From suneezahanif02 at gmail.com Fri Jan 1 17:17:36 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Fri, 1 Jan 2016 23:17:36 +0100 Subject: [ITK-users] Metric Evaluation Message-ID: Hello Everyone, I need help regarding metric calculation. When I run registration algorithm and use final results(e.g. rotation angle and translation) to calculate metric once again at the end of process I get different value as compared to the value of metric evaluated in last iteration. I am using same metric for registration and later. I also did this after one iteration but i still i get different values. Does anyone know how to solve this problem? Thanks in advance. Best Regards, Suneeza -------------- next part -------------- An HTML attachment was scrubbed... URL: From rfrank at dominionsw.com Sat Jan 2 12:48:18 2016 From: rfrank at dominionsw.com (Richard Frank) Date: Sat, 2 Jan 2016 17:48:18 +0000 Subject: [ITK-users] Metric Evaluation In-Reply-To: References: Message-ID: <9C83A080-3673-4ADF-9EE8-76292FCC84E8@dominionsw.com> What optimizer/ algorithm are you using? Some use random selections of data as a speed optimization which on average give good results for better performance. But possibly slightly different results. If the differences are great then you might have to look at how you pick the first "guess"...how the images are pre-positioned prior to registration. Rick Frank Sent from my iPad > On Jan 2, 2016, at 12:00 PM, "insight-users-request at itk.org" wrote: > > Send Insight-users mailing list submissions to > insight-users at itk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/insight-users > or, via email, send a message with subject or body 'help' to > insight-users-request at itk.org > > You can reach the person managing the list at > insight-users-owner at itk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Insight-users digest..." > > > Today's Topics: > > 1. Metric Evaluation (suneeza hanif) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Jan 2016 23:17:36 +0100 > From: suneeza hanif > To: insight-users at itk.org > Subject: [ITK-users] Metric Evaluation > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hello Everyone, > > I need help regarding metric calculation. When I run registration algorithm > and use final results(e.g. rotation angle and translation) to calculate > metric once again at the end of process I get different value as compared > to the value of metric evaluated in last iteration. I am using same metric > for registration and later. > > I also did this after one iteration but i still i get different values. > > Does anyone know how to solve this problem? > > Thanks in advance. > > Best Regards, > Suneeza > -------------- next part -------------- > From david.m.welch at gmail.com Sun Jan 3 21:22:21 2016 From: david.m.welch at gmail.com (David Welch) Date: Sun, 3 Jan 2016 20:22:21 -0600 Subject: [ITK-users] Mattes Mutual Information can produce a false positive? In-Reply-To: References: <1450211111544-7588261.post@n2.nabble.com> <79DC6C6D-D325-48E3-8F34-3FE0F614ABF2@urthecast.com> Message-ID: You're most likely finding a local minimum - you can't discount the implementation just because the minimization value is high. For example, two images of different patients would produce a "high" minimization value even though the registration might be very good. Each registration problem is unique, so you haven't found a "smoking gun" yet. Try plotting the metric value over the range of accepted values for your transform and I'll wager you'll see that the minimization is converging on a local minimum somewhere. That will tell you what parameter of your optimization you need to tweak. On Sunday, January 3, 2016, Gabriel A. Gim?nez wrote: > Hi again... > Thanks for your answer David, I was doing more tests to be sure of the > problem. I do not know the implementation of metrics and is beyond of the > scope of my work, but definitive think it's a bug of the implementation. > > This is the transformation that generates the error, and appears at random: > > Metric value: -0.571747, > Transformation: [0.45776567727601714, 0.041654583723424364, > -0.04058569867934432, -0.9751276082246223, -35.48376926584542, > -28.108117798651822] > > My optimizer generates random solutions, perhaps it could be generating an > "rare" solutions ... but the metric should not calculate a high value for > this types of solutions, no ? > > Attached results (difference before and after) to apply the transformation. > > Thanks... > > > 2015-12-16 14:55 GMT-03:00 David Welch >: > >> Hi Gabriel, >> >> I?m a little rusty, so maybe someone else can correct my example. >> >> 1) Consider a circle with one half ?dark: and one half ?bright" with a >> gray background. >> 2) Then consider the inverted image (max() - image). >> 3) Rotate the inverted image randomly about the center. >> 4) Now register the two using Mattes?. >> >> Do you see the problem? Statistically, both pairings of bright->bright >> and bright->dark have the same entropy to Mattes?, so neither would be >> preferred and the algorithm would settle on which ever solution it reaches >> first and would give a false positive 50% of the time. >> >> So Mattes? CAN produce false positives depending on the underlying >> statistics for the image pairs. >> >> Cheers, >> Dave >> >> >> >> >> On 12/15/15, 2:25 PM, "Gabriel A. Gim?nez" > > wrote: >> >> >Hi all, I hope you are well... >> > >> >My question is about a implementation of Mattes Mutual Information...is >> >possible to produce a false positive ? at times it gives me a high metric >> >value ... but the result of the recording is poor. We use it as a metric >> for >> >two implementations of optimizers (PSO and Scatter search). >> > >> >Attached results of two executions, using scatter search: >> > >> >Moving image: mr_pd >> >Fixed image: ct >> >Images source: http://www.insight-journal.org/rire/download_data.php >> >(patient_001) >> > >> >Thank you very much and I hope you can help me, regards. >> > >> > >> >ct_mr_pd_incorrect_result.zip >> >< >> http://itk-insight-users.2283740.n2.nabble.com/file/n7588261/ct_mr_pd_incorrect_result.zip >> > >> >ct_mr_pd_accurate_result.zip >> >< >> http://itk-insight-users.2283740.n2.nabble.com/file/n7588261/ct_mr_pd_accurate_result.zip >> > >> > >> > >> > >> >-- >> >View this message in context: >> http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-can-produce-a-false-positive-tp7588261.html >> >Sent from the ITK Insight Users mailing list archive at Nabble.com. >> > >> >> > > > -- > *Gabriel Alberto Gim?nez.* > -- Sent from a mobile device -------------- next part -------------- An HTML attachment was scrubbed... URL: From suneezahanif02 at gmail.com Mon Jan 4 08:29:21 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Mon, 4 Jan 2016 14:29:21 +0100 Subject: [ITK-users] InsightDocuments module Message-ID: Hello Everyone, Could someone please tell me where exactllay I can find the InsightDocuments module. I have downloaded InsightToolkit-4.8.1.zip from the http://www.itk.org/HTML/Download.htm website, but I can't find InsightDocuments there. Thanks, Suneeza -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabrielgimenez85 at gmail.com Mon Jan 4 08:52:33 2016 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Mon, 4 Jan 2016 10:52:33 -0300 Subject: [ITK-users] Mattes Mutual Information can produce a false positive? In-Reply-To: References: <1450211111544-7588261.post@n2.nabble.com> <79DC6C6D-D325-48E3-8F34-3FE0F614ABF2@urthecast.com> Message-ID: Hi David and all... David,really I do not understand some aspects of your answer ... ,first ... sorry for my bad english. With a "high" value of metrics I refer to a "good" value, not mathematically "high". Let's focus on this small part of the execution of the registration: 19 -0.56353 [0.019933984547764932, -0.010499154976998975, -0.00811108303741948, 0.6163571650068174, -24.641443477933247, -2.2643196247633544] 20 -0.56353 [0.019933984547764932, -0.010499154976998975, -0.00811108303741948, 0.6163571650068174, -24.641443477933247, -2.2643196247633544] 21 -0.56353 [0.019933984547764932, -0.010499154976998975, -0.00811108303741948, 0.6163571650068174, -24.641443477933247, -2.2643196247633544] 22 -0.56353 [0.019933984547764932, -0.010499154976998975, -0.00811108303741948, 0.6163571650068174, -24.641443477933247, -2.2643196247633544] *23 -0.570385 [0.5048258211954306, 0.029452473766705987, -0.060948117243475784, -2.7709477953906707, -36.32690303936296, -29.640626958681565] * The transformation in "bold" (23) is the erroneous, before this trasform definitely the optimizer is in a local minimum or perhaps in a global (the transformations 19 - 22 produce excellent registrations). The transform 23 is "better" (according to the metric value) but the registration is very bad (really bad). I do not understand the relationship of the optimizer is in a local optimum with the fact of the metric produces a wrong value ? Regards, 2016-01-03 23:22 GMT-03:00 David Welch : > You're most likely finding a local minimum - you can't discount the > implementation just because the minimization value is high. > > For example, two images of different patients would produce a "high" > minimization value even though the registration might be very good. Each > registration problem is unique, so you haven't found a "smoking gun" yet. > > Try plotting the metric value over the range of accepted values for your > transform and I'll wager you'll see that the minimization is converging on > a local minimum somewhere. That will tell you what parameter of your > optimization you need to tweak. > > > On Sunday, January 3, 2016, Gabriel A. Gim?nez > wrote: > >> Hi again... >> Thanks for your answer David, I was doing more tests to be sure of the >> problem. I do not know the implementation of metrics and is beyond of the >> scope of my work, but definitive think it's a bug of the implementation. >> >> This is the transformation that generates the error, and appears at >> random: >> >> Metric value: -0.571747, >> Transformation: [0.45776567727601714, 0.041654583723424364, >> -0.04058569867934432, -0.9751276082246223, -35.48376926584542, >> -28.108117798651822] >> >> My optimizer generates random solutions, perhaps it could be generating >> an "rare" solutions ... but the metric should not calculate a high value >> for this types of solutions, no ? >> >> Attached results (difference before and after) to apply the >> transformation. >> >> Thanks... >> >> >> 2015-12-16 14:55 GMT-03:00 David Welch : >> >>> Hi Gabriel, >>> >>> I?m a little rusty, so maybe someone else can correct my example. >>> >>> 1) Consider a circle with one half ?dark: and one half ?bright" with a >>> gray background. >>> 2) Then consider the inverted image (max() - image). >>> 3) Rotate the inverted image randomly about the center. >>> 4) Now register the two using Mattes?. >>> >>> Do you see the problem? Statistically, both pairings of bright->bright >>> and bright->dark have the same entropy to Mattes?, so neither would be >>> preferred and the algorithm would settle on which ever solution it reaches >>> first and would give a false positive 50% of the time. >>> >>> So Mattes? CAN produce false positives depending on the underlying >>> statistics for the image pairs. >>> >>> Cheers, >>> Dave >>> >>> >>> >>> >>> On 12/15/15, 2:25 PM, "Gabriel A. Gim?nez" >>> wrote: >>> >>> >Hi all, I hope you are well... >>> > >>> >My question is about a implementation of Mattes Mutual Information...is >>> >possible to produce a false positive ? at times it gives me a high >>> metric >>> >value ... but the result of the recording is poor. We use it as a >>> metric for >>> >two implementations of optimizers (PSO and Scatter search). >>> > >>> >Attached results of two executions, using scatter search: >>> > >>> >Moving image: mr_pd >>> >Fixed image: ct >>> >Images source: http://www.insight-journal.org/rire/download_data.php >>> >(patient_001) >>> > >>> >Thank you very much and I hope you can help me, regards. >>> > >>> > >>> >ct_mr_pd_incorrect_result.zip >>> >< >>> http://itk-insight-users.2283740.n2.nabble.com/file/n7588261/ct_mr_pd_incorrect_result.zip >>> > >>> >ct_mr_pd_accurate_result.zip >>> >< >>> http://itk-insight-users.2283740.n2.nabble.com/file/n7588261/ct_mr_pd_accurate_result.zip >>> > >>> > >>> > >>> > >>> >-- >>> >View this message in context: >>> http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-can-produce-a-false-positive-tp7588261.html >>> >Sent from the ITK Insight Users mailing list archive at Nabble.com. >>> > >>> >>> >> >> >> -- >> *Gabriel Alberto Gim?nez.* >> > > > -- > Sent from a mobile device > -- *Gabriel Alberto Gim?nez.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Jan 4 10:07:48 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 4 Jan 2016 10:07:48 -0500 Subject: [ITK-users] Visualize Intermediate result of ITK registration in vtk In-Reply-To: <1451450098542-36592.post@n7.nabble.com> References: <1451277758067-36590.post@n7.nabble.com> <1451450098542-36592.post@n7.nabble.com> Message-ID: Hi Vishal, You could perhaps have a static pointer to your VTK render window, which you could then just access from the Execute method (and have ITK optimizer as a parameter). HTH, D?enan On Tue, Dec 29, 2015 at 11:34 PM, vishal wrote: > hi D?enan, > thank you for ur help...But i have another doubt.. In the registration > algorithms in ITK in order to print the optimizer result, the optimizer > object is passed to the Execute() callback function.. to my understanding > only one object and one event object can be send to Execute()... inorder to > update my VTK render window il have to pass two objects (one ITK optimizer > and VTK renderer object) as argument to Execute()...get the transform from > the optimizer parameter and apply transform as you have suggested to the > VTK > object... This is where im having confusion.. How to achieve this? Is my > understanding about the registration algorithm correct? Please help me > out... > Regards > Vishal > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Visualize-Intermediate-result-of-ITK-registration-in-vtk-tp36590p36592.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Jan 4 10:47:35 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 4 Jan 2016 10:47:35 -0500 Subject: [ITK-users] Bug in ITK 4.8.2 In-Reply-To: <1451536488731-36593.post@n7.nabble.com> References: <1451536488731-36593.post@n7.nabble.com> Message-ID: Could it be related to this bug? https://issues.itk.org/jira/browse/ITK-3407 Could you try reproducing this bug with both 4.6 and 4.8? On Wed, Dec 30, 2015 at 11:34 PM, vishal wrote: > hi itk-users, > I recently switched from ITK 4.6 to ITK 4.8.2... In ITK 4.6 had no problems > when I was executing the DicomSeriesReadImageWrite2.cxx and > DigitallyReconstructedRadiograph1... But after switching to ITK 4.8.2 it is > showing the error as shown in the screenshots attached with this message... > Even thought the error is present* I get the expected result *but I would > like to solve this error.. could anyone please help me out?? > > > regards > Vishal > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Bug-in-ITK-4-8-2-tp36593.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From suneezahanif02 at gmail.com Mon Jan 4 10:51:01 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Mon, 4 Jan 2016 16:51:01 +0100 Subject: [ITK-users] GNU Plot Message-ID: Hello Everyone, I want to plot my optimizer parameters after registration. In ItkSoftwareGuide it is stated that the scripts used for plotting are available in the ITKSoftwareGuide git repository under the directory "SoftwareGuide/Art." I am unable to find such directory. Can anyone please tell me how to solve this problem? Best Regards, Suneeza -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Jan 4 10:54:33 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 4 Jan 2016 10:54:33 -0500 Subject: [ITK-users] GNU Plot In-Reply-To: References: Message-ID: ?Hi Suneeza, take one of the examples which display registration progress on screen on iteration events. Modify the example to write a new line to a file on each iteration event?, in a format which is suitable for plotting (a CSV might do). One possible example: http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv3_2ImageRegistration3_8cxx-example.html HTH, D?enan On Mon, Jan 4, 2016 at 10:51 AM, suneeza hanif wrote: > Hello Everyone, > > I want to plot my optimizer parameters after registration. > > In ItkSoftwareGuide it is stated that the scripts used for plotting are > available in the ITKSoftwareGuide git repository under the directory > "SoftwareGuide/Art." I am unable to find such directory. > > Can anyone please tell me how to solve this problem? > > Best Regards, > Suneeza > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From dzenanz at gmail.com Mon Jan 4 11:05:15 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 4 Jan 2016 11:05:15 -0500 Subject: [ITK-users] InsightDocuments module In-Reply-To: References: Message-ID: Hi Suneeza, I don't think InsightDocuments exist any more. A good new starting point would be: http://itk.org/ITK/help/documentation.html You can drill down from there. HTH, D?enan On Mon, Jan 4, 2016 at 8:29 AM, suneeza hanif wrote: > Hello Everyone, > > Could someone please tell me where exactllay I can find the > InsightDocuments module. I have downloaded InsightToolkit-4.8.1.zip > from the http://www.itk.org/HTML/Download.htm website, but I can't > find InsightDocuments there. > > Thanks, > Suneeza > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From sean at rogue-research.com Mon Jan 4 16:17:44 2016 From: sean at rogue-research.com (Sean McBride) Date: Mon, 4 Jan 2016 16:17:44 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: Message-ID: <20160104211744.1213332491@mail.rogue-research.com> On Tue, 22 Dec 2015 18:57:04 -0500, Matt McCormick said: >On behalf of the Insight Toolkit community, we are proud to announce >that ITK 4.9 release candidate 3 has been tagged and is available for >testing! Please take this opportunity to test the new features in the >release candidate. > >* Third Party Library Updates > * GDCM updated to the latest upstream If I understand ITK's git history correctly, ThirdParty/GDCM was last updated 2015-09-22: According to this: GDCM 2.6.1 was released 2015-11-02 and 2.6.2 on 2015-12-23. Try as I may, I don't see an easy way to determine which version of GDCM ITK actually includes... how does one determine this? Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From skalexander at gmail.com Mon Jan 4 19:56:54 2016 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 05 Jan 2016 00:56:54 +0000 Subject: [ITK-users] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: Message-ID: Thanks! Clean build and test on my machine this time, show's green on the dash for 4th. On Tue, 22 Dec 2015 at 15:57 Matt McCormick wrote: > On behalf of the Insight Toolkit community, we are proud to announce > that ITK 4.9 release candidate 3 has been tagged and is available for > testing! Please take this opportunity to test the new features in the > release candidate. > > > To obtain the source code, > > git clone http://itk.org/ITK.git > cd ITK > git checkout -q --detach v4.9rc03 > > For more details, please see the Git documentation [1]. > > > A few selected highlights for this release: > > * New Remote modules: the Cuberille module for smooth generation of > meshes from binary segmentation images, and the > AnisotropicDiffusionLBR module improved edge-preserving smoothing. > * Build your own ITK module outside the source tree, add continuous > integration testing on GitHub, and easily add Python wrapping for your > C++ algorithms. > * Python wrapping, including Python 3, builds faster with a more > standard installation > * Improved performance of itk::Image::GetPixel and operations on > itk::VariableLengthVector?s > * Generate a FlatStructuringElement from an image > * Point-set registration with time-varying B-splines > * Module dependencies can now be specified as public / private / compile / > test > > > Please test the release candidate and share your experiences on the > mailing list, issue tracker, and Gerrit Code Review. The new module > dependency specification mechanism may unearth missing dependencies > for projects that use ITK COMPONENTS with the CMake find_package > command. > > > An Experimental build, which demonstrates how the test suite performs > on your local build system, can be submitted to the dashboard [2] > with: > > mkdir ../ITK-build > cd ../ITK-build > cmake ../ITK > ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit > > Visual Studio builds must also add ?-C Release? to the ctest command. > > Notify the mailing list if there are any unexpected failures. Testing > your own applications against the RC is also appreciated. > > > Congratulations and well done to the 43 contributors to this release. > We would especially like to recognize the new contributors: Mikhail > Isakov, Betsy McPhail, Luc Hermitte, Shawn Waldon, Tobias Wood, > Ricardo Ortiz, Sreekanth Arikatla, Hyun Jae Kang, Lucas Gandel, Adam > Snyder, Junjie Bai, Seun Odutola, Abhishek Tiwari, Eugene Prilepin, > Zach Williamson, Alexander Leinoff, Alexis Girault, Laurentiu Nicola, > Floris Berendsen, Max Smolens, and Pablo Hernandez-Cerdan. > > Many community members stepped up to contribute fixes for this release > candidate. To allow testing and accommodate the upcoming holiday, the > final release is re-scheduled for mid-January. > > > Known issues in this release candidate, to be fixed before the final > release: > * TransformReadWriteTest fails on Mac OSX with shared libraries. > * Mac OSX 10.6 has build errors. > > > [1] http://www.itk.org/Wiki/ITK/Git > > [2] http://open.cdash.org/index.php?project=Insight > > > > New Features > --------------------- > > * Wrapping improvements > * Python 3 supported > * Wrapping builds much faster due to CastXML binaries > * LandmarkBasedTransformInitializer now wrapped > * NumPy bridge with VisualStudio > * Wrapping for the MinimalPathExtraction module > * Wrapping is now installed into Python?s site-packages directory > in the ?itk? package > * Wrapping package size is decreased > * Better package portability on Mac OSX > > * New Remote Modules > * Cuberille > * Insight Journal Article: http://hdl.handle.net/10380/3186 > * AnisotropicDiffusionLBR > * Insight Journal Article: http://hdl.handle.net/10380/3505 > * Web browser reproducibility: > http://www.kitware.com/blog/home/post/942 > > * Core Improvements > * External Modules can now be developed outside of the ITK source > tree and on GitHub > * Details: http://www.kitware.com/blog/home/post/997 > * New utilities in itk::Math: > * AlmostEquals > * NotAlmostEquals > * ExactlyEquals > * NotExactlyEquals > * New itk::NumericTraits > * IsInteger > * IsSigned > * Improved C++11 support > * New ITK_DELETE_FUNCTION macro for ?=delete? > * New ITK_NOEXCEPT macro for the ?noexcept? keyword > * Improved capabilities of itk::ResourceProbe and > itk::ResourceProbesCollectorBase > * Improve numerical stability in VNL eigen system estimation > * itksys_ios:: and itksys_stl:: have been remove (use std::) > > * Filtering Improvements > * Generate a FlatStructuringElement from an image > * WarpImageFilter support VectorImage?s > * ConvertLabelMap supports different LabelMap types > * ImageToPathFilter moved from the ITKReview to the ITKPath module > * itk::MovingHistogramImageFilter moved to the ITKImageFilterBase module > > * Registration Improvements > * Point-set registration with time-varying B-splines > > * Build Improvements > * Module dependencies can now be specified as public / private / > compile / test > * BUILD_EXAMPLES CMake option is now OFF by default > * Option to export all library symbols on Windows: > * Details: http://www.kitware.com/blog/home/post/939 > * Expat third party library is now name mangled > * Many more modules can be built as shared libraries > * KWStyle is automatically built and configured when tests are built > > * Performance Improvements > * New MetaProgrammingLibrary namespace (itk::mpl) holds members for > metaprogramming > * itk::mpl::{TrueType,FalseType} > * itk::mpl::{If,Not,And,Or,Xor} > * itk::mpl::EnableIf > * itk::mpl::IsBaseOf > * itk::mpl::IsConvertible > * itk::mpl::IsNumber > * itk::mpl::IsSame > * itk::mpl::PromoteType > * Image::GetPixel performance improvements > * Many itk::VariableLengthVector performance improvements > * AdaptiveHistogramEqualization uses a moving histogram > * WarpImageFilter performance improvements > > * Documentation Improvements > * Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples > * ITK Software Guide improvements > * How to use Python wrapping > * How to create an ITK module > * Improvements to segmentation examples > * Expanded Canny edge detection example > * Expanded tree container example > > * Third Party Library Updates > * FFTW updated to latest upstream > * Build with recent OpenCV 2 and 3 > * Build with the latest VTK > * PNG update to the latest upstream > * GDCM updated to the latest upstream > * KWSys updated to the latest upstream > * MINC updated to the latest upstream > * SWIG updated to the latest upstream > * Third party PNG and MINC are now Git subtrees > > * Style improvements -- ITK gets more stylish with every release! > * Private copy constructors and operator= use ITK_DELETE_FUNCTION > > * Improved code coverage -- we are at 84.9%! > > * *Lots* of important bug fixes > > * And much more! See details in the log below. > > > Changes from v4.9rc02..v4.9rc03 > ------------------------------------------------ > > Alexis Girault (1): > BUG: Implement SetAutoMinimumMaximum in > itkScalarImageToHistogramGenerator > > Bill Lorensen (1): > BUG: nifti_read_subregion_image was leaking file pointers > > Brad King (7): > ENH: Teach ITK module macros to support independent header-only > modules > ENH: Add script to import KWIML library source code > ENH: Add `ITKKWIML` module to provide external KWIML library > ENH: Port TIFF integer types from KWSys to KWIML > ENH: Port LSM integer types from KWSys to KWIML > ENH: Port itkIntTypes.h from KWSys to KWIML > ENH: Drop KWSys FundamentalType component > > Bradley Lowekamp (1): > ENH: Add option to choose scheme for git download > > Davis Vigneault (1): > STYLE: Use cstdlib return macros in ITK examples > > D?enan Zuki? (3): > BUG: do not pass 0,0,0 to Versor.Set() > STYLE: Removing the unused NeighborhoodRadius property > ENH: Write out transform in DeformableRegistration15 > > Gert Wollny (1): > BUG: Remove double-conversion from public interface, use system. > > Hyun Jae Kang (8): > ENH: Use a data struct to export the system information of a probe. > ENH: Create a test for the SpawnThread function ( ITK-3317) > STYLE: Remove an unnecessary file (-w) from source code > BUG: Fixed the failed case of itkStdStreamStateSaveTest on OS X 10.8 > BUG: Fixed the failed test case of itkThreadPoolTest on OS X 10.8 > BUG: Fixed a failed test of ITKDistanceMapTestDriver > BUG: Fixed the failed test VideoSourceTest > PERF: Improve the performance of a test of > ITKRegistrationMethodsv4TestDriver > COMP: Fixed the compiler error of > itkDisplacementFieldToBSplineImageFilterTest > > Jean-Christophe Fillion-Robin (25): > BUG: Build ITKIOTransformHDF5 as shared library. See #3393 > BUG: Build ITKIOTransformMINC as shared library. See #3393 > BUG: Build ITKIOTransformMatlab as shared library. See #3393 > BUG: Build ITKIOTransformInsightLegacy as shared library. See #3393 > STYLE: TransformIOFactory: Remove obsolete declaration. See #3393 > COMP: TransformIOFactory: Add missing ctor/dtor from hxx file. See > #3393 > COMP: TransformFileWriter: Remove method "OpenStream()" without > definition > COMP: TransformFileReaderTemplate: Remove undefined method > "CreateTransform()" > ENH: Update ITKIOPhilipsREC to allow static initialization. See #3393 > ENH: Update ITKIOTransformMINC to allow static initialization. See > #3393 > COMP: MINC: Fix VS2008 "unknown round" build error. See #3393 > COMP: MINC: Fix VS2008 "unknown arpa/inet.h" build error. See #3393 > COMP: Configure ENABLE_SHARED into .cmake file. See #3393 > COMP: Fix configuration of IOFactory header. See #3393 > STYLE: UseITK: Removed redundant code setting ImageIO factory > name. See #3393 > STYLE: UseITK: Re-factor introducing > _configure_IOFactoryRegisterManager > STYLE: UseITK: Set TransformIO factory and module name using > convention. > BUG: Ensure Image IO factories are registered once. See #3393 > BUG: Ensure Transform IO factories are registered once. > COMP: ITKIOXML: Fix VS11 "already defined std::string" link > error. See #3393 > BUG: TransformIO: Implement explicit template instantiation > using "extern". > COMP: TransformIO: Fix VS build errors removing extra EXPORT > COMP: TransformIO: Handle compiler not supporting "pragma > diagnostic". > COMP: TransformIO: TransformFile(Reader|Writer) still need to be > exported. > COMP: TransformIO: Fix explicit instantiation approach > > Johan Andruejol (1): > ENH: Add ITK_RUNTIME_LIBRARY_DIRS for external projects > > KWIML Upstream (1): > KWIML 2015-12-09 (43f9f8d0) > > Lucas Gandel (1): > BUG: PhysicsBasedNonRigidRegistrationMethod test failure on Debian > 32bit > > Matthew McCormick (16): > COMP: Fix PointDimension reference in AzimuthElevationToCartesian > test. > STYLE: Improve scoping in AzimuthElevationToCartesian test. > STYLE: Explicitly mark the ProcessObject methods virtual in > SignedMaurer. > BUG: Do not try to install targets that do not exist when > building externally. > BUG: ITKIOMeta needs a public dependency on ITKMetaIO. > COMP: Update LesionSizingToolkit for external build and style > test failures. > BUG: Add CMake OpenCV export code to ITKVideoBridgeOpenCV. > COMP: Improve compatibility with OpenCV 3. > DOC: Fix class references in StatisticsLabelMapFilter. > STYLE: Improved readability of > itkStatisticsUniqueLabelMapFilterTest1. > DOC: Correct ReverseOrdering description in > ShapeUniqueLabelMapFilter. > STYLE: Add own copy of GenerateExportHeader > COMP: Create _TEMPLATE_EXPORT macros. > COMP: TransformIOBaseTemplate must be explicitly instantiated. > BUG: Do not use dynamic_cast for DisplacementFieldType in HDF5 test. > COMP: Do not use string(MAKE_C_IDENTIFIER with CMake < 2.8.12 > > Max Smolens (1): > BUG: VoronoiSegmentationRGBImageFilter: add pixel dimension check > > Mikhail Isakov (1): > DOC: correction in DiffusionTensor3D Reconstruction > > Ricardo Ortiz (1): > BUG: Set itkBinaryImageTo*LabelMapFilter foreground/background values > > Seun Odutola (1): > BUG: absolute value of tolerance taken to cater for negative spacing > > Shawn Waldon (1): > COMP: OSX set deployment target when building fftw > > Simon Alexander (4): > STYLE: Change to make git bash on windows happy with the function > name > COMP: fixes for visual studio 2015update1 x86 in release mode > COMP: fixes for visual studio 2015update1 x86 in release mode > COMP: fixes for visual studio 2015update1 x86 in release mode > > Sreekanth Arikatla (2): > BUG: Resolved const correctness in itkMatrix.h > ENH: Fixes the symmetry of AzimuthElevationToCartesianTransform > and adds tests > > > Changes from v4.9rc01..v4.9rc02 > ------------------------------------------------ > > Bill Lorensen (1): > BUG: Valgrind detected an invalid read > > Davis Vigneault (1): > STYLE: Address some warnings when running cppcheck > > Hyun Jae Kang (2): > COMP: Fixed a warning message of data-conversion on VS14 > COMP: Update KWStyle to remove format-string warning message > > Matthew McCormick (3): > DOC: Remove invalid wrapping example. > BUG: Wrap AdaptiveEqualizationHistogram. > COMP: Ignore Doxygen endcond warning in itkIsConvertible.h. > > Seun Odutola (1): > COMP: Corrected minc2.h path installation from libsrc2/minc2.h to > minc2.h > > Ziv Yaniv (2): > BUG: Affine transformation was estimated without sufficient > number of points. > BUG: fixed BSpline initializer crash when reference image not set. > > > Changes from v4.8.0..v4.9rc01 > -------------------------------------------- > > Abhishek Tiwari (1): > BUG: "tmpImageIndex" not initialized to 0. > > Adam Snyder (1): > PERF: Reworked MMI Threading using a per-thread buffer > > Alexander Leinoff (6): > ENH: Adds IsInteger and IsSigned to NumericTraits. > COMP: Doxygen itkMath.h 'OneValue()' could not be resolved. > ENH: Adds ExactlyEquals and NotExactlyEquals functions to itkMath.h > COMP: Removes floating-point equality checks > ENH: COMP: Adds support for complex values to Math::AlmostEquals > ENH: Updates fftw dependency > > Arnaud Gelas (5): > COMP: fix warning (unused local typedef) > COMP: simplify ITKVideoBridgeOpenCV dependency > DOC: add doxgen documentation for BinaryImageToLevelSetImageAdaptor > ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner > COMP: fix compilation error with OpenCV2 and OpenCV3 > > Betsy McPhail (1): > BUG: Improve buffer alignment in OctreeNode . > > Bill Hoffman (2): > ENH: Use new CMake Windows export symbol dll feature. > COMP: Put vnl_export.h in the list of sources so it gets installed. > > Bill Lorensen (4): > COMP: VTkGlue linker errors > BUG: Inappropriate use of AlmostEquals > ENH: Bump tag for wiki examples > ENH: Better layout strategy > > Brad King (3): > ENH: Remove use of include and itksys_ios::* > ENH: Remove use of include and itksys_stl::* > ENH: Update CMake Policy settings in Testing/TestExternal project > > Bradley Lowekamp (31): > BUG: Avoid null deference in PrintSelf with default construction > ENH: Enable base classes for templates of landmark initializer > STYLE: Use "Swap" for ITK member name > BUG: Demonstrate Eigen analysis failure > BUG: Fix computation of Eigen analysis > ENH: Update DiscreteHessianGaussian Test baseline > ENH: Correctly demonstrate float point Eigen failure > ENH: compile vnl_math_hypot, and use at least double > ENH: Adding initial update script from used libpng version. > ENH: removing non-subtree files for itkpng > ENH: Ported ITK changes for building to subtree merged code > ENH: Update libpng update script for v1.6.9 > BUG: Use ParameterValueType for computation of landmark affine > ENH: Wrap LandmarkBasedTransformInitializer > BUG: Avoid potential exception in itk::Object::UnRegister > ENH: Update itkpng zlib, configuration, and rename > ENH: Update itkpng name mangling > BUG: Use const pointer in Set method for constant ReferenceImage ivar > BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod > BUG: Demonstrate side effect on registration due to BSplineScatter > change > ENH: Move MovingHistogramImageFilter base classes to ImageFilterBase > BUG: Avoid potential exception in itk::Object::UnRegister > BUG: Avoid null deference in PrintSelf with default construction > BUG: Use const pointer in Set method for constant ReferenceImage ivar > ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram base > COMP: address sign unsigned comparison warning > COMP: Address signed unsigned comparison warning > COMP: Address unused member variable and methods in anonymous ns > BUG: Fix segfault when with empty IsolatedWatershed Threshold range > BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test > BUG: Reduce number of targets with MSVC > > Davis Vigneault (7): > DOC: Minor improvements to segmentation examples. > DOC: Expanded Canny Edge Detection Example > DOC: Expanded TreeContainer Example > COMP: Warnings in itkVTKImageExport when compiling with c++11 > COMP: Warnings in FFTW Classes when compiling with c++11 > COMP: Update Git Tag for Subdivision Module > COMP: Warnings in FFTW Classes when compiling with c++11 > > D?enan Zuki? (1): > STYLE: better formatting of the "usage" message > > Eugene Prilepin (1): > BUG: Fix a template name formation in python wrappings > > Floris Berendsen (1): > STYLE: Improve naming conventions in comments. > > Hans Johnson (29): > STYLE: Instrument for FixedParameters typedef > BUG: Demonstrate DisplacementTransformFailure > BUG: FixedParameters should be double precision > STYLE: Minor code style issues for MGHIO > COMP: Update to version for WikiExamples > ENH: Update Sphinx for ITK 4.8.0 > ENH: Update MGHIO to be shared lib > ENH: Provide consistent floating point comparisons > BUG: Fix MGHIO to fix write failures > PERF: Remove floating point as sentinal value > COMP: Const correctness needs to be maintained > BUG: Preserve backwards compatibility > DOC: Provide consistent naming in comments > ENH: Conversion between transform type tolerance > STYLE: Prefer initialization to assignment > ENH: Missing ITK_OVERRIDE > COMP: Need to propagate ITKGDCM > COMP: Need to propagate ITKGDCM > COMP: Add missing ITK_OVERRIDE > STYLE: Minor code style issues for MGHIO > COMP: Update to version for WikiExamples > ENH: Update Sphinx for ITK 4.8.0 > ENH: Update MGHIO to be shared lib > BUG: Fix MGHIO to fix write failures > ENH: C++11 allows for rigorous =delete > COMP: Remove unnecessary failing assert test > ENH: Ignore internal files for the Clion editor > COMP: Fix VNL compilation for wider C++11 support > BUG: In configuration test need to mirror code > > Hyun Jae Kang (27): > BUG: Remove std::cout calls from class > BUG: Avoid an unexpected output of static_cast > BUG: Update python example codes for ImageRegistration > BUG: Retrieve the missed wrap file > BUG: itkVTKImageIO class does not handle blank lines in VTK file > header. > BUG: Fix HDF5 CMake configuration with VS2015 > BUG: Fix a compilation issue on ITK4 with FFTW and shared libraries > BUG: Fixed older XCode linking error > ENH: Use CastXML binaries when building with x86_64 Mac OS X > BUG: Remove std::cout calls from class > BUG: itkVTKImageIO class does not handle blank lines in VTK file > header. > BUG: Fixed older XCode linking error > ENH: Add automatic KWStyle build and configuration setup > COMP: KWStyle shadow, format-nonliteral and autological-compare > warning. > COMP: Fixed the warning messages from itkGPU Module > COMP: Fixed a warning message of unused-private-field > COMP: Apply latest version of KWStyle > COMP: Update KWStyle to fix its additional warning messages > COMP: Update KWStyle to fix its additional warning messages > COMP: Fix data-conversion warning messages on Windows > ENH: Update itkResourceProbe to calculate statistical data > COMP: Fix data-conversion warning messages on VS14 > COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function > ENH: Update the Report() function of itkResourceProbesCollectorBase > COMP: Fix data-conversion warning message on itkResourceProbe > COMP: Fix additional warning messages of KWStyle > COMP: Fix data-conversion warning messages > > Jon Haitz Legarreta (6): > ENH: Add test for itkStatisticsUniqueLabelMapFilter > BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest > BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter > BUG: Test for StatisticsUniqueLabelMapFilter stability > ENH: Add test for itkParametricStpaceToImageSpaceFilter > ENH: Improve code coverage for > itkParametricSpaceToImageSpaceMeshFilter > > Julien Michel (1): > ENH: Support of VectorImage as template parameters for WarpImageFilter > > Junjie Bai (2): > BUG: ConvertLabelMap with different LabelMapTypes > BUG: LabelObject CopyAttribute support different LabelObject type > > KWSys Robot (4): > KWSys 2015-07-10 (c9336bcf) > KWSys 2015-07-30 (f63febb7) > KWSys 2015-08-24 (cdaf522c) > KWSys 2015-08-28 (dc3fdd7f) > > LIBPNG Upstream (2): > PNG 2009-04-06 (e68f5a36) > PNG 2014-02-05 (3e753eb8) > > Laurentiu Nicola (2): > PERF: Avoid temporary smartptr in ProcessObject::GetInput > PERF: Optimize WarpImageFilter by avoiding refcount bouncing > > Luc Hermitte (8): > PERF: itk::Image::GetPixel() performance improvment. > PERF: Performance enhancements on VariableLengthVectors 1/... > ENH: Dependencies on itkVariableLengthVector.h reduced > BUG: Error in VariableLengthVector Unit Tests > PERF: Performance enhancements on VLV 2/... > PERF: Performances enhancements on VLV 3/... > COMP: Fix signed/unsigned warnings > BUG: std::copy/fill on empty VLV > > Lucas Gandel (4): > ENH: Move ImageToPathFilter from ITKReview to ITKPath module. > BUG: Fixing ImageToPathFilter wrapping call from Review Module > STYLE: Fix KWStyle dashboard errors > BUG: Fix external module BUILD_SHARED_LIBS status > > Mathieu Malaterre (1): > BUG: Name mangle the included expat third party library. > > Matthew McCormick (94): > ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest. > ENH: Add AnisotropicDiffusionLBR Remote Module. > ENH: Bump ITK version to 4.9.0. > BUG: Remove std::cout calls from classes. > COMP: Remove unused argument in ConditionVariableNoThreads. > BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. > COMP: Add link interface specification for wrapping > target_link_libraries. > STYLE: Fix indentation in itkMINCTransformIOFactory.cxx. > COMP: Fix MINCTransformIO factory registration. > COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1. > COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR. > BUG: Initialize mutex for 32 bit AtomicInt. > ENH: Use CastXML binaries when building with x86_64 Linux. > STYLE: Rename gccxml -> castxml in {idx,igenerator}.py. > COMP: Disable the gold linker for static builds on Ubuntu 14.04. > ENH: Use Windows binaries for CastXML. > ENH: Add better scoping in igenerator.py. > BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC. > BUG: LevelSetsv4 used signed char instead of char. > ENH: Add better scoping to idx.py. > COMP: Define newSize and oldSize in VariableLengthVector. > STYLE: Use prefix increment operator in ImageBase. > DOC: Correct spelling of Continuous. > ENH: Add more progress information to IterativeClosestPoint2. > BUG: Build BridgeNumPy with Visual Studio. > ENH: Add ITKModuleExternal.cmake > COMP: Wrap Image< bool, D > for FlatStructuringElement. > BUG: Use CastXML binary built in Release. > BUG: ContinuousIndex should not be templated over TCoordRep. > COMP: Set CMP0054 to new. > COMP: Address line length too long for Software Guide. > COMP: Fix CannyEdgeDetectionImageFilter.cxx types. > BUG: Support Python 3 wrapping module initialization. > BUG: Update itkTemplate.py for Python 3. > BUG: Update itkExtras.py for Python 3. > BUG: Prevent Python callback addition recursion. > BUG: Fix test scripts for Python 3. > BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. > ENH: Allow projects to build against an external module. > ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER. > ENH: Rename _cable_ to _wrappers_. > BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. > BUG: Define ITK_WRAPPING_PARSER when wrapping. > COMP: Do not use C++11 alignas in itkAlignedTypedef. > ENH: Bump CMakeLists.txt version to 4.8.1. > BUG: Pass the CMAKE_CXX_FLAGS to castxml. > ENH: Bump CastXML version to 2015-30-29. > ENH: Bump LLVM / Clang to 3.7.0. > COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5. > COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC. > COMP: Use itkSimpleNewMacro in ThreadedIteratorRangePartitionerTest. > ENH: Add wrapping support for building modules externally. > BUG: Fix KWStyle test paths when building a module externally. > ENH: Add Cuberille Remote module. > COMP: Remove carriage returns from Cuberille remote. > COMP: Remove unused argument in ConditionVariableNoThreads. > DOC: Correct spelling of Continuous. > ENH: Bump the MinimalPathExtraction Remote to 2015-10-20. > COMP: Fix KernelTransform SetFixedParameters argument type. > STYLE: Use prefix increment operator in ImageBase. > COMP: Use ITK's pygccxml by correctly setting up the sys.path > Revert "COMP: Put vnl_export.h in the list of sources so it gets > installed." > BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes" > ENH: Marking wrapping CMake configuration variables as advanced. > STYLE: Rename CASTXML to CASTXML_EXECUTABLE. > COMP: Non-virtual copy attribute members in LabelMap cannot have > override. > COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter. > COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT. > ENH: Remove CMake version check in ITKModuleHeaderTest.cmake > BUG: Improve KWStyle ExternalProject utilization. > ENH: Remove old KWStyle build script. > COMP: Address VariableLengthVector Doxygen rhs @param not found. > ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER. > ENH: Install Python bindings into site-packages. > ENH: Improve readability of Python site-packages path detection. > COMP: DiscreteGaussianDerivativeImageFilter unsigned expression > warning. > BUG: ITKCommon publically depends on ITKDoubleConversion. > COMP: Improve scoping in CovariantVectorGeometryTest. > ENH: Improves names and export of module dependencies. > STYLE: Improve namespace bracket style in itkIsConvertible. > COMP: Set CMP0054 to new. > BUG: Remove unused wrapping files. > BUG: Do install install wrapping development files. > ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. > BUG: Remove duplicate inclusion of wrapping submodules. > COMP: Do not use C++ style comments for Doxygen cond. > BUG: Fix detection of the gold linker. > BUG: Update Python package installation locations. > ENH: Bump CMakeLists.txt version to 4.8.2. > ENH: Change BUILD_EXAMPLES default to OFF. > BUG: Use 'from itk import ITKCommon' in module2module test. > COMP: Link to VTK Python when built with Kits support. > BUG: Install itk_minc2.h header. > COMP: ITKIOMINC has a public dependency on ITKIOImageBase. > > Michka Popoff (9): > ENH: Update to swig 3.0.7 > ENH: Do not link against specific Python library on OS X > COMP: Fix wrapping warnings when building with ITK_WRAP_IMAGE_DIMS=2 > COMP: Add missing wrapping for TransformBase > COMP: Use ITK's pygccxml by correctly setting up the sys.path > COMP: Disable incompatible modules when using Python 3 wrapping > COMP: Move MovingHistogramImageFilterBase wrapping to > ImageFilterBase module > COMP: Disable incompatible modules when using Python 3 wrapping > ENH: Allow operations on Indexes and Offsets in Python > > Mikhail Isakov (1): > BUG: DiffusionTensor3DReconstruction segfault if no baseline image > > Nick Tustison (5): > BUG: Set a default b-spline epsilon. > ENH: Adding testing for closed loop. > BUG: Updating B-spline classes with the same epsilon strategy. > PERF: Switch vnl_vectors for fixed arrays. > ENH: Point-set registration with time-varying B-spline. > > Olivier Commowick (3): > BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen system > BUG: Correct under/overflows in vnl_math_hypot (taken from pythag > from V3P) > BUG: Switch eigenvalues computation to double > > Pablo Hernandez-Cerdan (2): > ENH: Help class for itkFlatStructuringElement with constructor from > images. > COMP: Fix test errors and warnings in FlatStructuringElement. > > Seun Odutola (1): > COMP: Fixed name clash with Apple header (check Macro), renamed > check to Check > > Shawn Waldon (1): > COMP: Set target OS X version in environment for tools using compiler > > Simon Alexander (1): > BUG: incorrect closest point computation > > Tobias Wood (2): > BUG: LBFGSB was printing messages even with debug switched off. > BUG: Removed an unguarded print statement. > > Vladimir S. FONOV (9): > BUG: Missing ITKIOMINC_EXPORT on __Private() > COMP: Changing the order of HDF5 library components > COMP: Splitting up IOMINC module into two parts: MINC and Transform > STYLE: updated comments to properly reference LIBMINC > ENH: Add script to merge upstream MINC as a subtree > MINC 2015-07-23 (c033d431) > COMP: Update MINC CMake code > MINC 2015-08-18 (6d7e3ba8) > MINC 2015-09-13 (95cd5374) > > Xiaoxiao Liu (1): > DOC: update email address for xiaoxiao. > > Zach Williamson (10): > BUG: Use correct libraries for ImageFusion tests > ENH: Consolidate Library Dependencies > COMP: Add a missing link to Review module > COMP: Use correct linking macro in DCMTK > BUG: Use correct libraries for TestKernel tests > COMP: Fix inconsistant naming of GPUPDEDeformableRegistration > ENH: Use new linking system macros > PERF: Avoid searching private dependencies for include directories > COMP: Recover missing dependencies > ENH: use new linking macros in Filtering module > > > > ----------------------------------------------------- > Errors or omissions? Please fix them here: > > > https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From digajjj62 at gmail.com Tue Jan 5 05:33:43 2016 From: digajjj62 at gmail.com (jud) Date: Tue, 5 Jan 2016 03:33:43 -0700 (MST) Subject: [ITK-users] Floating point exception (core dumped) ConnectedComponentFilter Message-ID: <1451990023554-36607.post@n7.nabble.com> Hi, I have a problem when I use big images to find the connected componnents. When I execute the ConnectedComponentImageFilter the following appears: Floating point exception (core dumped) typedef itk::Image ImageType; typedef itk::Image ImageType2; typedef itk::ConnectedComponentImageFilter ConnectedComponentImageFilterType; ConnectedComponentImageFilterType::Pointer connected = ConnectedComponentImageFilterType::New (); connected->SetInput(image); connected->Update(); With small images this error doesn't happen. Anyone have any idea? Thanks! -- View this message in context: http://itk-users.7.n7.nabble.com/Floating-point-exception-core-dumped-ConnectedComponentFilter-tp36607.html Sent from the ITK - Users mailing list archive at Nabble.com. From blowekamp at mail.nih.gov Tue Jan 5 08:51:12 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 5 Jan 2016 08:51:12 -0500 Subject: [ITK-users] Floating point exception (core dumped) ConnectedComponentFilter In-Reply-To: <1451990023554-36607.post@n7.nabble.com> References: <1451990023554-36607.post@n7.nabble.com> Message-ID: <005C231D-F4EA-40B8-A87C-676AEEFED064@mail.nih.gov> Hello, How big is your big image? About how many connected components do you have? Brad > On Jan 5, 2016, at 5:33 AM, jud wrote: > > Hi, > > I have a problem when I use big images to find the connected componnents. > When I execute the ConnectedComponentImageFilter the following appears: > Floating point exception (core dumped) > > typedef itk::Image ImageType; > typedef itk::Image ImageType2; > > typedef itk::ConnectedComponentImageFilter > ConnectedComponentImageFilterType; > ConnectedComponentImageFilterType::Pointer connected = > ConnectedComponentImageFilterType::New (); > connected->SetInput(image); > connected->Update(); > > With small images this error doesn't happen. > > Anyone have any idea? > > Thanks! > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Floating-point-exception-core-dumped-ConnectedComponentFilter-tp36607.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 Tue Jan 5 13:47:42 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 13:47:42 -0500 Subject: [ITK-users] Floating point exception (core dumped) ConnectedComponentFilter In-Reply-To: <005C231D-F4EA-40B8-A87C-676AEEFED064@mail.nih.gov> References: <1451990023554-36607.post@n7.nabble.com> <005C231D-F4EA-40B8-A87C-676AEEFED064@mail.nih.gov> Message-ID: Hi, Catching and print the exception can provide more information. See: http://itk.org/ITKExamples/src/Core/Common/TryCatchException/Documentation.html for an example. HTH, Matt On Tue, Jan 5, 2016 at 8:51 AM, Bradley Lowekamp wrote: > Hello, > > How big is your big image? > > About how many connected components do you have? > > Brad > >> On Jan 5, 2016, at 5:33 AM, jud wrote: >> >> Hi, >> >> I have a problem when I use big images to find the connected componnents. >> When I execute the ConnectedComponentImageFilter the following appears: >> Floating point exception (core dumped) >> >> typedef itk::Image ImageType; >> typedef itk::Image ImageType2; >> >> typedef itk::ConnectedComponentImageFilter >> ConnectedComponentImageFilterType; >> ConnectedComponentImageFilterType::Pointer connected = >> ConnectedComponentImageFilterType::New (); >> connected->SetInput(image); >> connected->Update(); >> >> With small images this error doesn't happen. >> >> Anyone have any idea? >> >> Thanks! >> >> >> >> -- >> View this message in context: http://itk-users.7.n7.nabble.com/Floating-point-exception-core-dumped-ConnectedComponentFilter-tp36607.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 > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Tue Jan 5 14:09:48 2016 From: blowekamp at mail.nih.gov (Bradly Lowekamp) Date: Tue, 5 Jan 2016 14:09:48 -0500 Subject: [ITK-users] Floating point exception (core dumped) ConnectedComponentFilter In-Reply-To: References: <1451990023554-36607.post@n7.nabble.com> <005C231D-F4EA-40B8-A87C-676AEEFED064@mail.nih.gov> Message-ID: <21A77A75-18A0-495C-B474-C05D5BD7C800@mail.nih.gov> Hello, Certainly more information about the nature of the exception would be good. If this is indeed an C++ exception either std::exception of itk::ExceptionObject based, the try catch block will work. However floating point exceptions are usually a difference beast from C++ exception objects. Floating point exception occur during floating point computation in the FPU [1]. Generally the FPU can be configure to silently assign a predefined floating point value such as ?nan?, or a signal can be generating terminating the program like in your case. The option can usually be configured with compilation flags, the run-time environment or the program itself. HTH, Brad [1] https://en.wikipedia.org/wiki/IEEE_floating_point#Exception_handling > On Jan 5, 2016, at 1:47 PM, Matt McCormick wrote: > > Hi, > > Catching and print the exception can provide more information. See: > > http://itk.org/ITKExamples/src/Core/Common/TryCatchException/Documentation.html > > for an example. > > HTH, > Matt > > On Tue, Jan 5, 2016 at 8:51 AM, Bradley Lowekamp wrote: >> Hello, >> >> How big is your big image? >> >> About how many connected components do you have? >> >> Brad >> >>> On Jan 5, 2016, at 5:33 AM, jud wrote: >>> >>> Hi, >>> >>> I have a problem when I use big images to find the connected componnents. >>> When I execute the ConnectedComponentImageFilter the following appears: >>> Floating point exception (core dumped) >>> >>> typedef itk::Image ImageType; >>> typedef itk::Image ImageType2; >>> >>> typedef itk::ConnectedComponentImageFilter >>> ConnectedComponentImageFilterType; >>> ConnectedComponentImageFilterType::Pointer connected = >>> ConnectedComponentImageFilterType::New (); >>> connected->SetInput(image); >>> connected->Update(); >>> >>> With small images this error doesn't happen. >>> >>> Anyone have any idea? >>> >>> Thanks! >>> >>> >>> >>> -- >>> View this message in context: http://itk-users.7.n7.nabble.com/Floating-point-exception-core-dumped-ConnectedComponentFilter-tp36607.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 >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 Jan 5 14:54:47 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 14:54:47 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: <20160104211744.1213332491@mail.rogue-research.com> References: <20160104211744.1213332491@mail.rogue-research.com> Message-ID: Hi Sean, On Mon, Jan 4, 2016 at 4:17 PM, Sean McBride wrote: > On Tue, 22 Dec 2015 18:57:04 -0500, Matt McCormick said: > >>On behalf of the Insight Toolkit community, we are proud to announce >>that ITK 4.9 release candidate 3 has been tagged and is available for >>testing! Please take this opportunity to test the new features in the >>release candidate. >> >>* Third Party Library Updates >> * GDCM updated to the latest upstream > > If I understand ITK's git history correctly, ThirdParty/GDCM was last updated 2015-09-22: > > > According to this: > > > GDCM 2.6.1 was released 2015-11-02 and 2.6.2 on 2015-12-23. > > Try as I may, I don't see an easy way to determine which version of GDCM ITK actually includes... how does one determine this? The upstream commits should have the author "GDCM Upstream". So, cd ~/src/ITK git log --author="GDCM Upstream" This shows that this release note item is an error -- the last time GDCM was updated was 2015-04-29, which was included for ITK 4.8. I have corrected the release notes. To update GDCM, run the Modules/ThirdParty/GDCM/UpdateFromUpstream.sh script. Since GDCM 2.6 has been released, we should switch from GDCM "master" to GDCM "release" before doing the update. This can be changed here: https://github.com/InsightSoftwareConsortium/ITK/blob/af6b2c82ba794ada4d487c5bbd83f2bd1ed39e2f/Modules/ThirdParty/GDCM/UpdateFromUpstream.sh#L6 Thanks, Matt From matt.mccormick at kitware.com Tue Jan 5 14:55:10 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 14:55:10 -0500 Subject: [ITK-users] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: Message-ID: Excellent! Thanks for the patches and feedback! On Mon, Jan 4, 2016 at 7:56 PM, Simon Alexander wrote: > Thanks! > > Clean build and test on my machine this time, show's green on the dash for > 4th. > > On Tue, 22 Dec 2015 at 15:57 Matt McCormick > wrote: >> >> On behalf of the Insight Toolkit community, we are proud to announce >> that ITK 4.9 release candidate 3 has been tagged and is available for >> testing! Please take this opportunity to test the new features in the >> release candidate. >> >> >> To obtain the source code, >> >> git clone http://itk.org/ITK.git >> cd ITK >> git checkout -q --detach v4.9rc03 >> >> For more details, please see the Git documentation [1]. >> >> >> A few selected highlights for this release: >> >> * New Remote modules: the Cuberille module for smooth generation of >> meshes from binary segmentation images, and the >> AnisotropicDiffusionLBR module improved edge-preserving smoothing. >> * Build your own ITK module outside the source tree, add continuous >> integration testing on GitHub, and easily add Python wrapping for your >> C++ algorithms. >> * Python wrapping, including Python 3, builds faster with a more >> standard installation >> * Improved performance of itk::Image::GetPixel and operations on >> itk::VariableLengthVector?s >> * Generate a FlatStructuringElement from an image >> * Point-set registration with time-varying B-splines >> * Module dependencies can now be specified as public / private / compile / >> test >> >> >> Please test the release candidate and share your experiences on the >> mailing list, issue tracker, and Gerrit Code Review. The new module >> dependency specification mechanism may unearth missing dependencies >> for projects that use ITK COMPONENTS with the CMake find_package >> command. >> >> >> An Experimental build, which demonstrates how the test suite performs >> on your local build system, can be submitted to the dashboard [2] >> with: >> >> mkdir ../ITK-build >> cd ../ITK-build >> cmake ../ITK >> ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit >> >> Visual Studio builds must also add ?-C Release? to the ctest command. >> >> Notify the mailing list if there are any unexpected failures. Testing >> your own applications against the RC is also appreciated. >> >> >> Congratulations and well done to the 43 contributors to this release. >> We would especially like to recognize the new contributors: Mikhail >> Isakov, Betsy McPhail, Luc Hermitte, Shawn Waldon, Tobias Wood, >> Ricardo Ortiz, Sreekanth Arikatla, Hyun Jae Kang, Lucas Gandel, Adam >> Snyder, Junjie Bai, Seun Odutola, Abhishek Tiwari, Eugene Prilepin, >> Zach Williamson, Alexander Leinoff, Alexis Girault, Laurentiu Nicola, >> Floris Berendsen, Max Smolens, and Pablo Hernandez-Cerdan. >> >> Many community members stepped up to contribute fixes for this release >> candidate. To allow testing and accommodate the upcoming holiday, the >> final release is re-scheduled for mid-January. >> >> >> Known issues in this release candidate, to be fixed before the final >> release: >> * TransformReadWriteTest fails on Mac OSX with shared libraries. >> * Mac OSX 10.6 has build errors. >> >> >> [1] http://www.itk.org/Wiki/ITK/Git >> >> [2] http://open.cdash.org/index.php?project=Insight >> >> >> >> New Features >> --------------------- >> >> * Wrapping improvements >> * Python 3 supported >> * Wrapping builds much faster due to CastXML binaries >> * LandmarkBasedTransformInitializer now wrapped >> * NumPy bridge with VisualStudio >> * Wrapping for the MinimalPathExtraction module >> * Wrapping is now installed into Python?s site-packages directory >> in the ?itk? package >> * Wrapping package size is decreased >> * Better package portability on Mac OSX >> >> * New Remote Modules >> * Cuberille >> * Insight Journal Article: http://hdl.handle.net/10380/3186 >> * AnisotropicDiffusionLBR >> * Insight Journal Article: http://hdl.handle.net/10380/3505 >> * Web browser reproducibility: >> http://www.kitware.com/blog/home/post/942 >> >> * Core Improvements >> * External Modules can now be developed outside of the ITK source >> tree and on GitHub >> * Details: http://www.kitware.com/blog/home/post/997 >> * New utilities in itk::Math: >> * AlmostEquals >> * NotAlmostEquals >> * ExactlyEquals >> * NotExactlyEquals >> * New itk::NumericTraits >> * IsInteger >> * IsSigned >> * Improved C++11 support >> * New ITK_DELETE_FUNCTION macro for ?=delete? >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >> * Improved capabilities of itk::ResourceProbe and >> itk::ResourceProbesCollectorBase >> * Improve numerical stability in VNL eigen system estimation >> * itksys_ios:: and itksys_stl:: have been remove (use std::) >> >> * Filtering Improvements >> * Generate a FlatStructuringElement from an image >> * WarpImageFilter support VectorImage?s >> * ConvertLabelMap supports different LabelMap types >> * ImageToPathFilter moved from the ITKReview to the ITKPath module >> * itk::MovingHistogramImageFilter moved to the ITKImageFilterBase >> module >> >> * Registration Improvements >> * Point-set registration with time-varying B-splines >> >> * Build Improvements >> * Module dependencies can now be specified as public / private / >> compile / test >> * BUILD_EXAMPLES CMake option is now OFF by default >> * Option to export all library symbols on Windows: >> * Details: http://www.kitware.com/blog/home/post/939 >> * Expat third party library is now name mangled >> * Many more modules can be built as shared libraries >> * KWStyle is automatically built and configured when tests are built >> >> * Performance Improvements >> * New MetaProgrammingLibrary namespace (itk::mpl) holds members for >> metaprogramming >> * itk::mpl::{TrueType,FalseType} >> * itk::mpl::{If,Not,And,Or,Xor} >> * itk::mpl::EnableIf >> * itk::mpl::IsBaseOf >> * itk::mpl::IsConvertible >> * itk::mpl::IsNumber >> * itk::mpl::IsSame >> * itk::mpl::PromoteType >> * Image::GetPixel performance improvements >> * Many itk::VariableLengthVector performance improvements >> * AdaptiveHistogramEqualization uses a moving histogram >> * WarpImageFilter performance improvements >> >> * Documentation Improvements >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples >> * ITK Software Guide improvements >> * How to use Python wrapping >> * How to create an ITK module >> * Improvements to segmentation examples >> * Expanded Canny edge detection example >> * Expanded tree container example >> >> * Third Party Library Updates >> * FFTW updated to latest upstream >> * Build with recent OpenCV 2 and 3 >> * Build with the latest VTK >> * PNG update to the latest upstream >> * GDCM updated to the latest upstream >> * KWSys updated to the latest upstream >> * MINC updated to the latest upstream >> * SWIG updated to the latest upstream >> * Third party PNG and MINC are now Git subtrees >> >> * Style improvements -- ITK gets more stylish with every release! >> * Private copy constructors and operator= use ITK_DELETE_FUNCTION >> >> * Improved code coverage -- we are at 84.9%! >> >> * *Lots* of important bug fixes >> >> * And much more! See details in the log below. >> >> >> Changes from v4.9rc02..v4.9rc03 >> ------------------------------------------------ >> >> Alexis Girault (1): >> BUG: Implement SetAutoMinimumMaximum in >> itkScalarImageToHistogramGenerator >> >> Bill Lorensen (1): >> BUG: nifti_read_subregion_image was leaking file pointers >> >> Brad King (7): >> ENH: Teach ITK module macros to support independent header-only >> modules >> ENH: Add script to import KWIML library source code >> ENH: Add `ITKKWIML` module to provide external KWIML library >> ENH: Port TIFF integer types from KWSys to KWIML >> ENH: Port LSM integer types from KWSys to KWIML >> ENH: Port itkIntTypes.h from KWSys to KWIML >> ENH: Drop KWSys FundamentalType component >> >> Bradley Lowekamp (1): >> ENH: Add option to choose scheme for git download >> >> Davis Vigneault (1): >> STYLE: Use cstdlib return macros in ITK examples >> >> D?enan Zuki? (3): >> BUG: do not pass 0,0,0 to Versor.Set() >> STYLE: Removing the unused NeighborhoodRadius property >> ENH: Write out transform in DeformableRegistration15 >> >> Gert Wollny (1): >> BUG: Remove double-conversion from public interface, use system. >> >> Hyun Jae Kang (8): >> ENH: Use a data struct to export the system information of a probe. >> ENH: Create a test for the SpawnThread function ( ITK-3317) >> STYLE: Remove an unnecessary file (-w) from source code >> BUG: Fixed the failed case of itkStdStreamStateSaveTest on OS X 10.8 >> BUG: Fixed the failed test case of itkThreadPoolTest on OS X 10.8 >> BUG: Fixed a failed test of ITKDistanceMapTestDriver >> BUG: Fixed the failed test VideoSourceTest >> PERF: Improve the performance of a test of >> ITKRegistrationMethodsv4TestDriver >> COMP: Fixed the compiler error of >> itkDisplacementFieldToBSplineImageFilterTest >> >> Jean-Christophe Fillion-Robin (25): >> BUG: Build ITKIOTransformHDF5 as shared library. See #3393 >> BUG: Build ITKIOTransformMINC as shared library. See #3393 >> BUG: Build ITKIOTransformMatlab as shared library. See #3393 >> BUG: Build ITKIOTransformInsightLegacy as shared library. See #3393 >> STYLE: TransformIOFactory: Remove obsolete declaration. See #3393 >> COMP: TransformIOFactory: Add missing ctor/dtor from hxx file. See >> #3393 >> COMP: TransformFileWriter: Remove method "OpenStream()" without >> definition >> COMP: TransformFileReaderTemplate: Remove undefined method >> "CreateTransform()" >> ENH: Update ITKIOPhilipsREC to allow static initialization. See >> #3393 >> ENH: Update ITKIOTransformMINC to allow static initialization. See >> #3393 >> COMP: MINC: Fix VS2008 "unknown round" build error. See #3393 >> COMP: MINC: Fix VS2008 "unknown arpa/inet.h" build error. See #3393 >> COMP: Configure ENABLE_SHARED into .cmake file. See >> #3393 >> COMP: Fix configuration of IOFactory header. See #3393 >> STYLE: UseITK: Removed redundant code setting ImageIO factory >> name. See #3393 >> STYLE: UseITK: Re-factor introducing >> _configure_IOFactoryRegisterManager >> STYLE: UseITK: Set TransformIO factory and module name using >> convention. >> BUG: Ensure Image IO factories are registered once. See #3393 >> BUG: Ensure Transform IO factories are registered once. >> COMP: ITKIOXML: Fix VS11 "already defined std::string" link >> error. See #3393 >> BUG: TransformIO: Implement explicit template instantiation >> using "extern". >> COMP: TransformIO: Fix VS build errors removing extra EXPORT >> COMP: TransformIO: Handle compiler not supporting "pragma >> diagnostic". >> COMP: TransformIO: TransformFile(Reader|Writer) still need to be >> exported. >> COMP: TransformIO: Fix explicit instantiation approach >> >> Johan Andruejol (1): >> ENH: Add ITK_RUNTIME_LIBRARY_DIRS for external projects >> >> KWIML Upstream (1): >> KWIML 2015-12-09 (43f9f8d0) >> >> Lucas Gandel (1): >> BUG: PhysicsBasedNonRigidRegistrationMethod test failure on Debian >> 32bit >> >> Matthew McCormick (16): >> COMP: Fix PointDimension reference in AzimuthElevationToCartesian >> test. >> STYLE: Improve scoping in AzimuthElevationToCartesian test. >> STYLE: Explicitly mark the ProcessObject methods virtual in >> SignedMaurer. >> BUG: Do not try to install targets that do not exist when >> building externally. >> BUG: ITKIOMeta needs a public dependency on ITKMetaIO. >> COMP: Update LesionSizingToolkit for external build and style >> test failures. >> BUG: Add CMake OpenCV export code to ITKVideoBridgeOpenCV. >> COMP: Improve compatibility with OpenCV 3. >> DOC: Fix class references in StatisticsLabelMapFilter. >> STYLE: Improved readability of >> itkStatisticsUniqueLabelMapFilterTest1. >> DOC: Correct ReverseOrdering description in >> ShapeUniqueLabelMapFilter. >> STYLE: Add own copy of GenerateExportHeader >> COMP: Create _TEMPLATE_EXPORT macros. >> COMP: TransformIOBaseTemplate must be explicitly instantiated. >> BUG: Do not use dynamic_cast for DisplacementFieldType in HDF5 test. >> COMP: Do not use string(MAKE_C_IDENTIFIER with CMake < 2.8.12 >> >> Max Smolens (1): >> BUG: VoronoiSegmentationRGBImageFilter: add pixel dimension check >> >> Mikhail Isakov (1): >> DOC: correction in DiffusionTensor3D Reconstruction >> >> Ricardo Ortiz (1): >> BUG: Set itkBinaryImageTo*LabelMapFilter foreground/background >> values >> >> Seun Odutola (1): >> BUG: absolute value of tolerance taken to cater for negative spacing >> >> Shawn Waldon (1): >> COMP: OSX set deployment target when building fftw >> >> Simon Alexander (4): >> STYLE: Change to make git bash on windows happy with the function >> name >> COMP: fixes for visual studio 2015update1 x86 in release mode >> COMP: fixes for visual studio 2015update1 x86 in release mode >> COMP: fixes for visual studio 2015update1 x86 in release mode >> >> Sreekanth Arikatla (2): >> BUG: Resolved const correctness in itkMatrix.h >> ENH: Fixes the symmetry of AzimuthElevationToCartesianTransform >> and adds tests >> >> >> Changes from v4.9rc01..v4.9rc02 >> ------------------------------------------------ >> >> Bill Lorensen (1): >> BUG: Valgrind detected an invalid read >> >> Davis Vigneault (1): >> STYLE: Address some warnings when running cppcheck >> >> Hyun Jae Kang (2): >> COMP: Fixed a warning message of data-conversion on VS14 >> COMP: Update KWStyle to remove format-string warning message >> >> Matthew McCormick (3): >> DOC: Remove invalid wrapping example. >> BUG: Wrap AdaptiveEqualizationHistogram. >> COMP: Ignore Doxygen endcond warning in itkIsConvertible.h. >> >> Seun Odutola (1): >> COMP: Corrected minc2.h path installation from libsrc2/minc2.h to >> minc2.h >> >> Ziv Yaniv (2): >> BUG: Affine transformation was estimated without sufficient >> number of points. >> BUG: fixed BSpline initializer crash when reference image not set. >> >> >> Changes from v4.8.0..v4.9rc01 >> -------------------------------------------- >> >> Abhishek Tiwari (1): >> BUG: "tmpImageIndex" not initialized to 0. >> >> Adam Snyder (1): >> PERF: Reworked MMI Threading using a per-thread buffer >> >> Alexander Leinoff (6): >> ENH: Adds IsInteger and IsSigned to NumericTraits. >> COMP: Doxygen itkMath.h 'OneValue()' could not be resolved. >> ENH: Adds ExactlyEquals and NotExactlyEquals functions to itkMath.h >> COMP: Removes floating-point equality checks >> ENH: COMP: Adds support for complex values to Math::AlmostEquals >> ENH: Updates fftw dependency >> >> Arnaud Gelas (5): >> COMP: fix warning (unused local typedef) >> COMP: simplify ITKVideoBridgeOpenCV dependency >> DOC: add doxgen documentation for BinaryImageToLevelSetImageAdaptor >> ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner >> COMP: fix compilation error with OpenCV2 and OpenCV3 >> >> Betsy McPhail (1): >> BUG: Improve buffer alignment in OctreeNode . >> >> Bill Hoffman (2): >> ENH: Use new CMake Windows export symbol dll feature. >> COMP: Put vnl_export.h in the list of sources so it gets installed. >> >> Bill Lorensen (4): >> COMP: VTkGlue linker errors >> BUG: Inappropriate use of AlmostEquals >> ENH: Bump tag for wiki examples >> ENH: Better layout strategy >> >> Brad King (3): >> ENH: Remove use of include and itksys_ios::* >> ENH: Remove use of include and itksys_stl::* >> ENH: Update