From dzenanz at gmail.com Mon Aug 1 09:38:18 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 1 Aug 2016 09:38:18 -0400 Subject: [ITK-users] ITK wrapping with VS2013 Message-ID: Hi Brad and everybody, I am trying to build ITK with Ultrasound module, FFTW and wrapping for Python. This builds without errors on Linux, but on Windows I run into issues: 165> Building Custom Rule C:/Libs/InsightToolkit-4.10.0/Modules/External/ITKUltrasound/wrapping/CMakeLists.txt ... 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(706): warning 401: Nothing known about base class 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex2 > >'. Ignored. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(706): warning 401: Maybe you forgot to instantiate 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex2 > >' using %template. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(776): warning 401: Nothing known about base class 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex3 > >'. Ignored. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(776): warning 401: Maybe you forgot to instantiate 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex3 > >' using %template. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(720): warning 476: Initialization using std::initializer_list. ... 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(793): warning 476: Initialization using std::initializer_list. 165>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(170,5): error MSB6006: "cmd.exe" exited with code 28. The same error happens with ITK 4.10.0 and ITK git from 10 days ago. Can someone shed some light on the error and how to fix it? Regards, D?enan -------------- next part -------------- An HTML attachment was scrubbed... URL: From anton.delehony at gmail.com Fri Aug 5 09:40:53 2016 From: anton.delehony at gmail.com (Anton Delehony) Date: Fri, 5 Aug 2016 09:40:53 -0400 Subject: [ITK-users] simpleitk question C# Message-ID: Hi all, I'm a new to C# and simple itk and have a very simple question. in the ImageRegistrationMethodBSpline1.cxx there is the line: std::vector transfromDomainMeshSize(fixed.GetDimension(),8); What is the equivlent line to this in C#? thanks, Anton -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Fri Aug 5 10:05:44 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 5 Aug 2016 10:05:44 -0400 Subject: [ITK-users] simpleitk question C# In-Reply-To: References: Message-ID: Hi Anton, I don't know C#'s syntax that well to give you direct translation, but here is another way to write the same C++ code which should be easier to translate: std::vector transfromDomainMeshSize; //C# eqivalent: unsigned int[] transfromDomainMeshSize; transfromDomainMeshSize.resize(8); //my stab in C#: transfromDomainMeshSize=new unsigned int[8]; for (int i=0; i<8; i++) transfromDomainMeshSize[i]=fixed.GetDimension(); HTH, D?enan On Fri, Aug 5, 2016 at 9:40 AM, Anton Delehony wrote: > Hi all, > > I'm a new to C# and simple itk and have a very simple question. > > in the ImageRegistrationMethodBSpline1.cxx there is the line: > > std::vector transfromDomainMeshSize(fixed.GetDimension(),8); > > What is the equivlent line to this in C#? > > thanks, > > Anton > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 brad at lowekamp.net Fri Aug 5 22:06:24 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Fri, 5 Aug 2016 22:06:24 -0400 Subject: [ITK-users] simpleitk question C# In-Reply-To: References: Message-ID: Hi This suggestion has the arguments backwards: http://en.cppreference.com/w/cpp/container/vector/vector This line creates an std::vector of Dimension size and fills it with the value of 8. You can use the for loop to fill the array as suggested or use an array initializer if the array size is fixed. HTH Brad > On Aug 5, 2016, at 10:05 AM, D?enan Zuki? wrote: > > Hi Anton, > > I don't know C#'s syntax that well to give you direct translation, but here is another way to write the same C++ code which should be easier to translate: > > std::vector transfromDomainMeshSize; > //C# eqivalent: unsigned int[] transfromDomainMeshSize; > transfromDomainMeshSize.resize(8); > //my stab in C#: transfromDomainMeshSize=new unsigned int[8]; > for (int i=0; i<8; i++) > transfromDomainMeshSize[i]=fixed.GetDimension(); > > HTH, > D?enan > >> On Fri, Aug 5, 2016 at 9:40 AM, Anton Delehony wrote: >> Hi all, >> >> I'm a new to C# and simple itk and have a very simple question. >> >> in the ImageRegistrationMethodBSpline1.cxx there is the line: >> >> std::vector transfromDomainMeshSize(fixed.GetDimension(),8); >> >> What is the equivlent line to this in C#? >> >> thanks, >> >> Anton >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 Sat Aug 6 02:35:46 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Sat, 6 Aug 2016 07:35:46 +0100 Subject: [ITK-users] FW: [ITK] Manual 3d image segmentation using itk In-Reply-To: References: , Message-ID: Hi, I would like to ask about the functions that may be used with ITK-SNAP for the manual segmentation. Thank you in advance. Kind regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland From: matt.mccormick at kitware.com Date: Wed, 6 Jul 2016 11:42:51 -0400 Subject: Re: [ITK] Manual 3d image segmentation using itk To: bakkari.abdelkhalek at hotmail.fr CC: insight-users at itk.org; community at itk.org Hi, You may want to investigate the open source, ITK-based ITK-SNAP project, which has similiar functionality. HTH, Matt On Wed, Jul 6, 2016 at 11:11 AM, Abdelkhalek Bakkari wrote: Hi, I would like to ask if you could help me with a code source related to Manual interactive 3d image segmentation using itk as described in the video below : https://www.youtube.com/watch?v=7wCC2NaVLjs Thank you in advance. Best regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Virus-free. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Aug 8 09:15:25 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 8 Aug 2016 09:15:25 -0400 Subject: [ITK-users] [ITK] FW: Manual 3d image segmentation using itk In-Reply-To: References: Message-ID: Hi Abdelkhalek, the manual does a pretty good job of explaining the built-in functions. It is also very graphical. Regards, D?enan On Sat, Aug 6, 2016 at 2:35 AM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > Hi, > > I would like to ask about the functions that may be used with ITK-SNAP for > the manual segmentation. > > Thank you in advance. > > Kind regards, > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > > ------------------------------ > From: matt.mccormick at kitware.com > Date: Wed, 6 Jul 2016 11:42:51 -0400 > Subject: Re: [ITK] Manual 3d image segmentation using itk > To: bakkari.abdelkhalek at hotmail.fr > CC: insight-users at itk.org; community at itk.org > > > Hi, > > You may want to investigate the open source, ITK-based ITK-SNAP project, > which has similiar functionality. > > HTH, > Matt > > On Wed, Jul 6, 2016 at 11:11 AM, Abdelkhalek Bakkari < > bakkari.abdelkhalek at hotmail.fr> wrote: > > Hi, > > I would like to ask if you could help me with a code source related > to Manual interactive 3d image segmentation using itk as described in the > video below : > https://www.youtube.com/watch?v=7wCC2NaVLjs > > Thank you in advance. > > Best regards, > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > Virus-free. > www.avast.com > > <#m_4781774733812301522_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.giord at gmail.com Wed Aug 17 10:26:20 2016 From: marco.giord at gmail.com (marco giordano) Date: Wed, 17 Aug 2016 16:26:20 +0200 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild Message-ID: Hi there, I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this: -- Fetching " http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 " -- [download 100% complete] -- Fetching " https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 " -- Fetching " https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") Call Stack (most recent call first): /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object) make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1 make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 Any help is welcome. Regards -- Marco -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Aug 17 10:48:59 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Aug 2016 10:48:59 -0400 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hi Marco, Your CMake needs HTTPS support. The binaries from cmake.org have this enabled or set CMAKE_USE_OPENSSL in CMake's build configuration. HTH, Matt On Wed, Aug 17, 2016 at 10:26 AM, marco giordano wrote: > Hi there, > > I just downloaded SimpleTK and I tried to build it on a linux cluster > (running Scientific Linux release 6.5- Carbon) using the superbuild. > > I use cmake 3.3.1. The Generation of build files is fine, then when I try to > build i get this: > > -- Fetching > "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- [download 100% complete] > -- Fetching > "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- Fetching > "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" > CMake Error at > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 > (message): > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > ("Unsupported protocol") > > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 > ("Unsupported protocol") > Call Stack (most recent call first): > > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 > (_ExternalData_download_object) > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error > 1 > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > Any help is welcome. > Regards > -- > Marco > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From blowekamp at mail.nih.gov Wed Aug 17 10:51:52 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 17 Aug 2016 14:51:52 +0000 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hello! OK, so it looks like you are using the current master branch of SimpleITK. I know this because you have the latest SimpleITK feature where CMake downloads the Superbuild dependencies with the CMake ?ExternalData? module. This enables some interesting options for your situation. You are on a cluster. On compute clusters, frequently the nodes don?t have access to the internet. So when cmake tries to download the URLS below it times out or errors. You can verify this with some command like ?wget https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. The alternative is that your version of CMake doesn?t support HTTPS. Yo can test this with the following script: https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake Frequently, there are nodes on a cluster which have access to the internet for situations like this. You may be able to just use one of them. With the new ExternalData download module you may be able to pre-download these dependencies on the log in node. If you set the environment variable ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache downloads to this directory. I assume your home directory is available on the log in nodes. You can configure the SuperBuild there and build just the ?SuperBuildSimpleITKSource? target. This will download the dependencies to the ExternaData directory. Then you can build in a cluster node, which should use this cache. Also note when testing is enabled for the actual SimpleITK sub-project, a bunch of testing data is downloaded too. You can disable testing to avoid this, download and un-tar a Data archive [1], or replace the above procedure for this subproject. HTH, Brad [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Source/ > On Aug 17, 2016, at 10:26 AM, marco giordano wrote: > > Hi there, > > I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. > > I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this: > > -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- [download 100% complete] > -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- Fetching "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" > CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") > Call Stack (most recent call first): > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object) > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1 > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > Any help is welcome. > Regards > -- > Marco > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 aharr8 at uwo.ca Wed Aug 17 14:52:08 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Wed, 17 Aug 2016 14:52:08 -0400 Subject: [ITK-users] [ITK] CorrelationImageToImageMetricv4 returns with very low correlation values Message-ID: Hello, I am attempting to register two 3D images using the CorrelationImageToImageMetricv4, the LBFGSBOptimizer, and a 3DVersorRigidRegistration. Even if I put the same volumes in to the registration for both the fixed and moving image, I get a very low value for correlation. One thought I had was I might be setting the origins incorrectly, as previously in the project the origin was defined as the centre of the image cubes and I have attempted to stay with that convention, and I haven?t found an example in the ITK examples where the origin is set to something other than 0. The other issue might be that the original data is a char array so I had to create a cast filter to change the image to floats, and the origins might be getting confused between the two. If anyone has any thoughts they would be welcome, I can provide source code if that would be helpful. -- AH ----------------------------------------------------------------------------------------------- *This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Aug 17 15:08:52 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 17 Aug 2016 19:08:52 +0000 Subject: [ITK-users] [ITK] CorrelationImageToImageMetricv4 returns with very low correlation values In-Reply-To: References: Message-ID: <1269FEDC-93AE-4349-A5EB-E4021AFAB399@mail.nih.gov> Hello, You seem to need a way to interactively explore your program, images and registration setup. All ITK registration metrics are designed to be minimized. So the correlations are negative if I recall correctly. You may want to look into Slicer3D (https://www.slicer.org) for a image visualizer which is aware of ITK?s image geometry. You also may want to look into using an interactive programing environment such as Python to better understand the image geometry and the properties of what you are trying to setup. You may find the SimpleITK Notebooks on Image Registration useful: http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/ HTH, Brad On Aug 17, 2016, at 2:52 PM, Andrew Harris > wrote: Hello, I am attempting to register two 3D images using the CorrelationImageToImageMetricv4, the LBFGSBOptimizer, and a 3DVersorRigidRegistration. Even if I put the same volumes in to the registration for both the fixed and moving image, I get a very low value for correlation. One thought I had was I might be setting the origins incorrectly, as previously in the project the origin was defined as the centre of the image cubes and I have attempted to stay with that convention, and I haven?t found an example in the ITK examples where the origin is set to something other than 0. The other issue might be that the original data is a char array so I had to create a cast filter to change the image to floats, and the origins might be getting confused between the two. If anyone has any thoughts they would be welcome, I can provide source code if that would be helpful. -- AH ----------------------------------------------------------------------------------------------- This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 marco.giord at gmail.com Thu Aug 18 05:37:57 2016 From: marco.giord at gmail.com (marco giordano) Date: Thu, 18 Aug 2016 11:37:57 +0200 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hi there, I checked the internet connection on the node and seems fine (I can download with wget the https://midas3.kitware.com/ midas/api/rest?method=midas.bitstream.download&checksum= 2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?). I run the script SSLTest.cmake but it fails (it downloads a LICENSE file but it is empty): CMake Error at SSLTest.cmake:5 (file): file DOWNLOAD HASH mismatch for file: [/home/mgiordano/code/SimpleITK/LICENSE] expected hash: [f8c925402b90f74566f71e64eea7bb9d83daac69cde71408ffd6c043be6a4991] actual