mean by "reinstalled" ? You should not have to install Slicer to be able to execute it from the build directory. After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work out. When done building, make sure to start the Slicer launcher: C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe and not the Slicer executable: C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe By using the launcher, you ensure that the PATH are properly setup and the expected libraries are loaded. Hth Jc On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > wrote: I hope I understand correctly. I added the line as shown to C:\Slicer\SuperBuild\External_ITKv4.cmake: ... # ZLIB -DITK_USE_SYSTEM_ZLIB:BOOL=ON -DZLIB_ROOT:PATH=${ZLIB_ROOT} -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} # Big TIFF -DITK_USE_64_BITS_IDS:BOOL=ON ... I then did ALL_BUILD in the root of the build directory (C:\s\b). I presume this is the "superbuild". I then redid ALL_BUILD in C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still crashes with the big tiff. Is there somewhere I can check in the project configuration files to see if setting ITK_USE_64_BITS_IDS actually took effect? Thanks Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Sunday, 14 September 2014 1:36 p.m. To: Gib Bogle Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hey Gib - Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the ITK build process [1] during the superbuild. I don't think much else was required except turning off the IKTv3 parts. [1] https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 -Steve p.s. I hear the ABs beat the Boks recently in a close match (we don't get it on TV). So the Jo'berg game should be a great rematch! On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > wrote: You did warn me. Here is the list of options not ticked: Slicer_BUILD_BRAINSTOOLS _LEGACY_CLI _LandmarkRegistration _TESTING_EXTENSIONS _UPDATE_TRANSLATION _USE_GIT_PROTOCOL _OpenIGTLink _PYTHONQT_WITH_OPENSSL _PYTHONQT_WITH_TCL _QtTesting _SimpleITK _VTK_DEBUG_LINKS Slicer_WITH_LIBRARY_VERSION USE_BRAINS* USE_ConvertBetweenFileFormats USE_DWIConvert USE_DebugImageViewer USE_GTRACT USE_ICCDEF USE_ImageCalculator USE_ReferenceAtlas ------- Progress! Process Monitor showed me that the exit code was C0000139, which means a DLL was not found. I then realized that I have different occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this prompted me to look more carefully at the PATH environment variable. I just tested with all the new paths at the start of the PATH string, and Slicer starts successfully! I can load a tiff! But ... it still crashes when I attempt to load a 4 GB tiff. I am now wondering (belatedly!) about the way I tried to build with big tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as 'bool'. It appears ticked in Ungrouped Entries. I really should have asked for directions before doing this - now I'm wondering if that switch actually had any effect. Is that the right thing to do, and if not, what is? Thanks Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Sunday, 14 September 2014 10:02 a.m. To: Gib Bogle Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Yes, well, don't say I didn't warn you! ; ) You do need loadable modules and you probably do want python (a lot of core stuff is in python, like the editor). BRAINSTools should be off for now, since it needs ITKv3. I'm not sure either what to do next, but I suggest maybe trying the Process Monitor from microsoft (sysinternals) and see what it was doing when it exited. But that may be a longshot. -Steve On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > wrote: Hi Steve, That was an interesting exercise. I managed to build Slicer without Qtloadablemodules. As you might expect, it was not much use. The program started up but without any capabilities, just an empty shell. (I'm a bit handicapped by not knowing anything about how Slicer is constructed.) So I built it again, this time selecting most things except BRAINTools. The build took a long time, partly because I turned on the Python option, which I don't need. This time there were no errors, except for a couple of occasions where the attempt to create a directory failed - this was because the directory already existed, and was easily solved by deleting the directory and building again. I installed everything that wanted to be installed, and modified the environment variables to suit. My sense of satisfaction was short-lived, however. When Slicer is invoked the Acknowledgements screen flashes up briefly then the program exits. There are no error messages. Dependency Walker shows that all the DLLs are being found. I am assuming that BRAINTools is not needed (not knowing what it is). I sense that I must be close to getting it working, but I'm not sure what to do next. Cheers Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Sunday, 14 September 2014 12:36 a.m. To: Gib Bogle Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Gib - A lot of the building goes on in parallel so you need to review the whole build log to see what is going on. I'm guessing ITK didn't build correctly. Typically I do a Control-A Control-C in the visual studio output window and then paste it into a text editor to look for issues. Definitely you don't want to be editing any of the visual studio files, since they are generated by cmake every configure -- much better to sort out what is going on at the cmake flag level. Best, Steve On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > wrote: Looking at the Project Properties for qSlicerBaseQTCore I notice something odd. Here is a snippet from the list of Linker > Input > Additional Dependencies: ... C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib ITKCommon.lib C:\Qt64\4.8.1\lib\QtOpenGL4.lib ... For some reason ITKCommon.lib is treated differently from all the other (at first sight) ITK libraries. Any ideas about how I might fix this? If I edit the linker configuration for qSlicerBaseQTCore to point correctly to the ITKCommon library it builds OK, but I'd rather not have to do this 40+ times. Thanks again Gib ________________________________ From: slicer-devel-bounces at bwh.harvard.edu [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Saturday, 13 September 2014 12:59 p.m. To: Steve Pieper Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Steve, All goes well until the point where the qSlicer*.lib get made. The first error, while building qSlicerBaseQTCore.lib, is: LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' I don't know how to interpret this. I am guessing that it wants to link the ITK library that was just built, i.e.: \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib This is the first of about 40 such link errors. I'm not sure if ITK really needed to be built, since it is already installed (64-bit) on my system, but I didn't see any option for skipping that step (same for VTK). Is an INSTALL step for ITK needed? Should I set ITK_DIR appropriately? Thanks Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Saturday, 13 September 2014 9:02 a.m. To: Gib Bogle Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Gib - I'd give a qualified 'yes' answer. Technically what you propose is quite reasonable, and would be workable. But if you haven't built a big package on windows before there are quite a few prerequites (qt, cmake, git, visual studio...) and odd things can go wrong if it isn't all done just right. That said, slicer is actually quite well supported on windows, better, IMHO, than many cross-platform systems. But windows is really the trickiest platform in my experience. -Steve On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > wrote: Hi Steve, Do you think I would be able to build Slicer myself, with ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that depends on either ITKDeprecated or ITKV3Compatibility? My need at this point is simply for a 3D viewer that can handle big images. Thanks Gib ________________________________ From: Gib Bogle Sent: Wednesday, 10 September 2014 10:34 a.m. To: Jean-Christophe Fillion-Robin; Steve Pieper Cc: slicer-devel at bwh.harvard.edu Subject: RE: [slicer-devel] BigTIFF Hi Jean-Christophe, Any idea when 4.5 will enter the world? Cheers Gib ________________________________ From: slicer-devel-bounces at bwh.harvard.edu [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Wednesday, 10 September 2014 10:31 a.m. To: Steve Pieper Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Folks, Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on either ITKDeprecated or ITKV3Compatibility. That said, BRAINSTools and some extensions are still depending on these module. All details are captured here: http://na-mic.org/Mantis/view.php?id=3825#c12486 Note also that this will NOT be addressed for Slicer 4.4 release. The enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is planned for 4.5. Thanks Jc On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > wrote: Hi Matt - Thanks, that's helpful. I suspect that for slicer, the only real issues will be in vtkITK, which includes all the file IO adapters. But I think it will be pretty straightforward. But there's no reason to start that until we know that BRAINSTools will work - right now at least some of them depend on ITKDeprecated. -Steve On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick > wrote: Here is what the process would look like: 0) Start with a clean software quality dashboard. 1) Set ITKV3_COMPATIBILITY to OFF in Superbuild/External_ITKv4.cmake 2) Rebuild and encounter errors and test failures. 3) Fix the errors with the help of the ITK migration guide [1] and the ITK mailing list [2]. They usually fairly strait forward changes (minor modifications to the API, etc). 4) Set ITK_USE_64BITS_IDS to ON. 5) Profit. HTH, Matt [1] http://itk.org/migrationv4/ [2] http://www.itk.org/ITK/help/mailing.html On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > wrote: > Yes, agreed it's a good goal and I believe the expertise exists, but it's > looking like there's a fair amount of code to retrofit. > > Maybe Hans, Brad, Matt or others could provide some idea just what is > involved? > > -Steve > > > > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle > wrote: >> >> :( I imagine that people are increasingly working with very large >> datasets, so the number of people who would like to have this capability >> will grow. I, alas, am not an ITK expert. >> ________________________________ >> From: Steve Pieper [pieper at isomics.com] >> Sent: Friday, 5 September 2014 8:42 a.m. >> >> To: Gib Bogle >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Alas the build where I enabled 64 bit id's failed to even configure >> properly. Lots of key code depends on the ITKDeprecated module, like vtkITK >> and various components of BRAINSTools. So I would say some ITK experts are >> going to need to dig in before this mode can be enabled. >> >> -Steve >> >> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle > wrote: >>> >>> I await the results with interest... >>> ________________________________ >>> From: slicer-devel-bounces at bwh.harvard.edu >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve Pieper >>> [pieper at isomics.com] >>> Sent: Friday, 5 September 2014 1:32 a.m. >>> To: Bradley Lowekamp >>> >>> Cc: slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out a lot of >>> legacy CLI code - perhaps those were the main places ITKV3_COMPATIBILITY was >>> required? I kicked off a build to see what will happen. >>> >>> -Steve >>> >>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp > >>> wrote: >>>> >>>> Steve, >>>> >>>> Yes, this is certainly an issue with how ITK has been configured in >>>> Slicer. >>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY needs to >>>> be disabled, and then the ITKDeprecated module can no longer be used. I have >>>> brought these issue up before and offered assistance but no one wanted to >>>> champion changing these configuration flags. >>>> >>>> Brad >>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > wrote: >>>> >>>> Hi Brad - >>>> >>>> Right, this is not tiff specific but is ITK specific. I was able to >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's vtkNRRDWriter >>>> and reload with vtkNRRDReader. Could not read the same file with ITK's NRRD >>>> reader. This was all on a slicer current trunk build with default options >>>> on win7 64bit. >>>> >>>> So are we out of luck enabling 64bit IDs or is it just something nobody >>>> has tried? >>>> >>>> -Steve >>>> >>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>> > wrote: >>>>> >>>>> Steve, >>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on windows 64? >>>>> >>>>> There should be some image source filters in the SimpleFilters modules >>>>> to generate images. I don't think this issue is tiff specific. >>>>> >>>>> Bread >>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper > wrote: >>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>> >>>>> I happens in the itk tiff reader. I created a bug report and pasted in >>>>> a stack trace and put a link to the data. >>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>> >>>>> -Steve >>>>> >>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>> > wrote: >>>>>> >>>>>> Matt, I was just about to point that out. >>>>>> >>>>>> The other things is the compatibility flag: >>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's still >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>> >>>>>> Brad >>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper > wrote: >>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can replicate the >>>>>> issue and then we can see if that has any side effects. >>>>>> >>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>> > wrote: >>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>> >>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle > >>>>>>> wrote: >>>>>>> > I have to do something else for a while now. I'll get back to this >>>>>>> > later. >>>>>>> > ________________________________ >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>> > >>>>>>> > To: Gib Bogle >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>> > >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how to >>>>>>> > generate a big >>>>>>> > file with SimpleITK. Or a statically linked executable for any >>>>>>> > standard >>>>>>> > platform should be fine too. >>>>>>> > >>>>>>> > >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle > >>>>>>> > wrote: >>>>>>> >> >>>>>>> >> On second thoughts a very simple image will compress to a >>>>>>> >> reasonable size. >>>>>>> >> Slicer seems to handle the compression modes used by ITK without >>>>>>> >> problems. >>>>>>> >> ________________________________ >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>> >> To: Gib Bogle >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >> >>>>>>> >> Hi - >>>>>>> >> >>>>>>> >> Is there an easy way to generate a big tiff like this, for example >>>>>>> >> with a >>>>>>> >> few lines of SimpleITK code? (Easier than trying to transfer a >>>>>>> >> 4.5GB file >>>>>>> >> from NZ). >>>>>>> >> >>>>>>> >> -Steve >>>>>>> >> >>>>>>> >> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle > >>>>>>> >> wrote: >>>>>>> >>> >>>>>>> >>> Hi Brad, >>>>>>> >>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. I can load >>>>>>> >>> a tiff >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), but a couple >>>>>>> >>> of bigger >>>>>>> >>> files fail. When I try to open a file that is about 4.5 GB >>>>>>> >>> (actually when I >>>>>>> >>> try to add data to the scene) the program crashes immediately, >>>>>>> >>> exception >>>>>>> >>> code c0000005. The result with an image of about half this size >>>>>>> >>> is the >>>>>>> >>> same. Sometimes the behaviour is slightly different - I see the >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the windows greys >>>>>>> >>> out. >>>>>>> >>> Nothing happens after that, until I click the x button on the >>>>>>> >>> popup, and the >>>>>>> >>> program crashes. >>>>>>> >>> >>>>>>> >>> These files were all written with ITK. The reason I installed >>>>>>> >>> Slicer is >>>>>>> >>> simply to be able to view big files - Irfanview is very good but >>>>>>> >>> BigTIFFs >>>>>>> >>> are not enabled. >>>>>>> >>> >>>>>>> >>> Is it a case of having to build Slicer myself, with different >>>>>>> >>> build >>>>>>> >>> options? >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> Gib >>>>>>> >>> ________________________________ >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>> >>> To: Gib Bogle >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>> >>>>>>> >>> Hello, >>>>>>> >>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, and the >>>>>>> >>> associated >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you please >>>>>>> >>> provide more >>>>>>> >>> detail about your issue? >>>>>>> >>> >>>>>>> >>> Brad >>>>>>> >>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle > >>>>>>> >>> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does not >>>>>>> >>> handle >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>> >>> Thanks >>>>>>> >>> Gib >>>>>>> >>> _______________________________________________ >>>>>>> >>> slicer-devel mailing list >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>> >>> To unsubscribe: send email to >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as >>>>>>> >>> the >>>>>>> >>> subject >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> The information in this e-mail is intended only for the person to >>>>>>> >>> whom it >>>>>>> >>> is >>>>>>> >>> addressed. If you believe this e-mail was sent to you in error >>>>>>> >>> and the >>>>>>> >>> e-mail >>>>>>> >>> contains patient information, please contact the Partners >>>>>>> >>> Compliance >>>>>>> >>> HelpLine at >>>>>>> >>> http://www.partners.org/complianceline . If the e-mail was sent >>>>>>> >>> to you in >>>>>>> >>> error >>>>>>> >>> but does not contain patient information, please contact the >>>>>>> >>> sender and >>>>>>> >>> properly >>>>>>> >>> dispose of the e-mail. >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> slicer-devel mailing list >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>> >>> To unsubscribe: send email to >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as >>>>>>> >>> the >>>>>>> >>> subject >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> The information in this e-mail is intended only for the person to >>>>>>> >>> whom it >>>>>>> >>> is >>>>>>> >>> addressed. If you believe this e-mail was sent to you in error >>>>>>> >>> and the >>>>>>> >>> e-mail >>>>>>> >>> contains patient information, please contact the Partners >>>>>>> >>> Compliance >>>>>>> >>> HelpLine at >>>>>>> >>> http://www.partners.org/complianceline . If the e-mail was sent >>>>>>> >>> to you in >>>>>>> >>> error >>>>>>> >>> but does not contain patient information, please contact the >>>>>>> >>> sender and >>>>>>> >>> properly >>>>>>> >>> dispose of the e-mail. >>>>>>> >>> >>>>>>> >> >>>>>>> > >>>>>>> > >>>>>>> > _______________________________________________ >>>>>>> > slicer-devel mailing list >>>>>>> > slicer-devel at bwh.harvard.edu >>>>>>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>> > To unsubscribe: send email to >>>>>>> > slicer-devel-request at massmail.spl.harvard.edu >>>>>>> > with unsubscribe as the subject >>>>>>> > >>>>>>> > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>> > >>>>>>> > >>>>>>> > The information in this e-mail is intended only for the person to >>>>>>> > whom it is >>>>>>> > addressed. If you believe this e-mail was sent to you in error and >>>>>>> > the >>>>>>> > e-mail >>>>>>> > contains patient information, please contact the Partners >>>>>>> > Compliance >>>>>>> > HelpLine at >>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>> > you in >>>>>>> > error >>>>>>> > but does not contain patient information, please contact the sender >>>>>>> > and >>>>>>> > properly >>>>>>> > dispose of the e-mail. >>>>>>> > >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> slicer-devel mailing list >>>>>> slicer-devel at bwh.harvard.edu >>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>> To unsubscribe: send email to >>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>> subject >>>>>> >>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom >>>>>> it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>>> in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >> > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu > with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- +1 919 869 8849 _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- +1 919 869 8849 _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Wed Sep 17 09:02:21 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:02:21 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM Message-ID: Hi all, I have been looking at the following wiki example: http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 Can anyone confirm? Is this code validated? are output images compared to input ones in the corresponding test? Thanks Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:04:17 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:04:17 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: <75058210-3021-4372-A59C-8880B69CABED@gmail.com> References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> Message-ID: Hi Nick, I work with CT images, Rescale Intercept / Slope: ( -1024, 1 ) I use system gdcm (release branch from official git repository) Thanks Arnaud On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson wrote: > Arnauld, > > Can you also say if you are using the version of GDCM bundled with ITK > release or have you compiled a system version of GDCM from the > git-repository? > > Nick. > > > On 17 Sep 2014, at 13:59, Nick Patterson > wrote: > > Arnauld, > > Which modality image are you working with, and what are the rescale slope > and intercept of the original image? > > Nick. > > > > > On 17 Sep 2014, at 14:02, Arnaud Gelas wrote: > > Hi all, > > I have been looking at the following wiki example: > > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > It seems to me that the section to rescale the image is not valid anymore > with latest ITK version (?) > > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > > Can anyone confirm? > > Is this code validated? are output images compared to input ones in the > corresponding test? > > Thanks > Arnaud > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:10:43 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:10:43 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> Message-ID: I have been modifying extensively this example... Rescale slope/intercept are saved with expected values -1024 and 1. Not sure if the error is in my code or in this example, but when I compare inputs and outputs with the ShiftScale part all pixels are different (and the difference is -1024)... that's why I am asking if this part is still valid? On Wed, Sep 17, 2014 at 3:06 PM, Nick Patterson wrote: > Ok thanks. When you say that it doesn?t work anymore would I be correct in > assuming that you mean that the output rescale slope/intercept are written > out as 1 and 0, rather than the expected value of -1024 and 1? Or do you > mean not working in some other way? > > Nick. > > > > On 17 Sep 2014, at 14:04, Arnaud Gelas wrote: > > Hi Nick, > > I work with CT images, Rescale Intercept / Slope: ( -1024, 1 ) > > I use system gdcm (release branch from official git repository) > > Thanks > Arnaud > > On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson < > pattersonnp.work at gmail.com> wrote: > >> Arnauld, >> >> Can you also say if you are using the version of GDCM bundled with ITK >> release or have you compiled a system version of GDCM from the >> git-repository? >> >> Nick. >> >> >> On 17 Sep 2014, at 13:59, Nick Patterson >> wrote: >> >> Arnauld, >> >> Which modality image are you working with, and what are the rescale slope >> and intercept of the original image? >> >> Nick. >> >> >> >> >> On 17 Sep 2014, at 14:02, Arnaud Gelas wrote: >> >> Hi all, >> >> I have been looking at the following wiki example: >> >> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >> >> It seems to me that the section to rescale the image is not valid anymore >> with latest ITK version (?) >> >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >> >> Can anyone confirm? >> >> Is this code validated? are output images compared to input ones in the >> corresponding test? >> >> Thanks >> Arnaud >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Wed Sep 17 09:13:12 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 17 Sep 2014 09:13:12 -0400 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: Message-ID: <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov> Arnaud, If using shared libraries causes the dynamic cast to fail, than this may be a side effect of some recent changes [1]. Brad [1] https://github.com/InsightSoftwareConsortium/ITK/commits/master/Modules/Core/Common/include/itkMetaDataObject.h On Sep 17, 2014, at 9:02 AM, Arnaud Gelas wrote: > Hi all, > > I have been looking at the following wiki example: > > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > > Can anyone confirm? > > Is this code validated? are output images compared to input ones in the corresponding test? > > Thanks > Arnaud > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Wed Sep 17 09:21:09 2014 From: matimontg at gmail.com (Matias Montroull) Date: Wed, 17 Sep 2014 10:21:09 -0300 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: Message-ID: I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine. The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version. On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas wrote: > Hi all, > > I have been looking at the following wiki example: > > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > It seems to me that the section to rescale the image is not valid anymore > with latest ITK version (?) > > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > > Can anyone confirm? > > Is this code validated? are output images compared to input ones in the > corresponding test? > > Thanks > Arnaud > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Wed Sep 17 09:23:50 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Wed, 17 Sep 2014 22:23:50 +0900 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support In-Reply-To: <1410913163921868.021894.ptmail04@ptmail04> References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> <1410913163921868.021894.ptmail04@ptmail04> Message-ID: <000c01cfd27a$9ed25020$dc76f060$@ac.kr> By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows: Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): Syntax error in cmake code at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 when parsing string D:\Toolbox\ITK-4.6.0 Invalid escape sequence \T Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set) CMake/ITKModuleEnablement.cmake:171 (include) CMakeLists.txt:322 (include) Configuring incomplete, errors occurred! See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Xiaopeng Yang Sent: Wednesday, September 17, 2014 9:19 AM To: 'insight-users' Subject: [ITK-users] Any instruction of compiling ITK with GPU support Hello, Is there any detailed instructions of how to compile ITK with GPU module on? I had a hard time to get it work properly. Any information or help is appreciated. Thanks, Xiaopeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From pattersonnp.work at gmail.com Wed Sep 17 09:25:00 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 17 Sep 2014 14:25:00 +0100 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com> References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com> Message-ID: Ok thanks, I have had various issues with this examples before. If you can re-test your CT images with the unmodified ResampleDICOM example and let me know the results. If you see the same problem, get back to me. Nick. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:32:08 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:32:08 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: Message-ID: Hi Matias, I guess you are referring to https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e v4.6.0 I use the release branch of ITK --- Matt, Can you comment on this, please? Thanks Arnaud On Sep 17, 2014, at 3:21 PM, Matias Montroull wrote: > I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine. > > The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version. > > On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas wrote: > Hi all, > > I have been looking at the following wiki example: > > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > > Can anyone confirm? > > Is this code validated? are output images compared to input ones in the corresponding test? > > Thanks > Arnaud > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Wed Sep 17 09:27:44 2014 From: matimontg at gmail.com (Matias Montroull) Date: Wed, 17 Sep 2014 10:27:44 -0300 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com> Message-ID: Nick, what do you mean by "the unmodified resampleDICOM"? thanks, On Wed, Sep 17, 2014 at 10:25 AM, Nick Patterson wrote: > > Ok thanks, > > > I have had various issues with this examples before. If you can re-test > your CT images with the unmodified ResampleDICOM example and let me know > the results. If you see the same problem, get back to me. > > Nick. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From chinander at gmail.com Wed Sep 17 09:28:45 2014 From: chinander at gmail.com (Mike Chinander) Date: Wed, 17 Sep 2014 08:28:45 -0500 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support In-Reply-To: <000c01cfd27a$9ed25020$dc76f060$@ac.kr> References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> <1410913163921868.021894.ptmail04@ptmail04> <000c01cfd27a$9ed25020$dc76f060$@ac.kr> Message-ID: Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with forward slashes instead, "D:/Toolbox/ITK-4.6.0" On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang wrote: > By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under > windows 7 64 bit. I set USE_GPU on, but I got the error as follows: > > > > Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib > > CMake Error at C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): > Syntax error in cmake code at > > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 > > when parsing string > > D:\Toolbox\ITK-4.6.0 > > Invalid escape sequence \T > Call Stack (most recent call first): > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 > (cpack_set_if_not_set) > CMake/ITKModuleEnablement.cmake:171 (include) > CMakeLists.txt:322 (include) > > Configuring incomplete, errors occurred! > > See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". > > See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From pattersonnp.work at gmail.com Wed Sep 17 09:29:04 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 17 Sep 2014 14:29:04 +0100 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: Message-ID: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> I should also mention Arnauld that I use ITK4.5.2. I have had many issues with using ITK 4.6 with the latest GDCM from git, so rolled back to ITK4.5.2. Nick. On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: > Hi Matias, > > I guess you are referring to > > https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e > > $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e > v4.6.0 > > I use the release branch of ITK > > --- > > Matt, > > Can you comment on this, please? > > Thanks > Arnaud > > On Sep 17, 2014, at 3:21 PM, Matias Montroull wrote: > >> I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine. >> >> The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version. >> >> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas wrote: >> Hi all, >> >> I have been looking at the following wiki example: >> >> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >> >> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >> >> Can anyone confirm? >> >> Is this code validated? are output images compared to input ones in the corresponding test? >> >> Thanks >> Arnaud >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:27:33 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:27:33 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> Message-ID: <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com> I have already done that change before sending the email? Unfortunately, I can' share the code; so I'll rather get back to the example and validate with this one. I'll get back to you once I have made the same test with the example. On Sep 17, 2014, at 3:13 PM, Nick Patterson wrote: > Ok, I will probably need to see your code if you have heavily modified the example. However, could you try the following:- > > after line 333 : shiftScale->SetShift( interceptShift ); > add shiftScale->Update(); > > > and try again? > > Let me know. > > Nick. > > > > On 17 Sep 2014, at 14:10, Arnaud Gelas wrote: > >> I have been modifying extensively this example... >> Rescale slope/intercept are saved with expected values -1024 and 1. >> >> Not sure if the error is in my code or in this example, but when I compare inputs and outputs with the ShiftScale part all pixels are different (and the difference is -1024)... that's why I am asking if this part is still valid? >> >> On Wed, Sep 17, 2014 at 3:06 PM, Nick Patterson wrote: >> Ok thanks. When you say that it doesn?t work anymore would I be correct in assuming that you mean that the output rescale slope/intercept are written out as 1 and 0, rather than the expected value of -1024 and 1? Or do you mean not working in some other way? >> >> Nick. >> >> >> >> On 17 Sep 2014, at 14:04, Arnaud Gelas wrote: >> >>> Hi Nick, >>> >>> I work with CT images, Rescale Intercept / Slope: ( -1024, 1 ) >>> >>> I use system gdcm (release branch from official git repository) >>> >>> Thanks >>> Arnaud >>> >>> On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson wrote: >>> Arnauld, >>> >>> Can you also say if you are using the version of GDCM bundled with ITK release or have you compiled a system version of GDCM from the git-repository? >>> >>> Nick. >>> >>> >>> On 17 Sep 2014, at 13:59, Nick Patterson wrote: >>> >>>> Arnauld, >>>> >>>> Which modality image are you working with, and what are the rescale slope and intercept of the original image? >>>> >>>> Nick. >>>> >>>> >>>> >>>> >>>> On 17 Sep 2014, at 14:02, Arnaud Gelas wrote: >>>> >>>>> Hi all, >>>>> >>>>> I have been looking at the following wiki example: >>>>> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>>>> >>>>> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) >>>>> >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>>>> >>>>> Can anyone confirm? >>>>> >>>>> Is this code validated? are output images compared to input ones in the corresponding test? >>>>> >>>>> Thanks >>>>> Arnaud >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:34:00 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:34:00 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Nick, I can't roll back to previous ITK version, important patches on itkGDCMImageIO were very recently merged... https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx e.g. https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c Arnaud On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson wrote: > I should also mention Arnauld that I use ITK4.5.2. I have had many issues > with using ITK 4.6 with the latest GDCM from git, so rolled back to > ITK4.5.2. > > Nick. > > > > On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: > > Hi Matias, > > I guess you are referring to > > > https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e > > $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e > v4.6.0 > > I use the release branch of ITK > > --- > > Matt, > > Can you comment on this, please? > > Thanks > Arnaud > > On Sep 17, 2014, at 3:21 PM, Matias Montroull wrote: > > I had an issue with the resampledicom example once (all my pixel values > were recalculated by adding rescaleintercept) and then downloaded the > latest ITK release (4.6) and worked fine. > > The issue was with the GDCMIO class I beleive but was fixed somehow in the > 4.6 version. > > On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas > wrote: > >> Hi all, >> >> I have been looking at the following wiki example: >> >> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >> >> It seems to me that the section to rescale the image is not valid anymore >> with latest ITK version (?) >> >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >> >> Can anyone confirm? >> >> Is this code validated? are output images compared to input ones in the >> corresponding test? >> >> Thanks >> Arnaud >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From pattersonnp.work at gmail.com Wed Sep 17 09:35:49 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 17 Sep 2014 14:35:49 +0100 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: OK, I will wait to hear the outcome of your run with the original example then. Cheers, Nick. On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: > Nick, > > I can't roll back to previous ITK version, important patches on itkGDCMImageIO were very recently merged... > > https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx > > e.g. > > https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 > https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c > > > Arnaud > > On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson wrote: > I should also mention Arnauld that I use ITK4.5.2. I have had many issues with using ITK 4.6 with the latest GDCM from git, so rolled back to ITK4.5.2. > Nick. > > > > On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: > >> Hi Matias, >> >> I guess you are referring to >> >> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >> >> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >> v4.6.0 >> >> I use the release branch of ITK >> >> --- >> >> Matt, >> >> Can you comment on this, please? >> >> Thanks >> Arnaud >> >> On Sep 17, 2014, at 3:21 PM, Matias Montroull wrote: >> >>> I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine. >>> >>> The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version. >>> >>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas wrote: >>> Hi all, >>> >>> I have been looking at the following wiki example: >>> >>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>> >>> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) >>> >>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>> >>> Can anyone confirm? >>> >>> Is this code validated? are output images compared to input ones in the corresponding test? >>> >>> Thanks >>> Arnaud >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 10:15:11 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 16:15:11 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Hi Nick, I can confirm that with the example I get a difference of -1024 (+/- 1) in between the input and the output, using the ShiftScaleImage part... While without this part of code the difference is (+/-1) I would like to make sure this is the expected behaviour!? On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson wrote: > OK, I will wait to hear the outcome of your run with the original example > then. > > Cheers, Nick. > > > > > On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: > > Nick, > > I can't roll back to previous ITK version, important patches on > itkGDCMImageIO were very recently merged... > > > https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx > > e.g. > > > https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 > > https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c > > > Arnaud > > On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson < > pattersonnp.work at gmail.com> wrote: > >> I should also mention Arnauld that I use ITK4.5.2. I have had many >> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to >> ITK4.5.2. >> Nick. >> >> >> >> On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: >> >> Hi Matias, >> >> I guess you are referring to >> >> >> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >> >> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >> v4.6.0 >> >> I use the release branch of ITK >> >> --- >> >> Matt, >> >> Can you comment on this, please? >> >> Thanks >> Arnaud >> >> On Sep 17, 2014, at 3:21 PM, Matias Montroull >> wrote: >> >> I had an issue with the resampledicom example once (all my pixel values >> were recalculated by adding rescaleintercept) and then downloaded the >> latest ITK release (4.6) and worked fine. >> >> The issue was with the GDCMIO class I beleive but was fixed somehow in >> the 4.6 version. >> >> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas >> wrote: >> >>> Hi all, >>> >>> I have been looking at the following wiki example: >>> >>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>> >>> It seems to me that the section to rescale the image is not valid >>> anymore with latest ITK version (?) >>> >>> >>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>> >>> Can anyone confirm? >>> >>> Is this code validated? are output images compared to input ones in the >>> corresponding test? >>> >>> Thanks >>> Arnaud >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 10:39:59 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 16:39:59 +0200 Subject: [ITK] [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData In-Reply-To: <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov> References: <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov> Message-ID: <4B7CF7FB-4669-403C-A892-98DD219EBDB5@gmail.com> Brad, I guess the email was more related to this topic than the ResampleDICOM's one? Your last commit on itkMetaDataObject.h seems of interest, I'll keep on investigating! Thanks Arnaud On Sep 17, 2014, at 3:13 PM, Bradley Lowekamp wrote: > Arnaud, > > If using shared libraries causes the dynamic cast to fail, than this may be a side effect of some recent changes [1]. > > Brad > > [1] https://github.com/InsightSoftwareConsortium/ITK/commits/master/Modules/Core/Common/include/itkMetaDataObject.h > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From bill.lorensen at gmail.com Wed Sep 17 10:41:12 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 17 Sep 2014 10:41:12 -0400 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: I wrote this example many years ago? 1) If the input has a non-trivial slope/intercept, the reader applies the slope/intercept to the raw data. 2) Rather than setting the slope/intercept in the output dicom, I apply the inverse of of the slope intercept to the resampled data before writing. The output dicom should not have the origin slope/intercept tags. I'll try to verify this with Slicer, but I may be out of touch for 2 weeks? Bill On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas wrote: > Hi Nick, > > I can confirm that with the example I get a difference of -1024 (+/- 1) in > between the input and the output, using the ShiftScaleImage part... > While without this part of code the difference is (+/-1) > > I would like to make sure this is the expected behaviour!? > > On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson > wrote: >> >> OK, I will wait to hear the outcome of your run with the original example >> then. >> >> Cheers, Nick. >> >> >> >> >> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: >> >> Nick, >> >> I can't roll back to previous ITK version, important patches on >> itkGDCMImageIO were very recently merged... >> >> >> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx >> >> e.g. >> >> >> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 >> >> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c >> >> >> Arnaud >> >> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson >> wrote: >>> >>> I should also mention Arnauld that I use ITK4.5.2. I have had many >>> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to >>> ITK4.5.2. >>> Nick. >>> >>> >>> >>> On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: >>> >>> Hi Matias, >>> >>> I guess you are referring to >>> >>> >>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >>> v4.6.0 >>> >>> I use the release branch of ITK >>> >>> --- >>> >>> Matt, >>> >>> Can you comment on this, please? >>> >>> Thanks >>> Arnaud >>> >>> On Sep 17, 2014, at 3:21 PM, Matias Montroull >>> wrote: >>> >>> I had an issue with the resampledicom example once (all my pixel values >>> were recalculated by adding rescaleintercept) and then downloaded the latest >>> ITK release (4.6) and worked fine. >>> >>> The issue was with the GDCMIO class I beleive but was fixed somehow in >>> the 4.6 version. >>> >>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas >>> wrote: >>>> >>>> Hi all, >>>> >>>> I have been looking at the following wiki example: >>>> >>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>>> >>>> It seems to me that the section to rescale the image is not valid >>>> anymore with latest ITK version (?) >>>> >>>> >>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>>> >>>> Can anyone confirm? >>>> >>>> Is this code validated? are output images compared to input ones in the >>>> corresponding test? >>>> >>>> Thanks >>>> Arnaud >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 17 11:13:20 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:13:20 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cg0n52cqd08ulpr6o9jgku32gj0?authkey=CJ-S7tP5s5_xAw On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/ctabd8pd4oasc3p5ejat27jgko4?authkey=COjR69z2toGlIQ For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 All are welcome. Hope to talk to you then! From matt.mccormick at kitware.com Wed Sep 17 11:29:30 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:29:30 -0400 Subject: [ITK] ITK-4.6 problem In-Reply-To: References: Message-ID: Hi Gib, On Tue, Sep 16, 2014 at 6:39 PM, Gib Bogle wrote: > Update on the bug in the version of ITK-4.6 installed by Slicer: > > What can we make of this: > > ImageType::Pointer im = ImageType::New(); > ImageType::SizeType imsize; > imsize[0] = width; > imsize[1] = height; > imsize[2] = depth; > ImageType::IndexType imstart; > imstart[0] = 0; > imstart[1] = 0; > imstart[2] = 0; > ImageType::RegionType imregion; > imregion.SetSize(imsize); > imregion.SetIndex(imstart); > im->SetRegions(imregion); > im->Allocate(); > p = (unsigned char *)(im->GetBufferPointer()); > > width = im->GetLargestPossibleRegion().GetSize()[0]; > height = im->GetLargestPossibleRegion().GetSize()[1]; > depth = im->GetLargestPossibleRegion().GetSize()[2]; > printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); > > printf("imregion size(0): %d\n",imregion.GetSize(0)); > printf("imregion size(1): %d\n",imregion.GetSize(1)); > printf("imregion size(2): %d\n",imregion.GetSize(2)); > > int i = 195000000; > for (int i=197160890; i<200000000;i++) { > printf("offset: %d\n",i); > p[i] = 0; > } > > yields (reproducibly): > > D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 > ... > Requested image dimensions: width, height, depth: 1650 1650 1650 > imregion size(0): 1650 > imregion size(1): 1650 > imregion size(2): 1650 > offset: 197160890 > offset: 197160891 > offset: 197160892 > offset: 197160893 > offset: 197160894 > offset: 197160895 > offset: 197160896 > > > (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) > > Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. > > I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. > > I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? If allocation failed, it should throw a MemoryAllocationError [1]. It may help to walk through the code with a debugger. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Core/Common/include/itkImportImageContainer.hxx;h=cf29eb3f95e0c22ddd32f1170bfe1aff69569634;hb=HEAD > > I'd appreciate some pointers. > > Thanks > Gib > > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Wednesday, 17 September 2014 1:48 a.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] ITK-4.6 problem > > Hi Gib, > >> >> There is something a bit funny about the installed ITK-4.6, in that the >> compiler complained about some missing include files, vnl_*.h and others, >> which are in my ITK-4.0 installation but not in 4.6. I just copied them >> across - I hope this is not a problem. >> > > This is probably a problem. Did the ITK 4.6 build complete > successfully and the install complete successfully? > > Thanks, > Matt From g.bogle at auckland.ac.nz Wed Sep 17 11:35:42 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 15:35:42 +0000 Subject: [ITK] ITK-4.6 problem In-Reply-To: References: , Message-ID: I found the problem, Matt (see my latest message) - I had a typo, and in fact ITK_USE_64BITS_IDS was off. Now I cannot build vtkITK, and the error is too abstruse for me with my meagre C++ understanding. Thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 3:29 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] ITK-4.6 problem Hi Gib, On Tue, Sep 16, 2014 at 6:39 PM, Gib Bogle wrote: > Update on the bug in the version of ITK-4.6 installed by Slicer: > > What can we make of this: > > ImageType::Pointer im = ImageType::New(); > ImageType::SizeType imsize; > imsize[0] = width; > imsize[1] = height; > imsize[2] = depth; > ImageType::IndexType imstart; > imstart[0] = 0; > imstart[1] = 0; > imstart[2] = 0; > ImageType::RegionType imregion; > imregion.SetSize(imsize); > imregion.SetIndex(imstart); > im->SetRegions(imregion); > im->Allocate(); > p = (unsigned char *)(im->GetBufferPointer()); > > width = im->GetLargestPossibleRegion().GetSize()[0]; > height = im->GetLargestPossibleRegion().GetSize()[1]; > depth = im->GetLargestPossibleRegion().GetSize()[2]; > printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); > > printf("imregion size(0): %d\n",imregion.GetSize(0)); > printf("imregion size(1): %d\n",imregion.GetSize(1)); > printf("imregion size(2): %d\n",imregion.GetSize(2)); > > int i = 195000000; > for (int i=197160890; i<200000000;i++) { > printf("offset: %d\n",i); > p[i] = 0; > } > > yields (reproducibly): > > D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 > ... > Requested image dimensions: width, height, depth: 1650 1650 1650 > imregion size(0): 1650 > imregion size(1): 1650 > imregion size(2): 1650 > offset: 197160890 > offset: 197160891 > offset: 197160892 > offset: 197160893 > offset: 197160894 > offset: 197160895 > offset: 197160896 > > > (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) > > Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. > > I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. > > I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? If allocation failed, it should throw a MemoryAllocationError [1]. It may help to walk through the code with a debugger. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Core/Common/include/itkImportImageContainer.hxx;h=cf29eb3f95e0c22ddd32f1170bfe1aff69569634;hb=HEAD > > I'd appreciate some pointers. > > Thanks > Gib > > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Wednesday, 17 September 2014 1:48 a.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] ITK-4.6 problem > > Hi Gib, > >> >> There is something a bit funny about the installed ITK-4.6, in that the >> compiler complained about some missing include files, vnl_*.h and others, >> which are in my ITK-4.0 installation but not in 4.6. I just copied them >> across - I hope this is not a problem. >> > > This is probably a problem. Did the ITK 4.6 build complete > successfully and the install complete successfully? > > Thanks, > Matt From matt.mccormick at kitware.com Wed Sep 17 11:42:33 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:42:33 -0400 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Hi, Do to this fix [1], if the writer is re-using the GDCMImageIO, the writer should apply the inverse rescale / slope intercept like the reader applied the rescale / slope intercept when reading. This was a long-standing bug that I fixed in 4.6.0. Arnaud, if the manual inverse rescale / slope operation is removed, does the correct output result? Thanks, Matt [1] https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen wrote: > I wrote this example many years ago? > 1) If the input has a non-trivial slope/intercept, the reader applies > the slope/intercept to the raw data. > 2) Rather than setting the slope/intercept in the output dicom, I > apply the inverse of of the slope intercept to the resampled data > before writing. The output dicom should not have the origin > slope/intercept tags. > > I'll try to verify this with Slicer, but I may be out of touch for 2 weeks? > > Bill > > > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas wrote: >> Hi Nick, >> >> I can confirm that with the example I get a difference of -1024 (+/- 1) in >> between the input and the output, using the ShiftScaleImage part... >> While without this part of code the difference is (+/-1) >> >> I would like to make sure this is the expected behaviour!? >> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson >> wrote: >>> >>> OK, I will wait to hear the outcome of your run with the original example >>> then. >>> >>> Cheers, Nick. >>> >>> >>> >>> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: >>> >>> Nick, >>> >>> I can't roll back to previous ITK version, important patches on >>> itkGDCMImageIO were very recently merged... >>> >>> >>> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx >>> >>> e.g. >>> >>> >>> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 >>> >>> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c >>> >>> >>> Arnaud >>> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson >>> wrote: >>>> >>>> I should also mention Arnauld that I use ITK4.5.2. I have had many >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to >>>> ITK4.5.2. >>>> Nick. >>>> >>>> >>>> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: >>>> >>>> Hi Matias, >>>> >>>> I guess you are referring to >>>> >>>> >>>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >>>> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >>>> v4.6.0 >>>> >>>> I use the release branch of ITK >>>> >>>> --- >>>> >>>> Matt, >>>> >>>> Can you comment on this, please? >>>> >>>> Thanks >>>> Arnaud >>>> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull >>>> wrote: >>>> >>>> I had an issue with the resampledicom example once (all my pixel values >>>> were recalculated by adding rescaleintercept) and then downloaded the latest >>>> ITK release (4.6) and worked fine. >>>> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow in >>>> the 4.6 version. >>>> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas >>>> wrote: >>>>> >>>>> Hi all, >>>>> >>>>> I have been looking at the following wiki example: >>>>> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>>>> >>>>> It seems to me that the section to rescale the image is not valid >>>>> anymore with latest ITK version (?) >>>>> >>>>> >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>>>> >>>>> Can anyone confirm? >>>>> >>>>> Is this code validated? are output images compared to input ones in the >>>>> corresponding test? >>>>> >>>>> Thanks >>>>> Arnaud >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > > -- > Unpaid intern in BillsBasement at noware dot com > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 17 11:44:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:44:32 -0400 Subject: [ITK] Bug in StatisticsImageFilter? In-Reply-To: References: Message-ID: Hi gowith, Please try calling rangetest.Update() This is required for the results to be computed. HTH, Matt On Tue, Sep 16, 2014 at 7:53 PM, gowith king wrote: > I was trying to use itk.StatisticsImageFilter to check the outcome of my > image reader. but all the results are wrong. > reader1 = itk.ImageFileReader.IUC3.New() > reader1.SetFileName(inputImagetest) > > rangetest=itk.StatisticsImageFilter.IUC3.New() > rangetest.SetInput(reader1) > print 'range: ', str(rangetest.GetMinimum()) > > result: > range: 255 > > obviously this is not true for my image : it is a binary image and has only > 1 and 100 two values. > > I am working on a python 2.7 wrapped ITK4 . if the python2 is incompatible > with itk? > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Wed Sep 17 11:48:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:48:13 -0400 Subject: [ITK] ITK-4.6 problem - OffsetValueType In-Reply-To: References: Message-ID: Hi Gib, OffsetValueType is defined here [1]. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Core/Common/include/itkIntTypes.h;h=c7fe398a593c79367631719e75104983efb27335;hb=HEAD#l137 On Tue, Sep 16, 2014 at 9:12 PM, Gib Bogle wrote: > Hi, > > I've been digging into the code, and trying to track down where the memory access problem occurs. By putting some printf statements in itkImage.hxx and itkImageBase.h I think I've got close to the source. As I suspected it is in the Image::Allocate() function. As the program output below shows, with N=1625 GetOffsetTable() returns the correct size of the image, but with N=1626 it returns 1626^3 - 2^32. The problem is that OffsetValueType is only 4 bytes. I'm reluctant to go further with this because I don't want to risk breaking something, but somebody should know why OffsetValueType has this size and how to increase it to 8 bytes in the case of ITK_USE_64BITS_IDS on. > > itkImage.hxx: > > void > Image< TPixel, VImageDimension > > ::Allocate(bool initializePixels) > { > SizeValueType num; > > this->ComputeOffsetTable(); > num = static_cast(this->GetOffsetTable()[VImageDimension]); > printf("Image::Allocate: GetOffsetTable(): %lld\n",this->GetOffsetTable()[VImageDimension]); //Gib > printf("Image::Allocate: num: %lld\n",num); //Gib > m_Buffer->Reserve(num, initializePixels); > } > > itkImageBase.h: > > const OffsetValueType * GetOffsetTable() const { > printf("Image::Allocate: sizeof(OffsetValueType): %d\n",sizeof(OffsetValueType)); //Gib > return m_OffsetTable; } > > > D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1625 1 > Output image file: zzz-4.6.tif > Desired image dimensions: width, height, depth: 1625 1625 1625 > Image::Allocate: sizeof(OffsetValueType): 4 > Image::Allocate: sizeof(OffsetValueType): 4 > Image::Allocate: GetOffsetTable(): 4291015625 > Image::Allocate: num: 4291015625 > Requested image dimensions: width, height, depth: 1625 1625 1625 > imregion size(0): 1625 > imregion size(1): 1625 > imregion size(2): 1625 > Image::FillBuffer: numberOfPixels: 4291015625 > > D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1626 1 > Output image file: zzz-4.6.tif > Desired image dimensions: width, height, depth: 1626 1626 1626 > Image::Allocate: sizeof(OffsetValueType): 4 > Image::Allocate: sizeof(OffsetValueType): 4 > Image::Allocate: GetOffsetTable(): 3975080 > Image::Allocate: num: 3975080 > Requested image dimensions: width, height, depth: 1626 1626 1626 > imregion size(0): 1626 > imregion size(1): 1626 > imregion size(2): 1626 > Image::FillBuffer: numberOfPixels: 3975080 > ________________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] > Sent: Wednesday, 17 September 2014 10:39 a.m. > To: Matt McCormick > Cc: community at itk.org > Subject: Re: [ITK] ITK-4.6 problem > > Update on the bug in the version of ITK-4.6 installed by Slicer: > > What can we make of this: > > ImageType::Pointer im = ImageType::New(); > ImageType::SizeType imsize; > imsize[0] = width; > imsize[1] = height; > imsize[2] = depth; > ImageType::IndexType imstart; > imstart[0] = 0; > imstart[1] = 0; > imstart[2] = 0; > ImageType::RegionType imregion; > imregion.SetSize(imsize); > imregion.SetIndex(imstart); > im->SetRegions(imregion); > im->Allocate(); > p = (unsigned char *)(im->GetBufferPointer()); > > width = im->GetLargestPossibleRegion().GetSize()[0]; > height = im->GetLargestPossibleRegion().GetSize()[1]; > depth = im->GetLargestPossibleRegion().GetSize()[2]; > printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); > > printf("imregion size(0): %d\n",imregion.GetSize(0)); > printf("imregion size(1): %d\n",imregion.GetSize(1)); > printf("imregion size(2): %d\n",imregion.GetSize(2)); > > int i = 195000000; > for (int i=197160890; i<200000000;i++) { > printf("offset: %d\n",i); > p[i] = 0; > } > > yields (reproducibly): > > D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 > ... > Requested image dimensions: width, height, depth: 1650 1650 1650 > imregion size(0): 1650 > imregion size(1): 1650 > imregion size(2): 1650 > offset: 197160890 > offset: 197160891 > offset: 197160892 > offset: 197160893 > offset: 197160894 > offset: 197160895 > offset: 197160896 > > > (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) > > Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. > > I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. > > I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? > > I'd appreciate some pointers. > > Thanks > Gib > > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Wednesday, 17 September 2014 1:48 a.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] ITK-4.6 problem > > Hi Gib, > >> >> There is something a bit funny about the installed ITK-4.6, in that the >> compiler complained about some missing include files, vnl_*.h and others, >> which are in my ITK-4.0 installation but not in 4.6. I just copied them >> across - I hope this is not a problem. >> > > This is probably a problem. Did the ITK 4.6 build complete > successfully and the install complete successfully? > > Thanks, > Matt > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Wed Sep 17 11:55:34 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:55:34 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Hi Gib, Getting the builds states to propagate and follow how the get set can be tricky. A few pointers on where to look for the status: 1) CMakeCache.txt (this file contains the build settings that CMake recognized from your input when you run CMake) 2) ITKConfig.cmake (this file will exist in the build tree or the install tree, and it contains CMake varables that may be used by other projects building against ITK) 3) itkConfigure.h (this is a header that has configured preprocessor definitions used when building) HTH, Matt On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: > Hi Bradley, Matt and Steve, > > Now for the embarrassing confession. In External_ITK4.cmake I turned > ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I > finally checked what the code that is being built was using (with #if > defined ...) I discovered that both ITKV3_COMPATIBILITY and > ITK_USE_64BITS_IDS were off. How can this be? > > It's easy, all it takes is a typo: > -DITK_USE_64_BITS_IDS:BOOL=ON > That typo has cost me a couple of days, and caused annoyance to a few > people, I suspect. > > Unfortunately... now Slicer's vtkITK does not build. There are very many > errors like this: > > 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ > 3>Build started 17/09/2014 7:25:52 p.m.. > 3>InitializeBuildStatus: > 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". > 3>CustomBuild: > 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt > 3> CMake does not need to re-run because > C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. > 3>ClCompile: > 3> vtkITKNumericTraits.cxx > 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx > 3> vtkITKArchetypeImageSeriesReader.cxx > 3> vtkITKArchetypeImageSeriesScalarReader.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx > 3> vtkITKImageWriter.cxx > 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx > 3> vtkITKDistanceTransform.cxx > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): > error C2679: binary '=' : no operator found which takes a right-hand operand > of type 'itk::ImportImageContainer *' (or there > is no acceptable conversion) > 3> with > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): > could be 'itk::SmartPointer > &itk::SmartPointer::operator =(const > itk::SmartPointer &)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): > or 'itk::SmartPointer > &itk::SmartPointer::operator > =(itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer, > 3> TElementIdentifier=unsigned long, > 3> TElement=double > 3> ] > 3> while trying to match the argument list > '(itk::SmartPointer, > itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> and > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > > I presume these are related to the use of 64-bit integers. > > Over to you guys :) > > Gib > ________________________________ > From: Bradley Lowekamp [blowekamp at mail.nih.gov] > Sent: Tuesday, 16 September 2014 12:45 a.m. > To: Steve Pieper > Cc: Gib Bogle; slicer-devel at bwh.harvard.edu > Subject: Re: [slicer-devel] BigTIFF > > Hello, > > For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: > https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 > > To test for ITK big tiff compatibility, I'd recommend getting python 2.7 > 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to > read and write files like these there. More information about getting > started is here[1]. > > You should be a able to generate a image with: > > import SimpleITK as sitk > img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) > img += 10 > stats = sitk.StatisticsImageFilter() > stats.Execute(img) > print stats > > This should give you basic access to ITK in python to interactively > experiment with options with these large images. I have been able to load > large images with the binaries of SimpleITK on windows 64-bits. I don't know > if I have tried big tiff though. > > A simular test could be done with C++ and ITK directly, but I think > SimpleITK in python may be quicker for experimentation. > > Brad > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted > [2] > http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee > > On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: > > Hi Gib - > > Are you testing only on windows? What we would often try to do for this > kind of debugging is to create a small example that other people can test on > their configurations. Slicer has a mechanism called a Self Test [1] to > allow easy replication and debugging across multiple platforms. It's ideal > if we can hone it down to something like what is described as a 'sscce' [2]. > The self tests will typically download some data from a public web site, run > some operations, and then print something out saying if it passed or failed > (or it may crash). Since it's possible to make a small data file that > expands into a giant tiff image it should be pretty tractable to pose this > issue in the form of a self test. > > Best, > Steve > > > [1] > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule > > [2] http://sscce.org/ > > On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >> >> Hi J-C, >> >> Some more info about Slicer with big tiff files. >> >> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >> 72) >> >> All suggestions will be gratefully received. >> >> Cheers >> Gib >> ________________________________ >> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >> Sent: Sunday, 14 September 2014 8:32 p.m. >> To: Gib Bogle >> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> What do you mean by "reinstalled" ? You should not have to install Slicer >> to be able to execute it from the build directory. >> >> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >> out. >> >> When done building, make sure to start the Slicer launcher: >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >> >> and not the Slicer executable: >> >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >> >> >> By using the launcher, you ensure that the PATH are properly setup and the >> expected libraries are loaded. >> >> >> Hth >> Jc >> >> >> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >> wrote: >>> >>> I hope I understand correctly. I added the line as shown to >>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>> ... >>> # ZLIB >>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>> # Big TIFF >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> ... >>> >>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>> presume this is the "superbuild". I then redid ALL_BUILD in >>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>> crashes with the big tiff. Is there somewhere I can check in the project >>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>> effect? >>> >>> Thanks >>> Gib >>> ________________________________ >>> From: Steve Pieper [pieper at isomics.com] >>> Sent: Sunday, 14 September 2014 1:36 p.m. >>> >>> To: Gib Bogle >>> Cc: slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hey Gib - >>> >>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>> ITK build process [1] during the superbuild. I don't think much else was >>> required except turning off the IKTv3 parts. >>> >>> [1] >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>> >>> -Steve >>> >>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>> it on TV). So the Jo'berg game should be a great rematch! >>> >>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>> wrote: >>>> >>>> You did warn me. >>>> >>>> Here is the list of options not ticked: >>>> >>>> Slicer_BUILD_BRAINSTOOLS >>>> _LEGACY_CLI >>>> _LandmarkRegistration >>>> _TESTING_EXTENSIONS >>>> _UPDATE_TRANSLATION >>>> _USE_GIT_PROTOCOL >>>> _OpenIGTLink >>>> _PYTHONQT_WITH_OPENSSL >>>> _PYTHONQT_WITH_TCL >>>> _QtTesting >>>> _SimpleITK >>>> _VTK_DEBUG_LINKS >>>> Slicer_WITH_LIBRARY_VERSION >>>> >>>> USE_BRAINS* >>>> USE_ConvertBetweenFileFormats >>>> USE_DWIConvert >>>> USE_DebugImageViewer >>>> USE_GTRACT >>>> USE_ICCDEF >>>> USE_ImageCalculator >>>> USE_ReferenceAtlas >>>> >>>> ------- >>>> >>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>> which means a DLL was not found. I then realized that I have different >>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>> prompted me to look more carefully at the PATH environment variable. I just >>>> tested with all the new paths at the start of the PATH string, and Slicer >>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>> attempt to load a 4 GB tiff. >>>> >>>> I am now wondering (belatedly!) about the way I tried to build with big >>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>> for directions before doing this - now I'm wondering if that switch actually >>>> had any effect. Is that the right thing to do, and if not, what is? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Yes, well, don't say I didn't warn you! ; ) >>>> >>>> You do need loadable modules and you probably do want python (a lot of >>>> core stuff is in python, like the editor). >>>> >>>> BRAINSTools should be off for now, since it needs ITKv3. >>>> >>>> I'm not sure either what to do next, but I suggest maybe trying the >>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>> it exited. But that may be a longshot. >>>> >>>> -Steve >>>> >>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>> wrote: >>>>> >>>>> Hi Steve, >>>>> >>>>> That was an interesting exercise. I managed to build Slicer without >>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>> built it again, this time selecting most things except BRAINTools. The >>>>> build took a long time, partly because I turned on the Python option, which >>>>> I don't need. This time there were no errors, except for a couple of >>>>> occasions where the attempt to create a directory failed - this was because >>>>> the directory already existed, and was easily solved by deleting the >>>>> directory and building again. I installed everything that wanted to be >>>>> installed, and modified the environment variables to suit. >>>>> >>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>> knowing what it is). >>>>> >>>>> I sense that I must be close to getting it working, but I'm not sure >>>>> what to do next. >>>>> >>>>> Cheers >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hi Gib - >>>>> >>>>> A lot of the building goes on in parallel so you need to review the >>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>> window and then paste it into a text editor to look for issues. Definitely >>>>> you don't want to be editing any of the visual studio files, since they are >>>>> generated by cmake every configure -- much better to sort out what is going >>>>> on at the cmake flag level. >>>>> >>>>> Best, >>>>> Steve >>>>> >>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>> Additional Dependencies: >>>>>> >>>>>> ... >>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>> ITKCommon.lib >>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>> ... >>>>>> >>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>> 40+ times. >>>>>> >>>>>> Thanks again >>>>>> Gib >>>>>> ________________________________ >>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>> [g.bogle at auckland.ac.nz] >>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>> >>>>>> To: Steve Pieper >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>> >>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>> >>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>> link the ITK library that was just built, i.e.: >>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>> This is the first of about 40 such link errors. >>>>>> >>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>> ITK_DIR appropriately? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>> trickiest platform in my experience. >>>>>> >>>>>> -Steve >>>>>> >>>>>> >>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Gib Bogle >>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Jean-Christophe, >>>>>>> >>>>>>> Any idea when 4.5 will enter the world? >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Folks, >>>>>>> >>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>> >>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>> these module. All details are captured here: >>>>>>> >>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>> >>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>> planned for 4.5. >>>>>>> >>>>>>> Thanks >>>>>>> Jc >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Matt - >>>>>>>> >>>>>>>> Thanks, that's helpful. >>>>>>>> >>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>> straightforward. >>>>>>>> >>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Here is what the process would look like: >>>>>>>>> >>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>> the >>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>> (minor modifications to the API, etc). >>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>> 5) Profit. >>>>>>>>> >>>>>>>>> HTH, >>>>>>>>> Matt >>>>>>>>> >>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>> >>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>> >>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>> > but it's >>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>> > >>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>> > what is >>>>>>>>> > involved? >>>>>>>>> > >>>>>>>>> > -Steve >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>> > wrote: >>>>>>>>> >> >>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>> >> large >>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>> >> capability >>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>> >> ________________________________ >>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>> >> >>>>>>>>> >> To: Gib Bogle >>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >> >>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>> >> configure >>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>> >> like vtkITK >>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>> >> experts are >>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>> >> >>>>>>>>> >> -Steve >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>> >> wrote: >>>>>>>>> >>> >>>>>>>>> >>> I await the results with interest... >>>>>>>>> >>> ________________________________ >>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>> >>> Pieper >>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>> >>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>> >>> a lot of >>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>> >>> >>>>>>>>> >>> -Steve >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Steve, >>>>>>>>> >>>> >>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>> >>>> configured in >>>>>>>>> >>>> Slicer. >>>>>>>>> >>>> >>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>> >>>> needs to >>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>> >>>> be used. I have >>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>> >>>> one wanted to >>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>> >>>> >>>>>>>>> >>>> Brad >>>>>>>>> >>>> >>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>> >>>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Hi Brad - >>>>>>>>> >>>> >>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>> >>>> able to >>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>> >>>> with ITK's NRRD >>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>> >>>> default options >>>>>>>>> >>>> on win7 64bit. >>>>>>>>> >>>> >>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>> >>>> something nobody >>>>>>>>> >>>> has tried? >>>>>>>>> >>>> >>>>>>>>> >>>> -Steve >>>>>>>>> >>>> >>>>>>>>> >>>> >>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>> >>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> Steve, >>>>>>>>> >>>>> >>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>> >>>>> windows 64? >>>>>>>>> >>>>> >>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>> >>>>> specific. >>>>>>>>> >>>>> >>>>>>>>> >>>>> Bread >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>> >>>>> >>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>> >>>>> pasted in >>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>> >>>>> >>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>> >>>>> >>>>>>>>> >>>>> -Steve >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>> >>>>>> still >>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Brad >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>> >>>>>> replicate the >>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> wrote: >>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>> >>>>>>> > back to this >>>>>>>>> >>>>>>> > later. >>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>> >>>>>>> > to >>>>>>>>> >>>>>>> > generate a big >>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>> >>>>>>> > for any >>>>>>>>> >>>>>>> > standard >>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > wrote: >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>> >>>>>>> >> a >>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>> >>>>>>> >> without >>>>>>>>> >>>>>>> >> problems. >>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Hi - >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>> >>>>>>> >> for example >>>>>>>>> >>>>>>> >> with a >>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>> >>>>>>> >> transfer a >>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> -Steve >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>> >>>>>>> >>> I can load >>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>> >>>>>>> >>> exception >>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>> >>>>>>> >>> this size >>>>>>>>> >>>>>>> >>> is the >>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>> >>>>>>> >>> I see the >>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>> >>>>>>> >>> out. >>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>> >>>>>>> >>> on the >>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>> >>>>>>> >>> installed >>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>> >>>>>>> >>> good but >>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>> >>>>>>> >>> different >>>>>>>>> >>>>>>> >>> build >>>>>>>>> >>>>>>> >>> options? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> associated >>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>> >>>>>>> >>> please >>>>>>>>> >>>>>>> >>> provide more >>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Brad >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>> >>>>>>> >>> not >>>>>>>>> >>>>>>> >>> handle >>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>> >>>>>>> >>> the >>>>>>>>> >>>>>>> >>> subject >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>>> >>> person to >>>>>>>>> >>>>>>> >>> whom it >>>>>>>>> >>>>>>> >>> is >>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>> >>>>>>> >>> in error >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>> >>>>>>> >>> Partners >>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If the e-mail was sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> +1 919 869 8849 >>>>>> >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>> subject >>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> >> -- >> +1 919 869 8849 > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu > with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > From matt.mccormick at kitware.com Wed Sep 17 12:01:05 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 12:01:05 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi gowith, Is an Update() call missing? HTH, Matt On Tue, Sep 16, 2014 at 4:27 AM, gowith king wrote: > Hi , Matt > I tried it , it does not work as well. the print > LabelFilter0.GetNumberOfObjects() always returns 0, > what i want to do it every nasty: sign 1 to label 1, 100 to label 2 > ,and there is no background at all. > My images all like the attached image but in 3D , the 3D version will > be attached later ,thank you for your attention > > On Mon, Sep 15, 2014 at 11:58 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> >> >> On Mon, Sep 15, 2014 at 5:31 PM, gowith king >> wrote: >> >>> Thanks McCormick , I use the dir(itk,Image) and dir(itk.LabelMap) and >>> dir(to get some information : UC3 is included in itk.image then it is good. >>> Then I tried all the other dir() for each of my filter , made lots of >>> correction , now the pepline works perfect [?] Thank you again . >>> >>> But I still could not get my result ... >>> because of the filters I may not really understand. >>> >>> I have three filters >>> BinaryThresholdImageFilter # to get a binary image for now I get only >>> two values 1 and 100 it works well. I what the labelmap contains both two >>> parts of them >>> BinaryImageToLabelMapFilter #I have no idea if it works well or not >>> LabelMapToLabelImageFilter # returns a empty image >>> >>> Do you have any idea about this ? >>> >> >> Perhaps SetInputForegroundValue [1] needs to be set? >> >> HTH, >> Matt >> >> [1] >> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToLabelMapFilter.html#a5c56958ec0ae8d3a9bf7ae759c680c4a >> >> >> >>> >>> On Mon, Sep 15, 2014 at 10:12 PM, Matt McCormick < >>> matt.mccormick at kitware.com> wrote: >>> >>>> Hi gowith, >>>> >>>> To see the available types for itk.Image, run >>>> >>>> dir(itk.Image) >>>> >>>> If a type is not available that is desired, enable the option in CMake >>>> for that pixel type. For unsigned short, set >>>> >>>> ITK_WRAP_unsigned_short >>>> >>>> to ON. >>>> >>>> Hope this helps, >>>> Matt >>>> >>>> On Mon, Sep 15, 2014 at 2:19 PM, gowith king >>> > wrote: >>>> >>>>> Hi McCormick >>>>> I think you give me a hint for the key error problem: I tried few >>>>> other types in my python such as US , UI, SI ... most of them could not >>>>> work well . another keyerror pops out for the template lose: when I try >>>>> itk.Image[itk.SI, 3] >>>>> KeyError: 'itkTemplate : No template (, 3) for >>>>> the itk::Image class' >>>>> >>>>> >>>>> >>>>> On Mon, Sep 15, 2014 at 8:11 PM, gowith king < >>>>> gowithking at googlemail.com> wrote: >>>>> >>>>>> Hi McCormick >>>>>> Thank you so much for your suggestion, when I use US it pops out >>>>>> a keyerror , not template for the us3 [?]. But then I change to SS it >>>>>> works well for now. >>>>>> any suggestion for the second issue ? >>>>>> I dig for really long time for this keyerror problem , but have >>>>>> no clue at all >>>>>> >>>>>> >>>>>> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >>>>>> matt.mccormick at kitware.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>>> >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>>>>>> image in all the itk instructions. But in my case it only has a range of >>>>>>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>>>>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>>>>>> 0-9000 . How could I read it proprietorially? >>>>>>>> >>>>>>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range >>>>>>> 0-255) and with three dimension. For the correspondence between mangled >>>>>>> names and basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>>>>>> >>>>>>> HTH, >>>>>>> Matt >>>>>>> >>>>>>> [1] >>>>>>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Selection_001.png Type: image/png Size: 23881 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From g.bogle at auckland.ac.nz Wed Sep 17 12:02:43 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 16:02:43 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Hi Matt, I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 3:55 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib, Getting the builds states to propagate and follow how the get set can be tricky. A few pointers on where to look for the status: 1) CMakeCache.txt (this file contains the build settings that CMake recognized from your input when you run CMake) 2) ITKConfig.cmake (this file will exist in the build tree or the install tree, and it contains CMake varables that may be used by other projects building against ITK) 3) itkConfigure.h (this is a header that has configured preprocessor definitions used when building) HTH, Matt On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: > Hi Bradley, Matt and Steve, > > Now for the embarrassing confession. In External_ITK4.cmake I turned > ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I > finally checked what the code that is being built was using (with #if > defined ...) I discovered that both ITKV3_COMPATIBILITY and > ITK_USE_64BITS_IDS were off. How can this be? > > It's easy, all it takes is a typo: > -DITK_USE_64_BITS_IDS:BOOL=ON > That typo has cost me a couple of days, and caused annoyance to a few > people, I suspect. > > Unfortunately... now Slicer's vtkITK does not build. There are very many > errors like this: > > 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ > 3>Build started 17/09/2014 7:25:52 p.m.. > 3>InitializeBuildStatus: > 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". > 3>CustomBuild: > 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt > 3> CMake does not need to re-run because > C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. > 3>ClCompile: > 3> vtkITKNumericTraits.cxx > 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx > 3> vtkITKArchetypeImageSeriesReader.cxx > 3> vtkITKArchetypeImageSeriesScalarReader.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx > 3> vtkITKImageWriter.cxx > 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx > 3> vtkITKDistanceTransform.cxx > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): > error C2679: binary '=' : no operator found which takes a right-hand operand > of type 'itk::ImportImageContainer *' (or there > is no acceptable conversion) > 3> with > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): > could be 'itk::SmartPointer > &itk::SmartPointer::operator =(const > itk::SmartPointer &)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): > or 'itk::SmartPointer > &itk::SmartPointer::operator > =(itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer, > 3> TElementIdentifier=unsigned long, > 3> TElement=double > 3> ] > 3> while trying to match the argument list > '(itk::SmartPointer, > itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> and > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > > I presume these are related to the use of 64-bit integers. > > Over to you guys :) > > Gib > ________________________________ > From: Bradley Lowekamp [blowekamp at mail.nih.gov] > Sent: Tuesday, 16 September 2014 12:45 a.m. > To: Steve Pieper > Cc: Gib Bogle; slicer-devel at bwh.harvard.edu > Subject: Re: [slicer-devel] BigTIFF > > Hello, > > For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: > https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 > > To test for ITK big tiff compatibility, I'd recommend getting python 2.7 > 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to > read and write files like these there. More information about getting > started is here[1]. > > You should be a able to generate a image with: > > import SimpleITK as sitk > img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) > img += 10 > stats = sitk.StatisticsImageFilter() > stats.Execute(img) > print stats > > This should give you basic access to ITK in python to interactively > experiment with options with these large images. I have been able to load > large images with the binaries of SimpleITK on windows 64-bits. I don't know > if I have tried big tiff though. > > A simular test could be done with C++ and ITK directly, but I think > SimpleITK in python may be quicker for experimentation. > > Brad > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted > [2] > http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee > > On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: > > Hi Gib - > > Are you testing only on windows? What we would often try to do for this > kind of debugging is to create a small example that other people can test on > their configurations. Slicer has a mechanism called a Self Test [1] to > allow easy replication and debugging across multiple platforms. It's ideal > if we can hone it down to something like what is described as a 'sscce' [2]. > The self tests will typically download some data from a public web site, run > some operations, and then print something out saying if it passed or failed > (or it may crash). Since it's possible to make a small data file that > expands into a giant tiff image it should be pretty tractable to pose this > issue in the form of a self test. > > Best, > Steve > > > [1] > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule > > [2] http://sscce.org/ > > On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >> >> Hi J-C, >> >> Some more info about Slicer with big tiff files. >> >> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >> 72) >> >> All suggestions will be gratefully received. >> >> Cheers >> Gib >> ________________________________ >> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >> Sent: Sunday, 14 September 2014 8:32 p.m. >> To: Gib Bogle >> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> What do you mean by "reinstalled" ? You should not have to install Slicer >> to be able to execute it from the build directory. >> >> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >> out. >> >> When done building, make sure to start the Slicer launcher: >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >> >> and not the Slicer executable: >> >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >> >> >> By using the launcher, you ensure that the PATH are properly setup and the >> expected libraries are loaded. >> >> >> Hth >> Jc >> >> >> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >> wrote: >>> >>> I hope I understand correctly. I added the line as shown to >>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>> ... >>> # ZLIB >>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>> # Big TIFF >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> ... >>> >>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>> presume this is the "superbuild". I then redid ALL_BUILD in >>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>> crashes with the big tiff. Is there somewhere I can check in the project >>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>> effect? >>> >>> Thanks >>> Gib >>> ________________________________ >>> From: Steve Pieper [pieper at isomics.com] >>> Sent: Sunday, 14 September 2014 1:36 p.m. >>> >>> To: Gib Bogle >>> Cc: slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hey Gib - >>> >>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>> ITK build process [1] during the superbuild. I don't think much else was >>> required except turning off the IKTv3 parts. >>> >>> [1] >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>> >>> -Steve >>> >>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>> it on TV). So the Jo'berg game should be a great rematch! >>> >>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>> wrote: >>>> >>>> You did warn me. >>>> >>>> Here is the list of options not ticked: >>>> >>>> Slicer_BUILD_BRAINSTOOLS >>>> _LEGACY_CLI >>>> _LandmarkRegistration >>>> _TESTING_EXTENSIONS >>>> _UPDATE_TRANSLATION >>>> _USE_GIT_PROTOCOL >>>> _OpenIGTLink >>>> _PYTHONQT_WITH_OPENSSL >>>> _PYTHONQT_WITH_TCL >>>> _QtTesting >>>> _SimpleITK >>>> _VTK_DEBUG_LINKS >>>> Slicer_WITH_LIBRARY_VERSION >>>> >>>> USE_BRAINS* >>>> USE_ConvertBetweenFileFormats >>>> USE_DWIConvert >>>> USE_DebugImageViewer >>>> USE_GTRACT >>>> USE_ICCDEF >>>> USE_ImageCalculator >>>> USE_ReferenceAtlas >>>> >>>> ------- >>>> >>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>> which means a DLL was not found. I then realized that I have different >>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>> prompted me to look more carefully at the PATH environment variable. I just >>>> tested with all the new paths at the start of the PATH string, and Slicer >>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>> attempt to load a 4 GB tiff. >>>> >>>> I am now wondering (belatedly!) about the way I tried to build with big >>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>> for directions before doing this - now I'm wondering if that switch actually >>>> had any effect. Is that the right thing to do, and if not, what is? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Yes, well, don't say I didn't warn you! ; ) >>>> >>>> You do need loadable modules and you probably do want python (a lot of >>>> core stuff is in python, like the editor). >>>> >>>> BRAINSTools should be off for now, since it needs ITKv3. >>>> >>>> I'm not sure either what to do next, but I suggest maybe trying the >>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>> it exited. But that may be a longshot. >>>> >>>> -Steve >>>> >>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>> wrote: >>>>> >>>>> Hi Steve, >>>>> >>>>> That was an interesting exercise. I managed to build Slicer without >>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>> built it again, this time selecting most things except BRAINTools. The >>>>> build took a long time, partly because I turned on the Python option, which >>>>> I don't need. This time there were no errors, except for a couple of >>>>> occasions where the attempt to create a directory failed - this was because >>>>> the directory already existed, and was easily solved by deleting the >>>>> directory and building again. I installed everything that wanted to be >>>>> installed, and modified the environment variables to suit. >>>>> >>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>> knowing what it is). >>>>> >>>>> I sense that I must be close to getting it working, but I'm not sure >>>>> what to do next. >>>>> >>>>> Cheers >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hi Gib - >>>>> >>>>> A lot of the building goes on in parallel so you need to review the >>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>> window and then paste it into a text editor to look for issues. Definitely >>>>> you don't want to be editing any of the visual studio files, since they are >>>>> generated by cmake every configure -- much better to sort out what is going >>>>> on at the cmake flag level. >>>>> >>>>> Best, >>>>> Steve >>>>> >>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>> Additional Dependencies: >>>>>> >>>>>> ... >>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>> ITKCommon.lib >>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>> ... >>>>>> >>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>> 40+ times. >>>>>> >>>>>> Thanks again >>>>>> Gib >>>>>> ________________________________ >>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>> [g.bogle at auckland.ac.nz] >>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>> >>>>>> To: Steve Pieper >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>> >>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>> >>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>> link the ITK library that was just built, i.e.: >>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>> This is the first of about 40 such link errors. >>>>>> >>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>> ITK_DIR appropriately? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>> trickiest platform in my experience. >>>>>> >>>>>> -Steve >>>>>> >>>>>> >>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Gib Bogle >>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Jean-Christophe, >>>>>>> >>>>>>> Any idea when 4.5 will enter the world? >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Folks, >>>>>>> >>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>> >>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>> these module. All details are captured here: >>>>>>> >>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>> >>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>> planned for 4.5. >>>>>>> >>>>>>> Thanks >>>>>>> Jc >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Matt - >>>>>>>> >>>>>>>> Thanks, that's helpful. >>>>>>>> >>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>> straightforward. >>>>>>>> >>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Here is what the process would look like: >>>>>>>>> >>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>> the >>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>> (minor modifications to the API, etc). >>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>> 5) Profit. >>>>>>>>> >>>>>>>>> HTH, >>>>>>>>> Matt >>>>>>>>> >>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>> >>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>> >>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>> > but it's >>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>> > >>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>> > what is >>>>>>>>> > involved? >>>>>>>>> > >>>>>>>>> > -Steve >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>> > wrote: >>>>>>>>> >> >>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>> >> large >>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>> >> capability >>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>> >> ________________________________ >>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>> >> >>>>>>>>> >> To: Gib Bogle >>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >> >>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>> >> configure >>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>> >> like vtkITK >>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>> >> experts are >>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>> >> >>>>>>>>> >> -Steve >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>> >> wrote: >>>>>>>>> >>> >>>>>>>>> >>> I await the results with interest... >>>>>>>>> >>> ________________________________ >>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>> >>> Pieper >>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>> >>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>> >>> a lot of >>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>> >>> >>>>>>>>> >>> -Steve >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Steve, >>>>>>>>> >>>> >>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>> >>>> configured in >>>>>>>>> >>>> Slicer. >>>>>>>>> >>>> >>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>> >>>> needs to >>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>> >>>> be used. I have >>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>> >>>> one wanted to >>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>> >>>> >>>>>>>>> >>>> Brad >>>>>>>>> >>>> >>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>> >>>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Hi Brad - >>>>>>>>> >>>> >>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>> >>>> able to >>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>> >>>> with ITK's NRRD >>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>> >>>> default options >>>>>>>>> >>>> on win7 64bit. >>>>>>>>> >>>> >>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>> >>>> something nobody >>>>>>>>> >>>> has tried? >>>>>>>>> >>>> >>>>>>>>> >>>> -Steve >>>>>>>>> >>>> >>>>>>>>> >>>> >>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>> >>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> Steve, >>>>>>>>> >>>>> >>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>> >>>>> windows 64? >>>>>>>>> >>>>> >>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>> >>>>> specific. >>>>>>>>> >>>>> >>>>>>>>> >>>>> Bread >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>> >>>>> >>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>> >>>>> pasted in >>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>> >>>>> >>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>> >>>>> >>>>>>>>> >>>>> -Steve >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>> >>>>>> still >>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Brad >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>> >>>>>> replicate the >>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> wrote: >>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>> >>>>>>> > back to this >>>>>>>>> >>>>>>> > later. >>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>> >>>>>>> > to >>>>>>>>> >>>>>>> > generate a big >>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>> >>>>>>> > for any >>>>>>>>> >>>>>>> > standard >>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > wrote: >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>> >>>>>>> >> a >>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>> >>>>>>> >> without >>>>>>>>> >>>>>>> >> problems. >>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Hi - >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>> >>>>>>> >> for example >>>>>>>>> >>>>>>> >> with a >>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>> >>>>>>> >> transfer a >>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> -Steve >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>> >>>>>>> >>> I can load >>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>> >>>>>>> >>> exception >>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>> >>>>>>> >>> this size >>>>>>>>> >>>>>>> >>> is the >>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>> >>>>>>> >>> I see the >>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>> >>>>>>> >>> out. >>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>> >>>>>>> >>> on the >>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>> >>>>>>> >>> installed >>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>> >>>>>>> >>> good but >>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>> >>>>>>> >>> different >>>>>>>>> >>>>>>> >>> build >>>>>>>>> >>>>>>> >>> options? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> associated >>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>> >>>>>>> >>> please >>>>>>>>> >>>>>>> >>> provide more >>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Brad >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>> >>>>>>> >>> not >>>>>>>>> >>>>>>> >>> handle >>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>> >>>>>>> >>> the >>>>>>>>> >>>>>>> >>> subject >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>>> >>> person to >>>>>>>>> >>>>>>> >>> whom it >>>>>>>>> >>>>>>> >>> is >>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>> >>>>>>> >>> in error >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>> >>>>>>> >>> Partners >>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . If the e-mail >>>>>>>>> >>>>>>> >>> was sent >>>>>>>>> >>>>>>> >>> to you in >>>>>>>>> >>>>>>> >>> error >>>>>>>>> >>>>>>> >>> but does not contain patient information, please >>>>>>>>> >>>>>>> >>> contact the >>>>>>>>> >>>>>>> >>> sender and >>>>>>>>> >>>>>>> >>> properly >>>>>>>>> >>>>>>> >>> dispose of the e-mail. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>> >>>>>>> >>> the >>>>>>>>> >>>>>>> >>> subject >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>>> >>> person to >>>>>>>>> >>>>>>> >>> whom it >>>>>>>>> >>>>>>> >>> is >>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>> >>>>>>> >>> in error >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>> >>>>>>> >>> Partners >>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . If the e-mail >>>>>>>>> >>>>>>> >>> was sent >>>>>>>>> >>>>>>> >>> to you in >>>>>>>>> >>>>>>> >>> error >>>>>>>>> >>>>>>> >>> but does not contain patient information, please >>>>>>>>> >>>>>>> >>> contact the >>>>>>>>> >>>>>>> >>> sender and >>>>>>>>> >>>>>>> >>> properly >>>>>>>>> >>>>>>> >>> dispose of the e-mail. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > _______________________________________________ >>>>>>>>> >>>>>>> > slicer-devel mailing list >>>>>>>>> >>>>>>> > slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>>> > To unsubscribe: send email to >>>>>>>>> >>>>>>> > slicer-devel-request at massmail.spl.harvard.edu >>>>>>>>> >>>>>>> > with unsubscribe as the subject >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > The information in this e-mail is intended only for the >>>>>>>>> >>>>>>> > person to >>>>>>>>> >>>>>>> > whom it is >>>>>>>>> >>>>>>> > addressed. If you believe this e-mail was sent to you in >>>>>>>>> >>>>>>> > error and >>>>>>>>> >>>>>>> > the >>>>>>>>> >>>>>>> > e-mail >>>>>>>>> >>>>>>> > contains patient information, please contact the Partners >>>>>>>>> >>>>>>> > Compliance >>>>>>>>> >>>>>>> > HelpLine at >>>>>>>>> >>>>>>> > http://www.partners.org/complianceline . If the e-mail >>>>>>>>> >>>>>>> > was sent to >>>>>>>>> >>>>>>> > you in >>>>>>>>> >>>>>>> > error >>>>>>>>> >>>>>>> > but does not contain patient information, please contact >>>>>>>>> >>>>>>> > the sender >>>>>>>>> >>>>>>> > and >>>>>>>>> >>>>>>> > properly >>>>>>>>> >>>>>>> > dispose of the e-mail. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> _______________________________________________ >>>>>>>>> >>>>>> slicer-devel mailing list >>>>>>>>> >>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>> To unsubscribe: send email to >>>>>>>>> >>>>>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>> unsubscribe as the >>>>>>>>> >>>>>> subject >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>> person to whom >>>>>>>>> >>>>>> it is >>>>>>>>> >>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>> >>>>>> error and the >>>>>>>>> >>>>>> e-mail >>>>>>>>> >>>>>> contains patient information, please contact the Partners >>>>>>>>> >>>>>> Compliance >>>>>>>>> >>>>>> HelpLine at >>>>>>>>> >>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>>>>> >>>>>> sent to you >>>>>>>>> >>>>>> in error >>>>>>>>> >>>>>> but does not contain patient information, please contact the >>>>>>>>> >>>>>> sender >>>>>>>>> >>>>>> and properly >>>>>>>>> >>>>>> dispose of the e-mail. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>> >>>>>>>>> >>>> >>>>>>>>> >>> >>>>>>>>> >> >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > _______________________________________________ >>>>>>>>> > slicer-devel mailing list >>>>>>>>> > slicer-devel at bwh.harvard.edu >>>>>>>>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> > To unsubscribe: send email to >>>>>>>>> > slicer-devel-request at massmail.spl.harvard.edu >>>>>>>>> > with unsubscribe as the subject >>>>>>>>> > >>>>>>>>> > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > The information in this e-mail is intended only for the person to >>>>>>>>> > whom it is >>>>>>>>> > addressed. If you believe this e-mail was sent to you in error >>>>>>>>> > and the >>>>>>>>> > e-mail >>>>>>>>> > contains patient information, please contact the Partners >>>>>>>>> > Compliance >>>>>>>>> > HelpLine at >>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent >>>>>>>>> > to you in >>>>>>>>> > error >>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>> > sender and >>>>>>>>> > properly >>>>>>>>> > dispose of the e-mail. >>>>>>>>> > >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> slicer-devel mailing list >>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>> To unsubscribe: send email to >>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>> subject >>>>>>>> >>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>> whom it is >>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>> the e-mail >>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>> HelpLine at >>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> +1 919 869 8849 >>>>>> >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>> subject >>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> >> -- >> +1 919 869 8849 > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu > with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > From g.bogle at auckland.ac.nz Wed Sep 17 12:04:27 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 16:04:27 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: I forgot to mention that ITK builds correctly, and my test program that uses it to create big tiffs now works fine. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 3:55 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib, Getting the builds states to propagate and follow how the get set can be tricky. A few pointers on where to look for the status: 1) CMakeCache.txt (this file contains the build settings that CMake recognized from your input when you run CMake) 2) ITKConfig.cmake (this file will exist in the build tree or the install tree, and it contains CMake varables that may be used by other projects building against ITK) 3) itkConfigure.h (this is a header that has configured preprocessor definitions used when building) HTH, Matt On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: > Hi Bradley, Matt and Steve, > > Now for the embarrassing confession. In External_ITK4.cmake I turned > ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I > finally checked what the code that is being built was using (with #if > defined ...) I discovered that both ITKV3_COMPATIBILITY and > ITK_USE_64BITS_IDS were off. How can this be? > > It's easy, all it takes is a typo: > -DITK_USE_64_BITS_IDS:BOOL=ON > That typo has cost me a couple of days, and caused annoyance to a few > people, I suspect. > > Unfortunately... now Slicer's vtkITK does not build. There are very many > errors like this: > > 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ > 3>Build started 17/09/2014 7:25:52 p.m.. > 3>InitializeBuildStatus: > 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". > 3>CustomBuild: > 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt > 3> CMake does not need to re-run because > C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. > 3>ClCompile: > 3> vtkITKNumericTraits.cxx > 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx > 3> vtkITKArchetypeImageSeriesReader.cxx > 3> vtkITKArchetypeImageSeriesScalarReader.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx > 3> vtkITKImageWriter.cxx > 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx > 3> vtkITKDistanceTransform.cxx > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): > error C2679: binary '=' : no operator found which takes a right-hand operand > of type 'itk::ImportImageContainer *' (or there > is no acceptable conversion) > 3> with > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): > could be 'itk::SmartPointer > &itk::SmartPointer::operator =(const > itk::SmartPointer &)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): > or 'itk::SmartPointer > &itk::SmartPointer::operator > =(itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer, > 3> TElementIdentifier=unsigned long, > 3> TElement=double > 3> ] > 3> while trying to match the argument list > '(itk::SmartPointer, > itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> and > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > > I presume these are related to the use of 64-bit integers. > > Over to you guys :) > > Gib > ________________________________ > From: Bradley Lowekamp [blowekamp at mail.nih.gov] > Sent: Tuesday, 16 September 2014 12:45 a.m. > To: Steve Pieper > Cc: Gib Bogle; slicer-devel at bwh.harvard.edu > Subject: Re: [slicer-devel] BigTIFF > > Hello, > > For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: > https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 > > To test for ITK big tiff compatibility, I'd recommend getting python 2.7 > 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to > read and write files like these there. More information about getting > started is here[1]. > > You should be a able to generate a image with: > > import SimpleITK as sitk > img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) > img += 10 > stats = sitk.StatisticsImageFilter() > stats.Execute(img) > print stats > > This should give you basic access to ITK in python to interactively > experiment with options with these large images. I have been able to load > large images with the binaries of SimpleITK on windows 64-bits. I don't know > if I have tried big tiff though. > > A simular test could be done with C++ and ITK directly, but I think > SimpleITK in python may be quicker for experimentation. > > Brad > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted > [2] > http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee > > On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: > > Hi Gib - > > Are you testing only on windows? What we would often try to do for this > kind of debugging is to create a small example that other people can test on > their configurations. Slicer has a mechanism called a Self Test [1] to > allow easy replication and debugging across multiple platforms. It's ideal > if we can hone it down to something like what is described as a 'sscce' [2]. > The self tests will typically download some data from a public web site, run > some operations, and then print something out saying if it passed or failed > (or it may crash). Since it's possible to make a small data file that > expands into a giant tiff image it should be pretty tractable to pose this > issue in the form of a self test. > > Best, > Steve > > > [1] > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule > > [2] http://sscce.org/ > > On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >> >> Hi J-C, >> >> Some more info about Slicer with big tiff files. >> >> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >> 72) >> >> All suggestions will be gratefully received. >> >> Cheers >> Gib >> ________________________________ >> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >> Sent: Sunday, 14 September 2014 8:32 p.m. >> To: Gib Bogle >> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> What do you mean by "reinstalled" ? You should not have to install Slicer >> to be able to execute it from the build directory. >> >> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >> out. >> >> When done building, make sure to start the Slicer launcher: >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >> >> and not the Slicer executable: >> >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >> >> >> By using the launcher, you ensure that the PATH are properly setup and the >> expected libraries are loaded. >> >> >> Hth >> Jc >> >> >> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >> wrote: >>> >>> I hope I understand correctly. I added the line as shown to >>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>> ... >>> # ZLIB >>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>> # Big TIFF >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> ... >>> >>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>> presume this is the "superbuild". I then redid ALL_BUILD in >>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>> crashes with the big tiff. Is there somewhere I can check in the project >>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>> effect? >>> >>> Thanks >>> Gib >>> ________________________________ >>> From: Steve Pieper [pieper at isomics.com] >>> Sent: Sunday, 14 September 2014 1:36 p.m. >>> >>> To: Gib Bogle >>> Cc: slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hey Gib - >>> >>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>> ITK build process [1] during the superbuild. I don't think much else was >>> required except turning off the IKTv3 parts. >>> >>> [1] >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>> >>> -Steve >>> >>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>> it on TV). So the Jo'berg game should be a great rematch! >>> >>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>> wrote: >>>> >>>> You did warn me. >>>> >>>> Here is the list of options not ticked: >>>> >>>> Slicer_BUILD_BRAINSTOOLS >>>> _LEGACY_CLI >>>> _LandmarkRegistration >>>> _TESTING_EXTENSIONS >>>> _UPDATE_TRANSLATION >>>> _USE_GIT_PROTOCOL >>>> _OpenIGTLink >>>> _PYTHONQT_WITH_OPENSSL >>>> _PYTHONQT_WITH_TCL >>>> _QtTesting >>>> _SimpleITK >>>> _VTK_DEBUG_LINKS >>>> Slicer_WITH_LIBRARY_VERSION >>>> >>>> USE_BRAINS* >>>> USE_ConvertBetweenFileFormats >>>> USE_DWIConvert >>>> USE_DebugImageViewer >>>> USE_GTRACT >>>> USE_ICCDEF >>>> USE_ImageCalculator >>>> USE_ReferenceAtlas >>>> >>>> ------- >>>> >>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>> which means a DLL was not found. I then realized that I have different >>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>> prompted me to look more carefully at the PATH environment variable. I just >>>> tested with all the new paths at the start of the PATH string, and Slicer >>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>> attempt to load a 4 GB tiff. >>>> >>>> I am now wondering (belatedly!) about the way I tried to build with big >>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>> for directions before doing this - now I'm wondering if that switch actually >>>> had any effect. Is that the right thing to do, and if not, what is? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Yes, well, don't say I didn't warn you! ; ) >>>> >>>> You do need loadable modules and you probably do want python (a lot of >>>> core stuff is in python, like the editor). >>>> >>>> BRAINSTools should be off for now, since it needs ITKv3. >>>> >>>> I'm not sure either what to do next, but I suggest maybe trying the >>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>> it exited. But that may be a longshot. >>>> >>>> -Steve >>>> >>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>> wrote: >>>>> >>>>> Hi Steve, >>>>> >>>>> That was an interesting exercise. I managed to build Slicer without >>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>> built it again, this time selecting most things except BRAINTools. The >>>>> build took a long time, partly because I turned on the Python option, which >>>>> I don't need. This time there were no errors, except for a couple of >>>>> occasions where the attempt to create a directory failed - this was because >>>>> the directory already existed, and was easily solved by deleting the >>>>> directory and building again. I installed everything that wanted to be >>>>> installed, and modified the environment variables to suit. >>>>> >>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>> knowing what it is). >>>>> >>>>> I sense that I must be close to getting it working, but I'm not sure >>>>> what to do next. >>>>> >>>>> Cheers >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hi Gib - >>>>> >>>>> A lot of the building goes on in parallel so you need to review the >>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>> window and then paste it into a text editor to look for issues. Definitely >>>>> you don't want to be editing any of the visual studio files, since they are >>>>> generated by cmake every configure -- much better to sort out what is going >>>>> on at the cmake flag level. >>>>> >>>>> Best, >>>>> Steve >>>>> >>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>> Additional Dependencies: >>>>>> >>>>>> ... >>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>> ITKCommon.lib >>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>> ... >>>>>> >>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>> 40+ times. >>>>>> >>>>>> Thanks again >>>>>> Gib >>>>>> ________________________________ >>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>> [g.bogle at auckland.ac.nz] >>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>> >>>>>> To: Steve Pieper >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>> >>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>> >>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>> link the ITK library that was just built, i.e.: >>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>> This is the first of about 40 such link errors. >>>>>> >>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>> ITK_DIR appropriately? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>> trickiest platform in my experience. >>>>>> >>>>>> -Steve >>>>>> >>>>>> >>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Gib Bogle >>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Jean-Christophe, >>>>>>> >>>>>>> Any idea when 4.5 will enter the world? >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Folks, >>>>>>> >>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>> >>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>> these module. All details are captured here: >>>>>>> >>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>> >>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>> planned for 4.5. >>>>>>> >>>>>>> Thanks >>>>>>> Jc >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Matt - >>>>>>>> >>>>>>>> Thanks, that's helpful. >>>>>>>> >>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>> straightforward. >>>>>>>> >>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Here is what the process would look like: >>>>>>>>> >>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>> the >>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>> (minor modifications to the API, etc). >>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>> 5) Profit. >>>>>>>>> >>>>>>>>> HTH, >>>>>>>>> Matt >>>>>>>>> >>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>> >>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>> >>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>> > but it's >>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>> > >>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>> > what is >>>>>>>>> > involved? >>>>>>>>> > >>>>>>>>> > -Steve >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>> > wrote: >>>>>>>>> >> >>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>> >> large >>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>> >> capability >>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>> >> ________________________________ >>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>> >> >>>>>>>>> >> To: Gib Bogle >>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >> >>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>> >> configure >>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>> >> like vtkITK >>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>> >> experts are >>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>> >> >>>>>>>>> >> -Steve >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>> >> wrote: >>>>>>>>> >>> >>>>>>>>> >>> I await the results with interest... >>>>>>>>> >>> ________________________________ >>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>> >>> Pieper >>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>> >>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>> >>> a lot of >>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>> >>> >>>>>>>>> >>> -Steve >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Steve, >>>>>>>>> >>>> >>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>> >>>> configured in >>>>>>>>> >>>> Slicer. >>>>>>>>> >>>> >>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>> >>>> needs to >>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>> >>>> be used. I have >>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>> >>>> one wanted to >>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>> >>>> >>>>>>>>> >>>> Brad >>>>>>>>> >>>> >>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>> >>>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Hi Brad - >>>>>>>>> >>>> >>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>> >>>> able to >>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>> >>>> with ITK's NRRD >>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>> >>>> default options >>>>>>>>> >>>> on win7 64bit. >>>>>>>>> >>>> >>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>> >>>> something nobody >>>>>>>>> >>>> has tried? >>>>>>>>> >>>> >>>>>>>>> >>>> -Steve >>>>>>>>> >>>> >>>>>>>>> >>>> >>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>> >>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> Steve, >>>>>>>>> >>>>> >>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>> >>>>> windows 64? >>>>>>>>> >>>>> >>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>> >>>>> specific. >>>>>>>>> >>>>> >>>>>>>>> >>>>> Bread >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>> >>>>> >>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>> >>>>> pasted in >>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>> >>>>> >>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>> >>>>> >>>>>>>>> >>>>> -Steve >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>> >>>>>> still >>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Brad >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>> >>>>>> replicate the >>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> wrote: >>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>> >>>>>>> > back to this >>>>>>>>> >>>>>>> > later. >>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>> >>>>>>> > to >>>>>>>>> >>>>>>> > generate a big >>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>> >>>>>>> > for any >>>>>>>>> >>>>>>> > standard >>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > wrote: >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>> >>>>>>> >> a >>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>> >>>>>>> >> without >>>>>>>>> >>>>>>> >> problems. >>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Hi - >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>> >>>>>>> >> for example >>>>>>>>> >>>>>>> >> with a >>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>> >>>>>>> >> transfer a >>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> -Steve >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>> >>>>>>> >>> I can load >>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>> >>>>>>> >>> exception >>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>> >>>>>>> >>> this size >>>>>>>>> >>>>>>> >>> is the >>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>> >>>>>>> >>> I see the >>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>> >>>>>>> >>> out. >>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>> >>>>>>> >>> on the >>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>> >>>>>>> >>> installed >>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>> >>>>>>> >>> good but >>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>> >>>>>>> >>> different >>>>>>>>> >>>>>>> >>> build >>>>>>>>> >>>>>>> >>> options? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> associated >>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>> >>>>>>> >>> please >>>>>>>>> >>>>>>> >>> provide more >>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Brad >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>> >>>>>>> >>> not >>>>>>>>> >>>>>>> >>> handle >>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>> >>>>>>> >>> the >>>>>>>>> >>>>>>> >>> subject >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>>> >>> person to >>>>>>>>> >>>>>>> >>> whom it >>>>>>>>> >>>>>>> >>> is >>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>> >>>>>>> >>> in error >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>> >>>>>>> >>> Partners >>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If the e-mail was sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> +1 919 869 8849 >>>>>> >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>> subject >>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> >> -- >> +1 919 869 8849 > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu > with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > From matt.mccormick at kitware.com Wed Sep 17 13:05:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 13:05:56 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Great to hear! On Wed, Sep 17, 2014 at 12:04 PM, Gib Bogle wrote: > I forgot to mention that ITK builds correctly, and my test program that uses it to create big tiffs now works fine. > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 3:55 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > > Hi Gib, > > Getting the builds states to propagate and follow how the get set can > be tricky. A few pointers on where to look for the status: > > 1) CMakeCache.txt (this file contains the build settings that CMake > recognized from your input when you run CMake) > 2) ITKConfig.cmake (this file will exist in the build tree or the > install tree, and it contains CMake varables that may be used by other > projects building against ITK) > 3) itkConfigure.h (this is a header that has configured preprocessor > definitions used when building) > > HTH, > Matt > > > > On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >> Hi Bradley, Matt and Steve, >> >> Now for the embarrassing confession. In External_ITK4.cmake I turned >> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >> finally checked what the code that is being built was using (with #if >> defined ...) I discovered that both ITKV3_COMPATIBILITY and >> ITK_USE_64BITS_IDS were off. How can this be? >> >> It's easy, all it takes is a typo: >> -DITK_USE_64_BITS_IDS:BOOL=ON >> That typo has cost me a couple of days, and caused annoyance to a few >> people, I suspect. >> >> Unfortunately... now Slicer's vtkITK does not build. There are very many >> errors like this: >> >> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >> 3>Build started 17/09/2014 7:25:52 p.m.. >> 3>InitializeBuildStatus: >> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >> 3>CustomBuild: >> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >> 3> CMake does not need to re-run because >> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >> 3>ClCompile: >> 3> vtkITKNumericTraits.cxx >> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesReader.cxx >> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >> 3> vtkITKImageWriter.cxx >> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >> 3> vtkITKDistanceTransform.cxx >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >> error C2679: binary '=' : no operator found which takes a right-hand operand >> of type 'itk::ImportImageContainer *' (or there >> is no acceptable conversion) >> 3> with >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >> could be 'itk::SmartPointer >> &itk::SmartPointer::operator =(const >> itk::SmartPointer &)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >> or 'itk::SmartPointer >> &itk::SmartPointer::operator >> =(itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer, >> 3> TElementIdentifier=unsigned long, >> 3> TElement=double >> 3> ] >> 3> while trying to match the argument list >> '(itk::SmartPointer, >> itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> and >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> >> I presume these are related to the use of 64-bit integers. >> >> Over to you guys :) >> >> Gib >> ________________________________ >> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >> Sent: Tuesday, 16 September 2014 12:45 a.m. >> To: Steve Pieper >> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hello, >> >> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >> >> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >> read and write files like these there. More information about getting >> started is here[1]. >> >> You should be a able to generate a image with: >> >> import SimpleITK as sitk >> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >> img += 10 >> stats = sitk.StatisticsImageFilter() >> stats.Execute(img) >> print stats >> >> This should give you basic access to ITK in python to interactively >> experiment with options with these large images. I have been able to load >> large images with the binaries of SimpleITK on windows 64-bits. I don't know >> if I have tried big tiff though. >> >> A simular test could be done with C++ and ITK directly, but I think >> SimpleITK in python may be quicker for experimentation. >> >> Brad >> >> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >> [2] >> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >> >> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >> >> Hi Gib - >> >> Are you testing only on windows? What we would often try to do for this >> kind of debugging is to create a small example that other people can test on >> their configurations. Slicer has a mechanism called a Self Test [1] to >> allow easy replication and debugging across multiple platforms. It's ideal >> if we can hone it down to something like what is described as a 'sscce' [2]. >> The self tests will typically download some data from a public web site, run >> some operations, and then print something out saying if it passed or failed >> (or it may crash). Since it's possible to make a small data file that >> expands into a giant tiff image it should be pretty tractable to pose this >> issue in the form of a self test. >> >> Best, >> Steve >> >> >> [1] >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >> >> [2] http://sscce.org/ >> >> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>> >>> Hi J-C, >>> >>> Some more info about Slicer with big tiff files. >>> >>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>> 72) >>> >>> All suggestions will be gratefully received. >>> >>> Cheers >>> Gib >>> ________________________________ >>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>> Sent: Sunday, 14 September 2014 8:32 p.m. >>> To: Gib Bogle >>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hi Gib, >>> >>> What do you mean by "reinstalled" ? You should not have to install Slicer >>> to be able to execute it from the build directory. >>> >>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>> out. >>> >>> When done building, make sure to start the Slicer launcher: >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>> >>> and not the Slicer executable: >>> >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>> >>> >>> By using the launcher, you ensure that the PATH are properly setup and the >>> expected libraries are loaded. >>> >>> >>> Hth >>> Jc >>> >>> >>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>> wrote: >>>> >>>> I hope I understand correctly. I added the line as shown to >>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>> ... >>>> # ZLIB >>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>> # Big TIFF >>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>> ... >>>> >>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>> crashes with the big tiff. Is there somewhere I can check in the project >>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>> effect? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hey Gib - >>>> >>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>> ITK build process [1] during the superbuild. I don't think much else was >>>> required except turning off the IKTv3 parts. >>>> >>>> [1] >>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>> >>>> -Steve >>>> >>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>> it on TV). So the Jo'berg game should be a great rematch! >>>> >>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>> wrote: >>>>> >>>>> You did warn me. >>>>> >>>>> Here is the list of options not ticked: >>>>> >>>>> Slicer_BUILD_BRAINSTOOLS >>>>> _LEGACY_CLI >>>>> _LandmarkRegistration >>>>> _TESTING_EXTENSIONS >>>>> _UPDATE_TRANSLATION >>>>> _USE_GIT_PROTOCOL >>>>> _OpenIGTLink >>>>> _PYTHONQT_WITH_OPENSSL >>>>> _PYTHONQT_WITH_TCL >>>>> _QtTesting >>>>> _SimpleITK >>>>> _VTK_DEBUG_LINKS >>>>> Slicer_WITH_LIBRARY_VERSION >>>>> >>>>> USE_BRAINS* >>>>> USE_ConvertBetweenFileFormats >>>>> USE_DWIConvert >>>>> USE_DebugImageViewer >>>>> USE_GTRACT >>>>> USE_ICCDEF >>>>> USE_ImageCalculator >>>>> USE_ReferenceAtlas >>>>> >>>>> ------- >>>>> >>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>> which means a DLL was not found. I then realized that I have different >>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>> attempt to load a 4 GB tiff. >>>>> >>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>> for directions before doing this - now I'm wondering if that switch actually >>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Yes, well, don't say I didn't warn you! ; ) >>>>> >>>>> You do need loadable modules and you probably do want python (a lot of >>>>> core stuff is in python, like the editor). >>>>> >>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>> >>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>> it exited. But that may be a longshot. >>>>> >>>>> -Steve >>>>> >>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>> build took a long time, partly because I turned on the Python option, which >>>>>> I don't need. This time there were no errors, except for a couple of >>>>>> occasions where the attempt to create a directory failed - this was because >>>>>> the directory already existed, and was easily solved by deleting the >>>>>> directory and building again. I installed everything that wanted to be >>>>>> installed, and modified the environment variables to suit. >>>>>> >>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>> knowing what it is). >>>>>> >>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>> what to do next. >>>>>> >>>>>> Cheers >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> A lot of the building goes on in parallel so you need to review the >>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>> on at the cmake flag level. >>>>>> >>>>>> Best, >>>>>> Steve >>>>>> >>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>> Additional Dependencies: >>>>>>> >>>>>>> ... >>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>> ITKCommon.lib >>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>> ... >>>>>>> >>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>> 40+ times. >>>>>>> >>>>>>> Thanks again >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>> [g.bogle at auckland.ac.nz] >>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>> >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>> >>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>> >>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>> link the ITK library that was just built, i.e.: >>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>> This is the first of about 40 such link errors. >>>>>>> >>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>> ITK_DIR appropriately? >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>> trickiest platform in my experience. >>>>>>> >>>>>>> -Steve >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Gib Bogle >>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Jean-Christophe, >>>>>>>> >>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>> >>>>>>>> Cheers >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Folks, >>>>>>>> >>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>> >>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>> these module. All details are captured here: >>>>>>>> >>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>> >>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>> planned for 4.5. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Jc >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Matt - >>>>>>>>> >>>>>>>>> Thanks, that's helpful. >>>>>>>>> >>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>> straightforward. >>>>>>>>> >>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>> >>>>>>>>> -Steve >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Here is what the process would look like: >>>>>>>>>> >>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>> the >>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>> 5) Profit. >>>>>>>>>> >>>>>>>>>> HTH, >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>> >>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>> >>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>> wrote: >>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>> > but it's >>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>> > >>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>> > what is >>>>>>>>>> > involved? >>>>>>>>>> > >>>>>>>>>> > -Steve >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>> > wrote: >>>>>>>>>> >> >>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>> >> large >>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>> >> capability >>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>> >> ________________________________ >>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>> >> >>>>>>>>>> >> To: Gib Bogle >>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >> >>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>> >> configure >>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>> >> like vtkITK >>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>> >> experts are >>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>> >> >>>>>>>>>> >> -Steve >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>> >> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> I await the results with interest... >>>>>>>>>> >>> ________________________________ >>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>> >>> Pieper >>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>> >>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>> >>> a lot of >>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>> >>> >>>>>>>>>> >>> -Steve >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Steve, >>>>>>>>>> >>>> >>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>> >>>> configured in >>>>>>>>>> >>>> Slicer. >>>>>>>>>> >>>> >>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>> >>>> needs to >>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>> >>>> be used. I have >>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>> >>>> one wanted to >>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>> >>>> >>>>>>>>>> >>>> Brad >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Hi Brad - >>>>>>>>>> >>>> >>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>> >>>> able to >>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>> >>>> default options >>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>> >>>> >>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>> >>>> something nobody >>>>>>>>>> >>>> has tried? >>>>>>>>>> >>>> >>>>>>>>>> >>>> -Steve >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Steve, >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>> >>>>> windows 64? >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>> >>>>> specific. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Bread >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>> >>>>> pasted in >>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> -Steve >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>> >>>>>> still >>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Brad >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>> >>>>>> replicate the >>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> wrote: >>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>> >>>>>>> > back to this >>>>>>>>>> >>>>>>> > later. >>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>> >>>>>>> > to >>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>> >>>>>>> > for any >>>>>>>>>> >>>>>>> > standard >>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>> >>>>>>> >> a >>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>> >>>>>>> >> without >>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>> >>>>>>> >> for example >>>>>>>>>> >>>>>>> >> with a >>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>> >>>>>>> >>> different >>>>>>>>>> >>>>>>> >>> build >>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>> >>>>>>> >>> please >>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>> >>>>>>> >>> not >>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>> >>>>>>> >>> the >>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>> >>>>>>> >>> is >>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent >>>>>>>>>> > to you in >>>>>>>>>> > error >>>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>>> > sender and >>>>>>>>>> > properly >>>>>>>>>> > dispose of the e-mail. >>>>>>>>>> > >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> slicer-devel mailing list >>>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> To unsubscribe: send email to >>>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>>> subject >>>>>>>>> >>>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>> whom it is >>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>> the e-mail >>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>> HelpLine at >>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> +1 919 869 8849 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> slicer-devel mailing list >>>> slicer-devel at bwh.harvard.edu >>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>> To unsubscribe: send email to >>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>> subject >>>> >>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >>> >>> -- >>> +1 919 869 8849 >> >> >> _______________________________________________ >> slicer-devel mailing list >> slicer-devel at bwh.harvard.edu >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >> with unsubscribe as the subject >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> From matt.mccormick at kitware.com Wed Sep 17 13:06:49 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 13:06:49 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) Is this with the latest version of Slicer? My line 179 says vtkITKExecuteDataFromFile(VTK_DOUBLE, double); Thanks, Matt On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: > Hi Matt, > I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? > thanks > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 3:55 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > > Hi Gib, > > Getting the builds states to propagate and follow how the get set can > be tricky. A few pointers on where to look for the status: > > 1) CMakeCache.txt (this file contains the build settings that CMake > recognized from your input when you run CMake) > 2) ITKConfig.cmake (this file will exist in the build tree or the > install tree, and it contains CMake varables that may be used by other > projects building against ITK) > 3) itkConfigure.h (this is a header that has configured preprocessor > definitions used when building) > > HTH, > Matt > > > > On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >> Hi Bradley, Matt and Steve, >> >> Now for the embarrassing confession. In External_ITK4.cmake I turned >> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >> finally checked what the code that is being built was using (with #if >> defined ...) I discovered that both ITKV3_COMPATIBILITY and >> ITK_USE_64BITS_IDS were off. How can this be? >> >> It's easy, all it takes is a typo: >> -DITK_USE_64_BITS_IDS:BOOL=ON >> That typo has cost me a couple of days, and caused annoyance to a few >> people, I suspect. >> >> Unfortunately... now Slicer's vtkITK does not build. There are very many >> errors like this: >> >> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >> 3>Build started 17/09/2014 7:25:52 p.m.. >> 3>InitializeBuildStatus: >> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >> 3>CustomBuild: >> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >> 3> CMake does not need to re-run because >> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >> 3>ClCompile: >> 3> vtkITKNumericTraits.cxx >> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesReader.cxx >> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >> 3> vtkITKImageWriter.cxx >> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >> 3> vtkITKDistanceTransform.cxx >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >> error C2679: binary '=' : no operator found which takes a right-hand operand >> of type 'itk::ImportImageContainer *' (or there >> is no acceptable conversion) >> 3> with >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >> could be 'itk::SmartPointer >> &itk::SmartPointer::operator =(const >> itk::SmartPointer &)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >> or 'itk::SmartPointer >> &itk::SmartPointer::operator >> =(itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer, >> 3> TElementIdentifier=unsigned long, >> 3> TElement=double >> 3> ] >> 3> while trying to match the argument list >> '(itk::SmartPointer, >> itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> and >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> >> I presume these are related to the use of 64-bit integers. >> >> Over to you guys :) >> >> Gib >> ________________________________ >> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >> Sent: Tuesday, 16 September 2014 12:45 a.m. >> To: Steve Pieper >> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hello, >> >> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >> >> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >> read and write files like these there. More information about getting >> started is here[1]. >> >> You should be a able to generate a image with: >> >> import SimpleITK as sitk >> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >> img += 10 >> stats = sitk.StatisticsImageFilter() >> stats.Execute(img) >> print stats >> >> This should give you basic access to ITK in python to interactively >> experiment with options with these large images. I have been able to load >> large images with the binaries of SimpleITK on windows 64-bits. I don't know >> if I have tried big tiff though. >> >> A simular test could be done with C++ and ITK directly, but I think >> SimpleITK in python may be quicker for experimentation. >> >> Brad >> >> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >> [2] >> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >> >> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >> >> Hi Gib - >> >> Are you testing only on windows? What we would often try to do for this >> kind of debugging is to create a small example that other people can test on >> their configurations. Slicer has a mechanism called a Self Test [1] to >> allow easy replication and debugging across multiple platforms. It's ideal >> if we can hone it down to something like what is described as a 'sscce' [2]. >> The self tests will typically download some data from a public web site, run >> some operations, and then print something out saying if it passed or failed >> (or it may crash). Since it's possible to make a small data file that >> expands into a giant tiff image it should be pretty tractable to pose this >> issue in the form of a self test. >> >> Best, >> Steve >> >> >> [1] >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >> >> [2] http://sscce.org/ >> >> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>> >>> Hi J-C, >>> >>> Some more info about Slicer with big tiff files. >>> >>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>> 72) >>> >>> All suggestions will be gratefully received. >>> >>> Cheers >>> Gib >>> ________________________________ >>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>> Sent: Sunday, 14 September 2014 8:32 p.m. >>> To: Gib Bogle >>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hi Gib, >>> >>> What do you mean by "reinstalled" ? You should not have to install Slicer >>> to be able to execute it from the build directory. >>> >>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>> out. >>> >>> When done building, make sure to start the Slicer launcher: >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>> >>> and not the Slicer executable: >>> >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>> >>> >>> By using the launcher, you ensure that the PATH are properly setup and the >>> expected libraries are loaded. >>> >>> >>> Hth >>> Jc >>> >>> >>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>> wrote: >>>> >>>> I hope I understand correctly. I added the line as shown to >>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>> ... >>>> # ZLIB >>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>> # Big TIFF >>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>> ... >>>> >>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>> crashes with the big tiff. Is there somewhere I can check in the project >>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>> effect? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hey Gib - >>>> >>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>> ITK build process [1] during the superbuild. I don't think much else was >>>> required except turning off the IKTv3 parts. >>>> >>>> [1] >>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>> >>>> -Steve >>>> >>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>> it on TV). So the Jo'berg game should be a great rematch! >>>> >>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>> wrote: >>>>> >>>>> You did warn me. >>>>> >>>>> Here is the list of options not ticked: >>>>> >>>>> Slicer_BUILD_BRAINSTOOLS >>>>> _LEGACY_CLI >>>>> _LandmarkRegistration >>>>> _TESTING_EXTENSIONS >>>>> _UPDATE_TRANSLATION >>>>> _USE_GIT_PROTOCOL >>>>> _OpenIGTLink >>>>> _PYTHONQT_WITH_OPENSSL >>>>> _PYTHONQT_WITH_TCL >>>>> _QtTesting >>>>> _SimpleITK >>>>> _VTK_DEBUG_LINKS >>>>> Slicer_WITH_LIBRARY_VERSION >>>>> >>>>> USE_BRAINS* >>>>> USE_ConvertBetweenFileFormats >>>>> USE_DWIConvert >>>>> USE_DebugImageViewer >>>>> USE_GTRACT >>>>> USE_ICCDEF >>>>> USE_ImageCalculator >>>>> USE_ReferenceAtlas >>>>> >>>>> ------- >>>>> >>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>> which means a DLL was not found. I then realized that I have different >>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>> attempt to load a 4 GB tiff. >>>>> >>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>> for directions before doing this - now I'm wondering if that switch actually >>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Yes, well, don't say I didn't warn you! ; ) >>>>> >>>>> You do need loadable modules and you probably do want python (a lot of >>>>> core stuff is in python, like the editor). >>>>> >>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>> >>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>> it exited. But that may be a longshot. >>>>> >>>>> -Steve >>>>> >>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>> build took a long time, partly because I turned on the Python option, which >>>>>> I don't need. This time there were no errors, except for a couple of >>>>>> occasions where the attempt to create a directory failed - this was because >>>>>> the directory already existed, and was easily solved by deleting the >>>>>> directory and building again. I installed everything that wanted to be >>>>>> installed, and modified the environment variables to suit. >>>>>> >>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>> knowing what it is). >>>>>> >>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>> what to do next. >>>>>> >>>>>> Cheers >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> A lot of the building goes on in parallel so you need to review the >>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>> on at the cmake flag level. >>>>>> >>>>>> Best, >>>>>> Steve >>>>>> >>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>> Additional Dependencies: >>>>>>> >>>>>>> ... >>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>> ITKCommon.lib >>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>> ... >>>>>>> >>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>> 40+ times. >>>>>>> >>>>>>> Thanks again >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>> [g.bogle at auckland.ac.nz] >>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>> >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>> >>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>> >>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>> link the ITK library that was just built, i.e.: >>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>> This is the first of about 40 such link errors. >>>>>>> >>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>> ITK_DIR appropriately? >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>> trickiest platform in my experience. >>>>>>> >>>>>>> -Steve >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Gib Bogle >>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Jean-Christophe, >>>>>>>> >>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>> >>>>>>>> Cheers >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Folks, >>>>>>>> >>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>> >>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>> these module. All details are captured here: >>>>>>>> >>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>> >>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>> planned for 4.5. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Jc >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Matt - >>>>>>>>> >>>>>>>>> Thanks, that's helpful. >>>>>>>>> >>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>> straightforward. >>>>>>>>> >>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>> >>>>>>>>> -Steve >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Here is what the process would look like: >>>>>>>>>> >>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>> the >>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>> 5) Profit. >>>>>>>>>> >>>>>>>>>> HTH, >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>> >>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>> >>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>> wrote: >>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>> > but it's >>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>> > >>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>> > what is >>>>>>>>>> > involved? >>>>>>>>>> > >>>>>>>>>> > -Steve >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>> > wrote: >>>>>>>>>> >> >>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>> >> large >>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>> >> capability >>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>> >> ________________________________ >>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>> >> >>>>>>>>>> >> To: Gib Bogle >>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >> >>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>> >> configure >>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>> >> like vtkITK >>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>> >> experts are >>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>> >> >>>>>>>>>> >> -Steve >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>> >> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> I await the results with interest... >>>>>>>>>> >>> ________________________________ >>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>> >>> Pieper >>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>> >>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>> >>> a lot of >>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>> >>> >>>>>>>>>> >>> -Steve >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Steve, >>>>>>>>>> >>>> >>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>> >>>> configured in >>>>>>>>>> >>>> Slicer. >>>>>>>>>> >>>> >>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>> >>>> needs to >>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>> >>>> be used. I have >>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>> >>>> one wanted to >>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>> >>>> >>>>>>>>>> >>>> Brad >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Hi Brad - >>>>>>>>>> >>>> >>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>> >>>> able to >>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>> >>>> default options >>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>> >>>> >>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>> >>>> something nobody >>>>>>>>>> >>>> has tried? >>>>>>>>>> >>>> >>>>>>>>>> >>>> -Steve >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Steve, >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>> >>>>> windows 64? >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>> >>>>> specific. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Bread >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>> >>>>> pasted in >>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> -Steve >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>> >>>>>> still >>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Brad >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>> >>>>>> replicate the >>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> wrote: >>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>> >>>>>>> > back to this >>>>>>>>>> >>>>>>> > later. >>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>> >>>>>>> > to >>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>> >>>>>>> > for any >>>>>>>>>> >>>>>>> > standard >>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>> >>>>>>> >> a >>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>> >>>>>>> >> without >>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>> >>>>>>> >> for example >>>>>>>>>> >>>>>>> >> with a >>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>> >>>>>>> >>> different >>>>>>>>>> >>>>>>> >>> build >>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>> >>>>>>> >>> please >>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>> >>>>>>> >>> not >>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>> >>>>>>> >>> the >>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>> >>>>>>> >>> is >>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If the e-mail was sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> +1 919 869 8849 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> slicer-devel mailing list >>>> slicer-devel at bwh.harvard.edu >>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>> To unsubscribe: send email to >>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>> subject >>>> >>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >>> >>> -- >>> +1 919 869 8849 >> >> >> _______________________________________________ >> slicer-devel mailing list >> slicer-devel at bwh.harvard.edu >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >> with unsubscribe as the subject >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> From matt.mccormick at kitware.com Wed Sep 17 16:16:27 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 16:16:27 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: Message-ID: On Wed, Sep 17, 2014 at 11:13 AM, Matt McCormick wrote: > There are a couple of upcoming opportunities to share, discuss, design, and > learn with your fellow ITK community members. > > > On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a > Google+ Hangout > where we will be doing code reviews: > > https://plus.google.com/events/cg0n52cqd08ulpr6o9jgku32gj0?authkey=CJ-S7tP5s5_xAw > Due to a conflict, this had to be changed to 1:00 PM Eastern USA time. Sorry for schedule variation. Matt From g.bogle at auckland.ac.nz Wed Sep 17 16:32:32 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 20:32:32 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. I appreciate your attention to it very much! Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 5:06 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) Is this with the latest version of Slicer? My line 179 says vtkITKExecuteDataFromFile(VTK_DOUBLE, double); Thanks, Matt On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: > Hi Matt, > I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? > thanks > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 3:55 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > > Hi Gib, > > Getting the builds states to propagate and follow how the get set can > be tricky. A few pointers on where to look for the status: > > 1) CMakeCache.txt (this file contains the build settings that CMake > recognized from your input when you run CMake) > 2) ITKConfig.cmake (this file will exist in the build tree or the > install tree, and it contains CMake varables that may be used by other > projects building against ITK) > 3) itkConfigure.h (this is a header that has configured preprocessor > definitions used when building) > > HTH, > Matt > > > > On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >> Hi Bradley, Matt and Steve, >> >> Now for the embarrassing confession. In External_ITK4.cmake I turned >> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >> finally checked what the code that is being built was using (with #if >> defined ...) I discovered that both ITKV3_COMPATIBILITY and >> ITK_USE_64BITS_IDS were off. How can this be? >> >> It's easy, all it takes is a typo: >> -DITK_USE_64_BITS_IDS:BOOL=ON >> That typo has cost me a couple of days, and caused annoyance to a few >> people, I suspect. >> >> Unfortunately... now Slicer's vtkITK does not build. There are very many >> errors like this: >> >> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >> 3>Build started 17/09/2014 7:25:52 p.m.. >> 3>InitializeBuildStatus: >> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >> 3>CustomBuild: >> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >> 3> CMake does not need to re-run because >> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >> 3>ClCompile: >> 3> vtkITKNumericTraits.cxx >> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesReader.cxx >> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >> 3> vtkITKImageWriter.cxx >> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >> 3> vtkITKDistanceTransform.cxx >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >> error C2679: binary '=' : no operator found which takes a right-hand operand >> of type 'itk::ImportImageContainer *' (or there >> is no acceptable conversion) >> 3> with >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >> could be 'itk::SmartPointer >> &itk::SmartPointer::operator =(const >> itk::SmartPointer &)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >> or 'itk::SmartPointer >> &itk::SmartPointer::operator >> =(itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer, >> 3> TElementIdentifier=unsigned long, >> 3> TElement=double >> 3> ] >> 3> while trying to match the argument list >> '(itk::SmartPointer, >> itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> and >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> >> I presume these are related to the use of 64-bit integers. >> >> Over to you guys :) >> >> Gib >> ________________________________ >> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >> Sent: Tuesday, 16 September 2014 12:45 a.m. >> To: Steve Pieper >> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hello, >> >> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >> >> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >> read and write files like these there. More information about getting >> started is here[1]. >> >> You should be a able to generate a image with: >> >> import SimpleITK as sitk >> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >> img += 10 >> stats = sitk.StatisticsImageFilter() >> stats.Execute(img) >> print stats >> >> This should give you basic access to ITK in python to interactively >> experiment with options with these large images. I have been able to load >> large images with the binaries of SimpleITK on windows 64-bits. I don't know >> if I have tried big tiff though. >> >> A simular test could be done with C++ and ITK directly, but I think >> SimpleITK in python may be quicker for experimentation. >> >> Brad >> >> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >> [2] >> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >> >> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >> >> Hi Gib - >> >> Are you testing only on windows? What we would often try to do for this >> kind of debugging is to create a small example that other people can test on >> their configurations. Slicer has a mechanism called a Self Test [1] to >> allow easy replication and debugging across multiple platforms. It's ideal >> if we can hone it down to something like what is described as a 'sscce' [2]. >> The self tests will typically download some data from a public web site, run >> some operations, and then print something out saying if it passed or failed >> (or it may crash). Since it's possible to make a small data file that >> expands into a giant tiff image it should be pretty tractable to pose this >> issue in the form of a self test. >> >> Best, >> Steve >> >> >> [1] >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >> >> [2] http://sscce.org/ >> >> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>> >>> Hi J-C, >>> >>> Some more info about Slicer with big tiff files. >>> >>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>> 72) >>> >>> All suggestions will be gratefully received. >>> >>> Cheers >>> Gib >>> ________________________________ >>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>> Sent: Sunday, 14 September 2014 8:32 p.m. >>> To: Gib Bogle >>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hi Gib, >>> >>> What do you mean by "reinstalled" ? You should not have to install Slicer >>> to be able to execute it from the build directory. >>> >>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>> out. >>> >>> When done building, make sure to start the Slicer launcher: >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>> >>> and not the Slicer executable: >>> >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>> >>> >>> By using the launcher, you ensure that the PATH are properly setup and the >>> expected libraries are loaded. >>> >>> >>> Hth >>> Jc >>> >>> >>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>> wrote: >>>> >>>> I hope I understand correctly. I added the line as shown to >>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>> ... >>>> # ZLIB >>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>> # Big TIFF >>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>> ... >>>> >>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>> crashes with the big tiff. Is there somewhere I can check in the project >>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>> effect? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hey Gib - >>>> >>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>> ITK build process [1] during the superbuild. I don't think much else was >>>> required except turning off the IKTv3 parts. >>>> >>>> [1] >>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>> >>>> -Steve >>>> >>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>> it on TV). So the Jo'berg game should be a great rematch! >>>> >>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>> wrote: >>>>> >>>>> You did warn me. >>>>> >>>>> Here is the list of options not ticked: >>>>> >>>>> Slicer_BUILD_BRAINSTOOLS >>>>> _LEGACY_CLI >>>>> _LandmarkRegistration >>>>> _TESTING_EXTENSIONS >>>>> _UPDATE_TRANSLATION >>>>> _USE_GIT_PROTOCOL >>>>> _OpenIGTLink >>>>> _PYTHONQT_WITH_OPENSSL >>>>> _PYTHONQT_WITH_TCL >>>>> _QtTesting >>>>> _SimpleITK >>>>> _VTK_DEBUG_LINKS >>>>> Slicer_WITH_LIBRARY_VERSION >>>>> >>>>> USE_BRAINS* >>>>> USE_ConvertBetweenFileFormats >>>>> USE_DWIConvert >>>>> USE_DebugImageViewer >>>>> USE_GTRACT >>>>> USE_ICCDEF >>>>> USE_ImageCalculator >>>>> USE_ReferenceAtlas >>>>> >>>>> ------- >>>>> >>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>> which means a DLL was not found. I then realized that I have different >>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>> attempt to load a 4 GB tiff. >>>>> >>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>> for directions before doing this - now I'm wondering if that switch actually >>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Yes, well, don't say I didn't warn you! ; ) >>>>> >>>>> You do need loadable modules and you probably do want python (a lot of >>>>> core stuff is in python, like the editor). >>>>> >>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>> >>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>> it exited. But that may be a longshot. >>>>> >>>>> -Steve >>>>> >>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>> build took a long time, partly because I turned on the Python option, which >>>>>> I don't need. This time there were no errors, except for a couple of >>>>>> occasions where the attempt to create a directory failed - this was because >>>>>> the directory already existed, and was easily solved by deleting the >>>>>> directory and building again. I installed everything that wanted to be >>>>>> installed, and modified the environment variables to suit. >>>>>> >>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>> knowing what it is). >>>>>> >>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>> what to do next. >>>>>> >>>>>> Cheers >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> A lot of the building goes on in parallel so you need to review the >>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>> on at the cmake flag level. >>>>>> >>>>>> Best, >>>>>> Steve >>>>>> >>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>> Additional Dependencies: >>>>>>> >>>>>>> ... >>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>> ITKCommon.lib >>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>> ... >>>>>>> >>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>> 40+ times. >>>>>>> >>>>>>> Thanks again >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>> [g.bogle at auckland.ac.nz] >>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>> >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>> >>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>> >>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>> link the ITK library that was just built, i.e.: >>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>> This is the first of about 40 such link errors. >>>>>>> >>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>> ITK_DIR appropriately? >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>> trickiest platform in my experience. >>>>>>> >>>>>>> -Steve >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Gib Bogle >>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Jean-Christophe, >>>>>>>> >>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>> >>>>>>>> Cheers >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Folks, >>>>>>>> >>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>> >>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>> these module. All details are captured here: >>>>>>>> >>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>> >>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>> planned for 4.5. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Jc >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Matt - >>>>>>>>> >>>>>>>>> Thanks, that's helpful. >>>>>>>>> >>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>> straightforward. >>>>>>>>> >>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>> >>>>>>>>> -Steve >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Here is what the process would look like: >>>>>>>>>> >>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>> the >>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>> 5) Profit. >>>>>>>>>> >>>>>>>>>> HTH, >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>> >>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>> >>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>> wrote: >>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>> > but it's >>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>> > >>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>> > what is >>>>>>>>>> > involved? >>>>>>>>>> > >>>>>>>>>> > -Steve >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>> > wrote: >>>>>>>>>> >> >>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>> >> large >>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>> >> capability >>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>> >> ________________________________ >>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>> >> >>>>>>>>>> >> To: Gib Bogle >>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >> >>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>> >> configure >>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>> >> like vtkITK >>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>> >> experts are >>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>> >> >>>>>>>>>> >> -Steve >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>> >> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> I await the results with interest... >>>>>>>>>> >>> ________________________________ >>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>> >>> Pieper >>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>> >>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>> >>> a lot of >>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>> >>> >>>>>>>>>> >>> -Steve >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Steve, >>>>>>>>>> >>>> >>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>> >>>> configured in >>>>>>>>>> >>>> Slicer. >>>>>>>>>> >>>> >>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>> >>>> needs to >>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>> >>>> be used. I have >>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>> >>>> one wanted to >>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>> >>>> >>>>>>>>>> >>>> Brad >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Hi Brad - >>>>>>>>>> >>>> >>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>> >>>> able to >>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>> >>>> default options >>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>> >>>> >>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>> >>>> something nobody >>>>>>>>>> >>>> has tried? >>>>>>>>>> >>>> >>>>>>>>>> >>>> -Steve >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Steve, >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>> >>>>> windows 64? >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>> >>>>> specific. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Bread >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>> >>>>> pasted in >>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> -Steve >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>> >>>>>> still >>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Brad >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>> >>>>>> replicate the >>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> wrote: >>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>> >>>>>>> > back to this >>>>>>>>>> >>>>>>> > later. >>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>> >>>>>>> > to >>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>> >>>>>>> > for any >>>>>>>>>> >>>>>>> > standard >>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>> >>>>>>> >> a >>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>> >>>>>>> >> without >>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>> >>>>>>> >> for example >>>>>>>>>> >>>>>>> >> with a >>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>> >>>>>>> >>> different >>>>>>>>>> >>>>>>> >>> build >>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>> >>>>>>> >>> please >>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>> >>>>>>> >>> not >>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>> >>>>>>> >>> the >>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>> >>>>>>> >>> is >>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If you believe this e-mail was sent to you in error >>>>>>>>>> > and the >>>>>>>>>> > e-mail >>>>>>>>>> > contains patient information, please contact the Partners >>>>>>>>>> > Compliance >>>>>>>>>> > HelpLine at >>>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent >>>>>>>>>> > to you in >>>>>>>>>> > error >>>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>>> > sender and >>>>>>>>>> > properly >>>>>>>>>> > dispose of the e-mail. >>>>>>>>>> > >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> slicer-devel mailing list >>>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> To unsubscribe: send email to >>>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>>> subject >>>>>>>>> >>>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>> whom it is >>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>> the e-mail >>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>> HelpLine at >>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> +1 919 869 8849 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> slicer-devel mailing list >>>> slicer-devel at bwh.harvard.edu >>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>> To unsubscribe: send email to >>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>> subject >>>> >>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >>> >>> -- >>> +1 919 869 8849 >> >> >> _______________________________________________ >> slicer-devel mailing list >> slicer-devel at bwh.harvard.edu >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >> with unsubscribe as the subject >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> From matt.mccormick at kitware.com Wed Sep 17 17:05:45 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 17:05:45 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 17:44:38 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 21:44:38 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: That fixed the error in that file, but there are still many elsewhere. I will now try making that change in other places. Thanks! Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If you believe this e-mail was sent to you in error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 17:51:08 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 21:51:08 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Sorry, my mistake, not fixed. I tried one suggestion, will try the second. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 18:01:33 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 22:01:33 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Your second suggestion fixed two occurrences :) The next error is in vtkITKTimeSeriesDatabase.cxx(66): itk::ImportImageContainer::Pointer PixelContainerShort; PixelContainerShort = this->m_Filter->GetOutput()->GetPixelContainer(); ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 18:12:10 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 22:12:10 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , Message-ID: I boldly (rashly?) did this: itk::ImportImageContainer< itk::SizeValueType, short>::Pointer PixelContainerShort; and it compiles. Is this OK? ________________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Thursday, 18 September 2014 10:01 a.m. To: Matt McCormick Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Your second suggestion fixed two occurrences :) The next error is in vtkITKTimeSeriesDatabase.cxx(66): itk::ImportImageContainer::Pointer PixelContainerShort; PixelContainerShort = this->m_Filter->GetOutput()->GetPixelContainer(); ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From g.bogle at auckland.ac.nz Wed Sep 17 18:20:17 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 22:20:17 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Those errors have gone for now. Now I'm seeing a slew of errors like this: 2> vtkITKTimeSeriesDatabase.cxx 2>c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(33): error C2782: 'T itk::TSD_MAX(T,T)' : template parameter 'T' is ambiguous 2> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(19) : see declaration of 'itk::TSD_MAX' 2> could be 'itk::Size::SizeValueType' 2> with 2> [ 2> VDimension=3 2> ] 2> or 'unsigned long' 2> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(27) : while compiling class template member function 'bool itk::TimeSeriesDatabase::CalculateIntersection(itk::Size,itk::ImageRegion,itk::ImageRegion &,itk::ImageRegion &)' 2> with 2> [ 2> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType, 2> VDimension=3, 2> VImageDimension=3 2> ] 2> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(340) : while compiling class template member function 'void itk::TimeSeriesDatabase::CreateFromFileArchetype(const char *,const char *)' 2> with 2> [ 2> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType 2> ] 2> c:\slicer\libs\vtkitk\vtkITKTimeSeriesDatabase.h(89) : see reference to class template instantiation 'itk::TimeSeriesDatabase' being compiled 2> with 2> [ 2> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType 2> ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If you believe this e-mail was sent to you in error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 18:35:12 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 22:35:12 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If you believe this e-mail was sent to you in error >>>>>>>>>>> > and the >>>>>>>>>>> > e-mail >>>>>>>>>>> > contains patient information, please contact the Partners >>>>>>>>>>> > Compliance >>>>>>>>>>> > HelpLine at >>>>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent >>>>>>>>>>> > to you in >>>>>>>>>>> > error >>>>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>>>> > sender and >>>>>>>>>>> > properly >>>>>>>>>>> > dispose of the e-mail. >>>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> slicer-devel mailing list >>>>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> To unsubscribe: send email to >>>>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>>>> subject >>>>>>>>>> >>>>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>>> whom it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From jchris.fillionr at kitware.com Wed Sep 17 19:09:58 2014 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Wed, 17 Sep 2014 19:09:58 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Hi Gib, Thanks for your hard work and perseverance. This is very much appreciated ! On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle wrote: > There are two more projects to go, vtkITKPython, and vtkITKPythonD. The source of these two projects are automatically generated by the VTK python wrapping tools, I wouldn't expect any issues with these. Hth Jc -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 17 19:13:31 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 23:13:31 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Hi Steve, I'm just addressing another different error. I hope it's just a matter of replacing unsigned long with itk::SizeValueType I guess this is a bit like the Y2K problem - everybody thought unsigned long was amply big enough. 24> N4ITKBiasFieldCorrection.cxx 24>..\..\..\..\..\..\Slicer\Modules\CLI\N4ITKBiasFieldCorrection\N4ITKBiasFieldCorrection.cxx(206): error C2664: 'void itk::PadImageFilter::SetPadLowerBound(const itk::Size)' : cannot convert parameter 1 from 'unsigned long [3]' to 'const itk::Size' [C:\s\b\Slicer-build\Modules\CLI\N4ITKBiasFieldCorrection\N4ITKBiasFieldCorrectionLib.vcxproj] 24> with 24> [ 24> TInputImage=`anonymous-namespace'::ImageType, 24> TOutputImage=`anonymous-namespace'::ImageType, 24> VDimension=3 24> ] 24> and 24> [ 24> VDimension=3 24> ] 24> No constructor could take the source type, or constructor overload resolution was ambiguous ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:10 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib - Way to see it through! those vtk*Python and vtk*PythonD should be autogenerated and not manually edited so maybe you are already there? -Steve On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle > wrote: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle > wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle > wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle > wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> > wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> > >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> > >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 17 19:34:44 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 23:34:44 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Thanks. It would not have taken so long if I had not made that typo, and if I were a bit more mentally agile. Slicer is now built on my machine, and I am about to test it on some files. One thing puzzles me - when I Load Data and ask to select a file (or directory) it takes an awfully long time for any files to appear - anything from 30 sec to more than a minute. Is this normal? Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:10 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib - Way to see it through! those vtk*Python and vtk*PythonD should be autogenerated and not manually edited so maybe you are already there? -Steve On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle > wrote: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle > wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle > wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle > wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> > wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> > >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> > >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 17 19:41:54 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 23:41:54 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: It's a mystery. There are no drives mounted. There are other machines visible on Network (via wifi), but no drives are mapped. Do you think it could be those network machines? ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:37 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF That might happen if you have a drive mounted that's not available or something (some windows thing). Otherwise I'm not sure... Good luck with the loading... Steve On Wed, Sep 17, 2014 at 7:34 PM, Gib Bogle > wrote: Thanks. It would not have taken so long if I had not made that typo, and if I were a bit more mentally agile. Slicer is now built on my machine, and I am about to test it on some files. One thing puzzles me - when I Load Data and ask to select a file (or directory) it takes an awfully long time for any files to appear - anything from 30 sec to more than a minute. Is this normal? Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:10 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib - Way to see it through! those vtk*Python and vtk*PythonD should be autogenerated and not manually edited so maybe you are already there? -Steve On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle > wrote: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle > wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle > wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle > wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> > wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> > >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> > >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. 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URL: From yxp233 at postech.ac.kr Wed Sep 17 20:11:55 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Thu, 18 Sep 2014 09:11:55 +0900 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support In-Reply-To: <1410960535981899.04578.ptmail04@ptmail04> References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> <1410913163921868.021894.ptmail04@ptmail04> <000c01cfd27a$9ed25020$dc76f060$@ac.kr> <1410960535981899.04578.ptmail04@ptmail04> Message-ID: <008301cfd2d5$27ecc890$77c659b0$@ac.kr> Hi Mike, If I turn USE_GPU off, then there is no CMake error. I guess there is something wrong with the GPU module. I am using CUDA toolkit 6.5 for compiling. Which version of CUDA toolkit should I use? Thanks, Xiaopeng From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Mike Chinander Sent: Wednesday, September 17, 2014 10:29 PM To: insight-users Subject: Re: [ITK-users] Any instruction of compiling ITK with GPU support Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with forward slashes instead, "D:/Toolbox/ITK-4.6.0" On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang wrote: By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows: Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): Syntax error in cmake code at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 when parsing string D:\Toolbox\ITK-4.6.0 Invalid escape sequence \T Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set) CMake/ITKModuleEnablement.cmake:171 (include) CMakeLists.txt:322 (include) Configuring incomplete, errors occurred! See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Wed Sep 17 20:36:06 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 00:36:06 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) I am seeing some odd behaviour. I can load and display a > 4GB tiff (N = 1650), but although I can load a tiff made with N = 1300 (a bit bigger than 2 GB) nothing is displayed. You have to admit that this is surprising :) There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:37 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF That might happen if you have a drive mounted that's not available or something (some windows thing). Otherwise I'm not sure... Good luck with the loading... Steve On Wed, Sep 17, 2014 at 7:34 PM, Gib Bogle > wrote: Thanks. It would not have taken so long if I had not made that typo, and if I were a bit more mentally agile. Slicer is now built on my machine, and I am about to test it on some files. One thing puzzles me - when I Load Data and ask to select a file (or directory) it takes an awfully long time for any files to appear - anything from 30 sec to more than a minute. Is this normal? Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:10 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib - Way to see it through! those vtk*Python and vtk*PythonD should be autogenerated and not manually edited so maybe you are already there? -Steve On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle > wrote: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle > wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle > wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle > wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> > wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> > >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> > >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If you believe this e-mail was sent to you >>>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If you believe this e-mail was sent to you in >>>>>>>>>>> >>>>>> error and the >>>>>>>>>>> >>>>>> e-mail >>>>>>>>>>> >>>>>> contains patient information, please contact the Partners >>>>>>>>>>> >>>>>> Compliance >>>>>>>>>>> >>>>>> HelpLine at >>>>>>>>>>> >>>>>> http://www.partners.org/complianceline . 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If you believe this e-mail was sent to you in error >>>>>>>>>>> > and the >>>>>>>>>>> > e-mail >>>>>>>>>>> > contains patient information, please contact the Partners >>>>>>>>>>> > Compliance >>>>>>>>>>> > HelpLine at >>>>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent >>>>>>>>>>> > to you in >>>>>>>>>>> > error >>>>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>>>> > sender and >>>>>>>>>>> > properly >>>>>>>>>>> > dispose of the e-mail. >>>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> slicer-devel mailing list >>>>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> To unsubscribe: send email to >>>>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>>>> subject >>>>>>>>>> >>>>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>>> whom it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From yxp233 at postech.ac.kr Wed Sep 17 21:48:11 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Thu, 18 Sep 2014 10:48:11 +0900 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> <1410913163921868.021894.ptmail04@ptmail04> <000c01cfd27a$9ed25020$dc76f060$@ac.kr> <1410960535981899.04578.ptmail04@ptmail04> Message-ID: <009401cfd2e2$9b13c640$d13b52c0$@ac.kr> Hi Mike, I found that you were right. I changed the forward slashes for the directories of OpenCL: OPENCL_INCLUDE_DIRS C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/include OPENCL_LIBRARIES C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib There was no CMake error, but many warning messages: WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. And when I tried to debug ITK, errors occurred as ?cannot find CL/opencl.h?. Can you tell me where I made a mistake? Thank you, Xiaopeng From: Xiaopeng Yang [mailto:yxp233 at postech.ac.kr] Sent: Thursday, September 18, 2014 9:12 AM To: 'Mike Chinander'; 'insight-users' Subject: RE: [ITK-users] Any instruction of compiling ITK with GPU support Hi Mike, If I turn USE_GPU off, then there is no CMake error. I guess there is something wrong with the GPU module. I am using CUDA toolkit 6.5 for compiling. Which version of CUDA toolkit should I use? Thanks, Xiaopeng From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Mike Chinander Sent: Wednesday, September 17, 2014 10:29 PM To: insight-users Subject: Re: [ITK-users] Any instruction of compiling ITK with GPU support Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with forward slashes instead, "D:/Toolbox/ITK-4.6.0" On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang wrote: By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows: Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): Syntax error in cmake code at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 when parsing string D:\Toolbox\ITK-4.6.0 Invalid escape sequence \T Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set) CMake/ITKModuleEnablement.cmake:171 (include) CMakeLists.txt:322 (include) Configuring incomplete, errors occurred! See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Wed Sep 17 21:54:06 2014 From: llliu at umich.edu (Lianli Liu) Date: Wed, 17 Sep 2014 21:54:06 -0400 Subject: [ITK] [ITK-users] Mask in metric calculation Message-ID: Hi all, I just wonder if I define two masks for fixed image and moving image that are of differnt size, will voxels that fall in both the masks will contribute to metric calculation? Thanks! Regards, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jchris.fillionr at kitware.com Wed Sep 17 22:51:21 2014 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Wed, 17 Sep 2014 22:51:21 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle wrote: > Correction! You were right. There was a network drive that I could not > see until I right-clicked on Network, then Disconnect network drive. Now > it's responsive :) > > There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" > > There is another wrinkle that I'm not concerned about right now. When I > execute the installed program, C:\Program files\Slicer.exe, the console > shows this error message: > > Traceback (most recent call last): > File "", line 7, in > File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in > > import vtk, qt, ctk > ImportError: No module named vtk > > but the program runs. I don't see that message when I run the executable > in Slicer-build. The files in both places are the same, also the > SlicerApp-real.exe files - of course, since INSTALL just copies them. I > have seen any difference in the ability to display the tiff files. > This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 17 23:07:23 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 03:07:23 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From gowithking at googlemail.com Thu Sep 18 02:03:52 2014 From: gowithking at googlemail.com (gowith king) Date: Thu, 18 Sep 2014 08:03:52 +0200 Subject: [ITK] Bug in StatisticsImageFilter? In-Reply-To: References: Message-ID: Hi Matt You are the best . It works. I thought it need only the last writer.Update() to call the whole pep-line. Thank you . I am going to catch my flight now, I will try the other one later. On Wed, Sep 17, 2014 at 5:44 PM, Matt McCormick wrote: > Hi gowith, > > Please try calling > > rangetest.Update() > > This is required for the results to be computed. > > HTH, > Matt > > On Tue, Sep 16, 2014 at 7:53 PM, gowith king > wrote: > > I was trying to use itk.StatisticsImageFilter to check the outcome of my > > image reader. but all the results are wrong. > > reader1 = itk.ImageFileReader.IUC3.New() > > reader1.SetFileName(inputImagetest) > > > > rangetest=itk.StatisticsImageFilter.IUC3.New() > > rangetest.SetInput(reader1) > > print 'range: ', str(rangetest.GetMinimum()) > > > > result: > > range: 255 > > > > obviously this is not true for my image : it is a binary image and has > only > > 1 and 100 two values. > > > > I am working on a python 2.7 wrapped ITK4 . if the python2 is > incompatible > > with itk? > > > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Thu Sep 18 02:36:05 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 18 Sep 2014 08:36:05 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Hi Matt, This is indeed the observed and, based on your answer, expected behaviour. Thank you very much for the confirmation (that's exactly what I needed!). To avoid confusion in future, I am going to modify the corresponding example on github and on the wiki! Best, Arnaud On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick wrote: > Hi, > > Do to this fix [1], if the writer is re-using the GDCMImageIO, the > writer should apply the inverse rescale / slope intercept like the > reader applied the rescale / slope intercept when reading. This was a > long-standing bug that I fixed in 4.6.0. Arnaud, if the manual > inverse rescale / slope operation is removed, does the correct output > result? > > Thanks, > Matt > > [1] > https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e > > On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen > wrote: > > I wrote this example many years ago? > > 1) If the input has a non-trivial slope/intercept, the reader applies > > the slope/intercept to the raw data. > > 2) Rather than setting the slope/intercept in the output dicom, I > > apply the inverse of of the slope intercept to the resampled data > > before writing. The output dicom should not have the origin > > slope/intercept tags. > > > > I'll try to verify this with Slicer, but I may be out of touch for 2 > weeks? > > > > Bill > > > > > > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas > wrote: > >> Hi Nick, > >> > >> I can confirm that with the example I get a difference of -1024 (+/- 1) > in > >> between the input and the output, using the ShiftScaleImage part... > >> While without this part of code the difference is (+/-1) > >> > >> I would like to make sure this is the expected behaviour!? > >> > >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson < > pattersonnp.work at gmail.com> > >> wrote: > >>> > >>> OK, I will wait to hear the outcome of your run with the original > example > >>> then. > >>> > >>> Cheers, Nick. > >>> > >>> > >>> > >>> > >>> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: > >>> > >>> Nick, > >>> > >>> I can't roll back to previous ITK version, important patches on > >>> itkGDCMImageIO were very recently merged... > >>> > >>> > >>> > https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx > >>> > >>> e.g. > >>> > >>> > >>> > https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 > >>> > >>> > https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c > >>> > >>> > >>> Arnaud > >>> > >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson > >>> wrote: > >>>> > >>>> I should also mention Arnauld that I use ITK4.5.2. I have had many > >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled > back to > >>>> ITK4.5.2. > >>>> Nick. > >>>> > >>>> > >>>> > >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: > >>>> > >>>> Hi Matias, > >>>> > >>>> I guess you are referring to > >>>> > >>>> > >>>> > https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e > >>>> > >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e > >>>> v4.6.0 > >>>> > >>>> I use the release branch of ITK > >>>> > >>>> --- > >>>> > >>>> Matt, > >>>> > >>>> Can you comment on this, please? > >>>> > >>>> Thanks > >>>> Arnaud > >>>> > >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull > >>>> wrote: > >>>> > >>>> I had an issue with the resampledicom example once (all my pixel > values > >>>> were recalculated by adding rescaleintercept) and then downloaded the > latest > >>>> ITK release (4.6) and worked fine. > >>>> > >>>> The issue was with the GDCMIO class I beleive but was fixed somehow in > >>>> the 4.6 version. > >>>> > >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas > > >>>> wrote: > >>>>> > >>>>> Hi all, > >>>>> > >>>>> I have been looking at the following wiki example: > >>>>> > >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > >>>>> > >>>>> It seems to me that the section to rescale the image is not valid > >>>>> anymore with latest ITK version (?) > >>>>> > >>>>> > >>>>> > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > >>>>> > >>>>> Can anyone confirm? > >>>>> > >>>>> Is this code validated? are output images compared to input ones in > the > >>>>> corresponding test? > >>>>> > >>>>> Thanks > >>>>> Arnaud > >>>>> > >>>>> _____________________________________ > >>>>> Powered by www.kitware.com > >>>>> > >>>>> Visit other Kitware open-source projects at > >>>>> http://www.kitware.com/opensource/opensource.html > >>>>> > >>>>> Kitware offers ITK Training Courses, for more information visit: > >>>>> http://www.kitware.com/products/protraining.php > >>>>> > >>>>> Please keep messages on-topic and check the ITK FAQ at: > >>>>> http://www.itk.org/Wiki/ITK_FAQ > >>>>> > >>>>> Follow this link to subscribe/unsubscribe: > >>>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>>> > >>>> > >>>> > >>>> _____________________________________ > >>>> Powered by www.kitware.com > >>>> > >>>> Visit other Kitware open-source projects at > >>>> http://www.kitware.com/opensource/opensource.html > >>>> > >>>> Kitware offers ITK Training Courses, for more information visit: > >>>> http://www.kitware.com/products/protraining.php > >>>> > >>>> Please keep messages on-topic and check the ITK FAQ at: > >>>> http://www.itk.org/Wiki/ITK_FAQ > >>>> > >>>> Follow this link to subscribe/unsubscribe: > >>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>> > >>>> > >>> > >>> > >> > >> > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-users > >> > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Thu Sep 18 02:43:36 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 18 Sep 2014 08:43:36 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Matt, I guess there should be migration report for this fix? Arnaud On Thu, Sep 18, 2014 at 8:36 AM, Arnaud Gelas wrote: > Hi Matt, > > This is indeed the observed and, based on your answer, expected behaviour. > Thank you very much for the confirmation (that's exactly what I needed!). > > To avoid confusion in future, I am going to modify the corresponding > example on github and on the wiki! > > Best, > Arnaud > > On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi, >> >> Do to this fix [1], if the writer is re-using the GDCMImageIO, the >> writer should apply the inverse rescale / slope intercept like the >> reader applied the rescale / slope intercept when reading. This was a >> long-standing bug that I fixed in 4.6.0. Arnaud, if the manual >> inverse rescale / slope operation is removed, does the correct output >> result? >> >> Thanks, >> Matt >> >> [1] >> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >> >> On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen >> wrote: >> > I wrote this example many years ago? >> > 1) If the input has a non-trivial slope/intercept, the reader applies >> > the slope/intercept to the raw data. >> > 2) Rather than setting the slope/intercept in the output dicom, I >> > apply the inverse of of the slope intercept to the resampled data >> > before writing. The output dicom should not have the origin >> > slope/intercept tags. >> > >> > I'll try to verify this with Slicer, but I may be out of touch for 2 >> weeks? >> > >> > Bill >> > >> > >> > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas >> wrote: >> >> Hi Nick, >> >> >> >> I can confirm that with the example I get a difference of -1024 (+/- >> 1) in >> >> between the input and the output, using the ShiftScaleImage part... >> >> While without this part of code the difference is (+/-1) >> >> >> >> I would like to make sure this is the expected behaviour!? >> >> >> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson < >> pattersonnp.work at gmail.com> >> >> wrote: >> >>> >> >>> OK, I will wait to hear the outcome of your run with the original >> example >> >>> then. >> >>> >> >>> Cheers, Nick. >> >>> >> >>> >> >>> >> >>> >> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: >> >>> >> >>> Nick, >> >>> >> >>> I can't roll back to previous ITK version, important patches on >> >>> itkGDCMImageIO were very recently merged... >> >>> >> >>> >> >>> >> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx >> >>> >> >>> e.g. >> >>> >> >>> >> >>> >> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 >> >>> >> >>> >> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c >> >>> >> >>> >> >>> Arnaud >> >>> >> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson >> >>> wrote: >> >>>> >> >>>> I should also mention Arnauld that I use ITK4.5.2. I have had many >> >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled >> back to >> >>>> ITK4.5.2. >> >>>> Nick. >> >>>> >> >>>> >> >>>> >> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas >> wrote: >> >>>> >> >>>> Hi Matias, >> >>>> >> >>>> I guess you are referring to >> >>>> >> >>>> >> >>>> >> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >> >>>> >> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >> >>>> v4.6.0 >> >>>> >> >>>> I use the release branch of ITK >> >>>> >> >>>> --- >> >>>> >> >>>> Matt, >> >>>> >> >>>> Can you comment on this, please? >> >>>> >> >>>> Thanks >> >>>> Arnaud >> >>>> >> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull >> >>>> wrote: >> >>>> >> >>>> I had an issue with the resampledicom example once (all my pixel >> values >> >>>> were recalculated by adding rescaleintercept) and then downloaded >> the latest >> >>>> ITK release (4.6) and worked fine. >> >>>> >> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow >> in >> >>>> the 4.6 version. >> >>>> >> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas < >> arnaudgelas at gmail.com> >> >>>> wrote: >> >>>>> >> >>>>> Hi all, >> >>>>> >> >>>>> I have been looking at the following wiki example: >> >>>>> >> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >> >>>>> >> >>>>> It seems to me that the section to rescale the image is not valid >> >>>>> anymore with latest ITK version (?) >> >>>>> >> >>>>> >> >>>>> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >> >>>>> >> >>>>> Can anyone confirm? >> >>>>> >> >>>>> Is this code validated? are output images compared to input ones in >> the >> >>>>> corresponding test? >> >>>>> >> >>>>> Thanks >> >>>>> Arnaud >> >>>>> >> >>>>> _____________________________________ >> >>>>> Powered by www.kitware.com >> >>>>> >> >>>>> Visit other Kitware open-source projects at >> >>>>> http://www.kitware.com/opensource/opensource.html >> >>>>> >> >>>>> Kitware offers ITK Training Courses, for more information visit: >> >>>>> http://www.kitware.com/products/protraining.php >> >>>>> >> >>>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>>> >> >>>>> Follow this link to subscribe/unsubscribe: >> >>>>> http://public.kitware.com/mailman/listinfo/insight-users >> >>>>> >> >>>> >> >>>> >> >>>> _____________________________________ >> >>>> Powered by www.kitware.com >> >>>> >> >>>> Visit other Kitware open-source projects at >> >>>> http://www.kitware.com/opensource/opensource.html >> >>>> >> >>>> Kitware offers ITK Training Courses, for more information visit: >> >>>> http://www.kitware.com/products/protraining.php >> >>>> >> >>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>> >> >>>> Follow this link to subscribe/unsubscribe: >> >>>> http://public.kitware.com/mailman/listinfo/insight-users >> >>>> >> >>>> >> >>> >> >>> >> >> >> >> >> >> _____________________________________ >> >> Powered by www.kitware.com >> >> >> >> Visit other Kitware open-source projects at >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> http://www.kitware.com/products/protraining.php >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> > >> > >> > >> > -- >> > Unpaid intern in BillsBasement at noware dot com >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From joel.schaerer at laposte.net Thu Sep 18 08:19:52 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 18 Sep 2014 14:19:52 +0200 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: References: <541848B5.9060901@laposte.net> Message-ID: <541ACDE8.4080508@laposte.net> Hi Matt, I just sent you a github pull request: https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2 Note that I ditched my old fork and started with a clean clone of the template. Jo?l On 09/16/2014 07:26 PM, Matt McCormick wrote: > Hi Jo?l, > > Yes, that the current best repository, and fixes are welcome! Please > add a pull request on the repository and ping the mailing list if it > is not merged after a few days. > > Thanks, > Matt > > On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer > wrote: >> Hi all, >> >> The template for Insight Journal submissions that is available on GitHub and >> recommended on the Insight Journal website >> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) does >> not build with ITK4. >> >> I can try to fix it, but before I do I would like to make sure it is still >> the current version? >> >> Thanks! >> >> Jo?l >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 18 09:02:44 2014 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 18 Sep 2014 13:02:44 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , Message-ID: Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From matt.mccormick at kitware.com Thu Sep 18 13:02:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Sep 2014 13:02:55 -0400 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Hi Arnaud, Great to hear it is working! Yes, good idea on the migration guide to better communicate and explain the development. Here is a patch to review. http://review.source.kitware.com/#/c/17098/ Thanks, Matt On Thu, Sep 18, 2014 at 2:43 AM, Arnaud Gelas wrote: > Matt, > > I guess there should be migration report for this fix? > > Arnaud > > On Thu, Sep 18, 2014 at 8:36 AM, Arnaud Gelas wrote: >> >> Hi Matt, >> >> This is indeed the observed and, based on your answer, expected behaviour. >> Thank you very much for the confirmation (that's exactly what I needed!). >> >> To avoid confusion in future, I am going to modify the corresponding >> example on github and on the wiki! >> >> Best, >> Arnaud >> >> On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick >> wrote: >>> >>> Hi, >>> >>> Do to this fix [1], if the writer is re-using the GDCMImageIO, the >>> writer should apply the inverse rescale / slope intercept like the >>> reader applied the rescale / slope intercept when reading. This was a >>> long-standing bug that I fixed in 4.6.0. Arnaud, if the manual >>> inverse rescale / slope operation is removed, does the correct output >>> result? >>> >>> Thanks, >>> Matt >>> >>> [1] >>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>> On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen >>> wrote: >>> > I wrote this example many years ago? >>> > 1) If the input has a non-trivial slope/intercept, the reader applies >>> > the slope/intercept to the raw data. >>> > 2) Rather than setting the slope/intercept in the output dicom, I >>> > apply the inverse of of the slope intercept to the resampled data >>> > before writing. The output dicom should not have the origin >>> > slope/intercept tags. >>> > >>> > I'll try to verify this with Slicer, but I may be out of touch for 2 >>> > weeks? >>> > >>> > Bill >>> > >>> > >>> > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas >>> > wrote: >>> >> Hi Nick, >>> >> >>> >> I can confirm that with the example I get a difference of -1024 (+/- >>> >> 1) in >>> >> between the input and the output, using the ShiftScaleImage part... >>> >> While without this part of code the difference is (+/-1) >>> >> >>> >> I would like to make sure this is the expected behaviour!? >>> >> >>> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson >>> >> >>> >> wrote: >>> >>> >>> >>> OK, I will wait to hear the outcome of your run with the original >>> >>> example >>> >>> then. >>> >>> >>> >>> Cheers, Nick. >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: >>> >>> >>> >>> Nick, >>> >>> >>> >>> I can't roll back to previous ITK version, important patches on >>> >>> itkGDCMImageIO were very recently merged... >>> >>> >>> >>> >>> >>> >>> >>> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx >>> >>> >>> >>> e.g. >>> >>> >>> >>> >>> >>> >>> >>> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 >>> >>> >>> >>> >>> >>> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c >>> >>> >>> >>> >>> >>> Arnaud >>> >>> >>> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson >>> >>> wrote: >>> >>>> >>> >>>> I should also mention Arnauld that I use ITK4.5.2. I have had many >>> >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled >>> >>>> back to >>> >>>> ITK4.5.2. >>> >>>> Nick. >>> >>>> >>> >>>> >>> >>>> >>> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas >>> >>>> wrote: >>> >>>> >>> >>>> Hi Matias, >>> >>>> >>> >>>> I guess you are referring to >>> >>>> >>> >>>> >>> >>>> >>> >>>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>>> >>> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>>> v4.6.0 >>> >>>> >>> >>>> I use the release branch of ITK >>> >>>> >>> >>>> --- >>> >>>> >>> >>>> Matt, >>> >>>> >>> >>>> Can you comment on this, please? >>> >>>> >>> >>>> Thanks >>> >>>> Arnaud >>> >>>> >>> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull >>> >>>> wrote: >>> >>>> >>> >>>> I had an issue with the resampledicom example once (all my pixel >>> >>>> values >>> >>>> were recalculated by adding rescaleintercept) and then downloaded >>> >>>> the latest >>> >>>> ITK release (4.6) and worked fine. >>> >>>> >>> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow >>> >>>> in >>> >>>> the 4.6 version. >>> >>>> >>> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas >>> >>>> >>> >>>> wrote: >>> >>>>> >>> >>>>> Hi all, >>> >>>>> >>> >>>>> I have been looking at the following wiki example: >>> >>>>> >>> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>> >>>>> >>> >>>>> It seems to me that the section to rescale the image is not valid >>> >>>>> anymore with latest ITK version (?) >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>> >>>>> >>> >>>>> Can anyone confirm? >>> >>>>> >>> >>>>> Is this code validated? are output images compared to input ones in >>> >>>>> the >>> >>>>> corresponding test? >>> >>>>> >>> >>>>> Thanks >>> >>>>> Arnaud >>> >>>>> >>> >>>>> _____________________________________ >>> >>>>> Powered by www.kitware.com >>> >>>>> >>> >>>>> Visit other Kitware open-source projects at >>> >>>>> http://www.kitware.com/opensource/opensource.html >>> >>>>> >>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>> >>>>> http://www.kitware.com/products/protraining.php >>> >>>>> >>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>> >>>>> http://www.itk.org/Wiki/ITK_FAQ >>> >>>>> >>> >>>>> Follow this link to subscribe/unsubscribe: >>> >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>>>> >>> >>>> >>> >>>> >>> >>>> _____________________________________ >>> >>>> Powered by www.kitware.com >>> >>>> >>> >>>> Visit other Kitware open-source projects at >>> >>>> http://www.kitware.com/opensource/opensource.html >>> >>>> >>> >>>> Kitware offers ITK Training Courses, for more information visit: >>> >>>> http://www.kitware.com/products/protraining.php >>> >>>> >>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>> >>>> http://www.itk.org/Wiki/ITK_FAQ >>> >>>> >>> >>>> Follow this link to subscribe/unsubscribe: >>> >>>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>>> >>> >>>> >>> >>> >>> >>> >>> >> >>> >> >>> >> _____________________________________ >>> >> Powered by www.kitware.com >>> >> >>> >> Visit other Kitware open-source projects at >>> >> http://www.kitware.com/opensource/opensource.html >>> >> >>> >> Kitware offers ITK Training Courses, for more information visit: >>> >> http://www.kitware.com/products/protraining.php >>> >> >>> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> http://www.itk.org/Wiki/ITK_FAQ >>> >> >>> >> Follow this link to subscribe/unsubscribe: >>> >> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >>> > >>> > >>> > >>> > -- >>> > Unpaid intern in BillsBasement at noware dot com >>> > _____________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://www.kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >> > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Sep 18 13:03:57 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Sep 2014 13:03:57 -0400 Subject: [ITK] [ITK-users] Mask in metric calculation In-Reply-To: References: Message-ID: Hi Lianli, Could you please specify in greater detail which metric class you are using and how the masks are being applied. Thanks, Matt On Wed, Sep 17, 2014 at 9:54 PM, Lianli Liu wrote: > Hi all, > > I just wonder if I define two masks for fixed image and moving image that > are of differnt size, will voxels that fall in both the masks will > contribute to metric calculation? Thanks! > > Regards, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Sep 18 14:58:39 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Sep 2014 14:58:39 -0400 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: <541ACDE8.4080508@laposte.net> References: <541848B5.9060901@laposte.net> <541ACDE8.4080508@laposte.net> Message-ID: Thanks, merged! Should the other pull request be closed? On Thu, Sep 18, 2014 at 8:19 AM, Jo?l Schaerer wrote: > Hi Matt, > > I just sent you a github pull request: > > https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2 > > Note that I ditched my old fork and started with a clean clone of the > template. > > Jo?l > > > > On 09/16/2014 07:26 PM, Matt McCormick wrote: >> >> Hi Jo?l, >> >> Yes, that the current best repository, and fixes are welcome! Please >> add a pull request on the repository and ping the mailing list if it >> is not merged after a few days. >> >> Thanks, >> Matt >> >> On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer >> wrote: >>> >>> Hi all, >>> >>> The template for Insight Journal submissions that is available on GitHub >>> and >>> recommended on the Insight Journal website >>> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) >>> does >>> not build with ITK4. >>> >>> I can try to fix it, but before I do I would like to make sure it is >>> still >>> the current version? >>> >>> Thanks! >>> >>> Jo?l >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From nikita at iitj.ac.in Thu Sep 18 15:45:34 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Thu, 18 Sep 2014 15:45:34 -0400 Subject: [ITK] [ITK-users] (no subject) Message-ID: Hello Admin I wanted to post this question. I have built the ITK libraries on my computer and I have made new projects using CMake but now I want to integarte my project that includes QT , Opencv and other libs with ITK libs. is there any way by including file paths in Visual Studio 2010 I would be able to use ITK functions. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Thu Sep 18 15:47:33 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 19:47:33 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , , Message-ID: Hi Bradley, I am using your itkTIFFImageIO.cxx. It does not seem to have any effect on the problem I'm having. I will check again that I am really compiling with this fix. I wonder whether the failure to display tiffs with size between 2^31 and 2^32 could be caused by the use of a 'long' somewhere instead of an 'unsigned long'. Just grasping at straws. Best Gib ________________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Friday, 19 September 2014 1:02 a.m. To: Gib Bogle; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From g.bogle at auckland.ac.nz Thu Sep 18 15:50:57 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 19:50:57 +0000 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Many people will tell you that it's much better to use cmake to create your VS projects. Cheers Gib ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Nikita Chopra [nikita at iitj.ac.in] Sent: Friday, 19 September 2014 7:45 a.m. To: Insight-users at itk.org Subject: [ITK-users] (no subject) Hello Admin I wanted to post this question. I have built the ITK libraries on my computer and I have made new projects using CMake but now I want to integarte my project that includes QT , Opencv and other libs with ITK libs. is there any way by including file paths in Visual Studio 2010 I would be able to use ITK functions. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From chinander at gmail.com Thu Sep 18 15:51:22 2014 From: chinander at gmail.com (Mike Chinander) Date: Thu, 18 Sep 2014 14:51:22 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: The easiest way is to use CMake to set up your VS project. Here's Qt's documentation on use CMake with Qt. On Thu, Sep 18, 2014 at 2:45 PM, Nikita Chopra wrote: > Hello Admin > I wanted to post this question. > I have built the ITK libraries on my computer and I have made new > projects using CMake but now I want to integarte my project that includes > QT , Opencv and other libs with ITK libs. is there any way by including > file paths in Visual Studio 2010 I would be able to use ITK functions. > Regards > Nikita > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From chinander at gmail.com Thu Sep 18 15:51:57 2014 From: chinander at gmail.com (Mike Chinander) Date: Thu, 18 Sep 2014 14:51:57 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Here's the link I forgot to include in my previous email: http://qt-project.org/doc/qt-5/cmake-manual.html On Thu, Sep 18, 2014 at 2:51 PM, Mike Chinander wrote: > The easiest way is to use CMake to set up your VS project. Here's Qt's > documentation on use CMake with Qt. > > On Thu, Sep 18, 2014 at 2:45 PM, Nikita Chopra wrote: > >> Hello Admin >> I wanted to post this question. >> I have built the ITK libraries on my computer and I have made new >> projects using CMake but now I want to integarte my project that includes >> QT , Opencv and other libs with ITK libs. is there any way by including >> file paths in Visual Studio 2010 I would be able to use ITK functions. >> Regards >> Nikita >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Thu Sep 18 15:51:56 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 18 Sep 2014 20:51:56 +0100 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi, Just to clarify, you want to use Qt, OpenCV and ITK together in a project. Is that correct? I use OpenCV and ITK together in my projects and use CMake to configure and generate build files for MSVS 2010. Is that something you have tried? On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra wrote: > Hello Admin > I wanted to post this question. > I have built the ITK libraries on my computer and I have made new > projects using CMake but now I want to integarte my project that includes > QT , Opencv and other libs with ITK libs. is there any way by including > file paths in Visual Studio 2010 I would be able to use ITK functions. > Regards > Nikita > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From nikita at iitj.ac.in Thu Sep 18 15:57:30 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Thu, 18 Sep 2014 15:57:30 -0400 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi Thanks a lot for quick responses . Can you suggest me the changes I should make in .pro file to add ITK libs there so I can use qmake to build the project .Thanks again I'm new to ITK and any help would be really appreciated. My .pro file is as follows. # ------------------------------ ------------------- # Project created by QtCreator 2010-10-25T15:08:18 # ------------------------------------------------- QT += opengl TARGET = Endoscopic3D TEMPLATE = app INCLUDEPATH += . \ "C:\Program Files\Matrox Imaging\Mil\Include" LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \ -lmil SOURCES += main.cpp \ mainwindow.cpp \ thread.cpp \ display3d.cpp \ matroxmeteorii.cpp HEADERS += mainwindow.h \ thread.h \ display3d.h \ core.h \ matroxmeteorii.h FORMS += mainwindow.ui On Thu, Sep 18, 2014 at 3:51 PM, Girish Mallya Udupi < indianzeppelin at gmail.com> wrote: > Hi, > > Just to clarify, you want to use Qt, OpenCV and ITK together in a project. > Is that correct? > > I use OpenCV and ITK together in my projects and use CMake to configure > and generate build files for MSVS 2010. Is that something you have tried? > > > On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra wrote: > >> Hello Admin >> I wanted to post this question. >> I have built the ITK libraries on my computer and I have made new >> projects using CMake but now I want to integarte my project that includes >> QT , Opencv and other libs with ITK libs. is there any way by including >> file paths in Visual Studio 2010 I would be able to use ITK functions. >> Regards >> Nikita >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Thu Sep 18 16:07:19 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 18 Sep 2014 21:07:19 +0100 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Never used Qt myself, so can't help you with that. But, have you considered using CMake? There are CMake 'find' modules available for OpenCV, ITK and Qt (from what I see in the link sent by Mike). That same link explains how to use Qt with CMake. On Thu, Sep 18, 2014 at 8:57 PM, Nikita Chopra wrote: > Hi > Thanks a lot for quick responses . Can you suggest me the changes I should > make in .pro file to add ITK libs there so I can use qmake to build the > project .Thanks again I'm new to ITK and any help would be really > appreciated. My .pro file is as follows. > # ------------------------------ > ------------------- > # Project created by QtCreator 2010-10-25T15:08:18 > # ------------------------------------------------- > QT += opengl > TARGET = Endoscopic3D > TEMPLATE = app > INCLUDEPATH += . \ > "C:\Program Files\Matrox Imaging\Mil\Include" > LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \ > -lmil > SOURCES += main.cpp \ > mainwindow.cpp \ > thread.cpp \ > display3d.cpp \ > matroxmeteorii.cpp > HEADERS += mainwindow.h \ > thread.h \ > display3d.h \ > core.h \ > matroxmeteorii.h > FORMS += mainwindow.ui > > On Thu, Sep 18, 2014 at 3:51 PM, Girish Mallya Udupi < > indianzeppelin at gmail.com> wrote: > >> Hi, >> >> Just to clarify, you want to use Qt, OpenCV and ITK together in a >> project. Is that correct? >> >> I use OpenCV and ITK together in my projects and use CMake to configure >> and generate build files for MSVS 2010. Is that something you have tried? >> >> >> On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra wrote: >> >>> Hello Admin >>> I wanted to post this question. >>> I have built the ITK libraries on my computer and I have made new >>> projects using CMake but now I want to integarte my project that includes >>> QT , Opencv and other libs with ITK libs. is there any way by including >>> file paths in Visual Studio 2010 I would be able to use ITK functions. >>> Regards >>> Nikita >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> >> -- >> Regards, >> Girish >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From joel.schaerer at gmail.com Thu Sep 18 16:12:09 2014 From: joel.schaerer at gmail.com (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 18 Sep 2014 22:12:09 +0200 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: References: <541848B5.9060901@laposte.net> <541ACDE8.4080508@laposte.net> Message-ID: <541B3C99.1070503@gmail.com> Done! On 09/18/2014 08:58 PM, Matt McCormick wrote: > Thanks, merged! > > Should the other pull request be closed? > > On Thu, Sep 18, 2014 at 8:19 AM, Jo?l Schaerer > wrote: >> Hi Matt, >> >> I just sent you a github pull request: >> >> https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2 >> >> Note that I ditched my old fork and started with a clean clone of the >> template. >> >> Jo?l >> >> >> >> On 09/16/2014 07:26 PM, Matt McCormick wrote: >>> Hi Jo?l, >>> >>> Yes, that the current best repository, and fixes are welcome! Please >>> add a pull request on the repository and ping the mailing list if it >>> is not merged after a few days. >>> >>> Thanks, >>> Matt >>> >>> On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer >>> wrote: >>>> Hi all, >>>> >>>> The template for Insight Journal submissions that is available on GitHub >>>> and >>>> recommended on the Insight Journal website >>>> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) >>>> does >>>> not build with ITK4. >>>> >>>> I can try to fix it, but before I do I would like to make sure it is >>>> still >>>> the current version? >>>> >>>> Thanks! >>>> >>>> Jo?l >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >> > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 18 16:32:19 2014 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 18 Sep 2014 20:32:19 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , , , Message-ID: Gib, I have continued to work on refactoring ITK's TIFFImageIO, fixing some bugs along the way: http://review.source.kitware.com/#/c/17111/ If you have some specific images that are problematic, it would be good if you could run "tiffinfo"[1] on them to look at the tags or provide a copy of them. Thanks, Brad [1] http://www.libtiff.org/tools.html ________________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Thursday, September 18, 2014 3:47 PM To: Lowekamp, Bradley (NIH/NLM/LHC) [C]; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hi Bradley, I am using your itkTIFFImageIO.cxx. It does not seem to have any effect on the problem I'm having. I will check again that I am really compiling with this fix. I wonder whether the failure to display tiffs with size between 2^31 and 2^32 could be caused by the use of a 'long' somewhere instead of an 'unsigned long'. Just grasping at straws. Best Gib ________________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Friday, 19 September 2014 1:02 a.m. To: Gib Bogle; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From chinander at gmail.com Thu Sep 18 16:46:51 2014 From: chinander at gmail.com (Mike Chinander) Date: Thu, 18 Sep 2014 15:46:51 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: A CMakeLists.txt files replaces your .pro project file. Yours would look something like the following. I don't use Qt Designer so I'm not quite sure about the .ui-related configuration (or the OpenGL module). cmake_minimum_required(VERSION 2.8.12) PROJECT(Endoscopic3D) set(CMAKE_AUTOMOC ON) set(CMAKE_INCLUDE_CURRENT_DIR ON) SET(ITK_DIR "C:/Program Files/ITK/lib/cmake/ITK-4.5") FIND_PACKAGE(Qt5Core REQUIRED ) FIND_PACKAGE(Qt5Widgets REQUIRED) FIND_PACKAGE(Qt5OpenGL REQUIRED) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) include_directories (${CMAKE_CURRENT_BINARY_DIR}) SET (SRCS main.cpp mainwindow.cpp thread.cpp display3d.cpp matroxmeteorii.cpp) SET (MOC_SRCS mainwindow.h thread.h display3d.h core.h matroxmeteorii.h) QT5_WRAP_UI(UIS_HDRS mainwindow.ui) ADD_EXECUTABLE(Endoscopic3D WIN32 ${SRCS} ${UIS_HDRS} ) TARGET_LINK_LIBRARIES(Endoscopic3D Qt5::Widgets Qt5::OpenGL ${ITK_LIBRARIES}) On Thu, Sep 18, 2014 at 2:57 PM, Nikita Chopra wrote: > Hi > Thanks a lot for quick responses . Can you suggest me the changes I should > make in .pro file to add ITK libs there so I can use qmake to build the > project .Thanks again I'm new to ITK and any help would be really > appreciated. My .pro file is as follows. > # ------------------------------ > ------------------- > # Project created by QtCreator 2010-10-25T15:08:18 > # ------------------------------------------------- > QT += opengl > TARGET = Endoscopic3D > TEMPLATE = app > INCLUDEPATH += . \ > "C:\Program Files\Matrox Imaging\Mil\Include" > LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \ > -lmil > SOURCES += main.cpp \ > mainwindow.cpp \ > thread.cpp \ > display3d.cpp \ > matroxmeteorii.cpp > HEADERS += mainwindow.h \ > thread.h \ > display3d.h \ > core.h \ > matroxmeteorii.h > FORMS += mainwindow.ui > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Thu Sep 18 17:13:11 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 21:13:11 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , , Message-ID: Hi Bradley, To be completely safe, I'd like to know exactly what steps I should follow to get the changes you've made. 1. Edit Superbuild/External_ITKv4.cmake: modify the repository to: git://itk.org/ITK.git change the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c 2. ... Thanks Gib ________________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Friday, 19 September 2014 1:02 a.m. To: Gib Bogle; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From g.bogle at auckland.ac.nz Fri Sep 19 01:26:27 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Fri, 19 Sep 2014 05:26:27 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , , Message-ID: Hi Bradley, I made that change to the cmake file, and rebuilt Slicer. The situation is unchanged - tiff files in the size range 2^31 - 2^32 load but do not display. Gib ________________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Friday, 19 September 2014 1:02 a.m. To: Gib Bogle; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From blowekamp at mail.nih.gov Fri Sep 19 09:37:40 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 19 Sep 2014 09:37:40 -0400 Subject: [ITK] [ITK-dev] ITK Gerrit Primer Message-ID: I just stumbled on this wiki web page ( it actually was a paraview url initially ): http://www.itk.org/Wiki/ITK/Gerrit/ReviewPrimer I don't recall seeing it before, it looks like it has some good detailed information in it about how to use gerrit and do reviews. Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From norman-k-williams at uiowa.edu Fri Sep 19 10:14:01 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 19 Sep 2014 14:14:01 +0000 Subject: [ITK] [ITK-dev] The fix for patch in which I torpedoed the Release build nightlies Message-ID: Je suis plus d?sol?e! I typed ?/ *? instead of ?/*? and if NDEBUG is set, it?s a compiler error every time vml_vector_fixed_ref.h is included, compilers get mad. http://review.source.kitware.com/#/c/17126/ ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From hiner at wisc.edu Fri Sep 19 11:09:13 2014 From: hiner at wisc.edu (Mark Hiner) Date: Fri, 19 Sep 2014 10:09:13 -0500 Subject: [ITK] [ITK-dev] SCIFIO nightly build e-mail Message-ID: Hello ITK developers, Would it be possible to add imagej-builds at imagej.net to get build failure notifications for the SCIFIO nightly build ? I didn't realize that I had broken the build a couple days ago. Much appreciated! Regards, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From g.bogle at auckland.ac.nz Sat Sep 20 02:30:53 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sat, 20 Sep 2014 06:30:53 +0000 Subject: [ITK] Question about BigTIFF Message-ID: I observe that an ITK-created tiff that is bigger than 2^31 but smaller than 2^32 is a BigTIFF - it has Version number = 43 in the header. I am suddenly wondering why such a file is a BigTIFF. On this site: http://www.awaresystems.be/imaging/tiff/bigtiff.html it says: "The TIFF file format uses 32bit offsets and, as such, is limited to 4 gigabytes. This has been quite sufficient for many years. Today however, there is a need for a good multi-purpose open image file format that can handle huge images, or very large collections of images, breaking the 4 gig boundary. There is currently an ongoing attempt to launch a new variant of TIFF, called BigTIFF, that closely resembles TIFF, but uses 64bit offsets instead...." In other words, BigTIFF is needed for files bigger than 2^32 bytes, or 4 GB. Can somebody explain this? Cheers Gib -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Sat Sep 20 12:09:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 20 Sep 2014 12:09:55 -0400 Subject: [ITK] Question about BigTIFF In-Reply-To: References: Message-ID: Hi Gib, It should be a BigTIFF and it is, correct? Thanks for your investigations. Matt On Sat, Sep 20, 2014 at 2:30 AM, Gib Bogle wrote: > I observe that an ITK-created tiff that is bigger than 2^31 but smaller than > 2^32 is a BigTIFF - it has Version number = 43 in the header. I am suddenly > wondering why such a file is a BigTIFF. On this site: > http://www.awaresystems.be/imaging/tiff/bigtiff.html > it says: > "The TIFF file format uses 32bit offsets and, as such, is limited to 4 > gigabytes. This has been quite sufficient for many years. Today however, > there is a need for a good multi-purpose open image file format that can > handle huge images, or very large collections of images, breaking the 4 gig > boundary. There is currently an ongoing attempt to launch a new variant of > TIFF, called BigTIFF, that closely resembles TIFF, but uses 64bit offsets > instead...." > > In other words, BigTIFF is needed for files bigger than 2^32 bytes, or 4 GB. > > Can somebody explain this? > > Cheers > Gib > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From g.bogle at auckland.ac.nz Sat Sep 20 15:24:18 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sat, 20 Sep 2014 19:24:18 +0000 Subject: [ITK] Question about BigTIFF In-Reply-To: References: , Message-ID: Hi Matt, The file big1300.tif, which is just bigger than 2^31, is a BigTIFF. I'm just wondering why, since strictly speaking the BigTIFF format is needed for files > 2^32. This is now academic, I think, since it appears that Slicer is reading this file correctly, and the question is why it is not being displayed. Best Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Sunday, 21 September 2014 4:09 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] Question about BigTIFF Hi Gib, It should be a BigTIFF and it is, correct? Thanks for your investigations. Matt On Sat, Sep 20, 2014 at 2:30 AM, Gib Bogle wrote: > I observe that an ITK-created tiff that is bigger than 2^31 but smaller than > 2^32 is a BigTIFF - it has Version number = 43 in the header. I am suddenly > wondering why such a file is a BigTIFF. On this site: > http://www.awaresystems.be/imaging/tiff/bigtiff.html > it says: > "The TIFF file format uses 32bit offsets and, as such, is limited to 4 > gigabytes. This has been quite sufficient for many years. Today however, > there is a need for a good multi-purpose open image file format that can > handle huge images, or very large collections of images, breaking the 4 gig > boundary. There is currently an ongoing attempt to launch a new variant of > TIFF, called BigTIFF, that closely resembles TIFF, but uses 64bit offsets > instead...." > > In other words, BigTIFF is needed for files bigger than 2^32 bytes, or 4 GB. > > Can somebody explain this? > > Cheers > Gib > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From g.bogle at auckland.ac.nz Sun Sep 21 18:45:23 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sun, 21 Sep 2014 22:45:23 +0000 Subject: [ITK] BigTIFF and tiffinfo Message-ID: The saga continues... I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has revealed a problem with the tiff files built using the ITK that Slicer has created. This version was pulled using this cmake line: set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # slicer-v4.6.0-2014-09-19-056d97b When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: ... TIFF Directory at offset 0x7fd0fcf4 (2144402676) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1265-1300 Software: InsightToolkit TIFF Directory at offset 0x7fead588 (2146096520) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1266-1300 Software: InsightToolkit TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. TIFFReadDirectory: Failed to read directory at offset 2147790364. There is no problem with the compressed version of the image. This has added to my confusion. A program built with the same ITK library can read this file, raising the possibility that it is tiffinfo itself that can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo using Win64. And Vaa3D also gets this seek error when reading the file. Any ideas? Gib PS It is probably totally irrelevant to the tiff issue, but I happened to notice that there are a few occurrences in other places of checks for _WIN64, which is not defined. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Sun Sep 21 20:21:42 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 22 Sep 2014 00:21:42 +0000 Subject: [ITK] BigTIFF and tiffinfo In-Reply-To: References: Message-ID: Followup: I ran tiffdump on this file, and surprisngly it was able to read to the end of the file, and all the offsets look fine. So it seems that tiffinfo is at fault - very strange since one would expect that tiffdump and tiffinfo would use identical methods. More tiff strangeness... ________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 22 September 2014 10:45 a.m. To: community at itk.org Subject: [ITK] BigTIFF and tiffinfo The saga continues... I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has revealed a problem with the tiff files built using the ITK that Slicer has created. This version was pulled using this cmake line: set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # slicer-v4.6.0-2014-09-19-056d97b When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: ... TIFF Directory at offset 0x7fd0fcf4 (2144402676) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1265-1300 Software: InsightToolkit TIFF Directory at offset 0x7fead588 (2146096520) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1266-1300 Software: InsightToolkit TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. TIFFReadDirectory: Failed to read directory at offset 2147790364. There is no problem with the compressed version of the image. This has added to my confusion. A program built with the same ITK library can read this file, raising the possibility that it is tiffinfo itself that can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo using Win64. And Vaa3D also gets this seek error when reading the file. Any ideas? Gib PS It is probably totally irrelevant to the tiff issue, but I happened to notice that there are a few occurrences in other places of checks for _WIN64, which is not defined. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Sun Sep 21 21:57:01 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 22 Sep 2014 01:57:01 +0000 Subject: [ITK] BigTIFF and tiffinfo In-Reply-To: References: , Message-ID: Something cleared up (sort of): I discovered that while the ITK build of the itktiff project links tif_win32.c, the tiff-4.0.3 build was not linking this file. It turns out that this is controlled by a build option in nmake.opt: # # Uncomment following line to enable using Windows Common RunTime Library # instead of Windows specific system calls. See notes on top of tif_unix.c # module for details. # #USE_WIN_CRT_LIB = 1 # Gib commented this When I commented out this line and rebuilt libtiff, tiffinfo no longer fails at the 2 GB boundary. I don't understand what it's about, but it does resolve that mystery. Gib ________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 22 September 2014 12:21 p.m. To: community at itk.org Subject: Re: [ITK] BigTIFF and tiffinfo Followup: I ran tiffdump on this file, and surprisngly it was able to read to the end of the file, and all the offsets look fine. So it seems that tiffinfo is at fault - very strange since one would expect that tiffdump and tiffinfo would use identical methods. More tiff strangeness... ________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 22 September 2014 10:45 a.m. To: community at itk.org Subject: [ITK] BigTIFF and tiffinfo The saga continues... I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has revealed a problem with the tiff files built using the ITK that Slicer has created. This version was pulled using this cmake line: set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # slicer-v4.6.0-2014-09-19-056d97b When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: ... TIFF Directory at offset 0x7fd0fcf4 (2144402676) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1265-1300 Software: InsightToolkit TIFF Directory at offset 0x7fead588 (2146096520) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1266-1300 Software: InsightToolkit TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. TIFFReadDirectory: Failed to read directory at offset 2147790364. There is no problem with the compressed version of the image. This has added to my confusion. A program built with the same ITK library can read this file, raising the possibility that it is tiffinfo itself that can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo using Win64. And Vaa3D also gets this seek error when reading the file. Any ideas? Gib PS It is probably totally irrelevant to the tiff issue, but I happened to notice that there are a few occurrences in other places of checks for _WIN64, which is not defined. -------------- next part -------------- An HTML attachment was scrubbed... URL: From llliu at umich.edu Sun Sep 21 22:30:37 2014 From: llliu at umich.edu (Lianli Liu) Date: Sun, 21 Sep 2014 22:30:37 -0400 Subject: [ITK] [ITK-users] B spline multi grid registration Message-ID: Hi all, I am trying to use the B spline multi grid registration method in ITK, as given by the example code deformableregistration7.cxx. I used to 3D MRI images in analyze format (.img). I received the following error information: terminate called after throwing an instance of 'std::bad_alloc' I was wondering what is wrong and how to fix it? Thanks! Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From nikita at iitj.ac.in Sun Sep 21 22:44:38 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Sun, 21 Sep 2014 22:44:38 -0400 Subject: [ITK] [ITK-users] B spline multi grid registration In-Reply-To: References: Message-ID: Did you tr to debug it , Can you share the specific line in code where the error occurs ? I have used the same example to register CT scans with slight modification. On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu wrote: > Hi all, > > I am trying to use the B spline multi grid registration method in ITK, as > given by the example code deformableregistration7.cxx. I used to 3D MRI > images in analyze format (.img). I received the following error information: > > terminate called after throwing an instance of 'std::bad_alloc' > > I was wondering what is wrong and how to fix it? > > Thanks! > > Lianli > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sun Sep 21 22:54:25 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 21 Sep 2014 22:54:25 -0400 Subject: [ITK] BigTIFF and tiffinfo In-Reply-To: References: Message-ID: Hi Gib, Thanks for sharing the information. A good program to validate TIFF behavior would be FIJI [1], whose primary image format is TIFF's. HTH, Matt [1] http://fiji.sc/wiki/index.php/Fiji On Sun, Sep 21, 2014 at 9:57 PM, Gib Bogle wrote: > Something cleared up (sort of): I discovered that while the ITK build of > the itktiff project links tif_win32.c, the tiff-4.0.3 build was not linking > this file. It turns out that this is controlled by a build option in > nmake.opt: > > # > # Uncomment following line to enable using Windows Common RunTime Library > # instead of Windows specific system calls. See notes on top of tif_unix.c > # module for details. > # > #USE_WIN_CRT_LIB = 1 # Gib commented this > > When I commented out this line and rebuilt libtiff, tiffinfo no longer fails > at the 2 GB boundary. I don't understand what it's about, but it does > resolve that mystery. > > Gib > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 22 September 2014 12:21 p.m. > To: community at itk.org > Subject: Re: [ITK] BigTIFF and tiffinfo > > Followup: I ran tiffdump on this file, and surprisngly it was able to read > to the end of the file, and all the offsets look fine. So it seems that > tiffinfo is at fault - very strange since one would expect that tiffdump and > tiffinfo would use identical methods. More tiff strangeness... > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 22 September 2014 10:45 a.m. > To: community at itk.org > Subject: [ITK] BigTIFF and tiffinfo > > The saga continues... > > I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has > revealed a problem with the tiff files built using the ITK that Slicer has > created. This version was pulled using this cmake line: > set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # > slicer-v4.6.0-2014-09-19-056d97b > > When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger > than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: > > ... > TIFF Directory at offset 0x7fd0fcf4 (2144402676) > Subfile Type: multi-page document (2 = 0x2) > Image Width: 1300 Image Length: 1300 > Resolution: 25.4, 25.4 pixels/inch > Bits/Sample: 8 > Compression Scheme: None > Photometric Interpretation: min-is-black > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 6 > Planar Configuration: single image plane > Page Number: 1265-1300 > Software: InsightToolkit > TIFF Directory at offset 0x7fead588 (2146096520) > Subfile Type: multi-page document (2 = 0x2) > Image Width: 1300 Image Length: 1300 > Resolution: 25.4, 25.4 pixels/inch > Bits/Sample: 8 > Compression Scheme: None > Photometric Interpretation: min-is-black > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 6 > Planar Configuration: single image plane > Page Number: 1266-1300 > Software: InsightToolkit > TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. > TIFFReadDirectory: Failed to read directory at offset 2147790364. > > There is no problem with the compressed version of the image. > > This has added to my confusion. A program built with the same ITK library > can read this file, raising the possibility that it is tiffinfo itself that > can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo > using Win64. And Vaa3D also gets this seek error when reading the file. > > Any ideas? > > Gib > > PS It is probably totally irrelevant to the tiff issue, but I happened to > notice that there are a few occurrences in other places of checks for > _WIN64, which is not defined. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Sun Sep 21 22:58:59 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 21 Sep 2014 22:58:59 -0400 Subject: [ITK] [ITK-users] B spline multi grid registration In-Reply-To: References: Message-ID: Hi Lianli, On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu wrote: > Hi all, > > I am trying to use the B spline multi grid registration method in ITK, as > given by the example code deformableregistration7.cxx. I used to 3D MRI > images in analyze format (.img). I received the following error information: > > terminate called after throwing an instance of 'std::bad_alloc' > > I was wondering what is wrong and how to fix it? Are you running out of memory? HTH, Matt _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Sun Sep 21 23:01:28 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 22 Sep 2014 03:01:28 +0000 Subject: [ITK] BigTIFF and tiffinfo In-Reply-To: References: , Message-ID: Hi Matt, Yes, I checked a while ago that Fiji can read these images. The issue with tiffinfo had me worried, because that's straight from the horse's mouth, so to speak. Knowing about that build option puts my mind at rest. I still need to find out the cause of Slicer's bizarre behaviour, which I don't expect to be related to this issue. I have also been trying to get Vaa3D to read the BigTIFFs. Using the experience with tiffinfo, I've just succeeded in building an executable that works OK. Cheers Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Monday, 22 September 2014 2:54 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] BigTIFF and tiffinfo Hi Gib, Thanks for sharing the information. A good program to validate TIFF behavior would be FIJI [1], whose primary image format is TIFF's. HTH, Matt [1] http://fiji.sc/wiki/index.php/Fiji On Sun, Sep 21, 2014 at 9:57 PM, Gib Bogle wrote: > Something cleared up (sort of): I discovered that while the ITK build of > the itktiff project links tif_win32.c, the tiff-4.0.3 build was not linking > this file. It turns out that this is controlled by a build option in > nmake.opt: > > # > # Uncomment following line to enable using Windows Common RunTime Library > # instead of Windows specific system calls. See notes on top of tif_unix.c > # module for details. > # > #USE_WIN_CRT_LIB = 1 # Gib commented this > > When I commented out this line and rebuilt libtiff, tiffinfo no longer fails > at the 2 GB boundary. I don't understand what it's about, but it does > resolve that mystery. > > Gib > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 22 September 2014 12:21 p.m. > To: community at itk.org > Subject: Re: [ITK] BigTIFF and tiffinfo > > Followup: I ran tiffdump on this file, and surprisngly it was able to read > to the end of the file, and all the offsets look fine. So it seems that > tiffinfo is at fault - very strange since one would expect that tiffdump and > tiffinfo would use identical methods. More tiff strangeness... > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 22 September 2014 10:45 a.m. > To: community at itk.org > Subject: [ITK] BigTIFF and tiffinfo > > The saga continues... > > I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has > revealed a problem with the tiff files built using the ITK that Slicer has > created. This version was pulled using this cmake line: > set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # > slicer-v4.6.0-2014-09-19-056d97b > > When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger > than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: > > ... > TIFF Directory at offset 0x7fd0fcf4 (2144402676) > Subfile Type: multi-page document (2 = 0x2) > Image Width: 1300 Image Length: 1300 > Resolution: 25.4, 25.4 pixels/inch > Bits/Sample: 8 > Compression Scheme: None > Photometric Interpretation: min-is-black > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 6 > Planar Configuration: single image plane > Page Number: 1265-1300 > Software: InsightToolkit > TIFF Directory at offset 0x7fead588 (2146096520) > Subfile Type: multi-page document (2 = 0x2) > Image Width: 1300 Image Length: 1300 > Resolution: 25.4, 25.4 pixels/inch > Bits/Sample: 8 > Compression Scheme: None > Photometric Interpretation: min-is-black > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 6 > Planar Configuration: single image plane > Page Number: 1266-1300 > Software: InsightToolkit > TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. > TIFFReadDirectory: Failed to read directory at offset 2147790364. > > There is no problem with the compressed version of the image. > > This has added to my confusion. A program built with the same ITK library > can read this file, raising the possibility that it is tiffinfo itself that > can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo > using Win64. And Vaa3D also gets this seek error when reading the file. > > Any ideas? > > Gib > > PS It is probably totally irrelevant to the tiff issue, but I happened to > notice that there are a few occurrences in other places of checks for > _WIN64, which is not defined. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From llliu at umich.edu Sun Sep 21 23:13:09 2014 From: llliu at umich.edu (Lianli Liu) Date: Sun, 21 Sep 2014 23:13:09 -0400 Subject: [ITK] [ITK-users] B spline multi grid registration In-Reply-To: References: Message-ID: Hi all, Thanks for help. The program runs after I change the metric from mean square error to mutual information. But the new problem is the transformed image looks really wired. Seems the intensity is distorted a lot. I was wondering what may be the possible cause of this? Regards, Lianli On Sun, Sep 21, 2014 at 10:58 PM, Matt McCormick wrote: > Hi Lianli, > > On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu wrote: > > Hi all, > > > > I am trying to use the B spline multi grid registration method in ITK, as > > given by the example code deformableregistration7.cxx. I used to 3D MRI > > images in analyze format (.img). I received the following error > information: > > > > terminate called after throwing an instance of 'std::bad_alloc' > > > > I was wondering what is wrong and how to fix it? > > Are you running out of memory? > > HTH, > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From vijayarani.shanmugavadivu at appasamy.com Mon Sep 22 07:52:36 2014 From: vijayarani.shanmugavadivu at appasamy.com (vijayarani) Date: Mon, 22 Sep 2014 04:52:36 -0700 (PDT) Subject: [ITK] [ITK-users] Picking 10000 samples from a larger mha image using ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram. Message-ID: <1411386756138-7586255.post@n2.nabble.com> Hi I tried to pick 10000 samples from a larger mha image (which size is 167 MB) using ImageRandomNonRepeatingConstIteratorWithIndex class and tried to find the histogram and percentile values for the resultant image. However it gives 0 to all the percentiles. When I do the same for a small image it gives the valid percentile values.How to achieve finding histogram and percentiles for a larger mha image by picking up only 10000 samples from the original image? Thanks & Regards Vijaya Rani S -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Mon Sep 22 09:08:11 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 22 Sep 2014 09:08:11 -0400 Subject: [ITK] [ITK-users] Picking 10000 samples from a larger mha image using ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram. In-Reply-To: <1411386756138-7586255.post@n2.nabble.com> References: <1411386756138-7586255.post@n2.nabble.com> Message-ID: Hello, Do you have a small compilable example of this problem? It's really impossible to give specific information without any code. The most frequent reason for this type of issue is that the Update method to the reader has not been called before a manual iteration over the image. So the size of the image is zero during iteration. Brad On Sep 22, 2014, at 7:52 AM, vijayarani wrote: > Hi > I tried to pick 10000 samples from a larger mha image (which size is 167 MB) > using ImageRandomNonRepeatingConstIteratorWithIndex class and tried to find > the histogram and percentile > values for the resultant image. However it gives 0 to all the percentiles. > When I do the same for a small image it gives the valid percentile > values.How to achieve finding histogram and percentiles for a larger mha > image by picking up only 10000 samples from the original image? > > Thanks & Regards > Vijaya Rani S > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From genet at biomed.ee.ethz.ch Mon Sep 22 15:49:25 2014 From: genet at biomed.ee.ethz.ch (Martin Genet) Date: Mon, 22 Sep 2014 21:49:25 +0200 Subject: [ITK] [ITK-users] FEMRegistration Message-ID: <54207D45.9070409@biomed.ee.ethz.ch> Dear all: Trying to use FEMRegistration on a bunch of images. Still trying to figure out the following: - What is the simplest way to convert an external mesh (e.g., vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and vice versa (for post-treatment, vizualization)? - If the mesh covers only a subset of the image, what happens to the rest of the image? Any help would be super appreciated. Sorry if that's too trivial. Thanks in advance. Martin _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Sep 22 16:54:40 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 Sep 2014 16:54:40 -0400 Subject: [ITK] [ITK-users] FEMRegistration In-Reply-To: <54207D45.9070409@biomed.ee.ethz.ch> References: <54207D45.9070409@biomed.ee.ethz.ch> Message-ID: Hi Martin, itk::MeshFileReader and itk::MeshFileWriter are great classes for importing / exporting meshes. HTH, Matt On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet wrote: > Dear all: > > Trying to use FEMRegistration on a bunch of images. Still trying to figure > out the following: > > - What is the simplest way to convert an external mesh (e.g., > vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and vice > versa (for post-treatment, vizualization)? > > - If the mesh covers only a subset of the image, what happens to the rest > of the image? > > Any help would be super appreciated. Sorry if that's too trivial. Thanks in > advance. > > Martin > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From vijayarani.shanmugavadivu at appasamy.com Tue Sep 23 02:10:56 2014 From: vijayarani.shanmugavadivu at appasamy.com (vijayarani) Date: Mon, 22 Sep 2014 23:10:56 -0700 (PDT) Subject: [ITK] [ITK-users] Picking 10000 samples from a larger mha image using ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram. In-Reply-To: References: <1411386756138-7586255.post@n2.nabble.com> Message-ID: <1411452656592-7586259.post@n2.nabble.com> Hi, Thanks for your reply.Here is my code and the output #include "itkImage.h" #include "itkImageFileReader.h" #include #include #include #include "itkImageFileWriter.h" #include "itkImageRandomNonRepeatingConstIteratorWithIndex.h" int main(int argc, char*argv[]) { const unsigned int Dimension = 3; typedef unsigned short PixelType; typedef itk::Image ImageType; typedef itk::ImageFileReader< ImageType > ImageReaderType; typedef itk::ImageFileWriter< ImageType > ImageWriterType; ImageReaderType::Pointer ImageReader = ImageReaderType::New(); ImageWriterType::Pointer ImageWriter = ImageWriterType::New(); ImageReader->SetFileName( "SampleMha.mha" ); ImageWriter->SetFileName( "RandomIterator.mha" ); ImageType::Pointer Image = ImageReader->GetOutput(); Image->Update(); ImageType::RegionType region=Image->GetRequestedRegion(); ImageType::SizeType size=region.GetSize(); ImageType::IndexType index=region.GetIndex(); ImageType::IndexType start = index; ImageType::SpacingType spacing = Image->GetSpacing(); ImageType::DirectionType direction = Image->GetDirection(); ImageType::RegionType newregion; newregion.SetSize(size); newregion.SetIndex(start); std::cout << "The size of the image is " << size <SetRegions(newregion); output->SetSpacing(spacing); output->SetDirection(direction); output->Allocate(); output->FillBuffer(0); output->Update(); typedef itk::ImageRandomNonRepeatingConstIteratorWithIndex ConstIteratorType; ConstIteratorType inputIt( Image, region ); unsigned int number = 10000; inputIt.SetNumberOfSamples( number ); std::cout << "The number of samples is " << number << std::endl; inputIt.ReinitializeSeed(); inputIt.GoToBegin(); while(!inputIt.IsAtEnd()) { output->SetPixel(inputIt.GetIndex(), inputIt.Get()); ++inputIt; } output->Update(); ImageWriter->SetInput( output ); ImageWriter->Update(); calculatePercentile("RandomIterator.mha"); return EXIT_SUCCESS; } void calculatePercentile(QString file) { qDebug()<<"Calling: calculatePercentile"; //Define the pixel type and dimension for reader typedef int InternalPixelType; const unsigned int Dimension=3; typedef itk::Image InternalImageType; //Define the reader typedef itk::ImageFileReader ReaderType; ReaderType::Pointer reader = ReaderType::New(); typedef InternalPixelType HistogramMeasurementType; typedef itk::Statistics::Histogram< HistogramMeasurementType > HistogramType; typedef itk::Statistics::ImageToListSampleAdaptor< InternalImageType > AdaptorType; AdaptorType::Pointer adaptor = AdaptorType::New(); typedef itk::Statistics::SampleToHistogramFilter FilterType; FilterType::Pointer filter = FilterType::New(); if(QFileInfo(file).suffix()=="mha") { typedef itk::MetaImageIO MetaImageIOType; MetaImageIOType::Pointer metaIO=MetaImageIOType::New(); metaIO->SetFileName(file.toLocal8Bit().data()); reader->SetFileName(file.toLocal8Bit().data()); metaIO->ReadImageInformation(); qDebug()<<"No of dimesnsions "<GetNumberOfDimensions()<<"No of Comps "<GetNumberOfComponents()<<"Comp size "<GetComponentSize(); qDebug()<<"Image size in bytes "<GetImageSizeInBytes()<<"Image size in Comps "<GetImageSizeInComponents()<<"Image size in Pixels "<GetImageSizeInPixels(); adaptor->SetImage(reader->GetOutput() ); try { reader->Update(); } catch( itk::ExceptionObject & excp ) { std::cerr << "Problem reading image file" << std::endl; std::cerr << excp << std::endl; } const unsigned int numberOfComponents = metaIO->GetNumberOfComponents(); HistogramType::SizeType size(numberOfComponents); size.Fill( metaIO->GetImageSizeInPixels() ); filter->SetInput( adaptor ); filter->SetHistogramSize( size ); filter->SetMarginalScale( 10 ); HistogramType::MeasurementVectorType min( numberOfComponents ); HistogramType::MeasurementVectorType max( numberOfComponents ); min.Fill( 0 ); max.Fill( metaIO->GetImageSizeInComponents() ); filter->SetHistogramBinMinimum( min ); filter->SetHistogramBinMaximum( max ); filter->Update(); } HistogramType::ConstPointer histogram = filter->GetOutput(); qDebug()<<"5th percentile is "<< histogram->Quantile( 0, 0.05 ) <<" 25th percentile is "<Quantile( 0, 0.25 )<<" 50th percentile is "<Quantile( 0, 0.50 )<<" 75th percentile is "<Quantile( 0, 0.75 )<<" 95th percentile is "<Quantile( 0, 0.95 ); } And the output is: The size of the image is [650, 450, 300] The number of samples is 10000 Calling: calculatePercentile No of dimesnsions 3 No of Comps 1 Comp size 2 Image size in bytes 175500000 Image size in Comps 87750000 Image size in Pixels 87750000 5th percentile is 0 25th percentile is 0 50th percentile is 0 75th percentile is 0 95th percentile is 0 I have uploaded the SampleMha.mha file. Thanks & Regards Vijaya Rani S -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255p7586259.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Tue Sep 23 02:40:01 2014 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Tue, 23 Sep 2014 02:40:01 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: InsightToolkit Kinetic Analysis (itk::ka) Library Message-ID: <20140923064001.A66743D6C194@insightsoftwareconsortium.org> Hello, A new submission has been added to the Insight Journal. Title: InsightToolkit Kinetic Analysis (itk::ka) Library Authors: Dowson N., Baker C., Raffelt D., Smith J., Thomas P., Salvado O., Rose S. Abstract: This paper describes how to compile and use the Insight Toolkit Kinetic Analysis library (itk::ka), to perform analysis of dynamic medical images, along with a brief overview of the library source code. A set of interfaces to facilitate application development (koala) and an application using Powell???s Dogleg optimisation (koalaDogleg) are also supplied, along with some sample data. Only versions of ITK4 and higher are currently supported. Download and review this publication at: http://hdl.handle.net/10380/3469 Generated by the Insight Journal You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://www.insight-journal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From karl.diedrich at azetech.com Tue Sep 23 11:59:22 2014 From: karl.diedrich at azetech.com (Karl Diedrich) Date: Tue, 23 Sep 2014 11:59:22 -0400 Subject: [ITK] [ITK-users] looking for itk:DomainThreader example Message-ID: <542198DA.2070604@azetech.com> Hello, Does anyone know where an example program using the itk::DomainThreader is? There is a missing link [ http://itk.org/ITKExamples/Examples/Core/Common/DoDataParallelThreading/DoDataParallelThreading.html ] to an example on an ITKBar camp website here http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/WriteMultiThreadedCode/index.html Thanks, Karl -- Karl Diedrich, Ph.D. Principal Engineer AZE Technology, Inc. 1 Broadway 14th Floor Cambridge, MA 02142, USA Phone: 1-617-475-1502 Fax: 1-617-588-1889 http://www.azetech.com/ _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Sep 23 14:24:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 23 Sep 2014 14:24:11 -0400 Subject: [ITK] [ITK-users] looking for itk:DomainThreader example In-Reply-To: <542198DA.2070604@azetech.com> References: <542198DA.2070604@azetech.com> Message-ID: Hii Karl, The example is here: http://itk.org/ITKExamples/src/Core/Common/DoDataParallelThreading/Documentation.html I have also fixed the link. Thanks, Matt On Tue, Sep 23, 2014 at 11:59 AM, Karl Diedrich wrote: > Hello, > > Does anyone know where an example program using the itk::DomainThreader is? > There is a missing link [ > http://itk.org/ITKExamples/Examples/Core/Common/DoDataParallelThreading/DoDataParallelThreading.html > ] to an example on an ITKBar camp website here > http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/WriteMultiThreadedCode/index.html > > Thanks, > > Karl > > -- > Karl Diedrich, Ph.D. > Principal Engineer > AZE Technology, Inc. > 1 Broadway 14th Floor > Cambridge, MA 02142, USA > Phone: 1-617-475-1502 > Fax: 1-617-588-1889 > http://www.azetech.com/ > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Tue Sep 23 21:51:17 2014 From: llliu at umich.edu (Lianli Liu) Date: Tue, 23 Sep 2014 21:51:17 -0400 Subject: [ITK] [ITK-users] format of mask file Message-ID: Hi all, I am a bit unclear about the format of mask file. Is it fine if I use an image of analyze format that has 0,1 value, but of integer type not boolean type? The reason I am asking is that when I use this mask in the mutual information metric, there is an error : joint PDF summed to zero... Thanks! Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From sebastian.ordas at gmail.com Tue Sep 23 23:26:08 2014 From: sebastian.ordas at gmail.com (Sebastian Ordas) Date: Wed, 24 Sep 2014 00:26:08 -0300 Subject: [ITK] VTK6 migration and vtkImageData: "No scalar values found for texture input!" error in vtkOpenGLTexture Message-ID: <542239D0.7060203@gmail.com> Dear List, I have started getting the error "No scalar values found for texture input!" coming from vtkOpenGLTexture, while porting my code to VTK6 More precisely, I have a vtkImageData, generated by itkImageToVTKImageFilter, which is mapped through vtkImageResliceMapper I have tried adding the following to itkImageToVTKImageFilter: m_Importer->UpdateInformation(); vtkStreamingDemandDrivenPipeline::SetUpdateExtent( m_Importer->GetOutputInformation(0 /*port number*/), 0 /*piece*/, 2 /*number of pieces*/, 0 /*number of ghost levels*/); m_Importer->Update(); .. but no luck! I have also tried: m_ImageData->GetPointData()->SetActiveAttribute (0, vtkPointData::SCALARS); didn?t work either... Any hint? thank you, sebastian From matt.mccormick at kitware.com Wed Sep 24 10:42:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Sep 2014 10:42:32 -0400 Subject: [ITK] VTK6 migration and vtkImageData: "No scalar values found for texture input!" error in vtkOpenGLTexture In-Reply-To: <542239D0.7060203@gmail.com> References: <542239D0.7060203@gmail.com> Message-ID: Hi Sebastian, What version of VTK are you using? Does the QuickViewTest (built as part of the ITKVtkGlue tests) executable work for you? Thanks, Matt On Tue, Sep 23, 2014 at 11:26 PM, Sebastian Ordas wrote: > Dear List, > > I have started getting the error "No scalar values found for texture input!" > coming from vtkOpenGLTexture, while porting my code to VTK6 > > More precisely, I have a vtkImageData, generated by > itkImageToVTKImageFilter, which is mapped through vtkImageResliceMapper > > I have tried adding the following to itkImageToVTKImageFilter: > > m_Importer->UpdateInformation(); > vtkStreamingDemandDrivenPipeline::SetUpdateExtent( > m_Importer->GetOutputInformation(0 /*port number*/), > 0 /*piece*/, > 2 /*number of pieces*/, > 0 /*number of ghost levels*/); > m_Importer->Update(); > > .. but no luck! > > I have also tried: > > m_ImageData->GetPointData()->SetActiveAttribute (0, vtkPointData::SCALARS); > > didn?t work either... > > Any hint? > > thank you, > sebastian > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From sebastian.ordas at gmail.com Wed Sep 24 10:48:55 2014 From: sebastian.ordas at gmail.com (Sebastian Ordas) Date: Wed, 24 Sep 2014 11:48:55 -0300 Subject: [ITK] VTK6 migration and vtkImageData: "No scalar values found for texture input!" error in vtkOpenGLTexture In-Reply-To: References: <542239D0.7060203@gmail.com> Message-ID: Hi Matt, I'm using almost the latest master (c0fa16c5) I will enable the tests in my ITK build. thank you! sebastian On Wed, Sep 24, 2014 at 11:42 AM, Matt McCormick wrote: > Hi Sebastian, > > What version of VTK are you using? Does the QuickViewTest (built as > part of the ITKVtkGlue tests) executable work for you? > > Thanks, > Matt > > On Tue, Sep 23, 2014 at 11:26 PM, Sebastian Ordas > wrote: > > Dear List, > > > > I have started getting the error "No scalar values found for texture > input!" > > coming from vtkOpenGLTexture, while porting my code to VTK6 > > > > More precisely, I have a vtkImageData, generated by > > itkImageToVTKImageFilter, which is mapped through vtkImageResliceMapper > > > > I have tried adding the following to itkImageToVTKImageFilter: > > > > m_Importer->UpdateInformation(); > > vtkStreamingDemandDrivenPipeline::SetUpdateExtent( > > m_Importer->GetOutputInformation(0 /*port number*/), > > 0 /*piece*/, > > 2 /*number of pieces*/, > > 0 /*number of ghost levels*/); > > m_Importer->Update(); > > > > .. but no luck! > > > > I have also tried: > > > > m_ImageData->GetPointData()->SetActiveAttribute (0, > vtkPointData::SCALARS); > > > > didn?t work either... > > > > Any hint? > > > > thank you, > > sebastian > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Sep 24 13:39:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Sep 2014 13:39:55 -0400 Subject: [ITK] [ITK-users] Image Rotation while preserving image In-Reply-To: <1411578386.9555.YahooMailNeo@web120603.mail.ne1.yahoo.com> References: <1411558020.53437.YahooMailNeo@web120605.mail.ne1.yahoo.com> <1411578386.9555.YahooMailNeo@web120603.mail.ne1.yahoo.com> Message-ID: Hi Emma, The resampled image will be sampled at the locations specified for the output image by setting the desired parameters on ResampleImageFilter. It does not does resize based on the transformation. To get a different output image domain, use SetOutputOrigin() and SetSize() on the ResampleImageFilter. Hope this helps, Matt On Wed, Sep 24, 2014 at 1:06 PM, Emma Ryan wrote: > HI Matt, > > Thank you for your reply. Attached is a snapshot of what is happening. The > square needs to rotate and become a diamond. But after rotation, I get a > chopped image. Ideally, I would just expect a larger sized matrix holding > the larger image. So I'm not sure I understand how the 'content' could be > missing. > > I couldn't experiment with SetExtrapolator as it is probably not available > in the version of itk that I am using . Version 3.X. > > Are you suggesting that using Extrapolation, I would be able to address this > specific problem ? > > regards, > Emma > > > > > > > > On Wednesday, September 24, 2014 7:44 AM, Matt McCormick > wrote: > > > Hi Emma, > > If there is no content to resample from after the transformation, then > a default pixel value is used. To use extrapolation instead, call > SetExtrapolator() [1] on the ResampleImageFilter. > > HTH, > Matt > > [1] > http://www.itk.org/Insight/Doxygen/html/classitk_1_1ResampleImageFilter.html#a89d912b5608fbe73a9a2ca0ebcfebb69 > > On Wed, Sep 24, 2014 at 7:27 AM, Emma Ryan via Insight-users > wrote: >> Hi, >> >> I would like to rotate an input mage by a few degrees. I was able to >> easily do this using rigid transforms available in itk. But the output >> image >> is cropped. The extent of cropping is directly related to the angle of >> rotation. How can one disallow this kind of cropping ? >> >> Thank you for your help. >> regards, >> Emma > >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > >> > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 24 14:14:38 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Sep 2014 14:14:38 -0400 Subject: [ITK] [ITK-users] format of mask file In-Reply-To: References: Message-ID: Hi Lianli, Any integer pixel type should work in the mask. To check how the mask applies to the image, the MaskImageFilter [1] can be applied. HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1MaskImageFilter.html On Tue, Sep 23, 2014 at 9:51 PM, Lianli Liu wrote: > Hi all, > > I am a bit unclear about the format of mask file. Is it fine if I use an > image of analyze format that has 0,1 value, but of integer type not boolean > type? > > The reason I am asking is that when I use this mask in the mutual > information metric, there is an error : joint PDF summed to zero... > > Thanks! > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 24 17:53:03 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Sep 2014 17:53:03 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4 For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 All are welcome. Hope to talk to you then! From arnaudgelas at gmail.com Thu Sep 25 09:09:26 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 25 Sep 2014 15:09:26 +0200 Subject: [ITK] [ITK-dev] minor release? Message-ID: Hi all, I just wanted to know if there were any plan to release v4.6.1 from the release branch? If so, when could it happen? Thanks, Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From sebastian.ordas at gmail.com Thu Sep 25 09:36:28 2014 From: sebastian.ordas at gmail.com (Sebastian Ordas) Date: Thu, 25 Sep 2014 10:36:28 -0300 Subject: [ITK] VTK6 migration and vtkImageData: "No scalar values found for texture input!" error in vtkOpenGLTexture In-Reply-To: References: <542239D0.7060203@gmail.com> Message-ID: <54241A5C.2040701@gmail.com> Hi Matt, QuickViewTest works fine. I will look deeper in its code and compare it with the vtkImageData creation as by itkImageToVTKImageFilter more soon, sebastian On 9/24/2014 11:42 AM, Matt McCormick wrote: > Hi Sebastian, > > What version of VTK are you using? Does the QuickViewTest (built as > part of the ITKVtkGlue tests) executable work for you? > > Thanks, > Matt > > On Tue, Sep 23, 2014 at 11:26 PM, Sebastian Ordas > wrote: >> Dear List, >> >> I have started getting the error "No scalar values found for texture input!" >> coming from vtkOpenGLTexture, while porting my code to VTK6 >> >> More precisely, I have a vtkImageData, generated by >> itkImageToVTKImageFilter, which is mapped through vtkImageResliceMapper >> >> I have tried adding the following to itkImageToVTKImageFilter: >> >> m_Importer->UpdateInformation(); >> vtkStreamingDemandDrivenPipeline::SetUpdateExtent( >> m_Importer->GetOutputInformation(0 /*port number*/), >> 0 /*piece*/, >> 2 /*number of pieces*/, >> 0 /*number of ghost levels*/); >> m_Importer->Update(); >> >> .. but no luck! >> >> I have also tried: >> >> m_ImageData->GetPointData()->SetActiveAttribute (0, vtkPointData::SCALARS); >> >> didn?t work either... >> >> Any hint? >> >> thank you, >> sebastian >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community From arnaudgelas at gmail.com Thu Sep 25 09:51:12 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 25 Sep 2014 15:51:12 +0200 Subject: [ITK] [ITK-dev] packaging ITK with system HDF5? Message-ID: Hi all, When installing ITK with system HDF5, I get in the file ${CMAKE_INSTALL_PREFIX}/lib64/cmake/InsightToolkit/Modules/ITKHDF5.cmake set( ITKHDF5_INCLUDE_DIRS "${ITK_INSTALL_PREFIX}/include/InsightToolkit;/home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src;/usr/include" ) Of course it works fine, if you do not delete /home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src and if you use the same user... I could not find anything related to this issue... It seems to me that the problem comes from: https://github.com/Kitware/ITK/blob/master/Modules/ThirdParty/HDF5/CMakeLists.txt#L10 I guess this path should not be added there?? Any idea? Thank you very much Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Thu Sep 25 10:00:55 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 25 Sep 2014 10:00:55 -0400 Subject: [ITK] [ITK-dev] packaging ITK with system HDF5? In-Reply-To: References: Message-ID: <9750EDA2-6F14-41FB-8E4E-4330207C0F17@mail.nih.gov> Arnaud, For comparison you can look at libtiff: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/TIFF/CMakeLists.txt#L9-L14 There the include are split between ITKTIFF_INCLUDE_DIRS and ITKTIFF_SYSTEM_INCLUDE_DIRS. Likely the SYSTEM variable doesn't get modified when installed. What to git a shot at making HDF5 follow this TIFF include pattern? Brad On Sep 25, 2014, at 9:51 AM, Arnaud Gelas wrote: > Hi all, > > When installing ITK with system HDF5, I get in the file ${CMAKE_INSTALL_PREFIX}/lib64/cmake/InsightToolkit/Modules/ITKHDF5.cmake > > set( ITKHDF5_INCLUDE_DIRS "${ITK_INSTALL_PREFIX}/include/InsightToolkit;/home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src;/usr/include" ) > > Of course it works fine, if you do not delete /home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src and if you use the same user... > > I could not find anything related to this issue... > > It seems to me that the problem comes from: > https://github.com/Kitware/ITK/blob/master/Modules/ThirdParty/HDF5/CMakeLists.txt#L10 > > I guess this path should not be added there?? > > Any idea? > > Thank you very much > Arnaud > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Sep 25 10:25:46 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 25 Sep 2014 10:25:46 -0400 Subject: [ITK] [ITK-dev] minor release? In-Reply-To: References: Message-ID: Hi Arnaud, Yes, good point. There are many great bug fixes on the release branch. I think we can release 4.6.1 next week. Thanks, Matt On Thu, Sep 25, 2014 at 9:09 AM, Arnaud Gelas wrote: > Hi all, > > I just wanted to know if there were any plan to release v4.6.1 from the > release branch? > If so, when could it happen? > > Thanks, > Arnaud > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Sep 25 10:29:22 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 25 Sep 2014 10:29:22 -0400 Subject: [ITK] Patches for v4.6.1 Message-ID: Hi, We currently have the patches below on the "release" branch for the v4.6.1 release. Are there any patches missing? Thanks, Matt Arnaud Gelas (3): BUG: fix gdcm version in GDCMImageIO. COMP: missing cast when calling gdcm::DataElement::SetByteValue BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false Brad King (1): COMP: Fix vxl_config_macros usage of CMake check macros Bradley Lowekamp (7): ENH: Adding License file from upstream MetaIO ENH: Adding script to update MetaIO from upstream ENH: Remove ITK MetaIO to prepare for upstream import COMP: Fix variable type for Set/Get macros BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit BUG: Fix overflows computing size of read tiff image Christopher Mullins (1): COMP: Allows latex to compile for ITKSoftwareGuide David T. Chen (1): DOC: Fixed HistogramThresholdImageFitler Gert Wollny (1): COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) Girish Mallya (1): BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. Hans Johnson (12): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components PERF: Remove large foot print of PDF derivatives. PERF: Revert Remove large foot print of PDF derivatives. STYLE: Test against almost equal for floating point values STYLE: Non-exact floating point testing PERF: Distribute initialization per thread buffers ENH: Remove unnecessary mutable qualifier. STYLE: Remove comment with no meaning. ENH: Moved accumlator logic to main MI class ENH: Allow staggering of accumulations per thread. PERF: Zero reset thread buffers during finalize KWSys Robot (2): KWSys 2014-07-18 (65b36ede) KWSys 2014-08-04 (e787837a) Matthew McCormick (30): BUG: ArchiveTestingData.py future imports must occur at the beginning. DOC: Remove Image2.cxx reference from Book 2. DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. DOC: Remove references to Book 1 sections from Book 2. DOC: Make BinaryThresholdImageFilter not floating. DOC: Fix Software Guide figure caption for FlipImageFilter. DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. DOC: ImageRandomConstIteratorWithIndex table reference. BUG: Bump GCCXML to 2014-08-06. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. BUG: Fix alpha assignment for RGBA TIFF. BUG: Fix Nifti IO read with large images. BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. DOC: itk::statistics -> itk::Statistics. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Fix missing prefix in ITKv3ImageRegistration20Test. BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform STYLE: Improve style in BinaryImageToLabelMapFilter. BUG: Fix BinaryImageToLabelMapFilter on 1D image. ENH: Improve precision of the joint PDF sum BUG: Fix BinShrinkImageFilter for different input/output image types. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. COMP: Add missing wrapping for TransformIOBaseTemplate. BUG: gdcm::StringFilter recognizes backslash delimiter. MetaIO Maintainers (1): MetaIO (reduced) Michka Popoff (4): BUG: Improve SWIG version check BUG: Add VTK_VERSION for older VTK versions BUG: Update VTK minimum version (for release) BUG: Fix memory leak in MetaImageIO after exception From arnaudgelas at gmail.com Thu Sep 25 10:31:22 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 25 Sep 2014 16:31:22 +0200 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: References: Message-ID: Matt, Following Brad's email, I am testing the following patch right now http://review.source.kitware.com/#/c/17232/1 If it fixes the issue, I would really like it to be part of 4.6.1 Best Arnaud On Thu, Sep 25, 2014 at 4:29 PM, Matt McCormick wrote: > Hi, > > We currently have the patches below on the "release" branch for the > v4.6.1 release. Are there any patches missing? > > Thanks, > Matt > > > Arnaud Gelas (3): > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is > false > > Brad King (1): > COMP: Fix vxl_config_macros usage of CMake check macros > > Bradley Lowekamp (7): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > COMP: Fix variable type for Set/Get macros > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Fix overflows computing size of read tiff image > > Christopher Mullins (1): > COMP: Allows latex to compile for ITKSoftwareGuide > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row > images. > > Hans Johnson (12): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > > KWSys Robot (2): > KWSys 2014-07-18 (65b36ede) > KWSys 2014-08-04 (e787837a) > > Matthew McCormick (30): > BUG: ArchiveTestingData.py future imports must occur at the > beginning. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > BUG: Bump GCCXML to 2014-08-06. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Call clear instead of empty on PatchBasedDenoising > EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > BUG: Fix alpha assignment for RGBA TIFF. > BUG: Fix Nifti IO read with large images. > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > COMP: Add missing wrapping for TransformIOBaseTemplate. > BUG: gdcm::StringFilter recognizes backslash delimiter. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (4): > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Sep 25 10:37:32 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 25 Sep 2014 10:37:32 -0400 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: References: Message-ID: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov> This minor one too, fixes something that was merged into release last week: http://review.source.kitware.com/#/c/17202/ On Sep 25, 2014, at 10:29 AM, Matt McCormick wrote: > Hi, > > We currently have the patches below on the "release" branch for the > v4.6.1 release. Are there any patches missing? > > Thanks, > Matt > > > Arnaud Gelas (3): > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false > > Brad King (1): > COMP: Fix vxl_config_macros usage of CMake check macros > > Bradley Lowekamp (7): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > COMP: Fix variable type for Set/Get macros > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Fix overflows computing size of read tiff image > > Christopher Mullins (1): > COMP: Allows latex to compile for ITKSoftwareGuide > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. > > Hans Johnson (12): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > > KWSys Robot (2): > KWSys 2014-07-18 (65b36ede) > KWSys 2014-08-04 (e787837a) > > Matthew McCormick (30): > BUG: ArchiveTestingData.py future imports must occur at the beginning. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > BUG: Bump GCCXML to 2014-08-06. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > BUG: Fix alpha assignment for RGBA TIFF. > BUG: Fix Nifti IO read with large images. > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > COMP: Add missing wrapping for TransformIOBaseTemplate. > BUG: gdcm::StringFilter recognizes backslash delimiter. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (4): > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers From matt at mmmccormick.com Thu Sep 25 10:38:56 2014 From: matt at mmmccormick.com (Matthew McCormick (thewtex)) Date: Thu, 25 Sep 2014 10:38:56 -0400 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: References: Message-ID: Cool! Please make a note in the commit if it has been verified that the fix works for you. On Thu, Sep 25, 2014 at 10:31 AM, Arnaud Gelas wrote: > Matt, > > Following Brad's email, I am testing the following patch right now > > http://review.source.kitware.com/#/c/17232/1 > > If it fixes the issue, I would really like it to be part of 4.6.1 > > Best > Arnaud > > > On Thu, Sep 25, 2014 at 4:29 PM, Matt McCormick > wrote: >> >> Hi, >> >> We currently have the patches below on the "release" branch for the >> v4.6.1 release. Are there any patches missing? >> >> Thanks, >> Matt >> >> >> Arnaud Gelas (3): >> BUG: fix gdcm version in GDCMImageIO. >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is >> false >> >> Brad King (1): >> COMP: Fix vxl_config_macros usage of CMake check macros >> >> Bradley Lowekamp (7): >> ENH: Adding License file from upstream MetaIO >> ENH: Adding script to update MetaIO from upstream >> ENH: Remove ITK MetaIO to prepare for upstream import >> COMP: Fix variable type for Set/Get macros >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> BUG: Fix overflows computing size of read tiff image >> >> Christopher Mullins (1): >> COMP: Allows latex to compile for ITKSoftwareGuide >> >> David T. Chen (1): >> DOC: Fixed HistogramThresholdImageFitler >> >> Gert Wollny (1): >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >> >> Girish Mallya (1): >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row >> images. >> >> Hans Johnson (12): >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> PERF: Remove large foot print of PDF derivatives. >> PERF: Revert Remove large foot print of PDF derivatives. >> STYLE: Test against almost equal for floating point values >> STYLE: Non-exact floating point testing >> PERF: Distribute initialization per thread buffers >> ENH: Remove unnecessary mutable qualifier. >> STYLE: Remove comment with no meaning. >> ENH: Moved accumlator logic to main MI class >> ENH: Allow staggering of accumulations per thread. >> PERF: Zero reset thread buffers during finalize >> >> KWSys Robot (2): >> KWSys 2014-07-18 (65b36ede) >> KWSys 2014-08-04 (e787837a) >> >> Matthew McCormick (30): >> BUG: ArchiveTestingData.py future imports must occur at the >> beginning. >> DOC: Remove Image2.cxx reference from Book 2. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. >> DOC: Remove references to Book 1 sections from Book 2. >> DOC: Make BinaryThresholdImageFilter not floating. >> DOC: Fix Software Guide figure caption for FlipImageFilter. >> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. >> DOC: Remove duplicate figure in >> LaplacianRecursiveGaussianImageFilter2.cxx. >> DOC: ImageRandomConstIteratorWithIndex table reference. >> BUG: Bump GCCXML to 2014-08-06. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> BUG: Call clear instead of empty on PatchBasedDenoising >> EmptyCaches(). >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >> BUG: Fix alpha assignment for RGBA TIFF. >> BUG: Fix Nifti IO read with large images. >> BUG: Improve thread-safety and performance of >> PCAShapeSignedDistanceFunction. >> DOC: itk::statistics -> itk::Statistics. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> DOC: Fix Software Guide page overruns in >> IterativeClosestPoint{1,2}.cxx. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >> BUG: Do not return SmartPointers in >> TimeVaryingVelocityFieldTransform >> STYLE: Improve style in BinaryImageToLabelMapFilter. >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. >> ENH: Improve precision of the joint PDF sum >> BUG: Fix BinShrinkImageFilter for different input/output image >> types. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> BUG: gdcm::StringFilter recognizes backslash delimiter. >> >> MetaIO Maintainers (1): >> MetaIO (reduced) >> >> Michka Popoff (4): >> BUG: Improve SWIG version check >> BUG: Add VTK_VERSION for older VTK versions >> BUG: Update VTK minimum version (for release) >> BUG: Fix memory leak in MetaImageIO after exception >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt at mmmccormick.com Thu Sep 25 10:41:53 2014 From: matt at mmmccormick.com (Matthew McCormick (thewtex)) Date: Thu, 25 Sep 2014 10:41:53 -0400 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov> References: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov> Message-ID: Great, thanks! Merged to master. Will merge to release tomorrow after hitting the dashboards. On Thu, Sep 25, 2014 at 10:37 AM, Bradley Lowekamp wrote: > This minor one too, fixes something that was merged into release last week: > > http://review.source.kitware.com/#/c/17202/ > > On Sep 25, 2014, at 10:29 AM, Matt McCormick wrote: > >> Hi, >> >> We currently have the patches below on the "release" branch for the >> v4.6.1 release. Are there any patches missing? >> >> Thanks, >> Matt >> >> >> Arnaud Gelas (3): >> BUG: fix gdcm version in GDCMImageIO. >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false >> >> Brad King (1): >> COMP: Fix vxl_config_macros usage of CMake check macros >> >> Bradley Lowekamp (7): >> ENH: Adding License file from upstream MetaIO >> ENH: Adding script to update MetaIO from upstream >> ENH: Remove ITK MetaIO to prepare for upstream import >> COMP: Fix variable type for Set/Get macros >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> BUG: Fix overflows computing size of read tiff image >> >> Christopher Mullins (1): >> COMP: Allows latex to compile for ITKSoftwareGuide >> >> David T. Chen (1): >> DOC: Fixed HistogramThresholdImageFitler >> >> Gert Wollny (1): >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >> >> Girish Mallya (1): >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. >> >> Hans Johnson (12): >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> PERF: Remove large foot print of PDF derivatives. >> PERF: Revert Remove large foot print of PDF derivatives. >> STYLE: Test against almost equal for floating point values >> STYLE: Non-exact floating point testing >> PERF: Distribute initialization per thread buffers >> ENH: Remove unnecessary mutable qualifier. >> STYLE: Remove comment with no meaning. >> ENH: Moved accumlator logic to main MI class >> ENH: Allow staggering of accumulations per thread. >> PERF: Zero reset thread buffers during finalize >> >> KWSys Robot (2): >> KWSys 2014-07-18 (65b36ede) >> KWSys 2014-08-04 (e787837a) >> >> Matthew McCormick (30): >> BUG: ArchiveTestingData.py future imports must occur at the beginning. >> DOC: Remove Image2.cxx reference from Book 2. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. >> DOC: Remove references to Book 1 sections from Book 2. >> DOC: Make BinaryThresholdImageFilter not floating. >> DOC: Fix Software Guide figure caption for FlipImageFilter. >> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. >> DOC: Remove duplicate figure in >> LaplacianRecursiveGaussianImageFilter2.cxx. >> DOC: ImageRandomConstIteratorWithIndex table reference. >> BUG: Bump GCCXML to 2014-08-06. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >> BUG: Fix alpha assignment for RGBA TIFF. >> BUG: Fix Nifti IO read with large images. >> BUG: Improve thread-safety and performance of >> PCAShapeSignedDistanceFunction. >> DOC: itk::statistics -> itk::Statistics. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >> BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform >> STYLE: Improve style in BinaryImageToLabelMapFilter. >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. >> ENH: Improve precision of the joint PDF sum >> BUG: Fix BinShrinkImageFilter for different input/output image types. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> BUG: gdcm::StringFilter recognizes backslash delimiter. >> >> MetaIO Maintainers (1): >> MetaIO (reduced) >> >> Michka Popoff (4): >> BUG: Improve SWIG version check >> BUG: Add VTK_VERSION for older VTK versions >> BUG: Update VTK minimum version (for release) >> BUG: Fix memory leak in MetaImageIO after exception >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Thu Sep 25 10:43:51 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 25 Sep 2014 10:43:51 -0400 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: Message-ID: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov> Matt, The URL for the Confab is from last week, I think this is the URL for the one tomorrow: https://plus.google.com/u/0/events/c5snoqnkhtkcv1tebfo1cl9quo4 On Sep 24, 2014, at 5:53 PM, Matt McCormick wrote: > There are a couple of upcoming opportunities to share, discuss, design, and > learn with your fellow ITK community members. > > > On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a > Google+ Hangout > where we will be doing code reviews: > > https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk > > > On Friday, 11:00 AM Eastern USA time, an ITK development conference, > > https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4 > > For those that cannot join via Hangout, telephone call-in is also possible. > Dial: > > 585-632-6296 > > Enter pin: > > 31423 > > > All are welcome. Hope to talk to you then! > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Sep 25 10:45:45 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 25 Sep 2014 10:45:45 -0400 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov> References: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov> Message-ID: Thanks for the correction! On Thu, Sep 25, 2014 at 10:43 AM, Bradley Lowekamp wrote: > Matt, > > The URL for the Confab is from last week, I think this is the URL for the one tomorrow: > > https://plus.google.com/u/0/events/c5snoqnkhtkcv1tebfo1cl9quo4 > > On Sep 24, 2014, at 5:53 PM, Matt McCormick wrote: > >> There are a couple of upcoming opportunities to share, discuss, design, and >> learn with your fellow ITK community members. >> >> >> On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a >> Google+ Hangout >> where we will be doing code reviews: >> >> https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk >> >> >> On Friday, 11:00 AM Eastern USA time, an ITK development conference, >> >> https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4 >> >> For those that cannot join via Hangout, telephone call-in is also possible. >> Dial: >> >> 585-632-6296 >> >> Enter pin: >> >> 31423 >> >> >> All are welcome. Hope to talk to you then! >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > From arnaudgelas at gmail.com Thu Sep 25 11:30:25 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 25 Sep 2014 17:30:25 +0200 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: References: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov> Message-ID: With system HDF5, the patch works great (thanks to Brad)! I have also submitted one patch that could go in ITK 4.6.1 with system GDCM: http://review.source.kitware.com/#/c/17234/ On Thu, Sep 25, 2014 at 4:41 PM, Matthew McCormick (thewtex) < matt at mmmccormick.com> wrote: > Great, thanks! Merged to master. Will merge to release tomorrow > after hitting the dashboards. > > On Thu, Sep 25, 2014 at 10:37 AM, Bradley Lowekamp > wrote: > > This minor one too, fixes something that was merged into release last > week: > > > > http://review.source.kitware.com/#/c/17202/ > > > > On Sep 25, 2014, at 10:29 AM, Matt McCormick > wrote: > > > >> Hi, > >> > >> We currently have the patches below on the "release" branch for the > >> v4.6.1 release. Are there any patches missing? > >> > >> Thanks, > >> Matt > >> > >> > >> Arnaud Gelas (3): > >> BUG: fix gdcm version in GDCMImageIO. > >> COMP: missing cast when calling gdcm::DataElement::SetByteValue > >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID > is false > >> > >> Brad King (1): > >> COMP: Fix vxl_config_macros usage of CMake check macros > >> > >> Bradley Lowekamp (7): > >> ENH: Adding License file from upstream MetaIO > >> ENH: Adding script to update MetaIO from upstream > >> ENH: Remove ITK MetaIO to prepare for upstream import > >> COMP: Fix variable type for Set/Get macros > >> BUG: Use METER of sCAL scale unit > >> BUG: Use PNG_SCALE_METER for PNG sCAL unit > >> BUG: Fix overflows computing size of read tiff image > >> > >> Christopher Mullins (1): > >> COMP: Allows latex to compile for ITKSoftwareGuide > >> > >> David T. Chen (1): > >> DOC: Fixed HistogramThresholdImageFitler > >> > >> Gert Wollny (1): > >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > >> > >> Girish Mallya (1): > >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row > images. > >> > >> Hans Johnson (12): > >> COMP: Add tolerance for comparing floating point > >> PERF: Remove non-threadable algorithm components > >> PERF: Remove large foot print of PDF derivatives. > >> PERF: Revert Remove large foot print of PDF derivatives. > >> STYLE: Test against almost equal for floating point values > >> STYLE: Non-exact floating point testing > >> PERF: Distribute initialization per thread buffers > >> ENH: Remove unnecessary mutable qualifier. > >> STYLE: Remove comment with no meaning. > >> ENH: Moved accumlator logic to main MI class > >> ENH: Allow staggering of accumulations per thread. > >> PERF: Zero reset thread buffers during finalize > >> > >> KWSys Robot (2): > >> KWSys 2014-07-18 (65b36ede) > >> KWSys 2014-08-04 (e787837a) > >> > >> Matthew McCormick (30): > >> BUG: ArchiveTestingData.py future imports must occur at the > beginning. > >> DOC: Remove Image2.cxx reference from Book 2. > >> DOC: Fix Software Guide page overruns in > IterativeClosestPoint3.cxx. > >> DOC: Remove references to Book 1 sections from Book 2. > >> DOC: Make BinaryThresholdImageFilter not floating. > >> DOC: Fix Software Guide figure caption for FlipImageFilter. > >> DOC: Avoid duplicate figure description in > ResampleImageFilter2.cxx. > >> DOC: Remove duplicate figure in > >> LaplacianRecursiveGaussianImageFilter2.cxx. > >> DOC: ImageRandomConstIteratorWithIndex table reference. > >> BUG: Bump GCCXML to 2014-08-06. > >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > >> BUG: Call clear instead of empty on PatchBasedDenoising > EmptyCaches(). > >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > >> BUG: Fix alpha assignment for RGBA TIFF. > >> BUG: Fix Nifti IO read with large images. > >> BUG: Improve thread-safety and performance of > >> PCAShapeSignedDistanceFunction. > >> DOC: itk::statistics -> itk::Statistics. > >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > >> DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > >> BUG: TransformFileReader does not clear its TransformList. > >> BUG: Prevent dangling pointer in HDF5TransformIO. > >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > >> BUG: Do not return SmartPointers in > TimeVaryingVelocityFieldTransform > >> STYLE: Improve style in BinaryImageToLabelMapFilter. > >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. > >> ENH: Improve precision of the joint PDF sum > >> BUG: Fix BinShrinkImageFilter for different input/output image > types. > >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > >> COMP: Add missing wrapping for TransformIOBaseTemplate. > >> BUG: gdcm::StringFilter recognizes backslash delimiter. > >> > >> MetaIO Maintainers (1): > >> MetaIO (reduced) > >> > >> Michka Popoff (4): > >> BUG: Improve SWIG version check > >> BUG: Add VTK_VERSION for older VTK versions > >> BUG: Update VTK minimum version (for release) > >> BUG: Fix memory leak in MetaImageIO after exception > >> _______________________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-developers > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From elena.bresciani87 at gmail.com Fri Sep 26 10:23:18 2014 From: elena.bresciani87 at gmail.com (elena bresciani) Date: Fri, 26 Sep 2014 16:23:18 +0200 Subject: [ITK] [ITK-users] OpenCV - ITK project Message-ID: Hello to everybody, for the project I'm working on I need to integrate ITK and OpenCV. I've read the dedicated tutorial here , but I can't find informations on how the CmakeList.txt file should be created or if I have to change some kind of building configuration of ITK and/or OpenCV. Can you please explain me what I have to do? Cheers Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Fri Sep 26 10:35:18 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Fri, 26 Sep 2014 15:35:18 +0100 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: Hi Elena, I use OpenCV and ITK together. The general procedure is to build OpenCV from source using CMake, and then build ITK from source using CMake, checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. During both the builds you generally do not have to modify the CMakeLists.txt For a project which uses the libraries, the CMakeLists.txt would simply look like - ---- cmake_minimum_required(VERSION 2.8) project(myProject) find_package(ITK REQUIRED) find_package(OpenCV REQUIRED) include(${ITK_USE_FILE}) add_executable(myProject test.cpp) target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) ---- Is there a specific problem you are facing while trying this? On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani < elena.bresciani87 at gmail.com> wrote: > Hello to everybody, > > for the project I'm working on I need to integrate ITK and OpenCV. > I've read the dedicated tutorial here > , but > I can't find informations on how the CmakeList.txt file should be created > or if I have to change some kind of building configuration of ITK and/or > OpenCV. > > Can you please explain me what I have to do? > > Cheers > Elena > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From elena.bresciani87 at gmail.com Fri Sep 26 11:28:25 2014 From: elena.bresciani87 at gmail.com (elena bresciani) Date: Fri, 26 Sep 2014 17:28:25 +0200 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: I get the CMake error " Error in configuration files. Project Files may be invalid " I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", I have to rebuild ITK by checking that option (I don't think I had done this when I compiled ITK), and I hope that then it will work. I installed OpenCV with brew on Mac, you suggest to recompile it from source or it should be good as well? Thank you so much Elena 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi : > Hi Elena, > > I use OpenCV and ITK together. The general procedure is to build OpenCV > from source using CMake, and then build ITK from source using CMake, > checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. > During both the builds you generally do not have to modify the > CMakeLists.txt > > For a project which uses the libraries, the CMakeLists.txt would simply > look like - > > ---- > cmake_minimum_required(VERSION 2.8) > > project(myProject) > > find_package(ITK REQUIRED) > find_package(OpenCV REQUIRED) > > include(${ITK_USE_FILE}) > > add_executable(myProject test.cpp) > > target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) > ---- > > Is there a specific problem you are facing while trying this? > > On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani < > elena.bresciani87 at gmail.com> wrote: > >> Hello to everybody, >> >> for the project I'm working on I need to integrate ITK and OpenCV. >> I've read the dedicated tutorial here >> , >> but I can't find informations on how the CmakeList.txt file should be >> created or if I have to change some kind of building configuration of ITK >> and/or OpenCV. >> >> Can you please explain me what I have to do? >> >> Cheers >> Elena >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Fri Sep 26 11:35:23 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Fri, 26 Sep 2014 16:35:23 +0100 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build ITK. I am not familiar with OpenCV installations on Mac. Do projects build fine when you use OpenCV alone? On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani < elena.bresciani87 at gmail.com> wrote: > I get the CMake error " Error in configuration files. Project Files may be > invalid " > > I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", > I have to rebuild ITK by checking that option (I don't think I had done > this when I compiled ITK), and I hope that then it will work. > I installed OpenCV with brew on Mac, you suggest to recompile it from > source or it should be good as well? > > Thank you so much > > Elena > > 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi : > >> Hi Elena, >> >> I use OpenCV and ITK together. The general procedure is to build OpenCV >> from source using CMake, and then build ITK from source using CMake, >> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. >> During both the builds you generally do not have to modify the >> CMakeLists.txt >> >> For a project which uses the libraries, the CMakeLists.txt would simply >> look like - >> >> ---- >> cmake_minimum_required(VERSION 2.8) >> >> project(myProject) >> >> find_package(ITK REQUIRED) >> find_package(OpenCV REQUIRED) >> >> include(${ITK_USE_FILE}) >> >> add_executable(myProject test.cpp) >> >> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) >> ---- >> >> Is there a specific problem you are facing while trying this? >> >> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani < >> elena.bresciani87 at gmail.com> wrote: >> >>> Hello to everybody, >>> >>> for the project I'm working on I need to integrate ITK and OpenCV. >>> I've read the dedicated tutorial here >>> , >>> but I can't find informations on how the CmakeList.txt file should be >>> created or if I have to change some kind of building configuration of ITK >>> and/or OpenCV. >>> >>> Can you please explain me what I have to do? >>> >>> Cheers >>> Elena >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> >> -- >> Regards, >> Girish >> > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From elena.bresciani87 at gmail.com Fri Sep 26 11:53:12 2014 From: elena.bresciani87 at gmail.com (elena bresciani) Date: Fri, 26 Sep 2014 17:53:12 +0200 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: Yes, I don't have problems with it alone, so I will leave it as it as and only try rebuilding itk with the "Module_ITKVideoBridgeOpenCV" flag on. Thanks 2014-09-26 17:35 GMT+02:00 Girish Mallya Udupi : > Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build > ITK. > I am not familiar with OpenCV installations on Mac. Do projects build fine > when you use OpenCV alone? > > On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani < > elena.bresciani87 at gmail.com> wrote: > >> I get the CMake error " Error in configuration files. Project Files may >> be invalid " >> >> I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", >> I have to rebuild ITK by checking that option (I don't think I had done >> this when I compiled ITK), and I hope that then it will work. >> I installed OpenCV with brew on Mac, you suggest to recompile it from >> source or it should be good as well? >> >> Thank you so much >> >> Elena >> >> 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi >> : >> >>> Hi Elena, >>> >>> I use OpenCV and ITK together. The general procedure is to build OpenCV >>> from source using CMake, and then build ITK from source using CMake, >>> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. >>> During both the builds you generally do not have to modify the >>> CMakeLists.txt >>> >>> For a project which uses the libraries, the CMakeLists.txt would simply >>> look like - >>> >>> ---- >>> cmake_minimum_required(VERSION 2.8) >>> >>> project(myProject) >>> >>> find_package(ITK REQUIRED) >>> find_package(OpenCV REQUIRED) >>> >>> include(${ITK_USE_FILE}) >>> >>> add_executable(myProject test.cpp) >>> >>> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) >>> ---- >>> >>> Is there a specific problem you are facing while trying this? >>> >>> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani < >>> elena.bresciani87 at gmail.com> wrote: >>> >>>> Hello to everybody, >>>> >>>> for the project I'm working on I need to integrate ITK and OpenCV. >>>> I've read the dedicated tutorial here >>>> , >>>> but I can't find informations on how the CmakeList.txt file should be >>>> created or if I have to change some kind of building configuration of ITK >>>> and/or OpenCV. >>>> >>>> Can you please explain me what I have to do? >>>> >>>> Cheers >>>> Elena >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >>> >>> -- >>> Regards, >>> Girish >>> >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Sep 26 14:39:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 26 Sep 2014 14:39:13 -0400 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: Hi Elena, This example may be helpful [1]. Matt [1] http://itk.org/ITKExamples/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.html?highlight=opencv On Fri, Sep 26, 2014 at 11:53 AM, elena bresciani wrote: > Yes, I don't have problems with it alone, so I will leave it as it as and > only try rebuilding itk with the "Module_ITKVideoBridgeOpenCV" flag on. > > Thanks > > 2014-09-26 17:35 GMT+02:00 Girish Mallya Udupi : >> >> Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build >> ITK. >> I am not familiar with OpenCV installations on Mac. Do projects build fine >> when you use OpenCV alone? >> >> On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani >> wrote: >>> >>> I get the CMake error " Error in configuration files. Project Files may >>> be invalid " >>> >>> I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", >>> I have to rebuild ITK by checking that option (I don't think I had done this >>> when I compiled ITK), and I hope that then it will work. >>> I installed OpenCV with brew on Mac, you suggest to recompile it from >>> source or it should be good as well? >>> >>> Thank you so much >>> >>> Elena >>> >>> 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi >>> : >>>> >>>> Hi Elena, >>>> >>>> I use OpenCV and ITK together. The general procedure is to build OpenCV >>>> from source using CMake, and then build ITK from source using CMake, >>>> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. >>>> During both the builds you generally do not have to modify the >>>> CMakeLists.txt >>>> >>>> For a project which uses the libraries, the CMakeLists.txt would simply >>>> look like - >>>> >>>> ---- >>>> cmake_minimum_required(VERSION 2.8) >>>> >>>> project(myProject) >>>> >>>> find_package(ITK REQUIRED) >>>> find_package(OpenCV REQUIRED) >>>> >>>> include(${ITK_USE_FILE}) >>>> >>>> add_executable(myProject test.cpp) >>>> >>>> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) >>>> ---- >>>> >>>> Is there a specific problem you are facing while trying this? >>>> >>>> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani >>>> wrote: >>>>> >>>>> Hello to everybody, >>>>> >>>>> for the project I'm working on I need to integrate ITK and OpenCV. >>>>> I've read the dedicated tutorial here, but I can't find informations on >>>>> how the CmakeList.txt file should be created or if I have to change some >>>>> kind of building configuration of ITK and/or OpenCV. >>>>> >>>>> Can you please explain me what I have to do? >>>>> >>>>> Cheers >>>>> Elena >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>> >>>> >>>> >>>> -- >>>> Regards, >>>> Girish >>> >>> >> >> >> >> -- >> Regards, >> Girish > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From genet at biomed.ee.ethz.ch Fri Sep 26 16:46:46 2014 From: genet at biomed.ee.ethz.ch (Martin Genet) Date: Fri, 26 Sep 2014 22:46:46 +0200 Subject: [ITK] [ITK-users] FEMRegistration In-Reply-To: References: <54207D45.9070409@biomed.ee.ethz.ch> Message-ID: <5425D0B6.1000009@biomed.ee.ethz.ch> Thanks a lot, Matt. I'm still a little confused though. I can access the mesh using: > typedef itk::fem::FEMObject< 2 > MeshType; > MeshType::Pointer mesh = registrationFilter->GetInputFEMObject(); However, when trying to create a writer using > typedef itk::MeshFileWriter< MeshType > MeshWriterType; > MeshWriterType::Pointer meshWriter = MeshWriterType::New(); , it complains that InputMeshType (itk::fem::FEMObject< 2 > I guess) is missing a lot of stuff (e.g., RegionType, PixelType, GetPoints, etc.). If I use > typedef itk::Mesh< float, 2 > MeshType; instead, I can define the writer, but then I can't access the mesh from the registration filter of course. Is there a way to write registrationFilter->GetInputFEMObject() into a vtk file? Thanks again, and sorry again for the confusion. Martin On 09/22/2014 10:54 PM, Matt McCormick wrote: > Hi Martin, > > itk::MeshFileReader and itk::MeshFileWriter are great classes for > importing / exporting meshes. > > HTH, > Matt > > On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet wrote: >> Dear all: >> >> Trying to use FEMRegistration on a bunch of images. Still trying to figure >> out the following: >> >> - What is the simplest way to convert an external mesh (e.g., >> vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and vice >> versa (for post-treatment, vizualization)? >> >> - If the mesh covers only a subset of the image, what happens to the rest >> of the image? >> >> Any help would be super appreciated. Sorry if that's too trivial. Thanks in >> advance. >> >> Martin >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Sep 26 17:11:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 26 Sep 2014 17:11:11 -0400 Subject: [ITK] [ITK-users] FEMRegistration In-Reply-To: <5425D0B6.1000009@biomed.ee.ethz.ch> References: <54207D45.9070409@biomed.ee.ethz.ch> <5425D0B6.1000009@biomed.ee.ethz.ch> Message-ID: Hi Martin, An itk::Mesh will need to be constructed from the the itk::fem::FEMObject manually. We could use a set of converter classes. HTH, Matt On Fri, Sep 26, 2014 at 4:46 PM, Martin Genet wrote: > Thanks a lot, Matt. I'm still a little confused though. I can access the > mesh using: >> >> typedef itk::fem::FEMObject< 2 > MeshType; >> MeshType::Pointer mesh = registrationFilter->GetInputFEMObject(); > > > However, when trying to create a writer using >> typedef itk::MeshFileWriter< MeshType > MeshWriterType; >> MeshWriterType::Pointer meshWriter = MeshWriterType::New(); > , it complains that InputMeshType (itk::fem::FEMObject< 2 > I guess) is > missing a lot of stuff (e.g., RegionType, PixelType, GetPoints, etc.). > > If I use >> typedef itk::Mesh< float, 2 > MeshType; > instead, I can define the writer, but then I can't access the mesh from the > registration filter of course. > > Is there a way to write registrationFilter->GetInputFEMObject() into a vtk > file? Thanks again, and sorry again for the confusion. > > Martin > > > On 09/22/2014 10:54 PM, Matt McCormick wrote: >> >> Hi Martin, >> >> itk::MeshFileReader and itk::MeshFileWriter are great classes for >> importing / exporting meshes. >> >> HTH, >> Matt >> >> On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet >> wrote: >>> >>> Dear all: >>> >>> Trying to use FEMRegistration on a bunch of images. Still trying to >>> figure >>> out the following: >>> >>> - What is the simplest way to convert an external mesh (e.g., >>> vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and >>> vice >>> versa (for post-treatment, vizualization)? >>> >>> - If the mesh covers only a subset of the image, what happens to the >>> rest >>> of the image? >>> >>> Any help would be super appreciated. Sorry if that's too trivial. Thanks >>> in >>> advance. >>> >>> Martin >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From suryarajan15 at gmail.com Sat Sep 27 10:12:44 2014 From: suryarajan15 at gmail.com (Surya Rajan) Date: Sat, 27 Sep 2014 19:42:44 +0530 Subject: [ITK] problem with pathiterator Message-ID: Hi, I'm having trouble in itkPathToImageFilter.hxx. The input is a closed Path (2D index type). The problem is in this line of the file: PathIterator< OutputImageType, InputPathType > pathIt(OutputImage, InputPath); for ( pathIt.GoToBegin(); !pathIt.IsAtEnd(); ++pathIt) { pathIt.Set(m_PathValue); } I'm noticing that the loop executes only once, taking the first value in the path. ++pathIt does not seem to work. Could anyone please help me with this? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From llliu at umich.edu Sun Sep 28 18:18:40 2014 From: llliu at umich.edu (Lianli Liu) Date: Sun, 28 Sep 2014 18:18:40 -0400 Subject: [ITK] [ITK-users] build itkvtkglue Message-ID: Hi all, I want to use vtk with itk and I set the BUILD_SHARED_LIBS option as ON. My cmake file looks like this # This is the root ITK CMakeLists file. cmake_minimum_required(VERSION 2.4) if(COMMAND CMAKE_POLICY) cmake_policy(SET CMP0003 NEW) endif() # This project is designed to be built outside the Insight source tree. project(vtiPCA) # Find ITK. find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED) find_package(VTK REQUIRED) include(${VTK_USE_FILE}) else() find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue) endif() add_executable(vtiPCA vtiPCA.cxx ) target_link_libraries(vtiPCA ${ITK_LIBRARIES}) But I receivde the error saying By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ItkVtkGlue", but CMake did not find one. . Can anyone help with this? Thanks! Best, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Sun Sep 28 22:01:57 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Sun, 28 Sep 2014 22:01:57 -0400 Subject: [ITK] [ITK-users] build itkvtkglue In-Reply-To: References: Message-ID: Remove these lines: else() find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue) On Sun, Sep 28, 2014 at 6:18 PM, Lianli Liu wrote: > Hi all, > > I want to use vtk with itk and I set the BUILD_SHARED_LIBS option as ON. My > cmake file looks like this > > # This is the root ITK CMakeLists file. > cmake_minimum_required(VERSION 2.4) > if(COMMAND CMAKE_POLICY) > cmake_policy(SET CMP0003 NEW) > endif() > > > # This project is designed to be built outside the Insight source tree. > project(vtiPCA) > > # Find ITK. > find_package(ITK REQUIRED) > include(${ITK_USE_FILE}) > > if (ITKVtkGlue_LOADED) > find_package(VTK REQUIRED) > include(${VTK_USE_FILE}) > else() > find_package(ItkVtkGlue REQUIRED) > include(${ItkVtkGlue_USE_FILE}) > set(Glue ItkVtkGlue) > endif() > > add_executable(vtiPCA vtiPCA.cxx ) > > target_link_libraries(vtiPCA ${ITK_LIBRARIES}) > > But I receivde the error saying > > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > has asked CMake to find a package configuration file provided by > "ItkVtkGlue", but CMake did not find one. > . > > Can anyone help with this? Thanks! > > Best, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Mon Sep 29 08:06:59 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 29 Sep 2014 08:06:59 -0400 Subject: [ITK] [ITK-dev] Linux CDash@home build missing Message-ID: Matt, I haven't seen the Linux CDash at Home robot for a while now. Does it need to be persuaded to resume building and testing our gerrit patches? Thanks, Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Sep 29 10:57:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 29 Sep 2014 10:57:21 -0400 Subject: [ITK] [ITK-dev] Linux CDash@home build missing In-Reply-To: References: Message-ID: Hi Brad, Thanks for the note. My persuasion skills have been applied :-). Thanks, Matt On Mon, Sep 29, 2014 at 8:06 AM, Bradley Lowekamp wrote: > Matt, > > I haven't seen the Linux CDash at Home robot for a while now. > > Does it need to be persuaded to resume building and testing our gerrit patches? > > Thanks, > Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From emmasaunders123 at gmail.com Mon Sep 29 15:25:16 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Mon, 29 Sep 2014 20:25:16 +0100 Subject: [ITK] [ITK-users] Push forward Pull Back Euler Lagrangian Frame Message-ID: Hi List I am experiencing some confusion with terms above, if someone could clarify that would be great: Does registration using a Eulerian frame correspond to a pull back framework of registration similarly: Does registration using a Lagrangian frame correspond to a push forward framework for registration? Thanks for any help Kind regards Emma -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Mon Sep 29 18:24:39 2014 From: llliu at umich.edu (Lianli Liu) Date: Mon, 29 Sep 2014 18:24:39 -0400 Subject: [ITK] [ITK-users] segmentation error in PCA estimator Message-ID: Hi all, I am applying the itk example code for PCA estimator (EstimatePCAModel.cxx). I have 10 training images and I intend to output all components (i.e. 10). But after writing 4 components, I get the segmentation fault. I was wondering what is the cause of this? I would really appreciate any help. Thanks! Regards, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michkapopoff at gmail.com Tue Sep 30 07:03:33 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Tue, 30 Sep 2014 13:03:33 +0200 Subject: [ITK] [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem In-Reply-To: <542A8B2E.6020404@utu.fi> References: <542A8B2E.6020404@utu.fi> Message-ID: <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> Hi once ITK is compiled, there is no more need for Swig at runtime. For the syntax, you should use the new wrapping syntax. Look at how it is done in this example, at the end there is python code [1] I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig. If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig. You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial. [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html Michka On 30 sept. 2014, at 12:51, Sami Koho wrote: > Hello, > > this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer. > > I am able to load itk in Python, but every time I try to execute anything, the following error appears: > >> in () >> ----> 1 reader = itk.ImageFileReader.IUC3.New() >> >> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr) >> 40 module = self.__lazy_attributes[attr] >> 41 namespace = {} >> ---> 42 itkBase.LoadModule(module, namespace) >> 43 # Load into 'namespace' first, then self.__dict__ (via setattr) to >> 44 # prevent the warnings about overwriting the 'NotLoaded' values >> >> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace) >> 51 if namespace is not None: >> 52 swig = namespace.setdefault('swig', imp.new_module('swig')) >> ---> 53 swig.__dict__.update(this_module.swig.__dict__) >> 54 >> 55 # don't worry about overwriting the symbols in namespace -- any >> >> AttributeError: 'module' object has no attribute 'swig' > > I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython, tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly. > > Should I manually set a path to swig? Or is something else wrong instead? > > I have installed ITK in the default path /usr/local/lib, as can be seen from the example. > > Best, > > Sami _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From sami.koho at gmail.com Tue Sep 30 08:51:32 2014 From: sami.koho at gmail.com (Sami Koho) Date: Tue, 30 Sep 2014 15:51:32 +0300 Subject: [ITK] [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem In-Reply-To: <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> References: <542A8B2E.6020404@utu.fi> <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> Message-ID: Thank you Michka! The solution was in the ldconfig file creation: > ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here. > cd /etc/ld.so.conf.d/ > add a file called itk-46.conf, which should contain only one line: /usr/local/lib > ldconfig # tells the system to read the files in ld.so.conf.d On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide: > /Path to a program. > PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python > > //Path to a file. > PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 > > //Path to a file. > PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7 > > //Path to a library. > PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 > > //Path to a library. > PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND > > //Directory where the arrayobject.h header file can be found. This > // file is part of the numarray package > PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy > > //Python site-packages directory to install a .pth file pointing > // at WrapITK Python modules. > PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages Best, Sami On Sep 30, 2014, at 14:03, Michka Popoff wrote: > Hi > > once ITK is compiled, there is no more need for Swig at runtime. > > For the syntax, you should use the new wrapping syntax. > Look at how it is done in this example, at the end there is python code [1] > > I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig. > If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig. > You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora > > The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial. > > [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html > > Michka > > On 30 sept. 2014, at 12:51, Sami Koho wrote: > >> Hello, >> >> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer. >> >> I am able to load itk in Python, but every time I try to execute anything, the following error appears: >> >>> in () >>> ----> 1 reader = itk.ImageFileReader.IUC3.New() >>> >>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr) >>> 40 module = self.__lazy_attributes[attr] >>> 41 namespace = {} >>> ---> 42 itkBase.LoadModule(module, namespace) >>> 43 # Load into 'namespace' first, then self.__dict__ (via setattr) to >>> 44 # prevent the warnings about overwriting the 'NotLoaded' values >>> >>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace) >>> 51 if namespace is not None: >>> 52 swig = namespace.setdefault('swig', imp.new_module('swig')) >>> ---> 53 swig.__dict__.update(this_module.swig.__dict__) >>> 54 >>> 55 # don't worry about overwriting the symbols in namespace -- any >>> >>> AttributeError: 'module' object has no attribute 'swig' >> >> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython, tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly. >> >> Should I manually set a path to swig? Or is something else wrong instead? >> >> I have installed ITK in the default path /usr/local/lib, as can be seen from the example. >> >> Best, >> >> Sami > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michkapopoff at gmail.com Tue Sep 30 09:14:21 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Tue, 30 Sep 2014 15:14:21 +0200 Subject: [ITK] [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem In-Reply-To: References: <542A8B2E.6020404@utu.fi> <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> Message-ID: Would it be possible for you to write this down for me, so I can update the guide on the wiki ? Michka On 30 sept. 2014, at 14:51, Sami Koho wrote: > Thank you Michka! The solution was in the ldconfig file creation: > >> ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here. >> cd /etc/ld.so.conf.d/ >> add a file called itk-46.conf, which should contain only one line: /usr/local/lib >> ldconfig # tells the system to read the files in ld.so.conf.d > > On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide: > >> /Path to a program. >> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python >> >> //Path to a file. >> PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 >> >> //Path to a file. >> PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7 >> >> //Path to a library. >> PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 >> >> //Path to a library. >> PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND >> >> //Directory where the arrayobject.h header file can be found. This >> // file is part of the numarray package >> PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy >> >> //Python site-packages directory to install a .pth file pointing >> // at WrapITK Python modules. >> PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages > > > Best, > > Sami > > On Sep 30, 2014, at 14:03, Michka Popoff wrote: > >> Hi >> >> once ITK is compiled, there is no more need for Swig at runtime. >> >> For the syntax, you should use the new wrapping syntax. >> Look at how it is done in this example, at the end there is python code [1] >> >> I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig. >> If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig. >> You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora >> >> The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial. >> >> [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html >> >> Michka >> >> On 30 sept. 2014, at 12:51, Sami Koho wrote: >> >>> Hello, >>> >>> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer. >>> >>> I am able to load itk in Python, but every time I try to execute anything, the following error appears: >>> >>>> in () >>>> ----> 1 reader = itk.ImageFileReader.IUC3.New() >>>> >>>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr) >>>> 40 module = self.__lazy_attributes[attr] >>>> 41 namespace = {} >>>> ---> 42 itkBase.LoadModule(module, namespace) >>>> 43 # Load into 'namespace' first, then self.__dict__ (via setattr) to >>>> 44 # prevent the warnings about overwriting the 'NotLoaded' values >>>> >>>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace) >>>> 51 if namespace is not None: >>>> 52 swig = namespace.setdefault('swig', imp.new_module('swig')) >>>> ---> 53 swig.__dict__.update(this_module.swig.__dict__) >>>> 54 >>>> 55 # don't worry about overwriting the symbols in namespace -- any >>>> >>>> AttributeError: 'module' object has no attribute 'swig' >>> >>> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython, tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly. >>> >>> Should I manually set a path to swig? Or is something else wrong instead? >>> >>> I have installed ITK in the default path /usr/local/lib, as can be seen from the example. >>> >>> Best, >>> >>> Sami >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michkapopoff at gmail.com Tue Sep 30 09:51:06 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Tue, 30 Sep 2014 15:51:06 +0200 Subject: [ITK] [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem In-Reply-To: References: <542A8B2E.6020404@utu.fi> <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> Message-ID: Just writing this down for the list archives Sami, thank you very much for all the informations. I updated an created a new page, for Fedora and Ubuntu, with all the details. http://www.itk.org/Wiki/ITK/WrapITKInstallLinux For the moment this page is somewhat hidden, because you need to click 3-4 links through the FAQ and multiple pages to get to it. I will maybe reorganize the wiki a little bit to move the installation procedures to the front page. Thanks again Michka On 30 sept. 2014, at 15:14, Michka Popoff wrote: > Would it be possible for you to write this down for me, so I can update the guide on the wiki ? > > Michka > > On 30 sept. 2014, at 14:51, Sami Koho wrote: > >> Thank you Michka! The solution was in the ldconfig file creation: >> >>> ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here. >>> cd /etc/ld.so.conf.d/ >>> add a file called itk-46.conf, which should contain only one line: /usr/local/lib >>> ldconfig # tells the system to read the files in ld.so.conf.d >> >> On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide: >> >>> /Path to a program. >>> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python >>> >>> //Path to a file. >>> PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 >>> >>> //Path to a file. >>> PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7 >>> >>> //Path to a library. >>> PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 >>> >>> //Path to a library. >>> PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND >>> >>> //Directory where the arrayobject.h header file can be found. This >>> // file is part of the numarray package >>> PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy >>> >>> //Python site-packages directory to install a .pth file pointing >>> // at WrapITK Python modules. >>> PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages >> >> >> Best, >> >> Sami >> >> On Sep 30, 2014, at 14:03, Michka Popoff wrote: >> >>> Hi >>> >>> once ITK is compiled, there is no more need for Swig at runtime. >>> >>> For the syntax, you should use the new wrapping syntax. >>> Look at how it is done in this example, at the end there is python code [1] >>> >>> I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig. >>> If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig. >>> You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora >>> >>> The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial. >>> >>> [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html >>> >>> Michka >>> >>> On 30 sept. 2014, at 12:51, Sami Koho wrote: >>> >>>> Hello, >>>> >>>> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer. >>>> >>>> I am able to load itk in Python, but every time I try to execute anything, the following error appears: >>>> >>>>> in () >>>>> ----> 1 reader = itk.ImageFileReader.IUC3.New() >>>>> >>>>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr) >>>>> 40 module = self.__lazy_attributes[attr] >>>>> 41 namespace = {} >>>>> ---> 42 itkBase.LoadModule(module, namespace) >>>>> 43 # Load into 'namespace' first, then self.__dict__ (via setattr) to >>>>> 44 # prevent the warnings about overwriting the 'NotLoaded' values >>>>> >>>>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace) >>>>> 51 if namespace is not None: >>>>> 52 swig = namespace.setdefault('swig', imp.new_module('swig')) >>>>> ---> 53 swig.__dict__.update(this_module.swig.__dict__) >>>>> 54 >>>>> 55 # don't worry about overwriting the symbols in namespace -- any >>>>> >>>>> AttributeError: 'module' object has no attribute 'swig' >>>> >>>> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython, tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly. >>>> >>>> Should I manually set a path to swig? Or is something else wrong instead? >>>> >>>> I have installed ITK in the default path /usr/local/lib, as can be seen from the example. >>>> >>>> Best, >>>> >>>> Sami >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Tue Sep 30 09:57:58 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Tue, 30 Sep 2014 09:57:58 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: On the Importance of Location and Features for the Patch-Based Segmentation of Parotid Glands Message-ID: <20140930135758.AC11E3D6C169@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: On the Importance of Location and Features for the Patch-Based Segmentation of Parotid Glands Authors: Wachinger C., Brennan M., Sharp G., Golland P. Abstract: The segmentation of parotid glands in CT scans of patients with head and neck cancer is an essential part of treatment planning. We introduce a new method for the automatic segmentation of parotid glands that extends existing patch-based approaches in three ways: (1) we promote the use of image features in combination with patch intensity values to increase discrimination; (2) we work with larger search windows than established methods by using an approximate nearest neighbor search; and (3) we demonstrate that location information is a crucial discriminator and add it explicitly to the description. In our experiments, we compare a large number of features and introduce a new multi-scale descriptor. The best performance is achieved with entropy image features in combination with patches and location information. Download and review this publication at: http://hdl.handle.net/10380/3472 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Tue Sep 30 10:14:15 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 30 Sep 2014 14:14:15 +0000 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) Message-ID: This is a problem that has been cropping up in our projects that use ITK, VTK and SlicerExecutionModel. You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules. The problem is this: if you find packages in this order: find_package(VTK REQUIRED) find_package(ITK REQUIRED) You can?t real compile anything that needs VTK, because down in the ITK deployment stuff, it calls find_package(VTK) like this: find_package(VTK COMPONENTS vtkCommonCore vtkRenderingCore vtkRenderingOpenGL vtkRenderingFreeType vtkInteractionStyle vtkIOImage vtkImagingSources REQUIRED) Which blows away the larger list of include directories and libraries that the first find_package(VTK REQUIRED) built. Even better ? or worse ? Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include find_package(VTK) ? so ITK tries to import VTK twice, with different module lists. It doesn?t even help to reverse the order: find_package(ITK REQUIRED) find_package(VTK REQUIRED) because apparently there?s some hangover from the find_package(VTK) inside the ITK CMake deployment files. The only thing that works is to use COMPONENTS, i.e. find_package(ITK REQUIRED) find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED) Which seems to trigger a proper re-scan and build of the library/include lists. It gets even worse if you use find_package(SlicerExecutionModel) after find_package(ITK), for the same reason ? SlicerExecutionModel depends on ITK, so it clobbers the include/library lists from the first find_package(ITK). ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 30 10:17:27 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 10:17:27 -0400 Subject: [ITK] [ITK-users] Push forward Pull Back Euler Lagrangian Frame In-Reply-To: References: Message-ID: Hi Emma, Yes, that sounds correct. Is there some context to where this language is being used? Thanks, Matt On Mon, Sep 29, 2014 at 3:25 PM, Emma Saunders wrote: > Hi List > > I am experiencing some confusion with terms above, if someone could clarify > that would be great: > > Does registration using a Eulerian frame correspond to a pull back framework > of registration > > similarly: > > Does registration using a Lagrangian frame correspond to a push forward > framework for registration? > > Thanks for any help > > Kind regards > > Emma > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Sep 30 10:21:26 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 10:21:26 -0400 Subject: [ITK] [ITK-users] segmentation error in PCA estimator In-Reply-To: References: Message-ID: Hi Lianli, Building the program with debugging symbols and running the executable in a debugger should shed more light. Or, sharing a SSCCE [1], i.e. the code and images and command (CTest test), should help others debug your issue. Thanks, Matt [1] http://sscce.org/ On Mon, Sep 29, 2014 at 6:24 PM, Lianli Liu wrote: > Hi all, > > I am applying the itk example code for PCA estimator (EstimatePCAModel.cxx). > I have 10 training images and I intend to output all components (i.e. 10). > But after writing 4 components, I get the segmentation fault. I was > wondering what is the cause of this? I would really appreciate any help. > Thanks! > > Regards, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Tue Sep 30 10:23:36 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 30 Sep 2014 10:23:36 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: References: Message-ID: Here is what I do for the WikiExamples remote module: find_package(VTK REQUIRED) include(${VTK_USE_FILE}) set(VTK_COMPONENTS ${VTK_LIBRARIES}) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) set(ITK_LIBRARIES ${ITK_LIBRARIES} ${VTK_COMPONENTS}) On Tue, Sep 30, 2014 at 10:14 AM, Williams, Norman K wrote: > This is a problem that has been cropping up in our projects that use ITK, > VTK and SlicerExecutionModel. > > You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules. > > The problem is this: if you find packages in this order: > > find_package(VTK REQUIRED) > find_package(ITK REQUIRED) > > You can?t real compile anything that needs VTK, because down in the ITK > deployment stuff, it calls find_package(VTK) like this: > find_package(VTK COMPONENTS > vtkCommonCore > vtkRenderingCore > vtkRenderingOpenGL > vtkRenderingFreeType > vtkInteractionStyle > vtkIOImage > vtkImagingSources > REQUIRED) > > Which blows away the larger list of include directories and libraries that > the first find_package(VTK REQUIRED) built. > > Even better ? or worse ? > Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include > find_package(VTK) ? so ITK tries to import VTK twice, with different module > lists. > > It doesn?t even help to reverse the order: > find_package(ITK REQUIRED) > find_package(VTK REQUIRED) > > because apparently there?s some hangover from the find_package(VTK) inside > the ITK CMake deployment files. The only thing that works is to use > COMPONENTS, i.e. > > find_package(ITK REQUIRED) > find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED) > > Which seems to trigger a proper re-scan and build of the library/include > lists. > > It gets even worse if you use find_package(SlicerExecutionModel) after > find_package(ITK), for the same reason ? SlicerExecutionModel depends on > ITK, so it clobbers the include/library lists from the first > find_package(ITK). > > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From brad.king at kitware.com Tue Sep 30 10:48:47 2014 From: brad.king at kitware.com (Brad King) Date: Tue, 30 Sep 2014 10:48:47 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: References: Message-ID: <542AC2CF.7030008@kitware.com> On 09/30/2014 10:14 AM, Williams, Norman K wrote: > find_package(VTK REQUIRED) > find_package(ITK REQUIRED) > > You can?t real compile anything that needs VTK, because down in > the ITK deployment stuff, it calls find_package(VTK) like this: [snip] > Which blows away the larger list of include directories and libraries One may use the itk_module_config and vtk_module_config macros from the *ModuleAPI.cmake modules that come with the respective packages to compute the list of libraries and include dirs for a given list of components. All ITKConfig and VTKConfig do with the list of components is: itk_module_config(ITK ${ITK_MODULES_REQUESTED}) # sets ITK_LIBRARIES, ITK_INCLUDE_DIRS, etc. and vtk_module_config(VTK ${VTK_MODULES_REQUESTED}) # sets VTK_LIBRARIES, VTK_INCLUDE_DIRS, etc. One can invoke these directly: itk_module_config(ITK ${MY_LIST_OF_ITK_COMPONENTS}) vtk_module_config(VTK ${MY_LIST_OF_VTK_COMPONENTS}) at any time after the find_package calls. One could even use a different prefix: itk_module_config(MyITK ${MY_LIST_OF_ITK_COMPONENTS}) # sets MyITK_LIBRARIES, MyITK_INCLUDE_DIRS, etc. In the long run the plan is to stop recommending use of component lists at find_package time and instead use imported targets and usage requirements: http://www.cmake.org/cmake/help/v3.0/manual/cmake-buildsystem.7.html#build-specification-and-usage-requirements but that will have to wait until we can require CMake 3.0. -Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Sep 30 11:13:22 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 30 Sep 2014 11:13:22 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: <542AC2CF.7030008@kitware.com> References: <542AC2CF.7030008@kitware.com> Message-ID: Brad, Do you have a suggestion on how to conditionally include a module if it's available? e.g. Use ITKDeprecated if ITK was configure with it? Thanks, Brad On Sep 30, 2014, at 10:48 AM, Brad King wrote: > On 09/30/2014 10:14 AM, Williams, Norman K wrote: >> find_package(VTK REQUIRED) >> find_package(ITK REQUIRED) >> >> You can?t real compile anything that needs VTK, because down in >> the ITK deployment stuff, it calls find_package(VTK) like this: > [snip] >> Which blows away the larger list of include directories and libraries > > One may use the itk_module_config and vtk_module_config macros > from the *ModuleAPI.cmake modules that come with the respective > packages to compute the list of libraries and include dirs for > a given list of components. All ITKConfig and VTKConfig do with > the list of components is: > > itk_module_config(ITK ${ITK_MODULES_REQUESTED}) > # sets ITK_LIBRARIES, ITK_INCLUDE_DIRS, etc. > > and > > vtk_module_config(VTK ${VTK_MODULES_REQUESTED}) > # sets VTK_LIBRARIES, VTK_INCLUDE_DIRS, etc. > > One can invoke these directly: > > itk_module_config(ITK ${MY_LIST_OF_ITK_COMPONENTS}) > vtk_module_config(VTK ${MY_LIST_OF_VTK_COMPONENTS}) > > at any time after the find_package calls. One could even use > a different prefix: > > itk_module_config(MyITK ${MY_LIST_OF_ITK_COMPONENTS}) > # sets MyITK_LIBRARIES, MyITK_INCLUDE_DIRS, etc. > > In the long run the plan is to stop recommending use of component > lists at find_package time and instead use imported targets and > usage requirements: > > http://www.cmake.org/cmake/help/v3.0/manual/cmake-buildsystem.7.html#build-specification-and-usage-requirements > > but that will have to wait until we can require CMake 3.0. > > -Brad > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From brad.king at kitware.com Tue Sep 30 11:22:57 2014 From: brad.king at kitware.com (Brad King) Date: Tue, 30 Sep 2014 11:22:57 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: References: <542AC2CF.7030008@kitware.com> Message-ID: <542ACAD1.2040805@kitware.com> On 09/30/2014 11:13 AM, Bradley Lowekamp wrote: > Do you have a suggestion on how to conditionally include a > module if it's available? e.g. Use ITKDeprecated if ITK was > configure with it? find_package(ITK REQUIRED) set(MY_ITK_COMPONENTS ...) # list required mods here if(";${ITK_MODULES_ENABLED};" MATCHES ";ITKDeprecated;") list(APPEND MY_ITK_COMPONENTS ITKDeprecated) endif() itk_module_config(ITK ${MY_ITK_COMPONENTS}) I think the if() line could also be written if(TARGET ITKDeprecated) but I don't remember off the top of my head whether the library names and module names always match exactly. -Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 30 12:59:39 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 12:59:39 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: References: Message-ID: Hi Kent, On Tue, Sep 30, 2014 at 10:14 AM, Williams, Norman K wrote: > This is a problem that has been cropping up in our projects that use ITK, > VTK and SlicerExecutionModel. > > You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules. > > The problem is this: if you find packages in this order: > > find_package(VTK REQUIRED) > find_package(ITK REQUIRED) > > You can?t real compile anything that needs VTK, because down in the ITK > deployment stuff, it calls find_package(VTK) like this: > find_package(VTK COMPONENTS > vtkCommonCore > vtkRenderingCore > vtkRenderingOpenGL > vtkRenderingFreeType > vtkInteractionStyle > vtkIOImage > vtkImagingSources > REQUIRED) > > Which blows away the larger list of include directories and libraries that > the first find_package(VTK REQUIRED) built. > > Even better ? or worse ? > Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include > find_package(VTK) ? so ITK tries to import VTK twice, with different module > lists. > > It doesn?t even help to reverse the order: > find_package(ITK REQUIRED) > find_package(VTK REQUIRED) > > because apparently there?s some hangover from the find_package(VTK) inside > the ITK CMake deployment files. The only thing that works is to use > COMPONENTS, i.e. > > find_package(ITK REQUIRED) > find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED) > > Which seems to trigger a proper re-scan and build of the library/include > lists. This was discussed in this thread [1]. There does not seem to be interest at this time to have mixed COMPONENTS / non-COMPONENTS calls to find_package. It is also recommended to use the MODULE option to find_package. A "newer" version of VTK 6 is also required. > It gets even worse if you use find_package(SlicerExecutionModel) after > find_package(ITK), for the same reason ? SlicerExecutionModel depends on > ITK, so it clobbers the include/library lists from the first > find_package(ITK). > A patch was merged a few days ago that might address this issue [2]. Is this behavior still see with current ITK? Thanks, Matt [1] http://public.kitware.com/pipermail/vtk-developers/2014-September/015376.html [2] http://review.source.kitware.com/#/c/16963/ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 30 16:43:49 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 16:43:49 -0400 Subject: [ITK] ITK 4.6.1 Downloads update Message-ID: Hi Comm, Could the ITK download links please be updated for v4.6.1? On this page: http://www.itk.org/ITK/resources/software.html The current release is version 4.6.0 from July 2014. The following downloads are available: to The current release is version 4.6.1 from September 2014. The following downloads are available: and Library Source InsightToolkit-4.6.0.tar.gz (hosted at Sourceforge) InsightToolkit-4.6.0.tar.xz (hosted at Sourceforge) InsightToolkit-4.6.0.zip (hosted at Sourceforge) to Library Source InsightToolkit-4.6.1.tar.gz (hosted at Sourceforge) InsightToolkit-4.6.1.tar.xz (hosted at Sourceforge) InsightToolkit-4.6.1.zip (hosted at Sourceforge) with the links adjusted accordingly. Release notes written in anticipation of the release are here: https://docs.google.com/a/kitware.com/document/d/1wXFV1a2hfnZS8rDx96iO42fC9dyti6Onl-3PUPTYjDU/edit Thanks, Matt From matt.mccormick at kitware.com Tue Sep 30 17:06:53 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 17:06:53 -0400 Subject: [ITK] ITK 4.6.1 Downloads update In-Reply-To: References: Message-ID: Note: this message was meant for people updating the ITK download pages -- but ITK 4.6.1 will be coming soon! :-) On Tue, Sep 30, 2014 at 4:43 PM, Matt McCormick wrote: > Hi Comm, > > Could the ITK download links please be updated for v4.6.1? > > On this page: > > http://www.itk.org/ITK/resources/software.html > > > The current release is version 4.6.0 from July 2014. The following > downloads are available: > > to > > The current release is version 4.6.1 from September 2014. The > following downloads are available: > > > and > > Library Source > > InsightToolkit-4.6.0.tar.gz (hosted at Sourceforge) > InsightToolkit-4.6.0.tar.xz (hosted at Sourceforge) > InsightToolkit-4.6.0.zip (hosted at Sourceforge) > > to > > Library Source > > InsightToolkit-4.6.1.tar.gz (hosted at Sourceforge) > InsightToolkit-4.6.1.tar.xz (hosted at Sourceforge) > InsightToolkit-4.6.1.zip (hosted at Sourceforge) > > > with the links adjusted accordingly. > > > Release notes written in anticipation of the release are here: > https://docs.google.com/a/kitware.com/document/d/1wXFV1a2hfnZS8rDx96iO42fC9dyti6Onl-3PUPTYjDU/edit > > > Thanks, > Matt From mikael.k.eriksson at philips.com Mon Sep 1 02:11:54 2014 From: mikael.k.eriksson at philips.com (Eriksson, Mikael) Date: Mon, 1 Sep 2014 06:11:54 +0000 Subject: [ITK] Registration of multislice images Message-ID: <2D9DC0609429E24BA87612C012C580C318A75ED3@AMSPRD9002MB028.MGDPHG.emi.philips.com> Hello, I have obtained multislice image data for trying to do real-time registration for motion correction purposes. Specifically, every 0.x seconds, one coronal, one sagittal and one axial slice is obtained during the imaging, and I would like to register pairs of such sets with each other, e.g. each set after the first set at time zero should be registered to this time zero set. The slices cover the entire body in the axial plane, and the upper body from the hips to the neck in the sagittal and coronal planes with a size of 336 x 336 and pixel spacing of 1.19 x 1.19. I have searched for possible implementations in ITK and haven't found anything. An interesting article on the subject which describes what I want to do can be found here: http://www.researchgate.net/publication/221623301_Intersection_based_registration_of_slice_stacks_to_form_3D_images_of_the_human_fetal_brain Essentially, what they did was to optimize the (rigid) transform the slices in the moving set until their intensity profiles along the intersections with orthogonal slices match the intensity profiles at the corresponding intersections in the fixed set, within a certain tolerance. Now, this is one way that I would be more than happy to try out on my data, but likewise, if there are other methods already implemented in ITK I'll try them out as well. If there isn't anything already implemented, could someone please give me some hints as for how to write a program which does something along the lines of what I described above (and is described in more detail in the link)? Oh, and just knowing whether anything like this already exists and can be used in ITK will be a huge help, since it would allow me to plan my work. Best regards, Mikael ....................................................................................................... Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies mikael.k.eriksson at philips.com ....................................................................................................... ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuetian926 at 163.com Mon Sep 1 02:32:05 2014 From: yuetian926 at 163.com (Yuetian Liu) Date: Mon, 1 Sep 2014 14:32:05 +0800 (CST) Subject: [ITK] [ITK-users] How to fusion the MR volume to the CT volume Message-ID: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> Hi itkusers, Recently I want to fuse the MR volume to the CT volume, but I search the itk mailist. I haven;t known how to realise it. And there isn't example in the InsightSoftwareGuide-4.5.0.pdf and InsightSphinxExamplesPDF-4.5.0.pdf. So I want to ask how to fuse the MR volume to the CT volume by itk. Thank you for helping me! Best Yuetian -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michael.meuli at gmail.com Mon Sep 1 09:38:40 2014 From: michael.meuli at gmail.com (Michael Meuli) Date: Mon, 1 Sep 2014 15:38:40 +0200 Subject: [ITK] Distances of objects in LabelMap Message-ID: I have objects in a LabelMap (having used BinaryImageToLabelMapFilter). How do I best get the distance to the closest neighbouring object for each of these objects? (As I would like to exclude objects if they are too close to each other.) Best regards and many thanks Michael From indianzeppelin at gmail.com Mon Sep 1 09:59:13 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Mon, 1 Sep 2014 14:59:13 +0100 Subject: [ITK] Distances of objects in LabelMap In-Reply-To: References: Message-ID: Did you look into LabelGeometryImageFilter? You could get the centroids of the objects using that, and then use some nearest-neighbor searching algorithm for each centroid. On Mon, Sep 1, 2014 at 2:38 PM, Michael Meuli wrote: > I have objects in a LabelMap (having used BinaryImageToLabelMapFilter). > How do I best get the distance to the closest neighbouring object for > each of these objects? > (As I would like to exclude objects if they are too close to each other.) > > Best regards and many thanks > Michael > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From lasso at queensu.ca Mon Sep 1 10:40:38 2014 From: lasso at queensu.ca (Andras Lasso) Date: Mon, 1 Sep 2014 14:40:38 +0000 Subject: [ITK] Registration of multislice images In-Reply-To: <2D9DC0609429E24BA87612C012C580C318A75ED3@AMSPRD9002MB028.MGDPHG.emi.philips.com> References: <2D9DC0609429E24BA87612C012C580C318A75ED3@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: Hi Mikael, You can copy the voxels from each slice into a volume and use that as fixed image, use a mask that has non-zero values only at valid pixels (usually you can use the constructed image itself as a mask), then do a usual volumetric registration. This works quite well, if you have orthogonal images and their resolution is similar (see for example http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5975205). You can use ITK as is, no modifications are needed. Alternatively, you can modify a similarity metric to accept multiple images and compute the metric value as sum of the metric value of each image (this is necessary when the image slices are not orthogonal). An IJCARS paper is in press, a high-level overview is given in this abstract: http://perk.cs.queensu.ca/contents/target-localization-mriguided-transperineal-prostate-biopsy-using-multislicetovolume-regist . Andras From: Eriksson, Mikael Sent: ?Monday?, ?September? ?1?, ?2014 ?1?:?26? ?AM To: community at itk.org Hello, I have obtained multislice image data for trying to do real-time registration for motion correction purposes. Specifically, every 0.x seconds, one coronal, one sagittal and one axial slice is obtained during the imaging, and I would like to register pairs of such sets with each other, e.g. each set after the first set at time zero should be registered to this time zero set. The slices cover the entire body in the axial plane, and the upper body from the hips to the neck in the sagittal and coronal planes with a size of 336 x 336 and pixel spacing of 1.19 x 1.19. I have searched for possible implementations in ITK and haven?t found anything. An interesting article on the subject which describes what I want to do can be found here: http://www.researchgate.net/publication/221623301_Intersection_based_registration_of_slice_stacks_to_form_3D_images_of_the_human_fetal_brain Essentially, what they did was to optimize the (rigid) transform the slices in the moving set until their intensity profiles along the intersections with orthogonal slices match the intensity profiles at the corresponding intersections in the fixed set, within a certain tolerance. Now, this is one way that I would be more than happy to try out on my data, but likewise, if there are other methods already implemented in ITK I?ll try them out as well. If there isn?t anything already implemented, could someone please give me some hints as for how to write a program which does something along the lines of what I described above (and is described in more detail in the link)? Oh, and just knowing whether anything like this already exists and can be used in ITK will be a huge help, since it would allow me to plan my work. Best regards, Mikael ??????????????????????????????????. Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies mikael.k.eriksson at philips.com ??????????????????????????????????. ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 1 15:09:38 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Sep 2014 15:09:38 -0400 Subject: [ITK] [ITK-dev] [ITK-users] How to fusion the MR volume to the CT volume In-Reply-To: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> References: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> Message-ID: Hi Yeutian, Try a registration algorithm using a mutual information based metric. See also the Slicer Registration Case Library [1], which uses ITK under the hood, for examples. HTH, Matt [1] http://www.na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory On Mon, Sep 1, 2014 at 2:32 AM, Yuetian Liu wrote: > > Hi itkusers, > > Recently I want to fuse the MR volume to the CT volume, but I search the itk > mailist. > I haven;t known how to realise it. And there isn't example in the > InsightSoftwareGuide-4.5.0.pdf > and InsightSphinxExamplesPDF-4.5.0.pdf. > So I want to ask how to fuse the MR volume to the CT volume by itk. > > Thank you for helping me! > > Best > Yuetian > > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Sep 1 15:09:38 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Sep 2014 15:09:38 -0400 Subject: [ITK] [ITK-users] How to fusion the MR volume to the CT volume In-Reply-To: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> References: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com> Message-ID: Hi Yeutian, Try a registration algorithm using a mutual information based metric. See also the Slicer Registration Case Library [1], which uses ITK under the hood, for examples. HTH, Matt [1] http://www.na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory On Mon, Sep 1, 2014 at 2:32 AM, Yuetian Liu wrote: > > Hi itkusers, > > Recently I want to fuse the MR volume to the CT volume, but I search the itk > mailist. > I haven;t known how to realise it. And there isn't example in the > InsightSoftwareGuide-4.5.0.pdf > and InsightSphinxExamplesPDF-4.5.0.pdf. > So I want to ask how to fuse the MR volume to the CT volume by itk. > > Thank you for helping me! > > Best > Yuetian > > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From mikael.k.eriksson at philips.com Tue Sep 2 01:04:53 2014 From: mikael.k.eriksson at philips.com (Eriksson, Mikael) Date: Tue, 2 Sep 2014 05:04:53 +0000 Subject: [ITK] Registration of multislice images In-Reply-To: References: <2D9DC0609429E24BA87612C012C580C318A75ED3@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: <2D9DC0609429E24BA87612C012C580C318A7607F@AMSPRD9002MB028.MGDPHG.emi.philips.com> Thank you Andras, this helps a lot! Glad to see that the solutions are simple and elegant. Best regards, Mikael ??????????????????????????????????. Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies +358 40 631 8500 mikael.k.eriksson at philips.com ??????????????????????????????????. From: Andras Lasso [mailto:lasso at queensu.ca] Sent: 1. syyskuuta 2014 17:41 To: Eriksson, Mikael; community at itk.org Subject: Re: [ITK] Registration of multislice images Hi Mikael, You can copy the voxels from each slice into a volume and use that as fixed image, use a mask that has non-zero values only at valid pixels (usually you can use the constructed image itself as a mask), then do a usual volumetric registration. This works quite well, if you have orthogonal images and their resolution is similar (see for example http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5975205). You can use ITK as is, no modifications are needed. Alternatively, you can modify a similarity metric to accept multiple images and compute the metric value as sum of the metric value of each image (this is necessary when the image slices are not orthogonal). An IJCARS paper is in press, a high-level overview is given in this abstract: http://perk.cs.queensu.ca/contents/target-localization-mriguided-transperineal-prostate-biopsy-using-multislicetovolume-regist . Andras From: Eriksson, Mikael Sent: ?Monday?, ?September? ?1?, ?2014 ?1?:?26? ?AM To: community at itk.org Hello, I have obtained multislice image data for trying to do real-time registration for motion correction purposes. Specifically, every 0.x seconds, one coronal, one sagittal and one axial slice is obtained during the imaging, and I would like to register pairs of such sets with each other, e.g. each set after the first set at time zero should be registered to this time zero set. The slices cover the entire body in the axial plane, and the upper body from the hips to the neck in the sagittal and coronal planes with a size of 336 x 336 and pixel spacing of 1.19 x 1.19. I have searched for possible implementations in ITK and haven?t found anything. An interesting article on the subject which describes what I want to do can be found here: http://www.researchgate.net/publication/221623301_Intersection_based_registration_of_slice_stacks_to_form_3D_images_of_the_human_fetal_brain Essentially, what they did was to optimize the (rigid) transform the slices in the moving set until their intensity profiles along the intersections with orthogonal slices match the intensity profiles at the corresponding intersections in the fixed set, within a certain tolerance. Now, this is one way that I would be more than happy to try out on my data, but likewise, if there are other methods already implemented in ITK I?ll try them out as well. If there isn?t anything already implemented, could someone please give me some hints as for how to write a program which does something along the lines of what I described above (and is described in more detail in the link)? Oh, and just knowing whether anything like this already exists and can be used in ITK will be a huge help, since it would allow me to plan my work. Best regards, Mikael ??????????????????????????????????. Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies mikael.k.eriksson at philips.com ??????????????????????????????????. ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Sep 2 09:18:47 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Sep 2014 09:18:47 -0400 Subject: [ITK] [ITK-dev] issues.itk.org maintenance In-Reply-To: References: Message-ID: Thanks again for running the server! Brad On Aug 28, 2014, at 2:37 PM, Johnson, Hans J wrote: > The ITK bug tracker will be down for approximately 30 minutes at 4:30CST today for routine maintenance. > > Hans > > > > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 2 11:52:03 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 2 Sep 2014 11:52:03 -0400 Subject: [ITK] [ITK-users] ResampleDICOM example and DCMTK In-Reply-To: References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com> Message-ID: Hi Nick, The DCMTKImageIO class does not yet populate and extract tag information to / from the an Image's MetaDataDictionary. This will have to be implemented for this to work. HTH, Matt On Sun, Aug 31, 2014 at 5:38 PM, Matt McCormick wrote: > Hi Nick, > > Nothing stands out from inspecting the code. Could you please send an > example dataset? > > Thanks, > Matt > > On Sun, Aug 31, 2014 at 4:06 PM, NPatterson wrote: >> Hi, I wondered if anyone could test the code attached in the thread header >> "ResampleDICOM example and DCMTK" regarding the use of DCMTK for DICOM >> reading writing in ITK. I adapted the ResampleDICOM example to work with >> DCMTK instead of GDCM, and although I get no errors, I also do not get any >> output dicom images. If someone has the time to test this code to see if >> they observe the same behaviour/or can suggest a fix, I would be very >> appreciative. >> >> Regards, Nick. >> >> >> >> -- >> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-ResampleDICOM-example-and-DCMTK-tp7586131p7586158.html >> Sent from the ITK Insight Users mailing list archive at Nabble.com. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From tejasl2603 at gmail.com Tue Sep 2 16:07:25 2014 From: tejasl2603 at gmail.com (tejas lunawat) Date: Wed, 3 Sep 2014 01:37:25 +0530 Subject: [ITK] Error while building ITK Message-ID: Hey... I am an engineering student, working on a project, based on ITK libraries. I am new to ITK. I have encounter an error while building 'itkhdf5.sln' file. Details of the error are as follows: Error 1 error MSB6006: "cmd.exe" exited with code 216. Error 2 error LNK1104: cannot open file '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' I have searched for the solution of this error, but I didn't found it. Is their any possible way to solve this error Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Sep 2 16:30:17 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 2 Sep 2014 20:30:17 +0000 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: You are building a Debug program. Check that you have Debug ITK libraries installed. If not change the build selection in Visual Studio to Release. ________________________________ From: Community [community-bounces at itk.org] on behalf of tejas lunawat [tejasl2603 at gmail.com] Sent: Wednesday, 3 September 2014 8:07 a.m. To: community at itk.org Subject: [ITK] Error while building ITK Hey... I am an engineering student, working on a project, based on ITK libraries. I am new to ITK. I have encounter an error while building 'itkhdf5.sln' file. Details of the error are as follows: Error 1 error MSB6006: "cmd.exe" exited with code 216. Error 2 error LNK1104: cannot open file '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' I have searched for the solution of this error, but I didn't found it. Is their any possible way to solve this error Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: From tejasl2603 at gmail.com Wed Sep 3 01:59:39 2014 From: tejasl2603 at gmail.com (tejas lunawat) Date: Wed, 3 Sep 2014 11:29:39 +0530 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: ?? Even after changing the build selection in Visual Studio to Release, same error still persisits. On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle wrote: > You are building a Debug program. Check that you have Debug ITK > libraries installed. If not change the build selection in Visual Studio to > Release. > ------------------------------ > *From:* Community [community-bounces at itk.org] on behalf of tejas lunawat [ > tejasl2603 at gmail.com] > *Sent:* Wednesday, 3 September 2014 8:07 a.m. > *To:* community at itk.org > *Subject:* [ITK] Error while building ITK > > Hey... > > I am an engineering student, working on a project, based on ITK libraries. > I am new to ITK. I have encounter an error while building 'itkhdf5.sln' > file. Details of the error are as follows: > > Error 1 error MSB6006: "cmd.exe" exited with code 216. > Error 2 error LNK1104: cannot open file > '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' > > I have searched for the solution of this error, but I didn't found it. > Is their any possible way to solve this error Thank you > -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 3 02:36:55 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 3 Sep 2014 06:36:55 +0000 Subject: [ITK] Error while building ITK In-Reply-To: References: , Message-ID: Are you using a CMakeLists.txt file and cmake to create your project files? ________________________________ From: tejas lunawat [tejasl2603 at gmail.com] Sent: Wednesday, 3 September 2014 5:59 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] Error while building ITK ?? Even after changing the build selection in Visual Studio to Release, same error still persisits. On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle > wrote: You are building a Debug program. Check that you have Debug ITK libraries installed. If not change the build selection in Visual Studio to Release. ________________________________ From: Community [community-bounces at itk.org] on behalf of tejas lunawat [tejasl2603 at gmail.com] Sent: Wednesday, 3 September 2014 8:07 a.m. To: community at itk.org Subject: [ITK] Error while building ITK Hey... I am an engineering student, working on a project, based on ITK libraries. I am new to ITK. I have encounter an error while building 'itkhdf5.sln' file. Details of the error are as follows: Error 1 error MSB6006: "cmd.exe" exited with code 216. Error 2 error LNK1104: cannot open file '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' I have searched for the solution of this error, but I didn't found it. Is their any possible way to solve this error Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Wed Sep 3 05:16:48 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Wed, 3 Sep 2014 10:16:48 +0100 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: 1) From your question, I understand that you are having a problem building the ITK library itself and not a project which uses the library. Is that correct? 2) If so, I assume you have used CMake for configuring and generating the .sln files from the ITK source files on your computer. Specifically, did you follow the steps described here - http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? 