CMake Policy settings in Testing/TestExternal project >> >> Bradley Lowekamp (31): >> BUG: Avoid null deference in PrintSelf with default construction >> ENH: Enable base classes for templates of landmark initializer >> STYLE: Use "Swap" for ITK member name >> BUG: Demonstrate Eigen analysis failure >> BUG: Fix computation of Eigen analysis >> ENH: Update DiscreteHessianGaussian Test baseline >> ENH: Correctly demonstrate float point Eigen failure >> ENH: compile vnl_math_hypot, and use at least double >> ENH: Adding initial update script from used libpng version. >> ENH: removing non-subtree files for itkpng >> ENH: Ported ITK changes for building to subtree merged code >> ENH: Update libpng update script for v1.6.9 >> BUG: Use ParameterValueType for computation of landmark affine >> ENH: Wrap LandmarkBasedTransformInitializer >> BUG: Avoid potential exception in itk::Object::UnRegister >> ENH: Update itkpng zlib, configuration, and rename >> ENH: Update itkpng name mangling >> BUG: Use const pointer in Set method for constant ReferenceImage ivar >> BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod >> BUG: Demonstrate side effect on registration due to BSplineScatter >> change >> ENH: Move MovingHistogramImageFilter base classes to ImageFilterBase >> BUG: Avoid potential exception in itk::Object::UnRegister >> BUG: Avoid null deference in PrintSelf with default construction >> BUG: Use const pointer in Set method for constant ReferenceImage ivar >> ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram base >> COMP: address sign unsigned comparison warning >> COMP: Address signed unsigned comparison warning >> COMP: Address unused member variable and methods in anonymous ns >> BUG: Fix segfault when with empty IsolatedWatershed Threshold range >> BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test >> BUG: Reduce number of targets with MSVC >> >> Davis Vigneault (7): >> DOC: Minor improvements to segmentation examples. >> DOC: Expanded Canny Edge Detection Example >> DOC: Expanded TreeContainer Example >> COMP: Warnings in itkVTKImageExport when compiling with c++11 >> COMP: Warnings in FFTW Classes when compiling with c++11 >> COMP: Update Git Tag for Subdivision Module >> COMP: Warnings in FFTW Classes when compiling with c++11 >> >> D?enan Zuki? (1): >> STYLE: better formatting of the "usage" message >> >> Eugene Prilepin (1): >> BUG: Fix a template name formation in python wrappings >> >> Floris Berendsen (1): >> STYLE: Improve naming conventions in comments. >> >> Hans Johnson (29): >> STYLE: Instrument for FixedParameters typedef >> BUG: Demonstrate DisplacementTransformFailure >> BUG: FixedParameters should be double precision >> STYLE: Minor code style issues for MGHIO >> COMP: Update to version for WikiExamples >> ENH: Update Sphinx for ITK 4.8.0 >> ENH: Update MGHIO to be shared lib >> ENH: Provide consistent floating point comparisons >> BUG: Fix MGHIO to fix write failures >> PERF: Remove floating point as sentinal value >> COMP: Const correctness needs to be maintained >> BUG: Preserve backwards compatibility >> DOC: Provide consistent naming in comments >> ENH: Conversion between transform type tolerance >> STYLE: Prefer initialization to assignment >> ENH: Missing ITK_OVERRIDE >> COMP: Need to propagate ITKGDCM >> COMP: Need to propagate ITKGDCM >> COMP: Add missing ITK_OVERRIDE >> STYLE: Minor code style issues for MGHIO >> COMP: Update to version for WikiExamples >> ENH: Update Sphinx for ITK 4.8.0 >> ENH: Update MGHIO to be shared lib >> BUG: Fix MGHIO to fix write failures >> ENH: C++11 allows for rigorous =delete >> COMP: Remove unnecessary failing assert test >> ENH: Ignore internal files for the Clion editor >> COMP: Fix VNL compilation for wider C++11 support >> BUG: In configuration test need to mirror code >> >> Hyun Jae Kang (27): >> BUG: Remove std::cout calls from class >> BUG: Avoid an unexpected output of static_cast >> BUG: Update python example codes for ImageRegistration >> BUG: Retrieve the missed wrap file >> BUG: itkVTKImageIO class does not handle blank lines in VTK file >> header. >> BUG: Fix HDF5 CMake configuration with VS2015 >> BUG: Fix a compilation issue on ITK4 with FFTW and shared libraries >> BUG: Fixed older XCode linking error >> ENH: Use CastXML binaries when building with x86_64 Mac OS X >> BUG: Remove std::cout calls from class >> BUG: itkVTKImageIO class does not handle blank lines in VTK file >> header. >> BUG: Fixed older XCode linking error >> ENH: Add automatic KWStyle build and configuration setup >> COMP: KWStyle shadow, format-nonliteral and autological-compare >> warning. >> COMP: Fixed the warning messages from itkGPU Module >> COMP: Fixed a warning message of unused-private-field >> COMP: Apply latest version of KWStyle >> COMP: Update KWStyle to fix its additional warning messages >> COMP: Update KWStyle to fix its additional warning messages >> COMP: Fix data-conversion warning messages on Windows >> ENH: Update itkResourceProbe to calculate statistical data >> COMP: Fix data-conversion warning messages on VS14 >> COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function >> ENH: Update the Report() function of itkResourceProbesCollectorBase >> COMP: Fix data-conversion warning message on itkResourceProbe >> COMP: Fix additional warning messages of KWStyle >> COMP: Fix data-conversion warning messages >> >> Jon Haitz Legarreta (6): >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >> BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest >> BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter >> BUG: Test for StatisticsUniqueLabelMapFilter stability >> ENH: Add test for itkParametricStpaceToImageSpaceFilter >> ENH: Improve code coverage for >> itkParametricSpaceToImageSpaceMeshFilter >> >> Julien Michel (1): >> ENH: Support of VectorImage as template parameters for >> WarpImageFilter >> >> Junjie Bai (2): >> BUG: ConvertLabelMap with different LabelMapTypes >> BUG: LabelObject CopyAttribute support different LabelObject type >> >> KWSys Robot (4): >> KWSys 2015-07-10 (c9336bcf) >> KWSys 2015-07-30 (f63febb7) >> KWSys 2015-08-24 (cdaf522c) >> KWSys 2015-08-28 (dc3fdd7f) >> >> LIBPNG Upstream (2): >> PNG 2009-04-06 (e68f5a36) >> PNG 2014-02-05 (3e753eb8) >> >> Laurentiu Nicola (2): >> PERF: Avoid temporary smartptr in ProcessObject::GetInput >> PERF: Optimize WarpImageFilter by avoiding refcount bouncing >> >> Luc Hermitte (8): >> PERF: itk::Image::GetPixel() performance improvment. >> PERF: Performance enhancements on VariableLengthVectors 1/... >> ENH: Dependencies on itkVariableLengthVector.h reduced >> BUG: Error in VariableLengthVector Unit Tests >> PERF: Performance enhancements on VLV 2/... >> PERF: Performances enhancements on VLV 3/... >> COMP: Fix signed/unsigned warnings >> BUG: std::copy/fill on empty VLV >> >> Lucas Gandel (4): >> ENH: Move ImageToPathFilter from ITKReview to ITKPath module. >> BUG: Fixing ImageToPathFilter wrapping call from Review Module >> STYLE: Fix KWStyle dashboard errors >> BUG: Fix external module BUILD_SHARED_LIBS status >> >> Mathieu Malaterre (1): >> BUG: Name mangle the included expat third party library. >> >> Matthew McCormick (94): >> ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest. >> ENH: Add AnisotropicDiffusionLBR Remote Module. >> ENH: Bump ITK version to 4.9.0. >> BUG: Remove std::cout calls from classes. >> COMP: Remove unused argument in ConditionVariableNoThreads. >> BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. >> COMP: Add link interface specification for wrapping >> target_link_libraries. >> STYLE: Fix indentation in itkMINCTransformIOFactory.cxx. >> COMP: Fix MINCTransformIO factory registration. >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1. >> COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR. >> BUG: Initialize mutex for 32 bit AtomicInt. >> ENH: Use CastXML binaries when building with x86_64 Linux. >> STYLE: Rename gccxml -> castxml in {idx,igenerator}.py. >> COMP: Disable the gold linker for static builds on Ubuntu 14.04. >> ENH: Use Windows binaries for CastXML. >> ENH: Add better scoping in igenerator.py. >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC. >> BUG: LevelSetsv4 used signed char instead of char. >> ENH: Add better scoping to idx.py. >> COMP: Define newSize and oldSize in VariableLengthVector. >> STYLE: Use prefix increment operator in ImageBase. >> DOC: Correct spelling of Continuous. >> ENH: Add more progress information to IterativeClosestPoint2. >> BUG: Build BridgeNumPy with Visual Studio. >> ENH: Add ITKModuleExternal.cmake >> COMP: Wrap Image< bool, D > for FlatStructuringElement. >> BUG: Use CastXML binary built in Release. >> BUG: ContinuousIndex should not be templated over TCoordRep. >> COMP: Set CMP0054 to new. >> COMP: Address line length too long for Software Guide. >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >> BUG: Support Python 3 wrapping module initialization. >> BUG: Update itkTemplate.py for Python 3. >> BUG: Update itkExtras.py for Python 3. >> BUG: Prevent Python callback addition recursion. >> BUG: Fix test scripts for Python 3. >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >> ENH: Allow projects to build against an external module. >> ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER. >> ENH: Rename _cable_ to _wrappers_. >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >> ENH: Bump CMakeLists.txt version to 4.8.1. >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >> ENH: Bump CastXML version to 2015-30-29. >> ENH: Bump LLVM / Clang to 3.7.0. >> COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5. >> COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC. >> COMP: Use itkSimpleNewMacro in ThreadedIteratorRangePartitionerTest. >> ENH: Add wrapping support for building modules externally. >> BUG: Fix KWStyle test paths when building a module externally. >> ENH: Add Cuberille Remote module. >> COMP: Remove carriage returns from Cuberille remote. >> COMP: Remove unused argument in ConditionVariableNoThreads. >> DOC: Correct spelling of Continuous. >> ENH: Bump the MinimalPathExtraction Remote to 2015-10-20. >> COMP: Fix KernelTransform SetFixedParameters argument type. >> STYLE: Use prefix increment operator in ImageBase. >> COMP: Use ITK's pygccxml by correctly setting up the sys.path >> Revert "COMP: Put vnl_export.h in the list of sources so it gets >> installed." >> BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes" >> ENH: Marking wrapping CMake configuration variables as advanced. >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >> COMP: Non-virtual copy attribute members in LabelMap cannot have >> override. >> COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter. >> COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT. >> ENH: Remove CMake version check in ITKModuleHeaderTest.cmake >> BUG: Improve KWStyle ExternalProject utilization. >> ENH: Remove old KWStyle build script. >> COMP: Address VariableLengthVector Doxygen rhs @param not found. >> ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER. >> ENH: Install Python bindings into site-packages. >> ENH: Improve readability of Python site-packages path detection. >> COMP: DiscreteGaussianDerivativeImageFilter unsigned expression >> warning. >> BUG: ITKCommon publically depends on ITKDoubleConversion. >> COMP: Improve scoping in CovariantVectorGeometryTest. >> ENH: Improves names and export of module dependencies. >> STYLE: Improve namespace bracket style in itkIsConvertible. >> COMP: Set CMP0054 to new. >> BUG: Remove unused wrapping files. >> BUG: Do install install wrapping development files. >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >> BUG: Remove duplicate inclusion of wrapping submodules. >> COMP: Do not use C++ style comments for Doxygen cond. >> BUG: Fix detection of the gold linker. >> BUG: Update Python package installation locations. >> ENH: Bump CMakeLists.txt version to 4.8.2. >> ENH: Change BUILD_EXAMPLES default to OFF. >> BUG: Use 'from itk import ITKCommon' in module2module test. >> COMP: Link to VTK Python when built with Kits support. >> BUG: Install itk_minc2.h header. >> COMP: ITKIOMINC has a public dependency on ITKIOImageBase. >> >> Michka Popoff (9): >> ENH: Update to swig 3.0.7 >> ENH: Do not link against specific Python library on OS X >> COMP: Fix wrapping warnings when building with ITK_WRAP_IMAGE_DIMS=2 >> COMP: Add missing wrapping for TransformBase >> COMP: Use ITK's pygccxml by correctly setting up the sys.path >> COMP: Disable incompatible modules when using Python 3 wrapping >> COMP: Move MovingHistogramImageFilterBase wrapping to >> ImageFilterBase module >> COMP: Disable incompatible modules when using Python 3 wrapping >> ENH: Allow operations on Indexes and Offsets in Python >> >> Mikhail Isakov (1): >> BUG: DiffusionTensor3DReconstruction segfault if no baseline image >> >> Nick Tustison (5): >> BUG: Set a default b-spline epsilon. >> ENH: Adding testing for closed loop. >> BUG: Updating B-spline classes with the same epsilon strategy. >> PERF: Switch vnl_vectors for fixed arrays. >> ENH: Point-set registration with time-varying B-spline. >> >> Olivier Commowick (3): >> BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen >> system >> BUG: Correct under/overflows in vnl_math_hypot (taken from pythag >> from V3P) >> BUG: Switch eigenvalues computation to double >> >> Pablo Hernandez-Cerdan (2): >> ENH: Help class for itkFlatStructuringElement with constructor from >> images. >> COMP: Fix test errors and warnings in FlatStructuringElement. >> >> Seun Odutola (1): >> COMP: Fixed name clash with Apple header (check Macro), renamed >> check to Check >> >> Shawn Waldon (1): >> COMP: Set target OS X version in environment for tools using compiler >> >> Simon Alexander (1): >> BUG: incorrect closest point computation >> >> Tobias Wood (2): >> BUG: LBFGSB was printing messages even with debug switched off. >> BUG: Removed an unguarded print statement. >> >> Vladimir S. FONOV (9): >> BUG: Missing ITKIOMINC_EXPORT on __Private() >> COMP: Changing the order of HDF5 library components >> COMP: Splitting up IOMINC module into two parts: MINC and Transform >> STYLE: updated comments to properly reference LIBMINC >> ENH: Add script to merge upstream MINC as a subtree >> MINC 2015-07-23 (c033d431) >> COMP: Update MINC CMake code >> MINC 2015-08-18 (6d7e3ba8) >> MINC 2015-09-13 (95cd5374) >> >> Xiaoxiao Liu (1): >> DOC: update email address for xiaoxiao. >> >> Zach Williamson (10): >> BUG: Use correct libraries for ImageFusion tests >> ENH: Consolidate Library Dependencies >> COMP: Add a missing link to Review module >> COMP: Use correct linking macro in DCMTK >> BUG: Use correct libraries for TestKernel tests >> COMP: Fix inconsistant naming of GPUPDEDeformableRegistration >> ENH: Use new linking system macros >> PERF: Avoid searching private dependencies for include directories >> COMP: Recover missing dependencies >> ENH: use new linking macros in Filtering module >> >> >> >> ----------------------------------------------------- >> Errors or omissions? Please fix them here: >> >> >> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 sean at rogue-research.com Tue Jan 5 16:22:22 2016 From: sean at rogue-research.com (Sean McBride) Date: Tue, 5 Jan 2016 16:22:22 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: <20160104211744.1213332491@mail.rogue-research.com> Message-ID: <20160105212222.570045939@mail.rogue-research.com> On Tue, 5 Jan 2016 14:54:47 -0500, Matt McCormick said: >To update GDCM, run the > > Modules/ThirdParty/GDCM/UpdateFromUpstream.sh I've just tried, but it looks like no one has tried this from OS X before... :) It seems that OS X's sed, dirname, and basename do not accept '--version', and so I hit the 'die' at line 67. If I change it to 'echo' and let it proceed, I get: Command "sed" not found Command "dirname" not found Command "basename" not found sed: 1: "/GDCM 20[0-9][0-9]-[0-9 ...": extra characters at the end of p command Modules/ThirdParty/GDCM/../../../Utilities/Maintenance/UpdateThirdPartyFromUpstream.sh: line 125: upstream-${thirdparty_module_name,,}: bad substitution I guess it's one of those subtle GNU vs BSD differences tripping things up... I didn't debug further though, I think the author of this script could find the issue faster than me. :) Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From matt.mccormick at kitware.com Tue Jan 5 16:41:16 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 16:41:16 -0500 Subject: [ITK-users] Floating point exception (core dumped) ConnectedComponentFilter In-Reply-To: <21A77A75-18A0-495C-B474-C05D5BD7C800@mail.nih.gov> References: <1451990023554-36607.post@n7.nabble.com> <005C231D-F4EA-40B8-A87C-676AEEFED064@mail.nih.gov> <21A77A75-18A0-495C-B474-C05D5BD7C800@mail.nih.gov> Message-ID: Hi, ITK has support that helps debugging floating point exceptions. Call the static method itk::FloatingPointExceptions::Enable(): http://www.itk.org/Doxygen/html/classitk_1_1FloatingPointExceptions.html#a404951e9dbb64d0a69a7eb1f63d8f1c1 If the floating point exception action is ABORT, a backtrace can be obtained when running in a debugger like gdb. HTH, Matt On Tue, Jan 5, 2016 at 2:09 PM, Bradly Lowekamp wrote: > Hello, > > Certainly more information about the nature of the exception would be good. > > If this is indeed an C++ exception either std::exception of itk::ExceptionObject based, the try catch block will work. > > However floating point exceptions are usually a difference beast from C++ exception objects. Floating point exception occur during floating point computation in the FPU [1]. Generally the FPU can be configure to silently assign a predefined floating point value such as ?nan?, or a signal can be generating terminating the program like in your case. The option can usually be configured with compilation flags, the run-time environment or the program itself. > > HTH, > Brad > > > [1] https://en.wikipedia.org/wiki/IEEE_floating_point#Exception_handling > >> On Jan 5, 2016, at 1:47 PM, Matt McCormick wrote: >> >> Hi, >> >> Catching and print the exception can provide more information. See: >> >> http://itk.org/ITKExamples/src/Core/Common/TryCatchException/Documentation.html >> >> for an example. >> >> HTH, >> Matt >> >> On Tue, Jan 5, 2016 at 8:51 AM, Bradley Lowekamp wrote: >>> Hello, >>> >>> How big is your big image? >>> >>> About how many connected components do you have? >>> >>> Brad >>> >>>> On Jan 5, 2016, at 5:33 AM, jud wrote: >>>> >>>> Hi, >>>> >>>> I have a problem when I use big images to find the connected componnents. >>>> When I execute the ConnectedComponentImageFilter the following appears: >>>> Floating point exception (core dumped) >>>> >>>> typedef itk::Image ImageType; >>>> typedef itk::Image ImageType2; >>>> >>>> typedef itk::ConnectedComponentImageFilter >>>> ConnectedComponentImageFilterType; >>>> ConnectedComponentImageFilterType::Pointer connected = >>>> ConnectedComponentImageFilterType::New (); >>>> connected->SetInput(image); >>>> connected->Update(); >>>> >>>> With small images this error doesn't happen. >>>> >>>> Anyone have any idea? >>>> >>>> Thanks! >>>> >>>> >>>> >>>> -- >>>> View this message in context: http://itk-users.7.n7.nabble.com/Floating-point-exception-core-dumped-ConnectedComponentFilter-tp36607.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 >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 Jan 5 22:01:50 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 22:01:50 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: <20160105212222.570045939@mail.rogue-research.com> References: <20160104211744.1213332491@mail.rogue-research.com> <20160105212222.570045939@mail.rogue-research.com> Message-ID: On Tue, Jan 5, 2016 at 4:22 PM, Sean McBride wrote: > On Tue, 5 Jan 2016 14:54:47 -0500, Matt McCormick said: > >>To update GDCM, run the >> >> Modules/ThirdParty/GDCM/UpdateFromUpstream.sh > > I've just tried, but it looks like no one has tried this from OS X before... :) > > It seems that OS X's sed, dirname, and basename do not accept '--version', and so I hit the 'die' at line 67. If I change it to 'echo' and let it proceed, I get: > > Command "sed" not found > Command "dirname" not found > Command "basename" not found > sed: 1: "/GDCM 20[0-9][0-9]-[0-9 ...": extra characters at the end of p command > Modules/ThirdParty/GDCM/../../../Utilities/Maintenance/UpdateThirdPartyFromUpstream.sh: line 125: upstream-${thirdparty_module_name,,}: bad substitution > > I guess it's one of those subtle GNU vs BSD differences tripping things up... I didn't debug further though, I think the author of this script could find the issue faster than me. :) Thanks for giving it a whirl. It is worth another try after this patch is merged: http://review.source.kitware.com/#/c/20400/ Thanks, Matt From matt.mccormick at kitware.com Tue Jan 5 22:19:45 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 22:19:45 -0500 Subject: [ITK-users] GNU Plot In-Reply-To: References: Message-ID: Hello Suneeza, > I want to plot my optimizer parameters after registration. > > In ItkSoftwareGuide it is stated that the scripts used for plotting are > available in the ITKSoftwareGuide git repository under the directory > "SoftwareGuide/Art." I am unable to find such directory. What version of the Software Guide is this? Where specifically is the reference? We should correct it if it still in the current version. Thanks, Matt From matt.mccormick at kitware.com Tue Jan 5 22:24:41 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 22:24:41 -0500 Subject: [ITK-users] Metric Evaluation In-Reply-To: References: Message-ID: Hi Suneeza, When transferring the parameters to your metric computation, are you also re-using the FixedParameters (center of rotation) in addition to the optimized Parameters (rotation angle and translation)? HTH, Matt On Fri, Jan 1, 2016 at 5:17 PM, suneeza hanif wrote: > Hello Everyone, > > I need help regarding metric calculation. When I run registration algorithm > and use final results(e.g. rotation angle and translation) to calculate > metric once again at the end of process I get different value as compared to > the value of metric evaluated in last iteration. I am using same metric for > registration and later. > > I also did this after one iteration but i still i get different values. > > Does anyone know how to solve this problem? > > Thanks in advance. > > Best Regards, > Suneeza > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 m.jawad at jacobs-university.de Wed Jan 6 08:25:43 2016 From: m.jawad at jacobs-university.de (Jawad, Muhammad) Date: Wed, 6 Jan 2016 13:25:43 +0000 Subject: [ITK-users] itk::MRIBiasFieldCorrectionFilter Message-ID: Dear Itk User, I am looking for some example about the usage pipeline of itk::MRIBiasFieldCorrectionFilter for dicom images. If some body know or has already worked on it, kinldy share it by the toy example. -- Muhammad Jawad From suneezahanif02 at gmail.com Wed Jan 6 10:25:36 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Wed, 6 Jan 2016 16:25:36 +0100 Subject: [ITK-users] GNU Plot In-Reply-To: References: Message-ID: Hello Matt, This is written under section 3.5 Multi-Modality Registration (Pg: 483) in ItkSoftwareGuide V4.8. Best Regards, Suneeza On Wed, Jan 6, 2016 at 4:19 AM, Matt McCormick wrote: > Hello Suneeza, > > > I want to plot my optimizer parameters after registration. > > > > In ItkSoftwareGuide it is stated that the scripts used for plotting are > > available in the ITKSoftwareGuide git repository under the directory > > "SoftwareGuide/Art." I am unable to find such directory. > > What version of the Software Guide is this? Where specifically is the > reference? We should correct it if it still in the current version. > > Thanks, > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From suneezahanif02 at gmail.com Wed Jan 6 11:59:57 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Wed, 6 Jan 2016 17:59:57 +0100 Subject: [ITK-users] Fwd: Metric Evaluation In-Reply-To: References: Message-ID: Hello Matt, Thank you for your reply. I am doing like this: transform->SetParameters( registration->GetOutput()->Get()->GetParameters()); TranslationTransformType::ParametersType initialParameters(transform->GetNumberOfParameters() ); initialParameters[0] = 0; initialParameters[1] = FixedCenterX; initialParameters[2] = FixedCenterY; initialParameters[3] = 0; initialParameters[5] = 0; transform->SetFixedParameters(initialParameters); metric->SetTransform(transform); metric->SetFixedImage( fixedImageReader->GetOutput() ); metric->SetMovingImage(movingImageReader->GetOutput() ); metric->Initialize(); metric->GetValue(); But still I get different value for metric. Best Regards, Suneeza On Wed, Jan 6, 2016 at 4:24 AM, Matt McCormick > wrote: > Hi Suneeza, > > When transferring the parameters to your metric computation, are you > also re-using the FixedParameters (center of rotation) in addition to > the optimized Parameters (rotation angle and translation)? > > HTH, > Matt > > On Fri, Jan 1, 2016 at 5:17 PM, suneeza hanif > wrote: > > Hello Everyone, > > > > I need help regarding metric calculation. When I run registration > algorithm > > and use final results(e.g. rotation angle and translation) to calculate > > metric once again at the end of process I get different value as > compared to > > the value of metric evaluated in last iteration. I am using same metric > for > > registration and later. > > > > I also did this after one iteration but i still i get different values. > > > > Does anyone know how to solve this problem? > > > > Thanks in advance. > > > > Best Regards, > > Suneeza > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the 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: From matt.mccormick at kitware.com Wed Jan 6 15:45:34 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 6 Jan 2016 15:45:34 -0500 Subject: [ITK-users] Fwd: Metric Evaluation In-Reply-To: References: Message-ID: Hi Suneeza, The code is not correct -- the number of FixedParameters is not the same as the number of Parameters. For a 3D rigid transform there are only three FixedParameters -- the x, y, z center of rotation. It is more convenient to use itk::Transform::Clone(). See here for an example: http://itk.org/ITKExamples/src/Core/Transform/CopyANonCompositeTransform/Documentation.html Hope this helps, Matt On Wed, Jan 6, 2016 at 11:59 AM, suneeza hanif wrote: > > Hello Matt, > > Thank you for your reply. > > I am doing like this: > > transform->SetParameters( > registration->GetOutput()->Get()->GetParameters()); > TranslationTransformType::ParametersType > initialParameters(transform->GetNumberOfParameters() ); > initialParameters[0] = 0; > initialParameters[1] = FixedCenterX; > initialParameters[2] = FixedCenterY; > initialParameters[3] = 0; > initialParameters[5] = 0; > transform->SetFixedParameters(initialParameters); > metric->SetTransform(transform); > metric->SetFixedImage( fixedImageReader->GetOutput() ); > metric->SetMovingImage(movingImageReader->GetOutput() ); > metric->Initialize(); > metric->GetValue(); > > But still I get different value for metric. > > Best Regards, > Suneeza > > > On Wed, Jan 6, 2016 at 4:24 AM, Matt McCormick > wrote: >> >> Hi Suneeza, >> >> When transferring the parameters to your metric computation, are you >> also re-using the FixedParameters (center of rotation) in addition to >> the optimized Parameters (rotation angle and translation)? >> >> HTH, >> Matt >> >> On Fri, Jan 1, 2016 at 5:17 PM, suneeza hanif >> wrote: >> > Hello Everyone, >> > >> > I need help regarding metric calculation. When I run registration >> > algorithm >> > and use final results(e.g. rotation angle and translation) to calculate >> > metric once again at the end of process I get different value as >> > compared to >> > the value of metric evaluated in last iteration. I am using same metric >> > for >> > registration and later. >> > >> > I also did this after one iteration but i still i get different values. >> > >> > Does anyone know how to solve this problem? >> > >> > Thanks in advance. >> > >> > Best Regards, >> > Suneeza >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the 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 suneezahanif02 at gmail.com Wed Jan 6 17:53:54 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Wed, 6 Jan 2016 23:53:54 +0100 Subject: [ITK-users] Fwd: Metric Evaluation In-Reply-To: References: Message-ID: Hello Matt, Thanks a lot for your help. I am still unable to get same metric even after using this. I am using Centered2DTransform and during registration I have not initialized it so it will take (0,0) as center of rotation. Then I defined FixedParameters again with (0,0) but metric value is still quite different. Best Regards, Suneeza -------------- next part -------------- An HTML attachment was scrubbed... URL: From suneezahanif02 at gmail.com Thu Jan 7 04:52:11 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Thu, 7 Jan 2016 10:52:11 +0100 Subject: [ITK-users] Fwd: Metric Evaluation In-Reply-To: References: Message-ID: Hello Matt, Here is the full version of code. Can you please guide me where am I doing something wrong because I am unable to get it. Even If I stop after one iteration the values are very different. I would be highly thankful to you. * const unsigned int Dimension = 2;* * typedef float PixelType;* * typedef itk::Image< PixelType, Dimension > FixedImageType;* * typedef itk::Image< PixelType, Dimension > MovingImageType;* * typedef itk::TranslationTransform< double, Dimension > TransformType;* * typedef itk::RegularStepGradientDescentOptimizerv4 OptimizerType;* * typedef itk::MeanSquaresImageToImageMetricv4< FixedImageType,MovingImageType > MetricType;* * typedef itk::ImageRegistrationMethodv4< FixedImageType, MovingImageType, TransformType > RegistrationType;* * MetricType::Pointer metric = MetricType::New();* * OptimizerType::Pointer optimizer = OptimizerType::New();* * RegistrationType::Pointer registration = RegistrationType::New();* * registration->SetMetric( metric );* * registration->SetOptimizer( optimizer );* * typedef itk::LinearInterpolateImageFunction< FixedImageType, double > FixedLinearInterpolatorType;* * typedef itk::LinearInterpolateImageFunction< MovingImageType, double > MovingLinearInterpolatorType;* * FixedLinearInterpolatorType::Pointer fixedInterpolator = FixedLinearInterpolatorType::New();* * MovingLinearInterpolatorType::Pointer movingInterpolator = MovingLinearInterpolatorType::New();* * metric->SetFixedInterpolator( fixedInterpolator );* * metric->SetMovingInterpolator( movingInterpolator );* * typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;* * typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;* * FixedImageReaderType::Pointer fixedImageReader = FixedImageReaderType::New();* * MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();* * fixedImageReader->SetFileName( input1 );* * movingImageReader->SetFileName( input2 );* * registration->SetFixedImage( fixedImageReader->GetOutput() );* * registration->SetMovingImage( movingImageReader->GetOutput() );* * typedef float OutputPixelType;* * typedef itk::Image< PixelType, Dimension > OutputImageType;* * TransformType::Pointer transform = TransformType::New();* * transform->SetIdentity();* * registration->SetInitialTransform( transform );* * optimizer->SetLearningRate( 4 );* * optimizer->SetMinimumStepLength( 0.001 );* * optimizer->SetRelaxationFactor( 0.5 );* * std::cout<<"Transform before registration: "<SetMetricSamplingStrategy( samplingStrategy );* * registration->SetMetricSamplingPercentage( samplingPercentage );* * optimizer->SetNumberOfIterations( 1 );* * CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();* * optimizer->AddObserver( itk::IterationEvent(), observer );* * const unsigned int numberOfLevels = 1;* * registration->SetNumberOfLevels ( numberOfLevels );* * try* * {* * std::cout<<"Evaluating registration parameters..."<Update();* * std::cout << "Optimizer stop condition: ";* * std::cout<< registration->GetOptimizer()->GetStopConditionDescription();* * std::cout << std::endl;* * }* * catch( itk::ExceptionObject & err )* * {* * std::cerr << "ExceptionObject caught !" << std::endl;* * std::cerr << err << std::endl;* * system("pause");* * return EXIT_FAILURE;* * }* * TransformType::ParametersType finalParameters = registration->GetTransform()->GetParameters();* * const double TranslationAlongX = finalParameters[0];* * const double TranslationAlongY = finalParameters[1];* * const unsigned int numberOfIterations = optimizer->GetCurrentIteration();* * const double bestValue = optimizer->GetValue();* * std::cout << "Result = " << std::endl;* * std::cout << " Translation X = " << TranslationAlongX << std::endl;* * std::cout << " Translation Y = " << TranslationAlongY << std::endl;* * std::cout << " Iterations = " << numberOfIterations << std::endl;* * std::cout << " Metric value = " << bestValue << std::endl;* * typedef itk::ResampleImageFilter< MovingImageType, FixedImageType > ResampleFilterType;* * ResampleFilterType::Pointer resampler = ResampleFilterType::New();* * resampler->SetInput( movingImageReader->GetOutput() );* * resampler->SetTransform( registration->GetTransform() );* * FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();* * resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );* * resampler->SetOutputOrigin( fixedImage->GetOrigin() );* * resampler->SetOutputSpacing( fixedImage->GetSpacing() );* * resampler->SetOutputDirection( fixedImage->GetDirection() );* * resampler->SetDefaultPixelValue( 0 );* * ////////////////////////////////////////////////////////////////////////////////////////////* * std::cout<<"Transform after registration: "<Clone();* * std::cout << "Transform copy: " << transformCopy << std::endl;* * metric2->SetFixedImage( fixedImageReader->GetOutput() );* * metric2->SetMovingImage(movingImageReader->GetOutput() );* * metric2->SetFixedInterpolator( fixedInterpolator );* * metric2->SetMovingInterpolator( movingInterpolator );* * metric2->SetTransform(transformCopy);* * try* * {* * metric2->Initialize();* * }* * catch( itk::ExceptionObject & err )* * {* * std::cerr << "ExceptionObject caught !" << std::endl;* * std::cerr << err << std::endl;* * }* * cout<GetValue()< wrote: > Hello Matt, > > Thanks a lot for your help. > > I am still unable to get same metric even after using this. > > I am using Centered2DTransform and during registration I have not > initialized it so it will take (0,0) as center of rotation. Then I defined > FixedParameters again with (0,0) but metric value is still quite different. > > Best Regards, > Suneeza > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From suneezahanif02 at gmail.com Thu Jan 7 09:42:44 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Thu, 7 Jan 2016 15:42:44 +0100 Subject: [ITK-users] Metric Evaluation In-Reply-To: <9C83A080-3673-4ADF-9EE8-76292FCC84E8@dominionsw.com> References: <9C83A080-3673-4ADF-9EE8-76292FCC84E8@dominionsw.com> Message-ID: Hello Richard, I am using "HelloWorld" registration example with RegularStepGradienDescent optimizer and MeanSquareImageToImage metric. At the end of registration algorithm I want to compute metric value again using transform calculated by the algorithm but I get different value as compared to the metric value evaluated in last iteration. Best Regards, Suneeza On Sat, Jan 2, 2016 at 6:48 PM, Richard Frank wrote: > What optimizer/ algorithm are you using? Some use random selections of > data as a speed optimization which on average give good results for better > performance. But possibly slightly different results. If the differences > are great then you might have to look at how you pick the first > "guess"...how the images are pre-positioned prior to registration. > > Rick Frank > > Sent from my iPad > > > On Jan 2, 2016, at 12:00 PM, "insight-users-request at itk.org" < > insight-users-request at itk.org> wrote: > > > > Send Insight-users mailing list submissions to > > insight-users at itk.