From simon.esneault at gmail.com Mon Dec 1 06:54:43 2014 From: simon.esneault at gmail.com (Simon ESNEAULT) Date: Mon, 1 Dec 2014 12:54:43 +0100 Subject: [ITK] [ITK-users] Exception in itk::ResampleImageFilter multithreaded part after ITK migration from 3.20.1 to 4.6.1 Message-ID: Hello ITK community After the migration from ITK 3.20.1 to ITK 4.6.1, I'm getting a runtime exception when using itk::ResampleImageFilter in our framework. The output looks like this : Problem during Resample filtering: D:\Dev\DevCpp-Qt5\cmake-externals\ITK\src\Modules\Core\Common\src\itkMultiThreader.cxx:358: itk::ERROR: MultiThreader(31CAAD18): Exception occurred during SingleMethodExecute c:\dev\Dev_qt5\externals\itk-4.6.1\win32\include\itkImageSource.hxx:267: itk::ERROR: ResampleImageFilter(31AC2E90): Subclass should override this method!!! The signature of ThreadedGenerateData() has been changed in ITK v4 to use the new ThreadIdType. ResampleImageFilter::ThreadedGenerateData() might need to be updated to used it. That is weird, because the itkResampleImageFilter is the one delivered with ITK 4.6.1, so it must have followed the API changed ... The context is : Visual Studio 2013 community, 32 bit build, ITK build in shared library mode. That's quite a big project, with VTK, Qt, OpenCV, DCMTK, zlib ... I'm not using cmake in the usual way (ie no find_package(ITK) include(${ITK_USE_FILE}) ) but we list the libraries and includes. I know there are some factories to register in that case, we're doing this in the main.cpp : itk::TransformFactoryBase::RegisterDefaultTransforms(); itk::PNGImageIOFactory::RegisterOneFactory(); itk::MetaImageIOFactory::RegisterOneFactory(); itk::NrrdImageIOFactory::RegisterOneFactory(); Am I missing some others factories to register in order to run properly the resampleImageFilter ? Anyone else had a similar runtime exception with a native ITK filte, or know what would raise such an exception ? Thanks -- ------------------------------------------------------------------ Simon Esneault ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From simon.esneault at gmail.com Mon Dec 1 07:53:20 2014 From: simon.esneault at gmail.com (Simon ESNEAULT) Date: Mon, 1 Dec 2014 13:53:20 +0100 Subject: [ITK] [ITK-dev] Exception in itk::ResampleImageFilter multithreaded part after ITK migration from 3.20.1 to 4.6.1 Message-ID: Hello ITK community After the migration from ITK 3.20.1 to ITK 4.6.1, I'm getting a runtime exception when using itk::ResampleImageFilter in our framework. The output looks like this : Problem during Resample filtering: D:\Dev\DevCpp-Qt5\cmake-externals\ITK\src\Modules\Core\Common\src\itkMultiThreader.cxx:358: itk::ERROR: MultiThreader(31CAAD18): Exception occurred during SingleMethodExecute c:\dev\Dev_qt5\externals\itk-4.6.1\win32\include\itkImageSource.hxx:267: itk::ERROR: ResampleImageFilter(31AC2E90): Subclass should override this method!!! The signature of ThreadedGenerateData() has been changed in ITK v4 to use the new ThreadIdType. ResampleImageFilter::ThreadedGenerateData() might need to be updated to used it. That is weird, because the itkResampleImageFilter is the one delivered with ITK 4.6.1, so it must have followed the API changed ... The context is : Visual Studio 2013 community, 32 bit build, ITK build in shared library mode. That's quite a big project, with VTK, Qt, OpenCV, DCMTK, zlib ... I'm not using cmake in the usual way (ie no find_package(ITK) include(${ITK_USE_FILE}) ) but we list the libraries and includes. I know there are some factories to register in that case, we're doing this in the main.cpp : itk::TransformFactoryBase::RegisterDefaultTransforms(); itk::PNGImageIOFactory::RegisterOneFactory(); itk::MetaImageIOFactory::RegisterOneFactory(); itk::NrrdImageIOFactory::RegisterOneFactory(); Am I missing some others factories to register in order to run properly the resampleImageFilter ? Anyone else had a similar runtime exception with a native ITK filte, or know what would raise such an exception ? Thanks -- ------------------------------------------------------------------ Simon Esneault ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From bill.lorensen at gmail.com Mon Dec 1 08:51:41 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 1 Dec 2014 08:51:41 -0500 Subject: [ITK] [ITK-dev] Exception in itk::ResampleImageFilter multithreaded part after ITK migration from 3.20.1 to 4.6.1 In-Reply-To: References: Message-ID: Very strange. Could you try building and running this example: http://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter Bill On Mon, Dec 1, 2014 at 7:53 AM, Simon ESNEAULT wrote: > Hello ITK community > > After the migration from ITK 3.20.1 to ITK 4.6.1, I'm getting a runtime > exception when using itk::ResampleImageFilter in our framework. The output > looks like this : > > Problem during Resample filtering: > D:\Dev\DevCpp-Qt5\cmake-externals\ITK\src\Modules\Core\Common\src\itkMultiThreader.cxx:358: > itk::ERROR: MultiThreader(31CAAD18): Exception occurred during > SingleMethodExecute > c:\dev\Dev_qt5\externals\itk-4.6.1\win32\include\itkImageSource.hxx:267: > itk::ERROR: ResampleImageFilter(31AC2E90): Subclass should override this > method!!! > The signature of ThreadedGenerateData() has been changed in ITK v4 to use > the new ThreadIdType. > ResampleImageFilter::ThreadedGenerateData() might need to be updated to used > it. > > That is weird, because the itkResampleImageFilter is the one delivered with > ITK 4.6.1, so it must have followed the API changed ... > > The context is : > Visual Studio 2013 community, 32 bit build, ITK build in shared library > mode. That's quite a big project, with VTK, Qt, OpenCV, DCMTK, zlib ... > I'm not using cmake in the usual way (ie no find_package(ITK) > include(${ITK_USE_FILE}) ) but we list the libraries and includes. I know > there are some factories to register in that case, we're doing this in the > main.cpp : > itk::TransformFactoryBase::RegisterDefaultTransforms(); > itk::PNGImageIOFactory::RegisterOneFactory(); > itk::MetaImageIOFactory::RegisterOneFactory(); > itk::NrrdImageIOFactory::RegisterOneFactory(); > > Am I missing some others factories to register in order to run properly the > resampleImageFilter ? > Anyone else had a similar runtime exception with a native ITK filte, or know > what would raise such an exception ? > > Thanks > > -- > ------------------------------------------------------------------ > Simon Esneault > ------------------------------------------------------------------ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From fdrakopo at gmail.com Mon Dec 1 11:56:47 2014 From: fdrakopo at gmail.com (Fotis Drakopoulos) Date: Mon, 1 Dec 2014 11:56:47 -0500 Subject: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti volume. In-Reply-To: References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> Message-ID: Hi all, I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader. The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300. The pixelType is short. Thanks Fotis On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick wrote: > Thanks! Added. > > On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos > wrote: > > Hi, > > I signed up for the ITK community on midas. > > > > Thanks, > > Fotis Drakopoulos > > > > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick > > wrote: > >> > >> Hi Fotis, > >> > >> Thanks for helping to improve large nifti file support. > >> > >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK > >> community [1], let the list know the name of your account, and myself > >> or one of the other administrators will add upload priviledges to the > >> account. > >> > >> The file could then be added to > >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. > >> > >> Thanks, > >> Matt > >> > >> [1] http://midas3.kitware.com/midas/community/12 > >> > >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos > >> wrote: > >> > Hi all, > >> > > >> > I created a test nifti image that reproduces the problem I mentioned > >> > before. > >> > How can I share this image with the ITK community? > >> > > >> > Best, > >> > Fotis Drakopoulos > >> > > >> > > >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp > >> > > >> > wrote: > >> >> > >> >> Shareable test data greatly helps determine the cause and fix these > >> >> types > >> >> of issues. > >> >> > >> >> Got data? > >> >> > >> >> Brad > >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle > wrote: > >> >> > >> >> This is reminiscent of the previous problem with big TIFF images, now > >> >> fixed. > >> >> > >> >> Gib > >> >> ________________________________ > >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of > Fotis > >> >> Drakopoulos [fdrakopo at gmail.com] > >> >> Sent: Monday, 24 November 2014 10:51 a.m. > >> >> To: insight-users at itk.org; insight-developers at itk.org > >> >> Subject: [ITK-users] Problem reading a big nifti volume. > >> >> > >> >> Hi all, > >> >> > >> >> For the last couple of days I have been trying reading > (unsuccessfully) > >> >> a > >> >> big nifti volume labeled image from my disk. > >> >> > >> >> The pixel type is unsigned char and the rest specs of the image are: > >> >> Size : [1001, 1001, 8345] (in voxels) > >> >> Spacing : [0.012, 0.012, 0.012] (in mm) > >> >> Origin : [0, 0, 0] > >> >> Direction : > >> >> 1 0 0 > >> >> 0 1 0 > >> >> 0 0 1 > >> >> > >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an > idea > >> >> how it looks like. Indeed the object in the volume looks as it was > >> >> expected. > >> >> So far no problems. The specs of the image on Slicer are the same as > >> >> above > >> >> (except the direction which has flipped signs for the first two > >> >> diagonal > >> >> entries, as we know ). > >> >> > >> >> Then I tried to load the image in the memory using the > >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After > >> >> loading > >> >> the image I noticed that there are pixels with zero values instead of > >> >> non-zero by comparing the same indexes with the loaded image on > Slicer. > >> >> > >> >> Then I decided to write the loaded image on the disk using the > >> >> itk::ImageFileWriter. > >> >> > >> >> After opening the (written from ITK) image on Slicer I checked the > >> >> specks > >> >> and were the same with the original image as above. However I noticed > >> >> that a > >> >> big portion of the image is completely empty (black)! > >> >> > >> >> My workstation has enough memory to load the image (768 GB 1600MHz > >> >> DDR3L) > >> >> and is using Red Hat Enterprise Linux Server 6.5. > >> >> The size of the original nifti volume is : > >> >> > >> >> 25.7 MB (.nii.gz) > >> >> 8.36 GB (.nii) > >> >> > >> >> Has anybody experienced similar difficulties trying to load so big > >> >> volume > >> >> data? > >> >> > >> >> Best, > >> >> Fotis Drakopoulos > >> >> CRTC > >> >> > >> >> _____________________________________ > >> >> Powered by www.kitware.com > >> >> > >> >> Visit other Kitware open-source projects at > >> >> http://www.kitware.com/opensource/opensource.html > >> >> > >> >> Kitware offers ITK Training Courses, for more information visit: > >> >> http://www.kitware.com/products/protraining.php > >> >> > >> >> Please keep messages on-topic and check the ITK FAQ at: > >> >> http://www.itk.org/Wiki/ITK_FAQ > >> >> > >> >> Follow this link to subscribe/unsubscribe: > >> >> http://public.kitware.com/mailman/listinfo/insight-users > >> >> > >> >> > >> >> ________________________________ > >> >> > >> >> Spam > >> >> Not spam > >> >> Forget previous vote > >> > > >> > > >> > > >> > _______________________________________________ > >> > Powered by www.kitware.com > >> > > >> > Visit other Kitware open-source projects at > >> > http://www.kitware.com/opensource/opensource.html > >> > > >> > Kitware offers ITK Training Courses, for more information visit: > >> > http://kitware.com/products/protraining.php > >> > > >> > Please keep messages on-topic and check the ITK FAQ at: > >> > http://www.itk.org/Wiki/ITK_FAQ > >> > > >> > Follow this link to subscribe/unsubscribe: > >> > http://public.kitware.com/mailman/listinfo/insight-developers > >> > > >> > >> > >> -- > >> > > > > > -- > BEGIN-ANTISPAM-VOTING-LINKS > ------------------------------------------------------ > > Teach CanIt if this mail (ID 03NkpHcqT) is spam: > Spam: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=s > Not spam: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=n > Forget vote: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=f > ------------------------------------------------------ > END-ANTISPAM-VOTING-LINKS > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From fdrakopo at gmail.com Mon Dec 1 11:56:47 2014 From: fdrakopo at gmail.com (Fotis Drakopoulos) Date: Mon, 1 Dec 2014 11:56:47 -0500 Subject: [ITK] [ITK-users] [ITK-dev] Problem reading a big nifti volume. In-Reply-To: References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> Message-ID: Hi all, I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader. The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300. The pixelType is short. Thanks Fotis On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick wrote: > Thanks! Added. > > On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos > wrote: > > Hi, > > I signed up for the ITK community on midas. > > > > Thanks, > > Fotis Drakopoulos > > > > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick > > wrote: > >> > >> Hi Fotis, > >> > >> Thanks for helping to improve large nifti file support. > >> > >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK > >> community [1], let the list know the name of your account, and myself > >> or one of the other administrators will add upload priviledges to the > >> account. > >> > >> The file could then be added to > >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. > >> > >> Thanks, > >> Matt > >> > >> [1] http://midas3.kitware.com/midas/community/12 > >> > >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos > >> wrote: > >> > Hi all, > >> > > >> > I created a test nifti image that reproduces the problem I mentioned > >> > before. > >> > How can I share this image with the ITK community? > >> > > >> > Best, > >> > Fotis Drakopoulos > >> > > >> > > >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp > >> > > >> > wrote: > >> >> > >> >> Shareable test data greatly helps determine the cause and fix these > >> >> types > >> >> of issues. > >> >> > >> >> Got data? > >> >> > >> >> Brad > >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle > wrote: > >> >> > >> >> This is reminiscent of the previous problem with big TIFF images, now > >> >> fixed. > >> >> > >> >> Gib > >> >> ________________________________ > >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of > Fotis > >> >> Drakopoulos [fdrakopo at gmail.com] > >> >> Sent: Monday, 24 November 2014 10:51 a.m. > >> >> To: insight-users at itk.org; insight-developers at itk.org > >> >> Subject: [ITK-users] Problem reading a big nifti volume. > >> >> > >> >> Hi all, > >> >> > >> >> For the last couple of days I have been trying reading > (unsuccessfully) > >> >> a > >> >> big nifti volume labeled image from my disk. > >> >> > >> >> The pixel type is unsigned char and the rest specs of the image are: > >> >> Size : [1001, 1001, 8345] (in voxels) > >> >> Spacing : [0.012, 0.012, 0.012] (in mm) > >> >> Origin : [0, 0, 0] > >> >> Direction : > >> >> 1 0 0 > >> >> 0 1 0 > >> >> 0 0 1 > >> >> > >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an > idea > >> >> how it looks like. Indeed the object in the volume looks as it was > >> >> expected. > >> >> So far no problems. The specs of the image on Slicer are the same as > >> >> above > >> >> (except the direction which has flipped signs for the first two > >> >> diagonal > >> >> entries, as we know ). > >> >> > >> >> Then I tried to load the image in the memory using the > >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After > >> >> loading > >> >> the image I noticed that there are pixels with zero values instead of > >> >> non-zero by comparing the same indexes with the loaded image on > Slicer. > >> >> > >> >> Then I decided to write the loaded image on the disk using the > >> >> itk::ImageFileWriter. > >> >> > >> >> After opening the (written from ITK) image on Slicer I checked the > >> >> specks > >> >> and were the same with the original image as above. However I noticed > >> >> that a > >> >> big portion of the image is completely empty (black)! > >> >> > >> >> My workstation has enough memory to load the image (768 GB 1600MHz > >> >> DDR3L) > >> >> and is using Red Hat Enterprise Linux Server 6.5. > >> >> The size of the original nifti volume is : > >> >> > >> >> 25.7 MB (.nii.gz) > >> >> 8.36 GB (.nii) > >> >> > >> >> Has anybody experienced similar difficulties trying to load so big > >> >> volume > >> >> data? > >> >> > >> >> Best, > >> >> Fotis Drakopoulos > >> >> CRTC > >> >> > >> >> _____________________________________ > >> >> Powered by www.kitware.com > >> >> > >> >> Visit other Kitware open-source projects at > >> >> http://www.kitware.com/opensource/opensource.html > >> >> > >> >> Kitware offers ITK Training Courses, for more information visit: > >> >> http://www.kitware.com/products/protraining.php > >> >> > >> >> Please keep messages on-topic and check the ITK FAQ at: > >> >> http://www.itk.org/Wiki/ITK_FAQ > >> >> > >> >> Follow this link to subscribe/unsubscribe: > >> >> http://public.kitware.com/mailman/listinfo/insight-users > >> >> > >> >> > >> >> ________________________________ > >> >> > >> >> Spam > >> >> Not spam > >> >> Forget previous vote > >> > > >> > > >> > > >> > _______________________________________________ > >> > Powered by www.kitware.com > >> > > >> > Visit other Kitware open-source projects at > >> > http://www.kitware.com/opensource/opensource.html > >> > > >> > Kitware offers ITK Training Courses, for more information visit: > >> > http://kitware.com/products/protraining.php > >> > > >> > Please keep messages on-topic and check the ITK FAQ at: > >> > http://www.itk.org/Wiki/ITK_FAQ > >> > > >> > Follow this link to subscribe/unsubscribe: > >> > http://public.kitware.com/mailman/listinfo/insight-developers > >> > > >> > >> > >> -- > >> > > > > > -- > BEGIN-ANTISPAM-VOTING-LINKS > ------------------------------------------------------ > > Teach CanIt if this mail (ID 03NkpHcqT) is spam: > Spam: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=s > Not spam: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=n > Forget vote: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=f > ------------------------------------------------------ > END-ANTISPAM-VOTING-LINKS > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From drcjaudet at gmail.com Tue Dec 2 03:55:23 2014 From: drcjaudet at gmail.com (Cyril Jaudet) Date: Tue, 2 Dec 2014 09:55:23 +0100 Subject: [ITK] Choose the number of decimal Message-ID: Hello everyone, I have a simple yet a little stupid question. I want to restrain to two the number of decimal in float type image (PET SUV image). For this type of image it is really enought and will reduce the amount of time to postreatment, i suppose. An approximate value will be better then truncate. Is there a filter in itk or simple itk to do it? Thank's a lot, Cyril -------------- next part -------------- An HTML attachment was scrubbed... URL: From chiara.magliaro at googlemail.com Tue Dec 2 04:40:06 2014 From: chiara.magliaro at googlemail.com (Chiara Magliaro) Date: Tue, 2 Dec 2014 10:40:06 +0100 Subject: [ITK] simple question about Volume From Slices Message-ID: Hi all, I'm new of Itk and C++ programming language. I tryed to use the Volume From Slices example (link: http://www.itk.org/Wiki/ITK/Examples/IO/VolumeFromSlices) The script works well, but the 3d image obtained is not smooth. In fact, I can discriminate the contourn of the 2d images glued together, as you can see in pre.png. I tryed with an anti alias filter (fig. post.png), but i "lost" the shape of my cell. It is not a probem of registration of the stack (the images are acquired with a confocal microscope, so they are just aligned) How can I have a 3d image more suitable for the visualization? Thanks in advance Chiara Magliaro -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pre.png Type: image/png Size: 83333 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: post.png Type: image/png Size: 67224 bytes Desc: not available URL: From simon.esneault at gmail.com Tue Dec 2 04:51:52 2014 From: simon.esneault at gmail.com (Simon ESNEAULT) Date: Tue, 2 Dec 2014 10:51:52 +0100 Subject: [ITK] [ITK-dev] Exception in itk::ResampleImageFilter multithreaded part after ITK migration from 3.20.1 to 4.6.1 In-Reply-To: References: Message-ID: Hi Bill, Thanks for your reply. I have downloaded and executed succesfully the Upsampling example ( http://itk.org/Wiki/ITK/Examples/ImageProcessing/Upsampling), using the version of ITK (4.6.1) we used in the framework. It appears our problem is probably related with our framework architecture, and some dll import/export on windows. We wrapped all our ITK code in a library WrapItk.dll. And there are some others libraries, all of them can make use of native ITK code or wrapped ITK code. This used to work fine with ITK 3.20.1, but it's seems broken in 4.6.1. Not only the Resample filter raise an exception but all the MultiThreaded filter in ITK. When debugging, we go through itk::ResampleImageFilter::BeforeThreadedGenerateData() just fine, and somehow, when ThreadedGenerateData() is called we fall back in the mother class ImageSource method, hence raising the exception. Anyone know how to use properly ITK code with multiple DLL's on windows ? ie having an image loaded with ITK code from one DLL, and some ITK filter executed in another DLL without trouble ? We use that sort of mechanism to export functions properly between DLLs. #if SOME_DLL_DEFINITIONS #define MY_EXPORT __declspec(dllexport) #else #define MY_EXPORT __declspec(dllimport) I will try to sum things up in scheme if that can help ... Thanks Simon 2014-12-01 14:51 GMT+01:00 Bill Lorensen : > Very strange. > > Could you try building and running this example: > http://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter > > Bill > > On Mon, Dec 1, 2014 at 7:53 AM, Simon ESNEAULT > wrote: > > Hello ITK community > > > > After the migration from ITK 3.20.1 to ITK 4.6.1, I'm getting a runtime > > exception when using itk::ResampleImageFilter in our framework. The > output > > looks like this : > > > > Problem during Resample filtering: > > > D:\Dev\DevCpp-Qt5\cmake-externals\ITK\src\Modules\Core\Common\src\itkMultiThreader.cxx:358: > > itk::ERROR: MultiThreader(31CAAD18): Exception occurred during > > SingleMethodExecute > > c:\dev\Dev_qt5\externals\itk-4.6.1\win32\include\itkImageSource.hxx:267: > > itk::ERROR: ResampleImageFilter(31AC2E90): Subclass should override this > > method!!! > > The signature of ThreadedGenerateData() has been changed in ITK v4 to use > > the new ThreadIdType. > > ResampleImageFilter::ThreadedGenerateData() might need to be updated to > used > > it. > > > > That is weird, because the itkResampleImageFilter is the one delivered > with > > ITK 4.6.1, so it must have followed the API changed ... > > > > The context is : > > Visual Studio 2013 community, 32 bit build, ITK build in shared library > > mode. That's quite a big project, with VTK, Qt, OpenCV, DCMTK, zlib ... > > I'm not using cmake in the usual way (ie no find_package(ITK) > > include(${ITK_USE_FILE}) ) but we list the libraries and includes. I know > > there are some factories to register in that case, we're doing this in > the > > main.cpp : > > itk::TransformFactoryBase::RegisterDefaultTransforms(); > > itk::PNGImageIOFactory::RegisterOneFactory(); > > itk::MetaImageIOFactory::RegisterOneFactory(); > > itk::NrrdImageIOFactory::RegisterOneFactory(); > > > > Am I missing some others factories to register in order to run properly > the > > resampleImageFilter ? > > Anyone else had a similar runtime exception with a native ITK filte, or > know > > what would raise such an exception ? > > > > Thanks > > > > -- > > ------------------------------------------------------------------ > > Simon Esneault > > ------------------------------------------------------------------ > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > > > > > -- > Unpaid intern in BillsBasement at noware dot com > -- ------------------------------------------------------------------ Simon Esneault ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From fitz at zhaw.ch Tue Dec 2 05:07:17 2014 From: fitz at zhaw.ch (Fitze Thomas (fitz)) Date: Tue, 2 Dec 2014 10:07:17 +0000 Subject: [ITK] simple question about Volume From Slices In-Reply-To: References: Message-ID: <849A0B6C-5F05-489B-99B1-24E09BB4FEEF@zhaw.ch> Hi Chiara, One option i had good results with, is creating a surface mesh from your volume and do a surface reconstruction. There are different reconstruction methods, which one to use depends or your use case. Poisson reconstruction would be a good starting point. To extract and reconstruct the surface, you could either use VTK (1) or some tools to do the extraction (2) and reconstruction (3). (1) http://www.vtkjournal.org/browse/publication/718 (2) http://mitk.org/wiki/Downloads (3) http://meshlab.sourceforge.net/ Cheers, Thomas On 02.12.2014, at 10:40, Chiara Magliaro > wrote: Hi all, I'm new of Itk and C++ programming language. I tryed to use the Volume From Slices example (link: http://www.itk.org/Wiki/ITK/Examples/IO/VolumeFromSlices) The script works well, but the 3d image obtained is not smooth. In fact, I can discriminate the contourn of the 2d images glued together, as you can see in pre.png. I tryed with an anti alias filter (fig. post.png), but i "lost" the shape of my cell. It is not a probem of registration of the stack (the images are acquired with a confocal microscope, so they are just aligned) How can I have a 3d image more suitable for the visualization? Thanks in advance Chiara Magliaro _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Dec 2 09:45:34 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 09:45:34 -0500 Subject: [ITK] [ITK-dev] Exception in itk::ResampleImageFilter multithreaded part after ITK migration from 3.20.1 to 4.6.1 In-Reply-To: References: Message-ID: Hello Simon, If you don't have your exports correct it'd likely result in a link error. Given the error message you report, it sounds like you are using an old version of the ResampleFilter. I'd look into seeing if there are old copies of ITK 3.20 laying around that may be included in your project. You can not use mix symbols and includes from different version of ITK. Brad On Dec 2, 2014, at 4:51 AM, Simon ESNEAULT wrote: > Hi Bill, > > Thanks for your reply. I have downloaded and executed succesfully the Upsampling example (http://itk.org/Wiki/ITK/Examples/ImageProcessing/Upsampling), using the version of ITK (4.6.1) we used in the framework. > > It appears our problem is probably related with our framework architecture, and some dll import/export on windows. We wrapped all our ITK code in a library WrapItk.dll. And there are some others libraries, all of them can make use of native ITK code or wrapped ITK code. This used to work fine with ITK 3.20.1, but it's seems broken in 4.6.1. > > Not only the Resample filter raise an exception but all the MultiThreaded filter in ITK. When debugging, we go through itk::ResampleImageFilter::BeforeThreadedGenerateData() just fine, and somehow, when ThreadedGenerateData() is called we fall back in the mother class ImageSource method, hence raising the exception. > > Anyone know how to use properly ITK code with multiple DLL's on windows ? ie having an image loaded with ITK code from one DLL, and some ITK filter executed in another DLL without trouble ? > We use that sort of mechanism to export functions properly between DLLs. > #if SOME_DLL_DEFINITIONS > #define MY_EXPORT __declspec(dllexport) > #else > #define MY_EXPORT __declspec(dllimport) > > I will try to sum things up in scheme if that can help ... > > Thanks > Simon > > > 2014-12-01 14:51 GMT+01:00 Bill Lorensen : > Very strange. > > Could you try building and running this example: > http://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter > > Bill > > On Mon, Dec 1, 2014 at 7:53 AM, Simon ESNEAULT wrote: > > Hello ITK community > > > > After the migration from ITK 3.20.1 to ITK 4.6.1, I'm getting a runtime > > exception when using itk::ResampleImageFilter in our framework. The output > > looks like this : > > > > Problem during Resample filtering: > > D:\Dev\DevCpp-Qt5\cmake-externals\ITK\src\Modules\Core\Common\src\itkMultiThreader.cxx:358: > > itk::ERROR: MultiThreader(31CAAD18): Exception occurred during > > SingleMethodExecute > > c:\dev\Dev_qt5\externals\itk-4.6.1\win32\include\itkImageSource.hxx:267: > > itk::ERROR: ResampleImageFilter(31AC2E90): Subclass should override this > > method!!! > > The signature of ThreadedGenerateData() has been changed in ITK v4 to use > > the new ThreadIdType. > > ResampleImageFilter::ThreadedGenerateData() might need to be updated to used > > it. > > > > That is weird, because the itkResampleImageFilter is the one delivered with > > ITK 4.6.1, so it must have followed the API changed ... > > > > The context is : > > Visual Studio 2013 community, 32 bit build, ITK build in shared library > > mode. That's quite a big project, with VTK, Qt, OpenCV, DCMTK, zlib ... > > I'm not using cmake in the usual way (ie no find_package(ITK) > > include(${ITK_USE_FILE}) ) but we list the libraries and includes. I know > > there are some factories to register in that case, we're doing this in the > > main.cpp : > > itk::TransformFactoryBase::RegisterDefaultTransforms(); > > itk::PNGImageIOFactory::RegisterOneFactory(); > > itk::MetaImageIOFactory::RegisterOneFactory(); > > itk::NrrdImageIOFactory::RegisterOneFactory(); > > > > Am I missing some others factories to register in order to run properly the > > resampleImageFilter ? > > Anyone else had a similar runtime exception with a native ITK filte, or know > > what would raise such an exception ? > > > > Thanks > > > > -- > > ------------------------------------------------------------------ > > Simon Esneault > > ------------------------------------------------------------------ > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > > > > > -- > Unpaid intern in BillsBasement at noware dot com > > > > -- > ------------------------------------------------------------------ > Simon Esneault > ------------------------------------------------------------------ > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 2 09:50:25 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 09:50:25 -0500 Subject: [ITK] [ITK-dev] FDFImageIO Pull request In-Reply-To: <025B8F34-0769-4625-AC4B-5F1B7C3B5806@gmail.com> References: <821CBBE2-3D5D-4526-B8BD-A5AE3049C921@mail.nih.gov> <025B8F34-0769-4625-AC4B-5F1B7C3B5806@gmail.com> Message-ID: Hello Nick, The patch adds the missing private registration method that results in a link error. Then the patch adds the correct export specifications so that it can be a shared library on windows, and utilize default internal linkage with GCC. This minimizes the number of symbols exported creating a more efficient library. The one issue here was what to do with the functions in the FDFCommonImage header[1]. I didn't mark them as exported. I think these are more like private methods, so perhaps the header should be moved to the src directory so that it's not installed and not usable outside the module. Brad [1] https://github.com/InsightSoftwareConsortium/itkFDFImageIO/blob/master/include/itkFDFCommonImageIO.h On Nov 25, 2014, at 8:28 PM, Nicholas Tustison wrote: > Hi Brad, > > I use it for a single collaborator who acquires images in this FDF format. > I apologize but I don?t understand the errors that you?re seeing. Kent and > I updated the code from a contributor who had posted it back in the early > 2000s. I didn?t think there was anything particularly complex about the > code. > > Nick > > > >> On Nov 25, 2014, at 6:17 AM, Bradley Lowekamp wrote: >> >> Hello, >> >> To address compilation errors with FDFImageIO I have a pull request. >> >> https://github.com/InsightSoftwareConsortium/itkFDFImageIO/pull/1 >> >> Reviews are appreciated. >> >> This module does not appear to have been working for a while. Is there continued support and usage from the community for this module? >> >> Thanks, >> Brad > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 2 10:27:28 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 10:27:28 -0500 Subject: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti volume. In-Reply-To: References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> Message-ID: <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> Hello, What software did you use to create and validate that this image is correct? Thanks, Brad On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos wrote: > Hi all, > > I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader. > The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300. > The pixelType is short. > > Thanks > Fotis > > On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick wrote: > Thanks! Added. > > On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos wrote: > > Hi, > > I signed up for the ITK community on midas. > > > > Thanks, > > Fotis Drakopoulos > > > > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick > > wrote: > >> > >> Hi Fotis, > >> > >> Thanks for helping to improve large nifti file support. > >> > >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK > >> community [1], let the list know the name of your account, and myself > >> or one of the other administrators will add upload priviledges to the > >> account. > >> > >> The file could then be added to > >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. > >> > >> Thanks, > >> Matt > >> > >> [1] http://midas3.kitware.com/midas/community/12 > >> > >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos > >> wrote: > >> > Hi all, > >> > > >> > I created a test nifti image that reproduces the problem I mentioned > >> > before. > >> > How can I share this image with the ITK community? > >> > > >> > Best, > >> > Fotis Drakopoulos > >> > > >> > > >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp > >> > > >> > wrote: > >> >> > >> >> Shareable test data greatly helps determine the cause and fix these > >> >> types > >> >> of issues. > >> >> > >> >> Got data? > >> >> > >> >> Brad > >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle wrote: > >> >> > >> >> This is reminiscent of the previous problem with big TIFF images, now > >> >> fixed. > >> >> > >> >> Gib > >> >> ________________________________ > >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis > >> >> Drakopoulos [fdrakopo at gmail.com] > >> >> Sent: Monday, 24 November 2014 10:51 a.m. > >> >> To: insight-users at itk.org; insight-developers at itk.org > >> >> Subject: [ITK-users] Problem reading a big nifti volume. > >> >> > >> >> Hi all, > >> >> > >> >> For the last couple of days I have been trying reading (unsuccessfully) > >> >> a > >> >> big nifti volume labeled image from my disk. > >> >> > >> >> The pixel type is unsigned char and the rest specs of the image are: > >> >> Size : [1001, 1001, 8345] (in voxels) > >> >> Spacing : [0.012, 0.012, 0.012] (in mm) > >> >> Origin : [0, 0, 0] > >> >> Direction : > >> >> 1 0 0 > >> >> 0 1 0 > >> >> 0 0 1 > >> >> > >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea > >> >> how it looks like. Indeed the object in the volume looks as it was > >> >> expected. > >> >> So far no problems. The specs of the image on Slicer are the same as > >> >> above > >> >> (except the direction which has flipped signs for the first two > >> >> diagonal > >> >> entries, as we know ). > >> >> > >> >> Then I tried to load the image in the memory using the > >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After > >> >> loading > >> >> the image I noticed that there are pixels with zero values instead of > >> >> non-zero by comparing the same indexes with the loaded image on Slicer. > >> >> > >> >> Then I decided to write the loaded image on the disk using the > >> >> itk::ImageFileWriter. > >> >> > >> >> After opening the (written from ITK) image on Slicer I checked the > >> >> specks > >> >> and were the same with the original image as above. However I noticed > >> >> that a > >> >> big portion of the image is completely empty (black)! > >> >> > >> >> My workstation has enough memory to load the image (768 GB 1600MHz > >> >> DDR3L) > >> >> and is using Red Hat Enterprise Linux Server 6.5. > >> >> The size of the original nifti volume is : > >> >> > >> >> 25.7 MB (.nii.gz) > >> >> 8.36 GB (.nii) > >> >> > >> >> Has anybody experienced similar difficulties trying to load so big > >> >> volume > >> >> data? > >> >> > >> >> Best, > >> >> Fotis Drakopoulos > >> >> CRTC > >> >> > >> >> _____________________________________ > >> >> Powered by www.kitware.com > >> >> > >> >> Visit other Kitware open-source projects at > >> >> http://www.kitware.com/opensource/opensource.html > >> >> > >> >> Kitware offers ITK Training Courses, for more information visit: > >> >> http://www.kitware.com/products/protraining.php > >> >> > >> >> Please keep messages on-topic and check the ITK FAQ at: > >> >> http://www.itk.org/Wiki/ITK_FAQ > >> >> > >> >> Follow this link to subscribe/unsubscribe: > >> >> http://public.kitware.com/mailman/listinfo/insight-users > >> >> > >> >> > >> >> ________________________________ > >> >> > >> >> Spam > >> >> Not spam > >> >> Forget previous vote > >> > > >> > > >> > > >> > _______________________________________________ > >> > Powered by www.kitware.com > >> > > >> > Visit other Kitware open-source projects at > >> > http://www.kitware.com/opensource/opensource.html > >> > > >> > Kitware offers ITK Training Courses, for more information visit: > >> > http://kitware.com/products/protraining.php > >> > > >> > Please keep messages on-topic and check the ITK FAQ at: > >> > http://www.itk.org/Wiki/ITK_FAQ > >> > > >> > Follow this link to subscribe/unsubscribe: > >> > http://public.kitware.com/mailman/listinfo/insight-developers > >> > > >> > >> > >> -- > >> > > > > > -- > BEGIN-ANTISPAM-VOTING-LINKS > ------------------------------------------------------ > > Teach CanIt if this mail (ID 03NkpHcqT) is spam: > Spam: https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=s > Not spam: https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=n > Forget vote: https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=f > ------------------------------------------------------ > END-ANTISPAM-VOTING-LINKS > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 2 10:27:28 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 10:27:28 -0500 Subject: [ITK] [ITK-users] [ITK-dev] Problem reading a big nifti volume. In-Reply-To: References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> Message-ID: <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> Hello, What software did you use to create and validate that this image is correct? Thanks, Brad On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos wrote: > Hi all, > > I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader. > The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300. > The pixelType is short. > > Thanks > Fotis > > On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick wrote: > Thanks! Added. > > On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos wrote: > > Hi, > > I signed up for the ITK community on midas. > > > > Thanks, > > Fotis Drakopoulos > > > > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick > > wrote: > >> > >> Hi Fotis, > >> > >> Thanks for helping to improve large nifti file support. > >> > >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK > >> community [1], let the list know the name of your account, and myself > >> or one of the other administrators will add upload priviledges to the > >> account. > >> > >> The file could then be added to > >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. > >> > >> Thanks, > >> Matt > >> > >> [1] http://midas3.kitware.com/midas/community/12 > >> > >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos > >> wrote: > >> > Hi all, > >> > > >> > I created a test nifti image that reproduces the problem I mentioned > >> > before. > >> > How can I share this image with the ITK community? > >> > > >> > Best, > >> > Fotis Drakopoulos > >> > > >> > > >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp > >> > > >> > wrote: > >> >> > >> >> Shareable test data greatly helps determine the cause and fix these > >> >> types > >> >> of issues. > >> >> > >> >> Got data? > >> >> > >> >> Brad > >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle wrote: > >> >> > >> >> This is reminiscent of the previous problem with big TIFF images, now > >> >> fixed. > >> >> > >> >> Gib > >> >> ________________________________ > >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis > >> >> Drakopoulos [fdrakopo at gmail.com] > >> >> Sent: Monday, 24 November 2014 10:51 a.m. > >> >> To: insight-users at itk.org; insight-developers at itk.org > >> >> Subject: [ITK-users] Problem reading a big nifti volume. > >> >> > >> >> Hi all, > >> >> > >> >> For the last couple of days I have been trying reading (unsuccessfully) > >> >> a > >> >> big nifti volume labeled image from my disk. > >> >> > >> >> The pixel type is unsigned char and the rest specs of the image are: > >> >> Size : [1001, 1001, 8345] (in voxels) > >> >> Spacing : [0.012, 0.012, 0.012] (in mm) > >> >> Origin : [0, 0, 0] > >> >> Direction : > >> >> 1 0 0 > >> >> 0 1 0 > >> >> 0 0 1 > >> >> > >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea > >> >> how it looks like. Indeed the object in the volume looks as it was > >> >> expected. > >> >> So far no problems. The specs of the image on Slicer are the same as > >> >> above > >> >> (except the direction which has flipped signs for the first two > >> >> diagonal > >> >> entries, as we know ). > >> >> > >> >> Then I tried to load the image in the memory using the > >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After > >> >> loading > >> >> the image I noticed that there are pixels with zero values instead of > >> >> non-zero by comparing the same indexes with the loaded image on Slicer. > >> >> > >> >> Then I decided to write the loaded image on the disk using the > >> >> itk::ImageFileWriter. > >> >> > >> >> After opening the (written from ITK) image on Slicer I checked the > >> >> specks > >> >> and were the same with the original image as above. However I noticed > >> >> that a > >> >> big portion of the image is completely empty (black)! > >> >> > >> >> My workstation has enough memory to load the image (768 GB 1600MHz > >> >> DDR3L) > >> >> and is using Red Hat Enterprise Linux Server 6.5. > >> >> The size of the original nifti volume is : > >> >> > >> >> 25.7 MB (.nii.gz) > >> >> 8.36 GB (.nii) > >> >> > >> >> Has anybody experienced similar difficulties trying to load so big > >> >> volume > >> >> data? > >> >> > >> >> Best, > >> >> Fotis Drakopoulos > >> >> CRTC > >> >> > >> >> _____________________________________ > >> >> Powered by www.kitware.com > >> >> > >> >> Visit other Kitware open-source projects at > >> >> http://www.kitware.com/opensource/opensource.html > >> >> > >> >> Kitware offers ITK Training Courses, for more information visit: > >> >> http://www.kitware.com/products/protraining.php > >> >> > >> >> Please keep messages on-topic and check the ITK FAQ at: > >> >> http://www.itk.org/Wiki/ITK_FAQ > >> >> > >> >> Follow this link to subscribe/unsubscribe: > >> >> http://public.kitware.com/mailman/listinfo/insight-users > >> >> > >> >> > >> >> ________________________________ > >> >> > >> >> Spam > >> >> Not spam > >> >> Forget previous vote > >> > > >> > > >> > > >> > _______________________________________________ > >> > Powered by www.kitware.com > >> > > >> > Visit other Kitware open-source projects at > >> > http://www.kitware.com/opensource/opensource.html > >> > > >> > Kitware offers ITK Training Courses, for more information visit: > >> > http://kitware.com/products/protraining.php > >> > > >> > Please keep messages on-topic and check the ITK FAQ at: > >> > http://www.itk.org/Wiki/ITK_FAQ > >> > > >> > Follow this link to subscribe/unsubscribe: > >> > http://public.kitware.com/mailman/listinfo/insight-developers > >> > > >> > >> > >> -- > >> > > > > > -- > BEGIN-ANTISPAM-VOTING-LINKS > ------------------------------------------------------ > > Teach CanIt if this mail (ID 03NkpHcqT) is spam: > Spam: https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=s > Not spam: https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=n > Forget vote: https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=f > ------------------------------------------------------ > END-ANTISPAM-VOTING-LINKS > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Tue Dec 2 10:21:54 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 10:21:54 -0500 Subject: [ITK] [ITK-users] Otsu Filter for object/background separation In-Reply-To: References: Message-ID: <2A284D8D-9690-433C-9456-949744057644@mail.nih.gov> Hello, ITK has a histogram based thresholding framework contributed by Richard Beare through the Insight Journal [1]. At the heart of the frame work is the HistrogramThrsholdImageFilter[2], and the HistogramThresholdCalculator[3]. With this framework you should be able to write a calculator to behave as you want and then pass it to the filter with the HistogramThreshold::SetCalculator method. Also you may want to run the binary segmentation results through the LabelMap framework to analyze the statistics of the shape of the objects and selecting the one you are looking for or rejecting the results. Brad [1] http://hdl.handle.net/10380/3279 [2] http://itk.org/Insight/Doxygen/html/classitk_1_1HistogramThresholdImageFilter.html [3] http://itk.org/Insight/Doxygen/html/classitk_1_1HistogramThresholdCalculator.html On Nov 12, 2014, at 8:14 AM, Girish Mallya Udupi wrote: > Hi Zein, > > As you might know, Otsu's method assumes that the histogram of the image is bi-modal. i.e., there are two classes of pixels forming two peaks separated by a valley. > All the method (and the corresponding ITK filter) does is calculate the threshold which maximizes the inter-class variance and apply it on the image. > > > On Wed, Nov 12, 2014 at 12:43 PM, Zein Salah wrote: > Hello, > > I have been using the otsu filter for doing object-from-background separation. However, I noticed that the filter always comes out with an separation threshold, even if the image does NOT actually have a "reasonable" background, see the attached image, e.g.. > > My question is: is it possible to control the filter in such a way that it only generate a threshold if there is really a background? > > Practically, I could, in a post-processing step, do a decision weather the separation is feasible or not, e.g. computing the comparing the statistics of the two separated areas (average intensity, variance, etc.). But I thought the otsu filter already does such things internally, right? Is it possible to inquire such data from the filter? > > Any ideas would be welcome!! > > Much thanks, > > Zein > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > -- > Regards, > Girish > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Tue Dec 2 10:32:01 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 10:32:01 -0500 Subject: [ITK] Choose the number of decimal In-Reply-To: References: Message-ID: Hello, Depending on what exactly you want to do and the interpretation of the value, you could multiply the image by 100 and then convert to an appropriate integer representation to emulate fixed point operations for certain image processing algorithms. This poor mans fixed point representation may be trouble-some and cause confusion and errors if not carefully managed. However, I would think that just performing the rounding at the end of the computation would be sufficient for many cases, Brad On Dec 2, 2014, at 3:55 AM, Cyril Jaudet wrote: > Hello everyone, > > I have a simple yet a little stupid question. I want to restrain to two the number of decimal in float type image (PET SUV image). For this type of image it is really enought and will reduce the amount of time to postreatment, i suppose. An approximate value will be better then truncate. > > Is there a filter in itk or simple itk to do it? > > Thank's a lot, > Cyril > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From blowekamp at mail.nih.gov Tue Dec 2 10:26:50 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 10:26:50 -0500 Subject: [ITK] [ITK-users] Future of WrapITK In-Reply-To: References: , <189A597A-010D-4BEC-8A76-29A5046E32DD@gmail.com> Message-ID: Hello, > We are using many image filters as well as the registration framework from the ITK. I think I read that the registration framework is not fully usable in SimpleITK. The development of the SimpleITK registration interface is wrapping up. The current interface is quite usable, and powerful, although there are some minor issue that still need to be addressed. I'd encourage you to give it a try. You may be able to solve you problem faster and better with the SimpleITK wrapping of the ITKv4 registration framework. Please let us know if it works for your problem and what you think of the interface [1]. Thanks, Brad [1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html > > I'll follow the developments for ITK 4.8 and will test and help in anyways possible. Thank you all for your efforts with ITK wrappings. > > Cheers, > Lassi > > From: michkapopoff at gmail.com [michkapopoff at gmail.com] > Sent: Thursday, November 27, 2014 17:39 > To: Paavolainen Lassi > Cc: insight-users at itk.org; community at itk.org > Subject: Re: [ITK-users] Future of WrapITK > > Hi > > we have been working on Wrapping so the development is going on. > Some small improvements were made for ITK 4.7. > > I ported most of the code to Python3, but we have still an error which we have been working on, but is tricky to tackle. > I hope to get this done for ITK 4.8, and it will need some testing. > > Fixing the problem for Clang is also under way, I don?t know how much resources we can put in it but I am hoping also for ITK 4.8, though I can not > promise anything here. > > If you really need ITK wrappings on OS X, you can try my ITK binaries for homebrew: https://github.com/iMichka/homebrew-MacVTKITKPythonBottles > (Please open a ticket on the github page if you have any trouble with these binaries). > > If you would like to help, there are a lot of things to do on the wrapping code. > (Writing examples for the ITK examples website is a good way to start with). > > For SimpleITK vs Wrapping, it all depends on what image types you want to analyse, and what filters you want to use. > > Michka > >> On 27 Nov 2014, at 14:08, Paavolainen Lassi wrote: >> >> Hi, >> >> I'm developing software that uses ITK through Python wrapping. After some period of slower development progress we are now moving from ITK 3.20 to ITK 4.x. The software is developed and packages are released for 64-bit Windows, Linux and OS X. The problem is that ITK 4.6.1 with Python wrappings can be built only for Linux. It seems that there is no way around the issues with GCCXML and new Visual Studio in Win or Clang in OS X 10.9. >> >> The issue has been raised before in: http://www.itk.org/pipermail/insight-users/2014-July/050562.html >> >> To follow up that question, has there been any progress related to GCCXML replacement or development of GCCXML to support new Visual Studio and Clang? Are there still plans for this or will wrapITK be deprecated and replaced by SimpleITK? Is there anything I can help with? >> >> I noticed the Wiki page (http://www.itk.org/Wiki/ITK/Wrapping) where it is said that ITK 4.7 will include support for Python 3 but will it also fix the problem with Clang or new Visual Studios? >> >> I have to admit that I haven't tried SimpleITK so I don't know whether it could provide the same flexibility as wrapITK and how much of ITK related code would need to be rewritten. >> >> Cheers, >> Lassi >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From fdrakopo at gmail.com Tue Dec 2 10:49:06 2014 From: fdrakopo at gmail.com (Fotis Drakopoulos) Date: Tue, 2 Dec 2014 10:49:06 -0500 Subject: [ITK] [ITK-users] [ITK-dev] Problem reading a big nifti volume. In-Reply-To: <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> Message-ID: Hi, I created and wrote the image on the disk using ITK 4.6.0. I visualized the image using Slicer 4.4.0. The properties are: Size : [1001, 1001, 8345] Spacing : [1,1,1] Origin : [0, 0, 0] Direction : 1 0 0 0 1 0 0 0 1 Fotis On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp wrote: > Hello, > > What software did you use to create and validate that this image is > correct? > > Thanks, > Brad > > On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos wrote: > > Hi all, > > I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. > The image cannot loaded correctly when I use the itk::ImageFileReader. > The test image contains non-zero values only at indexes (350,350,i) where > i=0 to 8300. > The pixelType is short. > > Thanks > Fotis > > On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Thanks! Added. >> >> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos >> wrote: >> > Hi, >> > I signed up for the ITK community on midas. >> > >> > Thanks, >> > Fotis Drakopoulos >> > >> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >> > wrote: >> >> >> >> Hi Fotis, >> >> >> >> Thanks for helping to improve large nifti file support. >> >> >> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >> >> community [1], let the list know the name of your account, and myself >> >> or one of the other administrators will add upload priviledges to the >> >> account. >> >> >> >> The file could then be added to >> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >> >> >> >> Thanks, >> >> Matt >> >> >> >> [1] http://midas3.kitware.com/midas/community/12 >> >> >> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos > > >> >> wrote: >> >> > Hi all, >> >> > >> >> > I created a test nifti image that reproduces the problem I mentioned >> >> > before. >> >> > How can I share this image with the ITK community? >> >> > >> >> > Best, >> >> > Fotis Drakopoulos >> >> > >> >> > >> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >> >> > >> >> > wrote: >> >> >> >> >> >> Shareable test data greatly helps determine the cause and fix these >> >> >> types >> >> >> of issues. >> >> >> >> >> >> Got data? >> >> >> >> >> >> Brad >> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle >> wrote: >> >> >> >> >> >> This is reminiscent of the previous problem with big TIFF images, >> now >> >> >> fixed. >> >> >> >> >> >> Gib >> >> >> ________________________________ >> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of >> Fotis >> >> >> Drakopoulos [fdrakopo at gmail.com] >> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >> >> >> To: insight-users at itk.org; insight-developers at itk.org >> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >> >> >> >> >> >> Hi all, >> >> >> >> >> >> For the last couple of days I have been trying reading >> (unsuccessfully) >> >> >> a >> >> >> big nifti volume labeled image from my disk. >> >> >> >> >> >> The pixel type is unsigned char and the rest specs of the image are: >> >> >> Size : [1001, 1001, 8345] (in voxels) >> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >> >> >> Origin : [0, 0, 0] >> >> >> Direction : >> >> >> 1 0 0 >> >> >> 0 1 0 >> >> >> 0 0 1 >> >> >> >> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an >> idea >> >> >> how it looks like. Indeed the object in the volume looks as it was >> >> >> expected. >> >> >> So far no problems. The specs of the image on Slicer are the same as >> >> >> above >> >> >> (except the direction which has flipped signs for the first two >> >> >> diagonal >> >> >> entries, as we know ). >> >> >> >> >> >> Then I tried to load the image in the memory using the >> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >> >> >> loading >> >> >> the image I noticed that there are pixels with zero values instead >> of >> >> >> non-zero by comparing the same indexes with the loaded image on >> Slicer. >> >> >> >> >> >> Then I decided to write the loaded image on the disk using the >> >> >> itk::ImageFileWriter. >> >> >> >> >> >> After opening the (written from ITK) image on Slicer I checked the >> >> >> specks >> >> >> and were the same with the original image as above. However I >> noticed >> >> >> that a >> >> >> big portion of the image is completely empty (black)! >> >> >> >> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >> >> >> DDR3L) >> >> >> and is using Red Hat Enterprise Linux Server 6.5. >> >> >> The size of the original nifti volume is : >> >> >> >> >> >> 25.7 MB (.nii.gz) >> >> >> 8.36 GB (.nii) >> >> >> >> >> >> Has anybody experienced similar difficulties trying to load so big >> >> >> volume >> >> >> data? >> >> >> >> >> >> Best, >> >> >> Fotis Drakopoulos >> >> >> CRTC >> >> >> >> >> >> _____________________________________ >> >> >> Powered by www.kitware.com >> >> >> >> >> >> Visit other Kitware open-source projects at >> >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> >> http://www.kitware.com/products/protraining.php >> >> >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> >> >> >> >> >> ________________________________ >> >> >> >> >> >> Spam >> >> >> Not spam >> >> >> Forget previous vote >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Powered by www.kitware.com >> >> > >> >> > Visit other Kitware open-source projects at >> >> > http://www.kitware.com/opensource/opensource.html >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > http://kitware.com/products/protraining.php >> >> > >> >> > Please keep messages on-topic and check the ITK FAQ at: >> >> > http://www.itk.org/Wiki/ITK_FAQ >> >> > >> >> > Follow this link to subscribe/unsubscribe: >> >> > http://public.kitware.com/mailman/listinfo/insight-developers >> >> > >> >> >> >> >> >> -- >> >> >> > >> >> >> -- >> BEGIN-ANTISPAM-VOTING-LINKS >> ------------------------------------------------------ >> >> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >> Spam: about:blank >> Not spam: about:blank >> Forget vote: about:blank >> ------------------------------------------------------ >> END-ANTISPAM-VOTING-LINKS >> >> > > ------------------------------ > > Spam > > Not spam > > Forget previous vote > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From fdrakopo at gmail.com Tue Dec 2 10:49:06 2014 From: fdrakopo at gmail.com (Fotis Drakopoulos) Date: Tue, 2 Dec 2014 10:49:06 -0500 Subject: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti volume. In-Reply-To: <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> Message-ID: Hi, I created and wrote the image on the disk using ITK 4.6.0. I visualized the image using Slicer 4.4.0. The properties are: Size : [1001, 1001, 8345] Spacing : [1,1,1] Origin : [0, 0, 0] Direction : 1 0 0 0 1 0 0 0 1 Fotis On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp wrote: > Hello, > > What software did you use to create and validate that this image is > correct? > > Thanks, > Brad > > On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos wrote: > > Hi all, > > I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. > The image cannot loaded correctly when I use the itk::ImageFileReader. > The test image contains non-zero values only at indexes (350,350,i) where > i=0 to 8300. > The pixelType is short. > > Thanks > Fotis > > On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Thanks! Added. >> >> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos >> wrote: >> > Hi, >> > I signed up for the ITK community on midas. >> > >> > Thanks, >> > Fotis Drakopoulos >> > >> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >> > wrote: >> >> >> >> Hi Fotis, >> >> >> >> Thanks for helping to improve large nifti file support. >> >> >> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >> >> community [1], let the list know the name of your account, and myself >> >> or one of the other administrators will add upload priviledges to the >> >> account. >> >> >> >> The file could then be added to >> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >> >> >> >> Thanks, >> >> Matt >> >> >> >> [1] http://midas3.kitware.com/midas/community/12 >> >> >> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos > > >> >> wrote: >> >> > Hi all, >> >> > >> >> > I created a test nifti image that reproduces the problem I mentioned >> >> > before. >> >> > How can I share this image with the ITK community? >> >> > >> >> > Best, >> >> > Fotis Drakopoulos >> >> > >> >> > >> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >> >> > >> >> > wrote: >> >> >> >> >> >> Shareable test data greatly helps determine the cause and fix these >> >> >> types >> >> >> of issues. >> >> >> >> >> >> Got data? >> >> >> >> >> >> Brad >> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle >> wrote: >> >> >> >> >> >> This is reminiscent of the previous problem with big TIFF images, >> now >> >> >> fixed. >> >> >> >> >> >> Gib >> >> >> ________________________________ >> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of >> Fotis >> >> >> Drakopoulos [fdrakopo at gmail.com] >> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >> >> >> To: insight-users at itk.org; insight-developers at itk.org >> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >> >> >> >> >> >> Hi all, >> >> >> >> >> >> For the last couple of days I have been trying reading >> (unsuccessfully) >> >> >> a >> >> >> big nifti volume labeled image from my disk. >> >> >> >> >> >> The pixel type is unsigned char and the rest specs of the image are: >> >> >> Size : [1001, 1001, 8345] (in voxels) >> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >> >> >> Origin : [0, 0, 0] >> >> >> Direction : >> >> >> 1 0 0 >> >> >> 0 1 0 >> >> >> 0 0 1 >> >> >> >> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an >> idea >> >> >> how it looks like. Indeed the object in the volume looks as it was >> >> >> expected. >> >> >> So far no problems. The specs of the image on Slicer are the same as >> >> >> above >> >> >> (except the direction which has flipped signs for the first two >> >> >> diagonal >> >> >> entries, as we know ). >> >> >> >> >> >> Then I tried to load the image in the memory using the >> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >> >> >> loading >> >> >> the image I noticed that there are pixels with zero values instead >> of >> >> >> non-zero by comparing the same indexes with the loaded image on >> Slicer. >> >> >> >> >> >> Then I decided to write the loaded image on the disk using the >> >> >> itk::ImageFileWriter. >> >> >> >> >> >> After opening the (written from ITK) image on Slicer I checked the >> >> >> specks >> >> >> and were the same with the original image as above. However I >> noticed >> >> >> that a >> >> >> big portion of the image is completely empty (black)! >> >> >> >> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >> >> >> DDR3L) >> >> >> and is using Red Hat Enterprise Linux Server 6.5. >> >> >> The size of the original nifti volume is : >> >> >> >> >> >> 25.7 MB (.nii.gz) >> >> >> 8.36 GB (.nii) >> >> >> >> >> >> Has anybody experienced similar difficulties trying to load so big >> >> >> volume >> >> >> data? >> >> >> >> >> >> Best, >> >> >> Fotis Drakopoulos >> >> >> CRTC >> >> >> >> >> >> _____________________________________ >> >> >> Powered by www.kitware.com >> >> >> >> >> >> Visit other Kitware open-source projects at >> >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> >> http://www.kitware.com/products/protraining.php >> >> >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> >> >> >> >> >> ________________________________ >> >> >> >> >> >> Spam >> >> >> Not spam >> >> >> Forget previous vote >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Powered by www.kitware.com >> >> > >> >> > Visit other Kitware open-source projects at >> >> > http://www.kitware.com/opensource/opensource.html >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > http://kitware.com/products/protraining.php >> >> > >> >> > Please keep messages on-topic and check the ITK FAQ at: >> >> > http://www.itk.org/Wiki/ITK_FAQ >> >> > >> >> > Follow this link to subscribe/unsubscribe: >> >> > http://public.kitware.com/mailman/listinfo/insight-developers >> >> > >> >> >> >> >> >> -- >> >> >> > >> >> >> -- >> BEGIN-ANTISPAM-VOTING-LINKS >> ------------------------------------------------------ >> >> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >> Spam: about:blank >> Not spam: about:blank >> Forget vote: about:blank >> ------------------------------------------------------ >> END-ANTISPAM-VOTING-LINKS >> >> > > ------------------------------ > > Spam > > Not spam > > Forget previous vote > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From lassi.paavolainen at jyu.fi Tue Dec 2 10:56:02 2014 From: lassi.paavolainen at jyu.fi (Paavolainen Lassi) Date: Tue, 2 Dec 2014 15:56:02 +0000 Subject: [ITK] [ITK-users] Future of WrapITK In-Reply-To: References: , <189A597A-010D-4BEC-8A76-29A5046E32DD@gmail.com> , Message-ID: Thanks Brad, I'll give SimpleITK a try and let you know how well its able to replace our current use of WrapITK. By the way, I found Visual Studio 2008 Pro on one of our development machines, and I was able to build VTK 6.1.0 and ITK 4.6.1 with Python wrappings. So at least we are set for now except the OS X package and library needing C++11. Cheers, Lassi ________________________________ From: Bradley Lowekamp [blowekamp at mail.nih.gov] Sent: Tuesday, December 02, 2014 17:26 To: Paavolainen Lassi Cc: michkapopoff at gmail.com; insight-users at itk.org Subject: Re: [ITK-users] Future of WrapITK Hello, We are using many image filters as well as the registration framework from the ITK. I think I read that the registration framework is not fully usable in SimpleITK. The development of the SimpleITK registration interface is wrapping up. The current interface is quite usable, and powerful, although there are some minor issue that still need to be addressed. I'd encourage you to give it a try. You may be able to solve you problem faster and better with the SimpleITK wrapping of the ITKv4 registration framework. Please let us know if it works for your problem and what you think of the interface [1]. Thanks, Brad [1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html I'll follow the developments for ITK 4.8 and will test and help in anyways possible. Thank you all for your efforts with ITK wrappings. Cheers, Lassi ________________________________ From: michkapopoff at gmail.com [michkapopoff at gmail.com] Sent: Thursday, November 27, 2014 17:39 To: Paavolainen Lassi Cc: insight-users at itk.org; community at itk.org Subject: Re: [ITK-users] Future of WrapITK Hi we have been working on Wrapping so the development is going on. Some small improvements were made for ITK 4.7. I ported most of the code to Python3, but we have still an error which we have been working on, but is tricky to tackle. I hope to get this done for ITK 4.8, and it will need some testing. Fixing the problem for Clang is also under way, I don?t know how much resources we can put in it but I am hoping also for ITK 4.8, though I can not promise anything here. If you really need ITK wrappings on OS X, you can try my ITK binaries for homebrew: https://github.com/iMichka/homebrew-MacVTKITKPythonBottles (Please open a ticket on the github page if you have any trouble with these binaries). If you would like to help, there are a lot of things to do on the wrapping code. (Writing examples for the ITK examples website is a good way to start with). For SimpleITK vs Wrapping, it all depends on what image types you want to analyse, and what filters you want to use. Michka On 27 Nov 2014, at 14:08, Paavolainen Lassi > wrote: Hi, I'm developing software that uses ITK through Python wrapping. After some period of slower development progress we are now moving from ITK 3.20 to ITK 4.x. The software is developed and packages are released for 64-bit Windows, Linux and OS X. The problem is that ITK 4.6.1 with Python wrappings can be built only for Linux. It seems that there is no way around the issues with GCCXML and new Visual Studio in Win or Clang in OS X 10.9. The issue has been raised before in: http://www.itk.org/pipermail/insight-users/2014-July/050562.html To follow up that question, has there been any progress related to GCCXML replacement or development of GCCXML to support new Visual Studio and Clang? Are there still plans for this or will wrapITK be deprecated and replaced by SimpleITK? Is there anything I can help with? I noticed the Wiki page (http://www.itk.org/Wiki/ITK/Wrapping) where it is said that ITK 4.7 will include support for Python 3 but will it also fix the problem with Clang or new Visual Studios? I have to admit that I haven't tried SimpleITK so I don't know whether it could provide the same flexibility as wrapITK and how much of ITK related code would need to be rewritten. Cheers, Lassi _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Tue Dec 2 10:58:40 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 10:58:40 -0500 Subject: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti volume. In-Reply-To: References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> Message-ID: <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> So if you wrote and read with ITK ( via Slicer ), how do you know that the file is correct as you expect? I see the file has a ".nii.gz" extension, meaning that it's compressed. Does the same issue occur when it's not compressed? Brad On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos wrote: > Hi, > > I created and wrote the image on the disk using ITK 4.6.0. > I visualized the image using Slicer 4.4.0. > > The properties are: > Size : [1001, 1001, 8345] > Spacing : [1,1,1] > Origin : [0, 0, 0] > Direction : > 1 0 0 > 0 1 0 > 0 0 1 > > Fotis > > On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp wrote: > Hello, > > What software did you use to create and validate that this image is correct? > > Thanks, > Brad > > On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos wrote: > >> Hi all, >> >> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader. >> The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300. >> The pixelType is short. >> >> Thanks >> Fotis >> >> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick wrote: >> Thanks! Added. >> >> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos wrote: >> > Hi, >> > I signed up for the ITK community on midas. >> > >> > Thanks, >> > Fotis Drakopoulos >> > >> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >> > wrote: >> >> >> >> Hi Fotis, >> >> >> >> Thanks for helping to improve large nifti file support. >> >> >> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >> >> community [1], let the list know the name of your account, and myself >> >> or one of the other administrators will add upload priviledges to the >> >> account. >> >> >> >> The file could then be added to >> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >> >> >> >> Thanks, >> >> Matt >> >> >> >> [1] http://midas3.kitware.com/midas/community/12 >> >> >> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos >> >> wrote: >> >> > Hi all, >> >> > >> >> > I created a test nifti image that reproduces the problem I mentioned >> >> > before. >> >> > How can I share this image with the ITK community? >> >> > >> >> > Best, >> >> > Fotis Drakopoulos >> >> > >> >> > >> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >> >> > >> >> > wrote: >> >> >> >> >> >> Shareable test data greatly helps determine the cause and fix these >> >> >> types >> >> >> of issues. >> >> >> >> >> >> Got data? >> >> >> >> >> >> Brad >> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle wrote: >> >> >> >> >> >> This is reminiscent of the previous problem with big TIFF images, now >> >> >> fixed. >> >> >> >> >> >> Gib >> >> >> ________________________________ >> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis >> >> >> Drakopoulos [fdrakopo at gmail.com] >> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >> >> >> To: insight-users at itk.org; insight-developers at itk.org >> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >> >> >> >> >> >> Hi all, >> >> >> >> >> >> For the last couple of days I have been trying reading (unsuccessfully) >> >> >> a >> >> >> big nifti volume labeled image from my disk. >> >> >> >> >> >> The pixel type is unsigned char and the rest specs of the image are: >> >> >> Size : [1001, 1001, 8345] (in voxels) >> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >> >> >> Origin : [0, 0, 0] >> >> >> Direction : >> >> >> 1 0 0 >> >> >> 0 1 0 >> >> >> 0 0 1 >> >> >> >> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea >> >> >> how it looks like. Indeed the object in the volume looks as it was >> >> >> expected. >> >> >> So far no problems. The specs of the image on Slicer are the same as >> >> >> above >> >> >> (except the direction which has flipped signs for the first two >> >> >> diagonal >> >> >> entries, as we know ). >> >> >> >> >> >> Then I tried to load the image in the memory using the >> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >> >> >> loading >> >> >> the image I noticed that there are pixels with zero values instead of >> >> >> non-zero by comparing the same indexes with the loaded image on Slicer. >> >> >> >> >> >> Then I decided to write the loaded image on the disk using the >> >> >> itk::ImageFileWriter. >> >> >> >> >> >> After opening the (written from ITK) image on Slicer I checked the >> >> >> specks >> >> >> and were the same with the original image as above. However I noticed >> >> >> that a >> >> >> big portion of the image is completely empty (black)! >> >> >> >> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >> >> >> DDR3L) >> >> >> and is using Red Hat Enterprise Linux Server 6.5. >> >> >> The size of the original nifti volume is : >> >> >> >> >> >> 25.7 MB (.nii.gz) >> >> >> 8.36 GB (.nii) >> >> >> >> >> >> Has anybody experienced similar difficulties trying to load so big >> >> >> volume >> >> >> data? >> >> >> >> >> >> Best, >> >> >> Fotis Drakopoulos >> >> >> CRTC >> >> >> >> >> >> _____________________________________ >> >> >> Powered by www.kitware.com >> >> >> >> >> >> Visit other Kitware open-source projects at >> >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> >> http://www.kitware.com/products/protraining.php >> >> >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> >> >> >> >> >> ________________________________ >> >> >> >> >> >> Spam >> >> >> Not spam >> >> >> Forget previous vote >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Powered by www.kitware.com >> >> > >> >> > Visit other Kitware open-source projects at >> >> > http://www.kitware.com/opensource/opensource.html >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > http://kitware.com/products/protraining.php >> >> > >> >> > Please keep messages on-topic and check the ITK FAQ at: >> >> > http://www.itk.org/Wiki/ITK_FAQ >> >> > >> >> > Follow this link to subscribe/unsubscribe: >> >> > http://public.kitware.com/mailman/listinfo/insight-developers >> >> > >> >> >> >> >> >> -- >> >> >> > >> >> >> -- >> BEGIN-ANTISPAM-VOTING-LINKS >> ------------------------------------------------------ >> >> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >> Spam: about:blank >> Not spam: about:blank >> Forget vote: about:blank >> ------------------------------------------------------ >> END-ANTISPAM-VOTING-LINKS >> >> > > > Spam > Not spam > Forget previous vote > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 2 10:58:40 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 10:58:40 -0500 Subject: [ITK] [ITK-users] [ITK-dev] Problem reading a big nifti volume. In-Reply-To: References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> Message-ID: <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> So if you wrote and read with ITK ( via Slicer ), how do you know that the file is correct as you expect? I see the file has a ".nii.gz" extension, meaning that it's compressed. Does the same issue occur when it's not compressed? Brad On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos wrote: > Hi, > > I created and wrote the image on the disk using ITK 4.6.0. > I visualized the image using Slicer 4.4.0. > > The properties are: > Size : [1001, 1001, 8345] > Spacing : [1,1,1] > Origin : [0, 0, 0] > Direction : > 1 0 0 > 0 1 0 > 0 0 1 > > Fotis > > On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp wrote: > Hello, > > What software did you use to create and validate that this image is correct? > > Thanks, > Brad > > On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos wrote: > >> Hi all, >> >> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader. >> The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300. >> The pixelType is short. >> >> Thanks >> Fotis >> >> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick wrote: >> Thanks! Added. >> >> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos wrote: >> > Hi, >> > I signed up for the ITK community on midas. >> > >> > Thanks, >> > Fotis Drakopoulos >> > >> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >> > wrote: >> >> >> >> Hi Fotis, >> >> >> >> Thanks for helping to improve large nifti file support. >> >> >> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >> >> community [1], let the list know the name of your account, and myself >> >> or one of the other administrators will add upload priviledges to the >> >> account. >> >> >> >> The file could then be added to >> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >> >> >> >> Thanks, >> >> Matt >> >> >> >> [1] http://midas3.kitware.com/midas/community/12 >> >> >> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos >> >> wrote: >> >> > Hi all, >> >> > >> >> > I created a test nifti image that reproduces the problem I mentioned >> >> > before. >> >> > How can I share this image with the ITK community? >> >> > >> >> > Best, >> >> > Fotis Drakopoulos >> >> > >> >> > >> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >> >> > >> >> > wrote: >> >> >> >> >> >> Shareable test data greatly helps determine the cause and fix these >> >> >> types >> >> >> of issues. >> >> >> >> >> >> Got data? >> >> >> >> >> >> Brad >> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle wrote: >> >> >> >> >> >> This is reminiscent of the previous problem with big TIFF images, now >> >> >> fixed. >> >> >> >> >> >> Gib >> >> >> ________________________________ >> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis >> >> >> Drakopoulos [fdrakopo at gmail.com] >> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >> >> >> To: insight-users at itk.org; insight-developers at itk.org >> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >> >> >> >> >> >> Hi all, >> >> >> >> >> >> For the last couple of days I have been trying reading (unsuccessfully) >> >> >> a >> >> >> big nifti volume labeled image from my disk. >> >> >> >> >> >> The pixel type is unsigned char and the rest specs of the image are: >> >> >> Size : [1001, 1001, 8345] (in voxels) >> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >> >> >> Origin : [0, 0, 0] >> >> >> Direction : >> >> >> 1 0 0 >> >> >> 0 1 0 >> >> >> 0 0 1 >> >> >> >> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea >> >> >> how it looks like. Indeed the object in the volume looks as it was >> >> >> expected. >> >> >> So far no problems. The specs of the image on Slicer are the same as >> >> >> above >> >> >> (except the direction which has flipped signs for the first two >> >> >> diagonal >> >> >> entries, as we know ). >> >> >> >> >> >> Then I tried to load the image in the memory using the >> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >> >> >> loading >> >> >> the image I noticed that there are pixels with zero values instead of >> >> >> non-zero by comparing the same indexes with the loaded image on Slicer. >> >> >> >> >> >> Then I decided to write the loaded image on the disk using the >> >> >> itk::ImageFileWriter. >> >> >> >> >> >> After opening the (written from ITK) image on Slicer I checked the >> >> >> specks >> >> >> and were the same with the original image as above. However I noticed >> >> >> that a >> >> >> big portion of the image is completely empty (black)! >> >> >> >> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >> >> >> DDR3L) >> >> >> and is using Red Hat Enterprise Linux Server 6.5. >> >> >> The size of the original nifti volume is : >> >> >> >> >> >> 25.7 MB (.nii.gz) >> >> >> 8.36 GB (.nii) >> >> >> >> >> >> Has anybody experienced similar difficulties trying to load so big >> >> >> volume >> >> >> data? >> >> >> >> >> >> Best, >> >> >> Fotis Drakopoulos >> >> >> CRTC >> >> >> >> >> >> _____________________________________ >> >> >> Powered by www.kitware.com >> >> >> >> >> >> Visit other Kitware open-source projects at >> >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> >> http://www.kitware.com/products/protraining.php >> >> >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> >> >> >> >> >> ________________________________ >> >> >> >> >> >> Spam >> >> >> Not spam >> >> >> Forget previous vote >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Powered by www.kitware.com >> >> > >> >> > Visit other Kitware open-source projects at >> >> > http://www.kitware.com/opensource/opensource.html >> >> > >> >> > Kitware offers ITK Training Courses, for more information visit: >> >> > http://kitware.com/products/protraining.php >> >> > >> >> > Please keep messages on-topic and check the ITK FAQ at: >> >> > http://www.itk.org/Wiki/ITK_FAQ >> >> > >> >> > Follow this link to subscribe/unsubscribe: >> >> > http://public.kitware.com/mailman/listinfo/insight-developers >> >> > >> >> >> >> >> >> -- >> >> >> > >> >> >> -- >> BEGIN-ANTISPAM-VOTING-LINKS >> ------------------------------------------------------ >> >> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >> Spam: about:blank >> Not spam: about:blank >> Forget vote: about:blank >> ------------------------------------------------------ >> END-ANTISPAM-VOTING-LINKS >> >> > > > Spam > Not spam > Forget previous vote > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Tue Dec 2 11:04:56 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 11:04:56 -0500 Subject: [ITK] [ITK-users] Future of WrapITK In-Reply-To: References: , <189A597A-010D-4BEC-8A76-29A5046E32DD@gmail.com> , Message-ID: <2C9D32C3-635E-4597-8829-ABE435259EBD@mail.nih.gov> Hello, The complications of OSX's clang 5.0 switching to libc++ from GNU's libstdc++ are complex. If you set CMAKE_OSX_DEPLOYMENT_TARGET < 10.9, then GNU's libstdc++ will still be used and support for tr1 will exists, so the C++11 requirement may be relaxed for some cases. Currently the SimpleITK's master has a linking issue on Visual Studio when static libraries are created. If you choose to create shared libraries you can get it too link, although the installation of all ITK and SimpleITK shared libraries is more complicated and not automatic. Brad On Dec 2, 2014, at 10:56 AM, Paavolainen Lassi wrote: > So at least we are set for now except the OS X package and library needing C++11. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From fdrakopo at gmail.com Tue Dec 2 11:14:46 2014 From: fdrakopo at gmail.com (Fotis Drakopoulos) Date: Tue, 2 Dec 2014 11:14:46 -0500 Subject: [ITK] [ITK-users] [ITK-dev] Problem reading a big nifti volume. In-Reply-To: <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> Message-ID: The image contains a single non-zero voxel on each axial slice. When I load the image on Slicer the non-zero voxels are preserved as you traverse the image using the window slider. When I read the image using a simple main program a big portion of the the non-zero voxels do not exist. I had the same issue when the file was .nii (not compressed). Fotis On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp wrote: > So if you wrote and read with ITK ( via Slicer ), how do you know that the > file is correct as you expect? > > I see the file has a ".nii.gz" extension, meaning that it's compressed. > Does the same issue occur when it's not compressed? > > Brad > > > > On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos wrote: > > Hi, > > I created and wrote the image on the disk using ITK 4.6.0. > I visualized the image using Slicer 4.4.0. > > The properties are: > Size : [1001, 1001, 8345] > Spacing : [1,1,1] > Origin : [0, 0, 0] > Direction : > 1 0 0 > 0 1 0 > 0 0 1 > > Fotis > > On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp > wrote: > >> Hello, >> >> What software did you use to create and validate that this image is >> correct? >> >> Thanks, >> Brad >> >> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos >> wrote: >> >> Hi all, >> >> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >> The image cannot loaded correctly when I use the itk::ImageFileReader. >> The test image contains non-zero values only at indexes (350,350,i) >> where i=0 to 8300. >> The pixelType is short. >> >> Thanks >> Fotis >> >> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick < >> matt.mccormick at kitware.com> wrote: >> >>> Thanks! Added. >>> >>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos >>> wrote: >>> > Hi, >>> > I signed up for the ITK community on midas. >>> > >>> > Thanks, >>> > Fotis Drakopoulos >>> > >>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >>> > wrote: >>> >> >>> >> Hi Fotis, >>> >> >>> >> Thanks for helping to improve large nifti file support. >>> >> >>> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >>> >> community [1], let the list know the name of your account, and myself >>> >> or one of the other administrators will add upload priviledges to the >>> >> account. >>> >> >>> >> The file could then be added to >>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >>> >> >>> >> Thanks, >>> >> Matt >>> >> >>> >> [1] http://midas3.kitware.com/midas/community/12 >>> >> >>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos < >>> fdrakopo at gmail.com> >>> >> wrote: >>> >> > Hi all, >>> >> > >>> >> > I created a test nifti image that reproduces the problem I mentioned >>> >> > before. >>> >> > How can I share this image with the ITK community? >>> >> > >>> >> > Best, >>> >> > Fotis Drakopoulos >>> >> > >>> >> > >>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >>> >> > >>> >> > wrote: >>> >> >> >>> >> >> Shareable test data greatly helps determine the cause and fix these >>> >> >> types >>> >> >> of issues. >>> >> >> >>> >> >> Got data? >>> >> >> >>> >> >> Brad >>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle >>> wrote: >>> >> >> >>> >> >> This is reminiscent of the previous problem with big TIFF images, >>> now >>> >> >> fixed. >>> >> >> >>> >> >> Gib >>> >> >> ________________________________ >>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of >>> Fotis >>> >> >> Drakopoulos [fdrakopo at gmail.com] >>> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >>> >> >> To: insight-users at itk.org; insight-developers at itk.org >>> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >>> >> >> >>> >> >> Hi all, >>> >> >> >>> >> >> For the last couple of days I have been trying reading >>> (unsuccessfully) >>> >> >> a >>> >> >> big nifti volume labeled image from my disk. >>> >> >> >>> >> >> The pixel type is unsigned char and the rest specs of the image >>> are: >>> >> >> Size : [1001, 1001, 8345] (in voxels) >>> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >>> >> >> Origin : [0, 0, 0] >>> >> >> Direction : >>> >> >> 1 0 0 >>> >> >> 0 1 0 >>> >> >> 0 0 1 >>> >> >> >>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an >>> idea >>> >> >> how it looks like. Indeed the object in the volume looks as it was >>> >> >> expected. >>> >> >> So far no problems. The specs of the image on Slicer are the same >>> as >>> >> >> above >>> >> >> (except the direction which has flipped signs for the first two >>> >> >> diagonal >>> >> >> entries, as we know ). >>> >> >> >>> >> >> Then I tried to load the image in the memory using the >>> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >>> >> >> loading >>> >> >> the image I noticed that there are pixels with zero values instead >>> of >>> >> >> non-zero by comparing the same indexes with the loaded image on >>> Slicer. >>> >> >> >>> >> >> Then I decided to write the loaded image on the disk using the >>> >> >> itk::ImageFileWriter. >>> >> >> >>> >> >> After opening the (written from ITK) image on Slicer I checked the >>> >> >> specks >>> >> >> and were the same with the original image as above. However I >>> noticed >>> >> >> that a >>> >> >> big portion of the image is completely empty (black)! >>> >> >> >>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >>> >> >> DDR3L) >>> >> >> and is using Red Hat Enterprise Linux Server 6.5. >>> >> >> The size of the original nifti volume is : >>> >> >> >>> >> >> 25.7 MB (.nii.gz) >>> >> >> 8.36 GB (.nii) >>> >> >> >>> >> >> Has anybody experienced similar difficulties trying to load so big >>> >> >> volume >>> >> >> data? >>> >> >> >>> >> >> Best, >>> >> >> Fotis Drakopoulos >>> >> >> CRTC >>> >> >> >>> >> >> _____________________________________ >>> >> >> Powered by www.kitware.com >>> >> >> >>> >> >> Visit other Kitware open-source projects at >>> >> >> http://www.kitware.com/opensource/opensource.html >>> >> >> >>> >> >> Kitware offers ITK Training Courses, for more information visit: >>> >> >> http://www.kitware.com/products/protraining.php >>> >> >> >>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>> >> >> >>> >> >> Follow this link to subscribe/unsubscribe: >>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >> >>> >> >> >>> >> >> ________________________________ >>> >> >> >>> >> >> Spam >>> >> >> Not spam >>> >> >> Forget previous vote >>> >> > >>> >> > >>> >> > >>> >> > _______________________________________________ >>> >> > Powered by www.kitware.com >>> >> > >>> >> > Visit other Kitware open-source projects at >>> >> > http://www.kitware.com/opensource/opensource.html >>> >> > >>> >> > Kitware offers ITK Training Courses, for more information visit: >>> >> > http://kitware.com/products/protraining.php >>> >> > >>> >> > Please keep messages on-topic and check the ITK FAQ at: >>> >> > http://www.itk.org/Wiki/ITK_FAQ >>> >> > >>> >> > Follow this link to subscribe/unsubscribe: >>> >> > http://public.kitware.com/mailman/listinfo/insight-developers >>> >> > >>> >> >>> >> >>> >> -- >>> >> >>> > >>> >>> >>> -- >>> BEGIN-ANTISPAM-VOTING-LINKS >>> ------------------------------------------------------ >>> >>> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >>> Spam: about:blank >>> Not spam: about:blank >>> Forget vote: about:blank >>> ------------------------------------------------------ >>> END-ANTISPAM-VOTING-LINKS >>> >>> >> >> ------------------------------ >> >> Spam >> Not spam >> Forget previous vote >> > > > ------------------------------ > > Spam > > Not spam > > Forget previous vote > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From fdrakopo at gmail.com Tue Dec 2 11:14:46 2014 From: fdrakopo at gmail.com (Fotis Drakopoulos) Date: Tue, 2 Dec 2014 11:14:46 -0500 Subject: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti volume. In-Reply-To: <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> Message-ID: The image contains a single non-zero voxel on each axial slice. When I load the image on Slicer the non-zero voxels are preserved as you traverse the image using the window slider. When I read the image using a simple main program a big portion of the the non-zero voxels do not exist. I had the same issue when the file was .nii (not compressed). Fotis On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp wrote: > So if you wrote and read with ITK ( via Slicer ), how do you know that the > file is correct as you expect? > > I see the file has a ".nii.gz" extension, meaning that it's compressed. > Does the same issue occur when it's not compressed? > > Brad > > > > On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos wrote: > > Hi, > > I created and wrote the image on the disk using ITK 4.6.0. > I visualized the image using Slicer 4.4.0. > > The properties are: > Size : [1001, 1001, 8345] > Spacing : [1,1,1] > Origin : [0, 0, 0] > Direction : > 1 0 0 > 0 1 0 > 0 0 1 > > Fotis > > On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp > wrote: > >> Hello, >> >> What software did you use to create and validate that this image is >> correct? >> >> Thanks, >> Brad >> >> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos >> wrote: >> >> Hi all, >> >> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >> The image cannot loaded correctly when I use the itk::ImageFileReader. >> The test image contains non-zero values only at indexes (350,350,i) >> where i=0 to 8300. >> The pixelType is short. >> >> Thanks >> Fotis >> >> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick < >> matt.mccormick at kitware.com> wrote: >> >>> Thanks! Added. >>> >>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos >>> wrote: >>> > Hi, >>> > I signed up for the ITK community on midas. >>> > >>> > Thanks, >>> > Fotis Drakopoulos >>> > >>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >>> > wrote: >>> >> >>> >> Hi Fotis, >>> >> >>> >> Thanks for helping to improve large nifti file support. >>> >> >>> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >>> >> community [1], let the list know the name of your account, and myself >>> >> or one of the other administrators will add upload priviledges to the >>> >> account. >>> >> >>> >> The file could then be added to >>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >>> >> >>> >> Thanks, >>> >> Matt >>> >> >>> >> [1] http://midas3.kitware.com/midas/community/12 >>> >> >>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos < >>> fdrakopo at gmail.com> >>> >> wrote: >>> >> > Hi all, >>> >> > >>> >> > I created a test nifti image that reproduces the problem I mentioned >>> >> > before. >>> >> > How can I share this image with the ITK community? >>> >> > >>> >> > Best, >>> >> > Fotis Drakopoulos >>> >> > >>> >> > >>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >>> >> > >>> >> > wrote: >>> >> >> >>> >> >> Shareable test data greatly helps determine the cause and fix these >>> >> >> types >>> >> >> of issues. >>> >> >> >>> >> >> Got data? >>> >> >> >>> >> >> Brad >>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle >>> wrote: >>> >> >> >>> >> >> This is reminiscent of the previous problem with big TIFF images, >>> now >>> >> >> fixed. >>> >> >> >>> >> >> Gib >>> >> >> ________________________________ >>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of >>> Fotis >>> >> >> Drakopoulos [fdrakopo at gmail.com] >>> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >>> >> >> To: insight-users at itk.org; insight-developers at itk.org >>> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >>> >> >> >>> >> >> Hi all, >>> >> >> >>> >> >> For the last couple of days I have been trying reading >>> (unsuccessfully) >>> >> >> a >>> >> >> big nifti volume labeled image from my disk. >>> >> >> >>> >> >> The pixel type is unsigned char and the rest specs of the image >>> are: >>> >> >> Size : [1001, 1001, 8345] (in voxels) >>> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >>> >> >> Origin : [0, 0, 0] >>> >> >> Direction : >>> >> >> 1 0 0 >>> >> >> 0 1 0 >>> >> >> 0 0 1 >>> >> >> >>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an >>> idea >>> >> >> how it looks like. Indeed the object in the volume looks as it was >>> >> >> expected. >>> >> >> So far no problems. The specs of the image on Slicer are the same >>> as >>> >> >> above >>> >> >> (except the direction which has flipped signs for the first two >>> >> >> diagonal >>> >> >> entries, as we know ). >>> >> >> >>> >> >> Then I tried to load the image in the memory using the >>> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >>> >> >> loading >>> >> >> the image I noticed that there are pixels with zero values instead >>> of >>> >> >> non-zero by comparing the same indexes with the loaded image on >>> Slicer. >>> >> >> >>> >> >> Then I decided to write the loaded image on the disk using the >>> >> >> itk::ImageFileWriter. >>> >> >> >>> >> >> After opening the (written from ITK) image on Slicer I checked the >>> >> >> specks >>> >> >> and were the same with the original image as above. However I >>> noticed >>> >> >> that a >>> >> >> big portion of the image is completely empty (black)! >>> >> >> >>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >>> >> >> DDR3L) >>> >> >> and is using Red Hat Enterprise Linux Server 6.5. >>> >> >> The size of the original nifti volume is : >>> >> >> >>> >> >> 25.7 MB (.nii.gz) >>> >> >> 8.36 GB (.nii) >>> >> >> >>> >> >> Has anybody experienced similar difficulties trying to load so big >>> >> >> volume >>> >> >> data? >>> >> >> >>> >> >> Best, >>> >> >> Fotis Drakopoulos >>> >> >> CRTC >>> >> >> >>> >> >> _____________________________________ >>> >> >> Powered by www.kitware.com >>> >> >> >>> >> >> Visit other Kitware open-source projects at >>> >> >> http://www.kitware.com/opensource/opensource.html >>> >> >> >>> >> >> Kitware offers ITK Training Courses, for more information visit: >>> >> >> http://www.kitware.com/products/protraining.php >>> >> >> >>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>> >> >> >>> >> >> Follow this link to subscribe/unsubscribe: >>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >> >>> >> >> >>> >> >> ________________________________ >>> >> >> >>> >> >> Spam >>> >> >> Not spam >>> >> >> Forget previous vote >>> >> > >>> >> > >>> >> > >>> >> > _______________________________________________ >>> >> > Powered by www.kitware.com >>> >> > >>> >> > Visit other Kitware open-source projects at >>> >> > http://www.kitware.com/opensource/opensource.html >>> >> > >>> >> > Kitware offers ITK Training Courses, for more information visit: >>> >> > http://kitware.com/products/protraining.php >>> >> > >>> >> > Please keep messages on-topic and check the ITK FAQ at: >>> >> > http://www.itk.org/Wiki/ITK_FAQ >>> >> > >>> >> > Follow this link to subscribe/unsubscribe: >>> >> > http://public.kitware.com/mailman/listinfo/insight-developers >>> >> > >>> >> >>> >> >>> >> -- >>> >> >>> > >>> >>> >>> -- >>> BEGIN-ANTISPAM-VOTING-LINKS >>> ------------------------------------------------------ >>> >>> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >>> Spam: about:blank >>> Not spam: about:blank >>> Forget vote: about:blank >>> ------------------------------------------------------ >>> END-ANTISPAM-VOTING-LINKS >>> >>> >> >> ------------------------------ >> >> Spam >> Not spam >> Forget previous vote >> > > > ------------------------------ > > Spam > > Not spam > > Forget previous vote > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 2 11:34:17 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 11:34:17 -0500 Subject: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti volume. In-Reply-To: References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> Message-ID: <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov> Hello, Unfortunately, I don't see the logic with it working with Slicer, but not working in native ITK as it uses the same code. I have perused the NIFT1 C library that ITK has in the ThirdParty group, which appears up to date with the latest released version: 2.0.0. There a quite a number of places where the calculation of the size of the image is not done at size_t/64-bits safe fashion, along with other 64-bit safe operations. I am concluding that the nifit file format doesn't readily support image > 4GB. Even if we then through the extensive effort of updating our version of the third party library the resulting images are very likely not going to work with other toosl that work with nifti images. Brad On Dec 2, 2014, at 11:14 AM, Fotis Drakopoulos wrote: > The image contains a single non-zero voxel on each axial slice. > > When I load the image on Slicer the non-zero voxels are preserved as you traverse the image using the window slider. > When I read the image using a simple main program a big portion of the the non-zero voxels do not exist. > > I had the same issue when the file was .nii (not compressed). > > Fotis > > > On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp wrote: > So if you wrote and read with ITK ( via Slicer ), how do you know that the file is correct as you expect? > > I see the file has a ".nii.gz" extension, meaning that it's compressed. Does the same issue occur when it's not compressed? > > Brad > > > > On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos wrote: > >> Hi, >> >> I created and wrote the image on the disk using ITK 4.6.0. >> I visualized the image using Slicer 4.4.0. >> >> The properties are: >> Size : [1001, 1001, 8345] >> Spacing : [1,1,1] >> Origin : [0, 0, 0] >> Direction : >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> Fotis >> >> On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp wrote: >> Hello, >> >> What software did you use to create and validate that this image is correct? >> >> Thanks, >> Brad >> >> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos wrote: >> >>> Hi all, >>> >>> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader. >>> The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300. >>> The pixelType is short. >>> >>> Thanks >>> Fotis >>> >>> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick wrote: >>> Thanks! Added. >>> >>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos wrote: >>> > Hi, >>> > I signed up for the ITK community on midas. >>> > >>> > Thanks, >>> > Fotis Drakopoulos >>> > >>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >>> > wrote: >>> >> >>> >> Hi Fotis, >>> >> >>> >> Thanks for helping to improve large nifti file support. >>> >> >>> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >>> >> community [1], let the list know the name of your account, and myself >>> >> or one of the other administrators will add upload priviledges to the >>> >> account. >>> >> >>> >> The file could then be added to >>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >>> >> >>> >> Thanks, >>> >> Matt >>> >> >>> >> [1] http://midas3.kitware.com/midas/community/12 >>> >> >>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos >>> >> wrote: >>> >> > Hi all, >>> >> > >>> >> > I created a test nifti image that reproduces the problem I mentioned >>> >> > before. >>> >> > How can I share this image with the ITK community? >>> >> > >>> >> > Best, >>> >> > Fotis Drakopoulos >>> >> > >>> >> > >>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >>> >> > >>> >> > wrote: >>> >> >> >>> >> >> Shareable test data greatly helps determine the cause and fix these >>> >> >> types >>> >> >> of issues. >>> >> >> >>> >> >> Got data? >>> >> >> >>> >> >> Brad >>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle wrote: >>> >> >> >>> >> >> This is reminiscent of the previous problem with big TIFF images, now >>> >> >> fixed. >>> >> >> >>> >> >> Gib >>> >> >> ________________________________ >>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis >>> >> >> Drakopoulos [fdrakopo at gmail.com] >>> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >>> >> >> To: insight-users at itk.org; insight-developers at itk.org >>> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >>> >> >> >>> >> >> Hi all, >>> >> >> >>> >> >> For the last couple of days I have been trying reading (unsuccessfully) >>> >> >> a >>> >> >> big nifti volume labeled image from my disk. >>> >> >> >>> >> >> The pixel type is unsigned char and the rest specs of the image are: >>> >> >> Size : [1001, 1001, 8345] (in voxels) >>> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >>> >> >> Origin : [0, 0, 0] >>> >> >> Direction : >>> >> >> 1 0 0 >>> >> >> 0 1 0 >>> >> >> 0 0 1 >>> >> >> >>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea >>> >> >> how it looks like. Indeed the object in the volume looks as it was >>> >> >> expected. >>> >> >> So far no problems. The specs of the image on Slicer are the same as >>> >> >> above >>> >> >> (except the direction which has flipped signs for the first two >>> >> >> diagonal >>> >> >> entries, as we know ). >>> >> >> >>> >> >> Then I tried to load the image in the memory using the >>> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >>> >> >> loading >>> >> >> the image I noticed that there are pixels with zero values instead of >>> >> >> non-zero by comparing the same indexes with the loaded image on Slicer. >>> >> >> >>> >> >> Then I decided to write the loaded image on the disk using the >>> >> >> itk::ImageFileWriter. >>> >> >> >>> >> >> After opening the (written from ITK) image on Slicer I checked the >>> >> >> specks >>> >> >> and were the same with the original image as above. However I noticed >>> >> >> that a >>> >> >> big portion of the image is completely empty (black)! >>> >> >> >>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >>> >> >> DDR3L) >>> >> >> and is using Red Hat Enterprise Linux Server 6.5. >>> >> >> The size of the original nifti volume is : >>> >> >> >>> >> >> 25.7 MB (.nii.gz) >>> >> >> 8.36 GB (.nii) >>> >> >> >>> >> >> Has anybody experienced similar difficulties trying to load so big >>> >> >> volume >>> >> >> data? >>> >> >> >>> >> >> Best, >>> >> >> Fotis Drakopoulos >>> >> >> CRTC >>> >> >> >>> >> >> _____________________________________ >>> >> >> Powered by www.kitware.com >>> >> >> >>> >> >> Visit other Kitware open-source projects at >>> >> >> http://www.kitware.com/opensource/opensource.html >>> >> >> >>> >> >> Kitware offers ITK Training Courses, for more information visit: >>> >> >> http://www.kitware.com/products/protraining.php >>> >> >> >>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>> >> >> >>> >> >> Follow this link to subscribe/unsubscribe: >>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >> >>> >> >> >>> >> >> ________________________________ >>> >> >> >>> >> >> Spam >>> >> >> Not spam >>> >> >> Forget previous vote >>> >> > >>> >> > >>> >> > >>> >> > _______________________________________________ >>> >> > Powered by www.kitware.com >>> >> > >>> >> > Visit other Kitware open-source projects at >>> >> > http://www.kitware.com/opensource/opensource.html >>> >> > >>> >> > Kitware offers ITK Training Courses, for more information visit: >>> >> > http://kitware.com/products/protraining.php >>> >> > >>> >> > Please keep messages on-topic and check the ITK FAQ at: >>> >> > http://www.itk.org/Wiki/ITK_FAQ >>> >> > >>> >> > Follow this link to subscribe/unsubscribe: >>> >> > http://public.kitware.com/mailman/listinfo/insight-developers >>> >> > >>> >> >>> >> >>> >> -- >>> >> >>> > >>> >>> >>> -- >>> BEGIN-ANTISPAM-VOTING-LINKS >>> ------------------------------------------------------ >>> >>> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >>> Spam: about:blank >>> Not spam: about:blank >>> Forget vote: about:blank >>> ------------------------------------------------------ >>> END-ANTISPAM-VOTING-LINKS >>> >>> >> >> >> Spam >> Not spam >> Forget previous vote >> > > > Spam > Not spam > Forget previous vote > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 2 11:34:17 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Dec 2014 11:34:17 -0500 Subject: [ITK] [ITK-users] [ITK-dev] Problem reading a big nifti volume. In-Reply-To: References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> Message-ID: <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov> Hello, Unfortunately, I don't see the logic with it working with Slicer, but not working in native ITK as it uses the same code. I have perused the NIFT1 C library that ITK has in the ThirdParty group, which appears up to date with the latest released version: 2.0.0. There a quite a number of places where the calculation of the size of the image is not done at size_t/64-bits safe fashion, along with other 64-bit safe operations. I am concluding that the nifit file format doesn't readily support image > 4GB. Even if we then through the extensive effort of updating our version of the third party library the resulting images are very likely not going to work with other toosl that work with nifti images. Brad On Dec 2, 2014, at 11:14 AM, Fotis Drakopoulos wrote: > The image contains a single non-zero voxel on each axial slice. > > When I load the image on Slicer the non-zero voxels are preserved as you traverse the image using the window slider. > When I read the image using a simple main program a big portion of the the non-zero voxels do not exist. > > I had the same issue when the file was .nii (not compressed). > > Fotis > > > On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp wrote: > So if you wrote and read with ITK ( via Slicer ), how do you know that the file is correct as you expect? > > I see the file has a ".nii.gz" extension, meaning that it's compressed. Does the same issue occur when it's not compressed? > > Brad > > > > On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos wrote: > >> Hi, >> >> I created and wrote the image on the disk using ITK 4.6.0. >> I visualized the image using Slicer 4.4.0. >> >> The properties are: >> Size : [1001, 1001, 8345] >> Spacing : [1,1,1] >> Origin : [0, 0, 0] >> Direction : >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> Fotis >> >> On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp wrote: >> Hello, >> >> What software did you use to create and validate that this image is correct? >> >> Thanks, >> Brad >> >> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos wrote: >> >>> Hi all, >>> >>> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader. >>> The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300. >>> The pixelType is short. >>> >>> Thanks >>> Fotis >>> >>> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick wrote: >>> Thanks! Added. >>> >>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos wrote: >>> > Hi, >>> > I signed up for the ITK community on midas. >>> > >>> > Thanks, >>> > Fotis Drakopoulos >>> > >>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >>> > wrote: >>> >> >>> >> Hi Fotis, >>> >> >>> >> Thanks for helping to improve large nifti file support. >>> >> >>> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >>> >> community [1], let the list know the name of your account, and myself >>> >> or one of the other administrators will add upload priviledges to the >>> >> account. >>> >> >>> >> The file could then be added to >>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >>> >> >>> >> Thanks, >>> >> Matt >>> >> >>> >> [1] http://midas3.kitware.com/midas/community/12 >>> >> >>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos >>> >> wrote: >>> >> > Hi all, >>> >> > >>> >> > I created a test nifti image that reproduces the problem I mentioned >>> >> > before. >>> >> > How can I share this image with the ITK community? >>> >> > >>> >> > Best, >>> >> > Fotis Drakopoulos >>> >> > >>> >> > >>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >>> >> > >>> >> > wrote: >>> >> >> >>> >> >> Shareable test data greatly helps determine the cause and fix these >>> >> >> types >>> >> >> of issues. >>> >> >> >>> >> >> Got data? >>> >> >> >>> >> >> Brad >>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle wrote: >>> >> >> >>> >> >> This is reminiscent of the previous problem with big TIFF images, now >>> >> >> fixed. >>> >> >> >>> >> >> Gib >>> >> >> ________________________________ >>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis >>> >> >> Drakopoulos [fdrakopo at gmail.com] >>> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >>> >> >> To: insight-users at itk.org; insight-developers at itk.org >>> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >>> >> >> >>> >> >> Hi all, >>> >> >> >>> >> >> For the last couple of days I have been trying reading (unsuccessfully) >>> >> >> a >>> >> >> big nifti volume labeled image from my disk. >>> >> >> >>> >> >> The pixel type is unsigned char and the rest specs of the image are: >>> >> >> Size : [1001, 1001, 8345] (in voxels) >>> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >>> >> >> Origin : [0, 0, 0] >>> >> >> Direction : >>> >> >> 1 0 0 >>> >> >> 0 1 0 >>> >> >> 0 0 1 >>> >> >> >>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea >>> >> >> how it looks like. Indeed the object in the volume looks as it was >>> >> >> expected. >>> >> >> So far no problems. The specs of the image on Slicer are the same as >>> >> >> above >>> >> >> (except the direction which has flipped signs for the first two >>> >> >> diagonal >>> >> >> entries, as we know ). >>> >> >> >>> >> >> Then I tried to load the image in the memory using the >>> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >>> >> >> loading >>> >> >> the image I noticed that there are pixels with zero values instead of >>> >> >> non-zero by comparing the same indexes with the loaded image on Slicer. >>> >> >> >>> >> >> Then I decided to write the loaded image on the disk using the >>> >> >> itk::ImageFileWriter. >>> >> >> >>> >> >> After opening the (written from ITK) image on Slicer I checked the >>> >> >> specks >>> >> >> and were the same with the original image as above. However I noticed >>> >> >> that a >>> >> >> big portion of the image is completely empty (black)! >>> >> >> >>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >>> >> >> DDR3L) >>> >> >> and is using Red Hat Enterprise Linux Server 6.5. >>> >> >> The size of the original nifti volume is : >>> >> >> >>> >> >> 25.7 MB (.nii.gz) >>> >> >> 8.36 GB (.nii) >>> >> >> >>> >> >> Has anybody experienced similar difficulties trying to load so big >>> >> >> volume >>> >> >> data? >>> >> >> >>> >> >> Best, >>> >> >> Fotis Drakopoulos >>> >> >> CRTC >>> >> >> >>> >> >> _____________________________________ >>> >> >> Powered by www.kitware.com >>> >> >> >>> >> >> Visit other Kitware open-source projects at >>> >> >> http://www.kitware.com/opensource/opensource.html >>> >> >> >>> >> >> Kitware offers ITK Training Courses, for more information visit: >>> >> >> http://www.kitware.com/products/protraining.php >>> >> >> >>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>> >> >> >>> >> >> Follow this link to subscribe/unsubscribe: >>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >> >>> >> >> >>> >> >> ________________________________ >>> >> >> >>> >> >> Spam >>> >> >> Not spam >>> >> >> Forget previous vote >>> >> > >>> >> > >>> >> > >>> >> > _______________________________________________ >>> >> > Powered by www.kitware.com >>> >> > >>> >> > Visit other Kitware open-source projects at >>> >> > http://www.kitware.com/opensource/opensource.html >>> >> > >>> >> > Kitware offers ITK Training Courses, for more information visit: >>> >> > http://kitware.com/products/protraining.php >>> >> > >>> >> > Please keep messages on-topic and check the ITK FAQ at: >>> >> > http://www.itk.org/Wiki/ITK_FAQ >>> >> > >>> >> > Follow this link to subscribe/unsubscribe: >>> >> > http://public.kitware.com/mailman/listinfo/insight-developers >>> >> > >>> >> >>> >> >>> >> -- >>> >> >>> > >>> >>> >>> -- >>> BEGIN-ANTISPAM-VOTING-LINKS >>> ------------------------------------------------------ >>> >>> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >>> Spam: about:blank >>> Not spam: about:blank >>> Forget vote: about:blank >>> ------------------------------------------------------ >>> END-ANTISPAM-VOTING-LINKS >>> >>> >> >> >> Spam >> Not spam >> Forget previous vote >> > > > Spam > Not spam > Forget previous vote > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dr.tim.allman at gmail.com Tue Dec 2 14:35:27 2014 From: dr.tim.allman at gmail.com (Tim Allman) Date: Tue, 2 Dec 2014 14:35:27 -0500 Subject: [ITK] [ITK-users] Float dicom images Message-ID: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com> I have been having a bit of trouble trying to write Dicom images using itk::GDCMImageIO. The code suggests that this is supported but I know that this is a new feature. Has anyone else had any experience with this? Thanks, 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 matimontg at gmail.com Tue Dec 2 14:44:59 2014 From: matimontg at gmail.com (Matias Montroull) Date: Tue, 2 Dec 2014 16:44:59 -0300 Subject: [ITK] [ITK-users] Float dicom images In-Reply-To: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com> References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com> Message-ID: are you trying to write float dicom images? On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman wrote: > I have been having a bit of trouble trying to write Dicom images using > itk::GDCMImageIO. The code suggests that this is supported but I know that > this is a new feature. Has anyone else had any experience with this? > > Thanks, > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Tue Dec 2 15:40:54 2014 From: matimontg at gmail.com (Matias Montroull) Date: Tue, 2 Dec 2014 17:40:54 -0300 Subject: [ITK] [ITK-users] Float dicom images In-Reply-To: <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com> References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com> <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com> Message-ID: adding insight users.. I've never dealt with float dicom images, can you send me a sample image? I can try to write and see what's the problem. isn's saving the image or you get a wrong saved image, such as WL WC changed etc? On Tue, Dec 2, 2014 at 4:53 PM, Tim Allman wrote: > > On Dec 2, 2014, at 14:44 , Matias Montroull wrote: > > > are you trying to write float dicom images? > > Yes. Sorry for noting that only in the subject line. :-( > > > > > On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman > wrote: > > I have been having a bit of trouble trying to write Dicom images using > itk::GDCMImageIO. The code suggests that this is supported but I know that > this is a new feature. Has anyone else had any experience with this? > > > > Thanks, > > 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 > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From davis.vigneault at gmail.com Tue Dec 2 15:56:19 2014 From: davis.vigneault at gmail.com (DVigneault) Date: Tue, 2 Dec 2014 13:56:19 -0700 (MST) Subject: [ITK] [ITK-users] Pointing CMake to Updated ITK Library Message-ID: <1417553779482-7586653.post@n2.nabble.com> All-- I'm wondering how I need to update my CMakeLists.txt file to point it to a particular version of ITK. I'm working on OsX. I previously had version 4.4.2 installed, and have recently installed 4.6.1. However, when I run this code... itk::Version::Pointer version = itk::Version::New(); std::cout << version->GetITKVersion() << std::endl; ...it outputs 4.4.2. I've copied my CMakeLists.txt file below. I have tried changing this line... find_package(ITK REQUIRED) ...to... find_package(ITK 4.6.1 REQUIRED) ...but when I do, I get the following error: dyld: Library not loaded: /Applications/ITK/build/fftw/lib/libfftw3.3.dylib Referenced from: /Volumes/NO NAME/Chicago/example_for_jack_yao/bin/./dv-simulated_phase Reason: image not found Trace/BPT trap: 5 Thanks in advance for your help! Best, --Davis # This is the root ITK CMakeLists file. cmake_minimum_required(VERSION 2.4) if(COMMAND CMAKE_POLICY) cmake_policy(SET CMP0003 NEW) endif() # This project is designed to be built outside the Insight source tree. project(dv-simulated_phase) # Find ITK. find_package(ITK REQUIRED) include(${ITK_USE_FILE}) add_executable(dv-simulated_phase dv-simulated_phase.cxx ) target_link_libraries(dv-simulated_phase ${ITK_LIBRARIES}) -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Pointing-CMake-to-Updated-ITK-Library-tp7586653.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Dec 2 16:20:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 2 Dec 2014 16:20:21 -0500 Subject: [ITK] [ITK-users] Pointing CMake to Updated ITK Library In-Reply-To: <1417553779482-7586653.post@n2.nabble.com> References: <1417553779482-7586653.post@n2.nabble.com> Message-ID: Hi Davis, The ITK build to use is usually selected in the CMake build configuration (not in the source file CMakeLists.txt), by setting the "ITK_DIR" variable. This should point to the path that has the desired ITKConfig.cmake file. HTH, Matt On Tue, Dec 2, 2014 at 3:56 PM, DVigneault wrote: > All-- > > I'm wondering how I need to update my CMakeLists.txt file to point it to a > particular version of ITK. I'm working on OsX. I previously had version > 4.4.2 installed, and have recently installed 4.6.1. However, when I run > this code... > > itk::Version::Pointer version = itk::Version::New(); > std::cout << version->GetITKVersion() << std::endl; > > ...it outputs 4.4.2. I've copied my CMakeLists.txt file below. I have > tried changing this line... > > find_package(ITK REQUIRED) > > ...to... > > find_package(ITK 4.6.1 REQUIRED) > > ...but when I do, I get the following error: > > dyld: Library not loaded: /Applications/ITK/build/fftw/lib/libfftw3.3.dylib > Referenced from: /Volumes/NO > NAME/Chicago/example_for_jack_yao/bin/./dv-simulated_phase > Reason: image not found > Trace/BPT trap: 5 > > Thanks in advance for your help! > > Best, > > --Davis > > # This is the root ITK CMakeLists file. > cmake_minimum_required(VERSION 2.4) > if(COMMAND CMAKE_POLICY) > cmake_policy(SET CMP0003 NEW) > endif() > > # This project is designed to be built outside the Insight source tree. > project(dv-simulated_phase) > > # Find ITK. > find_package(ITK REQUIRED) > include(${ITK_USE_FILE}) > > add_executable(dv-simulated_phase dv-simulated_phase.cxx ) > > target_link_libraries(dv-simulated_phase ${ITK_LIBRARIES}) > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Pointing-CMake-to-Updated-ITK-Library-tp7586653.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dclunie at dclunie.com Tue Dec 2 17:14:29 2014 From: dclunie at dclunie.com (David Clunie) Date: Tue, 02 Dec 2014 17:14:29 -0500 Subject: [ITK] [ITK-users] Float dicom images In-Reply-To: References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com> <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com> Message-ID: <547E39C5.9040801@dclunie.com> We (DICOM) have only recently added support for floating point pixel data in DICOM (Sup 172), so I don't know if any of the toolkits used by ITK support it yet. I know dcmtk will, hopefully soon, but I can't speak for GDCM. I have some samples at: https://www.dropbox.com/sh/n4iqdjbhmwljx5e/AABllea-Muk0C2oo576nm_Mua?dl=0 if you want to try them; not perfect yet, but they have the float pixel data payload. I am assuming that you actually want to write floating point pixels, rather than integer quantized pixels with a floating point scaling factor. David On 12/2/14 3:40 PM, Matias Montroull wrote: > adding insight users.. > > I've never dealt with float dicom images, can you send me a sample image? I > can try to write and see what's the problem. isn's saving the image or you > get a wrong saved image, such as WL WC changed etc? > > On Tue, Dec 2, 2014 at 4:53 PM, Tim Allman wrote: > >> >> On Dec 2, 2014, at 14:44 , Matias Montroull wrote: >> >>> are you trying to write float dicom images? >> >> Yes. Sorry for noting that only in the subject line. :-( >> >>> >>> On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman >> wrote: >>> I have been having a bit of trouble trying to write Dicom images using >> itk::GDCMImageIO. The code suggests that this is supported but I know that >> this is a new feature. Has anyone else had any experience with this? >>> >>> Thanks, >>> 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 richard.beare at gmail.com Wed Dec 3 01:03:06 2014 From: richard.beare at gmail.com (Richard Beare) Date: Wed, 3 Dec 2014 17:03:06 +1100 Subject: [ITK] [ITK-users] [ITK-dev] Problem reading a big nifti volume. In-Reply-To: <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov> References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov> Message-ID: Hi, I have, coincidentally, run into what I presume is the same issue. I'll add what I've observed, but note that I haven't gone into investigations very thoroughly. I started with a 5.9GB mha volume. I found that an old version of ITK snap crashed when attempting to view it. I converted to nifti using the ConvertBetweenFileFormats tool, and found that fslview crashed, itksnap crashed, mrview (from mrtrix) was able to view. I tested a newer version of itksnap and found crashing with nifti. The new version of itksnap would load the mha but would only display part of it (probably the first 2GB), the rest was blank. I also found that imageJ was able to view the nifti. So, I think writing large nifti files from ITK is OK. Reading appears broken. I think there may be additional issues with large files with itksnap. On Wed, Dec 3, 2014 at 3:34 AM, Bradley Lowekamp wrote: > Hello, > > Unfortunately, I don't see the logic with it working with Slicer, but not > working in native ITK as it uses the same code. > > I have perused the NIFT1 C library that ITK has in the ThirdParty group, > which appears up to date with the latest released version: 2.0.0. > > There a quite a number of places where the calculation of the size of the > image is not done at size_t/64-bits safe fashion, along with other 64-bit > safe operations. I am concluding that the nifit file format doesn't readily > support image > 4GB. Even if we then through the extensive effort of > updating our version of the third party library the resulting images are > very likely not going to work with other toosl that work with nifti images. > > Brad > > On Dec 2, 2014, at 11:14 AM, Fotis Drakopoulos wrote: > > The image contains a single non-zero voxel on each axial slice. > > When I load the image on Slicer the non-zero voxels are preserved as you > traverse the image using the window slider. > When I read the image using a simple main program a big portion of the > the non-zero voxels do not exist. > > I had the same issue when the file was .nii (not compressed). > > Fotis > > > On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp > wrote: > >> So if you wrote and read with ITK ( via Slicer ), how do you know that >> the file is correct as you expect? >> >> I see the file has a ".nii.gz" extension, meaning that it's compressed. >> Does the same issue occur when it's not compressed? >> >> Brad >> >> >> >> On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos >> wrote: >> >> Hi, >> >> I created and wrote the image on the disk using ITK 4.6.0. >> I visualized the image using Slicer 4.4.0. >> >> The properties are: >> Size : [1001, 1001, 8345] >> Spacing : [1,1,1] >> Origin : [0, 0, 0] >> Direction : >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> Fotis >> >> On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp > > wrote: >> >>> Hello, >>> >>> What software did you use to create and validate that this image is >>> correct? >>> >>> Thanks, >>> Brad >>> >>> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos >>> wrote: >>> >>> Hi all, >>> >>> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >>> The image cannot loaded correctly when I use the itk::ImageFileReader. >>> The test image contains non-zero values only at indexes (350,350,i) >>> where i=0 to 8300. >>> The pixelType is short. >>> >>> Thanks >>> Fotis >>> >>> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick < >>> matt.mccormick at kitware.com> wrote: >>> >>>> Thanks! Added. >>>> >>>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos >>>> wrote: >>>> > Hi, >>>> > I signed up for the ITK community on midas. >>>> > >>>> > Thanks, >>>> > Fotis Drakopoulos >>>> > >>>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >>>> > wrote: >>>> >> >>>> >> Hi Fotis, >>>> >> >>>> >> Thanks for helping to improve large nifti file support. >>>> >> >>>> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >>>> >> community [1], let the list know the name of your account, and myself >>>> >> or one of the other administrators will add upload priviledges to the >>>> >> account. >>>> >> >>>> >> The file could then be added to >>>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >>>> >> >>>> >> Thanks, >>>> >> Matt >>>> >> >>>> >> [1] http://midas3.kitware.com/midas/community/12 >>>> >> >>>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos < >>>> fdrakopo at gmail.com> >>>> >> wrote: >>>> >> > Hi all, >>>> >> > >>>> >> > I created a test nifti image that reproduces the problem I >>>> mentioned >>>> >> > before. >>>> >> > How can I share this image with the ITK community? >>>> >> > >>>> >> > Best, >>>> >> > Fotis Drakopoulos >>>> >> > >>>> >> > >>>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >>>> >> > >>>> >> > wrote: >>>> >> >> >>>> >> >> Shareable test data greatly helps determine the cause and fix >>>> these >>>> >> >> types >>>> >> >> of issues. >>>> >> >> >>>> >> >> Got data? >>>> >> >> >>>> >> >> Brad >>>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle >>>> wrote: >>>> >> >> >>>> >> >> This is reminiscent of the previous problem with big TIFF images, >>>> now >>>> >> >> fixed. >>>> >> >> >>>> >> >> Gib >>>> >> >> ________________________________ >>>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of >>>> Fotis >>>> >> >> Drakopoulos [fdrakopo at gmail.com] >>>> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >>>> >> >> To: insight-users at itk.org; insight-developers at itk.org >>>> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >>>> >> >> >>>> >> >> Hi all, >>>> >> >> >>>> >> >> For the last couple of days I have been trying reading >>>> (unsuccessfully) >>>> >> >> a >>>> >> >> big nifti volume labeled image from my disk. >>>> >> >> >>>> >> >> The pixel type is unsigned char and the rest specs of the image >>>> are: >>>> >> >> Size : [1001, 1001, 8345] (in voxels) >>>> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >>>> >> >> Origin : [0, 0, 0] >>>> >> >> Direction : >>>> >> >> 1 0 0 >>>> >> >> 0 1 0 >>>> >> >> 0 0 1 >>>> >> >> >>>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get >>>> an idea >>>> >> >> how it looks like. Indeed the object in the volume looks as it was >>>> >> >> expected. >>>> >> >> So far no problems. The specs of the image on Slicer are the same >>>> as >>>> >> >> above >>>> >> >> (except the direction which has flipped signs for the first two >>>> >> >> diagonal >>>> >> >> entries, as we know ). >>>> >> >> >>>> >> >> Then I tried to load the image in the memory using the >>>> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >>>> >> >> loading >>>> >> >> the image I noticed that there are pixels with zero values >>>> instead of >>>> >> >> non-zero by comparing the same indexes with the loaded image on >>>> Slicer. >>>> >> >> >>>> >> >> Then I decided to write the loaded image on the disk using the >>>> >> >> itk::ImageFileWriter. >>>> >> >> >>>> >> >> After opening the (written from ITK) image on Slicer I checked the >>>> >> >> specks >>>> >> >> and were the same with the original image as above. However I >>>> noticed >>>> >> >> that a >>>> >> >> big portion of the image is completely empty (black)! >>>> >> >> >>>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >>>> >> >> DDR3L) >>>> >> >> and is using Red Hat Enterprise Linux Server 6.5. >>>> >> >> The size of the original nifti volume is : >>>> >> >> >>>> >> >> 25.7 MB (.nii.gz) >>>> >> >> 8.36 GB (.nii) >>>> >> >> >>>> >> >> Has anybody experienced similar difficulties trying to load so big >>>> >> >> volume >>>> >> >> data? >>>> >> >> >>>> >> >> Best, >>>> >> >> Fotis Drakopoulos >>>> >> >> CRTC >>>> >> >> >>>> >> >> _____________________________________ >>>> >> >> Powered by www.kitware.com >>>> >> >> >>>> >> >> Visit other Kitware open-source projects at >>>> >> >> http://www.kitware.com/opensource/opensource.html >>>> >> >> >>>> >> >> Kitware offers ITK Training Courses, for more information visit: >>>> >> >> http://www.kitware.com/products/protraining.php >>>> >> >> >>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>> >> >> >>>> >> >> Follow this link to subscribe/unsubscribe: >>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>> >> >> >>>> >> >> >>>> >> >> ________________________________ >>>> >> >> >>>> >> >> Spam >>>> >> >> Not spam >>>> >> >> Forget previous vote >>>> >> > >>>> >> > >>>> >> > >>>> >> > _______________________________________________ >>>> >> > Powered by www.kitware.com >>>> >> > >>>> >> > Visit other Kitware open-source projects at >>>> >> > http://www.kitware.com/opensource/opensource.html >>>> >> > >>>> >> > Kitware offers ITK Training Courses, for more information visit: >>>> >> > http://kitware.com/products/protraining.php >>>> >> > >>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>> >> > >>>> >> > Follow this link to subscribe/unsubscribe: >>>> >> > http://public.kitware.com/mailman/listinfo/insight-developers >>>> >> > >>>> >> >>>> >> >>>> >> -- >>>> >> >>>> > >>>> >>>> >>>> -- >>>> BEGIN-ANTISPAM-VOTING-LINKS >>>> ------------------------------------------------------ >>>> >>>> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >>>> Spam: about:blank >>>> Not spam: about:blank >>>> Forget vote: about:blank >>>> ------------------------------------------------------ >>>> END-ANTISPAM-VOTING-LINKS >>>> >>>> >>> >>> ------------------------------ >>> >>> Spam >>> Not spam >>> Forget previous vote >>> >> >> >> ------------------------------ >> >> Spam >> >> Not spam >> >> Forget previous vote >> >> > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From richard.beare at gmail.com Wed Dec 3 01:03:06 2014 From: richard.beare at gmail.com (Richard Beare) Date: Wed, 3 Dec 2014 17:03:06 +1100 Subject: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti volume. In-Reply-To: <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov> References: <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov> <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov> <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov> <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov> Message-ID: Hi, I have, coincidentally, run into what I presume is the same issue. I'll add what I've observed, but note that I haven't gone into investigations very thoroughly. I started with a 5.9GB mha volume. I found that an old version of ITK snap crashed when attempting to view it. I converted to nifti using the ConvertBetweenFileFormats tool, and found that fslview crashed, itksnap crashed, mrview (from mrtrix) was able to view. I tested a newer version of itksnap and found crashing with nifti. The new version of itksnap would load the mha but would only display part of it (probably the first 2GB), the rest was blank. I also found that imageJ was able to view the nifti. So, I think writing large nifti files from ITK is OK. Reading appears broken. I think there may be additional issues with large files with itksnap. On Wed, Dec 3, 2014 at 3:34 AM, Bradley Lowekamp wrote: > Hello, > > Unfortunately, I don't see the logic with it working with Slicer, but not > working in native ITK as it uses the same code. > > I have perused the NIFT1 C library that ITK has in the ThirdParty group, > which appears up to date with the latest released version: 2.0.0. > > There a quite a number of places where the calculation of the size of the > image is not done at size_t/64-bits safe fashion, along with other 64-bit > safe operations. I am concluding that the nifit file format doesn't readily > support image > 4GB. Even if we then through the extensive effort of > updating our version of the third party library the resulting images are > very likely not going to work with other toosl that work with nifti images. > > Brad > > On Dec 2, 2014, at 11:14 AM, Fotis Drakopoulos wrote: > > The image contains a single non-zero voxel on each axial slice. > > When I load the image on Slicer the non-zero voxels are preserved as you > traverse the image using the window slider. > When I read the image using a simple main program a big portion of the > the non-zero voxels do not exist. > > I had the same issue when the file was .nii (not compressed). > > Fotis > > > On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp > wrote: > >> So if you wrote and read with ITK ( via Slicer ), how do you know that >> the file is correct as you expect? >> >> I see the file has a ".nii.gz" extension, meaning that it's compressed. >> Does the same issue occur when it's not compressed? >> >> Brad >> >> >> >> On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos >> wrote: >> >> Hi, >> >> I created and wrote the image on the disk using ITK 4.6.0. >> I visualized the image using Slicer 4.4.0. >> >> The properties are: >> Size : [1001, 1001, 8345] >> Spacing : [1,1,1] >> Origin : [0, 0, 0] >> Direction : >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> Fotis >> >> On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp > > wrote: >> >>> Hello, >>> >>> What software did you use to create and validate that this image is >>> correct? >>> >>> Thanks, >>> Brad >>> >>> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos >>> wrote: >>> >>> Hi all, >>> >>> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >>> The image cannot loaded correctly when I use the itk::ImageFileReader. >>> The test image contains non-zero values only at indexes (350,350,i) >>> where i=0 to 8300. >>> The pixelType is short. >>> >>> Thanks >>> Fotis >>> >>> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick < >>> matt.mccormick at kitware.com> wrote: >>> >>>> Thanks! Added. >>>> >>>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos >>>> wrote: >>>> > Hi, >>>> > I signed up for the ITK community on midas. >>>> > >>>> > Thanks, >>>> > Fotis Drakopoulos >>>> > >>>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >>>> > wrote: >>>> >> >>>> >> Hi Fotis, >>>> >> >>>> >> Thanks for helping to improve large nifti file support. >>>> >> >>>> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >>>> >> community [1], let the list know the name of your account, and myself >>>> >> or one of the other administrators will add upload priviledges to the >>>> >> account. >>>> >> >>>> >> The file could then be added to >>>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >>>> >> >>>> >> Thanks, >>>> >> Matt >>>> >> >>>> >> [1] http://midas3.kitware.com/midas/community/12 >>>> >> >>>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos < >>>> fdrakopo at gmail.com> >>>> >> wrote: >>>> >> > Hi all, >>>> >> > >>>> >> > I created a test nifti image that reproduces the problem I >>>> mentioned >>>> >> > before. >>>> >> > How can I share this image with the ITK community? >>>> >> > >>>> >> > Best, >>>> >> > Fotis Drakopoulos >>>> >> > >>>> >> > >>>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp >>>> >> > >>>> >> > wrote: >>>> >> >> >>>> >> >> Shareable test data greatly helps determine the cause and fix >>>> these >>>> >> >> types >>>> >> >> of issues. >>>> >> >> >>>> >> >> Got data? >>>> >> >> >>>> >> >> Brad >>>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle >>>> wrote: >>>> >> >> >>>> >> >> This is reminiscent of the previous problem with big TIFF images, >>>> now >>>> >> >> fixed. >>>> >> >> >>>> >> >> Gib >>>> >> >> ________________________________ >>>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of >>>> Fotis >>>> >> >> Drakopoulos [fdrakopo at gmail.com] >>>> >> >> Sent: Monday, 24 November 2014 10:51 a.m. >>>> >> >> To: insight-users at itk.org; insight-developers at itk.org >>>> >> >> Subject: [ITK-users] Problem reading a big nifti volume. >>>> >> >> >>>> >> >> Hi all, >>>> >> >> >>>> >> >> For the last couple of days I have been trying reading >>>> (unsuccessfully) >>>> >> >> a >>>> >> >> big nifti volume labeled image from my disk. >>>> >> >> >>>> >> >> The pixel type is unsigned char and the rest specs of the image >>>> are: >>>> >> >> Size : [1001, 1001, 8345] (in voxels) >>>> >> >> Spacing : [0.012, 0.012, 0.012] (in mm) >>>> >> >> Origin : [0, 0, 0] >>>> >> >> Direction : >>>> >> >> 1 0 0 >>>> >> >> 0 1 0 >>>> >> >> 0 0 1 >>>> >> >> >>>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get >>>> an idea >>>> >> >> how it looks like. Indeed the object in the volume looks as it was >>>> >> >> expected. >>>> >> >> So far no problems. The specs of the image on Slicer are the same >>>> as >>>> >> >> above >>>> >> >> (except the direction which has flipped signs for the first two >>>> >> >> diagonal >>>> >> >> entries, as we know ). >>>> >> >> >>>> >> >> Then I tried to load the image in the memory using the >>>> >> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After >>>> >> >> loading >>>> >> >> the image I noticed that there are pixels with zero values >>>> instead of >>>> >> >> non-zero by comparing the same indexes with the loaded image on >>>> Slicer. >>>> >> >> >>>> >> >> Then I decided to write the loaded image on the disk using the >>>> >> >> itk::ImageFileWriter. >>>> >> >> >>>> >> >> After opening the (written from ITK) image on Slicer I checked the >>>> >> >> specks >>>> >> >> and were the same with the original image as above. However I >>>> noticed >>>> >> >> that a >>>> >> >> big portion of the image is completely empty (black)! >>>> >> >> >>>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz >>>> >> >> DDR3L) >>>> >> >> and is using Red Hat Enterprise Linux Server 6.5. >>>> >> >> The size of the original nifti volume is : >>>> >> >> >>>> >> >> 25.7 MB (.nii.gz) >>>> >> >> 8.36 GB (.nii) >>>> >> >> >>>> >> >> Has anybody experienced similar difficulties trying to load so big >>>> >> >> volume >>>> >> >> data? >>>> >> >> >>>> >> >> Best, >>>> >> >> Fotis Drakopoulos >>>> >> >> CRTC >>>> >> >> >>>> >> >> _____________________________________ >>>> >> >> Powered by www.kitware.com >>>> >> >> >>>> >> >> Visit other Kitware open-source projects at >>>> >> >> http://www.kitware.com/opensource/opensource.html >>>> >> >> >>>> >> >> Kitware offers ITK Training Courses, for more information visit: >>>> >> >> http://www.kitware.com/products/protraining.php >>>> >> >> >>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>> >> >> >>>> >> >> Follow this link to subscribe/unsubscribe: >>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>> >> >> >>>> >> >> >>>> >> >> ________________________________ >>>> >> >> >>>> >> >> Spam >>>> >> >> Not spam >>>> >> >> Forget previous vote >>>> >> > >>>> >> > >>>> >> > >>>> >> > _______________________________________________ >>>> >> > Powered by www.kitware.com >>>> >> > >>>> >> > Visit other Kitware open-source projects at >>>> >> > http://www.kitware.com/opensource/opensource.html >>>> >> > >>>> >> > Kitware offers ITK Training Courses, for more information visit: >>>> >> > http://kitware.com/products/protraining.php >>>> >> > >>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>> >> > >>>> >> > Follow this link to subscribe/unsubscribe: >>>> >> > http://public.kitware.com/mailman/listinfo/insight-developers >>>> >> > >>>> >> >>>> >> >>>> >> -- >>>> >> >>>> > >>>> >>>> >>>> -- >>>> BEGIN-ANTISPAM-VOTING-LINKS >>>> ------------------------------------------------------ >>>> >>>> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >>>> Spam: about:blank >>>> Not spam: about:blank >>>> Forget vote: about:blank >>>> ------------------------------------------------------ >>>> END-ANTISPAM-VOTING-LINKS >>>> >>>> >>> >>> ------------------------------ >>> >>> Spam >>> Not spam >>> Forget previous vote >>> >> >> >> ------------------------------ >> >> Spam >> >> Not spam >> >> Forget previous vote >> >> > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matimontg at gmail.com Wed Dec 3 06:30:35 2014 From: matimontg at gmail.com (Matias Montroull) Date: Wed, 3 Dec 2014 08:30:35 -0300 Subject: [ITK] [ITK-users] CT MR Fusion Message-ID: Hi, I have a set of DICOM images (CT) and another set of images from the same patient (CT) which I need to fuse. Looking at the examples, I noticed most of them are 2D, is there any example that would fuse a set of CT/MR images? I looked at some examples where the input was a single file but I actually need to input a 2 directories, (the CT image directory and the MR image directory). (I hope is that easy) Thanks, Matias. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From simon.esneault at gmail.com Wed Dec 3 09:22:29 2014 From: simon.esneault at gmail.com (Simon ESNEAULT) Date: Wed, 3 Dec 2014 15:22:29 +0100 Subject: [ITK] [ITK-dev] Exception in itk::ResampleImageFilter multithreaded part after ITK migration from 3.20.1 to 4.6.1 In-Reply-To: References: Message-ID: Hi Bradley, Thanks for your answer. You're right it can not be the export otherwise it would not link. Plus, I can now reproduce the exact same exception at runtime on OSX (10.10, XCode 6) with our framework updated and build against ITK 4.6.1 I've search all copies of ResampleFilter and the only one left on the computers (Win and OSX) are the one from ITK 4.6.1. It must be something else ! Here is what we do with cmake : set( Itk_INCLUDE_DIR ${CMAKE_BINARY_DIR}/../externals/ITK-4.6.1/${OS_NAME}/include ) set( Itk_LIBRARY_DIR ${CMAKE_BINARY_DIR}/../externals/ITK-4.6.1/${OS_NAME}/lib/${CMAKE_BUILD_TYPE} ) set( Itk_LIBRARIES ITKBiasCorrection-4.6 ITKBioCell-4.6 ITKCommon-4.6 ITKDICOMParser-4.6 itkdouble-conversion-4.6 ITKEXPAT-4.6 ITKFEM-4.6 itkgdcmCommon-4.6 itkgdcmDICT-4.6 itkgdcmDSED-4.6 itkgdcmIOD-4.6 itkgdcmjpeg12-4.6 itkgdcmjpeg16-4.6 itkgdcmjpeg8-4.6 itkgdcmMSFF-4.6 ITKgiftiio-4.6 itkhdf5-4.6 itkhdf5_cpp-4.6 ITKIOBioRad-4.6 ITKIOBMP-4.6 ITKIOCSV-4.6 ITKIOGDCM-4.6 ITKIOGE-4.6 ITKIOGIPL-4.6 ITKIOHDF5-4.6 ITKIOImageBase-4.6 ITKIOIPL-4.6 ITKIOJPEG-4.6 ITKIOLSM-4.6 ITKIOMesh-4.6 ITKIOMeta-4.6 ITKIOMRC-4.6 ITKIONIFTI-4.6 ITKIONRRD-4.6 ITKIOPNG-4.6 ITKIOSiemens-4.6 ITKIOSpatialObjects-4.6 ITKIOStimulate-4.6 ITKIOTIFF-4.6 ITKIOTransformBase-4.6 ITKIOTransformHDF5-4.6 ITKIOTransformInsightLegacy-4.6 ITKIOTransformMatlab-4.6 ITKIOVTK-4.6 ITKIOXML-4.6 itkjpeg-4.6 ITKKLMRegionGrowing-4.6 ITKLabelMap-4.6 ITKMesh-4.6 ITKMetaIO-4.6 itkNetlibSlatec-4.6 ITKniftiio-4.6 ITKNrrdIO-4.6 itkopenjpeg-4.6 ITKOptimizers-4.6 ITKOptimizersv4-4.6 ITKPath-4.6 itkpng-4.6 ITKPolynomials-4.6 ITKQuadEdgeMesh-4.6 ITKSpatialObjects-4.6 ITKStatistics-4.6 itksys-4.6 itktiff-4.6 itkv3p_lsqr-4.6 itkv3p_netlib-4.6 itkvcl-4.6 ITKVideoCore-4.6 ITKVideoIO-4.6 itkvnl-4.6 ITKVNLInstantiation-4.6 itkvnl_algo-4.6 ITKVTK-4.6 ITKWatersheds-4.6 itkzlib-4.6 ITKznz-4.6 ) And later on, include_directories( ${Itk_INCLUDE_DIR} ) link_directories( ${Itk_LIBRARY_DIR} ) target_link_libraries( my_exec ${Itk_LIBRARIES} ) or target_link_libraries( my_lib ${Itk_LIBRARIES} ) After that we Register Itk factories as stated in the first mail. Is this sufficient? Can this be responsible of such a behavior ? Simon 2014-12-02 15:45 GMT+01:00 Bradley Lowekamp : > Hello Simon, > > If you don't have your exports correct it'd likely result in a link error. > > Given the error message you report, it sounds like you are using an old > version of the ResampleFilter. I'd look into seeing if there are old copies > of ITK 3.20 laying around that may be included in your project. You can not > use mix symbols and includes from different version of ITK. > > Brad > > On Dec 2, 2014, at 4:51 AM, Simon ESNEAULT > wrote: > > Hi Bill, > > Thanks for your reply. I have downloaded and executed succesfully the > Upsampling example ( > http://itk.org/Wiki/ITK/Examples/ImageProcessing/Upsampling), using the > version of ITK (4.6.1) we used in the framework. > > It appears our problem is probably related with our framework > architecture, and some dll import/export on windows. We wrapped all our ITK > code in a library WrapItk.dll. And there are some others libraries, all of > them can make use of native ITK code or wrapped ITK code. This used to work > fine with ITK 3.20.1, but it's seems broken in 4.6.1. > > Not only the Resample filter raise an exception but all the MultiThreaded > filter in ITK. When debugging, we go through > itk::ResampleImageFilter::BeforeThreadedGenerateData() just fine, and > somehow, when ThreadedGenerateData() is called we fall back in the mother > class ImageSource method, hence raising the exception. > > Anyone know how to use properly ITK code with multiple DLL's on windows ? > ie having an image loaded with ITK code from one DLL, and some ITK filter > executed in another DLL without trouble ? > We use that sort of mechanism to export functions properly between DLLs. > #if SOME_DLL_DEFINITIONS > #define MY_EXPORT __declspec(dllexport) > #else > #define MY_EXPORT __declspec(dllimport) > > I will try to sum things up in scheme if that can help ... > > Thanks > Simon > > > 2014-12-01 14:51 GMT+01:00 Bill Lorensen : > >> Very strange. >> >> Could you try building and running this example: >> http://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter >> >> Bill >> >> On Mon, Dec 1, 2014 at 7:53 AM, Simon ESNEAULT >> wrote: >> > Hello ITK community >> > >> > After the migration from ITK 3.20.1 to ITK 4.6.1, I'm getting a runtime >> > exception when using itk::ResampleImageFilter in our framework. The >> output >> > looks like this : >> > >> > Problem during Resample filtering: >> > >> D:\Dev\DevCpp-Qt5\cmake-externals\ITK\src\Modules\Core\Common\src\itkMultiThreader.cxx:358: >> > itk::ERROR: MultiThreader(31CAAD18): Exception occurred during >> > SingleMethodExecute >> > c:\dev\Dev_qt5\externals\itk-4.6.1\win32\include\itkImageSource.hxx:267: >> > itk::ERROR: ResampleImageFilter(31AC2E90): Subclass should override this >> > method!!! >> > The signature of ThreadedGenerateData() has been changed in ITK v4 to >> use >> > the new ThreadIdType. >> > ResampleImageFilter::ThreadedGenerateData() might need to be updated to >> used >> > it. >> > >> > That is weird, because the itkResampleImageFilter is the one delivered >> with >> > ITK 4.6.1, so it must have followed the API changed ... >> > >> > The context is : >> > Visual Studio 2013 community, 32 bit build, ITK build in shared library >> > mode. That's quite a big project, with VTK, Qt, OpenCV, DCMTK, zlib ... >> > I'm not using cmake in the usual way (ie no find_package(ITK) >> > include(${ITK_USE_FILE}) ) but we list the libraries and includes. I >> know >> > there are some factories to register in that case, we're doing this in >> the >> > main.cpp : >> > itk::TransformFactoryBase::RegisterDefaultTransforms(); >> > itk::PNGImageIOFactory::RegisterOneFactory(); >> > itk::MetaImageIOFactory::RegisterOneFactory(); >> > itk::NrrdImageIOFactory::RegisterOneFactory(); >> > >> > Am I missing some others factories to register in order to run properly >> the >> > resampleImageFilter ? >> > Anyone else had a similar runtime exception with a native ITK filte, or >> know >> > what would raise such an exception ? >> > >> > Thanks >> > >> > -- >> > ------------------------------------------------------------------ >> > Simon Esneault >> > ------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-developers >> > >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> > > > > -- > ------------------------------------------------------------------ > Simon Esneault > ------------------------------------------------------------------ > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > -- ------------------------------------------------------------------ Simon Esneault 13 rue Vasselot 35000 Rennes, France Tel : 06 64 61 30 94 Mail : simon.esneault at gmail.com ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From deu439 at gmail.com Wed Dec 3 10:18:53 2014 From: deu439 at gmail.com (Jan Dorazil) Date: Wed, 03 Dec 2014 16:18:53 +0100 Subject: [ITK] MRI intensity normalization Message-ID: <547F29DD.7090902@gmail.com> Hello, is it possible to use NormalizeImageFilter to normalize image intensities with background of the image excluded? Thanks, Jan Dorazil From simon.esneault at gmail.com Wed Dec 3 10:19:48 2014 From: simon.esneault at gmail.com (Simon ESNEAULT) Date: Wed, 3 Dec 2014 16:19:48 +0100 Subject: [ITK] [ITK-dev] Exception in itk::ResampleImageFilter multithreaded part after ITK migration from 3.20.1 to 4.6.1 In-Reply-To: References: Message-ID: Finally just found the error ... We had somewhere deep in our code the following lines ... #ifndef ThreadIdType #define ThreadIdType int #endif Depending on the code tested, that was picked at the first place, thus messing with the new ITK API ! Sorry for the noise, everything back in order Thanks for the support Simon 2014-12-03 15:22 GMT+01:00 Simon ESNEAULT : > Hi Bradley, > > Thanks for your answer. You're right it can not be the export otherwise it > would not link. > Plus, I can now reproduce the exact same exception at runtime on OSX > (10.10, XCode 6) with our framework updated and build against ITK 4.6.1 > > I've search all copies of ResampleFilter and the only one left on the > computers (Win and OSX) are the one from ITK 4.6.1. It must be something > else ! > > Here is what we do with cmake : > > set( Itk_INCLUDE_DIR > ${CMAKE_BINARY_DIR}/../externals/ITK-4.6.1/${OS_NAME}/include ) > set( Itk_LIBRARY_DIR > ${CMAKE_BINARY_DIR}/../externals/ITK-4.6.1/${OS_NAME}/lib/${CMAKE_BUILD_TYPE} > ) > set( Itk_LIBRARIES > ITKBiasCorrection-4.6 > ITKBioCell-4.6 > ITKCommon-4.6 > ITKDICOMParser-4.6 > itkdouble-conversion-4.6 > ITKEXPAT-4.6 > ITKFEM-4.6 > itkgdcmCommon-4.6 > itkgdcmDICT-4.6 > itkgdcmDSED-4.6 > itkgdcmIOD-4.6 > itkgdcmjpeg12-4.6 > itkgdcmjpeg16-4.6 > itkgdcmjpeg8-4.6 > itkgdcmMSFF-4.6 > ITKgiftiio-4.6 > itkhdf5-4.6 > itkhdf5_cpp-4.6 > ITKIOBioRad-4.6 > ITKIOBMP-4.6 > ITKIOCSV-4.6 > ITKIOGDCM-4.6 > ITKIOGE-4.6 > ITKIOGIPL-4.6 > ITKIOHDF5-4.6 > ITKIOImageBase-4.6 > ITKIOIPL-4.6 > ITKIOJPEG-4.6 > ITKIOLSM-4.6 > ITKIOMesh-4.6 > ITKIOMeta-4.6 > ITKIOMRC-4.6 > ITKIONIFTI-4.6 > ITKIONRRD-4.6 > ITKIOPNG-4.6 > ITKIOSiemens-4.6 > ITKIOSpatialObjects-4.6 > ITKIOStimulate-4.6 > ITKIOTIFF-4.6 > ITKIOTransformBase-4.6 > ITKIOTransformHDF5-4.6 > ITKIOTransformInsightLegacy-4.6 > ITKIOTransformMatlab-4.6 > ITKIOVTK-4.6 > ITKIOXML-4.6 > itkjpeg-4.6 > ITKKLMRegionGrowing-4.6 > ITKLabelMap-4.6 > ITKMesh-4.6 > ITKMetaIO-4.6 > itkNetlibSlatec-4.6 > ITKniftiio-4.6 > ITKNrrdIO-4.6 > itkopenjpeg-4.6 > ITKOptimizers-4.6 > ITKOptimizersv4-4.6 > ITKPath-4.6 > itkpng-4.6 > ITKPolynomials-4.6 > ITKQuadEdgeMesh-4.6 > ITKSpatialObjects-4.6 > ITKStatistics-4.6 > itksys-4.6 > itktiff-4.6 > itkv3p_lsqr-4.6 > itkv3p_netlib-4.6 > itkvcl-4.6 > ITKVideoCore-4.6 > ITKVideoIO-4.6 > itkvnl-4.6 > ITKVNLInstantiation-4.6 > itkvnl_algo-4.6 > ITKVTK-4.6 > ITKWatersheds-4.6 > itkzlib-4.6 > ITKznz-4.6 > ) > > And later on, > include_directories( ${Itk_INCLUDE_DIR} ) > link_directories( ${Itk_LIBRARY_DIR} ) > target_link_libraries( my_exec ${Itk_LIBRARIES} ) > or target_link_libraries( my_lib ${Itk_LIBRARIES} ) > > After that we Register Itk factories as stated in the first mail. > Is this sufficient? > Can this be responsible of such a behavior ? > > Simon > > > 2014-12-02 15:45 GMT+01:00 Bradley Lowekamp : > >> Hello Simon, >> >> If you don't have your exports correct it'd likely result in a link error. >> >> Given the error message you report, it sounds like you are using an old >> version of the ResampleFilter. I'd look into seeing if there are old copies >> of ITK 3.20 laying around that may be included in your project. You can not >> use mix symbols and includes from different version of ITK. >> >> Brad >> >> On Dec 2, 2014, at 4:51 AM, Simon ESNEAULT >> wrote: >> >> Hi Bill, >> >> Thanks for your reply. I have downloaded and executed succesfully the >> Upsampling example ( >> http://itk.org/Wiki/ITK/Examples/ImageProcessing/Upsampling), using the >> version of ITK (4.6.1) we used in the framework. >> >> It appears our problem is probably related with our framework >> architecture, and some dll import/export on windows. We wrapped all our ITK >> code in a library WrapItk.dll. And there are some others libraries, all of >> them can make use of native ITK code or wrapped ITK code. This used to work >> fine with ITK 3.20.1, but it's seems broken in 4.6.1. >> >> Not only the Resample filter raise an exception but all the MultiThreaded >> filter in ITK. When debugging, we go through >> itk::ResampleImageFilter::BeforeThreadedGenerateData() just fine, and >> somehow, when ThreadedGenerateData() is called we fall back in the mother >> class ImageSource method, hence raising the exception. >> >> Anyone know how to use properly ITK code with multiple DLL's on windows ? >> ie having an image loaded with ITK code from one DLL, and some ITK filter >> executed in another DLL without trouble ? >> We use that sort of mechanism to export functions properly between DLLs. >> #if SOME_DLL_DEFINITIONS >> #define MY_EXPORT __declspec(dllexport) >> #else >> #define MY_EXPORT __declspec(dllimport) >> >> I will try to sum things up in scheme if that can help ... >> >> Thanks >> Simon >> >> >> 2014-12-01 14:51 GMT+01:00 Bill Lorensen : >> >>> Very strange. >>> >>> Could you try building and running this example: >>> http://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter >>> >>> Bill >>> >>> On Mon, Dec 1, 2014 at 7:53 AM, Simon ESNEAULT >>> wrote: >>> > Hello ITK community >>> > >>> > After the migration from ITK 3.20.1 to ITK 4.6.1, I'm getting a runtime >>> > exception when using itk::ResampleImageFilter in our framework. The >>> output >>> > looks like this : >>> > >>> > Problem during Resample filtering: >>> > >>> D:\Dev\DevCpp-Qt5\cmake-externals\ITK\src\Modules\Core\Common\src\itkMultiThreader.cxx:358: >>> > itk::ERROR: MultiThreader(31CAAD18): Exception occurred during >>> > SingleMethodExecute >>> > >>> c:\dev\Dev_qt5\externals\itk-4.6.1\win32\include\itkImageSource.hxx:267: >>> > itk::ERROR: ResampleImageFilter(31AC2E90): Subclass should override >>> this >>> > method!!! >>> > The signature of ThreadedGenerateData() has been changed in ITK v4 to >>> use >>> > the new ThreadIdType. >>> > ResampleImageFilter::ThreadedGenerateData() might need to be updated >>> to used >>> > it. >>> > >>> > That is weird, because the itkResampleImageFilter is the one delivered >>> with >>> > ITK 4.6.1, so it must have followed the API changed ... >>> > >>> > The context is : >>> > Visual Studio 2013 community, 32 bit build, ITK build in shared library >>> > mode. That's quite a big project, with VTK, Qt, OpenCV, DCMTK, zlib ... >>> > I'm not using cmake in the usual way (ie no find_package(ITK) >>> > include(${ITK_USE_FILE}) ) but we list the libraries and includes. I >>> know >>> > there are some factories to register in that case, we're doing this in >>> the >>> > main.cpp : >>> > itk::TransformFactoryBase::RegisterDefaultTransforms(); >>> > itk::PNGImageIOFactory::RegisterOneFactory(); >>> > itk::MetaImageIOFactory::RegisterOneFactory(); >>> > itk::NrrdImageIOFactory::RegisterOneFactory(); >>> > >>> > Am I missing some others factories to register in order to run >>> properly the >>> > resampleImageFilter ? >>> > Anyone else had a similar runtime exception with a native ITK filte, >>> or know >>> > what would raise such an exception ? >>> > >>> > Thanks >>> > >>> > -- >>> > ------------------------------------------------------------------ >>> > Simon Esneault >>> > ------------------------------------------------------------------ >>> > >>> > _______________________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-developers >>> > >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >>> >> >> >> >> -- >> ------------------------------------------------------------------ >> Simon Esneault >> ------------------------------------------------------------------ >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> >> > > > -- > ------------------------------------------------------------------ > Simon Esneault > ------------------------------------------------------------------ > -- ------------------------------------------------------------------ Simon Esneault ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Dec 3 11:00:16 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Dec 2014 11:00:16 -0500 Subject: [ITK] MRI intensity normalization In-Reply-To: <547F29DD.7090902@gmail.com> References: <547F29DD.7090902@gmail.com> Message-ID: Hi Jan, A normalization could be performed with a few filters and defining a foreground/background with the LabelStatisticsImageFilter. HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1LabelStatisticsImageFilter.html On Wed, Dec 3, 2014 at 10:18 AM, Jan Dorazil wrote: > Hello, > is it possible to use NormalizeImageFilter to normalize image intensities > with background of the image excluded? > > Thanks, > Jan Dorazil > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From sebastian.ordas at gmail.com Wed Dec 3 11:21:20 2014 From: sebastian.ordas at gmail.com (Sebastian Ordas) Date: Wed, 03 Dec 2014 13:21:20 -0300 Subject: [ITK] How to get a vector of DICOM Series description strings in ITKv4 (GDCM 2.x)? Message-ID: <547F3880.4030404@gmail.com> Dear All, I used to be able with ITK 3.12 (GDCM 1.x) to populate a vector with series description strings, recursively, given the path to a folder with DICOM files. The goal is to fill in an "Open DICOM" dialog with such information, in order to let the user load a single DICOM Series. How can I do that with ITKv4 (GDCM 2.x)? thank you, sebastian Here?s my original code: typedef gdcm::FileList DICOMFileListType; m_GDCMScanner = itk::GDCMSeriesFileNames::New(); m_GDCMScanner->SetUseSeriesDetails(true); m_GDCMScanner->LoadPrivateTagsOff(); m_GDCMHelper = m_GDCMScanner->GetSeriesHelper(); m_GDCMScanner->SetInputDirectory( m_ImageDirectoryName ); if (!itksys::SystemTools::FileExists (ImageDirectoryName )) { return; } // we now scan from scratch all dicom file headers try { this->m_GDCMHelper->Clear(); unsigned long counter_im = 0; gdcm::DirList dirlist(dirname, m_UseRecursiveScan); gdcm::DirListType filenames_list = dirlist.GetFilenames(); unsigned long totalImages = filenames_list.size(); if (totalImages<10) return; for( gdcm::DirListType::const_iterator it = filenames_list.begin(); it != filenames_list.end(); ++it) { if (itksys::SystemTools::FileExists ((*it).c_str(), true)) m_GDCMHelper->AddFileName ((*it)); counter_im++; } } catch (itk::ExceptionObject & excp) { return; } std::vector UIDs; UIDs = m_GDCMScanner->GetSeriesUIDs(); if (!UIDs.size()) return; try { m_SeriesNames.clear(); int nSeries = 0; for (unsigned int uid=0; uidGetSingleSerieUIDFileSet(uidname); this->m_GDCMHelper->OrderFileList (t_filelist); DICOMFileListType::iterator it; it = t_filelist.begin(); for (; it != t_filelist.end(); it++) { DICOMFileListType* filelist = (*it); if ( !filelist->size() ) { continue; } std::stringstream stream; stream << "series# " << nSeries << ": " << this->GenerateName(filelist) << " (" << filelist->size() << " slices)"; m_SeriesNames.push_back( stream.str() ); nSeries++; } } } catch (itk::ExceptionObject & excp) { return; } template std::string DICOMImageReader::GenerateName (DICOMFileListType* filelist) { std::string description = (*filelist)[0]->GetEntryValue(0x0008, 0x103E); if (description == gdcm::GDCM_UNFOUND) { (*filelist)[0]->Load(); description = (*filelist)[0]->GetEntryValue(0x0008, 0x103E); } return description; } From matt.mccormick at kitware.com Wed Dec 3 11:30:57 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Dec 2014 11:30:57 -0500 Subject: [ITK] How to get a vector of DICOM Series description strings in ITKv4 (GDCM 2.x)? In-Reply-To: <547F3880.4030404@gmail.com> References: <547F3880.4030404@gmail.com> Message-ID: Hi Sebastian, What specifically is the issue using this code with ITKv4? Thanks, Matt On Wed, Dec 3, 2014 at 11:21 AM, Sebastian Ordas wrote: > Dear All, > > I used to be able with ITK 3.12 (GDCM 1.x) to populate a vector with series > description strings, recursively, given the path to a folder with DICOM > files. > The goal is to fill in an "Open DICOM" dialog with such information, in > order to let the user load a single DICOM Series. > How can I do that with ITKv4 (GDCM 2.x)? > > thank you, > sebastian > > Here?s my original code: > > typedef gdcm::FileList DICOMFileListType; > > m_GDCMScanner = itk::GDCMSeriesFileNames::New(); > m_GDCMScanner->SetUseSeriesDetails(true); > m_GDCMScanner->LoadPrivateTagsOff(); > m_GDCMHelper = m_GDCMScanner->GetSeriesHelper(); > > m_GDCMScanner->SetInputDirectory( m_ImageDirectoryName ); > > if (!itksys::SystemTools::FileExists (ImageDirectoryName )) > { > return; > } > > // we now scan from scratch all dicom file headers > try > { > this->m_GDCMHelper->Clear(); > > unsigned long counter_im = 0; > gdcm::DirList dirlist(dirname, m_UseRecursiveScan); > > gdcm::DirListType filenames_list = dirlist.GetFilenames(); > > unsigned long totalImages = filenames_list.size(); > if (totalImages<10) > return; > > for( gdcm::DirListType::const_iterator it = filenames_list.begin(); > it != filenames_list.end(); ++it) > { > if (itksys::SystemTools::FileExists ((*it).c_str(), true)) > m_GDCMHelper->AddFileName ((*it)); > counter_im++; > } > } > catch (itk::ExceptionObject & excp) > { > return; > } > > std::vector UIDs; > UIDs = m_GDCMScanner->GetSeriesUIDs(); > > if (!UIDs.size()) > return; > > try > { > m_SeriesNames.clear(); > > int nSeries = 0; > > for (unsigned int uid=0; uid { > std::string uidname = UIDs[uid]; > DICOMFileListType* t_filelist = > m_GDCMHelper->GetSingleSerieUIDFileSet(uidname); > this->m_GDCMHelper->OrderFileList (t_filelist); > > DICOMFileListType::iterator it; > it = t_filelist.begin(); > > for (; it != t_filelist.end(); it++) > { > DICOMFileListType* filelist = (*it); > if ( !filelist->size() ) > { > continue; > } > std::stringstream stream; > stream << "series# " << nSeries << ": " << > this->GenerateName(filelist) << " (" << filelist->size() << " slices)"; > m_SeriesNames.push_back( stream.str() ); > nSeries++; > } > } > } > catch (itk::ExceptionObject & excp) > { > return; > } > > template > std::string DICOMImageReader::GenerateName (DICOMFileListType* > filelist) > { > std::string description = (*filelist)[0]->GetEntryValue(0x0008, 0x103E); > if (description == gdcm::GDCM_UNFOUND) > { > (*filelist)[0]->Load(); > description = (*filelist)[0]->GetEntryValue(0x0008, 0x103E); > } > return description; > } > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From sebastian.ordas at gmail.com Wed Dec 3 11:43:26 2014 From: sebastian.ordas at gmail.com (Sebastian Ordas) Date: Wed, 03 Dec 2014 13:43:26 -0300 Subject: [ITK] How to get a vector of DICOM Series description strings in ITKv4 (GDCM 2.x)? In-Reply-To: References: <547F3880.4030404@gmail.com> Message-ID: <547F3DAE.1090201@gmail.com> Hi Matt, several issues: the GDCM API has changed in 2.x For instance, gdcm::DirList does not exist anymore, same for m_GDCMHelper->AddFileName(), etc I would also like to know whether to put the efforts on GDCM or DCMTK (I have seen a gdcm::SerieHelper2 class in plastimach that is worthy to explore) ... but there should be some basic functionality / approach already available for such a simple and general action (i.e. explore available DICOM Series and/or Studies in a folder with DICOM files) let me know if you have some useful links (I don?'t want to link against CTK in my app) thanks sebastian On 03/12/2014 01:30 p.m., Matt McCormick wrote: > Hi Sebastian, > > What specifically is the issue using this code with ITKv4? > > Thanks, > Matt > > On Wed, Dec 3, 2014 at 11:21 AM, Sebastian Ordas > wrote: >> Dear All, >> >> I used to be able with ITK 3.12 (GDCM 1.x) to populate a vector with series >> description strings, recursively, given the path to a folder with DICOM >> files. >> The goal is to fill in an "Open DICOM" dialog with such information, in >> order to let the user load a single DICOM Series. >> How can I do that with ITKv4 (GDCM 2.x)? >> >> thank you, >> sebastian >> >> Here?s my original code: >> >> typedef gdcm::FileList DICOMFileListType; >> >> m_GDCMScanner = itk::GDCMSeriesFileNames::New(); >> m_GDCMScanner->SetUseSeriesDetails(true); >> m_GDCMScanner->LoadPrivateTagsOff(); >> m_GDCMHelper = m_GDCMScanner->GetSeriesHelper(); >> >> m_GDCMScanner->SetInputDirectory( m_ImageDirectoryName ); >> >> if (!itksys::SystemTools::FileExists (ImageDirectoryName )) >> { >> return; >> } >> >> // we now scan from scratch all dicom file headers >> try >> { >> this->m_GDCMHelper->Clear(); >> >> unsigned long counter_im = 0; >> gdcm::DirList dirlist(dirname, m_UseRecursiveScan); >> >> gdcm::DirListType filenames_list = dirlist.GetFilenames(); >> >> unsigned long totalImages = filenames_list.size(); >> if (totalImages<10) >> return; >> >> for( gdcm::DirListType::const_iterator it = filenames_list.begin(); >> it != filenames_list.end(); ++it) >> { >> if (itksys::SystemTools::FileExists ((*it).c_str(), true)) >> m_GDCMHelper->AddFileName ((*it)); >> counter_im++; >> } >> } >> catch (itk::ExceptionObject & excp) >> { >> return; >> } >> >> std::vector UIDs; >> UIDs = m_GDCMScanner->GetSeriesUIDs(); >> >> if (!UIDs.size()) >> return; >> >> try >> { >> m_SeriesNames.clear(); >> >> int nSeries = 0; >> >> for (unsigned int uid=0; uid> { >> std::string uidname = UIDs[uid]; >> DICOMFileListType* t_filelist = >> m_GDCMHelper->GetSingleSerieUIDFileSet(uidname); >> this->m_GDCMHelper->OrderFileList (t_filelist); >> >> DICOMFileListType::iterator it; >> it = t_filelist.begin(); >> >> for (; it != t_filelist.end(); it++) >> { >> DICOMFileListType* filelist = (*it); >> if ( !filelist->size() ) >> { >> continue; >> } >> std::stringstream stream; >> stream << "series# " << nSeries << ": " << >> this->GenerateName(filelist) << " (" << filelist->size() << " slices)"; >> m_SeriesNames.push_back( stream.str() ); >> nSeries++; >> } >> } >> } >> catch (itk::ExceptionObject & excp) >> { >> return; >> } >> >> template >> std::string DICOMImageReader::GenerateName (DICOMFileListType* >> filelist) >> { >> std::string description = (*filelist)[0]->GetEntryValue(0x0008, 0x103E); >> if (description == gdcm::GDCM_UNFOUND) >> { >> (*filelist)[0]->Load(); >> description = (*filelist)[0]->GetEntryValue(0x0008, 0x103E); >> } >> return description; >> } >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Wed Dec 3 14:29:53 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Dec 2014 14:29:53 -0500 Subject: [ITK] How to get a vector of DICOM Series description strings in ITKv4 (GDCM 2.x)? In-Reply-To: <547F3DAE.1090201@gmail.com> References: <547F3880.4030404@gmail.com> <547F3DAE.1090201@gmail.com> Message-ID: Passing along nice follow-up from Mathieu Malaterre: You should be using gdcm::Scanner: http://gdcm.sourceforge.net/html/classgdcm_1_1Scanner.html See for example: http://gdcm.sourceforge.net/html/SimpleScanner_8cxx-example.html#_a7 >From the command line, you will discover it is much *much* faster than the very old GDCM 1.x implementation, see: http://gdcm.sourceforge.net/html/gdcmscanner.html On Wed, Dec 3, 2014 at 11:43 AM, Sebastian Ordas wrote: > Hi Matt, > several issues: the GDCM API has changed in 2.x > For instance, gdcm::DirList does not exist anymore, same for > m_GDCMHelper->AddFileName(), etc > I would also like to know whether to put the efforts on GDCM or DCMTK (I > have seen a gdcm::SerieHelper2 class in plastimach that is worthy to > explore) > > > ... but there should be some basic functionality / approach already > available for such a simple and general action (i.e. explore available DICOM > Series and/or Studies in a folder with DICOM files) > > let me know if you have some useful links (I don?'t want to link against CTK > in my app) > > thanks > sebastian > > > On 03/12/2014 01:30 p.m., Matt McCormick wrote: >> >> Hi Sebastian, >> >> What specifically is the issue using this code with ITKv4? >> >> Thanks, >> Matt >> >> On Wed, Dec 3, 2014 at 11:21 AM, Sebastian Ordas >> wrote: >>> >>> Dear All, >>> >>> I used to be able with ITK 3.12 (GDCM 1.x) to populate a vector with >>> series >>> description strings, recursively, given the path to a folder with DICOM >>> files. >>> The goal is to fill in an "Open