3) Are you trying to build only "ITKHDF5.sln" (located at "your_ITK_build_folder\Modules\ThirdParty\HDF5)? On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle wrote: > Are you using a CMakeLists.txt file and cmake to create your project > files? > ------------------------------ > *From:* tejas lunawat [tejasl2603 at gmail.com] > *Sent:* Wednesday, 3 September 2014 5:59 p.m. > *To:* Gib Bogle > *Cc:* community at itk.org > *Subject:* Re: [ITK] Error while building ITK > > ?? > Even after changing the build selection in Visual Studio to Release, > same error still persisits. > > > On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle wrote: > >> You are building a Debug program. Check that you have Debug ITK >> libraries installed. If not change the build selection in Visual Studio to >> Release. >> ------------------------------ >> *From:* Community [community-bounces at itk.org] on behalf of tejas lunawat >> [tejasl2603 at gmail.com] >> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >> *To:* community at itk.org >> *Subject:* [ITK] Error while building ITK >> >> Hey... >> >> I am an engineering student, working on a project, based on ITK libraries. >> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >> file. Details of the error are as follows: >> >> Error 1 error MSB6006: "cmd.exe" exited with code 216. >> Error 2 error LNK1104: cannot open file >> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >> >> I have searched for the solution of this error, but I didn't found it. >> Is their any possible way to solve this error Thank you >> > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From tejasl2603 at gmail.com Wed Sep 3 06:18:28 2014 From: tejasl2603 at gmail.com (tejas lunawat) Date: Wed, 3 Sep 2014 15:48:28 +0530 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Yes, You are right. I am having a problem in building the ITK library itself. I followed all the steps described in this link http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio I have used CMake for configuring and generating the .sln files from the ITK source file. And then I am building the libraries by using itk.sln. On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < indianzeppelin at gmail.com> wrote: > 1) From your question, I understand that you are having a problem building > the ITK library itself and not a project which uses the library. Is that > correct? > > 2) If so, I assume you have used CMake for configuring and generating the > .sln files from the ITK source files on your computer. Specifically, did > you follow the steps described here - > http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? > > 3) Are you trying to build only "ITKHDF5.sln" (located at > "your_ITK_build_folder\Modules\ThirdParty\HDF5)? > > > On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle wrote: > >> Are you using a CMakeLists.txt file and cmake to create your project >> files? >> ------------------------------ >> *From:* tejas lunawat [tejasl2603 at gmail.com] >> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >> *To:* Gib Bogle >> *Cc:* community at itk.org >> *Subject:* Re: [ITK] Error while building ITK >> >> ?? >> Even after changing the build selection in Visual Studio to Release, >> same error still persisits. >> >> >> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle wrote: >> >>> You are building a Debug program. Check that you have Debug ITK >>> libraries installed. If not change the build selection in Visual Studio to >>> Release. >>> ------------------------------ >>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>> lunawat [tejasl2603 at gmail.com] >>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>> *To:* community at itk.org >>> *Subject:* [ITK] Error while building ITK >>> >>> Hey... >>> >>> I am an engineering student, working on a project, based on ITK libraries. >>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>> file. Details of the error are as follows: >>> >>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>> Error 2 error LNK1104: cannot open file >>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>> >>> I have searched for the solution of this error, but I didn't found it. >>> Is their any possible way to solve this error Thank you >>> >> >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Wed Sep 3 06:23:16 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Wed, 3 Sep 2014 11:23:16 +0100 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Ok. So, when you build "ITK.sln", do all the projects in it build fine with only "itkhdf5" failing? On Wed, Sep 3, 2014 at 11:18 AM, tejas lunawat wrote: > Yes, You are right. > I am having a problem in building the ITK library itself. > I followed all the steps described in this link > http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio > I have used CMake for configuring and generating the .sln files from the > ITK source file. > And then I am building the libraries by using itk.sln. > > > > On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < > indianzeppelin at gmail.com> wrote: > >> 1) From your question, I understand that you are having a problem >> building the ITK library itself and not a project which uses the library. >> Is that correct? >> >> 2) If so, I assume you have used CMake for configuring and generating the >> .sln files from the ITK source files on your computer. Specifically, did >> you follow the steps described here - >> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? >> >> 3) Are you trying to build only "ITKHDF5.sln" (located at >> "your_ITK_build_folder\Modules\ThirdParty\HDF5)? >> >> >> On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle wrote: >> >>> Are you using a CMakeLists.txt file and cmake to create your project >>> files? >>> ------------------------------ >>> *From:* tejas lunawat [tejasl2603 at gmail.com] >>> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >>> *To:* Gib Bogle >>> *Cc:* community at itk.org >>> *Subject:* Re: [ITK] Error while building ITK >>> >>> ?? >>> Even after changing the build selection in Visual Studio to Release, >>> same error still persisits. >>> >>> >>> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle >>> wrote: >>> >>>> You are building a Debug program. Check that you have Debug ITK >>>> libraries installed. If not change the build selection in Visual Studio to >>>> Release. >>>> ------------------------------ >>>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>>> lunawat [tejasl2603 at gmail.com] >>>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>>> *To:* community at itk.org >>>> *Subject:* [ITK] Error while building ITK >>>> >>>> Hey... >>>> >>>> I am an engineering student, working on a project, based on ITK libraries. >>>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>>> file. Details of the error are as follows: >>>> >>>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>>> Error 2 error LNK1104: cannot open file >>>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>>> >>>> I have searched for the solution of this error, but I didn't found >>>> it. Is their any possible way to solve this error Thank you >>>> >>> >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >> >> >> -- >> Regards, >> Girish >> > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Wed Sep 3 10:04:03 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Wed, 3 Sep 2014 15:04:03 +0100 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Strange. Have you tried opening and building the solution "ITKHDF5.sln" alone (located in "your_ITK_Build_folder\Modules\ThirdParty\HDF5")? If not, please try it and paste the contents of the output window (not just the error list). PS: Please keep the discussion on the mailing list (by cc'ing the community or replying to all)...:) On Wed, Sep 3, 2014 at 11:34 AM, tejas lunawat wrote: > yes, the problem is with "itkhdf5" and all others which are dependent on > it. As error are: > > Error 1 error MSB6006: "cmd.exe" exited with code 216. > Error 2 error LNK1104: cannot open file > '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' > > > On Wed, Sep 3, 2014 at 3:53 PM, Girish Mallya Udupi < > indianzeppelin at gmail.com> wrote: > >> Ok. So, when you build "ITK.sln", do all the projects in it build fine >> with only "itkhdf5" failing? >> >> >> On Wed, Sep 3, 2014 at 11:18 AM, tejas lunawat >> wrote: >> >>> Yes, You are right. >>> I am having a problem in building the ITK library itself. >>> I followed all the steps described in this link >>> >>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio >>> I have used CMake for configuring and generating the .sln files from >>> the ITK source file. >>> And then I am building the libraries by using itk.sln. >>> >>> >>> >>> On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < >>> indianzeppelin at gmail.com> wrote: >>> >>>> 1) From your question, I understand that you are having a problem >>>> building the ITK library itself and not a project which uses the library. >>>> Is that correct? >>>> >>>> 2) If so, I assume you have used CMake for configuring and generating >>>> the .sln files from the ITK source files on your computer. Specifically, >>>> did you follow the steps described here - >>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? >>>> >>>> 3) Are you trying to build only "ITKHDF5.sln" (located at >>>> "your_ITK_build_folder\Modules\ThirdParty\HDF5)? >>>> >>>> >>>> On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle >>>> wrote: >>>> >>>>> Are you using a CMakeLists.txt file and cmake to create your project >>>>> files? >>>>> ------------------------------ >>>>> *From:* tejas lunawat [tejasl2603 at gmail.com] >>>>> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >>>>> *To:* Gib Bogle >>>>> *Cc:* community at itk.org >>>>> *Subject:* Re: [ITK] Error while building ITK >>>>> >>>>> ?? >>>>> Even after changing the build selection in Visual Studio to Release, >>>>> same error still persisits. >>>>> >>>>> >>>>> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle >>>>> wrote: >>>>> >>>>>> You are building a Debug program. Check that you have Debug ITK >>>>>> libraries installed. If not change the build selection in Visual Studio to >>>>>> Release. >>>>>> ------------------------------ >>>>>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>>>>> lunawat [tejasl2603 at gmail.com] >>>>>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>>>>> *To:* community at itk.org >>>>>> *Subject:* [ITK] Error while building ITK >>>>>> >>>>>> Hey... >>>>>> >>>>>> I am an engineering student, working on a project, based on ITK libraries. >>>>>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>>>>> file. Details of the error are as follows: >>>>>> >>>>>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>>>>> Error 2 error LNK1104: cannot open file >>>>>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>>>>> >>>>>> I have searched for the solution of this error, but I didn't found >>>>>> it. Is their any possible way to solve this error Thank you >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>>>> >>>> >>>> >>>> -- >>>> Regards, >>>> Girish >>>> >>> >>> >> >> >> -- >> Regards, >> Girish >> > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From tejasl2603 at gmail.com Wed Sep 3 10:17:47 2014 From: tejasl2603 at gmail.com (tejas lunawat) Date: Wed, 3 Sep 2014 19:47:47 +0530 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Output in build selection as Debug 1>------ Build started: Project: ZERO_CHECK, Configuration: Debug x64 ------ 1>Build started 9/3/2014 7:43:45 PM. 1>InitializeBuildStatus: 1> Creating "x64\Debug\ZERO_CHECK\ZERO_CHECK.tlog\unsuccessfulbuild" because "AlwaysCreate" was specified. 1>CustomBuild: 1> Checking Build System 1> CMake does not need to re-run because E:/mtp win/ITK-build/CMakeFiles/generate.stamp is up-to-date. 1> CMake does not need to re-run because E:/mtp win/ITK-build/Modules/Remote/CMakeFiles/generate.stamp is up-to-date. 1> CMake does not need to re-run because E:/mtp win/ITK-build/Modules/ThirdParty/DoubleConversion/CMakeFiles/generate.stamp is up-to-date. 1> CMake does not need to re-run because E:/mtp 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Configuration: Debug x64 ------ 3>------ Build started: Project: H5make_libsettings, Configuration: Debug x64 ------ 4>------ Build started: Project: itkzlib, Configuration: Debug x64 ------ 2>Build started 9/3/2014 7:44:00 PM. 2>InitializeBuildStatus: 2> Creating "H5detect.dir\Debug\H5detect.tlog\unsuccessfulbuild" because "AlwaysCreate" was specified. 2>CustomBuild: 2> All outputs are up-to-date. 3>Build started 9/3/2014 7:44:01 PM. 2>ClCompile: 2> All outputs are up-to-date. 4>Build started 9/3/2014 7:44:01 PM. 2>Link: 2> All outputs are up-to-date. 2> H5detect.vcxproj -> E:\mtp win\ITK-build\bin\Debug\H5detect.exe 2>FinalizeBuildStatus: 2> Deleting file "H5detect.dir\Debug\H5detect.tlog\unsuccessfulbuild". 2> Touching "H5detect.dir\Debug\H5detect.tlog\H5detect.lastbuildstate". 2> 2>Build succeeded. 2> 2>Time Elapsed 00:00:00.67 3>InitializeBuildStatus: 3> Creating "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\unsuccessfulbuild" because "AlwaysCreate" was specified. 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Elapsed 00:00:00.78 5>------ Build started: Project: itkhdf5, Configuration: Debug x64 ------ 5>Build started 9/3/2014 7:44:02 PM. 5>InitializeBuildStatus: 5> Touching "itkhdf5.dir\Debug\itkhdf5.tlog\unsuccessfulbuild". 5>CustomBuild: 5> Building Custom Rule E:/mtp win/ITK/InsightToolkit-4.6.0/Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeLists.txt 5> CMake does not need to re-run because E:\mtp win\ITK-build\Modules\ThirdParty\HDF5\src\itkhdf5\src\CMakeFiles\generate.stamp is up-to-date. 5> Generating ../H5Tinit.c 5> This version of E:\mtp win\ITK-build\bin\Debug\H5detect.exe is not compatible with the version of Windows you're running. Check your computer's system information to see whether you need a x86 (32-bit) or x64 (64-bit) version of the program, and then contact the software publisher. 5>C:\Program Files\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(170,5): error MSB6006: "cmd.exe" exited with code 216. 5> 5>Build FAILED. 5> 5>Time Elapsed 00:00:01.87 ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped ========== On Wed, Sep 3, 2014 at 7:34 PM, Girish Mallya Udupi < indianzeppelin at gmail.com> wrote: > Strange. Have you tried opening and building the solution "ITKHDF5.sln" > alone (located in "your_ITK_Build_folder\Modules\ThirdParty\HDF5")? If not, > please try it and paste the contents of the output window (not just the > error list). > > PS: Please keep the discussion on the mailing list (by cc'ing the > community or replying to all)...:) > > > > On Wed, Sep 3, 2014 at 11:34 AM, tejas lunawat > wrote: > >> yes, the problem is with "itkhdf5" and all others which are dependent on >> it. As error are: >> >> Error 1 error MSB6006: "cmd.exe" exited with code 216. >> Error 2 error LNK1104: cannot open file >> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >> >> >> On Wed, Sep 3, 2014 at 3:53 PM, Girish Mallya Udupi < >> indianzeppelin at gmail.com> wrote: >> >>> Ok. So, when you build "ITK.sln", do all the projects in it build fine >>> with only "itkhdf5" failing? >>> >>> >>> On Wed, Sep 3, 2014 at 11:18 AM, tejas lunawat >>> wrote: >>> >>>> Yes, You are right. >>>> I am having a problem in building the ITK library itself. >>>> I followed all the steps described in this link >>>> >>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio >>>> I have used CMake for configuring and generating the .sln files from >>>> the ITK source file. >>>> And then I am building the libraries by using itk.sln. >>>> >>>> >>>> >>>> On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < >>>> indianzeppelin at gmail.com> wrote: >>>> >>>>> 1) From your question, I understand that you are having a problem >>>>> building the ITK library itself and not a project which uses the library. >>>>> Is that correct? >>>>> >>>>> 2) If so, I assume you have used CMake for configuring and generating >>>>> the .sln files from the ITK source files on your computer. Specifically, >>>>> did you follow the steps described here - >>>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? >>>>> >>>>> 3) Are you trying to build only "ITKHDF5.sln" (located at >>>>> "your_ITK_build_folder\Modules\ThirdParty\HDF5)? >>>>> >>>>> >>>>> On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle >>>>> wrote: >>>>> >>>>>> Are you using a CMakeLists.txt file and cmake to create your >>>>>> project files? >>>>>> ------------------------------ >>>>>> *From:* tejas lunawat [tejasl2603 at gmail.com] >>>>>> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >>>>>> *To:* Gib Bogle >>>>>> *Cc:* community at itk.org >>>>>> *Subject:* Re: [ITK] Error while building ITK >>>>>> >>>>>> ?? >>>>>> Even after changing the build selection in Visual Studio to >>>>>> Release, same error still persisits. >>>>>> >>>>>> >>>>>> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle >>>>>> wrote: >>>>>> >>>>>>> You are building a Debug program. Check that you have Debug ITK >>>>>>> libraries installed. If not change the build selection in Visual Studio to >>>>>>> Release. >>>>>>> ------------------------------ >>>>>>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>>>>>> lunawat [tejasl2603 at gmail.com] >>>>>>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>>>>>> *To:* community at itk.org >>>>>>> *Subject:* [ITK] Error while building ITK >>>>>>> >>>>>>> Hey... >>>>>>> >>>>>>> I am an engineering student, working on a project, based on ITK libraries. >>>>>>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>>>>>> file. Details of the error are as follows: >>>>>>> >>>>>>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>>>>>> Error 2 error LNK1104: cannot open file >>>>>>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>>>>>> >>>>>>> I have searched for the solution of this error, but I didn't found >>>>>>> it. Is their any possible way to solve this error Thank you >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Community mailing list >>>>>> Community at itk.org >>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Regards, >>>>> Girish >>>>> >>>> >>>> >>> >>> >>> -- >>> Regards, >>> Girish >>> >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pattersonnp.work at gmail.com Wed Sep 3 11:10:02 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 3 Sep 2014 16:10:02 +0100 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) Message-ID: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Hi, This is a problem that I have had before and have reported it as a ticket on the GDCM Git page. I have written some code which is heavily dependent on being able to read in a series of DICOM images, in this case they are of PET/NM modality. When a series of images are provided, which have "non-integer" rescale slope, the following error is returned at the final stage when SeriesWriter->Update() is invoked. Assertion failed: (slope == (int)slope), function InverseRescaleFunction, file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, line 67. Abort trap: 6 I cannot provide my own code here, as it may make the problem less clear. However, the problem is directly recreated using the ResampleDICOM.cxx example from the ITK examples page. If a series of PT/NM images are run through the code the above problem occurs. This is particularly problematic since NM/PT modality images do often have non-integer rescale slopes and currently I am not able to deal with images of this modality. There are 2 things to note:- 1) I have reported this error with GDCM developer and this problem appeared to have been resolved. I have previously been resampling NM/PT DICOM images using the ResampleDICOM.cxx example in the past without issue. If I recall correctly, ITK 4.5.2 worked with the latest GDCM release. 2) CT images (where the slope/intercepts are integer) work fine. I shall re-log this on the GDCM pages, but since I am unsure that something didn?t change in latest versions of ITK I wanted to report it here too. I would be much obliged if anyone would be able to test the ResampleDICOM.cxx example with DICOM images which have a rescale slope which is not-integer - and see if the problem can be recreated. I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from Git Repo yesterday. Regards, Nick. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From pattersonnp.work at gmail.com Wed Sep 3 11:51:14 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 3 Sep 2014 16:51:14 +0100 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) In-Reply-To: References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Message-ID: Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the time being. It seems to reappear in any version after 4.6. Nick. >> Hi Nick, >> >> This issue may be coming up now because a bug was fixed before ITK 4.6 >> which makes sure the rescale slope is applied when using GDCMImageIO >> for writing [1]. >> >> HTH, >> Matt >> >> >> [1] http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c0677793aa23a1e >> >> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson >> wrote: >>> Hi, >>> >>> This is a problem that I have had before and have reported it as a ticket >>> on the GDCM Git page. I have written some code which is heavily dependent on >>> being able to read in a series of DICOM images, in this case they are of >>> PET/NM modality. >>> >>> When a series of images are provided, which have "non-integer" rescale >>> slope, the following error is returned at the final stage when >>> SeriesWriter->Update() is invoked. >>> >>> Assertion failed: (slope == (int)slope), function InverseRescaleFunction, >>> file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, >>> line 67. >>> Abort trap: 6 >>> >>> >>> I cannot provide my own code here, as it may make the problem less clear. >>> However, the problem is directly recreated using the ResampleDICOM.cxx >>> example from the ITK examples page. If a series of PT/NM images are run >>> through the code the above problem occurs. This is particularly problematic >>> since NM/PT modality images do often have non-integer rescale slopes and >>> currently I am not able to deal with images of this modality. >>> >>> There are 2 things to note:- >>> 1) I have reported this error with GDCM developer and this problem appeared >>> to have been resolved. I have previously been resampling NM/PT DICOM images >>> using the ResampleDICOM.cxx example in the past without issue. If I recall >>> correctly, ITK 4.5.2 worked with the latest GDCM release. >>> >>> 2) CT images (where the slope/intercepts are integer) work fine. >>> >>> >>> I shall re-log this on the GDCM pages, but since I am unsure that something >>> didn?t change in latest versions of ITK I wanted to report it here too. >>> >>> I would be much obliged if anyone would be able to test the >>> ResampleDICOM.cxx example with DICOM images which have a rescale slope which >>> is not-integer - and see if the problem can be recreated. >>> >>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from >>> Git Repo yesterday. >>> >>> >>> Regards, Nick. >>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Wed Sep 3 12:10:02 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Wed, 3 Sep 2014 16:10:02 +0000 Subject: [ITK] [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent topics OK now? Message-ID: I?ve been trying to help out with changes related to the HDF5ImageIO, and there?s a string of 4 different patches: http://review.source.kitware.com/#/c/16579 http://review.source.kitware.com/#/c/16578 http://review.source.kitware.com/#/c/16577 http://review.source.kitware.com/#/c/16576 Incredibly, 16578 and 16579 seem to be circularly dependent. I?ve just pushed a new version of 16576 which addresses the comments Matt made. Should those others be abandoned and one free-standing patch be made of the actually substantive changes? ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Sep 3 12:26:23 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 12:26:23 -0400 Subject: [ITK] [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent topics OK now? In-Reply-To: References: Message-ID: Hi Kent, Thanks for taking a look at these. We had a good discussion about them this morning at the Google Hangout [1]. New versions are likely coming soon. Thanks, Matt [1] https://plus.google.com/events/c04l669q5omm7oo5p2ov1dp7kb4?authkey=CIH2womZ7I_9Fw On Wed, Sep 3, 2014 at 12:10 PM, Williams, Norman K wrote: > I?ve been trying to help out with changes related to the HDF5ImageIO, and > there?s a string of 4 different patches: > > http://review.source.kitware.com/#/c/16579 > http://review.source.kitware.com/#/c/16578 > http://review.source.kitware.com/#/c/16577 > http://review.source.kitware.com/#/c/16576 > > Incredibly, 16578 and 16579 seem to be circularly dependent. > > I?ve just pushed a new version of 16576 which addresses the comments Matt > made. Should those others be abandoned and one free-standing patch be made > of the actually substantive changes? > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Sep 3 12:30:25 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 12:30:25 -0400 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) In-Reply-To: References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Message-ID: Hi Nick, A reasonable way move forward; 1) A patch could be made to ITK's internal GDCM to support non-integer slope's. 2) This patch could then be submitted to upstream GDCM. Thanks, Matt On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson wrote: > Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the time being. It seems to reappear in any version after 4.6. > > Nick. > > >>> Hi Nick, >>> >>> This issue may be coming up now because a bug was fixed before ITK 4.6 >>> which makes sure the rescale slope is applied when using GDCMImageIO >>> for writing [1]. >>> >>> HTH, >>> Matt >>> >>> >>> [1] http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson >>> wrote: >>>> Hi, >>>> >>>> This is a problem that I have had before and have reported it as a ticket >>>> on the GDCM Git page. I have written some code which is heavily dependent on >>>> being able to read in a series of DICOM images, in this case they are of >>>> PET/NM modality. >>>> >>>> When a series of images are provided, which have "non-integer" rescale >>>> slope, the following error is returned at the final stage when >>>> SeriesWriter->Update() is invoked. >>>> >>>> Assertion failed: (slope == (int)slope), function InverseRescaleFunction, >>>> file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, >>>> line 67. >>>> Abort trap: 6 >>>> >>>> >>>> I cannot provide my own code here, as it may make the problem less clear. >>>> However, the problem is directly recreated using the ResampleDICOM.cxx >>>> example from the ITK examples page. If a series of PT/NM images are run >>>> through the code the above problem occurs. This is particularly problematic >>>> since NM/PT modality images do often have non-integer rescale slopes and >>>> currently I am not able to deal with images of this modality. >>>> >>>> There are 2 things to note:- >>>> 1) I have reported this error with GDCM developer and this problem appeared >>>> to have been resolved. I have previously been resampling NM/PT DICOM images >>>> using the ResampleDICOM.cxx example in the past without issue. If I recall >>>> correctly, ITK 4.5.2 worked with the latest GDCM release. >>>> >>>> 2) CT images (where the slope/intercepts are integer) work fine. >>>> >>>> >>>> I shall re-log this on the GDCM pages, but since I am unsure that something >>>> didn?t change in latest versions of ITK I wanted to report it here too. >>>> >>>> I would be much obliged if anyone would be able to test the >>>> ResampleDICOM.cxx example with DICOM images which have a rescale slope which >>>> is not-integer - and see if the problem can be recreated. >>>> >>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from >>>> Git Repo yesterday. >>>> >>>> >>>> Regards, Nick. >>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Wed Sep 3 12:38:26 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Wed, 3 Sep 2014 16:38:26 +0000 Subject: [ITK] [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent topics OK now? In-Reply-To: References: Message-ID: Watch out for my new version of 16576 ;-) On 9/3/14, 11:26 AM, "Matt McCormick" wrote: >Hi Kent, > >Thanks for taking a look at these. > >We had a good discussion about them this morning at the Google Hangout >[1]. New versions are likely coming soon. > >Thanks, >Matt > > >[1] >https://plus.google.com/events/c04l669q5omm7oo5p2ov1dp7kb4?authkey=CIH2wom >Z7I_9Fw > >On Wed, Sep 3, 2014 at 12:10 PM, Williams, Norman K > wrote: >> I?ve been trying to help out with changes related to the HDF5ImageIO, >>and >> there?s a string of 4 different patches: >> >> http://review.source.kitware.com/#/c/16579 >> http://review.source.kitware.com/#/c/16578 >> http://review.source.kitware.com/#/c/16577 >> http://review.source.kitware.com/#/c/16576 >> >> Incredibly, 16578 and 16579 seem to be circularly dependent. >> >> I?ve just pushed a new version of 16576 which addresses the comments >>Matt >> made. Should those others be abandoned and one free-standing patch be >>made >> of the actually substantive changes? >> >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered >>by the >> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >>confidential >> and may be legally privileged. If you are not the intended recipient, >>you >> are hereby notified that any retention, dissemination, distribution, or >> copying of this communication is strictly prohibited. Please reply to >>the >> sender that you have received the message in error, then delete it. >>Thank >> you. >> ________________________________ >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From hans-johnson at uiowa.edu Wed Sep 3 13:58:53 2014 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Wed, 3 Sep 2014 17:58:53 +0000 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) In-Reply-To: References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Message-ID: Matt, Can you comment on the efforts to update GDCM to a newer version? The version of GDCM in ITK is very much out of date. Hans -----Original Message----- From: Matt McCormick Date: Wednesday, September 3, 2014 at 11:30 AM To: Nick Patterson Cc: "insight-users at itk.org" Subject: Re: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope == (int)slope) Hi Nick, A reasonable way move forward; 1) A patch could be made to ITK's internal GDCM to support non-integer slope's. 2) This patch could then be submitted to upstream GDCM. Thanks, Matt On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson wrote: > Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the >time being. It seems to reappear in any version after 4.6. > > Nick. > > >>> Hi Nick, >>> >>> This issue may be coming up now because a bug was fixed before ITK 4.6 >>> which makes sure the rescale slope is applied when using GDCMImageIO >>> for writing [1]. >>> >>> HTH, >>> Matt >>> >>> >>> [1] >>>http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c067 >>>7793aa23a1e >>> >>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson >>> wrote: >>>> Hi, >>>> >>>> This is a problem that I have had before and have reported it as a >>>>ticket >>>> on the GDCM Git page. I have written some code which is heavily >>>>dependent on >>>> being able to read in a series of DICOM images, in this case they are >>>>of >>>> PET/NM modality. >>>> >>>> When a series of images are provided, which have "non-integer" rescale >>>> slope, the following error is returned at the final stage when >>>> SeriesWriter->Update() is invoked. >>>> >>>> Assertion failed: (slope == (int)slope), function >>>>InverseRescaleFunction, >>>> file >>>>/opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, >>>> line 67. >>>> Abort trap: 6 >>>> >>>> >>>> I cannot provide my own code here, as it may make the problem less >>>>clear. >>>> However, the problem is directly recreated using the ResampleDICOM.cxx >>>> example from the ITK examples page. If a series of PT/NM images are >>>>run >>>> through the code the above problem occurs. This is particularly >>>>problematic >>>> since NM/PT modality images do often have non-integer rescale slopes >>>>and >>>> currently I am not able to deal with images of this modality. >>>> >>>> There are 2 things to note:- >>>> 1) I have reported this error with GDCM developer and this problem >>>>appeared >>>> to have been resolved. I have previously been resampling NM/PT DICOM >>>>images >>>> using the ResampleDICOM.cxx example in the past without issue. If I >>>>recall >>>> correctly, ITK 4.5.2 worked with the latest GDCM release. >>>> >>>> 2) CT images (where the slope/intercepts are integer) work fine. >>>> >>>> >>>> I shall re-log this on the GDCM pages, but since I am unsure that >>>>something >>>> didn?t change in latest versions of ITK I wanted to report it here >>>>too. >>>> >>>> I would be much obliged if anyone would be able to test the >>>> ResampleDICOM.cxx example with DICOM images which have a rescale >>>>slope which >>>> is not-integer - and see if the problem can be recreated. >>>> >>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM >>>>from >>>> Git Repo yesterday. >>>> >>>> >>>> Regards, Nick. >>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 3 14:28:19 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 14:28:19 -0400 Subject: [ITK] [ITK-users] ResampleDICOM and Assertion failed: (slope == (int)slope) In-Reply-To: References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com> Message-ID: Hi Hans, Brian did work on it, but those efforts stalled. I will not have resources to put on it until sometime after the 4.7 release. Thanks, Matt On Wed, Sep 3, 2014 at 1:58 PM, Johnson, Hans J wrote: > Matt, > > Can you comment on the efforts to update GDCM to a newer version? The > version of GDCM in ITK is very much out of date. > > Hans > > > -----Original Message----- > From: Matt McCormick > Date: Wednesday, September 3, 2014 at 11:30 AM > To: Nick Patterson > Cc: "insight-users at itk.org" > Subject: Re: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope > == (int)slope) > > Hi Nick, > > A reasonable way move forward; > > 1) A patch could be made to ITK's internal GDCM to support non-integer > slope's. > 2) This patch could then be submitted to upstream GDCM. > > Thanks, > Matt > > On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson > wrote: >> Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the >>time being. It seems to reappear in any version after 4.6. >> >> Nick. >> >> >>>> Hi Nick, >>>> >>>> This issue may be coming up now because a bug was fixed before ITK 4.6 >>>> which makes sure the rescale slope is applied when using GDCMImageIO >>>> for writing [1]. >>>> >>>> HTH, >>>> Matt >>>> >>>> >>>> [1] >>>>http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c067 >>>>7793aa23a1e >>>> >>>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson >>>> wrote: >>>>> Hi, >>>>> >>>>> This is a problem that I have had before and have reported it as a >>>>>ticket >>>>> on the GDCM Git page. I have written some code which is heavily >>>>>dependent on >>>>> being able to read in a series of DICOM images, in this case they are >>>>>of >>>>> PET/NM modality. >>>>> >>>>> When a series of images are provided, which have "non-integer" rescale >>>>> slope, the following error is returned at the final stage when >>>>> SeriesWriter->Update() is invoked. >>>>> >>>>> Assertion failed: (slope == (int)slope), function >>>>>InverseRescaleFunction, >>>>> file >>>>>/opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, >>>>> line 67. >>>>> Abort trap: 6 >>>>> >>>>> >>>>> I cannot provide my own code here, as it may make the problem less >>>>>clear. >>>>> However, the problem is directly recreated using the ResampleDICOM.cxx >>>>> example from the ITK examples page. If a series of PT/NM images are >>>>>run >>>>> through the code the above problem occurs. This is particularly >>>>>problematic >>>>> since NM/PT modality images do often have non-integer rescale slopes >>>>>and >>>>> currently I am not able to deal with images of this modality. >>>>> >>>>> There are 2 things to note:- >>>>> 1) I have reported this error with GDCM developer and this problem >>>>>appeared >>>>> to have been resolved. I have previously been resampling NM/PT DICOM >>>>>images >>>>> using the ResampleDICOM.cxx example in the past without issue. If I >>>>>recall >>>>> correctly, ITK 4.5.2 worked with the latest GDCM release. >>>>> >>>>> 2) CT images (where the slope/intercepts are integer) work fine. >>>>> >>>>> >>>>> I shall re-log this on the GDCM pages, but since I am unsure that >>>>>something >>>>> didn?t change in latest versions of ITK I wanted to report it here >>>>>too. >>>>> >>>>> I would be much obliged if anyone would be able to test the >>>>> ResampleDICOM.cxx example with DICOM images which have a rescale >>>>>slope which >>>>> is not-integer - and see if the problem can be recreated. >>>>> >>>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM >>>>>from >>>>> Git Repo yesterday. >>>>> >>>>> >>>>> Regards, Nick. >>>>> >>>>> >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > ________________________________ _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 3 14:34:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 14:34:21 -0400 Subject: [ITK] ITK Software Guide Development Environment Message-ID: Hi Katie, Please review the instructions in this patch [1] on how to get an ITK Software Guide build environment. Thanks, Matt [1] http://review.source.kitware.com/#/c/16881/ From blowekamp at mail.nih.gov Wed Sep 3 14:38:29 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 3 Sep 2014 14:38:29 -0400 Subject: [ITK] [ITK-dev] CMake test macro for standard streaming behavior Message-ID: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov> Hello, In ITK 3.20 there was a macro to test the expected behavior of ImageIOs when streaming. It was defined here: https://github.com/InsightSoftwareConsortium/ITK/blob/v3.20.1/Testing/Code/IO/CMakeLists.txt#L406-L470 The intention of this code block was to reuse this sequence for tests for different file formats. ( I thought it was working for VTK and MRC file formats too, but I think that didn't happen when integrating from the IJ ). I wish to create a new and improved version of this macro ( or function ) to help test the HDF5 streaming contributions to ensure it's behavior matches that of the other ImageIOs. The issues are: 1) Where can "common" cmake testing code go so that other modules can use it? 2) Dependencies with modules and test drivers. It appears that I can call the ImageIOBaseTestDriver from other modules i.e. mha and HDF5. Any problem with this? 3) ImageIO registration - Currently I can just add additional dependencies to the TestingKernel to ensure that the HDF5 imageIO is registered everywhere. Is there any other better alternative? Thanks, Brad p.s. Alternatively, the test could be refactored to include the different states internally, as opposed to defined in cmake code. But I don't think it should be hard to get the cmake stuff working... _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Sep 3 15:01:16 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Sep 2014 15:01:16 -0400 Subject: [ITK] [ITK-dev] CMake test macro for standard streaming behavior In-Reply-To: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov> References: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov> Message-ID: Hi Brad, > 1) Where can "common" cmake testing code go so that other modules can use it? This can be added in the CMakeLists.txt for module that other modules will depend on. See "include(CreateTestDriver.cmake)" in Modules/Core/TestKernal/CMakeLists.txt. > 2) Dependencies with modules and test drivers. It appears that I can call the ImageIOBaseTestDriver from other modules i.e. mha and HDF5. Any problem with this? I don't think so, as long as all the other modules TEST_DEPEND ITKImageIOBase. > 3) ImageIO registration - Currently I can just add additional dependencies to the TestingKernel to ensure that the HDF5 imageIO is registered everywhere. Is there any other better alternative? Hopefully this can be avoided -- cross-compiling HDF5 is a pain. Thanks, Matt _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From arman.eshaghi at gmail.com Thu Sep 4 03:39:52 2014 From: arman.eshaghi at gmail.com (Arman Eshaghi) Date: Thu, 4 Sep 2014 12:09:52 +0430 Subject: [ITK] [ITK-users] Update on integration with R Message-ID: Hi, I'm wondering whether this proposal below from 2009 had any progresses regarding the integration of R statistics with ITK? http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages Thanks Arman -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Sep 4 08:44:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 4 Sep 2014 08:44:21 -0400 Subject: [ITK] [ITK-users] Update on integration with R In-Reply-To: References: Message-ID: Hi Arman, Since WrapITK uses SWIG, generating an R interface should be possible, but I do not know anyone who has tried it recently. SimpleITK uses SWIG and the R interface is enabled [1]. HTH, Matt [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi wrote: > Hi, > > I'm wondering whether this proposal below from 2009 had any progresses > regarding the integration of R statistics with ITK? > > http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages > > Thanks > Arman > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 4 08:58:40 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 4 Sep 2014 08:58:40 -0400 Subject: [ITK] [ITK-users] Update on integration with R In-Reply-To: References: Message-ID: Hello, What are you looking to do with R and ITK? The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version and is tested on linux and OSX. There are some issue with building R on windows that have not been addressed. Please let us know if you have further questions about getting this built. Good luck, Brad On Sep 4, 2014, at 8:44 AM, Matt McCormick wrote: > Hi Arman, > > Since WrapITK uses SWIG, generating an R interface should be possible, > but I do not know anyone who has tried it recently. > > SimpleITK uses SWIG and the R interface is enabled [1]. > > HTH, > Matt > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation > > On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi wrote: >> Hi, >> >> I'm wondering whether this proposal below from 2009 had any progresses >> regarding the integration of R statistics with ITK? >> >> http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages >> >> Thanks >> Arman >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arman.eshaghi at gmail.com Thu Sep 4 09:09:57 2014 From: arman.eshaghi at gmail.com (Arman Eshaghi) Date: Thu, 4 Sep 2014 17:39:57 +0430 Subject: [ITK] [ITK-users] Update on integration with R In-Reply-To: References: Message-ID: Thanks Brad and Matt, just wanted to read and write files with ITK in R. SITK works fine on Linux. All the best, Arman ps Just found another package (Rcpp) that may be useful for this as well On Thu, Sep 4, 2014 at 5:28 PM, Bradley Lowekamp wrote: > Hello, > > What are you looking to do with R and ITK? > > The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version > and is tested on linux and OSX. There are some issue with building R on > windows that have not been addressed. Please let us know if you have > further questions about getting this built. > > Good luck, > Brad > > On Sep 4, 2014, at 8:44 AM, Matt McCormick > wrote: > > > Hi Arman, > > > > Since WrapITK uses SWIG, generating an R interface should be possible, > > but I do not know anyone who has tried it recently. > > > > SimpleITK uses SWIG and the R interface is enabled [1]. > > > > HTH, > > Matt > > > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation > > > > On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi > wrote: > >> Hi, > >> > >> I'm wondering whether this proposal below from 2009 had any progresses > >> regarding the integration of R statistics with ITK? > >> > >> > http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages > >> > >> Thanks > >> Arman > >> > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-users > >> > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From stnava at gmail.com Thu Sep 4 09:33:44 2014 From: stnava at gmail.com (brian avants) Date: Thu, 4 Sep 2014 09:33:44 -0400 Subject: [ITK] [ITK-users] Update on integration with R In-Reply-To: References: Message-ID: you can also do ( in R ) install.packages("devtools") library(devtools) install_github("stnava/ANTsR") library(ANTsR) img<-antsImageRead("image.nii.gz",3) antsImageWrite(img,'temp.nii.gz') it's itk underneath brian On Thu, Sep 4, 2014 at 9:09 AM, Arman Eshaghi wrote: > Thanks Brad and Matt, just wanted to read and write files with ITK in R. > SITK works fine on Linux. > > All the best, > Arman > > ps Just found another package (Rcpp) that may be useful for this as well > > > On Thu, Sep 4, 2014 at 5:28 PM, Bradley Lowekamp > wrote: > >> Hello, >> >> What are you looking to do with R and ITK? >> >> The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version >> and is tested on linux and OSX. There are some issue with building R on >> windows that have not been addressed. Please let us know if you have >> further questions about getting this built. >> >> Good luck, >> Brad >> >> On Sep 4, 2014, at 8:44 AM, Matt McCormick >> wrote: >> >> > Hi Arman, >> > >> > Since WrapITK uses SWIG, generating an R interface should be possible, >> > but I do not know anyone who has tried it recently. >> > >> > SimpleITK uses SWIG and the R interface is enabled [1]. >> > >> > HTH, >> > Matt >> > >> > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation >> > >> > On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi >> wrote: >> >> Hi, >> >> >> >> I'm wondering whether this proposal below from 2009 had any progresses >> >> regarding the integration of R statistics with ITK? >> >> >> >> >> http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages >> >> >> >> Thanks >> >> Arman >> >> >> >> _____________________________________ >> >> Powered by www.kitware.com >> >> >> >> Visit other Kitware open-source projects at >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> http://www.kitware.com/products/protraining.php >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Thu Sep 4 10:06:44 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 4 Sep 2014 15:06:44 +0100 Subject: [ITK] Error while building ITK In-Reply-To: References: Message-ID: Okay, looks like the problem occurs while executing H5detect.exe (generated by the project "H5detect"). This exe is executed to generate H5Tinit.c which is a source file required by the "itkhdf5" project. For some reason (and this is probably something to do with VS), it is not able to execute the exe. Have you tried to do a 32-bit build of ITK (by choosing the 32-bit version of VS during CMake configure)? Also, what versions of VS and Windows are you using? On Wed, Sep 3, 2014 at 3:17 PM, tejas lunawat wrote: > Output in build selection as Debug > > 1>------ Build started: Project: ZERO_CHECK, Configuration: Debug x64 > ------ > 1>Build started 9/3/2014 7:43:45 PM. > 1>InitializeBuildStatus: > 1> Creating "x64\Debug\ZERO_CHECK\ZERO_CHECK.tlog\unsuccessfulbuild" > because "AlwaysCreate" was specified. > 1>CustomBuild: > 1> Checking Build System > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/Remote/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/DoubleConversion/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/DoubleConversion/src/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/DoubleConversion/src/double-conversion/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/KWSys/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/KWSys/src/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/KWSys/src/KWSys/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/config/cmake/config/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/v3p/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/core/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/vcl/tests/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/tests/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/core/testlib/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/core/testlib/tests/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/VNL/src/vxl/core/vnl/tests/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > 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win/ITK-build/Modules/Filtering/CurvatureFlow/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/Core/ImageAdaptors/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/Netlib/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/Netlib/src/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/Netlib/src/netlib/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/ThirdParty/Netlib/src/netlib/slatec/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Modules/Numerics/Statistics/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > 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up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Iterators/test/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/DataRepresentation/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/DataRepresentation/Containers/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/DataRepresentation/Image/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/DataRepresentation/Image/test/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/DataRepresentation/Mesh/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/DataRepresentation/Mesh/test/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/DataRepresentation/Path/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/DataRepresentation/Path/test/CMakeFiles/generate.stamp > is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Filtering/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Filtering/test/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/IO/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/IO/test/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/IO/XML/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Numerics/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Segmentation/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Segmentation/test/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/SpatialObjects/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Statistics/CMakeFiles/generate.stamp is up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/Statistics/test/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/RegistrationITKv4/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Examples/RegistrationITKv4/test/CMakeFiles/generate.stamp is > up-to-date. > 1> CMake does not need to re-run because E:/mtp > win/ITK-build/Utilities/Doxygen/CMakeFiles/generate.stamp is up-to-date. > 1>FinalizeBuildStatus: > 1> Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.tlog\unsuccessfulbuild". > 1> Touching > "x64\Debug\ZERO_CHECK\ZERO_CHECK.tlog\ZERO_CHECK.lastbuildstate". > 1> > 1>Build succeeded. > 1> > 1>Time Elapsed 00:00:15.42 > 2>------ Build started: Project: H5detect, Configuration: Debug x64 ------ > 3>------ Build started: Project: H5make_libsettings, Configuration: Debug > x64 ------ > 4>------ Build started: Project: itkzlib, Configuration: Debug x64 ------ > 2>Build started 9/3/2014 7:44:00 PM. > 2>InitializeBuildStatus: > 2> Creating "H5detect.dir\Debug\H5detect.tlog\unsuccessfulbuild" because > "AlwaysCreate" was specified. > 2>CustomBuild: > 2> All outputs are up-to-date. > 3>Build started 9/3/2014 7:44:01 PM. > 2>ClCompile: > 2> All outputs are up-to-date. > 4>Build started 9/3/2014 7:44:01 PM. > 2>Link: > 2> All outputs are up-to-date. > 2> H5detect.vcxproj -> E:\mtp win\ITK-build\bin\Debug\H5detect.exe > 2>FinalizeBuildStatus: > 2> Deleting file "H5detect.dir\Debug\H5detect.tlog\unsuccessfulbuild". > 2> Touching "H5detect.dir\Debug\H5detect.tlog\H5detect.lastbuildstate". > 2> > 2>Build succeeded. > 2> > 2>Time Elapsed 00:00:00.67 > 3>InitializeBuildStatus: > 3> Creating > "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\unsuccessfulbuild" > because "AlwaysCreate" was specified. > 3>CustomBuild: > 3> All outputs are up-to-date. > 4>InitializeBuildStatus: > 4> Creating "itkzlib.dir\Debug\itkzlib.tlog\unsuccessfulbuild" because > "AlwaysCreate" was specified. > 4>CustomBuild: > 4> All outputs are up-to-date. > 3>ClCompile: > 3> All outputs are up-to-date. > 3>Link: > 3> All outputs are up-to-date. > 3> H5make_libsettings.vcxproj -> E:\mtp > win\ITK-build\bin\Debug\H5make_libsettings.exe > 3>FinalizeBuildStatus: > 3> Deleting file > "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\unsuccessfulbuild". > 3> Touching > "H5make_libsettings.dir\Debug\H5make_l.6621D5FB.tlog\H5make_libsettings.lastbuildstate". > 3> > 3>Build succeeded. > 3> > 3>Time Elapsed 00:00:00.79 > 4>ClCompile: > 4> All outputs are up-to-date. > 4>Lib: > 4> All outputs are up-to-date. > 4> itkzlib.vcxproj -> E:\mtp win\ITK-build\lib\Debug\itkzlib-4.6.lib > 4>FinalizeBuildStatus: > 4> Deleting file "itkzlib.dir\Debug\itkzlib.tlog\unsuccessfulbuild". > 4> Touching "itkzlib.dir\Debug\itkzlib.tlog\itkzlib.lastbuildstate". > 4> > 4>Build succeeded. > 4> > 4>Time Elapsed 00:00:00.78 > 5>------ Build started: Project: itkhdf5, Configuration: Debug x64 ------ > 5>Build started 9/3/2014 7:44:02 PM. > 5>InitializeBuildStatus: > 5> Touching "itkhdf5.dir\Debug\itkhdf5.tlog\unsuccessfulbuild". > 5>CustomBuild: > 5> Building Custom Rule E:/mtp > win/ITK/InsightToolkit-4.6.0/Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeLists.txt > 5> CMake does not need to re-run because E:\mtp > win\ITK-build\Modules\ThirdParty\HDF5\src\itkhdf5\src\CMakeFiles\generate.stamp > is up-to-date. > 5> Generating ../H5Tinit.c > 5> This version of E:\mtp win\ITK-build\bin\Debug\H5detect.exe is not > compatible with the version of Windows you're running. Check your > computer's system information to see whether you need a x86 (32-bit) or x64 > (64-bit) version of the program, and then contact the software publisher. > 5>C:\Program > Files\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(170,5): > error MSB6006: "cmd.exe" exited with code 216. > 5> > 5>Build FAILED. > 5> > 5>Time Elapsed 00:00:01.87 > ========== Build: 4 succeeded, 1 failed, 0 up-to-date, 0 skipped ========== > > > > On Wed, Sep 3, 2014 at 7:34 PM, Girish Mallya Udupi < > indianzeppelin at gmail.com> wrote: > >> Strange. Have you tried opening and building the solution "ITKHDF5.sln" >> alone (located in "your_ITK_Build_folder\Modules\ThirdParty\HDF5")? If not, >> please try it and paste the contents of the output window (not just the >> error list). >> >> PS: Please keep the discussion on the mailing list (by cc'ing the >> community or replying to all)...:) >> >> >> >> On Wed, Sep 3, 2014 at 11:34 AM, tejas lunawat >> wrote: >> >>> yes, the problem is with "itkhdf5" and all others which are dependent on >>> it. As error are: >>> >>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>> Error 2 error LNK1104: cannot open file >>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>> >>> >>> On Wed, Sep 3, 2014 at 3:53 PM, Girish Mallya Udupi < >>> indianzeppelin at gmail.com> wrote: >>> >>>> Ok. So, when you build "ITK.sln", do all the projects in it build fine >>>> with only "itkhdf5" failing? >>>> >>>> >>>> On Wed, Sep 3, 2014 at 11:18 AM, tejas lunawat >>>> wrote: >>>> >>>>> Yes, You are right. >>>>> I am having a problem in building the ITK library itself. >>>>> I followed all the steps described in this link >>>>> >>>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio >>>>> I have used CMake for configuring and generating the .sln files from >>>>> the ITK source file. >>>>> And then I am building the libraries by using itk.sln. >>>>> >>>>> >>>>> >>>>> On Wed, Sep 3, 2014 at 2:46 PM, Girish Mallya Udupi < >>>>> indianzeppelin at gmail.com> wrote: >>>>> >>>>>> 1) From your question, I understand that you are having a problem >>>>>> building the ITK library itself and not a project which uses the library. >>>>>> Is that correct? >>>>>> >>>>>> 2) If so, I assume you have used CMake for configuring and generating >>>>>> the .sln files from the ITK source files on your computer. Specifically, >>>>>> did you follow the steps described here - >>>>>> http://www.itk.org/Wiki/ITK/Configuring_and_Building/VisualStudio? >>>>>> >>>>>> 3) Are you trying to build only "ITKHDF5.sln" (located at >>>>>> "your_ITK_build_folder\Modules\ThirdParty\HDF5)? >>>>>> >>>>>> >>>>>> On Wed, Sep 3, 2014 at 7:36 AM, Gib Bogle >>>>>> wrote: >>>>>> >>>>>>> Are you using a CMakeLists.txt file and cmake to create your >>>>>>> project files? >>>>>>> ------------------------------ >>>>>>> *From:* tejas lunawat [tejasl2603 at gmail.com] >>>>>>> *Sent:* Wednesday, 3 September 2014 5:59 p.m. >>>>>>> *To:* Gib Bogle >>>>>>> *Cc:* community at itk.org >>>>>>> *Subject:* Re: [ITK] Error while building ITK >>>>>>> >>>>>>> ?? >>>>>>> Even after changing the build selection in Visual Studio to >>>>>>> Release, same error still persisits. >>>>>>> >>>>>>> >>>>>>> On Wed, Sep 3, 2014 at 2:00 AM, Gib Bogle >>>>>>> wrote: >>>>>>> >>>>>>>> You are building a Debug program. Check that you have Debug ITK >>>>>>>> libraries installed. If not change the build selection in Visual Studio to >>>>>>>> Release. >>>>>>>> ------------------------------ >>>>>>>> *From:* Community [community-bounces at itk.org] on behalf of tejas >>>>>>>> lunawat [tejasl2603 at gmail.com] >>>>>>>> *Sent:* Wednesday, 3 September 2014 8:07 a.m. >>>>>>>> *To:* community at itk.org >>>>>>>> *Subject:* [ITK] Error while building ITK >>>>>>>> >>>>>>>> Hey... >>>>>>>> >>>>>>>> I am an engineering student, working on a project, based on ITK libraries. >>>>>>>> I am new to ITK. I have encounter an error while building 'itkhdf5.sln' >>>>>>>> file. Details of the error are as follows: >>>>>>>> >>>>>>>> Error 1 error MSB6006: "cmd.exe" exited with code 216. >>>>>>>> Error 2 error LNK1104: cannot open file >>>>>>>> '..\..\..\..\lib\Debug\itkhdf5-4.6.lib' >>>>>>>> >>>>>>>> I have searched for the solution of this error, but I didn't >>>>>>>> found it. Is their any possible way to solve this error Thank you >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Community mailing list >>>>>>> Community at itk.org >>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Regards, >>>>>> Girish >>>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Regards, >>>> Girish >>>> >>> >>> >> >> >> -- >> Regards, >> Girish >> > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Thu Sep 4 11:29:42 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 4 Sep 2014 16:29:42 +0100 Subject: [ITK] [ITK-dev] New to the Gerrit review process Message-ID: Hello, I have a couple of questions about the Gerrit review process - 1) Is the creator of a topic automatically added as a reviewer on subsequent patches in the topic? 2) As a reviewer, if I am unable to understand the changes made to the code (simply because I am not an advanced programmer), should I leave the patch unscored? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Sep 4 11:34:47 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 4 Sep 2014 11:34:47 -0400 Subject: [ITK] [ITK-dev] New to the Gerrit review process In-Reply-To: References: Message-ID: Hi Girish, Thanks for participating on Gerrit. > 1) Is the creator of a topic automatically added as a reviewer on subsequent > patches in the topic? No, they have to be manually added at the moment. > 2) As a reviewer, if I am unable to understand the changes made to the code > (simply because I am not an advanced programmer), should I leave the patch > unscored? An feedback is welcome. If you do not feel very knowledgeable about a patch, give it a "+1" as opposed to a "+2". Some more information can be found here [1]. Thanks, Matt [1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/PerformAGerritReview/index.html _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Thu Sep 4 11:43:14 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 4 Sep 2014 11:43:14 -0400 Subject: [ITK] [ITK-dev] New to the Gerrit review process In-Reply-To: References: Message-ID: Hello Girish, I assume you are talking about this patch: http://review.source.kitware.com/#/c/16868/ Thanks again for contributing the patch which demonstrated the bug you encountered. For this particular case I would encourage you to download, checkout, and compile the patch and verify that is resolves the issue you initially encountered. Then report back if it fixes the problem. Brad On Sep 4, 2014, at 11:29 AM, Girish Mallya Udupi wrote: > Hello, > > I have a couple of questions about the Gerrit review process - > > 1) Is the creator of a topic automatically added as a reviewer on subsequent patches in the topic? > > 2) As a reviewer, if I am unable to understand the changes made to the code (simply because I am not an advanced programmer), should I leave the patch unscored? > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Sep 4 11:50:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 4 Sep 2014 11:50:13 -0400 Subject: [ITK] Opportunity to share, discuss, design, and learn with other ITK community members Message-ID: There is an opportunity to share, discuss, design, and learn with your fellow ITK community members. On Friday, 11 AM Eastern USA time, join us as we discuss ITK development. We will use the Hangout link for the Event. https://plus.google.com/events/c4np6cgd8oosd5je818d9r1n3j8 For those that cannot join via Hangout, telephone call-in is also possible. Dial: +1-585-632-6296 Enter pin: 31423? All are welcome. Hope to talk to you then! From indianzeppelin at gmail.com Thu Sep 4 11:58:19 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 4 Sep 2014 16:58:19 +0100 Subject: [ITK] [ITK-dev] New to the Gerrit review process In-Reply-To: References: Message-ID: Hi Brad, Yes, that one (and its parent). I did in fact pull the patch and compile it without any issues. I ran the related tests too, which passed. But it seemed to me that I couldn't give a "Verify" score alone and had to give a "Code Review" score as well. Matt's reply has made it clearer now. Thanks! On Thu, Sep 4, 2014 at 4:43 PM, Bradley Lowekamp wrote: > Hello Girish, > > I assume you are talking about this patch: > http://review.source.kitware.com/#/c/16868/ > > Thanks again for contributing the patch which demonstrated the bug you > encountered. > > For this particular case I would encourage you to download, checkout, and > compile the patch and verify that is resolves the issue you initially > encountered. Then report back if it fixes the problem. > > Brad > > On Sep 4, 2014, at 11:29 AM, Girish Mallya Udupi > wrote: > > > Hello, > > > > I have a couple of questions about the Gerrit review process - > > > > 1) Is the creator of a topic automatically added as a reviewer on > subsequent patches in the topic? > > > > 2) As a reviewer, if I am unable to understand the changes made to the > code (simply because I am not an advanced programmer), should I leave the > patch unscored? > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From marcus.hanwell at kitware.com Fri Sep 5 11:31:30 2014 From: marcus.hanwell at kitware.com (Marcus D. Hanwell) Date: Fri, 5 Sep 2014 11:31:30 -0400 Subject: [ITK] [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent topics OK now? In-Reply-To: <8D195ACD03190B6-15CC-C133@webmail-m269.sysops.aol.com> References: <8D195ACD03190B6-15CC-C133@webmail-m269.sysops.aol.com> Message-ID: On Wed, Sep 3, 2014 at 12:39 PM, David Cole via Insight-developers wrote: >> http://review.source.kitware.com/#/c/16579 >> http://review.source.kitware.com/#/c/16578 >> Incredibly, 16578 and 16579 seem to be circularly dependent. > > > Why do you say they're circularly dependent? It looks to me like 79 is > based on 78... I'm not seeing the circularity. > If you managed a circular dependency I would love to see it - is that even possible in git? _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Fri Sep 5 13:23:22 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 5 Sep 2014 13:23:22 -0400 Subject: [ITK] [ITK-dev] Using ITK with optional components Message-ID: <1C470533-952F-4836-81C1-1DA697FA8213@mail.nih.gov> Hello, I was wondering if anyone had looked into adding support for CMake's find_package OPTIONAL_COMPONENTS option? This would be quite convenient in some situations. Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From zeinsalah at gmail.com Mon Sep 8 04:18:10 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 8 Sep 2014 10:18:10 +0200 Subject: [ITK] [ITK-users] Background / Foreground separation Message-ID: Hello, I want to reliably define the main object in CT/MRI image from the background. I.e. I want to do some kind of defining the boundary (skin) of the patient. Are there filters in ITK dedicated for this? or should I adapt filters like the Otsu? Thanks, Zein Sorry! I have not been using ITK since Release 3.20 :). -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From zeinsalah at gmail.com Mon Sep 8 10:10:49 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 8 Sep 2014 16:10:49 +0200 Subject: [ITK] ITK mailing list Message-ID: Hi, I have not been using ITK in the last 2 years. Has anything been changed since then regarding the mailing list email address? used to write my questions to isight-users at itk.org. Is this still valid? Thanks, Zein -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Mon Sep 8 10:17:17 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Mon, 8 Sep 2014 15:17:17 +0100 Subject: [ITK] ITK mailing list In-Reply-To: References: Message-ID: Yes, it is (assuming there's a typo in your question and you actually meant insight-users at itk.org). On Mon, Sep 8, 2014 at 3:10 PM, Zein Salah wrote: > Hi, > > I have not been using ITK in the last 2 years. Has anything been changed > since then regarding the mailing list email address? used to write my > questions to isight-users at itk.org. Is this still valid? > > Thanks, > Zein > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 8 10:41:40 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Sep 2014 10:41:40 -0400 Subject: [ITK] ITK mailing list In-Reply-To: References: Message-ID: Hi, While insight-user at itk.org will still work, community at itk.org [1] is recommended. Subscribing to this list will receive mails from both insight-user at itk.org and insight-developers at itk.org. Thanks, Matt [1] http://www.itk.org/mailman/listinfo/community On Mon, Sep 8, 2014 at 10:17 AM, Girish Mallya Udupi wrote: > Yes, it is (assuming there's a typo in your question and you actually meant > insight-users at itk.org). > > On Mon, Sep 8, 2014 at 3:10 PM, Zein Salah wrote: >> >> Hi, >> >> I have not been using ITK in the last 2 years. Has anything been changed >> since then regarding the mailing list email address? used to write my >> questions to isight-users at itk.org. Is this still valid? >> >> Thanks, >> Zein >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > > > > -- > Regards, > Girish > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Mon Sep 8 10:52:54 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Sep 2014 10:52:54 -0400 Subject: [ITK] [ITK-users] Background / Foreground separation In-Reply-To: References: Message-ID: Hi Zein, Welcome back! :-) One possible sequence of filters to obtain the "skin": OtsuThresholdImageFilter [1] BinaryShapeKeepNObjectImageFilter (keep only the largest object) [2] BinaryClosingByReconstructionImageFilter or BinaryFillholeImageFilter [3][4] BinaryContourImageFilter [5] HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1OtsuThresholdImageFilter.html [2] http://www.itk.org/Doxygen/html/classitk_1_1BinaryShapeKeepNObjectsImageFilter.html [3] http://www.itk.org/Doxygen/html/classitk_1_1BinaryClosingByReconstructionImageFilter.html [4] http://www.itk.org/Doxygen/html/classitk_1_1BinaryFillholeImageFilter.html [5] http://www.itk.org/Doxygen/html/classitk_1_1BinaryContourImageFilter.html On Mon, Sep 8, 2014 at 4:18 AM, Zein Salah wrote: > Hello, > > I want to reliably define the main object in CT/MRI image from the > background. I.e. I want to do some kind of defining the boundary (skin) of > the patient. Are there filters in ITK dedicated for this? or should I adapt > filters like the Otsu? > > Thanks, > Zein > > Sorry! I have not been using ITK since Release 3.20 :). > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From zeinsalah at gmail.com Mon Sep 8 11:14:06 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 8 Sep 2014 17:14:06 +0200 Subject: [ITK] OtsuMultipleThresholdsCalculator Message-ID: Hi, I was trying to use the OtsuMultipleThresholdsCalculator. Bellow is the corresponding code from my program. The compiler reports an error that Compute() is not a member of itk::OtsuMultipleThresholdsCalculator. I can't figure out what the actual error is!! BTW, due to compatibly reasons within our working team, I have to use ITK3.14 and and not a newer release. Does this have to do with the error?? Much thanks, Z. typedef itk::Statistics::ScalarImageToHistogramGenerator< InputImageType > ScalarImageToHistogramGeneratorType; typedef ScalarImageToHistogramGeneratorType::HistogramType HistogramType; typedef itk::OtsuMultipleThresholdsCalculator< HistogramType > CalculatorType; ScalarImageToHistogramGeneratorType::Pointer scalarImageToHistogramGenerator = ScalarImageToHistogramGeneratorType::New(); CalculatorType::Pointer calculator = CalculatorType::New(); scalarImageToHistogramGenerator->SetNumberOfBins( 128 ); scalarImageToHistogramGenerator->SetInput( m_ShiftedImage ); scalarImageToHistogramGenerator->Compute(); calculator->SetNumberOfThresholds( 3 ); calculator->SetInputHistogram(scalarImageToHistogramGenerator->GetOutput()); calculator->Compute(); -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 8 11:22:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Sep 2014 11:22:24 -0400 Subject: [ITK] OtsuMultipleThresholdsCalculator In-Reply-To: References: Message-ID: Hi Zein, If looking at Doxygen, the documentation for ITK 3.14 will need to be used [1]. The documentation suggests that Update() should be called [2]. HTH, Matt [1] http://itk.org/Doxygen314/html/ [2] http://itk.org/Doxygen314/html/classitk_1_1OtsuMultipleThresholdsCalculator.html On Mon, Sep 8, 2014 at 11:14 AM, Zein Salah wrote: > Hi, > > I was trying to use the OtsuMultipleThresholdsCalculator. Bellow is the > corresponding > code from my program. The compiler reports an error that Compute() is not a > member > of itk::OtsuMultipleThresholdsCalculator. I can't figure out what the actual > error is!! > BTW, due to compatibly reasons within our working team, I have to use > ITK3.14 and > and not a newer release. Does this have to do with the error?? > > Much thanks, > Z. > > > typedef itk::Statistics::ScalarImageToHistogramGenerator< InputImageType > > ScalarImageToHistogramGeneratorType; > typedef ScalarImageToHistogramGeneratorType::HistogramType > HistogramType; > typedef itk::OtsuMultipleThresholdsCalculator< HistogramType > > CalculatorType; > > ScalarImageToHistogramGeneratorType::Pointer > scalarImageToHistogramGenerator = > ScalarImageToHistogramGeneratorType::New(); > CalculatorType::Pointer calculator = CalculatorType::New(); > > scalarImageToHistogramGenerator->SetNumberOfBins( 128 ); > scalarImageToHistogramGenerator->SetInput( m_ShiftedImage ); > scalarImageToHistogramGenerator->Compute(); > > calculator->SetNumberOfThresholds( 3 ); > > calculator->SetInputHistogram(scalarImageToHistogramGenerator->GetOutput()); > calculator->Compute(); > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From elena.bresciani87 at gmail.com Tue Sep 9 11:50:31 2014 From: elena.bresciani87 at gmail.com (elena bresciani) Date: Tue, 9 Sep 2014 17:50:31 +0200 Subject: [ITK] [ITK-users] Pipeline update problem (I suppose) Message-ID: Hello guys, I'm writing an ITK script using C++ functions in order to reduce the number of operations repetition. What I need to do is: given a scan with 4 objects I need to separate them in 4 images and, if vertically oriented, rotate them 90 degrees in order to have them horizontal. I already have successfully compiled the code necessary to crop ROIs and the rotation step separately, everything works well, but when I try to unify all in a single script I don't get the desired output. I suppose that the problem could be in a missing Update() or something but I can't identify it. Attached you can find a concise version of the code; whilst SegmentedImage1..4 are as attended OutputImage1..4 have right size but are all filled with gray level 100. As I said before, I can't understand the problem because the same code used alone (attachment rotation.cxx), works well. Any guess? Thanks Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: code Type: application/octet-stream Size: 6155 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rotation.cxx Type: application/octet-stream Size: 3565 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dagarshali at gmail.com Tue Sep 9 22:33:46 2014 From: dagarshali at gmail.com (dagarshali) Date: Tue, 9 Sep 2014 19:33:46 -0700 (PDT) Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution Message-ID: <1410316426142-7586179.post@n2.nabble.com> I downloaded the source code for simple itk and complied it as instructed. In the cmake configuration, I changed the python paths according to using the python distribution of anaconda. I was able to compile it. I have attached a snapshot of the cmake configuration I am not sure what to do after the compiling.. If I enter import SimpleITK as sitk, I get a fatal python error. Can anybody please suggest how to overcome this problem?Thanks in advance.dagarshali -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Sep 9 22:41:57 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 9 Sep 2014 22:41:57 -0400 Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution In-Reply-To: <1410316426142-7586179.post@n2.nabble.com> References: <1410316426142-7586179.post@n2.nabble.com> Message-ID: Hi dagarshall, There is a SimpleITK recipe for conda [1]. To install it from a manual build, use the same commands at the end of build.sh: cd ${BUILD_DIR}/SimpleITK-build/Wrapping ${PYTHON} PythonPackage/setup.py install HTH, Matt [1] https://github.com/conda/conda-recipes/tree/master/simpleitk On Tue, Sep 9, 2014 at 10:33 PM, dagarshali wrote: > I downloaded the source code for simple itk and complied it as instructed. In > the cmake configuration, I changed the python paths according to using the > python distribution of anaconda. I was able to compile it. I have attached a > snapshot of the cmake configuration > > I am not sure what to do after the compiling.. If I enter import SimpleITK > as sitk, I get a fatal python error. Can anybody please suggest how to > overcome this problem?Thanks in advance.dagarshali > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From 88172828 at qq.com Wed Sep 10 07:42:59 2014 From: 88172828 at qq.com (Eping Wang) Date: Wed, 10 Sep 2014 04:42:59 -0700 (MST) Subject: [ITK] =?utf-8?q?=5BITK-users=5D_itk=3A_=3AImageFileReader_to_igst?= =?utf-8?q?k=3A_=3AImageSpatialObject=E2=80=8F?= In-Reply-To: <1403279378508-34126.post@n7.nabble.com> References: <1403279378508-34126.post@n7.nabble.com> Message-ID: <1410349379582-34523.post@n7.nabble.com> Hi SeanLee, Try this: igstk::Friends::ImageReaderToImageSpatialObject::ConnectImage(&m_MhdImageReader,&m_ImageSpatialObject.GetPointer()); It worked in my project. -- View this message in context: http://itk-users.7.n7.nabble.com/itk-ImageFileReader-to-igstk-ImageSpatialObject-tp34126p34523.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 10 08:22:44 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 10 Sep 2014 08:22:44 -0400 Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> Message-ID: Hi, I think the best route is to use their package build system so the build environment is set up correctly. However, the SimpleITK package may need some tweaks. HTH, Matt On Wed, Sep 10, 2014 at 2:27 AM, Vishwa wrote: > I tried installing again. Get the same error. Any ideas as to why this might > be happening? or how to even debug the issue? > > Vishwa > > On Tue, Sep 9, 2014 at 10:44 PM, Matt McCormick > wrote: >> >> Instructions to build the recipe are here [1], although there is >> currently a bug in the clone url [2]. >> >> The error you get is usually from using incompatible versions of >> Python in the CMake configuration. Your screenshot in the first >> message look good, but conda may be doing some funny business. >> >> HTH, >> Matt >> >> [1] http://conda.pydata.org/docs/build_tutorials/pkgs.html >> >> [2] https://github.com/conda/conda-recipes/pull/176 >> >> On Tue, Sep 9, 2014 at 10:55 PM, Vishwa >> wrote: >> > Thanks for getting back to me.. I am not sure how to use the build.sh. >> > Am i >> > to create those variables mentioned in that file? >> > >> > In the previous mail, I forgot to mention after I compiled, I tried what >> > you >> > suggest here >> > >> > cd ${BUILD_DIR}/SimpleITK-build/Wrapping >> > ${PYTHON} PythonPackage/setup.py install >> > >> > The last few lines of the output is shown below >> > >> > Installed >> > >> > /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev584-py2.7-macosx-10.5-x86_64.egg >> > >> > Processing dependencies for SimpleITK==0.9.0.dev584 >> > >> > Finished processing dependencies for SimpleITK==0.9.0.dev584 >> > >> > However, when i import simple itk in python, >> > >> > import SimpleITK as sitk >> > >> > Fatal Python error: PyThreadState_Get: no current thread >> > >> > Abort trap: 6 >> > >> > >> > On Tue, Sep 9, 2014 at 9:41 PM, Matt McCormick >> > >> > wrote: >> >> >> >> Hi dagarshall, >> >> >> >> There is a SimpleITK recipe for conda [1]. To install it from a >> >> manual build, use the same commands at the end of build.sh: >> >> >> >> cd ${BUILD_DIR}/SimpleITK-build/Wrapping >> >> ${PYTHON} PythonPackage/setup.py install >> >> >> >> HTH, >> >> Matt >> >> >> >> [1] https://github.com/conda/conda-recipes/tree/master/simpleitk >> >> >> >> On Tue, Sep 9, 2014 at 10:33 PM, dagarshali >> >> wrote: >> >> > I downloaded the source code for simple itk and complied it as >> >> > instructed. In >> >> > the cmake configuration, I changed the python paths according to >> >> > using >> >> > the >> >> > python distribution of anaconda. I was able to compile it. I have >> >> > attached a >> >> > snapshot of the cmake configuration >> >> > >> >> > >> >> > >> >> > I am not sure what to do after the compiling.. If I enter import >> >> > SimpleITK >> >> > as sitk, I get a fatal python error. Can anybody please suggest how >> >> > to >> >> > overcome this problem?Thanks in advance.dagarshali >> >> > >> >> > >> >> > >> >> > -- >> >> > View this message in context: >> >> > >> >> > http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html >> >> > Sent from the ITK Insight Users mailing list archive at Nabble.com. >> >> > _____________________________________ >> >> > Powered by www.kitware.com >> >> > >> >> > Visit other Kitware open-source projects at >> >> > http://www.kitware.com/opensource/opensource.html >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > http://www.kitware.com/products/protraining.php >> >> > >> >> > Please keep messages on-topic and check the ITK FAQ at: >> >> > http://www.itk.org/Wiki/ITK_FAQ >> >> > >> >> > Follow this link to subscribe/unsubscribe: >> >> > http://public.kitware.com/mailman/listinfo/insight-users >> > >> > >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Wed Sep 10 10:13:10 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 10 Sep 2014 10:13:10 -0400 Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> Message-ID: <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> Hello, This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment. I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct. You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker. Also you can inspect the runtime libraries: otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0) [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme Hope this helps, Brad On Sep 9, 2014, at 10:55 PM, Vishwa wrote: > import SimpleITK as sitk > > Fatal Python error: PyThreadState_Get: no current thread > > > Abort trap: 6 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Wed Sep 10 11:10:37 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 10 Sep 2014 11:10:37 -0400 Subject: [ITK] [ITK-users] using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> Message-ID: <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> Hello, You need to use the conda build environment. Look at the readme in this repo[1]. Basically you'll need to do the following: $ conda install conda-build $ cd src $ git clone https://github.com/thewtex/conda-recipes.git $ git checkout simpleitk-clone-url $ conda build simpleitk [1] https://github.com/conda/conda-recipes On Sep 10, 2014, at 11:01 AM, Vishwa wrote: > Thanks very much for the information. I looked at the conda recipe. There are three files. > One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile.. > > There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. > > Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. > > Best regards, > Vishwa > > > > On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp wrote: > Hello, > > This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment. > > I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct. > > You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker. > > Also you can inspect the runtime libraries: > > otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so > /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: > @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0) > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1) > /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0) > /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0) > > [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme > > Hope this helps, > Brad > > On Sep 9, 2014, at 10:55 PM, Vishwa wrote: > >> import SimpleITK as sitk >> >> Fatal Python error: PyThreadState_Get: no current thread >> >> >> Abort trap: 6 >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From smrolfe at u.washington.edu Wed Sep 10 17:25:57 2014 From: smrolfe at u.washington.edu (smrolfe at u.washington.edu) Date: Wed, 10 Sep 2014 14:25:57 -0700 (PDT) Subject: [ITK] Image bounds question Message-ID: Hello, I've been using a program for adding a constant padding to an image. This has worked to pad each edge, resulting in negative bounds. Now I've added the code as a subroutine and the behavior has changed. The padding now appears on only the positive side of the bounds, so the bounds still start at 0, 0, 0. It appears that writing the image changes the behavior of the bounds? Does this have to do with the position of the origin? I'd like to understand this better. My subroutine is below. InternalImageType::Pointer PadImage(InternalImageType::Pointer origIm, double padFactor ) { typedef itk::ConstantPadImageFilter ConstantPadImageFilterType; InternalImageType::SizeType lowerExtendRegion; lowerExtendRegion[0] = padFactor ; lowerExtendRegion[1] = padFactor ; lowerExtendRegion[2] = padFactor ; InternalImageType::SizeType upperExtendRegion; upperExtendRegion[0] = padFactor ; upperExtendRegion[1] = padFactor ; upperExtendRegion[2] = padFactor ; InternalImageType::PixelType constantPixel = 0; ConstantPadImageFilterType::Pointer padFilter = ConstantPadImageFilterType::New(); padFilter->SetInput(origIm); padFilter->SetPadLowerBound(lowerExtendRegion); padFilter->SetPadUpperBound(upperExtendRegion); padFilter->SetConstant(0); padFilter->Update(); return padFilter->GetOutput(); } Thanks, Sara From biradarsumangala at gmail.com Wed Sep 10 18:06:29 2014 From: biradarsumangala at gmail.com (biradarsumangala at gmail.com) Date: Wed, 10 Sep 2014 17:06:29 -0500 Subject: [ITK] [ITK-users] biradarsumangala@gmail.com has indicated you're a friend. Accept? 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URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From gabrielgimenez85 at gmail.com Wed Sep 10 21:55:56 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Wed, 10 Sep 2014 18:55:56 -0700 (PDT) Subject: [ITK] [ITK-users] itkParticleSwarmOptimizer - Example Message-ID: <1410400556611-7586188.post@n2.nabble.com> Hello everyone, is there an example of using the ParticleSwarmOptimizer in ITK? I tried using it but it throws the following error: *itkParticleSwarmOptimizerBase.cxx Line: 360 Description: itk::ERROR: ParticleSwarmOptimizer(0xa2a19d8): cost function and parameter bounds dimensions mismatch* I found no information about the error nor the optimizer. Thank you very much. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/itkParticleSwarmOptimizer-Example-tp7586188.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 11 09:05:28 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 11 Sep 2014 09:05:28 -0400 Subject: [ITK] [ITK-users] Fwd: using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> Message-ID: <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov> Hello, First I would look at the output of the conda build. What that OK? Did it give a successful output? Next I would look into the site packages directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages) for the SimpleITK directory. Brad On Sep 11, 2014, at 12:43 AM, Vishwa wrote: > > > I did install anaconda again and ran the conda build like you suggest. It ran without and problem. However, when I import simpleitk, it gives a error saying no module found. > > Any ideas? > > Vishwa > > On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] wrote: > Hello, > > You need to use the conda build environment. Look at the readme in this repo[1]. > > Basically you'll need to do the following: > > $ conda install conda-build > $ cd src > $ git clone https://github.com/thewtex/conda-recipes.git > $ git checkout simpleitk-clone-url > $ conda build simpleitk > > > > [1] https://github.com/conda/conda-recipes > > On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]> wrote: > >> Thanks very much for the information. I looked at the conda recipe. There are three files. >> One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile.. >> >> There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. >> >> Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. >> >> Best regards, >> Vishwa >> >> >> >> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]> wrote: >> Hello, >> >> This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment. >> >> I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct. >> >> You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker. >> >> Also you can inspect the runtime libraries: >> >> otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so >> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: >> @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0) >> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0) >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1) >> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0) >> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0) >> >> [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme >> >> Hope this helps, >> Brad >> >> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]> wrote: >> >>> import SimpleITK as sitk >>> >>> Fatal Python error: PyThreadState_Get: no current thread >>> >>> >>> Abort trap: 6 >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > If you reply to this email, your message will be added to the discussion below: > http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179p7586186.html > To unsubscribe from using simpleITK with anaconda python distribution, click here. > NAML > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 11 20:36:50 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 11 Sep 2014 20:36:50 -0400 Subject: [ITK] [ITK-users] Fwd: using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov> Message-ID: <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov> From [1] did you try: conda install --use-local simpleitk Brad [1] http://conda.pydata.org/docs/build_tutorials/pkgs.html On Sep 11, 2014, at 1:06 PM, Vishwa wrote: > Hi All, > I think python PythonPackage/setup.py installed wasn't in the location that the recipe calls for. I manually went to the location and ran the command. It was in the following folder > > /Users/dagarshali/anaconda/conda-bld/work/build/SimpleITK-build/Wrapping > > After that when I checked for simpleITK in /Users/dagarshali/anaconda/lib/python2.7/site-packages, I found > > > /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK > > Now, when I try to import simpleitk, i get an error which is shown below. > > >>> import SimpleITK as sitk > > Traceback (most recent call last): > > File "", line 1, in > > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in > > from .SimpleITK import * > > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in > > _SimpleITK = swig_import_helper() > > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > > ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libjpeg.8.dylib > > Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so > > Reason: image not found > > > > I am guessing that's a progress from where I was. Any ideas to fix this one? > > > > Vishwa > > > On Thu, Sep 11, 2014 at 11:18 AM, Vishwa wrote: > Hi, > I looked in ~/anaconda//lib/python2.7/site-packages and couldn't find the simpleitk directory. I ran the conda build again and saved the log file. I am attaching here for your reference. Hopefully, that should tell us something. > > Vishwa > > On Thu, Sep 11, 2014 at 8:05 AM, Bradley Lowekamp wrote: > Hello, > > First I would look at the output of the conda build. What that OK? Did it give a successful output? Next I would look into the site packages directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages) for the SimpleITK directory. > > Brad > On Sep 11, 2014, at 12:43 AM, Vishwa wrote: > >> >> >> I did install anaconda again and ran the conda build like you suggest. It ran without and problem. However, when I import simpleitk, it gives a error saying no module found. >> >> Any ideas? >> >> Vishwa >> >> On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] wrote: >> Hello, >> >> You need to use the conda build environment. Look at the readme in this repo[1]. >> >> Basically you'll need to do the following: >> >> $ conda install conda-build >> $ cd src >> $ git clone https://github.com/thewtex/conda-recipes.git >> $ git checkout simpleitk-clone-url >> $ conda build simpleitk >> >> >> >> [1] https://github.com/conda/conda-recipes >> >> On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]> wrote: >> >>> Thanks very much for the information. I looked at the conda recipe. There are three files. >>> One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile.. >>> >>> There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. >>> >>> Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. >>> >>> Best regards, >>> Vishwa >>> >>> >>> >>> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]> wrote: >>> Hello, >>> >>> This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment. >>> >>> I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct. >>> >>> You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker. >>> >>> Also you can inspect the runtime libraries: >>> >>> otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so >>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: >>> @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0) >>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0) >>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1) >>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0) >>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0) >>> >>> [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme >>> >>> Hope this helps, >>> Brad >>> >>> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]> wrote: >>> >>>> import SimpleITK as sitk >>>> >>>> Fatal Python error: PyThreadState_Get: no current thread >>>> >>>> >>>> Abort trap: 6 >>>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> If you reply to this email, your message will be added to the discussion below: >> http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179p7586186.html >> To unsubscribe from using simpleITK with anaconda python distribution, click here. >> NAML >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Fri Sep 12 02:02:22 2014 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Fri, 12 Sep 2014 02:02:22 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: DICOM Spatial Transform IO in the Insight Toolkit Message-ID: <20140912060222.BDC953D6C18C@insightsoftwareconsortium.org> Hello, A new submission has been added to the Insight Journal. Title: DICOM Spatial Transform IO in the Insight Toolkit Authors: McCormick M., Wang K., Lasso A., Sharp G., Pieper S. Abstract: This document describes a module that extends the Insight Toolkit, ITK, which reads DICOM Spatial Rogistration Object files in itk::Transform's. Currently, DICOM files are read by applying the DCMTK library as a backend. An itk::DCMTKTransformIO class can be registration with the IO factory mechanism so itk::TransformFileReadertemplate will recognize and read these files. This paper is accompanied with the source code, input data, parameters and output data that the authors used for validating the algorithm described in this paper. This adhere to the fundamental principle that scientific publications must facilitate reproducibility of the reported results. Download and review this publication at: http://hdl.handle.net/10380/3468 Generated by the Insight Journal You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://insight-journal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jean-charles.quillet at alyotech.fr Fri Sep 12 03:59:22 2014 From: jean-charles.quillet at alyotech.fr (QUILLET Jean-Charles) Date: Fri, 12 Sep 2014 09:59:22 +0200 Subject: [ITK] Hyperspectral images resampling Message-ID: <06A7AD4E92172446ADDEB44F8A5D5C1032802DC904@ARE01.alyotech.fr> Hello, I need to resample hyperspectral images along the third dimension. I mean, let's say I have an image with 200 bands. Can I resample the image to have 100 bands ? I'm pretty sure it is possible to do it with Itk. Can you confirm me this ? Can someone point me to the right direction (documentation, example) ? Thanks, Jean-Charles -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilian_oliver.mordig at roche.com Fri Sep 12 07:10:51 2014 From: maximilian_oliver.mordig at roche.com (maximilian) Date: Fri, 12 Sep 2014 04:10:51 -0700 (PDT) Subject: [ITK] [ITK-users] Integrate SCIFIO into ITK Message-ID: <1410520251887-7586194.post@n2.nabble.com> Dear All, I have problems including the image IO that comes with SCIFIO. I rebuilt ITK with the MODULE_SCIFIO flag activated. Then, I created a new project with the same content as "itkSCIFIOImageIOTest.cxx" that comes with the SCIFIO plugin. ITK can't find the itkSCIFIOImageIO.h header. The error is: fatal error C1083: Cannot open include file: 'itkSCIFIOImageIO.h': No such file or directory What do I have to add in my CMake file? My current CMakeLists.txt is: cmake_minimum_required(VERSION 2.8) project( ReadFlex ) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) add_executable(ReadFlex ReadFlex.cxx) target_link_libraries( ReadFlex ${ITK_LIBRARIES} ) Thanks in advance -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Integrate-SCIFIO-into-ITK-tp7586194.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From mikael.k.eriksson at philips.com Fri Sep 12 08:48:04 2014 From: mikael.k.eriksson at philips.com (Eriksson, Mikael) Date: Fri, 12 Sep 2014 12:48:04 +0000 Subject: [ITK] Multiple ITK-builds and CMake Message-ID: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> Hello, I'm experiencing some problems trying to build BRAINSTools (https://github.com/BRAINSia/BRAINSTools), from where I wanted to run the registration algorithms implemented in the 3DSlicer gui from the command line. The initial situation was: I had ITK (4.5) and VTK built from downloaded files in debug mode on my computer. I managed to build the modules that I wanted from BRAINSTools (BRAINSFit and BRAINSDemonWarp and their dependencies) in debug mode. Everything was fine until I tried running a registration - I hadn't realized until then that debug mode would make the registrations run really slowly. So, since I now have git on my computer, I cloned fresh versions of ITK and VTK to new source folders at the same levels as the old source folders, and built one debug version and one release version for both ITK and VTK, into separate folders. So my directory structure looked like this. C:/ - ITK/ - srcOld (ITK 4.5, from files) binOld (debug) srcNewDebug (ITK 4.7, from source) srcNewRelease (ITK 4.7, from source) binNewDebug binNewRelease C:/ - VTK/ - corresponding... I probably have an unnecessary amount of builds and folders, but I was afraid to ruin any previous work. Now I tried to build BRAINSTools again with CMake. The problem here is that there is no option to specify ITK_DIR in the CMakeGUI, as there is in other programs. So I'm not sure how CMake finds and chooses an ITK-build, but I think it fails, because when compiling the BRAINSTools solution in Visual Studio 2010 as usual, using release mode this time, I got linking errors saying that some ITK-libraries couldn't be found: error LNK1181: cannot open input file '..\..\lib\Release\ITKCommon-4.7.lib' I changed my environment variables ITK_DIR to C:/ITK/binNewRelease and changed the old ITK and VTK entries in the PATH variables to the new ones (changed C:\ITK\binOld\bin\debug to C:\ITK\binNewRelease\bin\Release and same for VTK). The same problem persisted however. Can anybody, give any suggestions for how to solve this particular problem? Also, I would be very happy for an explanation or a good link for how CMake and ITK interconnect, and especially, how CMake chooses an ITK build. I looked at the findITK.CMake files, and the ITKConfig.cmake and useITK.cmake files and read the documentation for the find_package function, but it's still not clear to me how it works. Best regards, Mikael ....................................................................................................... Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies mikael.k.eriksson at philips.com ....................................................................................................... ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Sep 12 09:37:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 12 Sep 2014 09:37:24 -0400 Subject: [ITK] Hyperspectral images resampling In-Reply-To: <06A7AD4E92172446ADDEB44F8A5D5C1032802DC904@ARE01.alyotech.fr> References: <06A7AD4E92172446ADDEB44F8A5D5C1032802DC904@ARE01.alyotech.fr> Message-ID: Hi Jean-Charles, If the spectral components are treated as the third dimension, then the image can be resampled with the ResampleImageFilter with a low-pass filter to prevent aliasing [1] or with the BinShrinkFilter [2]. Hope this helps, Matt [1] http://www.itk.org/Doxygen/html/Filtering_2SubsampleVolume_8cxx-example.html [2] http://www.itk.org/Doxygen/html/classitk_1_1BinShrinkImageFilter.html On Fri, Sep 12, 2014 at 3:59 AM, QUILLET Jean-Charles wrote: > Hello, > > > > I need to resample hyperspectral images along the third dimension. I mean, > let's say I have an image with 200 bands. Can I resample the image to have > 100 bands ? > > > > I'm pretty sure it is possible to do it with Itk. Can you confirm me this ? > Can someone point me to the right direction (documentation, example) ? > > Thanks, > > > > Jean-Charles > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Fri Sep 12 09:54:31 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 12 Sep 2014 09:54:31 -0400 Subject: [ITK] Multiple ITK-builds and CMake In-Reply-To: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> References: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: Hi Mikael, A few pointers: - Only a single source per project directory is needed. - Set ITK_DIR in the cmake-gui explicitly for each configuration -- don't try to use environmental variables, etc. More details on how find_package works can be found here [1] and here [2]. Hope this helps, Matt [1] http://www.cmake.org/cmake/help/v3.0/command/find_package.html#command:find_package [2] http://www.cmake.org/cmake/help/v3.0/manual/cmake-packages.7.html On Fri, Sep 12, 2014 at 8:48 AM, Eriksson, Mikael wrote: > Hello, > > > > I?m experiencing some problems trying to build BRAINSTools > (https://github.com/BRAINSia/BRAINSTools), from where I wanted to run the > registration algorithms implemented in the 3DSlicer gui from the command > line. The initial situation was: I had ITK (4.5) and VTK built from > downloaded files in debug mode on my computer. I managed to build the > modules that I wanted from BRAINSTools (BRAINSFit and BRAINSDemonWarp and > their dependencies) in debug mode. Everything was fine until I tried running > a registration ? I hadn?t realized until then that debug mode would make the > registrations run really slowly. > > > > So, since I now have git on my computer, I cloned fresh versions of ITK and > VTK to new source folders at the same levels as the old source folders, and > built one debug version and one release version for both ITK and VTK, into > separate folders. So my directory structure looked like this. > > > > C:/ - ITK/ - srcOld (ITK 4.5, from > files) > > binOld > (debug) > > srcNewDebug (ITK 4.7, from source) > > srcNewRelease (ITK 4.7, from source) > > binNewDebug > > binNewRelease > > > > C:/ - VTK/ - corresponding? > > > > I probably have an unnecessary amount of builds and folders, but I was > afraid to ruin any previous work. > > > > Now I tried to build BRAINSTools again with CMake. The problem here is that > there is no option to specify ITK_DIR in the CMakeGUI, as there is in other > programs. So I?m not sure how CMake finds and chooses an ITK-build, but I > think it fails, because when compiling the BRAINSTools solution in Visual > Studio 2010 as usual, using release mode this time, I got linking errors > saying that some ITK-libraries couldn?t be found: > > > > error LNK1181: cannot open input file '..\..\lib\Release\ITKCommon-4.7.lib' > > > > I changed my environment variables ITK_DIR to C:/ITK/binNewRelease and > changed the old ITK and VTK entries in the PATH variables to the new ones > (changed C:\ITK\binOld\bin\debug to C:\ITK\binNewRelease\bin\Release and > same for VTK). The same problem persisted however. Can anybody, give any > suggestions for how to solve this particular problem? Also, I would be very > happy for an explanation or a good link for how CMake and ITK interconnect, > and especially, how CMake chooses an ITK build. I looked at the > findITK.CMake files, and the ITKConfig.cmake and useITK.cmake files and read > the documentation for the find_package function, but it?s still not clear to > me how it works. > > > > Best regards, > > Mikael > > > > ??????????????????????????????????. > > Mikael Eriksson > > R&D Physicist Trainee > > Philips Medical Systems MR Finland, Feasibility studies > > mikael.k.eriksson at philips.com > > ??????????????????????????????????. > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From HIROTATSU.ARMSTRONG at UCDENVER.EDU Fri Sep 12 14:05:52 2014 From: HIROTATSU.ARMSTRONG at UCDENVER.EDU (Armstrong, Hirotatsu) Date: Fri, 12 Sep 2014 18:05:52 +0000 Subject: [ITK] VTK Deplacement Field Format Message-ID: <6a5c51da2497473e9b17bc41ba196482@CO1PR05MB411.namprd05.prod.outlook.com> Hello, I am having some trouble understanding the format of a .vtk file. I am deformably registering 2 CT images and saving the displacement field in a .vtk file. According to a pdf I found (for VTK v4.2), when written in ASCII format, vector data should have 3 values on each line corresponding to the x,y,z components for each vector. When I write my .vtk file, I get this, # vtk DataFile Version 3.0 VTK File Generated by Insight Segmentation and Registration Toolkit (ITK) ASCII DATASET STRUCTURED_POINTS DIMENSIONS 512 512 88 SPACING 9.7656250000000000e-001 9.7656250000000000e-001 3.0000000000000000e+000 ORIGIN -2.5000000000000000e+002 -1.0900000000000000e+002 -1.5900000000000000e+002 POINT_DATA 23068672 VECTORS vectors float -0.0644559 -0.0859412 0 0.231144 -0.231144 0 0.242202 -0.201835 0 -0.211765 0 0 0.164835 -0.362637 0 0.159204 -0.437811 0 0.108108 -0.0405405 0 0.395062 -0.0493827 0 -0.0987654 0.00493827 0 0.447702 -0.127915 0 -0.167866 0.167866 0 -0.359551 -0.134831 0 . . . Which is giving 6 values on each line. I looked for some documentation but couldn't find anything other than the pdf. Could someone please point me to the latest documentation for the .vtk file format? Also, I originally wrote the files in binary format, but was having some issue with that as well, which is why I switched to ASCII so I can actually visualize the data. The documentation is not clear if there are newline characters included or not when binary data is written. I would assume not, but could this be clarified as well? Thanks James Armstrong, Ph.D. PostDoctoral Fellow, Physics Department of Radiation Oncology University of Colorado School of Medicine 1665 Aurora Ct, MS F706 Aurora, CO 80045 720-848-0257 -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Sep 12 14:44:50 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 12 Sep 2014 14:44:50 -0400 Subject: [ITK] VTK Deplacement Field Format In-Reply-To: <6a5c51da2497473e9b17bc41ba196482@CO1PR05MB411.namprd05.prod.outlook.com> References: <6a5c51da2497473e9b17bc41ba196482@CO1PR05MB411.namprd05.prod.outlook.com> Message-ID: Hi James, Yes, it looks like ITK's .vtk files writer is not following the standard very well, and it is printing six values per line [1]. The binary version will not have any newlines. Hope this helps, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/src/itkImageIOBase.cxx;h=ae10e65dee1ecff0579d9ba43db9118c4466eec7;hb=HEAD#l656 On Fri, Sep 12, 2014 at 2:05 PM, Armstrong, Hirotatsu wrote: > Hello, > > > > I am having some trouble understanding the format of a .vtk file. I am > deformably registering 2 CT images and saving the displacement field in a > .vtk file. According to a pdf I found (for VTK v4.2), when written in ASCII > format, vector data should have 3 values on each line corresponding to the > x,y,z components for each vector. When I write my .vtk file, I get this, > > > > > > # vtk DataFile Version 3.0 > > VTK File Generated by Insight Segmentation and Registration Toolkit (ITK) > > ASCII > > DATASET STRUCTURED_POINTS > > DIMENSIONS 512 512 88 > > SPACING 9.7656250000000000e-001 9.7656250000000000e-001 > 3.0000000000000000e+000 > > ORIGIN -2.5000000000000000e+002 -1.0900000000000000e+002 > -1.5900000000000000e+002 > > POINT_DATA 23068672 > > VECTORS vectors float > > -0.0644559 -0.0859412 0 0.231144 -0.231144 0 > > 0.242202 -0.201835 0 -0.211765 0 0 > > 0.164835 -0.362637 0 0.159204 -0.437811 0 > > 0.108108 -0.0405405 0 0.395062 -0.0493827 0 > > -0.0987654 0.00493827 0 0.447702 -0.127915 0 > > -0.167866 0.167866 0 -0.359551 -0.134831 0 > > . > > . > > . > > > > > > Which is giving 6 values on each line. I looked for some documentation but > couldn?t find anything other than the pdf. Could someone please point me to > the latest documentation for the .vtk file format? Also, I originally wrote > the files in binary format, but was having some issue with that as well, > which is why I switched to ASCII so I can actually visualize the data. The > documentation is not clear if there are newline characters included or not > when binary data is written. I would assume not, but could this be > clarified as well? > > > > Thanks > > > > James Armstrong, Ph.D. > > PostDoctoral Fellow, Physics > > Department of Radiation Oncology > > University of Colorado School of Medicine > > 1665 Aurora Ct, MS F706 > > Aurora, CO 80045 > > 720-848-0257 > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From lasso at queensu.ca Fri Sep 12 15:08:11 2014 From: lasso at queensu.ca (Andras Lasso) Date: Fri, 12 Sep 2014 19:08:11 +0000 Subject: [ITK] VTK Deplacement Field Format In-Reply-To: References: <6a5c51da2497473e9b17bc41ba196482@CO1PR05MB411.namprd05.prod.outlook.com> Message-ID: .vtk is the old generic VTK file format, replaced by the XML-based file formats (.vti, .vtp, ...). I would not recommend using .vtk file format for image storage, especially the ASCII version (because it's big and floating-point numbers are not represented accurately). You can use MetaIO (.mha, .mhd) or NRRD (.nrrd, .nhdr) formats instead. They are both widely supported (ITK, VTK, 3D Slicer, ParaView, Matlab, etc.), well documented, and simple and efficient to parse. Andras -----Original Message----- From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt McCormick Sent: Friday, September 12, 2014 2:45 PM To: Armstrong, Hirotatsu Cc: community at itk.org Subject: Re: [ITK] VTK Deplacement Field Format Hi James, Yes, it looks like ITK's .vtk files writer is not following the standard very well, and it is printing six values per line [1]. The binary version will not have any newlines. Hope this helps, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/src/itkImageIOBase.cxx;h=ae10e65dee1ecff0579d9ba43db9118c4466eec7;hb=HEAD#l656 On Fri, Sep 12, 2014 at 2:05 PM, Armstrong, Hirotatsu wrote: > Hello, > > > > I am having some trouble understanding the format of a .vtk file. I > am deformably registering 2 CT images and saving the displacement > field in a .vtk file. According to a pdf I found (for VTK v4.2), when > written in ASCII format, vector data should have 3 values on each line > corresponding to the x,y,z components for each vector. When I write > my .vtk file, I get this, > > > > > > # vtk DataFile Version 3.0 > > VTK File Generated by Insight Segmentation and Registration Toolkit > (ITK) > > ASCII > > DATASET STRUCTURED_POINTS > > DIMENSIONS 512 512 88 > > SPACING 9.7656250000000000e-001 9.7656250000000000e-001 > 3.0000000000000000e+000 > > ORIGIN -2.5000000000000000e+002 -1.0900000000000000e+002 > -1.5900000000000000e+002 > > POINT_DATA 23068672 > > VECTORS vectors float > > -0.0644559 -0.0859412 0 0.231144 -0.231144 0 > > 0.242202 -0.201835 0 -0.211765 0 0 > > 0.164835 -0.362637 0 0.159204 -0.437811 0 > > 0.108108 -0.0405405 0 0.395062 -0.0493827 0 > > -0.0987654 0.00493827 0 0.447702 -0.127915 0 > > -0.167866 0.167866 0 -0.359551 -0.134831 0 > > . > > . > > . > > > > > > Which is giving 6 values on each line. I looked for some > documentation but couldn?t find anything other than the pdf. Could > someone please point me to the latest documentation for the .vtk file > format? Also, I originally wrote the files in binary format, but was > having some issue with that as well, which is why I switched to ASCII > so I can actually visualize the data. The documentation is not clear > if there are newline characters included or not when binary data is > written. I would assume not, but could this be clarified as well? > > > > Thanks > > > > James Armstrong, Ph.D. > > PostDoctoral Fellow, Physics > > Department of Radiation Oncology > > University of Colorado School of Medicine > > 1665 Aurora Ct, MS F706 > > Aurora, CO 80045 > > 720-848-0257 > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From vijayarani.shanmugavadivu at appasamy.com Sat Sep 13 08:34:42 2014 From: vijayarani.shanmugavadivu at appasamy.com (vijayarani) Date: Sat, 13 Sep 2014 05:34:42 -0700 (PDT) Subject: [ITK] [ITK-users] Resampling a mha image and finding histogram Message-ID: <1410611682783-7586198.post@n2.nabble.com> Hi I have a mha image which is very large.How to subsample it and find histogram of the image? Thanks Vijaya Rani S -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Resampling-a-mha-image-and-finding-histogram-tp7586198.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From vijayarani.shanmugavadivu at appasamy.com Sat Sep 13 08:39:28 2014 From: vijayarani.shanmugavadivu at appasamy.com (vijayarani) Date: Sat, 13 Sep 2014 18:09:28 +0530 Subject: [ITK] [ITK-users] Subsampling a mha image and finding histogram Message-ID: <54143B00.1070906@appasamy.com> Hi I have a mha image which is very large in size.How to subsample it and find histogram? Thanks Vijaya Rani S _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Sat Sep 13 13:00:50 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Sat, 13 Sep 2014 13:00:50 -0400 Subject: [ITK] [ITK-users] Fwd: using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov> <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov> Message-ID: <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov> Did you remove the installed SimpleITK from the setup.py script before running "const install --use-local simpleitk". I am guessing conda didn't install simpleitk correctly because of the old version manually installed. Brad On Sep 12, 2014, at 10:52 PM, Vishwa wrote: > Hi Brad, > Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter.. > > Here is the thing that I noticed.. > > If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error. > > >>import SimpleITK as sitk > Traceback (most recent call last): > File "", line 1, in > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in > from .SimpleITK import * > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in > _SimpleITK = swig_import_helper() > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib > Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so > Reason: image not found > > Any suggestions? > > > On Fri, Sep 12, 2014 at 6:59 PM, Vishwa wrote: > Hi Brad, > Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter.. > > Here is the thing that I noticed.. > > If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error. > > >>import SimpleITK as sitk > Traceback (most recent call last): > File "", line 1, in > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in > from .SimpleITK import * > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in > _SimpleITK = swig_import_helper() > File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib > Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so > Reason: image not found > > Any suggestions? > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From brad at lowekamp.net Sat Sep 13 21:51:48 2014 From: brad at lowekamp.net (Bradley Lowekamp) Date: Sat, 13 Sep 2014 21:51:48 -0400 Subject: [ITK] [ITK-users] Fwd: using simpleITK with anaconda python distribution In-Reply-To: References: <1410316426142-7586179.post@n2.nabble.com> <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov> <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov> <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov> <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov> <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov> Message-ID: <358E123A-966E-4C49-B2ED-9EC69B663C37@mail.nih.gov> Great to hear you got it working!!! I'll add a FAQ with specific instruction and some of the lessons learned here. Brad > On Sep 13, 2014, at 8:20 PM, Vishwa wrote: > > It finally worked with the conda install --use-local simpleitk command. > > Thanks everyone > > Regards, > vishwa > >> On Sat, Sep 13, 2014 at 2:36 PM, Vishwa wrote: >> I didn't remove it. How exactly do I do that? Also, from which folder should i run the conda install --use-local simpleitk command. >> >> I changed to conda recipes folder and issued the command. I got an error >> >> conda install --use-local simpleitk >> Fetching package metadata: ...Error: Could not find URL: file:///Users/dagarshali/anaconda/conda-bld/osx-64/ >> >> >>> On Sat, Sep 13, 2014 at 12:00 PM, Bradley Lowekamp wrote: >>> Did you remove the installed SimpleITK from the setup.py script before running "const install --use-local simpleitk". I am guessing conda didn't install simpleitk correctly because of the old version manually installed. >>> >>> Brad >>> >>>> On Sep 12, 2014, at 10:52 PM, Vishwa wrote: >>>> >>>> Hi Brad, >>>> Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter.. >>>> >>>> Here is the thing that I noticed.. >>>> >>>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error. >>>> >>>> >>import SimpleITK as sitk >>>> Traceback (most recent call last): >>>> File "", line 1, in >>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in >>>> from .SimpleITK import * >>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in >>>> _SimpleITK = swig_import_helper() >>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >>>> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >>>> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib >>>> Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so >>>> Reason: image not found >>>> >>>> Any suggestions? >>>> >>>> >>>>> On Fri, Sep 12, 2014 at 6:59 PM, Vishwa wrote: >>>>> Hi Brad, >>>>> Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter.. >>>>> >>>>> Here is the thing that I noticed.. >>>>> >>>>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error. >>>>> >>>>> >>import SimpleITK as sitk >>>>> Traceback (most recent call last): >>>>> File "", line 1, in >>>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in >>>>> from .SimpleITK import * >>>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in >>>>> _SimpleITK = swig_import_helper() >>>>> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >>>>> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >>>>> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib >>>>> Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so >>>>> Reason: image not found >>>>> >>>>> Any suggestions? > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Sun Sep 14 13:26:09 2014 From: llliu at umich.edu (Lianli Liu) Date: Sun, 14 Sep 2014 13:26:09 -0400 Subject: [ITK] [ITK-users] how to modify existing algorithm in ITK Message-ID: Hi all, I am brand new to ITK and I want to modify some ITK registration functions for specific use. But I am not clear about how to do this. After installation, it seems that I cannot find source code in the ITK-build folder. I just wonder if I want to redefine some functions, do I need to download the source code again? Or is there a tutorial giving example on how to modify existing algorithms in ITK? Thanks a lot! Regards, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Sun Sep 14 18:28:32 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sun, 14 Sep 2014 22:28:32 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff Message-ID: Hi all, I have run into an issue with 4.6, triggered by a problem with Slicer (another story - unable to load big tiffs). I have built Slicer, which includes ITK-4.6, on Windows 7. In my efforts to track down the problem Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 installation that I now have (I have previously been using 4.0). In principle the failure to load a big tiff should be a problem with ITK, not with Slicer. When I run cmake to set up the Visual Studio 10 project files for my simple test program (which works with 4.0), I get errors concerning DCMTK: D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 (message): Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR DCMTK_dcmimgle_LIBRARY) Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 (find_package_handle_standard_args) C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 (find_package) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 (itk_module_load) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 (_itk_module_config_recurse) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 (itk_module_config) C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 (find_package) CMakeLists.txt:4 (FIND_PACKAGE) Here is the stock-standard CMakeLists.txt: cmake_minimum_required(VERSION 2.8) PROJECT(makebig) FIND_PACKAGE(ITK) IF(ITK_FOUND) INCLUDE(${ITK_USE_FILE}) ELSE(ITK_FOUND) MESSAGE(FATAL_ERROR "ITK not found. Please set ITK_DIR.") ENDIF(ITK_FOUND) MESSAGE (${ITK_USE_FILE}) MESSAGE (${ITK_INCLUDE_DIRS}) set(PROJECTNAME "makebig") ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the error messages did not change. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Sun Sep 14 18:34:02 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sun, 14 Sep 2014 22:34:02 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: cmake-3.0.2 ________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 15 September 2014 10:28 a.m. To: community at itk.org Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi all, I have run into an issue with 4.6, triggered by a problem with Slicer (another story - unable to load big tiffs). I have built Slicer, which includes ITK-4.6, on Windows 7. In my efforts to track down the problem Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 installation that I now have (I have previously been using 4.0). In principle the failure to load a big tiff should be a problem with ITK, not with Slicer. When I run cmake to set up the Visual Studio 10 project files for my simple test program (which works with 4.0), I get errors concerning DCMTK: D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 (message): Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR DCMTK_dcmimgle_LIBRARY) Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 (find_package_handle_standard_args) C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 (find_package) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 (itk_module_load) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 (_itk_module_config_recurse) C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 (itk_module_config) C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 (find_package) CMakeLists.txt:4 (FIND_PACKAGE) Here is the stock-standard CMakeLists.txt: cmake_minimum_required(VERSION 2.8) PROJECT(makebig) FIND_PACKAGE(ITK) IF(ITK_FOUND) INCLUDE(${ITK_USE_FILE}) ELSE(ITK_FOUND) MESSAGE(FATAL_ERROR "ITK not found. Please set ITK_DIR.") ENDIF(ITK_FOUND) MESSAGE (${ITK_USE_FILE}) MESSAGE (${ITK_INCLUDE_DIRS}) set(PROJECTNAME "makebig") ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the error messages did not change. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Sun Sep 14 20:12:48 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 14 Sep 2014 20:12:48 -0400 Subject: [ITK] [ITK-users] how to modify existing algorithm in ITK In-Reply-To: References: Message-ID: Hi Lianli, Welcome to ITK! ITK separates source from build artifacts. Usually, all source code is kept in the source tree, and all build artifacts are kept in the build tree. An install tree will install header files from the source tree and libraries from the build tree, and it will leave out the .cxx sources and .o object files. You can extend ITK by writing your own classes in a module as described here [1]. For investigating registration, some tools built on ITK like elastix [2] can be useful. As always, The ITK Software Guide is a great resource [3]. Hope this helps, Matt [1] http://www.kitware.com/blog/home/post/557 [2] http://elastix.isi.uu.nl/ [3] http://itk.org/ITK/resources/software.html On Sun, Sep 14, 2014 at 1:26 PM, Lianli Liu wrote: > Hi all, > > I am brand new to ITK and I want to modify some ITK registration functions > for specific use. But I am not clear about how to do this. After > installation, it seems that I cannot find source code in the ITK-build > folder. I just wonder if I want to redefine some functions, do I need to > download the source code again? Or is there a tutorial giving example on how > to modify existing algorithms in ITK? Thanks a lot! > > Regards, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sun Sep 14 22:51:04 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 14 Sep 2014 22:51:04 -0400 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: Hi Gib, Which version of DCMTK was built? Was it installed? Thanks, Matt On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: > cmake-3.0.2 > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 15 September 2014 10:28 a.m. > To: community at itk.org > Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi all, > > I have run into an issue with 4.6, triggered by a problem with Slicer > (another story - unable to load big tiffs). I have built Slicer, which > includes ITK-4.6, on Windows 7. In my efforts to track down the problem > Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 > installation that I now have (I have previously been using 4.0). In > principle the failure to load a big tiff should be a problem with ITK, not > with Slicer. > > When I run cmake to set up the Visual Studio 10 project files for my simple > test program (which works with 4.0), I get errors concerning DCMTK: > > D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" > -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ > CMake Error at C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 > (message): > Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY > DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR > DCMTK_dcmimgle_LIBRARY) > Call Stack (most recent call first): > C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard > Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 > (find_package_handle_standard_args) > C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 > (find_package) > > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 > (itk_module_load) > > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 > (_itk_module_config_recurse) > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 > (itk_module_config) > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 > (find_package) > CMakeLists.txt:4 (FIND_PACKAGE) > > Here is the stock-standard CMakeLists.txt: > > cmake_minimum_required(VERSION 2.8) > > PROJECT(makebig) > FIND_PACKAGE(ITK) > IF(ITK_FOUND) > INCLUDE(${ITK_USE_FILE}) > ELSE(ITK_FOUND) > MESSAGE(FATAL_ERROR > "ITK not found. Please set ITK_DIR.") > ENDIF(ITK_FOUND) > MESSAGE (${ITK_USE_FILE}) > MESSAGE (${ITK_INCLUDE_DIRS}) > set(PROJECTNAME "makebig") > ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) > TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) > > I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the > error messages did not change. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From g.bogle at auckland.ac.nz Sun Sep 14 22:56:30 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 15 Sep 2014 02:56:30 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: , Message-ID: Hi Matt, Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. Cheers Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Monday, 15 September 2014 2:51 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi Gib, Which version of DCMTK was built? Was it installed? Thanks, Matt On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: > cmake-3.0.2 > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 15 September 2014 10:28 a.m. > To: community at itk.org > Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi all, > > I have run into an issue with 4.6, triggered by a problem with Slicer > (another story - unable to load big tiffs). I have built Slicer, which > includes ITK-4.6, on Windows 7. In my efforts to track down the problem > Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 > installation that I now have (I have previously been using 4.0). In > principle the failure to load a big tiff should be a problem with ITK, not > with Slicer. > > When I run cmake to set up the Visual Studio 10 project files for my simple > test program (which works with 4.0), I get errors concerning DCMTK: > > D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" > -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ > CMake Error at C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 > (message): > Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY > DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR > DCMTK_dcmimgle_LIBRARY) > Call Stack (most recent call first): > C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard > Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 > (find_package_handle_standard_args) > C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 > (find_package) > > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 > (itk_module_load) > > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 > (_itk_module_config_recurse) > C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 > (itk_module_config) > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 > (find_package) > CMakeLists.txt:4 (FIND_PACKAGE) > > Here is the stock-standard CMakeLists.txt: > > cmake_minimum_required(VERSION 2.8) > > PROJECT(makebig) > FIND_PACKAGE(ITK) > IF(ITK_FOUND) > INCLUDE(${ITK_USE_FILE}) > ELSE(ITK_FOUND) > MESSAGE(FATAL_ERROR > "ITK not found. Please set ITK_DIR.") > ENDIF(ITK_FOUND) > MESSAGE (${ITK_USE_FILE}) > MESSAGE (${ITK_INCLUDE_DIRS}) > set(PROJECTNAME "makebig") > ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) > TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) > > I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the > error messages did not change. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Sun Sep 14 23:05:46 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 14 Sep 2014 23:05:46 -0400 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: Hi Gib, Thanks for the information. What happens if DCMTK_DIR is pointed to the DCMTK build directory in the Slicer build tree? Thanks, Matt On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: > Hi Matt, > > Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. > > Cheers > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 2:51 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Which version of DCMTK was built? Was it installed? > > Thanks, > Matt > > On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >> cmake-3.0.2 >> ________________________________ >> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >> [g.bogle at auckland.ac.nz] >> Sent: Monday, 15 September 2014 10:28 a.m. >> To: community at itk.org >> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi all, >> >> I have run into an issue with 4.6, triggered by a problem with Slicer >> (another story - unable to load big tiffs). I have built Slicer, which >> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >> installation that I now have (I have previously been using 4.0). In >> principle the failure to load a big tiff should be a problem with ITK, not >> with Slicer. >> >> When I run cmake to set up the Visual Studio 10 project files for my simple >> test program (which works with 4.0), I get errors concerning DCMTK: >> >> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >> CMake Error at C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >> (message): >> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >> DCMTK_dcmimgle_LIBRARY) >> Call Stack (most recent call first): >> C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >> (find_package_handle_standard_args) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >> (find_package) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >> (itk_module_load) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >> (_itk_module_config_recurse) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >> (itk_module_config) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >> (find_package) >> CMakeLists.txt:4 (FIND_PACKAGE) >> >> Here is the stock-standard CMakeLists.txt: >> >> cmake_minimum_required(VERSION 2.8) >> >> PROJECT(makebig) >> FIND_PACKAGE(ITK) >> IF(ITK_FOUND) >> INCLUDE(${ITK_USE_FILE}) >> ELSE(ITK_FOUND) >> MESSAGE(FATAL_ERROR >> "ITK not found. Please set ITK_DIR.") >> ENDIF(ITK_FOUND) >> MESSAGE (${ITK_USE_FILE}) >> MESSAGE (${ITK_INCLUDE_DIRS}) >> set(PROJECTNAME "makebig") >> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >> >> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >> error messages did not change. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> From g.bogle at auckland.ac.nz Sun Sep 14 23:09:33 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 15 Sep 2014 03:09:33 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: , Message-ID: The same result. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Monday, 15 September 2014 3:05 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi Gib, Thanks for the information. What happens if DCMTK_DIR is pointed to the DCMTK build directory in the Slicer build tree? Thanks, Matt On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: > Hi Matt, > > Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. > > Cheers > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 2:51 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Which version of DCMTK was built? Was it installed? > > Thanks, > Matt > > On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >> cmake-3.0.2 >> ________________________________ >> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >> [g.bogle at auckland.ac.nz] >> Sent: Monday, 15 September 2014 10:28 a.m. >> To: community at itk.org >> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi all, >> >> I have run into an issue with 4.6, triggered by a problem with Slicer >> (another story - unable to load big tiffs). I have built Slicer, which >> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >> installation that I now have (I have previously been using 4.0). In >> principle the failure to load a big tiff should be a problem with ITK, not >> with Slicer. >> >> When I run cmake to set up the Visual Studio 10 project files for my simple >> test program (which works with 4.0), I get errors concerning DCMTK: >> >> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >> CMake Error at C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >> (message): >> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >> DCMTK_dcmimgle_LIBRARY) >> Call Stack (most recent call first): >> C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >> (find_package_handle_standard_args) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >> (find_package) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >> (itk_module_load) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >> (_itk_module_config_recurse) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >> (itk_module_config) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >> (find_package) >> CMakeLists.txt:4 (FIND_PACKAGE) >> >> Here is the stock-standard CMakeLists.txt: >> >> cmake_minimum_required(VERSION 2.8) >> >> PROJECT(makebig) >> FIND_PACKAGE(ITK) >> IF(ITK_FOUND) >> INCLUDE(${ITK_USE_FILE}) >> ELSE(ITK_FOUND) >> MESSAGE(FATAL_ERROR >> "ITK not found. Please set ITK_DIR.") >> ENDIF(ITK_FOUND) >> MESSAGE (${ITK_USE_FILE}) >> MESSAGE (${ITK_INCLUDE_DIRS}) >> set(PROJECTNAME "makebig") >> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >> >> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >> error messages did not change. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> From g.bogle at auckland.ac.nz Sun Sep 14 23:45:24 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 15 Sep 2014 03:45:24 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: , , Message-ID: Slicer built OK before I added DCMTK_DIR. ________________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 15 September 2014 3:09 p.m. To: Matt McCormick Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff The same result. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Monday, 15 September 2014 3:05 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi Gib, Thanks for the information. What happens if DCMTK_DIR is pointed to the DCMTK build directory in the Slicer build tree? Thanks, Matt On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: > Hi Matt, > > Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. > > Cheers > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 2:51 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Which version of DCMTK was built? Was it installed? > > Thanks, > Matt > > On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >> cmake-3.0.2 >> ________________________________ >> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >> [g.bogle at auckland.ac.nz] >> Sent: Monday, 15 September 2014 10:28 a.m. >> To: community at itk.org >> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi all, >> >> I have run into an issue with 4.6, triggered by a problem with Slicer >> (another story - unable to load big tiffs). I have built Slicer, which >> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >> installation that I now have (I have previously been using 4.0). In >> principle the failure to load a big tiff should be a problem with ITK, not >> with Slicer. >> >> When I run cmake to set up the Visual Studio 10 project files for my simple >> test program (which works with 4.0), I get errors concerning DCMTK: >> >> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >> CMake Error at C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >> (message): >> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >> DCMTK_dcmimgle_LIBRARY) >> Call Stack (most recent call first): >> C:/Program Files >> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >> (find_package_handle_standard_args) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >> (find_package) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >> (itk_module_load) >> >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >> (_itk_module_config_recurse) >> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >> (itk_module_config) >> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >> (find_package) >> CMakeLists.txt:4 (FIND_PACKAGE) >> >> Here is the stock-standard CMakeLists.txt: >> >> cmake_minimum_required(VERSION 2.8) >> >> PROJECT(makebig) >> FIND_PACKAGE(ITK) >> IF(ITK_FOUND) >> INCLUDE(${ITK_USE_FILE}) >> ELSE(ITK_FOUND) >> MESSAGE(FATAL_ERROR >> "ITK not found. Please set ITK_DIR.") >> ENDIF(ITK_FOUND) >> MESSAGE (${ITK_USE_FILE}) >> MESSAGE (${ITK_INCLUDE_DIRS}) >> set(PROJECTNAME "makebig") >> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >> >> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >> error messages did not change. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From mikael.k.eriksson at philips.com Mon Sep 15 01:40:41 2014 From: mikael.k.eriksson at philips.com (Eriksson, Mikael) Date: Mon, 15 Sep 2014 05:40:41 +0000 Subject: [ITK] Multiple ITK-builds and CMake In-Reply-To: References: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: <2D9DC0609429E24BA87612C012C580C318A76AB7@AMSPRD9002MB028.MGDPHG.emi.philips.com> Hi Matt and community, - Got it! - That is the problem here, the CMake-gui for this application has no ITK_DIR entry so that I can explicitly specify which one to use. Any suggestions for how to get around this? Best, Mikael ??????????????????????????????????. Mikael Eriksson R&D Physicist Trainee Philips Medical Systems MR Finland, Feasibility studies +358 40 631 8500 mikael.k.eriksson at philips.com ??????????????????????????????????. -----Original Message----- From: Matt McCormick [mailto:matt.mccormick at kitware.com] Sent: 12. syyskuuta 2014 16:55 To: Eriksson, Mikael Cc: community at itk.org Subject: Re: [ITK] Multiple ITK-builds and CMake Hi Mikael, A few pointers: - Only a single source per project directory is needed. - Set ITK_DIR in the cmake-gui explicitly for each configuration -- don't try to use environmental variables, etc. More details on how find_package works can be found here [1] and here [2]. Hope this helps, Matt [1] http://www.cmake.org/cmake/help/v3.0/command/find_package.html#command:find_package [2] http://www.cmake.org/cmake/help/v3.0/manual/cmake-packages.7.html On Fri, Sep 12, 2014 at 8:48 AM, Eriksson, Mikael wrote: > Hello, > > > > I?m experiencing some problems trying to build BRAINSTools > (https://github.com/BRAINSia/BRAINSTools), from where I wanted to run > the registration algorithms implemented in the 3DSlicer gui from the > command line. The initial situation was: I had ITK (4.5) and VTK built > from downloaded files in debug mode on my computer. I managed to build > the modules that I wanted from BRAINSTools (BRAINSFit and > BRAINSDemonWarp and their dependencies) in debug mode. Everything was > fine until I tried running a registration ? I hadn?t realized until > then that debug mode would make the registrations run really slowly. > > > > So, since I now have git on my computer, I cloned fresh versions of > ITK and VTK to new source folders at the same levels as the old source > folders, and built one debug version and one release version for both > ITK and VTK, into separate folders. So my directory structure looked like this. > > > > C:/ - ITK/ - srcOld (ITK 4.5, from > files) > > binOld > (debug) > > srcNewDebug (ITK 4.7, from source) > > srcNewRelease (ITK 4.7, from source) > > binNewDebug > > binNewRelease > > > > C:/ - VTK/ - corresponding? > > > > I probably have an unnecessary amount of builds and folders, but I was > afraid to ruin any previous work. > > > > Now I tried to build BRAINSTools again with CMake. The problem here is > that there is no option to specify ITK_DIR in the CMakeGUI, as there > is in other programs. So I?m not sure how CMake finds and chooses an > ITK-build, but I think it fails, because when compiling the > BRAINSTools solution in Visual Studio 2010 as usual, using release > mode this time, I got linking errors saying that some ITK-libraries couldn?t be found: > > > > error LNK1181: cannot open input file '..\..\lib\Release\ITKCommon-4.7.lib' > > > > I changed my environment variables ITK_DIR to C:/ITK/binNewRelease and > changed the old ITK and VTK entries in the PATH variables to the new > ones (changed C:\ITK\binOld\bin\debug to > C:\ITK\binNewRelease\bin\Release and same for VTK). The same problem > persisted however. Can anybody, give any suggestions for how to solve > this particular problem? Also, I would be very happy for an > explanation or a good link for how CMake and ITK interconnect, and > especially, how CMake chooses an ITK build. I looked at the > findITK.CMake files, and the ITKConfig.cmake and useITK.cmake files > and read the documentation for the find_package function, but it?s still not clear to me how it works. > > > > Best regards, > > Mikael > > > > ??????????????????????????????????. > > Mikael Eriksson > > R&D Physicist Trainee > > Philips Medical Systems MR Finland, Feasibility studies > > mikael.k.eriksson at philips.com > > ??????????????????????????????????. > > > > > ________________________________ > The information contained in this message may be confidential and > legally protected under applicable law. The message is intended solely > for the addressee(s). If you are not the intended recipient, you are > hereby notified that any use, forwarding, dissemination, or > reproduction of this message is strictly prohibited and may be > unlawful. If you are not the intended recipient, please contact the > sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From arnaudgelas at gmail.com Mon Sep 15 06:05:02 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Mon, 15 Sep 2014 12:05:02 +0200 Subject: [ITK] [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData Message-ID: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com> Hi guys, I have been looking at GDCMImageIO this morning and I thought it would be great if it was possible to iterate directly on the Dictionary and do not use ExposeMetaData cause internally there are 2 finds (HasKeys and [] ) per iterator (in which we already know both keys and values). https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L700 https://github.com/Kitware/ITK/blob/master/Modules/Core/Common/include/itkMetaDataObject.h#L171-L189 I have tried to create a new function which would take an iterator as parameter, I have compilation error or a failing dynamic_cast? I guess I am missing something obvious? I have been testing something like that: http://review.source.kitware.com/#/c/17026/ Any idea on how to fix the code ( both compilation & dynamic_cast ), please? Thanks, Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Sep 15 11:36:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 11:36:11 -0400 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: Hi Gib, Please try building DCMTK by pointing a clean build directory to this directory [1]. Then, start a clean build of ITK with DCMTK_DIR pointing to that directory. Please let us know if this works. Thanks, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/DCMTK/WindowsBuild/CMakeLists.txt;h=70c5ef6cfc25895ed54755818d7aa49299869fe6;hb=HEAD On Sun, Sep 14, 2014 at 11:45 PM, Gib Bogle wrote: > Slicer built OK before I added DCMTK_DIR. > ________________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] > Sent: Monday, 15 September 2014 3:09 p.m. > To: Matt McCormick > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > The same result. > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 3:05 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Thanks for the information. > > What happens if DCMTK_DIR is pointed to the DCMTK build directory in > the Slicer build tree? > > Thanks, > Matt > > > On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: >> Hi Matt, >> >> Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. >> >> Cheers >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Monday, 15 September 2014 2:51 p.m. >> To: Gib Bogle >> Cc: community at itk.org >> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi Gib, >> >> Which version of DCMTK was built? Was it installed? >> >> Thanks, >> Matt >> >> On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >>> cmake-3.0.2 >>> ________________________________ >>> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >>> [g.bogle at auckland.ac.nz] >>> Sent: Monday, 15 September 2014 10:28 a.m. >>> To: community at itk.org >>> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >>> >>> Hi all, >>> >>> I have run into an issue with 4.6, triggered by a problem with Slicer >>> (another story - unable to load big tiffs). I have built Slicer, which >>> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >>> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >>> installation that I now have (I have previously been using 4.0). In >>> principle the failure to load a big tiff should be a problem with ITK, not >>> with Slicer. >>> >>> When I run cmake to set up the Visual Studio 10 project files for my simple >>> test program (which works with 4.0), I get errors concerning DCMTK: >>> >>> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >>> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >>> CMake Error at C:/Program Files >>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >>> (message): >>> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >>> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >>> DCMTK_dcmimgle_LIBRARY) >>> Call Stack (most recent call first): >>> C:/Program Files >>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >>> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >>> (find_package_handle_standard_args) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >>> (find_package) >>> >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >>> (itk_module_load) >>> >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >>> (_itk_module_config_recurse) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >>> (itk_module_config) >>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >>> (find_package) >>> CMakeLists.txt:4 (FIND_PACKAGE) >>> >>> Here is the stock-standard CMakeLists.txt: >>> >>> cmake_minimum_required(VERSION 2.8) >>> >>> PROJECT(makebig) >>> FIND_PACKAGE(ITK) >>> IF(ITK_FOUND) >>> INCLUDE(${ITK_USE_FILE}) >>> ELSE(ITK_FOUND) >>> MESSAGE(FATAL_ERROR >>> "ITK not found. Please set ITK_DIR.") >>> ENDIF(ITK_FOUND) >>> MESSAGE (${ITK_USE_FILE}) >>> MESSAGE (${ITK_INCLUDE_DIRS}) >>> set(PROJECTNAME "makebig") >>> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >>> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >>> >>> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >>> error messages did not change. >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Mon Sep 15 11:41:37 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 11:41:37 -0400 Subject: [ITK] Multiple ITK-builds and CMake In-Reply-To: <2D9DC0609429E24BA87612C012C580C318A76AB7@AMSPRD9002MB028.MGDPHG.emi.philips.com> References: <2D9DC0609429E24BA87612C012C580C318A76A2B@AMSPRD9002MB028.MGDPHG.emi.philips.com> <2D9DC0609429E24BA87612C012C580C318A76AB7@AMSPRD9002MB028.MGDPHG.emi.philips.com> Message-ID: Hi Mikael, Since BRAINSTools is a "superbuild", i.e. it will build its own ITK/VTK by default, you will need to tell the the build system to first not build its own, so that you can specify your manually built version. HTH, Matt On Mon, Sep 15, 2014 at 1:40 AM, Eriksson, Mikael wrote: > Hi Matt and community, > > - Got it! > - That is the problem here, the CMake-gui for this application has no ITK_DIR entry so that I can explicitly specify which one to use. Any suggestions for how to get around this? > > Best, > Mikael > > ??????????????????????????????????. > Mikael Eriksson > R&D Physicist Trainee > Philips Medical Systems MR Finland, Feasibility studies > > +358 40 631 8500 > mikael.k.eriksson at philips.com > ??????????????????????????????????. > > -----Original Message----- > From: Matt McCormick [mailto:matt.mccormick at kitware.com] > Sent: 12. syyskuuta 2014 16:55 > To: Eriksson, Mikael > Cc: community at itk.org > Subject: Re: [ITK] Multiple ITK-builds and CMake > > Hi Mikael, > > A few pointers: > > - Only a single source per project directory is needed. > - Set ITK_DIR in the cmake-gui explicitly for each configuration -- don't try to use environmental variables, etc. > > More details on how find_package works can be found here [1] and here [2]. > > Hope this helps, > Matt > > [1] http://www.cmake.org/cmake/help/v3.0/command/find_package.html#command:find_package > > [2] http://www.cmake.org/cmake/help/v3.0/manual/cmake-packages.7.html > > On Fri, Sep 12, 2014 at 8:48 AM, Eriksson, Mikael wrote: >> Hello, >> >> >> >> I?m experiencing some problems trying to build BRAINSTools >> (https://github.com/BRAINSia/BRAINSTools), from where I wanted to run >> the registration algorithms implemented in the 3DSlicer gui from the >> command line. The initial situation was: I had ITK (4.5) and VTK built >> from downloaded files in debug mode on my computer. I managed to build >> the modules that I wanted from BRAINSTools (BRAINSFit and >> BRAINSDemonWarp and their dependencies) in debug mode. Everything was >> fine until I tried running a registration ? I hadn?t realized until >> then that debug mode would make the registrations run really slowly. >> >> >> >> So, since I now have git on my computer, I cloned fresh versions of >> ITK and VTK to new source folders at the same levels as the old source >> folders, and built one debug version and one release version for both >> ITK and VTK, into separate folders. So my directory structure looked like this. >> >> >> >> C:/ - ITK/ - srcOld (ITK 4.5, from >> files) >> >> binOld >> (debug) >> >> srcNewDebug (ITK 4.7, from source) >> >> srcNewRelease (ITK 4.7, from source) >> >> binNewDebug >> >> binNewRelease >> >> >> >> C:/ - VTK/ - corresponding? >> >> >> >> I probably have an unnecessary amount of builds and folders, but I was >> afraid to ruin any previous work. >> >> >> >> Now I tried to build BRAINSTools again with CMake. The problem here is >> that there is no option to specify ITK_DIR in the CMakeGUI, as there >> is in other programs. So I?m not sure how CMake finds and chooses an >> ITK-build, but I think it fails, because when compiling the >> BRAINSTools solution in Visual Studio 2010 as usual, using release >> mode this time, I got linking errors saying that some ITK-libraries couldn?t be found: >> >> >> >> error LNK1181: cannot open input file '..\..\lib\Release\ITKCommon-4.7.lib' >> >> >> >> I changed my environment variables ITK_DIR to C:/ITK/binNewRelease and >> changed the old ITK and VTK entries in the PATH variables to the new >> ones (changed C:\ITK\binOld\bin\debug to >> C:\ITK\binNewRelease\bin\Release and same for VTK). The same problem >> persisted however. Can anybody, give any suggestions for how to solve >> this particular problem? Also, I would be very happy for an >> explanation or a good link for how CMake and ITK interconnect, and >> especially, how CMake chooses an ITK build. I looked at the >> findITK.CMake files, and the ITKConfig.cmake and useITK.cmake files >> and read the documentation for the find_package function, but it?s still not clear to me how it works. >> >> >> >> Best regards, >> >> Mikael >> >> >> >> ??????????????????????????????????. >> >> Mikael Eriksson >> >> R&D Physicist Trainee >> >> Philips Medical Systems MR Finland, Feasibility studies >> >> mikael.k.eriksson at philips.com >> >> ??????????????????????????????????. >> >> >> >> >> ________________________________ >> The information contained in this message may be confidential and >> legally protected under applicable law. The message is intended solely >> for the addressee(s). If you are not the intended recipient, you are >> hereby notified that any use, forwarding, dissemination, or >> reproduction of this message is strictly prohibited and may be >> unlawful. If you are not the intended recipient, please contact the >> sender by return e-mail and destroy all copies of the original message. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From bilgincc at gmail.com Mon Sep 15 11:50:51 2014 From: bilgincc at gmail.com (Cagatay Bilgin) Date: Mon, 15 Sep 2014 08:50:51 -0700 Subject: [ITK] [ITK-users] Motion under Mean Curvature with LevelSetv4 Framework In-Reply-To: References: Message-ID: Hi Arnaud, Sorry for the late response, I somehow missed this email. I have not done the same experiment in the old framework to compare against. I can giving it a shot but the old framework is more mysterious to me. Best, Cagatay Bilgin On Fri, Aug 8, 2014 at 1:44 AM, Arnaud Gelas wrote: > Hi Cagatay, > > I just came back from vacation... Have you solved this problem? > It would be great if we could make the equivalent code in the old > framework to compare and fix what could be wrong. Have you done something > like this? > > I'll start looking at it... > > Best, > Arnaud > > > On Tue, Jul 22, 2014 at 9:58 AM, Cagatay Bilgin > wrote: > >> Dear ITK Community, >> >> I am trying to familiarize myself with the new level set classes. My goal >> is to simulate motion under mean curvature using the new design. >> >> I have put together the following, looking at the examples and tests. >> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872740/ is a great source >> to understand the design and tests in source directory are very helpful, >> thank you for the resources! >> >> The test scenario I have is a L shaped object. I would expect the object >> to become somewhat ellipse and then disappear at the end of the evolution. >> However I get the following results attached to the email. I don't quite >> follow these results. Am I missing something obvious? >> >> Here is the code and CMakeLists.txt. I ran the program with ./Motion 100 >> 0 0 0.05 >> >> #include "itkBinaryImageToLevelSetImageAdaptor.h" >> #include "itkImageFileReader.h" >> #include "itkLevelSetContainer.h" >> #include "itkLevelSetEquationPropagationTerm.h" >> #include "itkLevelSetEquationAdvectionTerm2.h" >> #include "itkLevelSetEquationContainer.h" >> #include "itkLevelSetEquationTermContainer.h" >> #include "itkLevelSetEvolution.h" >> #include "itkLevelSetEvolutionNumberOfIterationsStoppingCriterion.h" >> #include "itkLevelSetDenseImage.h" >> #include "itkVTKVisualizeImageLevelSetIsoValues.h" >> #include "itkSinRegularizedHeavisideStepFunction.h" >> #include "itkLevelSetIterationUpdateCommand.h" >> #include "itkLevelSetEquationCurvatureTerm.h" >> #include "itkCastImageFilter.h" >> #include "itkWhitakerSparseLevelSetImage.h" >> #include "itkSpatialObjectToImageFilter.h" >> #include "itkEllipseSpatialObject.h" >> >> typedef itk::Image< float, 2 > FIT; >> >> /* >> * L Shape >> */ >> void CreateSquareImage(FIT::Pointer image) >> { >> FIT::RegionType region; >> FIT::IndexType start; >> start[0] = 0; >> start[1] = 0; >> >> FIT::SizeType size; >> size[0] = 200; >> size[1] = 300; >> >> region.SetSize(size); >> region.SetIndex(start); >> >> image->SetRegions(region); >> image->Allocate(); >> >> // Set pixels in a square to one value >> for(unsigned int r = 20; r < 160; r++) >> { >> for(unsigned int c = 30; c < 100; c++) >> { >> FIT::IndexType pixelIndex; >> pixelIndex[0] = r; >> pixelIndex[1] = c; >> >> image->SetPixel(pixelIndex, 255); >> } >> } >> >> for(unsigned int r = 20; r < 80; r++) >> { >> for(unsigned int c = 100; c < 200; c++) >> { >> FIT::IndexType pixelIndex; >> pixelIndex[0] = r; >> pixelIndex[1] = c; >> >> image->SetPixel(pixelIndex, 255); >> } >> } >> } >> >> >> /* >> */ >> int main( int argc, char* argv[] ) >> { >> if( argc != 5) >> { >> std::cerr << "Missing Arguments" << std::endl; >> std::cerr << argv[0] << std::endl; >> std::cerr << "1- Number of Iterations" << std::endl; >> std::cerr << "2- Propagation Term" << std::endl; >> std::cerr << "3- Advection Term" << std::endl; >> std::cerr << "4- Curvature Term" << std::endl; >> return EXIT_FAILURE; >> } >> >> // Image Dimension >> const unsigned int Dimension = 2; >> >> typedef unsigned char InputPixelType; >> typedef itk::Image< InputPixelType, Dimension > IIT; >> typedef itk::Image< float, 2 > FIT; >> >> FIT::Pointer input = FIT::New(); >> CreateSquareImage(input); >> >> int numberOfIterations = atoi( argv[1]); >> >> typedef float >> LevelSetPixelType; >> typedef itk::Image< LevelSetPixelType, Dimension > LSIT; >> typedef itk::LevelSetDenseImage< LSIT > LST; >> //typedef itk::WhitakerSparseLevelSetImage< LevelSetPixelType, 2 > >> LST; >> >> typedef LST::OutputType LevelSetOutputType; >> typedef LST::OutputRealType LevelSetRealType; >> >> // convert a binary mask to a level-set function >> typedef itk::BinaryImageToLevelSetImageAdaptor BI2LST; >> BI2LST::Pointer adaptor = BI2LST::New(); >> adaptor->SetInputImage( input ); >> adaptor->Initialize(); >> LST::Pointer levelSet = adaptor->GetLevelSet(); >> >> // The Heaviside function >> typedef itk::SinRegularizedHeavisideStepFunction< LevelSetRealType, >> LevelSetRealType > HeavisideFunctionType; >> HeavisideFunctionType::Pointer heaviside = >> HeavisideFunctionType::New(); >> heaviside->SetEpsilon( 1 ); >> >> // Create the level set container >> typedef itk::LevelSetContainer< itk::IdentifierType, LST > >> LSContainerT; >> LSContainerT::Pointer levelSetContainer = LSContainerT::New(); >> levelSetContainer->SetHeaviside( heaviside ); >> levelSetContainer->AddLevelSet( 0, levelSet ); >> >> // Create the terms. >> typedef itk::LevelSetEquationPropagationTerm >> PropagationTermType; >> PropagationTermType::Pointer propagationTerm = >> PropagationTermType::New(); >> propagationTerm->SetInput(input); >> propagationTerm->SetCoefficient(atof(argv[2])); >> >> typedef itk::LevelSetEquationAdvectionTerm2 >> AdvectionTermType; >> AdvectionTermType::Pointer advectionTerm = AdvectionTermType::New(); >> advectionTerm->SetInput(input); >> advectionTerm->SetCoefficient(atof(argv[3])); >> >> typedef itk::LevelSetEquationCurvatureTerm >> CurvatureTermType; >> CurvatureTermType::Pointer curvatureTerm = CurvatureTermType::New(); >> //curvatureTerm->SetInput(input); >> curvatureTerm->SetCoefficient(atof(argv[4])); >> >> >> // Create term container (equation rhs) >> typedef itk::LevelSetEquationTermContainer< FIT, LSContainerT > >> TermContainerType; >> TermContainerType::Pointer termContainer = TermContainerType::New(); >> termContainer->SetLevelSetContainer( levelSetContainer ); >> termContainer->SetInput( input ); >> //termContainer->AddTerm( 0, propagationTerm ); >> //termContainer->AddTerm( 1, advectionTerm ); >> termContainer->AddTerm( 0, curvatureTerm ); >> >> // Create equation container >> typedef itk::LevelSetEquationContainer< TermContainerType > >> EquationContainerType; >> EquationContainerType::Pointer equationContainer = >> EquationContainerType::New(); >> equationContainer->SetLevelSetContainer( levelSetContainer ); >> equationContainer->AddEquation( 0, termContainer ); >> >> // Create stopping criteria >> typedef itk::LevelSetEvolutionNumberOfIterationsStoppingCriterion< >> LSContainerT > StoppingCriterionType; >> StoppingCriterionType::Pointer criterion = >> StoppingCriterionType::New(); >> criterion->SetNumberOfIterations( numberOfIterations ); >> >> // Create the visualizer >> typedef itk::VTKVisualizeImageLevelSetIsoValues< FIT, LST > >> VisualizationType; >> VisualizationType::Pointer visualizer = VisualizationType::New(); >> visualizer->SetInputImage( input ); >> visualizer->SetLevelSet( levelSet ); >> visualizer->SetScreenCapture( true ); >> >> // Create evolution class >> typedef itk::LevelSetEvolution< EquationContainerType, LST > >> LevelSetEvolutionType; >> LevelSetEvolutionType::Pointer evolution = >> LevelSetEvolutionType::New(); >> evolution->SetEquationContainer( equationContainer ); >> evolution->SetStoppingCriterion( criterion ); >> evolution->SetLevelSetContainer( levelSetContainer ); >> >> typedef itk::LevelSetIterationUpdateCommand< LevelSetEvolutionType, >> VisualizationType > IterationUpdateCommandType; >> IterationUpdateCommandType::Pointer iterationUpdateCommand = >> IterationUpdateCommandType::New(); >> iterationUpdateCommand->SetFilterToUpdate( visualizer ); >> iterationUpdateCommand->SetUpdatePeriod( 1 ); >> >> evolution->AddObserver( itk::IterationEvent(), iterationUpdateCommand >> ); >> >> evolution->Update(); >> >> return EXIT_SUCCESS; >> } >> >> >> >> cmake_minimum_required(VERSION 2.8) >> >> project(CurvatureMotion) >> >> find_package(ITK REQUIRED) >> include(${ITK_USE_FILE}) >> >> find_package(VTK REQUIRED) >> include(${VTK_USE_FILE}) >> >> add_executable(Motion main.cpp) >> target_link_libraries(Motion ${ITK_LIBRARIES} ${VTK_LIBRARIES}) >> >> [image: Inline image 4][image: Inline image 3] >> -- >> Cemal Cagatay Bilgin, PhD >> Life Sciences Division >> Lawrence Berkeley National Lab >> MS977, One Cyclotron Road >> Berkeley, CA 94720, USA >> Email: ccbilgin at lbl.gov >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -- Cemal Cagatay Bilgin, PhD Life Sciences Division Lawrence Berkeley National Lab MS977, One Cyclotron Road Berkeley, CA 94720, USA Email: ccbilgin at lbl.gov -------------- next part -------------- An HTML attachment was scrubbed... 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Name: levelset_040.png Type: image/png Size: 3421 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bilgincc at gmail.com Mon Sep 15 11:53:06 2014 From: bilgincc at gmail.com (Cagatay Bilgin) Date: Mon, 15 Sep 2014 08:53:06 -0700 Subject: [ITK] [ITK-users] Different output with dense and sparse level set representations In-Reply-To: References: Message-ID: Arnaud, should I also try this with the old framework? This really looks like a bug to me regardless of the framework used. Best, Cagatay Bilgin On Thu, Aug 21, 2014 at 10:33 AM, Cagatay Bilgin wrote: > Hello everybody, > > I continue with my exploration of the new level set framework. I have > modified one of the examples and have an advection field in the positive x > direction. I would expect the initial contour to move in that direction and > that's the case with the sparse representation. Using the dense > representation however, only half of the contour moves to my surprise. Is > this a bug or I am missing something here. Here is the code and the cmake > file and snapshots of the movements. > > [image: Inline image 2][image: Inline image 1] > > > #include "itkBinaryImageToLevelSetImageAdaptor.h" > #include "itkLevelSetContainer.h" > #include "itkLevelSetEquationPropagationTerm.h" > #include "itkLevelSetEquationAdvectionTerm.h" > #include "itkLevelSetEquationContainer.h" > #include "itkLevelSetEquationTermContainer.h" > #include "itkLevelSetEvolution.h" > #include "itkLevelSetEvolutionNumberOfIterationsStoppingCriterion.h" > #include "itkLevelSetDenseImage.h" > #include "itkVTKVisualizeImageLevelSetIsoValues.h" > #include "itkSinRegularizedHeavisideStepFunction.h" > #include "itkLevelSetIterationUpdateCommand.h" > #include "itkLevelSetEquationCurvatureTerm.h" > #include "itkWhitakerSparseLevelSetImage.h" > #include "itkLevelSetSparseImage.h" > > typedef itk::Image< float, 2 > FIT; > > void CreateSquareImage(FIT::Pointer image, FIT::Pointer prop, FIT::Pointer > advec) > { > FIT::RegionType region; > FIT::IndexType start; > start[0] = 0; > start[1] = 0; > > FIT::SizeType size; > size[0] = 100; > size[1] = 100; > > region.SetSize(size); > region.SetIndex(start); > > image->SetRegions(region); > image->Allocate(); > image->FillBuffer(0); > > //constant grow in all directions > prop->SetRegions(image->GetLargestPossibleRegion()); > prop->Allocate(); > prop->FillBuffer(1); > > //advec will increase in positive x direction > advec->SetRegions(image->GetLargestPossibleRegion()); > advec->Allocate(); > advec->FillBuffer(0); > > // Set pixels in a square to one value > for(unsigned int x = 35; x < 65; x++){ > for(unsigned int y = 35; y < 65; y++){ > FIT::IndexType pixelIndex; > pixelIndex[0] = x; > pixelIndex[1] = y; > > image->SetPixel(pixelIndex, 255); > } > } > > //advection in positive x direction > for(unsigned int x = 0; x < 100; x++){ > for(unsigned int y = 0; y < 100; y++){ > FIT::IndexType pixelIndex; > pixelIndex[0] = x; > pixelIndex[1] = y; > > advec->SetPixel(pixelIndex, x); > } > } > } > > > /* > */ > int main(int argc, char* argv[] ) > { > using namespace itk; > if(argc != 5) > { > std::cerr << "Missing Arguments" << std::endl; > std::cerr << argv[0] << std::endl; > std::cerr << "1- Number of Iterations" << std::endl; > std::cerr << "2- Propagation Term" << std::endl; > std::cerr << "3- Advection Term" << std::endl; > std::cerr << "4- Curvature Term" << std::endl; > return EXIT_FAILURE; > } > > FIT::Pointer input = FIT::New(); > FIT::Pointer prop = FIT::New(); > FIT::Pointer advec = FIT::New(); > > CreateSquareImage(input, prop, advec); > > int numberOfIterations = atoi(argv[1]); > > typedef float LSPT; > typedef Image< LSPT, 2 > LSIT; > typedef LevelSetDenseImage< LSIT > LST; > //typedef WhitakerSparseLevelSetImage< LSPT, 2 > LST; > > typedef LST::OutputRealType LSOutputT; > > // convert a binary mask to a level-set function > typedef BinaryImageToLevelSetImageAdaptor BI2LST; > BI2LST::Pointer adaptor = BI2LST::New(); > adaptor->SetInputImage(input ); > adaptor->Initialize(); > LST::Pointer levelSet = adaptor->GetLevelSet(); > > // The Heaviside function > typedef SinRegularizedHeavisideStepFunction > HeavisideFunctionType; > HeavisideFunctionType::Pointer heaviside = > HeavisideFunctionType::New(); > heaviside->SetEpsilon(1 ); > > // Create the level set container > typedef LevelSetContainer< IdentifierType, LST > LSContainerT; > LSContainerT::Pointer levelSetContainer = LSContainerT::New(); > levelSetContainer->SetHeaviside(heaviside ); > levelSetContainer->AddLevelSet(0, levelSet ); > > // Create the terms. > typedef LevelSetEquationPropagationTerm PropT; > PropT::Pointer propagationTerm = PropT::New(); > propagationTerm->SetInput(prop); > propagationTerm->SetCoefficient(atof(argv[2])); > > typedef LevelSetEquationAdvectionTerm AdvecT; > AdvecT::Pointer advectionTerm = AdvecT::New(); > advectionTerm->SetInput(advec); > advectionTerm->SetCoefficient(atof(argv[3])); > > typedef LevelSetEquationCurvatureTerm CurvT; > CurvT::Pointer curvatureTerm = CurvT::New(); > curvatureTerm->SetCoefficient(atof(argv[4])); > > // Create term container (equation rhs) > typedef LevelSetEquationTermContainer< FIT, LSContainerT > > TermContainerT; > TermContainerT::Pointer termContainer = TermContainerT::New(); > termContainer->SetLevelSetContainer(levelSetContainer ); > termContainer->SetInput(input ); > termContainer->AddTerm(0, curvatureTerm ); > termContainer->AddTerm(1, advectionTerm ); > termContainer->AddTerm(2, propagationTerm ); > > // Create equation container > typedef LevelSetEquationContainer< TermContainerT > > EquationContainerType; > EquationContainerType::Pointer equationContainer = > EquationContainerType::New(); > equationContainer->SetLevelSetContainer(levelSetContainer ); > equationContainer->AddEquation(0, termContainer ); > > // Create stopping criteria > typedef LevelSetEvolutionNumberOfIterationsStoppingCriterion< > LSContainerT > StoppingCriterionType; > StoppingCriterionType::Pointer criterion = > StoppingCriterionType::New(); > criterion->SetNumberOfIterations(numberOfIterations ); > > // Create the visualizer > typedef VTKVisualizeImageLevelSetIsoValues< FIT, LST > VisT; > VisT::Pointer visualizer = VisT::New(); > visualizer->SetInputImage(input ); > visualizer->SetLevelSet(levelSet ); > visualizer->SetScreenCapture(true ); > > // Create evolution class > typedef LevelSetEvolution< EquationContainerType, LST > LSEvolT; > LSEvolT::Pointer evolution = LSEvolT::New(); > evolution->SetEquationContainer(equationContainer ); > evolution->SetStoppingCriterion(criterion ); > evolution->SetLevelSetContainer(levelSetContainer ); > > typedef LevelSetIterationUpdateCommand< LSEvolT, VisT > > IterationUpdateCommandType; > IterationUpdateCommandType::Pointer iterationUpdateCommand = > IterationUpdateCommandType::New(); > iterationUpdateCommand->SetFilterToUpdate(visualizer ); > iterationUpdateCommand->SetUpdatePeriod(1 ); > > evolution->AddObserver(IterationEvent(), iterationUpdateCommand ); > evolution->Update(); > > return EXIT_SUCCESS; > } > > > cmake_minimum_required(VERSION 2.8) > project(Motion) > > find_package(ITK REQUIRED) > include(${ITK_USE_FILE}) > > find_package(VTK REQUIRED) > include(${VTK_USE_FILE}) > > add_executable(Motion main.cpp) > target_link_libraries(Motion ${ITK_LIBRARIES} ${VTK_LIBRARIES}) > > Params used for the experiment: > Ran sparse representation with > ./Motion 15 0 1 1 > > Ran dense representation with > ./Motion 15 0 1 0 > > > Cemal Cagatay Bilgin, PhD > Life Sciences Division > Lawrence Berkeley National Lab > MS977, One Cyclotron Road > Berkeley, CA 94720, USA > Email: ccbilgin at lbl.gov > -- Cemal Cagatay Bilgin, PhD Life Sciences Division Lawrence Berkeley National Lab MS977, One Cyclotron Road Berkeley, CA 94720, USA Email: ccbilgin at lbl.gov -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sparse_00015.png Type: image/png Size: 2848 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dense_00010.png Type: image/png Size: 2737 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From gowithking at googlemail.com Mon Sep 15 13:04:36 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 19:04:36 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK Message-ID: Hi, my Itk friends, I am using python warped ITK to write my first itk process to analysis series of mhd images, I test my procedure in slicer4 first to make sure it works well. Then I start the programming. However, two problem block me for a whole day. - The imagetype of itk.Image.UC3 should be used for 16 bit image in all the itk instructions. But in my case it only has a range of 0-255. Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I read it proprietorially? - I need to get a label map with simply threshold method, and then make few statistics with LabelStatisticsImageFilter. So the BinaryImageToLabelMapFilter is taken. but then the key error occurs: LabelFilter = itk.BinaryImageToLabelMapFilter[IUC3].New() File "/usr/local/lib/ITK-4.7/Python/itkTemplate.py", line 263, in __getitem__ (str(parameters), self.__name__)) KeyError: "itkTemplate : No template [] for the itk::BinaryImageToLabelMapFilter class" What should I do to achieve the LabelStatisticsImageFilter ? Thank you in advance[?] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From blowekamp at mail.nih.gov Mon Sep 15 13:09:11 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 15 Sep 2014 13:09:11 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: <90BD17AA-DADF-4EAA-94A5-2863F7DAF4CF@mail.nih.gov> Hello, 2) I believe that is the error message when the the filter hasn't been instantiated with that template argument. Poke around itk.BinaryImageToLabelMapFilter's dict interface, some method along the lines 'keys()' should give you a list of the types that have been compiled and can be created. hope this helps, Brad On Sep 15, 2014, at 1:04 PM, gowith king wrote: > Hi, my Itk friends, > I am using python warped ITK to write my first itk process to analysis series of mhd images, I test my procedure in slicer4 first to make sure it works well. Then I start the programming. However, two problem block me for a whole day. > The imagetype of itk.Image.UC3 should be used for 16 bit image in all the itk instructions. But in my case it only has a range of 0-255. Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I read it proprietorially? > > > I need to get a label map with simply threshold method, and then make few statistics with LabelStatisticsImageFilter. So the BinaryImageToLabelMapFilter is taken. but then the key error occurs: > LabelFilter = itk.BinaryImageToLabelMapFilter[IUC3].New() > File "/usr/local/lib/ITK-4.7/Python/itkTemplate.py", line 263, in __getitem__ > (str(parameters), self.__name__)) > KeyError: "itkTemplate : No template [] for the itk::BinaryImageToLabelMapFilter class" > > > What should I do to achieve the LabelStatisticsImageFilter ? > Thank you in advance<330.gif> > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 15 13:54:09 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 13:54:09 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: > > Hi, > > > - The imagetype of itk.Image.UC3 should be used for 16 bit image > in all the itk instructions. But in my case it only has a range of 0-255. > Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 > 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I > read it proprietorially? > > itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) and with three dimension. For the correspondence between mangled names and basic types see [1]. For a 16 bit image use 'US' or 'SS'. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD -------------- next part -------------- An HTML attachment was scrubbed... URL: From gowithking at googlemail.com Mon Sep 15 13:49:27 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 19:49:27 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: <90BD17AA-DADF-4EAA-94A5-2863F7DAF4CF@mail.nih.gov> References: <90BD17AA-DADF-4EAA-94A5-2863F7DAF4CF@mail.nih.gov> Message-ID: Hi Lowekamp I think I may get your meaning: I have to define something before I can use this filter in python? I so glad to get your reply, but could not figure out how to achieve your suggestion: Poke around itk.BinaryImageToLabelMapFilter's dict interface, some method along the lines 'keys()' should give you a list of the types that have been compiled and can be created. [?] On Mon, Sep 15, 2014 at 7:09 PM, Bradley Lowekamp wrote: > Hello, > > 2) I believe that is the error message when the the filter hasn't been > instantiated with that template argument. Poke around > itk.BinaryImageToLabelMapFilter's dict interface, some method along the > lines 'keys()' should give you a list of the types that have been compiled > and can be created. > > hope this helps, > Brad > > On Sep 15, 2014, at 1:04 PM, gowith king > wrote: > > Hi, my Itk friends, > I am using python warped ITK to write my first itk process to > analysis series of mhd images, I test my procedure in slicer4 first to > make sure it works well. Then I start the programming. However, two problem > block me for a whole day. > > - The imagetype of itk.Image.UC3 should be used for 16 bit image > in all the itk instructions. But in my case it only has a range of 0-255. > Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 > 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I > read it proprietorially? > > > > - I need to get a label map with simply threshold method, and > then make few statistics with LabelStatisticsImageFilter. So the > BinaryImageToLabelMapFilter is taken. but then the key error occurs: > > LabelFilter = itk.BinaryImageToLabelMapFilter[IUC3].New() > File "/usr/local/lib/ITK-4.7/Python/itkTemplate.py", line 263, in > __getitem__ > (str(parameters), self.__name__)) > KeyError: "itkTemplate : No template [ 'itkImagePython.itkImageUC3'>] for the itk::BinaryImageToLabelMapFilter > class" > > > What should I do to achieve the LabelStatisticsImageFilter ? > Thank you in advance<330.gif> > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1C4.gif Type: image/gif Size: 667 bytes Desc: not available URL: From gowithking at googlemail.com Mon Sep 15 14:11:47 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 20:11:47 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi McCormick Thank you so much for your suggestion, when I use US it pops out a keyerror , not template for the us3 [?]. But then I change to SS it works well for now. any suggestion for the second issue ? I dig for really long time for this keyerror problem , but have no clue at all On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick wrote: > Hi, >> > > >> >> - The imagetype of itk.Image.UC3 should be used for 16 bit image >> in all the itk instructions. But in my case it only has a range of 0-255. >> Then I take itk.Image.F3, then it get a range of '-3.40282346639e+38 >> 3.40282346639e+38' . The grey value of my image is 0-9000 . How could I >> read it proprietorially? >> >> itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) > and with three dimension. For the correspondence between mangled names and > basic types see [1]. For a 16 bit image use 'US' or 'SS'. > > HTH, > Matt > > [1] > http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: From gowithking at googlemail.com Mon Sep 15 14:19:56 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 20:19:56 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi McCormick I think you give me a hint for the key error problem: I tried few other types in my python such as US , UI, SI ... most of them could not work well . another keyerror pops out for the template lose: when I try itk.Image[itk.SI, 3] KeyError: 'itkTemplate : No template (, 3) for the itk::Image class' On Mon, Sep 15, 2014 at 8:11 PM, gowith king wrote: > Hi McCormick > Thank you so much for your suggestion, when I use US it pops out a > keyerror , not template for the us3 [?]. But then I change to SS it works > well for now. > any suggestion for the second issue ? > I dig for really long time for this keyerror problem , but have no > clue at all > > > On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi, >>> >> >> >>> >>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>> image in all the itk instructions. But in my case it only has a range of >>> 0-255. Then I take itk.Image.F3, then it get a range of >>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>> 0-9000 . How could I read it proprietorially? >>> >>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) >> and with three dimension. For the correspondence between mangled names and >> basic types see [1]. For a 16 bit image use 'US' or 'SS'. >> >> HTH, >> Matt >> >> [1] >> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: From matt.mccormick at kitware.com Mon Sep 15 16:12:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 16:12:56 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi gowith, To see the available types for itk.Image, run dir(itk.Image) If a type is not available that is desired, enable the option in CMake for that pixel type. For unsigned short, set ITK_WRAP_unsigned_short to ON. Hope this helps, Matt On Mon, Sep 15, 2014 at 2:19 PM, gowith king wrote: > Hi McCormick > I think you give me a hint for the key error problem: I tried few > other types in my python such as US , UI, SI ... most of them could not > work well . another keyerror pops out for the template lose: when I try > itk.Image[itk.SI, 3] > KeyError: 'itkTemplate : No template (, 3) for the > itk::Image class' > > > > On Mon, Sep 15, 2014 at 8:11 PM, gowith king > wrote: > >> Hi McCormick >> Thank you so much for your suggestion, when I use US it pops out a >> keyerror , not template for the us3 [?]. But then I change to SS it works >> well for now. >> any suggestion for the second issue ? >> I dig for really long time for this keyerror problem , but have no >> clue at all >> >> >> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >> matt.mccormick at kitware.com> wrote: >> >>> Hi, >>>> >>> >>> >>>> >>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>> image in all the itk instructions. But in my case it only has a range of >>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>> 0-9000 . How could I read it proprietorially? >>>> >>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) >>> and with three dimension. For the correspondence between mangled names and >>> basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>> >>> HTH, >>> Matt >>> >>> [1] >>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>> >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: From gowithking at googlemail.com Mon Sep 15 17:31:14 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 23:31:14 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Thanks McCormick , I use the dir(itk,Image) and dir(itk.LabelMap) and dir(to get some information : UC3 is included in itk.image then it is good. Then I tried all the other dir() for each of my filter , made lots of correction , now the pepline works perfect [?] Thank you again . But I still could not get my result ... because of the filters I may not really understand. I have three filters BinaryThresholdImageFilter # to get a binary image for now I get only two values 1 and 100 it works well. I what the labelmap contains both two parts of them BinaryImageToLabelMapFilter #I have no idea if it works well or not LabelMapToLabelImageFilter # returns a empty image Do you have any idea about this ? On Mon, Sep 15, 2014 at 10:12 PM, Matt McCormick wrote: > Hi gowith, > > To see the available types for itk.Image, run > > dir(itk.Image) > > If a type is not available that is desired, enable the option in CMake for > that pixel type. For unsigned short, set > > ITK_WRAP_unsigned_short > > to ON. > > Hope this helps, > Matt > > On Mon, Sep 15, 2014 at 2:19 PM, gowith king > wrote: > >> Hi McCormick >> I think you give me a hint for the key error problem: I tried few >> other types in my python such as US , UI, SI ... most of them could not >> work well . another keyerror pops out for the template lose: when I try >> itk.Image[itk.SI, 3] >> KeyError: 'itkTemplate : No template (, 3) for the >> itk::Image class' >> >> >> >> On Mon, Sep 15, 2014 at 8:11 PM, gowith king >> wrote: >> >>> Hi McCormick >>> Thank you so much for your suggestion, when I use US it pops out a >>> keyerror , not template for the us3 [?]. But then I change to SS it >>> works well for now. >>> any suggestion for the second issue ? >>> I dig for really long time for this keyerror problem , but have no >>> clue at all >>> >>> >>> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >>> matt.mccormick at kitware.com> wrote: >>> >>>> Hi, >>>>> >>>> >>>> >>>>> >>>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>>> image in all the itk instructions. But in my case it only has a range of >>>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>>> 0-9000 . How could I read it proprietorially? >>>>> >>>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range 0-255) >>>> and with three dimension. For the correspondence between mangled names and >>>> basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>>> >>>> HTH, >>>> Matt >>>> >>>> [1] >>>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>>> >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From gowithking at googlemail.com Mon Sep 15 17:48:50 2014 From: gowithking at googlemail.com (gowith king) Date: Mon, 15 Sep 2014 23:48:50 +0200 Subject: [ITK] How to binary image to label image correctly Message-ID: Hi. My lovely ITK friends I got so much help from here today , However I still could not achieve my goal correctly. The main issue of me is the understanding of binary to labelimage process: from binary to label image and then labelstatistic since I get a binary image which means I have only two values in the image as I set itk.BinaryThresholdImageFilter.ISS3IUC3 itk.BinaryImageToLabelMapFilter.IUC3LM3 itk.LabelMapToLabelImageFilter.LM3IUC3 itk.LabelStatisticsImageFilter.ISS3IUC3 However I got nothing for the outcome of : GetValidLabelValues() Then I checked the pepline: binary image works well it only contains 1 and 100 as I set. But the Labelimage is empty anyong have any idea about it ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Sep 15 17:58:36 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 17:58:36 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: On Mon, Sep 15, 2014 at 5:31 PM, gowith king wrote: > Thanks McCormick , I use the dir(itk,Image) and dir(itk.LabelMap) and > dir(to get some information : UC3 is included in itk.image then it is good. > Then I tried all the other dir() for each of my filter , made lots of > correction , now the pepline works perfect [?] Thank you again . > > But I still could not get my result ... > because of the filters I may not really understand. > > I have three filters > BinaryThresholdImageFilter # to get a binary image for now I get only two > values 1 and 100 it works well. I what the labelmap contains both two parts > of them > BinaryImageToLabelMapFilter #I have no idea if it works well or not > LabelMapToLabelImageFilter # returns a empty image > > Do you have any idea about this ? > Perhaps SetInputForegroundValue [1] needs to be set? HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToLabelMapFilter.html#a5c56958ec0ae8d3a9bf7ae759c680c4a > > On Mon, Sep 15, 2014 at 10:12 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi gowith, >> >> To see the available types for itk.Image, run >> >> dir(itk.Image) >> >> If a type is not available that is desired, enable the option in CMake >> for that pixel type. For unsigned short, set >> >> ITK_WRAP_unsigned_short >> >> to ON. >> >> Hope this helps, >> Matt >> >> On Mon, Sep 15, 2014 at 2:19 PM, gowith king >> wrote: >> >>> Hi McCormick >>> I think you give me a hint for the key error problem: I tried few >>> other types in my python such as US , UI, SI ... most of them could not >>> work well . another keyerror pops out for the template lose: when I try >>> itk.Image[itk.SI, 3] >>> KeyError: 'itkTemplate : No template (, 3) for the >>> itk::Image class' >>> >>> >>> >>> On Mon, Sep 15, 2014 at 8:11 PM, gowith king >>> wrote: >>> >>>> Hi McCormick >>>> Thank you so much for your suggestion, when I use US it pops out a >>>> keyerror , not template for the us3 [?]. But then I change to SS it >>>> works well for now. >>>> any suggestion for the second issue ? >>>> I dig for really long time for this keyerror problem , but have no >>>> clue at all >>>> >>>> >>>> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >>>> matt.mccormick at kitware.com> wrote: >>>> >>>>> Hi, >>>>>> >>>>> >>>>> >>>>>> >>>>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>>>> image in all the itk instructions. But in my case it only has a range of >>>>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>>>> 0-9000 . How could I read it proprietorially? >>>>>> >>>>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range >>>>> 0-255) and with three dimension. For the correspondence between mangled >>>>> names and basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>>>> >>>>> HTH, >>>>> Matt >>>>> >>>>> [1] >>>>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>>>> >>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From g.bogle at auckland.ac.nz Mon Sep 15 17:59:51 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 15 Sep 2014 21:59:51 +0000 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: , Message-ID: I'm sorry, Matt, but I'm not sure what you mean by "pointing a clean build directory to this directory [1]." I tried copying the DCMTK-build tree somewhere else, deleting CMakeCache.txt then running cmake with the CMakeLists.txt you provided (downloaded), but it wants DCMTKGitTag.cmake: D:\testing\DCMTK-build>cmake -G "Visual Studio 10 Win64" -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ CMake Error at CMakeLists.txt:6 (include): include could not find load file: D:/testing/DCMTK-build/../DCMTKGitTag.cmake CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message): error: no download info for 'DCMTK' -- please specify existing/non-empty SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY, GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command) CMakeLists.txt:17 (ExternalProject_add) -- Configuring incomplete, errors occurred! See also "D:/testing/DCMTK-build/CMakeFiles/CMakeOutput.log". See also "D:/testing/DCMTK-build/CMakeFiles/CMakeError.log". Please tell me in more detail what I need to do. Thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Tuesday, 16 September 2014 3:36 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff Hi Gib, Please try building DCMTK by pointing a clean build directory to this directory [1]. Then, start a clean build of ITK with DCMTK_DIR pointing to that directory. Please let us know if this works. Thanks, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/DCMTK/WindowsBuild/CMakeLists.txt;h=70c5ef6cfc25895ed54755818d7aa49299869fe6;hb=HEAD On Sun, Sep 14, 2014 at 11:45 PM, Gib Bogle wrote: > Slicer built OK before I added DCMTK_DIR. > ________________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] > Sent: Monday, 15 September 2014 3:09 p.m. > To: Matt McCormick > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > The same result. > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Monday, 15 September 2014 3:05 p.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Thanks for the information. > > What happens if DCMTK_DIR is pointed to the DCMTK build directory in > the Slicer build tree? > > Thanks, > Matt > > > On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: >> Hi Matt, >> >> Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. >> >> Cheers >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Monday, 15 September 2014 2:51 p.m. >> To: Gib Bogle >> Cc: community at itk.org >> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi Gib, >> >> Which version of DCMTK was built? Was it installed? >> >> Thanks, >> Matt >> >> On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >>> cmake-3.0.2 >>> ________________________________ >>> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >>> [g.bogle at auckland.ac.nz] >>> Sent: Monday, 15 September 2014 10:28 a.m. >>> To: community at itk.org >>> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >>> >>> Hi all, >>> >>> I have run into an issue with 4.6, triggered by a problem with Slicer >>> (another story - unable to load big tiffs). I have built Slicer, which >>> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >>> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >>> installation that I now have (I have previously been using 4.0). In >>> principle the failure to load a big tiff should be a problem with ITK, not >>> with Slicer. >>> >>> When I run cmake to set up the Visual Studio 10 project files for my simple >>> test program (which works with 4.0), I get errors concerning DCMTK: >>> >>> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >>> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >>> CMake Error at C:/Program Files >>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >>> (message): >>> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >>> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >>> DCMTK_dcmimgle_LIBRARY) >>> Call Stack (most recent call first): >>> C:/Program Files >>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >>> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >>> (find_package_handle_standard_args) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >>> (find_package) >>> >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >>> (itk_module_load) >>> >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >>> (_itk_module_config_recurse) >>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >>> (itk_module_config) >>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >>> (find_package) >>> CMakeLists.txt:4 (FIND_PACKAGE) >>> >>> Here is the stock-standard CMakeLists.txt: >>> >>> cmake_minimum_required(VERSION 2.8) >>> >>> PROJECT(makebig) >>> FIND_PACKAGE(ITK) >>> IF(ITK_FOUND) >>> INCLUDE(${ITK_USE_FILE}) >>> ELSE(ITK_FOUND) >>> MESSAGE(FATAL_ERROR >>> "ITK not found. Please set ITK_DIR.") >>> ENDIF(ITK_FOUND) >>> MESSAGE (${ITK_USE_FILE}) >>> MESSAGE (${ITK_INCLUDE_DIRS}) >>> set(PROJECTNAME "makebig") >>> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >>> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >>> >>> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >>> error messages did not change. >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Mon Sep 15 18:08:37 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 15 Sep 2014 18:08:37 -0400 Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff In-Reply-To: References: Message-ID: Hi Gib, Sorry for the insufficient detail. - Delete everything in D:\testing\DCMTK-build - Run D:\testing\DCMTK-build>cmake -G "Visual Studio 10 Win64" D:\testing\ITK-source\Modules\ThirdParty\DCMTK\WindowsBuild Assuming that ITK sources are in ITK-source. - Build the resulting project, which should build DCMTK. - In a clean ITK-build, set DCMTK_DIR to D:\testing\DCMTK-build Please let me know if anything is unclear. Thanks, Matt On Mon, Sep 15, 2014 at 5:59 PM, Gib Bogle wrote: > I'm sorry, Matt, but I'm not sure what you mean by "pointing a clean build directory to this directory [1]." I tried copying the DCMTK-build tree somewhere else, deleting CMakeCache.txt then running cmake with the CMakeLists.txt you provided (downloaded), but it wants DCMTKGitTag.cmake: > > D:\testing\DCMTK-build>cmake -G "Visual Studio 10 Win64" > -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ > CMake Error at CMakeLists.txt:6 (include): > include could not find load file: > D:/testing/DCMTK-build/../DCMTKGitTag.cmake > > CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message): > error: no download info for 'DCMTK' -- please specify existing/non-empty > SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY, > GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND > Call Stack (most recent call first): > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command) > CMakeLists.txt:17 (ExternalProject_add) > > -- Configuring incomplete, errors occurred! > See also "D:/testing/DCMTK-build/CMakeFiles/CMakeOutput.log". > See also "D:/testing/DCMTK-build/CMakeFiles/CMakeError.log". > > Please tell me in more detail what I need to do. > > Thanks > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Tuesday, 16 September 2014 3:36 a.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff > > Hi Gib, > > Please try building DCMTK by pointing a clean build directory to this > directory [1]. Then, start a clean build of ITK with DCMTK_DIR > pointing to that directory. Please let us know if this works. > > Thanks, > Matt > > [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/DCMTK/WindowsBuild/CMakeLists.txt;h=70c5ef6cfc25895ed54755818d7aa49299869fe6;hb=HEAD > > On Sun, Sep 14, 2014 at 11:45 PM, Gib Bogle wrote: >> Slicer built OK before I added DCMTK_DIR. >> ________________________________________ >> From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] >> Sent: Monday, 15 September 2014 3:09 p.m. >> To: Matt McCormick >> Cc: community at itk.org >> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> The same result. >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Monday, 15 September 2014 3:05 p.m. >> To: Gib Bogle >> Cc: community at itk.org >> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >> >> Hi Gib, >> >> Thanks for the information. >> >> What happens if DCMTK_DIR is pointed to the DCMTK build directory in >> the Slicer build tree? >> >> Thanks, >> Matt >> >> >> On Sun, Sep 14, 2014 at 10:56 PM, Gib Bogle wrote: >>> Hi Matt, >>> >>> Yes, I installed it as part of the Slicer build. All the directories and files seem to be there. The version is 3.6.1_CVS. >>> >>> Cheers >>> Gib >>> ________________________________________ >>> From: Matt McCormick [matt.mccormick at kitware.com] >>> Sent: Monday, 15 September 2014 2:51 p.m. >>> To: Gib Bogle >>> Cc: community at itk.org >>> Subject: Re: [ITK] cmake/ITK-4.6/DCMTK/big tiff >>> >>> Hi Gib, >>> >>> Which version of DCMTK was built? Was it installed? >>> >>> Thanks, >>> Matt >>> >>> On Sun, Sep 14, 2014 at 6:34 PM, Gib Bogle wrote: >>>> cmake-3.0.2 >>>> ________________________________ >>>> From: Community [community-bounces at itk.org] on behalf of Gib Bogle >>>> [g.bogle at auckland.ac.nz] >>>> Sent: Monday, 15 September 2014 10:28 a.m. >>>> To: community at itk.org >>>> Subject: [ITK] cmake/ITK-4.6/DCMTK/big tiff >>>> >>>> Hi all, >>>> >>>> I have run into an issue with 4.6, triggered by a problem with Slicer >>>> (another story - unable to load big tiffs). I have built Slicer, which >>>> includes ITK-4.6, on Windows 7. In my efforts to track down the problem >>>> Slicer has with big tiffs, I am trying to do a simple test with the ITK-4.6 >>>> installation that I now have (I have previously been using 4.0). In >>>> principle the failure to load a big tiff should be a problem with ITK, not >>>> with Slicer. >>>> >>>> When I run cmake to set up the Visual Studio 10 project files for my simple >>>> test program (which works with 4.0), I get errors concerning DCMTK: >>>> >>>> D:\testing\ITK\bigtiff>cmake -G "Visual Studio 10 Win64" >>>> -- Found Windows SDK v7.1: C:\Program Files\Microsoft SDKs\Windows\v7.1\ >>>> CMake Error at C:/Program Files >>>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandardArgs.cmake:136 >>>> (message): >>>> Could NOT find DCMTK (missing: DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY >>>> DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR >>>> DCMTK_dcmimgle_LIBRARY) >>>> Call Stack (most recent call first): >>>> C:/Program Files >>>> (x86)/CMake/share/cmake-3.0/Modules/FindPackageHandleStandard >>>> Args.cmake:343 (_FPHSA_FAILURE_MESSAGE) >>>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindDCMTK.cmake:141 >>>> (find_package_handle_standard_args) >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/Modules/ITKDCMTK.cmake:8 >>>> (find_package) >>>> >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:48 (include) >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:25 >>>> (itk_module_load) >>>> >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKModuleAPI.cmake:67 >>>> (_itk_module_config_recurse) >>>> C:/Program Files/ITK/lib/cmake/ITK-4.6/ITKConfig.cmake:86 >>>> (itk_module_config) >>>> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/FindITK.cmake:52 >>>> (find_package) >>>> CMakeLists.txt:4 (FIND_PACKAGE) >>>> >>>> Here is the stock-standard CMakeLists.txt: >>>> >>>> cmake_minimum_required(VERSION 2.8) >>>> >>>> PROJECT(makebig) >>>> FIND_PACKAGE(ITK) >>>> IF(ITK_FOUND) >>>> INCLUDE(${ITK_USE_FILE}) >>>> ELSE(ITK_FOUND) >>>> MESSAGE(FATAL_ERROR >>>> "ITK not found. Please set ITK_DIR.") >>>> ENDIF(ITK_FOUND) >>>> MESSAGE (${ITK_USE_FILE}) >>>> MESSAGE (${ITK_INCLUDE_DIRS}) >>>> set(PROJECTNAME "makebig") >>>> ADD_EXECUTABLE(${PROJECTNAME} makebig.cpp) >>>> TARGET_LINK_LIBRARIES(${PROJECTNAME} ${ITK_LIBRARIES} ) >>>> >>>> I set the environment variable DCMTK_DIR to C:\Program Files\DCMTK, but the >>>> error messages did not change. >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community From g.bogle at auckland.ac.nz Tue Sep 16 01:15:09 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 16 Sep 2014 05:15:09 +0000 Subject: [ITK] ITK-4.6 problem Message-ID: Hi all, There definitely seems to be a problem with ITK-4.6, at least with the code that got installed while building Slicer. This was carried out with ITKV3_COMPATIBILITY off. I am doing some testing with this installation to try to understand why Slicer cannot handle big tiffs (on my Windows 7 system). There is something a bit funny about the installed ITK-4.6, in that the compiler complained about some missing include files, vnl_*.h and others, which are in my ITK-4.0 installation but not in 4.6. I just copied them across - I hope this is not a problem. Anyway, I now find that my very simple program that uses ITK to create a tiff file now crashes when built with 4.6. What is a big clue is that it fails while creating the image, i.e. writing to the buffer, on page 73 - it's surely more than a coincidence that Slicer fails when reading page 72 of a 4 GB tiff. In this case only 73 bytes have been written to buffer when it fails. The whole program is below. It fails having written x=0, y=0, z=0...73 to the console. Unless my code (which was fine with 4.0) is no longer OK with 4.6, this is a very basic bug, since all I do is set the image size, allocate memory, get a pointer to the buffer and start writing to it. The program is short enough to paste in its entirety, but the relevant section is just a few lines. #include #include #include #include #include #include #include #include #include #include "itkImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkSize.h" typedef itk::Image ImageType; ImageType::Pointer im; unsigned char *p; #define V(a,b,c) p[(c)*xysize+(b)*width+(a)] int main(int argc, char**argv) { int x1, x2, y1, y2, z1, z2; int x0, y0, z0, dx, dy, dz; int x, y, z, xx, yy, zz, n, comp_flag; long long width, height, depth, xysize; int R, R2; bool use_compression; bool use_sphere = false; if (argc != 4) { printf("Usage: makebig tiff_file N compress\n"); printf(" the image will be NxNxN\n"); printf(" set compress=1 to use compression, =0 otherwise\n"); return 1; } printf("Output image file: %s\n",argv[1]); sscanf(argv[2],"%d",&n); sscanf(argv[3],"%d",&comp_flag); use_compression = (comp_flag == 1); x0 = n/2; y0 = n/2; z0 = n/2; R = 5; R2 = R*R; width = n; height = n; depth = n; xysize = width*height; printf("Desired image dimensions: width, height, depth: %d %d %d\n",width,height,depth); ImageType::Pointer im = ImageType::New(); ImageType::SizeType imsize; imsize[0] = width; imsize[1] = height; imsize[2] = depth; ImageType::IndexType imstart; imstart[0] = 0; imstart[1] = 0; imstart[2] = 0; ImageType::RegionType imregion; imregion.SetSize(imsize); imregion.SetIndex(imstart); im->SetRegions(imregion); im->Allocate(); p = (unsigned char *)(im->GetBufferPointer()); width = im->GetLargestPossibleRegion().GetSize()[0]; height = im->GetLargestPossibleRegion().GetSize()[1]; depth = im->GetLargestPossibleRegion().GetSize()[2]; printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); for (x=0; x x0+R) { V(x,y,z) = 0; } else { V(x,y,z) = 255; } } } } } typedef itk::ImageFileWriter FileWriterType; FileWriterType::Pointer writer = FileWriterType::New(); writer->SetFileName(argv[1]); writer->SetInput(im); if (use_compression) { writer->UseCompressionOn(); } printf("Writing tiff file\n"); try { writer->Update(); } catch (itk::ExceptionObject &e) { std::cout << e << std::endl; return 4; } if (use_compression) { printf("Created compressed image file: %s\n",argv[1]); } else { printf("Created uncompressed image file: %s\n",argv[1]); } return 0; } -------------- next part -------------- An HTML attachment was scrubbed... URL: From gowithking at googlemail.com Tue Sep 16 04:27:49 2014 From: gowithking at googlemail.com (gowith king) Date: Tue, 16 Sep 2014 10:27:49 +0200 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi , Matt I tried it , it does not work as well. the print LabelFilter0.GetNumberOfObjects() always returns 0, what i want to do it every nasty: sign 1 to label 1, 100 to label 2 ,and there is no background at all. My images all like the attached image but in 3D , the 3D version will be attached later ,thank you for your attention On Mon, Sep 15, 2014 at 11:58 PM, Matt McCormick wrote: > > > On Mon, Sep 15, 2014 at 5:31 PM, gowith king > wrote: > >> Thanks McCormick , I use the dir(itk,Image) and dir(itk.LabelMap) and >> dir(to get some information : UC3 is included in itk.image then it is good. >> Then I tried all the other dir() for each of my filter , made lots of >> correction , now the pepline works perfect [?] Thank you again . >> >> But I still could not get my result ... >> because of the filters I may not really understand. >> >> I have three filters >> BinaryThresholdImageFilter # to get a binary image for now I get only two >> values 1 and 100 it works well. I what the labelmap contains both two parts >> of them >> BinaryImageToLabelMapFilter #I have no idea if it works well or not >> LabelMapToLabelImageFilter # returns a empty image >> >> Do you have any idea about this ? >> > > Perhaps SetInputForegroundValue [1] needs to be set? > > HTH, > Matt > > [1] > http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToLabelMapFilter.html#a5c56958ec0ae8d3a9bf7ae759c680c4a > > > >> >> On Mon, Sep 15, 2014 at 10:12 PM, Matt McCormick < >> matt.mccormick at kitware.com> wrote: >> >>> Hi gowith, >>> >>> To see the available types for itk.Image, run >>> >>> dir(itk.Image) >>> >>> If a type is not available that is desired, enable the option in CMake >>> for that pixel type. For unsigned short, set >>> >>> ITK_WRAP_unsigned_short >>> >>> to ON. >>> >>> Hope this helps, >>> Matt >>> >>> On Mon, Sep 15, 2014 at 2:19 PM, gowith king >>> wrote: >>> >>>> Hi McCormick >>>> I think you give me a hint for the key error problem: I tried few >>>> other types in my python such as US , UI, SI ... most of them could not >>>> work well . another keyerror pops out for the template lose: when I try >>>> itk.Image[itk.SI, 3] >>>> KeyError: 'itkTemplate : No template (, 3) for the >>>> itk::Image class' >>>> >>>> >>>> >>>> On Mon, Sep 15, 2014 at 8:11 PM, gowith king >>> > wrote: >>>> >>>>> Hi McCormick >>>>> Thank you so much for your suggestion, when I use US it pops out >>>>> a keyerror , not template for the us3 [?]. But then I change to SS it >>>>> works well for now. >>>>> any suggestion for the second issue ? >>>>> I dig for really long time for this keyerror problem , but have >>>>> no clue at all >>>>> >>>>> >>>>> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >>>>> matt.mccormick at kitware.com> wrote: >>>>> >>>>>> Hi, >>>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>>>>> image in all the itk instructions. But in my case it only has a range of >>>>>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>>>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>>>>> 0-9000 . How could I read it proprietorially? >>>>>>> >>>>>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range >>>>>> 0-255) and with three dimension. For the correspondence between mangled >>>>>> names and basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>>>>> >>>>>> HTH, >>>>>> Matt >>>>>> >>>>>> [1] >>>>>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Selection_001.png Type: image/png Size: 23881 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From gowithking at googlemail.com Tue Sep 16 05:32:16 2014 From: gowithking at googlemail.com (gowith king) Date: Tue, 16 Sep 2014 11:32:16 +0200 Subject: [ITK] Fwd: How to label this binary image into two labels In-Reply-To: References: Message-ID: Hi, I tried to label this image into two labels since yesterday , However it always give no label for result. Here is my code: LabelFilter0 = itk.BinaryImageToLabelMapFilter.IUC3LM3.New() LabelFilter0.SetInput(BinaryFilter.GetOutput()) LabelFilter0.SetInputForegroundValue(100) LabelFilter0.SetFullyConnected(False) print LabelFilter0.GetNumberOfObjects() LabelImage0 = itk.LabelMapToLabelImageFilter.LM3IUC3.New() LabelImage0.SetInput(LabelFilter0.GetOutput()) Sta0Filter = itk.LabelStatisticsImageFilter.ISS3IUC3.New() Sta0Filter.SetLabelInput(LabelImage0.GetOutput()) Sta0Filter.SetInput(reader0.GetOutput()) ?here is the mhd file : https://drive.google.com/file/d/0B6iiB8fojky9NXhOZXFVWTNIbHlLc01jdmFyT2FkdDVmdXFB/edit?usp=sharing https://drive.google.com/file/d/0B6iiB8fojky9dnlSSmNqOHk4NDM1WHRBLVRhWWpHLUxGZ1JF/edit?usp=sharing -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Selection_001.png Type: image/png Size: 23881 bytes Desc: not available URL: From matt.mccormick at kitware.com Tue Sep 16 09:48:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Sep 2014 09:48:17 -0400 Subject: [ITK] ITK-4.6 problem In-Reply-To: References: Message-ID: Hi Gib, > > There is something a bit funny about the installed ITK-4.6, in that the > compiler complained about some missing include files, vnl_*.h and others, > which are in my ITK-4.0 installation but not in 4.6. I just copied them > across - I hope this is not a problem. > This is probably a problem. Did the ITK 4.6 build complete successfully and the install complete successfully? Thanks, Matt From joel.schaerer at laposte.net Tue Sep 16 10:27:01 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Tue, 16 Sep 2014 16:27:01 +0200 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty Message-ID: <541848B5.9060901@laposte.net> Hi all, The template for Insight Journal submissions that is available on GitHub and recommended on the Insight Journal website (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) does not build with ITK4. I can try to fix it, but before I do I would like to make sure it is still the current version? Thanks! Jo?l _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Tue Sep 16 10:46:05 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 16 Sep 2014 14:46:05 +0000 Subject: [ITK] [ITK-dev] Coverity 'Uncaught Exception' errors Message-ID: Hans asked me to look at a couple of ITK Coverity defects, as they were in code written in our lab. A couple of them are understandable but problematic. Basically there?s an exception thrown at itkObjectFactoryBase.cxx at line 533: 531 if ( ObjectFactoryBase::m_StrictVersionChecking ) 532 { 1. exception_thrown: An exception of type "itk::ExceptionObject" is thrown. 533 itkGenericExceptionMacro(<< "Incompatible factory version load attempt:" 534 << "\nRunning itk version :\n" << Version::GetITKSourceVersion() 535 << "\nAttempted loading factory version:\n" << factory->GetITKSourceVersion() 536 << "\nAttempted factory:\n" << factory->m_LibraryPath << "\n"); 537 } 538 else 539 { 540 itkGenericOutputMacro(<< "Possible incompatible factory load:" 541 << "\nRunning itk version :\n" << Version::GetITKSourceVersion() 542 << "\nLoaded factory version:\n" << factory->GetITKSourceVersion() 543 << "\nLoading factory:\n" << factory->m_LibraryPath << "\n"); 544 } 545 } There are 4 Coverity defects reported that all point to this code. Given where the exceptions are thrown, it looks like every call to itk::::New() should be bracketed by a try/catch pair. But in fact Coverity only reports 4 instances of this being a problem. I can fix the reported defects for completeness? sake, but I find it mysterious that more defects caused by this occur. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From yxp233 at postech.ac.kr Tue Sep 16 10:37:18 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Tue, 16 Sep 2014 23:37:18 +0900 Subject: [ITK] [ITK-users] Compiling ITK 4.6.0 error In-Reply-To: <1410796270474129.115529.ptmail04@ptmail04> References: <1410796270474129.115529.ptmail04@ptmail04> Message-ID: <024f01cfd1bb$b7c4a0c0$274de240$@ac.kr> Dear Users, I was trying to compile ITK 4.6.0 with MSVS 2010 with GPU enabled, but I got the following error: Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): Syntax error in cmake code at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 when parsing string D:\Toolbox\ITK-4.6.0 Invalid escape sequence \T Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set) CMake/ITKModuleEnablement.cmake:171 (include) CMakeLists.txt:322 (include) Configuring incomplete, errors occurred! See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". Could anyone tell me what caused this error? Thank you. Best regards, Xiaopeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Tue Sep 16 10:53:10 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 16 Sep 2014 10:53:10 -0400 Subject: [ITK] [ITK-dev] Coverity 'Uncaught Exception' errors In-Reply-To: References: Message-ID: I think we ignored a number of those. On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K wrote: > Hans asked me to look at a couple of ITK Coverity defects, as they were in > code written in our lab. > > A couple of them are understandable but problematic. Basically there?s an > exception thrown at itkObjectFactoryBase.cxx at line 533: > > 531 if ( ObjectFactoryBase::m_StrictVersionChecking ) > 532 { > 1. exception_thrown: An exception of type "itk::ExceptionObject" is > thrown. > 533 itkGenericExceptionMacro(<< "Incompatible factory version load > attempt:" > 534 << "\nRunning itk version :\n" << > Version::GetITKSourceVersion() > 535 << "\nAttempted loading factory version:\n" > << factory->GetITKSourceVersion() > 536 << "\nAttempted factory:\n" << > factory->m_LibraryPath << "\n"); > 537 } > 538 else > 539 { > 540 itkGenericOutputMacro(<< "Possible incompatible factory load:" > 541 << "\nRunning itk version :\n" << > Version::GetITKSourceVersion() > 542 << "\nLoaded factory version:\n" << > factory->GetITKSourceVersion() > 543 << "\nLoading factory:\n" << > factory->m_LibraryPath << "\n"); > 544 } > 545 } > > There are 4 Coverity defects reported that all point to this code. Given > where the exceptions are thrown, it looks like every call to > itk::::New() should be bracketed by a try/catch pair. > > But in fact Coverity only reports 4 instances of this being a problem. > > I can fix the reported defects for completeness? sake, but I find it > mysterious that more defects caused by this occur. > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From norman-k-williams at uiowa.edu Tue Sep 16 12:25:02 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 16 Sep 2014 16:25:02 +0000 Subject: [ITK] [ITK-dev] Coverity 'Uncaught Exception' errors In-Reply-To: References: Message-ID: You mean we told Coverity to ignore them? I guess that makes sense. On 9/16/14, 9:53 AM, "Bill Lorensen" wrote: >I think we ignored a number of those. > > >On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K > wrote: >> Hans asked me to look at a couple of ITK Coverity defects, as they were >>in >> code written in our lab. >> >> A couple of them are understandable but problematic. Basically there?s >>an >> exception thrown at itkObjectFactoryBase.cxx at line 533: >> >> 531 if ( ObjectFactoryBase::m_StrictVersionChecking ) >> 532 { >> 1. exception_thrown: An exception of type "itk::ExceptionObject" is >> thrown. >> 533 itkGenericExceptionMacro(<< "Incompatible factory version load >> attempt:" >> 534 << "\nRunning itk version :\n" << >> Version::GetITKSourceVersion() >> 535 << "\nAttempted loading factory >>version:\n" >> << factory->GetITKSourceVersion() >> 536 << "\nAttempted factory:\n" << >> factory->m_LibraryPath << "\n"); >> 537 } >> 538 else >> 539 { >> 540 itkGenericOutputMacro(<< "Possible incompatible factory load:" >> 541 << "\nRunning itk version :\n" << >> Version::GetITKSourceVersion() >> 542 << "\nLoaded factory version:\n" << >> factory->GetITKSourceVersion() >> 543 << "\nLoading factory:\n" << >> factory->m_LibraryPath << "\n"); >> 544 } >> 545 } >> >> There are 4 Coverity defects reported that all point to this code. >>Given >> where the exceptions are thrown, it looks like every call to >> itk::::New() should be bracketed by a try/catch pair. >> >> But in fact Coverity only reports 4 instances of this being a problem. >> >> I can fix the reported defects for completeness? sake, but I find it >> mysterious that more defects caused by this occur. >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered >>by the >> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >>confidential >> and may be legally privileged. If you are not the intended recipient, >>you >> are hereby notified that any retention, dissemination, distribution, or >> copying of this communication is strictly prohibited. Please reply to >>the >> sender that you have received the message in error, then delete it. >>Thank >> you. >> ________________________________ >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > > > >-- >Unpaid intern in BillsBasement at noware dot com ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From norman-k-williams at uiowa.edu Tue Sep 16 12:50:39 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 16 Sep 2014 16:50:39 +0000 Subject: [ITK] [ITK-dev] Review.source.kitware.com down? Message-ID: Is it just me or is ITK Gerrit inaccessible? ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 16 13:02:06 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Sep 2014 13:02:06 -0400 Subject: [ITK] [ITK-dev] Review.source.kitware.com down? In-Reply-To: References: Message-ID: It's not just you. I will find the status. Thanks, Matt On Tue, Sep 16, 2014 at 12:50 PM, Williams, Norman K wrote: > Is it just me or is ITK Gerrit inaccessible? > > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From norman-k-williams at uiowa.edu Tue Sep 16 13:15:48 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 16 Sep 2014 17:15:48 +0000 Subject: [ITK] [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData In-Reply-To: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com> References: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com> Message-ID: I?ll have a look when review.source.kitware.com comes back up. It would be OK to replaces the [] operator with using the iterator directly. The only reason I can think of not to is that even with a DICOM file, the time spent in writing and reading the MetaDataDictionary is not going to have a significant computational cost, since it only happens when you read or write a DICOM file. It?s not something done in the inner loop of a big computation. From: Arnaud Gelas > Date: Monday, September 15, 2014 at 5:05 AM To: ITK > Subject: [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData Hi guys, I have been looking at GDCMImageIO this morning and I thought it would be great if it was possible to iterate directly on the Dictionary and do not use ExposeMetaData cause internally there are 2 finds (HasKeys and [] ) per iterator (in which we already know both keys and values). https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L700 https://github.com/Kitware/ITK/blob/master/Modules/Core/Common/include/itkMetaDataObject.h#L171-L189 I have tried to create a new function which would take an iterator as parameter, I have compilation error or a failing dynamic_cast? I guess I am missing something obvious? I have been testing something like that: http://review.source.kitware.com/#/c/17026/ Any idea on how to fix the code ( both compilation & dynamic_cast ), please? Thanks, Arnaud ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 16 13:26:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Sep 2014 13:26:17 -0400 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: <541848B5.9060901@laposte.net> References: <541848B5.9060901@laposte.net> Message-ID: Hi Jo?l, Yes, that the current best repository, and fixes are welcome! Please add a pull request on the repository and ping the mailing list if it is not merged after a few days. Thanks, Matt On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer wrote: > Hi all, > > The template for Insight Journal submissions that is available on GitHub and > recommended on the Insight Journal website > (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) does > not build with ITK4. > > I can try to fix it, but before I do I would like to make sure it is still > the current version? > > Thanks! > > Jo?l > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Sep 16 13:29:31 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Sep 2014 13:29:31 -0400 Subject: [ITK] [ITK-dev] Review.source.kitware.com down? In-Reply-To: References: Message-ID: And we're back :-) On Tue, Sep 16, 2014 at 1:02 PM, Matt McCormick wrote: > It's not just you. I will find the status. > > Thanks, > Matt > > On Tue, Sep 16, 2014 at 12:50 PM, Williams, Norman K > wrote: >> Is it just me or is ITK Gerrit inaccessible? >> >> >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered by the >> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential >> and may be legally privileged. If you are not the intended recipient, you >> are hereby notified that any retention, dissemination, distribution, or >> copying of this communication is strictly prohibited. Please reply to the >> sender that you have received the message in error, then delete it. Thank >> you. >> ________________________________ >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Sep 16 13:28:20 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 16 Sep 2014 13:28:20 -0400 Subject: [ITK] [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData In-Reply-To: References: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com> Message-ID: <6367ECBA-9742-4DCD-A0F7-387C11195CF7@mail.nih.gov> Kent, A long time ago, when I was working on IO streaming, I had modified the ImageSeries reader to populate the metadata dictionary on the GenerateOutputInformation phase of the pipeline. This ended up getting called 2 or 3 times, and it caused a significant performance penalty with the GDCM meta-data that the Slicer folks loudly complained and it was fixed [ likely here 1]. I have doubts about your assumption that there are not significant computation expenses with metadata IO. However I am not quite certain if my experience is relavent to this issue. just an FYI, Brad [1] https://github.com/InsightSoftwareConsortium/ITK/commit/e92d78ee3b26069d3aeb6aa9f6460a46f20ec2de On Sep 16, 2014, at 1:15 PM, Williams, Norman K wrote: > the time spent in writing and reading the MetaDataDictionary is not going to have a significant computational cost, since it only happens when you read or write a DICOM file. It?s not something done in the inner loop of a big computation. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From daviddoria at gmail.com Tue Sep 16 14:01:46 2014 From: daviddoria at gmail.com (David Doria) Date: Tue, 16 Sep 2014 14:01:46 -0400 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: References: <541848B5.9060901@laposte.net> Message-ID: On Tue, Sep 16, 2014 at 1:26 PM, Matt McCormick wrote: > Hi Jo?l, > > Yes, that the current best repository, and fixes are welcome! Please > add a pull request on the repository and ping the mailing list if it > is not merged after a few days. > > Thanks, > Matt > I found an email from Hans from almost 2 years ago where it looks like he fixed the compatibility problems here: https://github.com/BRAINSia/LogSymmetricDemons I had fixed a few things in the same thread as well: http://public.kitware.com/pipermail/insight-developers/2012-December/022304.html Both might be worth a look. David -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From huanhehot at gmail.com Tue Sep 16 17:07:35 2014 From: huanhehot at gmail.com (=?UTF-8?B?5L2V5qyi?=) Date: Tue, 16 Sep 2014 17:07:35 -0400 Subject: [ITK] 3d volume construction with itk/vtk Message-ID: Hello, I'm a new user to ITK and a beginner to medical image processing. I'm working on a task of constructing a 3d volume from a series of micro-CT brain slices, the volume will be used for registration in later stage. What preparations do I make on those 2-d images? noise reduction? Do I have to segment tissue? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Sep 16 18:39:47 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 16 Sep 2014 22:39:47 +0000 Subject: [ITK] ITK-4.6 problem In-Reply-To: References: , Message-ID: Update on the bug in the version of ITK-4.6 installed by Slicer: What can we make of this: ImageType::Pointer im = ImageType::New(); ImageType::SizeType imsize; imsize[0] = width; imsize[1] = height; imsize[2] = depth; ImageType::IndexType imstart; imstart[0] = 0; imstart[1] = 0; imstart[2] = 0; ImageType::RegionType imregion; imregion.SetSize(imsize); imregion.SetIndex(imstart); im->SetRegions(imregion); im->Allocate(); p = (unsigned char *)(im->GetBufferPointer()); width = im->GetLargestPossibleRegion().GetSize()[0]; height = im->GetLargestPossibleRegion().GetSize()[1]; depth = im->GetLargestPossibleRegion().GetSize()[2]; printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); printf("imregion size(0): %d\n",imregion.GetSize(0)); printf("imregion size(1): %d\n",imregion.GetSize(1)); printf("imregion size(2): %d\n",imregion.GetSize(2)); int i = 195000000; for (int i=197160890; i<200000000;i++) { printf("offset: %d\n",i); p[i] = 0; } yields (reproducibly): D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 ... Requested image dimensions: width, height, depth: 1650 1650 1650 imregion size(0): 1650 imregion size(1): 1650 imregion size(2): 1650 offset: 197160890 offset: 197160891 offset: 197160892 offset: 197160893 offset: 197160894 offset: 197160895 offset: 197160896 (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? I'd appreciate some pointers. Thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Wednesday, 17 September 2014 1:48 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] ITK-4.6 problem Hi Gib, > > There is something a bit funny about the installed ITK-4.6, in that the > compiler complained about some missing include files, vnl_*.h and others, > which are in my ITK-4.0 installation but not in 4.6. I just copied them > across - I hope this is not a problem. > This is probably a problem. Did the ITK 4.6 build complete successfully and the install complete successfully? Thanks, Matt From bill.lorensen at gmail.com Tue Sep 16 18:59:59 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 16 Sep 2014 18:59:59 -0400 Subject: [ITK] [ITK-dev] Coverity 'Uncaught Exception' errors In-Reply-To: References: Message-ID: Yes On Sep 16, 2014 12:25 PM, "Williams, Norman K" wrote: > You mean we told Coverity to ignore them? > > I guess that makes sense. > > On 9/16/14, 9:53 AM, "Bill Lorensen" wrote: > > >I think we ignored a number of those. > > > > > >On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K > > wrote: > >> Hans asked me to look at a couple of ITK Coverity defects, as they were > >>in > >> code written in our lab. > >> > >> A couple of them are understandable but problematic. Basically there?s > >>an > >> exception thrown at itkObjectFactoryBase.cxx at line 533: > >> > >> 531 if ( ObjectFactoryBase::m_StrictVersionChecking ) > >> 532 { > >> 1. exception_thrown: An exception of type "itk::ExceptionObject" is > >> thrown. > >> 533 itkGenericExceptionMacro(<< "Incompatible factory version load > >> attempt:" > >> 534 << "\nRunning itk version :\n" << > >> Version::GetITKSourceVersion() > >> 535 << "\nAttempted loading factory > >>version:\n" > >> << factory->GetITKSourceVersion() > >> 536 << "\nAttempted factory:\n" << > >> factory->m_LibraryPath << "\n"); > >> 537 } > >> 538 else > >> 539 { > >> 540 itkGenericOutputMacro(<< "Possible incompatible factory load:" > >> 541 << "\nRunning itk version :\n" << > >> Version::GetITKSourceVersion() > >> 542 << "\nLoaded factory version:\n" << > >> factory->GetITKSourceVersion() > >> 543 << "\nLoading factory:\n" << > >> factory->m_LibraryPath << "\n"); > >> 544 } > >> 545 } > >> > >> There are 4 Coverity defects reported that all point to this code. > >>Given > >> where the exceptions are thrown, it looks like every call to > >> itk::::New() should be bracketed by a try/catch pair. > >> > >> But in fact Coverity only reports 4 instances of this being a problem. > >> > >> I can fix the reported defects for completeness? sake, but I find it > >> mysterious that more defects caused by this occur. > >> > >> > >> ________________________________ > >> Notice: This UI Health Care e-mail (including attachments) is covered > >>by the > >> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is > >>confidential > >> and may be legally privileged. If you are not the intended recipient, > >>you > >> are hereby notified that any retention, dissemination, distribution, or > >> copying of this communication is strictly prohibited. Please reply to > >>the > >> sender that you have received the message in error, then delete it. > >>Thank > >> you. > >> ________________________________ > >> > >> _______________________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-developers > >> > >> _______________________________________________ > >> Community mailing list > >> Community at itk.org > >> http://public.kitware.com/mailman/listinfo/community > >> > > > > > > > >-- > >Unpaid intern in BillsBasement at noware dot com > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by > the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is > confidential and may be legally privileged. If you are not the intended > recipient, you are hereby notified that any retention, dissemination, > distribution, or copying of this communication is strictly prohibited. > Please reply to the sender that you have received the message in error, > then delete it. Thank you. > ________________________________ > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From gowithking at googlemail.com Tue Sep 16 19:53:39 2014 From: gowithking at googlemail.com (gowith king) Date: Wed, 17 Sep 2014 01:53:39 +0200 Subject: [ITK] Bug in StatisticsImageFilter? Message-ID: I was trying to use itk.StatisticsImageFilter to check the outcome of my image reader. but all the results are wrong. reader1 = itk.ImageFileReader.IUC3.New() reader1.SetFileName(inputImagetest) rangetest=itk.StatisticsImageFilter.IUC3.New() rangetest.SetInput(reader1) print 'range: ', str(rangetest.GetMinimum()) result: range: 255 obviously this is not true for my image : it is a binary image and has only 1 and 100 two values. I am working on a python 2.7 wrapped ITK4 . if the python2 is incompatible with itk? -------------- next part -------------- An HTML attachment was scrubbed... URL: From yxp233 at postech.ac.kr Tue Sep 16 20:19:21 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Wed, 17 Sep 2014 09:19:21 +0900 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support In-Reply-To: <1410878838500935.032749.ptmail04@ptmail04> References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> Message-ID: <02a501cfd20d$079448c0$16bcda40$@ac.kr> Hello, Is there any detailed instructions of how to compile ITK with GPU module on? I had a hard time to get it work properly. Any information or help is appreciated. Thanks, Xiaopeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Tue Sep 16 21:12:37 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 01:12:37 +0000 Subject: [ITK] ITK-4.6 problem - OffsetValueType Message-ID: Hi, I've been digging into the code, and trying to track down where the memory access problem occurs. By putting some printf statements in itkImage.hxx and itkImageBase.h I think I've got close to the source. As I suspected it is in the Image::Allocate() function. As the program output below shows, with N=1625 GetOffsetTable() returns the correct size of the image, but with N=1626 it returns 1626^3 - 2^32. The problem is that OffsetValueType is only 4 bytes. I'm reluctant to go further with this because I don't want to risk breaking something, but somebody should know why OffsetValueType has this size and how to increase it to 8 bytes in the case of ITK_USE_64BITS_IDS on. itkImage.hxx: void Image< TPixel, VImageDimension > ::Allocate(bool initializePixels) { SizeValueType num; this->ComputeOffsetTable(); num = static_cast(this->GetOffsetTable()[VImageDimension]); printf("Image::Allocate: GetOffsetTable(): %lld\n",this->GetOffsetTable()[VImageDimension]); //Gib printf("Image::Allocate: num: %lld\n",num); //Gib m_Buffer->Reserve(num, initializePixels); } itkImageBase.h: const OffsetValueType * GetOffsetTable() const { printf("Image::Allocate: sizeof(OffsetValueType): %d\n",sizeof(OffsetValueType)); //Gib return m_OffsetTable; } D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1625 1 Output image file: zzz-4.6.tif Desired image dimensions: width, height, depth: 1625 1625 1625 Image::Allocate: sizeof(OffsetValueType): 4 Image::Allocate: sizeof(OffsetValueType): 4 Image::Allocate: GetOffsetTable(): 4291015625 Image::Allocate: num: 4291015625 Requested image dimensions: width, height, depth: 1625 1625 1625 imregion size(0): 1625 imregion size(1): 1625 imregion size(2): 1625 Image::FillBuffer: numberOfPixels: 4291015625 D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1626 1 Output image file: zzz-4.6.tif Desired image dimensions: width, height, depth: 1626 1626 1626 Image::Allocate: sizeof(OffsetValueType): 4 Image::Allocate: sizeof(OffsetValueType): 4 Image::Allocate: GetOffsetTable(): 3975080 Image::Allocate: num: 3975080 Requested image dimensions: width, height, depth: 1626 1626 1626 imregion size(0): 1626 imregion size(1): 1626 imregion size(2): 1626 Image::FillBuffer: numberOfPixels: 3975080 ________________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, 17 September 2014 10:39 a.m. To: Matt McCormick Cc: community at itk.org Subject: Re: [ITK] ITK-4.6 problem Update on the bug in the version of ITK-4.6 installed by Slicer: What can we make of this: ImageType::Pointer im = ImageType::New(); ImageType::SizeType imsize; imsize[0] = width; imsize[1] = height; imsize[2] = depth; ImageType::IndexType imstart; imstart[0] = 0; imstart[1] = 0; imstart[2] = 0; ImageType::RegionType imregion; imregion.SetSize(imsize); imregion.SetIndex(imstart); im->SetRegions(imregion); im->Allocate(); p = (unsigned char *)(im->GetBufferPointer()); width = im->GetLargestPossibleRegion().GetSize()[0]; height = im->GetLargestPossibleRegion().GetSize()[1]; depth = im->GetLargestPossibleRegion().GetSize()[2]; printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); printf("imregion size(0): %d\n",imregion.GetSize(0)); printf("imregion size(1): %d\n",imregion.GetSize(1)); printf("imregion size(2): %d\n",imregion.GetSize(2)); int i = 195000000; for (int i=197160890; i<200000000;i++) { printf("offset: %d\n",i); p[i] = 0; } yields (reproducibly): D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 ... Requested image dimensions: width, height, depth: 1650 1650 1650 imregion size(0): 1650 imregion size(1): 1650 imregion size(2): 1650 offset: 197160890 offset: 197160891 offset: 197160892 offset: 197160893 offset: 197160894 offset: 197160895 offset: 197160896 (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? I'd appreciate some pointers. Thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Wednesday, 17 September 2014 1:48 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] ITK-4.6 problem Hi Gib, > > There is something a bit funny about the installed ITK-4.6, in that the > compiler complained about some missing include files, vnl_*.h and others, > which are in my ITK-4.0 installation but not in 4.6. I just copied them > across - I hope this is not a problem. > This is probably a problem. Did the ITK 4.6 build complete successfully and the install complete successfully? Thanks, Matt _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From g.bogle at auckland.ac.nz Wed Sep 17 03:35:18 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 07:35:18 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> References: , <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Hi Bradley, Matt and Steve, Now for the embarrassing confession. In External_ITK4.cmake I turned ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I finally checked what the code that is being built was using (with #if defined ...) I discovered that both ITKV3_COMPATIBILITY and ITK_USE_64BITS_IDS were off. How can this be? It's easy, all it takes is a typo: -DITK_USE_64_BITS_IDS:BOOL=ON That typo has cost me a couple of days, and caused annoyance to a few people, I suspect. Unfortunately... now Slicer's vtkITK does not build. There are very many errors like this: 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ 3>Build started 17/09/2014 7:25:52 p.m.. 3>InitializeBuildStatus: 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". 3>CustomBuild: 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt 3> CMake does not need to re-run because C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. 3>ClCompile: 3> vtkITKNumericTraits.cxx 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx 3> vtkITKArchetypeImageSeriesReader.cxx 3> vtkITKArchetypeImageSeriesScalarReader.cxx 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx 3> vtkITKImageWriter.cxx 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx 3> vtkITKDistanceTransform.cxx 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): error C2679: binary '=' : no operator found which takes a right-hand operand of type 'itk::ImportImageContainer *' (or there is no acceptable conversion) 3> with 3> [ 3> TElementIdentifier=unsigned __int64, 3> TElement=double 3> ] 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): could be 'itk::SmartPointer &itk::SmartPointer::operator =(const itk::SmartPointer &)' 3> with 3> [ 3> TObjectType=itk::ImportImageContainer 3> ] 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): or 'itk::SmartPointer &itk::SmartPointer::operator =(itk::ImportImageContainer *)' 3> with 3> [ 3> TObjectType=itk::ImportImageContainer, 3> TElementIdentifier=unsigned long, 3> TElement=double 3> ] 3> while trying to match the argument list '(itk::SmartPointer, itk::ImportImageContainer *)' 3> with 3> [ 3> TObjectType=itk::ImportImageContainer 3> ] 3> and 3> [ 3> TElementIdentifier=unsigned __int64, 3> TElement=double 3> ] I presume these are related to the use of 64-bit integers. Over to you guys :) Gib ________________________________ From: Bradley Lowekamp [blowekamp at mail.nih.gov] Sent: Tuesday, 16 September 2014 12:45 a.m. To: Steve Pieper Cc: Gib Bogle; slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hello, For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 To test for ITK big tiff compatibility, I'd recommend getting python 2.7 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to read and write files like these there. More information about getting started is here[1]. You should be a able to generate a image with: import SimpleITK as sitk img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) img += 10 stats = sitk.StatisticsImageFilter() stats.Execute(img) print stats This should give you basic access to ITK in python to interactively experiment with options with these large images. I have been able to load large images with the binaries of SimpleITK on windows 64-bits. I don't know if I have tried big tiff though. A simular test could be done with C++ and ITK directly, but I think SimpleITK in python may be quicker for experimentation. Brad [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted [2] http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: Hi Gib - Are you testing only on windows? What we would often try to do for this kind of debugging is to create a small example that other people can test on their configurations. Slicer has a mechanism called a Self Test [1] to allow easy replication and debugging across multiple platforms. It's ideal if we can hone it down to something like what is described as a 'sscce' [2]. The self tests will typically download some data from a public web site, run some operations, and then print something out saying if it passed or failed (or it may crash). Since it's possible to make a small data file that expands into a giant tiff image it should be pretty tractable to pose this issue in the form of a self test. Best, Steve [1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule [2] http://sscce.org/ On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: Hi J-C, Some more info about Slicer with big tiff files. 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page 72) All suggestions will be gratefully received. Cheers Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Sunday, 14 September 2014 8:32 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Gib, What do you mean by "reinstalled" ? You should not have to install Slicer to be able to execute it from the build directory. After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work out. When done building, make sure to start the Slicer launcher: C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe and not the Slicer executable: C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe By using the launcher, you ensure that the PATH are properly setup and the expected libraries are loaded. Hth Jc On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > wrote: I hope I understand correctly. I added the line as shown to C:\Slicer\SuperBuild\External_ITKv4.cmake: ... # ZLIB -DITK_USE_SYSTEM_ZLIB:BOOL=ON -DZLIB_ROOT:PATH=${ZLIB_ROOT} -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} # Big TIFF -DITK_USE_64_BITS_IDS:BOOL=ON ... I then did ALL_BUILD in the root of the build directory (C:\s\b). I presume this is the "superbuild". I then redid ALL_BUILD in C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still crashes with the big tiff. Is there somewhere I can check in the project configuration files to see if setting ITK_USE_64_BITS_IDS actually took effect? Thanks Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Sunday, 14 September 2014 1:36 p.m. To: Gib Bogle Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hey Gib - Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the ITK build process [1] during the superbuild. I don't think much else was required except turning off the IKTv3 parts. [1] https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 -Steve p.s. I hear the ABs beat the Boks recently in a close match (we don't get it on TV). So the Jo'berg game should be a great rematch! On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > wrote: You did warn me. Here is the list of options not ticked: Slicer_BUILD_BRAINSTOOLS _LEGACY_CLI _LandmarkRegistration _TESTING_EXTENSIONS _UPDATE_TRANSLATION _USE_GIT_PROTOCOL _OpenIGTLink _PYTHONQT_WITH_OPENSSL _PYTHONQT_WITH_TCL _QtTesting _SimpleITK _VTK_DEBUG_LINKS Slicer_WITH_LIBRARY_VERSION USE_BRAINS* USE_ConvertBetweenFileFormats USE_DWIConvert USE_DebugImageViewer USE_GTRACT USE_ICCDEF USE_ImageCalculator USE_ReferenceAtlas ------- Progress! Process Monitor showed me that the exit code was C0000139, which means a DLL was not found. I then realized that I have different occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this prompted me to look more carefully at the PATH environment variable. I just tested with all the new paths at the start of the PATH string, and Slicer starts successfully! I can load a tiff! But ... it still crashes when I attempt to load a 4 GB tiff. I am now wondering (belatedly!) about the way I tried to build with big tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as 'bool'. It appears ticked in Ungrouped Entries. I really should have asked for directions before doing this - now I'm wondering if that switch actually had any effect. Is that the right thing to do, and if not, what is? Thanks Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Sunday, 14 September 2014 10:02 a.m. To: Gib Bogle Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Yes, well, don't say I didn't warn you! ; ) You do need loadable modules and you probably do want python (a lot of core stuff is in python, like the editor). BRAINSTools should be off for now, since it needs ITKv3. I'm not sure either what to do next, but I suggest maybe trying the Process Monitor from microsoft (sysinternals) and see what it was doing when it exited. But that may be a longshot. -Steve On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > wrote: Hi Steve, That was an interesting exercise. I managed to build Slicer without Qtloadablemodules. As you might expect, it was not much use. The program started up but without any capabilities, just an empty shell. (I'm a bit handicapped by not knowing anything about how Slicer is constructed.) So I built it again, this time selecting most things except BRAINTools. The build took a long time, partly because I turned on the Python option, which I don't need. This time there were no errors, except for a couple of occasions where the attempt to create a directory failed - this was because the directory already existed, and was easily solved by deleting the directory and building again. I installed everything that wanted to be installed, and modified the environment variables to suit. My sense of satisfaction was short-lived, however. When Slicer is invoked the Acknowledgements screen flashes up briefly then the program exits. There are no error messages. Dependency Walker shows that all the DLLs are being found. I am assuming that BRAINTools is not needed (not knowing what it is). I sense that I must be close to getting it working, but I'm not sure what to do next. Cheers Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Sunday, 14 September 2014 12:36 a.m. To: Gib Bogle Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Gib - A lot of the building goes on in parallel so you need to review the whole build log to see what is going on. I'm guessing ITK didn't build correctly. Typically I do a Control-A Control-C in the visual studio output window and then paste it into a text editor to look for issues. Definitely you don't want to be editing any of the visual studio files, since they are generated by cmake every configure -- much better to sort out what is going on at the cmake flag level. Best, Steve On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > wrote: Looking at the Project Properties for qSlicerBaseQTCore I notice something odd. Here is a snippet from the list of Linker > Input > Additional Dependencies: ... C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib ITKCommon.lib C:\Qt64\4.8.1\lib\QtOpenGL4.lib ... For some reason ITKCommon.lib is treated differently from all the other (at first sight) ITK libraries. Any ideas about how I might fix this? If I edit the linker configuration for qSlicerBaseQTCore to point correctly to the ITKCommon library it builds OK, but I'd rather not have to do this 40+ times. Thanks again Gib ________________________________ From: slicer-devel-bounces at bwh.harvard.edu [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Saturday, 13 September 2014 12:59 p.m. To: Steve Pieper Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Steve, All goes well until the point where the qSlicer*.lib get made. The first error, while building qSlicerBaseQTCore.lib, is: LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' I don't know how to interpret this. I am guessing that it wants to link the ITK library that was just built, i.e.: \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib This is the first of about 40 such link errors. I'm not sure if ITK really needed to be built, since it is already installed (64-bit) on my system, but I didn't see any option for skipping that step (same for VTK). Is an INSTALL step for ITK needed? Should I set ITK_DIR appropriately? Thanks Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Saturday, 13 September 2014 9:02 a.m. To: Gib Bogle Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Gib - I'd give a qualified 'yes' answer. Technically what you propose is quite reasonable, and would be workable. But if you haven't built a big package on windows before there are quite a few prerequites (qt, cmake, git, visual studio...) and odd things can go wrong if it isn't all done just right. That said, slicer is actually quite well supported on windows, better, IMHO, than many cross-platform systems. But windows is really the trickiest platform in my experience. -Steve On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > wrote: Hi Steve, Do you think I would be able to build Slicer myself, with ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that depends on either ITKDeprecated or ITKV3Compatibility? My need at this point is simply for a 3D viewer that can handle big images. Thanks Gib ________________________________ From: Gib Bogle Sent: Wednesday, 10 September 2014 10:34 a.m. To: Jean-Christophe Fillion-Robin; Steve Pieper Cc: slicer-devel at bwh.harvard.edu Subject: RE: [slicer-devel] BigTIFF Hi Jean-Christophe, Any idea when 4.5 will enter the world? Cheers Gib ________________________________ From: slicer-devel-bounces at bwh.harvard.edu [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Wednesday, 10 September 2014 10:31 a.m. To: Steve Pieper Cc: slicer-devel at bwh.harvard.edu Subject: Re: [slicer-devel] BigTIFF Hi Folks, Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on either ITKDeprecated or ITKV3Compatibility. That said, BRAINSTools and some extensions are still depending on these module. All details are captured here: http://na-mic.org/Mantis/view.php?id=3825#c12486 Note also that this will NOT be addressed for Slicer 4.4 release. The enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is planned for 4.5. Thanks Jc On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > wrote: Hi Matt - Thanks, that's helpful. I suspect that for slicer, the only real issues will be in vtkITK, which includes all the file IO adapters. But I think it will be pretty straightforward. But there's no reason to start that until we know that BRAINSTools will work - right now at least some of them depend on ITKDeprecated. -Steve On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick > wrote: Here is what the process would look like: 0) Start with a clean software quality dashboard. 1) Set ITKV3_COMPATIBILITY to OFF in Superbuild/External_ITKv4.cmake 2) Rebuild and encounter errors and test failures. 3) Fix the errors with the help of the ITK migration guide [1] and the ITK mailing list [2]. They usually fairly strait forward changes (minor modifications to the API, etc). 