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/mailman/listinfo/insight-users > > or, via email, send a message with subject or body 'help' to > > insight-users-request at itk.org > > > > You can reach the person managing the list at > > insight-users-owner at itk.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Insight-users digest..." > > > > > > Today's Topics: > > > > 1. Metric Evaluation (suneeza hanif) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 1 Jan 2016 23:17:36 +0100 > > From: suneeza hanif > > To: insight-users at itk.org > > Subject: [ITK-users] Metric Evaluation > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > Hello Everyone, > > > > I need help regarding metric calculation. When I run registration > algorithm > > and use final results(e.g. rotation angle and translation) to calculate > > metric once again at the end of process I get different value as compared > > to the value of metric evaluated in last iteration. I am using same > metric > > for registration and later. > > > > I also did this after one iteration but i still i get different values. > > > > Does anyone know how to solve this problem? > > > > Thanks in advance. > > > > Best Regards, > > Suneeza > > -------------- next part -------------- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at rogue-research.com Thu Jan 7 12:42:37 2016 From: sean at rogue-research.com (Sean McBride) Date: Thu, 7 Jan 2016 12:42:37 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: <20160104211744.1213332491@mail.rogue-research.com> <20160105212222.570045939@mail.rogue-research.com> Message-ID: <20160107174237.459545705@mail.rogue-research.com> On Tue, 5 Jan 2016 22:01:50 -0500, Matt McCormick said: >> It seems that OS X's sed, dirname, and basename do not accept '-- >version', and so I hit the 'die' at line 67. If I change it to 'echo' >and let it proceed, I get: >> >> Command "sed" not found >> Command "dirname" not found >> Command "basename" not found >> sed: 1: "/GDCM 20[0-9][0-9]-[0-9 ...": extra characters at the end of >p command >> Modules/ThirdParty/GDCM/../../../Utilities/Maintenance/ >UpdateThirdPartyFromUpstream.sh: line 125: upstream-$ >{thirdparty_module_name,,}: bad substitution >> >> I guess it's one of those subtle GNU vs BSD differences tripping >things up... I didn't debug further though, I think the author of this >script could find the issue faster than me. :) > >Thanks for giving it a whirl. It is worth another try after this patch >is merged: > > http://review.source.kitware.com/#/c/20400/ Matt, Sorry I wasn't more clear... the '--version' thing is trivial and I bypassed it already (though that patch is great!), the problem is the last line of output: sed: 1: "/GDCM 20[0-9][0-9]-[0-9 ...": extra characters at the end of p command Modules/ThirdParty/GDCM/../../../Utilities/Maintenance/UpdateThirdPartyFromUpstream.sh: line 125: upstream-${thirdparty_module_name,,}: bad substitution This is the real problem. It's what I was referring to wrt 'subtle GNU vs BSD differences'. Commands like 'sed' don't behave exactly the same on GNU vs BSD. Or that's my guess anyway... for all I know, the script doesn't work on linux either... Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From matt.mccormick at kitware.com Thu Jan 7 17:24:48 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 7 Jan 2016 17:24:48 -0500 Subject: [ITK-users] Fwd: Metric Evaluation In-Reply-To: References: Message-ID: Hi Suneeza, As show here: http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MeanSquaresImageMetric1_8cxx-example.html Does calling metric->SetVirtualDomainFromImage( fixedImageReader->GetOutput() ); improve the result? HTH, Matt On Thu, Jan 7, 2016 at 4:52 AM, suneeza hanif wrote: > Hello Matt, > > Here is the full version of code. Can you please guide me where am I doing > something wrong because I am unable to get it. Even If I stop after one > iteration the values are very different. > > I would be highly thankful to you. > > const unsigned int Dimension = 2; > typedef float PixelType; > > typedef itk::Image< PixelType, Dimension > FixedImageType; > typedef itk::Image< PixelType, Dimension > MovingImageType; > > typedef itk::TranslationTransform< double, Dimension > TransformType; > > typedef itk::RegularStepGradientDescentOptimizerv4 OptimizerType; > > typedef itk::MeanSquaresImageToImageMetricv4< FixedImageType,MovingImageType >> MetricType; > > typedef itk::ImageRegistrationMethodv4< FixedImageType, MovingImageType, > TransformType > RegistrationType; > > MetricType::Pointer metric = MetricType::New(); > OptimizerType::Pointer optimizer = OptimizerType::New(); > RegistrationType::Pointer registration = RegistrationType::New(); > > registration->SetMetric( metric ); > registration->SetOptimizer( optimizer ); > > typedef itk::LinearInterpolateImageFunction< FixedImageType, double > > FixedLinearInterpolatorType; > > typedef itk::LinearInterpolateImageFunction< MovingImageType, double > > MovingLinearInterpolatorType; > > FixedLinearInterpolatorType::Pointer fixedInterpolator = > FixedLinearInterpolatorType::New(); > MovingLinearInterpolatorType::Pointer movingInterpolator = > MovingLinearInterpolatorType::New(); > > metric->SetFixedInterpolator( fixedInterpolator ); > metric->SetMovingInterpolator( movingInterpolator ); > > typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType; > typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType; > > FixedImageReaderType::Pointer fixedImageReader = > FixedImageReaderType::New(); > MovingImageReaderType::Pointer movingImageReader = > MovingImageReaderType::New(); > > fixedImageReader->SetFileName( input1 ); > movingImageReader->SetFileName( input2 ); > > registration->SetFixedImage( fixedImageReader->GetOutput() ); > registration->SetMovingImage( movingImageReader->GetOutput() ); > typedef float OutputPixelType; > > typedef itk::Image< PixelType, Dimension > OutputImageType; > TransformType::Pointer transform = TransformType::New(); > > transform->SetIdentity(); > registration->SetInitialTransform( transform ); > > optimizer->SetLearningRate( 4 ); > optimizer->SetMinimumStepLength( 0.001 ); > optimizer->SetRelaxationFactor( 0.5 ); > > std::cout<<"Transform before registration: "< RegistrationType::MetricSamplingStrategyType samplingStrategy = > RegistrationType::RANDOM; > double samplingPercentage = 0.20; > registration->SetMetricSamplingStrategy( samplingStrategy ); > registration->SetMetricSamplingPercentage( samplingPercentage ); > > optimizer->SetNumberOfIterations( 1 ); > > CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New(); > optimizer->AddObserver( itk::IterationEvent(), observer ); > > const unsigned int numberOfLevels = 1; > registration->SetNumberOfLevels ( numberOfLevels ); > try > { > std::cout<<"Evaluating registration parameters..."< registration->Update(); > std::cout << "Optimizer stop condition: "; > std::cout<< registration->GetOptimizer()->GetStopConditionDescription(); > std::cout << std::endl; > } > catch( itk::ExceptionObject & err ) > { > std::cerr << "ExceptionObject caught !" << std::endl; > std::cerr << err << std::endl; > system("pause"); > return EXIT_FAILURE; > } > > TransformType::ParametersType finalParameters = > registration->GetTransform()->GetParameters(); > const double TranslationAlongX = finalParameters[0]; > const double TranslationAlongY = finalParameters[1]; > > const unsigned int numberOfIterations = optimizer->GetCurrentIteration(); > > const double bestValue = optimizer->GetValue(); > > std::cout << "Result = " << std::endl; > std::cout << " Translation X = " << TranslationAlongX << std::endl; > std::cout << " Translation Y = " << TranslationAlongY << std::endl; > std::cout << " Iterations = " << numberOfIterations << std::endl; > std::cout << " Metric value = " << bestValue << std::endl; > > > > typedef itk::ResampleImageFilter< MovingImageType, FixedImageType > > ResampleFilterType; > > ResampleFilterType::Pointer resampler = ResampleFilterType::New(); > resampler->SetInput( movingImageReader->GetOutput() ); > resampler->SetTransform( registration->GetTransform() ); > FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput(); > > resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() ); > resampler->SetOutputOrigin( fixedImage->GetOrigin() ); > resampler->SetOutputSpacing( fixedImage->GetSpacing() ); > resampler->SetOutputDirection( fixedImage->GetDirection() ); > resampler->SetDefaultPixelValue( 0 ); > > > //////////////////////////////////////////////////////////////////////////////////////////// > > std::cout<<"Transform after registration: "< > MetricType::Pointer metric2 = MetricType::New(); > > TransformType::Pointer transformCopy = transform->Clone(); > std::cout << "Transform copy: " << transformCopy << std::endl; > > metric2->SetFixedImage( fixedImageReader->GetOutput() ); > metric2->SetMovingImage(movingImageReader->GetOutput() ); > metric2->SetFixedInterpolator( fixedInterpolator ); > metric2->SetMovingInterpolator( movingInterpolator ); > metric2->SetTransform(transformCopy); > > try > { > metric2->Initialize(); > } > catch( itk::ExceptionObject & err ) > { > std::cerr << "ExceptionObject caught !" << std::endl; > std::cerr << err << std::endl; > } > > cout< "<GetValue()< > //////////////////////////////////////////////////////////////////////////////////////////// > > Best Regards, > Suneeza > > On Wed, Jan 6, 2016 at 11:53 PM, suneeza hanif > wrote: >> >> Hello Matt, >> >> Thanks a lot for your help. >> >> I am still unable to get same metric even after using this. >> >> I am using Centered2DTransform and during registration I have not >> initialized it so it will take (0,0) as center of rotation. Then I defined >> FixedParameters again with (0,0) but metric value is still quite different. >> >> Best Regards, >> Suneeza >> > From matt.mccormick at kitware.com Thu Jan 7 17:27:06 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 7 Jan 2016 17:27:06 -0500 Subject: [ITK-users] GNU Plot In-Reply-To: References: Message-ID: Thanks for the note. Please review this patch, which updates the references to point to the ITKSoftwareGuide Git repository: http://review.source.kitware.com/#/c/20634 Thanks, Matt On Wed, Jan 6, 2016 at 10:25 AM, suneeza hanif wrote: > Hello Matt, > > This is written under section 3.5 Multi-Modality Registration (Pg: 483) in > ItkSoftwareGuide V4.8. > > > Best Regards, > Suneeza > > On Wed, Jan 6, 2016 at 4:19 AM, Matt McCormick > wrote: >> >> Hello Suneeza, >> >> > I want to plot my optimizer parameters after registration. >> > >> > In ItkSoftwareGuide it is stated that the scripts used for plotting are >> > available in the ITKSoftwareGuide git repository under the directory >> > "SoftwareGuide/Art." I am unable to find such directory. >> >> What version of the Software Guide is this? Where specifically is the >> reference? We should correct it if it still in the current version. >> >> Thanks, >> Matt > > From yxt227 at med.miami.edu Thu Jan 7 17:57:38 2016 From: yxt227 at med.miami.edu (Yohann Tschudi) Date: Thu, 7 Jan 2016 15:57:38 -0700 (MST) Subject: [ITK-users] Texture analysis - two basics questions Message-ID: <1452207458825-7588334.post@n2.nabble.com> Hello, It is the first time I am posting here and I hope I am doing it following the rules. I am working on the texture analysis exposed as an example here : http://www.itk.org/Doxygen/html/WikiExamples_2Statistics_2TextureFeatures_8cxx-example.html#_a3 and I have two questions in mind. This method take as input : - a 3D (or 2D, not tested yet) image. For that I used : http://itk.org/Wiki/ITK/Examples/IO/VolumeFromSlices to convert a set of DICOM images to a .mha file containing the volume. - Is it possible to give it directly a data matrix (ADC mean values from MR for each pixel in the ROI for example) ? I was thinking for example to change : /typedef itk::Image< PixelType, Dimension > ImageType;/ to /typedef itk::Image< float, Dimension > ImageType;/ but I do not really know how to fill the image (now a float matrix right ?) used in : /void calcTextureFeatureImage(OffsetType offset, InternalImageType::Pointer inputImage, InternalImageType::Pointer outInertia, InternalImageType::Pointer outCorrelation, InternalImageType::Pointer outEnergy) / - The second question is about the Neighborhood and offset : /NeighborhoodType neighborhood; neighborhood.SetRadius(1); unsigned int centerIndex = neighborhood.GetCenterNeighborhoodIndex(); offset = neighborhood.GetOffset(d);/ (in the loop) I do not understand at all what is this loop is doing and what is more generally the Neigborhood concept in this case. Here for example : http://stackoverflow.com/questions/29570064/itk-calculate-texture-features-for-segmented-3d-brain-mri/29582085#29582085 This is not used. Thank you for your help, Yohann -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Texture-analysis-two-basics-questions-tp7588334.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From tevain at telecom-paristech.fr Fri Jan 8 03:40:22 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Fri, 8 Jan 2016 09:40:22 +0100 (CET) Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: <1452207458825-7588334.post@n2.nabble.com> References: <1452207458825-7588334.post@n2.nabble.com> Message-ID: <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> Hello Yohann, Welcome to the ITK community! 1) I'm not sure I've fully understood your question,so feel free to correct me. PixelType is any of the type you want, so you could use float without problem in itkImage. I guess your question about the data matrix is related to the fact you already have your data in another form. You can initialize an itkImage from a memory buffer with itkImportImageFilter, read the GettingStarted-V for example ( http://www.itk.org/CourseWare/Training/GettingStarted-V.pdf ) But since you said you have a .mha file, it would be far easier to read it with itkImageFileReader 2)This is related to the method. To construct a co-occurrence matrix, you have to provide an offset which is the "step" for looking at intensities pairs. One is enough, but the example you provided computes the features images for all possible offsets. To do that, a Neighborhood is used to easily get the offsets ( offset = neighborhood.GetOffset(d); ). Each loop is computing and writing the feature images for one offset. HTH Tim ----- Mail original ----- De: "Yohann Tschudi" ?: insight-users at itk.org Envoy?: Jeudi 7 Janvier 2016 23:57:38 Objet: [ITK] [ITK-users] Texture analysis - two basics questions Hello, It is the first time I am posting here and I hope I am doing it following the rules. I am working on the texture analysis exposed as an example here : http://www.itk.org/Doxygen/html/WikiExamples_2Statistics_2TextureFeatures_8cxx-example.html#_a3 and I have two questions in mind. This method take as input : - a 3D (or 2D, not tested yet) image. For that I used : http://itk.org/Wiki/ITK/Examples/IO/VolumeFromSlices to convert a set of DICOM images to a .mha file containing the volume. - Is it possible to give it directly a data matrix (ADC mean values from MR for each pixel in the ROI for example) ? I was thinking for example to change : /typedef itk::Image< PixelType, Dimension > ImageType;/ to /typedef itk::Image< float, Dimension > ImageType;/ but I do not really know how to fill the image (now a float matrix right ?) used in : /void calcTextureFeatureImage(OffsetType offset, InternalImageType::Pointer inputImage, InternalImageType::Pointer outInertia, InternalImageType::Pointer outCorrelation, InternalImageType::Pointer outEnergy) / - The second question is about the Neighborhood and offset : /NeighborhoodType neighborhood; neighborhood.SetRadius(1); unsigned int centerIndex = neighborhood.GetCenterNeighborhoodIndex(); offset = neighborhood.GetOffset(d);/ (in the loop) I do not understand at all what is this loop is doing and what is more generally the Neigborhood concept in this case. Here for example : http://stackoverflow.com/questions/29570064/itk-calculate-texture-features-for-segmented-3d-brain-mri/29582085#29582085 This is not used. Thank you for your help, Yohann -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Texture-analysis-two-basics-questions-tp7588334.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 _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From dzenanz at gmail.com Fri Jan 8 08:12:19 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 8 Jan 2016 08:12:19 -0500 Subject: [ITK-users] itk::MRIBiasFieldCorrectionFilter In-Reply-To: References: Message-ID: Hi Muhammad, it looks to be a case of the simplest 1 input 1 output filter. Pseudocode: read3Dimage(); MRIbfcFilter->SetInput(image3D); MRIbfcFilter->Update(); corrected3Dimage=MRIbfcFilter->GetOutput(); HTH, D?enan (????) On Wed, Jan 6, 2016 at 8:25 AM, Jawad, Muhammad < m.jawad at jacobs-university.de> wrote: > > Dear Itk User, > > I am looking for some example about the usage pipeline of > itk::MRIBiasFieldCorrectionFilter for dicom images. > > If some body know or has already worked on it, kinldy share it by the toy > example. > > > > > -- > Muhammad Jawad > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From yxt227 at med.miami.edu Fri Jan 8 09:46:10 2016 From: yxt227 at med.miami.edu (Yohann Tschudi) Date: Fri, 8 Jan 2016 07:46:10 -0700 (MST) Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> Message-ID: <1452264370571-7588337.post@n2.nabble.com> Hello Timothee, Thank you for your answer. 1.) My data is a surface in a 3D float matrix format so I need to find a way either to transform this matrix to a .mha format or to fill the input image which is /typedef itk::Image InternalImageType;/ format (manually by loops ?). I look at the buffer method, it seems really very "heavy", seeing the quality of the code, I am sure a quick method should exist. 2.) Perfectly understood. Very clear. Thank you. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588337.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From m.jawad at jacobs-university.de Fri Jan 8 10:12:22 2016 From: m.jawad at jacobs-university.de (Jawad, Muhammad) Date: Fri, 8 Jan 2016 15:12:22 +0000 Subject: [ITK-users] itk::MRIBiasFieldCorrectionFilter In-Reply-To: References: , Message-ID: Dear D?enan I tried in this way but it is not working. As itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage > take three arguments, How we define the mask image ? -- Muhammad Jawad PhD Student Computer Science School of Engineering and Science Telephone: +49 421 200-3182 Fax: +49 421 200-3103 Office: Research I, Room 119 Mailing Address: Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany ________________________________________ From: D?enan Zuki? [dzenanz at gmail.com] Sent: Friday, January 08, 2016 2:12 PM To: Jawad, Muhammad Cc: insight-users at itk.org Subject: Re: [ITK-users] itk::MRIBiasFieldCorrectionFilter Hi Muhammad, it looks to be a case of the simplest 1 input 1 output filter. Pseudocode: read3Dimage(); MRIbfcFilter->SetInput(image3D); MRIbfcFilter->Update(); corrected3Dimage=MRIbfcFilter->GetOutput(); HTH, D?enan (????) On Wed, Jan 6, 2016 at 8:25 AM, Jawad, Muhammad > wrote: Dear Itk User, I am looking for some example about the usage pipeline of itk::MRIBiasFieldCorrectionFilter for dicom images. If some body know or has already worked on it, kinldy share it by the toy example. -- Muhammad Jawad _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 m.jawad at jacobs-university.de Fri Jan 8 10:17:18 2016 From: m.jawad at jacobs-university.de (Jawad, Muhammad) Date: Fri, 8 Jan 2016 15:17:18 +0000 Subject: [ITK-users] itk::MRIBiasFieldCorrectionFilter In-Reply-To: References: , , Message-ID: it give error, itk::ExceptionObject (0044B814) Location: "unknown" File: c:\program files (x86)\itk\include\itk-4.7\itkMRIBiasFieldCorrectionFilter.hxx Line: 595 Description: itk::ERROR: MRIBiasFieldCorrectionFilter(0952CD98): Tissue Class Means is empty Any one know the complete pipeline for this algorithm ? -- Muhammad Jawad PhD Student Computer Science School of Engineering and Science Telephone: +49 421 200-3182 Fax: +49 421 200-3103 Office: Research I, Room 119 Mailing Address: Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany ________________________________________ From: Jawad, Muhammad Sent: Friday, January 08, 2016 4:12 PM To: D?enan Zuki? Cc: insight-users at itk.org Subject: RE: [ITK-users] itk::MRIBiasFieldCorrectionFilter Dear D?enan I tried in this way but it is not working. As itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage > take three arguments, How we define the mask image ? -- Muhammad Jawad PhD Student Computer Science School of Engineering and Science Telephone: +49 421 200-3182 Fax: +49 421 200-3103 Office: Research I, Room 119 Mailing Address: Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany ________________________________________ From: D?enan Zuki? [dzenanz at gmail.com] Sent: Friday, January 08, 2016 2:12 PM To: Jawad, Muhammad Cc: insight-users at itk.org Subject: Re: [ITK-users] itk::MRIBiasFieldCorrectionFilter Hi Muhammad, it looks to be a case of the simplest 1 input 1 output filter. Pseudocode: read3Dimage(); MRIbfcFilter->SetInput(image3D); MRIbfcFilter->Update(); corrected3Dimage=MRIbfcFilter->GetOutput(); HTH, D?enan (????) On Wed, Jan 6, 2016 at 8:25 AM, Jawad, Muhammad > wrote: Dear Itk User, I am looking for some example about the usage pipeline of itk::MRIBiasFieldCorrectionFilter for dicom images. If some body know or has already worked on it, kinldy share it by the toy example. -- Muhammad Jawad _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 dzenanz at gmail.com Fri Jan 8 10:24:16 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 8 Jan 2016 10:24:16 -0500 Subject: [ITK-users] itk::MRIBiasFieldCorrectionFilter In-Reply-To: References: Message-ID: Hi Muhammad, after a quick glance at the source code, the class expects SetTissueClassStatistics() to be called, with arrays of mean values and standard deviations of tissues of interest. You should probably read the referenced paper to figure out how to do that. Regards On Fri, Jan 8, 2016 at 10:17 AM, Jawad, Muhammad < m.jawad at jacobs-university.de> wrote: > it give error, > > itk::ExceptionObject (0044B814) > Location: "unknown" > File: c:\program files > (x86)\itk\include\itk-4.7\itkMRIBiasFieldCorrectionFilter.hxx > Line: 595 > Description: itk::ERROR: MRIBiasFieldCorrectionFilter(0952CD98): Tissue > Class Means is empty > > Any one know the complete pipeline for this algorithm ? > > -- > Muhammad Jawad > PhD Student Computer Science > School of Engineering and Science > > Telephone: +49 421 200-3182 > Fax: +49 421 200-3103 > Office: Research I, Room 119 > > Mailing Address: > Jacobs University Bremen gGmbH > Campus Ring 1 > 28759 Bremen > Germany > ________________________________________ > From: Jawad, Muhammad > Sent: Friday, January 08, 2016 4:12 PM > To: D?enan Zuki? > Cc: insight-users at itk.org > Subject: RE: [ITK-users] itk::MRIBiasFieldCorrectionFilter > > Dear D?enan > > I tried in this way but it is not working. > > As itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, > TMaskImage > take three arguments, > > How we define the mask image ? > > -- > Muhammad Jawad > PhD Student Computer Science > School of Engineering and Science > > Telephone: +49 421 200-3182 > Fax: +49 421 200-3103 > Office: Research I, Room 119 > > Mailing Address: > Jacobs University Bremen gGmbH > Campus Ring 1 > 28759 Bremen > Germany > ________________________________________ > From: D?enan Zuki? [dzenanz at gmail.com] > Sent: Friday, January 08, 2016 2:12 PM > To: Jawad, Muhammad > Cc: insight-users at itk.org > Subject: Re: [ITK-users] itk::MRIBiasFieldCorrectionFilter > > Hi Muhammad, > > it looks to be a case of the simplest 1 input 1 output filter. Pseudocode: > > read3Dimage(); > MRIbfcFilter->SetInput(image3D); > MRIbfcFilter->Update(); > corrected3Dimage=MRIbfcFilter->GetOutput(); > > HTH, > D?enan (????) > > On Wed, Jan 6, 2016 at 8:25 AM, Jawad, Muhammad < > m.jawad at jacobs-university.de> wrote: > > Dear Itk User, > > I am looking for some example about the usage pipeline of > itk::MRIBiasFieldCorrectionFilter for dicom images. > > If some body know or has already worked on it, kinldy share it by the toy > example. > > > > > -- > Muhammad Jawad > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From dzenanz at gmail.com Fri Jan 8 10:28:02 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 8 Jan 2016 10:28:02 -0500 Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: <1452264370571-7588337.post@n2.nabble.com> References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> Message-ID: Hi Yohann, you can create an image from scratch and fill it with your values using loops. A lot of examples for creating an image which you can modify can be found on ExamplesWiki , e.g.: http://itk.org/Wiki/ITK/Examples/ImageProcessing/InvertIntensityImageFilter Regards, D?enan On Fri, Jan 8, 2016 at 9:46 AM, Yohann Tschudi wrote: > Hello Timothee, > > Thank you for your answer. > > 1.) My data is a surface in a 3D float matrix format so I need to find a > way > either to transform this matrix to a .mha format or to fill the input image > which is /typedef itk::Image InternalImageType;/ format (manually > by loops ?). I look at the buffer method, it seems really very "heavy", > seeing the quality of the code, I am sure a quick method should exist. > > 2.) Perfectly understood. Very clear. Thank you. > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588337.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabrielgimenez85 at gmail.com Fri Jan 8 21:17:26 2016 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Fri, 8 Jan 2016 23:17:26 -0300 Subject: [ITK-users] Write a result image witout resampling Message-ID: Hi everyone...how are you ? I'm going to point, to finish the registration process build the new transformed fixed image (based on the manual examples), but the quality of the generated image is degraded...how I can create a new image with the same quality as the original image? I just need to apply the transformation parameters. Regards and thanks in advance, -- *Gabriel Alberto Gim?nez.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Sun Jan 10 14:22:58 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sun, 10 Jan 2016 14:22:58 -0500 Subject: [ITK-users] Write a result image witout resampling In-Reply-To: References: Message-ID: Hi Gabriel, you probably need to use interpolation method of a higher quality for the final resampling, i.e. windowed sinc instead of linear . Regards, D?enan On Fri, Jan 8, 2016 at 9:17 PM, Gabriel A. Gim?nez < gabrielgimenez85 at gmail.com> wrote: > Hi everyone...how are you ? > > I'm going to point, to finish the registration process build the new > transformed fixed image (based on the manual examples), but the quality of > the generated image is degraded...how I can create a new image with the > same quality as the original image? I just need to apply the transformation > parameters. > > Regards and thanks in advance, > > -- > *Gabriel Alberto Gim?nez.* > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From itkhelpacc at gmail.com Mon Jan 11 00:15:34 2016 From: itkhelpacc at gmail.com (vishal) Date: Sun, 10 Jan 2016 22:15:34 -0700 (MST) Subject: [ITK-users] Problem with Callback function Message-ID: <1452489334957-36638.post@n7.nabble.com> hi, Im trying to printout the rotation values(rotation abt x,y,z) of a volume using callback function... im follwing the example [1]http://www.vtk.org/Wiki/VTK/Examples/Cxx/Interaction/ClientData .... the flow of mycode goes something like this.. read 3D volume in ITK--> Visualize in VTK(using itkImageToVTKImageFilter.h)--> interact with volume -> upon press any key through callbackFunction called and using volume->GetOrientation() method in the callback function....I can get the angles values-> print to console... upon building the example code the radius was printed out ... but then i did some changes so that it matches my requirements the angles are not printed out... no errors were found during building the code is found below-> #include #include #include #include #include #include #include #include #include #include //////////////////////////// #include #include "itkImageToVTKImageFilter.h" #include #include #include #include #include #include #include #include #include #include #include "vtkSmartVolumeMapper.h" #include #include #include #include #include #include #include /////////////////////////// static void KeypressCallbackFunction ( vtkObject* caller, long unsigned int eventId, void* clientData, void* callData ); double printOrient[3]; double org[3]; int main(int argc, char *argv[]) { argv[1] ="OS_Volume.dcm"; // 3D volume that i want to display typedef itk::Image VisualizingImageType; typedef itk::ImageFileReader< VisualizingImageType > ReaderType; ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName( argv[1] ); reader->Update(); VisualizingImageType::Pointer image=reader->GetOutput(); vtkSmartPointer renWin = vtkSmartPointer::New(); vtkSmartPointer ren1 = vtkSmartPointer::New(); ren1->SetBackground(0.5f,0.5f,1.0f); renWin->AddRenderer(ren1); renWin->SetSize(1280,1024); vtkSmartPointer iren = vtkSmartPointer::New(); iren->SetRenderWindow(renWin); renWin->Render(); // make sure we have an OpenGL context. typedef itk::ImageToVTKImageFilter itkVtkConverter; itkVtkConverter::Pointer conv=itkVtkConverter::New(); conv->SetInput(image); conv->Update(); vtkSmartPointer image2=vtkSmartPointer::New(); image2->ShallowCopy(conv->GetOutput()); //shallow copy is vtk's equivalent of disconnect pipeline vtkSmartPointer volumeMapper = vtkSmartPointer::New(); volumeMapper->SetInputData(image2); vtkSmartPointer volumeProperty = vtkSmartPointer::New(); vtkSmartPointer compositeOpacity = vtkSmartPointer::New(); compositeOpacity->AddPoint(-3024, 0, 0.5, 0.0 ); compositeOpacity->AddPoint(-16, 0, .49, .61 ); compositeOpacity->AddPoint(641, .72, .5, 0.0 ); compositeOpacity->AddPoint(3071, .71, 0.5, 0.0); volumeProperty->SetScalarOpacity(compositeOpacity); volumeMapper->SetBlendModeToComposite(); vtkSmartPointer color = vtkSmartPointer::New(); color->AddRGBPoint( -3024, 0, 0, 0, 0.5, 0.0 ); color->AddRGBPoint( -16, 0.73, 0.25, 0.30, 0.49, .61 ); color->AddRGBPoint( 641, .90, .82, .56, .5, 0.0 ); color->AddRGBPoint( 3071, 1, 1, 1, .5, 0.0 ); volumeProperty->SetColor(color); //changes volumeProperty->SetInterpolationTypeToLinear(); volumeProperty->ShadeOn(); volumeProperty->SetAmbient(0.1); volumeProperty->SetDiffuse(0.9); volumeProperty->SetSpecular(0.2); volumeProperty->SetSpecularPower(10.0); volumeProperty->SetScalarOpacityUnitDistance(0.8919); vtkSmartPointer volume = vtkSmartPointer::New(); volume->SetMapper(volumeMapper); volume->SetProperty(volumeProperty); volume->SetScale(1.5); //Here we take care of position and orientation //so that volume is in DICOM patient physical space VisualizingImageType::DirectionType d=image->GetDirection(); vtkMatrix4x4 *mat=vtkMatrix4x4::New(); //start with identity matrix for (int i=0; i<3; i++) for (int k=0; k<3; k++) mat->SetElement(i,k, d(i,k)); //counteract the built-in translation by origin VisualizingImageType::PointType origin=image->GetOrigin(); volume->SetPosition(-origin[0], -origin[1], -origin[2]); //add translation to the user matrix for (int i=0; i<3; i++) mat->SetElement(i,3, origin[i]); volume->SetUserMatrix(mat); vtkSmartPointer keypressCallback = vtkSmartPointer::New(); // // Allow the observer to access the sphereSource keypressCallback->SetClientData(volume); keypressCallback->SetCallback(KeypressCallbackFunction ); renWin->AddObserver(vtkCommand::KeyPressEvent, keypressCallback); //Add coordinate system axes, so we have a reference for position and orientation vtkSmartPointer axes = vtkSmartPointer::New(); axes->SetTotalLength(250,250,250); //ORIGINAL axes->SetShaftTypeToCylinder(); axes->SetCylinderRadius(0.01); ren1->AddActor(axes); ren1->AddVolume( volume ); ren1->ResetCamera(); renWin->Render(); iren->Start(); return EXIT_SUCCESS; } void KeypressCallbackFunction(vtkObject *, long unsigned int vtkNotUsed(eventId), void* clientData, void* vtkNotUsed(callData) ) { // Prove that we can access the sphere source vtkVolume* volume = static_cast(clientData); volume->GetOrigin(org); volume->GetOrientation(printOrient); std::cout << "Radius is " << printOrient[1]<<" "< References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> Message-ID: <1452526554285-7588345.post@n2.nabble.com> I misunderstood the example. Thank you very much, that is perfect. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588345.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From m.jawad at jacobs-university.de Mon Jan 11 12:27:15 2016 From: m.jawad at jacobs-university.de (Jawad, Muhammad) Date: Mon, 11 Jan 2016 17:27:15 +0000 Subject: [ITK-users] itk::MRIBiasFieldCorrectionFilter In-Reply-To: References: Message-ID: Dear Itk User's, How to use the itk::MRIBiasFieldCorrectionFilter ? There is no example available. -- Muhammad Jawad ________________________________________ From: Jawad, Muhammad Sent: Wednesday, January 06, 2016 2:25 PM To: insight-users at itk.org Subject: itk::MRIBiasFieldCorrectionFilter Dear Itk User, I am looking for some example about the usage pipeline of itk::MRIBiasFieldCorrectionFilter for dicom images. If some body know or has already worked on it, kinldy share it by the toy example. -- Muhammad Jawad From noreply at insightsoftwareconsortium.org Tue Jan 12 11:29:52 2016 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Tue, 12 Jan 2016 11:29:52 -0500 (EST) Subject: [ITK-users] New Submission: Integration of the Java Image Science Toolkit with E-Science Platform Message-ID: <20160112162952.A1E9D3D6207C@insight-journal.org> Hello, A new submission has been added to the Insight Journal. Title: Integration of the Java Image Science Toolkit with E-Science Platform Authors: Damon S., Panjwani S., Bao S., Kochunov P., Landman B. Abstract: Medical image analyses rely on diverse software packages assembled into a ???pipeline???. The Java Image Science Toolkit (JIST) has served as a standalone plugin into the Medical Image Processing Analysis and Visualization (MIPAV). We addressed shortcomings that previously prevented deeper integration of JIST with other E-science platforms. First, we developed an interface for integrating externally compiled packages (similar to the interfaces in NiPy) such that the application can become a ???draggable module??? in the module tree. This allows for connection of inputs and outputs to other JIST modules while maintaining external processing and monitoring. Second, we develop an integration interface with the Neuroimaging Informatics Tools and Resources Clearinghouse Cloud Environment (NITRC-CE). User can launch and terminate pre-configured nodes to utilize computational resources of the Amazon cloud. Finally, we define a new external data source, which can connect to the eX tensible Neuroimaging Archive Toolkit (XNAT) to query and retrieve remote data using XNAT's REST API. Specifically, we define dataflow for files that can readily be converted into volumes and collections of volumes to interface with any JIST module that expects volumetric image data as an input. Users now have the ability to run their pipelines from a well-defined external data source and no longer are required to already have data on the disk. With these upgrades we have extended JIST???s capabilities outside of complied java source code and enhanced capabilities to seamlessly interface with E-science platforms. Download and review this publication at: http://hdl.handle.net/10380/3535 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/ . From yxt227 at med.miami.edu Tue Jan 12 18:18:12 2016 From: yxt227 at med.miami.edu (Yohann Tschudi) Date: Tue, 12 Jan 2016 16:18:12 -0700 (MST) Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: <1452526554285-7588345.post@n2.nabble.com> References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> <1452526554285-7588345.post@n2.nabble.com> Message-ID: <1452640692677-7588348.post@n2.nabble.com> Ok, I finally implemented everything and I got a "result". It means I got an 3D image (.mha) for each features with some numbers different from nan (I do not understand yet how that is possible). Here is an example of outputs for this study: _Energy0.mha _Correlation0.mha However for another study, I got 0 or nan or out of frame (I am using 3Dslicer to vizualise .mha, it gives me directly the value for each pixel pointed by the mouse). Example2_Energy0.mha Example2_Correlation0.mha I am a bit confused but I think this is coming from the construction of the input/3d data matrix. Let me explain what I am trying to do: I have an input file containing all the information of the data (a cube containing a prostate volume with T2 values (0 outside the prostate)): -> the first line contains the size of the matrix width, height and depth -> for each line, the value for each pixel Example: Example_DataMatrix.csv 74 60 17 0 0 0 0.0 0 0 1 0.0 0 0 2 0.0 ... 