hash: [e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855] status: [1;"Unsupported protocol"] So I assume the HTTPS is not supported. Now if I understand correctly the alternative is to download the modules manually in $HOME/ExternalData and point to that folder through the variable ExternalData_OBJECT_STORES. The question is what do I need to download, is that the only the two links above or there is more ? Is it maybe an option to change version of Cmake that can support that or/and how do I enable the support ? Any help is appreciated. Regards, Marco 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov>: > Hello! > > OK, so it looks like you are using the current master branch of SimpleITK. > I know this because you have the latest SimpleITK feature where CMake > downloads the Superbuild dependencies with the CMake ?ExternalData? module. > This enables some interesting options for your situation. > > You are on a cluster. On compute clusters, frequently the nodes don?t have > access to the internet. So when cmake tries to download the URLS below it > times out or errors. You can verify this with some command like ?wget > https://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. > The alternative is that your version of CMake doesn?t support HTTPS. Yo can > test this with the following script: https://github.com/conda- > forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake > > Frequently, there are nodes on a cluster which have access to the internet > for situations like this. You may be able to just use one of them. > > With the new ExternalData download module you may be able to pre-download > these dependencies on the log in node. If you set the environment variable > ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache > downloads to this directory. I assume your home directory is available on > the log in nodes. You can configure the SuperBuild there and build just the > ?SuperBuildSimpleITKSource? target. This will download the dependencies to > the ExternaData directory. Then you can build in a cluster node, which > should use this cache. > > Also note when testing is enabled for the actual SimpleITK sub-project, a > bunch of testing data is downloaded too. You can disable testing to avoid > this, download and un-tar a Data archive [1], or replace the above > procedure for this subproject. > > HTH, > Brad > > [1] https://sourceforge.net/projects/simpleitk/files/ > SimpleITK/0.10.0/Source/ > > > > On Aug 17, 2016, at 10:26 AM, marco giordano > wrote: > > > > Hi there, > > > > I just downloaded SimpleTK and I tried to build it on a linux cluster > (running Scientific Linux release 6.5- Carbon) using the superbuild. > > > > I use cmake 3.3.1. The Generation of build files is fine, then when I > try to build i get this: > > > > -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > " > > -- [download 100% complete] > > -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > " > > -- Fetching "https://itk.org/files/ExternalData/MD5/ > 2e115fe26e435e33b0d5c022e4490567" > > CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/ > Modules/ExternalData.cmake:1012 (message): > > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > > > http://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > ("Unsupported protocol") > > https://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > ("Unsupported protocol") > > https://itk.org/files/ExternalData/MD5/ > 2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") > > Call Stack (most recent call first): > > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/ > Modules/ExternalData.cmake:1034 (_ExternalData_download_object) > > > > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] > Error 1 > > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > > > Any help is welcome. > > Regards > > -- > > Marco > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > -- Marco Giordano SKYPE:marcogiord81 -------------- next part -------------- An HTML attachment was scrubbed... URL: From richard.beare at gmail.com Thu Aug 18 06:14:43 2016 From: richard.beare at gmail.com (Richard Beare) Date: Thu, 18 Aug 2016 20:14:43 +1000 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: A related problem, which I've never found a solution for, is that some cluster software (probably the curl library) is built without ssl support at a critical point. You may have the same issue. Maybe the configuration info for curl will tell you one way or another whether this is the case and you can request a reinstall. On Thu, Aug 18, 2016 at 7:37 PM, marco giordano wrote: > Hi there, > I checked the internet connection on the node and seems fine (I can > download with wget the https://midas3.kitware.com/mid > as/api/rest?method=midas.bitstream.download&checksum=2e115fe > 26e435e33b0d5c022e4490567&algorithm=MD5?). > > I run the script SSLTest.cmake > > but it fails (it downloads a LICENSE file but it is empty): > CMake Error at SSLTest.cmake:5 (file): > file DOWNLOAD HASH mismatch > > for file: [/home/mgiordano/code/SimpleITK/LICENSE] > expected hash: [f8c925402b90f74566f71e64eea7bb > 9d83daac69cde71408ffd6c043be6a4991] > actual hash: [e3b0c44298fc1c149afbf4c8996fb9 > 2427ae41e4649b934ca495991b7852b855] > status: [1;"Unsupported protocol"] > > So I assume the HTTPS is not supported. Now if I understand correctly the > alternative is to download the modules manually in $HOME/ExternalData and > point to that folder through the variable ExternalData_OBJECT_STORES. The > question is what do I need to download, is that the only the two links > above or there is more ? Is it maybe an option to change version of Cmake > that can support that or/and how do I enable the support ? > > Any help is appreciated. > Regards, > Marco > > 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < > blowekamp at mail.nih.gov>: > >> Hello! >> >> OK, so it looks like you are using the current master branch of >> SimpleITK. I know this because you have the latest SimpleITK feature where >> CMake downloads the Superbuild dependencies with the CMake ?ExternalData? >> module. This enables some interesting options for your situation. >> >> You are on a cluster. On compute clusters, frequently the nodes don?t >> have access to the internet. So when cmake tries to download the URLS below >> it times out or errors. You can verify this with some command like ?wget >> https://midas3.kitware.com/midas/api/rest?method=midas.bitst >> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. >> The alternative is that your version of CMake doesn?t support HTTPS. Yo can >> test this with the following script: https://github.com/conda-forge >> /cmake-feedstock/blob/master/recipe/SSLTest.cmake >> >> Frequently, there are nodes on a cluster which have access to the >> internet for situations like this. You may be able to just use one of them. >> >> With the new ExternalData download module you may be able to pre-download >> these dependencies on the log in node. If you set the environment variable >> ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache >> downloads to this directory. I assume your home directory is available on >> the log in nodes. You can configure the SuperBuild there and build just the >> ?SuperBuildSimpleITKSource? target. This will download the dependencies to >> the ExternaData directory. Then you can build in a cluster node, which >> should use this cache. >> >> Also note when testing is enabled for the actual SimpleITK sub-project, a >> bunch of testing data is downloaded too. You can disable testing to avoid >> this, download and un-tar a Data archive [1], or replace the above >> procedure for this subproject. >> >> HTH, >> Brad >> >> [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/ >> 0.10.0/Source/ >> >> >> > On Aug 17, 2016, at 10:26 AM, marco giordano >> wrote: >> > >> > Hi there, >> > >> > I just downloaded SimpleTK and I tried to build it on a linux cluster >> (running Scientific Linux release 6.5- Carbon) using the superbuild. >> > >> > I use cmake 3.3.1. The Generation of build files is fine, then when I >> try to build i get this: >> > >> > -- Fetching "http://midas3.kitware.com/mid >> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >> 26e435e33b0d5c022e4490567&algorithm=MD5" >> > -- [download 100% complete] >> > -- Fetching "https://midas3.kitware.com/mi >> das/api/rest?method=midas.bitstream.download&checksum=2e115f >> e26e435e33b0d5c022e4490567&algorithm=MD5" >> > -- Fetching "https://itk.org/files/Externa >> lData/MD5/2e115fe26e435e33b0d5c022e4490567" >> > CMake Error at /cm/shared/apps/cmake/3.3.1/in >> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): >> > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: >> > >> > http://midas3.kitware.com/midas/api/rest?method=midas.bitst >> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >> ("Unsupported protocol") >> > https://midas3.kitware.com/midas/api/rest?method=midas.bits >> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >> ("Unsupported protocol") >> > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5 >> c022e4490567 ("Unsupported protocol") >> > Call Stack (most recent call first): >> > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 >> (_ExternalData_download_object) >> > >> > >> > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] >> Error 1 >> > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 >> > >> > Any help is welcome. >> > Regards >> > -- >> > Marco >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Marco Giordano > SKYPE:marcogiord81 > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 p.zaffino at yahoo.it Thu Aug 18 07:09:21 2016 From: p.zaffino at yahoo.it (Paolo Zaffino) Date: Thu, 18 Aug 2016 13:09:21 +0200 Subject: [ITK-users] [ITK] Best similarity measure for deformable image registration In-Reply-To: References: Message-ID: <04164068-d766-bc76-d3f9-c8a595e3ab9d@yahoo.it> In this case I would suggest mutual information (there are different "versions"). I would also try different settings for the numbers of bins and for the sampling percentage. HTH. Paolo On 18/08/2016 12:18, Constantinus Spanakis wrote: > Helo Paolo. Sorry for omitting details. It's about 3D multimodal > registration > > On Thu, Aug 18, 2016 at 12:33 PM, Paolo Zaffino > wrote: > > Hi, > monomodal or multimodal registration? > > Paolo > > > On 18/08/2016 11:19, Constantinus Spanakis wrote: >> Hello. I am working on deformable image registration and I am >> puzzled by the variety of the similarity measures that ITK has >> and I don't know which to use. Any susggestions? >> >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Thu Aug 18 08:53:48 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 18 Aug 2016 08:53:48 -0400 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hi Marco, as Matt said, you can build CMake from source and while configuring it turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead of the system one. Regards, D?enan On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare wrote: > A related problem, which I've never found a solution for, is that some > cluster software (probably the curl library) is built without ssl support > at a critical point. You may have the same issue. Maybe the configuration > info for curl will tell you one way or another whether this is the case and > you can request a reinstall. > > On Thu, Aug 18, 2016 at 7:37 PM, marco giordano > wrote: > >> Hi there, >> I checked the internet connection on the node and seems fine (I can >> download with wget the https://midas3.kitware.com/mid >> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >> 26e435e33b0d5c022e4490567&algorithm=MD5?). >> >> I run the script SSLTest.cmake >> >> but it fails (it downloads a LICENSE file but it is empty): >> CMake Error at SSLTest.cmake:5 (file): >> file DOWNLOAD HASH mismatch >> >> for file: [/home/mgiordano/code/SimpleITK/LICENSE] >> expected hash: [f8c925402b90f74566f71e64eea7b >> b9d83daac69cde71408ffd6c043be6a4991] >> actual hash: [e3b0c44298fc1c149afbf4c8996fb >> 92427ae41e4649b934ca495991b7852b855] >> status: [1;"Unsupported protocol"] >> >> So I assume the HTTPS is not supported. Now if I understand correctly the >> alternative is to download the modules manually in $HOME/ExternalData and >> point to that folder through the variable ExternalData_OBJECT_STORES. The >> question is what do I need to download, is that the only the two links >> above or there is more ? Is it maybe an option to change version of Cmake >> that can support that or/and how do I enable the support ? >> >> Any help is appreciated. >> Regards, >> Marco >> >> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < >> blowekamp at mail.nih.gov>: >> >>> Hello! >>> >>> OK, so it looks like you are using the current master branch of >>> SimpleITK. I know this because you have the latest SimpleITK feature where >>> CMake downloads the Superbuild dependencies with the CMake ?ExternalData? >>> module. This enables some interesting options for your situation. >>> >>> You are on a cluster. On compute clusters, frequently the nodes don?t >>> have access to the internet. So when cmake tries to download the URLS below >>> it times out or errors. You can verify this with some command like ?wget >>> https://midas3.kitware.com/midas/api/rest?method=midas.bitst >>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. >>> The alternative is that your version of CMake doesn?t support HTTPS. Yo can >>> test this with the following script: https://github.com/conda-forge >>> /cmake-feedstock/blob/master/recipe/SSLTest.cmake >>> >>> Frequently, there are nodes on a cluster which have access to the >>> internet for situations like this. You may be able to just use one of them. >>> >>> With the new ExternalData download module you may be able to >>> pre-download these dependencies on the log in node. If you set the >>> environment variable ExternalData_OBJECT_STORES to say >>> ?