4) Set ITK_USE_64BITS_IDS to ON. 5) Profit. HTH, Matt [1] http://itk.org/migrationv4/ [2] http://www.itk.org/ITK/help/mailing.html On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > wrote: > Yes, agreed it's a good goal and I believe the expertise exists, but it's > looking like there's a fair amount of code to retrofit. > > Maybe Hans, Brad, Matt or others could provide some idea just what is > involved? > > -Steve > > > > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle > wrote: >> >> :( I imagine that people are increasingly working with very large >> datasets, so the number of people who would like to have this capability >> will grow. I, alas, am not an ITK expert. >> ________________________________ >> From: Steve Pieper [pieper at isomics.com] >> Sent: Friday, 5 September 2014 8:42 a.m. >> >> To: Gib Bogle >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Alas the build where I enabled 64 bit id's failed to even configure >> properly. Lots of key code depends on the ITKDeprecated module, like vtkITK >> and various components of BRAINSTools. So I would say some ITK experts are >> going to need to dig in before this mode can be enabled. >> >> -Steve >> >> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle > wrote: >>> >>> I await the results with interest... >>> ________________________________ >>> From: slicer-devel-bounces at bwh.harvard.edu >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve Pieper >>> [pieper at isomics.com] >>> Sent: Friday, 5 September 2014 1:32 a.m. >>> To: Bradley Lowekamp >>> >>> Cc: slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out a lot of >>> legacy CLI code - perhaps those were the main places ITKV3_COMPATIBILITY was >>> required? I kicked off a build to see what will happen. >>> >>> -Steve >>> >>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp > >>> wrote: >>>> >>>> Steve, >>>> >>>> Yes, this is certainly an issue with how ITK has been configured in >>>> Slicer. >>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY needs to >>>> be disabled, and then the ITKDeprecated module can no longer be used. I have >>>> brought these issue up before and offered assistance but no one wanted to >>>> champion changing these configuration flags. >>>> >>>> Brad >>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > wrote: >>>> >>>> Hi Brad - >>>> >>>> Right, this is not tiff specific but is ITK specific. I was able to >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's vtkNRRDWriter >>>> and reload with vtkNRRDReader. Could not read the same file with ITK's NRRD >>>> reader. This was all on a slicer current trunk build with default options >>>> on win7 64bit. >>>> >>>> So are we out of luck enabling 64bit IDs or is it just something nobody >>>> has tried? >>>> >>>> -Steve >>>> >>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>> > wrote: >>>>> >>>>> Steve, >>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on windows 64? >>>>> >>>>> There should be some image source filters in the SimpleFilters modules >>>>> to generate images. I don't think this issue is tiff specific. >>>>> >>>>> Bread >>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper > wrote: >>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>> >>>>> I happens in the itk tiff reader. I created a bug report and pasted in >>>>> a stack trace and put a link to the data. >>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>> >>>>> -Steve >>>>> >>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>> > wrote: >>>>>> >>>>>> Matt, I was just about to point that out. >>>>>> >>>>>> The other things is the compatibility flag: >>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's still >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>> >>>>>> Brad >>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper > wrote: >>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can replicate the >>>>>> issue and then we can see if that has any side effects. >>>>>> >>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>> > wrote: >>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>> >>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle > >>>>>>> wrote: >>>>>>> > I have to do something else for a while now. I'll get back to this >>>>>>> > later. >>>>>>> > ________________________________ >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>> > >>>>>>> > To: Gib Bogle >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>> > >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how to >>>>>>> > generate a big >>>>>>> > file with SimpleITK. Or a statically linked executable for any >>>>>>> > standard >>>>>>> > platform should be fine too. >>>>>>> > >>>>>>> > >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle > >>>>>>> > wrote: >>>>>>> >> >>>>>>> >> On second thoughts a very simple image will compress to a >>>>>>> >> reasonable size. >>>>>>> >> Slicer seems to handle the compression modes used by ITK without >>>>>>> >> problems. >>>>>>> >> ________________________________ >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>> >> To: Gib Bogle >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >> >>>>>>> >> Hi - >>>>>>> >> >>>>>>> >> Is there an easy way to generate a big tiff like this, for example >>>>>>> >> with a >>>>>>> >> few lines of SimpleITK code? (Easier than trying to transfer a >>>>>>> >> 4.5GB file >>>>>>> >> from NZ). >>>>>>> >> >>>>>>> >> -Steve >>>>>>> >> >>>>>>> >> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle > >>>>>>> >> wrote: >>>>>>> >>> >>>>>>> >>> Hi Brad, >>>>>>> >>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. I can load >>>>>>> >>> a tiff >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), but a couple >>>>>>> >>> of bigger >>>>>>> >>> files fail. When I try to open a file that is about 4.5 GB >>>>>>> >>> (actually when I >>>>>>> >>> try to add data to the scene) the program crashes immediately, >>>>>>> >>> exception >>>>>>> >>> code c0000005. The result with an image of about half this size >>>>>>> >>> is the >>>>>>> >>> same. Sometimes the behaviour is slightly different - I see the >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the windows greys >>>>>>> >>> out. >>>>>>> >>> Nothing happens after that, until I click the x button on the >>>>>>> >>> popup, and the >>>>>>> >>> program crashes. >>>>>>> >>> >>>>>>> >>> These files were all written with ITK. The reason I installed >>>>>>> >>> Slicer is >>>>>>> >>> simply to be able to view big files - Irfanview is very good but >>>>>>> >>> BigTIFFs >>>>>>> >>> are not enabled. >>>>>>> >>> >>>>>>> >>> Is it a case of having to build Slicer myself, with different >>>>>>> >>> build >>>>>>> >>> options? >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> Gib >>>>>>> >>> ________________________________ >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>> >>> To: Gib Bogle >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>> >>>>>>> >>> Hello, >>>>>>> >>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, and the >>>>>>> >>> associated >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you please >>>>>>> >>> provide more >>>>>>> >>> detail about your issue? >>>>>>> >>> >>>>>>> >>> Brad >>>>>>> >>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle > >>>>>>> >>> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does not >>>>>>> >>> handle >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>> >>> Thanks >>>>>>> >>> Gib >>>>>>> >>> _______________________________________________ >>>>>>> >>> slicer-devel mailing list >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>> >>> To unsubscribe: send email to >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as >>>>>>> >>> the >>>>>>> >>> subject >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> The information in this e-mail is intended only for the person to >>>>>>> >>> whom it >>>>>>> >>> is >>>>>>> >>> addressed. If you believe this e-mail was sent to you in error >>>>>>> >>> and the >>>>>>> >>> e-mail >>>>>>> >>> contains patient information, please contact the Partners >>>>>>> >>> Compliance >>>>>>> >>> HelpLine at >>>>>>> >>> http://www.partners.org/complianceline . If the e-mail was sent >>>>>>> >>> to you in >>>>>>> >>> error >>>>>>> >>> but does not contain patient information, please contact the >>>>>>> >>> sender and >>>>>>> >>> properly >>>>>>> >>> dispose of the e-mail. >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> slicer-devel mailing list >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>> >>> To unsubscribe: send email to >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as >>>>>>> >>> the >>>>>>> >>> subject >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> The information in this e-mail is intended only for the person to >>>>>>> >>> whom it >>>>>>> >>> is >>>>>>> >>> addressed. If you believe this e-mail was sent to you in error >>>>>>> >>> and the >>>>>>> >>> e-mail >>>>>>> >>> contains patient information, please contact the Partners >>>>>>> >>> Compliance >>>>>>> >>> HelpLine at >>>>>>> >>> http://www.partners.org/complianceline . If the e-mail was sent >>>>>>> >>> to you in >>>>>>> >>> error >>>>>>> >>> but does not contain patient information, please contact the >>>>>>> >>> sender and >>>>>>> >>> properly >>>>>>> >>> dispose of the e-mail. >>>>>>> >>> >>>>>>> >> >>>>>>> > >>>>>>> > >>>>>>> > _______________________________________________ >>>>>>> > slicer-devel mailing list >>>>>>> > slicer-devel at bwh.harvard.edu >>>>>>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>> > To unsubscribe: send email to >>>>>>> > slicer-devel-request at massmail.spl.harvard.edu >>>>>>> > with unsubscribe as the subject >>>>>>> > >>>>>>> > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>> > >>>>>>> > >>>>>>> > The information in this e-mail is intended only for the person to >>>>>>> > whom it is >>>>>>> > addressed. If you believe this e-mail was sent to you in error and >>>>>>> > the >>>>>>> > e-mail >>>>>>> > contains patient information, please contact the Partners >>>>>>> > Compliance >>>>>>> > HelpLine at >>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>> > you in >>>>>>> > error >>>>>>> > but does not contain patient information, please contact the sender >>>>>>> > and >>>>>>> > properly >>>>>>> > dispose of the e-mail. >>>>>>> > >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> slicer-devel mailing list >>>>>> slicer-devel at bwh.harvard.edu >>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>> To unsubscribe: send email to >>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>> subject >>>>>> >>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom >>>>>> it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>>> in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>> >> > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu > with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- +1 919 869 8849 _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- +1 919 869 8849 _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Wed Sep 17 09:02:21 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:02:21 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM Message-ID: Hi all, I have been looking at the following wiki example: http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 Can anyone confirm? Is this code validated? are output images compared to input ones in the corresponding test? Thanks Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:04:17 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:04:17 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: <75058210-3021-4372-A59C-8880B69CABED@gmail.com> References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> Message-ID: Hi Nick, I work with CT images, Rescale Intercept / Slope: ( -1024, 1 ) I use system gdcm (release branch from official git repository) Thanks Arnaud On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson wrote: > Arnauld, > > Can you also say if you are using the version of GDCM bundled with ITK > release or have you compiled a system version of GDCM from the > git-repository? > > Nick. > > > On 17 Sep 2014, at 13:59, Nick Patterson > wrote: > > Arnauld, > > Which modality image are you working with, and what are the rescale slope > and intercept of the original image? > > Nick. > > > > > On 17 Sep 2014, at 14:02, Arnaud Gelas wrote: > > Hi all, > > I have been looking at the following wiki example: > > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > It seems to me that the section to rescale the image is not valid anymore > with latest ITK version (?) > > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > > Can anyone confirm? > > Is this code validated? are output images compared to input ones in the > corresponding test? > > Thanks > Arnaud > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:10:43 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:10:43 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> Message-ID: I have been modifying extensively this example... Rescale slope/intercept are saved with expected values -1024 and 1. Not sure if the error is in my code or in this example, but when I compare inputs and outputs with the ShiftScale part all pixels are different (and the difference is -1024)... that's why I am asking if this part is still valid? On Wed, Sep 17, 2014 at 3:06 PM, Nick Patterson wrote: > Ok thanks. When you say that it doesn?t work anymore would I be correct in > assuming that you mean that the output rescale slope/intercept are written > out as 1 and 0, rather than the expected value of -1024 and 1? Or do you > mean not working in some other way? > > Nick. > > > > On 17 Sep 2014, at 14:04, Arnaud Gelas wrote: > > Hi Nick, > > I work with CT images, Rescale Intercept / Slope: ( -1024, 1 ) > > I use system gdcm (release branch from official git repository) > > Thanks > Arnaud > > On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson < > pattersonnp.work at gmail.com> wrote: > >> Arnauld, >> >> Can you also say if you are using the version of GDCM bundled with ITK >> release or have you compiled a system version of GDCM from the >> git-repository? >> >> Nick. >> >> >> On 17 Sep 2014, at 13:59, Nick Patterson >> wrote: >> >> Arnauld, >> >> Which modality image are you working with, and what are the rescale slope >> and intercept of the original image? >> >> Nick. >> >> >> >> >> On 17 Sep 2014, at 14:02, Arnaud Gelas wrote: >> >> Hi all, >> >> I have been looking at the following wiki example: >> >> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >> >> It seems to me that the section to rescale the image is not valid anymore >> with latest ITK version (?) >> >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >> >> Can anyone confirm? >> >> Is this code validated? are output images compared to input ones in the >> corresponding test? >> >> Thanks >> Arnaud >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Wed Sep 17 09:13:12 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 17 Sep 2014 09:13:12 -0400 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: Message-ID: <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov> Arnaud, If using shared libraries causes the dynamic cast to fail, than this may be a side effect of some recent changes [1]. Brad [1] https://github.com/InsightSoftwareConsortium/ITK/commits/master/Modules/Core/Common/include/itkMetaDataObject.h On Sep 17, 2014, at 9:02 AM, Arnaud Gelas wrote: > Hi all, > > I have been looking at the following wiki example: > > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > > Can anyone confirm? > > Is this code validated? are output images compared to input ones in the corresponding test? > > Thanks > Arnaud > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Wed Sep 17 09:21:09 2014 From: matimontg at gmail.com (Matias Montroull) Date: Wed, 17 Sep 2014 10:21:09 -0300 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: Message-ID: I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine. The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version. On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas wrote: > Hi all, > > I have been looking at the following wiki example: > > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > It seems to me that the section to rescale the image is not valid anymore > with latest ITK version (?) > > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > > Can anyone confirm? > > Is this code validated? are output images compared to input ones in the > corresponding test? > > Thanks > Arnaud > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Wed Sep 17 09:23:50 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Wed, 17 Sep 2014 22:23:50 +0900 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support In-Reply-To: <1410913163921868.021894.ptmail04@ptmail04> References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> <1410913163921868.021894.ptmail04@ptmail04> Message-ID: <000c01cfd27a$9ed25020$dc76f060$@ac.kr> By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows: Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): Syntax error in cmake code at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 when parsing string D:\Toolbox\ITK-4.6.0 Invalid escape sequence \T Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set) CMake/ITKModuleEnablement.cmake:171 (include) CMakeLists.txt:322 (include) Configuring incomplete, errors occurred! See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Xiaopeng Yang Sent: Wednesday, September 17, 2014 9:19 AM To: 'insight-users' Subject: [ITK-users] Any instruction of compiling ITK with GPU support Hello, Is there any detailed instructions of how to compile ITK with GPU module on? I had a hard time to get it work properly. Any information or help is appreciated. Thanks, Xiaopeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From pattersonnp.work at gmail.com Wed Sep 17 09:25:00 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 17 Sep 2014 14:25:00 +0100 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com> References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com> Message-ID: Ok thanks, I have had various issues with this examples before. If you can re-test your CT images with the unmodified ResampleDICOM example and let me know the results. If you see the same problem, get back to me. Nick. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:32:08 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:32:08 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: Message-ID: Hi Matias, I guess you are referring to https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e v4.6.0 I use the release branch of ITK --- Matt, Can you comment on this, please? Thanks Arnaud On Sep 17, 2014, at 3:21 PM, Matias Montroull wrote: > I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine. > > The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version. > > On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas wrote: > Hi all, > > I have been looking at the following wiki example: > > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > > Can anyone confirm? > > Is this code validated? are output images compared to input ones in the corresponding test? > > Thanks > Arnaud > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Wed Sep 17 09:27:44 2014 From: matimontg at gmail.com (Matias Montroull) Date: Wed, 17 Sep 2014 10:27:44 -0300 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com> Message-ID: Nick, what do you mean by "the unmodified resampleDICOM"? thanks, On Wed, Sep 17, 2014 at 10:25 AM, Nick Patterson wrote: > > Ok thanks, > > > I have had various issues with this examples before. If you can re-test > your CT images with the unmodified ResampleDICOM example and let me know > the results. If you see the same problem, get back to me. > > Nick. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From chinander at gmail.com Wed Sep 17 09:28:45 2014 From: chinander at gmail.com (Mike Chinander) Date: Wed, 17 Sep 2014 08:28:45 -0500 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support In-Reply-To: <000c01cfd27a$9ed25020$dc76f060$@ac.kr> References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> <1410913163921868.021894.ptmail04@ptmail04> <000c01cfd27a$9ed25020$dc76f060$@ac.kr> Message-ID: Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with forward slashes instead, "D:/Toolbox/ITK-4.6.0" On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang wrote: > By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under > windows 7 64 bit. I set USE_GPU on, but I got the error as follows: > > > > Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib > > CMake Error at C:/Program Files > (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): > Syntax error in cmake code at > > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 > > when parsing string > > D:\Toolbox\ITK-4.6.0 > > Invalid escape sequence \T > Call Stack (most recent call first): > C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 > (cpack_set_if_not_set) > CMake/ITKModuleEnablement.cmake:171 (include) > CMakeLists.txt:322 (include) > > Configuring incomplete, errors occurred! > > See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". > > See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From pattersonnp.work at gmail.com Wed Sep 17 09:29:04 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 17 Sep 2014 14:29:04 +0100 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: Message-ID: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> I should also mention Arnauld that I use ITK4.5.2. I have had many issues with using ITK 4.6 with the latest GDCM from git, so rolled back to ITK4.5.2. Nick. On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: > Hi Matias, > > I guess you are referring to > > https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e > > $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e > v4.6.0 > > I use the release branch of ITK > > --- > > Matt, > > Can you comment on this, please? > > Thanks > Arnaud > > On Sep 17, 2014, at 3:21 PM, Matias Montroull wrote: > >> I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine. >> >> The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version. >> >> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas wrote: >> Hi all, >> >> I have been looking at the following wiki example: >> >> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >> >> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >> >> Can anyone confirm? >> >> Is this code validated? are output images compared to input ones in the corresponding test? >> >> Thanks >> Arnaud >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:27:33 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:27:33 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com> <75058210-3021-4372-A59C-8880B69CABED@gmail.com> Message-ID: <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com> I have already done that change before sending the email? Unfortunately, I can' share the code; so I'll rather get back to the example and validate with this one. I'll get back to you once I have made the same test with the example. On Sep 17, 2014, at 3:13 PM, Nick Patterson wrote: > Ok, I will probably need to see your code if you have heavily modified the example. However, could you try the following:- > > after line 333 : shiftScale->SetShift( interceptShift ); > add shiftScale->Update(); > > > and try again? > > Let me know. > > Nick. > > > > On 17 Sep 2014, at 14:10, Arnaud Gelas wrote: > >> I have been modifying extensively this example... >> Rescale slope/intercept are saved with expected values -1024 and 1. >> >> Not sure if the error is in my code or in this example, but when I compare inputs and outputs with the ShiftScale part all pixels are different (and the difference is -1024)... that's why I am asking if this part is still valid? >> >> On Wed, Sep 17, 2014 at 3:06 PM, Nick Patterson wrote: >> Ok thanks. When you say that it doesn?t work anymore would I be correct in assuming that you mean that the output rescale slope/intercept are written out as 1 and 0, rather than the expected value of -1024 and 1? Or do you mean not working in some other way? >> >> Nick. >> >> >> >> On 17 Sep 2014, at 14:04, Arnaud Gelas wrote: >> >>> Hi Nick, >>> >>> I work with CT images, Rescale Intercept / Slope: ( -1024, 1 ) >>> >>> I use system gdcm (release branch from official git repository) >>> >>> Thanks >>> Arnaud >>> >>> On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson wrote: >>> Arnauld, >>> >>> Can you also say if you are using the version of GDCM bundled with ITK release or have you compiled a system version of GDCM from the git-repository? >>> >>> Nick. >>> >>> >>> On 17 Sep 2014, at 13:59, Nick Patterson wrote: >>> >>>> Arnauld, >>>> >>>> Which modality image are you working with, and what are the rescale slope and intercept of the original image? >>>> >>>> Nick. >>>> >>>> >>>> >>>> >>>> On 17 Sep 2014, at 14:02, Arnaud Gelas wrote: >>>> >>>>> Hi all, >>>>> >>>>> I have been looking at the following wiki example: >>>>> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>>>> >>>>> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) >>>>> >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>>>> >>>>> Can anyone confirm? >>>>> >>>>> Is this code validated? are output images compared to input ones in the corresponding test? >>>>> >>>>> Thanks >>>>> Arnaud >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 09:34:00 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 15:34:00 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Nick, I can't roll back to previous ITK version, important patches on itkGDCMImageIO were very recently merged... https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx e.g. https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c Arnaud On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson wrote: > I should also mention Arnauld that I use ITK4.5.2. I have had many issues > with using ITK 4.6 with the latest GDCM from git, so rolled back to > ITK4.5.2. > > Nick. > > > > On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: > > Hi Matias, > > I guess you are referring to > > > https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e > > $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e > v4.6.0 > > I use the release branch of ITK > > --- > > Matt, > > Can you comment on this, please? > > Thanks > Arnaud > > On Sep 17, 2014, at 3:21 PM, Matias Montroull wrote: > > I had an issue with the resampledicom example once (all my pixel values > were recalculated by adding rescaleintercept) and then downloaded the > latest ITK release (4.6) and worked fine. > > The issue was with the GDCMIO class I beleive but was fixed somehow in the > 4.6 version. > > On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas > wrote: > >> Hi all, >> >> I have been looking at the following wiki example: >> >> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >> >> It seems to me that the section to rescale the image is not valid anymore >> with latest ITK version (?) >> >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >> >> Can anyone confirm? >> >> Is this code validated? are output images compared to input ones in the >> corresponding test? >> >> Thanks >> Arnaud >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From pattersonnp.work at gmail.com Wed Sep 17 09:35:49 2014 From: pattersonnp.work at gmail.com (Nick Patterson) Date: Wed, 17 Sep 2014 14:35:49 +0100 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: OK, I will wait to hear the outcome of your run with the original example then. Cheers, Nick. On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: > Nick, > > I can't roll back to previous ITK version, important patches on itkGDCMImageIO were very recently merged... > > https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx > > e.g. > > https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 > https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c > > > Arnaud > > On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson wrote: > I should also mention Arnauld that I use ITK4.5.2. I have had many issues with using ITK 4.6 with the latest GDCM from git, so rolled back to ITK4.5.2. > Nick. > > > > On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: > >> Hi Matias, >> >> I guess you are referring to >> >> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >> >> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >> v4.6.0 >> >> I use the release branch of ITK >> >> --- >> >> Matt, >> >> Can you comment on this, please? >> >> Thanks >> Arnaud >> >> On Sep 17, 2014, at 3:21 PM, Matias Montroull wrote: >> >>> I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine. >>> >>> The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version. >>> >>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas wrote: >>> Hi all, >>> >>> I have been looking at the following wiki example: >>> >>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>> >>> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?) >>> >>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>> >>> Can anyone confirm? >>> >>> Is this code validated? are output images compared to input ones in the corresponding test? >>> >>> Thanks >>> Arnaud >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 10:15:11 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 16:15:11 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Hi Nick, I can confirm that with the example I get a difference of -1024 (+/- 1) in between the input and the output, using the ShiftScaleImage part... While without this part of code the difference is (+/-1) I would like to make sure this is the expected behaviour!? On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson wrote: > OK, I will wait to hear the outcome of your run with the original example > then. > > Cheers, Nick. > > > > > On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: > > Nick, > > I can't roll back to previous ITK version, important patches on > itkGDCMImageIO were very recently merged... > > > https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx > > e.g. > > > https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 > > https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c > > > Arnaud > > On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson < > pattersonnp.work at gmail.com> wrote: > >> I should also mention Arnauld that I use ITK4.5.2. I have had many >> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to >> ITK4.5.2. >> Nick. >> >> >> >> On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: >> >> Hi Matias, >> >> I guess you are referring to >> >> >> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >> >> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >> v4.6.0 >> >> I use the release branch of ITK >> >> --- >> >> Matt, >> >> Can you comment on this, please? >> >> Thanks >> Arnaud >> >> On Sep 17, 2014, at 3:21 PM, Matias Montroull >> wrote: >> >> I had an issue with the resampledicom example once (all my pixel values >> were recalculated by adding rescaleintercept) and then downloaded the >> latest ITK release (4.6) and worked fine. >> >> The issue was with the GDCMIO class I beleive but was fixed somehow in >> the 4.6 version. >> >> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas >> wrote: >> >>> Hi all, >>> >>> I have been looking at the following wiki example: >>> >>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>> >>> It seems to me that the section to rescale the image is not valid >>> anymore with latest ITK version (?) >>> >>> >>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>> >>> Can anyone confirm? >>> >>> Is this code validated? are output images compared to input ones in the >>> corresponding test? >>> >>> Thanks >>> Arnaud >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Sep 17 10:39:59 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 17 Sep 2014 16:39:59 +0200 Subject: [ITK] [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData In-Reply-To: <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov> References: <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov> Message-ID: <4B7CF7FB-4669-403C-A892-98DD219EBDB5@gmail.com> Brad, I guess the email was more related to this topic than the ResampleDICOM's one? Your last commit on itkMetaDataObject.h seems of interest, I'll keep on investigating! Thanks Arnaud On Sep 17, 2014, at 3:13 PM, Bradley Lowekamp wrote: > Arnaud, > > If using shared libraries causes the dynamic cast to fail, than this may be a side effect of some recent changes [1]. > > Brad > > [1] https://github.com/InsightSoftwareConsortium/ITK/commits/master/Modules/Core/Common/include/itkMetaDataObject.h > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From bill.lorensen at gmail.com Wed Sep 17 10:41:12 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 17 Sep 2014 10:41:12 -0400 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: I wrote this example many years ago? 1) If the input has a non-trivial slope/intercept, the reader applies the slope/intercept to the raw data. 2) Rather than setting the slope/intercept in the output dicom, I apply the inverse of of the slope intercept to the resampled data before writing. The output dicom should not have the origin slope/intercept tags. I'll try to verify this with Slicer, but I may be out of touch for 2 weeks? Bill On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas wrote: > Hi Nick, > > I can confirm that with the example I get a difference of -1024 (+/- 1) in > between the input and the output, using the ShiftScaleImage part... > While without this part of code the difference is (+/-1) > > I would like to make sure this is the expected behaviour!? > > On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson > wrote: >> >> OK, I will wait to hear the outcome of your run with the original example >> then. >> >> Cheers, Nick. >> >> >> >> >> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: >> >> Nick, >> >> I can't roll back to previous ITK version, important patches on >> itkGDCMImageIO were very recently merged... >> >> >> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx >> >> e.g. >> >> >> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 >> >> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c >> >> >> Arnaud >> >> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson >> wrote: >>> >>> I should also mention Arnauld that I use ITK4.5.2. I have had many >>> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to >>> ITK4.5.2. >>> Nick. >>> >>> >>> >>> On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: >>> >>> Hi Matias, >>> >>> I guess you are referring to >>> >>> >>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >>> v4.6.0 >>> >>> I use the release branch of ITK >>> >>> --- >>> >>> Matt, >>> >>> Can you comment on this, please? >>> >>> Thanks >>> Arnaud >>> >>> On Sep 17, 2014, at 3:21 PM, Matias Montroull >>> wrote: >>> >>> I had an issue with the resampledicom example once (all my pixel values >>> were recalculated by adding rescaleintercept) and then downloaded the latest >>> ITK release (4.6) and worked fine. >>> >>> The issue was with the GDCMIO class I beleive but was fixed somehow in >>> the 4.6 version. >>> >>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas >>> wrote: >>>> >>>> Hi all, >>>> >>>> I have been looking at the following wiki example: >>>> >>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>>> >>>> It seems to me that the section to rescale the image is not valid >>>> anymore with latest ITK version (?) >>>> >>>> >>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>>> >>>> Can anyone confirm? >>>> >>>> Is this code validated? are output images compared to input ones in the >>>> corresponding test? >>>> >>>> Thanks >>>> Arnaud >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 17 11:13:20 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:13:20 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cg0n52cqd08ulpr6o9jgku32gj0?authkey=CJ-S7tP5s5_xAw On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/ctabd8pd4oasc3p5ejat27jgko4?authkey=COjR69z2toGlIQ For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 All are welcome. Hope to talk to you then! From matt.mccormick at kitware.com Wed Sep 17 11:29:30 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:29:30 -0400 Subject: [ITK] ITK-4.6 problem In-Reply-To: References: Message-ID: Hi Gib, On Tue, Sep 16, 2014 at 6:39 PM, Gib Bogle wrote: > Update on the bug in the version of ITK-4.6 installed by Slicer: > > What can we make of this: > > ImageType::Pointer im = ImageType::New(); > ImageType::SizeType imsize; > imsize[0] = width; > imsize[1] = height; > imsize[2] = depth; > ImageType::IndexType imstart; > imstart[0] = 0; > imstart[1] = 0; > imstart[2] = 0; > ImageType::RegionType imregion; > imregion.SetSize(imsize); > imregion.SetIndex(imstart); > im->SetRegions(imregion); > im->Allocate(); > p = (unsigned char *)(im->GetBufferPointer()); > > width = im->GetLargestPossibleRegion().GetSize()[0]; > height = im->GetLargestPossibleRegion().GetSize()[1]; > depth = im->GetLargestPossibleRegion().GetSize()[2]; > printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); > > printf("imregion size(0): %d\n",imregion.GetSize(0)); > printf("imregion size(1): %d\n",imregion.GetSize(1)); > printf("imregion size(2): %d\n",imregion.GetSize(2)); > > int i = 195000000; > for (int i=197160890; i<200000000;i++) { > printf("offset: %d\n",i); > p[i] = 0; > } > > yields (reproducibly): > > D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 > ... > Requested image dimensions: width, height, depth: 1650 1650 1650 > imregion size(0): 1650 > imregion size(1): 1650 > imregion size(2): 1650 > offset: 197160890 > offset: 197160891 > offset: 197160892 > offset: 197160893 > offset: 197160894 > offset: 197160895 > offset: 197160896 > > > (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) > > Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. > > I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. > > I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? If allocation failed, it should throw a MemoryAllocationError [1]. It may help to walk through the code with a debugger. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Core/Common/include/itkImportImageContainer.hxx;h=cf29eb3f95e0c22ddd32f1170bfe1aff69569634;hb=HEAD > > I'd appreciate some pointers. > > Thanks > Gib > > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Wednesday, 17 September 2014 1:48 a.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] ITK-4.6 problem > > Hi Gib, > >> >> There is something a bit funny about the installed ITK-4.6, in that the >> compiler complained about some missing include files, vnl_*.h and others, >> which are in my ITK-4.0 installation but not in 4.6. I just copied them >> across - I hope this is not a problem. >> > > This is probably a problem. Did the ITK 4.6 build complete > successfully and the install complete successfully? > > Thanks, > Matt From g.bogle at auckland.ac.nz Wed Sep 17 11:35:42 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 15:35:42 +0000 Subject: [ITK] ITK-4.6 problem In-Reply-To: References: , Message-ID: I found the problem, Matt (see my latest message) - I had a typo, and in fact ITK_USE_64BITS_IDS was off. Now I cannot build vtkITK, and the error is too abstruse for me with my meagre C++ understanding. Thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 3:29 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] ITK-4.6 problem Hi Gib, On Tue, Sep 16, 2014 at 6:39 PM, Gib Bogle wrote: > Update on the bug in the version of ITK-4.6 installed by Slicer: > > What can we make of this: > > ImageType::Pointer im = ImageType::New(); > ImageType::SizeType imsize; > imsize[0] = width; > imsize[1] = height; > imsize[2] = depth; > ImageType::IndexType imstart; > imstart[0] = 0; > imstart[1] = 0; > imstart[2] = 0; > ImageType::RegionType imregion; > imregion.SetSize(imsize); > imregion.SetIndex(imstart); > im->SetRegions(imregion); > im->Allocate(); > p = (unsigned char *)(im->GetBufferPointer()); > > width = im->GetLargestPossibleRegion().GetSize()[0]; > height = im->GetLargestPossibleRegion().GetSize()[1]; > depth = im->GetLargestPossibleRegion().GetSize()[2]; > printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); > > printf("imregion size(0): %d\n",imregion.GetSize(0)); > printf("imregion size(1): %d\n",imregion.GetSize(1)); > printf("imregion size(2): %d\n",imregion.GetSize(2)); > > int i = 195000000; > for (int i=197160890; i<200000000;i++) { > printf("offset: %d\n",i); > p[i] = 0; > } > > yields (reproducibly): > > D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 > ... > Requested image dimensions: width, height, depth: 1650 1650 1650 > imregion size(0): 1650 > imregion size(1): 1650 > imregion size(2): 1650 > offset: 197160890 > offset: 197160891 > offset: 197160892 > offset: 197160893 > offset: 197160894 > offset: 197160895 > offset: 197160896 > > > (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) > > Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. > > I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. > > I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? If allocation failed, it should throw a MemoryAllocationError [1]. It may help to walk through the code with a debugger. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Core/Common/include/itkImportImageContainer.hxx;h=cf29eb3f95e0c22ddd32f1170bfe1aff69569634;hb=HEAD > > I'd appreciate some pointers. > > Thanks > Gib > > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Wednesday, 17 September 2014 1:48 a.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] ITK-4.6 problem > > Hi Gib, > >> >> There is something a bit funny about the installed ITK-4.6, in that the >> compiler complained about some missing include files, vnl_*.h and others, >> which are in my ITK-4.0 installation but not in 4.6. I just copied them >> across - I hope this is not a problem. >> > > This is probably a problem. Did the ITK 4.6 build complete > successfully and the install complete successfully? > > Thanks, > Matt From matt.mccormick at kitware.com Wed Sep 17 11:42:33 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:42:33 -0400 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Hi, Do to this fix [1], if the writer is re-using the GDCMImageIO, the writer should apply the inverse rescale / slope intercept like the reader applied the rescale / slope intercept when reading. This was a long-standing bug that I fixed in 4.6.0. Arnaud, if the manual inverse rescale / slope operation is removed, does the correct output result? Thanks, Matt [1] https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen wrote: > I wrote this example many years ago? > 1) If the input has a non-trivial slope/intercept, the reader applies > the slope/intercept to the raw data. > 2) Rather than setting the slope/intercept in the output dicom, I > apply the inverse of of the slope intercept to the resampled data > before writing. The output dicom should not have the origin > slope/intercept tags. > > I'll try to verify this with Slicer, but I may be out of touch for 2 weeks? > > Bill > > > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas wrote: >> Hi Nick, >> >> I can confirm that with the example I get a difference of -1024 (+/- 1) in >> between the input and the output, using the ShiftScaleImage part... >> While without this part of code the difference is (+/-1) >> >> I would like to make sure this is the expected behaviour!? >> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson >> wrote: >>> >>> OK, I will wait to hear the outcome of your run with the original example >>> then. >>> >>> Cheers, Nick. >>> >>> >>> >>> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: >>> >>> Nick, >>> >>> I can't roll back to previous ITK version, important patches on >>> itkGDCMImageIO were very recently merged... >>> >>> >>> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx >>> >>> e.g. >>> >>> >>> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 >>> >>> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c >>> >>> >>> Arnaud >>> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson >>> wrote: >>>> >>>> I should also mention Arnauld that I use ITK4.5.2. I have had many >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to >>>> ITK4.5.2. >>>> Nick. >>>> >>>> >>>> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: >>>> >>>> Hi Matias, >>>> >>>> I guess you are referring to >>>> >>>> >>>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >>>> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >>>> v4.6.0 >>>> >>>> I use the release branch of ITK >>>> >>>> --- >>>> >>>> Matt, >>>> >>>> Can you comment on this, please? >>>> >>>> Thanks >>>> Arnaud >>>> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull >>>> wrote: >>>> >>>> I had an issue with the resampledicom example once (all my pixel values >>>> were recalculated by adding rescaleintercept) and then downloaded the latest >>>> ITK release (4.6) and worked fine. >>>> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow in >>>> the 4.6 version. >>>> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas >>>> wrote: >>>>> >>>>> Hi all, >>>>> >>>>> I have been looking at the following wiki example: >>>>> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>>>> >>>>> It seems to me that the section to rescale the image is not valid >>>>> anymore with latest ITK version (?) >>>>> >>>>> >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>>>> >>>>> Can anyone confirm? >>>>> >>>>> Is this code validated? are output images compared to input ones in the >>>>> corresponding test? >>>>> >>>>> Thanks >>>>> Arnaud >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > > -- > Unpaid intern in BillsBasement at noware dot com > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 17 11:44:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:44:32 -0400 Subject: [ITK] Bug in StatisticsImageFilter? In-Reply-To: References: Message-ID: Hi gowith, Please try calling rangetest.Update() This is required for the results to be computed. HTH, Matt On Tue, Sep 16, 2014 at 7:53 PM, gowith king wrote: > I was trying to use itk.StatisticsImageFilter to check the outcome of my > image reader. but all the results are wrong. > reader1 = itk.ImageFileReader.IUC3.New() > reader1.SetFileName(inputImagetest) > > rangetest=itk.StatisticsImageFilter.IUC3.New() > rangetest.SetInput(reader1) > print 'range: ', str(rangetest.GetMinimum()) > > result: > range: 255 > > obviously this is not true for my image : it is a binary image and has only > 1 and 100 two values. > > I am working on a python 2.7 wrapped ITK4 . if the python2 is incompatible > with itk? > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Wed Sep 17 11:48:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:48:13 -0400 Subject: [ITK] ITK-4.6 problem - OffsetValueType In-Reply-To: References: Message-ID: Hi Gib, OffsetValueType is defined here [1]. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Core/Common/include/itkIntTypes.h;h=c7fe398a593c79367631719e75104983efb27335;hb=HEAD#l137 On Tue, Sep 16, 2014 at 9:12 PM, Gib Bogle wrote: > Hi, > > I've been digging into the code, and trying to track down where the memory access problem occurs. By putting some printf statements in itkImage.hxx and itkImageBase.h I think I've got close to the source. As I suspected it is in the Image::Allocate() function. As the program output below shows, with N=1625 GetOffsetTable() returns the correct size of the image, but with N=1626 it returns 1626^3 - 2^32. The problem is that OffsetValueType is only 4 bytes. I'm reluctant to go further with this because I don't want to risk breaking something, but somebody should know why OffsetValueType has this size and how to increase it to 8 bytes in the case of ITK_USE_64BITS_IDS on. > > itkImage.hxx: > > void > Image< TPixel, VImageDimension > > ::Allocate(bool initializePixels) > { > SizeValueType num; > > this->ComputeOffsetTable(); > num = static_cast(this->GetOffsetTable()[VImageDimension]); > printf("Image::Allocate: GetOffsetTable(): %lld\n",this->GetOffsetTable()[VImageDimension]); //Gib > printf("Image::Allocate: num: %lld\n",num); //Gib > m_Buffer->Reserve(num, initializePixels); > } > > itkImageBase.h: > > const OffsetValueType * GetOffsetTable() const { > printf("Image::Allocate: sizeof(OffsetValueType): %d\n",sizeof(OffsetValueType)); //Gib > return m_OffsetTable; } > > > D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1625 1 > Output image file: zzz-4.6.tif > Desired image dimensions: width, height, depth: 1625 1625 1625 > Image::Allocate: sizeof(OffsetValueType): 4 > Image::Allocate: sizeof(OffsetValueType): 4 > Image::Allocate: GetOffsetTable(): 4291015625 > Image::Allocate: num: 4291015625 > Requested image dimensions: width, height, depth: 1625 1625 1625 > imregion size(0): 1625 > imregion size(1): 1625 > imregion size(2): 1625 > Image::FillBuffer: numberOfPixels: 4291015625 > > D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1626 1 > Output image file: zzz-4.6.tif > Desired image dimensions: width, height, depth: 1626 1626 1626 > Image::Allocate: sizeof(OffsetValueType): 4 > Image::Allocate: sizeof(OffsetValueType): 4 > Image::Allocate: GetOffsetTable(): 3975080 > Image::Allocate: num: 3975080 > Requested image dimensions: width, height, depth: 1626 1626 1626 > imregion size(0): 1626 > imregion size(1): 1626 > imregion size(2): 1626 > Image::FillBuffer: numberOfPixels: 3975080 > ________________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] > Sent: Wednesday, 17 September 2014 10:39 a.m. > To: Matt McCormick > Cc: community at itk.org > Subject: Re: [ITK] ITK-4.6 problem > > Update on the bug in the version of ITK-4.6 installed by Slicer: > > What can we make of this: > > ImageType::Pointer im = ImageType::New(); > ImageType::SizeType imsize; > imsize[0] = width; > imsize[1] = height; > imsize[2] = depth; > ImageType::IndexType imstart; > imstart[0] = 0; > imstart[1] = 0; > imstart[2] = 0; > ImageType::RegionType imregion; > imregion.SetSize(imsize); > imregion.SetIndex(imstart); > im->SetRegions(imregion); > im->Allocate(); > p = (unsigned char *)(im->GetBufferPointer()); > > width = im->GetLargestPossibleRegion().GetSize()[0]; > height = im->GetLargestPossibleRegion().GetSize()[1]; > depth = im->GetLargestPossibleRegion().GetSize()[2]; > printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth); > > printf("imregion size(0): %d\n",imregion.GetSize(0)); > printf("imregion size(1): %d\n",imregion.GetSize(1)); > printf("imregion size(2): %d\n",imregion.GetSize(2)); > > int i = 195000000; > for (int i=197160890; i<200000000;i++) { > printf("offset: %d\n",i); > p[i] = 0; > } > > yields (reproducibly): > > D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0 > ... > Requested image dimensions: width, height, depth: 1650 1650 1650 > imregion size(0): 1650 > imregion size(1): 1650 > imregion size(2): 1650 > offset: 197160890 > offset: 197160891 > offset: 197160892 > offset: 197160893 > offset: 197160894 > offset: 197160895 > offset: 197160896 > > > (If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().) > > Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant). 1626^3 is slightly bigger than 2^32. > > I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on. > > I'm wondering if the image buffer allocation im->Allocate() is successful in the cases that crash. How can I check that? > > I'd appreciate some pointers. > > Thanks > Gib > > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Wednesday, 17 September 2014 1:48 a.m. > To: Gib Bogle > Cc: community at itk.org > Subject: Re: [ITK] ITK-4.6 problem > > Hi Gib, > >> >> There is something a bit funny about the installed ITK-4.6, in that the >> compiler complained about some missing include files, vnl_*.h and others, >> which are in my ITK-4.0 installation but not in 4.6. I just copied them >> across - I hope this is not a problem. >> > > This is probably a problem. Did the ITK 4.6 build complete > successfully and the install complete successfully? > > Thanks, > Matt > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Wed Sep 17 11:55:34 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 11:55:34 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Hi Gib, Getting the builds states to propagate and follow how the get set can be tricky. A few pointers on where to look for the status: 1) CMakeCache.txt (this file contains the build settings that CMake recognized from your input when you run CMake) 2) ITKConfig.cmake (this file will exist in the build tree or the install tree, and it contains CMake varables that may be used by other projects building against ITK) 3) itkConfigure.h (this is a header that has configured preprocessor definitions used when building) HTH, Matt On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: > Hi Bradley, Matt and Steve, > > Now for the embarrassing confession. In External_ITK4.cmake I turned > ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I > finally checked what the code that is being built was using (with #if > defined ...) I discovered that both ITKV3_COMPATIBILITY and > ITK_USE_64BITS_IDS were off. How can this be? > > It's easy, all it takes is a typo: > -DITK_USE_64_BITS_IDS:BOOL=ON > That typo has cost me a couple of days, and caused annoyance to a few > people, I suspect. > > Unfortunately... now Slicer's vtkITK does not build. There are very many > errors like this: > > 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ > 3>Build started 17/09/2014 7:25:52 p.m.. > 3>InitializeBuildStatus: > 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". > 3>CustomBuild: > 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt > 3> CMake does not need to re-run because > C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. > 3>ClCompile: > 3> vtkITKNumericTraits.cxx > 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx > 3> vtkITKArchetypeImageSeriesReader.cxx > 3> vtkITKArchetypeImageSeriesScalarReader.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx > 3> vtkITKImageWriter.cxx > 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx > 3> vtkITKDistanceTransform.cxx > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): > error C2679: binary '=' : no operator found which takes a right-hand operand > of type 'itk::ImportImageContainer *' (or there > is no acceptable conversion) > 3> with > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): > could be 'itk::SmartPointer > &itk::SmartPointer::operator =(const > itk::SmartPointer &)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): > or 'itk::SmartPointer > &itk::SmartPointer::operator > =(itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer, > 3> TElementIdentifier=unsigned long, > 3> TElement=double > 3> ] > 3> while trying to match the argument list > '(itk::SmartPointer, > itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> and > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > > I presume these are related to the use of 64-bit integers. > > Over to you guys :) > > Gib > ________________________________ > From: Bradley Lowekamp [blowekamp at mail.nih.gov] > Sent: Tuesday, 16 September 2014 12:45 a.m. > To: Steve Pieper > Cc: Gib Bogle; slicer-devel at bwh.harvard.edu > Subject: Re: [slicer-devel] BigTIFF > > Hello, > > For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: > https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 > > To test for ITK big tiff compatibility, I'd recommend getting python 2.7 > 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to > read and write files like these there. More information about getting > started is here[1]. > > You should be a able to generate a image with: > > import SimpleITK as sitk > img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) > img += 10 > stats = sitk.StatisticsImageFilter() > stats.Execute(img) > print stats > > This should give you basic access to ITK in python to interactively > experiment with options with these large images. I have been able to load > large images with the binaries of SimpleITK on windows 64-bits. I don't know > if I have tried big tiff though. > > A simular test could be done with C++ and ITK directly, but I think > SimpleITK in python may be quicker for experimentation. > > Brad > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted > [2] > http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee > > On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: > > Hi Gib - > > Are you testing only on windows? What we would often try to do for this > kind of debugging is to create a small example that other people can test on > their configurations. Slicer has a mechanism called a Self Test [1] to > allow easy replication and debugging across multiple platforms. It's ideal > if we can hone it down to something like what is described as a 'sscce' [2]. > The self tests will typically download some data from a public web site, run > some operations, and then print something out saying if it passed or failed > (or it may crash). Since it's possible to make a small data file that > expands into a giant tiff image it should be pretty tractable to pose this > issue in the form of a self test. > > Best, > Steve > > > [1] > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule > > [2] http://sscce.org/ > > On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >> >> Hi J-C, >> >> Some more info about Slicer with big tiff files. >> >> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >> 72) >> >> All suggestions will be gratefully received. >> >> Cheers >> Gib >> ________________________________ >> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >> Sent: Sunday, 14 September 2014 8:32 p.m. >> To: Gib Bogle >> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> What do you mean by "reinstalled" ? You should not have to install Slicer >> to be able to execute it from the build directory. >> >> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >> out. >> >> When done building, make sure to start the Slicer launcher: >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >> >> and not the Slicer executable: >> >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >> >> >> By using the launcher, you ensure that the PATH are properly setup and the >> expected libraries are loaded. >> >> >> Hth >> Jc >> >> >> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >> wrote: >>> >>> I hope I understand correctly. I added the line as shown to >>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>> ... >>> # ZLIB >>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>> # Big TIFF >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> ... >>> >>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>> presume this is the "superbuild". I then redid ALL_BUILD in >>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>> crashes with the big tiff. Is there somewhere I can check in the project >>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>> effect? >>> >>> Thanks >>> Gib >>> ________________________________ >>> From: Steve Pieper [pieper at isomics.com] >>> Sent: Sunday, 14 September 2014 1:36 p.m. >>> >>> To: Gib Bogle >>> Cc: slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hey Gib - >>> >>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>> ITK build process [1] during the superbuild. I don't think much else was >>> required except turning off the IKTv3 parts. >>> >>> [1] >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>> >>> -Steve >>> >>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>> it on TV). So the Jo'berg game should be a great rematch! >>> >>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>> wrote: >>>> >>>> You did warn me. >>>> >>>> Here is the list of options not ticked: >>>> >>>> Slicer_BUILD_BRAINSTOOLS >>>> _LEGACY_CLI >>>> _LandmarkRegistration >>>> _TESTING_EXTENSIONS >>>> _UPDATE_TRANSLATION >>>> _USE_GIT_PROTOCOL >>>> _OpenIGTLink >>>> _PYTHONQT_WITH_OPENSSL >>>> _PYTHONQT_WITH_TCL >>>> _QtTesting >>>> _SimpleITK >>>> _VTK_DEBUG_LINKS >>>> Slicer_WITH_LIBRARY_VERSION >>>> >>>> USE_BRAINS* >>>> USE_ConvertBetweenFileFormats >>>> USE_DWIConvert >>>> USE_DebugImageViewer >>>> USE_GTRACT >>>> USE_ICCDEF >>>> USE_ImageCalculator >>>> USE_ReferenceAtlas >>>> >>>> ------- >>>> >>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>> which means a DLL was not found. I then realized that I have different >>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>> prompted me to look more carefully at the PATH environment variable. I just >>>> tested with all the new paths at the start of the PATH string, and Slicer >>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>> attempt to load a 4 GB tiff. >>>> >>>> I am now wondering (belatedly!) about the way I tried to build with big >>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>> for directions before doing this - now I'm wondering if that switch actually >>>> had any effect. Is that the right thing to do, and if not, what is? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Yes, well, don't say I didn't warn you! ; ) >>>> >>>> You do need loadable modules and you probably do want python (a lot of >>>> core stuff is in python, like the editor). >>>> >>>> BRAINSTools should be off for now, since it needs ITKv3. >>>> >>>> I'm not sure either what to do next, but I suggest maybe trying the >>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>> it exited. But that may be a longshot. >>>> >>>> -Steve >>>> >>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>> wrote: >>>>> >>>>> Hi Steve, >>>>> >>>>> That was an interesting exercise. I managed to build Slicer without >>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>> built it again, this time selecting most things except BRAINTools. The >>>>> build took a long time, partly because I turned on the Python option, which >>>>> I don't need. This time there were no errors, except for a couple of >>>>> occasions where the attempt to create a directory failed - this was because >>>>> the directory already existed, and was easily solved by deleting the >>>>> directory and building again. I installed everything that wanted to be >>>>> installed, and modified the environment variables to suit. >>>>> >>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>> knowing what it is). >>>>> >>>>> I sense that I must be close to getting it working, but I'm not sure >>>>> what to do next. >>>>> >>>>> Cheers >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hi Gib - >>>>> >>>>> A lot of the building goes on in parallel so you need to review the >>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>> window and then paste it into a text editor to look for issues. Definitely >>>>> you don't want to be editing any of the visual studio files, since they are >>>>> generated by cmake every configure -- much better to sort out what is going >>>>> on at the cmake flag level. >>>>> >>>>> Best, >>>>> Steve >>>>> >>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>> Additional Dependencies: >>>>>> >>>>>> ... >>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>> ITKCommon.lib >>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>> ... >>>>>> >>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>> 40+ times. >>>>>> >>>>>> Thanks again >>>>>> Gib >>>>>> ________________________________ >>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>> [g.bogle at auckland.ac.nz] >>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>> >>>>>> To: Steve Pieper >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>> >>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>> >>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>> link the ITK library that was just built, i.e.: >>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>> This is the first of about 40 such link errors. >>>>>> >>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>> ITK_DIR appropriately? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>> trickiest platform in my experience. >>>>>> >>>>>> -Steve >>>>>> >>>>>> >>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Gib Bogle >>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Jean-Christophe, >>>>>>> >>>>>>> Any idea when 4.5 will enter the world? >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Folks, >>>>>>> >>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>> >>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>> these module. All details are captured here: >>>>>>> >>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>> >>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>> planned for 4.5. >>>>>>> >>>>>>> Thanks >>>>>>> Jc >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Matt - >>>>>>>> >>>>>>>> Thanks, that's helpful. >>>>>>>> >>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>> straightforward. >>>>>>>> >>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Here is what the process would look like: >>>>>>>>> >>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>> the >>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>> (minor modifications to the API, etc). >>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>> 5) Profit. >>>>>>>>> >>>>>>>>> HTH, >>>>>>>>> Matt >>>>>>>>> >>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>> >>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>> >>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>> > but it's >>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>> > >>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>> > what is >>>>>>>>> > involved? >>>>>>>>> > >>>>>>>>> > -Steve >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>> > wrote: >>>>>>>>> >> >>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>> >> large >>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>> >> capability >>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>> >> ________________________________ >>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>> >> >>>>>>>>> >> To: Gib Bogle >>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >> >>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>> >> configure >>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>> >> like vtkITK >>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>> >> experts are >>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>> >> >>>>>>>>> >> -Steve >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>> >> wrote: >>>>>>>>> >>> >>>>>>>>> >>> I await the results with interest... >>>>>>>>> >>> ________________________________ >>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>> >>> Pieper >>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>> >>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>> >>> a lot of >>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>> >>> >>>>>>>>> >>> -Steve >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Steve, >>>>>>>>> >>>> >>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>> >>>> configured in >>>>>>>>> >>>> Slicer. >>>>>>>>> >>>> >>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>> >>>> needs to >>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>> >>>> be used. I have >>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>> >>>> one wanted to >>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>> >>>> >>>>>>>>> >>>> Brad >>>>>>>>> >>>> >>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>> >>>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Hi Brad - >>>>>>>>> >>>> >>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>> >>>> able to >>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>> >>>> with ITK's NRRD >>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>> >>>> default options >>>>>>>>> >>>> on win7 64bit. >>>>>>>>> >>>> >>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>> >>>> something nobody >>>>>>>>> >>>> has tried? >>>>>>>>> >>>> >>>>>>>>> >>>> -Steve >>>>>>>>> >>>> >>>>>>>>> >>>> >>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>> >>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> Steve, >>>>>>>>> >>>>> >>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>> >>>>> windows 64? >>>>>>>>> >>>>> >>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>> >>>>> specific. >>>>>>>>> >>>>> >>>>>>>>> >>>>> Bread >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>> >>>>> >>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>> >>>>> pasted in >>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>> >>>>> >>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>> >>>>> >>>>>>>>> >>>>> -Steve >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>> >>>>>> still >>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Brad >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>> >>>>>> replicate the >>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> wrote: >>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>> >>>>>>> > back to this >>>>>>>>> >>>>>>> > later. >>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>> >>>>>>> > to >>>>>>>>> >>>>>>> > generate a big >>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>> >>>>>>> > for any >>>>>>>>> >>>>>>> > standard >>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > wrote: >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>> >>>>>>> >> a >>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>> >>>>>>> >> without >>>>>>>>> >>>>>>> >> problems. >>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Hi - >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>> >>>>>>> >> for example >>>>>>>>> >>>>>>> >> with a >>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>> >>>>>>> >> transfer a >>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> -Steve >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>> >>>>>>> >>> I can load >>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>> >>>>>>> >>> exception >>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>> >>>>>>> >>> this size >>>>>>>>> >>>>>>> >>> is the >>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>> >>>>>>> >>> I see the >>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>> >>>>>>> >>> out. >>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>> >>>>>>> >>> on the >>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>> >>>>>>> >>> installed >>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>> >>>>>>> >>> good but >>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>> >>>>>>> >>> different >>>>>>>>> >>>>>>> >>> build >>>>>>>>> >>>>>>> >>> options? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> associated >>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>> >>>>>>> >>> please >>>>>>>>> >>>>>>> >>> provide more >>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Brad >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>> >>>>>>> >>> not >>>>>>>>> >>>>>>> >>> handle >>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>> >>>>>>> >>> the >>>>>>>>> >>>>>>> >>> subject >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>>> >>> person to >>>>>>>>> >>>>>>> >>> whom it >>>>>>>>> >>>>>>> >>> is >>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> +1 919 869 8849 >>>>>> >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>> subject >>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> >> -- >> +1 919 869 8849 > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu > with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > From matt.mccormick at kitware.com Wed Sep 17 12:01:05 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 12:01:05 -0400 Subject: [ITK] pixeltype define and template lost in python warped ITK In-Reply-To: References: Message-ID: Hi gowith, Is an Update() call missing? HTH, Matt On Tue, Sep 16, 2014 at 4:27 AM, gowith king wrote: > Hi , Matt > I tried it , it does not work as well. the print > LabelFilter0.GetNumberOfObjects() always returns 0, > what i want to do it every nasty: sign 1 to label 1, 100 to label 2 > ,and there is no background at all. > My images all like the attached image but in 3D , the 3D version will > be attached later ,thank you for your attention > > On Mon, Sep 15, 2014 at 11:58 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> >> >> On Mon, Sep 15, 2014 at 5:31 PM, gowith king >> wrote: >> >>> Thanks McCormick , I use the dir(itk,Image) and dir(itk.LabelMap) and >>> dir(to get some information : UC3 is included in itk.image then it is good. >>> Then I tried all the other dir() for each of my filter , made lots of >>> correction , now the pepline works perfect [?] Thank you again . >>> >>> But I still could not get my result ... >>> because of the filters I may not really understand. >>> >>> I have three filters >>> BinaryThresholdImageFilter # to get a binary image for now I get only >>> two values 1 and 100 it works well. I what the labelmap contains both two >>> parts of them >>> BinaryImageToLabelMapFilter #I have no idea if it works well or not >>> LabelMapToLabelImageFilter # returns a empty image >>> >>> Do you have any idea about this ? >>> >> >> Perhaps SetInputForegroundValue [1] needs to be set? >> >> HTH, >> Matt >> >> [1] >> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToLabelMapFilter.html#a5c56958ec0ae8d3a9bf7ae759c680c4a >> >> >> >>> >>> On Mon, Sep 15, 2014 at 10:12 PM, Matt McCormick < >>> matt.mccormick at kitware.com> wrote: >>> >>>> Hi gowith, >>>> >>>> To see the available types for itk.Image, run >>>> >>>> dir(itk.Image) >>>> >>>> If a type is not available that is desired, enable the option in CMake >>>> for that pixel type. For unsigned short, set >>>> >>>> ITK_WRAP_unsigned_short >>>> >>>> to ON. >>>> >>>> Hope this helps, >>>> Matt >>>> >>>> On Mon, Sep 15, 2014 at 2:19 PM, gowith king >>> > wrote: >>>> >>>>> Hi McCormick >>>>> I think you give me a hint for the key error problem: I tried few >>>>> other types in my python such as US , UI, SI ... most of them could not >>>>> work well . another keyerror pops out for the template lose: when I try >>>>> itk.Image[itk.SI, 3] >>>>> KeyError: 'itkTemplate : No template (, 3) for >>>>> the itk::Image class' >>>>> >>>>> >>>>> >>>>> On Mon, Sep 15, 2014 at 8:11 PM, gowith king < >>>>> gowithking at googlemail.com> wrote: >>>>> >>>>>> Hi McCormick >>>>>> Thank you so much for your suggestion, when I use US it pops out >>>>>> a keyerror , not template for the us3 [?]. But then I change to SS it >>>>>> works well for now. >>>>>> any suggestion for the second issue ? >>>>>> I dig for really long time for this keyerror problem , but have >>>>>> no clue at all >>>>>> >>>>>> >>>>>> On Mon, Sep 15, 2014 at 7:54 PM, Matt McCormick < >>>>>> matt.mccormick at kitware.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>>> >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> - The imagetype of itk.Image.UC3 should be used for 16 bit >>>>>>>> image in all the itk instructions. But in my case it only has a range of >>>>>>>> 0-255. Then I take itk.Image.F3, then it get a range of >>>>>>>> '-3.40282346639e+38 3.40282346639e+38' . The grey value of my image is >>>>>>>> 0-9000 . How could I read it proprietorially? >>>>>>>> >>>>>>>> itk.Image.UC3 is an itk::Image with unsigned char pixels (range >>>>>>> 0-255) and with three dimension. For the correspondence between mangled >>>>>>> names and basic types see [1]. For a 16 bit image use 'US' or 'SS'. >>>>>>> >>>>>>> HTH, >>>>>>> Matt >>>>>>> >>>>>>> [1] >>>>>>> http://itk.org/gitweb?p=ITK.git;a=blob;f=Wrapping/WrapBasicTypes.cmake;h=f303a1c245a541e702674f969dac8209b12f2e93;hb=HEAD >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Selection_001.png Type: image/png Size: 23881 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 33A.gif Type: image/gif Size: 581 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 330.gif Type: image/gif Size: 96 bytes Desc: not available URL: From g.bogle at auckland.ac.nz Wed Sep 17 12:02:43 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 16:02:43 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Hi Matt, I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? thanks Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 3:55 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib, Getting the builds states to propagate and follow how the get set can be tricky. A few pointers on where to look for the status: 1) CMakeCache.txt (this file contains the build settings that CMake recognized from your input when you run CMake) 2) ITKConfig.cmake (this file will exist in the build tree or the install tree, and it contains CMake varables that may be used by other projects building against ITK) 3) itkConfigure.h (this is a header that has configured preprocessor definitions used when building) HTH, Matt On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: > Hi Bradley, Matt and Steve, > > Now for the embarrassing confession. In External_ITK4.cmake I turned > ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I > finally checked what the code that is being built was using (with #if > defined ...) I discovered that both ITKV3_COMPATIBILITY and > ITK_USE_64BITS_IDS were off. How can this be? > > It's easy, all it takes is a typo: > -DITK_USE_64_BITS_IDS:BOOL=ON > That typo has cost me a couple of days, and caused annoyance to a few > people, I suspect. > > Unfortunately... now Slicer's vtkITK does not build. There are very many > errors like this: > > 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ > 3>Build started 17/09/2014 7:25:52 p.m.. > 3>InitializeBuildStatus: > 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". > 3>CustomBuild: > 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt > 3> CMake does not need to re-run because > C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. > 3>ClCompile: > 3> vtkITKNumericTraits.cxx > 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx > 3> vtkITKArchetypeImageSeriesReader.cxx > 3> vtkITKArchetypeImageSeriesScalarReader.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx > 3> vtkITKImageWriter.cxx > 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx > 3> vtkITKDistanceTransform.cxx > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): > error C2679: binary '=' : no operator found which takes a right-hand operand > of type 'itk::ImportImageContainer *' (or there > is no acceptable conversion) > 3> with > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): > could be 'itk::SmartPointer > &itk::SmartPointer::operator =(const > itk::SmartPointer &)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): > or 'itk::SmartPointer > &itk::SmartPointer::operator > =(itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer, > 3> TElementIdentifier=unsigned long, > 3> TElement=double > 3> ] > 3> while trying to match the argument list > '(itk::SmartPointer, > itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> and > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > > I presume these are related to the use of 64-bit integers. > > Over to you guys :) > > Gib > ________________________________ > From: Bradley Lowekamp [blowekamp at mail.nih.gov] > Sent: Tuesday, 16 September 2014 12:45 a.m. > To: Steve Pieper > Cc: Gib Bogle; slicer-devel at bwh.harvard.edu > Subject: Re: [slicer-devel] BigTIFF > > Hello, > > For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: > https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 > > To test for ITK big tiff compatibility, I'd recommend getting python 2.7 > 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to > read and write files like these there. More information about getting > started is here[1]. > > You should be a able to generate a image with: > > import SimpleITK as sitk > img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) > img += 10 > stats = sitk.StatisticsImageFilter() > stats.Execute(img) > print stats > > This should give you basic access to ITK in python to interactively > experiment with options with these large images. I have been able to load > large images with the binaries of SimpleITK on windows 64-bits. I don't know > if I have tried big tiff though. > > A simular test could be done with C++ and ITK directly, but I think > SimpleITK in python may be quicker for experimentation. > > Brad > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted > [2] > http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee > > On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: > > Hi Gib - > > Are you testing only on windows? What we would often try to do for this > kind of debugging is to create a small example that other people can test on > their configurations. Slicer has a mechanism called a Self Test [1] to > allow easy replication and debugging across multiple platforms. It's ideal > if we can hone it down to something like what is described as a 'sscce' [2]. > The self tests will typically download some data from a public web site, run > some operations, and then print something out saying if it passed or failed > (or it may crash). Since it's possible to make a small data file that > expands into a giant tiff image it should be pretty tractable to pose this > issue in the form of a self test. > > Best, > Steve > > > [1] > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule > > [2] http://sscce.org/ > > On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >> >> Hi J-C, >> >> Some more info about Slicer with big tiff files. >> >> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >> 72) >> >> All suggestions will be gratefully received. >> >> Cheers >> Gib >> ________________________________ >> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >> Sent: Sunday, 14 September 2014 8:32 p.m. >> To: Gib Bogle >> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> What do you mean by "reinstalled" ? You should not have to install Slicer >> to be able to execute it from the build directory. >> >> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >> out. >> >> When done building, make sure to start the Slicer launcher: >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >> >> and not the Slicer executable: >> >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >> >> >> By using the launcher, you ensure that the PATH are properly setup and the >> expected libraries are loaded. >> >> >> Hth >> Jc >> >> >> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >> wrote: >>> >>> I hope I understand correctly. I added the line as shown to >>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>> ... >>> # ZLIB >>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>> # Big TIFF >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> ... >>> >>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>> presume this is the "superbuild". I then redid ALL_BUILD in >>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>> crashes with the big tiff. Is there somewhere I can check in the project >>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>> effect? >>> >>> Thanks >>> Gib >>> ________________________________ >>> From: Steve Pieper [pieper at isomics.com] >>> Sent: Sunday, 14 September 2014 1:36 p.m. >>> >>> To: Gib Bogle >>> Cc: slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hey Gib - >>> >>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>> ITK build process [1] during the superbuild. I don't think much else was >>> required except turning off the IKTv3 parts. >>> >>> [1] >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>> >>> -Steve >>> >>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>> it on TV). So the Jo'berg game should be a great rematch! >>> >>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>> wrote: >>>> >>>> You did warn me. >>>> >>>> Here is the list of options not ticked: >>>> >>>> Slicer_BUILD_BRAINSTOOLS >>>> _LEGACY_CLI >>>> _LandmarkRegistration >>>> _TESTING_EXTENSIONS >>>> _UPDATE_TRANSLATION >>>> _USE_GIT_PROTOCOL >>>> _OpenIGTLink >>>> _PYTHONQT_WITH_OPENSSL >>>> _PYTHONQT_WITH_TCL >>>> _QtTesting >>>> _SimpleITK >>>> _VTK_DEBUG_LINKS >>>> Slicer_WITH_LIBRARY_VERSION >>>> >>>> USE_BRAINS* >>>> USE_ConvertBetweenFileFormats >>>> USE_DWIConvert >>>> USE_DebugImageViewer >>>> USE_GTRACT >>>> USE_ICCDEF >>>> USE_ImageCalculator >>>> USE_ReferenceAtlas >>>> >>>> ------- >>>> >>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>> which means a DLL was not found. I then realized that I have different >>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>> prompted me to look more carefully at the PATH environment variable. I just >>>> tested with all the new paths at the start of the PATH string, and Slicer >>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>> attempt to load a 4 GB tiff. >>>> >>>> I am now wondering (belatedly!) about the way I tried to build with big >>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>> for directions before doing this - now I'm wondering if that switch actually >>>> had any effect. Is that the right thing to do, and if not, what is? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Yes, well, don't say I didn't warn you! ; ) >>>> >>>> You do need loadable modules and you probably do want python (a lot of >>>> core stuff is in python, like the editor). >>>> >>>> BRAINSTools should be off for now, since it needs ITKv3. >>>> >>>> I'm not sure either what to do next, but I suggest maybe trying the >>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>> it exited. But that may be a longshot. >>>> >>>> -Steve >>>> >>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>> wrote: >>>>> >>>>> Hi Steve, >>>>> >>>>> That was an interesting exercise. I managed to build Slicer without >>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>> built it again, this time selecting most things except BRAINTools. The >>>>> build took a long time, partly because I turned on the Python option, which >>>>> I don't need. This time there were no errors, except for a couple of >>>>> occasions where the attempt to create a directory failed - this was because >>>>> the directory already existed, and was easily solved by deleting the >>>>> directory and building again. I installed everything that wanted to be >>>>> installed, and modified the environment variables to suit. >>>>> >>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>> knowing what it is). >>>>> >>>>> I sense that I must be close to getting it working, but I'm not sure >>>>> what to do next. >>>>> >>>>> Cheers >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hi Gib - >>>>> >>>>> A lot of the building goes on in parallel so you need to review the >>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>> window and then paste it into a text editor to look for issues. Definitely >>>>> you don't want to be editing any of the visual studio files, since they are >>>>> generated by cmake every configure -- much better to sort out what is going >>>>> on at the cmake flag level. >>>>> >>>>> Best, >>>>> Steve >>>>> >>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>> Additional Dependencies: >>>>>> >>>>>> ... >>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>> ITKCommon.lib >>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>> ... >>>>>> >>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>> 40+ times. >>>>>> >>>>>> Thanks again >>>>>> Gib >>>>>> ________________________________ >>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>> [g.bogle at auckland.ac.nz] >>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>> >>>>>> To: Steve Pieper >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>> >>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>> >>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>> link the ITK library that was just built, i.e.: >>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>> This is the first of about 40 such link errors. >>>>>> >>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>> ITK_DIR appropriately? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>> trickiest platform in my experience. >>>>>> >>>>>> -Steve >>>>>> >>>>>> >>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Gib Bogle >>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Jean-Christophe, >>>>>>> >>>>>>> Any idea when 4.5 will enter the world? >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Folks, >>>>>>> >>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>> >>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>> these module. All details are captured here: >>>>>>> >>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>> >>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>> planned for 4.5. >>>>>>> >>>>>>> Thanks >>>>>>> Jc >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Matt - >>>>>>>> >>>>>>>> Thanks, that's helpful. >>>>>>>> >>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>> straightforward. >>>>>>>> >>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Here is what the process would look like: >>>>>>>>> >>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>> the >>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>> (minor modifications to the API, etc). >>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>> 5) Profit. >>>>>>>>> >>>>>>>>> HTH, >>>>>>>>> Matt >>>>>>>>> >>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>> >>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>> >>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>> > but it's >>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>> > >>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>> > what is >>>>>>>>> > involved? >>>>>>>>> > >>>>>>>>> > -Steve >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>> > wrote: >>>>>>>>> >> >>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>> >> large >>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>> >> capability >>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>> >> ________________________________ >>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>> >> >>>>>>>>> >> To: Gib Bogle >>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >> >>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>> >> configure >>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>> >> like vtkITK >>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>> >> experts are >>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>> >> >>>>>>>>> >> -Steve >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>> >> wrote: >>>>>>>>> >>> >>>>>>>>> >>> I await the results with interest... >>>>>>>>> >>> ________________________________ >>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>> >>> Pieper >>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>> >>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>> >>> a lot of >>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>> >>> >>>>>>>>> >>> -Steve >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Steve, >>>>>>>>> >>>> >>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>> >>>> configured in >>>>>>>>> >>>> Slicer. >>>>>>>>> >>>> >>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>> >>>> needs to >>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>> >>>> be used. I have >>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>> >>>> one wanted to >>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>> >>>> >>>>>>>>> >>>> Brad >>>>>>>>> >>>> >>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>> >>>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Hi Brad - >>>>>>>>> >>>> >>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>> >>>> able to >>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>> >>>> with ITK's NRRD >>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>> >>>> default options >>>>>>>>> >>>> on win7 64bit. >>>>>>>>> >>>> >>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>> >>>> something nobody >>>>>>>>> >>>> has tried? >>>>>>>>> >>>> >>>>>>>>> >>>> -Steve >>>>>>>>> >>>> >>>>>>>>> >>>> >>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>> >>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> Steve, >>>>>>>>> >>>>> >>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>> >>>>> windows 64? >>>>>>>>> >>>>> >>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>> >>>>> specific. >>>>>>>>> >>>>> >>>>>>>>> >>>>> Bread >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>> >>>>> >>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>> >>>>> pasted in >>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>> >>>>> >>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>> >>>>> >>>>>>>>> >>>>> -Steve >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>> >>>>>> still >>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Brad >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>> >>>>>> replicate the >>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> wrote: >>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>> >>>>>>> > back to this >>>>>>>>> >>>>>>> > later. >>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>> >>>>>>> > to >>>>>>>>> >>>>>>> > generate a big >>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>> >>>>>>> > for any >>>>>>>>> >>>>>>> > standard >>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > wrote: >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>> >>>>>>> >> a >>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>> >>>>>>> >> without >>>>>>>>> >>>>>>> >> problems. >>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Hi - >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>> >>>>>>> >> for example >>>>>>>>> >>>>>>> >> with a >>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>> >>>>>>> >> transfer a >>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> -Steve >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>> >>>>>>> >>> I can load >>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>> >>>>>>> >>> exception >>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>> >>>>>>> >>> this size >>>>>>>>> >>>>>>> >>> is the >>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>> >>>>>>> >>> I see the >>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>> >>>>>>> >>> out. >>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>> >>>>>>> >>> on the >>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>> >>>>>>> >>> installed >>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>> >>>>>>> >>> good but >>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>> >>>>>>> >>> different >>>>>>>>> >>>>>>> >>> build >>>>>>>>> >>>>>>> >>> options? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> associated >>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>> >>>>>>> >>> please >>>>>>>>> >>>>>>> >>> provide more >>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Brad >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>> >>>>>>> >>> not >>>>>>>>> >>>>>>> >>> handle >>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>> >>>>>>> >>> the >>>>>>>>> >>>>>>> >>> subject >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>>> >>> person to >>>>>>>>> >>>>>>> >>> whom it >>>>>>>>> >>>>>>> >>> is >>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>> >>>>>>> >>> in error >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>> >>>>>>> >>> Partners >>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If the e-mail was sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> +1 919 869 8849 >>>>>> >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>> subject >>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> >> -- >> +1 919 869 8849 > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu > with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > From g.bogle at auckland.ac.nz Wed Sep 17 12:04:27 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 16:04:27 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: I forgot to mention that ITK builds correctly, and my test program that uses it to create big tiffs now works fine. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 3:55 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib, Getting the builds states to propagate and follow how the get set can be tricky. A few pointers on where to look for the status: 1) CMakeCache.txt (this file contains the build settings that CMake recognized from your input when you run CMake) 2) ITKConfig.cmake (this file will exist in the build tree or the install tree, and it contains CMake varables that may be used by other projects building against ITK) 3) itkConfigure.h (this is a header that has configured preprocessor definitions used when building) HTH, Matt On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: > Hi Bradley, Matt and Steve, > > Now for the embarrassing confession. In External_ITK4.cmake I turned > ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I > finally checked what the code that is being built was using (with #if > defined ...) I discovered that both ITKV3_COMPATIBILITY and > ITK_USE_64BITS_IDS were off. How can this be? > > It's easy, all it takes is a typo: > -DITK_USE_64_BITS_IDS:BOOL=ON > That typo has cost me a couple of days, and caused annoyance to a few > people, I suspect. > > Unfortunately... now Slicer's vtkITK does not build. There are very many > errors like this: > > 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ > 3>Build started 17/09/2014 7:25:52 p.m.. > 3>InitializeBuildStatus: > 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". > 3>CustomBuild: > 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt > 3> CMake does not need to re-run because > C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. > 3>ClCompile: > 3> vtkITKNumericTraits.cxx > 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx > 3> vtkITKArchetypeImageSeriesReader.cxx > 3> vtkITKArchetypeImageSeriesScalarReader.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx > 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx > 3> vtkITKImageWriter.cxx > 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx > 3> vtkITKDistanceTransform.cxx > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): > error C2679: binary '=' : no operator found which takes a right-hand operand > of type 'itk::ImportImageContainer *' (or there > is no acceptable conversion) > 3> with > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): > could be 'itk::SmartPointer > &itk::SmartPointer::operator =(const > itk::SmartPointer &)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): > or 'itk::SmartPointer > &itk::SmartPointer::operator > =(itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer, > 3> TElementIdentifier=unsigned long, > 3> TElement=double > 3> ] > 3> while trying to match the argument list > '(itk::SmartPointer, > itk::ImportImageContainer *)' > 3> with > 3> [ > 3> TObjectType=itk::ImportImageContainer > 3> ] > 3> and > 3> [ > 3> TElementIdentifier=unsigned __int64, > 3> TElement=double > 3> ] > > I presume these are related to the use of 64-bit integers. > > Over to you guys :) > > Gib > ________________________________ > From: Bradley Lowekamp [blowekamp at mail.nih.gov] > Sent: Tuesday, 16 September 2014 12:45 a.m. > To: Steve Pieper > Cc: Gib Bogle; slicer-devel at bwh.harvard.edu > Subject: Re: [slicer-devel] BigTIFF > > Hello, > > For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: > https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 > > To test for ITK big tiff compatibility, I'd recommend getting python 2.7 > 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to > read and write files like these there. More information about getting > started is here[1]. > > You should be a able to generate a image with: > > import SimpleITK as sitk > img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) > img += 10 > stats = sitk.StatisticsImageFilter() > stats.Execute(img) > print stats > > This should give you basic access to ITK in python to interactively > experiment with options with these large images. I have been able to load > large images with the binaries of SimpleITK on windows 64-bits. I don't know > if I have tried big tiff though. > > A simular test could be done with C++ and ITK directly, but I think > SimpleITK in python may be quicker for experimentation. > > Brad > > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted > [2] > http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee > > On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: > > Hi Gib - > > Are you testing only on windows? What we would often try to do for this > kind of debugging is to create a small example that other people can test on > their configurations. Slicer has a mechanism called a Self Test [1] to > allow easy replication and debugging across multiple platforms. It's ideal > if we can hone it down to something like what is described as a 'sscce' [2]. > The self tests will typically download some data from a public web site, run > some operations, and then print something out saying if it passed or failed > (or it may crash). Since it's possible to make a small data file that > expands into a giant tiff image it should be pretty tractable to pose this > issue in the form of a self test. > > Best, > Steve > > > [1] > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule > > [2] http://sscce.org/ > > On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >> >> Hi J-C, >> >> Some more info about Slicer with big tiff files. >> >> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >> 72) >> >> All suggestions will be gratefully received. >> >> Cheers >> Gib >> ________________________________ >> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >> Sent: Sunday, 14 September 2014 8:32 p.m. >> To: Gib Bogle >> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> What do you mean by "reinstalled" ? You should not have to install Slicer >> to be able to execute it from the build directory. >> >> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >> out. >> >> When done building, make sure to start the Slicer launcher: >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >> >> and not the Slicer executable: >> >> >> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >> >> >> By using the launcher, you ensure that the PATH are properly setup and the >> expected libraries are loaded. >> >> >> Hth >> Jc >> >> >> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >> wrote: >>> >>> I hope I understand correctly. I added the line as shown to >>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>> ... >>> # ZLIB >>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>> # Big TIFF >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> ... >>> >>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>> presume this is the "superbuild". I then redid ALL_BUILD in >>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>> crashes with the big tiff. Is there somewhere I can check in the project >>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>> effect? >>> >>> Thanks >>> Gib >>> ________________________________ >>> From: Steve Pieper [pieper at isomics.com] >>> Sent: Sunday, 14 September 2014 1:36 p.m. >>> >>> To: Gib Bogle >>> Cc: slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hey Gib - >>> >>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>> ITK build process [1] during the superbuild. I don't think much else was >>> required except turning off the IKTv3 parts. >>> >>> [1] >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>> >>> -Steve >>> >>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>> it on TV). So the Jo'berg game should be a great rematch! >>> >>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>> wrote: >>>> >>>> You did warn me. >>>> >>>> Here is the list of options not ticked: >>>> >>>> Slicer_BUILD_BRAINSTOOLS >>>> _LEGACY_CLI >>>> _LandmarkRegistration >>>> _TESTING_EXTENSIONS >>>> _UPDATE_TRANSLATION >>>> _USE_GIT_PROTOCOL >>>> _OpenIGTLink >>>> _PYTHONQT_WITH_OPENSSL >>>> _PYTHONQT_WITH_TCL >>>> _QtTesting >>>> _SimpleITK >>>> _VTK_DEBUG_LINKS >>>> Slicer_WITH_LIBRARY_VERSION >>>> >>>> USE_BRAINS* >>>> USE_ConvertBetweenFileFormats >>>> USE_DWIConvert >>>> USE_DebugImageViewer >>>> USE_GTRACT >>>> USE_ICCDEF >>>> USE_ImageCalculator >>>> USE_ReferenceAtlas >>>> >>>> ------- >>>> >>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>> which means a DLL was not found. I then realized that I have different >>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>> prompted me to look more carefully at the PATH environment variable. I just >>>> tested with all the new paths at the start of the PATH string, and Slicer >>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>> attempt to load a 4 GB tiff. >>>> >>>> I am now wondering (belatedly!) about the way I tried to build with big >>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>> for directions before doing this - now I'm wondering if that switch actually >>>> had any effect. Is that the right thing to do, and if not, what is? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Yes, well, don't say I didn't warn you! ; ) >>>> >>>> You do need loadable modules and you probably do want python (a lot of >>>> core stuff is in python, like the editor). >>>> >>>> BRAINSTools should be off for now, since it needs ITKv3. >>>> >>>> I'm not sure either what to do next, but I suggest maybe trying the >>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>> it exited. But that may be a longshot. >>>> >>>> -Steve >>>> >>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>> wrote: >>>>> >>>>> Hi Steve, >>>>> >>>>> That was an interesting exercise. I managed to build Slicer without >>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>> built it again, this time selecting most things except BRAINTools. The >>>>> build took a long time, partly because I turned on the Python option, which >>>>> I don't need. This time there were no errors, except for a couple of >>>>> occasions where the attempt to create a directory failed - this was because >>>>> the directory already existed, and was easily solved by deleting the >>>>> directory and building again. I installed everything that wanted to be >>>>> installed, and modified the environment variables to suit. >>>>> >>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>> knowing what it is). >>>>> >>>>> I sense that I must be close to getting it working, but I'm not sure >>>>> what to do next. >>>>> >>>>> Cheers >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hi Gib - >>>>> >>>>> A lot of the building goes on in parallel so you need to review the >>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>> window and then paste it into a text editor to look for issues. Definitely >>>>> you don't want to be editing any of the visual studio files, since they are >>>>> generated by cmake every configure -- much better to sort out what is going >>>>> on at the cmake flag level. >>>>> >>>>> Best, >>>>> Steve >>>>> >>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>> Additional Dependencies: >>>>>> >>>>>> ... >>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>> ITKCommon.lib >>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>> ... >>>>>> >>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>> 40+ times. >>>>>> >>>>>> Thanks again >>>>>> Gib >>>>>> ________________________________ >>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>> [g.bogle at auckland.ac.nz] >>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>> >>>>>> To: Steve Pieper >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>> >>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>> >>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>> link the ITK library that was just built, i.e.: >>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>> This is the first of about 40 such link errors. >>>>>> >>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>> ITK_DIR appropriately? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>> trickiest platform in my experience. >>>>>> >>>>>> -Steve >>>>>> >>>>>> >>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Gib Bogle >>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Jean-Christophe, >>>>>>> >>>>>>> Any idea when 4.5 will enter the world? >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Folks, >>>>>>> >>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>> >>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>> these module. All details are captured here: >>>>>>> >>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>> >>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>> planned for 4.5. >>>>>>> >>>>>>> Thanks >>>>>>> Jc >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Matt - >>>>>>>> >>>>>>>> Thanks, that's helpful. >>>>>>>> >>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>> straightforward. >>>>>>>> >>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Here is what the process would look like: >>>>>>>>> >>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>> the >>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>> (minor modifications to the API, etc). >>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>> 5) Profit. >>>>>>>>> >>>>>>>>> HTH, >>>>>>>>> Matt >>>>>>>>> >>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>> >>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>> >>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>> > but it's >>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>> > >>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>> > what is >>>>>>>>> > involved? >>>>>>>>> > >>>>>>>>> > -Steve >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>> > wrote: >>>>>>>>> >> >>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>> >> large >>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>> >> capability >>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>> >> ________________________________ >>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>> >> >>>>>>>>> >> To: Gib Bogle >>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >> >>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>> >> configure >>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>> >> like vtkITK >>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>> >> experts are >>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>> >> >>>>>>>>> >> -Steve >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>> >> wrote: >>>>>>>>> >>> >>>>>>>>> >>> I await the results with interest... >>>>>>>>> >>> ________________________________ >>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>> >>> Pieper >>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>> >>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>> >>> a lot of >>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>> >>> >>>>>>>>> >>> -Steve >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>> >>> >>>>>>>>> >>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Steve, >>>>>>>>> >>>> >>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>> >>>> configured in >>>>>>>>> >>>> Slicer. >>>>>>>>> >>>> >>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>> >>>> needs to >>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>> >>>> be used. I have >>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>> >>>> one wanted to >>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>> >>>> >>>>>>>>> >>>> Brad >>>>>>>>> >>>> >>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>> >>>> wrote: >>>>>>>>> >>>> >>>>>>>>> >>>> Hi Brad - >>>>>>>>> >>>> >>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>> >>>> able to >>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>> >>>> with ITK's NRRD >>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>> >>>> default options >>>>>>>>> >>>> on win7 64bit. >>>>>>>>> >>>> >>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>> >>>> something nobody >>>>>>>>> >>>> has tried? >>>>>>>>> >>>> >>>>>>>>> >>>> -Steve >>>>>>>>> >>>> >>>>>>>>> >>>> >>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>> >>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> Steve, >>>>>>>>> >>>>> >>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>> >>>>> windows 64? >>>>>>>>> >>>>> >>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>> >>>>> specific. >>>>>>>>> >>>>> >>>>>>>>> >>>>> Bread >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>> >>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>> >>>>> >>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>> >>>>> pasted in >>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>> >>>>> >>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>> >>>>> >>>>>>>>> >>>>> -Steve >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>> >>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>> >>>>>> still >>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Brad >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>> >>>>>> replicate the >>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> wrote: >>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>> >>>>>>> > back to this >>>>>>>>> >>>>>>> > later. >>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>> >>>>>>> > to >>>>>>>>> >>>>>>> > generate a big >>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>> >>>>>>> > for any >>>>>>>>> >>>>>>> > standard >>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > wrote: >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>> >>>>>>> >> a >>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>> >>>>>>> >> without >>>>>>>>> >>>>>>> >> problems. >>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Hi - >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>> >>>>>>> >> for example >>>>>>>>> >>>>>>> >> with a >>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>> >>>>>>> >> transfer a >>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> -Steve >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>> >>>>>>> >>> I can load >>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>> >>>>>>> >>> exception >>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>> >>>>>>> >>> this size >>>>>>>>> >>>>>>> >>> is the >>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>> >>>>>>> >>> I see the >>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>> >>>>>>> >>> out. >>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>> >>>>>>> >>> on the >>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>> >>>>>>> >>> installed >>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>> >>>>>>> >>> good but >>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>> >>>>>>> >>> different >>>>>>>>> >>>>>>> >>> build >>>>>>>>> >>>>>>> >>> options? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> associated >>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>> >>>>>>> >>> please >>>>>>>>> >>>>>>> >>> provide more >>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Brad >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>> >>>>>>> >>> not >>>>>>>>> >>>>>>> >>> handle >>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>> >>>>>>> >>> Gib >>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>> >>>>>>> >>> the >>>>>>>>> >>>>>>> >>> subject >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> >>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>>> >>> person to >>>>>>>>> >>>>>>> >>> whom it >>>>>>>>> >>>>>>> >>> is >>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>> >>>>>>> >>> in error >>>>>>>>> >>>>>>> >>> and the >>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>> >>>>>>> >>> Partners >>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If you believe this e-mail was sent to you in >>>>>>>>> >>>>>>> > error and >>>>>>>>> >>>>>>> > the >>>>>>>>> >>>>>>> > e-mail >>>>>>>>> >>>>>>> > contains patient information, please contact the Partners >>>>>>>>> >>>>>>> > Compliance >>>>>>>>> >>>>>>> > HelpLine at >>>>>>>>> >>>>>>> > http://www.partners.org/complianceline . If the e-mail >>>>>>>>> >>>>>>> > was sent to >>>>>>>>> >>>>>>> > you in >>>>>>>>> >>>>>>> > error >>>>>>>>> >>>>>>> > but does not contain patient information, please contact >>>>>>>>> >>>>>>> > the sender >>>>>>>>> >>>>>>> > and >>>>>>>>> >>>>>>> > properly >>>>>>>>> >>>>>>> > dispose of the e-mail. >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> _______________________________________________ >>>>>>>>> >>>>>> slicer-devel mailing list >>>>>>>>> >>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> >>>>>> To unsubscribe: send email to >>>>>>>>> >>>>>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>> >>>>>> unsubscribe as the >>>>>>>>> >>>>>> subject >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> The information in this e-mail is intended only for the >>>>>>>>> >>>>>> person to whom >>>>>>>>> >>>>>> it is >>>>>>>>> >>>>>> addressed. 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If the e-mail was >>>>>>>>> >>>>>> sent to you >>>>>>>>> >>>>>> in error >>>>>>>>> >>>>>> but does not contain patient information, please contact the >>>>>>>>> >>>>>> sender >>>>>>>>> >>>>>> and properly >>>>>>>>> >>>>>> dispose of the e-mail. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>> >>>>>>>>> >>>> >>>>>>>>> >>> >>>>>>>>> >> >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > _______________________________________________ >>>>>>>>> > slicer-devel mailing list >>>>>>>>> > slicer-devel at bwh.harvard.edu >>>>>>>>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> > To unsubscribe: send email to >>>>>>>>> > slicer-devel-request at massmail.spl.harvard.edu >>>>>>>>> > with unsubscribe as the subject >>>>>>>>> > >>>>>>>>> > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > The information in this e-mail is intended only for the person to >>>>>>>>> > whom it is >>>>>>>>> > addressed. If you believe this e-mail was sent to you in error >>>>>>>>> > and the >>>>>>>>> > e-mail >>>>>>>>> > contains patient information, please contact the Partners >>>>>>>>> > Compliance >>>>>>>>> > HelpLine at >>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent >>>>>>>>> > to you in >>>>>>>>> > error >>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>> > sender and >>>>>>>>> > properly >>>>>>>>> > dispose of the e-mail. >>>>>>>>> > >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> slicer-devel mailing list >>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>> To unsubscribe: send email to >>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>> subject >>>>>>>> >>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>> whom it is >>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>> the e-mail >>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>> HelpLine at >>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>> you in error >>>>>>>> but does not contain patient information, please contact the sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> +1 919 869 8849 >>>>>> >>>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to >>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>> subject >>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >> >> -- >> +1 919 869 8849 > > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu > with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > From matt.mccormick at kitware.com Wed Sep 17 13:05:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 13:05:56 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Great to hear! On Wed, Sep 17, 2014 at 12:04 PM, Gib Bogle wrote: > I forgot to mention that ITK builds correctly, and my test program that uses it to create big tiffs now works fine. > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 3:55 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > > Hi Gib, > > Getting the builds states to propagate and follow how the get set can > be tricky. A few pointers on where to look for the status: > > 1) CMakeCache.txt (this file contains the build settings that CMake > recognized from your input when you run CMake) > 2) ITKConfig.cmake (this file will exist in the build tree or the > install tree, and it contains CMake varables that may be used by other > projects building against ITK) > 3) itkConfigure.h (this is a header that has configured preprocessor > definitions used when building) > > HTH, > Matt > > > > On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >> Hi Bradley, Matt and Steve, >> >> Now for the embarrassing confession. In External_ITK4.cmake I turned >> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >> finally checked what the code that is being built was using (with #if >> defined ...) I discovered that both ITKV3_COMPATIBILITY and >> ITK_USE_64BITS_IDS were off. How can this be? >> >> It's easy, all it takes is a typo: >> -DITK_USE_64_BITS_IDS:BOOL=ON >> That typo has cost me a couple of days, and caused annoyance to a few >> people, I suspect. >> >> Unfortunately... now Slicer's vtkITK does not build. There are very many >> errors like this: >> >> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >> 3>Build started 17/09/2014 7:25:52 p.m.. >> 3>InitializeBuildStatus: >> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >> 3>CustomBuild: >> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >> 3> CMake does not need to re-run because >> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >> 3>ClCompile: >> 3> vtkITKNumericTraits.cxx >> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesReader.cxx >> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >> 3> vtkITKImageWriter.cxx >> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >> 3> vtkITKDistanceTransform.cxx >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >> error C2679: binary '=' : no operator found which takes a right-hand operand >> of type 'itk::ImportImageContainer *' (or there >> is no acceptable conversion) >> 3> with >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >> could be 'itk::SmartPointer >> &itk::SmartPointer::operator =(const >> itk::SmartPointer &)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >> or 'itk::SmartPointer >> &itk::SmartPointer::operator >> =(itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer, >> 3> TElementIdentifier=unsigned long, >> 3> TElement=double >> 3> ] >> 3> while trying to match the argument list >> '(itk::SmartPointer, >> itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> and >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> >> I presume these are related to the use of 64-bit integers. >> >> Over to you guys :) >> >> Gib >> ________________________________ >> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >> Sent: Tuesday, 16 September 2014 12:45 a.m. >> To: Steve Pieper >> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hello, >> >> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >> >> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >> read and write files like these there. More information about getting >> started is here[1]. >> >> You should be a able to generate a image with: >> >> import SimpleITK as sitk >> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >> img += 10 >> stats = sitk.StatisticsImageFilter() >> stats.Execute(img) >> print stats >> >> This should give you basic access to ITK in python to interactively >> experiment with options with these large images. I have been able to load >> large images with the binaries of SimpleITK on windows 64-bits. I don't know >> if I have tried big tiff though. >> >> A simular test could be done with C++ and ITK directly, but I think >> SimpleITK in python may be quicker for experimentation. >> >> Brad >> >> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >> [2] >> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >> >> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >> >> Hi Gib - >> >> Are you testing only on windows? What we would often try to do for this >> kind of debugging is to create a small example that other people can test on >> their configurations. Slicer has a mechanism called a Self Test [1] to >> allow easy replication and debugging across multiple platforms. It's ideal >> if we can hone it down to something like what is described as a 'sscce' [2]. >> The self tests will typically download some data from a public web site, run >> some operations, and then print something out saying if it passed or failed >> (or it may crash). Since it's possible to make a small data file that >> expands into a giant tiff image it should be pretty tractable to pose this >> issue in the form of a self test. >> >> Best, >> Steve >> >> >> [1] >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >> >> [2] http://sscce.org/ >> >> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>> >>> Hi J-C, >>> >>> Some more info about Slicer with big tiff files. >>> >>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>> 72) >>> >>> All suggestions will be gratefully received. >>> >>> Cheers >>> Gib >>> ________________________________ >>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>> Sent: Sunday, 14 September 2014 8:32 p.m. >>> To: Gib Bogle >>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hi Gib, >>> >>> What do you mean by "reinstalled" ? You should not have to install Slicer >>> to be able to execute it from the build directory. >>> >>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>> out. >>> >>> When done building, make sure to start the Slicer launcher: >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>> >>> and not the Slicer executable: >>> >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>> >>> >>> By using the launcher, you ensure that the PATH are properly setup and the >>> expected libraries are loaded. >>> >>> >>> Hth >>> Jc >>> >>> >>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>> wrote: >>>> >>>> I hope I understand correctly. I added the line as shown to >>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>> ... >>>> # ZLIB >>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>> # Big TIFF >>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>> ... >>>> >>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>> crashes with the big tiff. Is there somewhere I can check in the project >>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>> effect? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hey Gib - >>>> >>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>> ITK build process [1] during the superbuild. I don't think much else was >>>> required except turning off the IKTv3 parts. >>>> >>>> [1] >>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>> >>>> -Steve >>>> >>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>> it on TV). So the Jo'berg game should be a great rematch! >>>> >>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>> wrote: >>>>> >>>>> You did warn me. >>>>> >>>>> Here is the list of options not ticked: >>>>> >>>>> Slicer_BUILD_BRAINSTOOLS >>>>> _LEGACY_CLI >>>>> _LandmarkRegistration >>>>> _TESTING_EXTENSIONS >>>>> _UPDATE_TRANSLATION >>>>> _USE_GIT_PROTOCOL >>>>> _OpenIGTLink >>>>> _PYTHONQT_WITH_OPENSSL >>>>> _PYTHONQT_WITH_TCL >>>>> _QtTesting >>>>> _SimpleITK >>>>> _VTK_DEBUG_LINKS >>>>> Slicer_WITH_LIBRARY_VERSION >>>>> >>>>> USE_BRAINS* >>>>> USE_ConvertBetweenFileFormats >>>>> USE_DWIConvert >>>>> USE_DebugImageViewer >>>>> USE_GTRACT >>>>> USE_ICCDEF >>>>> USE_ImageCalculator >>>>> USE_ReferenceAtlas >>>>> >>>>> ------- >>>>> >>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>> which means a DLL was not found. I then realized that I have different >>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>> attempt to load a 4 GB tiff. >>>>> >>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>> for directions before doing this - now I'm wondering if that switch actually >>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Yes, well, don't say I didn't warn you! ; ) >>>>> >>>>> You do need loadable modules and you probably do want python (a lot of >>>>> core stuff is in python, like the editor). >>>>> >>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>> >>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>> it exited. But that may be a longshot. >>>>> >>>>> -Steve >>>>> >>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>> build took a long time, partly because I turned on the Python option, which >>>>>> I don't need. This time there were no errors, except for a couple of >>>>>> occasions where the attempt to create a directory failed - this was because >>>>>> the directory already existed, and was easily solved by deleting the >>>>>> directory and building again. I installed everything that wanted to be >>>>>> installed, and modified the environment variables to suit. >>>>>> >>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>> knowing what it is). >>>>>> >>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>> what to do next. >>>>>> >>>>>> Cheers >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> A lot of the building goes on in parallel so you need to review the >>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>> on at the cmake flag level. >>>>>> >>>>>> Best, >>>>>> Steve >>>>>> >>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>> Additional Dependencies: >>>>>>> >>>>>>> ... >>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>> ITKCommon.lib >>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>> ... >>>>>>> >>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>> 40+ times. >>>>>>> >>>>>>> Thanks again >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>> [g.bogle at auckland.ac.nz] >>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>> >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>> >>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>> >>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>> link the ITK library that was just built, i.e.: >>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>> This is the first of about 40 such link errors. >>>>>>> >>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>> ITK_DIR appropriately? >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>> trickiest platform in my experience. >>>>>>> >>>>>>> -Steve >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Gib Bogle >>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Jean-Christophe, >>>>>>>> >>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>> >>>>>>>> Cheers >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Folks, >>>>>>>> >>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>> >>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>> these module. All details are captured here: >>>>>>>> >>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>> >>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>> planned for 4.5. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Jc >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Matt - >>>>>>>>> >>>>>>>>> Thanks, that's helpful. >>>>>>>>> >>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>> straightforward. >>>>>>>>> >>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>> >>>>>>>>> -Steve >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Here is what the process would look like: >>>>>>>>>> >>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>> the >>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>> 5) Profit. >>>>>>>>>> >>>>>>>>>> HTH, >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>> >>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>> >>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>> wrote: >>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>> > but it's >>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>> > >>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>> > what is >>>>>>>>>> > involved? >>>>>>>>>> > >>>>>>>>>> > -Steve >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>> > wrote: >>>>>>>>>> >> >>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>> >> large >>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>> >> capability >>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>> >> ________________________________ >>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>> >> >>>>>>>>>> >> To: Gib Bogle >>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >> >>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>> >> configure >>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>> >> like vtkITK >>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>> >> experts are >>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>> >> >>>>>>>>>> >> -Steve >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>> >> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> I await the results with interest... >>>>>>>>>> >>> ________________________________ >>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>> >>> Pieper >>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>> >>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>> >>> a lot of >>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>> >>> >>>>>>>>>> >>> -Steve >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Steve, >>>>>>>>>> >>>> >>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>> >>>> configured in >>>>>>>>>> >>>> Slicer. >>>>>>>>>> >>>> >>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>> >>>> needs to >>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>> >>>> be used. I have >>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>> >>>> one wanted to >>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>> >>>> >>>>>>>>>> >>>> Brad >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Hi Brad - >>>>>>>>>> >>>> >>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>> >>>> able to >>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>> >>>> default options >>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>> >>>> >>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>> >>>> something nobody >>>>>>>>>> >>>> has tried? >>>>>>>>>> >>>> >>>>>>>>>> >>>> -Steve >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Steve, >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>> >>>>> windows 64? >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>> >>>>> specific. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Bread >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>> >>>>> pasted in >>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> -Steve >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>> >>>>>> still >>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Brad >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>> >>>>>> replicate the >>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> wrote: >>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>> >>>>>>> > back to this >>>>>>>>>> >>>>>>> > later. >>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>> >>>>>>> > to >>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>> >>>>>>> > for any >>>>>>>>>> >>>>>>> > standard >>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>> >>>>>>> >> a >>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>> >>>>>>> >> without >>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>> >>>>>>> >> for example >>>>>>>>>> >>>>>>> >> with a >>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>> >>>>>>> >>> different >>>>>>>>>> >>>>>>> >>> build >>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>> >>>>>>> >>> please >>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>> >>>>>>> >>> not >>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>> >>>>>>> >>> the >>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>> >>>>>>> >>> is >>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If the e-mail was sent >>>>>>>>>> > to you in >>>>>>>>>> > error >>>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>>> > sender and >>>>>>>>>> > properly >>>>>>>>>> > dispose of the e-mail. >>>>>>>>>> > >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> slicer-devel mailing list >>>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> To unsubscribe: send email to >>>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>>> subject >>>>>>>>> >>>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>> whom it is >>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>> the e-mail >>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>> HelpLine at >>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> +1 919 869 8849 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> slicer-devel mailing list >>>> slicer-devel at bwh.harvard.edu >>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>> To unsubscribe: send email to >>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>> subject >>>> >>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >>> >>> -- >>> +1 919 869 8849 >> >> >> _______________________________________________ >> slicer-devel mailing list >> slicer-devel at bwh.harvard.edu >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >> with unsubscribe as the subject >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> From matt.mccormick at kitware.com Wed Sep 17 13:06:49 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 13:06:49 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) Is this with the latest version of Slicer? My line 179 says vtkITKExecuteDataFromFile(VTK_DOUBLE, double); Thanks, Matt On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: > Hi Matt, > I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? > thanks > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 3:55 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > > Hi Gib, > > Getting the builds states to propagate and follow how the get set can > be tricky. A few pointers on where to look for the status: > > 1) CMakeCache.txt (this file contains the build settings that CMake > recognized from your input when you run CMake) > 2) ITKConfig.cmake (this file will exist in the build tree or the > install tree, and it contains CMake varables that may be used by other > projects building against ITK) > 3) itkConfigure.h (this is a header that has configured preprocessor > definitions used when building) > > HTH, > Matt > > > > On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >> Hi Bradley, Matt and Steve, >> >> Now for the embarrassing confession. In External_ITK4.cmake I turned >> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >> finally checked what the code that is being built was using (with #if >> defined ...) I discovered that both ITKV3_COMPATIBILITY and >> ITK_USE_64BITS_IDS were off. How can this be? >> >> It's easy, all it takes is a typo: >> -DITK_USE_64_BITS_IDS:BOOL=ON >> That typo has cost me a couple of days, and caused annoyance to a few >> people, I suspect. >> >> Unfortunately... now Slicer's vtkITK does not build. There are very many >> errors like this: >> >> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >> 3>Build started 17/09/2014 7:25:52 p.m.. >> 3>InitializeBuildStatus: >> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >> 3>CustomBuild: >> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >> 3> CMake does not need to re-run because >> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >> 3>ClCompile: >> 3> vtkITKNumericTraits.cxx >> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesReader.cxx >> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >> 3> vtkITKImageWriter.cxx >> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >> 3> vtkITKDistanceTransform.cxx >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >> error C2679: binary '=' : no operator found which takes a right-hand operand >> of type 'itk::ImportImageContainer *' (or there >> is no acceptable conversion) >> 3> with >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >> could be 'itk::SmartPointer >> &itk::SmartPointer::operator =(const >> itk::SmartPointer &)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >> or 'itk::SmartPointer >> &itk::SmartPointer::operator >> =(itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer, >> 3> TElementIdentifier=unsigned long, >> 3> TElement=double >> 3> ] >> 3> while trying to match the argument list >> '(itk::SmartPointer, >> itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> and >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> >> I presume these are related to the use of 64-bit integers. >> >> Over to you guys :) >> >> Gib >> ________________________________ >> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >> Sent: Tuesday, 16 September 2014 12:45 a.m. >> To: Steve Pieper >> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hello, >> >> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >> >> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >> read and write files like these there. More information about getting >> started is here[1]. >> >> You should be a able to generate a image with: >> >> import SimpleITK as sitk >> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >> img += 10 >> stats = sitk.StatisticsImageFilter() >> stats.Execute(img) >> print stats >> >> This should give you basic access to ITK in python to interactively >> experiment with options with these large images. I have been able to load >> large images with the binaries of SimpleITK on windows 64-bits. I don't know >> if I have tried big tiff though. >> >> A simular test could be done with C++ and ITK directly, but I think >> SimpleITK in python may be quicker for experimentation. >> >> Brad >> >> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >> [2] >> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >> >> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >> >> Hi Gib - >> >> Are you testing only on windows? What we would often try to do for this >> kind of debugging is to create a small example that other people can test on >> their configurations. Slicer has a mechanism called a Self Test [1] to >> allow easy replication and debugging across multiple platforms. It's ideal >> if we can hone it down to something like what is described as a 'sscce' [2]. >> The self tests will typically download some data from a public web site, run >> some operations, and then print something out saying if it passed or failed >> (or it may crash). Since it's possible to make a small data file that >> expands into a giant tiff image it should be pretty tractable to pose this >> issue in the form of a self test. >> >> Best, >> Steve >> >> >> [1] >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >> >> [2] http://sscce.org/ >> >> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>> >>> Hi J-C, >>> >>> Some more info about Slicer with big tiff files. >>> >>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>> 72) >>> >>> All suggestions will be gratefully received. >>> >>> Cheers >>> Gib >>> ________________________________ >>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>> Sent: Sunday, 14 September 2014 8:32 p.m. >>> To: Gib Bogle >>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hi Gib, >>> >>> What do you mean by "reinstalled" ? You should not have to install Slicer >>> to be able to execute it from the build directory. >>> >>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>> out. >>> >>> When done building, make sure to start the Slicer launcher: >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>> >>> and not the Slicer executable: >>> >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>> >>> >>> By using the launcher, you ensure that the PATH are properly setup and the >>> expected libraries are loaded. >>> >>> >>> Hth >>> Jc >>> >>> >>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>> wrote: >>>> >>>> I hope I understand correctly. I added the line as shown to >>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>> ... >>>> # ZLIB >>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>> # Big TIFF >>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>> ... >>>> >>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>> crashes with the big tiff. Is there somewhere I can check in the project >>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>> effect? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hey Gib - >>>> >>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>> ITK build process [1] during the superbuild. I don't think much else was >>>> required except turning off the IKTv3 parts. >>>> >>>> [1] >>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>> >>>> -Steve >>>> >>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>> it on TV). So the Jo'berg game should be a great rematch! >>>> >>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>> wrote: >>>>> >>>>> You did warn me. >>>>> >>>>> Here is the list of options not ticked: >>>>> >>>>> Slicer_BUILD_BRAINSTOOLS >>>>> _LEGACY_CLI >>>>> _LandmarkRegistration >>>>> _TESTING_EXTENSIONS >>>>> _UPDATE_TRANSLATION >>>>> _USE_GIT_PROTOCOL >>>>> _OpenIGTLink >>>>> _PYTHONQT_WITH_OPENSSL >>>>> _PYTHONQT_WITH_TCL >>>>> _QtTesting >>>>> _SimpleITK >>>>> _VTK_DEBUG_LINKS >>>>> Slicer_WITH_LIBRARY_VERSION >>>>> >>>>> USE_BRAINS* >>>>> USE_ConvertBetweenFileFormats >>>>> USE_DWIConvert >>>>> USE_DebugImageViewer >>>>> USE_GTRACT >>>>> USE_ICCDEF >>>>> USE_ImageCalculator >>>>> USE_ReferenceAtlas >>>>> >>>>> ------- >>>>> >>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>> which means a DLL was not found. I then realized that I have different >>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>> attempt to load a 4 GB tiff. >>>>> >>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>> for directions before doing this - now I'm wondering if that switch actually >>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Yes, well, don't say I didn't warn you! ; ) >>>>> >>>>> You do need loadable modules and you probably do want python (a lot of >>>>> core stuff is in python, like the editor). >>>>> >>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>> >>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>> it exited. But that may be a longshot. >>>>> >>>>> -Steve >>>>> >>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>> build took a long time, partly because I turned on the Python option, which >>>>>> I don't need. This time there were no errors, except for a couple of >>>>>> occasions where the attempt to create a directory failed - this was because >>>>>> the directory already existed, and was easily solved by deleting the >>>>>> directory and building again. I installed everything that wanted to be >>>>>> installed, and modified the environment variables to suit. >>>>>> >>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>> knowing what it is). >>>>>> >>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>> what to do next. >>>>>> >>>>>> Cheers >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> A lot of the building goes on in parallel so you need to review the >>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>> on at the cmake flag level. >>>>>> >>>>>> Best, >>>>>> Steve >>>>>> >>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>> Additional Dependencies: >>>>>>> >>>>>>> ... >>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>> ITKCommon.lib >>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>> ... >>>>>>> >>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>> 40+ times. >>>>>>> >>>>>>> Thanks again >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>> [g.bogle at auckland.ac.nz] >>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>> >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>> >>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>> >>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>> link the ITK library that was just built, i.e.: >>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>> This is the first of about 40 such link errors. >>>>>>> >>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>> ITK_DIR appropriately? >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>> trickiest platform in my experience. >>>>>>> >>>>>>> -Steve >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Gib Bogle >>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Jean-Christophe, >>>>>>>> >>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>> >>>>>>>> Cheers >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Folks, >>>>>>>> >>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>> >>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>> these module. All details are captured here: >>>>>>>> >>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>> >>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>> planned for 4.5. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Jc >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Matt - >>>>>>>>> >>>>>>>>> Thanks, that's helpful. >>>>>>>>> >>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>> straightforward. >>>>>>>>> >>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>> >>>>>>>>> -Steve >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Here is what the process would look like: >>>>>>>>>> >>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>> the >>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>> 5) Profit. >>>>>>>>>> >>>>>>>>>> HTH, >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>> >>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>> >>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>> wrote: >>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>> > but it's >>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>> > >>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>> > what is >>>>>>>>>> > involved? >>>>>>>>>> > >>>>>>>>>> > -Steve >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>> > wrote: >>>>>>>>>> >> >>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>> >> large >>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>> >> capability >>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>> >> ________________________________ >>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>> >> >>>>>>>>>> >> To: Gib Bogle >>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >> >>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>> >> configure >>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>> >> like vtkITK >>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>> >> experts are >>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>> >> >>>>>>>>>> >> -Steve >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>> >> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> I await the results with interest... >>>>>>>>>> >>> ________________________________ >>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>> >>> Pieper >>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>> >>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>> >>> a lot of >>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>> >>> >>>>>>>>>> >>> -Steve >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Steve, >>>>>>>>>> >>>> >>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>> >>>> configured in >>>>>>>>>> >>>> Slicer. >>>>>>>>>> >>>> >>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>> >>>> needs to >>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>> >>>> be used. I have >>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>> >>>> one wanted to >>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>> >>>> >>>>>>>>>> >>>> Brad >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Hi Brad - >>>>>>>>>> >>>> >>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>> >>>> able to >>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>> >>>> default options >>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>> >>>> >>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>> >>>> something nobody >>>>>>>>>> >>>> has tried? >>>>>>>>>> >>>> >>>>>>>>>> >>>> -Steve >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Steve, >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>> >>>>> windows 64? >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>> >>>>> specific. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Bread >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>> >>>>> pasted in >>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> -Steve >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>> >>>>>> still >>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Brad >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>> >>>>>> replicate the >>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> wrote: >>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>> >>>>>>> > back to this >>>>>>>>>> >>>>>>> > later. >>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>> >>>>>>> > to >>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>> >>>>>>> > for any >>>>>>>>>> >>>>>>> > standard >>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>> >>>>>>> >> a >>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>> >>>>>>> >> without >>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>> >>>>>>> >> for example >>>>>>>>>> >>>>>>> >> with a >>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>> >>>>>>> >>> different >>>>>>>>>> >>>>>>> >>> build >>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>> >>>>>>> >>> please >>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>> >>>>>>> >>> not >>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>> >>>>>>> >>> the >>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>> >>>>>>> >>> is >>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> +1 919 869 8849 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> slicer-devel mailing list >>>> slicer-devel at bwh.harvard.edu >>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>> To unsubscribe: send email to >>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>> subject >>>> >>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >>>> is >>>> addressed. 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If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> From matt.mccormick at kitware.com Wed Sep 17 16:16:27 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 16:16:27 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: Message-ID: On Wed, Sep 17, 2014 at 11:13 AM, Matt McCormick wrote: > There are a couple of upcoming opportunities to share, discuss, design, and > learn with your fellow ITK community members. > > > On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a > Google+ Hangout > where we will be doing code reviews: > > https://plus.google.com/events/cg0n52cqd08ulpr6o9jgku32gj0?authkey=CJ-S7tP5s5_xAw > Due to a conflict, this had to be changed to 1:00 PM Eastern USA time. Sorry for schedule variation. Matt From g.bogle at auckland.ac.nz Wed Sep 17 16:32:32 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 20:32:32 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. I appreciate your attention to it very much! Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 5:06 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF > 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) Is this with the latest version of Slicer? My line 179 says vtkITKExecuteDataFromFile(VTK_DOUBLE, double); Thanks, Matt On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: > Hi Matt, > I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? > thanks > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 3:55 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > > Hi Gib, > > Getting the builds states to propagate and follow how the get set can > be tricky. A few pointers on where to look for the status: > > 1) CMakeCache.txt (this file contains the build settings that CMake > recognized from your input when you run CMake) > 2) ITKConfig.cmake (this file will exist in the build tree or the > install tree, and it contains CMake varables that may be used by other > projects building against ITK) > 3) itkConfigure.h (this is a header that has configured preprocessor > definitions used when building) > > HTH, > Matt > > > > On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >> Hi Bradley, Matt and Steve, >> >> Now for the embarrassing confession. In External_ITK4.cmake I turned >> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >> finally checked what the code that is being built was using (with #if >> defined ...) I discovered that both ITKV3_COMPATIBILITY and >> ITK_USE_64BITS_IDS were off. How can this be? >> >> It's easy, all it takes is a typo: >> -DITK_USE_64_BITS_IDS:BOOL=ON >> That typo has cost me a couple of days, and caused annoyance to a few >> people, I suspect. >> >> Unfortunately... now Slicer's vtkITK does not build. There are very many >> errors like this: >> >> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >> 3>Build started 17/09/2014 7:25:52 p.m.. >> 3>InitializeBuildStatus: >> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >> 3>CustomBuild: >> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >> 3> CMake does not need to re-run because >> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >> 3>ClCompile: >> 3> vtkITKNumericTraits.cxx >> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesReader.cxx >> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >> 3> vtkITKImageWriter.cxx >> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >> 3> vtkITKDistanceTransform.cxx >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >> error C2679: binary '=' : no operator found which takes a right-hand operand >> of type 'itk::ImportImageContainer *' (or there >> is no acceptable conversion) >> 3> with >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >> could be 'itk::SmartPointer >> &itk::SmartPointer::operator =(const >> itk::SmartPointer &)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >> or 'itk::SmartPointer >> &itk::SmartPointer::operator >> =(itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer, >> 3> TElementIdentifier=unsigned long, >> 3> TElement=double >> 3> ] >> 3> while trying to match the argument list >> '(itk::SmartPointer, >> itk::ImportImageContainer *)' >> 3> with >> 3> [ >> 3> TObjectType=itk::ImportImageContainer >> 3> ] >> 3> and >> 3> [ >> 3> TElementIdentifier=unsigned __int64, >> 3> TElement=double >> 3> ] >> >> I presume these are related to the use of 64-bit integers. >> >> Over to you guys :) >> >> Gib >> ________________________________ >> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >> Sent: Tuesday, 16 September 2014 12:45 a.m. >> To: Steve Pieper >> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >> Subject: Re: [slicer-devel] BigTIFF >> >> Hello, >> >> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >> >> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >> read and write files like these there. More information about getting >> started is here[1]. >> >> You should be a able to generate a image with: >> >> import SimpleITK as sitk >> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >> img += 10 >> stats = sitk.StatisticsImageFilter() >> stats.Execute(img) >> print stats >> >> This should give you basic access to ITK in python to interactively >> experiment with options with these large images. I have been able to load >> large images with the binaries of SimpleITK on windows 64-bits. I don't know >> if I have tried big tiff though. >> >> A simular test could be done with C++ and ITK directly, but I think >> SimpleITK in python may be quicker for experimentation. >> >> Brad >> >> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >> [2] >> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >> >> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >> >> Hi Gib - >> >> Are you testing only on windows? What we would often try to do for this >> kind of debugging is to create a small example that other people can test on >> their configurations. Slicer has a mechanism called a Self Test [1] to >> allow easy replication and debugging across multiple platforms. It's ideal >> if we can hone it down to something like what is described as a 'sscce' [2]. >> The self tests will typically download some data from a public web site, run >> some operations, and then print something out saying if it passed or failed >> (or it may crash). Since it's possible to make a small data file that >> expands into a giant tiff image it should be pretty tractable to pose this >> issue in the form of a self test. >> >> Best, >> Steve >> >> >> [1] >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >> >> [2] http://sscce.org/ >> >> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>> >>> Hi J-C, >>> >>> Some more info about Slicer with big tiff files. >>> >>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>> 72) >>> >>> All suggestions will be gratefully received. >>> >>> Cheers >>> Gib >>> ________________________________ >>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>> Sent: Sunday, 14 September 2014 8:32 p.m. >>> To: Gib Bogle >>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hi Gib, >>> >>> What do you mean by "reinstalled" ? You should not have to install Slicer >>> to be able to execute it from the build directory. >>> >>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>> out. >>> >>> When done building, make sure to start the Slicer launcher: >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>> >>> and not the Slicer executable: >>> >>> >>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>> >>> >>> By using the launcher, you ensure that the PATH are properly setup and the >>> expected libraries are loaded. >>> >>> >>> Hth >>> Jc >>> >>> >>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>> wrote: >>>> >>>> I hope I understand correctly. I added the line as shown to >>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>> ... >>>> # ZLIB >>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>> # Big TIFF >>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>> ... >>>> >>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>> crashes with the big tiff. Is there somewhere I can check in the project >>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>> effect? >>>> >>>> Thanks >>>> Gib >>>> ________________________________ >>>> From: Steve Pieper [pieper at isomics.com] >>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>> >>>> To: Gib Bogle >>>> Cc: slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hey Gib - >>>> >>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>> ITK build process [1] during the superbuild. I don't think much else was >>>> required except turning off the IKTv3 parts. >>>> >>>> [1] >>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>> >>>> -Steve >>>> >>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>> it on TV). So the Jo'berg game should be a great rematch! >>>> >>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>> wrote: >>>>> >>>>> You did warn me. >>>>> >>>>> Here is the list of options not ticked: >>>>> >>>>> Slicer_BUILD_BRAINSTOOLS >>>>> _LEGACY_CLI >>>>> _LandmarkRegistration >>>>> _TESTING_EXTENSIONS >>>>> _UPDATE_TRANSLATION >>>>> _USE_GIT_PROTOCOL >>>>> _OpenIGTLink >>>>> _PYTHONQT_WITH_OPENSSL >>>>> _PYTHONQT_WITH_TCL >>>>> _QtTesting >>>>> _SimpleITK >>>>> _VTK_DEBUG_LINKS >>>>> Slicer_WITH_LIBRARY_VERSION >>>>> >>>>> USE_BRAINS* >>>>> USE_ConvertBetweenFileFormats >>>>> USE_DWIConvert >>>>> USE_DebugImageViewer >>>>> USE_GTRACT >>>>> USE_ICCDEF >>>>> USE_ImageCalculator >>>>> USE_ReferenceAtlas >>>>> >>>>> ------- >>>>> >>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>> which means a DLL was not found. I then realized that I have different >>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>> attempt to load a 4 GB tiff. >>>>> >>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>> for directions before doing this - now I'm wondering if that switch actually >>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Yes, well, don't say I didn't warn you! ; ) >>>>> >>>>> You do need loadable modules and you probably do want python (a lot of >>>>> core stuff is in python, like the editor). >>>>> >>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>> >>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>> it exited. But that may be a longshot. >>>>> >>>>> -Steve >>>>> >>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> Hi Steve, >>>>>> >>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>> build took a long time, partly because I turned on the Python option, which >>>>>> I don't need. This time there were no errors, except for a couple of >>>>>> occasions where the attempt to create a directory failed - this was because >>>>>> the directory already existed, and was easily solved by deleting the >>>>>> directory and building again. I installed everything that wanted to be >>>>>> installed, and modified the environment variables to suit. >>>>>> >>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>> knowing what it is). >>>>>> >>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>> what to do next. >>>>>> >>>>>> Cheers >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Hi Gib - >>>>>> >>>>>> A lot of the building goes on in parallel so you need to review the >>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>> on at the cmake flag level. >>>>>> >>>>>> Best, >>>>>> Steve >>>>>> >>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>> Additional Dependencies: >>>>>>> >>>>>>> ... >>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>> ITKCommon.lib >>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>> ... >>>>>>> >>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>> 40+ times. >>>>>>> >>>>>>> Thanks again >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>> [g.bogle at auckland.ac.nz] >>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>> >>>>>>> To: Steve Pieper >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>> >>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>> >>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>> link the ITK library that was just built, i.e.: >>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>> This is the first of about 40 such link errors. >>>>>>> >>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>> ITK_DIR appropriately? >>>>>>> >>>>>>> Thanks >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>> trickiest platform in my experience. >>>>>>> >>>>>>> -Steve >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Gib Bogle >>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Jean-Christophe, >>>>>>>> >>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>> >>>>>>>> Cheers >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Folks, >>>>>>>> >>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>> >>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>> these module. All details are captured here: >>>>>>>> >>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>> >>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>> planned for 4.5. >>>>>>>> >>>>>>>> Thanks >>>>>>>> Jc >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Matt - >>>>>>>>> >>>>>>>>> Thanks, that's helpful. >>>>>>>>> >>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>> straightforward. >>>>>>>>> >>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>> >>>>>>>>> -Steve >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Here is what the process would look like: >>>>>>>>>> >>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>> the >>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>> 5) Profit. >>>>>>>>>> >>>>>>>>>> HTH, >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>> >>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>> >>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>> wrote: >>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>> > but it's >>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>> > >>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>> > what is >>>>>>>>>> > involved? >>>>>>>>>> > >>>>>>>>>> > -Steve >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>> > wrote: >>>>>>>>>> >> >>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>> >> large >>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>> >> capability >>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>> >> ________________________________ >>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>> >> >>>>>>>>>> >> To: Gib Bogle >>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >> >>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>> >> configure >>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>> >> like vtkITK >>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>> >> experts are >>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>> >> >>>>>>>>>> >> -Steve >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>> >> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> I await the results with interest... >>>>>>>>>> >>> ________________________________ >>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>> >>> Pieper >>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>> >>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>> >>> a lot of >>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>> >>> >>>>>>>>>> >>> -Steve >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>> >>> >>>>>>>>>> >>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Steve, >>>>>>>>>> >>>> >>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>> >>>> configured in >>>>>>>>>> >>>> Slicer. >>>>>>>>>> >>>> >>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>> >>>> needs to >>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>> >>>> be used. I have >>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>> >>>> one wanted to >>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>> >>>> >>>>>>>>>> >>>> Brad >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>> >>>>>>>>>> >>>> Hi Brad - >>>>>>>>>> >>>> >>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>> >>>> able to >>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>> >>>> default options >>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>> >>>> >>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>> >>>> something nobody >>>>>>>>>> >>>> has tried? >>>>>>>>>> >>>> >>>>>>>>>> >>>> -Steve >>>>>>>>>> >>>> >>>>>>>>>> >>>> >>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>> >>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Steve, >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>> >>>>> windows 64? >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>> >>>>> specific. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> Bread >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>> >>>>> pasted in >>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> -Steve >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>> >>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>> >>>>>> still >>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Brad >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>> >>>>>> replicate the >>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> wrote: >>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>> >>>>>>> > back to this >>>>>>>>>> >>>>>>> > later. >>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>> >>>>>>> > to >>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>> >>>>>>> > for any >>>>>>>>>> >>>>>>> > standard >>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>> >>>>>>> >> a >>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>> >>>>>>> >> without >>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>> >>>>>>> >> for example >>>>>>>>>> >>>>>>> >> with a >>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>> >>>>>>> >>> different >>>>>>>>>> >>>>>>> >>> build >>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>> >>>>>>> >>> please >>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>> >>>>>>> >>> not >>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>> >>>>>>> >>> the >>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> >>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>> >>>>>>> >>> is >>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If you believe this e-mail was sent to you in error >>>>>>>>>> > and the >>>>>>>>>> > e-mail >>>>>>>>>> > contains patient information, please contact the Partners >>>>>>>>>> > Compliance >>>>>>>>>> > HelpLine at >>>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent >>>>>>>>>> > to you in >>>>>>>>>> > error >>>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>>> > sender and >>>>>>>>>> > properly >>>>>>>>>> > dispose of the e-mail. >>>>>>>>>> > >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> slicer-devel mailing list >>>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>> To unsubscribe: send email to >>>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>>> subject >>>>>>>>> >>>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>> whom it is >>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>> the e-mail >>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>> HelpLine at >>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> +1 919 869 8849 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> slicer-devel mailing list >>>> slicer-devel at bwh.harvard.edu >>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>> To unsubscribe: send email to >>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>> subject >>>> >>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >>> >>> -- >>> +1 919 869 8849 >> >> >> _______________________________________________ >> slicer-devel mailing list >> slicer-devel at bwh.harvard.edu >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >> with unsubscribe as the subject >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> From matt.mccormick at kitware.com Wed Sep 17 17:05:45 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Sep 2014 17:05:45 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 17:44:38 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 21:44:38 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: That fixed the error in that file, but there are still many elsewhere. I will now try making that change in other places. Thanks! Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 17:51:08 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 21:51:08 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Sorry, my mistake, not fixed. I tried one suggestion, will try the second. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 18:01:33 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 22:01:33 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Your second suggestion fixed two occurrences :) The next error is in vtkITKTimeSeriesDatabase.cxx(66): itk::ImportImageContainer::Pointer PixelContainerShort; PixelContainerShort = this->m_Filter->GetOutput()->GetPixelContainer(); ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent >>>>>>>>>>> > to you in >>>>>>>>>>> > error >>>>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>>>> > sender and >>>>>>>>>>> > properly >>>>>>>>>>> > dispose of the e-mail. >>>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> slicer-devel mailing list >>>>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> To unsubscribe: send email to >>>>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>>>> subject >>>>>>>>>> >>>>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>>> whom it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 18:12:10 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 22:12:10 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , Message-ID: I boldly (rashly?) did this: itk::ImportImageContainer< itk::SizeValueType, short>::Pointer PixelContainerShort; and it compiles. Is this OK? ________________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Thursday, 18 September 2014 10:01 a.m. To: Matt McCormick Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Your second suggestion fixed two occurrences :) The next error is in vtkITKTimeSeriesDatabase.cxx(66): itk::ImportImageContainer::Pointer PixelContainerShort; PixelContainerShort = this->m_Filter->GetOutput()->GetPixelContainer(); ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From g.bogle at auckland.ac.nz Wed Sep 17 18:20:17 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 22:20:17 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Those errors have gone for now. Now I'm seeing a slew of errors like this: 2> vtkITKTimeSeriesDatabase.cxx 2>c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(33): error C2782: 'T itk::TSD_MAX(T,T)' : template parameter 'T' is ambiguous 2> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(19) : see declaration of 'itk::TSD_MAX' 2> could be 'itk::Size::SizeValueType' 2> with 2> [ 2> VDimension=3 2> ] 2> or 'unsigned long' 2> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(27) : while compiling class template member function 'bool itk::TimeSeriesDatabase::CalculateIntersection(itk::Size,itk::ImageRegion,itk::ImageRegion &,itk::ImageRegion &)' 2> with 2> [ 2> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType, 2> VDimension=3, 2> VImageDimension=3 2> ] 2> c:\slicer\libs\vtkitk\itkTimeSeriesDatabase.txx(340) : while compiling class template member function 'void itk::TimeSeriesDatabase::CreateFromFileArchetype(const char *,const char *)' 2> with 2> [ 2> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType 2> ] 2> c:\slicer\libs\vtkitk\vtkITKTimeSeriesDatabase.h(89) : see reference to class template instantiation 'itk::TimeSeriesDatabase' being compiled 2> with 2> [ 2> TPixel=vtkITKTimeSeriesDatabase::OutputImagePixelType 2> ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From g.bogle at auckland.ac.nz Wed Sep 17 18:35:12 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 22:35:12 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. If you believe this e-mail was sent to you >>>>>>>>>>> >>>>>>> >>> in error >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> e-mail >>>>>>>>>>> >>>>>>> >>> contains patient information, please contact the >>>>>>>>>>> >>>>>>> >>> Partners >>>>>>>>>>> >>>>>>> >>> Compliance >>>>>>>>>>> >>>>>>> >>> HelpLine at >>>>>>>>>>> >>>>>>> >>> http://www.partners.org/complianceline . 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If the e-mail was sent >>>>>>>>>>> > to you in >>>>>>>>>>> > error >>>>>>>>>>> > but does not contain patient information, please contact the >>>>>>>>>>> > sender and >>>>>>>>>>> > properly >>>>>>>>>>> > dispose of the e-mail. >>>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> slicer-devel mailing list >>>>>>>>>> slicer-devel at bwh.harvard.edu >>>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>> To unsubscribe: send email to >>>>>>>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>>>>>>> subject >>>>>>>>>> >>>>>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>>> whom it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> From jchris.fillionr at kitware.com Wed Sep 17 19:09:58 2014 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Wed, 17 Sep 2014 19:09:58 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Hi Gib, Thanks for your hard work and perseverance. This is very much appreciated ! On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle wrote: > There are two more projects to go, vtkITKPython, and vtkITKPythonD. The source of these two projects are automatically generated by the VTK python wrapping tools, I wouldn't expect any issues with these. Hth Jc -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 17 19:13:31 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 23:13:31 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Hi Steve, I'm just addressing another different error. I hope it's just a matter of replacing unsigned long with itk::SizeValueType I guess this is a bit like the Y2K problem - everybody thought unsigned long was amply big enough. 24> N4ITKBiasFieldCorrection.cxx 24>..\..\..\..\..\..\Slicer\Modules\CLI\N4ITKBiasFieldCorrection\N4ITKBiasFieldCorrection.cxx(206): error C2664: 'void itk::PadImageFilter::SetPadLowerBound(const itk::Size)' : cannot convert parameter 1 from 'unsigned long [3]' to 'const itk::Size' [C:\s\b\Slicer-build\Modules\CLI\N4ITKBiasFieldCorrection\N4ITKBiasFieldCorrectionLib.vcxproj] 24> with 24> [ 24> TInputImage=`anonymous-namespace'::ImageType, 24> TOutputImage=`anonymous-namespace'::ImageType, 24> VDimension=3 24> ] 24> and 24> [ 24> VDimension=3 24> ] 24> No constructor could take the source type, or constructor overload resolution was ambiguous ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:10 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib - Way to see it through! those vtk*Python and vtk*PythonD should be autogenerated and not manually edited so maybe you are already there? -Steve On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle > wrote: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle > wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle > wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle > wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> > wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> > >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> > >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If you believe this e-mail was sent to you in error and >>>>>>>>>> the e-mail >>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 17 19:34:44 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 23:34:44 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Thanks. It would not have taken so long if I had not made that typo, and if I were a bit more mentally agile. Slicer is now built on my machine, and I am about to test it on some files. One thing puzzles me - when I Load Data and ask to select a file (or directory) it takes an awfully long time for any files to appear - anything from 30 sec to more than a minute. Is this normal? Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:10 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib - Way to see it through! those vtk*Python and vtk*PythonD should be autogenerated and not manually edited so maybe you are already there? -Steve On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle > wrote: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle > wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle > wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle > wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> > wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> > >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> > >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 17 19:41:54 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 17 Sep 2014 23:41:54 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: It's a mystery. There are no drives mounted. There are other machines visible on Network (via wifi), but no drives are mapped. Do you think it could be those network machines? ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:37 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF That might happen if you have a drive mounted that's not available or something (some windows thing). Otherwise I'm not sure... Good luck with the loading... Steve On Wed, Sep 17, 2014 at 7:34 PM, Gib Bogle > wrote: Thanks. It would not have taken so long if I had not made that typo, and if I were a bit more mentally agile. Slicer is now built on my machine, and I am about to test it on some files. One thing puzzles me - when I Load Data and ask to select a file (or directory) it takes an awfully long time for any files to appear - anything from 30 sec to more than a minute. Is this normal? Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:10 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib - Way to see it through! those vtk*Python and vtk*PythonD should be autogenerated and not manually edited so maybe you are already there? -Steve On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle > wrote: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle > wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle > wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle > wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> > wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> > >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> > >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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URL: From yxp233 at postech.ac.kr Wed Sep 17 20:11:55 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Thu, 18 Sep 2014 09:11:55 +0900 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support In-Reply-To: <1410960535981899.04578.ptmail04@ptmail04> References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> <1410913163921868.021894.ptmail04@ptmail04> <000c01cfd27a$9ed25020$dc76f060$@ac.kr> <1410960535981899.04578.ptmail04@ptmail04> Message-ID: <008301cfd2d5$27ecc890$77c659b0$@ac.kr> Hi Mike, If I turn USE_GPU off, then there is no CMake error. I guess there is something wrong with the GPU module. I am using CUDA toolkit 6.5 for compiling. Which version of CUDA toolkit should I use? Thanks, Xiaopeng From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Mike Chinander Sent: Wednesday, September 17, 2014 10:29 PM To: insight-users Subject: Re: [ITK-users] Any instruction of compiling ITK with GPU support Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with forward slashes instead, "D:/Toolbox/ITK-4.6.0" On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang wrote: By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows: Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): Syntax error in cmake code at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 when parsing string D:\Toolbox\ITK-4.6.0 Invalid escape sequence \T Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set) CMake/ITKModuleEnablement.cmake:171 (include) CMakeLists.txt:322 (include) Configuring incomplete, errors occurred! See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Wed Sep 17 20:36:06 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 00:36:06 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) I am seeing some odd behaviour. I can load and display a > 4GB tiff (N = 1650), but although I can load a tiff made with N = 1300 (a bit bigger than 2 GB) nothing is displayed. You have to admit that this is surprising :) There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:37 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF That might happen if you have a drive mounted that's not available or something (some windows thing). Otherwise I'm not sure... Good luck with the loading... Steve On Wed, Sep 17, 2014 at 7:34 PM, Gib Bogle > wrote: Thanks. It would not have taken so long if I had not made that typo, and if I were a bit more mentally agile. Slicer is now built on my machine, and I am about to test it on some files. One thing puzzles me - when I Load Data and ask to select a file (or directory) it takes an awfully long time for any files to appear - anything from 30 sec to more than a minute. Is this normal? Gib ________________________________ From: Steve Pieper [pieper at isomics.com] Sent: Thursday, 18 September 2014 11:10 a.m. To: Gib Bogle Cc: Matt McCormick; Bradley Lowekamp; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF Hi Gib - Way to see it through! those vtk*Python and vtk*PythonD should be autogenerated and not manually edited so maybe you are already there? -Steve On Wed, Sep 17, 2014 at 6:35 PM, Gib Bogle > wrote: Yay! The vtkITK project built OK. That doesn't mean what I did is right, of course. There are two more projects to go, vtkITKPython, and vtkITKPythonD. ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Thursday, 18 September 2014 9:05 a.m. To: Gib Bogle Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [slicer-devel] BigTIFF OK, thanks for the information Does changing the content on line 161 from itk::ImportImageContainer< unsigned long, type >::Pointer to image2##typeN::PixelContainer or at least itk::ImportImageContainer< itk::SizeValueType, type >::Pointer fix the issue? Thanks, Matt On Wed, Sep 17, 2014 at 4:32 PM, Gib Bogle > wrote: > Yes Matt. That's my line 179 too. The error message is confusing because vtkITKExecuteDataFromFile is a complex macro. It does things that I do not have a good grasp of. Every occurrence of vtkITKExecuteDataFromFile gives a similar error, and there are similar macros in other files that also give the same type of error. It is all somehow related to 'unsigned __int64', and I didn't get this error before when I was building (without knowing it) with ITK_USE_64BITS_IDS off. > > It is not clear to me who would be best equipped to address this - ITK, VTK or Slicer experts. > > I appreciate your attention to it very much! > Gib > ________________________________________ > From: Matt McCormick [matt.mccormick at kitware.com] > Sent: Thursday, 18 September 2014 5:06 a.m. > To: Gib Bogle > Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org > Subject: Re: [slicer-devel] BigTIFF > >> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179) > > Is this with the latest version of Slicer? > > My line 179 says > > vtkITKExecuteDataFromFile(VTK_DOUBLE, double); > > Thanks, > Matt > > On Wed, Sep 17, 2014 at 12:02 PM, Gib Bogle > wrote: >> Hi Matt, >> I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS? >> thanks >> Gib >> ________________________________________ >> From: Matt McCormick [matt.mccormick at kitware.com] >> Sent: Thursday, 18 September 2014 3:55 a.m. >> To: Gib Bogle >> Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org >> Subject: Re: [slicer-devel] BigTIFF >> >> Hi Gib, >> >> Getting the builds states to propagate and follow how the get set can >> be tricky. A few pointers on where to look for the status: >> >> 1) CMakeCache.txt (this file contains the build settings that CMake >> recognized from your input when you run CMake) >> 2) ITKConfig.cmake (this file will exist in the build tree or the >> install tree, and it contains CMake varables that may be used by other >> projects building against ITK) >> 3) itkConfigure.h (this is a header that has configured preprocessor >> definitions used when building) >> >> HTH, >> Matt >> >> >> >> On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle > wrote: >>> Hi Bradley, Matt and Steve, >>> >>> Now for the embarrassing confession. In External_ITK4.cmake I turned >>> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I >>> finally checked what the code that is being built was using (with #if >>> defined ...) I discovered that both ITKV3_COMPATIBILITY and >>> ITK_USE_64BITS_IDS were off. How can this be? >>> >>> It's easy, all it takes is a typo: >>> -DITK_USE_64_BITS_IDS:BOOL=ON >>> That typo has cost me a couple of days, and caused annoyance to a few >>> people, I suspect. >>> >>> Unfortunately... now Slicer's vtkITK does not build. There are very many >>> errors like this: >>> >>> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------ >>> 3>Build started 17/09/2014 7:25:52 p.m.. >>> 3>InitializeBuildStatus: >>> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild". >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date. >>> 3>ClCompile: >>> 3> vtkITKNumericTraits.cxx >>> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesReader.cxx >>> 3> vtkITKArchetypeImageSeriesScalarReader.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx >>> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx >>> 3> vtkITKImageWriter.cxx >>> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx >>> 3> vtkITKDistanceTransform.cxx >>> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179): >>> error C2679: binary '=' : no operator found which takes a right-hand operand >>> of type 'itk::ImportImageContainer *' (or there >>> is no acceptable conversion) >>> 3> with >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124): >>> could be 'itk::SmartPointer >>> &itk::SmartPointer::operator =(const >>> itk::SmartPointer &)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128): >>> or 'itk::SmartPointer >>> &itk::SmartPointer::operator >>> =(itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer, >>> 3> TElementIdentifier=unsigned long, >>> 3> TElement=double >>> 3> ] >>> 3> while trying to match the argument list >>> '(itk::SmartPointer, >>> itk::ImportImageContainer *)' >>> 3> with >>> 3> [ >>> 3> TObjectType=itk::ImportImageContainer >>> 3> ] >>> 3> and >>> 3> [ >>> 3> TElementIdentifier=unsigned __int64, >>> 3> TElement=double >>> 3> ] >>> >>> I presume these are related to the use of 64-bit integers. >>> >>> Over to you guys :) >>> >>> Gib >>> ________________________________ >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>> Sent: Tuesday, 16 September 2014 12:45 a.m. >>> To: Steve Pieper >>> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu >>> Subject: Re: [slicer-devel] BigTIFF >>> >>> Hello, >>> >>> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here: >>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>> >>> To test for ITK big tiff compatibility, I'd recommend getting python 2.7 >>> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to >>> read and write files like these there. More information about getting >>> started is here[1]. >>> >>> You should be a able to generate a image with: >>> >>> import SimpleITK as sitk >>> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8) >>> img += 10 >>> stats = sitk.StatisticsImageFilter() >>> stats.Execute(img) >>> print stats >>> >>> This should give you basic access to ITK in python to interactively >>> experiment with options with these large images. I have been able to load >>> large images with the binaries of SimpleITK on windows 64-bits. I don't know >>> if I have tried big tiff though. >>> >>> A simular test could be done with C++ and ITK directly, but I think >>> SimpleITK in python may be quicker for experimentation. >>> >>> Brad >>> >>> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted >>> [2] >>> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee >>> >>> On Sep 15, 2014, at 7:37 AM, Steve Pieper > wrote: >>> >>> Hi Gib - >>> >>> Are you testing only on windows? What we would often try to do for this >>> kind of debugging is to create a small example that other people can test on >>> their configurations. Slicer has a mechanism called a Self Test [1] to >>> allow easy replication and debugging across multiple platforms. It's ideal >>> if we can hone it down to something like what is described as a 'sscce' [2]. >>> The self tests will typically download some data from a public web site, run >>> some operations, and then print something out saying if it passed or failed >>> (or it may crash). Since it's possible to make a small data file that >>> expands into a giant tiff image it should be pretty tractable to pose this >>> issue in the form of a self test. >>> >>> Best, >>> Steve >>> >>> >>> [1] >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule >>> >>> [2] http://sscce.org/ >>> >>> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle > wrote: >>>> >>>> Hi J-C, >>>> >>>> Some more info about Slicer with big tiff files. >>>> >>>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly >>>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything >>>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page >>>> 72) >>>> >>>> All suggestions will be gratefully received. >>>> >>>> Cheers >>>> Gib >>>> ________________________________ >>>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] >>>> Sent: Sunday, 14 September 2014 8:32 p.m. >>>> To: Gib Bogle >>>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu >>>> Subject: Re: [slicer-devel] BigTIFF >>>> >>>> Hi Gib, >>>> >>>> What do you mean by "reinstalled" ? You should not have to install Slicer >>>> to be able to execute it from the build directory. >>>> >>>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option >>>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work >>>> out. >>>> >>>> When done building, make sure to start the Slicer launcher: >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe >>>> >>>> and not the Slicer executable: >>>> >>>> >>>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe >>>> >>>> >>>> By using the launcher, you ensure that the PATH are properly setup and the >>>> expected libraries are loaded. >>>> >>>> >>>> Hth >>>> Jc >>>> >>>> >>>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle > >>>> wrote: >>>>> >>>>> I hope I understand correctly. I added the line as shown to >>>>> C:\Slicer\SuperBuild\External_ITKv4.cmake: >>>>> ... >>>>> # ZLIB >>>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON >>>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT} >>>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR} >>>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY} >>>>> # Big TIFF >>>>> -DITK_USE_64_BITS_IDS:BOOL=ON >>>>> ... >>>>> >>>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I >>>>> presume this is the "superbuild". I then redid ALL_BUILD in >>>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still >>>>> crashes with the big tiff. Is there somewhere I can check in the project >>>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took >>>>> effect? >>>>> >>>>> Thanks >>>>> Gib >>>>> ________________________________ >>>>> From: Steve Pieper [pieper at isomics.com] >>>>> Sent: Sunday, 14 September 2014 1:36 p.m. >>>>> >>>>> To: Gib Bogle >>>>> Cc: slicer-devel at bwh.harvard.edu >>>>> Subject: Re: [slicer-devel] BigTIFF >>>>> >>>>> Hey Gib - >>>>> >>>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the >>>>> ITK build process [1] during the superbuild. I don't think much else was >>>>> required except turning off the IKTv3 parts. >>>>> >>>>> [1] >>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68 >>>>> >>>>> -Steve >>>>> >>>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get >>>>> it on TV). So the Jo'berg game should be a great rematch! >>>>> >>>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle > >>>>> wrote: >>>>>> >>>>>> You did warn me. >>>>>> >>>>>> Here is the list of options not ticked: >>>>>> >>>>>> Slicer_BUILD_BRAINSTOOLS >>>>>> _LEGACY_CLI >>>>>> _LandmarkRegistration >>>>>> _TESTING_EXTENSIONS >>>>>> _UPDATE_TRANSLATION >>>>>> _USE_GIT_PROTOCOL >>>>>> _OpenIGTLink >>>>>> _PYTHONQT_WITH_OPENSSL >>>>>> _PYTHONQT_WITH_TCL >>>>>> _QtTesting >>>>>> _SimpleITK >>>>>> _VTK_DEBUG_LINKS >>>>>> Slicer_WITH_LIBRARY_VERSION >>>>>> >>>>>> USE_BRAINS* >>>>>> USE_ConvertBetweenFileFormats >>>>>> USE_DWIConvert >>>>>> USE_DebugImageViewer >>>>>> USE_GTRACT >>>>>> USE_ICCDEF >>>>>> USE_ImageCalculator >>>>>> USE_ReferenceAtlas >>>>>> >>>>>> ------- >>>>>> >>>>>> Progress! Process Monitor showed me that the exit code was C0000139, >>>>>> which means a DLL was not found. I then realized that I have different >>>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this >>>>>> prompted me to look more carefully at the PATH environment variable. I just >>>>>> tested with all the new paths at the start of the PATH string, and Slicer >>>>>> starts successfully! I can load a tiff! But ... it still crashes when I >>>>>> attempt to load a 4 GB tiff. >>>>>> >>>>>> I am now wondering (belatedly!) about the way I tried to build with big >>>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as >>>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked >>>>>> for directions before doing this - now I'm wondering if that switch actually >>>>>> had any effect. Is that the right thing to do, and if not, what is? >>>>>> >>>>>> Thanks >>>>>> Gib >>>>>> ________________________________ >>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>> Sent: Sunday, 14 September 2014 10:02 a.m. >>>>>> >>>>>> To: Gib Bogle >>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>> >>>>>> Yes, well, don't say I didn't warn you! ; ) >>>>>> >>>>>> You do need loadable modules and you probably do want python (a lot of >>>>>> core stuff is in python, like the editor). >>>>>> >>>>>> BRAINSTools should be off for now, since it needs ITKv3. >>>>>> >>>>>> I'm not sure either what to do next, but I suggest maybe trying the >>>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when >>>>>> it exited. But that may be a longshot. >>>>>> >>>>>> -Steve >>>>>> >>>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle > >>>>>> wrote: >>>>>>> >>>>>>> Hi Steve, >>>>>>> >>>>>>> That was an interesting exercise. I managed to build Slicer without >>>>>>> Qtloadablemodules. As you might expect, it was not much use. The program >>>>>>> started up but without any capabilities, just an empty shell. (I'm a bit >>>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I >>>>>>> built it again, this time selecting most things except BRAINTools. The >>>>>>> build took a long time, partly because I turned on the Python option, which >>>>>>> I don't need. This time there were no errors, except for a couple of >>>>>>> occasions where the attempt to create a directory failed - this was because >>>>>>> the directory already existed, and was easily solved by deleting the >>>>>>> directory and building again. I installed everything that wanted to be >>>>>>> installed, and modified the environment variables to suit. >>>>>>> >>>>>>> My sense of satisfaction was short-lived, however. When Slicer is >>>>>>> invoked the Acknowledgements screen flashes up briefly then the program >>>>>>> exits. There are no error messages. Dependency Walker shows that all the >>>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not >>>>>>> knowing what it is). >>>>>>> >>>>>>> I sense that I must be close to getting it working, but I'm not sure >>>>>>> what to do next. >>>>>>> >>>>>>> Cheers >>>>>>> Gib >>>>>>> ________________________________ >>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>> Sent: Sunday, 14 September 2014 12:36 a.m. >>>>>>> >>>>>>> To: Gib Bogle >>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>> >>>>>>> Hi Gib - >>>>>>> >>>>>>> A lot of the building goes on in parallel so you need to review the >>>>>>> whole build log to see what is going on. I'm guessing ITK didn't build >>>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output >>>>>>> window and then paste it into a text editor to look for issues. Definitely >>>>>>> you don't want to be editing any of the visual studio files, since they are >>>>>>> generated by cmake every configure -- much better to sort out what is going >>>>>>> on at the cmake flag level. >>>>>>> >>>>>>> Best, >>>>>>> Steve >>>>>>> >>>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle > >>>>>>> wrote: >>>>>>>> >>>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice >>>>>>>> something odd. Here is a snippet from the list of Linker > Input > >>>>>>>> Additional Dependencies: >>>>>>>> >>>>>>>> ... >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib >>>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib >>>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib >>>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib >>>>>>>> ITKCommon.lib >>>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib >>>>>>>> ... >>>>>>>> >>>>>>>> For some reason ITKCommon.lib is treated differently from all the >>>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this? >>>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly >>>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this >>>>>>>> 40+ times. >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle >>>>>>>> [g.bogle at auckland.ac.nz] >>>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m. >>>>>>>> >>>>>>>> To: Steve Pieper >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Steve, >>>>>>>> >>>>>>>> All goes well until the point where the qSlicer*.lib get made. The >>>>>>>> first error, while building qSlicerBaseQTCore.lib, is: >>>>>>>> >>>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib' >>>>>>>> >>>>>>>> I don't know how to interpret this. I am guessing that it wants to >>>>>>>> link the ITK library that was just built, i.e.: >>>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib >>>>>>>> This is the first of about 40 such link errors. >>>>>>>> >>>>>>>> I'm not sure if ITK really needed to be built, since it is already >>>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping >>>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set >>>>>>>> ITK_DIR appropriately? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Gib >>>>>>>> ________________________________ >>>>>>>> From: Steve Pieper [pieper at isomics.com] >>>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m. >>>>>>>> To: Gib Bogle >>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>> >>>>>>>> Hi Gib - >>>>>>>> >>>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is >>>>>>>> quite reasonable, and would be workable. But if you haven't built a big >>>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git, >>>>>>>> visual studio...) and odd things can go wrong if it isn't all done just >>>>>>>> right. That said, slicer is actually quite well supported on windows, >>>>>>>> better, IMHO, than many cross-platform systems. But windows is really the >>>>>>>> trickiest platform in my experience. >>>>>>>> >>>>>>>> -Steve >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle > >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi Steve, >>>>>>>>> >>>>>>>>> Do you think I would be able to build Slicer myself, with >>>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that >>>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this >>>>>>>>> point is simply for a 3D viewer that can handle big images. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: Gib Bogle >>>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m. >>>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: RE: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Jean-Christophe, >>>>>>>>> >>>>>>>>> Any idea when 4.5 will enter the world? >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Gib >>>>>>>>> ________________________________ >>>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe >>>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com] >>>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m. >>>>>>>>> To: Steve Pieper >>>>>>>>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>> >>>>>>>>> Hi Folks, >>>>>>>>> >>>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on >>>>>>>>> either ITKDeprecated or ITKV3Compatibility. >>>>>>>>> >>>>>>>>> That said, BRAINSTools and some extensions are still depending on >>>>>>>>> these module. All details are captured here: >>>>>>>>> >>>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486 >>>>>>>>> >>>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The >>>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is >>>>>>>>> planned for 4.5. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jc >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper > >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi Matt - >>>>>>>>>> >>>>>>>>>> Thanks, that's helpful. >>>>>>>>>> >>>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK, >>>>>>>>>> which includes all the file IO adapters. But I think it will be pretty >>>>>>>>>> straightforward. >>>>>>>>>> >>>>>>>>>> But there's no reason to start that until we know that BRAINSTools >>>>>>>>>> will work - right now at least some of them depend on ITKDeprecated. >>>>>>>>>> >>>>>>>>>> -Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick >>>>>>>>>> > wrote: >>>>>>>>>>> >>>>>>>>>>> Here is what the process would look like: >>>>>>>>>>> >>>>>>>>>>> 0) Start with a clean software quality dashboard. >>>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in >>>>>>>>>>> Superbuild/External_ITKv4.cmake >>>>>>>>>>> 2) Rebuild and encounter errors and test failures. >>>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and >>>>>>>>>>> the >>>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes >>>>>>>>>>> (minor modifications to the API, etc). >>>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON. >>>>>>>>>>> 5) Profit. >>>>>>>>>>> >>>>>>>>>>> HTH, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> [1] http://itk.org/migrationv4/ >>>>>>>>>>> >>>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper > >>>>>>>>>>> wrote: >>>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists, >>>>>>>>>>> > but it's >>>>>>>>>>> > looking like there's a fair amount of code to retrofit. >>>>>>>>>>> > >>>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just >>>>>>>>>>> > what is >>>>>>>>>>> > involved? >>>>>>>>>>> > >>>>>>>>>>> > -Steve >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle >>>>>>>>>>> > > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> :( I imagine that people are increasingly working with very >>>>>>>>>>> >> large >>>>>>>>>>> >> datasets, so the number of people who would like to have this >>>>>>>>>>> >> capability >>>>>>>>>>> >> will grow. I, alas, am not an ITK expert. >>>>>>>>>>> >> ________________________________ >>>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m. >>>>>>>>>>> >> >>>>>>>>>>> >> To: Gib Bogle >>>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >> >>>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even >>>>>>>>>>> >> configure >>>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module, >>>>>>>>>>> >> like vtkITK >>>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK >>>>>>>>>>> >> experts are >>>>>>>>>>> >> going to need to dig in before this mode can be enabled. >>>>>>>>>>> >> >>>>>>>>>>> >> -Steve >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I await the results with interest... >>>>>>>>>>> >>> ________________________________ >>>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu >>>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve >>>>>>>>>>> >>> Pieper >>>>>>>>>>> >>> [pieper at isomics.com] >>>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m. >>>>>>>>>>> >>> To: Bradley Lowekamp >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>> >>>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out >>>>>>>>>>> >>> a lot of >>>>>>>>>>> >>> legacy CLI code - perhaps those were the main places >>>>>>>>>>> >>> ITKV3_COMPATIBILITY was >>>>>>>>>>> >>> required? I kicked off a build to see what will happen. >>>>>>>>>>> >>> >>>>>>>>>>> >>> -Steve >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp >>>>>>>>>>> >>> > >>>>>>>>>>> >>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Steve, >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been >>>>>>>>>>> >>>> configured in >>>>>>>>>>> >>>> Slicer. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY >>>>>>>>>>> >>>> needs to >>>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer >>>>>>>>>>> >>>> be used. I have >>>>>>>>>>> >>>> brought these issue up before and offered assistance but no >>>>>>>>>>> >>>> one wanted to >>>>>>>>>>> >>>> champion changing these configuration flags. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Brad >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper > >>>>>>>>>>> >>>> wrote: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Hi Brad - >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was >>>>>>>>>>> >>>> able to >>>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's >>>>>>>>>>> >>>> vtkNRRDWriter >>>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file >>>>>>>>>>> >>>> with ITK's NRRD >>>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with >>>>>>>>>>> >>>> default options >>>>>>>>>>> >>>> on win7 64bit. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just >>>>>>>>>>> >>>> something nobody >>>>>>>>>>> >>>> has tried? >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> -Steve >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp >>>>>>>>>>> >>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Steve, >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on >>>>>>>>>>> >>>>> windows 64? >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> There should be some image source filters in the >>>>>>>>>>> >>>>> SimpleFilters modules >>>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff >>>>>>>>>>> >>>>> specific. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> Bread >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib! >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and >>>>>>>>>>> >>>>> pasted in >>>>>>>>>>> >>>>> a stack trace and put a link to the data. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825 >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> -Steve >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp >>>>>>>>>>> >>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Matt, I was just about to point that out. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> The other things is the compatibility flag: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's >>>>>>>>>>> >>>>>> still >>>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122 >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can >>>>>>>>>>> >>>>>> replicate the >>>>>>>>>>> >>>>>> issue and then we can see if that has any side effects. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick >>>>>>>>>>> >>>>>> > wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> wrote: >>>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get >>>>>>>>>>> >>>>>>> > back to this >>>>>>>>>>> >>>>>>> > later. >>>>>>>>>>> >>>>>>> > ________________________________ >>>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > To: Gib Bogle >>>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how >>>>>>>>>>> >>>>>>> > to >>>>>>>>>>> >>>>>>> > generate a big >>>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable >>>>>>>>>>> >>>>>>> > for any >>>>>>>>>>> >>>>>>> > standard >>>>>>>>>>> >>>>>>> > platform should be fine too. >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle >>>>>>>>>>> >>>>>>> > > >>>>>>>>>>> >>>>>>> > wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to >>>>>>>>>>> >>>>>>> >> a >>>>>>>>>>> >>>>>>> >> reasonable size. >>>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK >>>>>>>>>>> >>>>>>> >> without >>>>>>>>>>> >>>>>>> >> problems. >>>>>>>>>>> >>>>>>> >> ________________________________ >>>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com] >>>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m. >>>>>>>>>>> >>>>>>> >> To: Gib Bogle >>>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Hi - >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this, >>>>>>>>>>> >>>>>>> >> for example >>>>>>>>>>> >>>>>>> >> with a >>>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to >>>>>>>>>>> >>>>>>> >> transfer a >>>>>>>>>>> >>>>>>> >> 4.5GB file >>>>>>>>>>> >>>>>>> >> from NZ). >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> -Steve >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi Brad, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7. >>>>>>>>>>> >>>>>>> >>> I can load >>>>>>>>>>> >>>>>>> >>> a tiff >>>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000), >>>>>>>>>>> >>>>>>> >>> but a couple >>>>>>>>>>> >>>>>>> >>> of bigger >>>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about >>>>>>>>>>> >>>>>>> >>> 4.5 GB >>>>>>>>>>> >>>>>>> >>> (actually when I >>>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes >>>>>>>>>>> >>>>>>> >>> immediately, >>>>>>>>>>> >>>>>>> >>> exception >>>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half >>>>>>>>>>> >>>>>>> >>> this size >>>>>>>>>>> >>>>>>> >>> is the >>>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different - >>>>>>>>>>> >>>>>>> >>> I see the >>>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the >>>>>>>>>>> >>>>>>> >>> windows greys >>>>>>>>>>> >>>>>>> >>> out. >>>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button >>>>>>>>>>> >>>>>>> >>> on the >>>>>>>>>>> >>>>>>> >>> popup, and the >>>>>>>>>>> >>>>>>> >>> program crashes. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I >>>>>>>>>>> >>>>>>> >>> installed >>>>>>>>>>> >>>>>>> >>> Slicer is >>>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very >>>>>>>>>>> >>>>>>> >>> good but >>>>>>>>>>> >>>>>>> >>> BigTIFFs >>>>>>>>>>> >>>>>>> >>> are not enabled. >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with >>>>>>>>>>> >>>>>>> >>> different >>>>>>>>>>> >>>>>>> >>> build >>>>>>>>>>> >>>>>>> >>> options? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> ________________________________ >>>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov] >>>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m. >>>>>>>>>>> >>>>>>> >>> To: Gib Bogle >>>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hello, >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3, >>>>>>>>>>> >>>>>>> >>> and the >>>>>>>>>>> >>>>>>> >>> associated >>>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you >>>>>>>>>>> >>>>>>> >>> please >>>>>>>>>>> >>>>>>> >>> provide more >>>>>>>>>>> >>>>>>> >>> detail about your issue? >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Brad >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle >>>>>>>>>>> >>>>>>> >>> > >>>>>>>>>>> >>>>>>> >>> wrote: >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> Hi, >>>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does >>>>>>>>>>> >>>>>>> >>> not >>>>>>>>>>> >>>>>>> >>> handle >>>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability? >>>>>>>>>>> >>>>>>> >>> Thanks >>>>>>>>>>> >>>>>>> >>> Gib >>>>>>>>>>> >>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>>>>>> >>> slicer-devel mailing list >>>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to >>>>>>>>>>> >>>>>>> >>> slicer-devel-request at massmail.spl.harvard.edu with >>>>>>>>>>> >>>>>>> >>> unsubscribe as >>>>>>>>>>> >>>>>>> >>> the >>>>>>>>>>> >>>>>>> >>> subject >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> >>>>>>>>>>> >>>>>>> >>> The information in this e-mail is intended only for the >>>>>>>>>>> >>>>>>> >>> person to >>>>>>>>>>> >>>>>>> >>> whom it >>>>>>>>>>> >>>>>>> >>> is >>>>>>>>>>> >>>>>>> >>> addressed. 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If the e-mail was sent to >>>>>>>>>> you in error >>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> +1 919 869 8849 >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> slicer-devel mailing list >>>>> slicer-devel at bwh.harvard.edu >>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>>>> To unsubscribe: send email to >>>>> slicer-devel-request at massmail.spl.harvard.edu with unsubscribe as the >>>>> subject >>>>> >>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> >>>> >>>> -- >>>> +1 919 869 8849 >>> >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at massmail.spl.harvard.edu >>> with unsubscribe as the subject >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From yxp233 at postech.ac.kr Wed Sep 17 21:48:11 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Thu, 18 Sep 2014 10:48:11 +0900 Subject: [ITK] [ITK-users] Any instruction of compiling ITK with GPU support References: <1410796270474129.115529.ptmail04@ptmail04> <1410878838500935.032749.ptmail04@ptmail04> <1410913163921868.021894.ptmail04@ptmail04> <000c01cfd27a$9ed25020$dc76f060$@ac.kr> <1410960535981899.04578.ptmail04@ptmail04> Message-ID: <009401cfd2e2$9b13c640$d13b52c0$@ac.kr> Hi Mike, I found that you were right. I changed the forward slashes for the directories of OpenCL: OPENCL_INCLUDE_DIRS C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/include OPENCL_LIBRARIES C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib There was no CMake error, but many warning messages: WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item. And when I tried to debug ITK, errors occurred as ?cannot find CL/opencl.h?. Can you tell me where I made a mistake? Thank you, Xiaopeng From: Xiaopeng Yang [mailto:yxp233 at postech.ac.kr] Sent: Thursday, September 18, 2014 9:12 AM To: 'Mike Chinander'; 'insight-users' Subject: RE: [ITK-users] Any instruction of compiling ITK with GPU support Hi Mike, If I turn USE_GPU off, then there is no CMake error. I guess there is something wrong with the GPU module. I am using CUDA toolkit 6.5 for compiling. Which version of CUDA toolkit should I use? Thanks, Xiaopeng From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Mike Chinander Sent: Wednesday, September 17, 2014 10:29 PM To: insight-users Subject: Re: [ITK-users] Any instruction of compiling ITK with GPU support Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with forward slashes instead, "D:/Toolbox/ITK-4.6.0" On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang wrote: By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows: Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set): Syntax error in cmake code at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 when parsing string D:\Toolbox\ITK-4.6.0 Invalid escape sequence \T Call Stack (most recent call first): C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set) CMake/ITKModuleEnablement.cmake:171 (include) CMakeLists.txt:322 (include) Configuring incomplete, errors occurred! See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log". See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log". -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Wed Sep 17 21:54:06 2014 From: llliu at umich.edu (Lianli Liu) Date: Wed, 17 Sep 2014 21:54:06 -0400 Subject: [ITK] [ITK-users] Mask in metric calculation Message-ID: Hi all, I just wonder if I define two masks for fixed image and moving image that are of differnt size, will voxels that fall in both the masks will contribute to metric calculation? Thanks! Regards, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jchris.fillionr at kitware.com Wed Sep 17 22:51:21 2014 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Wed, 17 Sep 2014 22:51:21 -0400 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> Message-ID: Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle wrote: > Correction! You were right. There was a network drive that I could not > see until I right-clicked on Network, then Disconnect network drive. Now > it's responsive :) > > There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" > > There is another wrinkle that I'm not concerned about right now. When I > execute the installed program, C:\Program files\Slicer.exe, the console > shows this error message: > > Traceback (most recent call last): > File "", line 7, in > File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in > > import vtk, qt, ctk > ImportError: No module named vtk > > but the program runs. I don't see that message when I run the executable > in Slicer-build. The files in both places are the same, also the > SlicerApp-real.exe files - of course, since INSTALL just copies them. I > have seen any difference in the ability to display the tiff files. > This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Wed Sep 17 23:07:23 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 03:07:23 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , Message-ID: Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From gowithking at googlemail.com Thu Sep 18 02:03:52 2014 From: gowithking at googlemail.com (gowith king) Date: Thu, 18 Sep 2014 08:03:52 +0200 Subject: [ITK] Bug in StatisticsImageFilter? In-Reply-To: References: Message-ID: Hi Matt You are the best . It works. I thought it need only the last writer.Update() to call the whole pep-line. Thank you . I am going to catch my flight now, I will try the other one later. On Wed, Sep 17, 2014 at 5:44 PM, Matt McCormick wrote: > Hi gowith, > > Please try calling > > rangetest.Update() > > This is required for the results to be computed. > > HTH, > Matt > > On Tue, Sep 16, 2014 at 7:53 PM, gowith king > wrote: > > I was trying to use itk.StatisticsImageFilter to check the outcome of my > > image reader. but all the results are wrong. > > reader1 = itk.ImageFileReader.IUC3.New() > > reader1.SetFileName(inputImagetest) > > > > rangetest=itk.StatisticsImageFilter.IUC3.New() > > rangetest.SetInput(reader1) > > print 'range: ', str(rangetest.GetMinimum()) > > > > result: > > range: 255 > > > > obviously this is not true for my image : it is a binary image and has > only > > 1 and 100 two values. > > > > I am working on a python 2.7 wrapped ITK4 . if the python2 is > incompatible > > with itk? > > > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Thu Sep 18 02:36:05 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 18 Sep 2014 08:36:05 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Hi Matt, This is indeed the observed and, based on your answer, expected behaviour. Thank you very much for the confirmation (that's exactly what I needed!). To avoid confusion in future, I am going to modify the corresponding example on github and on the wiki! Best, Arnaud On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick wrote: > Hi, > > Do to this fix [1], if the writer is re-using the GDCMImageIO, the > writer should apply the inverse rescale / slope intercept like the > reader applied the rescale / slope intercept when reading. This was a > long-standing bug that I fixed in 4.6.0. Arnaud, if the manual > inverse rescale / slope operation is removed, does the correct output > result? > > Thanks, > Matt > > [1] > https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e > > On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen > wrote: > > I wrote this example many years ago? > > 1) If the input has a non-trivial slope/intercept, the reader applies > > the slope/intercept to the raw data. > > 2) Rather than setting the slope/intercept in the output dicom, I > > apply the inverse of of the slope intercept to the resampled data > > before writing. The output dicom should not have the origin > > slope/intercept tags. > > > > I'll try to verify this with Slicer, but I may be out of touch for 2 > weeks? > > > > Bill > > > > > > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas > wrote: > >> Hi Nick, > >> > >> I can confirm that with the example I get a difference of -1024 (+/- 1) > in > >> between the input and the output, using the ShiftScaleImage part... > >> While without this part of code the difference is (+/-1) > >> > >> I would like to make sure this is the expected behaviour!? > >> > >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson < > pattersonnp.work at gmail.com> > >> wrote: > >>> > >>> OK, I will wait to hear the outcome of your run with the original > example > >>> then. > >>> > >>> Cheers, Nick. > >>> > >>> > >>> > >>> > >>> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: > >>> > >>> Nick, > >>> > >>> I can't roll back to previous ITK version, important patches on > >>> itkGDCMImageIO were very recently merged... > >>> > >>> > >>> > https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx > >>> > >>> e.g. > >>> > >>> > >>> > https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 > >>> > >>> > https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c > >>> > >>> > >>> Arnaud > >>> > >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson > >>> wrote: > >>>> > >>>> I should also mention Arnauld that I use ITK4.5.2. I have had many > >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled > back to > >>>> ITK4.5.2. > >>>> Nick. > >>>> > >>>> > >>>> > >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas wrote: > >>>> > >>>> Hi Matias, > >>>> > >>>> I guess you are referring to > >>>> > >>>> > >>>> > https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e > >>>> > >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e > >>>> v4.6.0 > >>>> > >>>> I use the release branch of ITK > >>>> > >>>> --- > >>>> > >>>> Matt, > >>>> > >>>> Can you comment on this, please? > >>>> > >>>> Thanks > >>>> Arnaud > >>>> > >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull > >>>> wrote: > >>>> > >>>> I had an issue with the resampledicom example once (all my pixel > values > >>>> were recalculated by adding rescaleintercept) and then downloaded the > latest > >>>> ITK release (4.6) and worked fine. > >>>> > >>>> The issue was with the GDCMIO class I beleive but was fixed somehow in > >>>> the 4.6 version. > >>>> > >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas > > >>>> wrote: > >>>>> > >>>>> Hi all, > >>>>> > >>>>> I have been looking at the following wiki example: > >>>>> > >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > >>>>> > >>>>> It seems to me that the section to rescale the image is not valid > >>>>> anymore with latest ITK version (?) > >>>>> > >>>>> > >>>>> > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 > >>>>> > >>>>> Can anyone confirm? > >>>>> > >>>>> Is this code validated? are output images compared to input ones in > the > >>>>> corresponding test? > >>>>> > >>>>> Thanks > >>>>> Arnaud > >>>>> > >>>>> _____________________________________ > >>>>> Powered by www.kitware.com > >>>>> > >>>>> Visit other Kitware open-source projects at > >>>>> http://www.kitware.com/opensource/opensource.html > >>>>> > >>>>> Kitware offers ITK Training Courses, for more information visit: > >>>>> http://www.kitware.com/products/protraining.php > >>>>> > >>>>> Please keep messages on-topic and check the ITK FAQ at: > >>>>> http://www.itk.org/Wiki/ITK_FAQ > >>>>> > >>>>> Follow this link to subscribe/unsubscribe: > >>>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>>> > >>>> > >>>> > >>>> _____________________________________ > >>>> Powered by www.kitware.com > >>>> > >>>> Visit other Kitware open-source projects at > >>>> http://www.kitware.com/opensource/opensource.html > >>>> > >>>> Kitware offers ITK Training Courses, for more information visit: > >>>> http://www.kitware.com/products/protraining.php > >>>> > >>>> Please keep messages on-topic and check the ITK FAQ at: > >>>> http://www.itk.org/Wiki/ITK_FAQ > >>>> > >>>> Follow this link to subscribe/unsubscribe: > >>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>> > >>>> > >>> > >>> > >> > >> > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-users > >> > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Thu Sep 18 02:43:36 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 18 Sep 2014 08:43:36 +0200 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Matt, I guess there should be migration report for this fix? Arnaud On Thu, Sep 18, 2014 at 8:36 AM, Arnaud Gelas wrote: > Hi Matt, > > This is indeed the observed and, based on your answer, expected behaviour. > Thank you very much for the confirmation (that's exactly what I needed!). > > To avoid confusion in future, I am going to modify the corresponding > example on github and on the wiki! > > Best, > Arnaud > > On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi, >> >> Do to this fix [1], if the writer is re-using the GDCMImageIO, the >> writer should apply the inverse rescale / slope intercept like the >> reader applied the rescale / slope intercept when reading. This was a >> long-standing bug that I fixed in 4.6.0. Arnaud, if the manual >> inverse rescale / slope operation is removed, does the correct output >> result? >> >> Thanks, >> Matt >> >> [1] >> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >> >> On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen >> wrote: >> > I wrote this example many years ago? >> > 1) If the input has a non-trivial slope/intercept, the reader applies >> > the slope/intercept to the raw data. >> > 2) Rather than setting the slope/intercept in the output dicom, I >> > apply the inverse of of the slope intercept to the resampled data >> > before writing. The output dicom should not have the origin >> > slope/intercept tags. >> > >> > I'll try to verify this with Slicer, but I may be out of touch for 2 >> weeks? >> > >> > Bill >> > >> > >> > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas >> wrote: >> >> Hi Nick, >> >> >> >> I can confirm that with the example I get a difference of -1024 (+/- >> 1) in >> >> between the input and the output, using the ShiftScaleImage part... >> >> While without this part of code the difference is (+/-1) >> >> >> >> I would like to make sure this is the expected behaviour!? >> >> >> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson < >> pattersonnp.work at gmail.com> >> >> wrote: >> >>> >> >>> OK, I will wait to hear the outcome of your run with the original >> example >> >>> then. >> >>> >> >>> Cheers, Nick. >> >>> >> >>> >> >>> >> >>> >> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: >> >>> >> >>> Nick, >> >>> >> >>> I can't roll back to previous ITK version, important patches on >> >>> itkGDCMImageIO were very recently merged... >> >>> >> >>> >> >>> >> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx >> >>> >> >>> e.g. >> >>> >> >>> >> >>> >> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 >> >>> >> >>> >> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c >> >>> >> >>> >> >>> Arnaud >> >>> >> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson >> >>> wrote: >> >>>> >> >>>> I should also mention Arnauld that I use ITK4.5.2. I have had many >> >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled >> back to >> >>>> ITK4.5.2. >> >>>> Nick. >> >>>> >> >>>> >> >>>> >> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas >> wrote: >> >>>> >> >>>> Hi Matias, >> >>>> >> >>>> I guess you are referring to >> >>>> >> >>>> >> >>>> >> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >> >>>> >> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >> >>>> v4.6.0 >> >>>> >> >>>> I use the release branch of ITK >> >>>> >> >>>> --- >> >>>> >> >>>> Matt, >> >>>> >> >>>> Can you comment on this, please? >> >>>> >> >>>> Thanks >> >>>> Arnaud >> >>>> >> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull >> >>>> wrote: >> >>>> >> >>>> I had an issue with the resampledicom example once (all my pixel >> values >> >>>> were recalculated by adding rescaleintercept) and then downloaded >> the latest >> >>>> ITK release (4.6) and worked fine. >> >>>> >> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow >> in >> >>>> the 4.6 version. >> >>>> >> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas < >> arnaudgelas at gmail.com> >> >>>> wrote: >> >>>>> >> >>>>> Hi all, >> >>>>> >> >>>>> I have been looking at the following wiki example: >> >>>>> >> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >> >>>>> >> >>>>> It seems to me that the section to rescale the image is not valid >> >>>>> anymore with latest ITK version (?) >> >>>>> >> >>>>> >> >>>>> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >> >>>>> >> >>>>> Can anyone confirm? >> >>>>> >> >>>>> Is this code validated? are output images compared to input ones in >> the >> >>>>> corresponding test? >> >>>>> >> >>>>> Thanks >> >>>>> Arnaud >> >>>>> >> >>>>> _____________________________________ >> >>>>> Powered by www.kitware.com >> >>>>> >> >>>>> Visit other Kitware open-source projects at >> >>>>> http://www.kitware.com/opensource/opensource.html >> >>>>> >> >>>>> Kitware offers ITK Training Courses, for more information visit: >> >>>>> http://www.kitware.com/products/protraining.php >> >>>>> >> >>>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>>> >> >>>>> Follow this link to subscribe/unsubscribe: >> >>>>> http://public.kitware.com/mailman/listinfo/insight-users >> >>>>> >> >>>> >> >>>> >> >>>> _____________________________________ >> >>>> Powered by www.kitware.com >> >>>> >> >>>> Visit other Kitware open-source projects at >> >>>> http://www.kitware.com/opensource/opensource.html >> >>>> >> >>>> Kitware offers ITK Training Courses, for more information visit: >> >>>> http://www.kitware.com/products/protraining.php >> >>>> >> >>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>> >> >>>> Follow this link to subscribe/unsubscribe: >> >>>> http://public.kitware.com/mailman/listinfo/insight-users >> >>>> >> >>>> >> >>> >> >>> >> >> >> >> >> >> _____________________________________ >> >> Powered by www.kitware.com >> >> >> >> Visit other Kitware open-source projects at >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> http://www.kitware.com/products/protraining.php >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> > >> > >> > >> > -- >> > Unpaid intern in BillsBasement at noware dot com >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From joel.schaerer at laposte.net Thu Sep 18 08:19:52 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 18 Sep 2014 14:19:52 +0200 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: References: <541848B5.9060901@laposte.net> Message-ID: <541ACDE8.4080508@laposte.net> Hi Matt, I just sent you a github pull request: https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2 Note that I ditched my old fork and started with a clean clone of the template. Jo?l On 09/16/2014 07:26 PM, Matt McCormick wrote: > Hi Jo?l, > > Yes, that the current best repository, and fixes are welcome! Please > add a pull request on the repository and ping the mailing list if it > is not merged after a few days. > > Thanks, > Matt > > On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer > wrote: >> Hi all, >> >> The template for Insight Journal submissions that is available on GitHub and >> recommended on the Insight Journal website >> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) does >> not build with ITK4. >> >> I can try to fix it, but before I do I would like to make sure it is still >> the current version? >> >> Thanks! >> >> Jo?l >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 18 09:02:44 2014 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 18 Sep 2014 13:02:44 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , Message-ID: Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From matt.mccormick at kitware.com Thu Sep 18 13:02:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Sep 2014 13:02:55 -0400 Subject: [ITK] [ITK-users] question about wiki example ResampleDICOM In-Reply-To: References: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com> Message-ID: Hi Arnaud, Great to hear it is working! Yes, good idea on the migration guide to better communicate and explain the development. Here is a patch to review. http://review.source.kitware.com/#/c/17098/ Thanks, Matt On Thu, Sep 18, 2014 at 2:43 AM, Arnaud Gelas wrote: > Matt, > > I guess there should be migration report for this fix? > > Arnaud > > On Thu, Sep 18, 2014 at 8:36 AM, Arnaud Gelas wrote: >> >> Hi Matt, >> >> This is indeed the observed and, based on your answer, expected behaviour. >> Thank you very much for the confirmation (that's exactly what I needed!). >> >> To avoid confusion in future, I am going to modify the corresponding >> example on github and on the wiki! >> >> Best, >> Arnaud >> >> On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick >> wrote: >>> >>> Hi, >>> >>> Do to this fix [1], if the writer is re-using the GDCMImageIO, the >>> writer should apply the inverse rescale / slope intercept like the >>> reader applied the rescale / slope intercept when reading. This was a >>> long-standing bug that I fixed in 4.6.0. Arnaud, if the manual >>> inverse rescale / slope operation is removed, does the correct output >>> result? >>> >>> Thanks, >>> Matt >>> >>> [1] >>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>> On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen >>> wrote: >>> > I wrote this example many years ago? >>> > 1) If the input has a non-trivial slope/intercept, the reader applies >>> > the slope/intercept to the raw data. >>> > 2) Rather than setting the slope/intercept in the output dicom, I >>> > apply the inverse of of the slope intercept to the resampled data >>> > before writing. The output dicom should not have the origin >>> > slope/intercept tags. >>> > >>> > I'll try to verify this with Slicer, but I may be out of touch for 2 >>> > weeks? >>> > >>> > Bill >>> > >>> > >>> > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas >>> > wrote: >>> >> Hi Nick, >>> >> >>> >> I can confirm that with the example I get a difference of -1024 (+/- >>> >> 1) in >>> >> between the input and the output, using the ShiftScaleImage part... >>> >> While without this part of code the difference is (+/-1) >>> >> >>> >> I would like to make sure this is the expected behaviour!? >>> >> >>> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson >>> >> >>> >> wrote: >>> >>> >>> >>> OK, I will wait to hear the outcome of your run with the original >>> >>> example >>> >>> then. >>> >>> >>> >>> Cheers, Nick. >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas wrote: >>> >>> >>> >>> Nick, >>> >>> >>> >>> I can't roll back to previous ITK version, important patches on >>> >>> itkGDCMImageIO were very recently merged... >>> >>> >>> >>> >>> >>> >>> >>> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx >>> >>> >>> >>> e.g. >>> >>> >>> >>> >>> >>> >>> >>> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273 >>> >>> >>> >>> >>> >>> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c >>> >>> >>> >>> >>> >>> Arnaud >>> >>> >>> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson >>> >>> wrote: >>> >>>> >>> >>>> I should also mention Arnauld that I use ITK4.5.2. I have had many >>> >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled >>> >>>> back to >>> >>>> ITK4.5.2. >>> >>>> Nick. >>> >>>> >>> >>>> >>> >>>> >>> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas >>> >>>> wrote: >>> >>>> >>> >>>> Hi Matias, >>> >>>> >>> >>>> I guess you are referring to >>> >>>> >>> >>>> >>> >>>> >>> >>>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>>> >>> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e >>> >>>> v4.6.0 >>> >>>> >>> >>>> I use the release branch of ITK >>> >>>> >>> >>>> --- >>> >>>> >>> >>>> Matt, >>> >>>> >>> >>>> Can you comment on this, please? >>> >>>> >>> >>>> Thanks >>> >>>> Arnaud >>> >>>> >>> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull >>> >>>> wrote: >>> >>>> >>> >>>> I had an issue with the resampledicom example once (all my pixel >>> >>>> values >>> >>>> were recalculated by adding rescaleintercept) and then downloaded >>> >>>> the latest >>> >>>> ITK release (4.6) and worked fine. >>> >>>> >>> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow >>> >>>> in >>> >>>> the 4.6 version. >>> >>>> >>> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas >>> >>>> >>> >>>> wrote: >>> >>>>> >>> >>>>> Hi all, >>> >>>>> >>> >>>>> I have been looking at the following wiki example: >>> >>>>> >>> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM >>> >>>>> >>> >>>>> It seems to me that the section to rescale the image is not valid >>> >>>>> anymore with latest ITK version (?) >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333 >>> >>>>> >>> >>>>> Can anyone confirm? >>> >>>>> >>> >>>>> Is this code validated? are output images compared to input ones in >>> >>>>> the >>> >>>>> corresponding test? >>> >>>>> >>> >>>>> Thanks >>> >>>>> Arnaud >>> >>>>> >>> >>>>> _____________________________________ >>> >>>>> Powered by www.kitware.com >>> >>>>> >>> >>>>> Visit other Kitware open-source projects at >>> >>>>> http://www.kitware.com/opensource/opensource.html >>> >>>>> >>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>> >>>>> http://www.kitware.com/products/protraining.php >>> >>>>> >>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>> >>>>> http://www.itk.org/Wiki/ITK_FAQ >>> >>>>> >>> >>>>> Follow this link to subscribe/unsubscribe: >>> >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>>>> >>> >>>> >>> >>>> >>> >>>> _____________________________________ >>> >>>> Powered by www.kitware.com >>> >>>> >>> >>>> Visit other Kitware open-source projects at >>> >>>> http://www.kitware.com/opensource/opensource.html >>> >>>> >>> >>>> Kitware offers ITK Training Courses, for more information visit: >>> >>>> http://www.kitware.com/products/protraining.php >>> >>>> >>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>> >>>> http://www.itk.org/Wiki/ITK_FAQ >>> >>>> >>> >>>> Follow this link to subscribe/unsubscribe: >>> >>>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>>> >>> >>>> >>> >>> >>> >>> >>> >> >>> >> >>> >> _____________________________________ >>> >> Powered by www.kitware.com >>> >> >>> >> Visit other Kitware open-source projects at >>> >> http://www.kitware.com/opensource/opensource.html >>> >> >>> >> Kitware offers ITK Training Courses, for more information visit: >>> >> http://www.kitware.com/products/protraining.php >>> >> >>> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> http://www.itk.org/Wiki/ITK_FAQ >>> >> >>> >> Follow this link to subscribe/unsubscribe: >>> >> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >>> > >>> > >>> > >>> > -- >>> > Unpaid intern in BillsBasement at noware dot com >>> > _____________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://www.kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >> > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Sep 18 13:03:57 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Sep 2014 13:03:57 -0400 Subject: [ITK] [ITK-users] Mask in metric calculation In-Reply-To: References: Message-ID: Hi Lianli, Could you please specify in greater detail which metric class you are using and how the masks are being applied. Thanks, Matt On Wed, Sep 17, 2014 at 9:54 PM, Lianli Liu wrote: > Hi all, > > I just wonder if I define two masks for fixed image and moving image that > are of differnt size, will voxels that fall in both the masks will > contribute to metric calculation? Thanks! > > Regards, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Sep 18 14:58:39 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Sep 2014 14:58:39 -0400 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: <541ACDE8.4080508@laposte.net> References: <541848B5.9060901@laposte.net> <541ACDE8.4080508@laposte.net> Message-ID: Thanks, merged! Should the other pull request be closed? On Thu, Sep 18, 2014 at 8:19 AM, Jo?l Schaerer wrote: > Hi Matt, > > I just sent you a github pull request: > > https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2 > > Note that I ditched my old fork and started with a clean clone of the > template. > > Jo?l > > > > On 09/16/2014 07:26 PM, Matt McCormick wrote: >> >> Hi Jo?l, >> >> Yes, that the current best repository, and fixes are welcome! Please >> add a pull request on the repository and ping the mailing list if it >> is not merged after a few days. >> >> Thanks, >> Matt >> >> On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer >> wrote: >>> >>> Hi all, >>> >>> The template for Insight Journal submissions that is available on GitHub >>> and >>> recommended on the Insight Journal website >>> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) >>> does >>> not build with ITK4. >>> >>> I can try to fix it, but before I do I would like to make sure it is >>> still >>> the current version? >>> >>> Thanks! >>> >>> Jo?l >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From nikita at iitj.ac.in Thu Sep 18 15:45:34 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Thu, 18 Sep 2014 15:45:34 -0400 Subject: [ITK] [ITK-users] (no subject) Message-ID: Hello Admin I wanted to post this question. I have built the ITK libraries on my computer and I have made new projects using CMake but now I want to integarte my project that includes QT , Opencv and other libs with ITK libs. is there any way by including file paths in Visual Studio 2010 I would be able to use ITK functions. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Thu Sep 18 15:47:33 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 19:47:33 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , , Message-ID: Hi Bradley, I am using your itkTIFFImageIO.cxx. It does not seem to have any effect on the problem I'm having. I will check again that I am really compiling with this fix. I wonder whether the failure to display tiffs with size between 2^31 and 2^32 could be caused by the use of a 'long' somewhere instead of an 'unsigned long'. Just grasping at straws. Best Gib ________________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Friday, 19 September 2014 1:02 a.m. To: Gib Bogle; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From g.bogle at auckland.ac.nz Thu Sep 18 15:50:57 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 19:50:57 +0000 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Many people will tell you that it's much better to use cmake to create your VS projects. Cheers Gib ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Nikita Chopra [nikita at iitj.ac.in] Sent: Friday, 19 September 2014 7:45 a.m. To: Insight-users at itk.org Subject: [ITK-users] (no subject) Hello Admin I wanted to post this question. I have built the ITK libraries on my computer and I have made new projects using CMake but now I want to integarte my project that includes QT , Opencv and other libs with ITK libs. is there any way by including file paths in Visual Studio 2010 I would be able to use ITK functions. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From chinander at gmail.com Thu Sep 18 15:51:22 2014 From: chinander at gmail.com (Mike Chinander) Date: Thu, 18 Sep 2014 14:51:22 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: The easiest way is to use CMake to set up your VS project. Here's Qt's documentation on use CMake with Qt. On Thu, Sep 18, 2014 at 2:45 PM, Nikita Chopra wrote: > Hello Admin > I wanted to post this question. > I have built the ITK libraries on my computer and I have made new > projects using CMake but now I want to integarte my project that includes > QT , Opencv and other libs with ITK libs. is there any way by including > file paths in Visual Studio 2010 I would be able to use ITK functions. > Regards > Nikita > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From chinander at gmail.com Thu Sep 18 15:51:57 2014 From: chinander at gmail.com (Mike Chinander) Date: Thu, 18 Sep 2014 14:51:57 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Here's the link I forgot to include in my previous email: http://qt-project.org/doc/qt-5/cmake-manual.html On Thu, Sep 18, 2014 at 2:51 PM, Mike Chinander wrote: > The easiest way is to use CMake to set up your VS project. Here's Qt's > documentation on use CMake with Qt. > > On Thu, Sep 18, 2014 at 2:45 PM, Nikita Chopra wrote: > >> Hello Admin >> I wanted to post this question. >> I have built the ITK libraries on my computer and I have made new >> projects using CMake but now I want to integarte my project that includes >> QT , Opencv and other libs with ITK libs. is there any way by including >> file paths in Visual Studio 2010 I would be able to use ITK functions. >> Regards >> Nikita >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Thu Sep 18 15:51:56 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 18 Sep 2014 20:51:56 +0100 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi, Just to clarify, you want to use Qt, OpenCV and ITK together in a project. Is that correct? I use OpenCV and ITK together in my projects and use CMake to configure and generate build files for MSVS 2010. Is that something you have tried? On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra wrote: > Hello Admin > I wanted to post this question. > I have built the ITK libraries on my computer and I have made new > projects using CMake but now I want to integarte my project that includes > QT , Opencv and other libs with ITK libs. is there any way by including > file paths in Visual Studio 2010 I would be able to use ITK functions. > Regards > Nikita > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From nikita at iitj.ac.in Thu Sep 18 15:57:30 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Thu, 18 Sep 2014 15:57:30 -0400 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi Thanks a lot for quick responses . Can you suggest me the changes I should make in .pro file to add ITK libs there so I can use qmake to build the project .Thanks again I'm new to ITK and any help would be really appreciated. My .pro file is as follows. # ------------------------------ ------------------- # Project created by QtCreator 2010-10-25T15:08:18 # ------------------------------------------------- QT += opengl TARGET = Endoscopic3D TEMPLATE = app INCLUDEPATH += . \ "C:\Program Files\Matrox Imaging\Mil\Include" LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \ -lmil SOURCES += main.cpp \ mainwindow.cpp \ thread.cpp \ display3d.cpp \ matroxmeteorii.cpp HEADERS += mainwindow.h \ thread.h \ display3d.h \ core.h \ matroxmeteorii.h FORMS += mainwindow.ui On Thu, Sep 18, 2014 at 3:51 PM, Girish Mallya Udupi < indianzeppelin at gmail.com> wrote: > Hi, > > Just to clarify, you want to use Qt, OpenCV and ITK together in a project. > Is that correct? > > I use OpenCV and ITK together in my projects and use CMake to configure > and generate build files for MSVS 2010. Is that something you have tried? > > > On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra wrote: > >> Hello Admin >> I wanted to post this question. >> I have built the ITK libraries on my computer and I have made new >> projects using CMake but now I want to integarte my project that includes >> QT , Opencv and other libs with ITK libs. is there any way by including >> file paths in Visual Studio 2010 I would be able to use ITK functions. >> Regards >> Nikita >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Thu Sep 18 16:07:19 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Thu, 18 Sep 2014 21:07:19 +0100 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Never used Qt myself, so can't help you with that. But, have you considered using CMake? There are CMake 'find' modules available for OpenCV, ITK and Qt (from what I see in the link sent by Mike). That same link explains how to use Qt with CMake. On Thu, Sep 18, 2014 at 8:57 PM, Nikita Chopra wrote: > Hi > Thanks a lot for quick responses . Can you suggest me the changes I should > make in .pro file to add ITK libs there so I can use qmake to build the > project .Thanks again I'm new to ITK and any help would be really > appreciated. My .pro file is as follows. > # ------------------------------ > ------------------- > # Project created by QtCreator 2010-10-25T15:08:18 > # ------------------------------------------------- > QT += opengl > TARGET = Endoscopic3D > TEMPLATE = app > INCLUDEPATH += . \ > "C:\Program Files\Matrox Imaging\Mil\Include" > LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \ > -lmil > SOURCES += main.cpp \ > mainwindow.cpp \ > thread.cpp \ > display3d.cpp \ > matroxmeteorii.cpp > HEADERS += mainwindow.h \ > thread.h \ > display3d.h \ > core.h \ > matroxmeteorii.h > FORMS += mainwindow.ui > > On Thu, Sep 18, 2014 at 3:51 PM, Girish Mallya Udupi < > indianzeppelin at gmail.com> wrote: > >> Hi, >> >> Just to clarify, you want to use Qt, OpenCV and ITK together in a >> project. Is that correct? >> >> I use OpenCV and ITK together in my projects and use CMake to configure >> and generate build files for MSVS 2010. Is that something you have tried? >> >> >> On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra wrote: >> >>> Hello Admin >>> I wanted to post this question. >>> I have built the ITK libraries on my computer and I have made new >>> projects using CMake but now I want to integarte my project that includes >>> QT , Opencv and other libs with ITK libs. is there any way by including >>> file paths in Visual Studio 2010 I would be able to use ITK functions. >>> Regards >>> Nikita >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> >> -- >> Regards, >> Girish >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From joel.schaerer at gmail.com Thu Sep 18 16:12:09 2014 From: joel.schaerer at gmail.com (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 18 Sep 2014 22:12:09 +0200 Subject: [ITK] [ITK-users] Insight Journal template ITKv4 compatibilty In-Reply-To: References: <541848B5.9060901@laposte.net> <541ACDE8.4080508@laposte.net> Message-ID: <541B3C99.1070503@gmail.com> Done! On 09/18/2014 08:58 PM, Matt McCormick wrote: > Thanks, merged! > > Should the other pull request be closed? > > On Thu, Sep 18, 2014 at 8:19 AM, Jo?l Schaerer > wrote: >> Hi Matt, >> >> I just sent you a github pull request: >> >> https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2 >> >> Note that I ditched my old fork and started with a clean clone of the >> template. >> >> Jo?l >> >> >> >> On 09/16/2014 07:26 PM, Matt McCormick wrote: >>> Hi Jo?l, >>> >>> Yes, that the current best repository, and fixes are welcome! Please >>> add a pull request on the repository and ping the mailing list if it >>> is not merged after a few days. >>> >>> Thanks, >>> Matt >>> >>> On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer >>> wrote: >>>> Hi all, >>>> >>>> The template for Insight Journal submissions that is available on GitHub >>>> and >>>> recommended on the Insight Journal website >>>> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) >>>> does >>>> not build with ITK4. >>>> >>>> I can try to fix it, but before I do I would like to make sure it is >>>> still >>>> the current version? >>>> >>>> Thanks! >>>> >>>> Jo?l >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >> > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Sep 18 16:32:19 2014 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 18 Sep 2014 20:32:19 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , , , Message-ID: Gib, I have continued to work on refactoring ITK's TIFFImageIO, fixing some bugs along the way: http://review.source.kitware.com/#/c/17111/ If you have some specific images that are problematic, it would be good if you could run "tiffinfo"[1] on them to look at the tags or provide a copy of them. Thanks, Brad [1] http://www.libtiff.org/tools.html ________________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Thursday, September 18, 2014 3:47 PM To: Lowekamp, Bradley (NIH/NLM/LHC) [C]; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hi Bradley, I am using your itkTIFFImageIO.cxx. It does not seem to have any effect on the problem I'm having. I will check again that I am really compiling with this fix. I wonder whether the failure to display tiffs with size between 2^31 and 2^32 could be caused by the use of a 'long' somewhere instead of an 'unsigned long'. Just grasping at straws. Best Gib ________________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Friday, 19 September 2014 1:02 a.m. To: Gib Bogle; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From chinander at gmail.com Thu Sep 18 16:46:51 2014 From: chinander at gmail.com (Mike Chinander) Date: Thu, 18 Sep 2014 15:46:51 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: A CMakeLists.txt files replaces your .pro project file. Yours would look something like the following. I don't use Qt Designer so I'm not quite sure about the .ui-related configuration (or the OpenGL module). cmake_minimum_required(VERSION 2.8.12) PROJECT(Endoscopic3D) set(CMAKE_AUTOMOC ON) set(CMAKE_INCLUDE_CURRENT_DIR ON) SET(ITK_DIR "C:/Program Files/ITK/lib/cmake/ITK-4.5") FIND_PACKAGE(Qt5Core REQUIRED ) FIND_PACKAGE(Qt5Widgets REQUIRED) FIND_PACKAGE(Qt5OpenGL REQUIRED) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) include_directories (${CMAKE_CURRENT_BINARY_DIR}) SET (SRCS main.cpp mainwindow.cpp thread.cpp display3d.cpp matroxmeteorii.cpp) SET (MOC_SRCS mainwindow.h thread.h display3d.h core.h matroxmeteorii.h) QT5_WRAP_UI(UIS_HDRS mainwindow.ui) ADD_EXECUTABLE(Endoscopic3D WIN32 ${SRCS} ${UIS_HDRS} ) TARGET_LINK_LIBRARIES(Endoscopic3D Qt5::Widgets Qt5::OpenGL ${ITK_LIBRARIES}) On Thu, Sep 18, 2014 at 2:57 PM, Nikita Chopra wrote: > Hi > Thanks a lot for quick responses . Can you suggest me the changes I should > make in .pro file to add ITK libs there so I can use qmake to build the > project .Thanks again I'm new to ITK and any help would be really > appreciated. My .pro file is as follows. > # ------------------------------ > ------------------- > # Project created by QtCreator 2010-10-25T15:08:18 > # ------------------------------------------------- > QT += opengl > TARGET = Endoscopic3D > TEMPLATE = app > INCLUDEPATH += . \ > "C:\Program Files\Matrox Imaging\Mil\Include" > LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \ > -lmil > SOURCES += main.cpp \ > mainwindow.cpp \ > thread.cpp \ > display3d.cpp \ > matroxmeteorii.cpp > HEADERS += mainwindow.h \ > thread.h \ > display3d.h \ > core.h \ > matroxmeteorii.h > FORMS += mainwindow.ui > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Thu Sep 18 17:13:11 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Thu, 18 Sep 2014 21:13:11 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , , Message-ID: Hi Bradley, To be completely safe, I'd like to know exactly what steps I should follow to get the changes you've made. 1. Edit Superbuild/External_ITKv4.cmake: modify the repository to: git://itk.org/ITK.git change the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c 2. ... Thanks Gib ________________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Friday, 19 September 2014 1:02 a.m. To: Gib Bogle; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From g.bogle at auckland.ac.nz Fri Sep 19 01:26:27 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Fri, 19 Sep 2014 05:26:27 +0000 Subject: [ITK] [slicer-devel] BigTIFF In-Reply-To: References: <9422341B-4496-48BB-B9FA-CE5A5169E20B@mail.nih.gov> , , , Message-ID: Hi Bradley, I made that change to the cmake file, and rebuilt Slicer. The situation is unchanged - tiff files in the size range 2^31 - 2^32 load but do not display. Gib ________________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Friday, 19 September 2014 1:02 a.m. To: Gib Bogle; Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: RE: [ITK] [slicer-devel] BigTIFF Hello, I thought I sent this message last nigh, regarding the tiff reading issue. Did you update the ITK version to ITK master? I just committed a fix to ITK this week to likely address this issue: https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c You will need to modify the repository to: git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file. Brad ________________________________ From: Gib Bogle [g.bogle at auckland.ac.nz] Sent: Wednesday, September 17, 2014 11:07 PM To: Jean-Christophe Fillion-Robin Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper Subject: Re: [ITK] [slicer-devel] BigTIFF Hi J-C, OK, now that I know it's the Network drives I can easily take care of it. What do I need to do to ensure that the Python code is found? Is it just a matter of adding a directory to the PATH? Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size? Another observation: When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image. But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank). Thanks Gib ________________________________ From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com] Sent: Thursday, 18 September 2014 2:51 p.m. To: Gib Bogle Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org Subject: Re: [ITK] [slicer-devel] BigTIFF Hi Gib, On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle > wrote: Correction! You were right. There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive. Now it's responsive :) There is indeed known issue with network drive and file dialog. See https://bugreports.qt-project.org/browse/QTBUG-13182 If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded" There is another wrinkle that I'm not concerned about right now. When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message: Traceback (most recent call last): File "", line 7, in File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in import vtk, qt, ctk ImportError: No module named vtk but the program runs. I don't see that message when I run the executable in Slicer-build. The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them. I have seen any difference in the ability to display the tiff files. This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ... Hth JC -- +1 919 869 8849 From blowekamp at mail.nih.gov Fri Sep 19 09:37:40 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 19 Sep 2014 09:37:40 -0400 Subject: [ITK] [ITK-dev] ITK Gerrit Primer Message-ID: I just stumbled on this wiki web page ( it actually was a paraview url initially ): http://www.itk.org/Wiki/ITK/Gerrit/ReviewPrimer I don't recall seeing it before, it looks like it has some good detailed information in it about how to use gerrit and do reviews. Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From norman-k-williams at uiowa.edu Fri Sep 19 10:14:01 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 19 Sep 2014 14:14:01 +0000 Subject: [ITK] [ITK-dev] The fix for patch in which I torpedoed the Release build nightlies Message-ID: Je suis plus d?sol?e! I typed ?/ *? instead of ?/*? and if NDEBUG is set, it?s a compiler error every time vml_vector_fixed_ref.h is included, compilers get mad. http://review.source.kitware.com/#/c/17126/ ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From hiner at wisc.edu Fri Sep 19 11:09:13 2014 From: hiner at wisc.edu (Mark Hiner) Date: Fri, 19 Sep 2014 10:09:13 -0500 Subject: [ITK] [ITK-dev] SCIFIO nightly build e-mail Message-ID: Hello ITK developers, Would it be possible to add imagej-builds at imagej.net to get build failure notifications for the SCIFIO nightly build ? I didn't realize that I had broken the build a couple days ago. Much appreciated! Regards, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From g.bogle at auckland.ac.nz Sat Sep 20 02:30:53 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sat, 20 Sep 2014 06:30:53 +0000 Subject: [ITK] Question about BigTIFF Message-ID: I observe that an ITK-created tiff that is bigger than 2^31 but smaller than 2^32 is a BigTIFF - it has Version number = 43 in the header. I am suddenly wondering why such a file is a BigTIFF. On this site: http://www.awaresystems.be/imaging/tiff/bigtiff.html it says: "The TIFF file format uses 32bit offsets and, as such, is limited to 4 gigabytes. This has been quite sufficient for many years. Today however, there is a need for a good multi-purpose open image file format that can handle huge images, or very large collections of images, breaking the 4 gig boundary. There is currently an ongoing attempt to launch a new variant of TIFF, called BigTIFF, that closely resembles TIFF, but uses 64bit offsets instead...." In other words, BigTIFF is needed for files bigger than 2^32 bytes, or 4 GB. Can somebody explain this? Cheers Gib -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Sat Sep 20 12:09:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 20 Sep 2014 12:09:55 -0400 Subject: [ITK] Question about BigTIFF In-Reply-To: References: Message-ID: Hi Gib, It should be a BigTIFF and it is, correct? Thanks for your investigations. Matt On Sat, Sep 20, 2014 at 2:30 AM, Gib Bogle wrote: > I observe that an ITK-created tiff that is bigger than 2^31 but smaller than > 2^32 is a BigTIFF - it has Version number = 43 in the header. I am suddenly > wondering why such a file is a BigTIFF. On this site: > http://www.awaresystems.be/imaging/tiff/bigtiff.html > it says: > "The TIFF file format uses 32bit offsets and, as such, is limited to 4 > gigabytes. This has been quite sufficient for many years. Today however, > there is a need for a good multi-purpose open image file format that can > handle huge images, or very large collections of images, breaking the 4 gig > boundary. There is currently an ongoing attempt to launch a new variant of > TIFF, called BigTIFF, that closely resembles TIFF, but uses 64bit offsets > instead...." > > In other words, BigTIFF is needed for files bigger than 2^32 bytes, or 4 GB. > > Can somebody explain this? > > Cheers > Gib > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From g.bogle at auckland.ac.nz Sat Sep 20 15:24:18 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sat, 20 Sep 2014 19:24:18 +0000 Subject: [ITK] Question about BigTIFF In-Reply-To: References: , Message-ID: Hi Matt, The file big1300.tif, which is just bigger than 2^31, is a BigTIFF. I'm just wondering why, since strictly speaking the BigTIFF format is needed for files > 2^32. This is now academic, I think, since it appears that Slicer is reading this file correctly, and the question is why it is not being displayed. Best Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Sunday, 21 September 2014 4:09 a.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] Question about BigTIFF Hi Gib, It should be a BigTIFF and it is, correct? Thanks for your investigations. Matt On Sat, Sep 20, 2014 at 2:30 AM, Gib Bogle wrote: > I observe that an ITK-created tiff that is bigger than 2^31 but smaller than > 2^32 is a BigTIFF - it has Version number = 43 in the header. I am suddenly > wondering why such a file is a BigTIFF. On this site: > http://www.awaresystems.be/imaging/tiff/bigtiff.html > it says: > "The TIFF file format uses 32bit offsets and, as such, is limited to 4 > gigabytes. This has been quite sufficient for many years. Today however, > there is a need for a good multi-purpose open image file format that can > handle huge images, or very large collections of images, breaking the 4 gig > boundary. There is currently an ongoing attempt to launch a new variant of > TIFF, called BigTIFF, that closely resembles TIFF, but uses 64bit offsets > instead...." > > In other words, BigTIFF is needed for files bigger than 2^32 bytes, or 4 GB. > > Can somebody explain this? > > Cheers > Gib > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From g.bogle at auckland.ac.nz Sun Sep 21 18:45:23 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sun, 21 Sep 2014 22:45:23 +0000 Subject: [ITK] BigTIFF and tiffinfo Message-ID: The saga continues... I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has revealed a problem with the tiff files built using the ITK that Slicer has created. This version was pulled using this cmake line: set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # slicer-v4.6.0-2014-09-19-056d97b When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: ... TIFF Directory at offset 0x7fd0fcf4 (2144402676) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1265-1300 Software: InsightToolkit TIFF Directory at offset 0x7fead588 (2146096520) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1266-1300 Software: InsightToolkit TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. TIFFReadDirectory: Failed to read directory at offset 2147790364. There is no problem with the compressed version of the image. This has added to my confusion. A program built with the same ITK library can read this file, raising the possibility that it is tiffinfo itself that can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo using Win64. And Vaa3D also gets this seek error when reading the file. Any ideas? Gib PS It is probably totally irrelevant to the tiff issue, but I happened to notice that there are a few occurrences in other places of checks for _WIN64, which is not defined. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Sun Sep 21 20:21:42 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 22 Sep 2014 00:21:42 +0000 Subject: [ITK] BigTIFF and tiffinfo In-Reply-To: References: Message-ID: Followup: I ran tiffdump on this file, and surprisngly it was able to read to the end of the file, and all the offsets look fine. So it seems that tiffinfo is at fault - very strange since one would expect that tiffdump and tiffinfo would use identical methods. More tiff strangeness... ________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 22 September 2014 10:45 a.m. To: community at itk.org Subject: [ITK] BigTIFF and tiffinfo The saga continues... I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has revealed a problem with the tiff files built using the ITK that Slicer has created. This version was pulled using this cmake line: set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # slicer-v4.6.0-2014-09-19-056d97b When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: ... TIFF Directory at offset 0x7fd0fcf4 (2144402676) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1265-1300 Software: InsightToolkit TIFF Directory at offset 0x7fead588 (2146096520) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1266-1300 Software: InsightToolkit TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. TIFFReadDirectory: Failed to read directory at offset 2147790364. There is no problem with the compressed version of the image. This has added to my confusion. A program built with the same ITK library can read this file, raising the possibility that it is tiffinfo itself that can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo using Win64. And Vaa3D also gets this seek error when reading the file. Any ideas? Gib PS It is probably totally irrelevant to the tiff issue, but I happened to notice that there are a few occurrences in other places of checks for _WIN64, which is not defined. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Sun Sep 21 21:57:01 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 22 Sep 2014 01:57:01 +0000 Subject: [ITK] BigTIFF and tiffinfo In-Reply-To: References: , Message-ID: Something cleared up (sort of): I discovered that while the ITK build of the itktiff project links tif_win32.c, the tiff-4.0.3 build was not linking this file. It turns out that this is controlled by a build option in nmake.opt: # # Uncomment following line to enable using Windows Common RunTime Library # instead of Windows specific system calls. See notes on top of tif_unix.c # module for details. # #USE_WIN_CRT_LIB = 1 # Gib commented this When I commented out this line and rebuilt libtiff, tiffinfo no longer fails at the 2 GB boundary. I don't understand what it's about, but it does resolve that mystery. Gib ________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 22 September 2014 12:21 p.m. To: community at itk.org Subject: Re: [ITK] BigTIFF and tiffinfo Followup: I ran tiffdump on this file, and surprisngly it was able to read to the end of the file, and all the offsets look fine. So it seems that tiffinfo is at fault - very strange since one would expect that tiffdump and tiffinfo would use identical methods. More tiff strangeness... ________________________________ From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Monday, 22 September 2014 10:45 a.m. To: community at itk.org Subject: [ITK] BigTIFF and tiffinfo The saga continues... I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has revealed a problem with the tiff files built using the ITK that Slicer has created. This version was pulled using this cmake line: set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # slicer-v4.6.0-2014-09-19-056d97b When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: ... TIFF Directory at offset 0x7fd0fcf4 (2144402676) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1265-1300 Software: InsightToolkit TIFF Directory at offset 0x7fead588 (2146096520) Subfile Type: multi-page document (2 = 0x2) Image Width: 1300 Image Length: 1300 Resolution: 25.4, 25.4 pixels/inch Bits/Sample: 8 Compression Scheme: None Photometric Interpretation: min-is-black Orientation: row 0 top, col 0 lhs Samples/Pixel: 1 Rows/Strip: 6 Planar Configuration: single image plane Page Number: 1266-1300 Software: InsightToolkit TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. TIFFReadDirectory: Failed to read directory at offset 2147790364. There is no problem with the compressed version of the image. This has added to my confusion. A program built with the same ITK library can read this file, raising the possibility that it is tiffinfo itself that can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo using Win64. And Vaa3D also gets this seek error when reading the file. Any ideas? Gib PS It is probably totally irrelevant to the tiff issue, but I happened to notice that there are a few occurrences in other places of checks for _WIN64, which is not defined. -------------- next part -------------- An HTML attachment was scrubbed... URL: From llliu at umich.edu Sun Sep 21 22:30:37 2014 From: llliu at umich.edu (Lianli Liu) Date: Sun, 21 Sep 2014 22:30:37 -0400 Subject: [ITK] [ITK-users] B spline multi grid registration Message-ID: Hi all, I am trying to use the B spline multi grid registration method in ITK, as given by the example code deformableregistration7.cxx. I used to 3D MRI images in analyze format (.img). I received the following error information: terminate called after throwing an instance of 'std::bad_alloc' I was wondering what is wrong and how to fix it? Thanks! Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From nikita at iitj.ac.in Sun Sep 21 22:44:38 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Sun, 21 Sep 2014 22:44:38 -0400 Subject: [ITK] [ITK-users] B spline multi grid registration In-Reply-To: References: Message-ID: Did you tr to debug it , Can you share the specific line in code where the error occurs ? I have used the same example to register CT scans with slight modification. On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu wrote: > Hi all, > > I am trying to use the B spline multi grid registration method in ITK, as > given by the example code deformableregistration7.cxx. I used to 3D MRI > images in analyze format (.img). I received the following error information: > > terminate called after throwing an instance of 'std::bad_alloc' > > I was wondering what is wrong and how to fix it? > > Thanks! > > Lianli > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sun Sep 21 22:54:25 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 21 Sep 2014 22:54:25 -0400 Subject: [ITK] BigTIFF and tiffinfo In-Reply-To: References: Message-ID: Hi Gib, Thanks for sharing the information. A good program to validate TIFF behavior would be FIJI [1], whose primary image format is TIFF's. HTH, Matt [1] http://fiji.sc/wiki/index.php/Fiji On Sun, Sep 21, 2014 at 9:57 PM, Gib Bogle wrote: > Something cleared up (sort of): I discovered that while the ITK build of > the itktiff project links tif_win32.c, the tiff-4.0.3 build was not linking > this file. It turns out that this is controlled by a build option in > nmake.opt: > > # > # Uncomment following line to enable using Windows Common RunTime Library > # instead of Windows specific system calls. See notes on top of tif_unix.c > # module for details. > # > #USE_WIN_CRT_LIB = 1 # Gib commented this > > When I commented out this line and rebuilt libtiff, tiffinfo no longer fails > at the 2 GB boundary. I don't understand what it's about, but it does > resolve that mystery. > > Gib > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 22 September 2014 12:21 p.m. > To: community at itk.org > Subject: Re: [ITK] BigTIFF and tiffinfo > > Followup: I ran tiffdump on this file, and surprisngly it was able to read > to the end of the file, and all the offsets look fine. So it seems that > tiffinfo is at fault - very strange since one would expect that tiffdump and > tiffinfo would use identical methods. More tiff strangeness... > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 22 September 2014 10:45 a.m. > To: community at itk.org > Subject: [ITK] BigTIFF and tiffinfo > > The saga continues... > > I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has > revealed a problem with the tiff files built using the ITK that Slicer has > created. This version was pulled using this cmake line: > set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # > slicer-v4.6.0-2014-09-19-056d97b > > When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger > than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: > > ... > TIFF Directory at offset 0x7fd0fcf4 (2144402676) > Subfile Type: multi-page document (2 = 0x2) > Image Width: 1300 Image Length: 1300 > Resolution: 25.4, 25.4 pixels/inch > Bits/Sample: 8 > Compression Scheme: None > Photometric Interpretation: min-is-black > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 6 > Planar Configuration: single image plane > Page Number: 1265-1300 > Software: InsightToolkit > TIFF Directory at offset 0x7fead588 (2146096520) > Subfile Type: multi-page document (2 = 0x2) > Image Width: 1300 Image Length: 1300 > Resolution: 25.4, 25.4 pixels/inch > Bits/Sample: 8 > Compression Scheme: None > Photometric Interpretation: min-is-black > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 6 > Planar Configuration: single image plane > Page Number: 1266-1300 > Software: InsightToolkit > TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. > TIFFReadDirectory: Failed to read directory at offset 2147790364. > > There is no problem with the compressed version of the image. > > This has added to my confusion. A program built with the same ITK library > can read this file, raising the possibility that it is tiffinfo itself that > can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo > using Win64. And Vaa3D also gets this seek error when reading the file. > > Any ideas? > > Gib > > PS It is probably totally irrelevant to the tiff issue, but I happened to > notice that there are a few occurrences in other places of checks for > _WIN64, which is not defined. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Sun Sep 21 22:58:59 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 21 Sep 2014 22:58:59 -0400 Subject: [ITK] [ITK-users] B spline multi grid registration In-Reply-To: References: Message-ID: Hi Lianli, On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu wrote: > Hi all, > > I am trying to use the B spline multi grid registration method in ITK, as > given by the example code deformableregistration7.cxx. I used to 3D MRI > images in analyze format (.img). I received the following error information: > > terminate called after throwing an instance of 'std::bad_alloc' > > I was wondering what is wrong and how to fix it? Are you running out of memory? HTH, Matt _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Sun Sep 21 23:01:28 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Mon, 22 Sep 2014 03:01:28 +0000 Subject: [ITK] BigTIFF and tiffinfo In-Reply-To: References: , Message-ID: Hi Matt, Yes, I checked a while ago that Fiji can read these images. The issue with tiffinfo had me worried, because that's straight from the horse's mouth, so to speak. Knowing about that build option puts my mind at rest. I still need to find out the cause of Slicer's bizarre behaviour, which I don't expect to be related to this issue. I have also been trying to get Vaa3D to read the BigTIFFs. Using the experience with tiffinfo, I've just succeeded in building an executable that works OK. Cheers Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Monday, 22 September 2014 2:54 p.m. To: Gib Bogle Cc: community at itk.org Subject: Re: [ITK] BigTIFF and tiffinfo Hi Gib, Thanks for sharing the information. A good program to validate TIFF behavior would be FIJI [1], whose primary image format is TIFF's. HTH, Matt [1] http://fiji.sc/wiki/index.php/Fiji On Sun, Sep 21, 2014 at 9:57 PM, Gib Bogle wrote: > Something cleared up (sort of): I discovered that while the ITK build of > the itktiff project links tif_win32.c, the tiff-4.0.3 build was not linking > this file. It turns out that this is controlled by a build option in > nmake.opt: > > # > # Uncomment following line to enable using Windows Common RunTime Library > # instead of Windows specific system calls. See notes on top of tif_unix.c > # module for details. > # > #USE_WIN_CRT_LIB = 1 # Gib commented this > > When I commented out this line and rebuilt libtiff, tiffinfo no longer fails > at the 2 GB boundary. I don't understand what it's about, but it does > resolve that mystery. > > Gib > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 22 September 2014 12:21 p.m. > To: community at itk.org > Subject: Re: [ITK] BigTIFF and tiffinfo > > Followup: I ran tiffdump on this file, and surprisngly it was able to read > to the end of the file, and all the offsets look fine. So it seems that > tiffinfo is at fault - very strange since one would expect that tiffdump and > tiffinfo would use identical methods. More tiff strangeness... > ________________________________ > From: Community [community-bounces at itk.org] on behalf of Gib Bogle > [g.bogle at auckland.ac.nz] > Sent: Monday, 22 September 2014 10:45 a.m. > To: community at itk.org > Subject: [ITK] BigTIFF and tiffinfo > > The saga continues... > > I finally found and built tiff-4.0.2, to get tiffinfo.exe. This has > revealed a problem with the tiff files built using the ITK that Slicer has > created. This version was pulled using this cmake line: > set(ITKv4_GIT_TAG 056d97b66a1ddbae77e2217c5bd96e436c7e44fc) # > slicer-v4.6.0-2014-09-19-056d97b > > When I execute 'tiffinfo -D big1300.tif' or any uncompressed tiff bigger > than 2 GB tiffinfo gets a seek error when it tries to go over the 2 GB mark: > > ... > TIFF Directory at offset 0x7fd0fcf4 (2144402676) > Subfile Type: multi-page document (2 = 0x2) > Image Width: 1300 Image Length: 1300 > Resolution: 25.4, 25.4 pixels/inch > Bits/Sample: 8 > Compression Scheme: None > Photometric Interpretation: min-is-black > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 6 > Planar Configuration: single image plane > Page Number: 1265-1300 > Software: InsightToolkit > TIFF Directory at offset 0x7fead588 (2146096520) > Subfile Type: multi-page document (2 = 0x2) > Image Width: 1300 Image Length: 1300 > Resolution: 25.4, 25.4 pixels/inch > Bits/Sample: 8 > Compression Scheme: None > Photometric Interpretation: min-is-black > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 6 > Planar Configuration: single image plane > Page Number: 1266-1300 > Software: InsightToolkit > TIFFFetchDirectory: big1300.tif: Seek error accessing TIFF directory. > TIFFReadDirectory: Failed to read directory at offset 2147790364. > > There is no problem with the compressed version of the image. > > This has added to my confusion. A program built with the same ITK library > can read this file, raising the possibility that it is tiffinfo itself that > can't handle a memory pointer > 2 GB. But I did build libtiff and tiffinfo > using Win64. And Vaa3D also gets this seek error when reading the file. > > Any ideas? > > Gib > > PS It is probably totally irrelevant to the tiff issue, but I happened to > notice that there are a few occurrences in other places of checks for > _WIN64, which is not defined. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From llliu at umich.edu Sun Sep 21 23:13:09 2014 From: llliu at umich.edu (Lianli Liu) Date: Sun, 21 Sep 2014 23:13:09 -0400 Subject: [ITK] [ITK-users] B spline multi grid registration In-Reply-To: References: Message-ID: Hi all, Thanks for help. The program runs after I change the metric from mean square error to mutual information. But the new problem is the transformed image looks really wired. Seems the intensity is distorted a lot. I was wondering what may be the possible cause of this? Regards, Lianli On Sun, Sep 21, 2014 at 10:58 PM, Matt McCormick wrote: > Hi Lianli, > > On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu wrote: > > Hi all, > > > > I am trying to use the B spline multi grid registration method in ITK, as > > given by the example code deformableregistration7.cxx. I used to 3D MRI > > images in analyze format (.img). I received the following error > information: > > > > terminate called after throwing an instance of 'std::bad_alloc' > > > > I was wondering what is wrong and how to fix it? > > Are you running out of memory? > > HTH, > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From vijayarani.shanmugavadivu at appasamy.com Mon Sep 22 07:52:36 2014 From: vijayarani.shanmugavadivu at appasamy.com (vijayarani) Date: Mon, 22 Sep 2014 04:52:36 -0700 (PDT) Subject: [ITK] [ITK-users] Picking 10000 samples from a larger mha image using ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram. Message-ID: <1411386756138-7586255.post@n2.nabble.com> Hi I tried to pick 10000 samples from a larger mha image (which size is 167 MB) using ImageRandomNonRepeatingConstIteratorWithIndex class and tried to find the histogram and percentile values for the resultant image. However it gives 0 to all the percentiles. When I do the same for a small image it gives the valid percentile values.How to achieve finding histogram and percentiles for a larger mha image by picking up only 10000 samples from the original image? Thanks & Regards Vijaya Rani S -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Mon Sep 22 09:08:11 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 22 Sep 2014 09:08:11 -0400 Subject: [ITK] [ITK-users] Picking 10000 samples from a larger mha image using ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram. In-Reply-To: <1411386756138-7586255.post@n2.nabble.com> References: <1411386756138-7586255.post@n2.nabble.com> Message-ID: Hello, Do you have a small compilable example of this problem? It's really impossible to give specific information without any code. The most frequent reason for this type of issue is that the Update method to the reader has not been called before a manual iteration over the image. So the size of the image is zero during iteration. Brad On Sep 22, 2014, at 7:52 AM, vijayarani wrote: > Hi > I tried to pick 10000 samples from a larger mha image (which size is 167 MB) > using ImageRandomNonRepeatingConstIteratorWithIndex class and tried to find > the histogram and percentile > values for the resultant image. However it gives 0 to all the percentiles. > When I do the same for a small image it gives the valid percentile > values.How to achieve finding histogram and percentiles for a larger mha > image by picking up only 10000 samples from the original image? > > Thanks & Regards > Vijaya Rani S > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From genet at biomed.ee.ethz.ch Mon Sep 22 15:49:25 2014 From: genet at biomed.ee.ethz.ch (Martin Genet) Date: Mon, 22 Sep 2014 21:49:25 +0200 Subject: [ITK] [ITK-users] FEMRegistration Message-ID: <54207D45.9070409@biomed.ee.ethz.ch> Dear all: Trying to use FEMRegistration on a bunch of images. Still trying to figure out the following: - What is the simplest way to convert an external mesh (e.g., vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and vice versa (for post-treatment, vizualization)? - If the mesh covers only a subset of the image, what happens to the rest of the image? Any help would be super appreciated. Sorry if that's too trivial. Thanks in advance. Martin _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Sep 22 16:54:40 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 Sep 2014 16:54:40 -0400 Subject: [ITK] [ITK-users] FEMRegistration In-Reply-To: <54207D45.9070409@biomed.ee.ethz.ch> References: <54207D45.9070409@biomed.ee.ethz.ch> Message-ID: Hi Martin, itk::MeshFileReader and itk::MeshFileWriter are great classes for importing / exporting meshes. HTH, Matt On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet wrote: > Dear all: > > Trying to use FEMRegistration on a bunch of images. Still trying to figure > out the following: > > - What is the simplest way to convert an external mesh (e.g., > vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and vice > versa (for post-treatment, vizualization)? > > - If the mesh covers only a subset of the image, what happens to the rest > of the image? > > Any help would be super appreciated. Sorry if that's too trivial. Thanks in > advance. > > Martin > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From vijayarani.shanmugavadivu at appasamy.com Tue Sep 23 02:10:56 2014 From: vijayarani.shanmugavadivu at appasamy.com (vijayarani) Date: Mon, 22 Sep 2014 23:10:56 -0700 (PDT) Subject: [ITK] [ITK-users] Picking 10000 samples from a larger mha image using ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram. In-Reply-To: References: <1411386756138-7586255.post@n2.nabble.com> Message-ID: <1411452656592-7586259.post@n2.nabble.com> Hi, Thanks for your reply.Here is my code and the output #include "itkImage.h" #include "itkImageFileReader.h" #include #include #include #include "itkImageFileWriter.h" #include "itkImageRandomNonRepeatingConstIteratorWithIndex.h" int main(int argc, char*argv[]) { const unsigned int Dimension = 3; typedef unsigned short PixelType; typedef itk::Image ImageType; typedef itk::ImageFileReader< ImageType > ImageReaderType; typedef itk::ImageFileWriter< ImageType > ImageWriterType; ImageReaderType::Pointer ImageReader = ImageReaderType::New(); ImageWriterType::Pointer ImageWriter = ImageWriterType::New(); ImageReader->SetFileName( "SampleMha.mha" ); ImageWriter->SetFileName( "RandomIterator.mha" ); ImageType::Pointer Image = ImageReader->GetOutput(); Image->Update(); ImageType::RegionType region=Image->GetRequestedRegion(); ImageType::SizeType size=region.GetSize(); ImageType::IndexType index=region.GetIndex(); ImageType::IndexType start = index; ImageType::SpacingType spacing = Image->GetSpacing(); ImageType::DirectionType direction = Image->GetDirection(); ImageType::RegionType newregion; newregion.SetSize(size); newregion.SetIndex(start); std::cout << "The size of the image is " << size <SetRegions(newregion); output->SetSpacing(spacing); output->SetDirection(direction); output->Allocate(); output->FillBuffer(0); output->Update(); typedef itk::ImageRandomNonRepeatingConstIteratorWithIndex ConstIteratorType; ConstIteratorType inputIt( Image, region ); unsigned int number = 10000; inputIt.SetNumberOfSamples( number ); std::cout << "The number of samples is " << number << std::endl; inputIt.ReinitializeSeed(); inputIt.GoToBegin(); while(!inputIt.IsAtEnd()) { output->SetPixel(inputIt.GetIndex(), inputIt.Get()); ++inputIt; } output->Update(); ImageWriter->SetInput( output ); ImageWriter->Update(); calculatePercentile("RandomIterator.mha"); return EXIT_SUCCESS; } void calculatePercentile(QString file) { qDebug()<<"Calling: calculatePercentile"; //Define the pixel type and dimension for reader typedef int InternalPixelType; const unsigned int Dimension=3; typedef itk::Image InternalImageType; //Define the reader typedef itk::ImageFileReader ReaderType; ReaderType::Pointer reader = ReaderType::New(); typedef InternalPixelType HistogramMeasurementType; typedef itk::Statistics::Histogram< HistogramMeasurementType > HistogramType; typedef itk::Statistics::ImageToListSampleAdaptor< InternalImageType > AdaptorType; AdaptorType::Pointer adaptor = AdaptorType::New(); typedef itk::Statistics::SampleToHistogramFilter FilterType; FilterType::Pointer filter = FilterType::New(); if(QFileInfo(file).suffix()=="mha") { typedef itk::MetaImageIO MetaImageIOType; MetaImageIOType::Pointer metaIO=MetaImageIOType::New(); metaIO->SetFileName(file.toLocal8Bit().data()); reader->SetFileName(file.toLocal8Bit().data()); metaIO->ReadImageInformation(); qDebug()<<"No of dimesnsions "<GetNumberOfDimensions()<<"No of Comps "<GetNumberOfComponents()<<"Comp size "<GetComponentSize(); qDebug()<<"Image size in bytes "<GetImageSizeInBytes()<<"Image size in Comps "<GetImageSizeInComponents()<<"Image size in Pixels "<GetImageSizeInPixels(); adaptor->SetImage(reader->GetOutput() ); try { reader->Update(); } catch( itk::ExceptionObject & excp ) { std::cerr << "Problem reading image file" << std::endl; std::cerr << excp << std::endl; } const unsigned int numberOfComponents = metaIO->GetNumberOfComponents(); HistogramType::SizeType size(numberOfComponents); size.Fill( metaIO->GetImageSizeInPixels() ); filter->SetInput( adaptor ); filter->SetHistogramSize( size ); filter->SetMarginalScale( 10 ); HistogramType::MeasurementVectorType min( numberOfComponents ); HistogramType::MeasurementVectorType max( numberOfComponents ); min.Fill( 0 ); max.Fill( metaIO->GetImageSizeInComponents() ); filter->SetHistogramBinMinimum( min ); filter->SetHistogramBinMaximum( max ); filter->Update(); } HistogramType::ConstPointer histogram = filter->GetOutput(); qDebug()<<"5th percentile is "<< histogram->Quantile( 0, 0.05 ) <<" 25th percentile is "<Quantile( 0, 0.25 )<<" 50th percentile is "<Quantile( 0, 0.50 )<<" 75th percentile is "<Quantile( 0, 0.75 )<<" 95th percentile is "<Quantile( 0, 0.95 ); } And the output is: The size of the image is [650, 450, 300] The number of samples is 10000 Calling: calculatePercentile No of dimesnsions 3 No of Comps 1 Comp size 2 Image size in bytes 175500000 Image size in Comps 87750000 Image size in Pixels 87750000 5th percentile is 0 25th percentile is 0 50th percentile is 0 75th percentile is 0 95th percentile is 0 I have uploaded the SampleMha.mha file. Thanks & Regards Vijaya Rani S -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255p7586259.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Tue Sep 23 02:40:01 2014 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Tue, 23 Sep 2014 02:40:01 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: InsightToolkit Kinetic Analysis (itk::ka) Library Message-ID: <20140923064001.A66743D6C194@insightsoftwareconsortium.org> Hello, A new submission has been added to the Insight Journal. Title: InsightToolkit Kinetic Analysis (itk::ka) Library Authors: Dowson N., Baker C., Raffelt D., Smith J., Thomas P., Salvado O., Rose S. Abstract: This paper describes how to compile and use the Insight Toolkit Kinetic Analysis library (itk::ka), to perform analysis of dynamic medical images, along with a brief overview of the library source code. A set of interfaces to facilitate application development (koala) and an application using Powell???s Dogleg optimisation (koalaDogleg) are also supplied, along with some sample data. Only versions of ITK4 and higher are currently supported. Download and review this publication at: http://hdl.handle.net/10380/3469 Generated by the Insight Journal You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://www.insight-journal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From karl.diedrich at azetech.com Tue Sep 23 11:59:22 2014 From: karl.diedrich at azetech.com (Karl Diedrich) Date: Tue, 23 Sep 2014 11:59:22 -0400 Subject: [ITK] [ITK-users] looking for itk:DomainThreader example Message-ID: <542198DA.2070604@azetech.com> Hello, Does anyone know where an example program using the itk::DomainThreader is? There is a missing link [ http://itk.org/ITKExamples/Examples/Core/Common/DoDataParallelThreading/DoDataParallelThreading.html ] to an example on an ITKBar camp website here http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/WriteMultiThreadedCode/index.html Thanks, Karl -- Karl Diedrich, Ph.D. Principal Engineer AZE Technology, Inc. 1 Broadway 14th Floor Cambridge, MA 02142, USA Phone: 1-617-475-1502 Fax: 1-617-588-1889 http://www.azetech.com/ _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Sep 23 14:24:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 23 Sep 2014 14:24:11 -0400 Subject: [ITK] [ITK-users] looking for itk:DomainThreader example In-Reply-To: <542198DA.2070604@azetech.com> References: <542198DA.2070604@azetech.com> Message-ID: Hii Karl, The example is here: http://itk.org/ITKExamples/src/Core/Common/DoDataParallelThreading/Documentation.html I have also fixed the link. Thanks, Matt On Tue, Sep 23, 2014 at 11:59 AM, Karl Diedrich wrote: > Hello, > > Does anyone know where an example program using the itk::DomainThreader is? > There is a missing link [ > http://itk.org/ITKExamples/Examples/Core/Common/DoDataParallelThreading/DoDataParallelThreading.html > ] to an example on an ITKBar camp website here > http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/WriteMultiThreadedCode/index.html > > Thanks, > > Karl > > -- > Karl Diedrich, Ph.D. > Principal Engineer > AZE Technology, Inc. > 1 Broadway 14th Floor > Cambridge, MA 02142, USA > Phone: 1-617-475-1502 > Fax: 1-617-588-1889 > http://www.azetech.com/ > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Tue Sep 23 21:51:17 2014 From: llliu at umich.edu (Lianli Liu) Date: Tue, 23 Sep 2014 21:51:17 -0400 Subject: [ITK] [ITK-users] format of mask file Message-ID: Hi all, I am a bit unclear about the format of mask file. Is it fine if I use an image of analyze format that has 0,1 value, but of integer type not boolean type? The reason I am asking is that when I use this mask in the mutual information metric, there is an error : joint PDF summed to zero... Thanks! Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From sebastian.ordas at gmail.com Tue Sep 23 23:26:08 2014 From: sebastian.ordas at gmail.com (Sebastian Ordas) Date: Wed, 24 Sep 2014 00:26:08 -0300 Subject: [ITK] VTK6 migration and vtkImageData: "No scalar values found for texture input!" error in vtkOpenGLTexture Message-ID: <542239D0.7060203@gmail.com> Dear List, I have started getting the error "No scalar values found for texture input!" coming from vtkOpenGLTexture, while porting my code to VTK6 More precisely, I have a vtkImageData, generated by itkImageToVTKImageFilter, which is mapped through vtkImageResliceMapper I have tried adding the following to itkImageToVTKImageFilter: m_Importer->UpdateInformation(); vtkStreamingDemandDrivenPipeline::SetUpdateExtent( m_Importer->GetOutputInformation(0 /*port number*/), 0 /*piece*/, 2 /*number of pieces*/, 0 /*number of ghost levels*/); m_Importer->Update(); .. but no luck! I have also tried: m_ImageData->GetPointData()->SetActiveAttribute (0, vtkPointData::SCALARS); didn?t work either... Any hint? thank you, sebastian From matt.mccormick at kitware.com Wed Sep 24 10:42:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Sep 2014 10:42:32 -0400 Subject: [ITK] VTK6 migration and vtkImageData: "No scalar values found for texture input!" error in vtkOpenGLTexture In-Reply-To: <542239D0.7060203@gmail.com> References: <542239D0.7060203@gmail.com> Message-ID: Hi Sebastian, What version of VTK are you using? Does the QuickViewTest (built as part of the ITKVtkGlue tests) executable work for you? Thanks, Matt On Tue, Sep 23, 2014 at 11:26 PM, Sebastian Ordas wrote: > Dear List, > > I have started getting the error "No scalar values found for texture input!" > coming from vtkOpenGLTexture, while porting my code to VTK6 > > More precisely, I have a vtkImageData, generated by > itkImageToVTKImageFilter, which is mapped through vtkImageResliceMapper > > I have tried adding the following to itkImageToVTKImageFilter: > > m_Importer->UpdateInformation(); > vtkStreamingDemandDrivenPipeline::SetUpdateExtent( > m_Importer->GetOutputInformation(0 /*port number*/), > 0 /*piece*/, > 2 /*number of pieces*/, > 0 /*number of ghost levels*/); > m_Importer->Update(); > > .. but no luck! > > I have also tried: > > m_ImageData->GetPointData()->SetActiveAttribute (0, vtkPointData::SCALARS); > > didn?t work either... > > Any hint? > > thank you, > sebastian > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From sebastian.ordas at gmail.com Wed Sep 24 10:48:55 2014 From: sebastian.ordas at gmail.com (Sebastian Ordas) Date: Wed, 24 Sep 2014 11:48:55 -0300 Subject: [ITK] VTK6 migration and vtkImageData: "No scalar values found for texture input!" error in vtkOpenGLTexture In-Reply-To: References: <542239D0.7060203@gmail.com> Message-ID: Hi Matt, I'm using almost the latest master (c0fa16c5) I will enable the tests in my ITK build. thank you! sebastian On Wed, Sep 24, 2014 at 11:42 AM, Matt McCormick wrote: > Hi Sebastian, > > What version of VTK are you using? Does the QuickViewTest (built as > part of the ITKVtkGlue tests) executable work for you? > > Thanks, > Matt > > On Tue, Sep 23, 2014 at 11:26 PM, Sebastian Ordas > wrote: > > Dear List, > > > > I have started getting the error "No scalar values found for texture > input!" > > coming from vtkOpenGLTexture, while porting my code to VTK6 > > > > More precisely, I have a vtkImageData, generated by > > itkImageToVTKImageFilter, which is mapped through vtkImageResliceMapper > > > > I have tried adding the following to itkImageToVTKImageFilter: > > > > m_Importer->UpdateInformation(); > > vtkStreamingDemandDrivenPipeline::SetUpdateExtent( > > m_Importer->GetOutputInformation(0 /*port number*/), > > 0 /*piece*/, > > 2 /*number of pieces*/, > > 0 /*number of ghost levels*/); > > m_Importer->Update(); > > > > .. but no luck! > > > > I have also tried: > > > > m_ImageData->GetPointData()->SetActiveAttribute (0, > vtkPointData::SCALARS); > > > > didn?t work either... > > > > Any hint? > > > > thank you, > > sebastian > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Sep 24 13:39:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Sep 2014 13:39:55 -0400 Subject: [ITK] [ITK-users] Image Rotation while preserving image In-Reply-To: <1411578386.9555.YahooMailNeo@web120603.mail.ne1.yahoo.com> References: <1411558020.53437.YahooMailNeo@web120605.mail.ne1.yahoo.com> <1411578386.9555.YahooMailNeo@web120603.mail.ne1.yahoo.com> Message-ID: Hi Emma, The resampled image will be sampled at the locations specified for the output image by setting the desired parameters on ResampleImageFilter. It does not does resize based on the transformation. To get a different output image domain, use SetOutputOrigin() and SetSize() on the ResampleImageFilter. Hope this helps, Matt On Wed, Sep 24, 2014 at 1:06 PM, Emma Ryan wrote: > HI Matt, > > Thank you for your reply. Attached is a snapshot of what is happening. The > square needs to rotate and become a diamond. But after rotation, I get a > chopped image. Ideally, I would just expect a larger sized matrix holding > the larger image. So I'm not sure I understand how the 'content' could be > missing. > > I couldn't experiment with SetExtrapolator as it is probably not available > in the version of itk that I am using . Version 3.X. > > Are you suggesting that using Extrapolation, I would be able to address this > specific problem ? > > regards, > Emma > > > > > > > > On Wednesday, September 24, 2014 7:44 AM, Matt McCormick > wrote: > > > Hi Emma, > > If there is no content to resample from after the transformation, then > a default pixel value is used. To use extrapolation instead, call > SetExtrapolator() [1] on the ResampleImageFilter. > > HTH, > Matt > > [1] > http://www.itk.org/Insight/Doxygen/html/classitk_1_1ResampleImageFilter.html#a89d912b5608fbe73a9a2ca0ebcfebb69 > > On Wed, Sep 24, 2014 at 7:27 AM, Emma Ryan via Insight-users > wrote: >> Hi, >> >> I would like to rotate an input mage by a few degrees. I was able to >> easily do this using rigid transforms available in itk. But the output >> image >> is cropped. The extent of cropping is directly related to the angle of >> rotation. How can one disallow this kind of cropping ? >> >> Thank you for your help. >> regards, >> Emma > >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > >> > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 24 14:14:38 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Sep 2014 14:14:38 -0400 Subject: [ITK] [ITK-users] format of mask file In-Reply-To: References: Message-ID: Hi Lianli, Any integer pixel type should work in the mask. To check how the mask applies to the image, the MaskImageFilter [1] can be applied. HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1MaskImageFilter.html On Tue, Sep 23, 2014 at 9:51 PM, Lianli Liu wrote: > Hi all, > > I am a bit unclear about the format of mask file. Is it fine if I use an > image of analyze format that has 0,1 value, but of integer type not boolean > type? > > The reason I am asking is that when I use this mask in the mutual > information metric, there is an error : joint PDF summed to zero... > > Thanks! > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Sep 24 17:53:03 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Sep 2014 17:53:03 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4 For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 All are welcome. Hope to talk to you then! From arnaudgelas at gmail.com Thu Sep 25 09:09:26 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 25 Sep 2014 15:09:26 +0200 Subject: [ITK] [ITK-dev] minor release? Message-ID: Hi all, I just wanted to know if there were any plan to release v4.6.1 from the release branch? If so, when could it happen? Thanks, Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From sebastian.ordas at gmail.com Thu Sep 25 09:36:28 2014 From: sebastian.ordas at gmail.com (Sebastian Ordas) Date: Thu, 25 Sep 2014 10:36:28 -0300 Subject: [ITK] VTK6 migration and vtkImageData: "No scalar values found for texture input!" error in vtkOpenGLTexture In-Reply-To: References: <542239D0.7060203@gmail.com> Message-ID: <54241A5C.2040701@gmail.com> Hi Matt, QuickViewTest works fine. I will look deeper in its code and compare it with the vtkImageData creation as by itkImageToVTKImageFilter more soon, sebastian On 9/24/2014 11:42 AM, Matt McCormick wrote: > Hi Sebastian, > > What version of VTK are you using? Does the QuickViewTest (built as > part of the ITKVtkGlue tests) executable work for you? > > Thanks, > Matt > > On Tue, Sep 23, 2014 at 11:26 PM, Sebastian Ordas > wrote: >> Dear List, >> >> I have started getting the error "No scalar values found for texture input!" >> coming from vtkOpenGLTexture, while porting my code to VTK6 >> >> More precisely, I have a vtkImageData, generated by >> itkImageToVTKImageFilter, which is mapped through vtkImageResliceMapper >> >> I have tried adding the following to itkImageToVTKImageFilter: >> >> m_Importer->UpdateInformation(); >> vtkStreamingDemandDrivenPipeline::SetUpdateExtent( >> m_Importer->GetOutputInformation(0 /*port number*/), >> 0 /*piece*/, >> 2 /*number of pieces*/, >> 0 /*number of ghost levels*/); >> m_Importer->Update(); >> >> .. but no luck! >> >> I have also tried: >> >> m_ImageData->GetPointData()->SetActiveAttribute (0, vtkPointData::SCALARS); >> >> didn?t work either... >> >> Any hint? >> >> thank you, >> sebastian >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community From arnaudgelas at gmail.com Thu Sep 25 09:51:12 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 25 Sep 2014 15:51:12 +0200 Subject: [ITK] [ITK-dev] packaging ITK with system HDF5? Message-ID: Hi all, When installing ITK with system HDF5, I get in the file ${CMAKE_INSTALL_PREFIX}/lib64/cmake/InsightToolkit/Modules/ITKHDF5.cmake set( ITKHDF5_INCLUDE_DIRS "${ITK_INSTALL_PREFIX}/include/InsightToolkit;/home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src;/usr/include" ) Of course it works fine, if you do not delete /home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src and if you use the same user... I could not find anything related to this issue... It seems to me that the problem comes from: https://github.com/Kitware/ITK/blob/master/Modules/ThirdParty/HDF5/CMakeLists.txt#L10 I guess this path should not be added there?? Any idea? Thank you very much Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Thu Sep 25 10:00:55 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 25 Sep 2014 10:00:55 -0400 Subject: [ITK] [ITK-dev] packaging ITK with system HDF5? In-Reply-To: References: Message-ID: <9750EDA2-6F14-41FB-8E4E-4330207C0F17@mail.nih.gov> Arnaud, For comparison you can look at libtiff: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/TIFF/CMakeLists.txt#L9-L14 There the include are split between ITKTIFF_INCLUDE_DIRS and ITKTIFF_SYSTEM_INCLUDE_DIRS. Likely the SYSTEM variable doesn't get modified when installed. What to git a shot at making HDF5 follow this TIFF include pattern? Brad On Sep 25, 2014, at 9:51 AM, Arnaud Gelas wrote: > Hi all, > > When installing ITK with system HDF5, I get in the file ${CMAKE_INSTALL_PREFIX}/lib64/cmake/InsightToolkit/Modules/ITKHDF5.cmake > > set( ITKHDF5_INCLUDE_DIRS "${ITK_INSTALL_PREFIX}/include/InsightToolkit;/home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src;/usr/include" ) > > Of course it works fine, if you do not delete /home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src and if you use the same user... > > I could not find anything related to this issue... > > It seems to me that the problem comes from: > https://github.com/Kitware/ITK/blob/master/Modules/ThirdParty/HDF5/CMakeLists.txt#L10 > > I guess this path should not be added there?? > > Any idea? > > Thank you very much > Arnaud > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Sep 25 10:25:46 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 25 Sep 2014 10:25:46 -0400 Subject: [ITK] [ITK-dev] minor release? In-Reply-To: References: Message-ID: Hi Arnaud, Yes, good point. There are many great bug fixes on the release branch. I think we can release 4.6.1 next week. Thanks, Matt On Thu, Sep 25, 2014 at 9:09 AM, Arnaud Gelas wrote: > Hi all, > > I just wanted to know if there were any plan to release v4.6.1 from the > release branch? > If so, when could it happen? > > Thanks, > Arnaud > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Sep 25 10:29:22 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 25 Sep 2014 10:29:22 -0400 Subject: [ITK] Patches for v4.6.1 Message-ID: Hi, We currently have the patches below on the "release" branch for the v4.6.1 release. Are there any patches missing? Thanks, Matt Arnaud Gelas (3): BUG: fix gdcm version in GDCMImageIO. COMP: missing cast when calling gdcm::DataElement::SetByteValue BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false Brad King (1): COMP: Fix vxl_config_macros usage of CMake check macros Bradley Lowekamp (7): ENH: Adding License file from upstream MetaIO ENH: Adding script to update MetaIO from upstream ENH: Remove ITK MetaIO to prepare for upstream import COMP: Fix variable type for Set/Get macros BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit BUG: Fix overflows computing size of read tiff image Christopher Mullins (1): COMP: Allows latex to compile for ITKSoftwareGuide David T. Chen (1): DOC: Fixed HistogramThresholdImageFitler Gert Wollny (1): COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) Girish Mallya (1): BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. Hans Johnson (12): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components PERF: Remove large foot print of PDF derivatives. PERF: Revert Remove large foot print of PDF derivatives. STYLE: Test against almost equal for floating point values STYLE: Non-exact floating point testing PERF: Distribute initialization per thread buffers ENH: Remove unnecessary mutable qualifier. STYLE: Remove comment with no meaning. ENH: Moved accumlator logic to main MI class ENH: Allow staggering of accumulations per thread. PERF: Zero reset thread buffers during finalize KWSys Robot (2): KWSys 2014-07-18 (65b36ede) KWSys 2014-08-04 (e787837a) Matthew McCormick (30): BUG: ArchiveTestingData.py future imports must occur at the beginning. DOC: Remove Image2.cxx reference from Book 2. DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. DOC: Remove references to Book 1 sections from Book 2. DOC: Make BinaryThresholdImageFilter not floating. DOC: Fix Software Guide figure caption for FlipImageFilter. DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. DOC: ImageRandomConstIteratorWithIndex table reference. BUG: Bump GCCXML to 2014-08-06. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. BUG: Fix alpha assignment for RGBA TIFF. BUG: Fix Nifti IO read with large images. BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. DOC: itk::statistics -> itk::Statistics. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Fix missing prefix in ITKv3ImageRegistration20Test. BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform STYLE: Improve style in BinaryImageToLabelMapFilter. BUG: Fix BinaryImageToLabelMapFilter on 1D image. ENH: Improve precision of the joint PDF sum BUG: Fix BinShrinkImageFilter for different input/output image types. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. COMP: Add missing wrapping for TransformIOBaseTemplate. BUG: gdcm::StringFilter recognizes backslash delimiter. MetaIO Maintainers (1): MetaIO (reduced) Michka Popoff (4): BUG: Improve SWIG version check BUG: Add VTK_VERSION for older VTK versions BUG: Update VTK minimum version (for release) BUG: Fix memory leak in MetaImageIO after exception From arnaudgelas at gmail.com Thu Sep 25 10:31:22 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 25 Sep 2014 16:31:22 +0200 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: References: Message-ID: Matt, Following Brad's email, I am testing the following patch right now http://review.source.kitware.com/#/c/17232/1 If it fixes the issue, I would really like it to be part of 4.6.1 Best Arnaud On Thu, Sep 25, 2014 at 4:29 PM, Matt McCormick wrote: > Hi, > > We currently have the patches below on the "release" branch for the > v4.6.1 release. Are there any patches missing? > > Thanks, > Matt > > > Arnaud Gelas (3): > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is > false > > Brad King (1): > COMP: Fix vxl_config_macros usage of CMake check macros > > Bradley Lowekamp (7): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > COMP: Fix variable type for Set/Get macros > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Fix overflows computing size of read tiff image > > Christopher Mullins (1): > COMP: Allows latex to compile for ITKSoftwareGuide > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row > images. > > Hans Johnson (12): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > > KWSys Robot (2): > KWSys 2014-07-18 (65b36ede) > KWSys 2014-08-04 (e787837a) > > Matthew McCormick (30): > BUG: ArchiveTestingData.py future imports must occur at the > beginning. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > BUG: Bump GCCXML to 2014-08-06. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Call clear instead of empty on PatchBasedDenoising > EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > BUG: Fix alpha assignment for RGBA TIFF. > BUG: Fix Nifti IO read with large images. > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > COMP: Add missing wrapping for TransformIOBaseTemplate. > BUG: gdcm::StringFilter recognizes backslash delimiter. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (4): > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Sep 25 10:37:32 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 25 Sep 2014 10:37:32 -0400 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: References: Message-ID: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov> This minor one too, fixes something that was merged into release last week: http://review.source.kitware.com/#/c/17202/ On Sep 25, 2014, at 10:29 AM, Matt McCormick wrote: > Hi, > > We currently have the patches below on the "release" branch for the > v4.6.1 release. Are there any patches missing? > > Thanks, > Matt > > > Arnaud Gelas (3): > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false > > Brad King (1): > COMP: Fix vxl_config_macros usage of CMake check macros > > Bradley Lowekamp (7): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > COMP: Fix variable type for Set/Get macros > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Fix overflows computing size of read tiff image > > Christopher Mullins (1): > COMP: Allows latex to compile for ITKSoftwareGuide > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. > > Hans Johnson (12): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > > KWSys Robot (2): > KWSys 2014-07-18 (65b36ede) > KWSys 2014-08-04 (e787837a) > > Matthew McCormick (30): > BUG: ArchiveTestingData.py future imports must occur at the beginning. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > BUG: Bump GCCXML to 2014-08-06. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > BUG: Fix alpha assignment for RGBA TIFF. > BUG: Fix Nifti IO read with large images. > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > COMP: Add missing wrapping for TransformIOBaseTemplate. > BUG: gdcm::StringFilter recognizes backslash delimiter. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (4): > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers From matt at mmmccormick.com Thu Sep 25 10:38:56 2014 From: matt at mmmccormick.com (Matthew McCormick (thewtex)) Date: Thu, 25 Sep 2014 10:38:56 -0400 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: References: Message-ID: Cool! Please make a note in the commit if it has been verified that the fix works for you. On Thu, Sep 25, 2014 at 10:31 AM, Arnaud Gelas wrote: > Matt, > > Following Brad's email, I am testing the following patch right now > > http://review.source.kitware.com/#/c/17232/1 > > If it fixes the issue, I would really like it to be part of 4.6.1 > > Best > Arnaud > > > On Thu, Sep 25, 2014 at 4:29 PM, Matt McCormick > wrote: >> >> Hi, >> >> We currently have the patches below on the "release" branch for the >> v4.6.1 release. Are there any patches missing? >> >> Thanks, >> Matt >> >> >> Arnaud Gelas (3): >> BUG: fix gdcm version in GDCMImageIO. >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is >> false >> >> Brad King (1): >> COMP: Fix vxl_config_macros usage of CMake check macros >> >> Bradley Lowekamp (7): >> ENH: Adding License file from upstream MetaIO >> ENH: Adding script to update MetaIO from upstream >> ENH: Remove ITK MetaIO to prepare for upstream import >> COMP: Fix variable type for Set/Get macros >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> BUG: Fix overflows computing size of read tiff image >> >> Christopher Mullins (1): >> COMP: Allows latex to compile for ITKSoftwareGuide >> >> David T. Chen (1): >> DOC: Fixed HistogramThresholdImageFitler >> >> Gert Wollny (1): >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >> >> Girish Mallya (1): >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row >> images. >> >> Hans Johnson (12): >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> PERF: Remove large foot print of PDF derivatives. >> PERF: Revert Remove large foot print of PDF derivatives. >> STYLE: Test against almost equal for floating point values >> STYLE: Non-exact floating point testing >> PERF: Distribute initialization per thread buffers >> ENH: Remove unnecessary mutable qualifier. >> STYLE: Remove comment with no meaning. >> ENH: Moved accumlator logic to main MI class >> ENH: Allow staggering of accumulations per thread. >> PERF: Zero reset thread buffers during finalize >> >> KWSys Robot (2): >> KWSys 2014-07-18 (65b36ede) >> KWSys 2014-08-04 (e787837a) >> >> Matthew McCormick (30): >> BUG: ArchiveTestingData.py future imports must occur at the >> beginning. >> DOC: Remove Image2.cxx reference from Book 2. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. >> DOC: Remove references to Book 1 sections from Book 2. >> DOC: Make BinaryThresholdImageFilter not floating. >> DOC: Fix Software Guide figure caption for FlipImageFilter. >> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. >> DOC: Remove duplicate figure in >> LaplacianRecursiveGaussianImageFilter2.cxx. >> DOC: ImageRandomConstIteratorWithIndex table reference. >> BUG: Bump GCCXML to 2014-08-06. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> BUG: Call clear instead of empty on PatchBasedDenoising >> EmptyCaches(). >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >> BUG: Fix alpha assignment for RGBA TIFF. >> BUG: Fix Nifti IO read with large images. >> BUG: Improve thread-safety and performance of >> PCAShapeSignedDistanceFunction. >> DOC: itk::statistics -> itk::Statistics. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> DOC: Fix Software Guide page overruns in >> IterativeClosestPoint{1,2}.cxx. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >> BUG: Do not return SmartPointers in >> TimeVaryingVelocityFieldTransform >> STYLE: Improve style in BinaryImageToLabelMapFilter. >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. >> ENH: Improve precision of the joint PDF sum >> BUG: Fix BinShrinkImageFilter for different input/output image >> types. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> BUG: gdcm::StringFilter recognizes backslash delimiter. >> >> MetaIO Maintainers (1): >> MetaIO (reduced) >> >> Michka Popoff (4): >> BUG: Improve SWIG version check >> BUG: Add VTK_VERSION for older VTK versions >> BUG: Update VTK minimum version (for release) >> BUG: Fix memory leak in MetaImageIO after exception >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt at mmmccormick.com Thu Sep 25 10:41:53 2014 From: matt at mmmccormick.com (Matthew McCormick (thewtex)) Date: Thu, 25 Sep 2014 10:41:53 -0400 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov> References: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov> Message-ID: Great, thanks! Merged to master. Will merge to release tomorrow after hitting the dashboards. On Thu, Sep 25, 2014 at 10:37 AM, Bradley Lowekamp wrote: > This minor one too, fixes something that was merged into release last week: > > http://review.source.kitware.com/#/c/17202/ > > On Sep 25, 2014, at 10:29 AM, Matt McCormick wrote: > >> Hi, >> >> We currently have the patches below on the "release" branch for the >> v4.6.1 release. Are there any patches missing? >> >> Thanks, >> Matt >> >> >> Arnaud Gelas (3): >> BUG: fix gdcm version in GDCMImageIO. >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false >> >> Brad King (1): >> COMP: Fix vxl_config_macros usage of CMake check macros >> >> Bradley Lowekamp (7): >> ENH: Adding License file from upstream MetaIO >> ENH: Adding script to update MetaIO from upstream >> ENH: Remove ITK MetaIO to prepare for upstream import >> COMP: Fix variable type for Set/Get macros >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> BUG: Fix overflows computing size of read tiff image >> >> Christopher Mullins (1): >> COMP: Allows latex to compile for ITKSoftwareGuide >> >> David T. Chen (1): >> DOC: Fixed HistogramThresholdImageFitler >> >> Gert Wollny (1): >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >> >> Girish Mallya (1): >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. >> >> Hans Johnson (12): >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> PERF: Remove large foot print of PDF derivatives. >> PERF: Revert Remove large foot print of PDF derivatives. >> STYLE: Test against almost equal for floating point values >> STYLE: Non-exact floating point testing >> PERF: Distribute initialization per thread buffers >> ENH: Remove unnecessary mutable qualifier. >> STYLE: Remove comment with no meaning. >> ENH: Moved accumlator logic to main MI class >> ENH: Allow staggering of accumulations per thread. >> PERF: Zero reset thread buffers during finalize >> >> KWSys Robot (2): >> KWSys 2014-07-18 (65b36ede) >> KWSys 2014-08-04 (e787837a) >> >> Matthew McCormick (30): >> BUG: ArchiveTestingData.py future imports must occur at the beginning. >> DOC: Remove Image2.cxx reference from Book 2. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. >> DOC: Remove references to Book 1 sections from Book 2. >> DOC: Make BinaryThresholdImageFilter not floating. >> DOC: Fix Software Guide figure caption for FlipImageFilter. >> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. >> DOC: Remove duplicate figure in >> LaplacianRecursiveGaussianImageFilter2.cxx. >> DOC: ImageRandomConstIteratorWithIndex table reference. >> BUG: Bump GCCXML to 2014-08-06. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >> BUG: Fix alpha assignment for RGBA TIFF. >> BUG: Fix Nifti IO read with large images. >> BUG: Improve thread-safety and performance of >> PCAShapeSignedDistanceFunction. >> DOC: itk::statistics -> itk::Statistics. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >> BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform >> STYLE: Improve style in BinaryImageToLabelMapFilter. >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. >> ENH: Improve precision of the joint PDF sum >> BUG: Fix BinShrinkImageFilter for different input/output image types. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> BUG: gdcm::StringFilter recognizes backslash delimiter. >> >> MetaIO Maintainers (1): >> MetaIO (reduced) >> >> Michka Popoff (4): >> BUG: Improve SWIG version check >> BUG: Add VTK_VERSION for older VTK versions >> BUG: Update VTK minimum version (for release) >> BUG: Fix memory leak in MetaImageIO after exception >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Thu Sep 25 10:43:51 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 25 Sep 2014 10:43:51 -0400 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: Message-ID: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov> Matt, The URL for the Confab is from last week, I think this is the URL for the one tomorrow: https://plus.google.com/u/0/events/c5snoqnkhtkcv1tebfo1cl9quo4 On Sep 24, 2014, at 5:53 PM, Matt McCormick wrote: > There are a couple of upcoming opportunities to share, discuss, design, and > learn with your fellow ITK community members. > > > On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a > Google+ Hangout > where we will be doing code reviews: > > https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk > > > On Friday, 11:00 AM Eastern USA time, an ITK development conference, > > https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4 > > For those that cannot join via Hangout, telephone call-in is also possible. > Dial: > > 585-632-6296 > > Enter pin: > > 31423 > > > All are welcome. Hope to talk to you then! > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Sep 25 10:45:45 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 25 Sep 2014 10:45:45 -0400 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov> References: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov> Message-ID: Thanks for the correction! On Thu, Sep 25, 2014 at 10:43 AM, Bradley Lowekamp wrote: > Matt, > > The URL for the Confab is from last week, I think this is the URL for the one tomorrow: > > https://plus.google.com/u/0/events/c5snoqnkhtkcv1tebfo1cl9quo4 > > On Sep 24, 2014, at 5:53 PM, Matt McCormick wrote: > >> There are a couple of upcoming opportunities to share, discuss, design, and >> learn with your fellow ITK community members. >> >> >> On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a >> Google+ Hangout >> where we will be doing code reviews: >> >> https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk >> >> >> On Friday, 11:00 AM Eastern USA time, an ITK development conference, >> >> https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4 >> >> For those that cannot join via Hangout, telephone call-in is also possible. >> Dial: >> >> 585-632-6296 >> >> Enter pin: >> >> 31423 >> >> >> All are welcome. Hope to talk to you then! >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > From arnaudgelas at gmail.com Thu Sep 25 11:30:25 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 25 Sep 2014 17:30:25 +0200 Subject: [ITK] [ITK-dev] Patches for v4.6.1 In-Reply-To: References: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov> Message-ID: With system HDF5, the patch works great (thanks to Brad)! I have also submitted one patch that could go in ITK 4.6.1 with system GDCM: http://review.source.kitware.com/#/c/17234/ On Thu, Sep 25, 2014 at 4:41 PM, Matthew McCormick (thewtex) < matt at mmmccormick.com> wrote: > Great, thanks! Merged to master. Will merge to release tomorrow > after hitting the dashboards. > > On Thu, Sep 25, 2014 at 10:37 AM, Bradley Lowekamp > wrote: > > This minor one too, fixes something that was merged into release last > week: > > > > http://review.source.kitware.com/#/c/17202/ > > > > On Sep 25, 2014, at 10:29 AM, Matt McCormick > wrote: > > > >> Hi, > >> > >> We currently have the patches below on the "release" branch for the > >> v4.6.1 release. Are there any patches missing? > >> > >> Thanks, > >> Matt > >> > >> > >> Arnaud Gelas (3): > >> BUG: fix gdcm version in GDCMImageIO. > >> COMP: missing cast when calling gdcm::DataElement::SetByteValue > >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID > is false > >> > >> Brad King (1): > >> COMP: Fix vxl_config_macros usage of CMake check macros > >> > >> Bradley Lowekamp (7): > >> ENH: Adding License file from upstream MetaIO > >> ENH: Adding script to update MetaIO from upstream > >> ENH: Remove ITK MetaIO to prepare for upstream import > >> COMP: Fix variable type for Set/Get macros > >> BUG: Use METER of sCAL scale unit > >> BUG: Use PNG_SCALE_METER for PNG sCAL unit > >> BUG: Fix overflows computing size of read tiff image > >> > >> Christopher Mullins (1): > >> COMP: Allows latex to compile for ITKSoftwareGuide > >> > >> David T. Chen (1): > >> DOC: Fixed HistogramThresholdImageFitler > >> > >> Gert Wollny (1): > >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > >> > >> Girish Mallya (1): > >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row > images. > >> > >> Hans Johnson (12): > >> COMP: Add tolerance for comparing floating point > >> PERF: Remove non-threadable algorithm components > >> PERF: Remove large foot print of PDF derivatives. > >> PERF: Revert Remove large foot print of PDF derivatives. > >> STYLE: Test against almost equal for floating point values > >> STYLE: Non-exact floating point testing > >> PERF: Distribute initialization per thread buffers > >> ENH: Remove unnecessary mutable qualifier. > >> STYLE: Remove comment with no meaning. > >> ENH: Moved accumlator logic to main MI class > >> ENH: Allow staggering of accumulations per thread. > >> PERF: Zero reset thread buffers during finalize > >> > >> KWSys Robot (2): > >> KWSys 2014-07-18 (65b36ede) > >> KWSys 2014-08-04 (e787837a) > >> > >> Matthew McCormick (30): > >> BUG: ArchiveTestingData.py future imports must occur at the > beginning. > >> DOC: Remove Image2.cxx reference from Book 2. > >> DOC: Fix Software Guide page overruns in > IterativeClosestPoint3.cxx. > >> DOC: Remove references to Book 1 sections from Book 2. > >> DOC: Make BinaryThresholdImageFilter not floating. > >> DOC: Fix Software Guide figure caption for FlipImageFilter. > >> DOC: Avoid duplicate figure description in > ResampleImageFilter2.cxx. > >> DOC: Remove duplicate figure in > >> LaplacianRecursiveGaussianImageFilter2.cxx. > >> DOC: ImageRandomConstIteratorWithIndex table reference. > >> BUG: Bump GCCXML to 2014-08-06. > >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > >> BUG: Call clear instead of empty on PatchBasedDenoising > EmptyCaches(). > >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > >> BUG: Fix alpha assignment for RGBA TIFF. > >> BUG: Fix Nifti IO read with large images. > >> BUG: Improve thread-safety and performance of > >> PCAShapeSignedDistanceFunction. > >> DOC: itk::statistics -> itk::Statistics. > >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > >> DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > >> BUG: TransformFileReader does not clear its TransformList. > >> BUG: Prevent dangling pointer in HDF5TransformIO. > >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > >> BUG: Do not return SmartPointers in > TimeVaryingVelocityFieldTransform > >> STYLE: Improve style in BinaryImageToLabelMapFilter. > >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. > >> ENH: Improve precision of the joint PDF sum > >> BUG: Fix BinShrinkImageFilter for different input/output image > types. > >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > >> COMP: Add missing wrapping for TransformIOBaseTemplate. > >> BUG: gdcm::StringFilter recognizes backslash delimiter. > >> > >> MetaIO Maintainers (1): > >> MetaIO (reduced) > >> > >> Michka Popoff (4): > >> BUG: Improve SWIG version check > >> BUG: Add VTK_VERSION for older VTK versions > >> BUG: Update VTK minimum version (for release) > >> BUG: Fix memory leak in MetaImageIO after exception > >> _______________________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-developers > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From elena.bresciani87 at gmail.com Fri Sep 26 10:23:18 2014 From: elena.bresciani87 at gmail.com (elena bresciani) Date: Fri, 26 Sep 2014 16:23:18 +0200 Subject: [ITK] [ITK-users] OpenCV - ITK project Message-ID: Hello to everybody, for the project I'm working on I need to integrate ITK and OpenCV. I've read the dedicated tutorial here , but I can't find informations on how the CmakeList.txt file should be created or if I have to change some kind of building configuration of ITK and/or OpenCV. Can you please explain me what I have to do? Cheers Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Fri Sep 26 10:35:18 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Fri, 26 Sep 2014 15:35:18 +0100 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: Hi Elena, I use OpenCV and ITK together. The general procedure is to build OpenCV from source using CMake, and then build ITK from source using CMake, checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. During both the builds you generally do not have to modify the CMakeLists.txt For a project which uses the libraries, the CMakeLists.txt would simply look like - ---- cmake_minimum_required(VERSION 2.8) project(myProject) find_package(ITK REQUIRED) find_package(OpenCV REQUIRED) include(${ITK_USE_FILE}) add_executable(myProject test.cpp) target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) ---- Is there a specific problem you are facing while trying this? On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani < elena.bresciani87 at gmail.com> wrote: > Hello to everybody, > > for the project I'm working on I need to integrate ITK and OpenCV. > I've read the dedicated tutorial here > , but > I can't find informations on how the CmakeList.txt file should be created > or if I have to change some kind of building configuration of ITK and/or > OpenCV. > > Can you please explain me what I have to do? > > Cheers > Elena > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From elena.bresciani87 at gmail.com Fri Sep 26 11:28:25 2014 From: elena.bresciani87 at gmail.com (elena bresciani) Date: Fri, 26 Sep 2014 17:28:25 +0200 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: I get the CMake error " Error in configuration files. Project Files may be invalid " I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", I have to rebuild ITK by checking that option (I don't think I had done this when I compiled ITK), and I hope that then it will work. I installed OpenCV with brew on Mac, you suggest to recompile it from source or it should be good as well? Thank you so much Elena 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi : > Hi Elena, > > I use OpenCV and ITK together. The general procedure is to build OpenCV > from source using CMake, and then build ITK from source using CMake, > checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. > During both the builds you generally do not have to modify the > CMakeLists.txt > > For a project which uses the libraries, the CMakeLists.txt would simply > look like - > > ---- > cmake_minimum_required(VERSION 2.8) > > project(myProject) > > find_package(ITK REQUIRED) > find_package(OpenCV REQUIRED) > > include(${ITK_USE_FILE}) > > add_executable(myProject test.cpp) > > target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) > ---- > > Is there a specific problem you are facing while trying this? > > On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani < > elena.bresciani87 at gmail.com> wrote: > >> Hello to everybody, >> >> for the project I'm working on I need to integrate ITK and OpenCV. >> I've read the dedicated tutorial here >> , >> but I can't find informations on how the CmakeList.txt file should be >> created or if I have to change some kind of building configuration of ITK >> and/or OpenCV. >> >> Can you please explain me what I have to do? >> >> Cheers >> Elena >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From indianzeppelin at gmail.com Fri Sep 26 11:35:23 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Fri, 26 Sep 2014 16:35:23 +0100 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build ITK. I am not familiar with OpenCV installations on Mac. Do projects build fine when you use OpenCV alone? On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani < elena.bresciani87 at gmail.com> wrote: > I get the CMake error " Error in configuration files. Project Files may be > invalid " > > I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", > I have to rebuild ITK by checking that option (I don't think I had done > this when I compiled ITK), and I hope that then it will work. > I installed OpenCV with brew on Mac, you suggest to recompile it from > source or it should be good as well? > > Thank you so much > > Elena > > 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi : > >> Hi Elena, >> >> I use OpenCV and ITK together. The general procedure is to build OpenCV >> from source using CMake, and then build ITK from source using CMake, >> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. >> During both the builds you generally do not have to modify the >> CMakeLists.txt >> >> For a project which uses the libraries, the CMakeLists.txt would simply >> look like - >> >> ---- >> cmake_minimum_required(VERSION 2.8) >> >> project(myProject) >> >> find_package(ITK REQUIRED) >> find_package(OpenCV REQUIRED) >> >> include(${ITK_USE_FILE}) >> >> add_executable(myProject test.cpp) >> >> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) >> ---- >> >> Is there a specific problem you are facing while trying this? >> >> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani < >> elena.bresciani87 at gmail.com> wrote: >> >>> Hello to everybody, >>> >>> for the project I'm working on I need to integrate ITK and OpenCV. >>> I've read the dedicated tutorial here >>> , >>> but I can't find informations on how the CmakeList.txt file should be >>> created or if I have to change some kind of building configuration of ITK >>> and/or OpenCV. >>> >>> Can you please explain me what I have to do? >>> >>> Cheers >>> Elena >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> >> -- >> Regards, >> Girish >> > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From elena.bresciani87 at gmail.com Fri Sep 26 11:53:12 2014 From: elena.bresciani87 at gmail.com (elena bresciani) Date: Fri, 26 Sep 2014 17:53:12 +0200 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: Yes, I don't have problems with it alone, so I will leave it as it as and only try rebuilding itk with the "Module_ITKVideoBridgeOpenCV" flag on. Thanks 2014-09-26 17:35 GMT+02:00 Girish Mallya Udupi : > Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build > ITK. > I am not familiar with OpenCV installations on Mac. Do projects build fine > when you use OpenCV alone? > > On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani < > elena.bresciani87 at gmail.com> wrote: > >> I get the CMake error " Error in configuration files. Project Files may >> be invalid " >> >> I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", >> I have to rebuild ITK by checking that option (I don't think I had done >> this when I compiled ITK), and I hope that then it will work. >> I installed OpenCV with brew on Mac, you suggest to recompile it from >> source or it should be good as well? >> >> Thank you so much >> >> Elena >> >> 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi >> : >> >>> Hi Elena, >>> >>> I use OpenCV and ITK together. The general procedure is to build OpenCV >>> from source using CMake, and then build ITK from source using CMake, >>> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. >>> During both the builds you generally do not have to modify the >>> CMakeLists.txt >>> >>> For a project which uses the libraries, the CMakeLists.txt would simply >>> look like - >>> >>> ---- >>> cmake_minimum_required(VERSION 2.8) >>> >>> project(myProject) >>> >>> find_package(ITK REQUIRED) >>> find_package(OpenCV REQUIRED) >>> >>> include(${ITK_USE_FILE}) >>> >>> add_executable(myProject test.cpp) >>> >>> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) >>> ---- >>> >>> Is there a specific problem you are facing while trying this? >>> >>> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani < >>> elena.bresciani87 at gmail.com> wrote: >>> >>>> Hello to everybody, >>>> >>>> for the project I'm working on I need to integrate ITK and OpenCV. >>>> I've read the dedicated tutorial here >>>> , >>>> but I can't find informations on how the CmakeList.txt file should be >>>> created or if I have to change some kind of building configuration of ITK >>>> and/or OpenCV. >>>> >>>> Can you please explain me what I have to do? >>>> >>>> Cheers >>>> Elena >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >>> >>> -- >>> Regards, >>> Girish >>> >> >> > > > -- > Regards, > Girish > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Sep 26 14:39:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 26 Sep 2014 14:39:13 -0400 Subject: [ITK] [ITK-users] OpenCV - ITK project In-Reply-To: References: Message-ID: Hi Elena, This example may be helpful [1]. Matt [1] http://itk.org/ITKExamples/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.html?highlight=opencv On Fri, Sep 26, 2014 at 11:53 AM, elena bresciani wrote: > Yes, I don't have problems with it alone, so I will leave it as it as and > only try rebuilding itk with the "Module_ITKVideoBridgeOpenCV" flag on. > > Thanks > > 2014-09-26 17:35 GMT+02:00 Girish Mallya Udupi : >> >> Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build >> ITK. >> I am not familiar with OpenCV installations on Mac. Do projects build fine >> when you use OpenCV alone? >> >> On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani >> wrote: >>> >>> I get the CMake error " Error in configuration files. Project Files may >>> be invalid " >>> >>> I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", >>> I have to rebuild ITK by checking that option (I don't think I had done this >>> when I compiled ITK), and I hope that then it will work. >>> I installed OpenCV with brew on Mac, you suggest to recompile it from >>> source or it should be good as well? >>> >>> Thank you so much >>> >>> Elena >>> >>> 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi >>> : >>>> >>>> Hi Elena, >>>> >>>> I use OpenCV and ITK together. The general procedure is to build OpenCV >>>> from source using CMake, and then build ITK from source using CMake, >>>> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built. >>>> During both the builds you generally do not have to modify the >>>> CMakeLists.txt >>>> >>>> For a project which uses the libraries, the CMakeLists.txt would simply >>>> look like - >>>> >>>> ---- >>>> cmake_minimum_required(VERSION 2.8) >>>> >>>> project(myProject) >>>> >>>> find_package(ITK REQUIRED) >>>> find_package(OpenCV REQUIRED) >>>> >>>> include(${ITK_USE_FILE}) >>>> >>>> add_executable(myProject test.cpp) >>>> >>>> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS}) >>>> ---- >>>> >>>> Is there a specific problem you are facing while trying this? >>>> >>>> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani >>>> wrote: >>>>> >>>>> Hello to everybody, >>>>> >>>>> for the project I'm working on I need to integrate ITK and OpenCV. >>>>> I've read the dedicated tutorial here, but I can't find informations on >>>>> how the CmakeList.txt file should be created or if I have to change some >>>>> kind of building configuration of ITK and/or OpenCV. >>>>> >>>>> Can you please explain me what I have to do? >>>>> >>>>> Cheers >>>>> Elena >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>> >>>> >>>> >>>> -- >>>> Regards, >>>> Girish >>> >>> >> >> >> >> -- >> Regards, >> Girish > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From genet at biomed.ee.ethz.ch Fri Sep 26 16:46:46 2014 From: genet at biomed.ee.ethz.ch (Martin Genet) Date: Fri, 26 Sep 2014 22:46:46 +0200 Subject: [ITK] [ITK-users] FEMRegistration In-Reply-To: References: <54207D45.9070409@biomed.ee.ethz.ch> Message-ID: <5425D0B6.1000009@biomed.ee.ethz.ch> Thanks a lot, Matt. I'm still a little confused though. I can access the mesh using: > typedef itk::fem::FEMObject< 2 > MeshType; > MeshType::Pointer mesh = registrationFilter->GetInputFEMObject(); However, when trying to create a writer using > typedef itk::MeshFileWriter< MeshType > MeshWriterType; > MeshWriterType::Pointer meshWriter = MeshWriterType::New(); , it complains that InputMeshType (itk::fem::FEMObject< 2 > I guess) is missing a lot of stuff (e.g., RegionType, PixelType, GetPoints, etc.). If I use > typedef itk::Mesh< float, 2 > MeshType; instead, I can define the writer, but then I can't access the mesh from the registration filter of course. Is there a way to write registrationFilter->GetInputFEMObject() into a vtk file? Thanks again, and sorry again for the confusion. Martin On 09/22/2014 10:54 PM, Matt McCormick wrote: > Hi Martin, > > itk::MeshFileReader and itk::MeshFileWriter are great classes for > importing / exporting meshes. > > HTH, > Matt > > On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet wrote: >> Dear all: >> >> Trying to use FEMRegistration on a bunch of images. Still trying to figure >> out the following: >> >> - What is the simplest way to convert an external mesh (e.g., >> vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and vice >> versa (for post-treatment, vizualization)? >> >> - If the mesh covers only a subset of the image, what happens to the rest >> of the image? >> >> Any help would be super appreciated. Sorry if that's too trivial. Thanks in >> advance. >> >> Martin >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Sep 26 17:11:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 26 Sep 2014 17:11:11 -0400 Subject: [ITK] [ITK-users] FEMRegistration In-Reply-To: <5425D0B6.1000009@biomed.ee.ethz.ch> References: <54207D45.9070409@biomed.ee.ethz.ch> <5425D0B6.1000009@biomed.ee.ethz.ch> Message-ID: Hi Martin, An itk::Mesh will need to be constructed from the the itk::fem::FEMObject manually. We could use a set of converter classes. HTH, Matt On Fri, Sep 26, 2014 at 4:46 PM, Martin Genet wrote: > Thanks a lot, Matt. I'm still a little confused though. I can access the > mesh using: >> >> typedef itk::fem::FEMObject< 2 > MeshType; >> MeshType::Pointer mesh = registrationFilter->GetInputFEMObject(); > > > However, when trying to create a writer using >> typedef itk::MeshFileWriter< MeshType > MeshWriterType; >> MeshWriterType::Pointer meshWriter = MeshWriterType::New(); > , it complains that InputMeshType (itk::fem::FEMObject< 2 > I guess) is > missing a lot of stuff (e.g., RegionType, PixelType, GetPoints, etc.). > > If I use >> typedef itk::Mesh< float, 2 > MeshType; > instead, I can define the writer, but then I can't access the mesh from the > registration filter of course. > > Is there a way to write registrationFilter->GetInputFEMObject() into a vtk > file? Thanks again, and sorry again for the confusion. > > Martin > > > On 09/22/2014 10:54 PM, Matt McCormick wrote: >> >> Hi Martin, >> >> itk::MeshFileReader and itk::MeshFileWriter are great classes for >> importing / exporting meshes. >> >> HTH, >> Matt >> >> On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet >> wrote: >>> >>> Dear all: >>> >>> Trying to use FEMRegistration on a bunch of images. Still trying to >>> figure >>> out the following: >>> >>> - What is the simplest way to convert an external mesh (e.g., >>> vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and >>> vice >>> versa (for post-treatment, vizualization)? >>> >>> - If the mesh covers only a subset of the image, what happens to the >>> rest >>> of the image? >>> >>> Any help would be super appreciated. Sorry if that's too trivial. Thanks >>> in >>> advance. >>> >>> Martin >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From suryarajan15 at gmail.com Sat Sep 27 10:12:44 2014 From: suryarajan15 at gmail.com (Surya Rajan) Date: Sat, 27 Sep 2014 19:42:44 +0530 Subject: [ITK] problem with pathiterator Message-ID: Hi, I'm having trouble in itkPathToImageFilter.hxx. The input is a closed Path (2D index type). The problem is in this line of the file: PathIterator< OutputImageType, InputPathType > pathIt(OutputImage, InputPath); for ( pathIt.GoToBegin(); !pathIt.IsAtEnd(); ++pathIt) { pathIt.Set(m_PathValue); } I'm noticing that the loop executes only once, taking the first value in the path. ++pathIt does not seem to work. Could anyone please help me with this? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From llliu at umich.edu Sun Sep 28 18:18:40 2014 From: llliu at umich.edu (Lianli Liu) Date: Sun, 28 Sep 2014 18:18:40 -0400 Subject: [ITK] [ITK-users] build itkvtkglue Message-ID: Hi all, I want to use vtk with itk and I set the BUILD_SHARED_LIBS option as ON. My cmake file looks like this # This is the root ITK CMakeLists file. cmake_minimum_required(VERSION 2.4) if(COMMAND CMAKE_POLICY) cmake_policy(SET CMP0003 NEW) endif() # This project is designed to be built outside the Insight source tree. project(vtiPCA) # Find ITK. find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED) find_package(VTK REQUIRED) include(${VTK_USE_FILE}) else() find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue) endif() add_executable(vtiPCA vtiPCA.cxx ) target_link_libraries(vtiPCA ${ITK_LIBRARIES}) But I receivde the error saying By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ItkVtkGlue", but CMake did not find one. . Can anyone help with this? Thanks! Best, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Sun Sep 28 22:01:57 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Sun, 28 Sep 2014 22:01:57 -0400 Subject: [ITK] [ITK-users] build itkvtkglue In-Reply-To: References: Message-ID: Remove these lines: else() find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue) On Sun, Sep 28, 2014 at 6:18 PM, Lianli Liu wrote: > Hi all, > > I want to use vtk with itk and I set the BUILD_SHARED_LIBS option as ON. My > cmake file looks like this > > # This is the root ITK CMakeLists file. > cmake_minimum_required(VERSION 2.4) > if(COMMAND CMAKE_POLICY) > cmake_policy(SET CMP0003 NEW) > endif() > > > # This project is designed to be built outside the Insight source tree. > project(vtiPCA) > > # Find ITK. > find_package(ITK REQUIRED) > include(${ITK_USE_FILE}) > > if (ITKVtkGlue_LOADED) > find_package(VTK REQUIRED) > include(${VTK_USE_FILE}) > else() > find_package(ItkVtkGlue REQUIRED) > include(${ItkVtkGlue_USE_FILE}) > set(Glue ItkVtkGlue) > endif() > > add_executable(vtiPCA vtiPCA.cxx ) > > target_link_libraries(vtiPCA ${ITK_LIBRARIES}) > > But I receivde the error saying > > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > has asked CMake to find a package configuration file provided by > "ItkVtkGlue", but CMake did not find one. > . > > Can anyone help with this? Thanks! > > Best, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Mon Sep 29 08:06:59 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 29 Sep 2014 08:06:59 -0400 Subject: [ITK] [ITK-dev] Linux CDash@home build missing Message-ID: Matt, I haven't seen the Linux CDash at Home robot for a while now. Does it need to be persuaded to resume building and testing our gerrit patches? Thanks, Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Sep 29 10:57:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 29 Sep 2014 10:57:21 -0400 Subject: [ITK] [ITK-dev] Linux CDash@home build missing In-Reply-To: References: Message-ID: Hi Brad, Thanks for the note. My persuasion skills have been applied :-). Thanks, Matt On Mon, Sep 29, 2014 at 8:06 AM, Bradley Lowekamp wrote: > Matt, > > I haven't seen the Linux CDash at Home robot for a while now. > > Does it need to be persuaded to resume building and testing our gerrit patches? > > Thanks, > Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From emmasaunders123 at gmail.com Mon Sep 29 15:25:16 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Mon, 29 Sep 2014 20:25:16 +0100 Subject: [ITK] [ITK-users] Push forward Pull Back Euler Lagrangian Frame Message-ID: Hi List I am experiencing some confusion with terms above, if someone could clarify that would be great: Does registration using a Eulerian frame correspond to a pull back framework of registration similarly: Does registration using a Lagrangian frame correspond to a push forward framework for registration? Thanks for any help Kind regards Emma -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Mon Sep 29 18:24:39 2014 From: llliu at umich.edu (Lianli Liu) Date: Mon, 29 Sep 2014 18:24:39 -0400 Subject: [ITK] [ITK-users] segmentation error in PCA estimator Message-ID: Hi all, I am applying the itk example code for PCA estimator (EstimatePCAModel.cxx). I have 10 training images and I intend to output all components (i.e. 10). But after writing 4 components, I get the segmentation fault. I was wondering what is the cause of this? I would really appreciate any help. Thanks! Regards, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michkapopoff at gmail.com Tue Sep 30 07:03:33 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Tue, 30 Sep 2014 13:03:33 +0200 Subject: [ITK] [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem In-Reply-To: <542A8B2E.6020404@utu.fi> References: <542A8B2E.6020404@utu.fi> Message-ID: <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> Hi once ITK is compiled, there is no more need for Swig at runtime. For the syntax, you should use the new wrapping syntax. Look at how it is done in this example, at the end there is python code [1] I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig. If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig. You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial. [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html Michka On 30 sept. 2014, at 12:51, Sami Koho wrote: > Hello, > > this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer. > > I am able to load itk in Python, but every time I try to execute anything, the following error appears: > >> in () >> ----> 1 reader = itk.ImageFileReader.IUC3.New() >> >> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr) >> 40 module = self.__lazy_attributes[attr] >> 41 namespace = {} >> ---> 42 itkBase.LoadModule(module, namespace) >> 43 # Load into 'namespace' first, then self.__dict__ (via setattr) to >> 44 # prevent the warnings about overwriting the 'NotLoaded' values >> >> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace) >> 51 if namespace is not None: >> 52 swig = namespace.setdefault('swig', imp.new_module('swig')) >> ---> 53 swig.__dict__.update(this_module.swig.__dict__) >> 54 >> 55 # don't worry about overwriting the symbols in namespace -- any >> >> AttributeError: 'module' object has no attribute 'swig' > > I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython, tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly. > > Should I manually set a path to swig? Or is something else wrong instead? > > I have installed ITK in the default path /usr/local/lib, as can be seen from the example. > > Best, > > Sami _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From sami.koho at gmail.com Tue Sep 30 08:51:32 2014 From: sami.koho at gmail.com (Sami Koho) Date: Tue, 30 Sep 2014 15:51:32 +0300 Subject: [ITK] [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem In-Reply-To: <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> References: <542A8B2E.6020404@utu.fi> <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> Message-ID: Thank you Michka! The solution was in the ldconfig file creation: > ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here. > cd /etc/ld.so.conf.d/ > add a file called itk-46.conf, which should contain only one line: /usr/local/lib > ldconfig # tells the system to read the files in ld.so.conf.d On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide: > /Path to a program. > PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python > > //Path to a file. > PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 > > //Path to a file. > PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7 > > //Path to a library. > PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 > > //Path to a library. > PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND > > //Directory where the arrayobject.h header file can be found. This > // file is part of the numarray package > PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy > > //Python site-packages directory to install a .pth file pointing > // at WrapITK Python modules. > PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages Best, Sami On Sep 30, 2014, at 14:03, Michka Popoff wrote: > Hi > > once ITK is compiled, there is no more need for Swig at runtime. > > For the syntax, you should use the new wrapping syntax. > Look at how it is done in this example, at the end there is python code [1] > > I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig. > If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig. > You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora > > The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial. > > [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html > > Michka > > On 30 sept. 2014, at 12:51, Sami Koho wrote: > >> Hello, >> >> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer. >> >> I am able to load itk in Python, but every time I try to execute anything, the following error appears: >> >>> in () >>> ----> 1 reader = itk.ImageFileReader.IUC3.New() >>> >>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr) >>> 40 module = self.__lazy_attributes[attr] >>> 41 namespace = {} >>> ---> 42 itkBase.LoadModule(module, namespace) >>> 43 # Load into 'namespace' first, then self.__dict__ (via setattr) to >>> 44 # prevent the warnings about overwriting the 'NotLoaded' values >>> >>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace) >>> 51 if namespace is not None: >>> 52 swig = namespace.setdefault('swig', imp.new_module('swig')) >>> ---> 53 swig.__dict__.update(this_module.swig.__dict__) >>> 54 >>> 55 # don't worry about overwriting the symbols in namespace -- any >>> >>> AttributeError: 'module' object has no attribute 'swig' >> >> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython, tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly. >> >> Should I manually set a path to swig? Or is something else wrong instead? >> >> I have installed ITK in the default path /usr/local/lib, as can be seen from the example. >> >> Best, >> >> Sami > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michkapopoff at gmail.com Tue Sep 30 09:14:21 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Tue, 30 Sep 2014 15:14:21 +0200 Subject: [ITK] [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem In-Reply-To: References: <542A8B2E.6020404@utu.fi> <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> Message-ID: Would it be possible for you to write this down for me, so I can update the guide on the wiki ? Michka On 30 sept. 2014, at 14:51, Sami Koho wrote: > Thank you Michka! The solution was in the ldconfig file creation: > >> ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here. >> cd /etc/ld.so.conf.d/ >> add a file called itk-46.conf, which should contain only one line: /usr/local/lib >> ldconfig # tells the system to read the files in ld.so.conf.d > > On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide: > >> /Path to a program. >> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python >> >> //Path to a file. >> PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 >> >> //Path to a file. >> PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7 >> >> //Path to a library. >> PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 >> >> //Path to a library. >> PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND >> >> //Directory where the arrayobject.h header file can be found. This >> // file is part of the numarray package >> PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy >> >> //Python site-packages directory to install a .pth file pointing >> // at WrapITK Python modules. >> PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages > > > Best, > > Sami > > On Sep 30, 2014, at 14:03, Michka Popoff wrote: > >> Hi >> >> once ITK is compiled, there is no more need for Swig at runtime. >> >> For the syntax, you should use the new wrapping syntax. >> Look at how it is done in this example, at the end there is python code [1] >> >> I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig. >> If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig. >> You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora >> >> The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial. >> >> [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html >> >> Michka >> >> On 30 sept. 2014, at 12:51, Sami Koho wrote: >> >>> Hello, >>> >>> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer. >>> >>> I am able to load itk in Python, but every time I try to execute anything, the following error appears: >>> >>>> in () >>>> ----> 1 reader = itk.ImageFileReader.IUC3.New() >>>> >>>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr) >>>> 40 module = self.__lazy_attributes[attr] >>>> 41 namespace = {} >>>> ---> 42 itkBase.LoadModule(module, namespace) >>>> 43 # Load into 'namespace' first, then self.__dict__ (via setattr) to >>>> 44 # prevent the warnings about overwriting the 'NotLoaded' values >>>> >>>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace) >>>> 51 if namespace is not None: >>>> 52 swig = namespace.setdefault('swig', imp.new_module('swig')) >>>> ---> 53 swig.__dict__.update(this_module.swig.__dict__) >>>> 54 >>>> 55 # don't worry about overwriting the symbols in namespace -- any >>>> >>>> AttributeError: 'module' object has no attribute 'swig' >>> >>> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython, tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly. >>> >>> Should I manually set a path to swig? Or is something else wrong instead? >>> >>> I have installed ITK in the default path /usr/local/lib, as can be seen from the example. >>> >>> Best, >>> >>> Sami >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michkapopoff at gmail.com Tue Sep 30 09:51:06 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Tue, 30 Sep 2014 15:51:06 +0200 Subject: [ITK] [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem In-Reply-To: References: <542A8B2E.6020404@utu.fi> <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com> Message-ID: Just writing this down for the list archives Sami, thank you very much for all the informations. I updated an created a new page, for Fedora and Ubuntu, with all the details. http://www.itk.org/Wiki/ITK/WrapITKInstallLinux For the moment this page is somewhat hidden, because you need to click 3-4 links through the FAQ and multiple pages to get to it. I will maybe reorganize the wiki a little bit to move the installation procedures to the front page. Thanks again Michka On 30 sept. 2014, at 15:14, Michka Popoff wrote: > Would it be possible for you to write this down for me, so I can update the guide on the wiki ? > > Michka > > On 30 sept. 2014, at 14:51, Sami Koho wrote: > >> Thank you Michka! The solution was in the ldconfig file creation: >> >>> ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here. >>> cd /etc/ld.so.conf.d/ >>> add a file called itk-46.conf, which should contain only one line: /usr/local/lib >>> ldconfig # tells the system to read the files in ld.so.conf.d >> >> On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide: >> >>> /Path to a program. >>> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python >>> >>> //Path to a file. >>> PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 >>> >>> //Path to a file. >>> PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7 >>> >>> //Path to a library. >>> PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 >>> >>> //Path to a library. >>> PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND >>> >>> //Directory where the arrayobject.h header file can be found. This >>> // file is part of the numarray package >>> PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy >>> >>> //Python site-packages directory to install a .pth file pointing >>> // at WrapITK Python modules. >>> PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages >> >> >> Best, >> >> Sami >> >> On Sep 30, 2014, at 14:03, Michka Popoff wrote: >> >>> Hi >>> >>> once ITK is compiled, there is no more need for Swig at runtime. >>> >>> For the syntax, you should use the new wrapping syntax. >>> Look at how it is done in this example, at the end there is python code [1] >>> >>> I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig. >>> If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig. >>> You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora >>> >>> The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial. >>> >>> [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html >>> >>> Michka >>> >>> On 30 sept. 2014, at 12:51, Sami Koho wrote: >>> >>>> Hello, >>>> >>>> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer. >>>> >>>> I am able to load itk in Python, but every time I try to execute anything, the following error appears: >>>> >>>>> in () >>>>> ----> 1 reader = itk.ImageFileReader.IUC3.New() >>>>> >>>>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr) >>>>> 40 module = self.__lazy_attributes[attr] >>>>> 41 namespace = {} >>>>> ---> 42 itkBase.LoadModule(module, namespace) >>>>> 43 # Load into 'namespace' first, then self.__dict__ (via setattr) to >>>>> 44 # prevent the warnings about overwriting the 'NotLoaded' values >>>>> >>>>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace) >>>>> 51 if namespace is not None: >>>>> 52 swig = namespace.setdefault('swig', imp.new_module('swig')) >>>>> ---> 53 swig.__dict__.update(this_module.swig.__dict__) >>>>> 54 >>>>> 55 # don't worry about overwriting the symbols in namespace -- any >>>>> >>>>> AttributeError: 'module' object has no attribute 'swig' >>>> >>>> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython, tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly. >>>> >>>> Should I manually set a path to swig? Or is something else wrong instead? >>>> >>>> I have installed ITK in the default path /usr/local/lib, as can be seen from the example. >>>> >>>> Best, >>>> >>>> Sami >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Tue Sep 30 09:57:58 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Tue, 30 Sep 2014 09:57:58 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: On the Importance of Location and Features for the Patch-Based Segmentation of Parotid Glands Message-ID: <20140930135758.AC11E3D6C169@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: On the Importance of Location and Features for the Patch-Based Segmentation of Parotid Glands Authors: Wachinger C., Brennan M., Sharp G., Golland P. Abstract: The segmentation of parotid glands in CT scans of patients with head and neck cancer is an essential part of treatment planning. We introduce a new method for the automatic segmentation of parotid glands that extends existing patch-based approaches in three ways: (1) we promote the use of image features in combination with patch intensity values to increase discrimination; (2) we work with larger search windows than established methods by using an approximate nearest neighbor search; and (3) we demonstrate that location information is a crucial discriminator and add it explicitly to the description. In our experiments, we compare a large number of features and introduce a new multi-scale descriptor. The best performance is achieved with entropy image features in combination with patches and location information. Download and review this publication at: http://hdl.handle.net/10380/3472 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Tue Sep 30 10:14:15 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 30 Sep 2014 14:14:15 +0000 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) Message-ID: This is a problem that has been cropping up in our projects that use ITK, VTK and SlicerExecutionModel. You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules. The problem is this: if you find packages in this order: find_package(VTK REQUIRED) find_package(ITK REQUIRED) You can?t real compile anything that needs VTK, because down in the ITK deployment stuff, it calls find_package(VTK) like this: find_package(VTK COMPONENTS vtkCommonCore vtkRenderingCore vtkRenderingOpenGL vtkRenderingFreeType vtkInteractionStyle vtkIOImage vtkImagingSources REQUIRED) Which blows away the larger list of include directories and libraries that the first find_package(VTK REQUIRED) built. Even better ? or worse ? Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include find_package(VTK) ? so ITK tries to import VTK twice, with different module lists. It doesn?t even help to reverse the order: find_package(ITK REQUIRED) find_package(VTK REQUIRED) because apparently there?s some hangover from the find_package(VTK) inside the ITK CMake deployment files. The only thing that works is to use COMPONENTS, i.e. find_package(ITK REQUIRED) find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED) Which seems to trigger a proper re-scan and build of the library/include lists. It gets even worse if you use find_package(SlicerExecutionModel) after find_package(ITK), for the same reason ? SlicerExecutionModel depends on ITK, so it clobbers the include/library lists from the first find_package(ITK). ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 30 10:17:27 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 10:17:27 -0400 Subject: [ITK] [ITK-users] Push forward Pull Back Euler Lagrangian Frame In-Reply-To: References: Message-ID: Hi Emma, Yes, that sounds correct. Is there some context to where this language is being used? Thanks, Matt On Mon, Sep 29, 2014 at 3:25 PM, Emma Saunders wrote: > Hi List > > I am experiencing some confusion with terms above, if someone could clarify > that would be great: > > Does registration using a Eulerian frame correspond to a pull back framework > of registration > > similarly: > > Does registration using a Lagrangian frame correspond to a push forward > framework for registration? > > Thanks for any help > > Kind regards > > Emma > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Sep 30 10:21:26 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 10:21:26 -0400 Subject: [ITK] [ITK-users] segmentation error in PCA estimator In-Reply-To: References: Message-ID: Hi Lianli, Building the program with debugging symbols and running the executable in a debugger should shed more light. Or, sharing a SSCCE [1], i.e. the code and images and command (CTest test), should help others debug your issue. Thanks, Matt [1] http://sscce.org/ On Mon, Sep 29, 2014 at 6:24 PM, Lianli Liu wrote: > Hi all, > > I am applying the itk example code for PCA estimator (EstimatePCAModel.cxx). > I have 10 training images and I intend to output all components (i.e. 10). > But after writing 4 components, I get the segmentation fault. I was > wondering what is the cause of this? I would really appreciate any help. > Thanks! > > Regards, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Tue Sep 30 10:23:36 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 30 Sep 2014 10:23:36 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: References: Message-ID: Here is what I do for the WikiExamples remote module: find_package(VTK REQUIRED) include(${VTK_USE_FILE}) set(VTK_COMPONENTS ${VTK_LIBRARIES}) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) set(ITK_LIBRARIES ${ITK_LIBRARIES} ${VTK_COMPONENTS}) On Tue, Sep 30, 2014 at 10:14 AM, Williams, Norman K wrote: > This is a problem that has been cropping up in our projects that use ITK, > VTK and SlicerExecutionModel. > > You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules. > > The problem is this: if you find packages in this order: > > find_package(VTK REQUIRED) > find_package(ITK REQUIRED) > > You can?t real compile anything that needs VTK, because down in the ITK > deployment stuff, it calls find_package(VTK) like this: > find_package(VTK COMPONENTS > vtkCommonCore > vtkRenderingCore > vtkRenderingOpenGL > vtkRenderingFreeType > vtkInteractionStyle > vtkIOImage > vtkImagingSources > REQUIRED) > > Which blows away the larger list of include directories and libraries that > the first find_package(VTK REQUIRED) built. > > Even better ? or worse ? > Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include > find_package(VTK) ? so ITK tries to import VTK twice, with different module > lists. > > It doesn?t even help to reverse the order: > find_package(ITK REQUIRED) > find_package(VTK REQUIRED) > > because apparently there?s some hangover from the find_package(VTK) inside > the ITK CMake deployment files. The only thing that works is to use > COMPONENTS, i.e. > > find_package(ITK REQUIRED) > find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED) > > Which seems to trigger a proper re-scan and build of the library/include > lists. > > It gets even worse if you use find_package(SlicerExecutionModel) after > find_package(ITK), for the same reason ? SlicerExecutionModel depends on > ITK, so it clobbers the include/library lists from the first > find_package(ITK). > > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From brad.king at kitware.com Tue Sep 30 10:48:47 2014 From: brad.king at kitware.com (Brad King) Date: Tue, 30 Sep 2014 10:48:47 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: References: Message-ID: <542AC2CF.7030008@kitware.com> On 09/30/2014 10:14 AM, Williams, Norman K wrote: > find_package(VTK REQUIRED) > find_package(ITK REQUIRED) > > You can?t real compile anything that needs VTK, because down in > the ITK deployment stuff, it calls find_package(VTK) like this: [snip] > Which blows away the larger list of include directories and libraries One may use the itk_module_config and vtk_module_config macros from the *ModuleAPI.cmake modules that come with the respective packages to compute the list of libraries and include dirs for a given list of components. All ITKConfig and VTKConfig do with the list of components is: itk_module_config(ITK ${ITK_MODULES_REQUESTED}) # sets ITK_LIBRARIES, ITK_INCLUDE_DIRS, etc. and vtk_module_config(VTK ${VTK_MODULES_REQUESTED}) # sets VTK_LIBRARIES, VTK_INCLUDE_DIRS, etc. One can invoke these directly: itk_module_config(ITK ${MY_LIST_OF_ITK_COMPONENTS}) vtk_module_config(VTK ${MY_LIST_OF_VTK_COMPONENTS}) at any time after the find_package calls. One could even use a different prefix: itk_module_config(MyITK ${MY_LIST_OF_ITK_COMPONENTS}) # sets MyITK_LIBRARIES, MyITK_INCLUDE_DIRS, etc. In the long run the plan is to stop recommending use of component lists at find_package time and instead use imported targets and usage requirements: http://www.cmake.org/cmake/help/v3.0/manual/cmake-buildsystem.7.html#build-specification-and-usage-requirements but that will have to wait until we can require CMake 3.0. -Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Sep 30 11:13:22 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 30 Sep 2014 11:13:22 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: <542AC2CF.7030008@kitware.com> References: <542AC2CF.7030008@kitware.com> Message-ID: Brad, Do you have a suggestion on how to conditionally include a module if it's available? e.g. Use ITKDeprecated if ITK was configure with it? Thanks, Brad On Sep 30, 2014, at 10:48 AM, Brad King wrote: > On 09/30/2014 10:14 AM, Williams, Norman K wrote: >> find_package(VTK REQUIRED) >> find_package(ITK REQUIRED) >> >> You can?t real compile anything that needs VTK, because down in >> the ITK deployment stuff, it calls find_package(VTK) like this: > [snip] >> Which blows away the larger list of include directories and libraries > > One may use the itk_module_config and vtk_module_config macros > from the *ModuleAPI.cmake modules that come with the respective > packages to compute the list of libraries and include dirs for > a given list of components. All ITKConfig and VTKConfig do with > the list of components is: > > itk_module_config(ITK ${ITK_MODULES_REQUESTED}) > # sets ITK_LIBRARIES, ITK_INCLUDE_DIRS, etc. > > and > > vtk_module_config(VTK ${VTK_MODULES_REQUESTED}) > # sets VTK_LIBRARIES, VTK_INCLUDE_DIRS, etc. > > One can invoke these directly: > > itk_module_config(ITK ${MY_LIST_OF_ITK_COMPONENTS}) > vtk_module_config(VTK ${MY_LIST_OF_VTK_COMPONENTS}) > > at any time after the find_package calls. One could even use > a different prefix: > > itk_module_config(MyITK ${MY_LIST_OF_ITK_COMPONENTS}) > # sets MyITK_LIBRARIES, MyITK_INCLUDE_DIRS, etc. > > In the long run the plan is to stop recommending use of component > lists at find_package time and instead use imported targets and > usage requirements: > > http://www.cmake.org/cmake/help/v3.0/manual/cmake-buildsystem.7.html#build-specification-and-usage-requirements > > but that will have to wait until we can require CMake 3.0. > > -Brad > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From brad.king at kitware.com Tue Sep 30 11:22:57 2014 From: brad.king at kitware.com (Brad King) Date: Tue, 30 Sep 2014 11:22:57 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: References: <542AC2CF.7030008@kitware.com> Message-ID: <542ACAD1.2040805@kitware.com> On 09/30/2014 11:13 AM, Bradley Lowekamp wrote: > Do you have a suggestion on how to conditionally include a > module if it's available? e.g. Use ITKDeprecated if ITK was > configure with it? find_package(ITK REQUIRED) set(MY_ITK_COMPONENTS ...) # list required mods here if(";${ITK_MODULES_ENABLED};" MATCHES ";ITKDeprecated;") list(APPEND MY_ITK_COMPONENTS ITKDeprecated) endif() itk_module_config(ITK ${MY_ITK_COMPONENTS}) I think the if() line could also be written if(TARGET ITKDeprecated) but I don't remember off the top of my head whether the library names and module names always match exactly. -Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 30 12:59:39 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 12:59:39 -0400 Subject: [ITK] [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution Model) In-Reply-To: References: Message-ID: Hi Kent, On Tue, Sep 30, 2014 at 10:14 AM, Williams, Norman K wrote: > This is a problem that has been cropping up in our projects that use ITK, > VTK and SlicerExecutionModel. > > You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules. > > The problem is this: if you find packages in this order: > > find_package(VTK REQUIRED) > find_package(ITK REQUIRED) > > You can?t real compile anything that needs VTK, because down in the ITK > deployment stuff, it calls find_package(VTK) like this: > find_package(VTK COMPONENTS > vtkCommonCore > vtkRenderingCore > vtkRenderingOpenGL > vtkRenderingFreeType > vtkInteractionStyle > vtkIOImage > vtkImagingSources > REQUIRED) > > Which blows away the larger list of include directories and libraries that > the first find_package(VTK REQUIRED) built. > > Even better ? or worse ? > Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include > find_package(VTK) ? so ITK tries to import VTK twice, with different module > lists. > > It doesn?t even help to reverse the order: > find_package(ITK REQUIRED) > find_package(VTK REQUIRED) > > because apparently there?s some hangover from the find_package(VTK) inside > the ITK CMake deployment files. The only thing that works is to use > COMPONENTS, i.e. > > find_package(ITK REQUIRED) > find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED) > > Which seems to trigger a proper re-scan and build of the library/include > lists. This was discussed in this thread [1]. There does not seem to be interest at this time to have mixed COMPONENTS / non-COMPONENTS calls to find_package. It is also recommended to use the MODULE option to find_package. A "newer" version of VTK 6 is also required. > It gets even worse if you use find_package(SlicerExecutionModel) after > find_package(ITK), for the same reason ? SlicerExecutionModel depends on > ITK, so it clobbers the include/library lists from the first > find_package(ITK). > A patch was merged a few days ago that might address this issue [2]. Is this behavior still see with current ITK? Thanks, Matt [1] http://public.kitware.com/pipermail/vtk-developers/2014-September/015376.html [2] http://review.source.kitware.com/#/c/16963/ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Sep 30 16:43:49 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 16:43:49 -0400 Subject: [ITK] ITK 4.6.1 Downloads update Message-ID: Hi Comm, Could the ITK download links please be updated for v4.6.1? On this page: http://www.itk.org/ITK/resources/software.html The current release is version 4.6.0 from July 2014. The following downloads are available: to The current release is version 4.6.1 from September 2014. The following downloads are available: and Library Source InsightToolkit-4.6.0.tar.gz (hosted at Sourceforge) InsightToolkit-4.6.0.tar.xz (hosted at Sourceforge) InsightToolkit-4.6.0.zip (hosted at Sourceforge) to Library Source InsightToolkit-4.6.1.tar.gz (hosted at Sourceforge) InsightToolkit-4.6.1.tar.xz (hosted at Sourceforge) InsightToolkit-4.6.1.zip (hosted at Sourceforge) with the links adjusted accordingly. Release notes written in anticipation of the release are here: https://docs.google.com/a/kitware.com/document/d/1wXFV1a2hfnZS8rDx96iO42fC9dyti6Onl-3PUPTYjDU/edit Thanks, Matt From matt.mccormick at kitware.com Tue Sep 30 17:06:53 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Sep 2014 17:06:53 -0400 Subject: [ITK] ITK 4.6.1 Downloads update In-Reply-To: References: Message-ID: Note: this message was meant for people updating the ITK download pages -- but ITK 4.6.1 will be coming soon! :-) On Tue, Sep 30, 2014 at 4:43 PM, Matt McCormick wrote: > Hi Comm, > > Could the ITK download links please be updated for v4.6.1? > > On this page: > > http://www.itk.org/ITK/resources/software.html > > > The current release is version 4.6.0 from July 2014. The following > downloads are available: > > to > > The current release is version 4.6.1 from September 2014. The > following downloads are available: > > > and > > Library Source > > InsightToolkit-4.6.0.tar.gz (hosted at Sourceforge) > InsightToolkit-4.6.0.tar.xz (hosted at Sourceforge) > InsightToolkit-4.6.0.zip (hosted at Sourceforge) > > to > > Library Source > > InsightToolkit-4.6.1.tar.gz (hosted at Sourceforge) > InsightToolkit-4.6.1.tar.xz (hosted at Sourceforge) > InsightToolkit-4.6.1.zip (hosted at Sourceforge) > > > with the links adjusted accordingly. > > > Release notes written in anticipation of the release are here: > https://docs.google.com/a/kitware.com/document/d/1wXFV1a2hfnZS8rDx96iO42fC9dyti6Onl-3PUPTYjDU/edit > > > Thanks, > Matt From gowithking at googlemail.com Tue Sep 16 05:24:24 2014 From: gowithking at googlemail.com (gowith king) Date: Tue, 16 Sep 2014 09:24:24 -0000 Subject: [ITK] How to label this binary image into two labels Message-ID: Hi, I tried to label this image into two labels since yesterday , However it always give no label for result. Here is my code: LabelFilter0 = itk.BinaryImageToLabelMapFilter.IUC3LM3.New() LabelFilter0.SetInput(BinaryFilter.GetOutput()) LabelFilter0.SetInputForegroundValue(100) LabelFilter0.SetFullyConnected(False) print LabelFilter0.GetNumberOfObjects() LabelImage0 = itk.LabelMapToLabelImageFilter.LM3IUC3.New() LabelImage0.SetInput(LabelFilter0.GetOutput()) Sta0Filter = itk.LabelStatisticsImageFilter.ISS3IUC3.New() Sta0Filter.SetLabelInput(LabelImage0.GetOutput()) Sta0Filter.SetInput(reader0.GetOutput()) ? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Selection_001.png Type: image/png Size: 23881 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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