11 42 3 0.0 11 42 4 290.0 11 42 5 265.0 11 42 6 269.0 ... 73 59 14 0.0 73 59 15 0.0 73 59 16 0.0 This data matrix is then transformed in itk::Image InternalImageType image (I think there is a problem here maybe): /int Create3DImageFromMatrix(InternalImageType::Pointer &_image, string _dataMatrixFile) { //Create image InternalImageType::Pointer image = InternalImageType::New(); // Get file std::cout << "Get data matrix file " << _dataMatrixFile << endl; ifstream dataFile(_dataMatrixFile); //Read file string line; int xSize = 0; int ySize = 0; int zSize = 0; int iLine = 0; while (getline(dataFile, line)) { istringstream iss(line); if (iLine == 0) { //First line size of matrix iss >> xSize >> ySize >> zSize; std::cout << "Data matrix size verification: " << xSize << "x" << ySize << "x" << zSize << endl; //Initialize image InternalImageType::RegionType region; InternalImageType::IndexType start; start[0] = 0; start[1] = 0; start[2] = 0; InternalImageType::SizeType size; size[0] = xSize; size[1] = ySize; size[2] = zSize; region.SetSize(size); region.SetIndex(start); image->SetRegions(region); image->Allocate(); ++iLine; } else { //Fill image int x, y, z; double value; if (!(iss >> x >> y >> z >> value)) { return -1; } else { InternalImageType::IndexType pixelIndex; pixelIndex[0] = x; pixelIndex[1] = y; pixelIndex[2] = z; image->SetPixel(pixelIndex, value); ++iLine; } } } _image = image; std::cout << "Image created from data matrix file" << endl; return 0; }/ Finally, the code to compute the features is the same (in 3D) than in the example : http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures / int index0 = inputImage->GetLargestPossibleRegion().GetSize(0); int index1 = inputImage->GetLargestPossibleRegion().GetSize(1); int index2 = inputImage->GetLargestPossibleRegion().GetSize(2); //slide window over the entire image for (unsigned x = 1; x < index0 - 1; x++) { pi.SetElement(0, x); window.SetIndex(0, x - 1); for (unsigned y = 1; y < index1 - 1; y++) { pi.SetElement(1, y); window.SetIndex(1, y - 1); for (unsigned z = 1; z < index2 - 1; z++) { pi.SetElement(2, z); window.SetIndex(2, z - 1); roi->SetRegionOfInterest(window); roi->Update(); glcmGenerator->SetInput(roi->GetOutput()); glcmGenerator->Update(); featureCalc->SetInput(glcmGenerator->GetOutput()); featureCalc->Update(); outInertia->SetPixel(pi,featureCalc->GetFeature(Hist2FeaturesType::Inertia)); outCorrelation->SetPixel(pi, featureCalc->GetFeature(Hist2FeaturesType::Correlation)); outEnergy->SetPixel(pi, featureCalc->GetFeature(Hist2FeaturesType::Energy)); outEntropy->SetPixel(pi, featureCalc->GetFeature(Hist2FeaturesType::Entropy)); } } //Print step int total = index0 - 2; string step = to_string(x) + " on " + to_string(total); std::cout << step << endl; }/ As I wrote upper, the output values for this last example are either 0 or nan or out of frame. I am pretty sure that for the first example, getting values different from 0 are lucky (I still have nan values in it though). I am missing something and I am looking since hours without seeing what is wrong. Hope this is obvious ... Here is the c++ file I am using : TextureFeatures.cxx Thank you for your help -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588348.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From dzenanz at gmail.com Wed Jan 13 11:08:20 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 13 Jan 2016 11:08:20 -0500 Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: <1452640692677-7588348.post@n2.nabble.com> References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> <1452526554285-7588345.post@n2.nabble.com> <1452640692677-7588348.post@n2.nabble.com> Message-ID: ?Hi Yohann, line 56 in your TextureFeature.cxx: glcmGenerator->SetPixelValueMinMax(0, 255); //for input UCHAR pixel type could be the culprit.? The input files in my example were uchar, and 0-255 range was OK. For general processing, you should use minMax finder and pass those 2 values to calcTextureFeatureImage function. Your *Example_DataMatrix.csv* contained values over 255 (300+), but not a lot of them. The other image might have higher maximum values or negative minimum values, which would cause more anomalies such as NaNs. As for conversion of DICOM to MHA or NRRD, you can use Slicer for that. Just import it via DICOM module, and then save them with .mha or .nrrd extension. Then you can read them easily via itk::ImageFileReader. HTH, D?enan On Tue, Jan 12, 2016 at 6:18 PM, Yohann Tschudi wrote: > Ok, I finally implemented everything and I got a "result". > It means I got an 3D image (.mha) for each features with some numbers > different from nan (I do not understand yet how that is possible). > Here is an example of outputs for this study: > _Energy0.mha > > > _Correlation0.mha > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/_Correlation0.mha > > > > However for another study, I got 0 or nan or out of frame (I am using > 3Dslicer to vizualise .mha, it gives me directly the value for each pixel > pointed by the mouse). > Example2_Energy0.mha > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/Example2_Energy0.mha > > > Example2_Correlation0.mha > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/Example2_Correlation0.mha > > > > I am a bit confused but I think this is coming from the construction of the > input/3d data matrix. > > Let me explain what I am trying to do: > I have an input file containing all the information of the data (a cube > containing a prostate volume with T2 values (0 outside the prostate)): > -> the first line contains the size of the matrix width, height and depth > -> for each line, the value for each pixel > Example: > Example_DataMatrix.csv > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/Example_DataMatrix.csv > > > 74 60 17 > 0 0 0 0.0 > 0 0 1 0.0 > 0 0 2 0.0 > ... > 11 42 3 0.0 > 11 42 4 290.0 > 11 42 5 265.0 > 11 42 6 269.0 > ... > 73 59 14 0.0 > 73 59 15 0.0 > 73 59 16 0.0 > > This data matrix is then transformed in itk::Image > InternalImageType image (I think there is a problem here maybe): > /int Create3DImageFromMatrix(InternalImageType::Pointer &_image, string > _dataMatrixFile) > { > //Create image > InternalImageType::Pointer image = InternalImageType::New(); > > // Get file > std::cout << "Get data matrix file " << _dataMatrixFile << endl; > ifstream dataFile(_dataMatrixFile); > > //Read file > string line; > int xSize = 0; > int ySize = 0; > int zSize = 0; > int iLine = 0; > while (getline(dataFile, line)) > { > istringstream iss(line); > if (iLine == 0) > { > //First line size of matrix > iss >> xSize >> ySize >> zSize; > std::cout << "Data matrix size verification: " << > xSize << "x" << ySize > << "x" << zSize << endl; > > //Initialize image > InternalImageType::RegionType region; > InternalImageType::IndexType start; > start[0] = 0; > start[1] = 0; > start[2] = 0; > InternalImageType::SizeType size; > size[0] = xSize; > size[1] = ySize; > size[2] = zSize; > region.SetSize(size); > region.SetIndex(start); > image->SetRegions(region); > image->Allocate(); > > ++iLine; > } > else > { > //Fill image > int x, y, z; > double value; > if (!(iss >> x >> y >> z >> value)) > { > return -1; > } > else > { > InternalImageType::IndexType pixelIndex; > pixelIndex[0] = x; > pixelIndex[1] = y; > pixelIndex[2] = z; > image->SetPixel(pixelIndex, value); > ++iLine; > } > } > } > > _image = image; > std::cout << "Image created from data matrix file" << endl; > return 0; > }/ > > Finally, the code to compute the features is the same (in 3D) than in the > example : > http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > / int index0 = inputImage->GetLargestPossibleRegion().GetSize(0); > int index1 = inputImage->GetLargestPossibleRegion().GetSize(1); > int index2 = inputImage->GetLargestPossibleRegion().GetSize(2); > > //slide window over the entire image > for (unsigned x = 1; x < index0 - 1; x++) > { > pi.SetElement(0, x); > window.SetIndex(0, x - 1); > for (unsigned y = 1; y < index1 - 1; y++) > { > pi.SetElement(1, y); > window.SetIndex(1, y - 1); > for (unsigned z = 1; z < index2 - 1; z++) > { > pi.SetElement(2, z); > window.SetIndex(2, z - 1); > roi->SetRegionOfInterest(window); > roi->Update(); > glcmGenerator->SetInput(roi->GetOutput()); > glcmGenerator->Update(); > > featureCalc->SetInput(glcmGenerator->GetOutput()); > featureCalc->Update(); > > > outInertia->SetPixel(pi,featureCalc->GetFeature(Hist2FeaturesType::Inertia)); > outCorrelation->SetPixel(pi, > featureCalc->GetFeature(Hist2FeaturesType::Correlation)); > outEnergy->SetPixel(pi, > featureCalc->GetFeature(Hist2FeaturesType::Energy)); > outEntropy->SetPixel(pi, > featureCalc->GetFeature(Hist2FeaturesType::Entropy)); > } > } > > //Print step > int total = index0 - 2; > string step = to_string(x) + " on " + to_string(total); > std::cout << step << endl; > }/ > > As I wrote upper, the output values for this last example are either 0 or > nan or out of frame. > I am pretty sure that for the first example, getting values different from > 0 are lucky (I still have nan values in it though). > I am missing something and I am looking since hours without seeing what is > wrong. Hope this is obvious ... > > Here is the c++ file I am using : > TextureFeatures.cxx > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588348/TextureFeatures.cxx > > > > Thank you for your help > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588348.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yxt227 at med.miami.edu Wed Jan 13 17:01:04 2016 From: yxt227 at med.miami.edu (Yohann Tschudi) Date: Wed, 13 Jan 2016 15:01:04 -0700 (MST) Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> <1452526554285-7588345.post@n2.nabble.com> <1452640692677-7588348.post@n2.nabble.com> Message-ID: <1452722464220-7588350.post@n2.nabble.com> Thank you very much ! I let the default min and max pixel values ... Everything is corrected and is running correctly /a priori/ (not finished but first results seem ok). I am trying now on two examples : 74x60x17 pixels and 28x27x13 (short example) It takes very long for the first one (5-7hours), a lot less for the second one (around 1h30). I will test several parameters: size of the window 5x5x5 (literature), number of bins (16), fix the offset (to be determined). You can find the two input examples here : Example_DataMatrix.csv ExampleShort_DataMatrix.csv and the code : TextureFeatures.cxx Hope this will help someone. Thank you again for your really quick answers. I ll post some results if they are ok. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588350.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From dzenanz at gmail.com Wed Jan 13 17:28:12 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 13 Jan 2016 17:28:12 -0500 Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: <1452722464220-7588350.post@n2.nabble.com> References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> <1452526554285-7588345.post@n2.nabble.com> <1452640692677-7588348.post@n2.nabble.com> <1452722464220-7588350.post@n2.nabble.com> Message-ID: If some computation is taking more than a few minutes, it is best to switch to Release mode (or RelWithDebInfo) and then run it. With ITK code, Release mode is many times faster than Debug. Completely running your example 1 on my PC took 2-3 minutes in Release mode (I switched after noticing how slow it is in Debug). HTH On Wed, Jan 13, 2016 at 5:01 PM, Yohann Tschudi wrote: > Thank you very much ! > I let the default min and max pixel values ... > > Everything is corrected and is running correctly /a priori/ (not finished > but first results seem ok). > I am trying now on two examples : > 74x60x17 pixels and 28x27x13 (short example) > It takes very long for the first one (5-7hours), a lot less for the second > one (around 1h30). > I will test several parameters: size of the window 5x5x5 (literature), > number of bins (16), fix the offset (to be determined). > > You can find the two input examples here : > Example_DataMatrix.csv > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588350/Example_DataMatrix.csv > > > ExampleShort_DataMatrix.csv > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588350/ExampleShort_DataMatrix.csv > > > > and the code : > TextureFeatures.cxx > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588350/TextureFeatures.cxx > > > > Hope this will help someone. > > Thank you again for your really quick answers. > I ll post some results if they are ok. > > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588350.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yxt227 at med.miami.edu Wed Jan 13 18:16:45 2016 From: yxt227 at med.miami.edu (Yohann Tschudi) Date: Wed, 13 Jan 2016 16:16:45 -0700 (MST) Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> <1452526554285-7588345.post@n2.nabble.com> <1452640692677-7588348.post@n2.nabble.com> <1452722464220-7588350.post@n2.nabble.com> Message-ID: <1452727005415-7588352.post@n2.nabble.com> It is really much better in release but still took me 20-30 min to run the 1st one and I have a pretty good computer (Intel Xeon 3.5GHz, 16GB, 64-bit Windows 7, VC++). The project config seems ok too (ITK compiled in release, TextureFeatures too...), I am very curious on how you get these 2-3min ! Btw the results are ok, thank you again -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588352.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From rccm.kyoshimi at gmail.com Thu Jan 14 01:12:22 2016 From: rccm.kyoshimi at gmail.com (kenichiro yoshimi) Date: Thu, 14 Jan 2016 15:12:22 +0900 Subject: [ITK-users] Filters using Sparse Modeling technique Message-ID: Hello, I am aiming to study Sparse Modeling approaches to visual recoginition and image processing. I search for some filters based on Sparse Models in ITK and I can't find something like that. Could anyone tell me if there is any ITK filter or framework to apply Sparse Modelling technique? Best regards, yoshimi -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Thu Jan 14 09:17:18 2016 From: itkhelpacc at gmail.com (vis) Date: Thu, 14 Jan 2016 07:17:18 -0700 (MST) Subject: [ITK-users] Visualize Intermediate result of ITK registration in vtk In-Reply-To: References: <1451277758067-36590.post@n7.nabble.com> <1451450098542-36592.post@n7.nabble.com> Message-ID: <1452781038666-7588354.post@n2.nabble.com> hi dzenanz, thanks for the suggestion....il try it and post the results.. Regards Vishal -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Visualize-Intermediate-result-of-ITK-registration-in-vtk-tp7588295p7588354.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From dzenanz at gmail.com Thu Jan 14 09:59:31 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 14 Jan 2016 09:59:31 -0500 Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: <1452727005415-7588352.post@n2.nabble.com> References: <1452207458825-7588334.post@n2.nabble.com> <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> <1452526554285-7588345.post@n2.nabble.com> <1452640692677-7588348.post@n2.nabble.com> <1452722464220-7588350.post@n2.nabble.com> <1452727005415-7588352.post@n2.nabble.com> Message-ID: Run without debugging (Ctrl+F5) in release mode. I have a similar spec PC (quad-core Xeon E3-1220). What might make a difference is that I have an SSD too - your example does a lot of I/O writing all those images to disk. If you don't have an SSD, try to not write all those debug files and see how that affects performance. Even if you do have an SSD, not writing those files will speed up things. HTH On Wed, Jan 13, 2016 at 6:16 PM, Yohann Tschudi wrote: > It is really much better in release but still took me 20-30 min to run the > 1st one and I have a pretty good computer (Intel Xeon 3.5GHz, 16GB, 64-bit > Windows 7, VC++). > The project config seems ok too (ITK compiled in release, TextureFeatures > too...), I am very curious on how you get these 2-3min ! > > Btw the results are ok, thank you again > > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588352.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Fri Jan 15 03:28:26 2016 From: itkhelpacc at gmail.com (vishal) Date: Fri, 15 Jan 2016 01:28:26 -0700 (MST) Subject: [ITK-users] How to analyse the time taken by each module? and use of ELASTIX in ITK !?! Message-ID: <1452846506007-36650.post@n7.nabble.com> Hi, I have three question: [1] I working on a registration algorithm that takes half an hour to converge... I want to optimize my code.. so I need to no which module takes the most computation time.. is there any method to do this? [2] after analysing the code is it possible to convert the CPU based module to GPU based module? Can any one guide to do that? [3] I came across this software called ELASTIX.. wherein there are many ITK modules written to run on GPU.. is it possible for me to include these modules into my code directly?? any suggestion is appreciated... thank you Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.html Sent from the ITK - Users mailing list archive at Nabble.com. From dzenanz at gmail.com Fri Jan 15 08:47:25 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 15 Jan 2016 08:47:25 -0500 Subject: [ITK-users] How to analyse the time taken by each module? and use of ELASTIX in ITK !?! In-Reply-To: <1452846506007-36650.post@n7.nabble.com> References: <1452846506007-36650.post@n7.nabble.com> Message-ID: Hi Vishal, finding out how much time each which function takes is called code profiling. VisualStudio, Xcode and valgrind can do it. You can offload the heaviest computation to GPU. And the exact problem with GPU is that programming GPUs is cumbersome. Demons algorithm is already implemented for the GPU, you can take a look at how it is done. Do you have a link to this Elastix? Regards, D?enan On Fri, Jan 15, 2016 at 3:28 AM, vishal wrote: > Hi, > I have three question: > > [1] I working on a registration algorithm that takes half an hour to > converge... I want to optimize my code.. so I need to no which module takes > the most computation time.. is there any method to do this? > > [2] after analysing the code is it possible to convert the CPU based module > to GPU based module? Can any one guide to do that? > > [3] I came across this software called ELASTIX.. wherein there are many ITK > modules written to run on GPU.. is it possible for me to include these > modules into my code directly?? > > any suggestion is appreciated... > thank you > > Regards > Vishal > > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Jan 15 10:46:56 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 15 Jan 2016 10:46:56 -0500 Subject: [ITK-users] How to analyse the time taken by each module? and use of ELASTIX in ITK !?! In-Reply-To: References: <1452846506007-36650.post@n7.nabble.com> Message-ID: Hi, In addition to profiling tools, which is a good recommendation, ITK has cross-platform tools to do more high level timing. Here is an example that uses itk::TimeProbe. http://itk.org/ITKExamples/src/Core/Common/ComputeTimeBetweenPoints/Documentation.html HTH, Matt On Fri, Jan 15, 2016 at 8:47 AM, D?enan Zuki? wrote: > Hi Vishal, > > finding out how much time each which function takes is called code > profiling. VisualStudio, Xcode and valgrind can do it. > > You can offload the heaviest computation to GPU. And the exact problem with > GPU is that programming GPUs is cumbersome. Demons algorithm is already > implemented for the GPU, you can take a look at how it is done. > > Do you have a link to this Elastix? > > Regards, > D?enan > > On Fri, Jan 15, 2016 at 3:28 AM, vishal wrote: >> >> Hi, >> I have three question: >> >> [1] I working on a registration algorithm that takes half an hour to >> converge... I want to optimize my code.. so I need to no which module >> takes >> the most computation time.. is there any method to do this? >> >> [2] after analysing the code is it possible to convert the CPU based >> module >> to GPU based module? Can any one guide to do that? >> >> [3] I came across this software called ELASTIX.. wherein there are many >> ITK >> modules written to run on GPU.. is it possible for me to include these >> modules into my code directly?? >> >> any suggestion is appreciated... >> thank you >> >> Regards >> Vishal >> >> >> >> >> -- >> View this message in context: >> http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.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 > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 yxt227 at med.miami.edu Fri Jan 15 10:52:52 2016 From: yxt227 at med.miami.edu (Yohann Tschudi) Date: Fri, 15 Jan 2016 08:52:52 -0700 (MST) Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: References: <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> <1452526554285-7588345.post@n2.nabble.com> <1452640692677-7588348.post@n2.nabble.com> <1452722464220-7588350.post@n2.nabble.com> <1452727005415-7588352.post@n2.nabble.com> Message-ID: <1452873172762-7588359.post@n2.nabble.com> Here is the final code : TextureFeatures.cxx Hope this will be useful for someone. Some results from prostate: Slide13.PNG And brain : Slide15.PNG Thank you Timothee and Dzenan for your answers. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588359.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From dzenanz at gmail.com Fri Jan 15 11:04:22 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 15 Jan 2016 11:04:22 -0500 Subject: [ITK-users] [ITK] Texture analysis - two basics questions In-Reply-To: <1452873172762-7588359.post@n2.nabble.com> References: <637016711.7426094.1452242422659.JavaMail.zimbra@enst.fr> <1452264370571-7588337.post@n2.nabble.com> <1452526554285-7588345.post@n2.nabble.com> <1452640692677-7588348.post@n2.nabble.com> <1452722464220-7588350.post@n2.nabble.com> <1452727005415-7588352.post@n2.nabble.com> <1452873172762-7588359.post@n2.nabble.com> Message-ID: Thanks Yohann for sharing for posterity both your code and illustrative figures. On Fri, Jan 15, 2016 at 10:52 AM, Yohann Tschudi wrote: > Here is the final code : > TextureFeatures.cxx > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588359/TextureFeatures.cxx > > > Hope this will be useful for someone. > > Some results from prostate: > Slide13.PNG > > And brain : > Slide15.PNG > > > > Thank you Timothee and Dzenan for your answers. > > > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-analysis-two-basics-questions-tp7588334p7588359.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hyunjae.kang at kitware.com Fri Jan 15 13:56:18 2016 From: hyunjae.kang at kitware.com (Hyun Jae Kang) Date: Fri, 15 Jan 2016 11:56:18 -0700 (MST) Subject: [ITK-users] How to analyse the time taken by each module? and use of ELASTIX in ITK !?! In-Reply-To: References: <1452846506007-36650.post@n7.nabble.com> Message-ID: <1452884178401-36655.post@n7.nabble.com> Hi, Here are other examples of itk::TimeProbe: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbeTest.cxx https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbeTest2.cxx Also, You can measure computation times of multiple functions by using itk::TimeProbesCollectorBase. Please check the following example code. https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/test/itkTimeProbesTest.cxx Thanks, Hyun Jae -- View this message in context: http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650p36655.html Sent from the ITK - Users mailing list archive at Nabble.com. From andinet.enqu at kitware.com Sun Jan 17 08:10:04 2016 From: andinet.enqu at kitware.com (Andinet Enquobahrie) Date: Sun, 17 Jan 2016 08:10:04 -0500 Subject: [ITK-users] ANN: Kitware is hiring Image Guided Intervention Applications Research and Development Engineers in the Medical Computing Group Message-ID: Apologies for duplicate postings. =================== Hi folks, We are looking to hire image guided intervention applications research and development engineers in our Medical Computing group. If you are a talented medical image analysis and visualization expert with image guided intervention software applications development experience, please consider applying. For the full posting see: http://tinyurl.com/zxlpyyj JOB DESCRIPTION =============== Kitware is actively seeking talented individuals to contribute to the creation and development of image guided intervention software applications. The candidate will participate in research projects focused on building intelligent virtual surgical planning and guidance applications for a variety of clinical procedures including orthopedic, neurological and abdominal surgeries and other types of interventions such as needle biopsy. We aim to develop advanced algorithms to process pre-operative images, to localize surgical instruments and register pre-operative images with intraoperative images to guide surgeons and interventional radiologists for better clinical outcomes. Our efforts build upon our extensive C++ software libraries as well as our expertise in a variety of synergistic disciplines including machine learning, pattern recognition, medical image analysis, visualization, informatics, and computer vision. In these projects, the employee will collaborate with world-renowned researchers and talented engineers in industry, academia, and at government agencies. Qualifications *Masters or PhD in computer science, biomedical engineering, or a related field that has emphasis in medical image analysis and visualization *Concrete experience implementing image guided intervention applications using open-source libraries such as ITK, VTK, 3D Slicer and Qt. *Experience implementing biomedical analysis solutions such as: image registration, segmentation, volume rendering, statistical computing, visualization, etc. *Strong C++ programming skills *Excellent communication and writing skills =============== For other job openings at Kitware, please check http://jobs.kitware.com/opportunities.html -- Andinet Enquobahrie, Ph.D., MBA Assistant Director of Medical Computing Kitware, Inc. http://www.kitware.com (919) 969-6990 x311 -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Mon Jan 18 04:48:28 2016 From: itkhelpacc at gmail.com (vishal) Date: Mon, 18 Jan 2016 02:48:28 -0700 (MST) Subject: [ITK-users] How to analyse the time taken by each module? and use of ELASTIX in ITK !?! In-Reply-To: References: <1452846506007-36650.post@n7.nabble.com> Message-ID: <1453110508748-36657.post@n7.nabble.com> hi, Thank you all for the reply it was very helpful... and D?enan this is the Elastix link http://elastix.isi.uu.nl/... click on download.. two types of file is available source code and .exe file... pls download the source code.. browse file D:\compressed\elastix_sources_v4.8.zip\src\Common\OpenCL\Filters.... ul find some classes implemented in GPU.. i still have to look into it .. please tell me if u figure out some thing.. thank you regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650p36657.html Sent from the ITK - Users mailing list archive at Nabble.com. From dshamoni at gmail.com Mon Jan 18 10:16:13 2016 From: dshamoni at gmail.com (Denis Shamonin) Date: Mon, 18 Jan 2016 16:16:13 +0100 Subject: [ITK-users] How to analyse the time taken by each module? and use of ELASTIX in ITK !?! In-Reply-To: <1452846506007-36650.post@n7.nabble.com> References: <1452846506007-36650.post@n7.nabble.com> Message-ID: Hi Vishal, 1. One of the ways of profiling on Linux is using callgrind for collecting the performance profiling information http://linux.die.net/man/1/callgrind command = "valgrind --tool=callgrind " + appname + call + " -out " + out That will generate profile files like callgrind.out.xxxx. Then you could use the KCachegrind tool http://kcachegrind.sourceforge.net/html/Home.html to visualize this files and see all the timings. No special code injections or compilation flags are needed. 2. The resampling (itk::ResampleImageFilter) part of the image registration is highly optimized for GPU. The performance reaches incredible 0.1 sec execution time on modern cards, depending on image size, interpolator and transformations. The work and source code could be found at Insight Journal http://insight-journal.org/browse/publication/884 It is possible to convert some algorithms to GPU, but would require skill, time and a lot of testing. Good luck with that ;) You could relatively easy integrate (itk::GPUResampleImageFilter) in your application, see itkGPUResampleImageFilterTest.cxx of the submission. One way to use ::RegisterOneFactory() calls to replace CPU version with GPU, other way explicit creation. - See test\itkGPUResampleImageFilterTest.cxx for implicit replacement of the itk::ResampleImageFilter to GPU version. - See the elastix component called OpenCLResampler in elastix\ src\Components\Resamplers\OpenCLResampler. 3. The elastix a toolbox for rigid and nonrigid registration of images http://elastix.isi.uu.nl To enable GPU resampling (itk::GPUResampleImageFilter) in elastix, just set this two parameters (below) to true and enjoy. Resampler "OpenCLResampler" OpenCLResamplerUseOpenCL "true" Regards, Denis P. Shamonin, Division of Image Processing (LKEB) Department of Radiology Leiden University Medical Center On 15 January 2016 at 09:28, vishal wrote: > Hi, > I have three question: > > [1] I working on a registration algorithm that takes half an hour to > converge... I want to optimize my code.. so I need to no which module takes > the most computation time.. is there any method to do this? > > [2] after analysing the code is it possible to convert the CPU based module > to GPU based module? Can any one guide to do that? > > [3] I came across this software called ELASTIX.. wherein there are many ITK > modules written to run on GPU.. is it possible for me to include these > modules into my code directly?? > > any suggestion is appreciated... > thank you > > Regards > Vishal > > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/How-to-analyse-the-time-taken-by-each-module-and-use-of-ELASTIX-in-ITK-tp36650.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Mon Jan 18 10:51:32 2016 From: julien.jomier at kitware.com (Julien Jomier) Date: Mon, 18 Jan 2016 16:51:32 +0100 Subject: [ITK-users] ANN: CMake Course - March 14 in Lyon, France Message-ID: <569D0A04.4080704@kitware.com> Happy New Year! To start the new year right, Kitware will be holding a CMake training course on March 14, 2016 at Kitware's office in Lyon, France. This one-day course will cover CMake, CTest, CPack and CDash. Visit our website for more information and registration details (early registration and student discounts available): http://training.kitware.fr/browse/120 Note that the course will be taught in English. If you have any questions, please contact me directly or training at kitware.fr. We are looking forward to seeing you in Lyon, Julien -- Kitware SAS 26 rue Louis Gu?rin 69100 Villeurbanne, France http://www.kitware.eu From bill.lorensen at gmail.com Mon Jan 18 11:38:08 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 18 Jan 2016 11:38:08 -0500 Subject: [ITK-users] Visualize Intermediate result of ITK registration in vtk In-Reply-To: <1452781038666-7588354.post@n2.nabble.com> References: <1451277758067-36590.post@n7.nabble.com> <1451450098542-36592.post@n7.nabble.com> <1452781038666-7588354.post@n2.nabble.com> Message-ID: Vishal, I just added a wiki example that watches the iterations of a registration: http://itk.org/Wiki/ITK/Examples/Registration/WatchRegistration Bill On Thu, Jan 14, 2016 at 9:17 AM, vis wrote: > hi dzenanz, > thanks for the suggestion....il try it and post the results.. > Regards > Vishal > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Visualize-Intermediate-result-of-ITK-registration-in-vtk-tp7588295p7588354.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 -- Unpaid intern in BillsBasement at noware dot com From itkhelpacc at gmail.com Mon Jan 18 23:18:07 2016 From: itkhelpacc at gmail.com (vishal) Date: Mon, 18 Jan 2016 21:18:07 -0700 (MST) Subject: [ITK-users] Visualize Intermediate result of ITK registration in vtk In-Reply-To: References: <1451277758067-36590.post@n7.nabble.com> <1451450098542-36592.post@n7.nabble.com> <1452781038666-7588354.post@n2.nabble.com> Message-ID: <1453177087814-36661.post@n7.nabble.com> hi Bill, Thank you, this example very helpful for me!! Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Visualize-Intermediate-result-of-ITK-registration-in-vtk-tp36590p36661.html Sent from the ITK - Users mailing list archive at Nabble.com. From itkhelpacc at gmail.com Wed Jan 20 06:16:41 2016 From: itkhelpacc at gmail.com (vishal) Date: Wed, 20 Jan 2016 04:16:41 -0700 (MST) Subject: [ITK-users] Is this a bug in euler 3D transform?? Message-ID: <1453288601423-36662.post@n7.nabble.com> hi, Im working on a 2d/3d registration algorithm... Im using Euler3dtransform... the registration doesnt converge since the 3d volume tends to translate during the registration process... i have tried these examples [1]http://www.itk.org/Doxygen/html/SphinxExamples_2src_2Core_2Transform_2CopyANonCompositeTransform_2Code_8cxx-example.html#_a0 [2]http://www.itk.org/Doxygen/html/SphinxExamples_2src_2Core_2Transform_2CopyACompositeTransform_2Code_8cxx-example.html#_a0 in [1] they use TransformType::ParametersType fixedParameters(3); to set the rotation constant and only allow the volume to translate( this is my understanding of the code...pls correct me if im wrong) when i applied this to my code it ISNT working properly.... i was expecting euler parameters to be [-3.5;-4.5;-5.5; some-X-axis-translation;some-Yaxis--translation,some-Zaxis--translation]; this doesnt happen... here is a piece of my code where i attempt to STOP the volume from translating during registration and only allow the volume to rotate about the z-axis:- #if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 TransformType::FixedParametersType fixedParameters(3); #else //Pre 4.8.1 TransformType::ParametersType fixedParameters(6); #endif fixedParameters[3] = 0.0; fixedParameters[4] = 0.0; fixedParameters[5] = 0.0; transform->SetFixedParameters( fixedParameters ); registration->SetInitialTransformParameters( transform->GetParameters() ); i was expecting euler parameters to be [some-X axis-rotation;some-Y axis-rotation,some-Z axis-rotation,0.0,0.0,0.0]; this doesnt happen... please advice if this is an error [OR] a wrong implementation [OR] is disabling translation in euler transform is IMPOSSIBLE? any advice is appreciated... Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Is-this-a-bug-in-euler-3D-transform-tp36662.html Sent from the ITK - Users mailing list archive at Nabble.com. From itkhelpacc at gmail.com Thu Jan 21 01:35:11 2016 From: itkhelpacc at gmail.com (vishal) Date: Wed, 20 Jan 2016 23:35:11 -0700 (MST) Subject: [ITK-users] Bug in ITK 4.8.2 In-Reply-To: References: <1451536488731-36593.post@n7.nabble.com> Message-ID: <1453358111000-36663.post@n7.nabble.com> hi D?enan, I tried the running the code (DicomSeriesReadImageWrite2.cxx of ITK 4.7.2 IO examples) again in ITK 4.7.2 seemed to be working properly... but when i tried to run the IO examples code (DicomSeriesReadImageWrite2.cxx of ITK 4.8.2) in ITK 4.8.2 for the same data the following error occurred please look into the screenshot i have attached.. there seems to be some bug GDCM module.. the dataset im using is http://www.osirix-viewer.com/datasets/ (BREBIX dataset).... regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Bug-in-ITK-4-8-2-tp36593p36663.html Sent from the ITK - Users mailing list archive at Nabble.com. From wer.wie.was.wiso.weshalb.warum at googlemail.com Thu Jan 21 12:46:51 2016 From: wer.wie.was.wiso.weshalb.warum at googlemail.com (JE) Date: Thu, 21 Jan 2016 18:46:51 +0100 Subject: [ITK-users] Image stack with varying slice thickness Message-ID: <20160121174651.GA26277@jerng.de> Hi all, Is ITK capable of dealing with image stacks which are stored slice-by-slice and which have a varying slice thickness? I.e., the first 20 slices have a thickness of .5mm whereas the remaining slices have a thickness of 1.0mm? If so, how does ITK handle that? Best, JE From matt.mccormick at kitware.com Thu Jan 21 13:05:20 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jan 2016 13:05:20 -0500 Subject: [ITK-users] Image stack with varying slice thickness In-Reply-To: <20160121174651.GA26277@jerng.de> References: <20160121174651.GA26277@jerng.de> Message-ID: Hi JE, ITK can read in image stacks (see itk::ImageSeriesReader). The primary data structure (itk::Image) assumes possibly anisotropic, although consistent, spacing different directions. HTH, Matt On Thu, Jan 21, 2016 at 12:46 PM, JE via Insight-users wrote: > Hi all, > > Is ITK capable of dealing with image stacks which are stored > slice-by-slice and which have a varying slice thickness? I.e., the first > 20 slices have a thickness of .5mm whereas the remaining slices have a > thickness of 1.0mm? If so, how does ITK handle that? > > Best, > JE > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Jan 21 13:48:50 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jan 2016 13:48:50 -0500 Subject: [ITK-users] Is this a bug in euler 3D transform?? In-Reply-To: <1453288601423-36662.post@n7.nabble.com> References: <1453288601423-36662.post@n7.nabble.com> Message-ID: Hi, It sounds like there is confusion between FixedParameters and Parameters. When the FixedParameters are set, the Parameters are not affected. To mask out a transform's Parameters, call SetWeights [1]. When performing a 3D rigid registration, the VersorTransform behaves better than the Euler3DTransform. HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1ObjectToObjectOptimizerBaseTemplate.html On Wed, Jan 20, 2016 at 6:16 AM, vishal wrote: > hi, > Im working on a 2d/3d registration algorithm... Im using Euler3dtransform... > the registration doesnt converge since the 3d volume tends to translate > during the registration process... i have tried these examples > [1]http://www.itk.org/Doxygen/html/SphinxExamples_2src_2Core_2Transform_2CopyANonCompositeTransform_2Code_8cxx-example.html#_a0 > [2]http://www.itk.org/Doxygen/html/SphinxExamples_2src_2Core_2Transform_2CopyACompositeTransform_2Code_8cxx-example.html#_a0 > > in [1] they use TransformType::ParametersType fixedParameters(3); to set the > rotation constant and only allow the volume to translate( this is my > understanding of the code...pls correct me if im wrong) when i applied this > to my code it ISNT working properly.... i was expecting euler parameters to > be [-3.5;-4.5;-5.5; > some-X-axis-translation;some-Yaxis--translation,some-Zaxis--translation]; > this doesnt happen... > > here is a piece of my code where i attempt to STOP the volume from > translating during registration and only allow the volume to rotate about > the z-axis:- > > #if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 > TransformType::FixedParametersType fixedParameters(3); > #else //Pre 4.8.1 > TransformType::ParametersType fixedParameters(6); > #endif > fixedParameters[3] = 0.0; > fixedParameters[4] = 0.0; > fixedParameters[5] = 0.0; > transform->SetFixedParameters( fixedParameters ); > registration->SetInitialTransformParameters( transform->GetParameters() ); > > i was expecting euler parameters to be [some-X axis-rotation;some-Y > axis-rotation,some-Z axis-rotation,0.0,0.0,0.0]; this doesnt happen... > please advice if this is an error [OR] a wrong implementation [OR] is > disabling translation in euler transform is IMPOSSIBLE? any advice is > appreciated... > Regards > Vishal > > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Is-this-a-bug-in-euler-3D-transform-tp36662.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 sean at rogue-research.com Thu Jan 21 14:28:54 2016 From: sean at rogue-research.com (Sean McBride) Date: Thu, 21 Jan 2016 14:28:54 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: <20160104211744.1213332491@mail.rogue-research.com> Message-ID: <20160121192854.4986335@mail.rogue-research.com> On Tue, 5 Jan 2016 14:54:47 -0500, Matt McCormick said: >To update GDCM, run the > > Modules/ThirdParty/GDCM/UpdateFromUpstream.sh > >script. > > >Since GDCM 2.6 has been released, we should switch from GDCM "master" >to GDCM "release" before doing the update. Even more conservatively, I'll start from the "release-2-4" branch. So now the update script works on OS X, I've run it successfully and did: git merge -X subtree=Modules/ThirdParty/GDCM/src/gdcm upstream-gdcm as it instructs. This leaves one file conflicted: Modules/ThirdParty/GDCM/src/gdcm/Utilities/socketxx/socket++/CMakeLists.txt Due to the change in git SHA 70306386. What is the correct way to deal with that? Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From matt.mccormick at kitware.com Thu Jan 21 14:49:29 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jan 2016 14:49:29 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: <20160121192854.4986335@mail.rogue-research.com> References: <20160104211744.1213332491@mail.rogue-research.com> <20160121192854.4986335@mail.rogue-research.com> Message-ID: On Thu, Jan 21, 2016 at 2:28 PM, Sean McBride wrote: > On Tue, 5 Jan 2016 14:54:47 -0500, Matt McCormick said: > >>To update GDCM, run the >> >> Modules/ThirdParty/GDCM/UpdateFromUpstream.sh >> >>script. >> >> >>Since GDCM 2.6 has been released, we should switch from GDCM "master" >>to GDCM "release" before doing the update. > > Even more conservatively, I'll start from the "release-2-4" branch. Sounds good. > So now the update script works on OS X, Cool! > I've run it successfully and did: > > git merge -X subtree=Modules/ThirdParty/GDCM/src/gdcm upstream-gdcm > > as it instructs. This leaves one file conflicted: > > Modules/ThirdParty/GDCM/src/gdcm/Utilities/socketxx/socket++/CMakeLists.txt > > Due to the change in git SHA 70306386. It should probably still be kept. If it is still relevant to upstream, it could be submitted. Thanks, Matt From sean at rogue-research.com Thu Jan 21 15:05:33 2016 From: sean at rogue-research.com (Sean McBride) Date: Thu, 21 Jan 2016 15:05:33 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: <20160104211744.1213332491@mail.rogue-research.com> <20160121192854.4986335@mail.rogue-research.com> Message-ID: <20160121200533.74631707@mail.rogue-research.com> On Thu, 21 Jan 2016 14:49:29 -0500, Matt McCormick said: >> I've run it successfully and did: >> >> git merge -X subtree=Modules/ThirdParty/GDCM/src/gdcm upstream-gdcm >> >> as it instructs. This leaves one file conflicted: >> >> Modules/ThirdParty/GDCM/src/gdcm/Utilities/socketxx/socket++/CMakeLists.txt >> >> Due to the change in git SHA 70306386. > >It should probably still be kept. If it is still relevant to >upstream, it could be submitted. Sorry, what I mean is: what must I do git-wise? Do I just manually fix the conflict in the same commit as my gdcm update, or do I need to make it a separate commit to indicate it's not part of gdcm proper, or...? Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From matt.mccormick at kitware.com Thu Jan 21 15:09:12 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jan 2016 15:09:12 -0500 Subject: [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: <20160121200533.74631707@mail.rogue-research.com> References: <20160104211744.1213332491@mail.rogue-research.com> <20160121192854.4986335@mail.rogue-research.com> <20160121200533.74631707@mail.rogue-research.com> Message-ID: On Thu, Jan 21, 2016 at 3:05 PM, Sean McBride wrote: > On Thu, 21 Jan 2016 14:49:29 -0500, Matt McCormick said: > >>> I've run it successfully and did: >>> >>> git merge -X subtree=Modules/ThirdParty/GDCM/src/gdcm upstream-gdcm >>> >>> as it instructs. This leaves one file conflicted: >>> >>> Modules/ThirdParty/GDCM/src/gdcm/Utilities/socketxx/socket++/CMakeLists.txt >>> >>> Due to the change in git SHA 70306386. >> >>It should probably still be kept. If it is still relevant to >>upstream, it could be submitted. > > Sorry, what I mean is: what must I do git-wise? Do I just manually fix the conflict in the same commit as my gdcm update, or do I need to make it a separate commit to indicate it's not part of gdcm proper, or...? It can be included in the update commit. Thanks, Matt From dzenanz at gmail.com Thu Jan 21 15:10:22 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 21 Jan 2016 15:10:22 -0500 Subject: [ITK-users] Bug in ITK 4.8.2 In-Reply-To: <1453358111000-36663.post@n7.nabble.com> References: <1451536488731-36593.post@n7.nabble.com> <1453358111000-36663.post@n7.nabble.com> Message-ID: Hi Vishal, running this example in debug mode on a recent git version also produces the assertion. However running it in release mode produces a file (which seems correct to me) without any errors or warnings. Looking at the pixel types which mismatch in the assertion, this image series uses 11-bit pixel representation (which is either uncommon or non-standard). I would say that some metadata perhaps contradicts another, which causes the assertion. HTH, D?enan On Thu, Jan 21, 2016 at 1:35 AM, vishal wrote: > hi D?enan, > I tried the running the code (DicomSeriesReadImageWrite2.cxx of ITK 4.7.2 > IO > examples) again in ITK 4.7.2 seemed to be working properly... but when i > tried to run the IO examples code (DicomSeriesReadImageWrite2.cxx of ITK > 4.8.2) in ITK 4.8.2 for the same data the following error occurred please > look into the screenshot i have attached.. there seems to be some bug GDCM > module.. the dataset im using is http://www.osirix-viewer.com/datasets/ > (BREBIX dataset).... > > > regards > Vishal > > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Bug-in-ITK-4-8-2-tp36593p36663.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at rogue-research.com Thu Jan 21 17:47:58 2016 From: sean at rogue-research.com (Sean McBride) Date: Thu, 21 Jan 2016 17:47:58 -0500 Subject: [ITK-users] Bug in ITK 4.8.2 In-Reply-To: References: <1451536488731-36593.post@n7.nabble.com> <1453358111000-36663.post@n7.nabble.com> Message-ID: <20160121224758.1311363458@mail.rogue-research.com> On Thu, 21 Jan 2016 15:10:22 -0500, D?enan Zuki? said: >running this example in debug mode on a recent git version also produces >the assertion. However running it in release mode produces a file (which >seems correct to me) without any errors or warnings. A recent git version of? ITK? GDCM? I ask because ITK git master still uses GDCM from circa 2015-04-29. You might want to build GDCM git master and then rebuild ITK using the ITK_USE_SYSTEM_GDCM option to point to your GDCM. I'm working on updating ITK's GDCM to something newer... Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From dzenanz at gmail.com Thu Jan 21 18:02:19 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 21 Jan 2016 18:02:19 -0500 Subject: [ITK-users] Bug in ITK 4.8.2 In-Reply-To: <20160121224758.1311363458@mail.rogue-research.com> References: <1451536488731-36593.post@n7.nabble.com> <1453358111000-36663.post@n7.nabble.com> <20160121224758.1311363458@mail.rogue-research.com> Message-ID: I was not specific enough. My previous reply was concerning recent ITK (git commit af6b2c82ba794ada4d487c5bbd83f2bd1ed39e2f from 3rd January 2016) which I had lying around. Regards On Thu, Jan 21, 2016 at 5:47 PM, Sean McBride wrote: > On Thu, 21 Jan 2016 15:10:22 -0500, D?enan Zuki? said: > > >running this example in debug mode on a recent git version also produces > >the assertion. However running it in release mode produces a file (which > >seems correct to me) without any errors or warnings. > > A recent git version of? ITK? GDCM? I ask because ITK git master still > uses GDCM from circa 2015-04-29. You might want to build GDCM git master > and then rebuild ITK using the ITK_USE_SYSTEM_GDCM option to point to your > GDCM. > > I'm working on updating ITK's GDCM to something newer... > > Cheers, > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mike.jackson at bluequartz.net Fri Jan 22 09:28:58 2016 From: mike.jackson at bluequartz.net (Michael Jackson) Date: Fri, 22 Jan 2016 09:28:58 -0500 Subject: [ITK-users] Reading Gray Scale Palette Image Message-ID: We have a Tiff image that is GrayScale (8 bit) and Palette (photometric interpretation=3) and the indices into the palette are 16 bit but the values in the palette are 8 bit? When trying to use ITK to figure out what type of array we should be allocating our logic is coming back with 16 bit unsigned shorts because we have the following code: itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(getInputFileName(), itk::ImageIOFactory::ReadMode); itk::ImageIOBase::IOComponentType componentType = imageIO->GetComponentType(); ? else if(itk::ImageIOBase::USHORT == componentType) { data = UInt16ArrayType::CreateArray(0, "Temp", false); } ? Here is the header of the tiff file as put out by ?tiffdump? /Users/XXXXXXXX/Downloads/image_01.tif: Magic: 0x4949 Version: 0x2a Directory 0: offset 8 (0x8) next 113277976 (0x6c07c18) ImageWidth (256) LONG (4) 1<12288> ImageLength (257) LONG (4) 1<9216> BitsPerSample (258) SHORT (3) 1<8> Compression (259) SHORT (3) 1<1> Photometric (262) SHORT (3) 1<3> StripOffsets (273) LONG (4) 1<31768> RowsPerStrip (278) LONG (4) 1<4294967295> StripByteCounts (279) LONG (4) 1<113246208> XResolution (282) RATIONAL (5) 1<1> YResolution (283) RATIONAL (5) 1<1> ResolutionUnit (296) SHORT (3) 1<1> Colormap (320) SHORT (3) 768<0 256 512 768 1024 1280 1536 1792 2048 2304 2560 2816 3072 3328 3584 3840 4096 4352 4608 4864 5120 5376 5632 5888 ?> My question is this: what can we interrogate from the imageIO object to really nail down that this really turns out to be an 8 bit image? Thanks -- Michael A. Jackson BlueQuartz Software, LLC [e]: mike.jackson at bluequartz.net -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Fri Jan 22 10:39:05 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Fri, 22 Jan 2016 10:39:05 -0500 Subject: [ITK-users] Reading Gray Scale Palette Image In-Reply-To: References: Message-ID: <84C95810-9657-45A8-829D-F67818C28E3A@mail.nih.gov> Hello Michael, The current itkTIFFIO does handle some special cases for palette. Namely when all RGB palette entries are equal[1], the image palette is interpreted as grayscale. The other is when all the entires are less that 256, the component is interpreted as unsigned char. On the bright side you are not getting an RGB of uint16 :) But we are not handling the case where the upper bits of the palette entries are used and not the lower, so you are still getting uint16. While it is quite possible to modify TIFFIO to load this data as you expect, it likely would be easiest to just shift the palette in the file. As I have used this format before I was surprised with the support from a number of viewers. HTH, Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/6871f6f2c9510057ca253727d8487d88724cf2d8/Modules/IO/TIFF/src/itkTIFFImageIO.cxx#L122-L131 [2] https://github.com/InsightSoftwareConsortium/ITK/blob/6871f6f2c9510057ca253727d8487d88724cf2d8/Modules/IO/TIFF/src/itkTIFFImageIO.cxx#L392-L402 > On Jan 22, 2016, at 9:28 AM, Michael Jackson wrote: > > We have a Tiff image that is GrayScale (8 bit) and Palette (photometric interpretation=3) and the indices into the palette are 16 bit but the values in the palette are 8 bit? When trying to use ITK to figure out what type of array we should be allocating our logic is coming back with 16 bit unsigned shorts because we have the following code: > > itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(getInputFileName(), itk::ImageIOFactory::ReadMode); > > itk::ImageIOBase::IOComponentType componentType = imageIO->GetComponentType(); > ? > else if(itk::ImageIOBase::USHORT == componentType) > { > data = UInt16ArrayType::CreateArray(0, "Temp", false); > } > ? > > Here is the header of the tiff file as put out by ?tiffdump? > > /Users/XXXXXXXX/Downloads/image_01.tif: > Magic: 0x4949 Version: 0x2a > Directory 0: offset 8 (0x8) next 113277976 (0x6c07c18) > ImageWidth (256) LONG (4) 1<12288> > ImageLength (257) LONG (4) 1<9216> > BitsPerSample (258) SHORT (3) 1<8> > Compression (259) SHORT (3) 1<1> > Photometric (262) SHORT (3) 1<3> > StripOffsets (273) LONG (4) 1<31768> > RowsPerStrip (278) LONG (4) 1<4294967295> > StripByteCounts (279) LONG (4) 1<113246208> > XResolution (282) RATIONAL (5) 1<1> > YResolution (283) RATIONAL (5) 1<1> > ResolutionUnit (296) SHORT (3) 1<1> > Colormap (320) SHORT (3) 768<0 256 512 768 1024 1280 1536 1792 2048 2304 2560 2816 3072 3328 3584 3840 4096 4352 4608 4864 5120 5376 5632 5888 ?> > > > My question is this: what can we interrogate from the imageIO object to really nail down that this really turns out to be an 8 bit image? > > Thanks > -- > Michael A. Jackson > BlueQuartz Software, LLC > [e]: mike.jackson at bluequartz.net _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From franciscolopezdelafranca at gmail.com Mon Jan 25 06:50:35 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Mon, 25 Jan 2016 12:50:35 +0100 Subject: [ITK-users] Texture pixel by pixel In-Reply-To: References: <729B1C07-6BAA-41AD-8B16-A1A2ECE039DF@mail.nih.gov> <1443521320260-7587935.post@n2.nabble.com> <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hello Bradley again. Sorry but I'd like to re-open this issue because I need your class but with some modification. I pass to tell you. As my tests with your external class were not good taking into account the performance, I wonder if you could create a variant of it, but in which I can set a mask image and your class just return the VectorImage with all the features for that region (the masked locations) as itk::ScalarImageToTextureFeaturesFilter class does. I mean, to get the vector image with all the features but just calculate it for the regions belonging to the mask image. Positions not belonging to the mask region could have a pixel value of 0, for instance. I don?t know if it is very costly for you, but I would thank you so much. Otherwise, I could try it but I'd need your suggestions on how to do it. Thanks a lot. Best regards. 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com>: > Hello Bradley again, > I would like to ask you for a couple of favours. In the one hand, could > you please send me your 3D image so that I can test on it? And on the other > hand, could you test the example I have referenced in the previous email > with your image, not changing anything in the code, such as it is, and tell > me if the execution time is normal? > Thank you very much. > Regards, > /Francisco > > PS: All my application trace is printed via standard 'cout' command, not > due to a debugging compilation mode. > > > El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp < > blowekamp at mail.nih.gov> escribi?: > >> Hello, >> >> Did you compile TextureFeatureImage in Release mode? >> >> 1) The filter does not scale well with a large radius. And given by your >> initial report of print a very large number of offset you, it sounds like >> you are using a large radius with many offsets. I created a 224x224x300 >> unsigned short image and ran with the default offset and a radius of 2 in 5 >> minutes on my laptop. When I wrote this filter is was ~10x faster than this >> example... things change though... >> >> >> 2) I sounds like the boundaries/limits of the histogram may be clipping >> you values. I would inspect the co-occurance matrix. >> >> >> HTH, >> Brad >> >> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca < >> franciscolopezdelafranca at gmail.com> wrote: >> >> I've tested with itkTextureFeatureImageFilter, with >> itk::ScalarImageToTextureFeaturesFilter and also with the >> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example, for >> a 3D image and here are my comments: >> >> >> 1. I had to interrupt the test after several hours and it kept on >> calculating. And this is for only a 3D image (224x224x300). I need to >> process around 35 images. >> 2. The result (texture features: entropy, energy, correlation, LH, >> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247]. >> These values were not what I expected based on my experience on another >> application I developed, but in that case, I calculated the texture >> features for an image as a whole, not voxel by voxel. >> >> Regards. >> >> 2015-09-30 8:46 GMT+02:00 vis : >> >>> i yes i have tried radius = 3; >>> still no luck >>> >>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK Insight >>> Users] wrote: >>> >>> > Have you tried with a radius of 3 instead of 1? >>> > >>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>> > >: >>> > >>> >> hey Matt, >>> >> thanks for ur advice.. it did build successfully... but im not able >>> to run >>> >> the code for 2D png image... i tried to change the dimension to 2 and >>> >> build >>> >> it which it did.. but when i run the code using the command >>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png 1... >>> i see >>> >> this output >>> >> >>> >> offset: [-1, -1] [0, -1] >>> >> offset: [0, -1] [1, -1] >>> >> offset: [-1, 0] [0, 0] >>> >> offset: [0, 0] [1, 0] >>> >> offset: [-1, 1] [0, 1] >>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls tel >>> me >>> >> how can i modify this code to work wid 2d image... forgive me if my >>> ques >>> >> are really silly im trying to learn something.. >>> >> regards >>> >> Vis >>> >> >>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK Insight >>> Users] >>> >> < >>> >> [hidden email] >> >> >>> >> wrote: >>> >> >>> >> > Hi, >>> >> > >>> >> > The function: >>> >> > >>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>> >> > >>> >> > must be renamed to >>> >> > >>> >> > main(int argc, char* argv[]) >>> >> > >>> >> > HTH, >>> >> > Matt >>> >> > >>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>> >> > > wrote: >>> >> > >>> >> > > hi all, >>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx code >>> but >>> >> im >>> >> > not >>> >> > > able to it is showing the following error >>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, Configuration: >>> >> Debug >>> >> > x64 >>> >> > > ------ >>> >> > > 1> Checking Build System >>> >> > > 1> CMake does not need to re-run because >>> >> > > >>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>> >> > is >>> >> > > up-to-date. >>> >> > > 2>------ Rebuild All started: Project: >>> >> itkTextureFeatureImageFilterTest, >>> >> > > Configuration: Debug x64 ------ >>> >> > > 2> Building Custom Rule >>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>> >> > > 2> CMake does not need to re-run because >>> >> > > >>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>> >> > is >>> >> > > up-to-date. >>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>> >> > > 11.0\VC\include\xutility(2176): warning C4996: 'std::_Copy_impl': >>> >> > Function >>> >> > > call with parameters that may be unsafe - this call relies on the >>> >> caller >>> >> > to >>> >> > > check that the passed values are correct. To disable this >>> warning, use >>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use Visual >>> C++ >>> >> > > 'Checked Iterators' >>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>> 'std::_Copy_impl' >>> >> > > 2> >>> >> > > >>> >> >>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>> >> > see >>> >> > > reference to function template instantiation '_OutIt >>> std::copy>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being compiled >>> >> > > 2> with >>> >> > > 2> [ >>> >> > > 2> _OutIt=unsigned char *, >>> >> > > 2> _InIt=const unsigned char * >>> >> > > 2> ] >>> >> > > 2> >>> >> > > >>> >> >>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>> >> > > while compiling class template member function 'void >>> >> > > itk::ImageFileReader::GenerateData(void)' >>> >> > > 2> with >>> >> > > 2> [ >>> >> > > 2> TOutputImage=InputImageType >>> >> > > 2> ] >>> >> > > 2> >>> >> > > >>> >> > >>> >> >>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>> >> > >>> >> > > : see reference to class template instantiation >>> >> > > 'itk::ImageFileReader' being compiled >>> >> > > 2> with >>> >> > > 2> [ >>> >> > > 2> TOutputImage=InputImageType >>> >> > > 2> ] >>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>> 'std::_Copy_impl' >>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>> 'std::_Copy_impl' >>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>> 'std::_Copy_impl' >>> >> > > 2> Creating library >>> >> > > >>> >> > >>> >> >>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>> >> > >>> >> > > and object >>> >> > > >>> >> > >>> >> >>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>> >> > >>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved external >>> symbol >>> >> > main >>> >> > > referenced in function __tmainCRTStartup >>> >> > > >>> >> > >>> >> >>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>> >> > >>> >> > > : fatal error LNK1120: 1 unresolved externals >>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, Configuration: >>> Debug >>> >> > x64 >>> >> > > ------ >>> >> > > 3> Building Custom Rule >>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>> >> > > 3> CMake does not need to re-run because >>> >> > > >>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>> >> > is >>> >> > > up-to-date. >>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>> ========== >>> >> > > im using the follwing CMakeList.txt >>> >> > > # 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(HelloWorld) >>> >> > > >>> >> > > # Find ITK. >>> >> > > find_package(ITK REQUIRED) >>> >> > > include(${ITK_USE_FILE}) >>> >> > > >>> >> > > add_executable(itkTextureFeatureImageFilterTest >>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>> >> > > >>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>> >> ${ITK_LIBRARIES}) >>> >> > > >>> >> > > please tel me wat the error is?? >>> >> > > >>> >> > > >>> >> > > >>> >> > > -- >>> >> > > View this message in context: >>> >> > >>> >> >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.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 >>> >> > >>> >> > >>> >> > ------------------------------ >>> >> > If you reply to this email, your message will be added to the >>> discussion >>> >> > below: >>> >> > >>> >> > >>> >> >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click here >>> >> > < > . >>> >> > NAML >>> >> > < >>> >> >>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>> >> > >>> >> > >>> >> >>> >> >>> >> >>> >> >>> >> -- >>> >> View this message in context: >>> >> >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.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 >>> > >>> > >>> > ------------------------------ >>> > If you reply to this email, your message will be added to the >>> discussion >>> > below: >>> > >>> > >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>> > To unsubscribe from [ITK-users] Texture pixel by pixel, click here >>> > < >>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=7587867&code=aXRraGVscGFjY0BnbWFpbC5jb218NzU4Nzg2N3wzNzEzNjYzNzk= >>> > >>> > . >>> > NAML >>> > < >>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>> > >>> > >>> >>> >>> >>> >>> -- >>> View this message in context: >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.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 >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From davis.vigneault at gmail.com Mon Jan 25 10:12:02 2016 From: davis.vigneault at gmail.com (DVigneault) Date: Mon, 25 Jan 2016 08:12:02 -0700 (MST) Subject: [ITK-users] External Modules: Passing data to unit tests? Message-ID: <1453734722405-7588384.post@n2.nabble.com> All-- I'm working on an external module for ITK [1], and am having trouble passing image data to my unit tests. I understand from this link [2] that the build system will detect binary images and store them in a gitignored location, which is referenced by a hash. So if I have an image ITKPhase/test/Input/swi_wrapped.vtk, it will be moved somewhere else in the source tree, and the image file will be replaced by an md5--which is what has happened. However, I don't know how to reference the file in the ITKPhase/test/CMakeList.txt file when defining the command. I've tried this... itk_add_test(NAME itkDCTPhaseUnwrappingImageFilterTest COMMAND ${itk-module}TestDriver itkDCTPhaseUnwrappingImageFilterTest $(.ExternalData_MD5_$(cat swi_wrapped.vtk.md5)) "1") ...but, understandably, CMake isn't parsing it the way BASH would, and is instead breaking the link up into individual tokens: test 2 Start 2: itkDCTPhaseUnwrappingImageFilterTest 2: Test command: /local/pemb3433/Developer/ITK/bin/bin/ITKPhaseTestDriver "itkDCTPhaseUnwrappingImageFilterTest" "DATA{" ".ExternalData_MD5_$(cat Input//swi_wrapped.vtk.md5)" "}" "1" 2: Test timeout computed to be: 9.99988e+06 2: Usage: itkDCTPhaseUnwrappingImageFilterTest 1/1 Test #2: itkDCTPhaseUnwrappingImageFilterTest ...***Failed 0.04 sec 0% tests passed, 1 tests failed out of 1 What is the correct way to reference images in external module unit tests? Apologies if this is explained somewhere on the Wiki and I've missed it, or if this is more of a CMake question than an ITK question. Thanks in advance for your help! Best, --Davis [1] https://github.com/DVigneault/ITKPhase [2] http://www.itk.org/Wiki/ITK/Git/Develop/Data#ExternalData -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/External-Modules-Passing-data-to-unit-tests-tp7588384.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From davis.vigneault at gmail.com Mon Jan 25 11:36:08 2016 From: davis.vigneault at gmail.com (DVigneault) Date: Mon, 25 Jan 2016 09:36:08 -0700 (MST) Subject: [ITK-users] External Modules: Passing data to unit tests? In-Reply-To: <1453734722405-7588384.post@n2.nabble.com> References: <1453734722405-7588384.post@n2.nabble.com> Message-ID: <1453739768868-7588385.post@n2.nabble.com> All-- I have it working now--here's what I didn't understand: 1. The hash replacement happens in the source tree only (not the bin). 2. The data files can be referenced as usual, e.g. DATA{Input//swi_wrapped.vtk} 3. The data files should be copied into bin/ExternalData/Modules/External/ITKPhase/text/Input, but if they are not, copying them in manually may fix this (as it did in my case). Best, --Davis -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/External-Modules-Passing-data-to-unit-tests-tp7588384p7588385.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From matt.mccormick at kitware.com Mon Jan 25 13:23:37 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 25 Jan 2016 13:23:37 -0500 Subject: [ITK-users] External Modules: Passing data to unit tests? In-Reply-To: <1453739768868-7588385.post@n2.nabble.com> References: <1453734722405-7588384.post@n2.nabble.com> <1453739768868-7588385.post@n2.nabble.com> Message-ID: Hi Davis, ITKPhase looks like a very interesting module. It sounds like you have a handle on the ExternalData. Another approach for ExternalData is to upload it to the "ITK" community on midas3.kitware.com: http://midas3.kitware.com/midas/folder/10126 If you sign up for the community, please send me an email, and I will give you upload permissions. Then, there is an icon for each file to download the .md5 file. This process is illustrated here: http://itk.org/ITKExamples/Documentation/Contribute/UploadBinaryData.html#upload-via-the-web-interface HTH, Matt On Mon, Jan 25, 2016 at 11:36 AM, DVigneault wrote: > All-- > > I have it working now--here's what I didn't understand: > > 1. The hash replacement happens in the source tree only (not the bin). > 2. The data files can be referenced as usual, e.g. > DATA{Input//swi_wrapped.vtk} > 3. The data files should be copied into > bin/ExternalData/Modules/External/ITKPhase/text/Input, but if they are not, > copying them in manually may fix this (as it did in my case). > > Best, > > --Davis > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/External-Modules-Passing-data-to-unit-tests-tp7588384p7588385.