${HOME}/.ExternalData?, it will cache downloads to this directory. I >>> assume your home directory is available on the log in nodes. You can >>> configure the SuperBuild there and build just the >>> ?SuperBuildSimpleITKSource? target. This will download the dependencies to >>> the ExternaData directory. Then you can build in a cluster node, which >>> should use this cache. >>> >>> Also note when testing is enabled for the actual SimpleITK sub-project, >>> a bunch of testing data is downloaded too. You can disable testing to avoid >>> this, download and un-tar a Data archive [1], or replace the above >>> procedure for this subproject. >>> >>> HTH, >>> Brad >>> >>> [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0 >>> .10.0/Source/ >>> >>> >>> > On Aug 17, 2016, at 10:26 AM, marco giordano >>> wrote: >>> > >>> > Hi there, >>> > >>> > I just downloaded SimpleTK and I tried to build it on a linux cluster >>> (running Scientific Linux release 6.5- Carbon) using the superbuild. >>> > >>> > I use cmake 3.3.1. The Generation of build files is fine, then when I >>> try to build i get this: >>> > >>> > -- Fetching "http://midas3.kitware.com/mid >>> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >>> 26e435e33b0d5c022e4490567&algorithm=MD5" >>> > -- [download 100% complete] >>> > -- Fetching "https://midas3.kitware.com/mi >>> das/api/rest?method=midas.bitstream.download&checksum=2e115f >>> e26e435e33b0d5c022e4490567&algorithm=MD5" >>> > -- Fetching "https://itk.org/files/Externa >>> lData/MD5/2e115fe26e435e33b0d5c022e4490567" >>> > CMake Error at /cm/shared/apps/cmake/3.3.1/in >>> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): >>> > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: >>> > >>> > http://midas3.kitware.com/midas/api/rest?method=midas.bitst >>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >>> ("Unsupported protocol") >>> > https://midas3.kitware.com/midas/api/rest?method=midas.bits >>> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >>> ("Unsupported protocol") >>> > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5 >>> c022e4490567 ("Unsupported protocol") >>> > Call Stack (most recent call first): >>> > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 >>> (_ExternalData_download_object) >>> > >>> > >>> > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] >>> Error 1 >>> > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error >>> 2 >>> > >>> > Any help is welcome. >>> > Regards >>> > -- >>> > Marco >>> > _____________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://www.kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> >> -- >> Marco Giordano >> SKYPE:marcogiord81 >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 blowekamp at mail.nih.gov Thu Aug 18 09:28:41 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 18 Aug 2016 13:28:41 +0000 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: And for the lazier there are now CMake binaries for Linux i386 and x86_64. https://cmake.org/download/ On Aug 18, 2016, at 8:53 AM, D?enan Zuki? wrote: Hi Marco, as Matt said, you can build CMake from source and while configuring it turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead of the system one. Regards, D?enan On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare > wrote: A related problem, which I've never found a solution for, is that some cluster software (probably the curl library) is built without ssl support at a critical point. You may have the same issue. Maybe the configuration info for curl will tell you one way or another whether this is the case and you can request a reinstall. On Thu, Aug 18, 2016 at 7:37 PM, marco giordano > wrote: Hi there, I checked the internet connection on the node and seems fine (I can download with wget the https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?). I run the script SSLTest.cmake but it fails (it downloads a LICENSE file but it is empty): CMake Error at SSLTest.cmake:5 (file): file DOWNLOAD HASH mismatch for file: [/home/mgiordano/code/SimpleITK/LICENSE] expected hash: [f8c925402b90f74566f71e64eea7bb9d83daac69cde71408ffd6c043be6a4991] actual hash: [e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855] status: [1;"Unsupported protocol"] So I assume the HTTPS is not supported. Now if I understand correctly the alternative is to download the modules manually in $HOME/ExternalData and point to that folder through the variable ExternalData_OBJECT_STORES. The question is what do I need to download, is that the only the two links above or there is more ? Is it maybe an option to change version of Cmake that can support that or/and how do I enable the support ? Any help is appreciated. Regards, Marco 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] >: Hello! OK, so it looks like you are using the current master branch of SimpleITK. I know this because you have the latest SimpleITK feature where CMake downloads the Superbuild dependencies with the CMake ?ExternalData? module. This enables some interesting options for your situation. You are on a cluster. On compute clusters, frequently the nodes don?t have access to the internet. So when cmake tries to download the URLS below it times out or errors. You can verify this with some command like ?wget https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. The alternative is that your version of CMake doesn?t support HTTPS. Yo can test this with the following script: https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake Frequently, there are nodes on a cluster which have access to the internet for situations like this. You may be able to just use one of them. With the new ExternalData download module you may be able to pre-download these dependencies on the log in node. If you set the environment variable ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache downloads to this directory. I assume your home directory is available on the log in nodes. You can configure the SuperBuild there and build just the ?SuperBuildSimpleITKSource? target. This will download the dependencies to the ExternaData directory. Then you can build in a cluster node, which should use this cache. Also note when testing is enabled for the actual SimpleITK sub-project, a bunch of testing data is downloaded too. You can disable testing to avoid this, download and un-tar a Data archive [1], or replace the above procedure for this subproject. HTH, Brad [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Source/ > On Aug 17, 2016, at 10:26 AM, marco giordano > wrote: > > Hi there, > > I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. > > I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this: > > -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- [download 100% complete] > -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- Fetching "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" > CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") > Call Stack (most recent call first): > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object) > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1 > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > Any help is welcome. > Regards > -- > Marco > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -- Marco Giordano SKYPE:marcogiord81 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 marco.giord at gmail.com Thu Aug 18 12:04:47 2016 From: marco.giord at gmail.com (marco giordano) Date: Thu, 18 Aug 2016 18:04:47 +0200 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Thanks a lot for the help, I downloaded the Cmake binary and now it seems it is able to download, however the build process gets stuck at cloning ITK: -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua [ 18%] Completed 'Lua' [ 18%] Built target Lua [ 20%] Creating directories for 'ITK' [ 21%] Performing download step (git clone) for 'ITK' Cloning into 'ITK'... Install the project... -- Install configuration: "Release" -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua [ 18%] Completed 'Lua' [ 18%] Built target Lua [ 20%] Creating directories for 'ITK' [ 21%] Performing download step (git clone) for 'ITK' Cloning into 'ITK'... Maybe a wrong link somewhere ? Regards 2016-08-18 15:28 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov>: > And for the lazier there are now CMake binaries for Linux i386 and x86_64. > > https://cmake.org/download/ > > > On Aug 18, 2016, at 8:53 AM, D?enan Zuki? wrote: > > Hi Marco, > > as Matt said, you can build CMake from source and while configuring it > turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead > of the system one. > > Regards, > D?enan > > On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare > wrote: > >> A related problem, which I've never found a solution for, is that some >> cluster software (probably the curl library) is built without ssl support >> at a critical point. You may have the same issue. Maybe the configuration >> info for curl will tell you one way or another whether this is the case and >> you can request a reinstall. >> >> On Thu, Aug 18, 2016 at 7:37 PM, marco giordano >> wrote: >> >>> Hi there, >>> I checked the internet connection on the node and seems fine (I can >>> download with wget the https://midas3.kitware.com/midas/api/rest?method= >>> midas.bitstream.download&checksum=2e115fe26e435e33b0d5c >>> 022e4490567&algorithm=MD5?). >>> >>> I run the script SSLTest.cmake >>> >>> but it fails (it downloads a LICENSE file but it is empty): >>> CMake Error at SSLTest.cmake:5 (file): >>> file DOWNLOAD HASH mismatch >>> >>> for file: [/home/mgiordano/code/SimpleITK/LICENSE] >>> expected hash: [f8c925402b90f74566f71e64eea7b >>> b9d83daac69cde71408ffd6c043be6a4991] >>> actual hash: [e3b0c44298fc1c149afbf4c8996fb >>> 92427ae41e4649b934ca495991b7852b855] >>> status: [1;"Unsupported protocol"] >>> >>> So I assume the HTTPS is not supported. Now if I understand correctly >>> the alternative is to download the modules manually in $HOME/ExternalData >>> and point to that folder through the variable ExternalData_OBJECT_STORES. >>> The question is what do I need to download, is that the only the two links >>> above or there is more ? Is it maybe an option to change version of Cmake >>> that can support that or/and how do I enable the support ? >>> >>> Any help is appreciated. >>> Regards, >>> Marco >>> >>> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < >>> blowekamp at mail.nih.gov>: >>> >>>> Hello! >>>> >>>> OK, so it looks like you are using the current master branch of >>>> SimpleITK. I know this because you have the latest SimpleITK feature where >>>> CMake downloads the Superbuild dependencies with the CMake ?ExternalData? >>>> module. This enables some interesting options for your situation. >>>> >>>> You are on a cluster. On compute clusters, frequently the nodes don?t >>>> have access to the internet. So when cmake tries to download the URLS below >>>> it times out or errors. You can verify this with some command like ?wget >>>> https://midas3.kitware.com/midas/api/rest?method= >>>> midas.bitstream.download&checksum=2e115fe26e435e33b0d5c >>>> 022e4490567&algorithm=MD5?. The alternative is that your version of >>>> CMake doesn?t support HTTPS. Yo can test this with the following script: >>>> https://github.com/conda-forge/cmake-feedstock/ >>>> blob/master/recipe/SSLTest.cmake >>>> >>>> Frequently, there are nodes on a cluster which have access to the >>>> internet for situations like this. You may be able to just use one of them. >>>> >>>> With the new ExternalData download module you may be able to >>>> pre-download these dependencies on the log in node. If you set the >>>> environment variable ExternalData_OBJECT_STORES to say >>>> ?${HOME}/.ExternalData?, it will cache downloads to this directory. I >>>> assume your home directory is available on the log in nodes. You can >>>> configure the SuperBuild there and build just the >>>> ?SuperBuildSimpleITKSource? target. This will download the dependencies to >>>> the ExternaData directory. Then you can build in a cluster node, which >>>> should use this cache. >>>> >>>> Also note when testing is enabled for the actual SimpleITK sub-project, >>>> a bunch of testing data is downloaded too. You can disable testing to avoid >>>> this, download and un-tar a Data archive [1], or replace the above >>>> procedure for this subproject. >>>> >>>> HTH, >>>> Brad >>>> >>>> [1] https://sourceforge.net/projects/simpleitk/files/ >>>> SimpleITK/0.10.0/Source/ >>>> >>>> >>>> > On Aug 17, 2016, at 10:26 AM, marco giordano >>>> wrote: >>>> > >>>> > Hi there, >>>> > >>>> > I just downloaded SimpleTK and I tried to build it on a linux cluster >>>> (running Scientific Linux release 6.5- Carbon) using the superbuild. >>>> > >>>> > I use cmake 3.3.1. The Generation of build files is fine, then when I >>>> try to build i get this: >>>> > >>>> > -- Fetching "http://midas3.kitware.com/mid >>>> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >>>> 26e435e33b0d5c022e4490567&algorithm=MD5" >>>> > -- [download 100% complete] >>>> > -- Fetching "https://midas3.kitware.com/mi >>>> das/api/rest?method=midas.bitstream.download&checksum=2e115f >>>> e26e435e33b0d5c022e4490567&algorithm=MD5" >>>> > -- Fetching "https://itk.org/files/Externa >>>> lData/MD5/2e115fe26e435e33b0d5c022e4490567" >>>> > CMake Error at /cm/shared/apps/cmake/3.3.1/in >>>> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): >>>> > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: >>>> > >>>> > http://midas3.kitware.com/midas/api/rest?method=midas.bitst >>>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported >>>> protocol") >>>> > https://midas3.kitware.com/midas/api/rest?method=midas.bits >>>> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported >>>> protocol") >>>> > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5 >>>> c022e4490567 ("Unsupported protocol") >>>> > Call Stack (most recent call first): >>>> > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 >>>> (_ExternalData_download_object) >>>> > >>>> > >>>> > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] >>>> Error 1 >>>> > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] >>>> Error 2 >>>> > >>>> > Any help is welcome. >>>> > Regards >>>> > -- >>>> > Marco >>>> > _____________________________________ >>>> > Powered by www.kitware.com >>>> > >>>> > Visit other Kitware open-source projects at >>>> > http://www.kitware.com/opensource/opensource.html >>>> > >>>> > Kitware offers ITK Training Courses, for more information visit: >>>> > http://www.kitware.com/products/protraining.php >>>> > >>>> > Please keep messages on-topic and check the ITK FAQ at: >>>> > http://www.itk.org/Wiki/ITK_FAQ >>>> > >>>> > Follow this link to subscribe/unsubscribe: >>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >>> >>> -- >>> Marco Giordano >>> SKYPE:marcogiord81 >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Marco Giordano SKYPE:marcogiord81 -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Aug 18 12:13:56 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 18 Aug 2016 16:13:56 +0000 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hi! The lack of error message is not helpful to assist with debugging. You must try to reproduce the problem on the node then. Try running ?git clone https://itk.org/ITK.git? and see if it produces more output. The probable problems are there is network restrictions on your cluster node, or that your git version is too old and does not support the https protocol. You could try changing the CMake variable SITK_GIT_PROTOCOL from ?https? to ?git? [1]. Currently there is not ?ExternalData? cache work around for this. HTH, Brad [1] https://github.com/SimpleITK/SimpleITK/blob/master/SuperBuild/External_ITK.cmake#L36 On Aug 18, 2016, at 12:04 PM, marco giordano > wrote: Thanks a lot for the help, I downloaded the Cmake binary and now it seems it is able to download, however the build process gets stuck at cloning ITK: -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua [ 18%] Completed 'Lua' [ 18%] Built target Lua [ 20%] Creating directories for 'ITK' [ 21%] Performing download step (git clone) for 'ITK' Cloning into 'ITK'... Install the project... -- Install configuration: "Release" -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua [ 18%] Completed 'Lua' [ 18%] Built target Lua [ 20%] Creating directories for 'ITK' [ 21%] Performing download step (git clone) for 'ITK' Cloning into 'ITK'... Maybe a wrong link somewhere ? Regards 2016-08-18 15:28 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] >: And for the lazier there are now CMake binaries for Linux i386 and x86_64. https://cmake.org/download/ On Aug 18, 2016, at 8:53 AM, D?enan Zuki? > wrote: Hi Marco, as Matt said, you can build CMake from source and while configuring it turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead of the system one. Regards, D?enan On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare > wrote: A related problem, which I've never found a solution for, is that some cluster software (probably the curl library) is built without ssl support at a critical point. You may have the same issue. Maybe the configuration info for curl will tell you one way or another whether this is the case and you can request a reinstall. On Thu, Aug 18, 2016 at 7:37 PM, marco giordano > wrote: Hi there, I checked the internet connection on the node and seems fine (I can download with wget the https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?). I run the script SSLTest.cmake but it fails (it downloads a LICENSE file but it is empty): CMake Error at SSLTest.cmake:5 (file): file DOWNLOAD HASH mismatch for file: [/home/mgiordano/code/SimpleITK/LICENSE] expected hash: [f8c925402b90f74566f71e64eea7bb9d83daac69cde71408ffd6c043be6a4991] actual hash: [e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855] status: [1;"Unsupported protocol"] So I assume the HTTPS is not supported. Now if I understand correctly the alternative is to download the modules manually in $HOME/ExternalData and point to that folder through the variable ExternalData_OBJECT_STORES. The question is what do I need to download, is that the only the two links above or there is more ? Is it maybe an option to change version of Cmake that can support that or/and how do I enable the support ? Any help is appreciated. Regards, Marco 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] >: Hello! OK, so it looks like you are using the current master branch of SimpleITK. I know this because you have the latest SimpleITK feature where CMake downloads the Superbuild dependencies with the CMake ?ExternalData? module. This enables some interesting options for your situation. You are on a