From dominik.hofer at gmail.com Tue Dec 1 04:26:27 2015 From: dominik.hofer at gmail.com (dominik) Date: Tue, 1 Dec 2015 02:26:27 -0700 (MST) Subject: [ITK] [ITK-users] Examples for ITK-based 2D/3D registration In-Reply-To: <5E843F0B86B47846B72559B57A54F96217BE836658@MBX02.ad.uni-heidelberg.de> References: <5E843F0B86B47846B72559B57A54F96217BE836658@MBX02.ad.uni-heidelberg.de> Message-ID: <1448961987594-7588225.post@n2.nabble.com> I suggest checking out 3DSlicer because it already has a lot of visualization and registration features and is built on ITK and VTK. And you can write your own plugins in C++ or Python using ITK or SimpleITK. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Examples-for-ITK-based-2D-3D-registration-tp7587004p7588225.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dominik.hofer at gmail.com Tue Dec 1 04:47:20 2015 From: dominik.hofer at gmail.com (dominik) Date: Tue, 1 Dec 2015 02:47:20 -0700 (MST) Subject: [ITK] [ITK-users] Own Transformation Class In-Reply-To: References: <1448627334852-7588218.post@n2.nabble.com> Message-ID: <1448963240154-7588226.post@n2.nabble.com> Hey Matt, thanks for your answer! :) > A new transformation can often be avoided by calling SetWeights() on the > optimizer as explained here [1]. This can be used to hold parameters > constant for a given transform during the optimization process. > > However, it sounds like goal is to limit registration to information from > a particular region in the image (the urethra). To achieve this goal, you > may consider setting the Fixed and Moving image masks on the metric as > described here [2]. I'm already using registration masks on the prostate itself to exclude the surrounding tissue. However, the registration is always a bit off because in the result the urethras are not in the same place. In the histology the urethra is more or less a point and in the MRI the urethra is like a vector (well actually it is more like a curve). So I'd like the transformation to edit it in a way that the point follows that curve. I hope my explanation is not too confusing :) > If every histology slice is registered independently, when they are merged > together there will be gaps and overlap in the histology slice locations. > Therefore, if a histology volume is desired, the histology slices could be > registered to each other first to generate a single histology slice > volume, then that volume is registered to the MRI volume. The histology slices all have a certain distance to each other (and are not even parallel I think), so I think gaps in the merged volume are desirable. Therefore I can't just stack them. Cheers, Dominik -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Own-Transformation-Class-tp7588218p7588226.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From skalexander at gmail.com Tue Dec 1 09:19:31 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 01 Dec 2015 14:19:31 +0000 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Hi Matt, So I pulled origin/master and rebuilt last night. I have different failures now, all by timeout: *Total Test time (real) = 6363.39 sec* *The following tests FAILED:* * 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo (Timeout)* * 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo (Timeout)* * 728 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout)* * 2025 - itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest (Timeout)* *Errors while running CTest* Any thoughts on what's going on there? On Mon, 30 Nov 2015 at 20:42 Matt McCormick wrote: > Hi Simon, > > I am returning from holiday, and also catching up on activity. > > > Hyun Jae has taken care of the KWStyle warnings and the data conversion > warning: > > http://review.source.kitware.com/#/c/20430/ > http://review.source.kitware.com/#/c/20446/ > > > And Dzenan and Bill have addressed Wiki examples errors: > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 > > > It is likely that the test failures on your build still remain. Did you > want to take them on? > > Thanks, > Matt > > On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? wrote: > >> Looking at the master branch is the right thing to do. I am not doing any >> active development regarding this right now. >> >> On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander >> wrote: >> >>> Hi All, >>> >>> I had hoped to be able to look at this over the weekend, but no such >>> luck. Is there somewhere useful I can help with it now? Not sure what >>> state we are in (or what branch). >>> >>> On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? wrote: >>> >>>> It turns out that all the compile errors were occurring in >>>> WikiExamples. I solved all except one: >>>> ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in >>>> file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line >>>> 23, but it should be judging from the comment on that line. >>>> >>>> For the rest, I created a pull request: >>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>>> >>>> On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander >>> > wrote: >>>> >>>>> Perfect. I'm under a deadline that is likely to eat the rest of the >>>>> week but if that clears up I'll try and jump in earlier. >>>>> >>>>> On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? wrote: >>>>> >>>>>> OK I will work on it for an hour or two now, and I will make a branch >>>>>> and push it to Gerrit so whoever wants can pick up from there and keep >>>>>> updating it. >>>>>> >>>>>> On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander < >>>>>> skalexander at gmail.com> wrote: >>>>>> >>>>>>> Makes sense. At this point I am unlikely to have time to look at >>>>>>> this until Saturday, but have hopes for a few free hours there. >>>>>>> >>>>>>> On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? wrote: >>>>>>> >>>>>>>> Building git master from Nov 23rd with examples and testing enabled >>>>>>>> I get 14 compile errors in VS2015 debug x64. Should we coordinate our >>>>>>>> efforts in fixing them? >>>>>>>> >>>>>>>> On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander < >>>>>>>> skalexander at gmail.com> wrote: >>>>>>>> >>>>>>>>> Two of the three failures look like truncation issues (like >>>>>>>>> https://open.cdash.org/testDetails.php?test=395263772&build=4117158 >>>>>>>>> ) >>>>>>>>> >>>>>>>>> The other ( >>>>>>>>> https://open.cdash.org/testDetails.php?test=395264938&build=4117158) >>>>>>>>> is less obvious. >>>>>>>>> >>>>>>>>> If I have time this evening I'll try and have a look at these. >>>>>>>>> >>>>>>>>> Is your standard test build in 32 bit ? That might explain the >>>>>>>>> difference if there are some underlying type assumptions, but not obvious >>>>>>>>> why 2015 would trigger but not 2013. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, 25 Nov 2015 at 11:01 Matt McCormick < >>>>>>>>> matt.mccormick at kitware.com> wrote: >>>>>>>>> >>>>>>>>>> Ah, cool! Here: >>>>>>>>>> >>>>>>>>>> https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 >>>>>>>>>> >>>>>>>>>> Could you please look into the test failures? >>>>>>>>>> >>>>>>>>>> @Hyun Jae, could you please look into the KWStyle warnings? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander < >>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>> > Sorry, if I wasn't clear - I submitted two builds yesterday >>>>>>>>>> from SIMON-LAP, >>>>>>>>>> > (actually 3 as I wasn't sure the config was right on the first >>>>>>>>>> one). VS2013 >>>>>>>>>> > was green, three failures on VS2015 (and 18 warnings). Looks >>>>>>>>>> like a >>>>>>>>>> > truncation problem on the resuts. >>>>>>>>>> > >>>>>>>>>> > On Wed, 25 Nov 2015 at 10:51 Matt McCormick < >>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>> > wrote: >>>>>>>>>> >> >>>>>>>>>> >> Hi Simon, >>>>>>>>>> >> >>>>>>>>>> >> Thanks for testing. >>>>>>>>>> >> >>>>>>>>>> >> We have a Visual Studio 2015 build on the dashboard that is >>>>>>>>>> green: >>>>>>>>>> >> >>>>>>>>>> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >>>>>>>>>> >> >>>>>>>>>> >> Are there any different flags? Could you please submit an >>>>>>>>>> Experimental >>>>>>>>>> >> build? >>>>>>>>>> >> >>>>>>>>>> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test -T >>>>>>>>>> Submit -C >>>>>>>>>> >> Release >>>>>>>>>> >> >>>>>>>>>> >> from a fresh build tree. >>>>>>>>>> >> >>>>>>>>>> >> Thanks, >>>>>>>>>> >> Matt >>>>>>>>>> >> >>>>>>>>>> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander < >>>>>>>>>> skalexander at gmail.com> >>>>>>>>>> >> wrote: >>>>>>>>>> >> > Looks like a few problems with x64 build on visual studio >>>>>>>>>> 2015 - do you >>>>>>>>>> >> > have >>>>>>>>>> >> > a test machine in this configuration? >>>>>>>>>> >> > >>>>>>>>>> >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick < >>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>> >> > wrote: >>>>>>>>>> >> >> >>>>>>>>>> >> >> On behalf of the Insight Toolkit community, we are proud to >>>>>>>>>> announce >>>>>>>>>> >> >> that >>>>>>>>>> >> >> ITK 4.9 release candidate 1 has been tagged and is >>>>>>>>>> available for >>>>>>>>>> >> >> testing! >>>>>>>>>> >> >> >>>>>>>>>> >> >> Please take this opportunity to test the new features in >>>>>>>>>> the release >>>>>>>>>> >> >> candidate. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> To obtain the source code, >>>>>>>>>> >> >> >>>>>>>>>> >> >> git clone http://itk.org/ITK.git >>>>>>>>>> >> >> cd ITK >>>>>>>>>> >> >> git checkout -q --detach v4.9rc01 >>>>>>>>>> >> >> >>>>>>>>>> >> >> For more details, please see the Git documentation [1]. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> A few selected highlights for this release: >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * New Remote modules: the Cuberille module for smooth >>>>>>>>>> generation of >>>>>>>>>> >> >> meshes >>>>>>>>>> >> >> from binary segmentation images, and the >>>>>>>>>> AnisotropicDiffusionLBR module >>>>>>>>>> >> >> improved edge-preserving smoothing. >>>>>>>>>> >> >> * Build your own ITK module outside the source tree, add >>>>>>>>>> continuous >>>>>>>>>> >> >> integration testing on GitHub, and easily add Python >>>>>>>>>> wrapping for your >>>>>>>>>> >> >> C++ >>>>>>>>>> >> >> algorithms. >>>>>>>>>> >> >> * Python wrapping, including Python 3, builds faster with a >>>>>>>>>> more >>>>>>>>>> >> >> standard >>>>>>>>>> >> >> installation >>>>>>>>>> >> >> * Improved performance of itk::Image::GetPixel and >>>>>>>>>> operations on >>>>>>>>>> >> >> itk::VariableLengthVector?s >>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>> private / >>>>>>>>>> >> >> compile / >>>>>>>>>> >> >> test >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Please test the release candidate and share your >>>>>>>>>> experiences on the >>>>>>>>>> >> >> mailing list, issue tracker, and Gerrit Code Review. The >>>>>>>>>> new module >>>>>>>>>> >> >> dependency specification mechanism may unearth missing >>>>>>>>>> dependencies for >>>>>>>>>> >> >> projects that use ITK COMPONENTS with the CMake >>>>>>>>>> find_package command. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> An Experimental build, which demonstrates how the test >>>>>>>>>> suite performs >>>>>>>>>> >> >> on >>>>>>>>>> >> >> your local build system, can be submitted to the dashboard >>>>>>>>>> [2] with: >>>>>>>>>> >> >> >>>>>>>>>> >> >> mkdir ../ITK-build >>>>>>>>>> >> >> cd ../ITK-build >>>>>>>>>> >> >> cmake ../ITK >>>>>>>>>> >> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test >>>>>>>>>> -T Submit >>>>>>>>>> >> >> >>>>>>>>>> >> >> Visual Studio builds must also add ?