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 bert.alberto at gmail.com Tue Jan 26 05:07:49 2016 From: bert.alberto at gmail.com (Alberto Bert) Date: Tue, 26 Jan 2016 11:07:49 +0100 Subject: [ITK-users] Merging segmentation masks in different region of interests Message-ID: Hi, I have several rectangular regions of interest from a single image (extracted using RegionOfInterestImageFilter), and I am processing one at a time to extract from each of them a segmentation masks (image of labels with 0 or 1). Finally, I would need to ?merge? (i.e. ?combine? or ?and?) the various ROI masks (different size and origin) in a single mask having the same size and origin of the original image. Let?s say I would need to ?put back in the right place? the ROI masks. The AndImageFilter does not allow me to combine the various ROI masks ("Inputs do not occupy the same physical space!?). I browsed the documentation but I could not find a viable solution... I am currently using SimpleITK. Can you help me please? Thanks a lot! Best Alberto From tevain at telecom-paristech.fr Tue Jan 26 05:31:21 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Tue, 26 Jan 2016 11:31:21 +0100 (CET) Subject: [ITK-users] [ITK] Merging segmentation masks in different region of interests In-Reply-To: References: Message-ID: <1708259882.6072050.1453804281916.JavaMail.zimbra@enst.fr> Hello Alberto, If I remember well, the RegionOfInterestImageFilter keeps the subparts in the same physical space, i.e. a same index will get you the same pixel/voxel in the ROI as in the original. So I would use an iterator to create your full mask image. Something like : itk::Image::Pointer FullMask=itk::Image::New(); FullMask->SetRegions(OriginalImage->GetLargestPossibleRegion()); FullMask->Allocate(); itk::ImageRegionIteratorWithIndex> Iter(FullMask,FullMask->GetLargestPossibleRegion()); Iter.GoToBegin(); while(!Iter.IsAtEnd()) { itk::Index CurrentPoint=Iter.GetIndex(); if(//There you test the index to know from which subimage it belong//) { Iter.Set(SubImage->GetPixel(CurrentPoint)); } ++Iter; } HTH, Tim ----- Mail original ----- De: "Alberto Bert" ?: "ITK Users" Envoy?: Mardi 26 Janvier 2016 11:07:49 Objet: [ITK] [ITK-users] Merging segmentation masks in different region of interests Hi, I have several rectangular regions of interest from a single image (extracted using RegionOfInterestImageFilter), and I am processing one at a time to extract from each of them a segmentation masks (image of labels with 0 or 1). Finally, I would need to ?merge? (i.e. ?combine? or ?and?) the various ROI masks (different size and origin) in a single mask having the same size and origin of the original image. Let?s say I would need to ?put back in the right place? the ROI masks. The AndImageFilter does not allow me to combine the various ROI masks ("Inputs do not occupy the same physical space!?). I browsed the documentation but I could not find a viable solution... I am currently using SimpleITK. Can you help me please? Thanks a lot! Best Alberto _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 From bert.alberto at gmail.com Tue Jan 26 09:21:31 2016 From: bert.alberto at gmail.com (Alberto Bert) Date: Tue, 26 Jan 2016 15:21:31 +0100 Subject: [ITK-users] [ITK] Merging segmentation masks in different region of interests In-Reply-To: <1708259882.6072050.1453804281916.JavaMail.zimbra@enst.fr> References: <1708259882.6072050.1453804281916.JavaMail.zimbra@enst.fr> Message-ID: <2CD5E0E5-7B5E-44DD-B38C-843FD87F3E84@gmail.com> Thanks Tim, according to the documentation, RegionOfInterestImageFilter should do what you say, that is why I tried to used it. Unfortunately, it seems not to keep the original logical references... I am not sure I can efficiently do what you suggest with SimpleITK, but if it turns out to be the only way, I guess I will need to switch to the original ITK. I hoped there was a way to do it without a pixel by pixel copy? Any other suggestions? Thanks! Alberto > On 26 Jan 2016, at 11:31, Timothee Evain wrote: > > Hello Alberto, > > If I remember well, the RegionOfInterestImageFilter keeps the subparts in the same physical space, i.e. a same index will get you the same pixel/voxel in the ROI as in the original. So I would use an iterator to create your full mask image. Something like : > > itk::Image::Pointer FullMask=itk::Image::New(); > FullMask->SetRegions(OriginalImage->GetLargestPossibleRegion()); > FullMask->Allocate(); > > itk::ImageRegionIteratorWithIndex> Iter(FullMask,FullMask->GetLargestPossibleRegion()); > Iter.GoToBegin(); > > while(!Iter.IsAtEnd()) > { > itk::Index CurrentPoint=Iter.GetIndex(); > if(//There you test the index to know from which subimage it belong//) > { > Iter.Set(SubImage->GetPixel(CurrentPoint)); > } > ++Iter; > } > > HTH, > > Tim > > ----- Mail original ----- > De: "Alberto Bert" > ?: "ITK Users" > Envoy?: Mardi 26 Janvier 2016 11:07:49 > Objet: [ITK] [ITK-users] Merging segmentation masks in different region of interests > > Hi, > > I have several rectangular regions of interest from a single image (extracted using RegionOfInterestImageFilter), and I am processing one at a time to extract from each of them a segmentation masks (image of labels with 0 or 1). Finally, I would need to ?merge? (i.e. ?combine? or ?and?) the various ROI masks (different size and origin) in a single mask having the same size and origin of the original image. Let?s say I would need to ?put back in the right place? the ROI masks. > > The AndImageFilter does not allow me to combine the various ROI masks ("Inputs do not occupy the same physical space!?). I browsed the documentation but I could not find a viable solution... > > I am currently using SimpleITK. > > Can you help me please? > > Thanks a lot! > Best > Alberto > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Tue Jan 26 09:33:32 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Tue, 26 Jan 2016 09:33:32 -0500 Subject: [ITK-users] [ITK] Merging segmentation masks in different region of interests In-Reply-To: <2CD5E0E5-7B5E-44DD-B38C-843FD87F3E84@gmail.com> References: <1708259882.6072050.1453804281916.JavaMail.zimbra@enst.fr> <2CD5E0E5-7B5E-44DD-B38C-843FD87F3E84@gmail.com> Message-ID: Hello, In general You can not efficiently iterate on pixel on an Image in Python or another scripting language. There are however filters which can efficiently accomplish similar things. You should look into the ResampleImageFilter[1], and the PasteImageFilter[2]. The most logical way to is to use the ResampleImageFilters?s SetReferenceImage parameter. Use an image to represent the domain of the composite images you have ( or the original image). Then resample each segmentation on the reference image. Then you can use the AndImageFilter or overloaded operators to compose the images together. It?s also possible to convert your segmented images into LabelMaps, so that they are represented as run-length-encoded elements. This can be more efficient for some operations, but it?s a bit more tricky. HTH, Brad [1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ResampleImageFilter.html [2] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1PasteImageFilter.html > On Jan 26, 2016, at 9:21 AM, Alberto Bert wrote: > > Thanks Tim, > > according to the documentation, RegionOfInterestImageFilter should do what you say, that is why I tried to used it. Unfortunately, it seems not to keep the original logical references... > > I am not sure I can efficiently do what you suggest with SimpleITK, but if it turns out to be the only way, I guess I will need to switch to the original ITK. I hoped there was a way to do it without a pixel by pixel copy? > > Any other suggestions? > > Thanks! > Alberto > >> On 26 Jan 2016, at 11:31, Timothee Evain > wrote: >> >> Hello Alberto, >> >> If I remember well, the RegionOfInterestImageFilter keeps the subparts in the same physical space, i.e. a same index will get you the same pixel/voxel in the ROI as in the original. So I would use an iterator to create your full mask image. Something like : >> >> itk::Image::Pointer FullMask=itk::Image::New(); >> FullMask->SetRegions(OriginalImage->GetLargestPossibleRegion()); >> FullMask->Allocate(); >> >> itk::ImageRegionIteratorWithIndex> Iter(FullMask,FullMask->GetLargestPossibleRegion()); >> Iter.GoToBegin(); >> >> while(!Iter.IsAtEnd()) >> { >> itk::Index CurrentPoint=Iter.GetIndex(); >> if(//There you test the index to know from which subimage it belong//) >> { >> Iter.Set(SubImage->GetPixel(CurrentPoint)); >> } >> ++Iter; >> } >> >> HTH, >> >> Tim >> >> ----- Mail original ----- >> De: "Alberto Bert" > >> ?: "ITK Users" > >> Envoy?: Mardi 26 Janvier 2016 11:07:49 >> Objet: [ITK] [ITK-users] Merging segmentation masks in different region of interests >> >> Hi, >> >> I have several rectangular regions of interest from a single image (extracted using RegionOfInterestImageFilter), and I am processing one at a time to extract from each of them a segmentation masks (image of labels with 0 or 1). Finally, I would need to ?merge? (i.e. ?combine? or ?and?) the various ROI masks (different size and origin) in a single mask having the same size and origin of the original image. Let?s say I would need to ?put back in the right place? the ROI masks. >> >> The AndImageFilter does not allow me to combine the various ROI masks ("Inputs do not occupy the same physical space!?). I browsed the documentation but I could not find a viable solution... >> >> I am currently using SimpleITK. >> >> Can you help me please? >> >> Thanks a lot! >> Best >> Alberto >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Jan 26 10:57:22 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 26 Jan 2016 10:57:22 -0500 Subject: [ITK-users] [ITK] Merging segmentation masks in different region of interests In-Reply-To: References: <1708259882.6072050.1453804281916.JavaMail.zimbra@enst.fr> <2CD5E0E5-7B5E-44DD-B38C-843FD87F3E84@gmail.com> Message-ID: Try PasteImageFilter: http://itk.org/Wiki/ITK/Examples/ImageProcessing/PasteImageFilter On Tue, Jan 26, 2016 at 9:33 AM, Bradley Lowekamp wrote: > Hello, > > In general You can not efficiently iterate on pixel on an Image in Python or > another scripting language. There are however filters which can efficiently > accomplish similar things. > > You should look into the ResampleImageFilter[1], and the > PasteImageFilter[2]. > > The most logical way to is to use the ResampleImageFilters?s > SetReferenceImage parameter. Use an image to represent the domain of the > composite images you have ( or the original image). Then resample each > segmentation on the reference image. Then you can use the AndImageFilter or > overloaded operators to compose the images together. > > It?s also possible to convert your segmented images into LabelMaps, so that > they are represented as run-length-encoded elements. This can be more > efficient for some operations, but it?s a bit more tricky. > > HTH, > Brad > > [1] > http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ResampleImageFilter.html > [2] > http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1PasteImageFilter.html > > On Jan 26, 2016, at 9:21 AM, Alberto Bert wrote: > > Thanks Tim, > > according to the documentation, RegionOfInterestImageFilter should do what > you say, that is why I tried to used it. Unfortunately, it seems not to keep > the original logical references... > > I am not sure I can efficiently do what you suggest with SimpleITK, but if > it turns out to be the only way, I guess I will need to switch to the > original ITK. I hoped there was a way to do it without a pixel by pixel > copy? > > Any other suggestions? > > Thanks! > Alberto > > On 26 Jan 2016, at 11:31, Timothee Evain > wrote: > > Hello Alberto, > > If I remember well, the RegionOfInterestImageFilter keeps the subparts in > the same physical space, i.e. a same index will get you the same pixel/voxel > in the ROI as in the original. So I would use an iterator to create your > full mask image. Something like : > > itk::Image::Pointer FullMask=itk::Image::New(); > FullMask->SetRegions(OriginalImage->GetLargestPossibleRegion()); > FullMask->Allocate(); > > itk::ImageRegionIteratorWithIndex> > Iter(FullMask,FullMask->GetLargestPossibleRegion()); > Iter.GoToBegin(); > > while(!Iter.IsAtEnd()) > { > itk::Index CurrentPoint=Iter.GetIndex(); > if(//There you test the index to know from which subimage it belong//) > { > Iter.Set(SubImage->GetPixel(CurrentPoint)); > } > ++Iter; > } > > HTH, > > Tim > > ----- Mail original ----- > De: "Alberto Bert" > ?: "ITK Users" > Envoy?: Mardi 26 Janvier 2016 11:07:49 > Objet: [ITK] [ITK-users] Merging segmentation masks in different region of > interests > > Hi, > > I have several rectangular regions of interest from a single image > (extracted using RegionOfInterestImageFilter), and I am processing one at a > time to extract from each of them a segmentation masks (image of labels with > 0 or 1). Finally, I would need to ?merge? (i.e. ?combine? or ?and?) the > various ROI masks (different size and origin) in a single mask having the > same size and origin of the original image. Let?s say I would need to ?put > back in the right place? the ROI masks. > > The AndImageFilter does not allow me to combine the various ROI masks > ("Inputs do not occupy the same physical space!?). I browsed the > documentation but I could not find a viable solution... > > I am currently using SimpleITK. > > Can you help me please? > > Thanks a lot! > Best > Alberto > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 > -- Unpaid intern in BillsBasement at noware dot com From gabrielgimenez85 at gmail.com Tue Jan 26 12:54:04 2016 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Tue, 26 Jan 2016 14:54:04 -0300 Subject: [ITK-users] VersorRigid3DTransform with other Optimizer Message-ID: Hi! how are you ? VersorRigid3DTransform, It can be used with other optimizer other than itkRegularStepGradientDescentOptimizerv4.h ? The method UpdateTransformParameters have code associated to approach GradientDescent...which it makes me think that can not be used with other optimizer. Thanks and regards, -- *Gabriel Alberto Gim?nez.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabrielgimenez85 at gmail.com Tue Jan 26 12:57:46 2016 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Tue, 26 Jan 2016 14:57:46 -0300 Subject: [ITK-users] Write a result image witout resampling In-Reply-To: References: Message-ID: Thanks D?enan Zuki?...., I changed the cast filter type to RescaleIntensityImageFilter and I got the expected result. Best Regards... 2016-01-10 16:22 GMT-03:00 D?enan Zuki? : > Hi Gabriel, > > you probably need to use interpolation method of a higher quality for the > final resampling, i.e. windowed sinc > > instead of linear > > . > > Regards, > D?enan > > On Fri, Jan 8, 2016 at 9:17 PM, Gabriel A. Gim?nez < > gabrielgimenez85 at gmail.com> wrote: > >> Hi everyone...how are you ? >> >> I'm going to point, to finish the registration process build the new >> transformed fixed image (based on the manual examples), but the quality of >> the generated image is degraded...how I can create a new image with the >> same quality as the original image? I just need to apply the transformation >> parameters. >> >> Regards and thanks in advance, >> >> -- >> *Gabriel Alberto Gim?nez.* >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -- *Gabriel Alberto Gim?nez.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Tue Jan 26 13:00:32 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Tue, 26 Jan 2016 13:00:32 -0500 Subject: [ITK-users] VersorRigid3DTransform with other Optimizer In-Reply-To: References: Message-ID: Hello, I don?t believe there are any programmatic obstacles preventing you from using other optimizers only the theoretical mathematics of trying to optimize the non-Eucldian versor space as a Euclidian space. HTH, Brad > On Jan 26, 2016, at 12:54 PM, Gabriel A. Gim?nez wrote: > > Hi! how are you ? > > VersorRigid3DTransform, It can be used with other optimizer other than itkRegularStepGradientDescentOptimizerv4.h ? > > The method UpdateTransformParameters have code associated to approach GradientDescent...which it makes me think that can not be used with other optimizer. > > Thanks and regards, > > > -- > Gabriel Alberto Gim?nez. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From bakkari.abdelkhalek at hotmail.fr Tue Jan 26 13:17:15 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Tue, 26 Jan 2016 19:17:15 +0100 Subject: [ITK-users] fatal error LNK1120: 33 unresolved externals Message-ID: Dear Insight-users, I tried to build my application using Visual Studio 2010. But, some errors appear during running. Creating library C:/Application_26_01_2016/Build/Release/main.lib and object C:/Application_26_01_2016/Build/Release/main.exp2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkResliceImageViewer * __cdecl vtkResliceImageViewer::New(void)" (__imp_?New at vtkResliceImageViewer@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkResliceImageViewer@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageLuminance * __cdecl vtkImageLuminance::New(void)" (__imp_?New at vtkImageLuminance@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkImageLuminance@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderWindow * __cdecl vtkRenderWindow::New(void)" (__imp_?New at vtkRenderWindow@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderWindow@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderer * __cdecl vtkRenderer::New(void)" (__imp_?New at vtkRenderer@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderer@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderWindowInteractor * __cdecl vtkRenderWindowInteractor::New(void)" (__imp_?New at vtkRenderWindowInteractor@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderWindowInteractor@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkSmartVolumeMapper * __cdecl vtkSmartVolumeMapper::New(void)" (__imp_?New at vtkSmartVolumeMapper@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkSmartVolumeMapper@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkVolumeProperty * __cdecl vtkVolumeProperty::New(void)" (__imp_?New at vtkVolumeProperty@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkVolumeProperty@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkVolume * __cdecl vtkVolume::New(void)" (__imp_?New at vtkVolume@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkVolume@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageViewer2 * __cdecl vtkImageViewer2::New(void)" (__imp_?New at vtkImageViewer2@@SAPAV1 at XZ) referenced in function "private: void __thiscall MainWindow::prepareImageViews(void)" (?prepareImageViews at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkSmartVolumeMapper::SetRequestedRenderModeToRayCast(void)" (__imp_?SetRequestedRenderModeToRayCast at vtkSmartVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkSmartVolumeMapper::SetRequestedRenderModeToRayCastAndTexture(void)" (__imp_?SetRequestedRenderModeToRayCastAndTexture at vtkSmartVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkRenderer::ResetCamera(void)" (__imp_?ResetCamera at vtkRenderer@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolume::SetProperty(class vtkVolumeProperty *)" (__imp_?SetProperty at vtkVolume@@QAEXPAVvtkVolumeProperty@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolume::SetMapper(class vtkAbstractVolumeMapper *)" (__imp_?SetMapper at vtkVolume@@QAEXPAVvtkAbstractVolumeMapper@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::SetColor(int,class vtkColorTransferFunction *)" (__imp_?SetColor at vtkVolumeProperty@@QAEXHPAVvtkColorTransferFunction@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::SetScalarOpacity(int,class vtkPiecewiseFunction *)" (__imp_?SetScalarOpacity at vtkVolumeProperty@@QAEXHPAVvtkPiecewiseFunction@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::ShadeOff(int)" (__imp_?ShadeOff at vtkVolumeProperty@@QAEXH at Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeMapper::SetBlendModeToComposite(void)" (__imp_?SetBlendModeToComposite at vtkVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkRenderWindowInteractor::SetRenderWindow(class vtkRenderWindow *)" (__imp_?SetRenderWindow at vtkRenderWindowInteractor@@QAEXPAVvtkRenderWindow@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void * __thiscall vtkImageExport::GetCallbackUserData(void)" (__imp_?GetCallbackUserData at vtkImageExport@@QAEPAXXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void * (__cdecl*__thiscall vtkImageExport::GetBufferPointerCallback(void)const )(void *)" (__imp_?GetBufferPointerCallback at vtkImageExport@@QBEP6APAXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int * (__cdecl*__thiscall vtkImageExport::GetDataExtentCallback(void)const )(void *)" (__imp_?GetDataExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetUpdateDataCallback(void)const )(void *)" (__imp_?GetUpdateDataCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetPropagateUpdateExtentCallback(void)const )(void *,int *)" (__imp_?GetPropagateUpdateExtentCallback at vtkImageExport@@QBEP6AXPAXPAH at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int (__cdecl*__thiscall vtkImageExport::GetNumberOfComponentsCallback(void)const )(void *)" (__imp_?GetNumberOfComponentsCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: char const * (__cdecl*__thiscall vtkImageExport::GetScalarTypeCallback(void)const )(void *)" (__imp_?GetScalarTypeCallback at vtkImageExport@@QBEP6APBDPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: double * (__cdecl*__thiscall vtkImageExport::GetOriginCallback(void)const )(void *)" (__imp_?GetOriginCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: double * (__cdecl*__thiscall vtkImageExport::GetSpacingCallback(void)const )(void *)" (__imp_?GetSpacingCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int * (__cdecl*__thiscall vtkImageExport::GetWholeExtentCallback(void)const )(void *)" (__imp_?GetWholeExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int (__cdecl*__thiscall vtkImageExport::GetPipelineModifiedCallback(void)const )(void *)" (__imp_?GetPipelineModifiedCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetUpdateInformationCallback(void)const )(void *)" (__imp_?GetUpdateInformationCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageExport * __cdecl vtkImageExport::New(void)" (__imp_?New at vtkImageExport@@SAPAV1 at XZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageImport * __cdecl vtkImageImport::New(void)" (__imp_?New at vtkImageImport@@SAPAV1 at XZ) referenced in function "protected: __thiscall itk::ImageToVTKImageFilter,3> >::ImageToVTKImageFilter,3> >(void)" (??0?$ImageToVTKImageFilter at V?$Image at V?$RGBPixel at E@itk@@$02 at itk@@@itk@@IAE at XZ)2>C:\Application_26_01_2016\Build\Release\main.exe : fatal error LNK1120: 33 unresolved externals2>2>Build FAILED. Please, help me to solve these problems. Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From chinander at gmail.com Tue Jan 26 13:25:06 2016 From: chinander at gmail.com (Mike Chinander) Date: Tue, 26 Jan 2016 12:25:06 -0600 Subject: [ITK-users] fatal error LNK1120: 33 unresolved externals In-Reply-To: References: Message-ID: Can you post your CMakeLists.txt file? On Tue, Jan 26, 2016 at 12:17 PM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > > Dear Insight-users, > > I tried to build my application using Visual Studio 2010. But, some errors > appear during running. > > Creating library C:/Application_26_01_2016/Build/Release/main.lib and > object C:/Application_26_01_2016/Build/Release/main.exp > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkResliceImageViewer * __cdecl > vtkResliceImageViewer::New(void)" (__imp_?New at vtkResliceImageViewer > @@SAPAV1 at XZ) referenced in function "public: static class > vtkSmartPointer __cdecl vtkSmartPointer vtkResliceImageViewer>::New(void)" (?New@ > ?$vtkSmartPointer at VvtkResliceImageViewer@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkImageLuminance * __cdecl > vtkImageLuminance::New(void)" (__imp_?New at vtkImageLuminance@@SAPAV1 at XZ) > referenced in function "public: static class vtkSmartPointer vtkImageLuminance> __cdecl vtkSmartPointer vtkImageLuminance>::New(void)" (?New@?$vtkSmartPointer at VvtkImageLuminance > @@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkRenderWindow * __cdecl > vtkRenderWindow::New(void)" (__imp_?New at vtkRenderWindow@@SAPAV1 at XZ) > referenced in function "public: static class vtkSmartPointer vtkRenderWindow> __cdecl vtkSmartPointer::New(void)" > (?New@?$vtkSmartPointer at VvtkRenderWindow@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkRenderer * __cdecl > vtkRenderer::New(void)" (__imp_?New at vtkRenderer@@SAPAV1 at XZ) referenced in > function "public: static class vtkSmartPointer __cdecl > vtkSmartPointer::New(void)" (?New@ > ?$vtkSmartPointer at VvtkRenderer@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkRenderWindowInteractor * > __cdecl vtkRenderWindowInteractor::New(void)" > (__imp_?New at vtkRenderWindowInteractor@@SAPAV1 at XZ) referenced in function > "public: static class vtkSmartPointer > __cdecl vtkSmartPointer::New(void)" (?New@ > ?$vtkSmartPointer at VvtkRenderWindowInteractor@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkSmartVolumeMapper * __cdecl > vtkSmartVolumeMapper::New(void)" (__imp_?New at vtkSmartVolumeMapper > @@SAPAV1 at XZ) referenced in function "public: static class > vtkSmartPointer __cdecl vtkSmartPointer vtkSmartVolumeMapper>::New(void)" (?New@ > ?$vtkSmartPointer at VvtkSmartVolumeMapper@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkVolumeProperty * __cdecl > vtkVolumeProperty::New(void)" (__imp_?New at vtkVolumeProperty@@SAPAV1 at XZ) > referenced in function "public: static class vtkSmartPointer vtkVolumeProperty> __cdecl vtkSmartPointer vtkVolumeProperty>::New(void)" (?New@?$vtkSmartPointer at VvtkVolumeProperty > @@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkVolume * __cdecl > vtkVolume::New(void)" (__imp_?New at vtkVolume@@SAPAV1 at XZ) referenced in > function "public: static class vtkSmartPointer __cdecl > vtkSmartPointer::New(void)" (?New@ > ?$vtkSmartPointer at VvtkVolume@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkImageViewer2 * __cdecl > vtkImageViewer2::New(void)" (__imp_?New at vtkImageViewer2@@SAPAV1 at XZ) > referenced in function "private: void __thiscall > MainWindow::prepareImageViews(void)" (?prepareImageViews at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkSmartVolumeMapper::SetRequestedRenderModeToRayCast(void)" > (__imp_?SetRequestedRenderModeToRayCast at vtkSmartVolumeMapper@@QAEXXZ) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkSmartVolumeMapper::SetRequestedRenderModeToRayCastAndTexture(void)" > (__imp_?SetRequestedRenderModeToRayCastAndTexture at vtkSmartVolumeMapper@@QAEXXZ) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkRenderer::ResetCamera(void)" (__imp_?ResetCamera at vtkRenderer@@QAEXXZ) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall vtkVolume::SetProperty(class > vtkVolumeProperty *)" (__imp_?SetProperty at vtkVolume > @@QAEXPAVvtkVolumeProperty@@@Z) referenced in function "private: void > __thiscall MainWindow::on_button_3d_clicked(void)" > (?on_button_3d_clicked at MainWindow@@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall vtkVolume::SetMapper(class > vtkAbstractVolumeMapper *)" (__imp_?SetMapper at vtkVolume > @@QAEXPAVvtkAbstractVolumeMapper@@@Z) referenced in function "private: > void __thiscall MainWindow::on_button_3d_clicked(void)" > (?on_button_3d_clicked at MainWindow@@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkVolumeProperty::SetColor(int,class vtkColorTransferFunction *)" > (__imp_?SetColor at vtkVolumeProperty@@QAEXHPAVvtkColorTransferFunction@@@Z) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkVolumeProperty::SetScalarOpacity(int,class vtkPiecewiseFunction *)" > (__imp_?SetScalarOpacity at vtkVolumeProperty@@QAEXHPAVvtkPiecewiseFunction@@@Z) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkVolumeProperty::ShadeOff(int)" (__imp_?ShadeOff at vtkVolumeProperty > @@QAEXH at Z) referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkVolumeMapper::SetBlendModeToComposite(void)" > (__imp_?SetBlendModeToComposite at vtkVolumeMapper@@QAEXXZ) referenced in > function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" > (?on_button_3d_clicked at MainWindow@@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkRenderWindowInteractor::SetRenderWindow(class vtkRenderWindow *)" > (__imp_?SetRenderWindow at vtkRenderWindowInteractor@@QAEXPAVvtkRenderWindow@@@Z) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void * __thiscall > vtkImageExport::GetCallbackUserData(void)" > (__imp_?GetCallbackUserData at vtkImageExport@@QAEPAXXZ) referenced in > function "protected: __thiscall itk::VTKImageToImageFilter itk::Image >::VTKImageToImageFilter > >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void * (__cdecl*__thiscall > vtkImageExport::GetBufferPointerCallback(void)const )(void *)" > (__imp_?GetBufferPointerCallback at vtkImageExport@@QBEP6APAXPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: int * (__cdecl*__thiscall > vtkImageExport::GetDataExtentCallback(void)const )(void *)" > (__imp_?GetDataExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void (__cdecl*__thiscall > vtkImageExport::GetUpdateDataCallback(void)const )(void *)" > (__imp_?GetUpdateDataCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) referenced > in function "protected: __thiscall itk::VTKImageToImageFilter itk::Image >::VTKImageToImageFilter > >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void (__cdecl*__thiscall > vtkImageExport::GetPropagateUpdateExtentCallback(void)const )(void *,int > *)" (__imp_?GetPropagateUpdateExtentCallback at vtkImageExport > @@QBEP6AXPAXPAH at ZXZ) referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: int (__cdecl*__thiscall > vtkImageExport::GetNumberOfComponentsCallback(void)const )(void *)" > (__imp_?GetNumberOfComponentsCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: char const * (__cdecl*__thiscall > vtkImageExport::GetScalarTypeCallback(void)const )(void *)" > (__imp_?GetScalarTypeCallback at vtkImageExport@@QBEP6APBDPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: double * (__cdecl*__thiscall > vtkImageExport::GetOriginCallback(void)const )(void *)" > (__imp_?GetOriginCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced in > function "protected: __thiscall itk::VTKImageToImageFilter itk::Image >::VTKImageToImageFilter > >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: double * (__cdecl*__thiscall > vtkImageExport::GetSpacingCallback(void)const )(void *)" > (__imp_?GetSpacingCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced > in function "protected: __thiscall itk::VTKImageToImageFilter itk::Image >::VTKImageToImageFilter > >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: int * (__cdecl*__thiscall > vtkImageExport::GetWholeExtentCallback(void)const )(void *)" > (__imp_?GetWholeExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: int (__cdecl*__thiscall > vtkImageExport::GetPipelineModifiedCallback(void)const )(void *)" > (__imp_?GetPipelineModifiedCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void (__cdecl*__thiscall > vtkImageExport::GetUpdateInformationCallback(void)const )(void *)" > (__imp_?GetUpdateInformationCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkImageExport * __cdecl > vtkImageExport::New(void)" (__imp_?New at vtkImageExport@@SAPAV1 at XZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkImageImport * __cdecl > vtkImageImport::New(void)" (__imp_?New at vtkImageImport@@SAPAV1 at XZ) > referenced in function "protected: __thiscall > itk::ImageToVTKImageFilter char>,3> >::ImageToVTKImageFilter itk::RGBPixel,3> >(void)" (??0?$ImageToVTKImageFilter at V > ?$Image at V?$RGBPixel at E@itk@@$02 at itk@@@itk@@IAE at XZ) > 2>C:\Application_26_01_2016\Build\Release\main.exe : fatal error LNK1120: > 33 unresolved externals > 2> > 2>Build FAILED. > > > > Please, help me to solve these problems. > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From bakkari.abdelkhalek at hotmail.fr Tue Jan 26 14:28:11 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Tue, 26 Jan 2016 20:28:11 +0100 Subject: [ITK-users] fatal error LNK1120: 33 unresolved externals In-Reply-To: References: , Message-ID: Date: Tue, 26 Jan 2016 12:25:06 -0600 From: chinander at gmail.com To: insight-users at itk.org Subject: Re: [ITK-users] fatal error LNK1120: 33 unresolved externals Can you post your CMakeLists.txt file? On Tue, Jan 26, 2016 at 12:17 PM, Abdelkhalek Bakkari wrote: Dear Insight-users, I tried to build my application using Visual Studio 2010. But, some errors appear during running. Creating library C:/Application_26_01_2016/Build/Release/main.lib and object C:/Application_26_01_2016/Build/Release/main.exp2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkResliceImageViewer * __cdecl vtkResliceImageViewer::New(void)" (__imp_?New at vtkResliceImageViewer@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkResliceImageViewer@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageLuminance * __cdecl vtkImageLuminance::New(void)" (__imp_?New at vtkImageLuminance@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkImageLuminance@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderWindow * __cdecl vtkRenderWindow::New(void)" (__imp_?New at vtkRenderWindow@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderWindow@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderer * __cdecl vtkRenderer::New(void)" (__imp_?New at vtkRenderer@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderer@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderWindowInteractor * __cdecl vtkRenderWindowInteractor::New(void)" (__imp_?New at vtkRenderWindowInteractor@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderWindowInteractor@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkSmartVolumeMapper * __cdecl vtkSmartVolumeMapper::New(void)" (__imp_?New at vtkSmartVolumeMapper@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkSmartVolumeMapper@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkVolumeProperty * __cdecl vtkVolumeProperty::New(void)" (__imp_?New at vtkVolumeProperty@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkVolumeProperty@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkVolume * __cdecl vtkVolume::New(void)" (__imp_?New at vtkVolume@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkVolume@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageViewer2 * __cdecl vtkImageViewer2::New(void)" (__imp_?New at vtkImageViewer2@@SAPAV1 at XZ) referenced in function "private: void __thiscall MainWindow::prepareImageViews(void)" (?prepareImageViews at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkSmartVolumeMapper::SetRequestedRenderModeToRayCast(void)" (__imp_?SetRequestedRenderModeToRayCast at vtkSmartVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkSmartVolumeMapper::SetRequestedRenderModeToRayCastAndTexture(void)" (__imp_?SetRequestedRenderModeToRayCastAndTexture at vtkSmartVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkRenderer::ResetCamera(void)" (__imp_?ResetCamera at vtkRenderer@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolume::SetProperty(class vtkVolumeProperty *)" (__imp_?SetProperty at vtkVolume@@QAEXPAVvtkVolumeProperty@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolume::SetMapper(class vtkAbstractVolumeMapper *)" (__imp_?SetMapper at vtkVolume@@QAEXPAVvtkAbstractVolumeMapper@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::SetColor(int,class vtkColorTransferFunction *)" (__imp_?SetColor at vtkVolumeProperty@@QAEXHPAVvtkColorTransferFunction@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::SetScalarOpacity(int,class vtkPiecewiseFunction *)" (__imp_?SetScalarOpacity at vtkVolumeProperty@@QAEXHPAVvtkPiecewiseFunction@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::ShadeOff(int)" (__imp_?ShadeOff at vtkVolumeProperty@@QAEXH at Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeMapper::SetBlendModeToComposite(void)" (__imp_?SetBlendModeToComposite at vtkVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkRenderWindowInteractor::SetRenderWindow(class vtkRenderWindow *)" (__imp_?SetRenderWindow at vtkRenderWindowInteractor@@QAEXPAVvtkRenderWindow@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void * __thiscall vtkImageExport::GetCallbackUserData(void)" (__imp_?GetCallbackUserData at vtkImageExport@@QAEPAXXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void * (__cdecl*__thiscall vtkImageExport::GetBufferPointerCallback(void)const )(void *)" (__imp_?GetBufferPointerCallback at vtkImageExport@@QBEP6APAXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int * (__cdecl*__thiscall vtkImageExport::GetDataExtentCallback(void)const )(void *)" (__imp_?GetDataExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetUpdateDataCallback(void)const )(void *)" (__imp_?GetUpdateDataCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetPropagateUpdateExtentCallback(void)const )(void *,int *)" (__imp_?GetPropagateUpdateExtentCallback at vtkImageExport@@QBEP6AXPAXPAH at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int (__cdecl*__thiscall vtkImageExport::GetNumberOfComponentsCallback(void)const )(void *)" (__imp_?GetNumberOfComponentsCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: char const * (__cdecl*__thiscall vtkImageExport::GetScalarTypeCallback(void)const )(void *)" (__imp_?GetScalarTypeCallback at vtkImageExport@@QBEP6APBDPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: double * (__cdecl*__thiscall vtkImageExport::GetOriginCallback(void)const )(void *)" (__imp_?GetOriginCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: double * (__cdecl*__thiscall vtkImageExport::GetSpacingCallback(void)const )(void *)" (__imp_?GetSpacingCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int * (__cdecl*__thiscall vtkImageExport::GetWholeExtentCallback(void)const )(void *)" (__imp_?GetWholeExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int (__cdecl*__thiscall vtkImageExport::GetPipelineModifiedCallback(void)const )(void *)" (__imp_?GetPipelineModifiedCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetUpdateInformationCallback(void)const )(void *)" (__imp_?GetUpdateInformationCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageExport * __cdecl vtkImageExport::New(void)" (__imp_?New at vtkImageExport@@SAPAV1 at XZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageImport * __cdecl vtkImageImport::New(void)" (__imp_?New at vtkImageImport@@SAPAV1 at XZ) referenced in function "protected: __thiscall itk::ImageToVTKImageFilter,3> >::ImageToVTKImageFilter,3> >(void)" (??0?