cluster. On compute clusters, frequently the nodes don?t have access to the internet. So when cmake tries to download the URLS below it times out or errors. You can verify this with some command like ?wget https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. The alternative is that your version of CMake doesn?t support HTTPS. Yo can test this with the following script: https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake Frequently, there are nodes on a cluster which have access to the internet for situations like this. You may be able to just use one of them. With the new ExternalData download module you may be able to pre-download these dependencies on the log in node. If you set the environment variable ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache downloads to this directory. I assume your home directory is available on the log in nodes. You can configure the SuperBuild there and build just the ?SuperBuildSimpleITKSource? target. This will download the dependencies to the ExternaData directory. Then you can build in a cluster node, which should use this cache. Also note when testing is enabled for the actual SimpleITK sub-project, a bunch of testing data is downloaded too. You can disable testing to avoid this, download and un-tar a Data archive [1], or replace the above procedure for this subproject. HTH, Brad [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Source/ > On Aug 17, 2016, at 10:26 AM, marco giordano > wrote: > > Hi there, > > I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. > > I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this: > > -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- [download 100% complete] > -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- Fetching "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" > CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") > Call Stack (most recent call first): > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object) > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1 > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > Any help is welcome. > Regards > -- > Marco > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -- Marco Giordano SKYPE:marcogiord81 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -- Marco Giordano SKYPE:marcogiord81 -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at insightsoftwareconsortium.org Fri Aug 19 09:51:30 2016 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Fri, 19 Aug 2016 09:51:30 -0400 (EDT) Subject: [ITK-users] New Submission: Cubic and Hermite splines for VTK Message-ID: <20160819135131.04CFE3D6208D@insight-journal.org> Hello, A new submission has been added to the MIDAS Journal. Title: Cubic and Hermite splines for VTK Authors: Kovacs N., Peters T., Chen E. Abstract: A cubic spline is a spline where each curve is defined by a third-order polynomial, while a Hermite spline has each polynomial specified in Hermite form, being computed using tangent information as well as the position of the points. We propose two new classes for VTK, vtkCubicSpline and vtkHermiteSpline, which compute interpolating splines using a Cubic and a Hermite Spline Interpolation function, respectively. We also propose two new auxiliary classes, vtkParametricCubicSpline and vtkParametricHermiteSpline, that create parametric functions for the 1D interpolating aforementioned splines. Download and review this publication at: http://hdl.handle.net/10380/3561 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Aug 22 03:11:36 2016 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Mon, 22 Aug 2016 03:11:36 -0400 (EDT) Subject: [ITK-users] New Submission: ND morphological contour interpolation Message-ID: <20160822071136.020FE3D620D3@insight-journal.org> Hello, A new submission has been added to the Insight Journal. Title: ND morphological contour interpolation Authors: Zuki?? D., Vicory J., McCormick M., Wisse L., Gerig G., Yushkevich P., Aylward S. Abstract: This document describes a new class, itk::MorphologicalContourInterpolator, which implements a method proposed by Albu et al. in 2008. Interpolation is done by first determining correspondence between shapes on adjacent segmented slices by detecting overlaps, then aligning the corresponding shapes, generating transition sequence of one-pixel dilations and taking the median as result. Recursion is employed if the original segmented slices are separated by more than one empty slice. This class is n-dimensional, and supports inputs of 3 or more dimensions. `Slices' are n-1-dimensional, and can be both automatically detected and manually set. The class is efficient in both memory used and execution time. It requires little memory in addition to allocation of input and output images. The implementation is multi-threaded, and processing one of the test inputs takes around 1-2 seconds on a quad-core processor. The class is tested to operate on both itk::Image and itk::RLEImage. Since all the processing is done on extracted slices, usage of itk::RLEImage for input and/or output affects performance to a limited degree. This class is implemented to ease manual segmentation in ITK-SNAP (www.itksnap.org). The class, along with test data and automated regression tests is packaged as an ITK remote module https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation. Download and review this publication at: http://hdl.handle.net/10380/3563 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 marco.giord at gmail.com Mon Aug 22 04:53:04 2016 From: marco.giord at gmail.com (marco giordano) Date: Mon, 22 Aug 2016 10:53:04 +0200 Subject: [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Finally I managed to build SimpleITK on the cluster node. Despite the suggestions I could not manage to clone ITK through the build process (still not sure why, maybe the git version 1.7.7.3?) but I could clone it separately and then set the ITK_REPOSITORY variable to the repository and it worked. Thanks a lot. regards 2016-08-18 18:13 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov>: > Hi! > > The lack of error message is not helpful to assist with debugging. You > must try to reproduce the problem on the node then. > > Try running ?git clone https://itk.org/ITK.git? and see if it produces > more output. > > The probable problems are there is network restrictions on your cluster > node, or that your git version is too old and does not support the https > protocol. > > You could try changing the CMake variable SITK_GIT_PROTOCOL from ?https? > to ?git? [1]. Currently there is not ?ExternalData? cache work around for > this. > > HTH, > Brad > > [1] https://github.com/SimpleITK/SimpleITK/blob/master/ > SuperBuild/External_ITK.cmake#L36 > > On Aug 18, 2016, at 12:04 PM, marco giordano > wrote: > > Thanks a lot for the help, > I downloaded the Cmake binary and now it seems it is able to download, > however the build process gets stuck at cloning ITK: > > -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua > [ 18%] Completed 'Lua' > [ 18%] Built target Lua > [ 20%] Creating directories for 'ITK' > [ 21%] Performing download step (git clone) for 'ITK' > Cloning into 'ITK'... > Install the project... > -- Install configuration: "Release" > -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua > [ 18%] Completed 'Lua' > [ 18%] Built target Lua > [ 20%] Creating directories for 'ITK' > [ 21%] Performing download step (git clone) for 'ITK' > Cloning into 'ITK'... > > Maybe a wrong link somewhere ? > Regards > > 2016-08-18 15:28 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < > blowekamp at mail.nih.gov>: > >> And for the lazier there are now CMake binaries for Linux i386 and >> x86_64. >> >> https://cmake.org/download/ >> >> >> On Aug 18, 2016, at 8:53 AM, D?enan Zuki? wrote: >> >> Hi Marco, >> >> as Matt said, you can build CMake from source and while configuring it >> turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead >> of the system one. >> >> Regards, >> D?enan >> >> On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare >> wrote: >> >>> A related problem, which I've never found a solution for, is that some >>> cluster software (probably the curl library) is built without ssl support >>> at a critical point. You may have the same issue. Maybe the configuration >>> info for curl will tell you one way or another whether this is the case and >>> you can request a reinstall. >>> >>> On Thu, Aug 18, 2016 at 7:37 PM, marco giordano >>> wrote: >>> >>>> Hi there, >>>> I checked the internet connection on the node and seems fine (I can >>>> download with wget the https://midas3.kitware.com >>>> /midas/api/rest?method=midas.bitstream.download&checksum= >>>> 2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?). >>>> >>>> I run the script SSLTest.cmake >>>> >>>> but it fails (it downloads a LICENSE file but it is empty): >>>> CMake Error at SSLTest.cmake:5 (file): >>>> file DOWNLOAD HASH mismatch >>>> >>>> for file: [/home/mgiordano/code/SimpleITK/LICENSE] >>>> expected hash: [f8c925402b90f74566f71e64eea7b >>>> b9d83daac69cde71408ffd6c043be6a4991] >>>> actual hash: [e3b0c44298fc1c149afbf4c8996fb >>>> 92427ae41e4649b934ca495991b7852b855] >>>> status: [1;"Unsupported protocol"] >>>> >>>> So I assume the HTTPS is not supported. Now if I understand correctly >>>> the alternative is to download the modules manually in $HOME/ExternalData >>>> and point to that folder through the variable ExternalData_OBJECT_STORES. >>>> The question is what do I need to download, is that the only the two links >>>> above or there is more ? Is it maybe an option to change version of Cmake >>>> that can support that or/and how do I enable the support ? >>>> >>>> Any help is appreciated. >>>> Regards, >>>> Marco >>>> >>>> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < >>>> blowekamp at mail.nih.gov>: >>>> >>>>> Hello! >>>>> >>>>> OK, so it looks like you are using the current master branch of >>>>> SimpleITK. I know this because you have the latest SimpleITK feature where >>>>> CMake downloads the Superbuild dependencies with the CMake ?ExternalData? >>>>> module. This enables some interesting options for your situation. >>>>> >>>>> You are on a cluster. On compute clusters, frequently the nodes don?t >>>>> have access to the internet. So when cmake tries to download the URLS below >>>>> it times out or errors. You can verify this with some command like ?wget >>>>> https://midas3.kitware.com/midas/api/rest?method=midas >>>>> .bitstream.download&checksum=2e115fe26e435e33b0d5c022e44905 >>>>> 67&algorithm=MD5?. The alternative is that your version of CMake >>>>> doesn?t support HTTPS. Yo can test this with the following script: >>>>> https://github.com/conda-forge/cmake-feedstock/blob/ >>>>> master/recipe/SSLTest.cmake >>>>> >>>>> Frequently, there are nodes on a cluster which have access to the >>>>> internet for situations like this. You may be able to just use one of them. >>>>> >>>>> With the new ExternalData download module you may be able to >>>>> pre-download these dependencies on the log in node. If you set the >>>>> environment variable ExternalData_OBJECT_STORES to say >>>>> ?${HOME}/.ExternalData?, it will cache downloads to this directory. I >>>>> assume your home directory is available on the log in nodes. You can >>>>> configure the SuperBuild there and build just the >>>>> ?SuperBuildSimpleITKSource? target. This will download the dependencies to >>>>> the ExternaData directory. Then you can build in a cluster node, which >>>>> should use this cache. >>>>> >>>>> Also note when testing is enabled for the actual SimpleITK >>>>> sub-project, a bunch of testing data is downloaded too. You can disable >>>>> testing to avoid this, download and un-tar a Data archive [1], or replace >>>>> the above procedure for this subproject. >>>>> >>>>> HTH, >>>>> Brad >>>>> >>>>> [1] https://sourceforge.net/projects/simpleitk/files/SimpleI >>>>> TK/0.10.0/Source/ >>>>> >>>>> >>>>> > On Aug 17, 2016, at 10:26 AM, marco giordano >>>>> wrote: >>>>> > >>>>> > Hi there, >>>>> > >>>>> > I just downloaded SimpleTK and I tried to build it on a linux >>>>> cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. >>>>> > >>>>> > I use cmake 3.3.1. The Generation of build files is fine, then when >>>>> I try to build i get this: >>>>> > >>>>> > -- Fetching "http://midas3.kitware.com/mid >>>>> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >>>>> 26e435e33b0d5c022e4490567&algorithm=MD5" >>>>> > -- [download 100% complete] >>>>> > -- Fetching "https://midas3.kitware.com/mi >>>>> das/api/rest?method=midas.bitstream.download&checksum=2e115f >>>>> e26e435e33b0d5c022e4490567&algorithm=MD5" >>>>> > -- Fetching "https://itk.org/files/Externa >>>>> lData/MD5/2e115fe26e435e33b0d5c022e4490567" >>>>> > CMake Error at /cm/shared/apps/cmake/3.3.1/in >>>>> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): >>>>> > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: >>>>> > >>>>> > http://midas3.kitware.com/midas/api/rest?method=midas.bitst >>>>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported >>>>> protocol") >>>>> > https://midas3.kitware.com/midas/api/rest?method=midas.bits >>>>> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >>>>> ("Unsupported protocol") >>>>> > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5 >>>>> c022e4490567 ("Unsupported protocol") >>>>> > Call Stack (most recent call first): >>>>> > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 >>>>> (_ExternalData_download_object) >>>>> > >>>>> > >>>>> > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] >>>>> Error 1 >>>>> > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] >>>>> Error 2 >>>>> > >>>>> > Any help is welcome. >>>>> > Regards >>>>> > -- >>>>> > Marco >>>>> > _____________________________________ >>>>> > Powered by www.kitware.com >>>>> > >>>>> > Visit other Kitware open-source projects at >>>>> > http://www.kitware.com/opensource/opensource.html >>>>> > >>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>> > http://www.kitware.com/products/protraining.php >>>>> > >>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>> > >>>>> > Follow this link to subscribe/unsubscribe: >>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> >>>> >>>> >>>> -- >>>> Marco Giordano >>>> SKYPE:marcogiord81 >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the 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 >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Marco Giordano > SKYPE:marcogiord81 > > > -- Marco Giordano SKYPE:marcogiord81 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Aug 22 09:33:03 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 22 Aug 2016 09:33:03 -0400 Subject: [ITK-users] RLEImage Message-ID: Hi everybody, an article was recently published in Insight ?Journal, but for some reason was not automatically announce to this list. The title is "RLEImage: run-length encoded memory compression scheme for an itk::Image" and can be accessed here: http://www.insight-journal.org/browse/publication/978 Regards, D?enan -------------- next part -------------- An HTML attachment was scrubbed... URL: From aharr8 at uwo.ca Mon Aug 22 15:25:56 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Mon, 22 Aug 2016 15:25:56 -0400 Subject: [ITK-users] [ITK] CorrelationImageToImageMetricv4 returns 0 from GetValue() Message-ID: Hello all, I am having a devil of a time setting up the CorrelationImageToImageMetricv4 and getting a result that makes sense. I have written an observer that outputs to a text file the iteration number, correlation value, and current position. I have generated a virtual phantom image of a white cube on a black background, and when I put the same image through for fixed and moving images, I get [0,0,0,0,0,0], meaning that no rotation or translation is required for the images to be aligned. This is the correct versor and vector transform, and if I apply a translation the correct distance values are returned to have the images align, however the metric value returned is also 0 and a perfect registration like this should yield a metric of -1 according to the documentation. Additionally, it doesn?t seem to be analyzing rotation properly, as when I introduce a rotation around any axis the metric returns a translation on the other two axes but the rotation versor remains at zero. I?m attaching my code as well, it?s possible I?ve not set some parameters up properly: -- AH ------------------------------------------------------------ ----------------------------------- *This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.