-C Release? to the >>>>>>>>>> ctest command. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Notify the mailing list if there are any unexpected >>>>>>>>>> failures. Testing >>>>>>>>>> >> >> your own applications against the RC is also appreciated. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Congratulations and well done to the 35 contributors to >>>>>>>>>> this release. >>>>>>>>>> >> >> We >>>>>>>>>> >> >> would especially like to recognize the new contributors: >>>>>>>>>> Mikhail >>>>>>>>>> >> >> Isakov, >>>>>>>>>> >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias >>>>>>>>>> Wood, Seun >>>>>>>>>> >> >> Odutola, >>>>>>>>>> >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo >>>>>>>>>> >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach >>>>>>>>>> Williamson, >>>>>>>>>> >> >> Luc >>>>>>>>>> >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> The final release is scheduled for mid-December. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> [1] http://www.itk.org/Wiki/ITK/Git >>>>>>>>>> >> >> >>>>>>>>>> >> >> [2] http://open.cdash.org/index.php?project=Insight >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> New Features >>>>>>>>>> >> >> --------------------- >>>>>>>>>> >> >> >>>>>>>>>> >> >> Wrapping improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Python 3 supported >>>>>>>>>> >> >> * Wrapping builds much faster due to CastXML binaries >>>>>>>>>> >> >> * LandmarkBasedTransformInitializer now wrapped >>>>>>>>>> >> >> * NumPy bridge with VisualStudio >>>>>>>>>> >> >> * Wrapping for the MinimalPathExtraction module >>>>>>>>>> >> >> * Wrapping is now installed into Python?s site-packages >>>>>>>>>> directory in >>>>>>>>>> >> >> the >>>>>>>>>> >> >> ?itk? package >>>>>>>>>> >> >> * Wrapping package size is decreased >>>>>>>>>> >> >> * Better package portability on Mac OSX >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> New Remote Modules >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Cuberille >>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>> http://hdl.handle.net/10380/3186 >>>>>>>>>> >> >> * AnisotropicDiffusionLBR >>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>> http://hdl.handle.net/10380/3505 >>>>>>>>>> >> >> * Web browser reproducibility: >>>>>>>>>> >> >> http://www.kitware.com/blog/home/post/942 >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Core Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * External Modules can now be developed outside of the ITK >>>>>>>>>> source tree >>>>>>>>>> >> >> and >>>>>>>>>> >> >> on GitHub >>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/997 >>>>>>>>>> >> >> * New utilities in itk::Math: >>>>>>>>>> >> >> * AlmostEquals >>>>>>>>>> >> >> * NotAlmostEquals >>>>>>>>>> >> >> * ExactlyEquals >>>>>>>>>> >> >> * NotExactlyEquals >>>>>>>>>> >> >> * New itk::NumericTraits >>>>>>>>>> >> >> * IsInteger >>>>>>>>>> >> >> * IsSigned >>>>>>>>>> >> >> * Improved C++11 support >>>>>>>>>> >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >>>>>>>>>> >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >>>>>>>>>> >> >> * Improved capabilities of itk::ResourceProbe and >>>>>>>>>> >> >> itk::ResourceProbesCollectorBase >>>>>>>>>> >> >> * Improve numerical stability in VNL eigen system estimation >>>>>>>>>> >> >> * itksys_ios:: and itksys_stl:: have been remove (use std::) >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Filtering Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>> >> >> * WarpImageFilter support VectorImage?s >>>>>>>>>> >> >> * ConvertLabelMap