$ImageToVTKImageFilter at V?$Image at V?$RGBPixel at E@itk@@$02 at itk@@@itk@@IAE at XZ)2>C:\Application_26_01_2016\Build\Release\main.exe : fatal error LNK1120: 33 unresolved externals2>2>Build FAILED. Please, help me to solve these problems. Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 -------------- An embedded and charset-unspecified text was scrubbed... Name: CmakeLists.txt URL: From dzenanz at gmail.com Tue Jan 26 17:21:47 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 26 Jan 2016 17:21:47 -0500 Subject: [ITK-users] fatal error LNK1120: 33 unresolved externals In-Reply-To: References: Message-ID: ?Hi Abdelkhalek, most of these errors are VTK related. Can you replace the following line in you CMakeLists.txt: TARGET_LINK_LIBRARIES( main ${QT_LIBRARIES} vtkGraphics vtkIO vtkCommon QVTK QVTKWidgetPlugin ${ITK_LIBRARIES}) with this: TARGET_LINK_LIBRARIES( main ${QT_LIBRARIES} ${VTK_LIBRARIES} ${ITK_LIBRARIES}) and report? HTH?, D?enan On Tue, Jan 26, 2016 at 2:28 PM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > > > > > ------------------------------ > Date: Tue, 26 Jan 2016 12:25:06 -0600 > From: chinander at gmail.com > To: insight-users at itk.org > Subject: Re: [ITK-users] fatal error LNK1120: 33 unresolved externals > > > Can you post your CMakeLists.txt file? > > On Tue, Jan 26, 2016 at 12:17 PM, Abdelkhalek Bakkari < > bakkari.abdelkhalek at hotmail.fr> wrote: > > > Dear Insight-users, > > I tried to build my application using Visual Studio 2010. But, some errors > appear during running. > > Creating library C:/Application_26_01_2016/Build/Release/main.lib and > object C:/Application_26_01_2016/Build/Release/main.exp > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkResliceImageViewer * __cdecl > vtkResliceImageViewer::New(void)" (__imp_?New at vtkResliceImageViewer > @@SAPAV1 at XZ) referenced in function "public: static class > vtkSmartPointer __cdecl vtkSmartPointer vtkResliceImageViewer>::New(void)" (?New@ > ?$vtkSmartPointer at VvtkResliceImageViewer@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkImageLuminance * __cdecl > vtkImageLuminance::New(void)" (__imp_?New at vtkImageLuminance@@SAPAV1 at XZ) > referenced in function "public: static class vtkSmartPointer vtkImageLuminance> __cdecl vtkSmartPointer vtkImageLuminance>::New(void)" (?New@?$vtkSmartPointer at VvtkImageLuminance > @@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkRenderWindow * __cdecl > vtkRenderWindow::New(void)" (__imp_?New at vtkRenderWindow@@SAPAV1 at XZ) > referenced in function "public: static class vtkSmartPointer vtkRenderWindow> __cdecl vtkSmartPointer::New(void)" > (?New@?$vtkSmartPointer at VvtkRenderWindow@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkRenderer * __cdecl > vtkRenderer::New(void)" (__imp_?New at vtkRenderer@@SAPAV1 at XZ) referenced in > function "public: static class vtkSmartPointer __cdecl > vtkSmartPointer::New(void)" (?New@ > ?$vtkSmartPointer at VvtkRenderer@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkRenderWindowInteractor * > __cdecl vtkRenderWindowInteractor::New(void)" > (__imp_?New at vtkRenderWindowInteractor@@SAPAV1 at XZ) referenced in function > "public: static class vtkSmartPointer > __cdecl vtkSmartPointer::New(void)" (?New@ > ?$vtkSmartPointer at VvtkRenderWindowInteractor@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkSmartVolumeMapper * __cdecl > vtkSmartVolumeMapper::New(void)" (__imp_?New at vtkSmartVolumeMapper > @@SAPAV1 at XZ) referenced in function "public: static class > vtkSmartPointer __cdecl vtkSmartPointer vtkSmartVolumeMapper>::New(void)" (?New@ > ?$vtkSmartPointer at VvtkSmartVolumeMapper@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkVolumeProperty * __cdecl > vtkVolumeProperty::New(void)" (__imp_?New at vtkVolumeProperty@@SAPAV1 at XZ) > referenced in function "public: static class vtkSmartPointer vtkVolumeProperty> __cdecl vtkSmartPointer vtkVolumeProperty>::New(void)" (?New@?$vtkSmartPointer at VvtkVolumeProperty > @@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkVolume * __cdecl > vtkVolume::New(void)" (__imp_?New at vtkVolume@@SAPAV1 at XZ) referenced in > function "public: static class vtkSmartPointer __cdecl > vtkSmartPointer::New(void)" (?New@ > ?$vtkSmartPointer at VvtkVolume@@@@SA?AV1 at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkImageViewer2 * __cdecl > vtkImageViewer2::New(void)" (__imp_?New at vtkImageViewer2@@SAPAV1 at XZ) > referenced in function "private: void __thiscall > MainWindow::prepareImageViews(void)" (?prepareImageViews at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkSmartVolumeMapper::SetRequestedRenderModeToRayCast(void)" > (__imp_?SetRequestedRenderModeToRayCast at vtkSmartVolumeMapper@@QAEXXZ) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkSmartVolumeMapper::SetRequestedRenderModeToRayCastAndTexture(void)" > (__imp_?SetRequestedRenderModeToRayCastAndTexture at vtkSmartVolumeMapper@@QAEXXZ) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkRenderer::ResetCamera(void)" (__imp_?ResetCamera at vtkRenderer@@QAEXXZ) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall vtkVolume::SetProperty(class > vtkVolumeProperty *)" (__imp_?SetProperty at vtkVolume > @@QAEXPAVvtkVolumeProperty@@@Z) referenced in function "private: void > __thiscall MainWindow::on_button_3d_clicked(void)" > (?on_button_3d_clicked at MainWindow@@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall vtkVolume::SetMapper(class > vtkAbstractVolumeMapper *)" (__imp_?SetMapper at vtkVolume > @@QAEXPAVvtkAbstractVolumeMapper@@@Z) referenced in function "private: > void __thiscall MainWindow::on_button_3d_clicked(void)" > (?on_button_3d_clicked at MainWindow@@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkVolumeProperty::SetColor(int,class vtkColorTransferFunction *)" > (__imp_?SetColor at vtkVolumeProperty@@QAEXHPAVvtkColorTransferFunction@@@Z) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkVolumeProperty::SetScalarOpacity(int,class vtkPiecewiseFunction *)" > (__imp_?SetScalarOpacity at vtkVolumeProperty@@QAEXHPAVvtkPiecewiseFunction@@@Z) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkVolumeProperty::ShadeOff(int)" (__imp_?ShadeOff at vtkVolumeProperty > @@QAEXH at Z) referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkVolumeMapper::SetBlendModeToComposite(void)" > (__imp_?SetBlendModeToComposite at vtkVolumeMapper@@QAEXXZ) referenced in > function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" > (?on_button_3d_clicked at MainWindow@@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void __thiscall > vtkRenderWindowInteractor::SetRenderWindow(class vtkRenderWindow *)" > (__imp_?SetRenderWindow at vtkRenderWindowInteractor@@QAEXPAVvtkRenderWindow@@@Z) > referenced in function "private: void __thiscall > MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow > @@AAEXXZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void * __thiscall > vtkImageExport::GetCallbackUserData(void)" > (__imp_?GetCallbackUserData at vtkImageExport@@QAEPAXXZ) referenced in > function "protected: __thiscall itk::VTKImageToImageFilter itk::Image >::VTKImageToImageFilter > >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void * (__cdecl*__thiscall > vtkImageExport::GetBufferPointerCallback(void)const )(void *)" > (__imp_?GetBufferPointerCallback at vtkImageExport@@QBEP6APAXPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: int * (__cdecl*__thiscall > vtkImageExport::GetDataExtentCallback(void)const )(void *)" > (__imp_?GetDataExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void (__cdecl*__thiscall > vtkImageExport::GetUpdateDataCallback(void)const )(void *)" > (__imp_?GetUpdateDataCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) referenced > in function "protected: __thiscall itk::VTKImageToImageFilter itk::Image >::VTKImageToImageFilter > >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void (__cdecl*__thiscall > vtkImageExport::GetPropagateUpdateExtentCallback(void)const )(void *,int > *)" (__imp_?GetPropagateUpdateExtentCallback at vtkImageExport > @@QBEP6AXPAXPAH at ZXZ) referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: int (__cdecl*__thiscall > vtkImageExport::GetNumberOfComponentsCallback(void)const )(void *)" > (__imp_?GetNumberOfComponentsCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: char const * (__cdecl*__thiscall > vtkImageExport::GetScalarTypeCallback(void)const )(void *)" > (__imp_?GetScalarTypeCallback at vtkImageExport@@QBEP6APBDPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: double * (__cdecl*__thiscall > vtkImageExport::GetOriginCallback(void)const )(void *)" > (__imp_?GetOriginCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced in > function "protected: __thiscall itk::VTKImageToImageFilter itk::Image >::VTKImageToImageFilter > >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: double * (__cdecl*__thiscall > vtkImageExport::GetSpacingCallback(void)const )(void *)" > (__imp_?GetSpacingCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced > in function "protected: __thiscall itk::VTKImageToImageFilter itk::Image >::VTKImageToImageFilter > >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: int * (__cdecl*__thiscall > vtkImageExport::GetWholeExtentCallback(void)const )(void *)" > (__imp_?GetWholeExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: int (__cdecl*__thiscall > vtkImageExport::GetPipelineModifiedCallback(void)const )(void *)" > (__imp_?GetPipelineModifiedCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: void (__cdecl*__thiscall > vtkImageExport::GetUpdateInformationCallback(void)const )(void *)" > (__imp_?GetUpdateInformationCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkImageExport * __cdecl > vtkImageExport::New(void)" (__imp_?New at vtkImageExport@@SAPAV1 at XZ) > referenced in function "protected: __thiscall > itk::VTKImageToImageFilter > >::VTKImageToImageFilter >(void)" > (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ) > 2>mainwindow.obj : error LNK2019: unresolved external symbol > "__declspec(dllimport) public: static class vtkImageImport * __cdecl > vtkImageImport::New(void)" (__imp_?New at vtkImageImport@@SAPAV1 at XZ) > referenced in function "protected: __thiscall > itk::ImageToVTKImageFilter char>,3> >::ImageToVTKImageFilter itk::RGBPixel,3> >(void)" (??0?$ImageToVTKImageFilter at V > ?$Image at V?$RGBPixel at E@itk@@$02 at itk@@@itk@@IAE at XZ) > 2>C:\Application_26_01_2016\Build\Release\main.exe : fatal error LNK1120: > 33 unresolved externals > 2> > 2>Build FAILED. > > > > Please, help me to solve these problems. > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From bakkari.abdelkhalek at hotmail.fr Tue Jan 26 19:45:33 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Wed, 27 Jan 2016 01:45:33 +0100 Subject: [ITK-users] fatal error LNK1120: 33 unresolved externals In-Reply-To: References: , , Message-ID: Thank you so much D?enan. Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland From: dzenanz at gmail.com Date: Tue, 26 Jan 2016 17:21:47 -0500 Subject: Re: [ITK-users] fatal error LNK1120: 33 unresolved externals To: bakkari.abdelkhalek at hotmail.fr CC: chinander at gmail.com; insight-users at itk.org ?Hi Abdelkhalek, most of these errors are VTK related. Can you replace the following line in you CMakeLists.txt:TARGET_LINK_LIBRARIES( main ${QT_LIBRARIES} vtkGraphics vtkIO vtkCommon QVTK QVTKWidgetPlugin ${ITK_LIBRARIES})with this:TARGET_LINK_LIBRARIES( main ${QT_LIBRARIES} ${VTK_LIBRARIES} ${ITK_LIBRARIES})and report? HTH?,D?enan On Tue, Jan 26, 2016 at 2:28 PM, Abdelkhalek Bakkari wrote: Date: Tue, 26 Jan 2016 12:25:06 -0600 From: chinander at gmail.com To: insight-users at itk.org Subject: Re: [ITK-users] fatal error LNK1120: 33 unresolved externals Can you post your CMakeLists.txt file? On Tue, Jan 26, 2016 at 12:17 PM, Abdelkhalek Bakkari wrote: Dear Insight-users, I tried to build my application using Visual Studio 2010. But, some errors appear during running. Creating library C:/Application_26_01_2016/Build/Release/main.lib and object C:/Application_26_01_2016/Build/Release/main.exp2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkResliceImageViewer * __cdecl vtkResliceImageViewer::New(void)" (__imp_?New at vtkResliceImageViewer@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkResliceImageViewer@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageLuminance * __cdecl vtkImageLuminance::New(void)" (__imp_?New at vtkImageLuminance@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkImageLuminance@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderWindow * __cdecl vtkRenderWindow::New(void)" (__imp_?New at vtkRenderWindow@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderWindow@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderer * __cdecl vtkRenderer::New(void)" (__imp_?New at vtkRenderer@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderer@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkRenderWindowInteractor * __cdecl vtkRenderWindowInteractor::New(void)" (__imp_?New at vtkRenderWindowInteractor@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkRenderWindowInteractor@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkSmartVolumeMapper * __cdecl vtkSmartVolumeMapper::New(void)" (__imp_?New at vtkSmartVolumeMapper@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkSmartVolumeMapper@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkVolumeProperty * __cdecl vtkVolumeProperty::New(void)" (__imp_?New at vtkVolumeProperty@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkVolumeProperty@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkVolume * __cdecl vtkVolume::New(void)" (__imp_?New at vtkVolume@@SAPAV1 at XZ) referenced in function "public: static class vtkSmartPointer __cdecl vtkSmartPointer::New(void)" (?New@?$vtkSmartPointer at VvtkVolume@@@@SA?AV1 at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageViewer2 * __cdecl vtkImageViewer2::New(void)" (__imp_?New at vtkImageViewer2@@SAPAV1 at XZ) referenced in function "private: void __thiscall MainWindow::prepareImageViews(void)" (?prepareImageViews at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkSmartVolumeMapper::SetRequestedRenderModeToRayCast(void)" (__imp_?SetRequestedRenderModeToRayCast at vtkSmartVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkSmartVolumeMapper::SetRequestedRenderModeToRayCastAndTexture(void)" (__imp_?SetRequestedRenderModeToRayCastAndTexture at vtkSmartVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkRenderer::ResetCamera(void)" (__imp_?ResetCamera at vtkRenderer@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolume::SetProperty(class vtkVolumeProperty *)" (__imp_?SetProperty at vtkVolume@@QAEXPAVvtkVolumeProperty@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolume::SetMapper(class vtkAbstractVolumeMapper *)" (__imp_?SetMapper at vtkVolume@@QAEXPAVvtkAbstractVolumeMapper@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::SetColor(int,class vtkColorTransferFunction *)" (__imp_?SetColor at vtkVolumeProperty@@QAEXHPAVvtkColorTransferFunction@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::SetScalarOpacity(int,class vtkPiecewiseFunction *)" (__imp_?SetScalarOpacity at vtkVolumeProperty@@QAEXHPAVvtkPiecewiseFunction@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeProperty::ShadeOff(int)" (__imp_?ShadeOff at vtkVolumeProperty@@QAEXH at Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkVolumeMapper::SetBlendModeToComposite(void)" (__imp_?SetBlendModeToComposite at vtkVolumeMapper@@QAEXXZ) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkRenderWindowInteractor::SetRenderWindow(class vtkRenderWindow *)" (__imp_?SetRenderWindow at vtkRenderWindowInteractor@@QAEXPAVvtkRenderWindow@@@Z) referenced in function "private: void __thiscall MainWindow::on_button_3d_clicked(void)" (?on_button_3d_clicked at MainWindow@@AAEXXZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void * __thiscall vtkImageExport::GetCallbackUserData(void)" (__imp_?GetCallbackUserData at vtkImageExport@@QAEPAXXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void * (__cdecl*__thiscall vtkImageExport::GetBufferPointerCallback(void)const )(void *)" (__imp_?GetBufferPointerCallback at vtkImageExport@@QBEP6APAXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int * (__cdecl*__thiscall vtkImageExport::GetDataExtentCallback(void)const )(void *)" (__imp_?GetDataExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetUpdateDataCallback(void)const )(void *)" (__imp_?GetUpdateDataCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetPropagateUpdateExtentCallback(void)const )(void *,int *)" (__imp_?GetPropagateUpdateExtentCallback at vtkImageExport@@QBEP6AXPAXPAH at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int (__cdecl*__thiscall vtkImageExport::GetNumberOfComponentsCallback(void)const )(void *)" (__imp_?GetNumberOfComponentsCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: char const * (__cdecl*__thiscall vtkImageExport::GetScalarTypeCallback(void)const )(void *)" (__imp_?GetScalarTypeCallback at vtkImageExport@@QBEP6APBDPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: double * (__cdecl*__thiscall vtkImageExport::GetOriginCallback(void)const )(void *)" (__imp_?GetOriginCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: double * (__cdecl*__thiscall vtkImageExport::GetSpacingCallback(void)const )(void *)" (__imp_?GetSpacingCallback at vtkImageExport@@QBEP6APANPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int * (__cdecl*__thiscall vtkImageExport::GetWholeExtentCallback(void)const )(void *)" (__imp_?GetWholeExtentCallback at vtkImageExport@@QBEP6APAHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int (__cdecl*__thiscall vtkImageExport::GetPipelineModifiedCallback(void)const )(void *)" (__imp_?GetPipelineModifiedCallback at vtkImageExport@@QBEP6AHPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void (__cdecl*__thiscall vtkImageExport::GetUpdateInformationCallback(void)const )(void *)" (__imp_?GetUpdateInformationCallback at vtkImageExport@@QBEP6AXPAX at ZXZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageExport * __cdecl vtkImageExport::New(void)" (__imp_?New at vtkImageExport@@SAPAV1 at XZ) referenced in function "protected: __thiscall itk::VTKImageToImageFilter >::VTKImageToImageFilter >(void)" (??0?$VTKImageToImageFilter at V?$Image at F$02 at itk@@@itk@@IAE at XZ)2>mainwindow.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class vtkImageImport * __cdecl vtkImageImport::New(void)" (__imp_?New at vtkImageImport@@SAPAV1 at XZ) referenced in function "protected: __thiscall itk::ImageToVTKImageFilter,3> >::ImageToVTKImageFilter,3> >(void)" (??0?$ImageToVTKImageFilter at V?$Image at V?$RGBPixel at E@itk@@$02 at itk@@@itk@@IAE at XZ)2>C:\Application_26_01_2016\Build\Release\main.exe : fatal error LNK1120: 33 unresolved externals2>2>Build FAILED. Please, help me to solve these problems. Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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: From bert.alberto at gmail.com Wed Jan 27 03:51:57 2016 From: bert.alberto at gmail.com (Alberto Bert) Date: Wed, 27 Jan 2016 09:51:57 +0100 Subject: [ITK-users] [ITK] Merging segmentation masks in different region of interests In-Reply-To: References: <1708259882.6072050.1453804281916.JavaMail.zimbra@enst.fr> <2CD5E0E5-7B5E-44DD-B38C-843FD87F3E84@gmail.com> Message-ID: With the PasteImageFilter seems to be working. Thank you all ! Alberto > On 26 Jan 2016, at 16:57, Bill Lorensen wrote: > > Try PasteImageFilter: > http://itk.org/Wiki/ITK/Examples/ImageProcessing/PasteImageFilter > > > On Tue, Jan 26, 2016 at 9:33 AM, Bradley Lowekamp wrote: >> Hello, >> >> In general You can not efficiently iterate on pixel on an Image in Python or >> another scripting language. There are however filters which can efficiently >> accomplish similar things. >> >> You should look into the ResampleImageFilter[1], and the >> PasteImageFilter[2]. >> >> The most logical way to is to use the ResampleImageFilters?s >> SetReferenceImage parameter. Use an image to represent the domain of the >> composite images you have ( or the original image). Then resample each >> segmentation on the reference image. Then you can use the AndImageFilter or >> overloaded operators to compose the images together. >> >> It?s also possible to convert your segmented images into LabelMaps, so that >> they are represented as run-length-encoded elements. This can be more >> efficient for some operations, but it?s a bit more tricky. >> >> HTH, >> Brad >> >> [1] >> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ResampleImageFilter.html >> [2] >> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1PasteImageFilter.html >> >> On Jan 26, 2016, at 9:21 AM, Alberto Bert wrote: >> >> Thanks Tim, >> >> according to the documentation, RegionOfInterestImageFilter should do what >> you say, that is why I tried to used it. Unfortunately, it seems not to keep >> the original logical references... >> >> I am not sure I can efficiently do what you suggest with SimpleITK, but if >> it turns out to be the only way, I guess I will need to switch to the >> original ITK. I hoped there was a way to do it without a pixel by pixel >> copy? >> >> Any other suggestions? >> >> Thanks! >> Alberto >> >> On 26 Jan 2016, at 11:31, Timothee Evain >> wrote: >> >> Hello Alberto, >> >> If I remember well, the RegionOfInterestImageFilter keeps the subparts in >> the same physical space, i.e. a same index will get you the same pixel/voxel >> in the ROI as in the original. So I would use an iterator to create your >> full mask image. Something like : >> >> itk::Image::Pointer FullMask=itk::Image::New(); >> FullMask->SetRegions(OriginalImage->GetLargestPossibleRegion()); >> FullMask->Allocate(); >> >> itk::ImageRegionIteratorWithIndex> >> Iter(FullMask,FullMask->GetLargestPossibleRegion()); >> Iter.GoToBegin(); >> >> while(!Iter.IsAtEnd()) >> { >> itk::Index CurrentPoint=Iter.GetIndex(); >> if(//There you test the index to know from which subimage it belong//) >> { >> Iter.Set(SubImage->GetPixel(CurrentPoint)); >> } >> ++Iter; >> } >> >> HTH, >> >> Tim >> >> ----- Mail original ----- >> De: "Alberto Bert" >> ?: "ITK Users" >> Envoy?: Mardi 26 Janvier 2016 11:07:49 >> Objet: [ITK] [ITK-users] Merging segmentation masks in different region of >> interests >> >> Hi, >> >> I have several rectangular regions of interest from a single image >> (extracted using RegionOfInterestImageFilter), and I am processing one at a >> time to extract from each of them a segmentation masks (image of labels with >> 0 or 1). Finally, I would need to ?merge? (i.e. ?combine? or ?and?) the >> various ROI masks (different size and origin) in a single mask having the >> same size and origin of the original image. Let?s say I would need to ?put >> back in the right place? the ROI masks. >> >> The AndImageFilter does not allow me to combine the various ROI masks >> ("Inputs do not occupy the same physical space!?). I browsed the >> documentation but I could not find a viable solution... >> >> I am currently using SimpleITK. >> >> Can you help me please? >> >> Thanks a lot! >> Best >> Alberto >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 >> > > > > -- > Unpaid intern in BillsBasement at noware dot com From bakkari.abdelkhalek at hotmail.fr Wed Jan 27 04:57:53 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Wed, 27 Jan 2016 10:57:53 +0100 Subject: [ITK-users] GPU with ITK and VTK Message-ID: Dear Insight Users, I would like to speed up my algorithm using GPU with ITK and VTK. Any suggestion for this issue ? Thank you in advance, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Jan 27 08:47:57 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 27 Jan 2016 08:47:57 -0500 Subject: [ITK-users] GPU with ITK and VTK In-Reply-To: References: Message-ID: Hi Abdelkhalek, you might want to take a look at ITK GPU page. An example whose source code you could look at for reference: GPUGradientAnisotropicDiffusionImageFilter HTH, D?enan On Wed, Jan 27, 2016 at 4:57 AM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > > Dear Insight Users, > > I would like to speed up my algorithm using GPU with ITK and VTK. > Any suggestion for this issue ? > > Thank you in advance, > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From bert.alberto at gmail.com Thu Jan 28 05:30:09 2016 From: bert.alberto at gmail.com (Alberto Bert) Date: Thu, 28 Jan 2016 11:30:09 +0100 Subject: [ITK-users] LabelOverlayImageFilter with a binary mask: everything red Message-ID: <9C7FB885-87F2-4F63-BBA0-310D131AC3F2@gmail.com> Hi all, I am trying to produce a coloured overlay between a UInt16 grey-level image and a segmentation mask extracted from such image. The segmentation mask is a UInt8 image valued 1 in the segmented area and 0 elsewhere. If I try to: mask_overlay = sitk.LabelOverlay(image, mask, opacity = 0, backgroundValue = 0) # I am using SimpleITK 0.9.1 with Python 2.7 and then I write the mask_overlay (as .nii), I get an image almost completely reddish, while I expected to get the original grey-level image, with some red (or other color) corresponding only to the pixels valued 1 in the mask. (I did check the mask itself, and very few pixels are valued 1) What am I doing (or expecting) wrong? Thank you in advance, Best Alberto -------------- next part -------------- An HTML attachment was scrubbed... URL: From bert.alberto at gmail.com Thu Jan 28 06:51:02 2016 From: bert.alberto at gmail.com (Alberto Bert) Date: Thu, 28 Jan 2016 12:51:02 +0100 Subject: [ITK-users] LabelOverlayImageFilter with a binary mask: everything red In-Reply-To: <9C7FB885-87F2-4F63-BBA0-310D131AC3F2@gmail.com> References: <9C7FB885-87F2-4F63-BBA0-310D131AC3F2@gmail.com> Message-ID: <3B466288-BAC1-48A6-894B-3773ADCA04F3@gmail.com> Hi, a few updates... Instead of using .nii, I tried to save the output overlay image in: .png - the resulting image is in grey levels, but I cannot see any red (or other colors) .dcm - the resulting image looks corrupted both opened with imagej and Osirix Any ideas? Thanks Alberto > On 28 Jan 2016, at 11:30, Alberto Bert wrote: > > Hi all, > > I am trying to produce a coloured overlay between a UInt16 grey-level image and a segmentation mask extracted from such image. The segmentation mask is a UInt8 image valued 1 in the segmented area and 0 elsewhere. > > If I try to: > > mask_overlay = sitk.LabelOverlay(image, mask, opacity = 0, backgroundValue = 0) # I am using SimpleITK 0.9.1 with Python 2.7 > > and then I write the mask_overlay (as .nii), I get an image almost completely reddish, while I expected to get the original grey-level image, with some red (or other color) corresponding only to the pixels valued 1 in the mask. (I did check the mask itself, and very few pixels are valued 1) > > What am I doing (or expecting) wrong? > > Thank you in advance, > Best > Alberto -------------- next part -------------- An HTML attachment was scrubbed... URL: From bert.alberto at gmail.com Thu Jan 28 07:13:12 2016 From: bert.alberto at gmail.com (Alberto Bert) Date: Thu, 28 Jan 2016 13:13:12 +0100 Subject: [ITK-users] How to add two RGB images? Message-ID: <2D5836EB-AC9B-40A0-A424-94EBBEF9B1B3@gmail.com> Hi all, I have got an grey level image and a binary segmentation mask extracted from it, and I would like to produce a third image, showing the segmented area in color on top the original grey level image. Here is what I am doing: image_rgb = sitk.ScalarToRGBColormap(image, colormap = sitk.ScalarToRGBColormapImageFilter.Grey) mask_rgb = sitk.ScalarToRGBColormap(mask, colormap = sitk.ScalarToRGBColormapImageFilter.Red) mask_overlay = image_rgb + mask_rgb Unfortunately, mask_overlay looks just the same as image_rgb, as the addition were not doing any action. Any help will be appreciated, Thanks, Alberto PS I am using SimpleITK 0.9.1 and Python 2.7 PPS I have already tried the LabelOverlayImageFilter. In fact that was my first choice, but I cannot make it working either (see my previous email, please). From bert.alberto at gmail.com Thu Jan 28 08:07:45 2016 From: bert.alberto at gmail.com (Alberto Bert) Date: Thu, 28 Jan 2016 14:07:45 +0100 Subject: [ITK-users] How to add two RGB images? In-Reply-To: <2D5836EB-AC9B-40A0-A424-94EBBEF9B1B3@gmail.com> References: <2D5836EB-AC9B-40A0-A424-94EBBEF9B1B3@gmail.com> Message-ID: Hi, I understood why it wasn?t working. It was an overflow problem of the red channel. Sorry for bothering. Alb > On 28 Jan 2016, at 13:13, Alberto Bert wrote: > > Hi all, > > I have got an grey level image and a binary segmentation mask extracted from it, and I would like to produce a third image, showing the segmented area in color on top the original grey level image. > > Here is what I am doing: > > image_rgb = sitk.ScalarToRGBColormap(image, colormap = sitk.ScalarToRGBColormapImageFilter.Grey) > mask_rgb = sitk.ScalarToRGBColormap(mask, colormap = sitk.ScalarToRGBColormapImageFilter.Red) > mask_overlay = image_rgb + mask_rgb > > Unfortunately, mask_overlay looks just the same as image_rgb, as the addition were not doing any action. > > Any help will be appreciated, > Thanks, > > Alberto > > PS > I am using SimpleITK 0.9.1 and Python 2.7 > > PPS > I have already tried the LabelOverlayImageFilter. In fact that was my first choice, but I cannot make it working either (see my previous email, please). From blowekamp at mail.nih.gov Thu Jan 28 09:13:40 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 28 Jan 2016 09:13:40 -0500 Subject: [ITK-users] LabelOverlayImageFilter with a binary mask: everything red In-Reply-To: <3B466288-BAC1-48A6-894B-3773ADCA04F3@gmail.com> References: <9C7FB885-87F2-4F63-BBA0-310D131AC3F2@gmail.com> <3B466288-BAC1-48A6-894B-3773ADCA04F3@gmail.com> Message-ID: <214E8D88-987D-4AA1-B52A-CE33968BDB3D@mail.nih.gov> Hello, There two potential issues here you need to isolate. The first: Is the filter behaving the way you expect? And the second: Is the image being written correctly? also related is: Does the view support the file type you created? Start by inspecting the pixel values of output image. Also keep in mind that many gray scale viewers apply window and leveling, while RGB viewers don?t. So you may need to scale the intensity of you gray scale image before apply the LabelOverlay filter. HTH, Brad > On Jan 28, 2016, at 6:51 AM, Alberto Bert wrote: > > Hi, > > a few updates... > > Instead of using .nii, I tried to save the output overlay image in: > .png - the resulting image is in grey levels, but I cannot see any red (or other colors) > .dcm - the resulting image looks corrupted both opened with imagej and Osirix > > Any ideas? > > Thanks > Alberto > >> On 28 Jan 2016, at 11:30, Alberto Bert > wrote: >> >> Hi all, >> >> I am trying to produce a coloured overlay between a UInt16 grey-level image and a segmentation mask extracted from such image. The segmentation mask is a UInt8 image valued 1 in the segmented area and 0 elsewhere. >> >> If I try to: >> >> mask_overlay = sitk.LabelOverlay(image, mask, opacity = 0, backgroundValue = 0) # I am using SimpleITK 0.9.1 with Python 2.7 >> >> and then I write the mask_overlay (as .nii), I get an image almost completely reddish, while I expected to get the original grey-level image, with some red (or other color) corresponding only to the pixels valued 1 in the mask. (I did check the mask itself, and very few pixels are valued 1) >> >> What am I doing (or expecting) wrong? >> >> Thank you in advance, >> Best >> Alberto > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: From zivrafael.yaniv at nih.gov Thu Jan 28 15:55:23 2016 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Thu, 28 Jan 2016 20:55:23 +0000 Subject: [ITK-users] Pill Image Recognition Challenge Message-ID: Dear ITK community, As developers of image analysis algorithms I belive the following NLM sponsored challenge may be of interest to you: Pill Image Recognition Challenge (http://pir.nlm.nih.gov/challenge) In this Challenge, the National Library of Medicine at the U.S. National Institutes of Health invites individuals and teams to submit algorithms and software for pill image recognition. The submissions are to rank images taken from NLM's RxIMAGE database of high-quality prescription pill images by similarity to consumer-quality images of the same pills. NLM plans to use the submissions in creating a future software system and a future Application Programming Interface (API) that can be used in identifying an unknown prescription pill from a photo taken of that pill by a smart phone. Prizes: 1st place: $25,000 2nd place: $15,000 3rd place: $5,000 Honorable mentions (2): $2,500 The submission period for the Challenge is April 4, 2016 to May 31, 2016, with winners to be announced August 1, 2016. Parties wishing to participate in the Challenge are provided with a training data set. The Challenge will be judged by calculating mean average precision (MAP) on a similar judging data set. The eligible submission with the highest MAP score will be recommended as the first place winner, with the second, third, fourth, and fifth best MAPs, respectively being recommended to earn second place, third place, and two honorable mentions. best regards Ziv -------------- next part -------------- An HTML attachment was scrubbed... URL: From bakkari.abdelkhalek at hotmail.fr Thu Jan 28 16:58:03 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Thu, 28 Jan 2016 22:58:03 +0100 Subject: [ITK-users] itk::ERROR: VarianceImageFilter(060CFF60): Message-ID: Hi ! I tried to adopt the itkImageVarianceFilter into my code. But, an error appears during execution : " Exception detected: itk::ERROR: MultiThreader(060E4078): Exception occurred during SingleMethodExecutec:\itk 4.8.1\source\modules\core\common\include\itkImageSource.hxx:279:itk::ERROR: VarianceImageFilter(060CFF60): Subclass should override this method!!!The signature of ThreadedGenerateData() has been changed in ITK v4 to use the new ThreadIdType. " Any help, please! Best regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Jan 28 17:07:35 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 28 Jan 2016 17:07:35 -0500 Subject: [ITK-users] itk::ERROR: VarianceImageFilter(060CFF60): In-Reply-To: References: Message-ID: Hi, > The signature of ThreadedGenerateData() has been changed in ITK v4 to use the ne w ThreadIdType. " This means the type of the arguments to method have to be changed as directed. HTH, Matt On Thu, Jan 28, 2016 at 4:58 PM, Abdelkhalek Bakkari wrote: > > > Hi ! > > I tried to adopt the itkImageVarianceFilter into my code. But, an error > appears during execution : > > " Exception detected: itk::ERROR: MultiThreader(060E4078): Exception > occurred duri > ng SingleMethodExecute > c:\itk 4.8.1\source\modules\core\common\include\itkImageSource.hxx:279: > itk::ERROR: VarianceImageFilter(060CFF60): Subclass should override this > method! > !! > The signature of ThreadedGenerateData() has been changed in ITK v4 to use > the ne > w ThreadIdType. " > > Any help, please! > > Best regards, > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Jan 29 11:22:24 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 29 Jan 2016 11:22:24 -0500 Subject: [ITK-users] http support on midas3.kitware.com Message-ID: Hi folks, The server that hosts ITK data -- midas3.kitware.com now only supports https, and does not support downloading via the http protocol. This may result in build errors like: error: downloading 'http://midas3.kitware.com/midas/download/bitstream/457653/castxml-linux.tar.gz' failed status_code: 1 status_string: "Unsupported protocol" log: Trying 192.168.120.111... Connected to midas3.kitware.com (192.168.120.111) port 80 (#0) To address this error, the CMake client needs OpenSSL support. Newer binaries from cmake.org have this support. When building from source, this is not enabled by default -- enable the configuration option CMAKE_USE_OPENSSL. Matt