* -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Correlator3D.cpp Type: text/x-c++src Size: 16036 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Correlator3D.h Type: text/x-chdr Size: 4336 bytes Desc: not available URL: From dzenanz at gmail.com Tue Aug 23 09:53:45 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 23 Aug 2016 09:53:45 -0400 Subject: [ITK-users] [ITK] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: Hi Andrew, you are doing so many things in a nonstandard way, starting with passing around pointers to buffers and metadata as plain parameters, instead of just once converting to itk::Image and then using itk::Image::Pointer to pass the images around. Your approach is more prone to errors. Can you provide the inputs and the main function which invokes this class to have a runnable example? I will try to find the problem. Regards, D?enan On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: > Hello all, > I am having a devil of a time setting up the CorrelationImageToImageMetricv4 > and getting a result that makes sense. I have written an observer that > outputs to a text file the iteration number, correlation value, and current > position. I have generated a virtual phantom image of a white cube on a > black background, and when I put the same image through for fixed and > moving images, I get [0,0,0,0,0,0], meaning that no rotation or translation > is required for the images to be aligned. This is the correct versor and > vector transform, and if I apply a translation the correct distance values > are returned to have the images align, however the metric value returned is > also 0 and a perfect registration like this should yield a metric of -1 > according to the documentation. Additionally, it doesn?t seem to be > analyzing rotation properly, as when I introduce a rotation around any axis > the metric returns a translation on the other two axes but the rotation > versor remains at zero. > > I?m attaching my code as well, it?s possible I?ve not set some parameters > up properly: > > > -- > > AH > > > ------------------------------------------------------------ > ----------------------------------- > > *This email and any attachments thereto may contain private, > confidential, and privileged materials for the sole use of the intended > recipient. Any reviewing, copying, or distribution of this email (or any > attachments thereto) by other than the intended recipient is strictly > prohibited. If you are not the intended recipient, please contact the > sender immediately and permanently destroy this email and any attachments > thereto.* > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 kolin9105 at gmail.com Tue Aug 23 14:50:57 2016 From: kolin9105 at gmail.com (meikolin saimara) Date: Wed, 24 Aug 2016 01:50:57 +0700 Subject: [ITK-users] (no subject) Message-ID: hello every one... how I can found sp x and sp y of my image with itk -------------- next part -------------- An HTML attachment was scrubbed... URL: From andinet.enqu at kitware.com Tue Aug 23 20:15:34 2016 From: andinet.enqu at kitware.com (Andinet Enquobahrie) Date: Tue, 23 Aug 2016 20:15:34 -0400 Subject: [ITK-users] ANN:Kitware is hiring software developers for ITK and 3D Slicer Message-ID: Apologies for duplicate postings. =================== Hi folks, Kitware is seeking to hire highly skilled software developers to assist us in creating high quality software by utilizing and extending ITK and 3D Slicer for our research and commercial collaborations. If you are interested in this opportunity, please consider applying. Software Developer for ITK and Slicer http://tinyurl.com/h3e6ukh Another opportunity in the Medical Computing group: Research and Development Involving Machine Learning and Medical Image Analysis http://tinyurl.com/hy58kq8 For other job openings including internships 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhuangming.shen at sphic.org.cn Tue Aug 23 21:53:03 2016 From: zhuangming.shen at sphic.org.cn (=?utf-8?B?5rKI5bqE5piO?=) Date: Wed, 24 Aug 2016 01:53:03 +0000 Subject: [ITK-users] How to use itk::LandmarkBasedTransformInitializer for python supported ITK? Message-ID: <1472003582182.51985@sphic.org.cn> Hi all, I'd like to do landmark based image registration using python supported ITK. I referred to this example (https://itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer) and want to modify the code to python. In this example, itk::LandmarkBasedTransformInitializer can be wrapped to python. But how to SetFixedLandmarks/SetMovingLandmarks? using python? Because the input of SetFixedLandmarks/SetMovingLandmarks? is fixedLandmarks/movingLandmarks, whose actual type is std::vector. Could anyone give me a short example on how to write it? Thanks in advance. Regards, Zhuangming Shen -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Aug 24 00:02:03 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Aug 2016 00:02:03 -0400 Subject: [ITK-users] How to use itk::LandmarkBasedTransformInitializer for python supported ITK? In-Reply-To: <1472003582182.51985@sphic.org.cn> References: <1472003582182.51985@sphic.org.cn> Message-ID: Hi, I added a Python version of the example to the wiki page, although it required a few fixes to the wrapping. This patch fixes wrapping of the LandmarkTransformInitializer class for 2D Transform's: http://review.source.kitware.com/#/c/21481/ and this patch adds wrapping for std::vector< itk::Point > so the landmarks can be added. http://review.source.kitware.com/#/c/21480/ Please review the patches. Thanks, Matt On Tue, Aug 23, 2016 at 9:53 PM, ??? wrote: > Hi all, > > > I'd like to do landmark based image registration using python supported ITK. > I referred to this example > (https://itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer) > and want to modify the code to python. In this example, > itk::LandmarkBasedTransformInitializer can be wrapped to python. But how to > SetFixedLandmarks/SetMovingLandmarks using python? Because the input of > SetFixedLandmarks/SetMovingLandmarks is fixedLandmarks/movingLandmarks, > whose actual type is std::vector. Could anyone give me a short example on > how to write it? Thanks in advance. > > > > Regards, > > > Zhuangming Shen > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 zhuangming.shen at sphic.org.cn Wed Aug 24 00:51:32 2016 From: zhuangming.shen at sphic.org.cn (=?gb2312?B?yfLXr8P3?=) Date: Wed, 24 Aug 2016 04:51:32 +0000 Subject: [ITK-users] How to use itk::LandmarkBasedTransformInitializer for python supported ITK? In-Reply-To: References: <1472003582182.51985@sphic.org.cn>, Message-ID: <1472014291321.59445@sphic.org.cn> Thank you so much. ________________________________________ From: Matt McCormick Sent: Wednesday, August 24, 2016 12:02 PM To: ??? Cc: insight-users at itk.org Subject: Re: [ITK-users] How to use itk::LandmarkBasedTransformInitializer for python supported ITK? Hi, I added a Python version of the example to the wiki page, although it required a few fixes to the wrapping. This patch fixes wrapping of the LandmarkTransformInitializer class for 2D Transform's: http://review.source.kitware.com/#/c/21481/ and this patch adds wrapping for std::vector< itk::Point > so the landmarks can be added. http://review.source.kitware.com/#/c/21480/ Please review the patches. Thanks, Matt On Tue, Aug 23, 2016 at 9:53 PM, ??? wrote: > Hi all, > > > I'd like to do landmark based image registration using python supported ITK. > I referred to this example > (https://itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer) > and want to modify the code to python. In this example, > itk::LandmarkBasedTransformInitializer can be wrapped to python. But how to > SetFixedLandmarks/SetMovingLandmarks using python? Because the input of > SetFixedLandmarks/SetMovingLandmarks is fixedLandmarks/movingLandmarks, > whose actual type is std::vector. Could anyone give me a short example on > how to write it? Thanks in advance. > > > > Regards, > > > Zhuangming Shen > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 jhlegarreta at vicomtech.org Wed Aug 24 03:12:47 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Wed, 24 Aug 2016 09:12:47 +0200 Subject: [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi, section 4.1.4 in the ITK software guide [1] may be of help. In essence, image->GetSpacing(); will give you the image spacing. HTH, JON HAITZ [1] https://itk.org/ItkSoftwareGuide.pdf -- On 23 August 2016 at 20:50, meikolin saimara wrote: > hello every one... > how I can found sp x and sp y of my image with itk > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 aharr8 at uwo.ca Wed Aug 24 11:13:13 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Wed, 24 Aug 2016 11:13:13 -0400 Subject: [ITK-users] [ITK] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: Thanks for getting back to me. I know the approach isn?t ideal, I?m building my class on top of an existing project, so that?s the reason for using the primative types. I?m going to write a main function as well as sending you a data set so that you can skip figuring out how to get data in to the class and can focus directly on the problem, should have both the program and data to you by the end of the day. Thanks again. -- AH ----------------------------------------------------------------------------------------------- *This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.* On Tue, Aug 23, 2016 at 9:53 AM, D?enan Zuki? wrote: > Hi Andrew, > > you are doing so many things in a nonstandard way, starting with passing > around pointers to buffers and metadata as plain parameters, instead of > just once converting to itk::Image and then using itk::Image::Pointer to > pass the images around. Your approach is more prone to errors. > > Can you provide the inputs and the main function which invokes this class > to have a runnable example? I will try to find the problem. > > Regards, > D?enan > > On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: > >> Hello all, >> I am having a devil of a time setting up the >> CorrelationImageToImageMetricv4 and getting a result that makes sense. >> I have written an observer that outputs to a text file the iteration >> number, correlation value, and current position. I have generated a >> virtual phantom image of a white cube on a black background, and when I put >> the same image through for fixed and moving images, I get [0,0,0,0,0,0], >> meaning that no rotation or translation is required for the images to be >> aligned. This is the correct versor and vector transform, and if I apply a >> translation the correct distance values are returned to have the images >> align, however the metric value returned is also 0 and a perfect >> registration like this should yield a metric of -1 according to the >> documentation. Additionally, it doesn?t seem to be analyzing rotation >> properly, as when I introduce a rotation around any axis the metric returns >> a translation on the other two axes but the rotation versor remains at zero. >> >> I?m attaching my code as well, it?s possible I?ve not set some parameters >> up properly: >> >> >> -- >> >> AH >> >> >> ------------------------------------------------------------ >> ----------------------------------- >> >> *This email and any attachments thereto may contain private, >> confidential, and privileged materials for the sole use of the intended >> recipient. Any reviewing, copying, or distribution of this email (or any >> attachments thereto) by other than the intended recipient is strictly >> prohibited. If you are not the intended recipient, please contact the >> sender immediately and permanently destroy this email and any attachments >> thereto.* >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 sepideh.movaghati at gmail.com Wed Aug 24 13:52:21 2016 From: sepideh.movaghati at gmail.com (Sepide Movaghati) Date: Wed, 24 Aug 2016 13:52:21 -0400 Subject: [ITK-users] Problem Using ScaleEstimator in V4 Registration Message-ID: Hi, I found a problem while I was using ScaleEstimator in v4 registration: In itkRegistrationParametersScaleEstimator class there are two functions SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the sampling strategy is chosen based on the Transformation type. For example if the transformation is of type displacement field or BSpline, it uses all of the samples. If transformation is any regular affine or rigid transformation (child of class MatrixOffsetTransformBase) it performs corner sampling. However, if the transformation is none of the known ones, it uses Random Sampling. Here is the problem: in itkImageRegistrationMethodv4.hxx the Metric transformation is set using ->SetMovingTransform() and it is always a CompositeTransform! Therefore, ScaleEstimator cannot detect the transformation type and it always fall into "else" which is using Random Sampling! It does not matter if you do a multilevel registration or not. The transformation is always of type CompositeTransform even if you do just a one level rigid transform! I would appreciate if you let me know if I was correct about this issue and whether we can consider this a bug and hope to get it fixed for the upcoming versions. Thanks a lot for your consideration in advance, Sepide From dzenanz at gmail.com Wed Aug 24 14:45:00 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 24 Aug 2016 14:45:00 -0400 Subject: [ITK-users] Problem Using ScaleEstimator in V4 Registration In-Reply-To: References: Message-ID: Hi Sepide, if I remember correctly, registration framework is advertised as using random sampling. And the function you mention is not used for sampling the registration metric, but rather for parameter scale estimation. So even if random sampling usage for scale estimation is unintentional, I don't believe it is a major problem. Perhaps someone who participated in writing the registration framework can chime in? Regards, D?enan On Wed, Aug 24, 2016 at 1:52 PM, Sepide Movaghati < sepideh.movaghati at gmail.com> wrote: > Hi, > > I found a problem while I was using ScaleEstimator in v4 registration: > > In itkRegistrationParametersScaleEstimator class there are two functions > SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the > sampling strategy is chosen based on the Transformation type. For example > if the transformation is of type displacement field or BSpline, it uses all > of the samples. If transformation is any regular affine or rigid > transformation (child of class MatrixOffsetTransformBase) it performs > corner sampling. However, if the transformation is none of the known ones, > it uses Random Sampling. > > Here is the problem: in itkImageRegistrationMethodv4.hxx the Metric > transformation is set using ->SetMovingTransform() and it is always a > CompositeTransform! Therefore, ScaleEstimator cannot detect the > transformation type and it always fall into "else" which is using Random > Sampling! It does not matter if you do a multilevel registration or not. > The transformation is always of type CompositeTransform even if you do just > a one level rigid transform! > > I would appreciate if you let me know if I was correct about this issue > and whether we can consider this a bug and hope to get it fixed for the > upcoming versions. > > Thanks a lot for your consideration in advance, > Sepide > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 tevain at telecom-paristech.fr Thu Aug 25 04:59:24 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Thu, 25 Aug 2016 10:59:24 +0200 (CEST) Subject: [ITK-users] ASM and AAM in ITK In-Reply-To: <1121240625.46335790.1472114394416.JavaMail.zimbra@enst.fr> Message-ID: <1090038339.46348680.1472115564462.JavaMail.zimbra@enst.fr> Hi everybody, I'm currently trying to build teeth models to guide segmentation in CBCT data. With the help of the ImagePCAShapeModelEstimator I was able to build an ASM model. But that's not enough and I would like to add the intensity information, thus building an appearance model. Since there isn't build-in solution, I have two questions: -Is anyone aware of a code project for AAM which could be used with itk? -In the perspective of coding my own method, I've taken a look to the ImagePCAShapeModelEstimator code. The way the PCA is performed puzzle me. The principal component are computed by combining the data matrix to the eigenvectors of the inner product matrix, not by taking the eigenvector of covariance matrix, for computational efficiency. I don't see the equivalence between these methods. Is there somewhere I could get information on this, a math sheet or something like that ? Tim From aharr8 at uwo.ca Thu Aug 25 07:53:47 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Thu, 25 Aug 2016 07:53:47 -0400 Subject: [ITK-users] [ITK] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: It's taking me longer than I thought it would to put a main function together, so I thought I would get you some image data to look at. This is a virtual phantom I generated, a white cube on a black background. The second image is the same cube but rotated by 5 degrees in the X direction. The .nfo files contain information about the image size and spacing. Let me know if you find anything out, I'll keep working on getting you a simple main function in case you need it. Thanks again.? PhantomBox.nfo ?? PhantomBox.raw ?? PhantomBoxRotX2.nfo ?? PhantomBoxRotX2.raw ? -- AH ----------------------------------------------------------------------------------------------- *This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.