DICOM" dialog with such information, in >>> order to let the user load a single DICOM Series. >>> How can I do that with ITKv4 (GDCM 2.x)? >>> >>> thank you, >>> sebastian >>> >>> Here?s my original code: >>> >>> typedef gdcm::FileList DICOMFileListType; >>> >>> m_GDCMScanner = itk::GDCMSeriesFileNames::New(); >>> m_GDCMScanner->SetUseSeriesDetails(true); >>> m_GDCMScanner->LoadPrivateTagsOff(); >>> m_GDCMHelper = m_GDCMScanner->GetSeriesHelper(); >>> >>> m_GDCMScanner->SetInputDirectory( m_ImageDirectoryName ); >>> >>> if (!itksys::SystemTools::FileExists (ImageDirectoryName )) >>> { >>> return; >>> } >>> >>> // we now scan from scratch all dicom file headers >>> try >>> { >>> this->m_GDCMHelper->Clear(); >>> >>> unsigned long counter_im = 0; >>> gdcm::DirList dirlist(dirname, m_UseRecursiveScan); >>> >>> gdcm::DirListType filenames_list = dirlist.GetFilenames(); >>> >>> unsigned long totalImages = filenames_list.size(); >>> if (totalImages<10) >>> return; >>> >>> for( gdcm::DirListType::const_iterator it = filenames_list.begin(); >>> it != filenames_list.end(); ++it) >>> { >>> if (itksys::SystemTools::FileExists ((*it).c_str(), true)) >>> m_GDCMHelper->AddFileName ((*it)); >>> counter_im++; >>> } >>> } >>> catch (itk::ExceptionObject & excp) >>> { >>> return; >>> } >>> >>> std::vector UIDs; >>> UIDs = m_GDCMScanner->GetSeriesUIDs(); >>> >>> if (!UIDs.size()) >>> return; >>> >>> try >>> { >>> m_SeriesNames.clear(); >>> >>> int nSeries = 0; >>> >>> for (unsigned int uid=0; uid>> { >>> std::string uidname = UIDs[uid]; >>> DICOMFileListType* t_filelist = >>> m_GDCMHelper->GetSingleSerieUIDFileSet(uidname); >>> this->m_GDCMHelper->OrderFileList (t_filelist); >>> >>> DICOMFileListType::iterator it; >>> it = t_filelist.begin(); >>> >>> for (; it != t_filelist.end(); it++) >>> { >>> DICOMFileListType* filelist = (*it); >>> if ( !filelist->size() ) >>> { >>> continue; >>> } >>> std::stringstream stream; >>> stream << "series# " << nSeries << ": " << >>> this->GenerateName(filelist) << " (" << filelist->size() << " slices)"; >>> m_SeriesNames.push_back( stream.str() ); >>> nSeries++; >>> } >>> } >>> } >>> catch (itk::ExceptionObject & excp) >>> { >>> return; >>> } >>> >>> template >>> std::string DICOMImageReader::GenerateName >>> (DICOMFileListType* >>> filelist) >>> { >>> std::string description = (*filelist)[0]->GetEntryValue(0x0008, >>> 0x103E); >>> if (description == gdcm::GDCM_UNFOUND) >>> { >>> (*filelist)[0]->Load(); >>> description = (*filelist)[0]->GetEntryValue(0x0008, 0x103E); >>> } >>> return description; >>> } >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community > > From yxp233 at postech.ac.kr Wed Dec 3 21:55:01 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Thu, 4 Dec 2014 11:55:01 +0900 Subject: [ITK] [ITK-users] GPU Manual In-Reply-To: <1417620036528671.016779.ptmail04@ptmail04> References: <1417620036528671.016779.ptmail04@ptmail04> Message-ID: <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr> Hi, I have tried to build ITK with GPU ON to use GPU filters for a couple of months but unfortunately I still cannot get it work. I searched with Google but found little instruction or documentation available for how to compile. May I ask whether there is any manual for how to compile ITK with GPU ON and how to setup OpenCL directories? I have been feeling so frustrated with ITK GPU. If you can share your knowledge about ITK GPU, I would appreciate it very much. Thank you very much. Best regards, Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Wed Dec 3 21:55:01 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Thu, 4 Dec 2014 11:55:01 +0900 Subject: [ITK] [ITK-dev] GPU Manual In-Reply-To: <1417620036528671.016779.ptmail04@ptmail04> References: <1417620036528671.016779.ptmail04@ptmail04> Message-ID: <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr> Hi, I have tried to build ITK with GPU ON to use GPU filters for a couple of months but unfortunately I still cannot get it work. I searched with Google but found little instruction or documentation available for how to compile. May I ask whether there is any manual for how to compile ITK with GPU ON and how to setup OpenCL directories? I have been feeling so frustrated with ITK GPU. If you can share your knowledge about ITK GPU, I would appreciate it very much. Thank you very much. Best regards, Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From zeinsalah at gmail.com Thu Dec 4 04:46:36 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Thu, 4 Dec 2014 10:46:36 +0100 Subject: [ITK] itkShapeLabelObject and itkBinaryImageToShapeLabelMapFilter. are missing Message-ID: Hi, I am trying to do binary image labelling. My program claims that the files itkShapeLabelObject.h and itkBinaryImageToShapeLabelMapFilter.h are missing. I am using ITK 3.14.0. Are the filters not included in this release? Or I am should configure something? Thanks, Zein From waldovalenzuela at yahoo.com Thu Dec 4 05:04:36 2014 From: waldovalenzuela at yahoo.com (Waldo Valenzuela) Date: Thu, 4 Dec 2014 11:04:36 +0100 Subject: [ITK] About Compile ITK Ubuntu c++11 Message-ID: Hi Guys, I have been using ITK on Mac and Windows for a while, but I started to do it on linux and I have some problems enabling c++11 feature. On my Scientific Linux 7 machine, I didn?t have any problem to compile ITK adding CMAKE_CXX_FLAG= -std=gnu++11, but in a Ubuntu 14.04 machine with gcc 4.8.2, I have the error ?constexpr needed? from the VNL library. I know that this was a common error in the past with c++11, but I google it to solve it and couldn?t find any answer that really works. There is a special configuration on CMAKE to solve this in Ubuntu? Any help or guide is really welcome. Cheers, Waldo. From blowekamp at mail.nih.gov Thu Dec 4 08:33:22 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 4 Dec 2014 08:33:22 -0500 Subject: [ITK] [ITK-users] About Compile ITK Ubuntu c++11 In-Reply-To: References: Message-ID: Hello, When CMake does it's initial configuration it does a bunch of try compiles. The correct compiler and language flags are needed when this initial configuration is done. I suggest starting with a completely empty directory, then do some thing like: cmake -DCMAKE_CXX_FLAGS=-std=c++11 ~/src/ITK This will ensure the flags are there for the initial configuration to correctly detect C++11 features. Brad On Dec 4, 2014, at 5:04 AM, Waldo Valenzuela via Insight-users wrote: > Hi Guys, > > I have been using ITK on Mac and Windows for a while, but I started to do it on linux and I have some problems enabling c++11 feature. > > On my Scientific Linux 7 machine, I didn?t have any problem to compile ITK adding CMAKE_CXX_FLAG= -std=gnu++11, but in a Ubuntu 14.04 machine with gcc 4.8.2, I have the error ?constexpr needed? from the VNL library. > > I know that this was a common error in the past with c++11, but I google it to solve it and couldn?t find any answer that really works. > > There is a special configuration on CMAKE to solve this in Ubuntu? > > Any help or guide is really welcome. > > Cheers, > > Waldo. > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From zeinsalah at gmail.com Thu Dec 4 10:35:28 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Thu, 4 Dec 2014 16:35:28 +0100 Subject: [ITK] registration of two point sets Message-ID: Hi, as I am not a registration expert, I have the following question. I have two point sets to be registered with each other, e.g., A and B, where points in A correspond to a subset of the points in B. The correspondences are not known. Moreover, I want need to register the points in A to the best fitting corresponding points in B, in a pair point fashion. Has someone dealt with such an issue? Does ITK or IGSTK have suitable mechanisms for such thing? Much thanks, Zeno From matimontg at gmail.com Thu Dec 4 10:41:49 2014 From: matimontg at gmail.com (Matias Montroull) Date: Thu, 4 Dec 2014 12:41:49 -0300 Subject: [ITK] registration of two point sets In-Reply-To: References: Message-ID: I've done that using VTK in C# if it helps On Thu, Dec 4, 2014 at 12:35 PM, Zein Salah wrote: > Hi, > > as I am not a registration expert, I have the following question. > > I have two point sets to be registered with each other, e.g., A and B, > where points in A correspond to a subset of the points in B. The > correspondences > are not known. Moreover, I want need to register the points in A to the > best fitting corresponding points in B, in a pair point fashion. > > Has someone dealt with such an issue? Does ITK or IGSTK have suitable > mechanisms for such thing? > > Much thanks, > Zeno > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Dec 4 13:13:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 4 Dec 2014 13:13:21 -0500 Subject: [ITK] ITK Development Confab Message-ID: Tomorrow we will to share, discuss, design, and learn with your fellow ITK community members at the ITK Development Confab. Bring your ITK related topic of interest. We will also discuss the 4.7 Software Guide printing and 4.7 release candidate. Details: Friday, 11:00 AM Eastern USA time: https://plus.google.com/events/cstc9fe3njoggjqlaiacpiae9a4 For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From dr.tim.allman at gmail.com Thu Dec 4 13:42:11 2014 From: dr.tim.allman at gmail.com (Tim Allman) Date: Thu, 04 Dec 2014 13:42:11 -0500 Subject: [ITK] [ITK-users] Float dicom images In-Reply-To: <547E39C5.9040801@dclunie.com> References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com> <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com> <547E39C5.9040801@dclunie.com> Message-ID: <5480AB03.1080705@gmail.com> I just read Supplement 172 and it certainly addresses what I want which is to create parametric maps and not lose information (sign, dynamic range etc.) on storage. My situation is that I am writing a plugin for Osirix, a DICOM (only) viewer which runs on OSX (only). I can create the maps I want internally as the viewer uses float as its pixel type internally but it saves everything as unsigned 16 bit integers. It will read floating point images however so perhaps writing them will come soon. I single stepped through the writing of a float image and discovered that GDCM has some code clearly intended to support I/O of these images but it is incomplete. It will indeed write float images but they are rescaled to have a range of 0 - MAXFLOAT. Tim On 14-12-02 05:14 PM, David Clunie wrote: > We (DICOM) have only recently added support for floating point > pixel data in DICOM (Sup 172), so I don't know if any of the > toolkits used by ITK support it yet. > > I know dcmtk will, hopefully soon, but I can't speak for GDCM. > > I have some samples at: > > https://www.dropbox.com/sh/n4iqdjbhmwljx5e/AABllea-Muk0C2oo576nm_Mua?dl=0 > > if you want to try them; not perfect yet, but they have the float pixel > data payload. > > I am assuming that you actually want to write floating point pixels, > rather than integer quantized pixels with a floating point scaling > factor. > > David > > On 12/2/14 3:40 PM, Matias Montroull wrote: >> adding insight users.. >> >> I've never dealt with float dicom images, can you send me a sample >> image? I >> can try to write and see what's the problem. isn's saving the image >> or you >> get a wrong saved image, such as WL WC changed etc? >> >> On Tue, Dec 2, 2014 at 4:53 PM, Tim Allman >> wrote: >> >>> >>> On Dec 2, 2014, at 14:44 , Matias Montroull >>> wrote: >>> >>>> are you trying to write float dicom images? >>> >>> Yes. Sorry for noting that only in the subject line. :-( >>> >>>> >>>> On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman >>> wrote: >>>> I have been having a bit of trouble trying to write Dicom images using >>> itk::GDCMImageIO. The code suggests that this is supported but I >>> know that >>> this is a new feature. Has anyone else had any experience with this? >>>> >>>> Thanks, >>>> 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 -- Tim Allman, Ph.D. 35 Margaret Street, Guelph Ontario N1E 5R6 Canada -------------- next part -------------- A non-text attachment was scrubbed... Name: dr_tim_allman.vcf Type: text/x-vcard Size: 151 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Thu Dec 4 15:41:42 2014 From: millerjv at gmail.com (Jim Miller) Date: Thu, 4 Dec 2014 15:41:42 -0500 Subject: [ITK] [ITK-users] GPU Manual In-Reply-To: <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr> References: <1417620036528671.016779.ptmail04@ptmail04> <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr> Message-ID: <6738AC11-E741-4152-AFAC-0E79FDD36CF9@gmail.com> I just did a fresh checkout of ITK and clean build on the Mac. When configuring with CMake, I turned on BUILD_EXAMPLES, BUILD_TESTING, and ITK_USE_GPU. All the GPU related tests passed. Jim > On Dec 3, 2014, at 9:55 PM, Xiaopeng Yang wrote: > > Hi, > > I have tried to build ITK with GPU ON to use GPU filters for a couple of months but unfortunately I still cannot get it work. I searched with Google but found little instruction or documentation available for how to compile. May I ask whether there is any manual for how to compile ITK with GPU ON and how to setup OpenCL directories? I have been feeling so frustrated with ITK GPU. If you can share your knowledge about ITK GPU, I would appreciate it very much. Thank you very much. > > Best regards, > Yang > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Thu Dec 4 15:41:42 2014 From: millerjv at gmail.com (Jim Miller) Date: Thu, 4 Dec 2014 15:41:42 -0500 Subject: [ITK] [ITK-dev] [ITK-users] GPU Manual In-Reply-To: <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr> References: <1417620036528671.016779.ptmail04@ptmail04> <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr> Message-ID: <6738AC11-E741-4152-AFAC-0E79FDD36CF9@gmail.com> I just did a fresh checkout of ITK and clean build on the Mac. When configuring with CMake, I turned on BUILD_EXAMPLES, BUILD_TESTING, and ITK_USE_GPU. All the GPU related tests passed. Jim > On Dec 3, 2014, at 9:55 PM, Xiaopeng Yang wrote: > > Hi, > > I have tried to build ITK with GPU ON to use GPU filters for a couple of months but unfortunately I still cannot get it work. I searched with Google but found little instruction or documentation available for how to compile. May I ask whether there is any manual for how to compile ITK with GPU ON and how to setup OpenCL directories? I have been feeling so frustrated with ITK GPU. If you can share your knowledge about ITK GPU, I would appreciate it very much. Thank you very much. > > Best regards, > Yang > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From millerjv at gmail.com Thu Dec 4 16:25:59 2014 From: millerjv at gmail.com (Jim Miller) Date: Thu, 4 Dec 2014 16:25:59 -0500 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> Message-ID: Xiaopeng, I changed your target_link_libraries line to be target_link_libraries(itkGPUDemonsRegistrationFilterTest ITKGPUPDEDeformable ${ITK_LIBRARIES} ) Without adding ITKGPUPDEDeformable to the target_link_libraries, I would get an error in linking like you had. When ITK is built, the kernel functions (OpenCL code) are "compiled into" the C++ code. Basically, the .cl files are converted into a C++ file where the OpenCL code is encoded as a C++ string. This C++ code implements the method GetOpenCLSource() which returns that string containing the OpenCL code. The PDE registration OpenCL kernels are compiled into the library ITKGPUPDEDeformable. If you had used other GPU filters, you would have had to add the libraries that contain those kernels as well to your target_link_libraries. Jim On Thu, Nov 27, 2014 at 7:34 AM, Xiaopeng Yang wrote: > Hi Jim, > > I am sorry but could you please build the code enclosed to check whether > you > also have that kind of errors or not? > > Thank you very much. > > Best, > Xiaopeng > > -----Original Message----- > From: Xiaopeng Yang [mailto:yxp233 at postech.ac.kr] > Sent: Wednesday, November 26, 2014 9:34 PM > To: 'Jim Miller' > Cc: 'Michael Pinkert'; 'insight-users at itk.org' > Subject: RE: [ITK-users] GPU Implementation > > Hi, > > I tried to compile the code from Modules\Registration\GPUPDEDeformable\test > folder. Enclosed please find the code and CMakeLists file. I am quite new > to > GPU, sorry I could not understand your explanation. Could you point out > what > I missed please? > > Thanks, > Xiaopeng > > -----Original Message----- > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Wednesday, November 26, 2014 9:10 PM > To: Xiaopeng Yang > Cc: Michael Pinkert; insight-users at itk.org > Subject: Re: [ITK-users] GPU Implementation > > This doesn't look like any issue with finding OpenCL. The link error is > saying it cannot find the implementation of an ITK method. > > I think GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void) is > supposed to return the kernel's implementation (probably as a string > containing the OpenCL code). > > Is there a txx file that is not being included? Does your program contain > the same headers and test? > > (I guess the error could occur if OpenCL was not found if the > implementation > of this method in GPUPDEDeformableRegistrationFilterKernel is within > #ifdef/#endif on OpenCL.) > > Jim > > > On Nov 25, 2014, at 10:03 PM, Xiaopeng Yang > wrote: > > > > Hi Michael, > > > > I also had the same errors while building my GPU registration program. > > Have you solved the problems? I guess the error was caused by improper > > setting in CMakeLists.txt file, but I could not find any > > CMakeLists.txt sample regarding GPU implementation in ITK. I doubt > > whether there are users using this GPU module or not. > > > > Best regards, > > Xiaopeng Yang > > > > > > This is the question you raised: > > > > I am trying to implement the GPU demons registration algorithm, but I > > have been having difficulty getting the program to compile. I believe > > the errors are because it cannot find the OpenCL library correctly, > > but I'm not sure how to fix it. > > > > I am using a NVIDIA Quadro FX 570 and am currently using OpenCL > > through the CUDA Computing Toolkit 4.2. My cmake file is attached, > > but I have had to manually enter in the directory locations to CMake > > because I have not been able to find a FindOpenCL.cmake file that > > works correctly. My operating system is Windows 7 x64. > > > > I am able to compile ITK after generating it in CMake with manually > > linked directories and Itk_Use_Gpu checked, but I have not been able > > to compile my program without getting errors, which are listed at the > bottom. > > > > Does anyone have suggestions as to how to fix this? > > > > Best regards, > > Michael Pinkert > > > > 2>registrationFunctions.obj : error LNK2019: unresolved external > > 2>symbol > > "public: static char const * __cdecl > > itk::GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void)" > > (?GetOpenCLSource at GPUPDEDeformableRegistrationFilterKernel@itk@@SAPEBD > > XZ) referenced in function "public: static char const * __cdecl > > itk::GPUPDEDeformableRegistrationFilter > itk::GPUImage,class itk::GPUImage,class > > itk::GPUImage,3>,class > > itk::DemonsRegistrationFilter > itk::GPUImage,class itk::GPUImage,class > > itk::GPUImage,3> > >::GetOpenCLSource(void)" > > (?GetOpenCLSource@?$GPUPDEDeformableRegistrationFilter at V?$GPUImage at M$0 > > 2 at itk@ > > @V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@V?$DemonsRegistrationFilter > > @V?$GP > > UImage at M$02 at itk@@V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@2@@itk@@SA > > PEBDXZ > > ) > > > > 2>registrationFunctions.obj : error LNK2019: unresolved external > > 2>symbol > > "public: static char const * __cdecl > > itk::GPUDemonsRegistrationFunctionKernel::GetOpenCLSource(void)" > > (?GetOpenCLSource at GPUDemonsRegistrationFunctionKernel@itk@@SAPEBDXZ) > > referenced in function "public: static char const * __cdecl > > itk::GPUDemonsRegistrationFunction,class > > itk::GPUImage,classitk::GPUImage > itk::Vector,3> > >> ::GetOpenCLSource(void)" > > (?GetOpenCLSource@?$GPUDemonsRegistrationFunction at V?$GPUImage at M$02 at itk > > @@V12@ > > V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@itk@@SAPEBDXZ) > > > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lloyd at itis.ethz.ch Thu Dec 4 17:18:11 2014 From: lloyd at itis.ethz.ch (Bryn Lloyd) Date: Thu, 04 Dec 2014 23:18:11 +0100 Subject: [ITK] [ITK-users] How to abort execution of ImageRegistrationMethodv4 / Optimizer Message-ID: <5480DDA3.905@itis.ethz.ch> Hi I recently started using ITK again and am trying out the ITK registration framework v4. I am trying to gracefully abort/stop the ImageRegistrationMethodv4 process, however it just continues. In my Command class, which observes an IterationEvent of the ImageRegistrationMethodv4 and Optimizer I call 1. registration_method_v4->SetAbortGenerateData( true ); // object of type ImageRegistrationMethodv4<...> 2. optimizer->StopOptimization(); However, the process just continues to execute. Is this supposed to work? What am I doing wrong? Thanks and best regards Bryn _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 lloyd at itis.ethz.ch Thu Dec 4 17:48:09 2014 From: lloyd at itis.ethz.ch (Bryn Lloyd) Date: Thu, 04 Dec 2014 23:48:09 +0100 Subject: [ITK] [ITK-users] How to abort execution of ImageRegistrationMethodv4 / Optimizer In-Reply-To: <5480DDA3.905@itis.ethz.ch> References: <5480DDA3.905@itis.ethz.ch> Message-ID: <5480E4A9.3050304@itis.ethz.ch> At a first glance it seems that ImageRegistrationMethodv4 does not check for the abort flag: ImageRegistrationMethodv4 ::GenerateData() { this->AllocateOutputs(); for( this->m_CurrentLevel = 0; this->m_CurrentLevel < this->m_NumberOfLevels; this->m_CurrentLevel++ ) { this->InitializeRegistrationAtEachLevel( this->m_CurrentLevel ); this->m_Metric->Initialize(); this->m_Optimizer->StartOptimization(); } } If I modify this code to check for m_AbortGenerateData, the registration terminates as expected. In addition it seems that the members m_CurrentMetricValue, m_CurrentIteration etc. are never updated during optimization. Best regards Bryn On 04.12.2014 23:18, Bryn Lloyd wrote: > Hi > > I recently started using ITK again and am trying out the ITK > registration framework v4. > > > I am trying to gracefully abort/stop the ImageRegistrationMethodv4 > process, however it just continues. > > In my Command class, which observes an IterationEvent of the > ImageRegistrationMethodv4 and Optimizer I call > 1. registration_method_v4->SetAbortGenerateData( true ); // object of > type ImageRegistrationMethodv4<...> > > 2. optimizer->StopOptimization(); > > However, the process just continues to execute. Is this supposed to > work? What am I doing wrong? > > Thanks and best regards > Bryn > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Fri Dec 5 00:41:20 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Fri, 5 Dec 2014 14:41:20 +0900 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <141772836420039.030290.ptmail04@ptmail04> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> Message-ID: <001801d0104e$19711800$4c534800$@ac.kr> Dear Jim, Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. Best, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Friday, December 05, 2014 6:26 AM To: Xiaopeng Yang Cc: Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation Xiaopeng, I changed your target_link_libraries line to be target_link_libraries(itkGPUDemonsRegistrationFilterTest ITKGPUPDEDeformable ${ITK_LIBRARIES} ) Without adding ITKGPUPDEDeformable to the target_link_libraries, I would get an error in linking like you had. When ITK is built, the kernel functions (OpenCL code) are "compiled into" the C++ code. Basically, the .cl files are converted into a C++ file where the OpenCL code is encoded as a C++ string. This C++ code implements the method GetOpenCLSource() which returns that string containing the OpenCL code. The PDE registration OpenCL kernels are compiled into the library ITKGPUPDEDeformable. If you had used other GPU filters, you would have had to add the libraries that contain those kernels as well to your target_link_libraries. Jim On Thu, Nov 27, 2014 at 7:34 AM, Xiaopeng Yang wrote: Hi Jim, I am sorry but could you please build the code enclosed to check whether you also have that kind of errors or not? Thank you very much. Best, Xiaopeng -----Original Message----- From: Xiaopeng Yang [mailto:yxp233 at postech.ac.kr] Sent: Wednesday, November 26, 2014 9:34 PM To: 'Jim Miller' Cc: 'Michael Pinkert'; 'insight-users at itk.org' Subject: RE: [ITK-users] GPU Implementation Hi, I tried to compile the code from Modules\Registration\GPUPDEDeformable\test folder. Enclosed please find the code and CMakeLists file. I am quite new to GPU, sorry I could not understand your explanation. Could you point out what I missed please? Thanks, Xiaopeng -----Original Message----- From: Jim Miller [mailto:millerjv at gmail.com] Sent: Wednesday, November 26, 2014 9:10 PM To: Xiaopeng Yang Cc: Michael Pinkert; insight-users at itk.org Subject: Re: [ITK-users] GPU Implementation This doesn't look like any issue with finding OpenCL. The link error is saying it cannot find the implementation of an ITK method. I think GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void) is supposed to return the kernel's implementation (probably as a string containing the OpenCL code). Is there a txx file that is not being included? Does your program contain the same headers and test? (I guess the error could occur if OpenCL was not found if the implementation of this method in GPUPDEDeformableRegistrationFilterKernel is within #ifdef/#endif on OpenCL.) Jim > On Nov 25, 2014, at 10:03 PM, Xiaopeng Yang wrote: > > Hi Michael, > > I also had the same errors while building my GPU registration program. > Have you solved the problems? I guess the error was caused by improper > setting in CMakeLists.txt file, but I could not find any > CMakeLists.txt sample regarding GPU implementation in ITK. I doubt > whether there are users using this GPU module or not. > > Best regards, > Xiaopeng Yang > > > This is the question you raised: > > I am trying to implement the GPU demons registration algorithm, but I > have been having difficulty getting the program to compile. I believe > the errors are because it cannot find the OpenCL library correctly, > but I'm not sure how to fix it. > > I am using a NVIDIA Quadro FX 570 and am currently using OpenCL > through the CUDA Computing Toolkit 4.2. My cmake file is attached, > but I have had to manually enter in the directory locations to CMake > because I have not been able to find a FindOpenCL.cmake file that > works correctly. My operating system is Windows 7 x64. > > I am able to compile ITK after generating it in CMake with manually > linked directories and Itk_Use_Gpu checked, but I have not been able > to compile my program without getting errors, which are listed at the bottom. > > Does anyone have suggestions as to how to fix this? > > Best regards, > Michael Pinkert > > 2>registrationFunctions.obj : error LNK2019: unresolved external > 2>symbol > "public: static char const * __cdecl > itk::GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void)" > (?GetOpenCLSource at GPUPDEDeformableRegistrationFilterKernel@itk@@SAPEBD > XZ) referenced in function "public: static char const * __cdecl > itk::GPUPDEDeformableRegistrationFilter itk::GPUImage,class itk::GPUImage,class > itk::GPUImage,3>,class > itk::DemonsRegistrationFilter itk::GPUImage,class itk::GPUImage,class > itk::GPUImage,3> > >::GetOpenCLSource(void)" > (?GetOpenCLSource@?$GPUPDEDeformableRegistrationFilter at V?$GPUImage at M$0 > 2 at itk@ > @V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@V?$DemonsRegistrationFilter > @V?$GP > UImage at M$02 at itk@@V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@2@@itk@@SA > PEBDXZ > ) > > 2>registrationFunctions.obj : error LNK2019: unresolved external > 2>symbol > "public: static char const * __cdecl > itk::GPUDemonsRegistrationFunctionKernel::GetOpenCLSource(void)" > (?GetOpenCLSource at GPUDemonsRegistrationFunctionKernel@itk@@SAPEBDXZ) > referenced in function "public: static char const * __cdecl > itk::GPUDemonsRegistrationFunction,class > itk::GPUImage,classitk::GPUImage itk::Vector,3> >> ::GetOpenCLSource(void)" > (?GetOpenCLSource@?$GPUDemonsRegistrationFunction at V?$GPUImage at M$02 at itk > @@V12@ > V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@itk@@SAPEBDXZ) > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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: image001.png Type: image/png Size: 43723 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From drescherjm at gmail.com Fri Dec 5 02:23:52 2014 From: drescherjm at gmail.com (John Drescher) Date: Fri, 5 Dec 2014 02:23:52 -0500 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <001801d0104e$19711800$4c534800$@ac.kr> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> Message-ID: On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: > Dear Jim, > > > > Thanks for your help. I built the test successfully, but I met an error > when I run the program. Please see the attached image file. > > > > Best, > > Xiaopeng > > > > > Is that an error? John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 43723 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Fri Dec 5 02:43:10 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Fri, 5 Dec 2014 16:43:10 +0900 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <141776427270398.129323.ptmail04@ptmail04> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> Message-ID: <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> Hi John, Sorry I mean the program got crashed after showing #define T float. Thanks, Xiaopeng From: John Drescher [mailto:drescherjm at gmail.com] Sent: Friday, December 05, 2014 4:24 PM To: Xiaopeng Yang Cc: Jim Miller; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: Dear Jim, Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. Best, Xiaopeng Is that an error? John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 43723 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Fri Dec 5 09:14:43 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 5 Dec 2014 09:14:43 -0500 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> Message-ID: <40B2E025-88FB-4EB1-B23D-64CB2C983C0D@gmail.com> How large are the images that you are using? Jim > On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: > > Hi John, > > Sorry I mean the program got crashed after showing #define T float. > > Thanks, > Xiaopeng > > From: John Drescher [mailto:drescherjm at gmail.com] > Sent: Friday, December 05, 2014 4:24 PM > To: Xiaopeng Yang > Cc: Jim Miller; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > > > On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: > Dear Jim, > > Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. > > Best, > Xiaopeng > > > > > Is that an error? > > John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Fri Dec 5 11:57:17 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 5 Dec 2014 11:57:17 -0500 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> Message-ID: <5D56294F-D85B-4F45-AAE5-3CE151862C03@gmail.com> Do the GPU tests run our system? $ cd ITK-build $ ctest -V -R GPU Jim > On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: > > Hi John, > > Sorry I mean the program got crashed after showing #define T float. > > Thanks, > Xiaopeng > > From: John Drescher [mailto:drescherjm at gmail.com] > Sent: Friday, December 05, 2014 4:24 PM > To: Xiaopeng Yang > Cc: Jim Miller; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > > > On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: > Dear Jim, > > Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. > > Best, > Xiaopeng > > > > > Is that an error? > > John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From llliu at umich.edu Fri Dec 5 17:19:18 2014 From: llliu at umich.edu (Lianli Liu) Date: Fri, 5 Dec 2014 17:19:18 -0500 Subject: [ITK] [ITK-users] compling itkScaleInvariantFeatureImageFilter Message-ID: Hi all, I want to use the itkScaleInvariantFeatureImageFilter but I am getting several errors when compiling, such as: error: ?FeatureType? was not declared in this scope error: ?PointSetType? is not a class or namespace Does anyone has experience in using this filter? Also, I am unclear how where to specify input image in the filter. Thanks! Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Fri Dec 5 18:45:13 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Sat, 6 Dec 2014 08:45:13 +0900 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <1417788892216194.03990.ptmail04@ptmail04> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> Message-ID: <008c01d010e5$84172950$8c457bf0$@ac.kr> Dear Jim, The images are quite large: 512 * 512 *300. I did not build test when I compile ITK. Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Friday, December 05, 2014 11:15 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation How large are the images that you are using? Jim On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: Hi John, Sorry I mean the program got crashed after showing #define T float. Thanks, Xiaopeng From: John Drescher [mailto:drescherjm at gmail.com] Sent: Friday, December 05, 2014 4:24 PM To: Xiaopeng Yang Cc: Jim Miller; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: Dear Jim, Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. Best, Xiaopeng Is that an error? John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Fri Dec 5 20:11:04 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 5 Dec 2014 20:11:04 -0500 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <008c01d010e5$84172950$8c457bf0$@ac.kr> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> <008c01d010e5$84172950$8c457bf0$@ac.kr> Message-ID: I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. Jim > On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang wrote: > > Dear Jim, > > The images are quite large: 512 * 512 *300. > > I did not build test when I compile ITK. > > Thanks, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Friday, December 05, 2014 11:15 PM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > How large are the images that you are using? > > Jim > > On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: > > Hi John, > > Sorry I mean the program got crashed after showing #define T float. > > Thanks, > Xiaopeng > > From: John Drescher [mailto:drescherjm at gmail.com] > Sent: Friday, December 05, 2014 4:24 PM > To: Xiaopeng Yang > Cc: Jim Miller; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > > > On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: > Dear Jim, > > Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. > > Best, > Xiaopeng > > > > > Is that an error? > > John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Fri Dec 5 20:39:33 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Sat, 6 Dec 2014 10:39:33 +0900 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <1417828271180838.110987.ptmail04@ptmail04> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> <008c01d010e5$84172950$8c457bf0$@ac.kr> <1417828271180838.110987.ptmail04@ptmail04> Message-ID: <009a01d010f5$7d4043e0$77c0cba0$@ac.kr> Hi Jim, So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Saturday, December 06, 2014 10:11 AM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. Jim On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang wrote: Dear Jim, The images are quite large: 512 * 512 *300. I did not build test when I compile ITK. Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Friday, December 05, 2014 11:15 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation How large are the images that you are using? Jim On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: Hi John, Sorry I mean the program got crashed after showing #define T float. Thanks, Xiaopeng From: John Drescher [mailto:drescherjm at gmail.com] Sent: Friday, December 05, 2014 4:24 PM To: Xiaopeng Yang Cc: Jim Miller; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: Dear Jim, Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. Best, Xiaopeng Is that an error? John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Fri Dec 5 22:50:04 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 5 Dec 2014 22:50:04 -0500 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <009a01d010f5$7d4043e0$77c0cba0$@ac.kr> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> <008c01d010e5$84172950$8c457bf0$@ac.kr> <1417828271180838.110987.ptmail04@ptmail04> <009a01d010f5$7d4043e0$77c0cba0$@ac.kr> Message-ID: <0C9B1AAB-2795-4526-BE27-008DB18EE7F1@gmail.com> I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. Jim > On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang wrote: > > Hi Jim, > > So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? > > Thanks, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Saturday, December 06, 2014 10:11 AM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. > > Jim > > On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang wrote: > > Dear Jim, > > The images are quite large: 512 * 512 *300. > > I did not build test when I compile ITK. > > Thanks, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Friday, December 05, 2014 11:15 PM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > How large are the images that you are using? > > Jim > > On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: > > Hi John, > > Sorry I mean the program got crashed after showing #define T float. > > Thanks, > Xiaopeng > > From: John Drescher [mailto:drescherjm at gmail.com] > Sent: Friday, December 05, 2014 4:24 PM > To: Xiaopeng Yang > Cc: Jim Miller; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > > > On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: > Dear Jim, > > Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. > > Best, > Xiaopeng > > > > > Is that an error? > > John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From boxerab at gmail.com Sat Dec 6 09:12:52 2014 From: boxerab at gmail.com (Aaron Boxer) Date: Sat, 6 Dec 2014 09:12:52 -0500 Subject: [ITK] LibTiff and CMake Message-ID: Hello! I would like to use libtiff via CMake. I understand that ITK maintains a CMake file for libtiff. Can anyone recommend how I could pull this file out and use it with the standard libtiff distribution? Thanks so much, Aaron -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Sat Dec 6 10:44:25 2014 From: matimontg at gmail.com (Matias Montroull) Date: Sat, 6 Dec 2014 12:44:25 -0300 Subject: [ITK] [ITK-users] registration->StartRegistration(); Message-ID: Hi, I was trying to compile some registration examples and I get this: 2 IntelliSense: class "itk::ImageRegistrationMethod, itk::Image>" has no member "StartRegistration" Should I use Update(); instead? I tried but I get an error when running the program. (I tried both examples registration8 and registration20 Thanks, -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Sat Dec 6 11:19:39 2014 From: matimontg at gmail.com (Matias Montroull) Date: Sat, 6 Dec 2014 13:19:39 -0300 Subject: [ITK] [ITK-users] convert mha to stack of dicom images Message-ID: HI, I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this? Thanks, Matias. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dr.tim.allman at gmail.com Sat Dec 6 14:08:31 2014 From: dr.tim.allman at gmail.com (Tim Allman) Date: Sat, 6 Dec 2014 14:08:31 -0500 Subject: [ITK] [ITK-users] convert mha to stack of dicom images In-Reply-To: References: Message-ID: <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com> I wrote a program for OSX to convert any file format recognized by ITK to DICOM. I wrote it for myself so most of the formats, including mha, haven?t been tested. If you have a Mac then you may even be able to run it. If not, the code should be helpful in showing how to construct a DICOM series. source and binary: https://github.com/TimAllman/ConvertToDicom/releases/tag/v0.1-beta I hope you find this helpful. If you have questions about the program feel free to email me. Tim On Dec 6, 2014, at 11:19 , Matias Montroull wrote: > HI, > > I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this? > > Thanks, > > Matias. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dclunie at dclunie.com Sat Dec 6 19:18:06 2014 From: dclunie at dclunie.com (David Clunie) Date: Sat, 06 Dec 2014 19:18:06 -0500 Subject: [ITK] [ITK-users] DICOM Floating point output from Osirix, was Re: Float dicom images In-Reply-To: <5480AB03.1080705@gmail.com> References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com> <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com> <547E39C5.9040801@dclunie.com> <5480AB03.1080705@gmail.com> Message-ID: <54839CBE.1090807@dclunie.com> Hi Tim Antoine Rosset was going to implement this in Osirix when we finalized the SOP Class UID and data element tags in DICOM, so you might want to check with him about how far he has got, before writing any code yourself. I have cc'd him. Osirix uses dcmtk (or Papyrus). David On 12/4/14 1:42 PM, Tim Allman wrote: > I just read Supplement 172 and it certainly addresses what I want which > is to create parametric maps and not lose information (sign, dynamic > range etc.) on storage. > > My situation is that I am writing a plugin for Osirix, a DICOM (only) > viewer which runs on OSX (only). I can create the maps I want internally > as the viewer uses float as its pixel type internally but it saves > everything as unsigned 16 bit integers. It will read floating point > images however so perhaps writing them will come soon. > > I single stepped through the writing of a float image and discovered > that GDCM has some code clearly intended to support I/O of these images > but it is incomplete. It will indeed write float images but they are > rescaled to have a range of 0 - MAXFLOAT. > > Tim > > On 14-12-02 05:14 PM, David Clunie wrote: >> We (DICOM) have only recently added support for floating point >> pixel data in DICOM (Sup 172), so I don't know if any of the >> toolkits used by ITK support it yet. >> >> I know dcmtk will, hopefully soon, but I can't speak for GDCM. >> >> I have some samples at: >> >> https://www.dropbox.com/sh/n4iqdjbhmwljx5e/AABllea-Muk0C2oo576nm_Mua?dl=0 >> >> if you want to try them; not perfect yet, but they have the float pixel >> data payload. >> >> I am assuming that you actually want to write floating point pixels, >> rather than integer quantized pixels with a floating point scaling >> factor. >> >> David >> >> On 12/2/14 3:40 PM, Matias Montroull wrote: >>> adding insight users.. >>> >>> I've never dealt with float dicom images, can you send me a sample >>> image? I >>> can try to write and see what's the problem. isn's saving the image >>> or you >>> get a wrong saved image, such as WL WC changed etc? >>> >>> On Tue, Dec 2, 2014 at 4:53 PM, Tim Allman >>> wrote: >>> >>>> >>>> On Dec 2, 2014, at 14:44 , Matias Montroull >>>> wrote: >>>> >>>>> are you trying to write float dicom images? >>>> >>>> Yes. Sorry for noting that only in the subject line. :-( >>>> >>>>> >>>>> On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman >>>> wrote: >>>>> I have been having a bit of trouble trying to write Dicom images using >>>> itk::GDCMImageIO. The code suggests that this is supported but I >>>> know that >>>> this is a new feature. Has anyone else had any experience with this? >>>>> >>>>> Thanks, >>>>> 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 > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dclunie at dclunie.com Sun Dec 7 17:42:07 2014 From: dclunie at dclunie.com (David Clunie) Date: Sun, 07 Dec 2014 17:42:07 -0500 Subject: [ITK] [ITK-users] convert mha to stack of dicom images In-Reply-To: <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com> References: <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com> Message-ID: <5484D7BF.4070403@dclunie.com> Make sure you run dciodvfy and dcentvfy on DICOM files that you create, to check that they are compliant (within the limits of what these tools can mechanically check). See: http://www.dclunie.com/dicom3tools/dciodvfy.html David On 12/6/14 2:08 PM, Tim Allman wrote: > I wrote a program for OSX to convert any file format recognized by ITK to DICOM. I wrote it for myself so most of the formats, including mha, haven?t been tested. If you have a Mac then you may even be able to run it. If not, the code should be helpful in showing how to construct a DICOM series. > > source and binary: https://github.com/TimAllman/ConvertToDicom/releases/tag/v0.1-beta > > I hope you find this helpful. If you have questions about the program feel free to email me. > > Tim > > On Dec 6, 2014, at 11:19 , Matias Montroull wrote: > >> HI, >> >> I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this? >> >> Thanks, >> >> Matias. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michael.meuli at gmail.com Mon Dec 8 07:07:47 2014 From: michael.meuli at gmail.com (Michael Meuli) Date: Mon, 8 Dec 2014 13:07:47 +0100 Subject: [ITK] Colocalization of bacteria and lysosome Message-ID: Hi all I've written a little program to analyse the colocalization of bacteria and lysosome within macrophages. As main result it should write the mean values of pixels located in the objects (bacteria) but taking the value from the channel used to visualize the lysosomes (image3Dred) into a file. Image acquisition is done with a fancy confocal laser scanning microscope. Bacteria, lysosomes and the nuclei of the macrophages are labeld with different fluorochromes. As the cells are seeded as monolayer, the images are quite flat and maximum intensity projections are done to visually check the result. The programm compiles and runs but I'm not yet fully convinced if it does what it should do. I'm not a professional programmer and wanted to ask if some itk guru could have a look at it. The programm and some more information can be found here: https://github.com/michaelmeuli/bactelize My main question is, if the following piece of code really does what it shoud do: BinaryImageToShapeLabelMapFilterType::Pointer binaryImageToShapeLabelMapFilter = BinaryImageToShapeLabelMapFilterType::New(); binaryImageToShapeLabelMapFilter->SetInput(binaryimage3Dbacteria); binaryImageToShapeLabelMapFilter->Update(); ... StatisticsLabelMapFilterType::Pointer statisticsLabelMapFilter = StatisticsLabelMapFilterType::New(); statisticsLabelMapFilter->SetInput1(binaryImageToShapeLabelMapFilter->GetOutput()); statisticsLabelMapFilter->SetInput2(image3Dred); statisticsLabelMapFilter->InPlaceOn(); statisticsLabelMapFilter->Update(); unsigned int bacteriacount = statisticsLabelMapFilter->GetOutput()->GetNumberOfLabelObjects(); for(unsigned int i = 0; i < statisticsLabelMapFilter->GetOutput()->GetNumberOfLabelObjects(); i++) { StatisticsLabelMapFilterType::OutputImageType::LabelObjectType* labelObjectMe = statisticsLabelMapFilter->GetOutput()->GetNthLabelObject(i); double mean = labelObjectMe->GetMean(); fileout << mean << "\t"; std::cout << "Mean value of object with label " << static_cast(labelObjectMe->GetLabel()) << " in lysosomechannel: " << mean << std::endl; } fileout << "\n"; fileout.close(); std::cout << "Total bacteria counted (in statisticsLabelMapFilter): " << bacteriacount << std::endl; std::cout << std::endl; Do I really get the mean value from within my objects (bacteria) but calculating it using the values in image3Dred because I did: statisticsLabelMapFilter->SetInput2(image3Dred); and double mean = labelObjectMe->GetMean(); Best regards Michael Meuli From zeinsalah at gmail.com Mon Dec 8 08:20:29 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 8 Dec 2014 14:20:29 +0100 Subject: [ITK] GetOrigin of an itk image Message-ID: Hi, To saome reason I don't know, I fail to get the origin of itk images. The following simple code prints the spacing. for the origin, it always prints 0,0,0. typedef itk::Image ImageType; ImageType::SpacingType spacing = image->GetSpacing(); ImageType::PointType origin = image->GetOrigin(); printf("Spacing: %f %f %f\n", spacing[0], spacing[1], spacing[2]); printf("Origin: %f %f %f\n", origin[0], origin[1], origin[2]); The values of the Offset field in the Header og the input file (mhd) are definitely not zero. Was this the right way to read out the origin? o I am missing something? thanks zein From bill.lorensen at gmail.com Mon Dec 8 08:25:11 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 8 Dec 2014 08:25:11 -0500 Subject: [ITK] GetOrigin of an itk image In-Reply-To: References: Message-ID: That is correct. What does the rest of your code look like? Have you done an Update() on the reader? On Mon, Dec 8, 2014 at 8:20 AM, Zein Salah wrote: > Hi, > > To saome reason I don't know, I fail to get the origin of itk images. > The following simple code prints the spacing. for the origin, it always > prints 0,0,0. > > typedef itk::Image ImageType; > ImageType::SpacingType spacing = image->GetSpacing(); > ImageType::PointType origin = image->GetOrigin(); > printf("Spacing: %f %f %f\n", spacing[0], spacing[1], spacing[2]); > printf("Origin: %f %f %f\n", origin[0], origin[1], origin[2]); > > The values of the Offset field in the Header og the input file (mhd) > are definitely not zero. > > Was this the right way to read out the origin? o I am missing something? > > thanks > > zein > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -- Unpaid intern in BillsBasement at noware dot com From blowekamp at mail.nih.gov Mon Dec 8 08:44:29 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 8 Dec 2014 08:44:29 -0500 Subject: [ITK] Colocalization of bacteria and lysosome In-Reply-To: References: Message-ID: Hello, I am not sure anyone else can validate your code for you. What I'd recommend is developing some test images with known answers, and then adding them at test to you code to validate the results. This testing process can easily be done with cmake and ctest. Brad On Dec 8, 2014, at 7:07 AM, Michael Meuli wrote: > Hi all > > I've written a little program to analyse the colocalization of > bacteria and lysosome within macrophages. As main result it should > write the mean values of pixels located in the objects (bacteria) but > taking the value from the channel used to visualize the lysosomes > (image3Dred) into a file. > Image acquisition is done with a fancy confocal laser scanning > microscope. Bacteria, lysosomes and the nuclei of the macrophages are > labeld with different fluorochromes. As the cells are seeded as > monolayer, the images are quite flat and maximum intensity projections > are done to visually check the result. > > The programm compiles and runs but I'm not yet fully convinced if it > does what it should do. > I'm not a professional programmer and wanted to ask if some itk guru > could have a look at it. > The programm and some more information can be found here: > > https://github.com/michaelmeuli/bactelize > > My main question is, if the following piece of code really does what > it shoud do: > > BinaryImageToShapeLabelMapFilterType::Pointer > binaryImageToShapeLabelMapFilter = > BinaryImageToShapeLabelMapFilterType::New(); > binaryImageToShapeLabelMapFilter->SetInput(binaryimage3Dbacteria); > binaryImageToShapeLabelMapFilter->Update(); > ... > StatisticsLabelMapFilterType::Pointer statisticsLabelMapFilter = > StatisticsLabelMapFilterType::New(); > statisticsLabelMapFilter->SetInput1(binaryImageToShapeLabelMapFilter->GetOutput()); > statisticsLabelMapFilter->SetInput2(image3Dred); > statisticsLabelMapFilter->InPlaceOn(); > statisticsLabelMapFilter->Update(); > > unsigned int bacteriacount = > statisticsLabelMapFilter->GetOutput()->GetNumberOfLabelObjects(); > for(unsigned int i = 0; i < > statisticsLabelMapFilter->GetOutput()->GetNumberOfLabelObjects(); i++) > { > StatisticsLabelMapFilterType::OutputImageType::LabelObjectType* > labelObjectMe = > statisticsLabelMapFilter->GetOutput()->GetNthLabelObject(i); > double mean = labelObjectMe->GetMean(); > fileout << mean << "\t"; > std::cout << "Mean value of object with label " << > static_cast(labelObjectMe->GetLabel()) << " in lysosomechannel: " > << mean << std::endl; > } > fileout << "\n"; > fileout.close(); > std::cout << "Total bacteria counted (in statisticsLabelMapFilter): " > << bacteriacount << std::endl; > std::cout << std::endl; > > > Do I really get the mean value from within my objects (bacteria) but > calculating it using the values in image3Dred because I did: > statisticsLabelMapFilter->SetInput2(image3Dred); > and > double mean = labelObjectMe->GetMean(); > > Best regards > Michael Meuli > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From dr.tim.allman at gmail.com Mon Dec 8 09:01:54 2014 From: dr.tim.allman at gmail.com (Tim Allman) Date: Mon, 8 Dec 2014 09:01:54 -0500 Subject: [ITK] [ITK-users] convert mha to stack of dicom images In-Reply-To: <5484D7BF.4070403@dclunie.com> References: <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com> <5484D7BF.4070403@dclunie.com> Message-ID: Good idea. I have not done that. I was merely happy if Osirix would read the files. Tim On Dec 7, 2014, at 17:42 , David Clunie wrote: > Make sure you run dciodvfy and dcentvfy on DICOM files that you > create, to check that they are compliant (within the limits of > what these tools can mechanically check). See: > > http://www.dclunie.com/dicom3tools/dciodvfy.html > > David > > On 12/6/14 2:08 PM, Tim Allman wrote: >> I wrote a program for OSX to convert any file format recognized by ITK to DICOM. I wrote it for myself so most of the formats, including mha, haven?t been tested. If you have a Mac then you may even be able to run it. If not, the code should be helpful in showing how to construct a DICOM series. >> >> source and binary: https://github.com/TimAllman/ConvertToDicom/releases/tag/v0.1-beta >> >> I hope you find this helpful. If you have questions about the program feel free to email me. >> >> Tim >> >> On Dec 6, 2014, at 11:19 , Matias Montroull wrote: >> >>> HI, >>> >>> I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this? >>> >>> Thanks, >>> >>> Matias. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Dec 8 09:58:38 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Dec 2014 09:58:38 -0500 Subject: [ITK] [ITK-users] compling itkScaleInvariantFeatureImageFilter In-Reply-To: References: Message-ID: Hi Lianli, I assume you are using the code with this article [1] ? It looks like there is example test code in testnD.cxx. HTH, Matt [1] http://hdl.handle.net/1926/1321 On Fri, Dec 5, 2014 at 5:19 PM, Lianli Liu wrote: > Hi all, > > I want to use the itkScaleInvariantFeatureImageFilter but I am getting > several errors when compiling, such as: > error: ?FeatureType? was not declared in this scope > error: ?PointSetType? is not a class or namespace > > Does anyone has experience in using this filter? > > Also, I am unclear how where to specify input image in the filter. > > Thanks! > Lianli > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Dec 8 10:02:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Dec 2014 10:02:56 -0500 Subject: [ITK] LibTiff and CMake In-Reply-To: References: Message-ID: Hi Aaron, ITK's libtiff CMake configuration was not meant to be used stand-alone, but it can be used as a good starting point. This file is where to start [1]. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/TIFF/src/itktiff/CMakeLists.txt;h=b08a7fa1f76cdf6e88db83f1ee2933a738a64f7c;hb=HEAD On Sat, Dec 6, 2014 at 9:12 AM, Aaron Boxer wrote: > Hello! > I would like to use libtiff via CMake. I understand that ITK maintains a > CMake file for libtiff. > Can anyone recommend how I could pull this file out and use it with the > standard libtiff distribution? > > Thanks so much, > Aaron > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From zeinsalah at gmail.com Mon Dec 8 10:11:06 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 8 Dec 2014 16:11:06 +0100 Subject: [ITK] BinaryImageToShapeLabelMapFilter problem Message-ID: Hi, I am using the BinaryImageToShapeLabelMapFilter to label connected component in a binaty image. I recycled some code as follows: typedef unsigned long LabelType; typedef itk::ShapeLabelObject< LabelType, 3 > LabelObjectType; typedef itk::LabelMap< LabelObjectType > LabelMapType; typedef itk::BinaryImageToShapeLabelMapFilter< BinaryImageType, LabelMapType > ConverterType; ConverterType::Pointer converter = ConverterType::New(); converter->SetInput(m_SegmentedImage); converter->SetInputForegroundValue(255); converter->Update(); LabelMapType::Pointer labelMap = converter->GetOutput(); MarkerPositions detectedMarkers; for( unsigned int label=0; labelGetNumberOfLabelObjects(); label++ ) { const LabelObjectType * labelObject = labelMap->GetNthLabelObject(label); ImageType::PointType point = labelObject->GetCentroid(); std::cout << label << "\t" << labelObject->GetPhysicalSize() << " at: " << point[0] << "," << point[1] << "," << point[2] << std::endl; } The code actually generates some labels (for the image I used, it generates 35 labels). The thing I could not understand is that the centroids of the labeled object do not correspond to components in the image. I.e., when I take one centroid and select the point in the image, in most, if not all, cases it is an empty area. Are elements in a label map no more related to there position in the image? or I am missing some point here?? Centroids are computed in the pixels coordinates, not physical locations. Right? thanks, Zein From blowekamp at mail.nih.gov Mon Dec 8 10:18:28 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 8 Dec 2014 10:18:28 -0500 Subject: [ITK] [ITK-users] BinaryImageToShapeLabelMapFilter problem In-Reply-To: References: Message-ID: <1DC38089-CFCC-43BF-9C6D-8BD148DC8BF5@mail.nih.gov> Hello, The BinaryImageToShapeLabelMapFilter's Centroids are computed in physical space and are represented as a point. ITK uses strong type which makes this type of issue clear. The type of itk::ShapreLabelObject::CentroidType[1] is an itk::Point. This is used for physical coordinates. While the itk::Index type ( or itk::ContinuousIndex ) is used for indices. Also the PhysicalSize is going to be in your physical units, and not the number of voxels. Brad [1] http://www.itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#a34402f70c483dfe5b7e412d891d5abf6 On Dec 8, 2014, at 10:11 AM, Zein Salah wrote: > Are elements in > a label map no more related to there position in the image? or I am > missing some point here?? -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Mon Dec 8 10:18:31 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Mon, 8 Dec 2014 15:18:31 +0000 Subject: [ITK] Colocalization of bacteria and lysosome In-Reply-To: References: Message-ID: Hi Michael, That snippet of code should do what you expect (although, as Brad suggested, it would be a good idea to validate it). "image3Dred" is used as the feature image. This is the image from which the statistics are calculated. The label-map input defines the regions of the feature image for the calculations. By the way, you could use a single filter - BinaryImageToStatisticsLabelMapFilter [1], to achieve the same. [1] http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToStatisticsLabelMapFilter.html On Mon, Dec 8, 2014 at 1:44 PM, Bradley Lowekamp wrote: > Hello, > > I am not sure anyone else can validate your code for you. > > What I'd recommend is developing some test images with known answers, and > then adding them at test to you code to validate the results. This testing > process can easily be done with cmake and ctest. > > Brad > > On Dec 8, 2014, at 7:07 AM, Michael Meuli wrote: > > > Hi all > > > > I've written a little program to analyse the colocalization of > > bacteria and lysosome within macrophages. As main result it should > > write the mean values of pixels located in the objects (bacteria) but > > taking the value from the channel used to visualize the lysosomes > > (image3Dred) into a file. > > Image acquisition is done with a fancy confocal laser scanning > > microscope. Bacteria, lysosomes and the nuclei of the macrophages are > > labeld with different fluorochromes. As the cells are seeded as > > monolayer, the images are quite flat and maximum intensity projections > > are done to visually check the result. > > > > The programm compiles and runs but I'm not yet fully convinced if it > > does what it should do. > > I'm not a professional programmer and wanted to ask if some itk guru > > could have a look at it. > > The programm and some more information can be found here: > > > > https://github.com/michaelmeuli/bactelize > > > > My main question is, if the following piece of code really does what > > it shoud do: > > > > BinaryImageToShapeLabelMapFilterType::Pointer > > binaryImageToShapeLabelMapFilter = > > BinaryImageToShapeLabelMapFilterType::New(); > > binaryImageToShapeLabelMapFilter->SetInput(binaryimage3Dbacteria); > > binaryImageToShapeLabelMapFilter->Update(); > > ... > > StatisticsLabelMapFilterType::Pointer statisticsLabelMapFilter = > > StatisticsLabelMapFilterType::New(); > > > statisticsLabelMapFilter->SetInput1(binaryImageToShapeLabelMapFilter->GetOutput()); > > statisticsLabelMapFilter->SetInput2(image3Dred); > > statisticsLabelMapFilter->InPlaceOn(); > > statisticsLabelMapFilter->Update(); > > > > unsigned int bacteriacount = > > statisticsLabelMapFilter->GetOutput()->GetNumberOfLabelObjects(); > > for(unsigned int i = 0; i < > > statisticsLabelMapFilter->GetOutput()->GetNumberOfLabelObjects(); i++) > > { > > StatisticsLabelMapFilterType::OutputImageType::LabelObjectType* > > labelObjectMe = > > statisticsLabelMapFilter->GetOutput()->GetNthLabelObject(i); > > double mean = labelObjectMe->GetMean(); > > fileout << mean << "\t"; > > std::cout << "Mean value of object with label " << > > static_cast(labelObjectMe->GetLabel()) << " in lysosomechannel: " > > << mean << std::endl; > > } > > fileout << "\n"; > > fileout.close(); > > std::cout << "Total bacteria counted (in statisticsLabelMapFilter): " > > << bacteriacount << std::endl; > > std::cout << std::endl; > > > > > > Do I really get the mean value from within my objects (bacteria) but > > calculating it using the values in image3Dred because I did: > > statisticsLabelMapFilter->SetInput2(image3Dred); > > and > > double mean = labelObjectMe->GetMean(); > > > > Best regards > > Michael Meuli > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Dec 8 10:36:18 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Dec 2014 10:36:18 -0500 Subject: [ITK] [ITK-users] registration->StartRegistration(); In-Reply-To: References: Message-ID: Hi Matias, ->StartRegistration(); has been deprecated in favor of ->Update(); which is more consistent with how the rest of the algorithms are start in ITK. HTH, Matt On Sat, Dec 6, 2014 at 10:44 AM, Matias Montroull wrote: > Hi, > > I was trying to compile some registration examples and I get this: > 2 IntelliSense: class "itk::ImageRegistrationMethod short, 3U>, itk::Image>" has no member "StartRegistration" > > Should I use Update(); instead? > > I tried but I get an error when running the program. > > (I tried both examples registration8 and registration20 > > 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 > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 lasso at queensu.ca Mon Dec 8 12:00:16 2014 From: lasso at queensu.ca (Andras Lasso) Date: Mon, 8 Dec 2014 17:00:16 +0000 Subject: [ITK] [ITK-users] convert mha to stack of dicom images In-Reply-To: References: <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com> <5484D7BF.4070403@dclunie.com> Message-ID: You may also use latest nightly version of 3D Slicer to load data in almost any research format (nrrd, mha, stl, ...), process it (apply deformation, filters, etc.) and export it to DICOM (image, structure set, etc). http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DICOM Andras -----Original Message----- From: Community [mailto:community-bounces at itk.org] On Behalf Of Tim Allman Sent: Monday, December 8, 2014 09:02 To: insight-users at itk.org Users Subject: Re: [ITK] [ITK-users] convert mha to stack of dicom images Good idea. I have not done that. I was merely happy if Osirix would read the files. Tim On Dec 7, 2014, at 17:42 , David Clunie wrote: > Make sure you run dciodvfy and dcentvfy on DICOM files that you > create, to check that they are compliant (within the limits of what > these tools can mechanically check). See: > > http://www.dclunie.com/dicom3tools/dciodvfy.html > > David > > On 12/6/14 2:08 PM, Tim Allman wrote: >> I wrote a program for OSX to convert any file format recognized by ITK to DICOM. I wrote it for myself so most of the formats, including mha, haven't been tested. If you have a Mac then you may even be able to run it. If not, the code should be helpful in showing how to construct a DICOM series. >> >> source and binary: >> https://github.com/TimAllman/ConvertToDicom/releases/tag/v0.1-beta >> >> I hope you find this helpful. If you have questions about the program feel free to email me. >> >> Tim >> >> On Dec 6, 2014, at 11:19 , Matias Montroull wrote: >> >>> HI, >>> >>> I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this? >>> >>> Thanks, >>> >>> Matias. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Dec 8 12:37:42 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Dec 2014 12:37:42 -0500 Subject: [ITK] [ITK-users] How to abort execution of ImageRegistrationMethodv4 / Optimizer In-Reply-To: <5480E4A9.3050304@itis.ethz.ch> References: <5480DDA3.905@itis.ethz.ch> <5480E4A9.3050304@itis.ethz.ch> Message-ID: Hi Bryn, Thanks for looking into these issues. Could a patches please be created to address them? [1]. I think a separate patch could be created for each member. The check for AbortGenerateData should use the method: this->GetAbortGenerateData() Thanks, Matt [1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/SubmitAPatchToGerrit/index.html On Thu, Dec 4, 2014 at 5:48 PM, Bryn Lloyd wrote: > At a first glance it seems that ImageRegistrationMethodv4 does not check for > the abort flag: > > ImageRegistrationMethodv4 TVirtualImage> > ::GenerateData() > { > this->AllocateOutputs(); > for( this->m_CurrentLevel = 0; this->m_CurrentLevel < > this->m_NumberOfLevels; this->m_CurrentLevel++ ) > { > this->InitializeRegistrationAtEachLevel( this->m_CurrentLevel ); > > this->m_Metric->Initialize(); > > this->m_Optimizer->StartOptimization(); > } > } > > If I modify this code to check for m_AbortGenerateData, the registration > terminates as expected. > > > In addition it seems that the members m_CurrentMetricValue, > m_CurrentIteration etc. are never updated during optimization. > > Best regards > Bryn > > > > > On 04.12.2014 23:18, Bryn Lloyd wrote: >> >> Hi >> >> I recently started using ITK again and am trying out the ITK registration >> framework v4. >> >> >> I am trying to gracefully abort/stop the ImageRegistrationMethodv4 >> process, however it just continues. >> >> In my Command class, which observes an IterationEvent of the >> ImageRegistrationMethodv4 and Optimizer I call >> 1. registration_method_v4->SetAbortGenerateData( true ); // object of >> type ImageRegistrationMethodv4<...> >> >> 2. optimizer->StopOptimization(); >> >> However, the process just continues to execute. Is this supposed to work? >> What am I doing wrong? >> >> Thanks and best regards >> Bryn >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Mon Dec 8 12:51:42 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 8 Dec 2014 12:51:42 -0500 Subject: [ITK] [ITK-users] How to abort execution of ImageRegistrationMethodv4 / Optimizer In-Reply-To: References: <5480DDA3.905@itis.ethz.ch> <5480E4A9.3050304@itis.ethz.ch> Message-ID: <3B98C36F-15E5-4D7E-9DB6-4DD056EE5EDE@mail.nih.gov> Hello, I think that the optimizer needs to be stopped or told to abort. Perhaps the registration method should forward the request to the optimizer? Brad On Dec 8, 2014, at 12:37 PM, Matt McCormick wrote: > Hi Bryn, > > Thanks for looking into these issues. > > Could a patches please be created to address them? [1]. I think a > separate patch could be created for each member. The check for > AbortGenerateData should use the method: > > this->GetAbortGenerateData() > > Thanks, > Matt > > [1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/SubmitAPatchToGerrit/index.html > > On Thu, Dec 4, 2014 at 5:48 PM, Bryn Lloyd wrote: >> At a first glance it seems that ImageRegistrationMethodv4 does not check for >> the abort flag: >> >> ImageRegistrationMethodv4> TVirtualImage> >> ::GenerateData() >> { >> this->AllocateOutputs(); >> for( this->m_CurrentLevel = 0; this->m_CurrentLevel < >> this->m_NumberOfLevels; this->m_CurrentLevel++ ) >> { >> this->InitializeRegistrationAtEachLevel( this->m_CurrentLevel ); >> >> this->m_Metric->Initialize(); >> >> this->m_Optimizer->StartOptimization(); >> } >> } >> >> If I modify this code to check for m_AbortGenerateData, the registration >> terminates as expected. >> >> >> In addition it seems that the members m_CurrentMetricValue, >> m_CurrentIteration etc. are never updated during optimization. >> >> Best regards >> Bryn >> >> >> >> >> On 04.12.2014 23:18, Bryn Lloyd wrote: >>> >>> Hi >>> >>> I recently started using ITK again and am trying out the ITK registration >>> framework v4. >>> >>> >>> I am trying to gracefully abort/stop the ImageRegistrationMethodv4 >>> process, however it just continues. >>> >>> In my Command class, which observes an IterationEvent of the >>> ImageRegistrationMethodv4 and Optimizer I call >>> 1. registration_method_v4->SetAbortGenerateData( true ); // object of >>> type ImageRegistrationMethodv4<...> >>> >>> 2. optimizer->StopOptimization(); >>> >>> However, the process just continues to execute. Is this supposed to work? >>> What am I doing wrong? >>> >>> Thanks and best regards >>> Bryn >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 From blowekamp at mail.nih.gov Mon Dec 8 15:19:01 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 8 Dec 2014 15:19:01 -0500 Subject: [ITK] [ITK-dev] ImageToImageFilterCommon Wrapping Message-ID: <2EBAA106-1975-47F4-B95D-E64F54CAD78C@mail.nih.gov> Michka, I just saw this new warning for this funky class I added: /scratch/dashboards/Linux-x86_64-gcc4.8-WrapITK/ITK-build/Wrapping/Modules/ITKCommon/itkImageToImageFilterA.xml: warning(4): ITK type not wrapped, or currently not known: itk::ImageToImageFilterCommon http://open.cdash.org/viewBuildError.php?type=1&buildid=3603076 This class is privately inherited, and should not need to be directly used/wrapped. However the similar ImageSourceCommon is explicitly wrapped [1]. How sure what's best for the WrapITK interface. Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/wrapping/itkImageSource.wrap -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From marina.bendersky at gmail.com Mon Dec 8 15:39:20 2014 From: marina.bendersky at gmail.com (MB) Date: Mon, 8 Dec 2014 13:39:20 -0700 (MST) Subject: [ITK] [ITK-users] convert mha to stack of dicom images In-Reply-To: References: <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com> <5484D7BF.4070403@dclunie.com> Message-ID: <1418071160353-35033.post@n7.nabble.com> What about extracting the 2D images from the 3D volume using, for example, IO/ImageReadExtractWrite.cxx? Maybe this is not the most efficient way, but you could call the program in a loop and extract all of the slices automatically. (I'm a newbie so I tried this solution using a bash script.). Thanks -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-convert-mha-to-stack-of-dicom-images-tp35019p35033.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From michkapopoff at gmail.com Mon Dec 8 16:28:24 2014 From: michkapopoff at gmail.com (michkapopoff at gmail.com) Date: Mon, 8 Dec 2014 22:28:24 +0100 Subject: [ITK] [ITK-dev] ImageToImageFilterCommon Wrapping In-Reply-To: <2EBAA106-1975-47F4-B95D-E64F54CAD78C@mail.nih.gov> References: <2EBAA106-1975-47F4-B95D-E64F54CAD78C@mail.nih.gov> Message-ID: <23755723-ECF5-44B6-BFE8-8E20DCFC071A@gmail.com> Hi Brad I guess the ?fast? way is to just wrap it, like ImageSourceCommon. Then just open a ticket on JIRA so that we can think about it. We may have to find a way not to wrap privatly inherited classes, which should be doable. I?m still working on the python 3 support which is taking some time, so I will not have much time to spend on this right now. Michka > On 08 Dec 2014, at 21:19, Bradley Lowekamp wrote: > > Michka, > > I just saw this new warning for this funky class I added: > > > > /scratch/dashboards/Linux-x86_64-gcc4.8-WrapITK/ITK-build/Wrapping/Modules/ITKCommon/itkImageToImageFilterA.xml: warning(4): ITK type not wrapped, or currently not known: itk::ImageToImageFilterCommon > > http://open.cdash.org/viewBuildError.php?type=1&buildid=3603076 > > This class is privately inherited, and should not need to be directly used/wrapped. However the similar ImageSourceCommon is explicitly wrapped [1]. How sure what's best for the WrapITK interface. > > Brad > > > [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/wrapping/itkImageSource.wrap -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From senan.doyle at gmail.com Mon Dec 8 21:36:33 2014 From: senan.doyle at gmail.com (Senan Doyle) Date: Tue, 9 Dec 2014 03:36:33 +0100 Subject: [ITK] [ITK-dev] itkImageMaskSpatialObject malloc error Message-ID: Hi, I'm having trouble with the ImageMaskSpatialObject class The simple code below produces malloc: *** error for object 0x109043840: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug A quick debugging shows the call to m_Property = PropertyType::New(); in itkSpatialObject results in the smartpointer destructor for spatialobject property being called Anyone seen this before?Any ideas? int main ( int argc, char* argv[] ) { for(int i=0;i<100;i++){ typedef itk::ImageMaskSpatialObject< 3 > MaskSpatialObjectType; MaskSpatialObjectType::Pointer spatialObjectMask = MaskSpatialObjectType::New(); typedef itk::Image< unsigned char, 3 > ImageMaskType; typedef itk::ImageFileReader< ImageMaskType > MaskReaderType; MaskReaderType::Pointer maskReader = MaskReaderType::New(); maskReader->SetFileName( "/some/path/to/mask.nii"); try { maskReader->Update(); } catch( itk::ExceptionObject & err ) { std::cerr << "ExceptionObject caught !" << std::endl; std::cerr << err << std::endl; return 0; } spatialObjectMask->SetImage( maskReader->GetOutput() ); } } -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Dec 8 23:44:31 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 8 Dec 2014 23:44:31 -0500 Subject: [ITK] [ANNOUNCE] ITK 4.7 Release Candidate 1 has been tagged! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.7.0 release candidate 1 has been tagged and is available for testing! To obtain the source code, git clone http://itk.org/ITK.git cd ITK git checkout -q --detach v4.7rc01 For more details, please see the Git documentation [1]. Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review. Please help identify issues submitting an Experimental build to the dashboard [2] with: ctest -M Experimental -T Configure -T Build -T Test -T Submit and notifying the mailing list. Testing your own applications against the RC is also appreciated. Congratulations and well done to everyone that has contributed to this release. Release candidates are tagged every week. The final release is scheduled for December 18th. [1] http://www.itk.org/Wiki/ITK/Git [2] http://open.cdash.org/index.php?project=Insight New Features ------------------ * Documentation Improvements - Update Software Guide registration examples to ITKv4 framework - Wiki and Sphinx examples are indexed in Doxygen - Clean Software Guide dashboard build * Filtering Improvements - New Laplacian deformation filter?s for QuadEdgeMesh?s - IJ article: http://hdl.handle.net/10380/3410 - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations * ImageIO improvements - PNG sCAL unit support - TIFF IO performance greatly improved - TIFF tags read into Image MetaDataDictionary - MetaIO updated - Better support for system GDCM * Infrastructure improvements - New method to erase a MetaDataDictionary entry - New global method to set physical space tolerance - New, experimental thread pool support - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue() and ::OneValue() * New Remote Modules - Higher Order Accurate Gradient - http://hdl.handle.net/10380/3231 - IO Transform DCMTK - http://hdl.handle.net/10380/3468 * Registration improvements - LandmarkBasedTransformInitializer supports BSplineTransform - Transverse inverse consistency increased - Automatic initialization of the transform center for multi-stage registrations - Sparse point B-spline field estimate * Performance improvements - Faster recursive Gaussian on VectorImage - Mutual information faster, lower memory usage * Wrapping improvements - Wrapping now builds without type warnings - pygccxml bumped to 1.6.2 - Latest GCCXML - CMake wrapping infrastructure cleanup - Build with Ninja CMake generator - New GetTypes() and GetTypesAsList() methods - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake * Many style improvements -- ITK gets more stylish with every release! * Improved code coverage -- we are over 85%! * *Lots* of important bug fixes * And much more! See details in the log below. List of changes since v4.5.0 -------------------------------------- Alexander Schmidt-Richberg (1): ENH: Updated Remote Module VariationalRegistration to new git tag Ali Ghayoor (10): ENH: Make ITKv4 compatible with ITKSoftwareGuide ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 ENH: Convert three ImageRegistration Examples to ITKv4 ENH: Add multi-Res and multistage registration Examples to ITKv4 ENH: Convert DeformableReg examples to ITKv4 reg framework BUG: Expand a test to reflect multi-metric registration bug BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 ENH: Add direct initialization to SyN registration ENH: Direct initialization of SyN by restoring the state ENH: LandmarkBasedTransformInitializer supports BSplineTransformType Arnaud Gelas (15): COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization ENH: Importing Laplacian Deformation for QuadEdgeMesh DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter BUG: fix gdcm version in GDCMImageIO. COMP: missing cast when calling gdcm::DataElement::SetByteValue COMP: missing cast when calling gdcm::DataElement::SetByteValue ENH: increase LaplacianDeformation code coverage STYLE: use typedef rather than inheritance BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false BUG: split include directories into appropriate cmake variables HDF5 BUG: missing gdcm libraries when using system GDCM DOC: fix doxygen documentaiton for itk::LaplacianDeformationQuadEdgeMeshFilter ENH: Add one method to erase a tag into MetaDataDictionary Bill Lorensen (5): ENH: Specify required VTK modules COMP: Wiki examples require additional vtk modules ENH: Modify WikiExamples remote config COMP: Bad test signature COMP: Update tag for wiki examples Brad King (6): COMP: Fix vxl_config_macros usage of CMake check macros ENH: Use if(DEFINED) to simplify conditions COMP: Fix vxl_config_macros checks broken by refactoring COMP: Fix one more vxl_config_macros check broken by refactoring BUG: Fix itk_module_config for repeated calls BUG: Fix itk_module_config for repeated calls Bradley Lowekamp (52): ENH: Adding License file from upstream MetaIO ENH: Adding script to update MetaIO from upstream ENH: Remove ITK MetaIO to prepare for upstream import PERF: Remove dynamically allocated temporary in evaluate method COMP: Fix variable type for Set/Get macros BUG: Implement ITK Style Singleton design pattern ENH: Add no throw exception specification for UnRegister methods COMP: Must specify order as "noexcept override" BUG: Add GetInverse for IdentityTransform ENH: Adding SetIdentity method to base DisplacementField class BUG: Remove unused redefinition of NULL BUG: Don't print to std::cout in PrintSelf ENH: Prefer the PrintSelfObjectMacro for printing nested objects BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit COMP: Fix signed to unsigned int comparison BUG: Fix overflows computing size of read tiff image ENH: Extract TiffReaderInternal to separate file ENH: Refactor ReadTwoSamplePerPixelImage into template function ENH: Refactor GenericReadImage into template function BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) ENH: Refactor method to convert RGBA image to output buffer ENH: Refactor duplicated code to read a page BUG: Fix right oriented tiff images BUG: Remove dead separated plannar code, add test STYLE: Fix minor kwstyle defects in test and test results BUG: Use array delete operator for array new allocations ENH: add arbitrary TIFF TAGs to meta-data dictionary ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage BUG: Address Coverity warning about null pointer dereferences ENH: Remove support for TIFF tile as 3D and dead code ENH: RGBA read images should stay unchanged. BUG: Override method to MakeOutput by name ENH: Refactor per pixel conversion function to per scan-line method PERF: Refactor color table lookup BUG: Adding missing parentheses around boolean expression ENH: adding TIFFImageIO test for RGB palette images PERF: Improve recursive Gaussian perfromance with VectorImages ENH: Query libtiff to determine compression support BUG: Support TIFF tiled image with TIFFReadRGBAImage BUG: Use SizeValueType for length of scanline PERF: Store causal results directly in output buffers COMP: Add explicit conversion to const char COMP: Explicitly add override to GetNameOfClass method COMP: Address internal segmentation fault with Intel compiler ENH: Adding method to set global physical space tolerance COMP: Explicitly add override to GetNameOfClass method BUG: Add new TypeMacro for non-overloaded classes BUG: Fix obscure race condition on access thread pool initialization BUG: Updating FDFImageIO remote module Christopher Mullins (15): COMP: Allows latex to compile for ITKSoftwareGuide COMP: Allows latex to compile for ITKSoftwareGuide COMP: Wrap MeshBase templates COMP: Wrap MeshBase templates COMP: Fix warning in BlockMatchingImageFilter STYLE: Line lengths in examples should be no longer than 80 chars. COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. COMP: Fix LaTeX warnings. STYLE: Fix formatting/punctuation errors. STYLE: Formatting and punctuation fixes. DOC: Edits for Book 2 Chapter 1 documentation in the Examples. DOC: Edits for book 2 chapter 2. DOC: More chapter 2 edits DOC: Book 2 Chapter 3 edits (part 1) DOC: book 2 chapter 4 Segmentation edits Danny Perry (2): BUG: adding test for vnl_sparse_matrix::mult() BUG: size of q buffer should actually be (this->rows())*pcols. David T. Chen (1): DOC: Fixed HistogramThresholdImageFitler Dirk Padfield (1): BUG: Corrected processing of last sigma GCC-XML Upstream (1): ENH: pygccxml v1.6.2 (reduced) Gert Wollny (1): COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) Girish Mallya (1): BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. Hans Johnson (24): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components PERF: Remove large foot print of PDF derivatives. PERF: Revert Remove large foot print of PDF derivatives. STYLE: Test against almost equal for floating point values STYLE: Non-exact floating point testing PERF: Distribute initialization per thread buffers ENH: Remove unnecessary mutable qualifier. STYLE: Remove comment with no meaning. ENH: Moved accumlator logic to main MI class ENH: Allow staggering of accumulations per thread. PERF: Zero reset thread buffers during finalize BUG: Syntax error in comment PERF: Add non-blocking mutex locking. ENH: Use TryLock minimize thread stalls BUG: ThreadedIndexedContainerPartitioner is inclusive STYLE: Remove include_regular_expression from Examples BUG: Demonstrate Inv(Inv(T)) != T BUG: Ensure Inv(Inv(T)) == T for transforms COMP: Valgrind detects uninitialized memory read COMP: Missing required base class API component ENH: Expand interface for selecting threadpool Ismael Belghiti (1): DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter Jim Miller (1): STYLE: Removing what appears to be a temporary file Johan Andruejol (1): ENH: Fix normalization for null vectors and return the norm Jon Haitz Legarreta (1): ENH: New test for itkLabelShapeOpeningImageFilter Kent Williams (9): COMP: use find_package(VTK COMPONENTS) to specify just needed VTK Components BUG: ImageSources/test/CMakeLists.txt incorrect library var reference COMP: Fix coverity defects related to RegistrationV4 examples COMP: silence warning of vnl_vector_fixed_ref::assert_size COMP: Fix various Coverity warnings COMP: Fix a typo in an error message print statement. COMP: itk::Command-derived class used pointless dynamic_cast. PERF: Don't recompute InternalInverse repeatedly COMP: Correct orientation/spacing for Philips MultiFrame Mark Hiner (2): ENH: Update SCIFIO remote module hash BUG: Fix duplicate variables in Windows Matthew McCormick (105): DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. ENH: Move FFTComplexToComplexImageFilter out of Review. ENH: Add VnlComplexToComplexFFTImageFilter. BUG: Use fixed seed for Vnl FFT tests for repeatibility. ENH: Bump CMakeLists.txt version to 4.7.0. BUG: ArchiveTestingData.py future imports must occur at the beginning. BUG: Do not run vnl_test_na with broken libc++. DOC: Remove Image2.cxx reference from Book 2. DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. DOC: Remove references to Book 1 sections from Book 2. DOC: Make BinaryThresholdImageFilter not floating. DOC: Fix Software Guide figure caption for FlipImageFilter. DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. DOC: ImageRandomConstIteratorWithIndex table reference. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter. BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. STYLE: Fix style in VoronoiDiagram2D. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Bump GCCXML to 2014-08-06. BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. BUG: Fix Win MultiThreader check for successful process creation. BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. DOC: itk::statistics -> itk::Statistics. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. COMP: Improve const correctness of GradientRecursiveGaussianImageFilter. BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. COMP: ThreadJob NULL not defined. BUG: Fix alpha assignment for RGBA TIFF. COMP: Remove unused typedefs in LevelSetsv4Visualization. COMP: Remove unused typedef's in VtkGlue. ENH: Mark BSplineWarping2Test as RUNS_LONG. BUG: Fix Nifti IO read with large images. COMP: Remove call for non-existent variable in Nifti debugging. BUG: Close the file on Read and Write in HDF5TransformIO. BUG: Remove InsightLegacy test code from TransformHDF5Test. ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. STYLE: Use SeriesUIDContainerType and FileNamesContainerType ENH: Allow specification of orthogonality tolerance in rigid transforms. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Do not use _stat64 with MinGW-32. BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. DOC: itk::statistics -> itk::Statistics. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. COMP: Address LaplacianDeformation Doxygen warnings. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Fix missing prefix in ITKv3ImageRegistration20Test. BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform COMP: Do not wrap the FixedArray of Image SmartPointer's. COMP: Add missing wrapping for TransformIOBaseTemplate. COMP: Mark DeformableRegistration6Test as RUNS_LONG. STYLE: Improve style in BinaryImageToLabelMapFilter. BUG: Fix BinaryImageToLabelMapFilter on 1D image. ENH: Improve precision of the joint PDF sum BUG: Fix BinShrinkImageFilter for different input/output image types. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. BUG: Use -py3 when building wrapping for Python 3. COMP: Add missing wrapping for TransformIOBaseTemplate. DOC: Improve ImageRegistration4 grammar. ENH: Add IOTransformDCMTK Remote module. BUG: gdcm::StringFilter recognizes backslash delimiter. DOC: Add migration guide for GDCM Rescale slope intercept apply on write. COMP: Remove unused typedef's in GPU code. STYLE: Improve style of HoughTransform2DLinesImageFilter example. COMP: Use ConceptChecking for IterativeInverse dimension check. COMP: Wrap TransformIOBaseTemplate for const SmartPointer. COMP: Add warning exceptions for third party pcre, swig, gccxml. ENH: Bump ITK version to 4.6.1. BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. BUG: Remove GaussianImageSource members shadowing GenerateImageSource. STYLE: Style fixes to ITKImageSources module. BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType. BUG: Do not perform itk_download_attempt_check when not building ITK. DOC: Update GDCMImageIO rescale slope intercept doc. BUG: Only register requestion IO COMPONENT modules. BUG: Fix wrapping .i, .idx CMake dependencies. COMP: Add VTK Python module when wrapping ITKVtkGlue. STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. COMP: Add missing VTK module dependency for LevelSetsv4Visualization. BUG: By default, do not create any fixed parameters. STYLE: Remove trivial method comments in itkTransform.hxx. BUG: PolylineMask Filter's GenerateData is protected / virtual. ENH: Add HigherOrderAccurateGradient Module. BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal. COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. STYLE: Style fixes for Transform classes. DOC: Increase Doxygen LOOKUP_CACHE_SIZE. BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. DOC: Index Wiki examples with Doxygen. COMP: Bump SphinxExamples remote module. DOC: Index Sphinx examples in Doxygen. COMP: Remove old java examples. COMP: Remove duplicate DiffusionTensor3DReconstruction example reference. COMP: Address GradientAnisotropicDiffusionImageFilter example settings. COMP: Bump Sphinx Examples remote. COMP: Bump WikiExamples remote. MetaIO Maintainers (1): MetaIO (reduced) Michka Popoff (40): ENH: Fixes for python 3 support BUG: Add VTK_VERSION for older VTK versions BUG: Improve SWIG version check COMP: Add wrapping for ThreadPool and ThreadJob COMP: Remove unimplemented DestroyPool method COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping COMP: Do not hide pygccxml warnings ENH: Update links in readme file BUG: Improve SWIG version check BUG: Add VTK_VERSION for older VTK versions STYLE: Remove trailing whitespaces STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP BUG: Fix memory leak in MetaImageIO after exception ENH: Add script to update pygccxml from upstream BUG: Update VTK minimum version (for release) BUG: Fix memory leak in MetaImageIO after exception ENH: Remove Sun OS compatibility for the wrappings COMP: Fix for conversion to non-pointer like type warning STYLE: LabelObject style DOC: Remove broken link from LabelObject class description ENH: Do not setup the python tests if not asked ENH: Add new GetTypes() and GetTypesAsList() methods to the template class COMP: Fix CMP0054 warnings in wrappings STYLE: Remove old cmake < 2.8.4 specific code STYLE: Remove old cmake < 2.8.5 specific code ENH: Update to PCRE 8.36 COMP: Refactor Wrapping setup and fix legacy warnings ENH: Add wrapping configuration to ITKConfig.cmake STYLE: Some minor code cleanup in the wrapping setup DOC: Fix typo in RelabelComponentImageFilter ENH: Deprecate VectorResampleImageFilter DOC: Add migration guide for ::Zero and ::One ENH: Deprecate ::Zero and ::One ENH: Add option to disable sorting by size in itkRelabelComponentImageFilter ENH: Add Vector and RGB wrapping to linear interpolator STYLE: Remove SORT macro in wrappings COMP: Fix warning for InterpolateImageFunction wrapping COMP: Add a check for Blocks in GPU module COMP: Bump SCIFIO to fix test build warnings COMP: Fix wrapping of itkImageFunctionBase Nick Tustison (7): BUG: Need to explicitly specify spline order. ENH: Initializing the transform center. BUG: Need to check the dynamic cast before any calls. ENH: Adding modifications for point set metrics. BUG: Need to specify TInternalComputationValueType for default metric. ENH: Adding sparse points to B-spline field estimate. BUG: Uninitialized variables. Richard Beare (1): ENH: Include TIFF tags in the MetaDataDictionary Taylor Braun-Jones (1): BUG: Fix SliceBySliceImageFilter doesn't propagate information internally Umang B (1): ENH: Use thread pool to dispatch multithreading tasks Vivien Delmon (2): BUG: ExtractImageFilter::CollapseToSubMatrix fix ENH: Add a test on extracted directions in CollapseToSubMatrix mode Vladimir S. FONOV (1): BUG: Fixing incorrect MINC style inverse transform ----------------------------------------------------- Errors or omissions? Please fix them here: https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing From zeinsalah at gmail.com Tue Dec 9 08:25:21 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Tue, 9 Dec 2014 14:25:21 +0100 Subject: [ITK] Computing/Getting the attributes of ShapeLabelObject Message-ID: Hi, I want to compute some shape properties of segmented objects in a binary image. S I used the code below to create a labelmap. BTW, I am using ITK 3.14. typedef unsigned long LabelType; typedef itk::ShapeLabelObject< LabelType, 3 > LabelObjectType; typedef itk::LabelMap< LabelObjectType > LabelMapType; typedef itk::BinaryImageToShapeLabelMapFilter< OverlayImageType, LabelMapType > ConverterType; ConverterType::Pointer converter = ConverterType::New(); converter->SetInput(m_SegmentedImage); converter->SetInputForegroundValue(255); converter->Update(); LabelMapType::Pointer labelMap = converter->GetOutput(); for( unsigned int label=0; label < labelMap->GetNumberOfLabelObjects(); label++ ) { const LabelObjectType * labelObject = labelMap->GetNthLabelObject(label); LabelObjectType::CentroidType centroid = labelObject->GetCentroid(); std::cout << label << ": " << labelObject->GetCentroid() << " " << labelObject->GetPhysicalSize() << " " << labelObject->GetRegionElongation() << " " << labelObject->GeRoundness() << std::endl; } Strangely, the output of the Roundness is always 0. Moreover, it seems that some attrubutes are not implemented, e.g. GetElongation, GetboundingBox. From the corresponding IJ paper, I could not really understand if the the attributes are computed or need to computed elsewhere. Any hints how this should work? Thanks, Zein From zeinsalah at gmail.com Tue Dec 9 09:03:58 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Tue, 9 Dec 2014 15:03:58 +0100 Subject: [ITK] Computing/Getting the attributes of ShapeLabelObject In-Reply-To: References: Message-ID: And by the way, some attributes, like centroid, physical size, regionelongation are computed. Others, like roundness are not ! On Tue, Dec 9, 2014 at 2:25 PM, Zein Salah wrote: > Hi, > > I want to compute some shape properties of segmented objects in a binary image. > S I used the code below to create a labelmap. BTW, I am using ITK 3.14. > > typedef unsigned long LabelType; > typedef itk::ShapeLabelObject< LabelType, 3 > LabelObjectType; > typedef itk::LabelMap< LabelObjectType > LabelMapType; > > typedef itk::BinaryImageToShapeLabelMapFilter< OverlayImageType, > LabelMapType > ConverterType; > ConverterType::Pointer converter = ConverterType::New(); > converter->SetInput(m_SegmentedImage); > converter->SetInputForegroundValue(255); > converter->Update(); > > LabelMapType::Pointer labelMap = converter->GetOutput(); > > for( unsigned int label=0; label < > labelMap->GetNumberOfLabelObjects(); label++ ) > { > const LabelObjectType * labelObject = labelMap->GetNthLabelObject(label); > LabelObjectType::CentroidType centroid = labelObject->GetCentroid(); > std::cout << label << ": " << labelObject->GetCentroid() << " " > << labelObject->GetPhysicalSize() << " " > << labelObject->GetRegionElongation() << " " > << labelObject->GeRoundness() > << std::endl; > } > > > Strangely, the output of the Roundness is always 0. Moreover, it seems that > some attrubutes are not implemented, e.g. GetElongation, > GetboundingBox. From the > corresponding IJ paper, I could not really understand if the the > attributes are computed > or need to computed elsewhere. > > Any hints how this should work? > > Thanks, > Zein From blowekamp at mail.nih.gov Tue Dec 9 09:11:06 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 9 Dec 2014 09:11:06 -0500 Subject: [ITK] Computing/Getting the attributes of ShapeLabelObject In-Reply-To: References: Message-ID: <6235C0ED-0277-40A9-9B97-D46DFF3280A6@mail.nih.gov> Hello, ITK 3.14 is over 5 years old, and appears not to even have this IJ paper merged into the Review directory. I _strongly_ recommend upgrading! I don't even know what code you are using. It looks like the IJ paper says the roundness is related to the ratio of the areas, but currently (4.7rc1) it computation is does as a ratio of the perimeters[1]. The BinaryImageToShapeLabelMapFilter has some optional computation, among those are computing the peremeter, did you try calling BinaryImageToShapeLabelMapFilter::ComputePerimeterOn()? Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkShapeLabelMapFilter.hxx#L625 On Dec 9, 2014, at 8:25 AM, Zein Salah wrote: > Hi, > > I want to compute some shape properties of segmented objects in a binary image. > S I used the code below to create a labelmap. BTW, I am using ITK 3.14. > > typedef unsigned long LabelType; > typedef itk::ShapeLabelObject< LabelType, 3 > LabelObjectType; > typedef itk::LabelMap< LabelObjectType > LabelMapType; > > typedef itk::BinaryImageToShapeLabelMapFilter< OverlayImageType, > LabelMapType > ConverterType; > ConverterType::Pointer converter = ConverterType::New(); > converter->SetInput(m_SegmentedImage); > converter->SetInputForegroundValue(255); > converter->Update(); > > LabelMapType::Pointer labelMap = converter->GetOutput(); > > for( unsigned int label=0; label < > labelMap->GetNumberOfLabelObjects(); label++ ) > { > const LabelObjectType * labelObject = labelMap->GetNthLabelObject(label); > LabelObjectType::CentroidType centroid = labelObject->GetCentroid(); > std::cout << label << ": " << labelObject->GetCentroid() << " " > << labelObject->GetPhysicalSize() << " " > << labelObject->GetRegionElongation() << " " > << labelObject->GeRoundness() > << std::endl; > } > > > Strangely, the output of the Roundness is always 0. Moreover, it seems that > some attrubutes are not implemented, e.g. GetElongation, > GetboundingBox. From the > corresponding IJ paper, I could not really understand if the the > attributes are computed > or need to computed elsewhere. > > Any hints how this should work? > > Thanks, > Zein > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From blowekamp at mail.nih.gov Tue Dec 9 09:29:17 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 9 Dec 2014 09:29:17 -0500 Subject: [ITK] [ANNOUNCE] ITK 4.7 Release Candidate 1 has been tagged! In-Reply-To: References: Message-ID: <45FEEDBD-1DEF-4D1B-B9D0-46EC83FAE6CC@mail.nih.gov> Matt, I don't think you sufficiently highlighted that now all ITK examples from the Software Guide, Wiki Examples, and SphinxExamples are indexed and crossed linked in Doxygen[1]. So now when you go to your favorite filter or other object, say the ResampleImageFilter[2], there is a large selection of examples in the examples sections. This should make it much easier to fine sample code on how to use an ITK class! Brad [1] http://itk.org/Insight/Doxygen/html/examples.html [2] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html On Dec 8, 2014, at 11:44 PM, Matt McCormick wrote: > On behalf of the Insight Toolkit community, we are proud to announce > that ITK 4.7.0 release candidate 1 has been tagged and is available > for testing! > > > To obtain the source code, > > git clone http://itk.org/ITK.git > cd ITK > git checkout -q --detach v4.7rc01 > > For more details, please see the Git documentation [1]. > > > Please test the release candidate and share your experiences on the > mailing list, issue tracker, and Gerrit Code Review. Please help > identify issues submitting an Experimental build to the dashboard [2] > with: > > ctest -M Experimental -T Configure -T Build -T Test -T Submit > > and notifying the mailing list. Testing your own applications against > the RC is also appreciated. > > > Congratulations and well done to everyone that has contributed to this > release. Release candidates are tagged every week. The final release > is scheduled for December 18th. > > > [1] http://www.itk.org/Wiki/ITK/Git > > [2] http://open.cdash.org/index.php?project=Insight > > > > New Features > ------------------ > * Documentation Improvements > - Update Software Guide registration examples to ITKv4 framework > - Wiki and Sphinx examples are indexed in Doxygen > - Clean Software Guide dashboard build > > * Filtering Improvements > - New Laplacian deformation filter?s for QuadEdgeMesh?s > - IJ article: http://hdl.handle.net/10380/3410 > - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations > > * ImageIO improvements > - PNG sCAL unit support > - TIFF IO performance greatly improved > - TIFF tags read into Image MetaDataDictionary > - MetaIO updated > - Better support for system GDCM > > * Infrastructure improvements > - New method to erase a MetaDataDictionary entry > - New global method to set physical space tolerance > - New, experimental thread pool support > - NumericTraits::Zero and ::One are deprecated in favor of > ::ZeroValue() and ::OneValue() > > * New Remote Modules > - Higher Order Accurate Gradient > - http://hdl.handle.net/10380/3231 > - IO Transform DCMTK > - http://hdl.handle.net/10380/3468 > > * Registration improvements > - LandmarkBasedTransformInitializer supports BSplineTransform > - Transverse inverse consistency increased > - Automatic initialization of the transform center for multi-stage > registrations > - Sparse point B-spline field estimate > > * Performance improvements > - Faster recursive Gaussian on VectorImage > - Mutual information faster, lower memory usage > > * Wrapping improvements > - Wrapping now builds without type warnings > - pygccxml bumped to 1.6.2 > - Latest GCCXML > - CMake wrapping infrastructure cleanup > - Build with Ninja CMake generator > - New GetTypes() and GetTypesAsList() methods > - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake > > * Many style improvements -- ITK gets more stylish with every release! > > * Improved code coverage -- we are over 85%! > > * *Lots* of important bug fixes > > * And much more! See details in the log below. > > > List of changes since v4.5.0 > -------------------------------------- > > Alexander Schmidt-Richberg (1): > ENH: Updated Remote Module VariationalRegistration to new git tag > > Ali Ghayoor (10): > ENH: Make ITKv4 compatible with ITKSoftwareGuide > ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 > ENH: Convert three ImageRegistration Examples to ITKv4 > ENH: Add multi-Res and multistage registration Examples to ITKv4 > ENH: Convert DeformableReg examples to ITKv4 reg framework > BUG: Expand a test to reflect multi-metric registration bug > BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 > ENH: Add direct initialization to SyN registration > ENH: Direct initialization of SyN by restoring the state > ENH: LandmarkBasedTransformInitializer supports BSplineTransformType > > Arnaud Gelas (15): > COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization > ENH: Importing Laplacian Deformation for QuadEdgeMesh > DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage > ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() > ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > COMP: missing cast when calling gdcm::DataElement::SetByteValue > ENH: increase LaplacianDeformation code coverage > STYLE: use typedef rather than inheritance > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false > BUG: split include directories into appropriate cmake variables HDF5 > BUG: missing gdcm libraries when using system GDCM > DOC: fix doxygen documentaiton for > itk::LaplacianDeformationQuadEdgeMeshFilter > ENH: Add one method to erase a tag into MetaDataDictionary > > Bill Lorensen (5): > ENH: Specify required VTK modules > COMP: Wiki examples require additional vtk modules > ENH: Modify WikiExamples remote config > COMP: Bad test signature > COMP: Update tag for wiki examples > > Brad King (6): > COMP: Fix vxl_config_macros usage of CMake check macros > ENH: Use if(DEFINED) to simplify conditions > COMP: Fix vxl_config_macros checks broken by refactoring > COMP: Fix one more vxl_config_macros check broken by refactoring > BUG: Fix itk_module_config for repeated calls > BUG: Fix itk_module_config for repeated calls > > Bradley Lowekamp (52): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > PERF: Remove dynamically allocated temporary in evaluate method > COMP: Fix variable type for Set/Get macros > BUG: Implement ITK Style Singleton design pattern > ENH: Add no throw exception specification for UnRegister methods > COMP: Must specify order as "noexcept override" > BUG: Add GetInverse for IdentityTransform > ENH: Adding SetIdentity method to base DisplacementField class > BUG: Remove unused redefinition of NULL > BUG: Don't print to std::cout in PrintSelf > ENH: Prefer the PrintSelfObjectMacro for printing nested objects > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > COMP: Fix signed to unsigned int comparison > BUG: Fix overflows computing size of read tiff image > ENH: Extract TiffReaderInternal to separate file > ENH: Refactor ReadTwoSamplePerPixelImage into template function > ENH: Refactor GenericReadImage into template function > BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) > ENH: Refactor method to convert RGBA image to output buffer > ENH: Refactor duplicated code to read a page > BUG: Fix right oriented tiff images > BUG: Remove dead separated plannar code, add test > STYLE: Fix minor kwstyle defects in test and test results > BUG: Use array delete operator for array new allocations > ENH: add arbitrary TIFF TAGs to meta-data dictionary > ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage > BUG: Address Coverity warning about null pointer dereferences > ENH: Remove support for TIFF tile as 3D and dead code > ENH: RGBA read images should stay unchanged. > BUG: Override method to MakeOutput by name > ENH: Refactor per pixel conversion function to per scan-line method > PERF: Refactor color table lookup > BUG: Adding missing parentheses around boolean expression > ENH: adding TIFFImageIO test for RGB palette images > PERF: Improve recursive Gaussian perfromance with VectorImages > ENH: Query libtiff to determine compression support > BUG: Support TIFF tiled image with TIFFReadRGBAImage > BUG: Use SizeValueType for length of scanline > PERF: Store causal results directly in output buffers > COMP: Add explicit conversion to const char > COMP: Explicitly add override to GetNameOfClass method > COMP: Address internal segmentation fault with Intel compiler > ENH: Adding method to set global physical space tolerance > COMP: Explicitly add override to GetNameOfClass method > BUG: Add new TypeMacro for non-overloaded classes > BUG: Fix obscure race condition on access thread pool initialization > BUG: Updating FDFImageIO remote module > > Christopher Mullins (15): > COMP: Allows latex to compile for ITKSoftwareGuide > COMP: Allows latex to compile for ITKSoftwareGuide > COMP: Wrap MeshBase templates > COMP: Wrap MeshBase templates > COMP: Fix warning in BlockMatchingImageFilter > STYLE: Line lengths in examples should be no longer than 80 chars. > COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. > COMP: Fix LaTeX warnings. > STYLE: Fix formatting/punctuation errors. > STYLE: Formatting and punctuation fixes. > DOC: Edits for Book 2 Chapter 1 documentation in the Examples. > DOC: Edits for book 2 chapter 2. > DOC: More chapter 2 edits > DOC: Book 2 Chapter 3 edits (part 1) > DOC: book 2 chapter 4 Segmentation edits > > Danny Perry (2): > BUG: adding test for vnl_sparse_matrix::mult() > BUG: size of q buffer should actually be (this->rows())*pcols. > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Dirk Padfield (1): > BUG: Corrected processing of last sigma > > GCC-XML Upstream (1): > ENH: pygccxml v1.6.2 (reduced) > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. > > Hans Johnson (24): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > BUG: Syntax error in comment > PERF: Add non-blocking mutex locking. > ENH: Use TryLock minimize thread stalls > BUG: ThreadedIndexedContainerPartitioner is inclusive > STYLE: Remove include_regular_expression from Examples > BUG: Demonstrate Inv(Inv(T)) != T > BUG: Ensure Inv(Inv(T)) == T for transforms > COMP: Valgrind detects uninitialized memory read > COMP: Missing required base class API component > ENH: Expand interface for selecting threadpool > > Ismael Belghiti (1): > DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter > > Jim Miller (1): > STYLE: Removing what appears to be a temporary file > > Johan Andruejol (1): > ENH: Fix normalization for null vectors and return the norm > > Jon Haitz Legarreta (1): > ENH: New test for itkLabelShapeOpeningImageFilter > > Kent Williams (9): > COMP: use find_package(VTK COMPONENTS) to specify just needed > VTK Components > BUG: ImageSources/test/CMakeLists.txt incorrect library var reference > COMP: Fix coverity defects related to RegistrationV4 examples > COMP: silence warning of vnl_vector_fixed_ref::assert_size > COMP: Fix various Coverity warnings > COMP: Fix a typo in an error message print statement. > COMP: itk::Command-derived class used pointless dynamic_cast. > PERF: Don't recompute InternalInverse repeatedly > COMP: Correct orientation/spacing for Philips MultiFrame > > Mark Hiner (2): > ENH: Update SCIFIO remote module hash > BUG: Fix duplicate variables in Windows > > Matthew McCormick (105): > DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. > ENH: Move FFTComplexToComplexImageFilter out of Review. > ENH: Add VnlComplexToComplexFFTImageFilter. > BUG: Use fixed seed for Vnl FFT tests for repeatibility. > ENH: Bump CMakeLists.txt version to 4.7.0. > BUG: ArchiveTestingData.py future imports must occur at the beginning. > BUG: Do not run vnl_test_na with broken libc++. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter. > BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. > STYLE: Fix style in VoronoiDiagram2D. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Bump GCCXML to 2014-08-06. > BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. > BUG: Fix Win MultiThreader check for successful process creation. > BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. > COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. > DOC: itk::statistics -> itk::Statistics. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > COMP: Improve const correctness of GradientRecursiveGaussianImageFilter. > BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > COMP: ThreadJob NULL not defined. > BUG: Fix alpha assignment for RGBA TIFF. > COMP: Remove unused typedefs in LevelSetsv4Visualization. > COMP: Remove unused typedef's in VtkGlue. > ENH: Mark BSplineWarping2Test as RUNS_LONG. > BUG: Fix Nifti IO read with large images. > COMP: Remove call for non-existent variable in Nifti debugging. > BUG: Close the file on Read and Write in HDF5TransformIO. > BUG: Remove InsightLegacy test code from TransformHDF5Test. > ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. > STYLE: Use SeriesUIDContainerType and FileNamesContainerType > ENH: Allow specification of orthogonality tolerance in rigid transforms. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Do not use _stat64 with MinGW-32. > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. > COMP: Address LaplacianDeformation Doxygen warnings. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > COMP: Do not wrap the FixedArray of Image SmartPointer's. > COMP: Add missing wrapping for TransformIOBaseTemplate. > COMP: Mark DeformableRegistration6Test as RUNS_LONG. > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > BUG: Use -py3 when building wrapping for Python 3. > COMP: Add missing wrapping for TransformIOBaseTemplate. > DOC: Improve ImageRegistration4 grammar. > ENH: Add IOTransformDCMTK Remote module. > BUG: gdcm::StringFilter recognizes backslash delimiter. > DOC: Add migration guide for GDCM Rescale slope intercept apply on write. > COMP: Remove unused typedef's in GPU code. > STYLE: Improve style of HoughTransform2DLinesImageFilter example. > COMP: Use ConceptChecking for IterativeInverse dimension check. > COMP: Wrap TransformIOBaseTemplate for const SmartPointer. > COMP: Add warning exceptions for third party pcre, swig, gccxml. > ENH: Bump ITK version to 4.6.1. > BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. > BUG: Remove GaussianImageSource members shadowing GenerateImageSource. > STYLE: Style fixes to ITKImageSources module. > BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType. > BUG: Do not perform itk_download_attempt_check when not building ITK. > DOC: Update GDCMImageIO rescale slope intercept doc. > BUG: Only register requestion IO COMPONENT modules. > BUG: Fix wrapping .i, .idx CMake dependencies. > COMP: Add VTK Python module when wrapping ITKVtkGlue. > STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. > STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. > COMP: Add missing VTK module dependency for LevelSetsv4Visualization. > BUG: By default, do not create any fixed parameters. > STYLE: Remove trivial method comments in itkTransform.hxx. > BUG: PolylineMask Filter's GenerateData is protected / virtual. > ENH: Add HigherOrderAccurateGradient Module. > BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal. > COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. > STYLE: Style fixes for Transform classes. > DOC: Increase Doxygen LOOKUP_CACHE_SIZE. > BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. > DOC: Index Wiki examples with Doxygen. > COMP: Bump SphinxExamples remote module. > DOC: Index Sphinx examples in Doxygen. > COMP: Remove old java examples. > COMP: Remove duplicate DiffusionTensor3DReconstruction example reference. > COMP: Address GradientAnisotropicDiffusionImageFilter example settings. > COMP: Bump Sphinx Examples remote. > COMP: Bump WikiExamples remote. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (40): > ENH: Fixes for python 3 support > BUG: Add VTK_VERSION for older VTK versions > BUG: Improve SWIG version check > COMP: Add wrapping for ThreadPool and ThreadJob > COMP: Remove unimplemented DestroyPool method > COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping > COMP: Do not hide pygccxml warnings > ENH: Update links in readme file > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > STYLE: Remove trailing whitespaces > STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP > BUG: Fix memory leak in MetaImageIO after exception > ENH: Add script to update pygccxml from upstream > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > ENH: Remove Sun OS compatibility for the wrappings > COMP: Fix for conversion to non-pointer like type warning > STYLE: LabelObject style > DOC: Remove broken link from LabelObject class description > ENH: Do not setup the python tests if not asked > ENH: Add new GetTypes() and GetTypesAsList() methods to the template class > COMP: Fix CMP0054 warnings in wrappings > STYLE: Remove old cmake < 2.8.4 specific code > STYLE: Remove old cmake < 2.8.5 specific code > ENH: Update to PCRE 8.36 > COMP: Refactor Wrapping setup and fix legacy warnings > ENH: Add wrapping configuration to ITKConfig.cmake > STYLE: Some minor code cleanup in the wrapping setup > DOC: Fix typo in RelabelComponentImageFilter > ENH: Deprecate VectorResampleImageFilter > DOC: Add migration guide for ::Zero and ::One > ENH: Deprecate ::Zero and ::One > ENH: Add option to disable sorting by size in > itkRelabelComponentImageFilter > ENH: Add Vector and RGB wrapping to linear interpolator > STYLE: Remove SORT macro in wrappings > COMP: Fix warning for InterpolateImageFunction wrapping > COMP: Add a check for Blocks in GPU module > COMP: Bump SCIFIO to fix test build warnings > COMP: Fix wrapping of itkImageFunctionBase > > Nick Tustison (7): > BUG: Need to explicitly specify spline order. > ENH: Initializing the transform center. > BUG: Need to check the dynamic cast before any calls. > ENH: Adding modifications for point set metrics. > BUG: Need to specify TInternalComputationValueType for default metric. > ENH: Adding sparse points to B-spline field estimate. > BUG: Uninitialized variables. > > Richard Beare (1): > ENH: Include TIFF tags in the MetaDataDictionary > > Taylor Braun-Jones (1): > BUG: Fix SliceBySliceImageFilter doesn't propagate information internally > > Umang B (1): > ENH: Use thread pool to dispatch multithreading tasks > > Vivien Delmon (2): > BUG: ExtractImageFilter::CollapseToSubMatrix fix > ENH: Add a test on extracted directions in CollapseToSubMatrix mode > > Vladimir S. FONOV (1): > BUG: Fixing incorrect MINC style inverse transform > > > > ----------------------------------------------------- > Errors or omissions? Please fix them here: > > https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From blowekamp at mail.nih.gov Tue Dec 9 09:37:58 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 9 Dec 2014 09:37:58 -0500 Subject: [ITK] [ITK-dev] Dashboard systems now stable. Message-ID: <3463F3B7-5F1B-4E18-8B31-001659E600CA@mail.nih.gov> Matt, These builds should be considered for moving to the Expected Nightly Section: http://open.cdash.org/buildSummary.php?buildid=3604304 http://open.cdash.org/buildSummary.php?buildid=3604093 I am poking at mini6's instability again today, to fix system/build issues. Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Dec 9 11:22:23 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 9 Dec 2014 11:22:23 -0500 Subject: [ITK] [ANNOUNCE] ITK 4.7 Release Candidate 1 has been tagged! In-Reply-To: <45FEEDBD-1DEF-4D1B-B9D0-46EC83FAE6CC@mail.nih.gov> References: <45FEEDBD-1DEF-4D1B-B9D0-46EC83FAE6CC@mail.nih.gov> Message-ID: Hi Brad, Thanks for the feedback. I've tweaked the release text accordingly. On a side note, I also created this issue [1], so that we will remember to allow modules to declare their own examples in the future. Thanks, Matt [1] https://issues.itk.org/jira/browse/ITK-3336 On Tue, Dec 9, 2014 at 9:29 AM, Bradley Lowekamp wrote: > Matt, > > I don't think you sufficiently highlighted that now all ITK examples from the Software Guide, Wiki Examples, and SphinxExamples are indexed and crossed linked in Doxygen[1]. So now when you go to your favorite filter or other object, say the ResampleImageFilter[2], there is a large selection of examples in the examples sections. This should make it much easier to fine sample code on how to use an ITK class! > > Brad > > [1] http://itk.org/Insight/Doxygen/html/examples.html > [2] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html > > On Dec 8, 2014, at 11:44 PM, Matt McCormick wrote: > >> On behalf of the Insight Toolkit community, we are proud to announce >> that ITK 4.7.0 release candidate 1 has been tagged and is available >> for testing! >> >> >> To obtain the source code, >> >> git clone http://itk.org/ITK.git >> cd ITK >> git checkout -q --detach v4.7rc01 >> >> For more details, please see the Git documentation [1]. >> >> >> Please test the release candidate and share your experiences on the >> mailing list, issue tracker, and Gerrit Code Review. Please help >> identify issues submitting an Experimental build to the dashboard [2] >> with: >> >> ctest -M Experimental -T Configure -T Build -T Test -T Submit >> >> and notifying the mailing list. Testing your own applications against >> the RC is also appreciated. >> >> >> Congratulations and well done to everyone that has contributed to this >> release. Release candidates are tagged every week. The final release >> is scheduled for December 18th. >> >> >> [1] http://www.itk.org/Wiki/ITK/Git >> >> [2] http://open.cdash.org/index.php?project=Insight >> >> >> >> New Features >> ------------------ >> * Documentation Improvements >> - Update Software Guide registration examples to ITKv4 framework >> - Wiki and Sphinx examples are indexed in Doxygen >> - Clean Software Guide dashboard build >> >> * Filtering Improvements >> - New Laplacian deformation filter?s for QuadEdgeMesh?s >> - IJ article: http://hdl.handle.net/10380/3410 >> - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations >> >> * ImageIO improvements >> - PNG sCAL unit support >> - TIFF IO performance greatly improved >> - TIFF tags read into Image MetaDataDictionary >> - MetaIO updated >> - Better support for system GDCM >> >> * Infrastructure improvements >> - New method to erase a MetaDataDictionary entry >> - New global method to set physical space tolerance >> - New, experimental thread pool support >> - NumericTraits::Zero and ::One are deprecated in favor of >> ::ZeroValue() and ::OneValue() >> >> * New Remote Modules >> - Higher Order Accurate Gradient >> - http://hdl.handle.net/10380/3231 >> - IO Transform DCMTK >> - http://hdl.handle.net/10380/3468 >> >> * Registration improvements >> - LandmarkBasedTransformInitializer supports BSplineTransform >> - Transverse inverse consistency increased >> - Automatic initialization of the transform center for multi-stage >> registrations >> - Sparse point B-spline field estimate >> >> * Performance improvements >> - Faster recursive Gaussian on VectorImage >> - Mutual information faster, lower memory usage >> >> * Wrapping improvements >> - Wrapping now builds without type warnings >> - pygccxml bumped to 1.6.2 >> - Latest GCCXML >> - CMake wrapping infrastructure cleanup >> - Build with Ninja CMake generator >> - New GetTypes() and GetTypesAsList() methods >> - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake >> >> * Many style improvements -- ITK gets more stylish with every release! >> >> * Improved code coverage -- we are over 85%! >> >> * *Lots* of important bug fixes >> >> * And much more! See details in the log below. >> >> >> List of changes since v4.5.0 >> -------------------------------------- >> >> Alexander Schmidt-Richberg (1): >> ENH: Updated Remote Module VariationalRegistration to new git tag >> >> Ali Ghayoor (10): >> ENH: Make ITKv4 compatible with ITKSoftwareGuide >> ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 >> ENH: Convert three ImageRegistration Examples to ITKv4 >> ENH: Add multi-Res and multistage registration Examples to ITKv4 >> ENH: Convert DeformableReg examples to ITKv4 reg framework >> BUG: Expand a test to reflect multi-metric registration bug >> BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 >> ENH: Add direct initialization to SyN registration >> ENH: Direct initialization of SyN by restoring the state >> ENH: LandmarkBasedTransformInitializer supports BSplineTransformType >> >> Arnaud Gelas (15): >> COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization >> ENH: Importing Laplacian Deformation for QuadEdgeMesh >> DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage >> ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() >> ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter >> BUG: fix gdcm version in GDCMImageIO. >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> ENH: increase LaplacianDeformation code coverage >> STYLE: use typedef rather than inheritance >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false >> BUG: split include directories into appropriate cmake variables HDF5 >> BUG: missing gdcm libraries when using system GDCM >> DOC: fix doxygen documentaiton for >> itk::LaplacianDeformationQuadEdgeMeshFilter >> ENH: Add one method to erase a tag into MetaDataDictionary >> >> Bill Lorensen (5): >> ENH: Specify required VTK modules >> COMP: Wiki examples require additional vtk modules >> ENH: Modify WikiExamples remote config >> COMP: Bad test signature >> COMP: Update tag for wiki examples >> >> Brad King (6): >> COMP: Fix vxl_config_macros usage of CMake check macros >> ENH: Use if(DEFINED) to simplify conditions >> COMP: Fix vxl_config_macros checks broken by refactoring >> COMP: Fix one more vxl_config_macros check broken by refactoring >> BUG: Fix itk_module_config for repeated calls >> BUG: Fix itk_module_config for repeated calls >> >> Bradley Lowekamp (52): >> ENH: Adding License file from upstream MetaIO >> ENH: Adding script to update MetaIO from upstream >> ENH: Remove ITK MetaIO to prepare for upstream import >> PERF: Remove dynamically allocated temporary in evaluate method >> COMP: Fix variable type for Set/Get macros >> BUG: Implement ITK Style Singleton design pattern >> ENH: Add no throw exception specification for UnRegister methods >> COMP: Must specify order as "noexcept override" >> BUG: Add GetInverse for IdentityTransform >> ENH: Adding SetIdentity method to base DisplacementField class >> BUG: Remove unused redefinition of NULL >> BUG: Don't print to std::cout in PrintSelf >> ENH: Prefer the PrintSelfObjectMacro for printing nested objects >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> COMP: Fix signed to unsigned int comparison >> BUG: Fix overflows computing size of read tiff image >> ENH: Extract TiffReaderInternal to separate file >> ENH: Refactor ReadTwoSamplePerPixelImage into template function >> ENH: Refactor GenericReadImage into template function >> BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) >> ENH: Refactor method to convert RGBA image to output buffer >> ENH: Refactor duplicated code to read a page >> BUG: Fix right oriented tiff images >> BUG: Remove dead separated plannar code, add test >> STYLE: Fix minor kwstyle defects in test and test results >> BUG: Use array delete operator for array new allocations >> ENH: add arbitrary TIFF TAGs to meta-data dictionary >> ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage >> BUG: Address Coverity warning about null pointer dereferences >> ENH: Remove support for TIFF tile as 3D and dead code >> ENH: RGBA read images should stay unchanged. >> BUG: Override method to MakeOutput by name >> ENH: Refactor per pixel conversion function to per scan-line method >> PERF: Refactor color table lookup >> BUG: Adding missing parentheses around boolean expression >> ENH: adding TIFFImageIO test for RGB palette images >> PERF: Improve recursive Gaussian perfromance with VectorImages >> ENH: Query libtiff to determine compression support >> BUG: Support TIFF tiled image with TIFFReadRGBAImage >> BUG: Use SizeValueType for length of scanline >> PERF: Store causal results directly in output buffers >> COMP: Add explicit conversion to const char >> COMP: Explicitly add override to GetNameOfClass method >> COMP: Address internal segmentation fault with Intel compiler >> ENH: Adding method to set global physical space tolerance >> COMP: Explicitly add override to GetNameOfClass method >> BUG: Add new TypeMacro for non-overloaded classes >> BUG: Fix obscure race condition on access thread pool initialization >> BUG: Updating FDFImageIO remote module >> >> Christopher Mullins (15): >> COMP: Allows latex to compile for ITKSoftwareGuide >> COMP: Allows latex to compile for ITKSoftwareGuide >> COMP: Wrap MeshBase templates >> COMP: Wrap MeshBase templates >> COMP: Fix warning in BlockMatchingImageFilter >> STYLE: Line lengths in examples should be no longer than 80 chars. >> COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. >> COMP: Fix LaTeX warnings. >> STYLE: Fix formatting/punctuation errors. >> STYLE: Formatting and punctuation fixes. >> DOC: Edits for Book 2 Chapter 1 documentation in the Examples. >> DOC: Edits for book 2 chapter 2. >> DOC: More chapter 2 edits >> DOC: Book 2 Chapter 3 edits (part 1) >> DOC: book 2 chapter 4 Segmentation edits >> >> Danny Perry (2): >> BUG: adding test for vnl_sparse_matrix::mult() >> BUG: size of q buffer should actually be (this->rows())*pcols. >> >> David T. Chen (1): >> DOC: Fixed HistogramThresholdImageFitler >> >> Dirk Padfield (1): >> BUG: Corrected processing of last sigma >> >> GCC-XML Upstream (1): >> ENH: pygccxml v1.6.2 (reduced) >> >> Gert Wollny (1): >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >> >> Girish Mallya (1): >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. >> >> Hans Johnson (24): >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> PERF: Remove large foot print of PDF derivatives. >> PERF: Revert Remove large foot print of PDF derivatives. >> STYLE: Test against almost equal for floating point values >> STYLE: Non-exact floating point testing >> PERF: Distribute initialization per thread buffers >> ENH: Remove unnecessary mutable qualifier. >> STYLE: Remove comment with no meaning. >> ENH: Moved accumlator logic to main MI class >> ENH: Allow staggering of accumulations per thread. >> PERF: Zero reset thread buffers during finalize >> BUG: Syntax error in comment >> PERF: Add non-blocking mutex locking. >> ENH: Use TryLock minimize thread stalls >> BUG: ThreadedIndexedContainerPartitioner is inclusive >> STYLE: Remove include_regular_expression from Examples >> BUG: Demonstrate Inv(Inv(T)) != T >> BUG: Ensure Inv(Inv(T)) == T for transforms >> COMP: Valgrind detects uninitialized memory read >> COMP: Missing required base class API component >> ENH: Expand interface for selecting threadpool >> >> Ismael Belghiti (1): >> DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter >> >> Jim Miller (1): >> STYLE: Removing what appears to be a temporary file >> >> Johan Andruejol (1): >> ENH: Fix normalization for null vectors and return the norm >> >> Jon Haitz Legarreta (1): >> ENH: New test for itkLabelShapeOpeningImageFilter >> >> Kent Williams (9): >> COMP: use find_package(VTK COMPONENTS) to specify just needed >> VTK Components >> BUG: ImageSources/test/CMakeLists.txt incorrect library var reference >> COMP: Fix coverity defects related to RegistrationV4 examples >> COMP: silence warning of vnl_vector_fixed_ref::assert_size >> COMP: Fix various Coverity warnings >> COMP: Fix a typo in an error message print statement. >> COMP: itk::Command-derived class used pointless dynamic_cast. >> PERF: Don't recompute InternalInverse repeatedly >> COMP: Correct orientation/spacing for Philips MultiFrame >> >> Mark Hiner (2): >> ENH: Update SCIFIO remote module hash >> BUG: Fix duplicate variables in Windows >> >> Matthew McCormick (105): >> DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. >> ENH: Move FFTComplexToComplexImageFilter out of Review. >> ENH: Add VnlComplexToComplexFFTImageFilter. >> BUG: Use fixed seed for Vnl FFT tests for repeatibility. >> ENH: Bump CMakeLists.txt version to 4.7.0. >> BUG: ArchiveTestingData.py future imports must occur at the beginning. >> BUG: Do not run vnl_test_na with broken libc++. >> DOC: Remove Image2.cxx reference from Book 2. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. >> DOC: Remove references to Book 1 sections from Book 2. >> DOC: Make BinaryThresholdImageFilter not floating. >> DOC: Fix Software Guide figure caption for FlipImageFilter. >> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. >> DOC: Remove duplicate figure in >> LaplacianRecursiveGaussianImageFilter2.cxx. >> DOC: ImageRandomConstIteratorWithIndex table reference. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter. >> BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. >> STYLE: Fix style in VoronoiDiagram2D. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> BUG: Bump GCCXML to 2014-08-06. >> BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. >> BUG: Fix Win MultiThreader check for successful process creation. >> BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. >> COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. >> DOC: itk::statistics -> itk::Statistics. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> COMP: Improve const correctness of GradientRecursiveGaussianImageFilter. >> BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >> COMP: ThreadJob NULL not defined. >> BUG: Fix alpha assignment for RGBA TIFF. >> COMP: Remove unused typedefs in LevelSetsv4Visualization. >> COMP: Remove unused typedef's in VtkGlue. >> ENH: Mark BSplineWarping2Test as RUNS_LONG. >> BUG: Fix Nifti IO read with large images. >> COMP: Remove call for non-existent variable in Nifti debugging. >> BUG: Close the file on Read and Write in HDF5TransformIO. >> BUG: Remove InsightLegacy test code from TransformHDF5Test. >> ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. >> STYLE: Use SeriesUIDContainerType and FileNamesContainerType >> ENH: Allow specification of orthogonality tolerance in rigid transforms. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Do not use _stat64 with MinGW-32. >> BUG: Improve thread-safety and performance of >> PCAShapeSignedDistanceFunction. >> DOC: itk::statistics -> itk::Statistics. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. >> COMP: Address LaplacianDeformation Doxygen warnings. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >> BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform >> COMP: Do not wrap the FixedArray of Image SmartPointer's. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> COMP: Mark DeformableRegistration6Test as RUNS_LONG. >> STYLE: Improve style in BinaryImageToLabelMapFilter. >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. >> ENH: Improve precision of the joint PDF sum >> BUG: Fix BinShrinkImageFilter for different input/output image types. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> BUG: Use -py3 when building wrapping for Python 3. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> DOC: Improve ImageRegistration4 grammar. >> ENH: Add IOTransformDCMTK Remote module. >> BUG: gdcm::StringFilter recognizes backslash delimiter. >> DOC: Add migration guide for GDCM Rescale slope intercept apply on write. >> COMP: Remove unused typedef's in GPU code. >> STYLE: Improve style of HoughTransform2DLinesImageFilter example. >> COMP: Use ConceptChecking for IterativeInverse dimension check. >> COMP: Wrap TransformIOBaseTemplate for const SmartPointer. >> COMP: Add warning exceptions for third party pcre, swig, gccxml. >> ENH: Bump ITK version to 4.6.1. >> BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. >> BUG: Remove GaussianImageSource members shadowing GenerateImageSource. >> STYLE: Style fixes to ITKImageSources module. >> BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType. >> BUG: Do not perform itk_download_attempt_check when not building ITK. >> DOC: Update GDCMImageIO rescale slope intercept doc. >> BUG: Only register requestion IO COMPONENT modules. >> BUG: Fix wrapping .i, .idx CMake dependencies. >> COMP: Add VTK Python module when wrapping ITKVtkGlue. >> STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. >> STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. >> COMP: Add missing VTK module dependency for LevelSetsv4Visualization. >> BUG: By default, do not create any fixed parameters. >> STYLE: Remove trivial method comments in itkTransform.hxx. >> BUG: PolylineMask Filter's GenerateData is protected / virtual. >> ENH: Add HigherOrderAccurateGradient Module. >> BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal. >> COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. >> STYLE: Style fixes for Transform classes. >> DOC: Increase Doxygen LOOKUP_CACHE_SIZE. >> BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. >> DOC: Index Wiki examples with Doxygen. >> COMP: Bump SphinxExamples remote module. >> DOC: Index Sphinx examples in Doxygen. >> COMP: Remove old java examples. >> COMP: Remove duplicate DiffusionTensor3DReconstruction example reference. >> COMP: Address GradientAnisotropicDiffusionImageFilter example settings. >> COMP: Bump Sphinx Examples remote. >> COMP: Bump WikiExamples remote. >> >> MetaIO Maintainers (1): >> MetaIO (reduced) >> >> Michka Popoff (40): >> ENH: Fixes for python 3 support >> BUG: Add VTK_VERSION for older VTK versions >> BUG: Improve SWIG version check >> COMP: Add wrapping for ThreadPool and ThreadJob >> COMP: Remove unimplemented DestroyPool method >> COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping >> COMP: Do not hide pygccxml warnings >> ENH: Update links in readme file >> BUG: Improve SWIG version check >> BUG: Add VTK_VERSION for older VTK versions >> STYLE: Remove trailing whitespaces >> STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP >> BUG: Fix memory leak in MetaImageIO after exception >> ENH: Add script to update pygccxml from upstream >> BUG: Update VTK minimum version (for release) >> BUG: Fix memory leak in MetaImageIO after exception >> ENH: Remove Sun OS compatibility for the wrappings >> COMP: Fix for conversion to non-pointer like type warning >> STYLE: LabelObject style >> DOC: Remove broken link from LabelObject class description >> ENH: Do not setup the python tests if not asked >> ENH: Add new GetTypes() and GetTypesAsList() methods to the template class >> COMP: Fix CMP0054 warnings in wrappings >> STYLE: Remove old cmake < 2.8.4 specific code >> STYLE: Remove old cmake < 2.8.5 specific code >> ENH: Update to PCRE 8.36 >> COMP: Refactor Wrapping setup and fix legacy warnings >> ENH: Add wrapping configuration to ITKConfig.cmake >> STYLE: Some minor code cleanup in the wrapping setup >> DOC: Fix typo in RelabelComponentImageFilter >> ENH: Deprecate VectorResampleImageFilter >> DOC: Add migration guide for ::Zero and ::One >> ENH: Deprecate ::Zero and ::One >> ENH: Add option to disable sorting by size in >> itkRelabelComponentImageFilter >> ENH: Add Vector and RGB wrapping to linear interpolator >> STYLE: Remove SORT macro in wrappings >> COMP: Fix warning for InterpolateImageFunction wrapping >> COMP: Add a check for Blocks in GPU module >> COMP: Bump SCIFIO to fix test build warnings >> COMP: Fix wrapping of itkImageFunctionBase >> >> Nick Tustison (7): >> BUG: Need to explicitly specify spline order. >> ENH: Initializing the transform center. >> BUG: Need to check the dynamic cast before any calls. >> ENH: Adding modifications for point set metrics. >> BUG: Need to specify TInternalComputationValueType for default metric. >> ENH: Adding sparse points to B-spline field estimate. >> BUG: Uninitialized variables. >> >> Richard Beare (1): >> ENH: Include TIFF tags in the MetaDataDictionary >> >> Taylor Braun-Jones (1): >> BUG: Fix SliceBySliceImageFilter doesn't propagate information internally >> >> Umang B (1): >> ENH: Use thread pool to dispatch multithreading tasks >> >> Vivien Delmon (2): >> BUG: ExtractImageFilter::CollapseToSubMatrix fix >> ENH: Add a test on extracted directions in CollapseToSubMatrix mode >> >> Vladimir S. FONOV (1): >> BUG: Fixing incorrect MINC style inverse transform >> >> >> >> ----------------------------------------------------- >> Errors or omissions? Please fix them here: >> >> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Tue Dec 9 11:30:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 9 Dec 2014 11:30:32 -0500 Subject: [ITK] [ITK-dev] Dashboard systems now stable. In-Reply-To: <3463F3B7-5F1B-4E18-8B31-001659E600CA@mail.nih.gov> References: <3463F3B7-5F1B-4E18-8B31-001659E600CA@mail.nih.gov> Message-ID: Hi Brad, Excellent, thanks for the note! The builds have been moved. Matt On Tue, Dec 9, 2014 at 9:37 AM, Bradley Lowekamp wrote: > Matt, > > These builds should be considered for moving to the Expected Nightly Section: > > http://open.cdash.org/buildSummary.php?buildid=3604304 > http://open.cdash.org/buildSummary.php?buildid=3604093 > > I am poking at mini6's instability again today, to fix system/build issues. > > Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From tj.jackson1226 at gmail.com Tue Dec 9 14:01:40 2014 From: tj.jackson1226 at gmail.com (Tim Jackson) Date: Tue, 9 Dec 2014 14:01:40 -0500 Subject: [ITK] [ITK-dev] FFTWForwardFFTImageFilter and FFTWInverseFFTImageFilter Message-ID: Hello, I am currently writing a C++ program that I've called FTTC using VS2012 to compile. I'm having problems including the FFTW libraries, which I downloaded v3.3.4 of the precompiled libraries for Windows, into ITK. I reconfigured and rebuilt ITK v4.6.1, changing the variables in CMake to turn on ITK_USE_FFTWF and set the path for both FFTWF_LIB and FFTWF_THREADS_LIB to the downloaded version of libfftw3-3.lib. I also set FFTW_INCLUDE_PATH to where all of the downloaded files for the FFTW are located. ITK built without a problem, but when I now compile my program that uses the FFTWForwardFFTImageFilter and FFTWInverseFFTImageFilter, I get a whole host of linker error messages: fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_execute referenced in function "protected: virtual void __thiscall itk::FFTWInverseFFTImageFilter,class itk::Image >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@?$FFTWInverseFFTImageFilter at V?$Image at M$01 at itk @@V12@@itk@@MAEXXZ) fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_r2c referenced in function "public: static struct fftwf_plan_s * __cdecl itk::fftw::Proxy::Plan_dft_r2c(int,int const *,float *,float (*)[2],unsigned int,int,bool)" (?Plan_dft_r2c@?$Proxy at M @fftw at itk@@SAPAUfftwf_plan_s@@HPBHPAMPAY01MIH_N at Z) fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_c2r referenced in function "public: static struct fftwf_plan_s * __cdecl itk::fftw::Proxy::Plan_dft_c2r(int,int const *,float (*)[2],float *,unsigned int,int,bool)" (?Plan_dft_c2r@?$Proxy at M @fftw at itk@@SAPAUfftwf_plan_s@@HPBHPAY01MPAMIH_N at Z) fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_destroy_plan referenced in function "protected: virtual void __thiscall itk::FFTWInverseFFTImageFilter,class itk::Image >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@?$FFTWInverseFFTImageFilter at V?$Image at M$01 at itk @@V12@@itk@@MAEXXZ) fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_plan_with_nthreads referenced in function "public: static struct fftwf_plan_s * __cdecl itk::fftw::Proxy::Plan_dft_c2r(int,int const *,float (*)[2],float *,unsigned int,int,bool)" (?Plan_dft_c2r@ ?$Proxy at M@fftw at itk@@SAPAUfftwf_plan_s@@HPBHPAY01MPAMIH_N at Z) ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_cleanup referenced in function "private: virtual __thiscall itk::FFTWGlobalConfiguration::~FFTWGlobalConfiguration(void)" (??1FFTWGlobalConfiguration at itk@@EAE at XZ) ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_init_threads referenced in function __catch$??0FFTWGlobalConfiguration at itk@@AAE at XZ$0 ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_cleanup_threads referenced in function "private: virtual __thiscall itk::FFTWGlobalConfiguration::~FFTWGlobalConfiguration(void)" (??1FFTWGlobalConfiguration at itk@@EAE at XZ) ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_import_system_wisdom referenced in function __catch$??0FFTWGlobalConfiguration at itk@@AAE at XZ$0 ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_import_wisdom_from_file referenced in function "public: static bool __cdecl itk::FFTWGlobalConfiguration::ExportWisdomFileFloat(class std::basic_string,class std::allocator > const &)" (?ExportWisdomFileFloat at FFTWGlobalConfiguration@itk@ @SA_NABV?$basic_string at DU?$char_traits at D@std@@V?$allocator at D@2@@std@@@Z) C:\MIIA\FTTCBin\Release\FTTC.exe : fatal error LNK1120: 10 unresolved externals I've spent a long time searching the help forums and looked for ways to resolve this, but to no avail. Does anyone know what I may be doing wrong? I'm guessing I did something wrong when setting variables in CMake, but haven't been able to find any information on how to set them correctly. Thanks for your time and assistance! Best, Tim -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 9 14:04:08 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 9 Dec 2014 14:04:08 -0500 Subject: [ITK] [ITK-dev] FFTWForwardFFTImageFilter and FFTWInverseFFTImageFilter In-Reply-To: References: Message-ID: Hello, One guess I have is that the Visual Studio version used to compile FFTW is different than the one you are using. This could cause linking problems due to the different versions. Just a guess though. Brad On Dec 9, 2014, at 2:01 PM, Tim Jackson wrote: > Hello, > > I am currently writing a C++ program that I've called FTTC using VS2012 to compile. I'm having problems including the FFTW libraries, which I downloaded v3.3.4 of the precompiled libraries for Windows, into ITK. I reconfigured and rebuilt ITK v4.6.1, changing the variables in CMake to turn on ITK_USE_FFTWF and set the path for both FFTWF_LIB and FFTWF_THREADS_LIB to the downloaded version of libfftw3-3.lib. I also set FFTW_INCLUDE_PATH to where all of the downloaded files for the FFTW are located. > > ITK built without a problem, but when I now compile my program that uses the FFTWForwardFFTImageFilter and FFTWInverseFFTImageFilter, I get a whole host of linker error messages: > > fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_execute referenced in function "protected: virtual void __thiscall itk::FFTWInverseFFTImageFilter,class itk::Image >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@?$FFTWInverseFFTImageFilter at V?$Image at M$01 at itk@@V12@@itk@@MAEXXZ) > > fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_r2c referenced in function "public: static struct fftwf_plan_s * __cdecl itk::fftw::Proxy::Plan_dft_r2c(int,int const *,float *,float (*)[2],unsigned int,int,bool)" (?Plan_dft_r2c@?$Proxy at M@fftw at itk@@SAPAUfftwf_plan_s@@HPBHPAMPAY01MIH_N at Z) > > fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_c2r referenced in function "public: static struct fftwf_plan_s * __cdecl itk::fftw::Proxy::Plan_dft_c2r(int,int const *,float (*)[2],float *,unsigned int,int,bool)" (?Plan_dft_c2r@?$Proxy at M@fftw at itk@@SAPAUfftwf_plan_s@@HPBHPAY01MPAMIH_N at Z) > > fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_destroy_plan referenced in function "protected: virtual void __thiscall itk::FFTWInverseFFTImageFilter,class itk::Image >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@?$FFTWInverseFFTImageFilter at V?$Image at M$01 at itk@@V12@@itk@@MAEXXZ) > > fttc.obj : error LNK2019: unresolved external symbol __imp__fftwf_plan_with_nthreads referenced in function "public: static struct fftwf_plan_s * __cdecl itk::fftw::Proxy::Plan_dft_c2r(int,int const *,float (*)[2],float *,unsigned int,int,bool)" (?Plan_dft_c2r@?$Proxy at M@fftw at itk@@SAPAUfftwf_plan_s@@HPBHPAY01MPAMIH_N at Z) > > ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_cleanup referenced in function "private: virtual __thiscall itk::FFTWGlobalConfiguration::~FFTWGlobalConfiguration(void)" (??1FFTWGlobalConfiguration at itk@@EAE at XZ) > > ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_init_threads referenced in function __catch$??0FFTWGlobalConfiguration at itk@@AAE at XZ$0 > > ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_cleanup_threads referenced in function "private: virtual __thiscall itk::FFTWGlobalConfiguration::~FFTWGlobalConfiguration(void)" (??1FFTWGlobalConfiguration at itk@@EAE at XZ) > > ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_import_system_wisdom referenced in function __catch$??0FFTWGlobalConfiguration at itk@@AAE at XZ$0 > > ITKFFT-4.6.lib(itkFFTWGlobalConfiguration.obj) : error LNK2019: unresolved external symbol __imp__fftwf_import_wisdom_from_file referenced in function "public: static bool __cdecl itk::FFTWGlobalConfiguration::ExportWisdomFileFloat(class std::basic_string,class std::allocator > const &)" (?ExportWisdomFileFloat at FFTWGlobalConfiguration@itk@@SA_NABV?$basic_string at DU?$char_traits at D@std@@V?$allocator at D@2@@std@@@Z) > > C:\MIIA\FTTCBin\Release\FTTC.exe : fatal error LNK1120: 10 unresolved externals > > > I've spent a long time searching the help forums and looked for ways to resolve this, but to no avail. Does anyone know what I may be doing wrong? I'm guessing I did something wrong when setting variables in CMake, but haven't been able to find any information on how to set them correctly. > > Thanks for your time and assistance! > > Best, > 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://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From mpinkert at wisc.edu Tue Dec 9 14:15:56 2014 From: mpinkert at wisc.edu (Michael Pinkert) Date: Tue, 09 Dec 2014 13:15:56 -0600 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <76f08a62167ec.54874a47@wiscmail.wisc.edu> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <039601d00975$3f03c660$bd0b5320$@ac.kr> <76f08a62167ec.54874a47@wiscmail.wisc.edu> Message-ID: <76a0870a10478.5486f60c@wiscmail.wisc.edu> Hi Xiaopeng, Unfortunately, I was not able to fix this problem in my code. Please let us know if Jim's explanation is accurate. Best regards, Michael Pinkert On 11/26/14, Xiaopeng Yang wrote: > Hi, > > I tried to compile the code from Modules\Registration\GPUPDEDeformable\test > folder. Enclosed please find the code and CMakeLists file. I am quite new to > GPU, sorry I could not understand your explanation. Could you point out what > I missed please? > > Thanks, > Xiaopeng > > -----Original Message----- > From: Jim Miller [mailto:millerjv at gmail.com](javascript:main.compose() > Sent: Wednesday, November 26, 2014 9:10 PM > To: Xiaopeng Yang > Cc: Michael Pinkert; insight-users at itk.org > Subject: Re: [ITK-users] GPU Implementation > > This doesn't look like any issue with finding OpenCL. The link error is > saying it cannot find the implementation of an ITK method. > > I think GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void) is > supposed to return the kernel's implementation (probably as a string > containing the OpenCL code). > > Is there a txx file that is not being included? Does your program contain > the same headers and test? > > (I guess the error could occur if OpenCL was not found if the implementation > of this method in GPUPDEDeformableRegistrationFilterKernel is within > #ifdef/#endif on OpenCL.) > > Jim > > > On Nov 25, 2014, at 10:03 PM, Xiaopeng Yang wrote: > > > > Hi Michael, > > > > I also had the same errors while building my GPU registration program. > > Have you solved the problems? I guess the error was caused by improper > > setting in CMakeLists.txt file, but I could not find any > > CMakeLists.txt sample regarding GPU implementation in ITK. I doubt > > whether there are users using this GPU module or not. > > > > Best regards, > > Xiaopeng Yang > > > > > > This is the question you raised: > > > > I am trying to implement the GPU demons registration algorithm, but I > > have been having difficulty getting the program to compile. I believe > > the errors are because it cannot find the OpenCL library correctly, > > but I'm not sure how to fix it. > > > > I am using a NVIDIA Quadro FX 570 and am currently using OpenCL > > through the CUDA Computing Toolkit 4.2. My cmake file is attached, > > but I have had to manually enter in the directory locations to CMake > > because I have not been able to find a FindOpenCL.cmake file that > > works correctly. My operating system is Windows 7 x64. > > > > I am able to compile ITK after generating it in CMake with manually > > linked directories and Itk_Use_Gpu checked, but I have not been able > > to compile my program without getting errors, which are listed at the > bottom. > > > > Does anyone have suggestions as to how to fix this? > > > > Best regards, > > Michael Pinkert > > > > 2>registrationFunctions.obj : error LNK2019: unresolved external > > 2>symbol > > "public: static char const * __cdecl > > itk::GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void)" > > (?GetOpenCLSource at GPUPDEDeformableRegistrationFilterKernel@itk@@SAPEBD > > XZ) referenced in function "public: static char const * __cdecl > > itk::GPUPDEDeformableRegistrationFilter > itk::GPUImage,class itk::GPUImage,class > > itk::GPUImage,3>,class > > itk::DemonsRegistrationFilter > itk::GPUImage,class itk::GPUImage,class > > itk::GPUImage,3> > >::GetOpenCLSource(void)" > > (?GetOpenCLSource@?$GPUPDEDeformableRegistrationFilter at V?$GPUImage at M$0 > > 2 at itk@ > > @V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@V?$DemonsRegistrationFilter > > @V?$GP > > UImage at M$02 at itk@@V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@2@@itk@@SA > > PEBDXZ > > ) > > > > 2>registrationFunctions.obj : error LNK2019: unresolved external > > 2>symbol > > "public: static char const * __cdecl > > itk::GPUDemonsRegistrationFunctionKernel::GetOpenCLSource(void)" > > (?GetOpenCLSource at GPUDemonsRegistrationFunctionKernel@itk@@SAPEBDXZ) > > referenced in function "public: static char const * __cdecl > > itk::GPUDemonsRegistrationFunction,class > > itk::GPUImage,classitk::GPUImage > itk::Vector,3> > >> ::GetOpenCLSource(void)" > > (?GetOpenCLSource@?$GPUDemonsRegistrationFunction at V?$GPUImage at M$02 at itk > > @@V12@ > > V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@itk@@SAPEBDXZ) > > > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Dec 9 17:51:21 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 9 Dec 2014 17:51:21 -0500 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday, 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cqe0krqo83kpfnsc4nvkursl8r8 On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/ctoce1bib4f557omdapue9s49hk For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From franciscolopezdelafranca at gmail.com Wed Dec 10 02:08:35 2014 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Wed, 10 Dec 2014 08:08:35 +0100 Subject: [ITK] [ITK-users] Description of ShapeLabelObject attributes Message-ID: Hi everybody. Is there any place with a description of the different attributes contained in the ShapeLabelObject? For instance, what elongation, flatness, roundness, etc. are? Thank you very much. Best regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From zeinsalah at gmail.com Wed Dec 10 03:11:24 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Wed, 10 Dec 2014 09:11:24 +0100 Subject: [ITK] [ITK-users] Description of ShapeLabelObject attributes In-Reply-To: References: Message-ID: Probably the related Insight Journal paper. http://www.insight-journal.org/browse/publication/176 On Wed, Dec 10, 2014 at 8:08 AM, Francisco Lopez de la Franca wrote: > Hi everybody. > Is there any place with a description of the different attributes contained > in the ShapeLabelObject? > > For instance, what elongation, flatness, roundness, etc. are? > > Thank you very much. > Best regards. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Wed Dec 10 04:32:25 2014 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Wed, 10 Dec 2014 10:32:25 +0100 Subject: [ITK] [ITK-users] Description of ShapeLabelObject attributes In-Reply-To: References: Message-ID: Thanks a lot, but I've read the paper and don?t find the criteria to segment the objects and label them, I mean, how does the filter know that a group of pixels/voxels belong to the same blob? Does it use, for example, some x-connectivity mechanism? Thanks. 2014-12-10 9:11 GMT+01:00 Zein Salah : > Probably the related Insight Journal paper. > > http://www.insight-journal.org/browse/publication/176 > > > On Wed, Dec 10, 2014 at 8:08 AM, Francisco Lopez de la Franca > wrote: > > Hi everybody. > > Is there any place with a description of the different attributes > contained > > in the ShapeLabelObject? > > > > For instance, what elongation, flatness, roundness, etc. are? > > > > Thank you very much. > > Best regards. > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From zeinsalah at gmail.com Wed Dec 10 07:17:13 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Wed, 10 Dec 2014 13:17:13 +0100 Subject: [ITK] Question about ShapeLabelObject attribute Message-ID: Hi, i need to compute the maximum length of objects in a a LabelMap, i.e. something like LabelGeometryImageFilter::GetMajorAxisLength. Does any of the attributes of ShapeLabelObject stores this? Is there a way to compute this from the existing attribute, preferably without the need to compute perimeters? One more question: what do binary principal moments of an object practically mean? thanks. z. From yxp233 at postech.ac.kr Wed Dec 10 09:02:06 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Wed, 10 Dec 2014 23:02:06 +0900 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <1418152562580616.023858.ptmail04@ptmail04> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <039601d00975$3f03c660$bd0b5320$@ac.kr> <76f08a62167ec.54874a47@wiscmail.wisc.edu> <1418152562580616.023858.ptmail04@ptmail04> Message-ID: <02e801d01481$e1d82540$a5886fc0$@ac.kr> Hi Michael, I solved the problem according to Jim's explanation. You need to add ITKGPUPDEDeformable to your target_link_libraries line in CMakeLists: target_link_libraries(itkGPUDemonsRegistrationFilterTest ITKGPUPDEDeformable ${ITK_LIBRARIES} ). Best regards, Xiaopeng -----Original Message----- From: Michael Pinkert [mailto:mpinkert at wisc.edu] Sent: Wednesday, December 10, 2014 4:16 AM To: Xiaopeng Yang; 'Jim Miller' Cc: insight-users at itk.org Subject: RE: [ITK-users] GPU Implementation Hi Xiaopeng, Unfortunately, I was not able to fix this problem in my code. Please let us know if Jim's explanation is accurate. Best regards, Michael Pinkert On 11/26/14, Xiaopeng Yang wrote: > Hi, > > I tried to compile the code from > Modules\Registration\GPUPDEDeformable\test > folder. Enclosed please find the code and CMakeLists file. I am quite > new to GPU, sorry I could not understand your explanation. Could you > point out what I missed please? > > Thanks, > Xiaopeng > > -----Original Message----- > From: Jim Miller [mailto:millerjv at gmail.com](javascript:main.compose() > Sent: Wednesday, November 26, 2014 9:10 PM > To: Xiaopeng Yang > Cc: Michael Pinkert; insight-users at itk.org > Subject: Re: [ITK-users] GPU Implementation > > This doesn't look like any issue with finding OpenCL. The link error > is saying it cannot find the implementation of an ITK method. > > I think > GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void) is > supposed to return the kernel's implementation (probably as a string containing the OpenCL code). > > Is there a txx file that is not being included? Does your program > contain the same headers and test? > > (I guess the error could occur if OpenCL was not found if the > implementation of this method in > GPUPDEDeformableRegistrationFilterKernel is within #ifdef/#endif on > OpenCL.) > > Jim > > > On Nov 25, 2014, at 10:03 PM, Xiaopeng Yang wrote: > > > > Hi Michael, > > > > I also had the same errors while building my GPU registration program. > > Have you solved the problems? I guess the error was caused by > > improper setting in CMakeLists.txt file, but I could not find any > > CMakeLists.txt sample regarding GPU implementation in ITK. I doubt > > whether there are users using this GPU module or not. > > > > Best regards, > > Xiaopeng Yang > > > > > > This is the question you raised: > > > > I am trying to implement the GPU demons registration algorithm, but > > I have been having difficulty getting the program to compile. I > > believe the errors are because it cannot find the OpenCL library > > correctly, but I'm not sure how to fix it. > > > > I am using a NVIDIA Quadro FX 570 and am currently using OpenCL > > through the CUDA Computing Toolkit 4.2. My cmake file is attached, > > but I have had to manually enter in the directory locations to CMake > > because I have not been able to find a FindOpenCL.cmake file that > > works correctly. My operating system is Windows 7 x64. > > > > I am able to compile ITK after generating it in CMake with manually > > linked directories and Itk_Use_Gpu checked, but I have not been able > > to compile my program without getting errors, which are listed at > > the > bottom. > > > > Does anyone have suggestions as to how to fix this? > > > > Best regards, > > Michael Pinkert > > > > 2>registrationFunctions.obj : error LNK2019: unresolved external > > 2>symbol > > "public: static char const * __cdecl > > itk::GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void)" > > (?GetOpenCLSource at GPUPDEDeformableRegistrationFilterKernel@itk@@SAPE > > BD > > XZ) referenced in function "public: static char const * __cdecl > > itk::GPUPDEDeformableRegistrationFilter > itk::GPUImage,class itk::GPUImage,class > > itk::GPUImage,3>,class > > itk::DemonsRegistrationFilter > itk::GPUImage,class itk::GPUImage,class > > itk::GPUImage,3> > >::GetOpenCLSource(void)" > > (?GetOpenCLSource@?$GPUPDEDeformableRegistrationFilter at V?$GPUImage at M > > $0 > > 2 at itk@ > > @V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@V?$DemonsRegistrationFilt > > er > > @V?$GP > > UImage at M$02 at itk@@V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@2@@itk@@ > > SA > > PEBDXZ > > ) > > > > 2>registrationFunctions.obj : error LNK2019: unresolved external > > 2>symbol > > "public: static char const * __cdecl > > itk::GPUDemonsRegistrationFunctionKernel::GetOpenCLSource(void)" > > (?GetOpenCLSource at GPUDemonsRegistrationFunctionKernel@itk@@SAPEBDXZ) > > referenced in function "public: static char const * __cdecl > > itk::GPUDemonsRegistrationFunction > itk::GPUImage,class > > itk::GPUImage,classitk::GPUImage > itk::Vector,3> > >> ::GetOpenCLSource(void)" > > (?GetOpenCLSource@?$GPUDemonsRegistrationFunction at V?$GPUImage at M$02 at i > > tk > > @@V12@ > > V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@itk@@SAPEBDXZ) > > > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Wed Dec 10 09:04:04 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Wed, 10 Dec 2014 23:04:04 +0900 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <1417837813159280.04286.ptmail04@ptmail04> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> <008c01d010e5$84172950$8c457bf0$@ac.kr> <1417828271180838.110987.ptmail04@ptmail04> <009a01d010f5$7d4043e0$77c0cba0$@ac.kr> <1417837813159280.04286.ptmail04@ptmail04> Message-ID: <02e901d01482$28372130$78a56390$@ac.kr> Hi Jim, Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred. Best regards, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Saturday, December 06, 2014 12:50 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. Jim On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang wrote: Hi Jim, So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Saturday, December 06, 2014 10:11 AM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. Jim On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang wrote: Dear Jim, The images are quite large: 512 * 512 *300. I did not build test when I compile ITK. Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Friday, December 05, 2014 11:15 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation How large are the images that you are using? Jim On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: Hi John, Sorry I mean the program got crashed after showing #define T float. Thanks, Xiaopeng From: John Drescher [mailto:drescherjm at gmail.com] Sent: Friday, December 05, 2014 4:24 PM To: Xiaopeng Yang Cc: Jim Miller; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: Dear Jim, Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. Best, Xiaopeng Is that an error? John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Wed Dec 10 09:43:03 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 10 Dec 2014 09:43:03 -0500 Subject: [ITK] Question about ShapeLabelObject attribute In-Reply-To: References: Message-ID: <64D53F04-F156-4E1C-8D84-EC6A613DB15A@mail.nih.gov> Hello, There are many ways to measure the maximum length of an object. Principal moments of share are an important shape description that is common an I suggest further reading to be done on. You may be able to start on the wikipedia [1]. For some case I prefer to use second principle moments to measure the size of an object over length as it is a more robust statistics. It similar to using the standard deviation as opposed to the range to describe a set of samples. So the second principle moments in the shape label object are similar to the LabelGeometryFilter's axis measurements. I have an external module which computes an oriented bounding box based on the second principle moments and provide access to this value you are looking for [2]. The computation done there should be much more efficient that what's done in the LabelGeometryImageFilter. If you want a simular interface to the LabelGeometryImageFilter that the LabelShapeStatisticsImageFilter should be the interface you are looking for[3][4]. Hope that helps, Brad [1] http://en.wikipedia.org/wiki/Second_moment_of_area [2] https://github.com/blowekamp/itkOBBLabelMap [3] https://github.com/blowekamp/itkOBBLabelMap/blob/master/include/itkLabelShapeStatisticsImageFilter.h [4] https://github.com/blowekamp/itkOBBLabelMap/blob/master/test/itkLabelShapeStatisticsImageFilterTest.cxx On Dec 10, 2014, at 7:17 AM, Zein Salah wrote: > Hi, > > i need to compute the maximum length of objects in a a LabelMap, i.e. > something like LabelGeometryImageFilter::GetMajorAxisLength. > Does any of the attributes of ShapeLabelObject stores this? Is there a > way to compute this from the existing attribute, preferably without > the need to compute perimeters? > > One more question: what do binary principal moments of an object > practically mean? > > thanks. > z. > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From millerjv at gmail.com Wed Dec 10 10:48:50 2014 From: millerjv at gmail.com (Jim Miller) Date: Wed, 10 Dec 2014 10:48:50 -0500 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <02e901d01482$28372130$78a56390$@ac.kr> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> <008c01d010e5$84172950$8c457bf0$@ac.kr> <1417828271180838.110987.ptmail04@ptmail04> <009a01d010f5$7d4043e0$77c0cba0$@ac.kr> <1417837813159280.04286.ptmail04@ptmail04> <02e901d01482$28372130$78a56390$@ac.kr> Message-ID: <58B0CB8C-557C-4F16-A283-F65D69F850A3@gmail.com> Great. You can experiment further to see how large of a dataset you can handle. Then decide if you need to upgrade your graphic card to one with more memory to support the dataset size you want to process. Jim > On Dec 10, 2014, at 9:04 AM, Xiaopeng Yang wrote: > > Hi Jim, > > Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred. > > Best regards, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Saturday, December 06, 2014 12:50 PM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. > > Jim > > On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang wrote: > > Hi Jim, > > So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? > > Thanks, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Saturday, December 06, 2014 10:11 AM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. > > Jim > > On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang wrote: > > Dear Jim, > > The images are quite large: 512 * 512 *300. > > I did not build test when I compile ITK. > > Thanks, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Friday, December 05, 2014 11:15 PM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > How large are the images that you are using? > > Jim > > On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: > > Hi John, > > Sorry I mean the program got crashed after showing #define T float. > > Thanks, > Xiaopeng > > From: John Drescher [mailto:drescherjm at gmail.com] > Sent: Friday, December 05, 2014 4:24 PM > To: Xiaopeng Yang > Cc: Jim Miller; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > > > On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: > Dear Jim, > > Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. > > Best, > Xiaopeng > > > > > Is that an error? > > John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From senan.doyle at gmail.com Wed Dec 10 17:35:39 2014 From: senan.doyle at gmail.com (Senan Doyle) Date: Wed, 10 Dec 2014 23:35:39 +0100 Subject: [ITK] [ITK-dev] itkImageMaskSpatialObject malloc error In-Reply-To: References: Message-ID: Posting the solution in case anyone else encounters this ... It's a problem concerning Mac+Qt+ITK setups, as solved by Christian Lackas here: http://itk-insight-users.2283740.n2.nabble.com/ITK-crash-on-Lion-Qt-td6894083.html On 9 December 2014 at 03:36, Senan Doyle wrote: > > Hi, > I'm having trouble with the ImageMaskSpatialObject class > The simple code below produces > > malloc: *** error for object 0x109043840: pointer being freed was not > allocated > > *** set a breakpoint in malloc_error_break to debug > > A quick debugging shows the call to > > m_Property = PropertyType::New(); > > in itkSpatialObject results in the smartpointer destructor for > spatialobject property being called > > > Anyone seen this before?Any ideas? > > > > > int main ( int argc, char* argv[] ) > > { > > > for(int i=0;i<100;i++){ > > typedef itk::ImageMaskSpatialObject< 3 > MaskSpatialObjectType; > > MaskSpatialObjectType::Pointer spatialObjectMask = MaskSpatialObjectType::New(); > > > typedef itk::Image< unsigned char, 3 > ImageMaskType; > > > typedef itk::ImageFileReader< ImageMaskType > MaskReaderType; > > MaskReaderType::Pointer maskReader = MaskReaderType::New(); > > maskReader->SetFileName( "/some/path/to/mask.nii"); > > try > > { > > maskReader->Update(); > > } > > catch( itk::ExceptionObject & err ) > > { > > std::cerr << "ExceptionObject caught !" << std::endl; > > std::cerr << err << std::endl; > > return 0; > > } > > > spatialObjectMask->SetImage( maskReader->GetOutput() ); > > > } > > } > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From michael.meuli at gmail.com Thu Dec 11 04:25:50 2014 From: michael.meuli at gmail.com (Michael Meuli) Date: Thu, 11 Dec 2014 10:25:50 +0100 Subject: [ITK] Colocalization of bacteria and lysosome In-Reply-To: References: Message-ID: Hi all, thanks a lot for your responses. I think the results are correct, but there's a bug in the 2D "heat map" which should actually serve to visually verify that the program is running correct. Actually yesterday I fully evaluated my experiment with the output of my little program and for the first time could see the effect we wanted to see and which I wasn't fully able to demonstrate using Imaris. As it's my first programm which does something useful I really like it and I wanted to thank all the itk people for this cool toolkit and for all the help! Some synthetic images for testing would be nice but I've no idea how to draw a 3D bacterium. Are there some tools or programms available? Also I don't get it how to write a test. If somebody could point me to a nice starting point would be nice. Best regards Michael On 8 December 2014 at 16:18, Girish Mallya Udupi wrote: > Hi Michael, > > That snippet of code should do what you expect (although, as Brad suggested, > it would be a good idea to validate it). "image3Dred" is used as the feature > image. This is the image from which the statistics are calculated. The > label-map input defines the regions of the feature image for the > calculations. > > By the way, you could use a single filter - > BinaryImageToStatisticsLabelMapFilter [1], to achieve the same. > > > [1] > http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToStatisticsLabelMapFilter.html > > On Mon, Dec 8, 2014 at 1:44 PM, Bradley Lowekamp > wrote: >> >> Hello, >> >> I am not sure anyone else can validate your code for you. >> >> What I'd recommend is developing some test images with known answers, and >> then adding them at test to you code to validate the results. This testing >> process can easily be done with cmake and ctest. >> >> Brad >> >> On Dec 8, 2014, at 7:07 AM, Michael Meuli wrote: >> >> > Hi all >> > >> > I've written a little program to analyse the colocalization of >> > bacteria and lysosome within macrophages. As main result it should >> > write the mean values of pixels located in the objects (bacteria) but >> > taking the value from the channel used to visualize the lysosomes >> > (image3Dred) into a file. >> > Image acquisition is done with a fancy confocal laser scanning >> > microscope. Bacteria, lysosomes and the nuclei of the macrophages are >> > labeld with different fluorochromes. As the cells are seeded as >> > monolayer, the images are quite flat and maximum intensity projections >> > are done to visually check the result. >> > >> > The programm compiles and runs but I'm not yet fully convinced if it >> > does what it should do. >> > I'm not a professional programmer and wanted to ask if some itk guru >> > could have a look at it. >> > The programm and some more information can be found here: >> > >> > https://github.com/michaelmeuli/bactelize >> > >> > My main question is, if the following piece of code really does what >> > it shoud do: >> > >> > BinaryImageToShapeLabelMapFilterType::Pointer >> > binaryImageToShapeLabelMapFilter = >> > BinaryImageToShapeLabelMapFilterType::New(); >> > binaryImageToShapeLabelMapFilter->SetInput(binaryimage3Dbacteria); >> > binaryImageToShapeLabelMapFilter->Update(); >> > ... >> > StatisticsLabelMapFilterType::Pointer statisticsLabelMapFilter = >> > StatisticsLabelMapFilterType::New(); >> > >> > statisticsLabelMapFilter->SetInput1(binaryImageToShapeLabelMapFilter->GetOutput()); >> > statisticsLabelMapFilter->SetInput2(image3Dred); >> > statisticsLabelMapFilter->InPlaceOn(); >> > statisticsLabelMapFilter->Update(); >> > >> > unsigned int bacteriacount = >> > statisticsLabelMapFilter->GetOutput()->GetNumberOfLabelObjects(); >> > for(unsigned int i = 0; i < >> > statisticsLabelMapFilter->GetOutput()->GetNumberOfLabelObjects(); i++) >> > { >> > StatisticsLabelMapFilterType::OutputImageType::LabelObjectType* >> > labelObjectMe = >> > statisticsLabelMapFilter->GetOutput()->GetNthLabelObject(i); >> > double mean = labelObjectMe->GetMean(); >> > fileout << mean << "\t"; >> > std::cout << "Mean value of object with label " << >> > static_cast(labelObjectMe->GetLabel()) << " in lysosomechannel: " >> > << mean << std::endl; >> > } >> > fileout << "\n"; >> > fileout.close(); >> > std::cout << "Total bacteria counted (in statisticsLabelMapFilter): " >> > << bacteriacount << std::endl; >> > std::cout << std::endl; >> > >> > >> > Do I really get the mean value from within my objects (bacteria) but >> > calculating it using the values in image3Dred because I did: >> > statisticsLabelMapFilter->SetInput2(image3Dred); >> > and >> > double mean = labelObjectMe->GetMean(); >> > >> > Best regards >> > Michael Meuli >> > _______________________________________________ >> > Community mailing list >> > Community at itk.org >> > http://public.kitware.com/mailman/listinfo/community >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community > > > > > -- > Regards, > Girish From jhlegarreta at vicomtech.org Thu Dec 11 11:19:25 2014 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Thu, 11 Dec 2014 17:19:25 +0100 Subject: [ITK] ITK 4.6.1 linking problems in OS X Message-ID: Hi there, we are experiencing some issues when liking a project of our own to ITK 4.6.1 in OS X using XCode. The Xcode output says: *ld: library not found for -litkdouble-conversion* However, the library is actually in the lib/{Debug/Release} folder in the ITK binaries, together with the rest of the ITK libraries compiled. I would dare to say that XCode is unable to find any of the ITK libraries; that is, the message mentions the double-conversion library because it may be the first library it looks for. Any guess? Thanks, JON HAITZ -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Dec 11 12:23:41 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 11 Dec 2014 12:23:41 -0500 Subject: [ITK] ITK 4.6.1 linking problems in OS X In-Reply-To: References: Message-ID: <79128020-43E2-430B-BEA5-2B6EAFE3528D@mail.nih.gov> Hello, I am going to assume you are using CMake's XCode generator, and you are finding and using ITK from the build tree in CMake Unfortunately, the XCode environment has some limitation with the command line length causing paths to be truncated when a large number of include and link library paths are listed. I presume this may be the cause of the error you are seeing. Three possible solutions: 1) install ITK into a directory and use it from there. This will significantly reduce the number of include paths and option needed. 