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-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: 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-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 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-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: 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-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: 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-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: 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-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 > 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-dev] 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 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-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: 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-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: 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-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: 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-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: 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-dev] [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 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-dev] [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-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 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-dev] [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-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 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-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: 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-dev] [ITK] 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 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-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: 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-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 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-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 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-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 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-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. ________________________________ 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-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 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-dev] [ITK] 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 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-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 > > 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-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 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-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 > > 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-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 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-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 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-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 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-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 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-dev] 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-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: 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-dev] [ITK] 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: 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-dev] [ITK] 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: 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-dev] [ITK] 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: 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-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 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-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 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-dev] [ITK] 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: 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-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-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-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-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 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-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: 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-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 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-dev] [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 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-dev] [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