* On Tue, Aug 23, 2016 at 9:53 AM, D?enan Zuki? wrote: > Hi Andrew, > > you are doing so many things in a nonstandard way, starting with passing > around pointers to buffers and metadata as plain parameters, instead of > just once converting to itk::Image and then using itk::Image::Pointer to > pass the images around. Your approach is more prone to errors. > > Can you provide the inputs and the main function which invokes this class > to have a runnable example? I will try to find the problem. > > Regards, > D?enan > > On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: > >> Hello all, >> I am having a devil of a time setting up the >> CorrelationImageToImageMetricv4 and getting a result that makes sense. >> I have written an observer that outputs to a text file the iteration >> number, correlation value, and current position. I have generated a >> virtual phantom image of a white cube on a black background, and when I put >> the same image through for fixed and moving images, I get [0,0,0,0,0,0], >> meaning that no rotation or translation is required for the images to be >> aligned. This is the correct versor and vector transform, and if I apply a >> translation the correct distance values are returned to have the images >> align, however the metric value returned is also 0 and a perfect >> registration like this should yield a metric of -1 according to the >> documentation. Additionally, it doesn?t seem to be analyzing rotation >> properly, as when I introduce a rotation around any axis the metric returns >> a translation on the other two axes but the rotation versor remains at zero. >> >> I?m attaching my code as well, it?s possible I?ve not set some parameters >> up properly: >> >> >> -- >> >> AH >> >> >> ------------------------------------------------------------ >> ----------------------------------- >> >> *This email and any attachments thereto may contain private, >> confidential, and privileged materials for the sole use of the intended >> recipient. Any reviewing, copying, or distribution of this email (or any >> attachments thereto) by other than the intended recipient is strictly >> prohibited. If you are not the intended recipient, please contact the >> sender immediately and permanently destroy this email and any attachments >> thereto.* >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 Aug 25 09:25:06 2016 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Thu, 25 Aug 2016 13:25:06 +0000 Subject: [ITK-users] ASM and AAM in ITK Message-ID: Hi Tim, Before you continue on this path I would recommend that you take a look at the Statismo project (http://www.si-cas.com/ncssm/software.htm) . It may be doing what you want, to quote from their github documentation "Although the main focus of statismo lies on shape modeling, it is designed such that it supports any kind of PCA based statistical model, including statistical deformation models and intensity models." It is built on top of ITK. hope this helps Ziv On 8/25/16, 4:59 AM, "Timothee Evain" wrote: >Hi everybody, > >I'm currently trying to build teeth models to guide segmentation in CBCT >data. > >With the help of the ImagePCAShapeModelEstimator I was able to build an >ASM model. But that's not enough and I would like to add the intensity >information, thus building an appearance model. >Since there isn't build-in solution, I have two questions: > >-Is anyone aware of a code project for AAM which could be used with itk? > >-In the perspective of coding my own method, I've taken a look to the >ImagePCAShapeModelEstimator code. The way the PCA is performed puzzle me. >The principal component are computed by combining the data matrix to the >eigenvectors of the inner product matrix, not by taking the eigenvector >of covariance matrix, for computational efficiency. I don't see the >equivalence between these methods. Is there somewhere I could get >information on this, a math sheet or something like that ? > >Tim >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the 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 tevain at telecom-paristech.fr Thu Aug 25 11:59:24 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Thu, 25 Aug 2016 17:59:24 +0200 (CEST) Subject: [ITK-users] ASM and AAM in ITK In-Reply-To: References: Message-ID: <1528465751.46616463.1472140764261.JavaMail.zimbra@enst.fr> Thanks a lot Ziv! I will take a look into that library. From a quick search, I'm not sure it will be able to model the intensity of the data, I will see. Anyway, this project is a quite interesting contribution to statistical modelling with it implementation-independant model approach, and deserve to be known. Thanks for the hint :) Tim ----- Mail original ----- De: "Ziv Rafael Yaniv (NIH/NLM/LHC) [C]" ?: "Timothee Evain" , "Insight Users" Envoy?: Jeudi 25 Ao?t 2016 15:25:06 Objet: Re: [ITK-users] ASM and AAM in ITK Hi Tim, Before you continue on this path I would recommend that you take a look at the Statismo project (http://www.si-cas.com/ncssm/software.htm) . It may be doing what you want, to quote from their github documentation "Although the main focus of statismo lies on shape modeling, it is designed such that it supports any kind of PCA based statistical model, including statistical deformation models and intensity models." It is built on top of ITK. hope this helps Ziv On 8/25/16, 4:59 AM, "Timothee Evain" wrote: >Hi everybody, > >I'm currently trying to build teeth models to guide segmentation in CBCT >data. > >With the help of the ImagePCAShapeModelEstimator I was able to build an >ASM model. But that's not enough and I would like to add the intensity >information, thus building an appearance model. >Since there isn't build-in solution, I have two questions: > >-Is anyone aware of a code project for AAM which could be used with itk? > >-In the perspective of coding my own method, I've taken a look to the >ImagePCAShapeModelEstimator code. The way the PCA is performed puzzle me. >The principal component are computed by combining the data matrix to the >eigenvectors of the inner product matrix, not by taking the eigenvector >of covariance matrix, for computational efficiency. I don't see the >equivalence between these methods. Is there somewhere I could get >information on this, a math sheet or something like that ? > >Tim >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the 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 aharr8 at uwo.ca Fri Aug 26 15:14:41 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Fri, 26 Aug 2016 15:14:41 -0400 Subject: [ITK-users] [ITK] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: Sorry again for the delay, we determined the images we were creating were too big so we created a smaller phantom image, attached. In addition, there is a main() function in CorrelationTest.cpp that runs the correlation and outputs it to a file called observer.txt, and I have included the most up-to-date versions of my class and header files. The function is expecting the phantom to exist in a folder at c:/Scans/Phantom. Let me know if you need further info, and thanks again for your help.? SmallPhantomBox.raw ?? CorrelationTest.cpp ?? Correlator3D.cpp ?? Correlator3D.h ? -- AH ----------------------------------------------------------------------------------------------- *This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.* On Tue, Aug 23, 2016 at 9:53 AM, D?enan Zuki? wrote: > Hi Andrew, > > you are doing so many things in a nonstandard way, starting with passing > around pointers to buffers and metadata as plain parameters, instead of > just once converting to itk::Image and then using itk::Image::Pointer to > pass the images around. Your approach is more prone to errors. > > Can you provide the inputs and the main function which invokes this class > to have a runnable example? I will try to find the problem. > > Regards, > D?enan > > On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: > >> Hello all, >> I am having a devil of a time setting up the >> CorrelationImageToImageMetricv4 and getting a result that makes sense. >> I have written an observer that outputs to a text file the iteration >> number, correlation value, and current position. I have generated a >> virtual phantom image of a white cube on a black background, and when I put >> the same image through for fixed and moving images, I get [0,0,0,0,0,0], >> meaning that no rotation or translation is required for the images to be >> aligned. This is the correct versor and vector transform, and if I apply a >> translation the correct distance values are returned to have the images >> align, however the metric value returned is also 0 and a perfect >> registration like this should yield a metric of -1 according to the >> documentation. Additionally, it doesn?t seem to be analyzing rotation >> properly, as when I introduce a rotation around any axis the metric returns >> a translation on the other two axes but the rotation versor remains at zero. >> >> I?m attaching my code as well, it?s possible I?ve not set some parameters >> up properly: >> >> >> -- >> >> AH >> >> >> ------------------------------------------------------------ >> ----------------------------------- >> >> *This email and any attachments thereto may contain private, >> confidential, and privileged materials for the sole use of the intended >> recipient. Any reviewing, copying, or distribution of this email (or any >> attachments thereto) by other than the intended recipient is strictly >> prohibited. If you are not the intended recipient, please contact the >> sender immediately and permanently destroy this email and any attachments >> thereto.* >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 Aug 26 16:50:14 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 26 Aug 2016 16:50:14 -0400 Subject: [ITK-users] [ITK] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: Hi Andrew, the problem was that you were setting the mask to just the white box. This caused the metric to only be evaluated on one pixel intensity, which is a degenerate case and is probably what caused the correlation to be 0. Without setting either mask, the registration does something - I did not examine whether the result is correct or even meaningful. The modified files are attached - you can do a diff to see the few differences. If you need the mask for a similar case in practice, you could use dilate filter to enlarge the mask by a few voxels. Regards, D?enan On Fri, Aug 26, 2016 at 3:14 PM, Andrew Harris wrote: > Sorry again for the delay, we determined the images we were creating were > too big so we created a smaller phantom image, attached. In addition, > there is a main() function in CorrelationTest.cpp that runs the correlation > and outputs it to a file called observer.txt, and I have included the most > up-to-date versions of my class and header files. The function is > expecting the phantom to exist in a folder at c:/Scans/Phantom. Let me > know if you need further info, and thanks again for your help.? > SmallPhantomBox.raw > > ?? > CorrelationTest.cpp > > ?? > Correlator3D.cpp > > ?? > Correlator3D.h > > ? > > -- > > AH > > > ------------------------------------------------------------ > ----------------------------------- > > *This email and any attachments thereto may contain private, > confidential, and privileged materials for the sole use of the intended > recipient. Any reviewing, copying, or distribution of this email (or any > attachments thereto) by other than the intended recipient is strictly > prohibited. If you are not the intended recipient, please contact the > sender immediately and permanently destroy this email and any attachments > thereto.* > > On Tue, Aug 23, 2016 at 9:53 AM, D?enan Zuki? wrote: > >> Hi Andrew, >> >> you are doing so many things in a nonstandard way, starting with passing >> around pointers to buffers and metadata as plain parameters, instead of >> just once converting to itk::Image and then using itk::Image::Pointer to >> pass the images around. Your approach is more prone to errors. >> >> Can you provide the inputs and the main function which invokes this class >> to have a runnable example? I will try to find the problem. >> >> Regards, >> D?enan >> >> On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: >> >>> Hello all, >>> I am having a devil of a time setting up the >>> CorrelationImageToImageMetricv4 and getting a result that makes sense. >>> I have written an observer that outputs to a text file the iteration >>> number, correlation value, and current position. I have generated a >>> virtual phantom image of a white cube on a black background, and when I put >>> the same image through for fixed and moving images, I get [0,0,0,0,0,0], >>> meaning that no rotation or translation is required for the images to be >>> aligned. This is the correct versor and vector transform, and if I apply a >>> translation the correct distance values are returned to have the images >>> align, however the metric value returned is also 0 and a perfect >>> registration like this should yield a metric of -1 according to the >>> documentation. Additionally, it doesn?t seem to be analyzing rotation >>> properly, as when I introduce a rotation around any axis the metric returns >>> a translation on the other two axes but the rotation versor remains at zero. >>> >>> I?m attaching my code as well, it?s possible I?ve not set some >>> parameters up properly: >>> >>> >>> -- >>> >>> AH >>> >>> >>> ------------------------------------------------------------ >>> ----------------------------------- >>> >>> *This email and any attachments thereto may contain private, >>> confidential, and privileged materials for the sole use of the intended >>> recipient. Any reviewing, copying, or distribution of this email (or any >>> attachments thereto) by other than the intended recipient is strictly >>> prohibited. If you are not the intended recipient, please contact the >>> sender immediately and permanently destroy this email and any attachments >>> thereto.