2) Use ITK in a modular fashion and specify only the ITK components needed in the CMake FIND_PACKAGE command. 3) Switch to another generator, such as unix make Doing 3 is probably the quickest to test if this really is a caused by the XCode generator limitations. Brad On Dec 11, 2014, at 11:19 AM, Jon Haitz Legarreta wrote: > Hi there, > we are experiencing some issues when liking a project of our own to ITK 4.6.1 in OS X using XCode. > > The Xcode output says: > ld: library not found for -litkdouble-conversion > > However, the library is actually in the lib/{Debug/Release} folder in the ITK binaries, together with the rest of the ITK libraries compiled. > > I would dare to say that XCode is unable to find any of the ITK libraries; that is, the message mentions the double-conversion library because it may be the first library it looks for. > > Any guess? > > > Thanks, > > JON HAITZ > > > > > > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Dec 11 12:32:49 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 11 Dec 2014 12:32:49 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro Message-ID: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> I am seeing these new warnings on the dashboard from Mac10.8-clang-dbg-x86_64-static-torture: In file included from /Users/builder/external/ITK/Modules/Core/Common/src/itkHexahedronCellTopology.cxx:18: In file included from /Users/builder/external/ITK/Modules/Core/Common/include/itkHexahedronCellTopology.h:21: /Users/builder/external/ITK/Modules/Core/Common/include/itkMacro.h:39:9: warning: reserved identifier is used as macro name [-Wreserved-id-macro] #define __itkMacro_h Should this warning be disabled or do we need to invoke some sed wizardry to try to fix this? Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From sean at rogue-research.com Thu Dec 11 12:48:35 2014 From: sean at rogue-research.com (Sean McBride) Date: Thu, 11 Dec 2014 12:48:35 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> Message-ID: <20141211174835.1382825240@mail.rogue-research.com> On Thu, 11 Dec 2014 12:32:49 -0500, Bradley Lowekamp said: >I am seeing these new warnings on the dashboard from Mac10.8-clang-dbg- >x86_64-static-torture: > >In file included from /Users/builder/external/ITK/Modules/Core/Common/ >src/itkHexahedronCellTopology.cxx:18: >In file included from /Users/builder/external/ITK/Modules/Core/Common/ >include/itkHexahedronCellTopology.h:21: >/Users/builder/external/ITK/Modules/Core/Common/include/itkMacro.h:39:9: >warning: reserved identifier is used as macro name [-Wreserved-id-macro] >#define __itkMacro_h > >Should this warning be disabled or do we need to invoke some sed >wizardry to try to fix this? Brad, I was just writing about this, but you beat me to it. :) The new warnings are because I updated clang on that machine to a newer svn trunk version (it's my bleeding edge machine). C & C++ in fact reserve double underscores: I'm turning the warning off to keep the dashboards clean, but ideally we should fix the warnings. KWSys, CMake, VTK, and ITK all seem to have the same naming scheme for header guard #defines, namely "___h", ex: __itkMacro_h, __vtkFooBar_h, etc. Fixing this naming scheme would fix about 80% of the warnings. I volunteer to make the changes, but we should agree on a scheme. Maybe just drop the __ prefix would be enough. Could throw another _ at the end too perhaps. Thoughts? Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From brad.king at kitware.com Thu Dec 11 13:00:10 2014 From: brad.king at kitware.com (Brad King) Date: Thu, 11 Dec 2014 13:00:10 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <20141211174835.1382825240@mail.rogue-research.com> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211174835.1382825240@mail.rogue-research.com> Message-ID: <5489DBAA.8010408@kitware.com> On 12/11/2014 12:48 PM, Sean McBride wrote: > C & C++ in fact reserve double underscores: Yes. > KWSys, CMake KWSys and CMake do not use "__" guards AFAIK. It looks like there might be a couple in CMake by accident. > VTK, and ITK all seem to have the same naming scheme > for header guard #defines, namely "___h", > ex: __itkMacro_h, __vtkFooBar_h, etc. Yes, and this does step on the namespace reserved for the C and C++ implementations. > I volunteer to make the changes, but we should agree on a scheme. Thanks! > Maybe just drop the __ prefix would be enough. Yes. > Could throw another _ at the end too perhaps. They all end in "_h" or something already, so that should not be needed. Thanks, -Brad K _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From hans-johnson at uiowa.edu Thu Dec 11 13:48:15 2014 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Thu, 11 Dec 2014 18:48:15 +0000 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <5489DBAA.8010408@kitware.com> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211174835.1382825240@mail.rogue-research.com> <5489DBAA.8010408@kitware.com> Message-ID: Sean, Thanks! I am very appreciative of you taking on this tedious task. Hans -----Original Message----- From: Brad King Date: Thursday, December 11, 2014 at 12:00 PM To: Sean McBride Cc: Insight Developers Subject: Re: [ITK-dev] New clang warnings: reserved-id-macro On 12/11/2014 12:48 PM, Sean McBride wrote: > C & C++ in fact reserve double underscores: Yes. > KWSys, CMake KWSys and CMake do not use "__" guards AFAIK. It looks like there might be a couple in CMake by accident. > VTK, and ITK all seem to have the same naming scheme > for header guard #defines, namely "___h", > ex: __itkMacro_h, __vtkFooBar_h, etc. Yes, and this does step on the namespace reserved for the C and C++ implementations. > I volunteer to make the changes, but we should agree on a scheme. Thanks! > Maybe just drop the __ prefix would be enough. Yes. > Could throw another _ at the end too perhaps. They all end in "_h" or something already, so that should not be needed. Thanks, -Brad K _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From sean at rogue-research.com Thu Dec 11 15:15:10 2014 From: sean at rogue-research.com (Sean McBride) Date: Thu, 11 Dec 2014 15:15:10 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> Message-ID: <20141211201510.1661524377@mail.rogue-research.com> On Thu, 11 Dec 2014 12:32:49 -0500, Bradley Lowekamp said: >warning: reserved identifier is used as macro name [-Wreserved-id-macro] >#define __itkMacro_h So I did some find/replace, but when I try to commit, I get: --------------------------- Examples/IO/XML/itkParticleSwarmOptimizerDOMReader.h:29: error: itkParticleSwarmOptimizerDOMReader_h v.s. __itkParticleSwarmOptimizerDOMReader_h pre-commit hook failure ----------------------- KWStyle check failed. Line numbers in the errors shown refer to the file: Examples/IO/XML/itkParticleSwarmOptimizerDOMReader.h.kws --------------------------- Is there a style check that's checking for a header guard format?! Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Dec 11 15:19:20 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 11 Dec 2014 15:19:20 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <20141211201510.1661524377@mail.rogue-research.com> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> Message-ID: Hi Sean, Thanks for working on this! The KWStyle configuration can be updated here: http://itk.org/gitweb?p=ITK.git;a=blob;f=Utilities/KWStyle/ITK.kws.xml;h=34569cf363cf65a2f7936d564d09793dca95006f;hb=HEAD#l14 Thanks, Matt On Thu, Dec 11, 2014 at 3:15 PM, Sean McBride wrote: > On Thu, 11 Dec 2014 12:32:49 -0500, Bradley Lowekamp said: > >>warning: reserved identifier is used as macro name [-Wreserved-id-macro] >>#define __itkMacro_h > > So I did some find/replace, but when I try to commit, I get: > > --------------------------- > Examples/IO/XML/itkParticleSwarmOptimizerDOMReader.h:29: error: itkParticleSwarmOptimizerDOMReader_h v.s. __itkParticleSwarmOptimizerDOMReader_h > pre-commit hook failure > ----------------------- > > KWStyle check failed. > > Line numbers in the errors shown refer to the file: > Examples/IO/XML/itkParticleSwarmOptimizerDOMReader.h.kws > --------------------------- > > Is there a style check that's checking for a header guard format?! > > Cheers, > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Thu Dec 11 15:20:31 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 11 Dec 2014 15:20:31 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <20141211201510.1661524377@mail.rogue-research.com> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> Message-ID: <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> I Think so: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Utilities/KWStyle/ITK.kws.xml#L14 Having the header guarder not begin with an '_' seems wrong to me. What about __? Brad On Dec 11, 2014, at 3:15 PM, Sean McBride wrote: > On Thu, 11 Dec 2014 12:32:49 -0500, Bradley Lowekamp said: > >> warning: reserved identifier is used as macro name [-Wreserved-id-macro] >> #define __itkMacro_h > > So I did some find/replace, but when I try to commit, I get: > > --------------------------- > Examples/IO/XML/itkParticleSwarmOptimizerDOMReader.h:29: error: itkParticleSwarmOptimizerDOMReader_h v.s. __itkParticleSwarmOptimizerDOMReader_h > pre-commit hook failure > ----------------------- > > KWStyle check failed. > > Line numbers in the errors shown refer to the file: > Examples/IO/XML/itkParticleSwarmOptimizerDOMReader.h.kws > --------------------------- > > Is there a style check that's checking for a header guard format?! > > Cheers, > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From sean at rogue-research.com Thu Dec 11 15:30:14 2014 From: sean at rogue-research.com (Sean McBride) Date: Thu, 11 Dec 2014 15:30:14 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> Message-ID: <20141211203014.425400305@mail.rogue-research.com> On Thu, 11 Dec 2014 15:20:31 -0500, Bradley Lowekamp said: >Having the header guarder not begin with an '_' seems wrong to me. > >What about __? That works too as long as starts lowercase, as starting with underscore+uppercase is also reserved. So "_itkFooBar_h" would be ok, but not "_ITKFOOBAR_H" for example. Adding another underscore between seems gratuitous though. This change will touch hundreds and hundreds of files, so you guys decide on the scheme, then I'll do it. :) Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Fri Dec 12 09:22:06 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 12 Dec 2014 09:22:06 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <20141211203014.425400305@mail.rogue-research.com> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> <20141211203014.425400305@mail.rogue-research.com> Message-ID: <89CF8EC3-F5DF-478E-A140-C375C8A7F5AB@mail.nih.gov> And all the remote modules should be updated as well... On Dec 11, 2014, at 3:30 PM, Sean McBride wrote: > On Thu, 11 Dec 2014 15:20:31 -0500, Bradley Lowekamp said: > >> Having the header guarder not begin with an '_' seems wrong to me. >> >> What about __? > > That works too as long as starts lowercase, as starting with underscore+uppercase is also reserved. So "_itkFooBar_h" would be ok, but not "_ITKFOOBAR_H" for example. > > Adding another underscore between seems gratuitous though. > > This change will touch hundreds and hundreds of files, so you guys decide on the scheme, then I'll do it. :) > > Cheers, > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Fri Dec 12 10:34:05 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 12 Dec 2014 10:34:05 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <89CF8EC3-F5DF-478E-A140-C375C8A7F5AB@mail.nih.gov> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> <20141211203014.425400305@mail.rogue-research.com> <89CF8EC3-F5DF-478E-A140-C375C8A7F5AB@mail.nih.gov> Message-ID: Personally, I don't have any strong preference. How about itkFooBar_h , since it seems to be the most compatible. Thanks, Matt On Fri, Dec 12, 2014 at 9:22 AM, Bradley Lowekamp wrote: > And all the remote modules should be updated as well... > > > On Dec 11, 2014, at 3:30 PM, Sean McBride wrote: > >> On Thu, 11 Dec 2014 15:20:31 -0500, Bradley Lowekamp said: >> >>> Having the header guarder not begin with an '_' seems wrong to me. >>> >>> What about __? >> >> That works too as long as starts lowercase, as starting with underscore+uppercase is also reserved. So "_itkFooBar_h" would be ok, but not "_ITKFOOBAR_H" for example. >> >> Adding another underscore between seems gratuitous though. >> >> This change will touch hundreds and hundreds of files, so you guys decide on the scheme, then I'll do it. :) >> >> Cheers, >> >> -- >> ____________________________________________________________ >> Sean McBride, B. Eng sean at rogue-research.com >> Rogue Research www.rogue-research.com >> Mac Software Developer Montr?al, Qu?bec, Canada >> >> > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Fri Dec 12 12:11:13 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 12 Dec 2014 12:11:13 -0500 Subject: [ITK] [ITK-dev] Compositions in ScaleVersor3D and ScaleSkewVersor3D Transforms Message-ID: <93A27D3A-D855-4A62-9E04-50D63041765B@mail.nih.gov> Hello, This seems very wrong to me... I was looking into the inverse of the classes. And I saw how the matrix was composed from the scale and versor components[1] newMatrix[0][0] = m_Scale[0] - 2.0 * ( yy + zz ); newMatrix[1][1] = m_Scale[1] - 2.0 * ( xx + zz ); newMatrix[2][2] = m_Scale[2] - 2.0 * ( xx + yy ); newMatrix[0][1] = 2.0 * ( xy - zw ) + ( m_Skew[0] ); newMatrix[0][2] = 2.0 * ( xz + yw ) + ( m_Skew[1] ); newMatrix[1][0] = 2.0 * ( xy + zw ) + ( m_Skew[2] ); newMatrix[1][2] = 2.0 * ( yz - xw ) + ( m_Skew[3] ); newMatrix[2][0] = 2.0 * ( xz - yw ) + ( m_Skew[4] ); newMatrix[2][1] = 2.0 * ( yz + xw ) + ( m_Skew[5] ); Similarly both classes just add the scale/skew component and don't do correct matrix composition. Let R be the versor, S scale, and K skew matrices, and p be a point. Currently we have: (R+S+K)*p = R*p+S*p+K*p Where I expected these classes would be implementing: R*S*K*p which is a traditional composition of transform matrices. Anyone know where the current math came from? Or what it's really doing? Is this something that we should fix/improve/evaluate? Or just document what's actually happening? Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Transform/include/itkScaleVersor3DTransform.hxx#L219-L227 _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matimontg at gmail.com Sat Dec 13 10:09:37 2014 From: matimontg at gmail.com (Matias Montroull) Date: Sat, 13 Dec 2014 12:09:37 -0300 Subject: [ITK] [ITK-users] Fusion | Need the resulting image, not the fused image Message-ID: Hi, I've ran the example ImageRegistration5 to do RM-CT fusion and works pretty well for 2D images, now, the resulting image is a fused image. How can I obtain the moving image in the position of the fixed image? I'm trying to overlap, not fuse. Thanks, Matias. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sun Dec 14 22:54:45 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 14 Dec 2014 22:54:45 -0500 Subject: [ITK] [ITK-users] Fusion | Need the resulting image, not the fused image In-Reply-To: References: Message-ID: Hi Matias, The moving image in the position of the fixed image is the output of the ResampleImageFilter in ImageRegistration5. HTH, Matt On Sat, Dec 13, 2014 at 10:09 AM, Matias Montroull wrote: > Hi, > > I've ran the example ImageRegistration5 to do RM-CT fusion and works pretty > well for 2D images, now, the resulting image is a fused image. How can I > obtain the moving image in the position of the fixed image? > I'm trying to overlap, not fuse. > Thanks, > Matias. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jhlegarreta at vicomtech.org Mon Dec 15 05:17:31 2014 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Mon, 15 Dec 2014 11:17:31 +0100 Subject: [ITK] ITK 4.6.1 linking problems in OS X In-Reply-To: <79128020-43E2-430B-BEA5-2B6EAFE3528D@mail.nih.gov> References: <79128020-43E2-430B-BEA5-2B6EAFE3528D@mail.nih.gov> Message-ID: Dear Brad, thanks for your quick reply. Your assumptions were right :-) Thanks for the explanations. We tried using shorter paths for all third-party libraries (including ITK) and ours, but did not solve the issue. We then tried 3). And that solved the problem indeed. So thanks again Brad. Kind regards, JON HAITZ On 11 December 2014 at 18:23, Bradley Lowekamp wrote: > > Hello, > > I am going to assume you are using CMake's XCode generator, and you are > finding and using ITK from the build tree in CMake > > Unfortunately, the XCode environment has some limitation with the command > line length causing paths to be truncated when a large number of include > and link library paths are listed. I presume this may be the cause of the > error you are seeing. > > Three possible solutions: > > 1) install ITK into a directory and use it from there. This will > significantly reduce the number of include paths and option needed. > 2) Use ITK in a modular fashion and specify only the ITK components needed > in the CMake FIND_PACKAGE command. > 3) Switch to another generator, such as unix make > > Doing 3 is probably the quickest to test if this really is a caused by the > XCode generator limitations. > > Brad > > On Dec 11, 2014, at 11:19 AM, Jon Haitz Legarreta < > jhlegarreta at vicomtech.org> wrote: > > Hi there, > we are experiencing some issues when liking a project of our own to ITK > 4.6.1 in OS X using XCode. > > The Xcode output says: > *ld: library not found for -litkdouble-conversion* > > However, the library is actually in the lib/{Debug/Release} folder in the > ITK binaries, together with the rest of the ITK libraries compiled. > > I would dare to say that XCode is unable to find any of the ITK libraries; > that is, the message mentions the double-conversion library because it may > be the first library it looks for. > > Any guess? > > > Thanks, > > JON HAITZ > > > > > > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Mon Dec 15 07:14:24 2014 From: matimontg at gmail.com (Matias Montroull) Date: Mon, 15 Dec 2014 09:14:24 -0300 Subject: [ITK] [ITK-users] Fusion | Need the resulting image, not the fused image In-Reply-To: References: Message-ID: Thanks Matt, I'll give it a try On Mon, Dec 15, 2014 at 12:54 AM, Matt McCormick wrote: > > Hi Matias, > > The moving image in the position of the fixed image is the output of > the ResampleImageFilter in ImageRegistration5. > > HTH, > Matt > > On Sat, Dec 13, 2014 at 10:09 AM, Matias Montroull > wrote: > > Hi, > > > > I've ran the example ImageRegistration5 to do RM-CT fusion and works > pretty > > well for 2D images, now, the resulting image is a fused image. How can I > > obtain the moving image in the position of the fixed image? > > I'm trying to overlap, not fuse. > > Thanks, > > Matias. > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Mon Dec 15 09:08:43 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 15 Dec 2014 09:08:43 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> <20141211203014.425400305@mail.rogue-research.com> <89CF8EC3-F5DF-478E-A140-C375C8A7F5AB@mail.nih.gov> Message-ID: <1FC3831A-8A7A-4677-9461-E822B83B5C99@mail.nih.gov> Sean, Thanks for taking this on. I believe at the TCON on friday we agreed with Matt's suggestion: itkFooBar_h I hope that there will be a fairly robust command line to do this work. Please include it in the commit messages so that it can easily be done again later for others modules. Thanks, Brad On Dec 12, 2014, at 10:34 AM, Matt McCormick wrote: > Personally, I don't have any strong preference. > > How about > > itkFooBar_h > > , since it seems to be the most compatible. > > Thanks, > Matt > > > On Fri, Dec 12, 2014 at 9:22 AM, Bradley Lowekamp > wrote: >> And all the remote modules should be updated as well... >> >> >> On Dec 11, 2014, at 3:30 PM, Sean McBride wrote: >> >>> On Thu, 11 Dec 2014 15:20:31 -0500, Bradley Lowekamp said: >>> >>>> Having the header guarder not begin with an '_' seems wrong to me. >>>> >>>> What about __? >>> >>> That works too as long as starts lowercase, as starting with underscore+uppercase is also reserved. So "_itkFooBar_h" would be ok, but not "_ITKFOOBAR_H" for example. >>> >>> Adding another underscore between seems gratuitous though. >>> >>> This change will touch hundreds and hundreds of files, so you guys decide on the scheme, then I'll do it. :) >>> >>> Cheers, >>> >>> -- >>> ____________________________________________________________ >>> Sean McBride, B. Eng sean at rogue-research.com >>> Rogue Research www.rogue-research.com >>> Mac Software Developer Montr?al, Qu?bec, Canada >>> >>> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From sean at rogue-research.com Mon Dec 15 16:47:20 2014 From: sean at rogue-research.com (Sean McBride) Date: Mon, 15 Dec 2014 16:47:20 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <1FC3831A-8A7A-4677-9461-E822B83B5C99@mail.nih.gov> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> <20141211203014.425400305@mail.rogue-research.com> <89CF8EC3-F5DF-478E-A140-C375C8A7F5AB@mail.nih.gov> <1FC3831A-8A7A-4677-9461-E822B83B5C99@mail.nih.gov> Message-ID: <20141215214720.1396295766@mail.rogue-research.com> On Mon, 15 Dec 2014 09:08:43 -0500, Bradley Lowekamp said: >Thanks for taking this on. > >I believe at the TCON on friday we agreed with Matt's suggestion: > >itkFooBar_h > >I hope that there will be a fairly robust command line to do this work. >Please include it in the commit messages so that it can easily be done >again later for others modules. OK, my first patch is here, hopefully it won't explode gerrit: Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Dec 16 02:42:34 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Dec 2014 02:42:34 -0500 Subject: [ITK] ITK 4.7 Release Candidate 2 has been tagged! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.7.0 release candidate 2 has been tagged and is available for testing! Please test the release candidate in the coming days for an imminent release. To obtain the source code, git clone http://itk.org/ITK.git cd ITK git checkout -q --detach v4.7rc02 For more details, please see the Git documentation [1]. A few highlights for this release: all ITK examples from the Software Guide, Wiki Examples, and SphinxExamples are new indexed and crossed linked in Doxygen . So now when you go to your favorite filter or other object, say the ResampleImageFilter , there is a large selection of examples in the examples sections. This should make it much easier to fine sample code on how to use an ITK class! TIFF IO has undergone a significant cleanup and speed-up, and now TIFF tags are read into the MetaDataDictionary. Three new Remote Modules are available, for gradient computation, DICOM IO, and QuadEdgeMesh filtering. Python wrapping, CMake configuration, and registration continue to improve. A new, experimental thread pool is available -- to enable set the ITK_USE_THREADPOOL or call itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review. Please help identify issues submitting an Experimental build to the dashboard [2] with: ctest -M Experimental -T Configure -T Build -T Test -T Submit and notifying the mailing list. Testing your own applications against the RC is also appreciated. Congratulations and well done to the 29 contributors to this release. We would especially like to recognize the new contributors, Gert Wollny, Girish Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan Andruejol, and Ismael Belghiti. The final release is scheduled for December 18th. [1] http://www.itk.org/Wiki/ITK/Git [2] http://itk.org/Insight/Doxygen/html/examples.html [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html [2] http://open.cdash.org/index.php?project=Insight New Features ------------------ * Documentation Improvements - Update Software Guide registration examples to ITKv4 framework - Wiki and Sphinx examples are indexed in Doxygen - Clean Software Guide dashboard build * Filtering Improvements - New Laplacian deformation filter?s for QuadEdgeMesh?s - IJ article: http://hdl.handle.net/10380/3410 - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations - Faster recursive Gaussian on VectorImage * ImageIO improvements - PNG sCAL unit support - TIFF IO performance greatly improved - TIFF tags read into Image MetaDataDictionary - MetaIO updated - Better support for system GDCM * Infrastructure improvements - New method to erase a MetaDataDictionary entry - New global method to set physical space tolerance - New, experimental thread pool support - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue() and ::OneValue() - VTK bridge modules only request required VTK modules * New Remote Modules - Higher Order Accurate Gradient - http://hdl.handle.net/10380/3231 - IO Transform DCMTK - http://hdl.handle.net/10380/3468 - Subdivision Quad Edge Mesh Filters - http://hdl.handle.net/10380/3307 * Registration improvements - LandmarkBasedTransformInitializer supports BSplineTransform - Transverse inverse consistency increased - Automatic initialization of the transform center for multi-stage registrations - Sparse point B-spline field estimate - Mutual information faster, lower memory usage * Wrapping improvements - Wrapping now builds without type warnings - pygccxml bumped to 1.6.2 - Latest GCCXML - CMake wrapping infrastructure cleanup - Build with Ninja CMake generator - New GetTypes() and GetTypesAsList() methods - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake * Many style improvements -- ITK gets more stylish with every release! * Improved code coverage -- we are over 85%! * *Lots* of important bug fixes * And much more! See details in the log below. List of changes since v4.7-rc01 -------------------------------------- Ali Ghayoor (1): DOC: Revise the registration examples of ITKSoftwareGuide Arnaud Gelas (3): ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh COMP: fix warnings on dashboard for Subdivision remote module Bradley Lowekamp (5): BUG: Fix segfault when setting displacement field as null BUG: Don't enable SSE rounding with OSX and gccxml BUG: Add portable access to Tiff field name BUG: Fix conversion compilation error BUG: Rename remote module FDFImageIO -> IOFDF Christopher Mullins (6): STYLE: Fix line length in OpenJPEG license for 80 character. DOC: Finish the ImageLinearIteratorWithIndex example. DOC: Text and picture problems, book2 BUG: Fix text in margin issues DOC: Edits for the beginning of chapter 5, Statistics DOC: Fix empty code block. Cory Quammen (1): COMP: Avoid including VTK_USE_FILE within ITK Kent Williams (1): ENH: Add test to exercise issue with Transform::GetInverse Matthew McCormick (7): BUG: Register AzimuthElevationToCartesianTransform to factories. DOC: Update texture feature class references. BUG: Fix texture feature correlation computation for constant image. STYLE: Put ImageToImageFilterCommon in its own file. BUG: Wrap ImageToImageFilterCommon. STYLE: Put ImageSourceCommon in its own file. COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. Michka Popoff (1): ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter wrappings Ziv Yaniv (1): COMP: fixed warnings from gcc4.1.2, made implicit casts explicit List of changes since v4.6.0 -------------------------------------- Alexander Schmidt-Richberg (1): ENH: Updated Remote Module VariationalRegistration to new git tag Ali Ghayoor (10): ENH: Make ITKv4 compatible with ITKSoftwareGuide ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 ENH: Convert three ImageRegistration Examples to ITKv4 ENH: Add multi-Res and multistage registration Examples to ITKv4 ENH: Convert DeformableReg examples to ITKv4 reg framework BUG: Expand a test to reflect multi-metric registration bug BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 ENH: Add direct initialization to SyN registration ENH: Direct initialization of SyN by restoring the state ENH: LandmarkBasedTransformInitializer supports BSplineTransformType Arnaud Gelas (15): COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization ENH: Importing Laplacian Deformation for QuadEdgeMesh DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter BUG: fix gdcm version in GDCMImageIO. COMP: missing cast when calling gdcm::DataElement::SetByteValue COMP: missing cast when calling gdcm::DataElement::SetByteValue ENH: increase LaplacianDeformation code coverage STYLE: use typedef rather than inheritance BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false BUG: split include directories into appropriate cmake variables HDF5 BUG: missing gdcm libraries when using system GDCM DOC: fix doxygen documentaiton for itk::LaplacianDeformationQuadEdgeMeshFilter ENH: Add one method to erase a tag into MetaDataDictionary Bill Lorensen (5): ENH: Specify required VTK modules COMP: Wiki examples require additional vtk modules ENH: Modify WikiExamples remote config COMP: Bad test signature COMP: Update tag for wiki examples Brad King (6): COMP: Fix vxl_config_macros usage of CMake check macros ENH: Use if(DEFINED) to simplify conditions COMP: Fix vxl_config_macros checks broken by refactoring COMP: Fix one more vxl_config_macros check broken by refactoring BUG: Fix itk_module_config for repeated calls BUG: Fix itk_module_config for repeated calls Bradley Lowekamp (52): ENH: Adding License file from upstream MetaIO ENH: Adding script to update MetaIO from upstream ENH: Remove ITK MetaIO to prepare for upstream import PERF: Remove dynamically allocated temporary in evaluate method COMP: Fix variable type for Set/Get macros BUG: Implement ITK Style Singleton design pattern ENH: Add no throw exception specification for UnRegister methods COMP: Must specify order as "noexcept override" BUG: Add GetInverse for IdentityTransform ENH: Adding SetIdentity method to base DisplacementField class BUG: Remove unused redefinition of NULL BUG: Don't print to std::cout in PrintSelf ENH: Prefer the PrintSelfObjectMacro for printing nested objects BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit COMP: Fix signed to unsigned int comparison BUG: Fix overflows computing size of read tiff image ENH: Extract TiffReaderInternal to separate file ENH: Refactor ReadTwoSamplePerPixelImage into template function ENH: Refactor GenericReadImage into template function BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) ENH: Refactor method to convert RGBA image to output buffer ENH: Refactor duplicated code to read a page BUG: Fix right oriented tiff images BUG: Remove dead separated plannar code, add test STYLE: Fix minor kwstyle defects in test and test results BUG: Use array delete operator for array new allocations ENH: add arbitrary TIFF TAGs to meta-data dictionary ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage BUG: Address Coverity warning about null pointer dereferences ENH: Remove support for TIFF tile as 3D and dead code ENH: RGBA read images should stay unchanged. BUG: Override method to MakeOutput by name ENH: Refactor per pixel conversion function to per scan-line method PERF: Refactor color table lookup BUG: Adding missing parentheses around boolean expression ENH: adding TIFFImageIO test for RGB palette images PERF: Improve recursive Gaussian perfromance with VectorImages ENH: Query libtiff to determine compression support BUG: Support TIFF tiled image with TIFFReadRGBAImage BUG: Use SizeValueType for length of scanline PERF: Store causal results directly in output buffers COMP: Add explicit conversion to const char COMP: Explicitly add override to GetNameOfClass method COMP: Address internal segmentation fault with Intel compiler ENH: Adding method to set global physical space tolerance COMP: Explicitly add override to GetNameOfClass method BUG: Add new TypeMacro for non-overloaded classes BUG: Fix obscure race condition on access thread pool initialization BUG: Updating FDFImageIO remote module Christopher Mullins (15): COMP: Allows latex to compile for ITKSoftwareGuide COMP: Allows latex to compile for ITKSoftwareGuide COMP: Wrap MeshBase templates COMP: Wrap MeshBase templates COMP: Fix warning in BlockMatchingImageFilter STYLE: Line lengths in examples should be no longer than 80 chars. COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. COMP: Fix LaTeX warnings. STYLE: Fix formatting/punctuation errors. STYLE: Formatting and punctuation fixes. DOC: Edits for Book 2 Chapter 1 documentation in the Examples. DOC: Edits for book 2 chapter 2. DOC: More chapter 2 edits DOC: Book 2 Chapter 3 edits (part 1) DOC: book 2 chapter 4 Segmentation edits Danny Perry (2): BUG: adding test for vnl_sparse_matrix::mult() BUG: size of q buffer should actually be (this->rows())*pcols. David T. Chen (1): DOC: Fixed HistogramThresholdImageFitler Dirk Padfield (1): BUG: Corrected processing of last sigma GCC-XML Upstream (1): ENH: pygccxml v1.6.2 (reduced) Gert Wollny (1): COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) Girish Mallya (1): BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. Hans Johnson (24): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components PERF: Remove large foot print of PDF derivatives. PERF: Revert Remove large foot print of PDF derivatives. STYLE: Test against almost equal for floating point values STYLE: Non-exact floating point testing PERF: Distribute initialization per thread buffers ENH: Remove unnecessary mutable qualifier. STYLE: Remove comment with no meaning. ENH: Moved accumlator logic to main MI class ENH: Allow staggering of accumulations per thread. PERF: Zero reset thread buffers during finalize BUG: Syntax error in comment PERF: Add non-blocking mutex locking. ENH: Use TryLock minimize thread stalls BUG: ThreadedIndexedContainerPartitioner is inclusive STYLE: Remove include_regular_expression from Examples BUG: Demonstrate Inv(Inv(T)) != T BUG: Ensure Inv(Inv(T)) == T for transforms COMP: Valgrind detects uninitialized memory read COMP: Missing required base class API component ENH: Expand interface for selecting threadpool Ismael Belghiti (1): DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter Jim Miller (1): STYLE: Removing what appears to be a temporary file Johan Andruejol (1): ENH: Fix normalization for null vectors and return the norm Jon Haitz Legarreta (1): ENH: New test for itkLabelShapeOpeningImageFilter Kent Williams (9): COMP: use find_package(VTK COMPONENTS) to specify just needed VTK Components BUG: ImageSources/test/CMakeLists.txt incorrect library var reference COMP: Fix coverity defects related to RegistrationV4 examples COMP: silence warning of vnl_vector_fixed_ref::assert_size COMP: Fix various Coverity warnings COMP: Fix a typo in an error message print statement. COMP: itk::Command-derived class used pointless dynamic_cast. PERF: Don't recompute InternalInverse repeatedly COMP: Correct orientation/spacing for Philips MultiFrame Mark Hiner (2): ENH: Update SCIFIO remote module hash BUG: Fix duplicate variables in Windows Matthew McCormick (105): DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. ENH: Move FFTComplexToComplexImageFilter out of Review. ENH: Add VnlComplexToComplexFFTImageFilter. BUG: Use fixed seed for Vnl FFT tests for repeatibility. ENH: Bump CMakeLists.txt version to 4.7.0. BUG: ArchiveTestingData.py future imports must occur at the beginning. BUG: Do not run vnl_test_na with broken libc++. DOC: Remove Image2.cxx reference from Book 2. DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. DOC: Remove references to Book 1 sections from Book 2. DOC: Make BinaryThresholdImageFilter not floating. DOC: Fix Software Guide figure caption for FlipImageFilter. DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. DOC: ImageRandomConstIteratorWithIndex table reference. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter. BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. STYLE: Fix style in VoronoiDiagram2D. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Bump GCCXML to 2014-08-06. BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. BUG: Fix Win MultiThreader check for successful process creation. BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. DOC: itk::statistics -> itk::Statistics. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. COMP: Improve const correctness of GradientRecursiveGaussianImageFilter. BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. COMP: ThreadJob NULL not defined. BUG: Fix alpha assignment for RGBA TIFF. COMP: Remove unused typedefs in LevelSetsv4Visualization. COMP: Remove unused typedef's in VtkGlue. ENH: Mark BSplineWarping2Test as RUNS_LONG. BUG: Fix Nifti IO read with large images. COMP: Remove call for non-existent variable in Nifti debugging. BUG: Close the file on Read and Write in HDF5TransformIO. BUG: Remove InsightLegacy test code from TransformHDF5Test. ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. STYLE: Use SeriesUIDContainerType and FileNamesContainerType ENH: Allow specification of orthogonality tolerance in rigid transforms. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Do not use _stat64 with MinGW-32. BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. DOC: itk::statistics -> itk::Statistics. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. COMP: Address LaplacianDeformation Doxygen warnings. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Fix missing prefix in ITKv3ImageRegistration20Test. BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform COMP: Do not wrap the FixedArray of Image SmartPointer's. COMP: Add missing wrapping for TransformIOBaseTemplate. COMP: Mark DeformableRegistration6Test as RUNS_LONG. STYLE: Improve style in BinaryImageToLabelMapFilter. BUG: Fix BinaryImageToLabelMapFilter on 1D image. ENH: Improve precision of the joint PDF sum BUG: Fix BinShrinkImageFilter for different input/output image types. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. BUG: Use -py3 when building wrapping for Python 3. COMP: Add missing wrapping for TransformIOBaseTemplate. DOC: Improve ImageRegistration4 grammar. ENH: Add IOTransformDCMTK Remote module. BUG: gdcm::StringFilter recognizes backslash delimiter. DOC: Add migration guide for GDCM Rescale slope intercept apply on write. COMP: Remove unused typedef's in GPU code. STYLE: Improve style of HoughTransform2DLinesImageFilter example. COMP: Use ConceptChecking for IterativeInverse dimension check. COMP: Wrap TransformIOBaseTemplate for const SmartPointer. COMP: Add warning exceptions for third party pcre, swig, gccxml. ENH: Bump ITK version to 4.6.1. BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. BUG: Remove GaussianImageSource members shadowing GenerateImageSource. STYLE: Style fixes to ITKImageSources module. BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType. BUG: Do not perform itk_download_attempt_check when not building ITK. DOC: Update GDCMImageIO rescale slope intercept doc. BUG: Only register requestion IO COMPONENT modules. BUG: Fix wrapping .i, .idx CMake dependencies. COMP: Add VTK Python module when wrapping ITKVtkGlue. STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. COMP: Add missing VTK module dependency for LevelSetsv4Visualization. BUG: By default, do not create any fixed parameters. STYLE: Remove trivial method comments in itkTransform.hxx. BUG: PolylineMask Filter's GenerateData is protected / virtual. ENH: Add HigherOrderAccurateGradient Module. BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal. COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. STYLE: Style fixes for Transform classes. DOC: Increase Doxygen LOOKUP_CACHE_SIZE. BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. DOC: Index Wiki examples with Doxygen. COMP: Bump SphinxExamples remote module. DOC: Index Sphinx examples in Doxygen. COMP: Remove old java examples. COMP: Remove duplicate DiffusionTensor3DReconstruction example reference. COMP: Address GradientAnisotropicDiffusionImageFilter example settings. COMP: Bump Sphinx Examples remote. COMP: Bump WikiExamples remote. MetaIO Maintainers (1): MetaIO (reduced) Michka Popoff (40): ENH: Fixes for python 3 support BUG: Add VTK_VERSION for older VTK versions BUG: Improve SWIG version check COMP: Add wrapping for ThreadPool and ThreadJob COMP: Remove unimplemented DestroyPool method COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping COMP: Do not hide pygccxml warnings ENH: Update links in readme file BUG: Improve SWIG version check BUG: Add VTK_VERSION for older VTK versions STYLE: Remove trailing whitespaces STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP BUG: Fix memory leak in MetaImageIO after exception ENH: Add script to update pygccxml from upstream BUG: Update VTK minimum version (for release) BUG: Fix memory leak in MetaImageIO after exception ENH: Remove Sun OS compatibility for the wrappings COMP: Fix for conversion to non-pointer like type warning STYLE: LabelObject style DOC: Remove broken link from LabelObject class description ENH: Do not setup the python tests if not asked ENH: Add new GetTypes() and GetTypesAsList() methods to the template class COMP: Fix CMP0054 warnings in wrappings STYLE: Remove old cmake < 2.8.4 specific code STYLE: Remove old cmake < 2.8.5 specific code ENH: Update to PCRE 8.36 COMP: Refactor Wrapping setup and fix legacy warnings ENH: Add wrapping configuration to ITKConfig.cmake STYLE: Some minor code cleanup in the wrapping setup DOC: Fix typo in RelabelComponentImageFilter ENH: Deprecate VectorResampleImageFilter DOC: Add migration guide for ::Zero and ::One ENH: Deprecate ::Zero and ::One ENH: Add option to disable sorting by size in itkRelabelComponentImageFilter ENH: Add Vector and RGB wrapping to linear interpolator STYLE: Remove SORT macro in wrappings COMP: Fix warning for InterpolateImageFunction wrapping COMP: Add a check for Blocks in GPU module COMP: Bump SCIFIO to fix test build warnings COMP: Fix wrapping of itkImageFunctionBase Nick Tustison (7): BUG: Need to explicitly specify spline order. ENH: Initializing the transform center. BUG: Need to check the dynamic cast before any calls. ENH: Adding modifications for point set metrics. BUG: Need to specify TInternalComputationValueType for default metric. ENH: Adding sparse points to B-spline field estimate. BUG: Uninitialized variables. Richard Beare (1): ENH: Include TIFF tags in the MetaDataDictionary Taylor Braun-Jones (1): BUG: Fix SliceBySliceImageFilter doesn't propagate information internally Umang B (1): ENH: Use thread pool to dispatch multithreading tasks Vivien Delmon (2): BUG: ExtractImageFilter::CollapseToSubMatrix fix ENH: Add a test on extracted directions in CollapseToSubMatrix mode Vladimir S. FONOV (1): BUG: Fixing incorrect MINC style inverse transform ----------------------------------------------------- Errors or omissions? Please fix them here: https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Dec 16 03:06:41 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Dec 2014 03:06:41 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: <20141215214720.1396295766@mail.rogue-research.com> References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> <20141211203014.425400305@mail.rogue-research.com> <89CF8EC3-F5DF-478E-A140-C375C8A7F5AB@mail.nih.gov> <1FC3831A-8A7A-4677-9461-E822B83B5C99@mail.nih.gov> <20141215214720.1396295766@mail.rogue-research.com> Message-ID: On Mon, Dec 15, 2014 at 4:47 PM, Sean McBride wrote: > > On Mon, 15 Dec 2014 09:08:43 -0500, Bradley Lowekamp said: > > >Thanks for taking this on. > > > >I believe at the TCON on friday we agreed with Matt's suggestion: > > > >itkFooBar_h > > > >I hope that there will be a fairly robust command line to do this work. > >Please include it in the commit messages so that it can easily be done > >again later for others modules. > > OK, my first patch is here, hopefully it won't explode gerrit: > > < > http://review.source.kitware.com/#/q/status:open+project:ITK+branch:master+topic:include-guards,n,z > > > > Looks great! I added a few minor comments on removing most of the .cxx entries and improving the commit messages. Thanks, Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 16 08:53:00 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 16 Dec 2014 08:53:00 -0500 Subject: [ITK] [ITK-dev] ITK 4.7 Release Candidate 2 has been tagged! In-Reply-To: References: Message-ID: <1E677360-2968-4613-B82F-28ED35D5D836@mail.nih.gov> Hello, Looking over SimpleITK's dashboard I have found an interesting failure: https://open.cdash.org/testSummary.php?project=40&name=BasicFilters.MorphologicalWatershedFromMarkersImageFilter&date=2014-12-16 This system is using the system PNG library, and it appears to be failing because the spacing is different than expected. This is specifically a Redhat 7 system, and does have an ITK build with the system png library: https://open.cdash.org/buildSummary.php?buildid=3613486 I'll look into this to see if the recent PNG sCAL changes are related. Brad On Dec 16, 2014, at 2:42 AM, Matt McCormick wrote: > On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.7.0 release candidate 2 has been tagged and is available for testing! Please test the release candidate in the coming days for an imminent release. > > To obtain the source code, > > git clone http://itk.org/ITK.git > cd ITK > git checkout -q --detach v4.7rc02 > > For more details, please see the Git documentation [1]. > > A few highlights for this release: all ITK examples from the Software Guide, Wiki Examples, and SphinxExamples are new indexed and crossed linked in Doxygen. So now when you go to your favorite filter or other object, say the ResampleImageFilter, there is a large selection of examples in the examples sections. This should make it much easier to fine sample code on how to use an ITK class! TIFF IO has undergone a significant cleanup and speed-up, and now TIFF tags are read into the MetaDataDictionary. Three new Remote Modules are available, for gradient computation, DICOM IO, and QuadEdgeMesh filtering. Python wrapping, CMake configuration, and registration continue to improve. A new, experimental thread pool is available -- to enable set the ITK_USE_THREADPOOL or call itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). > > > Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review. Please help identify issues submitting an Experimental build to the dashboard [2] with: > > ctest -M Experimental -T Configure -T Build -T Test -T Submit > > and notifying the mailing list. Testing your own applications against the RC is also appreciated. > > > Congratulations and well done to the 29 contributors to this release. We would especially like to recognize the new contributors, Gert Wollny, Girish Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan Andruejol, and Ismael Belghiti. > > The final release is scheduled for December 18th. > > [1] http://www.itk.org/Wiki/ITK/Git > > [2] http://itk.org/Insight/Doxygen/html/examples.html > > [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html > > [2] http://open.cdash.org/index.php?project=Insight > > > > New Features > ------------------ > * Documentation Improvements > - Update Software Guide registration examples to ITKv4 framework > - Wiki and Sphinx examples are indexed in Doxygen > - Clean Software Guide dashboard build > > * Filtering Improvements > - New Laplacian deformation filter?s for QuadEdgeMesh?s > - IJ article: http://hdl.handle.net/10380/3410 > - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations > - Faster recursive Gaussian on VectorImage > > * ImageIO improvements > - PNG sCAL unit support > - TIFF IO performance greatly improved > - TIFF tags read into Image MetaDataDictionary > - MetaIO updated > - Better support for system GDCM > > * Infrastructure improvements > - New method to erase a MetaDataDictionary entry > - New global method to set physical space tolerance > - New, experimental thread pool support > - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue() and ::OneValue() > - VTK bridge modules only request required VTK modules > > * New Remote Modules > - Higher Order Accurate Gradient > - http://hdl.handle.net/10380/3231 > - IO Transform DCMTK > - http://hdl.handle.net/10380/3468 > - Subdivision Quad Edge Mesh Filters > - http://hdl.handle.net/10380/3307 > > * Registration improvements > - LandmarkBasedTransformInitializer supports BSplineTransform > - Transverse inverse consistency increased > - Automatic initialization of the transform center for multi-stage registrations > - Sparse point B-spline field estimate > - Mutual information faster, lower memory usage > > * Wrapping improvements > - Wrapping now builds without type warnings > - pygccxml bumped to 1.6.2 > - Latest GCCXML > - CMake wrapping infrastructure cleanup > - Build with Ninja CMake generator > - New GetTypes() and GetTypesAsList() methods > - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake > > * Many style improvements -- ITK gets more stylish with every release! > > * Improved code coverage -- we are over 85%! > > * *Lots* of important bug fixes > > * And much more! See details in the log below. > > List of changes since v4.7-rc01 > -------------------------------------- > > Ali Ghayoor (1): > DOC: Revise the registration examples of ITKSoftwareGuide > > Arnaud Gelas (3): > ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module > COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh > COMP: fix warnings on dashboard for Subdivision remote module > > Bradley Lowekamp (5): > BUG: Fix segfault when setting displacement field as null > BUG: Don't enable SSE rounding with OSX and gccxml > BUG: Add portable access to Tiff field name > BUG: Fix conversion compilation error > BUG: Rename remote module FDFImageIO -> IOFDF > > Christopher Mullins (6): > STYLE: Fix line length in OpenJPEG license for 80 character. > DOC: Finish the ImageLinearIteratorWithIndex example. > DOC: Text and picture problems, book2 > BUG: Fix text in margin issues > DOC: Edits for the beginning of chapter 5, Statistics > DOC: Fix empty code block. > > Cory Quammen (1): > COMP: Avoid including VTK_USE_FILE within ITK > > Kent Williams (1): > ENH: Add test to exercise issue with Transform::GetInverse > > Matthew McCormick (7): > BUG: Register AzimuthElevationToCartesianTransform to factories. > DOC: Update texture feature class references. > BUG: Fix texture feature correlation computation for constant image. > STYLE: Put ImageToImageFilterCommon in its own file. > BUG: Wrap ImageToImageFilterCommon. > STYLE: Put ImageSourceCommon in its own file. > COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. > > Michka Popoff (1): > ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter wrappings > > Ziv Yaniv (1): > COMP: fixed warnings from gcc4.1.2, made implicit casts explicit > > > List of changes since v4.6.0 > -------------------------------------- > > Alexander Schmidt-Richberg (1): > ENH: Updated Remote Module VariationalRegistration to new git tag > > Ali Ghayoor (10): > ENH: Make ITKv4 compatible with ITKSoftwareGuide > ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 > ENH: Convert three ImageRegistration Examples to ITKv4 > ENH: Add multi-Res and multistage registration Examples to ITKv4 > ENH: Convert DeformableReg examples to ITKv4 reg framework > BUG: Expand a test to reflect multi-metric registration bug > BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 > ENH: Add direct initialization to SyN registration > ENH: Direct initialization of SyN by restoring the state > ENH: LandmarkBasedTransformInitializer supports BSplineTransformType > > Arnaud Gelas (15): > COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization > ENH: Importing Laplacian Deformation for QuadEdgeMesh > DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage > ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() > ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > COMP: missing cast when calling gdcm::DataElement::SetByteValue > ENH: increase LaplacianDeformation code coverage > STYLE: use typedef rather than inheritance > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false > BUG: split include directories into appropriate cmake variables HDF5 > BUG: missing gdcm libraries when using system GDCM > DOC: fix doxygen documentaiton for itk::LaplacianDeformationQuadEdgeMeshFilter > ENH: Add one method to erase a tag into MetaDataDictionary > > Bill Lorensen (5): > ENH: Specify required VTK modules > COMP: Wiki examples require additional vtk modules > ENH: Modify WikiExamples remote config > COMP: Bad test signature > COMP: Update tag for wiki examples > > Brad King (6): > COMP: Fix vxl_config_macros usage of CMake check macros > ENH: Use if(DEFINED) to simplify conditions > COMP: Fix vxl_config_macros checks broken by refactoring > COMP: Fix one more vxl_config_macros check broken by refactoring > BUG: Fix itk_module_config for repeated calls > BUG: Fix itk_module_config for repeated calls > > Bradley Lowekamp (52): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > PERF: Remove dynamically allocated temporary in evaluate method > COMP: Fix variable type for Set/Get macros > BUG: Implement ITK Style Singleton design pattern > ENH: Add no throw exception specification for UnRegister methods > COMP: Must specify order as "noexcept override" > BUG: Add GetInverse for IdentityTransform > ENH: Adding SetIdentity method to base DisplacementField class > BUG: Remove unused redefinition of NULL > BUG: Don't print to std::cout in PrintSelf > ENH: Prefer the PrintSelfObjectMacro for printing nested objects > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > COMP: Fix signed to unsigned int comparison > BUG: Fix overflows computing size of read tiff image > ENH: Extract TiffReaderInternal to separate file > ENH: Refactor ReadTwoSamplePerPixelImage into template function > ENH: Refactor GenericReadImage into template function > BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) > ENH: Refactor method to convert RGBA image to output buffer > ENH: Refactor duplicated code to read a page > BUG: Fix right oriented tiff images > BUG: Remove dead separated plannar code, add test > STYLE: Fix minor kwstyle defects in test and test results > BUG: Use array delete operator for array new allocations > ENH: add arbitrary TIFF TAGs to meta-data dictionary > ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage > BUG: Address Coverity warning about null pointer dereferences > ENH: Remove support for TIFF tile as 3D and dead code > ENH: RGBA read images should stay unchanged. > BUG: Override method to MakeOutput by name > ENH: Refactor per pixel conversion function to per scan-line method > PERF: Refactor color table lookup > BUG: Adding missing parentheses around boolean expression > ENH: adding TIFFImageIO test for RGB palette images > PERF: Improve recursive Gaussian perfromance with VectorImages > ENH: Query libtiff to determine compression support > BUG: Support TIFF tiled image with TIFFReadRGBAImage > BUG: Use SizeValueType for length of scanline > PERF: Store causal results directly in output buffers > COMP: Add explicit conversion to const char > COMP: Explicitly add override to GetNameOfClass method > COMP: Address internal segmentation fault with Intel compiler > ENH: Adding method to set global physical space tolerance > COMP: Explicitly add override to GetNameOfClass method > BUG: Add new TypeMacro for non-overloaded classes > BUG: Fix obscure race condition on access thread pool initialization > BUG: Updating FDFImageIO remote module > > Christopher Mullins (15): > COMP: Allows latex to compile for ITKSoftwareGuide > COMP: Allows latex to compile for ITKSoftwareGuide > COMP: Wrap MeshBase templates > COMP: Wrap MeshBase templates > COMP: Fix warning in BlockMatchingImageFilter > STYLE: Line lengths in examples should be no longer than 80 chars. > COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. > COMP: Fix LaTeX warnings. > STYLE: Fix formatting/punctuation errors. > STYLE: Formatting and punctuation fixes. > DOC: Edits for Book 2 Chapter 1 documentation in the Examples. > DOC: Edits for book 2 chapter 2. > DOC: More chapter 2 edits > DOC: Book 2 Chapter 3 edits (part 1) > DOC: book 2 chapter 4 Segmentation edits > > Danny Perry (2): > BUG: adding test for vnl_sparse_matrix::mult() > BUG: size of q buffer should actually be (this->rows())*pcols. > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Dirk Padfield (1): > BUG: Corrected processing of last sigma > > GCC-XML Upstream (1): > ENH: pygccxml v1.6.2 (reduced) > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. > > Hans Johnson (24): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > BUG: Syntax error in comment > PERF: Add non-blocking mutex locking. > ENH: Use TryLock minimize thread stalls > BUG: ThreadedIndexedContainerPartitioner is inclusive > STYLE: Remove include_regular_expression from Examples > BUG: Demonstrate Inv(Inv(T)) != T > BUG: Ensure Inv(Inv(T)) == T for transforms > COMP: Valgrind detects uninitialized memory read > COMP: Missing required base class API component > ENH: Expand interface for selecting threadpool > > Ismael Belghiti (1): > DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter > > Jim Miller (1): > STYLE: Removing what appears to be a temporary file > > Johan Andruejol (1): > ENH: Fix normalization for null vectors and return the norm > > Jon Haitz Legarreta (1): > ENH: New test for itkLabelShapeOpeningImageFilter > > Kent Williams (9): > COMP: use find_package(VTK COMPONENTS) to specify just needed VTK Components > BUG: ImageSources/test/CMakeLists.txt incorrect library var reference > COMP: Fix coverity defects related to RegistrationV4 examples > COMP: silence warning of vnl_vector_fixed_ref::assert_size > COMP: Fix various Coverity warnings > COMP: Fix a typo in an error message print statement. > COMP: itk::Command-derived class used pointless dynamic_cast. > PERF: Don't recompute InternalInverse repeatedly > COMP: Correct orientation/spacing for Philips MultiFrame > > Mark Hiner (2): > ENH: Update SCIFIO remote module hash > BUG: Fix duplicate variables in Windows > > Matthew McCormick (105): > DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. > ENH: Move FFTComplexToComplexImageFilter out of Review. > ENH: Add VnlComplexToComplexFFTImageFilter. > BUG: Use fixed seed for Vnl FFT tests for repeatibility. > ENH: Bump CMakeLists.txt version to 4.7.0. > BUG: ArchiveTestingData.py future imports must occur at the beginning. > BUG: Do not run vnl_test_na with broken libc++. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter. > BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. > STYLE: Fix style in VoronoiDiagram2D. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Bump GCCXML to 2014-08-06. > BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. > BUG: Fix Win MultiThreader check for successful process creation. > BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. > COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. > DOC: itk::statistics -> itk::Statistics. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > COMP: Improve const correctness of GradientRecursiveGaussianImageFilter. > BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > COMP: ThreadJob NULL not defined. > BUG: Fix alpha assignment for RGBA TIFF. > COMP: Remove unused typedefs in LevelSetsv4Visualization. > COMP: Remove unused typedef's in VtkGlue. > ENH: Mark BSplineWarping2Test as RUNS_LONG. > BUG: Fix Nifti IO read with large images. > COMP: Remove call for non-existent variable in Nifti debugging. > BUG: Close the file on Read and Write in HDF5TransformIO. > BUG: Remove InsightLegacy test code from TransformHDF5Test. > ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. > STYLE: Use SeriesUIDContainerType and FileNamesContainerType > ENH: Allow specification of orthogonality tolerance in rigid transforms. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Do not use _stat64 with MinGW-32. > BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. > COMP: Address LaplacianDeformation Doxygen warnings. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > COMP: Do not wrap the FixedArray of Image SmartPointer's. > COMP: Add missing wrapping for TransformIOBaseTemplate. > COMP: Mark DeformableRegistration6Test as RUNS_LONG. > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > BUG: Use -py3 when building wrapping for Python 3. > COMP: Add missing wrapping for TransformIOBaseTemplate. > DOC: Improve ImageRegistration4 grammar. > ENH: Add IOTransformDCMTK Remote module. > BUG: gdcm::StringFilter recognizes backslash delimiter. > DOC: Add migration guide for GDCM Rescale slope intercept apply on write. > COMP: Remove unused typedef's in GPU code. > STYLE: Improve style of HoughTransform2DLinesImageFilter example. > COMP: Use ConceptChecking for IterativeInverse dimension check. > COMP: Wrap TransformIOBaseTemplate for const SmartPointer. > COMP: Add warning exceptions for third party pcre, swig, gccxml. > ENH: Bump ITK version to 4.6.1. > BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. > BUG: Remove GaussianImageSource members shadowing GenerateImageSource. > STYLE: Style fixes to ITKImageSources module. > BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType. > BUG: Do not perform itk_download_attempt_check when not building ITK. > DOC: Update GDCMImageIO rescale slope intercept doc. > BUG: Only register requestion IO COMPONENT modules. > BUG: Fix wrapping .i, .idx CMake dependencies. > COMP: Add VTK Python module when wrapping ITKVtkGlue. > STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. > STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. > COMP: Add missing VTK module dependency for LevelSetsv4Visualization. > BUG: By default, do not create any fixed parameters. > STYLE: Remove trivial method comments in itkTransform.hxx. > BUG: PolylineMask Filter's GenerateData is protected / virtual. > ENH: Add HigherOrderAccurateGradient Module. > BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal. > COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. > STYLE: Style fixes for Transform classes. > DOC: Increase Doxygen LOOKUP_CACHE_SIZE. > BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. > DOC: Index Wiki examples with Doxygen. > COMP: Bump SphinxExamples remote module. > DOC: Index Sphinx examples in Doxygen. > COMP: Remove old java examples. > COMP: Remove duplicate DiffusionTensor3DReconstruction example reference. > COMP: Address GradientAnisotropicDiffusionImageFilter example settings. > COMP: Bump Sphinx Examples remote. > COMP: Bump WikiExamples remote. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (40): > ENH: Fixes for python 3 support > BUG: Add VTK_VERSION for older VTK versions > BUG: Improve SWIG version check > COMP: Add wrapping for ThreadPool and ThreadJob > COMP: Remove unimplemented DestroyPool method > COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping > COMP: Do not hide pygccxml warnings > ENH: Update links in readme file > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > STYLE: Remove trailing whitespaces > STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP > BUG: Fix memory leak in MetaImageIO after exception > ENH: Add script to update pygccxml from upstream > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > ENH: Remove Sun OS compatibility for the wrappings > COMP: Fix for conversion to non-pointer like type warning > STYLE: LabelObject style > DOC: Remove broken link from LabelObject class description > ENH: Do not setup the python tests if not asked > ENH: Add new GetTypes() and GetTypesAsList() methods to the template class > COMP: Fix CMP0054 warnings in wrappings > STYLE: Remove old cmake < 2.8.4 specific code > STYLE: Remove old cmake < 2.8.5 specific code > ENH: Update to PCRE 8.36 > COMP: Refactor Wrapping setup and fix legacy warnings > ENH: Add wrapping configuration to ITKConfig.cmake > STYLE: Some minor code cleanup in the wrapping setup > DOC: Fix typo in RelabelComponentImageFilter > ENH: Deprecate VectorResampleImageFilter > DOC: Add migration guide for ::Zero and ::One > ENH: Deprecate ::Zero and ::One > ENH: Add option to disable sorting by size in itkRelabelComponentImageFilter > ENH: Add Vector and RGB wrapping to linear interpolator > STYLE: Remove SORT macro in wrappings > COMP: Fix warning for InterpolateImageFunction wrapping > COMP: Add a check for Blocks in GPU module > COMP: Bump SCIFIO to fix test build warnings > COMP: Fix wrapping of itkImageFunctionBase > > Nick Tustison (7): > BUG: Need to explicitly specify spline order. > ENH: Initializing the transform center. > BUG: Need to check the dynamic cast before any calls. > ENH: Adding modifications for point set metrics. > BUG: Need to specify TInternalComputationValueType for default metric. > ENH: Adding sparse points to B-spline field estimate. > BUG: Uninitialized variables. > > Richard Beare (1): > ENH: Include TIFF tags in the MetaDataDictionary > > Taylor Braun-Jones (1): > BUG: Fix SliceBySliceImageFilter doesn't propagate information internally > > Umang B (1): > ENH: Use thread pool to dispatch multithreading tasks > > Vivien Delmon (2): > BUG: ExtractImageFilter::CollapseToSubMatrix fix > ENH: Add a test on extracted directions in CollapseToSubMatrix mode > > Vladimir S. FONOV (1): > BUG: Fixing incorrect MINC style inverse transform > > > ----------------------------------------------------- > Errors or omissions? Please fix them here: > > https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 16 12:04:50 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 16 Dec 2014 12:04:50 -0500 Subject: [ITK] [ITK-dev] ITK 4.7 Release Candidate 2 has been tagged! In-Reply-To: References: <1E677360-2968-4613-B82F-28ED35D5D836@mail.nih.gov> Message-ID: Matt, Here is a the commit which provided insight: https://github.com/InsightSoftwareConsortium/ITK/commit/d7bd945330746905c5e813275690477ff8981e7b The png files previously written by ITK have an UNKNOW sCal field. With PNG 1.5, the value is ignored unlike the prior versions. ITK now writes the the sCAL field as METER. My solution was to take a version of SimpleITK with ITK's PNG and just read and re-write the files: import SimpleITK as sitk from glob import glob fn = glob("*/*.png") for f in fn: img = sitk.ReadImage(f) sitk.WriteImage(img, f) I don't see how to improve this behavior. This line just works differently with the new libpng [1]. Brad On Dec 16, 2014, at 11:53 AM, Matt McCormick wrote: > Thanks! > > On Tue, Dec 16, 2014 at 8:53 AM, Bradley Lowekamp wrote: > Hello, > > Looking over SimpleITK's dashboard I have found an interesting failure: > > https://open.cdash.org/testSummary.php?project=40&name=BasicFilters.MorphologicalWatershedFromMarkersImageFilter&date=2014-12-16 > > This system is using the system PNG library, and it appears to be failing because the spacing is different than expected. This is specifically a Redhat 7 system, and does have an ITK build with the system png library: > > https://open.cdash.org/buildSummary.php?buildid=3613486 > > I'll look into this to see if the recent PNG sCAL changes are related. > > Brad > > > On Dec 16, 2014, at 2:42 AM, Matt McCormick wrote: > >> On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.7.0 release candidate 2 has been tagged and is available for testing! Please test the release candidate in the coming days for an imminent release. >> >> To obtain the source code, >> >> git clone http://itk.org/ITK.git >> cd ITK >> git checkout -q --detach v4.7rc02 >> >> For more details, please see the Git documentation [1]. >> >> A few highlights for this release: all ITK examples from the Software Guide, Wiki Examples, and SphinxExamples are new indexed and crossed linked in Doxygen. So now when you go to your favorite filter or other object, say the ResampleImageFilter, there is a large selection of examples in the examples sections. This should make it much easier to fine sample code on how to use an ITK class! TIFF IO has undergone a significant cleanup and speed-up, and now TIFF tags are read into the MetaDataDictionary. Three new Remote Modules are available, for gradient computation, DICOM IO, and QuadEdgeMesh filtering. Python wrapping, CMake configuration, and registration continue to improve. A new, experimental thread pool is available -- to enable set the ITK_USE_THREADPOOL or call itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). >> >> >> Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review. Please help identify issues submitting an Experimental build to the dashboard [2] with: >> >> ctest -M Experimental -T Configure -T Build -T Test -T Submit >> >> and notifying the mailing list. Testing your own applications against the RC is also appreciated. >> >> >> Congratulations and well done to the 29 contributors to this release. We would especially like to recognize the new contributors, Gert Wollny, Girish Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan Andruejol, and Ismael Belghiti. >> >> The final release is scheduled for December 18th. >> >> [1] http://www.itk.org/Wiki/ITK/Git >> >> [2] http://itk.org/Insight/Doxygen/html/examples.html >> >> [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html >> >> [2] http://open.cdash.org/index.php?project=Insight >> >> >> >> New Features >> ------------------ >> * Documentation Improvements >> - Update Software Guide registration examples to ITKv4 framework >> - Wiki and Sphinx examples are indexed in Doxygen >> - Clean Software Guide dashboard build >> >> * Filtering Improvements >> - New Laplacian deformation filter?s for QuadEdgeMesh?s >> - IJ article: http://hdl.handle.net/10380/3410 >> - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations >> - Faster recursive Gaussian on VectorImage >> >> * ImageIO improvements >> - PNG sCAL unit support >> - TIFF IO performance greatly improved >> - TIFF tags read into Image MetaDataDictionary >> - MetaIO updated >> - Better support for system GDCM >> >> * Infrastructure improvements >> - New method to erase a MetaDataDictionary entry >> - New global method to set physical space tolerance >> - New, experimental thread pool support >> - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue() and ::OneValue() >> - VTK bridge modules only request required VTK modules >> >> * New Remote Modules >> - Higher Order Accurate Gradient >> - http://hdl.handle.net/10380/3231 >> - IO Transform DCMTK >> - http://hdl.handle.net/10380/3468 >> - Subdivision Quad Edge Mesh Filters >> - http://hdl.handle.net/10380/3307 >> >> * Registration improvements >> - LandmarkBasedTransformInitializer supports BSplineTransform >> - Transverse inverse consistency increased >> - Automatic initialization of the transform center for multi-stage registrations >> - Sparse point B-spline field estimate >> - Mutual information faster, lower memory usage >> >> * Wrapping improvements >> - Wrapping now builds without type warnings >> - pygccxml bumped to 1.6.2 >> - Latest GCCXML >> - CMake wrapping infrastructure cleanup >> - Build with Ninja CMake generator >> - New GetTypes() and GetTypesAsList() methods >> - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake >> >> * Many style improvements -- ITK gets more stylish with every release! >> >> * Improved code coverage -- we are over 85%! >> >> * *Lots* of important bug fixes >> >> * And much more! See details in the log below. >> >> List of changes since v4.7-rc01 >> -------------------------------------- >> >> Ali Ghayoor (1): >> DOC: Revise the registration examples of ITKSoftwareGuide >> >> Arnaud Gelas (3): >> ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module >> COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh >> COMP: fix warnings on dashboard for Subdivision remote module >> >> Bradley Lowekamp (5): >> BUG: Fix segfault when setting displacement field as null >> BUG: Don't enable SSE rounding with OSX and gccxml >> BUG: Add portable access to Tiff field name >> BUG: Fix conversion compilation error >> BUG: Rename remote module FDFImageIO -> IOFDF >> >> Christopher Mullins (6): >> STYLE: Fix line length in OpenJPEG license for 80 character. >> DOC: Finish the ImageLinearIteratorWithIndex example. >> DOC: Text and picture problems, book2 >> BUG: Fix text in margin issues >> DOC: Edits for the beginning of chapter 5, Statistics >> DOC: Fix empty code block. >> >> Cory Quammen (1): >> COMP: Avoid including VTK_USE_FILE within ITK >> >> Kent Williams (1): >> ENH: Add test to exercise issue with Transform::GetInverse >> >> Matthew McCormick (7): >> BUG: Register AzimuthElevationToCartesianTransform to factories. >> DOC: Update texture feature class references. >> BUG: Fix texture feature correlation computation for constant image. >> STYLE: Put ImageToImageFilterCommon in its own file. >> BUG: Wrap ImageToImageFilterCommon. >> STYLE: Put ImageSourceCommon in its own file. >> COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. >> >> Michka Popoff (1): >> ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter wrappings >> >> Ziv Yaniv (1): >> COMP: fixed warnings from gcc4.1.2, made implicit casts explicit >> >> >> List of changes since v4.6.0 >> -------------------------------------- >> >> Alexander Schmidt-Richberg (1): >> ENH: Updated Remote Module VariationalRegistration to new git tag >> >> Ali Ghayoor (10): >> ENH: Make ITKv4 compatible with ITKSoftwareGuide >> ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 >> ENH: Convert three ImageRegistration Examples to ITKv4 >> ENH: Add multi-Res and multistage registration Examples to ITKv4 >> ENH: Convert DeformableReg examples to ITKv4 reg framework >> BUG: Expand a test to reflect multi-metric registration bug >> BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 >> ENH: Add direct initialization to SyN registration >> ENH: Direct initialization of SyN by restoring the state >> ENH: LandmarkBasedTransformInitializer supports BSplineTransformType >> >> Arnaud Gelas (15): >> COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization >> ENH: Importing Laplacian Deformation for QuadEdgeMesh >> DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage >> ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() >> ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter >> BUG: fix gdcm version in GDCMImageIO. >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> ENH: increase LaplacianDeformation code coverage >> STYLE: use typedef rather than inheritance >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false >> BUG: split include directories into appropriate cmake variables HDF5 >> BUG: missing gdcm libraries when using system GDCM >> DOC: fix doxygen documentaiton for itk::LaplacianDeformationQuadEdgeMeshFilter >> ENH: Add one method to erase a tag into MetaDataDictionary >> >> Bill Lorensen (5): >> ENH: Specify required VTK modules >> COMP: Wiki examples require additional vtk modules >> ENH: Modify WikiExamples remote config >> COMP: Bad test signature >> COMP: Update tag for wiki examples >> >> Brad King (6): >> COMP: Fix vxl_config_macros usage of CMake check macros >> ENH: Use if(DEFINED) to simplify conditions >> COMP: Fix vxl_config_macros checks broken by refactoring >> COMP: Fix one more vxl_config_macros check broken by refactoring >> BUG: Fix itk_module_config for repeated calls >> BUG: Fix itk_module_config for repeated calls >> >> Bradley Lowekamp (52): >> ENH: Adding License file from upstream MetaIO >> ENH: Adding script to update MetaIO from upstream >> ENH: Remove ITK MetaIO to prepare for upstream import >> PERF: Remove dynamically allocated temporary in evaluate method >> COMP: Fix variable type for Set/Get macros >> BUG: Implement ITK Style Singleton design pattern >> ENH: Add no throw exception specification for UnRegister methods >> COMP: Must specify order as "noexcept override" >> BUG: Add GetInverse for IdentityTransform >> ENH: Adding SetIdentity method to base DisplacementField class >> BUG: Remove unused redefinition of NULL >> BUG: Don't print to std::cout in PrintSelf >> ENH: Prefer the PrintSelfObjectMacro for printing nested objects >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> COMP: Fix signed to unsigned int comparison >> BUG: Fix overflows computing size of read tiff image >> ENH: Extract TiffReaderInternal to separate file >> ENH: Refactor ReadTwoSamplePerPixelImage into template function >> ENH: Refactor GenericReadImage into template function >> BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) >> ENH: Refactor method to convert RGBA image to output buffer >> ENH: Refactor duplicated code to read a page >> BUG: Fix right oriented tiff images >> BUG: Remove dead separated plannar code, add test >> STYLE: Fix minor kwstyle defects in test and test results >> BUG: Use array delete operator for array new allocations >> ENH: add arbitrary TIFF TAGs to meta-data dictionary >> ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage >> BUG: Address Coverity warning about null pointer dereferences >> ENH: Remove support for TIFF tile as 3D and dead code >> ENH: RGBA read images should stay unchanged. >> BUG: Override method to MakeOutput by name >> ENH: Refactor per pixel conversion function to per scan-line method >> PERF: Refactor color table lookup >> BUG: Adding missing parentheses around boolean expression >> ENH: adding TIFFImageIO test for RGB palette images >> PERF: Improve recursive Gaussian perfromance with VectorImages >> ENH: Query libtiff to determine compression support >> BUG: Support TIFF tiled image with TIFFReadRGBAImage >> BUG: Use SizeValueType for length of scanline >> PERF: Store causal results directly in output buffers >> COMP: Add explicit conversion to const char >> COMP: Explicitly add override to GetNameOfClass method >> COMP: Address internal segmentation fault with Intel compiler >> ENH: Adding method to set global physical space tolerance >> COMP: Explicitly add override to GetNameOfClass method >> BUG: Add new TypeMacro for non-overloaded classes >> BUG: Fix obscure race condition on access thread pool initialization >> BUG: Updating FDFImageIO remote module >> >> Christopher Mullins (15): >> COMP: Allows latex to compile for ITKSoftwareGuide >> COMP: Allows latex to compile for ITKSoftwareGuide >> COMP: Wrap MeshBase templates >> COMP: Wrap MeshBase templates >> COMP: Fix warning in BlockMatchingImageFilter >> STYLE: Line lengths in examples should be no longer than 80 chars. >> COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. >> COMP: Fix LaTeX warnings. >> STYLE: Fix formatting/punctuation errors. >> STYLE: Formatting and punctuation fixes. >> DOC: Edits for Book 2 Chapter 1 documentation in the Examples. >> DOC: Edits for book 2 chapter 2. >> DOC: More chapter 2 edits >> DOC: Book 2 Chapter 3 edits (part 1) >> DOC: book 2 chapter 4 Segmentation edits >> >> Danny Perry (2): >> BUG: adding test for vnl_sparse_matrix::mult() >> BUG: size of q buffer should actually be (this->rows())*pcols. >> >> David T. Chen (1): >> DOC: Fixed HistogramThresholdImageFitler >> >> Dirk Padfield (1): >> BUG: Corrected processing of last sigma >> >> GCC-XML Upstream (1): >> ENH: pygccxml v1.6.2 (reduced) >> >> Gert Wollny (1): >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >> >> Girish Mallya (1): >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. >> >> Hans Johnson (24): >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> PERF: Remove large foot print of PDF derivatives. >> PERF: Revert Remove large foot print of PDF derivatives. >> STYLE: Test against almost equal for floating point values >> STYLE: Non-exact floating point testing >> PERF: Distribute initialization per thread buffers >> ENH: Remove unnecessary mutable qualifier. >> STYLE: Remove comment with no meaning. >> ENH: Moved accumlator logic to main MI class >> ENH: Allow staggering of accumulations per thread. >> PERF: Zero reset thread buffers during finalize >> BUG: Syntax error in comment >> PERF: Add non-blocking mutex locking. >> ENH: Use TryLock minimize thread stalls >> BUG: ThreadedIndexedContainerPartitioner is inclusive >> STYLE: Remove include_regular_expression from Examples >> BUG: Demonstrate Inv(Inv(T)) != T >> BUG: Ensure Inv(Inv(T)) == T for transforms >> COMP: Valgrind detects uninitialized memory read >> COMP: Missing required base class API component >> ENH: Expand interface for selecting threadpool >> >> Ismael Belghiti (1): >> DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter >> >> Jim Miller (1): >> STYLE: Removing what appears to be a temporary file >> >> Johan Andruejol (1): >> ENH: Fix normalization for null vectors and return the norm >> >> Jon Haitz Legarreta (1): >> ENH: New test for itkLabelShapeOpeningImageFilter >> >> Kent Williams (9): >> COMP: use find_package(VTK COMPONENTS) to specify just needed VTK Components >> BUG: ImageSources/test/CMakeLists.txt incorrect library var reference >> COMP: Fix coverity defects related to RegistrationV4 examples >> COMP: silence warning of vnl_vector_fixed_ref::assert_size >> COMP: Fix various Coverity warnings >> COMP: Fix a typo in an error message print statement. >> COMP: itk::Command-derived class used pointless dynamic_cast. >> PERF: Don't recompute InternalInverse repeatedly >> COMP: Correct orientation/spacing for Philips MultiFrame >> >> Mark Hiner (2): >> ENH: Update SCIFIO remote module hash >> BUG: Fix duplicate variables in Windows >> >> Matthew McCormick (105): >> DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. >> ENH: Move FFTComplexToComplexImageFilter out of Review. >> ENH: Add VnlComplexToComplexFFTImageFilter. >> BUG: Use fixed seed for Vnl FFT tests for repeatibility. >> ENH: Bump CMakeLists.txt version to 4.7.0. >> BUG: ArchiveTestingData.py future imports must occur at the beginning. >> BUG: Do not run vnl_test_na with broken libc++. >> DOC: Remove Image2.cxx reference from Book 2. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. >> DOC: Remove references to Book 1 sections from Book 2. >> DOC: Make BinaryThresholdImageFilter not floating. >> DOC: Fix Software Guide figure caption for FlipImageFilter. >> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. >> DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. >> DOC: ImageRandomConstIteratorWithIndex table reference. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter. >> BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. >> STYLE: Fix style in VoronoiDiagram2D. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> BUG: Bump GCCXML to 2014-08-06. >> BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. >> BUG: Fix Win MultiThreader check for successful process creation. >> BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. >> COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. >> DOC: itk::statistics -> itk::Statistics. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> COMP: Improve const correctness of GradientRecursiveGaussianImageFilter. >> BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >> COMP: ThreadJob NULL not defined. >> BUG: Fix alpha assignment for RGBA TIFF. >> COMP: Remove unused typedefs in LevelSetsv4Visualization. >> COMP: Remove unused typedef's in VtkGlue. >> ENH: Mark BSplineWarping2Test as RUNS_LONG. >> BUG: Fix Nifti IO read with large images. >> COMP: Remove call for non-existent variable in Nifti debugging. >> BUG: Close the file on Read and Write in HDF5TransformIO. >> BUG: Remove InsightLegacy test code from TransformHDF5Test. >> ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. >> STYLE: Use SeriesUIDContainerType and FileNamesContainerType >> ENH: Allow specification of orthogonality tolerance in rigid transforms. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Do not use _stat64 with MinGW-32. >> BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. >> DOC: itk::statistics -> itk::Statistics. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. >> COMP: Address LaplacianDeformation Doxygen warnings. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >> BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform >> COMP: Do not wrap the FixedArray of Image SmartPointer's. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> COMP: Mark DeformableRegistration6Test as RUNS_LONG. >> STYLE: Improve style in BinaryImageToLabelMapFilter. >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. >> ENH: Improve precision of the joint PDF sum >> BUG: Fix BinShrinkImageFilter for different input/output image types. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> BUG: Use -py3 when building wrapping for Python 3. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> DOC: Improve ImageRegistration4 grammar. >> ENH: Add IOTransformDCMTK Remote module. >> BUG: gdcm::StringFilter recognizes backslash delimiter. >> DOC: Add migration guide for GDCM Rescale slope intercept apply on write. >> COMP: Remove unused typedef's in GPU code. >> STYLE: Improve style of HoughTransform2DLinesImageFilter example. >> COMP: Use ConceptChecking for IterativeInverse dimension check. >> COMP: Wrap TransformIOBaseTemplate for const SmartPointer. >> COMP: Add warning exceptions for third party pcre, swig, gccxml. >> ENH: Bump ITK version to 4.6.1. >> BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. >> BUG: Remove GaussianImageSource members shadowing GenerateImageSource. >> STYLE: Style fixes to ITKImageSources module. >> BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType. >> BUG: Do not perform itk_download_attempt_check when not building ITK. >> DOC: Update GDCMImageIO rescale slope intercept doc. >> BUG: Only register requestion IO COMPONENT modules. >> BUG: Fix wrapping .i, .idx CMake dependencies. >> COMP: Add VTK Python module when wrapping ITKVtkGlue. >> STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. >> STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. >> COMP: Add missing VTK module dependency for LevelSetsv4Visualization. >> BUG: By default, do not create any fixed parameters. >> STYLE: Remove trivial method comments in itkTransform.hxx. >> BUG: PolylineMask Filter's GenerateData is protected / virtual. >> ENH: Add HigherOrderAccurateGradient Module. >> BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal. >> COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. >> STYLE: Style fixes for Transform classes. >> DOC: Increase Doxygen LOOKUP_CACHE_SIZE. >> BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. >> DOC: Index Wiki examples with Doxygen. >> COMP: Bump SphinxExamples remote module. >> DOC: Index Sphinx examples in Doxygen. >> COMP: Remove old java examples. >> COMP: Remove duplicate DiffusionTensor3DReconstruction example reference. >> COMP: Address GradientAnisotropicDiffusionImageFilter example settings. >> COMP: Bump Sphinx Examples remote. >> COMP: Bump WikiExamples remote. >> >> MetaIO Maintainers (1): >> MetaIO (reduced) >> >> Michka Popoff (40): >> ENH: Fixes for python 3 support >> BUG: Add VTK_VERSION for older VTK versions >> BUG: Improve SWIG version check >> COMP: Add wrapping for ThreadPool and ThreadJob >> COMP: Remove unimplemented DestroyPool method >> COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping >> COMP: Do not hide pygccxml warnings >> ENH: Update links in readme file >> BUG: Improve SWIG version check >> BUG: Add VTK_VERSION for older VTK versions >> STYLE: Remove trailing whitespaces >> STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP >> BUG: Fix memory leak in MetaImageIO after exception >> ENH: Add script to update pygccxml from upstream >> BUG: Update VTK minimum version (for release) >> BUG: Fix memory leak in MetaImageIO after exception >> ENH: Remove Sun OS compatibility for the wrappings >> COMP: Fix for conversion to non-pointer like type warning >> STYLE: LabelObject style >> DOC: Remove broken link from LabelObject class description >> ENH: Do not setup the python tests if not asked >> ENH: Add new GetTypes() and GetTypesAsList() methods to the template class >> COMP: Fix CMP0054 warnings in wrappings >> STYLE: Remove old cmake < 2.8.4 specific code >> STYLE: Remove old cmake < 2.8.5 specific code >> ENH: Update to PCRE 8.36 >> COMP: Refactor Wrapping setup and fix legacy warnings >> ENH: Add wrapping configuration to ITKConfig.cmake >> STYLE: Some minor code cleanup in the wrapping setup >> DOC: Fix typo in RelabelComponentImageFilter >> ENH: Deprecate VectorResampleImageFilter >> DOC: Add migration guide for ::Zero and ::One >> ENH: Deprecate ::Zero and ::One >> ENH: Add option to disable sorting by size in itkRelabelComponentImageFilter >> ENH: Add Vector and RGB wrapping to linear interpolator >> STYLE: Remove SORT macro in wrappings >> COMP: Fix warning for InterpolateImageFunction wrapping >> COMP: Add a check for Blocks in GPU module >> COMP: Bump SCIFIO to fix test build warnings >> COMP: Fix wrapping of itkImageFunctionBase >> >> Nick Tustison (7): >> BUG: Need to explicitly specify spline order. >> ENH: Initializing the transform center. >> BUG: Need to check the dynamic cast before any calls. >> ENH: Adding modifications for point set metrics. >> BUG: Need to specify TInternalComputationValueType for default metric. >> ENH: Adding sparse points to B-spline field estimate. >> BUG: Uninitialized variables. >> >> Richard Beare (1): >> ENH: Include TIFF tags in the MetaDataDictionary >> >> Taylor Braun-Jones (1): >> BUG: Fix SliceBySliceImageFilter doesn't propagate information internally >> >> Umang B (1): >> ENH: Use thread pool to dispatch multithreading tasks >> >> Vivien Delmon (2): >> BUG: ExtractImageFilter::CollapseToSubMatrix fix >> ENH: Add a test on extracted directions in CollapseToSubMatrix mode >> >> Vladimir S. FONOV (1): >> BUG: Fixing incorrect MINC style inverse transform >> >> >> ----------------------------------------------------- >> Errors or omissions? Please fix them here: >> >> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing >> >> >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Tue Dec 16 15:05:39 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Dec 2014 15:05:39 -0500 Subject: [ITK] [ITK-dev] ITK 4.7 Release Candidate 2 has been tagged! In-Reply-To: References: <1E677360-2968-4613-B82F-28ED35D5D836@mail.nih.gov> Message-ID: Hi Brad, Thanks for investigating. I will look into throwing a warning if a read file has UNKNOWN units with non-unit spacing. Thanks, Matt On Tue, Dec 16, 2014 at 12:04 PM, Bradley Lowekamp wrote: > > Matt, > > Here is a the commit which provided insight: > > > https://github.com/InsightSoftwareConsortium/ITK/commit/d7bd945330746905c5e813275690477ff8981e7b > > The png files previously written by ITK have an UNKNOW sCal field. With > PNG 1.5, the value is ignored unlike the prior versions. ITK now writes the > the sCAL field as METER. > > My solution was to take a version of SimpleITK with ITK's PNG and just > read and re-write the files: > > > import SimpleITK as sitk > from glob import glob > fn = glob("*/*.png") > for f in fn: > img = sitk.ReadImage(f) > sitk.WriteImage(img, f) > > > I don't see how to improve this behavior. This line just works differently > with the new libpng [1]. > > Brad > > On Dec 16, 2014, at 11:53 AM, Matt McCormick > wrote: > > Thanks! > > On Tue, Dec 16, 2014 at 8:53 AM, Bradley Lowekamp > wrote: >> >> Hello, >> >> Looking over SimpleITK's dashboard I have found an interesting failure: >> >> >> https://open.cdash.org/testSummary.php?project=40&name=BasicFilters.MorphologicalWatershedFromMarkersImageFilter&date=2014-12-16 >> >> This system is using the system PNG library, and it appears to be failing >> because the spacing is different than expected. This is specifically a >> Redhat 7 system, and does have an ITK build with the system png library: >> >> https://open.cdash.org/buildSummary.php?buildid=3613486 >> >> I'll look into this to see if the recent PNG sCAL changes are related. >> >> Brad >> >> >> On Dec 16, 2014, at 2:42 AM, Matt McCormick >> wrote: >> >> On behalf of the Insight Toolkit community, we are proud to announce that >> ITK 4.7.0 release candidate 2 has been tagged and is available for testing! >> Please test the release candidate in the coming days for an imminent >> release. >> >> To obtain the source code, >> >> git clone http://itk.org/ITK.git >> cd ITK >> git checkout -q --detach v4.7rc02 >> >> For more details, please see the Git documentation >> [1]. >> >> A few highlights for this release: all ITK examples from the Software >> Guide, Wiki Examples, and SphinxExamples are new indexed and crossed >> linked in Doxygen . >> So now when you go to your favorite filter or other object, say the >> ResampleImageFilter >> , >> there is a large selection of examples in the examples sections. This >> should make it much easier to fine sample code on how to use an ITK class! >> TIFF IO has undergone a significant cleanup and speed-up, and now TIFF tags >> are read into the MetaDataDictionary. Three new Remote Modules are >> available, for gradient computation, DICOM IO, and QuadEdgeMesh filtering. >> Python wrapping, CMake configuration, and registration continue to improve. >> A new, experimental thread pool is available -- to enable set the >> ITK_USE_THREADPOOL or call >> itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). >> >> >> Please test the release candidate and share your experiences on the >> mailing list, issue tracker, and Gerrit Code Review. Please help identify >> issues submitting an Experimental build to the dashboard >> [2] with: >> >> ctest -M Experimental -T Configure -T Build -T Test -T Submit >> >> and notifying the mailing list. Testing your own applications against >> the RC is also appreciated. >> >> >> Congratulations and well done to the 29 contributors to this release. We >> would especially like to recognize the new contributors, Gert Wollny, >> Girish Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, >> Johan Andruejol, and Ismael Belghiti. >> >> The final release is scheduled for December 18th. >> >> [1] http://www.itk.org/Wiki/ITK/Git >> >> [2] http://itk.org/Insight/Doxygen/html/examples.html >> >> [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html >> >> [2] http://open.cdash.org/index.php?project=Insight >> >> >> >> New Features >> ------------------ >> * Documentation Improvements >> - Update Software Guide registration examples to ITKv4 framework >> - Wiki and Sphinx examples are indexed in Doxygen >> - Clean Software Guide dashboard build >> >> * Filtering Improvements >> - New Laplacian deformation filter?s for QuadEdgeMesh?s >> - IJ article: http://hdl.handle.net/10380/3410 >> - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations >> - Faster recursive Gaussian on VectorImage >> >> * ImageIO improvements >> - PNG sCAL unit support >> - TIFF IO performance greatly improved >> - TIFF tags read into Image MetaDataDictionary >> - MetaIO updated >> - Better support for system GDCM >> >> * Infrastructure improvements >> - New method to erase a MetaDataDictionary entry >> - New global method to set physical space tolerance >> - New, experimental thread pool support >> - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue() >> and ::OneValue() >> - VTK bridge modules only request required VTK modules >> >> * New Remote Modules >> - Higher Order Accurate Gradient >> - http://hdl.handle.net/10380/3231 >> - IO Transform DCMTK >> - http://hdl.handle.net/10380/3468 >> - Subdivision Quad Edge Mesh Filters >> - http://hdl.handle.net/10380/3307 >> >> * Registration improvements >> - LandmarkBasedTransformInitializer supports BSplineTransform >> - Transverse inverse consistency increased >> - Automatic initialization of the transform center for multi-stage >> registrations >> - Sparse point B-spline field estimate >> - Mutual information faster, lower memory usage >> >> * Wrapping improvements >> - Wrapping now builds without type warnings >> - pygccxml bumped to 1.6.2 >> - Latest GCCXML >> - CMake wrapping infrastructure cleanup >> - Build with Ninja CMake generator >> - New GetTypes() and GetTypesAsList() methods >> - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake >> >> >> * Many style improvements -- ITK gets more stylish with every release! >> >> * Improved code coverage -- we are over 85%! >> >> * *Lots* of important bug fixes >> >> * And much more! See details in the log below. >> >> List of changes since v4.7-rc01 >> -------------------------------------- >> >> Ali Ghayoor (1): >> DOC: Revise the registration examples of ITKSoftwareGuide >> >> Arnaud Gelas (3): >> ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module >> COMP: address clang -Winconsistent-missing-override in >> ITKQuadEdgeMesh >> COMP: fix warnings on dashboard for Subdivision remote module >> >> Bradley Lowekamp (5): >> BUG: Fix segfault when setting displacement field as null >> BUG: Don't enable SSE rounding with OSX and gccxml >> BUG: Add portable access to Tiff field name >> BUG: Fix conversion compilation error >> BUG: Rename remote module FDFImageIO -> IOFDF >> >> Christopher Mullins (6): >> STYLE: Fix line length in OpenJPEG license for 80 character. >> DOC: Finish the ImageLinearIteratorWithIndex example. >> DOC: Text and picture problems, book2 >> BUG: Fix text in margin issues >> DOC: Edits for the beginning of chapter 5, Statistics >> DOC: Fix empty code block. >> >> Cory Quammen (1): >> COMP: Avoid including VTK_USE_FILE within ITK >> >> Kent Williams (1): >> ENH: Add test to exercise issue with Transform::GetInverse >> >> Matthew McCormick (7): >> BUG: Register AzimuthElevationToCartesianTransform to factories. >> DOC: Update texture feature class references. >> BUG: Fix texture feature correlation computation for constant image. >> STYLE: Put ImageToImageFilterCommon in its own file. >> BUG: Wrap ImageToImageFilterCommon. >> STYLE: Put ImageSourceCommon in its own file. >> COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. >> >> Michka Popoff (1): >> ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter >> wrappings >> >> Ziv Yaniv (1): >> COMP: fixed warnings from gcc4.1.2, made implicit casts explicit >> >> >> List of changes since v4.6.0 >> -------------------------------------- >> >> Alexander Schmidt-Richberg (1): >> ENH: Updated Remote Module VariationalRegistration to new git tag >> >> Ali Ghayoor (10): >> ENH: Make ITKv4 compatible with ITKSoftwareGuide >> ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 >> ENH: Convert three ImageRegistration Examples to ITKv4 >> ENH: Add multi-Res and multistage registration Examples to ITKv4 >> ENH: Convert DeformableReg examples to ITKv4 reg framework >> BUG: Expand a test to reflect multi-metric registration bug >> BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 >> ENH: Add direct initialization to SyN registration >> ENH: Direct initialization of SyN by restoring the state >> ENH: LandmarkBasedTransformInitializer supports BSplineTransformType >> >> Arnaud Gelas (15): >> COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization >> ENH: Importing Laplacian Deformation for QuadEdgeMesh >> DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage >> ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls >> Modified() >> ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter >> BUG: fix gdcm version in GDCMImageIO. >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> COMP: missing cast when calling gdcm::DataElement::SetByteValue >> ENH: increase LaplacianDeformation code coverage >> STYLE: use typedef rather than inheritance >> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is >> false >> BUG: split include directories into appropriate cmake variables HDF5 >> BUG: missing gdcm libraries when using system GDCM >> DOC: fix doxygen documentaiton for >> itk::LaplacianDeformationQuadEdgeMeshFilter >> ENH: Add one method to erase a tag into MetaDataDictionary >> >> Bill Lorensen (5): >> ENH: Specify required VTK modules >> COMP: Wiki examples require additional vtk modules >> ENH: Modify WikiExamples remote config >> COMP: Bad test signature >> COMP: Update tag for wiki examples >> >> Brad King (6): >> COMP: Fix vxl_config_macros usage of CMake check macros >> ENH: Use if(DEFINED) to simplify conditions >> COMP: Fix vxl_config_macros checks broken by refactoring >> COMP: Fix one more vxl_config_macros check broken by refactoring >> BUG: Fix itk_module_config for repeated calls >> BUG: Fix itk_module_config for repeated calls >> >> Bradley Lowekamp (52): >> ENH: Adding License file from upstream MetaIO >> ENH: Adding script to update MetaIO from upstream >> ENH: Remove ITK MetaIO to prepare for upstream import >> PERF: Remove dynamically allocated temporary in evaluate method >> COMP: Fix variable type for Set/Get macros >> BUG: Implement ITK Style Singleton design pattern >> ENH: Add no throw exception specification for UnRegister methods >> COMP: Must specify order as "noexcept override" >> BUG: Add GetInverse for IdentityTransform >> ENH: Adding SetIdentity method to base DisplacementField class >> BUG: Remove unused redefinition of NULL >> BUG: Don't print to std::cout in PrintSelf >> ENH: Prefer the PrintSelfObjectMacro for printing nested objects >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> BUG: Use METER of sCAL scale unit >> BUG: Use PNG_SCALE_METER for PNG sCAL unit >> COMP: Fix signed to unsigned int comparison >> BUG: Fix overflows computing size of read tiff image >> ENH: Extract TiffReaderInternal to separate file >> ENH: Refactor ReadTwoSamplePerPixelImage into template function >> ENH: Refactor GenericReadImage into template function >> BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and >> LSMImageIO ) >> ENH: Refactor method to convert RGBA image to output buffer >> ENH: Refactor duplicated code to read a page >> BUG: Fix right oriented tiff images >> BUG: Remove dead separated plannar code, add test >> STYLE: Fix minor kwstyle defects in test and test results >> BUG: Use array delete operator for array new allocations >> ENH: add arbitrary TIFF TAGs to meta-data dictionary >> ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage >> BUG: Address Coverity warning about null pointer dereferences >> ENH: Remove support for TIFF tile as 3D and dead code >> ENH: RGBA read images should stay unchanged. >> BUG: Override method to MakeOutput by name >> ENH: Refactor per pixel conversion function to per scan-line method >> PERF: Refactor color table lookup >> BUG: Adding missing parentheses around boolean expression >> ENH: adding TIFFImageIO test for RGB palette images >> PERF: Improve recursive Gaussian perfromance with VectorImages >> ENH: Query libtiff to determine compression support >> BUG: Support TIFF tiled image with TIFFReadRGBAImage >> BUG: Use SizeValueType for length of scanline >> PERF: Store causal results directly in output buffers >> COMP: Add explicit conversion to const char >> COMP: Explicitly add override to GetNameOfClass method >> COMP: Address internal segmentation fault with Intel compiler >> ENH: Adding method to set global physical space tolerance >> COMP: Explicitly add override to GetNameOfClass method >> BUG: Add new TypeMacro for non-overloaded classes >> BUG: Fix obscure race condition on access thread pool initialization >> BUG: Updating FDFImageIO remote module >> >> Christopher Mullins (15): >> COMP: Allows latex to compile for ITKSoftwareGuide >> COMP: Allows latex to compile for ITKSoftwareGuide >> COMP: Wrap MeshBase templates >> COMP: Wrap MeshBase templates >> COMP: Fix warning in BlockMatchingImageFilter >> STYLE: Line lengths in examples should be no longer than 80 chars. >> COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. >> COMP: Fix LaTeX warnings. >> STYLE: Fix formatting/punctuation errors. >> STYLE: Formatting and punctuation fixes. >> DOC: Edits for Book 2 Chapter 1 documentation in the Examples. >> DOC: Edits for book 2 chapter 2. >> DOC: More chapter 2 edits >> DOC: Book 2 Chapter 3 edits (part 1) >> DOC: book 2 chapter 4 Segmentation edits >> >> Danny Perry (2): >> BUG: adding test for vnl_sparse_matrix::mult() >> BUG: size of q buffer should actually be (this->rows())*pcols. >> >> David T. Chen (1): >> DOC: Fixed HistogramThresholdImageFitler >> >> Dirk Padfield (1): >> BUG: Corrected processing of last sigma >> >> GCC-XML Upstream (1): >> ENH: pygccxml v1.6.2 (reduced) >> >> Gert Wollny (1): >> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >> >> Girish Mallya (1): >> BUG: Tests added for BinaryImageToLabelMapFilter for single-row >> images. >> >> Hans Johnson (24): >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> COMP: Add tolerance for comparing floating point >> PERF: Remove non-threadable algorithm components >> PERF: Remove large foot print of PDF derivatives. >> PERF: Revert Remove large foot print of PDF derivatives. >> STYLE: Test against almost equal for floating point values >> STYLE: Non-exact floating point testing >> PERF: Distribute initialization per thread buffers >> ENH: Remove unnecessary mutable qualifier. >> STYLE: Remove comment with no meaning. >> ENH: Moved accumlator logic to main MI class >> ENH: Allow staggering of accumulations per thread. >> PERF: Zero reset thread buffers during finalize >> BUG: Syntax error in comment >> PERF: Add non-blocking mutex locking. >> ENH: Use TryLock minimize thread stalls >> BUG: ThreadedIndexedContainerPartitioner is inclusive >> STYLE: Remove include_regular_expression from Examples >> BUG: Demonstrate Inv(Inv(T)) != T >> BUG: Ensure Inv(Inv(T)) == T for transforms >> COMP: Valgrind detects uninitialized memory read >> COMP: Missing required base class API component >> ENH: Expand interface for selecting threadpool >> >> Ismael Belghiti (1): >> DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter >> >> Jim Miller (1): >> STYLE: Removing what appears to be a temporary file >> >> Johan Andruejol (1): >> ENH: Fix normalization for null vectors and return the norm >> >> Jon Haitz Legarreta (1): >> ENH: New test for itkLabelShapeOpeningImageFilter >> >> Kent Williams (9): >> COMP: use find_package(VTK COMPONENTS) to specify just needed VTK >> Components >> BUG: ImageSources/test/CMakeLists.txt incorrect library var reference >> COMP: Fix coverity defects related to RegistrationV4 examples >> COMP: silence warning of vnl_vector_fixed_ref::assert_size >> COMP: Fix various Coverity warnings >> COMP: Fix a typo in an error message print statement. >> COMP: itk::Command-derived class used pointless dynamic_cast. >> PERF: Don't recompute InternalInverse repeatedly >> COMP: Correct orientation/spacing for Philips MultiFrame >> >> Mark Hiner (2): >> ENH: Update SCIFIO remote module hash >> BUG: Fix duplicate variables in Windows >> >> Matthew McCormick (105): >> DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. >> ENH: Move FFTComplexToComplexImageFilter out of Review. >> ENH: Add VnlComplexToComplexFFTImageFilter. >> BUG: Use fixed seed for Vnl FFT tests for repeatibility. >> ENH: Bump CMakeLists.txt version to 4.7.0. >> BUG: ArchiveTestingData.py future imports must occur at the >> beginning. >> BUG: Do not run vnl_test_na with broken libc++. >> DOC: Remove Image2.cxx reference from Book 2. >> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. >> DOC: Remove references to Book 1 sections from Book 2. >> DOC: Make BinaryThresholdImageFilter not floating. >> DOC: Fix Software Guide figure caption for FlipImageFilter. >> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. >> DOC: Remove duplicate figure in >> LaplacianRecursiveGaussianImageFilter2.cxx. >> DOC: ImageRandomConstIteratorWithIndex table reference. >> DOC: Fix Software Guide page overruns in >> IterativeClosestPoint{1,2}.cxx. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> BUG: Uninitialized m_TransformDirection in >> ComplexToComplexFFTImageFilter. >> BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. >> STYLE: Fix style in VoronoiDiagram2D. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> BUG: Bump GCCXML to 2014-08-06. >> BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. >> BUG: Fix Win MultiThreader check for successful process creation. >> BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. >> COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. >> DOC: itk::statistics -> itk::Statistics. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> COMP: Improve const correctness of >> GradientRecursiveGaussianImageFilter. >> BUG: Call clear instead of empty on PatchBasedDenoising >> EmptyCaches(). >> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >> COMP: ThreadJob NULL not defined. >> BUG: Fix alpha assignment for RGBA TIFF. >> COMP: Remove unused typedefs in LevelSetsv4Visualization. >> COMP: Remove unused typedef's in VtkGlue. >> ENH: Mark BSplineWarping2Test as RUNS_LONG. >> BUG: Fix Nifti IO read with large images. >> COMP: Remove call for non-existent variable in Nifti debugging. >> BUG: Close the file on Read and Write in HDF5TransformIO. >> BUG: Remove InsightLegacy test code from TransformHDF5Test. >> ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. >> STYLE: Use SeriesUIDContainerType and FileNamesContainerType >> ENH: Allow specification of orthogonality tolerance in rigid >> transforms. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Do not use _stat64 with MinGW-32. >> BUG: Improve thread-safety and performance of >> PCAShapeSignedDistanceFunction. >> DOC: itk::statistics -> itk::Statistics. >> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> DOC: Fix Software Guide page overruns in >> IterativeClosestPoint{1,2}.cxx. >> COMP: Address LaplacianDeformation Doxygen warnings. >> BUG: TransformFileReader does not clear its TransformList. >> BUG: Prevent dangling pointer in HDF5TransformIO. >> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >> BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform >> COMP: Do not wrap the FixedArray of Image SmartPointer's. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> COMP: Mark DeformableRegistration6Test as RUNS_LONG. >> STYLE: Improve style in BinaryImageToLabelMapFilter. >> BUG: Fix BinaryImageToLabelMapFilter on 1D image. >> ENH: Improve precision of the joint PDF sum >> BUG: Fix BinShrinkImageFilter for different input/output image types. >> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> BUG: Use -py3 when building wrapping for Python 3. >> COMP: Add missing wrapping for TransformIOBaseTemplate. >> DOC: Improve ImageRegistration4 grammar. >> ENH: Add IOTransformDCMTK Remote module. >> BUG: gdcm::StringFilter recognizes backslash delimiter. >> DOC: Add migration guide for GDCM Rescale slope intercept apply on >> write. >> COMP: Remove unused typedef's in GPU code. >> STYLE: Improve style of HoughTransform2DLinesImageFilter example. >> COMP: Use ConceptChecking for IterativeInverse dimension check. >> COMP: Wrap TransformIOBaseTemplate for const SmartPointer. >> COMP: Add warning exceptions for third party pcre, swig, gccxml. >> ENH: Bump ITK version to 4.6.1. >> BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. >> BUG: Remove GaussianImageSource members shadowing >> GenerateImageSource. >> STYLE: Style fixes to ITKImageSources module. >> BUG: GaussianSpatialFunction and GaborImageSource use >> SpacePrecisionType. >> BUG: Do not perform itk_download_attempt_check when not building ITK. >> DOC: Update GDCMImageIO rescale slope intercept doc. >> BUG: Only register requestion IO COMPONENT modules. >> BUG: Fix wrapping .i, .idx CMake dependencies. >> COMP: Add VTK Python module when wrapping ITKVtkGlue. >> STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. >> STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType >> typedef. >> COMP: Add missing VTK module dependency for LevelSetsv4Visualization. >> BUG: By default, do not create any fixed parameters. >> STYLE: Remove trivial method comments in itkTransform.hxx. >> BUG: PolylineMask Filter's GenerateData is protected / virtual. >> ENH: Add HigherOrderAccurateGradient Module. >> BUG: Use input RequestedRegion Index in SliceBySliceImageFilter >> internal. >> COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. >> STYLE: Style fixes for Transform classes. >> DOC: Increase Doxygen LOOKUP_CACHE_SIZE. >> BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. >> DOC: Index Wiki examples with Doxygen. >> COMP: Bump SphinxExamples remote module. >> DOC: Index Sphinx examples in Doxygen. >> COMP: Remove old java examples. >> COMP: Remove duplicate DiffusionTensor3DReconstruction example >> reference. >> COMP: Address GradientAnisotropicDiffusionImageFilter example >> settings. >> COMP: Bump Sphinx Examples remote. >> COMP: Bump WikiExamples remote. >> >> MetaIO Maintainers (1): >> MetaIO (reduced) >> >> Michka Popoff (40): >> ENH: Fixes for python 3 support >> BUG: Add VTK_VERSION for older VTK versions >> BUG: Improve SWIG version check >> COMP: Add wrapping for ThreadPool and ThreadJob >> COMP: Remove unimplemented DestroyPool method >> COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping >> COMP: Do not hide pygccxml warnings >> ENH: Update links in readme file >> BUG: Improve SWIG version check >> BUG: Add VTK_VERSION for older VTK versions >> STYLE: Remove trailing whitespaces >> STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP >> BUG: Fix memory leak in MetaImageIO after exception >> ENH: Add script to update pygccxml from upstream >> BUG: Update VTK minimum version (for release) >> BUG: Fix memory leak in MetaImageIO after exception >> ENH: Remove Sun OS compatibility for the wrappings >> COMP: Fix for conversion to non-pointer like type warning >> STYLE: LabelObject style >> DOC: Remove broken link from LabelObject class description >> ENH: Do not setup the python tests if not asked >> ENH: Add new GetTypes() and GetTypesAsList() methods to the template >> class >> COMP: Fix CMP0054 warnings in wrappings >> STYLE: Remove old cmake < 2.8.4 specific code >> STYLE: Remove old cmake < 2.8.5 specific code >> ENH: Update to PCRE 8.36 >> COMP: Refactor Wrapping setup and fix legacy warnings >> ENH: Add wrapping configuration to ITKConfig.cmake >> STYLE: Some minor code cleanup in the wrapping setup >> DOC: Fix typo in RelabelComponentImageFilter >> ENH: Deprecate VectorResampleImageFilter >> DOC: Add migration guide for ::Zero and ::One >> ENH: Deprecate ::Zero and ::One >> ENH: Add option to disable sorting by size in >> itkRelabelComponentImageFilter >> ENH: Add Vector and RGB wrapping to linear interpolator >> STYLE: Remove SORT macro in wrappings >> COMP: Fix warning for InterpolateImageFunction wrapping >> COMP: Add a check for Blocks in GPU module >> COMP: Bump SCIFIO to fix test build warnings >> COMP: Fix wrapping of itkImageFunctionBase >> >> Nick Tustison (7): >> BUG: Need to explicitly specify spline order. >> ENH: Initializing the transform center. >> BUG: Need to check the dynamic cast before any calls. >> ENH: Adding modifications for point set metrics. >> BUG: Need to specify TInternalComputationValueType for default >> metric. >> ENH: Adding sparse points to B-spline field estimate. >> BUG: Uninitialized variables. >> >> Richard Beare (1): >> ENH: Include TIFF tags in the MetaDataDictionary >> >> Taylor Braun-Jones (1): >> BUG: Fix SliceBySliceImageFilter doesn't propagate information >> internally >> >> Umang B (1): >> ENH: Use thread pool to dispatch multithreading tasks >> >> Vivien Delmon (2): >> BUG: ExtractImageFilter::CollapseToSubMatrix fix >> ENH: Add a test on extracted directions in CollapseToSubMatrix mode >> >> Vladimir S. FONOV (1): >> BUG: Fixing incorrect MINC style inverse transform >> >> >> ----------------------------------------------------- >> Errors or omissions? Please fix them here: >> >> >> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing >> >> >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From sean at rogue-research.com Tue Dec 16 15:26:01 2014 From: sean at rogue-research.com (Sean McBride) Date: Tue, 16 Dec 2014 15:26:01 -0500 Subject: [ITK] [ITK-dev] New clang warnings: reserved-id-macro In-Reply-To: References: <30BB5441-6132-458C-A703-4B54B9DA3997@mail.nih.gov> <20141211201510.1661524377@mail.rogue-research.com> <17AE119A-CD75-4F2C-A5A1-6B09EBEF33B4@mail.nih.gov> <20141211203014.425400305@mail.rogue-research.com> <89CF8EC3-F5DF-478E-A140-C375C8A7F5AB@mail.nih.gov> <1FC3831A-8A7A-4677-9461-E822B83B5C99@mail.nih.gov> <20141215214720.1396295766@mail.rogue-research.com> Message-ID: <20141216202601.1994937373@mail.rogue-research.com> On Tue, 16 Dec 2014 03:06:41 -0500, Matt McCormick said: >Looks great! I added a few minor comments on removing most of the .cxx >entries and improving the commit messages. OK, I think I fixed things up... had to fight with git as usual, but I think I did it right... :) Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 16 17:32:07 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 16 Dec 2014 17:32:07 -0500 Subject: [ITK] [ITK-dev] Compositions in ScaleVersor3D and ScaleSkewVersor3D Transforms In-Reply-To: <93A27D3A-D855-4A62-9E04-50D63041765B@mail.nih.gov> References: <93A27D3A-D855-4A62-9E04-50D63041765B@mail.nih.gov> Message-ID: <3A7E6D09-D5EB-4C71-A101-17E333D9CAAB@mail.nih.gov> Hello, I thought I'd just update folks with my progress, I am using symbolic computation to compute the need jacobian, with sympy: http://nbviewer.ipython.org/urls/gist.githubusercontent.com/blowekamp/359f7d2e5221eae97a1b/raw/dd5614577474dc6b012406a238e702468c886e0b/ScaleSkewJacoboan.ipynb Looks a bit hairy... Brad On Dec 12, 2014, at 12:11 PM, Bradley Lowekamp wrote: > Hello, > > This seems very wrong to me... > > I was looking into the inverse of the classes. And I saw how the matrix was composed from the scale and versor components[1] > > newMatrix[0][0] = m_Scale[0] - 2.0 * ( yy + zz ); > newMatrix[1][1] = m_Scale[1] - 2.0 * ( xx + zz ); > newMatrix[2][2] = m_Scale[2] - 2.0 * ( xx + yy ); > newMatrix[0][1] = 2.0 * ( xy - zw ) + ( m_Skew[0] ); > newMatrix[0][2] = 2.0 * ( xz + yw ) + ( m_Skew[1] ); > newMatrix[1][0] = 2.0 * ( xy + zw ) + ( m_Skew[2] ); > newMatrix[1][2] = 2.0 * ( yz - xw ) + ( m_Skew[3] ); > newMatrix[2][0] = 2.0 * ( xz - yw ) + ( m_Skew[4] ); > newMatrix[2][1] = 2.0 * ( yz + xw ) + ( m_Skew[5] ); > > Similarly both classes just add the scale/skew component and don't do correct matrix composition. > > Let R be the versor, S scale, and K skew matrices, and p be a point. > > Currently we have: > > (R+S+K)*p = R*p+S*p+K*p > > Where I expected these classes would be implementing: > > R*S*K*p > > which is a traditional composition of transform matrices. > > Anyone know where the current math came from? Or what it's really doing? > > Is this something that we should fix/improve/evaluate? Or just document what's actually happening? > > Brad > > > > > [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Transform/include/itkScaleVersor3DTransform.hxx#L219-L227 > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Dec 17 01:55:18 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Dec 2014 01:55:18 -0500 Subject: [ITK] [ITK-dev] ITK 4.7 Release Candidate 2 has been tagged! In-Reply-To: References: <1E677360-2968-4613-B82F-28ED35D5D836@mail.nih.gov> Message-ID: Here is the patch: http://review.source.kitware.com/#/c/18511/ On Tue, Dec 16, 2014 at 3:05 PM, Matt McCormick wrote: > > Hi Brad, > > Thanks for investigating. > > I will look into throwing a warning if a read file has UNKNOWN units with > non-unit spacing. > > Thanks, > Matt > > > > On Tue, Dec 16, 2014 at 12:04 PM, Bradley Lowekamp > wrote: >> >> Matt, >> >> Here is a the commit which provided insight: >> >> >> https://github.com/InsightSoftwareConsortium/ITK/commit/d7bd945330746905c5e813275690477ff8981e7b >> >> The png files previously written by ITK have an UNKNOW sCal field. With >> PNG 1.5, the value is ignored unlike the prior versions. ITK now writes the >> the sCAL field as METER. >> >> My solution was to take a version of SimpleITK with ITK's PNG and just >> read and re-write the files: >> >> >> import SimpleITK as sitk >> from glob import glob >> fn = glob("*/*.png") >> for f in fn: >> img = sitk.ReadImage(f) >> sitk.WriteImage(img, f) >> >> >> I don't see how to improve this behavior. This line just works >> differently with the new libpng [1]. >> >> Brad >> >> On Dec 16, 2014, at 11:53 AM, Matt McCormick >> wrote: >> >> Thanks! >> >> On Tue, Dec 16, 2014 at 8:53 AM, Bradley Lowekamp > > wrote: >>> >>> Hello, >>> >>> Looking over SimpleITK's dashboard I have found an interesting failure: >>> >>> >>> https://open.cdash.org/testSummary.php?project=40&name=BasicFilters.MorphologicalWatershedFromMarkersImageFilter&date=2014-12-16 >>> >>> This system is using the system PNG library, and it appears to be >>> failing because the spacing is different than expected. This is >>> specifically a Redhat 7 system, and does have an ITK build with the system >>> png library: >>> >>> https://open.cdash.org/buildSummary.php?buildid=3613486 >>> >>> I'll look into this to see if the recent PNG sCAL changes are related. >>> >>> Brad >>> >>> >>> On Dec 16, 2014, at 2:42 AM, Matt McCormick >>> wrote: >>> >>> On behalf of the Insight Toolkit community, we are proud to announce >>> that ITK 4.7.0 release candidate 2 has been tagged and is available for >>> testing! Please test the release candidate in the coming days for an >>> imminent release. >>> >>> To obtain the source code, >>> >>> git clone http://itk.org/ITK.git >>> cd ITK >>> git checkout -q --detach v4.7rc02 >>> >>> For more details, please see the Git documentation >>> [1]. >>> >>> A few highlights for this release: all ITK examples from the Software >>> Guide, Wiki Examples, and SphinxExamples are new indexed and crossed >>> linked in Doxygen . >>> So now when you go to your favorite filter or other object, say the >>> ResampleImageFilter >>> , >>> there is a large selection of examples in the examples sections. This >>> should make it much easier to fine sample code on how to use an ITK class! >>> TIFF IO has undergone a significant cleanup and speed-up, and now TIFF tags >>> are read into the MetaDataDictionary. Three new Remote Modules are >>> available, for gradient computation, DICOM IO, and QuadEdgeMesh filtering. >>> Python wrapping, CMake configuration, and registration continue to improve. >>> A new, experimental thread pool is available -- to enable set the >>> ITK_USE_THREADPOOL or call >>> itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). >>> >>> >>> Please test the release candidate and share your experiences on the >>> mailing list, issue tracker, and Gerrit Code Review. Please help identify >>> issues submitting an Experimental build to the dashboard >>> [2] with: >>> >>> ctest -M Experimental -T Configure -T Build -T Test -T Submit >>> >>> and notifying the mailing list. Testing your own applications against >>> the RC is also appreciated. >>> >>> >>> Congratulations and well done to the 29 contributors to this release. We >>> would especially like to recognize the new contributors, Gert Wollny, >>> Girish Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, >>> Johan Andruejol, and Ismael Belghiti. >>> >>> The final release is scheduled for December 18th. >>> >>> [1] http://www.itk.org/Wiki/ITK/Git >>> >>> [2] http://itk.org/Insight/Doxygen/html/examples.html >>> >>> [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html >>> >>> [2] http://open.cdash.org/index.php?project=Insight >>> >>> >>> >>> New Features >>> ------------------ >>> * Documentation Improvements >>> - Update Software Guide registration examples to ITKv4 framework >>> - Wiki and Sphinx examples are indexed in Doxygen >>> - Clean Software Guide dashboard build >>> >>> * Filtering Improvements >>> - New Laplacian deformation filter?s for QuadEdgeMesh?s >>> - IJ article: http://hdl.handle.net/10380/3410 >>> - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations >>> - Faster recursive Gaussian on VectorImage >>> >>> * ImageIO improvements >>> - PNG sCAL unit support >>> - TIFF IO performance greatly improved >>> - TIFF tags read into Image MetaDataDictionary >>> - MetaIO updated >>> - Better support for system GDCM >>> >>> * Infrastructure improvements >>> - New method to erase a MetaDataDictionary entry >>> - New global method to set physical space tolerance >>> - New, experimental thread pool support >>> - NumericTraits::Zero and ::One are deprecated in favor of >>> ::ZeroValue() and ::OneValue() >>> - VTK bridge modules only request required VTK modules >>> >>> * New Remote Modules >>> - Higher Order Accurate Gradient >>> - http://hdl.handle.net/10380/3231 >>> - IO Transform DCMTK >>> - http://hdl.handle.net/10380/3468 >>> - Subdivision Quad Edge Mesh Filters >>> - http://hdl.handle.net/10380/3307 >>> >>> * Registration improvements >>> - LandmarkBasedTransformInitializer supports BSplineTransform >>> - Transverse inverse consistency increased >>> - Automatic initialization of the transform center for multi-stage >>> registrations >>> - Sparse point B-spline field estimate >>> - Mutual information faster, lower memory usage >>> >>> * Wrapping improvements >>> - Wrapping now builds without type warnings >>> - pygccxml bumped to 1.6.2 >>> - Latest GCCXML >>> - CMake wrapping infrastructure cleanup >>> - Build with Ninja CMake generator >>> - New GetTypes() and GetTypesAsList() methods >>> - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake >>> >>> >>> * Many style improvements -- ITK gets more stylish with every release! >>> >>> * Improved code coverage -- we are over 85%! >>> >>> * *Lots* of important bug fixes >>> >>> * And much more! See details in the log below. >>> >>> List of changes since v4.7-rc01 >>> -------------------------------------- >>> >>> Ali Ghayoor (1): >>> DOC: Revise the registration examples of ITKSoftwareGuide >>> >>> Arnaud Gelas (3): >>> ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module >>> COMP: address clang -Winconsistent-missing-override in >>> ITKQuadEdgeMesh >>> COMP: fix warnings on dashboard for Subdivision remote module >>> >>> Bradley Lowekamp (5): >>> BUG: Fix segfault when setting displacement field as null >>> BUG: Don't enable SSE rounding with OSX and gccxml >>> BUG: Add portable access to Tiff field name >>> BUG: Fix conversion compilation error >>> BUG: Rename remote module FDFImageIO -> IOFDF >>> >>> Christopher Mullins (6): >>> STYLE: Fix line length in OpenJPEG license for 80 character. >>> DOC: Finish the ImageLinearIteratorWithIndex example. >>> DOC: Text and picture problems, book2 >>> BUG: Fix text in margin issues >>> DOC: Edits for the beginning of chapter 5, Statistics >>> DOC: Fix empty code block. >>> >>> Cory Quammen (1): >>> COMP: Avoid including VTK_USE_FILE within ITK >>> >>> Kent Williams (1): >>> ENH: Add test to exercise issue with Transform::GetInverse >>> >>> Matthew McCormick (7): >>> BUG: Register AzimuthElevationToCartesianTransform to factories. >>> DOC: Update texture feature class references. >>> BUG: Fix texture feature correlation computation for constant image. >>> STYLE: Put ImageToImageFilterCommon in its own file. >>> BUG: Wrap ImageToImageFilterCommon. >>> STYLE: Put ImageSourceCommon in its own file. >>> COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. >>> >>> Michka Popoff (1): >>> ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter >>> wrappings >>> >>> Ziv Yaniv (1): >>> COMP: fixed warnings from gcc4.1.2, made implicit casts explicit >>> >>> >>> List of changes since v4.6.0 >>> -------------------------------------- >>> >>> Alexander Schmidt-Richberg (1): >>> ENH: Updated Remote Module VariationalRegistration to new git tag >>> >>> Ali Ghayoor (10): >>> ENH: Make ITKv4 compatible with ITKSoftwareGuide >>> ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 >>> ENH: Convert three ImageRegistration Examples to ITKv4 >>> ENH: Add multi-Res and multistage registration Examples to ITKv4 >>> ENH: Convert DeformableReg examples to ITKv4 reg framework >>> BUG: Expand a test to reflect multi-metric registration bug >>> BUG: Fix multi metric point sampling bug in >>> ImageRegistrationMethodv4 >>> ENH: Add direct initialization to SyN registration >>> ENH: Direct initialization of SyN by restoring the state >>> ENH: LandmarkBasedTransformInitializer supports BSplineTransformType >>> >>> Arnaud Gelas (15): >>> COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization >>> ENH: Importing Laplacian Deformation for QuadEdgeMesh >>> DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage >>> ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls >>> Modified() >>> ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter >>> BUG: fix gdcm version in GDCMImageIO. >>> COMP: missing cast when calling gdcm::DataElement::SetByteValue >>> COMP: missing cast when calling gdcm::DataElement::SetByteValue >>> ENH: increase LaplacianDeformation code coverage >>> STYLE: use typedef rather than inheritance >>> BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is >>> false >>> BUG: split include directories into appropriate cmake variables HDF5 >>> BUG: missing gdcm libraries when using system GDCM >>> DOC: fix doxygen documentaiton for >>> itk::LaplacianDeformationQuadEdgeMeshFilter >>> ENH: Add one method to erase a tag into MetaDataDictionary >>> >>> Bill Lorensen (5): >>> ENH: Specify required VTK modules >>> COMP: Wiki examples require additional vtk modules >>> ENH: Modify WikiExamples remote config >>> COMP: Bad test signature >>> COMP: Update tag for wiki examples >>> >>> Brad King (6): >>> COMP: Fix vxl_config_macros usage of CMake check macros >>> ENH: Use if(DEFINED) to simplify conditions >>> COMP: Fix vxl_config_macros checks broken by refactoring >>> COMP: Fix one more vxl_config_macros check broken by refactoring >>> BUG: Fix itk_module_config for repeated calls >>> BUG: Fix itk_module_config for repeated calls >>> >>> Bradley Lowekamp (52): >>> ENH: Adding License file from upstream MetaIO >>> ENH: Adding script to update MetaIO from upstream >>> ENH: Remove ITK MetaIO to prepare for upstream import >>> PERF: Remove dynamically allocated temporary in evaluate method >>> COMP: Fix variable type for Set/Get macros >>> BUG: Implement ITK Style Singleton design pattern >>> ENH: Add no throw exception specification for UnRegister methods >>> COMP: Must specify order as "noexcept override" >>> BUG: Add GetInverse for IdentityTransform >>> ENH: Adding SetIdentity method to base DisplacementField class >>> BUG: Remove unused redefinition of NULL >>> BUG: Don't print to std::cout in PrintSelf >>> ENH: Prefer the PrintSelfObjectMacro for printing nested objects >>> BUG: Use METER of sCAL scale unit >>> BUG: Use PNG_SCALE_METER for PNG sCAL unit >>> BUG: Use METER of sCAL scale unit >>> BUG: Use PNG_SCALE_METER for PNG sCAL unit >>> COMP: Fix signed to unsigned int comparison >>> BUG: Fix overflows computing size of read tiff image >>> ENH: Extract TiffReaderInternal to separate file >>> ENH: Refactor ReadTwoSamplePerPixelImage into template function >>> ENH: Refactor GenericReadImage into template function >>> BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and >>> LSMImageIO ) >>> ENH: Refactor method to convert RGBA image to output buffer >>> ENH: Refactor duplicated code to read a page >>> BUG: Fix right oriented tiff images >>> BUG: Remove dead separated plannar code, add test >>> STYLE: Fix minor kwstyle defects in test and test results >>> BUG: Use array delete operator for array new allocations >>> ENH: add arbitrary TIFF TAGs to meta-data dictionary >>> ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage >>> BUG: Address Coverity warning about null pointer dereferences >>> ENH: Remove support for TIFF tile as 3D and dead code >>> ENH: RGBA read images should stay unchanged. >>> BUG: Override method to MakeOutput by name >>> ENH: Refactor per pixel conversion function to per scan-line method >>> PERF: Refactor color table lookup >>> BUG: Adding missing parentheses around boolean expression >>> ENH: adding TIFFImageIO test for RGB palette images >>> PERF: Improve recursive Gaussian perfromance with VectorImages >>> ENH: Query libtiff to determine compression support >>> BUG: Support TIFF tiled image with TIFFReadRGBAImage >>> BUG: Use SizeValueType for length of scanline >>> PERF: Store causal results directly in output buffers >>> COMP: Add explicit conversion to const char >>> COMP: Explicitly add override to GetNameOfClass method >>> COMP: Address internal segmentation fault with Intel compiler >>> ENH: Adding method to set global physical space tolerance >>> COMP: Explicitly add override to GetNameOfClass method >>> BUG: Add new TypeMacro for non-overloaded classes >>> BUG: Fix obscure race condition on access thread pool initialization >>> BUG: Updating FDFImageIO remote module >>> >>> Christopher Mullins (15): >>> COMP: Allows latex to compile for ITKSoftwareGuide >>> COMP: Allows latex to compile for ITKSoftwareGuide >>> COMP: Wrap MeshBase templates >>> COMP: Wrap MeshBase templates >>> COMP: Fix warning in BlockMatchingImageFilter >>> STYLE: Line lengths in examples should be no longer than 80 chars. >>> COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. >>> COMP: Fix LaTeX warnings. >>> STYLE: Fix formatting/punctuation errors. >>> STYLE: Formatting and punctuation fixes. >>> DOC: Edits for Book 2 Chapter 1 documentation in the Examples. >>> DOC: Edits for book 2 chapter 2. >>> DOC: More chapter 2 edits >>> DOC: Book 2 Chapter 3 edits (part 1) >>> DOC: book 2 chapter 4 Segmentation edits >>> >>> Danny Perry (2): >>> BUG: adding test for vnl_sparse_matrix::mult() >>> BUG: size of q buffer should actually be (this->rows())*pcols. >>> >>> David T. Chen (1): >>> DOC: Fixed HistogramThresholdImageFitler >>> >>> Dirk Padfield (1): >>> BUG: Corrected processing of last sigma >>> >>> GCC-XML Upstream (1): >>> ENH: pygccxml v1.6.2 (reduced) >>> >>> Gert Wollny (1): >>> COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >>> >>> Girish Mallya (1): >>> BUG: Tests added for BinaryImageToLabelMapFilter for single-row >>> images. >>> >>> Hans Johnson (24): >>> COMP: Add tolerance for comparing floating point >>> PERF: Remove non-threadable algorithm components >>> COMP: Add tolerance for comparing floating point >>> PERF: Remove non-threadable algorithm components >>> PERF: Remove large foot print of PDF derivatives. >>> PERF: Revert Remove large foot print of PDF derivatives. >>> STYLE: Test against almost equal for floating point values >>> STYLE: Non-exact floating point testing >>> PERF: Distribute initialization per thread buffers >>> ENH: Remove unnecessary mutable qualifier. >>> STYLE: Remove comment with no meaning. >>> ENH: Moved accumlator logic to main MI class >>> ENH: Allow staggering of accumulations per thread. >>> PERF: Zero reset thread buffers during finalize >>> BUG: Syntax error in comment >>> PERF: Add non-blocking mutex locking. >>> ENH: Use TryLock minimize thread stalls >>> BUG: ThreadedIndexedContainerPartitioner is inclusive >>> STYLE: Remove include_regular_expression from Examples >>> BUG: Demonstrate Inv(Inv(T)) != T >>> BUG: Ensure Inv(Inv(T)) == T for transforms >>> COMP: Valgrind detects uninitialized memory read >>> COMP: Missing required base class API component >>> ENH: Expand interface for selecting threadpool >>> >>> Ismael Belghiti (1): >>> DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter >>> >>> Jim Miller (1): >>> STYLE: Removing what appears to be a temporary file >>> >>> Johan Andruejol (1): >>> ENH: Fix normalization for null vectors and return the norm >>> >>> Jon Haitz Legarreta (1): >>> ENH: New test for itkLabelShapeOpeningImageFilter >>> >>> Kent Williams (9): >>> COMP: use find_package(VTK COMPONENTS) to specify just needed VTK >>> Components >>> BUG: ImageSources/test/CMakeLists.txt incorrect library var >>> reference >>> COMP: Fix coverity defects related to RegistrationV4 examples >>> COMP: silence warning of vnl_vector_fixed_ref::assert_size >>> COMP: Fix various Coverity warnings >>> COMP: Fix a typo in an error message print statement. >>> COMP: itk::Command-derived class used pointless dynamic_cast. >>> PERF: Don't recompute InternalInverse repeatedly >>> COMP: Correct orientation/spacing for Philips MultiFrame >>> >>> Mark Hiner (2): >>> ENH: Update SCIFIO remote module hash >>> BUG: Fix duplicate variables in Windows >>> >>> Matthew McCormick (105): >>> DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. >>> ENH: Move FFTComplexToComplexImageFilter out of Review. >>> ENH: Add VnlComplexToComplexFFTImageFilter. >>> BUG: Use fixed seed for Vnl FFT tests for repeatibility. >>> ENH: Bump CMakeLists.txt version to 4.7.0. >>> BUG: ArchiveTestingData.py future imports must occur at the >>> beginning. >>> BUG: Do not run vnl_test_na with broken libc++. >>> DOC: Remove Image2.cxx reference from Book 2. >>> DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. >>> DOC: Remove references to Book 1 sections from Book 2. >>> DOC: Make BinaryThresholdImageFilter not floating. >>> DOC: Fix Software Guide figure caption for FlipImageFilter. >>> DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. >>> DOC: Remove duplicate figure in >>> LaplacianRecursiveGaussianImageFilter2.cxx. >>> DOC: ImageRandomConstIteratorWithIndex table reference. >>> DOC: Fix Software Guide page overruns in >>> IterativeClosestPoint{1,2}.cxx. >>> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >>> BUG: Uninitialized m_TransformDirection in >>> ComplexToComplexFFTImageFilter. >>> BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. >>> STYLE: Fix style in VoronoiDiagram2D. >>> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >>> BUG: Bump GCCXML to 2014-08-06. >>> BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. >>> BUG: Fix Win MultiThreader check for successful process creation. >>> BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. >>> COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. >>> DOC: itk::statistics -> itk::Statistics. >>> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >>> BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >>> COMP: Improve const correctness of >>> GradientRecursiveGaussianImageFilter. >>> BUG: Call clear instead of empty on PatchBasedDenoising >>> EmptyCaches(). >>> BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >>> COMP: ThreadJob NULL not defined. >>> BUG: Fix alpha assignment for RGBA TIFF. >>> COMP: Remove unused typedefs in LevelSetsv4Visualization. >>> COMP: Remove unused typedef's in VtkGlue. >>> ENH: Mark BSplineWarping2Test as RUNS_LONG. >>> BUG: Fix Nifti IO read with large images. >>> COMP: Remove call for non-existent variable in Nifti debugging. >>> BUG: Close the file on Read and Write in HDF5TransformIO. >>> BUG: Remove InsightLegacy test code from TransformHDF5Test. >>> ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. >>> STYLE: Use SeriesUIDContainerType and FileNamesContainerType >>> ENH: Allow specification of orthogonality tolerance in rigid >>> transforms. >>> BUG: TransformFileReader does not clear its TransformList. >>> BUG: Prevent dangling pointer in HDF5TransformIO. >>> COMP: Do not use _stat64 with MinGW-32. >>> BUG: Improve thread-safety and performance of >>> PCAShapeSignedDistanceFunction. >>> DOC: itk::statistics -> itk::Statistics. >>> DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >>> DOC: Fix Software Guide page overruns in >>> IterativeClosestPoint{1,2}.cxx. >>> COMP: Address LaplacianDeformation Doxygen warnings. >>> BUG: TransformFileReader does not clear its TransformList. >>> BUG: Prevent dangling pointer in HDF5TransformIO. >>> COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >>> BUG: Do not return SmartPointers in >>> TimeVaryingVelocityFieldTransform >>> COMP: Do not wrap the FixedArray of Image SmartPointer's. >>> COMP: Add missing wrapping for TransformIOBaseTemplate. >>> COMP: Mark DeformableRegistration6Test as RUNS_LONG. >>> STYLE: Improve style in BinaryImageToLabelMapFilter. >>> BUG: Fix BinaryImageToLabelMapFilter on 1D image. >>> ENH: Improve precision of the joint PDF sum >>> BUG: Fix BinShrinkImageFilter for different input/output image >>> types. >>> COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >>> BUG: Use -py3 when building wrapping for Python 3. >>> COMP: Add missing wrapping for TransformIOBaseTemplate. >>> DOC: Improve ImageRegistration4 grammar. >>> ENH: Add IOTransformDCMTK Remote module. >>> BUG: gdcm::StringFilter recognizes backslash delimiter. >>> DOC: Add migration guide for GDCM Rescale slope intercept apply on >>> write. >>> COMP: Remove unused typedef's in GPU code. >>> STYLE: Improve style of HoughTransform2DLinesImageFilter example. >>> COMP: Use ConceptChecking for IterativeInverse dimension check. >>> COMP: Wrap TransformIOBaseTemplate for const SmartPointer. >>> COMP: Add warning exceptions for third party pcre, swig, gccxml. >>> ENH: Bump ITK version to 4.6.1. >>> BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. >>> BUG: Remove GaussianImageSource members shadowing >>> GenerateImageSource. >>> STYLE: Style fixes to ITKImageSources module. >>> BUG: GaussianSpatialFunction and GaborImageSource use >>> SpacePrecisionType. >>> BUG: Do not perform itk_download_attempt_check when not building >>> ITK. >>> DOC: Update GDCMImageIO rescale slope intercept doc. >>> BUG: Only register requestion IO COMPONENT modules. >>> BUG: Fix wrapping .i, .idx CMake dependencies. >>> COMP: Add VTK Python module when wrapping ITKVtkGlue. >>> STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. >>> STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType >>> typedef. >>> COMP: Add missing VTK module dependency for >>> LevelSetsv4Visualization. >>> BUG: By default, do not create any fixed parameters. >>> STYLE: Remove trivial method comments in itkTransform.hxx. >>> BUG: PolylineMask Filter's GenerateData is protected / virtual. >>> ENH: Add HigherOrderAccurateGradient Module. >>> BUG: Use input RequestedRegion Index in SliceBySliceImageFilter >>> internal. >>> COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. >>> STYLE: Style fixes for Transform classes. >>> DOC: Increase Doxygen LOOKUP_CACHE_SIZE. >>> BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. >>> DOC: Index Wiki examples with Doxygen. >>> COMP: Bump SphinxExamples remote module. >>> DOC: Index Sphinx examples in Doxygen. >>> COMP: Remove old java examples. >>> COMP: Remove duplicate DiffusionTensor3DReconstruction example >>> reference. >>> COMP: Address GradientAnisotropicDiffusionImageFilter example >>> settings. >>> COMP: Bump Sphinx Examples remote. >>> COMP: Bump WikiExamples remote. >>> >>> MetaIO Maintainers (1): >>> MetaIO (reduced) >>> >>> Michka Popoff (40): >>> ENH: Fixes for python 3 support >>> BUG: Add VTK_VERSION for older VTK versions >>> BUG: Improve SWIG version check >>> COMP: Add wrapping for ThreadPool and ThreadJob >>> COMP: Remove unimplemented DestroyPool method >>> COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping >>> COMP: Do not hide pygccxml warnings >>> ENH: Update links in readme file >>> BUG: Improve SWIG version check >>> BUG: Add VTK_VERSION for older VTK versions >>> STYLE: Remove trailing whitespaces >>> STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP >>> BUG: Fix memory leak in MetaImageIO after exception >>> ENH: Add script to update pygccxml from upstream >>> BUG: Update VTK minimum version (for release) >>> BUG: Fix memory leak in MetaImageIO after exception >>> ENH: Remove Sun OS compatibility for the wrappings >>> COMP: Fix for conversion to non-pointer like type warning >>> STYLE: LabelObject style >>> DOC: Remove broken link from LabelObject class description >>> ENH: Do not setup the python tests if not asked >>> ENH: Add new GetTypes() and GetTypesAsList() methods to the >>> template class >>> COMP: Fix CMP0054 warnings in wrappings >>> STYLE: Remove old cmake < 2.8.4 specific code >>> STYLE: Remove old cmake < 2.8.5 specific code >>> ENH: Update to PCRE 8.36 >>> COMP: Refactor Wrapping setup and fix legacy warnings >>> ENH: Add wrapping configuration to ITKConfig.cmake >>> STYLE: Some minor code cleanup in the wrapping setup >>> DOC: Fix typo in RelabelComponentImageFilter >>> ENH: Deprecate VectorResampleImageFilter >>> DOC: Add migration guide for ::Zero and ::One >>> ENH: Deprecate ::Zero and ::One >>> ENH: Add option to disable sorting by size in >>> itkRelabelComponentImageFilter >>> ENH: Add Vector and RGB wrapping to linear interpolator >>> STYLE: Remove SORT macro in wrappings >>> COMP: Fix warning for InterpolateImageFunction wrapping >>> COMP: Add a check for Blocks in GPU module >>> COMP: Bump SCIFIO to fix test build warnings >>> COMP: Fix wrapping of itkImageFunctionBase >>> >>> Nick Tustison (7): >>> BUG: Need to explicitly specify spline order. >>> ENH: Initializing the transform center. >>> BUG: Need to check the dynamic cast before any calls. >>> ENH: Adding modifications for point set metrics. >>> BUG: Need to specify TInternalComputationValueType for default >>> metric. >>> ENH: Adding sparse points to B-spline field estimate. >>> BUG: Uninitialized variables. >>> >>> Richard Beare (1): >>> ENH: Include TIFF tags in the MetaDataDictionary >>> >>> Taylor Braun-Jones (1): >>> BUG: Fix SliceBySliceImageFilter doesn't propagate information >>> internally >>> >>> Umang B (1): >>> ENH: Use thread pool to dispatch multithreading tasks >>> >>> Vivien Delmon (2): >>> BUG: ExtractImageFilter::CollapseToSubMatrix fix >>> ENH: Add a test on extracted directions in CollapseToSubMatrix mode >>> >>> Vladimir S. FONOV (1): >>> BUG: Fixing incorrect MINC style inverse transform >>> >>> >>> ----------------------------------------------------- >>> Errors or omissions? Please fix them here: >>> >>> >>> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing >>> >>> >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From DLRdave at aol.com Wed Dec 17 14:40:08 2014 From: DLRdave at aol.com (David Cole) Date: Wed, 17 Dec 2014 14:40:08 -0500 Subject: [ITK] [ITK-dev] ITK 4.7 Release Candidate 2 has been tagged! In-Reply-To: References: Message-ID: I did this build with the VS 2013 compiler, and the Ninja cmake generator, and it basically worked: https://open.cdash.org/buildSummary.php?buildid=3614855 The 3 test timeouts I guess are expected because it's a Debug build. I tried to do it by following just the directions in this email to run the dashboard, and there are some things I would add to future emails to make it even easier: - running "ctest" like that works fine for submitting an Experimental dashboard, but: it assumes you've configured an ITK build tree already with CMake... perhaps it should be mentioned that you need to run cmake first - when running CMake, and using make files or Ninja generator, the default build type appears to be Debug -- when configuring, use -D CMAKE_BUILD_TYPE=Release to avoid the long long long test times of a Debug build on Windows - when running ctest, use "-j 4" or "-j 8" or however many processors you can spare to actually run the tests..... My dashboard took over 4 hours because it was a Debug build, and I was running the exact command line in the email with ctest, and just simply forgot that when running a dashboard this way, you have to tell ctest how many processes to test at once... Bottom line: 4.7rc02 looks good to me, go for it! Cheers, David C. On Tue, Dec 16, 2014 at 2:42 AM, Matt McCormick wrote: > On behalf of the Insight Toolkit community, we are proud to announce that > ITK 4.7.0 release candidate 2 has been tagged and is available for testing! > Please test the release candidate in the coming days for an imminent > release. > > > To obtain the source code, > > git clone http://itk.org/ITK.git > cd ITK > git checkout -q --detach v4.7rc02 > > For more details, please see the Git documentation [1]. > > A few highlights for this release: all ITK examples from the Software Guide, > Wiki Examples, and SphinxExamples are new indexed and crossed linked in > Doxygen. So now when you go to your favorite filter or other object, say the > ResampleImageFilter, there is a large selection of examples in the examples > sections. This should make it much easier to fine sample code on how to use > an ITK class! TIFF IO has undergone a significant cleanup and speed-up, and > now TIFF tags are read into the MetaDataDictionary. Three new Remote Modules > are available, for gradient computation, DICOM IO, and QuadEdgeMesh > filtering. Python wrapping, CMake configuration, and registration continue > to improve. A new, experimental thread pool is available -- to enable set > the ITK_USE_THREADPOOL or call > itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). > > > > Please test the release candidate and share your experiences on the mailing > list, issue tracker, and Gerrit Code Review. Please help identify issues > submitting an Experimental build to the dashboard [2] with: > > ctest -M Experimental -T Configure -T Build -T Test -T Submit > > and notifying the mailing list. Testing your own applications against the > RC is also appreciated. > > > > Congratulations and well done to the 29 contributors to this release. We > would especially like to recognize the new contributors, Gert Wollny, Girish > Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan > Andruejol, and Ismael Belghiti. > > > The final release is scheduled for December 18th. > > [1] http://www.itk.org/Wiki/ITK/Git > > > [2] http://itk.org/Insight/Doxygen/html/examples.html > > > [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html > > > [2] http://open.cdash.org/index.php?project=Insight > > > > > New Features > ------------------ > > * Documentation Improvements > > - Update Software Guide registration examples to ITKv4 framework > > - Wiki and Sphinx examples are indexed in Doxygen > > - Clean Software Guide dashboard build > > > * Filtering Improvements > > - New Laplacian deformation filter?s for QuadEdgeMesh?s > > - IJ article: http://hdl.handle.net/10380/3410 > > - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations > > - Faster recursive Gaussian on VectorImage > > > * ImageIO improvements > > - PNG sCAL unit support > > - TIFF IO performance greatly improved > > - TIFF tags read into Image MetaDataDictionary > > - MetaIO updated > > - Better support for system GDCM > > > * Infrastructure improvements > > - New method to erase a MetaDataDictionary entry > > - New global method to set physical space tolerance > > - New, experimental thread pool support > > - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue() > and ::OneValue() > > - VTK bridge modules only request required VTK modules > > > * New Remote Modules > > - Higher Order Accurate Gradient > > - http://hdl.handle.net/10380/3231 > > - IO Transform DCMTK > > - http://hdl.handle.net/10380/3468 > > - Subdivision Quad Edge Mesh Filters > > - http://hdl.handle.net/10380/3307 > > > * Registration improvements > > - LandmarkBasedTransformInitializer supports BSplineTransform > > - Transverse inverse consistency increased > > - Automatic initialization of the transform center for multi-stage > registrations > > - Sparse point B-spline field estimate > > - Mutual information faster, lower memory usage > > > * Wrapping improvements > > - Wrapping now builds without type warnings > > - pygccxml bumped to 1.6.2 > > - Latest GCCXML > > - CMake wrapping infrastructure cleanup > > - Build with Ninja CMake generator > > - New GetTypes() and GetTypesAsList() methods > > - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake > > > > * Many style improvements -- ITK gets more stylish with every release! > > > * Improved code coverage -- we are over 85%! > > > * *Lots* of important bug fixes > > > * And much more! See details in the log below. > > > List of changes since v4.7-rc01 > > -------------------------------------- > > > Ali Ghayoor (1): > DOC: Revise the registration examples of ITKSoftwareGuide > > Arnaud Gelas (3): > ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module > COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh > COMP: fix warnings on dashboard for Subdivision remote module > > Bradley Lowekamp (5): > BUG: Fix segfault when setting displacement field as null > BUG: Don't enable SSE rounding with OSX and gccxml > BUG: Add portable access to Tiff field name > BUG: Fix conversion compilation error > BUG: Rename remote module FDFImageIO -> IOFDF > > Christopher Mullins (6): > STYLE: Fix line length in OpenJPEG license for 80 character. > DOC: Finish the ImageLinearIteratorWithIndex example. > DOC: Text and picture problems, book2 > BUG: Fix text in margin issues > DOC: Edits for the beginning of chapter 5, Statistics > DOC: Fix empty code block. > > Cory Quammen (1): > COMP: Avoid including VTK_USE_FILE within ITK > > Kent Williams (1): > ENH: Add test to exercise issue with Transform::GetInverse > > Matthew McCormick (7): > BUG: Register AzimuthElevationToCartesianTransform to factories. > DOC: Update texture feature class references. > BUG: Fix texture feature correlation computation for constant image. > STYLE: Put ImageToImageFilterCommon in its own file. > BUG: Wrap ImageToImageFilterCommon. > STYLE: Put ImageSourceCommon in its own file. > COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. > > Michka Popoff (1): > ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter > wrappings > > Ziv Yaniv (1): > COMP: fixed warnings from gcc4.1.2, made implicit casts explicit > > > List of changes since v4.6.0 > > -------------------------------------- > > > Alexander Schmidt-Richberg (1): > > ENH: Updated Remote Module VariationalRegistration to new git tag > > > Ali Ghayoor (10): > > ENH: Make ITKv4 compatible with ITKSoftwareGuide > > ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 > > ENH: Convert three ImageRegistration Examples to ITKv4 > > ENH: Add multi-Res and multistage registration Examples to ITKv4 > > ENH: Convert DeformableReg examples to ITKv4 reg framework > > BUG: Expand a test to reflect multi-metric registration bug > > BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 > > ENH: Add direct initialization to SyN registration > > ENH: Direct initialization of SyN by restoring the state > > ENH: LandmarkBasedTransformInitializer supports BSplineTransformType > > > Arnaud Gelas (15): > > COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization > > ENH: Importing Laplacian Deformation for QuadEdgeMesh > > DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage > > ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() > > ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter > > BUG: fix gdcm version in GDCMImageIO. > > COMP: missing cast when calling gdcm::DataElement::SetByteValue > > COMP: missing cast when calling gdcm::DataElement::SetByteValue > > ENH: increase LaplacianDeformation code coverage > > STYLE: use typedef rather than inheritance > > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is > false > > BUG: split include directories into appropriate cmake variables HDF5 > > BUG: missing gdcm libraries when using system GDCM > > DOC: fix doxygen documentaiton for > itk::LaplacianDeformationQuadEdgeMeshFilter > > ENH: Add one method to erase a tag into MetaDataDictionary > > > Bill Lorensen (5): > > ENH: Specify required VTK modules > > COMP: Wiki examples require additional vtk modules > > ENH: Modify WikiExamples remote config > > COMP: Bad test signature > > COMP: Update tag for wiki examples > > > Brad King (6): > > COMP: Fix vxl_config_macros usage of CMake check macros > > ENH: Use if(DEFINED) to simplify conditions > > COMP: Fix vxl_config_macros checks broken by refactoring > > COMP: Fix one more vxl_config_macros check broken by refactoring > > BUG: Fix itk_module_config for repeated calls > > BUG: Fix itk_module_config for repeated calls > > > Bradley Lowekamp (52): > > ENH: Adding License file from upstream MetaIO > > ENH: Adding script to update MetaIO from upstream > > ENH: Remove ITK MetaIO to prepare for upstream import > > PERF: Remove dynamically allocated temporary in evaluate method > > COMP: Fix variable type for Set/Get macros > > BUG: Implement ITK Style Singleton design pattern > > ENH: Add no throw exception specification for UnRegister methods > > COMP: Must specify order as "noexcept override" > > BUG: Add GetInverse for IdentityTransform > > ENH: Adding SetIdentity method to base DisplacementField class > > BUG: Remove unused redefinition of NULL > > BUG: Don't print to std::cout in PrintSelf > > ENH: Prefer the PrintSelfObjectMacro for printing nested objects > > BUG: Use METER of sCAL scale unit > > BUG: Use PNG_SCALE_METER for PNG sCAL unit > > BUG: Use METER of sCAL scale unit > > BUG: Use PNG_SCALE_METER for PNG sCAL unit > > COMP: Fix signed to unsigned int comparison > > BUG: Fix overflows computing size of read tiff image > > ENH: Extract TiffReaderInternal to separate file > > ENH: Refactor ReadTwoSamplePerPixelImage into template function > > ENH: Refactor GenericReadImage into template function > > BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and > LSMImageIO ) > > ENH: Refactor method to convert RGBA image to output buffer > > ENH: Refactor duplicated code to read a page > > BUG: Fix right oriented tiff images > > BUG: Remove dead separated plannar code, add test > > STYLE: Fix minor kwstyle defects in test and test results > > BUG: Use array delete operator for array new allocations > > ENH: add arbitrary TIFF TAGs to meta-data dictionary > > ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage > > BUG: Address Coverity warning about null pointer dereferences > > ENH: Remove support for TIFF tile as 3D and dead code > > ENH: RGBA read images should stay unchanged. > > BUG: Override method to MakeOutput by name > > ENH: Refactor per pixel conversion function to per scan-line method > > PERF: Refactor color table lookup > > BUG: Adding missing parentheses around boolean expression > > ENH: adding TIFFImageIO test for RGB palette images > > PERF: Improve recursive Gaussian perfromance with VectorImages > > ENH: Query libtiff to determine compression support > > BUG: Support TIFF tiled image with TIFFReadRGBAImage > > BUG: Use SizeValueType for length of scanline > > PERF: Store causal results directly in output buffers > > COMP: Add explicit conversion to const char > > COMP: Explicitly add override to GetNameOfClass method > > COMP: Address internal segmentation fault with Intel compiler > > ENH: Adding method to set global physical space tolerance > > COMP: Explicitly add override to GetNameOfClass method > > BUG: Add new TypeMacro for non-overloaded classes > > BUG: Fix obscure race condition on access thread pool initialization > > BUG: Updating FDFImageIO remote module > > > Christopher Mullins (15): > > COMP: Allows latex to compile for ITKSoftwareGuide > > COMP: Allows latex to compile for ITKSoftwareGuide > > COMP: Wrap MeshBase templates > > COMP: Wrap MeshBase templates > > COMP: Fix warning in BlockMatchingImageFilter > > STYLE: Line lengths in examples should be no longer than 80 chars. > > COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. > > COMP: Fix LaTeX warnings. > > STYLE: Fix formatting/punctuation errors. > > STYLE: Formatting and punctuation fixes. > > DOC: Edits for Book 2 Chapter 1 documentation in the Examples. > > DOC: Edits for book 2 chapter 2. > > DOC: More chapter 2 edits > > DOC: Book 2 Chapter 3 edits (part 1) > > DOC: book 2 chapter 4 Segmentation edits > > > Danny Perry (2): > > BUG: adding test for vnl_sparse_matrix::mult() > > BUG: size of q buffer should actually be (this->rows())*pcols. > > > David T. Chen (1): > > DOC: Fixed HistogramThresholdImageFitler > > > Dirk Padfield (1): > > BUG: Corrected processing of last sigma > > > GCC-XML Upstream (1): > > ENH: pygccxml v1.6.2 (reduced) > > > Gert Wollny (1): > > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > > Girish Mallya (1): > > BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. > > > Hans Johnson (24): > > COMP: Add tolerance for comparing floating point > > PERF: Remove non-threadable algorithm components > > COMP: Add tolerance for comparing floating point > > PERF: Remove non-threadable algorithm components > > PERF: Remove large foot print of PDF derivatives. > > PERF: Revert Remove large foot print of PDF derivatives. > > STYLE: Test against almost equal for floating point values > > STYLE: Non-exact floating point testing > > PERF: Distribute initialization per thread buffers > > ENH: Remove unnecessary mutable qualifier. > > STYLE: Remove comment with no meaning. > > ENH: Moved accumlator logic to main MI class > > ENH: Allow staggering of accumulations per thread. > > PERF: Zero reset thread buffers during finalize > > BUG: Syntax error in comment > > PERF: Add non-blocking mutex locking. > > ENH: Use TryLock minimize thread stalls > > BUG: ThreadedIndexedContainerPartitioner is inclusive > > STYLE: Remove include_regular_expression from Examples > > BUG: Demonstrate Inv(Inv(T)) != T > > BUG: Ensure Inv(Inv(T)) == T for transforms > > COMP: Valgrind detects uninitialized memory read > > COMP: Missing required base class API component > > ENH: Expand interface for selecting threadpool > > > Ismael Belghiti (1): > > DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter > > > Jim Miller (1): > > STYLE: Removing what appears to be a temporary file > > > Johan Andruejol (1): > > ENH: Fix normalization for null vectors and return the norm > > > Jon Haitz Legarreta (1): > > ENH: New test for itkLabelShapeOpeningImageFilter > > > Kent Williams (9): > > COMP: use find_package(VTK COMPONENTS) to specify just needed VTK > Components > > BUG: ImageSources/test/CMakeLists.txt incorrect library var reference > > COMP: Fix coverity defects related to RegistrationV4 examples > > COMP: silence warning of vnl_vector_fixed_ref::assert_size > > COMP: Fix various Coverity warnings > > COMP: Fix a typo in an error message print statement. > > COMP: itk::Command-derived class used pointless dynamic_cast. > > PERF: Don't recompute InternalInverse repeatedly > > COMP: Correct orientation/spacing for Philips MultiFrame > > > Mark Hiner (2): > > ENH: Update SCIFIO remote module hash > > BUG: Fix duplicate variables in Windows > > > Matthew McCormick (105): > > DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. > > ENH: Move FFTComplexToComplexImageFilter out of Review. > > ENH: Add VnlComplexToComplexFFTImageFilter. > > BUG: Use fixed seed for Vnl FFT tests for repeatibility. > > ENH: Bump CMakeLists.txt version to 4.7.0. > > BUG: ArchiveTestingData.py future imports must occur at the beginning. > > BUG: Do not run vnl_test_na with broken libc++. > > DOC: Remove Image2.cxx reference from Book 2. > > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > > DOC: Remove references to Book 1 sections from Book 2. > > DOC: Make BinaryThresholdImageFilter not floating. > > DOC: Fix Software Guide figure caption for FlipImageFilter. > > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > > DOC: ImageRandomConstIteratorWithIndex table reference. > > DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > > BUG: Uninitialized m_TransformDirection in > ComplexToComplexFFTImageFilter. > > BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. > > STYLE: Fix style in VoronoiDiagram2D. > > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > > BUG: Bump GCCXML to 2014-08-06. > > BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. > > BUG: Fix Win MultiThreader check for successful process creation. > > BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. > > COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. > > DOC: itk::statistics -> itk::Statistics. > > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > > COMP: Improve const correctness of > GradientRecursiveGaussianImageFilter. > > BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). > > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > > COMP: ThreadJob NULL not defined. > > BUG: Fix alpha assignment for RGBA TIFF. > > COMP: Remove unused typedefs in LevelSetsv4Visualization. > > COMP: Remove unused typedef's in VtkGlue. > > ENH: Mark BSplineWarping2Test as RUNS_LONG. > > BUG: Fix Nifti IO read with large images. > > COMP: Remove call for non-existent variable in Nifti debugging. > > BUG: Close the file on Read and Write in HDF5TransformIO. > > BUG: Remove InsightLegacy test code from TransformHDF5Test. > > ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. > > STYLE: Use SeriesUIDContainerType and FileNamesContainerType > > ENH: Allow specification of orthogonality tolerance in rigid > transforms. > > BUG: TransformFileReader does not clear its TransformList. > > BUG: Prevent dangling pointer in HDF5TransformIO. > > COMP: Do not use _stat64 with MinGW-32. > > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > > DOC: itk::statistics -> itk::Statistics. > > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > > DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > > COMP: Address LaplacianDeformation Doxygen warnings. > > BUG: TransformFileReader does not clear its TransformList. > > BUG: Prevent dangling pointer in HDF5TransformIO. > > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > > COMP: Do not wrap the FixedArray of Image SmartPointer's. > > COMP: Add missing wrapping for TransformIOBaseTemplate. > > COMP: Mark DeformableRegistration6Test as RUNS_LONG. > > STYLE: Improve style in BinaryImageToLabelMapFilter. > > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > > ENH: Improve precision of the joint PDF sum > > BUG: Fix BinShrinkImageFilter for different input/output image types. > > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > > BUG: Use -py3 when building wrapping for Python 3. > > COMP: Add missing wrapping for TransformIOBaseTemplate. > > DOC: Improve ImageRegistration4 grammar. > > ENH: Add IOTransformDCMTK Remote module. > > BUG: gdcm::StringFilter recognizes backslash delimiter. > > DOC: Add migration guide for GDCM Rescale slope intercept apply on > write. > > COMP: Remove unused typedef's in GPU code. > > STYLE: Improve style of HoughTransform2DLinesImageFilter example. > > COMP: Use ConceptChecking for IterativeInverse dimension check. > > COMP: Wrap TransformIOBaseTemplate for const SmartPointer. > > COMP: Add warning exceptions for third party pcre, swig, gccxml. > > ENH: Bump ITK version to 4.6.1. > > BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. > > BUG: Remove GaussianImageSource members shadowing GenerateImageSource. > > STYLE: Style fixes to ITKImageSources module. > > BUG: GaussianSpatialFunction and GaborImageSource use > SpacePrecisionType. > > BUG: Do not perform itk_download_attempt_check when not building ITK. > > DOC: Update GDCMImageIO rescale slope intercept doc. > > BUG: Only register requestion IO COMPONENT modules. > > BUG: Fix wrapping .i, .idx CMake dependencies. > > COMP: Add VTK Python module when wrapping ITKVtkGlue. > > STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. > > STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. > > COMP: Add missing VTK module dependency for LevelSetsv4Visualization. > > BUG: By default, do not create any fixed parameters. > > STYLE: Remove trivial method comments in itkTransform.hxx. > > BUG: PolylineMask Filter's GenerateData is protected / virtual. > > ENH: Add HigherOrderAccurateGradient Module. > > BUG: Use input RequestedRegion Index in SliceBySliceImageFilter > internal. > > COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. > > STYLE: Style fixes for Transform classes. > > DOC: Increase Doxygen LOOKUP_CACHE_SIZE. > > BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. > > DOC: Index Wiki examples with Doxygen. > > COMP: Bump SphinxExamples remote module. > > DOC: Index Sphinx examples in Doxygen. > > COMP: Remove old java examples. > > COMP: Remove duplicate DiffusionTensor3DReconstruction example > reference. > > COMP: Address GradientAnisotropicDiffusionImageFilter example settings. > > COMP: Bump Sphinx Examples remote. > > COMP: Bump WikiExamples remote. > > > MetaIO Maintainers (1): > > MetaIO (reduced) > > > Michka Popoff (40): > > ENH: Fixes for python 3 support > > BUG: Add VTK_VERSION for older VTK versions > > BUG: Improve SWIG version check > > COMP: Add wrapping for ThreadPool and ThreadJob > > COMP: Remove unimplemented DestroyPool method > > COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping > > COMP: Do not hide pygccxml