* >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 -------------- Iteration: 0 Calculation: 1 Value = -0.714321 Position: [0, 0, 0, 0, 0, 0] Iteration: 0 Calculation: 2 Value = 0 Position: [-0.44869711458819234, -0.3193438163428909, 0.8322332598948731, -0.03702978345737059, 0.05202905520612079, 7.648517331413413e-11] Iteration: 0 Calculation: 3 Value = -0.259188 Position: [-0.05356018556689876, -0.03811950981379673, 0.09934222081152533, -0.004420180137104539, 0.00621061683061597, 9.129900644850814e-12] Iteration: 0 Calculation: 4 Value = -0.741777 Position: [-0.0018972980288040964, -0.0013503327156766355, 0.003519065472379799, -0.00015657897694571133, 0.0002200028051745136, 3.234145347576637e-13] Iteration: 0 Calculation: 5 Value = -0.741777 Position: [-0.0018972980288040964, -0.0013503327156766355, 0.003519065472379799, -0.00015657897694571133, 0.0002200028051745136, 3.234145347576637e-13] Iteration: 1 Calculation: 6 Value = -0.764069 Position: [-0.008864090218485405, -0.007374896592515705, 0.020338116205582384, -0.0006576375484633565, 0.0012860372951096447, 0.00022307664983305773] Iteration: 1 Calculation: 7 Value = -0.764069 Position: [-0.008864090218485405, -0.007374896592515705, 0.020338116205582384, -0.0006576375484633565, 0.0012860372951096447, 0.00022307664983305773] Iteration: 2 Calculation: 8 Value = -0.768639 Position: [-0.007362369143132123, -0.005453990604406128, 0.01819539033060534, -0.0003739565466923287, 0.0012063875812397637, 0.0002982793118707005] Iteration: 2 Calculation: 9 Value = -0.768639 Position: [-0.007362369143132123, -0.005453990604406128, 0.01819539033060534, -0.0003739565466923287, 0.0012063875812397637, 0.0002982793118707005] Iteration: 3 Calculation: 10 Value = -0.769345 Position: [-0.0063722110784427445, -0.004674860804162271, 0.01869368990204535, -0.0001296212038001693, 0.0012940408600778173, 0.0004709802964571845] Iteration: 3 Calculation: 11 Value = -0.769345 Position: [-0.0063722110784427445, -0.004674860804162271, 0.01869368990204535, -0.0001296212038001693, 0.0012940408600778173, 0.0004709802964571845] Iteration: 4 Calculation: 12 Value = -0.771464 Position: [0.007388884078228691, 0.008516254318087854, 0.0293297785177389, 0.003835853083661105, 0.00290783602505402, 0.0032057741175897177] Iteration: 4 Calculation: 13 Value = -0.771464 Position: [0.007388884078228691, 0.008516254318087854, 0.0293297785177389, 0.003835853083661105, 0.00290783602505402, 0.0032057741175897177] Iteration: 5 Calculation: 14 Value = -0.771616 Position: [0.03099193061558464, 0.032248721416564013, 0.05173840999553268, 0.011093456031267445, 0.006026166796194969, 0.008235101260558113] Iteration: 5 Calculation: 15 Value = -0.771616 Position: [0.03099193061558464, 0.032248721416564013, 0.05173840999553268, 0.011093456031267445, 0.006026166796194969, 0.008235101260558113] -------------- next part -------------- A non-text attachment was scrubbed... Name: tester.cpp Type: text/x-c++src Size: 1141 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Correlator3D.cpp Type: text/x-c++src Size: 18667 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Correlator3D.h Type: text/x-chdr Size: 4592 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rotatedImage.nrrd Type: application/octet-stream Size: 1366 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: fixedImage.nrrd Type: application/octet-stream Size: 1159 bytes Desc: not available URL: From tammy.diprima at stonybrook.edu Sat Aug 27 16:04:13 2016 From: tammy.diprima at stonybrook.edu (Tammy DiPrima) Date: Sat, 27 Aug 2016 16:04:13 -0400 Subject: [ITK-users] max min image matrix Message-ID: Hello, Is StatisticsImageFilter->GetMaximum() and GetMinimum() the ITK functions that calculate the max/min values in the 2D image array? I?m running the example code from ITKWikiExamples , and the output is: Mean: 23.5875 Std.: 73.8819 Min: Max: ? I modified the code to write the image to file (attached). As far as I can tell, statisticsImageFilter->GetMinimum() should be 0 and statisticsImageFilter->GetMaximum() should be 255. Is GetMinimum() and GetMaximum() not the right functions? Thanks in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 3886 bytes Desc: not available URL: From chinander at gmail.com Sat Aug 27 16:33:16 2016 From: chinander at gmail.com (Mike Chinander) Date: Sat, 27 Aug 2016 15:33:16 -0500 Subject: [ITK-users] max min image matrix In-Reply-To: References: Message-ID: Since the image type is unsigned char, cout is interpreting the values of GetMaximum() and GetMinimum as chars. Cast the result to int before sending to cout: std::cout << "Min: " << static_cast(statisticsImageFilter->GetMinimum()) << std::endl; std::cout << "Max: " << static_cast(statisticsImageFilter->GetMaximum()) << std::endl; On Sat, Aug 27, 2016 at 3:04 PM, Tammy DiPrima wrote: > Hello, > > Is StatisticsImageFilter->GetMaximum() and GetMinimum() the ITK functions > that calculate the max/min values in the 2D image array? > I?m running the example code from ITKWikiExamples > , > and the output is: > > Mean: 23.5875 > Std.: 73.8819 > Min: > Max: ? > > I modified the code to write the image to file (attached). As far as I > can tell, statisticsImageFilter->GetMinimum() should be 0 > and statisticsImageFilter->GetMaximum() should be 255. > > Is GetMinimum() and GetMaximum() not the right functions? > > Thanks in advance > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 3886 bytes Desc: not available URL: From jaroslawlobaza at gmail.com Sun Aug 28 05:23:36 2016 From: jaroslawlobaza at gmail.com (Krakers) Date: Sun, 28 Aug 2016 02:23:36 -0700 (MST) Subject: [ITK-users] Reopening data after conversion vtk -> itk -> vtk Message-ID: <1472376216630-37443.post@n7.nabble.com> Hello wise itk users. Context of my situation is : - I use vtk for opening dicom image and convert it to ITK image, with VTKImageToImageFilter - process it with MedianImageFilter - convert back to VTK and save to a file. I encounter a problem with opening saved data after conversion. I don't get any specific error, maybe I should compile with debug options? I will be greatfull for every advice. -- View this message in context: http://itk-users.7.n7.nabble.com/Reopening-data-after-conversion-vtk-itk-vtk-tp37443.html Sent from the ITK - Users mailing list archive at Nabble.com. From dzenanz at gmail.com Mon Aug 29 09:29:13 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 29 Aug 2016 09:29:13 -0400 Subject: [ITK-users] Reopening data after conversion vtk -> itk -> vtk In-Reply-To: <1472376216630-37443.post@n7.nabble.com> References: <1472376216630-37443.post@n7.nabble.com> Message-ID: Hi Jaroslaw, what kind of problem do you encounter? Crash? Exception? What is the error message? Or maybe the image loads incorrectly? Why are you using VTK to load DICOM data? Using ITK only simplifies things. Regards, D?enan On Sun, Aug 28, 2016 at 5:23 AM, Krakers wrote: > Hello wise itk users. > > Context of my situation is : > - I use vtk for opening dicom image and convert it to ITK image, with > VTKImageToImageFilter > - process it with MedianImageFilter > - convert back to VTK and save to a file. > > I encounter a problem with opening saved data after conversion. > I don't get any specific error, maybe I should compile with debug options? > I will be greatfull for every advice. > > > > > > -- > View this message in context: http://itk-users.7.n7.nabble. > com/Reopening-data-after-conversion-vtk-itk-vtk-tp37443.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 sepideh.movaghati at gmail.com Mon Aug 29 12:23:37 2016 From: sepideh.movaghati at gmail.com (sepideh movaghati) Date: Mon, 29 Aug 2016 12:23:37 -0400 Subject: [ITK-users] Problem Using ScaleEstimator in V4 Registration In-Reply-To: References: Message-ID: Hi D?enan, Thanks for your response. You are right. The functions I mentioned are setting the sampling strategy of the scale estimator not the registration metric. In my tests I made sure that I use a regular sampling for registration metric. The problem I mentioned is causing a non-deterministic behavior when changing the order of two completely unrelated registrations. I reposted the same issue in insight-developer mailing and there I explained this non-deterministic behavior in detail. Thanks a lot, Sepide On Wed, Aug 24, 2016 at 2:45 PM, D?enan Zuki? wrote: > Hi Sepide, > > if I remember correctly, registration framework is advertised as using > random sampling. And the function you mention is not used for sampling the > registration metric, but rather for parameter scale estimation. So even if > random sampling usage for scale estimation is unintentional, I don't > believe it is a major problem. Perhaps someone who participated in writing > the registration framework can chime in? > > Regards, > D?enan > > On Wed, Aug 24, 2016 at 1:52 PM, Sepide Movaghati < > sepideh.movaghati at gmail.com> wrote: > >> Hi, >> >> I found a problem while I was using ScaleEstimator in v4 registration: >> >> In itkRegistrationParametersScaleEstimator class there are two functions >> SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the >> sampling strategy is chosen based on the Transformation type. For example >> if the transformation is of type displacement field or BSpline, it uses all >> of the samples. If transformation is any regular affine or rigid >> transformation (child of class MatrixOffsetTransformBase) it performs >> corner sampling. However, if the transformation is none of the known ones, >> it uses Random Sampling. >> >> Here is the problem: in itkImageRegistrationMethodv4.hxx the Metric >> transformation is set using ->SetMovingTransform() and it is always a >> CompositeTransform! Therefore, ScaleEstimator cannot detect the >> transformation type and it always fall into "else" which is using Random >> Sampling! It does not matter if you do a multilevel registration or not. >> The transformation is always of type CompositeTransform even if you do just >> a one level rigid transform! >> >> I would appreciate if you let me know if I was correct about this issue >> and whether we can consider this a bug and hope to get it fixed for the >> upcoming versions. >> >> Thanks a lot for your consideration in advance, >> Sepide >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 tammy.diprima at stonybrook.edu Tue Aug 30 12:25:22 2016 From: tammy.diprima at stonybrook.edu (Tammy Diprima) Date: Tue, 30 Aug 2016 12:25:22 -0400 Subject: [ITK-users] built opencv bridge but can't find Message-ID: I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. I recompiled using make. In my C++ program I'm including the headers: #include *#include "itkOpenCVImageBridge.h"* But it's saying "cannot find itkOpenCVImageBridge.h" I put messaging output in my CMakeLists.txt: include_directories(${OpenCV_INCLUDE_DIRS}) MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) And the output shows that the directory is incorrect: *OpenCV_INCLUDE_DIRS* /usr/local/include/opencv*/usr/local/include* This might be what's causing the problem. I tried to do a set() but it didn't seem to fix it. Can somebody please advise? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tammy.diprima at stonybrook.edu Tue Aug 30 12:35:34 2016 From: tammy.diprima at stonybrook.edu (Tammy Diprima) Date: Tue, 30 Aug 2016 12:35:34 -0400 Subject: [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: OK I have an update. So, set() worked to reset the broken variable (workaround). And then I had to locate itkOpenCVImageBridge.* and copy the files to the location. That worked. But -- does anybody have an idea how I could have broken OpenCV_INCLUDE_DIRS in the first place? And also -- something tells me I shouldn't have had to copy the source files to the OpenCV_INCLUDE_DIRS. What did I do wrong? Thanks again. *30 August 2016 at 12:25:* > I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. > I recompiled using make. > > In my C++ program I'm including the headers: > #include > *#include "itkOpenCVImageBridge.h"* > > But it's saying "cannot find itkOpenCVImageBridge.h" > > I put messaging output in my CMakeLists.txt: > include_directories(${OpenCV_INCLUDE_DIRS}) > MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) > > And the output shows that the directory is incorrect: > *OpenCV_INCLUDE_DIRS* /usr/local/include/opencv*/usr/local/include* > > This might be what's causing the problem. I tried to do a set() but it > didn't seem to fix it. > > Can somebody please advise? > > Thanks. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Aug 30 13:28:38 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Aug 2016 13:28:38 -0400 Subject: [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: Hi Tammy, Your project's CMakeLists.txt needs: find_package(ITK) include(${ITK_USE_FILE}) The "include(${ITK_USE_FILE})" command calls "include_directories" with the directories containing itkOpenCVImageBridge.h. HTH, Matt On Tue, Aug 30, 2016 at 12:35 PM, Tammy Diprima wrote: > OK I have an update. So, set() worked to reset the broken variable > (workaround). And then I had to locate itkOpenCVImageBridge.* and copy the > files to the location. > > That worked. > > But -- does anybody have an idea how I could have broken OpenCV_INCLUDE_DIRS > in the first place? > And also -- something tells me I shouldn't have had to copy the source files > to the OpenCV_INCLUDE_DIRS. What did I do wrong? > > Thanks again. > > > > 30 August 2016 at 12:25: > >> I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. >> I recompiled using make. >> >> In my C++ program I'm including the headers: >> #include >> #include "itkOpenCVImageBridge.h" >> >> But it's saying "cannot find itkOpenCVImageBridge.h" >> >> I put messaging output in my CMakeLists.txt: >> include_directories(${OpenCV_INCLUDE_DIRS}) >> MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) >> >> And the output shows that the directory is incorrect: >> OpenCV_INCLUDE_DIRS /usr/local/include/opencv/usr/local/include >> >> This might be what's causing the problem. I tried to do a set() but it >> didn't seem to fix it. >> >> Can somebody please advise? >> >> Thanks. > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 ibr_ex at yahoo.com Tue Aug 30 15:14:00 2016 From: ibr_ex at yahoo.com (ibraheem aldhamari) Date: Tue, 30 Aug 2016 19:14:00 +0000 (UTC) Subject: [ITK-users] QVtkWidget beginner questions References: <1311842425.2660868.1472584440996.ref@mail.yahoo.com> Message-ID: <1311842425.2660868.1472584440996@mail.yahoo.com> I am writing some ITK examples while learning it following?different tutorials. I have Ubuntu 14.04. I build these tools from the source: ITK 4.10, VTK 7.0, QT5.7 and CMake 3.6.1 ?In example 2, I wrote a simple GUI application that read a DICOM volume from a folder, displays it in a QVtkWidget, thresholds the slice and displays it in another QVtkWidget. Save the resulted thresholded volume in a new folder.?I had some problems that I was able to solve like the dark output and the flipping, see the code comments. My questions:? ? 1- Is there a way to filter and write all the images at once instead of using the for loop?? 2- Writing the way I did make the output volume lost some origin information i.e value, 0,0 . What did I do wrong??? 3- I read some posts about using QVtkWidget2 and ?QVtkWidget3 but I couldn't find them in my vtk?build, is there some options I missed when I built?vtk??? 4- How can I display?a specific plane instead of the axial slices e.g. display a coronal slice. ? 5- How can I get the voxel information when I point in the QVTkWidget? I am not sure if the mapping I used is correct.Here is the link to the examples:?GUI ITK Examples using VTK Qt5 and CMake - IbraheemTutorials Actually, I am not sure if what I did is the correct way to combine QT, VTK and ITK so your?comments are welcome.?? ?? Best regards!Ibraheem -------------- next part -------------- An HTML attachment was scrubbed... URL: From tammy.diprima at stonybrook.edu Tue Aug 30 19:52:56 2016 From: tammy.diprima at stonybrook.edu (Tammy Diprima) Date: Tue, 30 Aug 2016 19:52:56 -0400 Subject: [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: Hi Matt, Thank you for the advice. You're right, in that I need not include any OpenCV dirs; it's all about ITK. The problem is, I'm already doing the: find_package( ITK REQUIRED ) include( ${ITK_USE_FILE} ) The compiler's not happy unless I physically copy the header and source files (itkOpenCVImageBridge.*) from [ ITK-SOURCE-DIR]/Modules/Video/BridgeOpenCV/include to a location CMakeLists knows about (in an include directory). Which makes sense, but I would have thought when I built ITK with the BridgeOpenCV flag turned on that it would have been copied during that particular process. Oh well. At least it's working now. Cheers, thanks a lot. Tammy On 30 August 2016 at 13:28, Matt McCormick wrote: > Hi Tammy, > > Your project's CMakeLists.txt needs: > > find_package(ITK) > include(${ITK_USE_FILE}) > > The "include(${ITK_USE_FILE})" command calls "include_directories" > with the directories containing itkOpenCVImageBridge.h. > > HTH, > Matt > > On Tue, Aug 30, 2016 at 12:35 PM, Tammy Diprima > wrote: > > OK I have an update. So, set() worked to reset the broken variable > > (workaround). And then I had to locate itkOpenCVImageBridge.