warnings > > ENH: Update links in readme file > > BUG: Improve SWIG version check > > BUG: Add VTK_VERSION for older VTK versions > > STYLE: Remove trailing whitespaces > > STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP > > BUG: Fix memory leak in MetaImageIO after exception > > ENH: Add script to update pygccxml from upstream > > BUG: Update VTK minimum version (for release) > > BUG: Fix memory leak in MetaImageIO after exception > > ENH: Remove Sun OS compatibility for the wrappings > > COMP: Fix for conversion to non-pointer like type warning > > STYLE: LabelObject style > > DOC: Remove broken link from LabelObject class description > > ENH: Do not setup the python tests if not asked > > ENH: Add new GetTypes() and GetTypesAsList() methods to the template > class > > COMP: Fix CMP0054 warnings in wrappings > > STYLE: Remove old cmake < 2.8.4 specific code > > STYLE: Remove old cmake < 2.8.5 specific code > > ENH: Update to PCRE 8.36 > > COMP: Refactor Wrapping setup and fix legacy warnings > > ENH: Add wrapping configuration to ITKConfig.cmake > > STYLE: Some minor code cleanup in the wrapping setup > > DOC: Fix typo in RelabelComponentImageFilter > > ENH: Deprecate VectorResampleImageFilter > > DOC: Add migration guide for ::Zero and ::One > > ENH: Deprecate ::Zero and ::One > > ENH: Add option to disable sorting by size in > itkRelabelComponentImageFilter > > ENH: Add Vector and RGB wrapping to linear interpolator > > STYLE: Remove SORT macro in wrappings > > COMP: Fix warning for InterpolateImageFunction wrapping > > COMP: Add a check for Blocks in GPU module > > COMP: Bump SCIFIO to fix test build warnings > > COMP: Fix wrapping of itkImageFunctionBase > > > Nick Tustison (7): > > BUG: Need to explicitly specify spline order. > > ENH: Initializing the transform center. > > BUG: Need to check the dynamic cast before any calls. > > ENH: Adding modifications for point set metrics. > > BUG: Need to specify TInternalComputationValueType for default metric. > > ENH: Adding sparse points to B-spline field estimate. > > BUG: Uninitialized variables. > > > Richard Beare (1): > > ENH: Include TIFF tags in the MetaDataDictionary > > > Taylor Braun-Jones (1): > > BUG: Fix SliceBySliceImageFilter doesn't propagate information > internally > > > Umang B (1): > > ENH: Use thread pool to dispatch multithreading tasks > > > Vivien Delmon (2): > > BUG: ExtractImageFilter::CollapseToSubMatrix fix > > ENH: Add a test on extracted directions in CollapseToSubMatrix mode > > > Vladimir S. FONOV (1): > > BUG: Fixing incorrect MINC style inverse transform > > > > ----------------------------------------------------- > > Errors or omissions? Please fix them here: > > > https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing > > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > From matt.mccormick at kitware.com Wed Dec 17 15:34:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Dec 2014 15:34:56 -0500 Subject: [ITK] [ITK-dev] ITK 4.7 Release Candidate 2 has been tagged! In-Reply-To: References: Message-ID: Hi Dave, Thanks for the build and feedback! I've improve the testing instructions based on your suggestions. There is now explicit cmake configuration steps, and a -j flag to ctest. I am surprised that you got a Debug build by default -- we try to make it Release for a clean build [1]. Thanks, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=CMakeLists.txt;h=a913e4e065239edbf8d89b51969a8a51fc67fb8e;hb=HEAD#l95 On Wed, Dec 17, 2014 at 2:40 PM, David Cole wrote: > > I did this build with the VS 2013 compiler, and the Ninja cmake > generator, and it basically worked: > > https://open.cdash.org/buildSummary.php?buildid=3614855 > > The 3 test timeouts I guess are expected because it's a Debug build. > > I tried to do it by following just the directions in this email to run > the dashboard, and there are some things I would add to future emails > to make it even easier: > > - running "ctest" like that works fine for submitting an Experimental > dashboard, but: it assumes you've configured an ITK build tree already > with CMake... perhaps it should be mentioned that you need to run > cmake first > > - when running CMake, and using make files or Ninja generator, the > default build type appears to be Debug -- when configuring, use -D > CMAKE_BUILD_TYPE=Release to avoid the long long long test times of a > Debug build on Windows > > - when running ctest, use "-j 4" or "-j 8" or however many processors > you can spare to actually run the tests..... My dashboard took over 4 > hours because it was a Debug build, and I was running the exact > command line in the email with ctest, and just simply forgot that when > running a dashboard this way, you have to tell ctest how many > processes to test at once... > > Bottom line: > 4.7rc02 looks good to me, go for it! > > > Cheers, > David C. > > > > On Tue, Dec 16, 2014 at 2:42 AM, Matt McCormick > wrote: > > On behalf of the Insight Toolkit community, we are proud to announce that > > ITK 4.7.0 release candidate 2 has been tagged and is available for > testing! > > Please test the release candidate in the coming days for an imminent > > release. > > > > > > To obtain the source code, > > > > git clone http://itk.org/ITK.git > > cd ITK > > git checkout -q --detach v4.7rc02 > > > > For more details, please see the Git documentation [1]. > > > > A few highlights for this release: all ITK examples from the Software > Guide, > > Wiki Examples, and SphinxExamples are new indexed and crossed linked in > > Doxygen. So now when you go to your favorite filter or other object, say > the > > ResampleImageFilter, there is a large selection of examples in the > examples > > sections. This should make it much easier to fine sample code on how to > use > > an ITK class! TIFF IO has undergone a significant cleanup and speed-up, > and > > now TIFF tags are read into the MetaDataDictionary. Three new Remote > Modules > > are available, for gradient computation, DICOM IO, and QuadEdgeMesh > > filtering. Python wrapping, CMake configuration, and registration > continue > > to improve. A new, experimental thread pool is available -- to enable set > > the ITK_USE_THREADPOOL or call > > itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). > > > > > > > > Please test the release candidate and share your experiences on the > mailing > > list, issue tracker, and Gerrit Code Review. Please help identify issues > > submitting an Experimental build to the dashboard [2] with: > > > > ctest -M Experimental -T Configure -T Build -T Test -T Submit > > > > and notifying the mailing list. Testing your own applications against > the > > RC is also appreciated. > > > > > > > > Congratulations and well done to the 29 contributors to this release. We > > would especially like to recognize the new contributors, Gert Wollny, > Girish > > Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan > > Andruejol, and Ismael Belghiti. > > > > > > The final release is scheduled for December 18th. > > > > [1] http://www.itk.org/Wiki/ITK/Git > > > > > > [2] http://itk.org/Insight/Doxygen/html/examples.html > > > > > > [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html > > > > > > [2] http://open.cdash.org/index.php?project=Insight > > > > > > > > > > New Features > > ------------------ > > > > * Documentation Improvements > > > > - Update Software Guide registration examples to ITKv4 framework > > > > - Wiki and Sphinx examples are indexed in Doxygen > > > > - Clean Software Guide dashboard build > > > > > > * Filtering Improvements > > > > - New Laplacian deformation filter?s for QuadEdgeMesh?s > > > > - IJ article: http://hdl.handle.net/10380/3410 > > > > - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations > > > > - Faster recursive Gaussian on VectorImage > > > > > > * ImageIO improvements > > > > - PNG sCAL unit support > > > > - TIFF IO performance greatly improved > > > > - TIFF tags read into Image MetaDataDictionary > > > > - MetaIO updated > > > > - Better support for system GDCM > > > > > > * Infrastructure improvements > > > > - New method to erase a MetaDataDictionary entry > > > > - New global method to set physical space tolerance > > > > - New, experimental thread pool support > > > > - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue() > > and ::OneValue() > > > > - VTK bridge modules only request required VTK modules > > > > > > * New Remote Modules > > > > - Higher Order Accurate Gradient > > > > - http://hdl.handle.net/10380/3231 > > > > - IO Transform DCMTK > > > > - http://hdl.handle.net/10380/3468 > > > > - Subdivision Quad Edge Mesh Filters > > > > - http://hdl.handle.net/10380/3307 > > > > > > * Registration improvements > > > > - LandmarkBasedTransformInitializer supports BSplineTransform > > > > - Transverse inverse consistency increased > > > > - Automatic initialization of the transform center for multi-stage > > registrations > > > > - Sparse point B-spline field estimate > > > > - Mutual information faster, lower memory usage > > > > > > * Wrapping improvements > > > > - Wrapping now builds without type warnings > > > > - pygccxml bumped to 1.6.2 > > > > - Latest GCCXML > > > > - CMake wrapping infrastructure cleanup > > > > - Build with Ninja CMake generator > > > > - New GetTypes() and GetTypesAsList() methods > > > > - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake > > > > > > > > * Many style improvements -- ITK gets more stylish with every release! > > > > > > * Improved code coverage -- we are over 85%! > > > > > > * *Lots* of important bug fixes > > > > > > * And much more! See details in the log below. > > > > > > List of changes since v4.7-rc01 > > > > -------------------------------------- > > > > > > Ali Ghayoor (1): > > DOC: Revise the registration examples of ITKSoftwareGuide > > > > Arnaud Gelas (3): > > ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module > > COMP: address clang -Winconsistent-missing-override in > ITKQuadEdgeMesh > > COMP: fix warnings on dashboard for Subdivision remote module > > > > Bradley Lowekamp (5): > > BUG: Fix segfault when setting displacement field as null > > BUG: Don't enable SSE rounding with OSX and gccxml > > BUG: Add portable access to Tiff field name > > BUG: Fix conversion compilation error > > BUG: Rename remote module FDFImageIO -> IOFDF > > > > Christopher Mullins (6): > > STYLE: Fix line length in OpenJPEG license for 80 character. > > DOC: Finish the ImageLinearIteratorWithIndex example. > > DOC: Text and picture problems, book2 > > BUG: Fix text in margin issues > > DOC: Edits for the beginning of chapter 5, Statistics > > DOC: Fix empty code block. > > > > Cory Quammen (1): > > COMP: Avoid including VTK_USE_FILE within ITK > > > > Kent Williams (1): > > ENH: Add test to exercise issue with Transform::GetInverse > > > > Matthew McCormick (7): > > BUG: Register AzimuthElevationToCartesianTransform to factories. > > DOC: Update texture feature class references. > > BUG: Fix texture feature correlation computation for constant image. > > STYLE: Put ImageToImageFilterCommon in its own file. > > BUG: Wrap ImageToImageFilterCommon. > > STYLE: Put ImageSourceCommon in its own file. > > COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. > > > > Michka Popoff (1): > > ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter > > wrappings > > > > Ziv Yaniv (1): > > COMP: fixed warnings from gcc4.1.2, made implicit casts explicit > > > > > > List of changes since v4.6.0 > > > > -------------------------------------- > > > > > > Alexander Schmidt-Richberg (1): > > > > ENH: Updated Remote Module VariationalRegistration to new git tag > > > > > > Ali Ghayoor (10): > > > > ENH: Make ITKv4 compatible with ITKSoftwareGuide > > > > ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 > > > > ENH: Convert three ImageRegistration Examples to ITKv4 > > > > ENH: Add multi-Res and multistage registration Examples to ITKv4 > > > > ENH: Convert DeformableReg examples to ITKv4 reg framework > > > > BUG: Expand a test to reflect multi-metric registration bug > > > > BUG: Fix multi metric point sampling bug in > ImageRegistrationMethodv4 > > > > ENH: Add direct initialization to SyN registration > > > > ENH: Direct initialization of SyN by restoring the state > > > > ENH: LandmarkBasedTransformInitializer supports BSplineTransformType > > > > > > Arnaud Gelas (15): > > > > COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization > > > > ENH: Importing Laplacian Deformation for QuadEdgeMesh > > > > DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage > > > > ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls > Modified() > > > > ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter > > > > BUG: fix gdcm version in GDCMImageIO. > > > > COMP: missing cast when calling gdcm::DataElement::SetByteValue > > > > COMP: missing cast when calling gdcm::DataElement::SetByteValue > > > > ENH: increase LaplacianDeformation code coverage > > > > STYLE: use typedef rather than inheritance > > > > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is > > false > > > > BUG: split include directories into appropriate cmake variables HDF5 > > > > BUG: missing gdcm libraries when using system GDCM > > > > DOC: fix doxygen documentaiton for > > itk::LaplacianDeformationQuadEdgeMeshFilter > > > > ENH: Add one method to erase a tag into MetaDataDictionary > > > > > > Bill Lorensen (5): > > > > ENH: Specify required VTK modules > > > > COMP: Wiki examples require additional vtk modules > > > > ENH: Modify WikiExamples remote config > > > > COMP: Bad test signature > > > > COMP: Update tag for wiki examples > > > > > > Brad King (6): > > > > COMP: Fix vxl_config_macros usage of CMake check macros > > > > ENH: Use if(DEFINED) to simplify conditions > > > > COMP: Fix vxl_config_macros checks broken by refactoring > > > > COMP: Fix one more vxl_config_macros check broken by refactoring > > > > BUG: Fix itk_module_config for repeated calls > > > > BUG: Fix itk_module_config for repeated calls > > > > > > Bradley Lowekamp (52): > > > > ENH: Adding License file from upstream MetaIO > > > > ENH: Adding script to update MetaIO from upstream > > > > ENH: Remove ITK MetaIO to prepare for upstream import > > > > PERF: Remove dynamically allocated temporary in evaluate method > > > > COMP: Fix variable type for Set/Get macros > > > > BUG: Implement ITK Style Singleton design pattern > > > > ENH: Add no throw exception specification for UnRegister methods > > > > COMP: Must specify order as "noexcept override" > > > > BUG: Add GetInverse for IdentityTransform > > > > ENH: Adding SetIdentity method to base DisplacementField class > > > > BUG: Remove unused redefinition of NULL > > > > BUG: Don't print to std::cout in PrintSelf > > > > ENH: Prefer the PrintSelfObjectMacro for printing nested objects > > > > BUG: Use METER of sCAL scale unit > > > > BUG: Use PNG_SCALE_METER for PNG sCAL unit > > > > BUG: Use METER of sCAL scale unit > > > > BUG: Use PNG_SCALE_METER for PNG sCAL unit > > > > COMP: Fix signed to unsigned int comparison > > > > BUG: Fix overflows computing size of read tiff image > > > > ENH: Extract TiffReaderInternal to separate file > > > > ENH: Refactor ReadTwoSamplePerPixelImage into template function > > > > ENH: Refactor GenericReadImage into template function > > > > BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and > > LSMImageIO ) > > > > ENH: Refactor method to convert RGBA image to output buffer > > > > ENH: Refactor duplicated code to read a page > > > > BUG: Fix right oriented tiff images > > > > BUG: Remove dead separated plannar code, add test > > > > STYLE: Fix minor kwstyle defects in test and test results > > > > BUG: Use array delete operator for array new allocations > > > > ENH: add arbitrary TIFF TAGs to meta-data dictionary > > > > ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage > > > > BUG: Address Coverity warning about null pointer dereferences > > > > ENH: Remove support for TIFF tile as 3D and dead code > > > > ENH: RGBA read images should stay unchanged. > > > > BUG: Override method to MakeOutput by name > > > > ENH: Refactor per pixel conversion function to per scan-line method > > > > PERF: Refactor color table lookup > > > > BUG: Adding missing parentheses around boolean expression > > > > ENH: adding TIFFImageIO test for RGB palette images > > > > PERF: Improve recursive Gaussian perfromance with VectorImages > > > > ENH: Query libtiff to determine compression support > > > > BUG: Support TIFF tiled image with TIFFReadRGBAImage > > > > BUG: Use SizeValueType for length of scanline > > > > PERF: Store causal results directly in output buffers > > > > COMP: Add explicit conversion to const char > > > > COMP: Explicitly add override to GetNameOfClass method > > > > COMP: Address internal segmentation fault with Intel compiler > > > > ENH: Adding method to set global physical space tolerance > > > > COMP: Explicitly add override to GetNameOfClass method > > > > BUG: Add new TypeMacro for non-overloaded classes > > > > BUG: Fix obscure race condition on access thread pool initialization > > > > BUG: Updating FDFImageIO remote module > > > > > > Christopher Mullins (15): > > > > COMP: Allows latex to compile for ITKSoftwareGuide > > > > COMP: Allows latex to compile for ITKSoftwareGuide > > > > COMP: Wrap MeshBase templates > > > > COMP: Wrap MeshBase templates > > > > COMP: Fix warning in BlockMatchingImageFilter > > > > STYLE: Line lengths in examples should be no longer than 80 chars. > > > > COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. > > > > COMP: Fix LaTeX warnings. > > > > STYLE: Fix formatting/punctuation errors. > > > > STYLE: Formatting and punctuation fixes. > > > > DOC: Edits for Book 2 Chapter 1 documentation in the Examples. > > > > DOC: Edits for book 2 chapter 2. > > > > DOC: More chapter 2 edits > > > > DOC: Book 2 Chapter 3 edits (part 1) > > > > DOC: book 2 chapter 4 Segmentation edits > > > > > > Danny Perry (2): > > > > BUG: adding test for vnl_sparse_matrix::mult() > > > > BUG: size of q buffer should actually be (this->rows())*pcols. > > > > > > David T. Chen (1): > > > > DOC: Fixed HistogramThresholdImageFitler > > > > > > Dirk Padfield (1): > > > > BUG: Corrected processing of last sigma > > > > > > GCC-XML Upstream (1): > > > > ENH: pygccxml v1.6.2 (reduced) > > > > > > Gert Wollny (1): > > > > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > > > > > Girish Mallya (1): > > > > BUG: Tests added for BinaryImageToLabelMapFilter for single-row > images. > > > > > > Hans Johnson (24): > > > > COMP: Add tolerance for comparing floating point > > > > PERF: Remove non-threadable algorithm components > > > > COMP: Add tolerance for comparing floating point > > > > PERF: Remove non-threadable algorithm components > > > > PERF: Remove large foot print of PDF derivatives. > > > > PERF: Revert Remove large foot print of PDF derivatives. > > > > STYLE: Test against almost equal for floating point values > > > > STYLE: Non-exact floating point testing > > > > PERF: Distribute initialization per thread buffers > > > > ENH: Remove unnecessary mutable qualifier. > > > > STYLE: Remove comment with no meaning. > > > > ENH: Moved accumlator logic to main MI class > > > > ENH: Allow staggering of accumulations per thread. > > > > PERF: Zero reset thread buffers during finalize > > > > BUG: Syntax error in comment > > > > PERF: Add non-blocking mutex locking. > > > > ENH: Use TryLock minimize thread stalls > > > > BUG: ThreadedIndexedContainerPartitioner is inclusive > > > > STYLE: Remove include_regular_expression from Examples > > > > BUG: Demonstrate Inv(Inv(T)) != T > > > > BUG: Ensure Inv(Inv(T)) == T for transforms > > > > COMP: Valgrind detects uninitialized memory read > > > > COMP: Missing required base class API component > > > > ENH: Expand interface for selecting threadpool > > > > > > Ismael Belghiti (1): > > > > DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter > > > > > > Jim Miller (1): > > > > STYLE: Removing what appears to be a temporary file > > > > > > Johan Andruejol (1): > > > > ENH: Fix normalization for null vectors and return the norm > > > > > > Jon Haitz Legarreta (1): > > > > ENH: New test for itkLabelShapeOpeningImageFilter > > > > > > Kent Williams (9): > > > > COMP: use find_package(VTK COMPONENTS) to specify just needed VTK > > Components > > > > BUG: ImageSources/test/CMakeLists.txt incorrect library var > reference > > > > COMP: Fix coverity defects related to RegistrationV4 examples > > > > COMP: silence warning of vnl_vector_fixed_ref::assert_size > > > > COMP: Fix various Coverity warnings > > > > COMP: Fix a typo in an error message print statement. > > > > COMP: itk::Command-derived class used pointless dynamic_cast. > > > > PERF: Don't recompute InternalInverse repeatedly > > > > COMP: Correct orientation/spacing for Philips MultiFrame > > > > > > Mark Hiner (2): > > > > ENH: Update SCIFIO remote module hash > > > > BUG: Fix duplicate variables in Windows > > > > > > Matthew McCormick (105): > > > > DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. > > > > ENH: Move FFTComplexToComplexImageFilter out of Review. > > > > ENH: Add VnlComplexToComplexFFTImageFilter. > > > > BUG: Use fixed seed for Vnl FFT tests for repeatibility. > > > > ENH: Bump CMakeLists.txt version to 4.7.0. > > > > BUG: ArchiveTestingData.py future imports must occur at the > beginning. > > > > BUG: Do not run vnl_test_na with broken libc++. > > > > DOC: Remove Image2.cxx reference from Book 2. > > > > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > > > > DOC: Remove references to Book 1 sections from Book 2. > > > > DOC: Make BinaryThresholdImageFilter not floating. > > > > DOC: Fix Software Guide figure caption for FlipImageFilter. > > > > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > > > > DOC: Remove duplicate figure in > > LaplacianRecursiveGaussianImageFilter2.cxx. > > > > DOC: ImageRandomConstIteratorWithIndex table reference. > > > > DOC: Fix Software Guide page overruns in > > IterativeClosestPoint{1,2}.cxx. > > > > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > > > > BUG: Uninitialized m_TransformDirection in > > ComplexToComplexFFTImageFilter. > > > > BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. > > > > STYLE: Fix style in VoronoiDiagram2D. > > > > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > > > > BUG: Bump GCCXML to 2014-08-06. > > > > BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. > > > > BUG: Fix Win MultiThreader check for successful process creation. > > > > BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. > > > > COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. > > > > DOC: itk::statistics -> itk::Statistics. > > > > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > > > > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > > > > COMP: Improve const correctness of > > GradientRecursiveGaussianImageFilter. > > > > BUG: Call clear instead of empty on PatchBasedDenoising > EmptyCaches(). > > > > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > > > > COMP: ThreadJob NULL not defined. > > > > BUG: Fix alpha assignment for RGBA TIFF. > > > > COMP: Remove unused typedefs in LevelSetsv4Visualization. > > > > COMP: Remove unused typedef's in VtkGlue. > > > > ENH: Mark BSplineWarping2Test as RUNS_LONG. > > > > BUG: Fix Nifti IO read with large images. > > > > COMP: Remove call for non-existent variable in Nifti debugging. > > > > BUG: Close the file on Read and Write in HDF5TransformIO. > > > > BUG: Remove InsightLegacy test code from TransformHDF5Test. > > > > ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. > > > > STYLE: Use SeriesUIDContainerType and FileNamesContainerType > > > > ENH: Allow specification of orthogonality tolerance in rigid > > transforms. > > > > BUG: TransformFileReader does not clear its TransformList. > > > > BUG: Prevent dangling pointer in HDF5TransformIO. > > > > COMP: Do not use _stat64 with MinGW-32. > > > > BUG: Improve thread-safety and performance of > > PCAShapeSignedDistanceFunction. > > > > DOC: itk::statistics -> itk::Statistics. > > > > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > > > > DOC: Fix Software Guide page overruns in > > IterativeClosestPoint{1,2}.cxx. > > > > COMP: Address LaplacianDeformation Doxygen warnings. > > > > BUG: TransformFileReader does not clear its TransformList. > > > > BUG: Prevent dangling pointer in HDF5TransformIO. > > > > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > > > > BUG: Do not return SmartPointers in > TimeVaryingVelocityFieldTransform > > > > COMP: Do not wrap the FixedArray of Image SmartPointer's. > > > > COMP: Add missing wrapping for TransformIOBaseTemplate. > > > > COMP: Mark DeformableRegistration6Test as RUNS_LONG. > > > > STYLE: Improve style in BinaryImageToLabelMapFilter. > > > > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > > > > ENH: Improve precision of the joint PDF sum > > > > BUG: Fix BinShrinkImageFilter for different input/output image > types. > > > > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > > > > BUG: Use -py3 when building wrapping for Python 3. > > > > COMP: Add missing wrapping for TransformIOBaseTemplate. > > > > DOC: Improve ImageRegistration4 grammar. > > > > ENH: Add IOTransformDCMTK Remote module. > > > > BUG: gdcm::StringFilter recognizes backslash delimiter. > > > > DOC: Add migration guide for GDCM Rescale slope intercept apply on > > write. > > > > COMP: Remove unused typedef's in GPU code. > > > > STYLE: Improve style of HoughTransform2DLinesImageFilter example. > > > > COMP: Use ConceptChecking for IterativeInverse dimension check. > > > > COMP: Wrap TransformIOBaseTemplate for const SmartPointer. > > > > COMP: Add warning exceptions for third party pcre, swig, gccxml. > > > > ENH: Bump ITK version to 4.6.1. > > > > BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. > > > > BUG: Remove GaussianImageSource members shadowing > GenerateImageSource. > > > > STYLE: Style fixes to ITKImageSources module. > > > > BUG: GaussianSpatialFunction and GaborImageSource use > > SpacePrecisionType. > > > > BUG: Do not perform itk_download_attempt_check when not building > ITK. > > > > DOC: Update GDCMImageIO rescale slope intercept doc. > > > > BUG: Only register requestion IO COMPONENT modules. > > > > BUG: Fix wrapping .i, .idx CMake dependencies. > > > > COMP: Add VTK Python module when wrapping ITKVtkGlue. > > > > STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. > > > > STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType > typedef. > > > > COMP: Add missing VTK module dependency for > LevelSetsv4Visualization. > > > > BUG: By default, do not create any fixed parameters. > > > > STYLE: Remove trivial method comments in itkTransform.hxx. > > > > BUG: PolylineMask Filter's GenerateData is protected / virtual. > > > > ENH: Add HigherOrderAccurateGradient Module. > > > > BUG: Use input RequestedRegion Index in SliceBySliceImageFilter > > internal. > > > > COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. > > > > STYLE: Style fixes for Transform classes. > > > > DOC: Increase Doxygen LOOKUP_CACHE_SIZE. > > > > BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. > > > > DOC: Index Wiki examples with Doxygen. > > > > COMP: Bump SphinxExamples remote module. > > > > DOC: Index Sphinx examples in Doxygen. > > > > COMP: Remove old java examples. > > > > COMP: Remove duplicate DiffusionTensor3DReconstruction example > > reference. > > > > COMP: Address GradientAnisotropicDiffusionImageFilter example > settings. > > > > COMP: Bump Sphinx Examples remote. > > > > COMP: Bump WikiExamples remote. > > > > > > MetaIO Maintainers (1): > > > > MetaIO (reduced) > > > > > > Michka Popoff (40): > > > > ENH: Fixes for python 3 support > > > > BUG: Add VTK_VERSION for older VTK versions > > > > BUG: Improve SWIG version check > > > > COMP: Add wrapping for ThreadPool and ThreadJob > > > > COMP: Remove unimplemented DestroyPool method > > > > COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping > > > > COMP: Do not hide pygccxml warnings > > > > ENH: Update links in readme file > > > > BUG: Improve SWIG version check > > > > BUG: Add VTK_VERSION for older VTK versions > > > > STYLE: Remove trailing whitespaces > > > > STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP > > > > BUG: Fix memory leak in MetaImageIO after exception > > > > ENH: Add script to update pygccxml from upstream > > > > BUG: Update VTK minimum version (for release) > > > > BUG: Fix memory leak in MetaImageIO after exception > > > > ENH: Remove Sun OS compatibility for the wrappings > > > > COMP: Fix for conversion to non-pointer like type warning > > > > STYLE: LabelObject style > > > > DOC: Remove broken link from LabelObject class description > > > > ENH: Do not setup the python tests if not asked > > > > ENH: Add new GetTypes() and GetTypesAsList() methods to the template > > class > > > > COMP: Fix CMP0054 warnings in wrappings > > > > STYLE: Remove old cmake < 2.8.4 specific code > > > > STYLE: Remove old cmake < 2.8.5 specific code > > > > ENH: Update to PCRE 8.36 > > > > COMP: Refactor Wrapping setup and fix legacy warnings > > > > ENH: Add wrapping configuration to ITKConfig.cmake > > > > STYLE: Some minor code cleanup in the wrapping setup > > > > DOC: Fix typo in RelabelComponentImageFilter > > > > ENH: Deprecate VectorResampleImageFilter > > > > DOC: Add migration guide for ::Zero and ::One > > > > ENH: Deprecate ::Zero and ::One > > > > ENH: Add option to disable sorting by size in > > itkRelabelComponentImageFilter > > > > ENH: Add Vector and RGB wrapping to linear interpolator > > > > STYLE: Remove SORT macro in wrappings > > > > COMP: Fix warning for InterpolateImageFunction wrapping > > > > COMP: Add a check for Blocks in GPU module > > > > COMP: Bump SCIFIO to fix test build warnings > > > > COMP: Fix wrapping of itkImageFunctionBase > > > > > > Nick Tustison (7): > > > > BUG: Need to explicitly specify spline order. > > > > ENH: Initializing the transform center. > > > > BUG: Need to check the dynamic cast before any calls. > > > > ENH: Adding modifications for point set metrics. > > > > BUG: Need to specify TInternalComputationValueType for default > metric. > > > > ENH: Adding sparse points to B-spline field estimate. > > > > BUG: Uninitialized variables. > > > > > > Richard Beare (1): > > > > ENH: Include TIFF tags in the MetaDataDictionary > > > > > > Taylor Braun-Jones (1): > > > > BUG: Fix SliceBySliceImageFilter doesn't propagate information > > internally > > > > > > Umang B (1): > > > > ENH: Use thread pool to dispatch multithreading tasks > > > > > > Vivien Delmon (2): > > > > BUG: ExtractImageFilter::CollapseToSubMatrix fix > > > > ENH: Add a test on extracted directions in CollapseToSubMatrix mode > > > > > > Vladimir S. FONOV (1): > > > > BUG: Fixing incorrect MINC style inverse transform > > > > > > > > ----------------------------------------------------- > > > > Errors or omissions? Please fix them here: > > > > > > > https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing > > > > > > > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From DLRdave at aol.com Wed Dec 17 20:46:39 2014 From: DLRdave at aol.com (David Cole) Date: Wed, 17 Dec 2014 20:46:39 -0500 Subject: [ITK] [ITK-dev] ITK 4.7 Release Candidate 2 has been tagged! In-Reply-To: References: Message-ID: I'm surprised too, after seeing the code you pointed to.... But there it is right in the CMakeCache.txt as seen in this test result: https://open.cdash.org/testDetails.php?test=300879476&build=3614855 I'm pretty sure I didn't ask for Debug... If I still have that prompt open on that machine next time I get to it, I'll double check the command history. Probably not till Friday. D On Wednesday, December 17, 2014, Matt McCormick wrote: > Hi Dave, > > Thanks for the build and feedback! > > I've improve the testing instructions based on your suggestions. There is > now explicit cmake configuration steps, and a -j flag to ctest. I am > surprised that you got a Debug build by default -- we try to make it > Release for a clean build [1]. > > Thanks, > Matt > > [1] > http://itk.org/gitweb?p=ITK.git;a=blob;f=CMakeLists.txt;h=a913e4e065239edbf8d89b51969a8a51fc67fb8e;hb=HEAD#l95 > > On Wed, Dec 17, 2014 at 2:40 PM, David Cole > wrote: >> >> I did this build with the VS 2013 compiler, and the Ninja cmake >> generator, and it basically worked: >> >> https://open.cdash.org/buildSummary.php?buildid=3614855 >> >> The 3 test timeouts I guess are expected because it's a Debug build. >> >> I tried to do it by following just the directions in this email to run >> the dashboard, and there are some things I would add to future emails >> to make it even easier: >> >> - running "ctest" like that works fine for submitting an Experimental >> dashboard, but: it assumes you've configured an ITK build tree already >> with CMake... perhaps it should be mentioned that you need to run >> cmake first >> >> - when running CMake, and using make files or Ninja generator, the >> default build type appears to be Debug -- when configuring, use -D >> CMAKE_BUILD_TYPE=Release to avoid the long long long test times of a >> Debug build on Windows >> >> - when running ctest, use "-j 4" or "-j 8" or however many processors >> you can spare to actually run the tests..... My dashboard took over 4 >> hours because it was a Debug build, and I was running the exact >> command line in the email with ctest, and just simply forgot that when >> running a dashboard this way, you have to tell ctest how many >> processes to test at once... >> >> Bottom line: >> 4.7rc02 looks good to me, go for it! >> >> >> Cheers, >> David C. >> >> >> >> On Tue, Dec 16, 2014 at 2:42 AM, Matt McCormick >> > > wrote: >> > On behalf of the Insight Toolkit community, we are proud to announce >> that >> > ITK 4.7.0 release candidate 2 has been tagged and is available for >> testing! >> > Please test the release candidate in the coming days for an imminent >> > release. >> > >> > >> > To obtain the source code, >> > >> > git clone http://itk.org/ITK.git >> > cd ITK >> > git checkout -q --detach v4.7rc02 >> > >> > For more details, please see the Git documentation [1]. >> > >> > A few highlights for this release: all ITK examples from the Software >> Guide, >> > Wiki Examples, and SphinxExamples are new indexed and crossed linked in >> > Doxygen. So now when you go to your favorite filter or other object, >> say the >> > ResampleImageFilter, there is a large selection of examples in the >> examples >> > sections. This should make it much easier to fine sample code on how to >> use >> > an ITK class! TIFF IO has undergone a significant cleanup and speed-up, >> and >> > now TIFF tags are read into the MetaDataDictionary. Three new Remote >> Modules >> > are available, for gradient computation, DICOM IO, and QuadEdgeMesh >> > filtering. Python wrapping, CMake configuration, and registration >> continue >> > to improve. A new, experimental thread pool is available -- to enable >> set >> > the ITK_USE_THREADPOOL or call >> > itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). >> > >> > >> > >> > Please test the release candidate and share your experiences on the >> mailing >> > list, issue tracker, and Gerrit Code Review. Please help identify issues >> > submitting an Experimental build to the dashboard [2] with: >> > >> > ctest -M Experimental -T Configure -T Build -T Test -T Submit >> > >> > and notifying the mailing list. Testing your own applications against >> the >> > RC is also appreciated. >> > >> > >> > >> > Congratulations and well done to the 29 contributors to this release. We >> > would especially like to recognize the new contributors, Gert Wollny, >> Girish >> > Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan >> > Andruejol, and Ismael Belghiti. >> > >> > >> > The final release is scheduled for December 18th. >> > >> > [1] http://www.itk.org/Wiki/ITK/Git >> > >> > >> > [2] http://itk.org/Insight/Doxygen/html/examples.html >> > >> > >> > [3] >> http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html >> > >> > >> > [2] http://open.cdash.org/index.php?project=Insight >> > >> > >> > >> > >> > New Features >> > ------------------ >> > >> > * Documentation Improvements >> > >> > - Update Software Guide registration examples to ITKv4 framework >> > >> > - Wiki and Sphinx examples are indexed in Doxygen >> > >> > - Clean Software Guide dashboard build >> > >> > >> > * Filtering Improvements >> > >> > - New Laplacian deformation filter?s for QuadEdgeMesh?s >> > >> > - IJ article: http://hdl.handle.net/10380/3410 >> > >> > - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW >> implementations >> > >> > - Faster recursive Gaussian on VectorImage >> > >> > >> > * ImageIO improvements >> > >> > - PNG sCAL unit support >> > >> > - TIFF IO performance greatly improved >> > >> > - TIFF tags read into Image MetaDataDictionary >> > >> > - MetaIO updated >> > >> > - Better support for system GDCM >> > >> > >> > * Infrastructure improvements >> > >> > - New method to erase a MetaDataDictionary entry >> > >> > - New global method to set physical space tolerance >> > >> > - New, experimental thread pool support >> > >> > - NumericTraits::Zero and ::One are deprecated in favor of >> ::ZeroValue() >> > and ::OneValue() >> > >> > - VTK bridge modules only request required VTK modules >> > >> > >> > * New Remote Modules >> > >> > - Higher Order Accurate Gradient >> > >> > - http://hdl.handle.net/10380/3231 >> > >> > - IO Transform DCMTK >> > >> > - http://hdl.handle.net/10380/3468 >> > >> > - Subdivision Quad Edge Mesh Filters >> > >> > - http://hdl.handle.net/10380/3307 >> > >> > >> > * Registration improvements >> > >> > - LandmarkBasedTransformInitializer supports BSplineTransform >> > >> > - Transverse inverse consistency increased >> > >> > - Automatic initialization of the transform center for multi-stage >> > registrations >> > >> > - Sparse point B-spline field estimate >> > >> > - Mutual information faster, lower memory usage >> > >> > >> > * Wrapping improvements >> > >> > - Wrapping now builds without type warnings >> > >> > - pygccxml bumped to 1.6.2 >> > >> > - Latest GCCXML >> > >> > - CMake wrapping infrastructure cleanup >> > >> > - Build with Ninja CMake generator >> > >> > - New GetTypes() and GetTypesAsList() methods >> > >> > - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake >> > >> > >> > >> > * Many style improvements -- ITK gets more stylish with every release! >> > >> > >> > * Improved code coverage -- we are over 85%! >> > >> > >> > * *Lots* of important bug fixes >> > >> > >> > * And much more! See details in the log below. >> > >> > >> > List of changes since v4.7-rc01 >> > >> > -------------------------------------- >> > >> > >> > Ali Ghayoor (1): >> > DOC: Revise the registration examples of ITKSoftwareGuide >> > >> > Arnaud Gelas (3): >> > ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module >> > COMP: address clang -Winconsistent-missing-override in >> ITKQuadEdgeMesh >> > COMP: fix warnings on dashboard for Subdivision remote module >> > >> > Bradley Lowekamp (5): >> > BUG: Fix segfault when setting displacement field as null >> > BUG: Don't enable SSE rounding with OSX and gccxml >> > BUG: Add portable access to Tiff field name >> > BUG: Fix conversion compilation error >> > BUG: Rename remote module FDFImageIO -> IOFDF >> > >> > Christopher Mullins (6): >> > STYLE: Fix line length in OpenJPEG license for 80 character. >> > DOC: Finish the ImageLinearIteratorWithIndex example. >> > DOC: Text and picture problems, book2 >> > BUG: Fix text in margin issues >> > DOC: Edits for the beginning of chapter 5, Statistics >> > DOC: Fix empty code block. >> > >> > Cory Quammen (1): >> > COMP: Avoid including VTK_USE_FILE within ITK >> > >> > Kent Williams (1): >> > ENH: Add test to exercise issue with Transform::GetInverse >> > >> > Matthew McCormick (7): >> > BUG: Register AzimuthElevationToCartesianTransform to factories. >> > DOC: Update texture feature class references. >> > BUG: Fix texture feature correlation computation for constant >> image. >> > STYLE: Put ImageToImageFilterCommon in its own file. >> > BUG: Wrap ImageToImageFilterCommon. >> > STYLE: Put ImageSourceCommon in its own file. >> > COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. >> > >> > Michka Popoff (1): >> > ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter >> > wrappings >> > >> > Ziv Yaniv (1): >> > COMP: fixed warnings from gcc4.1.2, made implicit casts explicit >> > >> > >> > List of changes since v4.6.0 >> > >> > -------------------------------------- >> > >> > >> > Alexander Schmidt-Richberg (1): >> > >> > ENH: Updated Remote Module VariationalRegistration to new git tag >> > >> > >> > Ali Ghayoor (10): >> > >> > ENH: Make ITKv4 compatible with ITKSoftwareGuide >> > >> > ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 >> > >> > ENH: Convert three ImageRegistration Examples to ITKv4 >> > >> > ENH: Add multi-Res and multistage registration Examples to ITKv4 >> > >> > ENH: Convert DeformableReg examples to ITKv4 reg framework >> > >> > BUG: Expand a test to reflect multi-metric registration bug >> > >> > BUG: Fix multi metric point sampling bug in >> ImageRegistrationMethodv4 >> > >> > ENH: Add direct initialization to SyN registration >> > >> > ENH: Direct initialization of SyN by restoring the state >> > >> > ENH: LandmarkBasedTransformInitializer supports >> BSplineTransformType >> > >> > >> > Arnaud Gelas (15): >> > >> > COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization >> > >> > ENH: Importing Laplacian Deformation for QuadEdgeMesh >> > >> > DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage >> > >> > ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls >> Modified() >> > >> > ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter >> > >> > BUG: fix gdcm version in GDCMImageIO. >> > >> > COMP: missing cast when calling gdcm::DataElement::SetByteValue >> > >> > COMP: missing cast when calling gdcm::DataElement::SetByteValue >> > >> > ENH: increase LaplacianDeformation code coverage >> > >> > STYLE: use typedef rather than inheritance >> > >> > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is >> > false >> > >> > BUG: split include directories into appropriate cmake variables >> HDF5 >> > >> > BUG: missing gdcm libraries when using system GDCM >> > >> > DOC: fix doxygen documentaiton for >> > itk::LaplacianDeformationQuadEdgeMeshFilter >> > >> > ENH: Add one method to erase a tag into MetaDataDictionary >> > >> > >> > Bill Lorensen (5): >> > >> > ENH: Specify required VTK modules >> > >> > COMP: Wiki examples require additional vtk modules >> > >> > ENH: Modify WikiExamples remote config >> > >> > COMP: Bad test signature >> > >> > COMP: Update tag for wiki examples >> > >> > >> > Brad King (6): >> > >> > COMP: Fix vxl_config_macros usage of CMake check macros >> > >> > ENH: Use if(DEFINED) to simplify conditions >> > >> > COMP: Fix vxl_config_macros checks broken by refactoring >> > >> > COMP: Fix one more vxl_config_macros check broken by refactoring >> > >> > BUG: Fix itk_module_config for repeated calls >> > >> > BUG: Fix itk_module_config for repeated calls >> > >> > >> > Bradley Lowekamp (52): >> > >> > ENH: Adding License file from upstream MetaIO >> > >> > ENH: Adding script to update MetaIO from upstream >> > >> > ENH: Remove ITK MetaIO to prepare for upstream import >> > >> > PERF: Remove dynamically allocated temporary in evaluate method >> > >> > COMP: Fix variable type for Set/Get macros >> > >> > BUG: Implement ITK Style Singleton design pattern >> > >> > ENH: Add no throw exception specification for UnRegister methods >> > >> > COMP: Must specify order as "noexcept override" >> > >> > BUG: Add GetInverse for IdentityTransform >> > >> > ENH: Adding SetIdentity method to base DisplacementField class >> > >> > BUG: Remove unused redefinition of NULL >> > >> > BUG: Don't print to std::cout in PrintSelf >> > >> > ENH: Prefer the PrintSelfObjectMacro for printing nested objects >> > >> > BUG: Use METER of sCAL scale unit >> > >> > BUG: Use PNG_SCALE_METER for PNG sCAL unit >> > >> > BUG: Use METER of sCAL scale unit >> > >> > BUG: Use PNG_SCALE_METER for PNG sCAL unit >> > >> > COMP: Fix signed to unsigned int comparison >> > >> > BUG: Fix overflows computing size of read tiff image >> > >> > ENH: Extract TiffReaderInternal to separate file >> > >> > ENH: Refactor ReadTwoSamplePerPixelImage into template function >> > >> > ENH: Refactor GenericReadImage into template function >> > >> > BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and >> > LSMImageIO ) >> > >> > ENH: Refactor method to convert RGBA image to output buffer >> > >> > ENH: Refactor duplicated code to read a page >> > >> > BUG: Fix right oriented tiff images >> > >> > BUG: Remove dead separated plannar code, add test >> > >> > STYLE: Fix minor kwstyle defects in test and test results >> > >> > BUG: Use array delete operator for array new allocations >> > >> > ENH: add arbitrary TIFF TAGs to meta-data dictionary >> > >> > ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage >> > >> > BUG: Address Coverity warning about null pointer dereferences >> > >> > ENH: Remove support for TIFF tile as 3D and dead code >> > >> > ENH: RGBA read images should stay unchanged. >> > >> > BUG: Override method to MakeOutput by name >> > >> > ENH: Refactor per pixel conversion function to per scan-line method >> > >> > PERF: Refactor color table lookup >> > >> > BUG: Adding missing parentheses around boolean expression >> > >> > ENH: adding TIFFImageIO test for RGB palette images >> > >> > PERF: Improve recursive Gaussian perfromance with VectorImages >> > >> > ENH: Query libtiff to determine compression support >> > >> > BUG: Support TIFF tiled image with TIFFReadRGBAImage >> > >> > BUG: Use SizeValueType for length of scanline >> > >> > PERF: Store causal results directly in output buffers >> > >> > COMP: Add explicit conversion to const char >> > >> > COMP: Explicitly add override to GetNameOfClass method >> > >> > COMP: Address internal segmentation fault with Intel compiler >> > >> > ENH: Adding method to set global physical space tolerance >> > >> > COMP: Explicitly add override to GetNameOfClass method >> > >> > BUG: Add new TypeMacro for non-overloaded classes >> > >> > BUG: Fix obscure race condition on access thread pool >> initialization >> > >> > BUG: Updating FDFImageIO remote module >> > >> > >> > Christopher Mullins (15): >> > >> > COMP: Allows latex to compile for ITKSoftwareGuide >> > >> > COMP: Allows latex to compile for ITKSoftwareGuide >> > >> > COMP: Wrap MeshBase templates >> > >> > COMP: Wrap MeshBase templates >> > >> > COMP: Fix warning in BlockMatchingImageFilter >> > >> > STYLE: Line lengths in examples should be no longer than 80 chars. >> > >> > COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. >> > >> > COMP: Fix LaTeX warnings. >> > >> > STYLE: Fix formatting/punctuation errors. >> > >> > STYLE: Formatting and punctuation fixes. >> > >> > DOC: Edits for Book 2 Chapter 1 documentation in the Examples. >> > >> > DOC: Edits for book 2 chapter 2. >> > >> > DOC: More chapter 2 edits >> > >> > DOC: Book 2 Chapter 3 edits (part 1) >> > >> > DOC: book 2 chapter 4 Segmentation edits >> > >> > >> > Danny Perry (2): >> > >> > BUG: adding test for vnl_sparse_matrix::mult() >> > >> > BUG: size of q buffer should actually be (this->rows())*pcols. >> > >> > >> > David T. Chen (1): >> > >> > DOC: Fixed HistogramThresholdImageFitler >> > >> > >> > Dirk Padfield (1): >> > >> > BUG: Corrected processing of last sigma >> > >> > >> > GCC-XML Upstream (1): >> > >> > ENH: pygccxml v1.6.2 (reduced) >> > >> > >> > Gert Wollny (1): >> > >> > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) >> > >> > >> > Girish Mallya (1): >> > >> > BUG: Tests added for BinaryImageToLabelMapFilter for single-row >> images. >> > >> > >> > Hans Johnson (24): >> > >> > COMP: Add tolerance for comparing floating point >> > >> > PERF: Remove non-threadable algorithm components >> > >> > COMP: Add tolerance for comparing floating point >> > >> > PERF: Remove non-threadable algorithm components >> > >> > PERF: Remove large foot print of PDF derivatives. >> > >> > PERF: Revert Remove large foot print of PDF derivatives. >> > >> > STYLE: Test against almost equal for floating point values >> > >> > STYLE: Non-exact floating point testing >> > >> > PERF: Distribute initialization per thread buffers >> > >> > ENH: Remove unnecessary mutable qualifier. >> > >> > STYLE: Remove comment with no meaning. >> > >> > ENH: Moved accumlator logic to main MI class >> > >> > ENH: Allow staggering of accumulations per thread. >> > >> > PERF: Zero reset thread buffers during finalize >> > >> > BUG: Syntax error in comment >> > >> > PERF: Add non-blocking mutex locking. >> > >> > ENH: Use TryLock minimize thread stalls >> > >> > BUG: ThreadedIndexedContainerPartitioner is inclusive >> > >> > STYLE: Remove include_regular_expression from Examples >> > >> > BUG: Demonstrate Inv(Inv(T)) != T >> > >> > BUG: Ensure Inv(Inv(T)) == T for transforms >> > >> > COMP: Valgrind detects uninitialized memory read >> > >> > COMP: Missing required base class API component >> > >> > ENH: Expand interface for selecting threadpool >> > >> > >> > Ismael Belghiti (1): >> > >> > DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter >> > >> > >> > Jim Miller (1): >> > >> > STYLE: Removing what appears to be a temporary file >> > >> > >> > Johan Andruejol (1): >> > >> > ENH: Fix normalization for null vectors and return the norm >> > >> > >> > Jon Haitz Legarreta (1): >> > >> > ENH: New test for itkLabelShapeOpeningImageFilter >> > >> > >> > Kent Williams (9): >> > >> > COMP: use find_package(VTK COMPONENTS) to specify just needed VTK >> > Components >> > >> > BUG: ImageSources/test/CMakeLists.txt incorrect library var >> reference >> > >> > COMP: Fix coverity defects related to RegistrationV4 examples >> > >> > COMP: silence warning of vnl_vector_fixed_ref::assert_size >> > >> > COMP: Fix various Coverity warnings >> > >> > COMP: Fix a typo in an error message print statement. >> > >> > COMP: itk::Command-derived class used pointless dynamic_cast. >> > >> > PERF: Don't recompute InternalInverse repeatedly >> > >> > COMP: Correct orientation/spacing for Philips MultiFrame >> > >> > >> > Mark Hiner (2): >> > >> > ENH: Update SCIFIO remote module hash >> > >> > BUG: Fix duplicate variables in Windows >> > >> > >> > Matthew McCormick (105): >> > >> > DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. >> > >> > ENH: Move FFTComplexToComplexImageFilter out of Review. >> > >> > ENH: Add VnlComplexToComplexFFTImageFilter. >> > >> > BUG: Use fixed seed for Vnl FFT tests for repeatibility. >> > >> > ENH: Bump CMakeLists.txt version to 4.7.0. >> > >> > BUG: ArchiveTestingData.py future imports must occur at the >> beginning. >> > >> > BUG: Do not run vnl_test_na with broken libc++. >> > >> > DOC: Remove Image2.cxx reference from Book 2. >> > >> > DOC: Fix Software Guide page overruns in >> IterativeClosestPoint3.cxx. >> > >> > DOC: Remove references to Book 1 sections from Book 2. >> > >> > DOC: Make BinaryThresholdImageFilter not floating. >> > >> > DOC: Fix Software Guide figure caption for FlipImageFilter. >> > >> > DOC: Avoid duplicate figure description in >> ResampleImageFilter2.cxx. >> > >> > DOC: Remove duplicate figure in >> > LaplacianRecursiveGaussianImageFilter2.cxx. >> > >> > DOC: ImageRandomConstIteratorWithIndex table reference. >> > >> > DOC: Fix Software Guide page overruns in >> > IterativeClosestPoint{1,2}.cxx. >> > >> > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> > >> > BUG: Uninitialized m_TransformDirection in >> > ComplexToComplexFFTImageFilter. >> > >> > BUG: Fix offset[2] in >> PointSetToSpatialObjectDemonsRegistrationTest. >> > >> > STYLE: Fix style in VoronoiDiagram2D. >> > >> > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> > >> > BUG: Bump GCCXML to 2014-08-06. >> > >> > BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. >> > >> > BUG: Fix Win MultiThreader check for successful process creation. >> > >> > BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. >> > >> > COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. >> > >> > DOC: itk::statistics -> itk::Statistics. >> > >> > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> > >> > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. >> > >> > COMP: Improve const correctness of >> > GradientRecursiveGaussianImageFilter. >> > >> > BUG: Call clear instead of empty on PatchBasedDenoising >> EmptyCaches(). >> > >> > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. >> > >> > COMP: ThreadJob NULL not defined. >> > >> > BUG: Fix alpha assignment for RGBA TIFF. >> > >> > COMP: Remove unused typedefs in LevelSetsv4Visualization. >> > >> > COMP: Remove unused typedef's in VtkGlue. >> > >> > ENH: Mark BSplineWarping2Test as RUNS_LONG. >> > >> > BUG: Fix Nifti IO read with large images. >> > >> > COMP: Remove call for non-existent variable in Nifti debugging. >> > >> > BUG: Close the file on Read and Write in HDF5TransformIO. >> > >> > BUG: Remove InsightLegacy test code from TransformHDF5Test. >> > >> > ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. >> > >> > STYLE: Use SeriesUIDContainerType and FileNamesContainerType >> > >> > ENH: Allow specification of orthogonality tolerance in rigid >> > transforms. >> > >> > BUG: TransformFileReader does not clear its TransformList. >> > >> > BUG: Prevent dangling pointer in HDF5TransformIO. >> > >> > COMP: Do not use _stat64 with MinGW-32. >> > >> > BUG: Improve thread-safety and performance of >> > PCAShapeSignedDistanceFunction. >> > >> > DOC: itk::statistics -> itk::Statistics. >> > >> > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. >> > >> > DOC: Fix Software Guide page overruns in >> > IterativeClosestPoint{1,2}.cxx. >> > >> > COMP: Address LaplacianDeformation Doxygen warnings. >> > >> > BUG: TransformFileReader does not clear its TransformList. >> > >> > BUG: Prevent dangling pointer in HDF5TransformIO. >> > >> > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. >> > >> > BUG: Do not return SmartPointers in >> TimeVaryingVelocityFieldTransform >> > >> > COMP: Do not wrap the FixedArray of Image SmartPointer's. >> > >> > COMP: Add missing wrapping for TransformIOBaseTemplate. >> > >> > COMP: Mark DeformableRegistration6Test as RUNS_LONG. >> > >> > STYLE: Improve style in BinaryImageToLabelMapFilter. >> > >> > BUG: Fix BinaryImageToLabelMapFilter on 1D image. >> > >> > ENH: Improve precision of the joint PDF sum >> > >> > BUG: Fix BinShrinkImageFilter for different input/output image >> types. >> > >> > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. >> > >> > BUG: Use -py3 when building wrapping for Python 3. >> > >> > COMP: Add missing wrapping for TransformIOBaseTemplate. >> > >> > DOC: Improve ImageRegistration4 grammar. >> > >> > ENH: Add IOTransformDCMTK Remote module. >> > >> > BUG: gdcm::StringFilter recognizes backslash delimiter. >> > >> > DOC: Add migration guide for GDCM Rescale slope intercept apply on >> > write. >> > >> > COMP: Remove unused typedef's in GPU code. >> > >> > STYLE: Improve style of HoughTransform2DLinesImageFilter example. >> > >> > COMP: Use ConceptChecking for IterativeInverse dimension check. >> > >> > COMP: Wrap TransformIOBaseTemplate for const SmartPointer. >> > >> > COMP: Add warning exceptions for third party pcre, swig, gccxml. >> > >> > ENH: Bump ITK version to 4.6.1. >> > >> > BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. >> > >> > BUG: Remove GaussianImageSource members shadowing >> GenerateImageSource. >> > >> > STYLE: Style fixes to ITKImageSources module. >> > >> > BUG: GaussianSpatialFunction and GaborImageSource use >> > SpacePrecisionType. >> > >> > BUG: Do not perform itk_download_attempt_check when not building >> ITK. >> > >> > DOC: Update GDCMImageIO rescale slope intercept doc. >> > >> > BUG: Only register requestion IO COMPONENT modules. >> > >> > BUG: Fix wrapping .i, .idx CMake dependencies. >> > >> > COMP: Add VTK Python module when wrapping ITKVtkGlue. >> > >> > STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. >> > >> > STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType >> typedef. >> > >> > COMP: Add missing VTK module dependency for >> LevelSetsv4Visualization. >> > >> > BUG: By default, do not create any fixed parameters. >> > >> > STYLE: Remove trivial method comments in itkTransform.hxx. >> > >> > BUG: PolylineMask Filter's GenerateData is protected / virtual. >> > >> > ENH: Add HigherOrderAccurateGradient Module. >> > >> > BUG: Use input RequestedRegion Index in SliceBySliceImageFilter >> > internal. >> > >> > COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. >> > >> > STYLE: Style fixes for Transform classes. >> > >> > DOC: Increase Doxygen LOOKUP_CACHE_SIZE. >> > >> > BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. >> > >> > DOC: Index Wiki examples with Doxygen. >> > >> > COMP: Bump SphinxExamples remote module. >> > >> > DOC: Index Sphinx examples in Doxygen. >> > >> > COMP: Remove old java examples. >> > >> > COMP: Remove duplicate DiffusionTensor3DReconstruction example >> > reference. >> > >> > COMP: Address GradientAnisotropicDiffusionImageFilter example >> settings. >> > >> > COMP: Bump Sphinx Examples remote. >> > >> > COMP: Bump WikiExamples remote. >> > >> > >> > MetaIO Maintainers (1): >> > >> > MetaIO (reduced) >> > >> > >> > Michka Popoff (40): >> > >> > ENH: Fixes for python 3 support >> > >> > BUG: Add VTK_VERSION for older VTK versions >> > >> > BUG: Improve SWIG version check >> > >> > COMP: Add wrapping for ThreadPool and ThreadJob >> > >> > COMP: Remove unimplemented DestroyPool method >> > >> > COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping >> > >> > COMP: Do not hide pygccxml warnings >> > >> > ENH: Update links in readme file >> > >> > BUG: Improve SWIG version check >> > >> > BUG: Add VTK_VERSION for older VTK versions >> > >> > STYLE: Remove trailing whitespaces >> > >> > STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP >> > >> > BUG: Fix memory leak in MetaImageIO after exception >> > >> > ENH: Add script to update pygccxml from upstream >> > >> > BUG: Update VTK minimum version (for release) >> > >> > BUG: Fix memory leak in MetaImageIO after exception >> > >> > ENH: Remove Sun OS compatibility for the wrappings >> > >> > COMP: Fix for conversion to non-pointer like type warning >> > >> > STYLE: LabelObject style >> > >> > DOC: Remove broken link from LabelObject class description >> > >> > ENH: Do not setup the python tests if not asked >> > >> > ENH: Add new GetTypes() and GetTypesAsList() methods to the >> template >> > class >> > >> > COMP: Fix CMP0054 warnings in wrappings >> > >> > STYLE: Remove old cmake < 2.8.4 specific code >> > >> > STYLE: Remove old cmake < 2.8.5 specific code >> > >> > ENH: Update to PCRE 8.36 >> > >> > COMP: Refactor Wrapping setup and fix legacy warnings >> > >> > ENH: Add wrapping configuration to ITKConfig.cmake >> > >> > STYLE: Some minor code cleanup in the wrapping setup >> > >> > DOC: Fix typo in RelabelComponentImageFilter >> > >> > ENH: Deprecate VectorResampleImageFilter >> > >> > DOC: Add migration guide for ::Zero and ::One >> > >> > ENH: Deprecate ::Zero and ::One >> > >> > ENH: Add option to disable sorting by size in >> > itkRelabelComponentImageFilter >> > >> > ENH: Add Vector and RGB wrapping to linear interpolator >> > >> > STYLE: Remove SORT macro in wrappings >> > >> > COMP: Fix warning for InterpolateImageFunction wrapping >> > >> > COMP: Add a check for Blocks in GPU module >> > >> > COMP: Bump SCIFIO to fix test build warnings >> > >> > COMP: Fix wrapping of itkImageFunctionBase >> > >> > >> > Nick Tustison (7): >> > >> > BUG: Need to explicitly specify spline order. >> > >> > ENH: Initializing the transform center. >> > >> > BUG: Need to check the dynamic cast before any calls. >> > >> > ENH: Adding modifications for point set metrics. >> > >> > BUG: Need to specify TInternalComputationValueType for default >> metric. >> > >> > ENH: Adding sparse points to B-spline field estimate. >> > >> > BUG: Uninitialized variables. >> > >> > >> > Richard Beare (1): >> > >> > ENH: Include TIFF tags in the MetaDataDictionary >> > >> > >> > Taylor Braun-Jones (1): >> > >> > BUG: Fix SliceBySliceImageFilter doesn't propagate information >> > internally >> > >> > >> > Umang B (1): >> > >> > ENH: Use thread pool to dispatch multithreading tasks >> > >> > >> > Vivien Delmon (2): >> > >> > BUG: ExtractImageFilter::CollapseToSubMatrix fix >> > >> > ENH: Add a test on extracted directions in CollapseToSubMatrix mode >> > >> > >> > Vladimir S. FONOV (1): >> > >> > BUG: Fixing incorrect MINC style inverse transform >> > >> > >> > >> > ----------------------------------------------------- >> > >> > Errors or omissions? Please fix them here: >> > >> > >> > >> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing >> > >> > >> > >> > >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-developers >> > >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Thu Dec 18 08:08:23 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Thu, 18 Dec 2014 08:08:23 -0500 Subject: [ITK] [ITK-dev] ITKApps and 4.7rc02 Message-ID: Matt, I tried to build ITKApps against the release candidate. The ITK external project will not configure since it uses VTK5 and tour recent patch for ItkVtkGlue is not in the rc. Bill -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Dec 18 11:20:47 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Dec 2014 11:20:47 -0500 Subject: [ITK] [ITK-dev] ITKApps and 4.7rc02 In-Reply-To: References: Message-ID: Hi Bill, Thanks for testing. Yes, this patch fixes the issue [1]. I will make sure it is in the release. Thanks, Matt [1] http://review.source.kitware.com/#/c/18531/ On Thu, Dec 18, 2014 at 8:08 AM, Bill Lorensen wrote: > > Matt, > > I tried to build ITKApps against the release candidate. The ITK > external project will not configure since it uses VTK5 and tour recent > patch for ItkVtkGlue is not in the rc. > > Bill > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From bill.lorensen at gmail.com Thu Dec 18 11:22:47 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Thu, 18 Dec 2014 11:22:47 -0500 Subject: [ITK] [ITK-dev] ITKApps and 4.7rc02 In-Reply-To: References: Message-ID: I built ITKApps fine with that patch applied to my local copy. On Thu, Dec 18, 2014 at 11:20 AM, Matt McCormick wrote: > Hi Bill, > > Thanks for testing. > > Yes, this patch fixes the issue [1]. I will make sure it is in the release. > > Thanks, > Matt > > [1] http://review.source.kitware.com/#/c/18531/ > > On Thu, Dec 18, 2014 at 8:08 AM, Bill Lorensen > wrote: >> >> Matt, >> >> I tried to build ITKApps against the release candidate. The ITK >> external project will not configure since it uses VTK5 and tour recent >> patch for ItkVtkGlue is not in the rc. >> >> Bill >> >> -- >> Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matimontg at gmail.com Fri Dec 19 08:16:13 2014 From: matimontg at gmail.com (Matias Montroull) Date: Fri, 19 Dec 2014 10:16:13 -0300 Subject: [ITK] [ITK-users] ITK Apps | MRIRegistration not included in compilation Message-ID: Hi, I downloaded ITK Apps from GIT and generated the .sln in Visual Studio (2012) with Cmake. Now, this particular example: MRIRegistration is not included in the build directory, any reason why this is happening? Thank you, Matias. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Fri Dec 19 08:34:32 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 19 Dec 2014 08:34:32 -0500 Subject: [ITK] [ITK-users] ITK Apps | MRIRegistration not included in compilation In-Reply-To: References: Message-ID: Are you using the superbuild to build itk and vtk or are you pointing to your own itk and vtk? On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull wrote: > Hi, > > I downloaded ITK Apps from GIT and generated the .sln in Visual Studio > (2012) with Cmake. > > Now, this particular example: MRIRegistration is not included in the build > directory, any reason why this is happening? > > Thank you, > > Matias. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Fri Dec 19 09:20:19 2014 From: matimontg at gmail.com (Matias Montroull) Date: Fri, 19 Dec 2014 11:20:19 -0300 Subject: [ITK] [ITK-users] ITK Apps | MRIRegistration not included in compilation In-Reply-To: References: Message-ID: Hi Bill, I've downloaded and compiled ITK in a directory and FLTK as well Regards, Matias. On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen wrote: > > Are you using the superbuild to build itk and vtk or are you pointing > to your own itk and vtk? > > > On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull > wrote: > > Hi, > > > > I downloaded ITK Apps from GIT and generated the .sln in Visual Studio > > (2012) with Cmake. > > > > Now, this particular example: MRIRegistration is not included in the > build > > directory, any reason why this is happening? > > > > Thank you, > > > > Matias. > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Fri Dec 19 09:23:09 2014 From: matimontg at gmail.com (Matias Montroull) Date: Fri, 19 Dec 2014 11:23:09 -0300 Subject: [ITK] [ITK-users] ITK Apps | MRIRegistration not included in compilation In-Reply-To: References: Message-ID: I've seen in the Cmake.txt list these lines: so how do I specidy these optional apps need to be included in the binaries build? IF(FLTK_FOUND) IF(WIN32) ADD_DEFINITIONS(-DWIN32) ENDIF(WIN32) * OPTIONAL_APP(MultiResMIRegistration)* OPTIONAL_APP(DigitalArchive) OPTIONAL_APP(DistanceMapFilter) OPTIONAL_APP(DicomImageViewer) ...... On Fri, Dec 19, 2014 at 11:20 AM, Matias Montroull wrote: > > Hi Bill, > > I've downloaded and compiled ITK in a directory and FLTK as well > > Regards, > > Matias. > > On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen > wrote: >> >> Are you using the superbuild to build itk and vtk or are you pointing >> to your own itk and vtk? >> >> >> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull >> wrote: >> > Hi, >> > >> > I downloaded ITK Apps from GIT and generated the .sln in Visual Studio >> > (2012) with Cmake. >> > >> > Now, this particular example: MRIRegistration is not included in the >> build >> > directory, any reason why this is happening? >> > >> > Thank you, >> > >> > Matias. >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From nekto1989 at gmail.com Fri Dec 19 09:28:56 2014 From: nekto1989 at gmail.com (=?UTF-8?B?0JzQsNGAJ9GP0L0g0JrQu9C40LzQvtCy?=) Date: Fri, 19 Dec 2014 16:28:56 +0200 Subject: [ITK] VS2013 Update 4 (RelWithDebInfo x64) crash with ITK 4.6.1 Message-ID: Hi, I've reproduced crash using VS2013 Update 4 (RelWithDebInfo x64) with pure ITK 4.6.1 code inside FiniteDifferenceImageFilter. I've reported it to https://connect.microsoft.com/VisualStudio/feedback/details/1060166/compiler-generates-divpd-instruction-on-non-aligned-data Can someone check if it's really compiler problem and upvote on connect? Don't really want to add one more __declspec(align(16)) inside ITK. I'm attaching .cpp and cmakelists.txt Best regards, Marian -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- cmake_minimum_required(VERSION 3.0) set(CMAKE_CONFIGURATION_TYPES "RelWithDebInfo" CACHE STRING "" FORCE) project(AlignCrashDivpd) # itk if(NOT DEFINED ITK_DIR) set(ITK_DIR "ITK_DIR-NOTFOUND" CACHE PATH "Path to UseITK.cmake") message(SEND_ERROR "Please specify ITK_DIR") endif() find_package(ITK REQUIRED) include(${ITK_USE_FILE}) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MP /Zo") add_executable(AlignCrashDivpd main.cpp) target_link_libraries(AlignCrashDivpd ${ITK_LIBRARIES}) add_custom_command(TARGET AlignCrashDivpd POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${ITK_INSTALL_PREFIX}/bin/ITKCommon-4.6.dll ${CMAKE_BINARY_DIR}/$(Configuration)/ COMMENT "Copy itk dlls") -------------- next part -------------- A non-text attachment was scrubbed... Name: main.cpp Type: text/x-c++src Size: 1548 bytes Desc: not available URL: From blowekamp at mail.nih.gov Fri Dec 19 09:59:31 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 19 Dec 2014 09:59:31 -0500 Subject: [ITK] VS2013 Update 4 (RelWithDebInfo x64) crash with ITK 4.6.1 In-Reply-To: References: Message-ID: <822C53AE-230F-48C3-9487-EF9D042C13BB@mail.nih.gov> Hello, We have been having significant issues with Visual Studio 2013 (VS12) Professional in with Release optimizations for a while now. Here is the nightly dashboard with the run time errors: https://open.cdash.org/buildSummary.php?buildid=3619048 It's been a while since I looked into this. If I recall correctly it appeared to be critical alignment issues with SSE optimization and just the code being generated was invalid. Your posted issue looks the same. However, I don't think your example posted with MS is simple enough to get traction there. I think what is needed is a single preprocessed file without dependencies on building all of ITK, or cmake to maximize chances of it being addressed. Brad On Dec 19, 2014, at 9:28 AM, ???'?? ?????? wrote: > Hi, > > I've reproduced crash using VS2013 Update 4 (RelWithDebInfo x64) with pure ITK 4.6.1 code inside FiniteDifferenceImageFilter. > > I've reported it to https://connect.microsoft.com/VisualStudio/feedback/details/1060166/compiler-generates-divpd-instruction-on-non-aligned-data > Can someone check if it's really compiler problem and upvote on connect? Don't really want to add one more __declspec(align(16)) inside ITK. I'm attaching .cpp and cmakelists.txt > > Best regards, > Marian > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Fri Dec 19 10:32:39 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 19 Dec 2014 10:32:39 -0500 Subject: [ITK] [ITK-users] ITK Apps | MRIRegistration not included in compilation In-Reply-To: References: Message-ID: You really should use the Superbuild for ITKApps. Configuration can be very tricky. On Fri, Dec 19, 2014 at 9:23 AM, Matias Montroull wrote: > I've seen in the Cmake.txt list these lines: > so how do I specidy these optional apps need to be included in the binaries > build? > IF(FLTK_FOUND) > IF(WIN32) > ADD_DEFINITIONS(-DWIN32) > ENDIF(WIN32) > OPTIONAL_APP(MultiResMIRegistration) > OPTIONAL_APP(DigitalArchive) > OPTIONAL_APP(DistanceMapFilter) > OPTIONAL_APP(DicomImageViewer) > ...... > > On Fri, Dec 19, 2014 at 11:20 AM, Matias Montroull > wrote: >> >> Hi Bill, >> >> I've downloaded and compiled ITK in a directory and FLTK as well >> >> Regards, >> >> Matias. >> >> On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen >> wrote: >>> >>> Are you using the superbuild to build itk and vtk or are you pointing >>> to your own itk and vtk? >>> >>> >>> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull >>> wrote: >>> > Hi, >>> > >>> > I downloaded ITK Apps from GIT and generated the .sln in Visual Studio >>> > (2012) with Cmake. >>> > >>> > Now, this particular example: MRIRegistration is not included in the >>> > build >>> > directory, any reason why this is happening? >>> > >>> > Thank you, >>> > >>> > Matias. >>> > >>> > _____________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://www.kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> > >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Fri Dec 19 13:34:52 2014 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 19 Dec 2014 13:34:52 -0500 Subject: [ITK] [ITK-users] [Insight-users] [ITK-USER]Compile ITK3.20.1 with VS2012 In-Reply-To: References: Message-ID: Probably too late for JX, but I found a solution. When configuring ITK with CMake, in the field CMAKE_CXX_FLAGS add the following: /D_ALLOW_KEYWORD_MACROS Article which helped me: http://mostlybuggy.wordpress.com/2012/12/18/getting-around-vs2012-c1189c4005-keyword-re-defined-in-macros/ On Wed, May 29, 2013 at 9:33 AM, Bradley Lowekamp wrote: > > Hi, > > Why no upgrade to ITK v4? > > ITK v3.20 was released in 2010, well before Visual Studio 2012. So it > should be no surprise it does not work with it. I believe VS 2010 should > work with it, and VS9, and VS8, and VS7.... > > > Brad > > > > On May 28, 2013, at 10:41 PM, JX NIE wrote: > > > Hi Everyone, > > I have tried to compile ITK(version 3.20.1 ) with VS2012, but failed. > > It has ended up with a lot of Redifine errors as follow. > > Could you please tell me how to solve this compile problem. > > Regards, > > > > NIE JUNXIAO > > > > > > >C:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\xkeycheck.h(242): fatal error C1189: #error : The C++ > Standard Library forbids macroizing keywords. Enable warning C4005 to find > the forbidden macro. > > > > 1 IntelliSense: #error directive: The C++ Standard Library > forbids macroizing keywords. Enable warning C4005 to find the forbidden > macro. c:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\xkeycheck.h 242 > > 2 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\sal.h 2367 > > 3 IntelliSense: expected a declaration c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\vadefs.h 139 > > 4 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 437 > > 5 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 446 > > 6 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 464 > > 7 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 475 > > 8 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 476 > > 9 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 497 > > 10 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 501 > > 11 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 506 > > 12 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 514 > > 13 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 571 > > 14 IntelliSense: attribute "noreturn" does not apply here > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h > 572 > > 15 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 572 > > 16 IntelliSense: attribute "noreturn" does not apply here > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h > 575 > > 17 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 576 > > 18 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1979 > > 19 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1980 > > 20 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1981 > > 21 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1982 > > 22 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1983 > > 23 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1985 > > 24 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1992 > > 25 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1999 > > 26 IntelliSense: expected a declaration c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 2023 > > 27 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 510 > > 28 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 528 > > 29 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 529 > > 30 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 542 > > 31 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 576 > > 32 IntelliSense: invalid destructor declaration c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 577 > > 33 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 583 > > 34 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 585 > > 35 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 586 > > 36 IntelliSense: explicit type is missing ('int' assumed) > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 588 > > 37 IntelliSense: identifier "EMIT" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 588 > > 38 IntelliSense: function "_Lockit" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 589 > > 39 IntelliSense: reference variable "EMIT" requires an > initializer c:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\yvals.h 589 > > 40 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 591 > > 41 IntelliSense: expected a declaration c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 606 > > 42 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 693 > > 43 IntelliSense: expected a declaration c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 726 > > 44 IntelliSense: expected a declaration c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 729 > > 45 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 740 > > 46 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 741 > > 47 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 23 > > 48 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 47 > > 49 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 48 > > 50 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 49 > > 51 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 50 > > 52 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 54 > > 53 IntelliSense: identifier "errno_t" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56 > > 54 IntelliSense: variable "memcpy_s" may not be initialized > c:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\string.h 56 > > 55 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56 > > 56 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 93 > > 57 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 97 > > 58 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 98 > > 59 IntelliSense: identifier "errno_t" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103 > > 60 IntelliSense: variable "_strset_s" may not be initialized > c:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\string.h 103 > > 61 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103 > > 62 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 104 > > 63 IntelliSense: identifier "errno_t" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107 > > 64 IntelliSense: variable "strcpy_s" may not be initialized > c:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\string.h 107 > > 65 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107 > > 66 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 109 > > 67 IntelliSense: identifier "errno_t" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112 > > 68 IntelliSense: variable "strcat_s" may not be initialized > c:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\string.h 112 > > 69 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112 > > 70 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 114 > > 71 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 116 > > 72 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 117 > > 73 IntelliSense: variable "strnlen" may not be initialized > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 121 > > 74 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 121 > > 75 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 123 > > 76 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 135 > > 77 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 142 > > 78 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 148 > > 79 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 149 > > 80 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 150 > > 81 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 151 > > 82 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 152 > > 83 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 153 > > 84 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 154 > > 85 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 155 > > 86 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 156 > > 87 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 157 > > 88 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 158 > > 89 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 159 > > 90 IntelliSense: variable "strcspn" may not be initialized > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 160 > > 91 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 160 > > 92 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 161 > > 93 IntelliSense: identifier "errno_t" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 162 > > 94 IntelliSense: variable "_strerror_s" may not be > initialized c:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\string.h 162 > > 95 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 162 > > 96 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 163 > > 97 IntelliSense: identifier "errno_t" is undefined c:\Program > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166 > > 98 IntelliSense: variable "strerror_s" may not be > initialized c:\Program Files (x86)\Microsoft Visual Studio > 11.0\VC\include\string.h 166 > > 99 IntelliSense: expected a ')' c:\Program Files > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166 > > 100 IntelliSense: variable "EMIT" is not a type name > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 168 > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://www.itk.org/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://www.itk.org/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Fri Dec 19 15:16:37 2014 From: matimontg at gmail.com (Matias Montroull) Date: Fri, 19 Dec 2014 17:16:37 -0300 Subject: [ITK] [ITK-users] ITK Apps | MRIRegistration not included in compilation In-Reply-To: References: Message-ID: Hi Bill, I was able to make it work, I had to enable use of FLTK in Cmake when building ITKApps binaries On Fri, Dec 19, 2014 at 12:32 PM, Bill Lorensen wrote: > > You really should use the Superbuild for ITKApps. Configuration can be > very tricky. > > > On Fri, Dec 19, 2014 at 9:23 AM, Matias Montroull > wrote: > > I've seen in the Cmake.txt list these lines: > > so how do I specidy these optional apps need to be included in the > binaries > > build? > > IF(FLTK_FOUND) > > IF(WIN32) > > ADD_DEFINITIONS(-DWIN32) > > ENDIF(WIN32) > > OPTIONAL_APP(MultiResMIRegistration) > > OPTIONAL_APP(DigitalArchive) > > OPTIONAL_APP(DistanceMapFilter) > > OPTIONAL_APP(DicomImageViewer) > > ...... > > > > On Fri, Dec 19, 2014 at 11:20 AM, Matias Montroull > > wrote: > >> > >> Hi Bill, > >> > >> I've downloaded and compiled ITK in a directory and FLTK as well > >> > >> Regards, > >> > >> Matias. > >> > >> On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen < > bill.lorensen at gmail.com> > >> wrote: > >>> > >>> Are you using the superbuild to build itk and vtk or are you pointing > >>> to your own itk and vtk? > >>> > >>> > >>> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull > > >>> wrote: > >>> > Hi, > >>> > > >>> > I downloaded ITK Apps from GIT and generated the .sln in Visual > Studio > >>> > (2012) with Cmake. > >>> > > >>> > Now, this particular example: MRIRegistration is not included in the > >>> > build > >>> > directory, any reason why this is happening? > >>> > > >>> > Thank you, > >>> > > >>> > Matias. > >>> > > >>> > _____________________________________ > >>> > Powered by www.kitware.com > >>> > > >>> > Visit other Kitware open-source projects at > >>> > http://www.kitware.com/opensource/opensource.html > >>> > > >>> > Kitware offers ITK Training Courses, for more information visit: > >>> > http://www.kitware.com/products/protraining.php > >>> > > >>> > Please keep messages on-topic and check the ITK FAQ at: > >>> > http://www.itk.org/Wiki/ITK_FAQ > >>> > > >>> > Follow this link to subscribe/unsubscribe: > >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>> > > >>> > >>> > >>> > >>> -- > >>> Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Fri Dec 19 15:31:52 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 19 Dec 2014 15:31:52 -0500 Subject: [ITK] [ITK-users] ITK Apps | MRIRegistration not included in compilation In-Reply-To: References: Message-ID: Excellent! On Fri, Dec 19, 2014 at 3:16 PM, Matias Montroull wrote: > Hi Bill, I was able to make it work, I had to enable use of FLTK in Cmake > when building ITKApps binaries > > On Fri, Dec 19, 2014 at 12:32 PM, Bill Lorensen > wrote: >> >> You really should use the Superbuild for ITKApps. Configuration can be >> very tricky. >> >> >> On Fri, Dec 19, 2014 at 9:23 AM, Matias Montroull >> wrote: >> > I've seen in the Cmake.txt list these lines: >> > so how do I specidy these optional apps need to be included in the >> > binaries >> > build? >> > IF(FLTK_FOUND) >> > IF(WIN32) >> > ADD_DEFINITIONS(-DWIN32) >> > ENDIF(WIN32) >> > OPTIONAL_APP(MultiResMIRegistration) >> > OPTIONAL_APP(DigitalArchive) >> > OPTIONAL_APP(DistanceMapFilter) >> > OPTIONAL_APP(DicomImageViewer) >> > ...... >> > >> > On Fri, Dec 19, 2014 at 11:20 AM, Matias Montroull >> > wrote: >> >> >> >> Hi Bill, >> >> >> >> I've downloaded and compiled ITK in a directory and FLTK as well >> >> >> >> Regards, >> >> >> >> Matias. >> >> >> >> On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen >> >> >> >> wrote: >> >>> >> >>> Are you using the superbuild to build itk and vtk or are you pointing >> >>> to your own itk and vtk? >> >>> >> >>> >> >>> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull >> >>> >> >>> wrote: >> >>> > Hi, >> >>> > >> >>> > I downloaded ITK Apps from GIT and generated the .sln in Visual >> >>> > Studio >> >>> > (2012) with Cmake. >> >>> > >> >>> > Now, this particular example: MRIRegistration is not included in the >> >>> > build >> >>> > directory, any reason why this is happening? >> >>> > >> >>> > Thank you, >> >>> > >> >>> > Matias. >> >>> > >> >>> > _____________________________________ >> >>> > Powered by www.kitware.com >> >>> > >> >>> > Visit other Kitware open-source projects at >> >>> > http://www.kitware.com/opensource/opensource.html >> >>> > >> >>> > Kitware offers ITK Training Courses, for more information visit: >> >>> > http://www.kitware.com/products/protraining.php >> >>> > >> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>> > >> >>> > Follow this link to subscribe/unsubscribe: >> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>> > >> >>> >> >>> >> >>> >> >>> -- >> >>> Unpaid intern in BillsBasement at noware dot com >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Dec 19 17:59:20 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 19 Dec 2014 17:59:20 -0500 Subject: [ITK] [ANNOUNCE] ITK 4.7.0 has been released! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.7.0 has been released! Links to the Sourceforge.net tarballs can be found on the download page: http://www.itk.org/ITK/resources/software.html Outline ---------- 1. Introduction 2. New Features 3. ITK Changelog 4. ITK Sphinx Examples Changelog 5. ITK Software Guide Changelog 6. ITK Apps Changelog Introduction ----------------- The 4.7 release is a major milestone that marks the hard work of many outstanding community members. Congratulations and well done to the 29 contributors to this release. We would especially like to recognize the new contributors, Gert Wollny, Girish Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan Andruejol, and Ismael Belghiti. Among the major contributions in this release: all ITK examples from the Software Guide, Wiki Examples, and SphinxExamples are new indexed and crossed linked in Doxygen -- when you visit the Doxygen page for your favorite filter or other object, say the ResampleImageFilter, there is a large selection of examples in the Examples section. TIFF IO has undergone a significant cleanup and speed-up, and TIFF tags are now read into the Image?s MetaDataDictionary. Three new Remote Modules are available, for gradient computation, DICOM IO, and QuadEdgeMesh filtering. Python wrapping, CMake configuration, and registration continue to improve. A new, experimental thread pool is available -- to enable set the ITK_USE_THREADPOOL or call itk::MultiThreader::SetGlobalDefaultUseThreadPool(true). Thanks to everyone for their hard work! Enjoy ITK! New Features ------------------ * Documentation Improvements - Update Software Guide registration examples to ITKv4 framework - Wiki and Sphinx examples are indexed in Doxygen - Clean Software Guide dashboard build * Filtering Improvements - New Laplacian deformation filter?s for QuadEdgeMesh?s - IJ article: http://hdl.handle.net/10380/3410 - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations - Faster recursive Gaussian on VectorImage * ImageIO improvements - PNG sCAL unit support - TIFF IO performance greatly improved - TIFF tags read into Image MetaDataDictionary - MetaIO updated - Better support for system GDCM * Infrastructure improvements - New method to erase a MetaDataDictionary entry - New global method to set physical space tolerance - New, experimental thread pool support - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue() and ::OneValue() - VTK bridge modules only request required VTK modules * New Remote Modules - Higher Order Accurate Gradient - http://hdl.handle.net/10380/3231 - IO Transform DCMTK - http://hdl.handle.net/10380/3468 - Subdivision Quad Edge Mesh Filters - http://hdl.handle.net/10380/3307 * Registration improvements - LandmarkBasedTransformInitializer supports BSplineTransform - Transverse inverse consistency increased - Automatic initialization of the transform center for multi-stage registrations - Sparse point B-spline field estimate - Mutual information faster, lower memory usage * Wrapping improvements - Wrapping now builds without type warnings - pygccxml bumped to 1.6.2 - Latest GCCXML - CMake wrapping infrastructure cleanup - Build with Ninja CMake generator - New GetTypes() and GetTypesAsList() methods - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake * Many style improvements -- ITK gets more stylish with every release! * Improved code coverage -- we are over 85%! * *Lots* of important bug fixes * And much more! See details in the log below. List of changes since v4.7-rc02 ----------------------------------------- Bradley Lowekamp (1): BUG: IOFDF remote module should stay with InsightConsortium repo Christopher Mullins (3): DOC: Fix code overlapping figure STYLE: Keep the text in the margins STYLE: Put newline before long doxygen reference Cory Quammen (1): BUG: Fix segfaults in ITKExamples Matthew McCormick (8): BUG: Reset ITK_MODULES_REQUESTED to all modules with multiple calls. BUG: Configure against VTK 5. COMP: Add ITK_SOURCE_DIR to doxygen EXAMPLE_PATH. COMP: Increase DOT_GRAPH_MAX_NODES. DOC: Add Doxygen macros for itkSetGetDecoratedObjectMacro. ENH: Warning when reading a PNG with UNKNOWN unit and non-unit spacing. BUG: Fix VTK5 module export code. BUG: Fix LevelSetsv4Visualization VTK variable names. Michka Popoff (1): DOC: Improvements for Book1, Chap4 List of changes since v4.7-rc01 ----------------------------------------- Ali Ghayoor (1): DOC: Revise the registration examples of ITKSoftwareGuide Arnaud Gelas (3): ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh COMP: fix warnings on dashboard for Subdivision remote module Bradley Lowekamp (5): BUG: Fix segfault when setting displacement field as null BUG: Don't enable SSE rounding with OSX and gccxml BUG: Add portable access to Tiff field name BUG: Fix conversion compilation error BUG: Rename remote module FDFImageIO -> IOFDF Christopher Mullins (6): STYLE: Fix line length in OpenJPEG license for 80 character. DOC: Finish the ImageLinearIteratorWithIndex example. DOC: Text and picture problems, book2 BUG: Fix text in margin issues DOC: Edits for the beginning of chapter 5, Statistics DOC: Fix empty code block. Cory Quammen (1): COMP: Avoid including VTK_USE_FILE within ITK Kent Williams (1): ENH: Add test to exercise issue with Transform::GetInverse Matthew McCormick (7): BUG: Register AzimuthElevationToCartesianTransform to factories. DOC: Update texture feature class references. BUG: Fix texture feature correlation computation for constant image. STYLE: Put ImageToImageFilterCommon in its own file. BUG: Wrap ImageToImageFilterCommon. STYLE: Put ImageSourceCommon in its own file. COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. Michka Popoff (1): ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter wrappings Ziv Yaniv (1): COMP: fixed warnings from gcc4.1.2, made implicit casts explicit List of changes since v4.6.0 -------------------------------------- Alexander Schmidt-Richberg (1): ENH: Updated Remote Module VariationalRegistration to new git tag Ali Ghayoor (10): ENH: Make ITKv4 compatible with ITKSoftwareGuide ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 ENH: Convert three ImageRegistration Examples to ITKv4 ENH: Add multi-Res and multistage registration Examples to ITKv4 ENH: Convert DeformableReg examples to ITKv4 reg framework BUG: Expand a test to reflect multi-metric registration bug BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 ENH: Add direct initialization to SyN registration ENH: Direct initialization of SyN by restoring the state ENH: LandmarkBasedTransformInitializer supports BSplineTransformType Arnaud Gelas (15): COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization ENH: Importing Laplacian Deformation for QuadEdgeMesh DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter BUG: fix gdcm version in GDCMImageIO. COMP: missing cast when calling gdcm::DataElement::SetByteValue COMP: missing cast when calling gdcm::DataElement::SetByteValue ENH: increase LaplacianDeformation code coverage STYLE: use typedef rather than inheritance BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false BUG: split include directories into appropriate cmake variables HDF5 BUG: missing gdcm libraries when using system GDCM DOC: fix doxygen documentaiton for itk::LaplacianDeformationQuadEdgeMeshFilter ENH: Add one method to erase a tag into MetaDataDictionary Bill Lorensen (5): ENH: Specify required VTK modules COMP: Wiki examples require additional vtk modules ENH: Modify WikiExamples remote config COMP: Bad test signature COMP: Update tag for wiki examples Brad King (6): COMP: Fix vxl_config_macros usage of CMake check macros ENH: Use if(DEFINED) to simplify conditions COMP: Fix vxl_config_macros checks broken by refactoring COMP: Fix one more vxl_config_macros check broken by refactoring BUG: Fix itk_module_config for repeated calls BUG: Fix itk_module_config for repeated calls Bradley Lowekamp (52): ENH: Adding License file from upstream MetaIO ENH: Adding script to update MetaIO from upstream ENH: Remove ITK MetaIO to prepare for upstream import PERF: Remove dynamically allocated temporary in evaluate method COMP: Fix variable type for Set/Get macros BUG: Implement ITK Style Singleton design pattern ENH: Add no throw exception specification for UnRegister methods COMP: Must specify order as "noexcept override" BUG: Add GetInverse for IdentityTransform ENH: Adding SetIdentity method to base DisplacementField class BUG: Remove unused redefinition of NULL BUG: Don't print to std::cout in PrintSelf ENH: Prefer the PrintSelfObjectMacro for printing nested objects BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit COMP: Fix signed to unsigned int comparison BUG: Fix overflows computing size of read tiff image ENH: Extract TiffReaderInternal to separate file ENH: Refactor ReadTwoSamplePerPixelImage into template function ENH: Refactor GenericReadImage into template function BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) ENH: Refactor method to convert RGBA image to output buffer ENH: Refactor duplicated code to read a page BUG: Fix right oriented tiff images BUG: Remove dead separated plannar code, add test STYLE: Fix minor kwstyle defects in test and test results BUG: Use array delete operator for array new allocations ENH: add arbitrary TIFF TAGs to meta-data dictionary ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage BUG: Address Coverity warning about null pointer dereferences ENH: Remove support for TIFF tile as 3D and dead code ENH: RGBA read images should stay unchanged. BUG: Override method to MakeOutput by name ENH: Refactor per pixel conversion function to per scan-line method PERF: Refactor color table lookup BUG: Adding missing parentheses around boolean expression ENH: adding TIFFImageIO test for RGB palette images PERF: Improve recursive Gaussian perfromance with VectorImages ENH: Query libtiff to determine compression support BUG: Support TIFF tiled image with TIFFReadRGBAImage BUG: Use SizeValueType for length of scanline PERF: Store causal results directly in output buffers COMP: Add explicit conversion to const char COMP: Explicitly add override to GetNameOfClass method COMP: Address internal segmentation fault with Intel compiler ENH: Adding method to set global physical space tolerance COMP: Explicitly add override to GetNameOfClass method BUG: Add new TypeMacro for non-overloaded classes BUG: Fix obscure race condition on access thread pool initialization BUG: Updating FDFImageIO remote module Christopher Mullins (15): COMP: Allows latex to compile for ITKSoftwareGuide COMP: Allows latex to compile for ITKSoftwareGuide COMP: Wrap MeshBase templates COMP: Wrap MeshBase templates COMP: Fix warning in BlockMatchingImageFilter STYLE: Line lengths in examples should be no longer than 80 chars. COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. COMP: Fix LaTeX warnings. STYLE: Fix formatting/punctuation errors. STYLE: Formatting and punctuation fixes. DOC: Edits for Book 2 Chapter 1 documentation in the Examples. DOC: Edits for book 2 chapter 2. DOC: More chapter 2 edits DOC: Book 2 Chapter 3 edits (part 1) DOC: book 2 chapter 4 Segmentation edits Danny Perry (2): BUG: adding test for vnl_sparse_matrix::mult() BUG: size of q buffer should actually be (this->rows())*pcols. David T. Chen (1): DOC: Fixed HistogramThresholdImageFitler Dirk Padfield (1): BUG: Corrected processing of last sigma GCC-XML Upstream (1): ENH: pygccxml v1.6.2 (reduced) Gert Wollny (1): COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) Girish Mallya (1): BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. Hans Johnson (24): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components PERF: Remove large foot print of PDF derivatives. PERF: Revert Remove large foot print of PDF derivatives. STYLE: Test against almost equal for floating point values STYLE: Non-exact floating point testing PERF: Distribute initialization per thread buffers ENH: Remove unnecessary mutable qualifier. STYLE: Remove comment with no meaning. ENH: Moved accumlator logic to main MI class ENH: Allow staggering of accumulations per thread. PERF: Zero reset thread buffers during finalize BUG: Syntax error in comment PERF: Add non-blocking mutex locking. ENH: Use TryLock minimize thread stalls BUG: ThreadedIndexedContainerPartitioner is inclusive STYLE: Remove include_regular_expression from Examples BUG: Demonstrate Inv(Inv(T)) != T BUG: Ensure Inv(Inv(T)) == T for transforms COMP: Valgrind detects uninitialized memory read COMP: Missing required base class API component ENH: Expand interface for selecting threadpool Ismael Belghiti (1): DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter Jim Miller (1): STYLE: Removing what appears to be a temporary file Johan Andruejol (1): ENH: Fix normalization for null vectors and return the norm Jon Haitz Legarreta (1): ENH: New test for itkLabelShapeOpeningImageFilter Kent Williams (9): COMP: use find_package(VTK COMPONENTS) to specify just needed VTK Components BUG: ImageSources/test/CMakeLists.txt incorrect library var reference COMP: Fix coverity defects related to RegistrationV4 examples COMP: silence warning of vnl_vector_fixed_ref::assert_size COMP: Fix various Coverity warnings COMP: Fix a typo in an error message print statement. COMP: itk::Command-derived class used pointless dynamic_cast. PERF: Don't recompute InternalInverse repeatedly COMP: Correct orientation/spacing for Philips MultiFrame Mark Hiner (2): ENH: Update SCIFIO remote module hash BUG: Fix duplicate variables in Windows Matthew McCormick (105): DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. ENH: Move FFTComplexToComplexImageFilter out of Review. ENH: Add VnlComplexToComplexFFTImageFilter. BUG: Use fixed seed for Vnl FFT tests for repeatibility. ENH: Bump CMakeLists.txt version to 4.7.0. BUG: ArchiveTestingData.py future imports must occur at the beginning. BUG: Do not run vnl_test_na with broken libc++. DOC: Remove Image2.cxx reference from Book 2. DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. DOC: Remove references to Book 1 sections from Book 2. DOC: Make BinaryThresholdImageFilter not floating. DOC: Fix Software Guide figure caption for FlipImageFilter. DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. DOC: ImageRandomConstIteratorWithIndex table reference. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter. BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. STYLE: Fix style in VoronoiDiagram2D. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Bump GCCXML to 2014-08-06. BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. BUG: Fix Win MultiThreader check for successful process creation. BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. DOC: itk::statistics -> itk::Statistics. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. COMP: Improve const correctness of GradientRecursiveGaussianImageFilter. BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. COMP: ThreadJob NULL not defined. BUG: Fix alpha assignment for RGBA TIFF. COMP: Remove unused typedefs in LevelSetsv4Visualization. COMP: Remove unused typedef's in VtkGlue. ENH: Mark BSplineWarping2Test as RUNS_LONG. BUG: Fix Nifti IO read with large images. COMP: Remove call for non-existent variable in Nifti debugging. BUG: Close the file on Read and Write in HDF5TransformIO. BUG: Remove InsightLegacy test code from TransformHDF5Test. ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. STYLE: Use SeriesUIDContainerType and FileNamesContainerType ENH: Allow specification of orthogonality tolerance in rigid transforms. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Do not use _stat64 with MinGW-32. BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. DOC: itk::statistics -> itk::Statistics. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. COMP: Address LaplacianDeformation Doxygen warnings. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Fix missing prefix in ITKv3ImageRegistration20Test. BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform COMP: Do not wrap the FixedArray of Image SmartPointer's. COMP: Add missing wrapping for TransformIOBaseTemplate. COMP: Mark DeformableRegistration6Test as RUNS_LONG. STYLE: Improve style in BinaryImageToLabelMapFilter. BUG: Fix BinaryImageToLabelMapFilter on 1D image. ENH: Improve precision of the joint PDF sum BUG: Fix BinShrinkImageFilter for different input/output image types. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. BUG: Use -py3 when building wrapping for Python 3. COMP: Add missing wrapping for TransformIOBaseTemplate. DOC: Improve ImageRegistration4 grammar. ENH: Add IOTransformDCMTK Remote module. BUG: gdcm::StringFilter recognizes backslash delimiter. DOC: Add migration guide for GDCM Rescale slope intercept apply on write. COMP: Remove unused typedef's in GPU code. STYLE: Improve style of HoughTransform2DLinesImageFilter example. COMP: Use ConceptChecking for IterativeInverse dimension check. COMP: Wrap TransformIOBaseTemplate for const SmartPointer. COMP: Add warning exceptions for third party pcre, swig, gccxml. ENH: Bump ITK version to 4.6.1. BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. BUG: Remove GaussianImageSource members shadowing GenerateImageSource. STYLE: Style fixes to ITKImageSources module. BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType. BUG: Do not perform itk_download_attempt_check when not building ITK. DOC: Update GDCMImageIO rescale slope intercept doc. BUG: Only register requestion IO COMPONENT modules. BUG: Fix wrapping .i, .idx CMake dependencies. COMP: Add VTK Python module when wrapping ITKVtkGlue. STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. COMP: Add missing VTK module dependency for LevelSetsv4Visualization. BUG: By default, do not create any fixed parameters. STYLE: Remove trivial method comments in itkTransform.hxx. BUG: PolylineMask Filter's GenerateData is protected / virtual. ENH: Add HigherOrderAccurateGradient Module. BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal. COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. STYLE: Style fixes for Transform classes. DOC: Increase Doxygen LOOKUP_CACHE_SIZE. BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. DOC: Index Wiki examples with Doxygen. COMP: Bump SphinxExamples remote module. DOC: Index Sphinx examples in Doxygen. COMP: Remove old java examples. COMP: Remove duplicate DiffusionTensor3DReconstruction example reference. COMP: Address GradientAnisotropicDiffusionImageFilter example settings. COMP: Bump Sphinx Examples remote. COMP: Bump WikiExamples remote. MetaIO Maintainers (1): MetaIO (reduced) Michka Popoff (40): ENH: Fixes for python 3 support BUG: Add VTK_VERSION for older VTK versions BUG: Improve SWIG version check COMP: Add wrapping for ThreadPool and ThreadJob COMP: Remove unimplemented DestroyPool method COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping COMP: Do not hide pygccxml warnings ENH: Update links in readme file BUG: Improve SWIG version check BUG: Add VTK_VERSION for older VTK versions STYLE: Remove trailing whitespaces STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP BUG: Fix memory leak in MetaImageIO after exception ENH: Add script to update pygccxml from upstream BUG: Update VTK minimum version (for release) BUG: Fix memory leak in MetaImageIO after exception ENH: Remove Sun OS compatibility for the wrappings COMP: Fix for conversion to non-pointer like type warning STYLE: LabelObject style DOC: Remove broken link from LabelObject class description ENH: Do not setup the python tests if not asked ENH: Add new GetTypes() and GetTypesAsList() methods to the template class COMP: Fix CMP0054 warnings in wrappings STYLE: Remove old cmake < 2.8.4 specific code STYLE: Remove old cmake < 2.8.5 specific code ENH: Update to PCRE 8.36 COMP: Refactor Wrapping setup and fix legacy warnings ENH: Add wrapping configuration to ITKConfig.cmake STYLE: Some minor code cleanup in the wrapping setup DOC: Fix typo in RelabelComponentImageFilter ENH: Deprecate VectorResampleImageFilter DOC: Add migration guide for ::Zero and ::One ENH: Deprecate ::Zero and ::One ENH: Add option to disable sorting by size in itkRelabelComponentImageFilter ENH: Add Vector and RGB wrapping to linear interpolator STYLE: Remove SORT macro in wrappings COMP: Fix warning for InterpolateImageFunction wrapping COMP: Add a check for Blocks in GPU module COMP: Bump SCIFIO to fix test build warnings COMP: Fix wrapping of itkImageFunctionBase Nick Tustison (7): BUG: Need to explicitly specify spline order. ENH: Initializing the transform center. BUG: Need to check the dynamic cast before any calls. ENH: Adding modifications for point set metrics. BUG: Need to specify TInternalComputationValueType for default metric. ENH: Adding sparse points to B-spline field estimate. BUG: Uninitialized variables. Richard Beare (1): ENH: Include TIFF tags in the MetaDataDictionary Taylor Braun-Jones (1): BUG: Fix SliceBySliceImageFilter doesn't propagate information internally Umang B (1): ENH: Use thread pool to dispatch multithreading tasks Vivien Delmon (2): BUG: ExtractImageFilter::CollapseToSubMatrix fix ENH: Add a test on extracted directions in CollapseToSubMatrix mode Vladimir S. FONOV (1): BUG: Fixing incorrect MINC style inverse transform ITK Sphinx Examples Changelog ----------------------------------------------------- Arnaud Gelas (12): add one example to translate one itk::Image add PasteImageFilter example fix path in ArchiveBinaryData.py.in BUG: error when TEST_IMAGE_PREFIX was used fix broken links as detected by linkcheck add example for PermuteAxesImageFilter Add one example to apply an affine transform given homogeneous matrix Add one example to multiply 2 images use ITK 4.6.1 for superbuild update breathe to 3.1.0 Add one example to generate slices from volume Add one example about RegionOfInterestImageFilter Brad King (1): setup-hooks: Create .git hooks directory if necessary Matt McCormick (15): ENH: Bump ITK Superbuild tag to 4.6.0. BUG: Fix ConvertAnITKGrayScaleImageToCVMat compare_to_baseline. COMP: Remove breathe link to ConstantPadImageFilter. BUG: Fix figure path for Iterative Hole Filling. BUG: Evolution.gif needs to be ..only:: html COMP: Content not permitted in image:: directive. BUG: Require CMake 2.8.6 in CreateNewExample template. BUG: Update CreateNewExample.py for new compare_to_baseline syntax. COMP: Fix ITKMathematicalMorphology COMPONENT dependency. COMP: Fix build as a Remote module. COMP: Fix fresh configuration as an ITK module. COMP: Fix configuration ITK_WRAP_PYTHON is not defined. BUG: Annotate ReadUnknownImageType component type correctly. ENH: Bump Superbuild VTK version to 6.1.0. ENH: Bump Superbuild ITK version to 4.7.0. Michka Popoff (15): COMP: Fix failing setup of SegmentBloodVessels example STYLE: Update title for Apply Affine Transform example ENH: Add GeodesicActiveContourLevelSetImageFilter example COMP: Fix failing MultiplyTwoImagesTestBaselineComparison test COMP: Add images to the MultiplyTwoImages documentation COMP: Fix and improve ForwardFFTExample COMP: Fix Multiply two images output COMP: Update all cmake versions to 2.8.6 COMP: Fix MultiplyTwoImagesTestBaselineComparison ENH: Add infrastructure for Python tests ENH: Add example on how to resample a RGB image BUG: Add missing images to ResampleAVectorImage documentation COMP: Fix path for favicon COMP: Fix for CleanQuadEdgeMesh documentation BUG: Add missing semicolon to example ITK Software Guide Changelog ------------------------------------------- Ali Ghayoor (4): ENH: Part one of converting Registration chapter to ITKv4 ENH: Part two of converting Registration chapter to ITKv4 ENH: Part three of converting Registration chapter to ITKv4 DOC: Revise the registration chapter Christopher Mullins (16): COMP: Use RegistrationITKv3 examples with ITKv3_COMPATIBILITY STYLE: Use minted to highlight code syntax DOC: Add instructions for using ITK from python COMP: Sort and run the examples topologically. COMP: add_custom_command no longer takes SOURCE parameter STYLE: Fix python indentation COMP: BuildTexFiles target should depend on SoftwareGuideExamples COMP: Update the .eps generation command to use the OUTPUT signature. STYLE: Fix quotes. DOC: Language edits mostly from Book 2 ENH: Only flip the images we want to flip BUG: Figure overlaps text in 4.3. DOC: More language fixes, use minted instead of code tags. STYLE: Put a new line before code blocks STYLE: Fix margin problems with filenames and floating figure overlaps STYLE: Change margins using the geometry package. Hans Johnson (1): ENH: Bring ITK code closer to the 4.7 release code Matt McCormick (25): ENH: Pass PDF_QUALITY_LEVEL in superbuild. BUG: Remove unused RunExamples.py imports. ENH: Reduce verbosity of RunExamples.py. BUG: Do not include RegistrationITKv4 example sources in the build. BUG: Fix caption on Confidence Connectened on BrainWeb figures. BUG: Bump the ITK superbuild for LaTeX fixes. ENH: Add new ISBN numbers. DOC: CDash has replaced Dart. DOC: itk::statistics -> itk::Statistics. ENH: Update ITK logo. STYLE: Remove box around CC logo. DOC: Document instructions for building from the Docker image. DOC: Docker build instruction improvements. ENH: New path for starting the docker environment. ENH: Change paper size. COMP: Improve arguments for GradientAnisotropicDiffusionImageFilter. ENH: Bump ITK Superbuild version to 2014-12-03. BUG: Add flags for PDF_QUALITY_LEVEL STREQUAL "" ENH: Add contributors for print release. ENH: Upsample when building with PDF_QUALITY_LEVEL "Printer". BUG: Specify cc-by logo size explicitly. BUG: Use original ITK configuration images. ENH: Use file(COPY to copy over .eps images. ENH: Margin tightening. ENH: Bump ITK ExternalProject to v4.7.0. Michka Popoff (5): ENH: Use the new licence file for MetaIO DOC: Fixes for the ITK 4.7 book DOC: Fixes for book1, part1, chapter 2 DOC: Fixes and improvements for Book 1, chapter 3 DOC: Minor fixes for Book 1, Chapter 4 Sandy McKenzie (1): STYLE: Add new line before code block ITKApps Changelog --------------------------- Bill Lorensen (1): COMP: Update CTEST_DROP_SITE Matt McCormick (4): COMP: Use ::ZeroValue() instead of ::Zero. COMP: Patch FLTK for build against newer freetype. COMP: Address %d type for VolviewPlugins. ENH: Bump ITK Superbuild version to v4.7.0. From matt.mccormick at kitware.com Fri Dec 19 19:29:00 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 19 Dec 2014 19:29:00 -0500 Subject: [ITK] VS2013 Update 4 (RelWithDebInfo x64) crash with ITK 4.6.1 In-Reply-To: <822C53AE-230F-48C3-9487-EF9D042C13BB@mail.nih.gov> References: <822C53AE-230F-48C3-9487-EF9D042C13BB@mail.nih.gov> Message-ID: Hi Marian, Thanks for taking the initiative to post this! I have upvoted the issue. I encourage others to do so, too. I added a comment to reflecting Brad's note that we have seen this on the dashboard. Other comments could help, too. Thanks, Matt On Fri, Dec 19, 2014 at 9:59 AM, Bradley Lowekamp wrote: > Hello, > > We have been having significant issues with Visual Studio 2013 (VS12) > Professional in with Release optimizations for a while now. Here is the > nightly dashboard with the run time errors: > > https://open.cdash.org/buildSummary.php?buildid=3619048 > > It's been a while since I looked into this. If I recall correctly it > appeared to be critical alignment issues with SSE optimization and just the > code being generated was invalid. Your posted issue looks the same. > > However, I don't think your example posted with MS is simple enough to get > traction there. I think what is needed is a single preprocessed file without > dependencies on building all of ITK, or cmake to maximize chances of it > being addressed. > > Brad > > > > On Dec 19, 2014, at 9:28 AM, ???'?? ?????? wrote: > > Hi, > > I've reproduced crash using VS2013 Update 4 (RelWithDebInfo x64) with pure > ITK 4.6.1 code inside FiniteDifferenceImageFilter. > > I've reported it to > https://connect.microsoft.com/VisualStudio/feedback/details/1060166/compiler-generates-divpd-instruction-on-non-aligned-data > Can someone check if it's really compiler problem and upvote on connect? > Don't really want to add one more __declspec(align(16)) inside ITK. I'm > attaching .cpp and cmakelists.txt > > Best regards, > Marian > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Fri Dec 19 19:47:39 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 19 Dec 2014 19:47:39 -0500 Subject: [ITK] [ITK-users] [Insight-users] [ITK-USER]Compile ITK3.20.1 with VS2012 In-Reply-To: References: Message-ID: Hi, Dzenan sent a patch for building ITKv3 with Visual Studio 2013. It has been pushed to Git "release-3.20" branch. For more information on ITK's Git, see [1]. Thanks, Matt [1] http://www.itk.org/Wiki/ITK/Git On Fri, Dec 19, 2014 at 1:34 PM, D?enan Zuki? wrote: > Probably too late for JX, but I found a solution. When configuring ITK with > CMake, in the field CMAKE_CXX_FLAGS add the following: > /D_ALLOW_KEYWORD_MACROS > Article which helped me: > http://mostlybuggy.wordpress.com/2012/12/18/getting-around-vs2012-c1189c4005-keyword-re-defined-in-macros/ > > > On Wed, May 29, 2013 at 9:33 AM, Bradley Lowekamp > wrote: >> >> Hi, >> >> Why no upgrade to ITK v4? >> >> ITK v3.20 was released in 2010, well before Visual Studio 2012. So it >> should be no surprise it does not work with it. I believe VS 2010 should >> work with it, and VS9, and VS8, and VS7.... >> >> >> Brad >> >> >> >> On May 28, 2013, at 10:41 PM, JX NIE wrote: >> >> > Hi Everyone, >> > I have tried to compile ITK(version 3.20.1 ) with VS2012, but >> > failed. >> > It has ended up with a lot of Redifine errors as follow. >> > Could you please tell me how to solve this compile problem. >> > Regards, >> > >> > NIE JUNXIAO >> > >> > >> > >C:\Program Files (x86)\Microsoft Visual Studio >> > > 11.0\VC\include\xkeycheck.h(242): fatal error C1189: #error : The C++ >> > > Standard Library forbids macroizing keywords. Enable warning C4005 to find >> > > the forbidden macro. >> > >> > 1 IntelliSense: #error directive: The C++ Standard Library >> > forbids macroizing keywords. Enable warning C4005 to find the forbidden >> > macro. c:\Program Files (x86)\Microsoft Visual Studio >> > 11.0\VC\include\xkeycheck.h 242 >> > 2 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\sal.h 2367 >> > 3 IntelliSense: expected a declaration c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\vadefs.h 139 >> > 4 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 437 >> > 5 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 446 >> > 6 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 464 >> > 7 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 475 >> > 8 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 476 >> > 9 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 497 >> > 10 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 501 >> > 11 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 506 >> > 12 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 514 >> > 13 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 571 >> > 14 IntelliSense: attribute "noreturn" does not apply here >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h >> > 572 >> > 15 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 572 >> > 16 IntelliSense: attribute "noreturn" does not apply here >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h >> > 575 >> > 17 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 576 >> > 18 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1979 >> > 19 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1980 >> > 20 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1981 >> > 21 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1982 >> > 22 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1983 >> > 23 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1985 >> > 24 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1992 >> > 25 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 1999 >> > 26 IntelliSense: expected a declaration c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h 2023 >> > 27 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 510 >> > 28 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 528 >> > 29 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 529 >> > 30 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 542 >> > 31 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 576 >> > 32 IntelliSense: invalid destructor declaration c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 577 >> > 33 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 583 >> > 34 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 585 >> > 35 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 586 >> > 36 IntelliSense: explicit type is missing ('int' assumed) >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 588 >> > 37 IntelliSense: identifier "EMIT" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 588 >> > 38 IntelliSense: function "_Lockit" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 589 >> > 39 IntelliSense: reference variable "EMIT" requires an >> > initializer c:\Program Files (x86)\Microsoft Visual Studio >> > 11.0\VC\include\yvals.h 589 >> > 40 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 591 >> > 41 IntelliSense: expected a declaration c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 606 >> > 42 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 693 >> > 43 IntelliSense: expected a declaration c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 726 >> > 44 IntelliSense: expected a declaration c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 729 >> > 45 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 740 >> > 46 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h 741 >> > 47 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 23 >> > 48 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 47 >> > 49 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 48 >> > 50 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 49 >> > 51 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 50 >> > 52 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 54 >> > 53 IntelliSense: identifier "errno_t" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56 >> > 54 IntelliSense: variable "memcpy_s" may not be initialized >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56 >> > 55 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56 >> > 56 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 93 >> > 57 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 97 >> > 58 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 98 >> > 59 IntelliSense: identifier "errno_t" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103 >> > 60 IntelliSense: variable "_strset_s" may not be initialized >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103 >> > 61 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103 >> > 62 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 104 >> > 63 IntelliSense: identifier "errno_t" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107 >> > 64 IntelliSense: variable "strcpy_s" may not be initialized >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107 >> > 65 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107 >> > 66 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 109 >> > 67 IntelliSense: identifier "errno_t" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112 >> > 68 IntelliSense: variable "strcat_s" may not be initialized >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112 >> > 69 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112 >> > 70 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 114 >> > 71 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 116 >> > 72 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 117 >> > 73 IntelliSense: variable "strnlen" may not be initialized >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 121 >> > 74 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 121 >> > 75 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 123 >> > 76 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 135 >> > 77 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 142 >> > 78 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 148 >> > 79 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 149 >> > 80 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 150 >> > 81 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 151 >> > 82 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 152 >> > 83 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 153 >> > 84 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 154 >> > 85 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 155 >> > 86 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 156 >> > 87 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 157 >> > 88 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 158 >> > 89 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 159 >> > 90 IntelliSense: variable "strcspn" may not be initialized >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 160 >> > 91 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 160 >> > 92 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 161 >> > 93 IntelliSense: identifier "errno_t" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 162 >> > 94 IntelliSense: variable "_strerror_s" may not be >> > initialized c:\Program Files (x86)\Microsoft Visual Studio >> > 11.0\VC\include\string.h 162 >> > 95 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 162 >> > 96 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 163 >> > 97 IntelliSense: identifier "errno_t" is undefined c:\Program >> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166 >> > 98 IntelliSense: variable "strerror_s" may not be initialized >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166 >> > 99 IntelliSense: expected a ')' c:\Program Files >> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166 >> > 100 IntelliSense: variable "EMIT" is not a type name >> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 168 >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://www.itk.org/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://www.itk.org/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From kevin.keraudren10 at imperial.ac.uk Sat Dec 20 05:24:58 2014 From: kevin.keraudren10 at imperial.ac.uk (Kevin Keraudren) Date: Sat, 20 Dec 2014 10:24:58 +0000 Subject: [ITK] [ITK-users] Medical Image Analysis IPython Notebooks Message-ID: <54954E7A.3050503@imperial.ac.uk> Hi, The IPython notebooks used for the tutorials in the Medical Image Analysis course at Imperial College London are now on github: https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials These might be of interest to the mailing list as they rely on SimpleITK and could be useful either as teaching material or example applications. They can be browsed directly in nbviewer: http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/ The following blog post is a quick presentation of the github repository: http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html Please do not hesitate to let us know if you have questions or comments regarding these tutorials. Kind regards, Kevin Keraudren, PhD student, Imperial College London -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Mon Dec 22 09:26:11 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 22 Dec 2014 09:26:11 -0500 Subject: [ITK] [ITK-users] Medical Image Analysis IPython Notebooks In-Reply-To: <54954E7A.3050503@imperial.ac.uk> References: <54954E7A.3050503@imperial.ac.uk> Message-ID: Hello Kevin, These notebooks look outstanding. Thank you very much for sharing. I very much like what you did here: http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/blob/master/tutorial_2/basics_reg.ipynb to illustrate the different metrics' values, and the impact of apply Gaussian smoothing to the images. Also please note that you were using the an experimental version of the ImageRegistrationMethod in SimpleITK which was based on ITKv3 registration frameworks. Since then the development has evolved to be based on the ITKv4 registration framework and many, many features have been added. This includes a couple transform initializers which estimate some basic transform parameters and very importantly set the fixed parameter for the center of the transform. Additionally the interface to the transforms is much improved. Brad On Dec 20, 2014, at 5:24 AM, Kevin Keraudren wrote: > Hi, > > The IPython notebooks used for the tutorials in the Medical Image Analysis course at Imperial College London are now on github: > https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials > > These might be of interest to the mailing list as they rely on SimpleITK and could be useful either as teaching material or example applications. > > They can be browsed directly in nbviewer: > http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/ > > The following blog post is a quick presentation of the github repository: > http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html > > Please do not hesitate to let us know if you have questions or comments regarding these tutorials. > > Kind regards, > > Kevin Keraudren, > PhD student, Imperial College London > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Dec 22 10:37:56 2014 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Mon, 22 Dec 2014 10:37:56 -0500 (EST) Subject: [ITK] [ITK-users] New Submission: A generic interpolator for multi-label images Message-ID: <20141222153756.61A7F3D6C186@insightsoftwareconsortium.org> Hello, A new submission has been added to the Insight Journal. Title: A generic interpolator for multi-label images Authors: Schaerer J., Roche F., Belaroussi B. Abstract: We present a generic interpolator for label images. The basic idea is to interpolate each label with an ordinary image interpolator, and return the label with the highest value. This is the idea used by the itk::LabelImageGaussianInterpolateImageFunction interpolator. Unfortunately, this class is currently limited to Gaussian interpolation. Using generic programming, our proposed interpolator extends this idea to any image interpolator. Combined with linear interpolation, this results in similar or better accuracy and much improved computation speeds on a test image. Download and review this publication at: http://hdl.handle.net/10380/3506 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/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 kevin.keraudren10 at imperial.ac.uk Mon Dec 22 13:04:23 2014 From: kevin.keraudren10 at imperial.ac.uk (Keraudren, Kevin) Date: Mon, 22 Dec 2014 18:04:23 +0000 Subject: [ITK] [ITK-users] Medical Image Analysis IPython Notebooks In-Reply-To: References: <54954E7A.3050503@imperial.ac.uk>, Message-ID: Hi Brad, I am glad the notebooks are appreciated, all the credit goes to Ozan (in copy) who is the main author! If I understand correctly you are mentioning in your email the ImageRegistrationMethod which will be in the next release of SimpleITK (0.9.0): http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html https://github.com/SimpleITK/SimpleITK/tree/next This will definitely be something to look at for the next iteration of these tutorials. Kind regards, Kevin ________________________________ From: Bradley Lowekamp [blowekamp at mail.nih.gov] Sent: Monday, December 22, 2014 2:26 PM To: Keraudren, Kevin Cc: insight-users at itk.org Users; Oktay, Ozan Subject: Re: [ITK-users] Medical Image Analysis IPython Notebooks Hello Kevin, These notebooks look outstanding. Thank you very much for sharing. I very much like what you did here: http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/blob/master/tutorial_2/basics_reg.ipynb to illustrate the different metrics' values, and the impact of apply Gaussian smoothing to the images. Also please note that you were using the an experimental version of the ImageRegistrationMethod in SimpleITK which was based on ITKv3 registration frameworks. Since then the development has evolved to be based on the ITKv4 registration framework and many, many features have been added. This includes a couple transform initializers which estimate some basic transform parameters and very importantly set the fixed parameter for the center of the transform. Additionally the interface to the transforms is much improved. Brad On Dec 20, 2014, at 5:24 AM, Kevin Keraudren > wrote: Hi, The IPython notebooks used for the tutorials in the Medical Image Analysis course at Imperial College London are now on github: https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials These might be of interest to the mailing list as they rely on SimpleITK and could be useful either as teaching material or example applications. They can be browsed directly in nbviewer: http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/ The following blog post is a quick presentation of the github repository: http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html Please do not hesitate to let us know if you have questions or comments regarding these tutorials. Kind regards, Kevin Keraudren, PhD student, Imperial College London _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Mon Dec 22 13:14:32 2014 From: matimontg at gmail.com (Matias Montroull) Date: Mon, 22 Dec 2014 15:14:32 -0300 Subject: [ITK] [ITK-users] SimpleITK | Read non dicom file and write it as series of slices Message-ID: Hi, is there an example out there similar to this but in C#: http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html Thank you, Matias. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Mon Dec 22 15:32:59 2014 From: millerjv at gmail.com (Jim Miller) Date: Mon, 22 Dec 2014 15:32:59 -0500 Subject: [ITK] [ITK-users] Medical Image Analysis IPython Notebooks In-Reply-To: References: <54954E7A.3050503@imperial.ac.uk> Message-ID: <6CDB3AF3-447E-4A51-822B-2C9187B52A67@gmail.com> How about we add a link to these off the ITK Wiki. Perhaps off the page http://itk.org/Wiki/ITK/Course_Ware Jim > On Dec 22, 2014, at 1:04 PM, Keraudren, Kevin wrote: > > Hi Brad, > > I am glad the notebooks are appreciated, all the credit goes to Ozan (in copy) who is the main author! > > If I understand correctly you are mentioning in your email the ImageRegistrationMethod which will be in the next release of SimpleITK (0.9.0): > http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html > https://github.com/SimpleITK/SimpleITK/tree/next > > This will definitely be something to look at for the next iteration of these tutorials. > > Kind regards, > > Kevin > > From: Bradley Lowekamp [blowekamp at mail.nih.gov] > Sent: Monday, December 22, 2014 2:26 PM > To: Keraudren, Kevin > Cc: insight-users at itk.org Users; Oktay, Ozan > Subject: Re: [ITK-users] Medical Image Analysis IPython Notebooks > > Hello Kevin, > > These notebooks look outstanding. Thank you very much for sharing. > > I very much like what you did here: > http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/blob/master/tutorial_2/basics_reg.ipynb > to illustrate the different metrics' values, and the impact of apply Gaussian smoothing to the images. > > Also please note that you were using the an experimental version of the ImageRegistrationMethod in SimpleITK which was based on ITKv3 registration frameworks. Since then the development has evolved to be based on the ITKv4 registration framework and many, many features have been added. > > This includes a couple transform initializers which estimate some basic transform parameters and very importantly set the fixed parameter for the center of the transform. Additionally the interface to the transforms is much improved. > > Brad > >> On Dec 20, 2014, at 5:24 AM, Kevin Keraudren wrote: >> >> Hi, >> >> The IPython notebooks used for the tutorials in the Medical Image Analysis course at Imperial College London are now on github: >> https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials >> >> These might be of interest to the mailing list as they rely on SimpleITK and could be useful either as teaching material or example applications. >> >> They can be browsed directly in nbviewer: >> http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/ >> >> The following blog post is a quick presentation of the github repository: >> http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html >> >> Please do not hesitate to let us know if you have questions or comments regarding these tutorials. >> >> Kind regards, >> >> Kevin Keraudren, >> PhD student, Imperial College London >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Dec 23 00:55:18 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 23 Dec 2014 00:55:18 -0500 Subject: [ITK] [ITK-users] Medical Image Analysis IPython Notebooks In-Reply-To: <6CDB3AF3-447E-4A51-822B-2C9187B52A67@gmail.com> References: <54954E7A.3050503@imperial.ac.uk> <6CDB3AF3-447E-4A51-822B-2C9187B52A67@gmail.com> Message-ID: I was unaware of this wiki page (thanks!). I added a link to that page and a link to the course here: http://www.itk.org/Wiki/ITK/Documentation#Courses This page is linked from the main ITK web page and from the http://www.itk.org/ITK/help/documentation.html page. Thanks again for sharing this wonderful resource! Well done! Matt On Mon, Dec 22, 2014 at 3:32 PM, Jim Miller wrote: > How about we add a link to these off the ITK Wiki. Perhaps off the page > > http://itk.org/Wiki/ITK/Course_Ware > > > Jim > > On Dec 22, 2014, at 1:04 PM, Keraudren, Kevin > wrote: > > Hi Brad, > > I am glad the notebooks are appreciated, all the credit goes to Ozan (in > copy) who is the main author! > > If I understand correctly you are mentioning in your email the > ImageRegistrationMethod which will be in the next release of SimpleITK > (0.9.0): > > http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html > https://github.com/SimpleITK/SimpleITK/tree/next > > This will definitely be something to look at for the next iteration of these > tutorials. > > Kind regards, > > Kevin > > ________________________________ > From: Bradley Lowekamp [blowekamp at mail.nih.gov] > Sent: Monday, December 22, 2014 2:26 PM > To: Keraudren, Kevin > Cc: insight-users at itk.org Users; Oktay, Ozan > Subject: Re: [ITK-users] Medical Image Analysis IPython Notebooks > > Hello Kevin, > > These notebooks look outstanding. Thank you very much for sharing. > > I very much like what you did here: > http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/blob/master/tutorial_2/basics_reg.ipynb > to illustrate the different metrics' values, and the impact of apply > Gaussian smoothing to the images. > > Also please note that you were using the an experimental version of the > ImageRegistrationMethod in SimpleITK which was based on ITKv3 registration > frameworks. Since then the development has evolved to be based on the ITKv4 > registration framework and many, many features have been added. > > This includes a couple transform initializers which estimate some basic > transform parameters and very importantly set the fixed parameter for the > center of the transform. Additionally the interface to the transforms is > much improved. > > Brad > > On Dec 20, 2014, at 5:24 AM, Kevin Keraudren > wrote: > > Hi, > > The IPython notebooks used for the tutorials in the Medical Image Analysis > course at Imperial College London are now on github: > https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials > > These might be of interest to the mailing list as they rely on SimpleITK and > could be useful either as teaching material or example applications. > > They can be browsed directly in nbviewer: > http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/ > > The following blog post is a quick presentation of the github repository: > http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html > > Please do not hesitate to let us know if you have questions or comments > regarding these tutorials. > > Kind regards, > > Kevin Keraudren, > PhD student, Imperial College London > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From nekto1989 at gmail.com Tue Dec 23 05:36:38 2014 From: nekto1989 at gmail.com (=?UTF-8?B?0JzQsNGAJ9GP0L0g0JrQu9C40LzQvtCy?=) Date: Tue, 23 Dec 2014 12:36:38 +0200 Subject: [ITK] ITK_NULLPTR and ITK_OVERRIDE on VS2012+ Message-ID: Hi, I've found out that ITK defines ITK_NULLPTR to NULL instead of nullptr and ITK_OVERRIDE to nothing. This happens in itkMacro.h. Can't this be done in some other way like check for HAS_OVERRIDE, HAS_NULLPTR instead of checking for __cplusplus? Best regards, Marian -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Dec 23 11:34:35 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 23 Dec 2014 11:34:35 -0500 Subject: [ITK] [ANNOUNCE] SimpleITK 0.8.1 Release Message-ID: <96262E2C-0CF1-4C15-B17C-5D063F830B45@mail.nih.gov> We are pleased to announce the SimpleITK 0.8.1 Release. SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education and interpreted languages. SimpleITK provides binaries for several wrapped languages to enable users to rapidly get started using ITK. Information on how to get started and download the binaries: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries This patch release updates the ITK version to the newly released 4.7.0. Additionally, this patch contains improved support for CMake 3.0, fixes for compilation issues, the addition of the LabelOverlapMeasures filter, and a fix for the ClampCast filter. Also, we are now compiling for Python 3.4, and have stopped compiling for Python 3.2. Lastly, we are providing some binaries for the Anaconda Python distribution on Binstar. Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.1/ Release Doxygen Documentation: http://www.itk.org/SimpleITKDoxygen08/html/index.html Additional Release Notes: http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.8.1_Release Enjoy, Brad From blowekamp at mail.nih.gov Tue Dec 23 11:36:27 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 23 Dec 2014 11:36:27 -0500 Subject: [ITK] ITK_NULLPTR and ITK_OVERRIDE on VS2012+ In-Reply-To: References: Message-ID: <44EA4124-D6D3-4AD6-ADEF-CEFBC68568E2@mail.nih.gov> Hello, Yes you could be done with CMake try compiles an what not. Checking to see if the C++ version is C++11 seems reasonable. Is this causing any problems? Brad On Dec 23, 2014, at 5:36 AM, ???'?? ?????? wrote: > Hi, > > I've found out that ITK defines ITK_NULLPTR to NULL instead of nullptr and ITK_OVERRIDE to nothing. This happens in itkMacro.h. Can't this be done in some other way like check for HAS_OVERRIDE, HAS_NULLPTR instead of checking for __cplusplus? > > Best regards, > Marian > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From nekto1989 at gmail.com Tue Dec 23 14:31:28 2014 From: nekto1989 at gmail.com (=?UTF-8?B?0JzQsNGAJ9GP0L0g0JrQu9C40LzQvtCy?=) Date: Tue, 23 Dec 2014 21:31:28 +0200 Subject: [ITK] ITK_NULLPTR and ITK_OVERRIDE on VS2012+ In-Reply-To: <44EA4124-D6D3-4AD6-ADEF-CEFBC68568E2@mail.nih.gov> References: <44EA4124-D6D3-4AD6-ADEF-CEFBC68568E2@mail.nih.gov> Message-ID: Hi, Even latest VS2013 has __cplusplus defined to 199711L. I just changed second compiler from mingw to mingw-w64 and GCC 4.9.2 found some problems in code because of ITK_OVERRIDE that was ignored by VS and mingw32. Marian 2014-12-23 18:36 GMT+02:00 Bradley Lowekamp : > Hello, > > Yes you could be done with CMake try compiles an what not. > > Checking to see if the C++ version is C++11 seems reasonable. Is this > causing any problems? > > Brad > > On Dec 23, 2014, at 5:36 AM, ???'?? ?????? wrote: > > > Hi, > > > > I've found out that ITK defines ITK_NULLPTR to NULL instead of nullptr > and ITK_OVERRIDE to nothing. This happens in itkMacro.h. Can't this be done > in some other way like check for HAS_OVERRIDE, HAS_NULLPTR instead of > checking for __cplusplus? > > > > Best regards, > > Marian > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ronn at rlkling.com Wed Dec 24 13:14:22 2014 From: ronn at rlkling.com (Ronn Kling) Date: Wed, 24 Dec 2014 13:14:22 -0500 Subject: [ITK] getting RawImageIO to work Message-ID: <549B027E.2020802@rlkling.com> Hello All, I am trying to read in a binary data file using RawImageIO. When I step through with the debugger I get an error on the last line below about memory corruption. As far as I can tell I have everything correct, what am I missing? typedef unsigned char fixedPixelType; typedef unsigned char movingPixelType; typedef itk::Image fixedImageType; typedef itk::Image movingImageType; // create a ImageIO for the raw data files typedef itk::RawImageIO ImageIOType; ImageIOType::Pointer fixedimageio = ImageIOType::New(); From bill.lorensen at gmail.com Wed Dec 24 14:07:45 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 24 Dec 2014 14:07:45 -0500 Subject: [ITK] getting RawImageIO to work In-Reply-To: <549B027E.2020802@rlkling.com> References: <549B027E.2020802@rlkling.com> Message-ID: Please provide a small, complete compilable example and I'm sure we can help. On Wed, Dec 24, 2014 at 1:14 PM, Ronn Kling wrote: > Hello All, > > I am trying to read in a binary data file using RawImageIO. When I step > through with the debugger I get an error on the last line below about memory > corruption. As far as I can tell I have everything correct, what am I > missing? > > typedef unsigned char fixedPixelType; > typedef unsigned char movingPixelType; > > typedef itk::Image fixedImageType; > typedef itk::Image movingImageType; > // create a ImageIO for the raw data files > typedef itk::RawImageIO ImageIOType; > ImageIOType::Pointer fixedimageio = ImageIOType::New(); > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -- Unpaid intern in BillsBasement at noware dot com From ronn at rlkling.com Wed Dec 24 14:26:10 2014 From: ronn at rlkling.com (Ronn Kling) Date: Wed, 24 Dec 2014 14:26:10 -0500 Subject: [ITK] getting RawImageIO to work In-Reply-To: References: <549B027E.2020802@rlkling.com> Message-ID: <549B1352.8090207@rlkling.com> I am using ITK 4.6.1, VS2010 and windows 7 64 bit. It gives this error on the last line in the try box #include #include #include #include #include #include #include "itkRawImageIO.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #using using namespace System; using namespace System::IO; using namespace System::Windows::Forms; using namespace System::Drawing; using namespace System::Collections; using namespace System::Runtime::InteropServices; int main() { try { typedef unsigned char fixedPixelType; typedef unsigned char movingPixelType; typedef itk::Image fixedImageType; typedef itk::Image movingImageType; // create a ImageIO for the raw data files typedef itk::RawImageIO ImageIOType; ImageIOType::Pointer fixedimageio = ImageIOType::New(); } catch(itk::ExceptionObject & err) {std::cerr << "itkWrapper caught an ITK exception:\n"; err.Print(std::cerr); } } On 12/24/2014 2:07 PM, Bill Lorensen wrote: > Please provide a small, complete compilable example and I'm sure we can help. > > > On Wed, Dec 24, 2014 at 1:14 PM, Ronn Kling wrote: >> Hello All, >> >> I am trying to read in a binary data file using RawImageIO. When I step >> through with the debugger I get an error on the last line below about memory >> corruption. As far as I can tell I have everything correct, what am I >> missing? >> >> typedef unsigned char fixedPixelType; >> typedef unsigned char movingPixelType; >> >> typedef itk::Image fixedImageType; >> typedef itk::Image movingImageType; >> // create a ImageIO for the raw data files >> typedef itk::RawImageIO ImageIOType; >> ImageIOType::Pointer fixedimageio = ImageIOType::New(); >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cjggacai.png Type: image/png Size: 18047 bytes Desc: not available URL: From m.mashdi at gmail.com Sun Dec 28 08:36:10 2014 From: m.mashdi at gmail.com (imashti) Date: Sun, 28 Dec 2014 06:36:10 -0700 (MST) Subject: [ITK] [ITK-users] Create java VM failure SimpleITK, Python, Windows In-Reply-To: <1419771563210-35074.post@n7.nabble.com> References: <1379456385734-32371.post@n7.nabble.com> <1379463383239-32376.post@n7.nabble.com> <1403721309106-34160.post@n7.nabble.com> <1419771563210-35074.post@n7.nabble.com> Message-ID: <1419773770742-35075.post@n7.nabble.com> Hi jmerkow, I have got the same error in Windows but I do not know how to change the mentioned environment variable. Could you please tell me how these variables could be changed in Windows OS? Regards jmerkow wrote > Hello, > > I solved this recently on my windows machine. > For some reason, on windows the -o was not working properly with the > ImageJ 64 (with jre) and ImageJ 32 (with jre). Even if you change your > cfg to use your system jre this option was not recognized. > > I followed Matt's suggestion and changed my SITK_SHOW_COMMAND environment > variable to %a %f > > This worked. Also, note that you can increase the memory in the > ImageJ.cfg file, and you do not need to set _JAVA_OPTIONS variable to > increase memory allocation. > > Hope this helps anyone else that runs into this problem! > > -Jameson -- View this message in context: http://itk-users.7.n7.nabble.com/Create-java-VM-failure-SimpleITK-Python-Windows-tp32371p35075.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Mon Dec 29 11:09:41 2014 From: matimontg at gmail.com (Matias Montroull) Date: Mon, 29 Dec 2014 13:09:41 -0300 Subject: [ITK] [ITK-users] VersorRigid3DTransformOptimizer question Message-ID: Hi, What are the components or what each element represents (0 to 5) in the VersorRigid3DTransformOptimizer? typedef OptimizerType::ScalesType OptimizerScalesType; OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() ); const double translationScale = 1.0 / 1000.0; optimizerScales[0] = 1.0; optimizerScales[1] = 1.0; optimizerScales[2] = 1.0; optimizerScales[3] = translationScale; optimizerScales[4] = translationScale; optimizerScales[5] = translationScale; Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From christopher.mullins at kitware.com Mon Dec 29 12:12:46 2014 From: christopher.mullins at kitware.com (Christopher Mullins) Date: Mon, 29 Dec 2014 12:12:46 -0500 Subject: [ITK] [ITK-users] VersorRigid3DTransformOptimizer question In-Reply-To: References: Message-ID: >From Examples/RegistrationITKv4/MultiResImageRegistration2.cxx [1]: *The set of parameters in the AffineTransform have different dynamic ranges. Typically the parameters associated with the matrix have values around [-1:1], although they are not restricted to this interval. Parameters associated with translations, on the other hand, tend to have much higher values, typically in the order of 10.0 to 100.0. This difference in dynamic range negatively affects the performance of gradient descent optimizers. ITK provides a mechanism to compensate for such differences in values among the parameters when they are passed to the optimizer. The mechanism consists of providing an array of scale factors to the optimizer. These factors re-normalize the gradient components before they are used to compute the step of the optimizer at the current iteration. In our particular case, a common choice for the scale parameters is to set to 1.0 all those associated with the matrix coefficients, that is, the first N x N factors. Then, we set the remaining scale factors to a small value. The following code sets up the scale coefficients.* >From the ImageRegistration7 example [5]: *Keeping in mind that the scale of units in scaling, rotation and translation are quite different, we take advantage of the scaling functionality provided by the optimizers. We know that the first element of the parameters array corresponds to the scale factor, the second corresponds to the angle, third and fourth are the center of rotation and fifth and sixth are the remaining translation. We use henceforth small factors in the scales associated with translations and the rotation center.* >From the ScalesType doxygen [2]: *Scale type. This array defines scale to be applied to parameters before being evaluated in the cost function. This allows to map to a more convenient space. In particular this is used to normalize parameter spaces in which some parameters have a different dynamic range.* [5] is the most specific I can find. Looking at how it's used in [1] might also be useful, as the example you mentioned doesn't provide much explanation (perhaps I or someone else should address that soon). >From [3] (warning, outdated (2002!)): *e.g. for an 3D AffineTransform, you get 12 parameters: the first 9 are the coefficients of the matrix (representing rotation, scale and shearing) the last 3 are the components of a translation vector. You want then to provide an array of 12 values with the first 9 being =1.0 and the last three being on the range of 1.0 / the image size (in millimeters).* Here is another useful thread which is only half a decade old [4]. Perhaps an explanation for this is deserving of better accommodations, maybe on the wiki. In the meantime, hope this helps! [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/MultiResImageRegistration2.cxx#L291-322 [2] http://www.itk.org/Doxygen/html/classitk_1_1Optimizer.html#a4c2e8eb9d9390e0e2988e78ea094492a [3] http://public.kitware.com/pipermail/insight-users/2002-October/001400.html [4] http://itk-insight-users.2283740.n2.nabble.com/Confused-abour-Optimizer-Scales-td4010857.html [5] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/ImageRegistration7.cxx On Mon, Dec 29, 2014 at 11:09 AM, Matias Montroull wrote: > Hi, > > What are the components or what each element represents (0 to 5) in > the VersorRigid3DTransformOptimizer? > > typedef OptimizerType::ScalesType OptimizerScalesType; > OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() > ); > const double translationScale = 1.0 / 1000.0; > > optimizerScales[0] = 1.0; > optimizerScales[1] = 1.0; > optimizerScales[2] = 1.0; > optimizerScales[3] = translationScale; > optimizerScales[4] = translationScale; > optimizerScales[5] = translationScale; > > 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 > > -- Christopher Mullins R&D Engineer Kitware Inc., 919.869.8871 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Mon Dec 29 14:48:03 2014 From: matimontg at gmail.com (Matias Montroull) Date: Mon, 29 Dec 2014 16:48:03 -0300 Subject: [ITK] [ITK-users] SimpleITK | read a 3D image from a non DICOM file and write it as a series of DICOM slices Message-ID: Hi, Is there an example for SimpleITK to read a 3D image from a non Dicom file such as mhd and then write it as a series of DICOM Slices? I can do this with C++ but I haven't been able to figure out how to do it using simpleITK. Thanks, Matias. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matimontg at gmail.com Mon Dec 29 14:48:32 2014 From: matimontg at gmail.com (Matias Montroull) Date: Mon, 29 Dec 2014 16:48:32 -0300 Subject: [ITK] [ITK-users] VersorRigid3DTransformOptimizer question In-Reply-To: References: Message-ID: Thanks Chris! very useful articles. On Mon, Dec 29, 2014 at 2:12 PM, Christopher Mullins < christopher.mullins at kitware.com> wrote: > From Examples/RegistrationITKv4/MultiResImageRegistration2.cxx [1]: > > *The set of parameters in the AffineTransform have different dynamic > ranges. Typically the parameters associated with the matrix have values > around [-1:1], although they are not restricted to this interval. > Parameters associated with translations, on the other hand, tend to have > much higher values, typically in the order of 10.0 to 100.0. This > difference in dynamic range negatively affects the performance of gradient > descent optimizers. ITK provides a mechanism to compensate for such > differences in values among the parameters when they are passed to the > optimizer. The mechanism consists of providing an array of scale factors to > the optimizer. These factors re-normalize the gradient components before > they are used to compute the step of the optimizer at the current > iteration. In our particular case, a common choice for the scale parameters > is to set to 1.0 all those associated with the matrix coefficients, that > is, the first N x N factors. Then, we set the remaining scale factors to a > small value. The following code sets up the scale coefficients.* > > From the ImageRegistration7 example [5]: > > *Keeping in mind that the scale of units in scaling, rotation > and translation are quite different, we take advantage of the > scaling functionality provided by the optimizers. We know that the first > element of the parameters array corresponds to the scale factor, the > second corresponds to the angle, third and fourth are the center of > rotation and fifth and sixth are the remaining translation. We use > henceforth small factors in the scales associated with translations and the > rotation center.* > > From the ScalesType doxygen [2]: > > *Scale type. This array defines scale to be applied to parameters before > being evaluated in the cost function. This allows to map to a more > convenient space. In particular this is used to normalize parameter spaces > in which some parameters have a different dynamic range.* > > [5] is the most specific I can find. Looking at how it's used in [1] > might also be useful, as the example you mentioned doesn't provide much > explanation (perhaps I or someone else should address that soon). > > From [3] (warning, outdated (2002!)): > > *e.g. for an 3D AffineTransform, you get 12 parameters: the first 9 are > the coefficients of the matrix (representing rotation, scale and shearing) > the last 3 are the components of a translation vector. You want then to > provide an array of 12 values with the first 9 being =1.0 and the last > three being on the range of 1.0 / the image size (in millimeters).* > > Here is another useful thread which is only half a decade old [4]. > > Perhaps an explanation for this is deserving of better accommodations, > maybe on the wiki. > > In the meantime, hope this helps! > > [1] > https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/MultiResImageRegistration2.cxx#L291-322 > > [2] > http://www.itk.org/Doxygen/html/classitk_1_1Optimizer.html#a4c2e8eb9d9390e0e2988e78ea094492a > > [3] > http://public.kitware.com/pipermail/insight-users/2002-October/001400.html > > [4] > http://itk-insight-users.2283740.n2.nabble.com/Confused-abour-Optimizer-Scales-td4010857.html > > [5] > https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/ImageRegistration7.cxx > > > On Mon, Dec 29, 2014 at 11:09 AM, Matias Montroull > wrote: > >> Hi, >> >> What are the components or what each element represents (0 to 5) in >> the VersorRigid3DTransformOptimizer? >> >> typedef OptimizerType::ScalesType OptimizerScalesType; >> OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() >> ); >> const double translationScale = 1.0 / 1000.0; >> >> optimizerScales[0] = 1.0; >> optimizerScales[1] = 1.0; >> optimizerScales[2] = 1.0; >> optimizerScales[3] = translationScale; >> optimizerScales[4] = translationScale; >> optimizerScales[5] = translationScale; >> >> 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 >> >> > > > -- > Christopher Mullins > R&D Engineer > Kitware Inc., > 919.869.8871 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Tue Dec 30 07:57:27 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Tue, 30 Dec 2014 21:57:27 +0900 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <1418226543917722.015107.ptmail04@ptmail04> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> <008c01d010e5$84172950$8c457bf0$@ac.kr> <1417828271180838.110987.ptmail04@ptmail04> <009a01d010f5$7d4043e0$77c0cba0$@ac.kr> <1417837813159280.04286.ptmail04@ptmail04> <02e901d01482$28372130$78a56390$@ac.kr> <1418226543917722.015107.ptmail04@ptmail04> Message-ID: <005001d02430$2a385770$7ea90650$@ac.kr> Hi Jim, How are you doing? I have a new question about dataset size. I did an experiment to see how large of a dataset I can handle and the result was 512 ? 512 ? 140 (140 CT slices). Then I upgraded my graphic card which has 12 GB memory (previous card has 4 GB memory) and did the same experiment. However, only up to 218 slices, the new graphic card worked properly. In my case, sometimes I need to process more than 350 slices, what would be a solution for processing this large dataset? I know there are 16 GB and 24 GB graphic cards, but I am not sure whether they can handle up to 350 slices or not and they are very expensive as you know. Maybe there should be any solution by coding? Thank you. Best regards, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Thursday, December 11, 2014 12:49 AM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation Great. You can experiment further to see how large of a dataset you can handle. Then decide if you need to upgrade your graphic card to one with more memory to support the dataset size you want to process. Jim On Dec 10, 2014, at 9:04 AM, Xiaopeng Yang wrote: Hi Jim, Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred. Best regards, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Saturday, December 06, 2014 12:50 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. Jim On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang wrote: Hi Jim, So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Saturday, December 06, 2014 10:11 AM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. Jim On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang wrote: Dear Jim, The images are quite large: 512 * 512 *300. I did not build test when I compile ITK. Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Friday, December 05, 2014 11:15 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation How large are the images that you are using? Jim On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: Hi John, Sorry I mean the program got crashed after showing #define T float. Thanks, Xiaopeng From: John Drescher [mailto:drescherjm at gmail.com] Sent: Friday, December 05, 2014 4:24 PM To: Xiaopeng Yang Cc: Jim Miller; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: Dear Jim, Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. Best, Xiaopeng Is that an error? John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Tue Dec 30 09:15:34 2014 From: millerjv at gmail.com (Jim Miller) Date: Tue, 30 Dec 2014 09:15:34 -0500 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <005001d02430$2a385770$7ea90650$@ac.kr> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> <008c01d010e5$84172950$8c457bf0$@ac.kr> <1417828271180838.110987.ptmail04@ptmail04> <009a01d010f5$7d4043e0$77c0cba0$@ac.kr> <1417837813159280.04286.ptmail04@ptmail04> <02e901d01482$28372130$78a56390$@ac.kr> <1418226543917722.015107.ptmail04@ptmail04> <005001d02430$2a385770$7ea90650$@ac.kr> Message-ID: A simple solution is to downsample the images. Instead of 512x512x350 images, downsample to 256x256x175 images. With the regularization in the registration algorithm, the results will be very similar on the two datasets. If you wanted, after running the registration on the downsampled versions, you can upsample the deformation field and run a few iterations of the algorithm on the cpu at full resolution. Jim > On Dec 30, 2014, at 7:57 AM, Xiaopeng Yang wrote: > > Hi Jim, > > How are you doing? > > I have a new question about dataset size. I did an experiment to see how large of a dataset I can handle and the result was 512 ? 512 ? 140 (140 CT slices). Then I upgraded my graphic card which has 12 GB memory (previous card has 4 GB memory) and did the same experiment. However, only up to 218 slices, the new graphic card worked properly. In my case, sometimes I need to process more than 350 slices, what would be a solution for processing this large dataset? I know there are 16 GB and 24 GB graphic cards, but I am not sure whether they can handle up to 350 slices or not and they are very expensive as you know. Maybe there should be any solution by coding? Thank you. > > Best regards, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Thursday, December 11, 2014 12:49 AM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > Great. You can experiment further to see how large of a dataset you can handle. Then decide if you need to upgrade your graphic card to one with more memory to support the dataset size you want to process. > > Jim > > On Dec 10, 2014, at 9:04 AM, Xiaopeng Yang wrote: > > Hi Jim, > > Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred. > > Best regards, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Saturday, December 06, 2014 12:50 PM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. > > Jim > > On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang wrote: > > Hi Jim, > > So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? > > Thanks, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Saturday, December 06, 2014 10:11 AM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. > > Jim > > On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang wrote: > > Dear Jim, > > The images are quite large: 512 * 512 *300. > > I did not build test when I compile ITK. > > Thanks, > Xiaopeng > > From: Jim Miller [mailto:millerjv at gmail.com] > Sent: Friday, December 05, 2014 11:15 PM > To: Xiaopeng Yang > Cc: John Drescher; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > How large are the images that you are using? > > Jim > > On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: > > Hi John, > > Sorry I mean the program got crashed after showing #define T float. > > Thanks, > Xiaopeng > > From: John Drescher [mailto:drescherjm at gmail.com] > Sent: Friday, December 05, 2014 4:24 PM > To: Xiaopeng Yang > Cc: Jim Miller; Insight-Users at Itk. Org > Subject: Re: [ITK-users] GPU Implementation > > > > On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: > Dear Jim, > > Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. > > Best, > Xiaopeng > > > > > Is that an error? > > John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From yxp233 at postech.ac.kr Tue Dec 30 18:41:57 2014 From: yxp233 at postech.ac.kr (Xiaopeng Yang) Date: Wed, 31 Dec 2014 08:41:57 +0900 Subject: [ITK] [ITK-users] GPU Implementation In-Reply-To: <1419948940352555.011699.ptmail03@ptmail03> References: <1405441657014-7585907.post@n2.nabble.com> <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov> <1405533203306221.02118.ptmail04@ptmail04> <035401d00925$9a422350$cec669f0$@ac.kr> <1417003820802645.09215.ptmail03@ptmail03> <042401d00a3e$7bea7f00$73bf7d00$@ac.kr> <141772836420039.030290.ptmail04@ptmail04> <001801d0104e$19711800$4c534800$@ac.kr> <141776427270398.129323.ptmail04@ptmail04> <003901d0105f$1e6a39c0$5b3ead40$@ac.kr> <1417788892216194.03990.ptmail04@ptmail04> <008c01d010e5$84172950$8c457bf0$@ac.kr> <1417828271180838.110987.ptmail04@ptmail04> <009a01d010f5$7d4043e0$77c0cba0$@ac.kr> <1417837813159280.04286.ptmail04@ptmail04> <02e901d01482$28372130$78a56390$@ac.kr> <1418226543917722.015107.ptmail04@ptmail04> <005001d02430$2a385770$7ea90650$@ac.kr> <1419948940352555.011699.ptmail03@ptmail03> Message-ID: <007301d0248a$333962b0$99ac2810$@ac.kr> Hi Jim, I also thought about sampling the images, but I was worried about losing accuracy after sampling. If they are very similar, this can be a very simple solution. I will try it first. Thank you very much. Best regards, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Tuesday, December 30, 2014 11:16 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation A simple solution is to downsample the images. Instead of 512x512x350 images, downsample to 256x256x175 images. With the regularization in the registration algorithm, the results will be very similar on the two datasets. If you wanted, after running the registration on the downsampled versions, you can upsample the deformation field and run a few iterations of the algorithm on the cpu at full resolution. Jim On Dec 30, 2014, at 7:57 AM, Xiaopeng Yang wrote: Hi Jim, How are you doing? I have a new question about dataset size. I did an experiment to see how large of a dataset I can handle and the result was 512 ? 512 ? 140 (140 CT slices). Then I upgraded my graphic card which has 12 GB memory (previous card has 4 GB memory) and did the same experiment. However, only up to 218 slices, the new graphic card worked properly. In my case, sometimes I need to process more than 350 slices, what would be a solution for processing this large dataset? I know there are 16 GB and 24 GB graphic cards, but I am not sure whether they can handle up to 350 slices or not and they are very expensive as you know. Maybe there should be any solution by coding? Thank you. Best regards, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Thursday, December 11, 2014 12:49 AM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation Great. You can experiment further to see how large of a dataset you can handle. Then decide if you need to upgrade your graphic card to one with more memory to support the dataset size you want to process. Jim On Dec 10, 2014, at 9:04 AM, Xiaopeng Yang wrote: Hi Jim, Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred. Best regards, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Saturday, December 06, 2014 12:50 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. Jim On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang wrote: Hi Jim, So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Saturday, December 06, 2014 10:11 AM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. Jim On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang wrote: Dear Jim, The images are quite large: 512 * 512 *300. I did not build test when I compile ITK. Thanks, Xiaopeng From: Jim Miller [mailto:millerjv at gmail.com] Sent: Friday, December 05, 2014 11:15 PM To: Xiaopeng Yang Cc: John Drescher; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation How large are the images that you are using? Jim On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang wrote: Hi John, Sorry I mean the program got crashed after showing #define T float. Thanks, Xiaopeng From: John Drescher [mailto:drescherjm at gmail.com] Sent: Friday, December 05, 2014 4:24 PM To: Xiaopeng Yang Cc: Jim Miller; Insight-Users at Itk. Org Subject: Re: [ITK-users] GPU Implementation On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang wrote: Dear Jim, Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. Best, Xiaopeng Is that an error? John -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dae.wong at gmail.com Wed Dec 31 06:22:22 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Wed, 31 Dec 2014 19:22:22 +0800 Subject: [ITK] [ITK-users] Itk mesh to stl Message-ID: Hi every one I have a segmented image (object in white, background in black) and I want to obtain a mesh for the segmented object. I am using tetgen software to use obtain a Delaunay tetrahedralization to obtain the mesh. With this software I obtain a list of nodes, a list of tethraedrons and a list of triangle faces. Is there a way to use the information obtained with tetgen with ITK and/or VTK to create a mesh that I can use in MeshLab or Comsol (.ply or .stl)? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Wed Dec 31 10:46:45 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 31 Dec 2014 10:46:45 -0500 Subject: [ITK] [ITK-users] SimpleITK | read a 3D image from a non DICOM file and write it as a series of DICOM slices In-Reply-To: References: Message-ID: Hello, Sorry for the slow reply. Earlier you linked to this nice example for reference: http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html With SimpleITK I have done the following when I needed to write a series in Python: for i in range(img.GetSize()[2]): sitk.WriteImage(img[:,:,i],"test_{0:04}.tif".format(i)) However it is not quite this simple for a DICOM series. The metadata tags need to be correct too. SimpleITK is not designed to be a full fledge interface to DICOM files. Other tools may be better for that. But this seems like a reasonable thing to do but it's not currently readily available in the SimpleITK interface. Perhaps after some discussion on the best way to do it it and be added. There are 3 main components to this example: 1) MetaDataDictionary In SimpleITK the MetaDataDictionary interface is only part of the Image class. Currently it provides a read only interface, with the GetMetaDataKeys(), and GetMetaData(key) methods[1]. This get method only returns the type of data in the dictionary converted to a string. The required method would be Image::SetMetaData(key,value). The issue would be what types of value need to be supported. For this example only std::string is needed, perhaps others should be overloaded? 2) NumericSeriesFileNameGenerator This class only produces a "list" of file names. I think that many of the languages may have a more convenient way to do this. For example in Python: [ "test_{0:04}.png".format(i) for i in range(img.GetSize()[2]) ] So I don't think this is so important. 3) SeriesWriter What we just used above is different then the SeriesWriter, as special metadata is passed from the ImageSeriesWriter to the ImageIO [2]. Here is the JIRA issue for this task [3]. So after these get done something like the following would do what you ask: import SimpleITK as sitk img = stik.ReadImage(argv[1]) img.SetMetaData("008|0060", "MR") // Modality img.SetMetaData("008|0008", "DERIVED\\SECONDARY") // Image Type img.SetMetaData("008|0064", "DV") // Conversion Type sitk.WriteImage(img, [ "test_{0:04}.dcm".format(i) for i in range(img.GetSize()[2]) ]) Does that look like what you are looking for? Brad [1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html#a3d6cb12a211352ee38da5405b9c75928 [2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/ImageBase/include/itkImageSeriesWriter.hxx#L327-L368 [3] https://issues.itk.org/jira/browse/SIMPLEITK-122 On Dec 29, 2014, at 2:48 PM, Matias Montroull wrote: > Hi, > > Is there an example for SimpleITK to read a 3D image from a non Dicom file such as mhd and then write it as a series of DICOM Slices? > > I can do this with C++ but I haven't been able to figure out how to do it using simpleITK. > > Thanks, > > Matias. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users