* and copy > the > > files to the location. > > > > That worked. > > > > But -- does anybody have an idea how I could have broken > OpenCV_INCLUDE_DIRS > > in the first place? > > And also -- something tells me I shouldn't have had to copy the source > files > > to the OpenCV_INCLUDE_DIRS. What did I do wrong? > > > > Thanks again. > > > > > > > > 30 August 2016 at 12:25: > > > >> I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. > >> I recompiled using make. > >> > >> In my C++ program I'm including the headers: > >> #include > >> #include "itkOpenCVImageBridge.h" > >> > >> But it's saying "cannot find itkOpenCVImageBridge.h" > >> > >> I put messaging output in my CMakeLists.txt: > >> include_directories(${OpenCV_INCLUDE_DIRS}) > >> MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) > >> > >> And the output shows that the directory is incorrect: > >> OpenCV_INCLUDE_DIRS /usr/local/include/opencv/usr/local/include > >> > >> This might be what's causing the problem. I tried to do a set() but it > >> didn't seem to fix it. > >> > >> Can somebody please advise? > >> > >> Thanks. > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the 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 ibr_ex at yahoo.com Wed Aug 31 03:01:30 2016 From: ibr_ex at yahoo.com (Ibraheem) Date: Wed, 31 Aug 2016 00:01:30 -0700 (MST) Subject: [ITK-users] QVtkWidget beginner questions Message-ID: <1472626890697-37451.post@n7.nabble.com> Dear all, I am writing some ITK examples while learning it following different tutorials . I have Ubuntu 14.04. I build these tools from the source: ITK 4.10, VTK 7.0, QT5.7 and CMake 3.6.1 In example 2, I wrote a simple GUI application that read a DICOM volume from a folder, displays it in a QVtkWidget, thresholds the slice and displays it in another QVtkWidget. Save the resulted thresholded volume in a new folder. I had some problems that I was able to solve like the dark output and the flipping, see the bellow code comments. My questions: 1- Is there a way to filter and write all the images at once instead of using the for loop? 2- Writing the way I did make the output volume lost some origin information i.e value, 0,0 . What did I do wrong? 3- I read some posts about using QVtkWidget2 and QVtkWidget3 but I couldn't find them in my vtk build, is there some options I missed when I built vtk? 4- How can I display a specific plane instead of the axial slices e.g. display a coronal slice. 5- How can I get the voxel information when I point in the QVTkWidget? I am not sure if the mapping I used is correct. Here is the link to the examples . Actually, I am not sure if what I did is the correct way to combine QT, VTK and ITK so your comments are welcome . Best regards! Ibraheem myDCMSeriesIO__src.zip // ================== Initialization ========================== typedef itk::Image< short, 3 > InputImageType; typedef itk::Image< short, 3 > OutputImageType; //---------------------------------- Reading -------------------------------------------------- typedef itk::GDCMSeriesFileNames InputFileNamesGeneratorType; InputFileNamesGeneratorType::Pointer inputNames = InputFileNamesGeneratorType::New(); typedef itk::GDCMImageIO ImageIOType; ImageIOType::Pointer gdcmIO = ImageIOType::New(); typedef itk::ImageSeriesReader< InputImageType > DCMReaderType; DCMReaderType::Pointer reader = DCMReaderType::New(); //---------------------------------- Writing -------------------------------------------------- typedef itk::NumericSeriesFileNames OutputNamesGeneratorType; OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New(); typedef itk::ImageSeriesWriter< InputImageType, InputImageType > DCMWriterType; DCMWriterType::Pointer writer = DCMWriterType::New(); //---------------------------------- Filtering -------------------------------------------------- typedef itk::ThresholdImageFilter< InputImageType > ThresholdImageType; ThresholdImageType::Pointer filterThresh = ThresholdImageType::New(); //---------------------------------- Display -------------------------------------------------- typedef itk::ImageToVTKImageFilter ConnectorSType;// ConnectorType typedef itk::ImageToVTKImageFilter ConnectorFType;// ConnectorType int nSlices, midS; // number of slices and middle slice //x,y,z of Camera parameters: Position, UpView and FocapPoint double CPx, CPy, CPz, CUx, CUy, CUz, CFx, CFy, CFz ; int myValue=0; // to filter the same slice from the source widget ConnectorSType::Pointer vtkImgS = ConnectorSType::New(); // connector of the Source itk Image ConnectorFType::Pointer vtkImgF = ConnectorFType::New(); // connector of the filtered itk Image // Viewers for the source and the filtered images vtkSmartPointer imageViewerS = vtkSmartPointer::New(); vtkSmartPointer imageViewerF = vtkSmartPointer::New(); vtkSmartPointer myStyleS = vtkSmartPointer::New(); vtkSmartPointer myStyleF = vtkSmartPointer::New(); void mWin::on_butF_clicked(){ reader->SetFileName(inputNames->GetInputFileNames()[myValue]); // get one slice reader->Update(); // filtering : get threshold filterThresh->SetInput( reader->GetOutput() ); QString thVals=ui->ThVal->text(); int ut= thVals.toInt() ; //filterThresh->ThresholdOutside(lt,ut); filterThresh->ThresholdAbove(ut); filterThresh->SetOutsideValue(0); filterThresh->Update(); // Convert to VTK image using ImageToVTKImageFilter vtkImgF->SetInput(filterThresh->GetOutput ()); vtkImgF->Update(); //vtk image imageViewerF->SetInputData( vtkImgF->GetOutput() ); // ok but the image currpted sometime CFx = ui->cFx->text().toDouble(); CFy = ui->cFy->text().toDouble(); CFz = ui->cFz->text().toDouble(); CPx = ui->cPx->text().toDouble(); CPy = ui->cPy->text().toDouble(); CPz = ui->cPz->text().toDouble(); CUx = ui->cUx->text().toDouble(); CUy = ui->cUx->text().toDouble(); CUz = ui->cUx->text().toDouble(); vtkCamera * cam2 = imageViewerF->GetRenderer()->GetActiveCamera(); cam2->SetFocalPoint(CFx, CFy, CFz); // 0 0 0 cam2->SetPosition (CPx, CPy, CPz); // 0 0 -1 cam2->SetViewUp (CUx, CUy, CUz); // -1 0 0 imageViewerF->GetRenderer()->ResetCamera( ); double * range = vtkImgF->GetOutput()->GetScalarRange(); std::cout<< " color range: "<< range[0] << " , "<SetColorLevel( 0.5 * ( range[1]+ range[0]) ); imageViewerS->SetColorWindow(range[1]-range[0]); imageViewerF->GetRenderWindow()->SetInteractor( ui->vtkWF->GetRenderWindow()->GetInteractor() ); imageViewerF->Render(); //Connect to the QVTKWidget ui->vtkWF->SetRenderWindow(imageViewerF->GetRenderWindow()); //ui->vtkW->GetRenderWindow()->GetInteractor()->SetInteractorStyle(0); // 3D ui->vtkWF->GetRenderWindow()->GetInteractor()->SetInteractorStyle(myStyleF); // contrast ui->vtkWF->update(); qApp->processEvents(); } -- View this message in context: http://itk-users.7.n7.nabble.com/QVtkWidget-beginner-questions-tp37451.html Sent from the ITK - Users mailing list archive at Nabble.com. From tammy.diprima at stonybrook.edu Wed Aug 31 09:32:11 2016 From: tammy.diprima at stonybrook.edu (Tammy Diprima) Date: Wed, 31 Aug 2016 09:32:11 -0400 Subject: [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: I think I just answered my own question. I forgot *sudo make install*. Now both itkOpenCVImageBridge files are where they're supposed to be, in /usr/local/include/ITK-4.8. Matt, the chat with you totally helped. Sorry to interrupt your day, but -- Thanks very much. I really appreciate it. -- T *30 August 2016 at 19:52:* > Hi Matt, > > Thank you for the advice. You're right, in that I need not include any > OpenCV dirs; it's all about ITK. > The problem is, I'm already doing the: > > find_package( ITK REQUIRED ) > include( ${ITK_USE_FILE} ) > > The compiler's not happy unless I physically copy the header and source > files (itkOpenCVImageBridge.*) from [ITK-SOURCE-DIR]/Modules/ > Video/BridgeOpenCV/include to a location CMakeLists knows about (in an > include directory). Which makes sense, but I would have thought when I > built ITK with the BridgeOpenCV flag turned on that it would have been > copied during that particular process. Oh well. At least it's working now. > > Cheers, thanks a lot. > Tammy > > > On 30 August 2016 at 13:28, Matt McCormick > wrote: > >> Hi Tammy, >> >> Your project's CMakeLists.txt needs: >> >> find_package(ITK) >> include(${ITK_USE_FILE}) >> >> The "include(${ITK_USE_FILE})" command calls "include_directories" >> with the directories containing itkOpenCVImageBridge.h. >> >> HTH, >> Matt >> >> On Tue, Aug 30, 2016 at 12:35 PM, Tammy Diprima >> wrote: >> > OK I have an update. So, set() worked to reset the broken variable >> > (workaround). And then I had to locate itkOpenCVImageBridge.* and copy >> the >> > files to the location. >> > >> > That worked. >> > >> > But -- does anybody have an idea how I could have broken >> OpenCV_INCLUDE_DIRS >> > in the first place? >> > And also -- something tells me I shouldn't have had to copy the source >> files >> > to the OpenCV_INCLUDE_DIRS. What did I do wrong? >> > >> > Thanks again. >> > >> > >> > >> > 30 August 2016 at 12:25: >> > >> >> I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. >> >> I recompiled using make. >> >> >> >> In my C++ program I'm including the headers: >> >> #include >> >> #include "itkOpenCVImageBridge.h" >> >> >> >> But it's saying "cannot find itkOpenCVImageBridge.h" >> >> >> >> I put messaging output in my CMakeLists.txt: >> >> include_directories(${OpenCV_INCLUDE_DIRS}) >> >> MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) >> >> >> >> And the output shows that the directory is incorrect: >> >> OpenCV_INCLUDE_DIRS /usr/local/include/opencv/usr/local/include >> >> >> >> This might be what's causing the problem. I tried to do a set() but it >> >> didn't seem to fix it. >> >> >> >> Can somebody please advise? >> >> >> >> Thanks. >> > >> > >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the 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 Aug 31 10:09:38 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 31 Aug 2016 10:09:38 -0400 Subject: [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: Hi Tammy, Thanks for sharing your progress and the update! Welcome to ITK :-) Matt On Wed, Aug 31, 2016 at 9:32 AM, Tammy Diprima wrote: > I think I just answered my own question. I forgot sudo make install. Now > both itkOpenCVImageBridge files are where they're supposed to be, in > /usr/local/include/ITK-4.8. > > Matt, the chat with you totally helped. Sorry to interrupt your day, but -- > Thanks very much. I really appreciate it. -- T > > > 30 August 2016 at 19:52: > >> Hi Matt, >> >> Thank you for the advice. You're right, in that I need not include any >> OpenCV dirs; it's all about ITK. >> The problem is, I'm already doing the: >> >> find_package( ITK REQUIRED ) >> include( ${ITK_USE_FILE} ) >> >> The compiler's not happy unless I physically copy the header and source >> files (itkOpenCVImageBridge.*) from >> [ITK-SOURCE-DIR]/Modules/Video/BridgeOpenCV/include to a location CMakeLists >> knows about (in an include directory). Which makes sense, but I would have >> thought when I built ITK with the BridgeOpenCV flag turned on that it would >> have been copied during that particular process. Oh well. At least it's >> working now. >> >> Cheers, thanks a lot. >> Tammy >> >> >> On 30 August 2016 at 13:28, Matt McCormick >> wrote: >>> >>> Hi Tammy, >>> >>> Your project's CMakeLists.txt needs: >>> >>> find_package(ITK) >>> include(${ITK_USE_FILE}) >>> >>> The "include(${ITK_USE_FILE})" command calls "include_directories" >>> with the directories containing itkOpenCVImageBridge.h. >>> >>> HTH, >>> Matt >>> >>> On Tue, Aug 30, 2016 at 12:35 PM, Tammy Diprima >>> wrote: >>> > OK I have an update. So, set() worked to reset the broken variable >>> > (workaround). And then I had to locate itkOpenCVImageBridge.* and copy >>> > the >>> > files to the location. >>> > >>> > That worked. >>> > >>> > But -- does anybody have an idea how I could have broken >>> > OpenCV_INCLUDE_DIRS >>> > in the first place? >>> > And also -- something tells me I shouldn't have had to copy the source >>> > files >>> > to the OpenCV_INCLUDE_DIRS. What did I do wrong? >>> > >>> > Thanks again. >>> > >>> > >>> > >>> > 30 August 2016 at 12:25: >>> > >>> >> I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. >>> >> I recompiled using make. >>> >> >>> >> In my C++ program I'm including the headers: >>> >> #include >>> >> #include "itkOpenCVImageBridge.h" >>> >> >>> >> But it's saying "cannot find itkOpenCVImageBridge.h" >>> >> >>> >> I put messaging output in my CMakeLists.txt: >>> >> include_directories(${OpenCV_INCLUDE_DIRS}) >>> >> MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) >>> >> >>> >> And the output shows that the directory is incorrect: >>> >> OpenCV_INCLUDE_DIRS /usr/local/include/opencv/usr/local/include >>> >> >>> >> This might be what's causing the problem. I tried to do a set() but >>> >> it >>> >> didn't seem to fix it. >>> >> >>> >> Can somebody please advise? >>> >> >>> >> Thanks. >>> > >>> > >>> > >>> > _____________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://www.kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> > >> >> > From matt.mccormick at kitware.com Wed Aug 31 10:16:38 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 31 Aug 2016 10:16:38 -0400 Subject: [ITK-users] QVtkWidget beginner questions In-Reply-To: <1472626890697-37451.post@n7.nabble.com> References: <1472626890697-37451.post@n7.nabble.com> Message-ID: Hello Ibraheem, Welcome to ITK :-) Please see comments inline below. On Wed, Aug 31, 2016 at 3:01 AM, Ibraheem via Insight-users wrote: > Dear all, > I am writing some ITK examples while learning it following different > tutorials . I have Ubuntu 14.04. I build these tools from the source: ITK > 4.10, VTK 7.0, QT5.7 and CMake 3.6.1 > In example 2, I wrote a simple GUI application that read a DICOM volume from > a folder, displays it in a QVtkWidget, thresholds the slice and displays it > in another QVtkWidget. Save the resulted thresholded volume in a new folder. > I had some problems that I was able to solve like the dark output and the > flipping, see the bellow code comments. Excellent. Thanks for sharing your efforts! > My questions: > 1- Is there a way to filter and write all the images at once instead of > using the for loop? To write to an image series in general, there is an itk::ImageSeriesWriter. > 2- Writing the way I did make the output volume lost some origin > information i.e value, 0,0 . What did I do wrong? Writing DICOMs (correctly) is currently a very tricky endeavour. There are currently some experiments underway to make this easier. However, until that time, it is recommended to use another format, like MetaImage, for writing files. > 3- I read some posts about using QVtkWidget2 and QVtkWidget3 but I > couldn't find them in my vtk build, is there some options I missed when I > built vtk? > 4- How can I display a specific plane instead of the axial slices e.g. > display a coronal slice. > 5- How can I get the voxel information when I point in the QVTkWidget? I > am not sure if the mapping I used is correct. These questions are welcome, but the VTK mailing list is a better place to discuss these issues. Matt From noreply at insightsoftwareconsortium.org Wed Aug 31 17:15:49 2016 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Wed, 31 Aug 2016 17:15:49 -0400 (EDT) Subject: [ITK-users] New Submission: Two Luis Miguel fans walk into a bar in Nagoya ---> (yada, yada, yada) ---> an ITK-implementation of a popular patch-based denoising filter Message-ID: <20160831211549.9CC363D620C4@insight-journal.org> Hello, A new submission has been added to the Insight Journal. Title: Two Luis Miguel fans walk into a bar in Nagoya ---> (yada, yada, yada) ---> an ITK-implementation of a popular patch-based denoising filter Authors: Tustison N., Manjon Herrera J. Abstract: This document describes an ITK implementation of the adaptive patch-based image denoising algorithm described in cite{Manjon:2010aa}. This offering consists of the templated class itkPatchBasedDenoisingImageFilter interfaced through the DenoiseImage program which includes its own interface program. We include a couple of examples. Download and review this publication at: http://hdl.handle.net/10380/3564 Generated by the Insight Journal You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://insight-journal.org/ .