supports different LabelMap types >>>>>>>>>> >> >> * ImageToPathFilter moved from the ITKReview to the ITKPath >>>>>>>>>> module >>>>>>>>>> >> >> * itk::MovingHistogramImageFilter moved to the >>>>>>>>>> ITKImageFilterBase >>>>>>>>>> >> >> module >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Registration Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Build Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>> private / >>>>>>>>>> >> >> compile / >>>>>>>>>> >> >> test >>>>>>>>>> >> >> * BUILD_EXAMPLES CMake option is now OFF by default >>>>>>>>>> >> >> * Option to export all library symbols on Windows: >>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/939 >>>>>>>>>> >> >> * Expat third party library is now name mangled >>>>>>>>>> >> >> * Many more modules can be built as shared libraries >>>>>>>>>> >> >> * KWStyle is automatically built and configured when tests >>>>>>>>>> are built >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Performance Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds >>>>>>>>>> members for >>>>>>>>>> >> >> metaprogramming >>>>>>>>>> >> >> * itk::mpl::{TrueType,FalseType} >>>>>>>>>> >> >> * itk::mpl::{If,Not,And,Or,Xor} >>>>>>>>>> >> >> * itk::mpl::EnableIf >>>>>>>>>> >> >> * itk::mpl::IsBaseOf >>>>>>>>>> >> >> * itk::mpl::IsConvertible >>>>>>>>>> >> >> * itk::mpl::IsNumber >>>>>>>>>> >> >> * itk::mpl::IsSame >>>>>>>>>> >> >> * itk::mpl::PromoteType >>>>>>>>>> >> >> * Image::GetPixel performance improvements >>>>>>>>>> >> >> * Many itk::VariableLengthVector performance improvements >>>>>>>>>> >> >> * AdaptiveHistogramEqualization uses a moving histogram >>>>>>>>>> >> >> * WarpImageFilter performance improvements >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Documentation Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx >>>>>>>>>> Examples >>>>>>>>>> >> >> * ITK Software Guide improvements >>>>>>>>>> >> >> * How to use Python wrapping >>>>>>>>>> >> >> * How to create an ITK module >>>>>>>>>> >> >> * Improvements to segmentation examples >>>>>>>>>> >> >> * Expanded Canny edge detection example >>>>>>>>>> >> >> * Expanded tree container example >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Third Party Library Updates >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * FFTW updated to latest upstream >>>>>>>>>> >> >> * Build with recent OpenCV 2 and 3 >>>>>>>>>> >> >> * Build with the latest VTK >>>>>>>>>> >> >> * PNG update to the latest upstream >>>>>>>>>> >> >> * GDCM updated to the latest upstream >>>>>>>>>> >> >> * KWSys updated to the latest upstream >>>>>>>>>> >> >> * MINC updated to the latest upstream >>>>>>>>>> >> >> * SWIG updated to the latest upstream >>>>>>>>>> >> >> * Third party PNG and MINC are now Git subtrees >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Style improvements -- ITK gets more stylish with every >>>>>>>>>> release! >>>>>>>>>> >> >> >>>>>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Private copy constructors and operator= use >>>>>>>>>> ITK_DELETE_FUNCTION >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Improved code coverage -- we are at 84.9%! >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> * *Lots* of important bug fixes >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> * And much more! See details in the log below. >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Changes from v4.8.0..v4.9rc01 >>>>>>>>>> >> >> -------------------------------------------- >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Abhishek Tiwari (1): >>>>>>>>>> >> >> BUG: "tmpImageIndex" not initialized to 0. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Adam Snyder (1): >>>>>>>>>> >> >> PERF: Reworked MMI Threading using a per-thread buffer >>>>>>>>>> >> >> >>>>>>>>>> >> >> Alexander Leinoff (6): >>>>>>>>>> >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >>>>>>>>>> >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be >>>>>>>>>> resolved. >>>>>>>>>> >> >> ENH: Adds ExactlyEquals and NotExactlyEquals functions >>>>>>>>>> to >>>>>>>>>> >> >> itkMath.h >>>>>>>>>> >> >> COMP: Removes floating-point equality checks >>>>>>>>>> >> >> ENH: COMP: Adds support for complex values to >>>>>>>>>> Math::AlmostEquals >>>>>>>>>> >> >> ENH: Updates fftw dependency >>>>>>>>>> >> >> >>>>>>>>>> >> >> Arnaud Gelas (5): >>>>>>>>>> >> >> COMP: fix warning (unused local typedef) >>>>>>>>>> >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >>>>>>>>>> >> >> DOC: add doxgen documentation for >>>>>>>>>> >> >> BinaryImageToLevelSetImageAdaptor >>>>>>>>>> >> >> ENH: add tests to exercise >>>>>>>>>> itk::ThreadedIteratorRangePartitioner >>>>>>>>>> >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >>>>>>>>>> >> >> >>>>>>>>>> >> >> Betsy McPhail (1): >>>>>>>>>> >> >> BUG: Improve buffer alignment in OctreeNode . >>>>>>>>>> >> >> >>>>>>>>>> >> >> Bill Hoffman (2): >>>>>>>>>> >> >> ENH: Use new CMake Windows export symbol dll feature. >>>>>>>>>> >> >> COMP: Put vnl_export.h in the list of sources so it >>>>>>>>>> gets >>>>>>>>>> >> >> installed. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Bill Lorensen (4): >>>>>>>>>> >> >> COMP: VTkGlue linker errors >>>>>>>>>> >> >> BUG: Inappropriate use of AlmostEquals >>>>>>>>>> >> >> ENH: Bump tag for wiki examples >>>>>>>>>> >> >> ENH: Better layout strategy >>>>>>>>>> >> >> >>>>>>>>>> >> >> Brad King (3): >>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>> itksys_ios::* >>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>> itksys_stl::* >>>>>>>>>> >> >> ENH: Update CMake Policy settings in >>>>>>>>>> Testing/TestExternal project >>>>>>>>>> >> >> >>>>>>>>>> >> >> Bradley Lowekamp (31): >>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>> construction >>>>>>>>>> >> >> ENH: Enable base classes for templates of landmark >>>>>>>>>> initializer >>>>>>>>>> >> >> STYLE: Use "Swap" for ITK member name >>>>>>>>>> >> >> BUG: Demonstrate Eigen analysis failure >>>>>>>>>> >> >> BUG: Fix computation of Eigen analysis >>>>>>>>>> >> >> ENH: Update DiscreteHessianGaussian Test baseline >>>>>>>>>> >> >> ENH: Correctly demonstrate float point Eigen failure >>>>>>>>>> >> >> ENH: compile vnl_math_hypot, and use at least double >>>>>>>>>> >> >> ENH: Adding initial update script from used libpng >>>>>>>>>> version. >>>>>>>>>> >> >> ENH: removing non-subtree files for itkpng >>>>>>>>>> >> >> ENH: Ported ITK changes for building to subtree merged >>>>>>>>>> code >>>>>>>>>> >> >> ENH: Update libpng update script for v1.6.9 >>>>>>>>>> >> >> BUG: Use ParameterValueType for computation of >>>>>>>>>> landmark affine >>>>>>>>>> >> >> ENH: Wrap LandmarkBasedTransformInitializer >>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>> itk::Object::UnRegister >>>>>>>>>> >> >> ENH: Update itkpng zlib, configuration, and rename >>>>>>>>>> >> >> ENH: Update itkpng name mangling >>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>> ReferenceImage >>>>>>>>>> >> >> ivar >>>>>>>>>> >> >> BUG: Increase tolerance for >>>>>>>>>> PhysicsBasedNonRigidRegistrationMethod >>>>>>>>>> >> >> BUG: Demonstrate side effect on registration due to >>>>>>>>>> BSplineScatter >>>>>>>>>> >> >> change >>>>>>>>>> >> >> ENH: Move MovingHistogramImageFilter base classes to >>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>> itk::Object::UnRegister >>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>> construction >>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>> ReferenceImage >>>>>>>>>> >> >> ivar >>>>>>>>>> >> >> ENH: Optimize AdaptiveHistogramEqualization with >>>>>>>>>> MovingHistogram >>>>>>>>>> >> >> base >>>>>>>>>> >> >> COMP: address sign unsigned comparison warning >>>>>>>>>> >> >> COMP: Address signed unsigned comparison warning >>>>>>>>>> >> >> COMP: Address unused member variable and methods in >>>>>>>>>> anonymous ns >>>>>>>>>> >> >> BUG: Fix segfault when with empty IsolatedWatershed >>>>>>>>>> Threshold >>>>>>>>>> >> >> range >>>>>>>>>> >> >> BUG: Adjust intensity tolerance for >>>>>>>>>> PhysicsBasedNonRigid test >>>>>>>>>> >> >> BUG: Reduce number of targets with MSVC >>>>>>>>>> >> >> >>>>>>>>>> >> >> Davis Vigneault (7): >>>>>>>>>> >> >> DOC: Minor improvements to segmentation examples. >>>>>>>>>> >> >> DOC: Expanded Canny Edge Detection Example >>>>>>>>>> >> >> DOC: Expanded TreeContainer Example >>>>>>>>>> >> >> COMP: Warnings in itkVTKImageExport when compiling >>>>>>>>>> with c++11 >>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>> c++11 >>>>>>>>>> >> >> COMP: Update Git Tag for Subdivision Module >>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>> c++11 >>>>>>>>>> >> >> >>>>>>>>>> >> >> D?enan Zuki? (1): >>>>>>>>>> >> >> STYLE: better formatting of the "usage" message >>>>>>>>>> >> >> >>>>>>>>>> >> >> Eugene Prilepin (1): >>>>>>>>>> >> >> BUG: Fix a template name formation in python wrappings >>>>>>>>>> >> >> >>>>>>>>>> >> >> Floris Berendsen (1): >>>>>>>>>> >> >> STYLE: Improve naming conventions in comments. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Hans Johnson (29): >>>>>>>>>> >> >> STYLE: Instrument for FixedParameters typedef >>>>>>>>>> >> >> BUG: Demonstrate DisplacementTransformFailure >>>>>>>>>> >> >> BUG: FixedParameters should be double precision >>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>> >> >> ENH: Provide consistent floating point comparisons >>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>> >> >> PERF: Remove floating point as sentinal value >>>>>>>>>> >> >> COMP: Const correctness needs to be maintained >>>>>>>>>> >> >> BUG: Preserve backwards compatibility >>>>>>>>>> >> >> DOC: Provide consistent naming in comments >>>>>>>>>> >> >> ENH: Conversion between transform type tolerance >>>>>>>>>> >> >> STYLE: Prefer initialization to assignment >>>>>>>>>> >> >> ENH: Missing ITK_OVERRIDE >>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>> >> >> COMP: Add missing ITK_OVERRIDE >>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>> >> >> ENH: C++11 allows for rigorous =delete >>>>>>>>>> >> >> COMP: Remove unnecessary failing assert test >>>>>>>>>> >> >> ENH: Ignore internal files for the Clion editor >>>>>>>>>> >> >> COMP: Fix VNL compilation for wider C++11 support >>>>>>>>>> >> >> BUG: In configuration test need to mirror code >>>>>>>>>> >> >> >>>>>>>>>> >> >> Hyun Jae Kang (27): >>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>> >> >> BUG: Avoid an unexpected output of static_cast >>>>>>>>>> >> >> BUG: Update python example codes for ImageRegistration >>>>>>>>>> >> >> BUG: Retrieve the missed wrap file >>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>> in VTK file >>>>>>>>>> >> >> header. >>>>>>>>>> >> >> BUG: Fix HDF5 CMake configuration with VS2015 >>>>>>>>>> >> >> BUG: Fix a compilation issue on ITK4 with FFTW and >>>>>>>>>> shared >>>>>>>>>> >> >> libraries >>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>> Mac OS X >>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>> in VTK file >>>>>>>>>> >> >> header. >>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>> >> >> ENH: Add automatic KWStyle build and configuration >>>>>>>>>> setup >>>>>>>>>> >> >> COMP: KWStyle shadow, format-nonliteral and >>>>>>>>>> autological-compare >>>>>>>>>> >> >> warning. >>>>>>>>>> >> >> COMP: Fixed the warning messages from itkGPU Module >>>>>>>>>> >> >> COMP: Fixed a warning message of unused-private-field >>>>>>>>>> >> >> COMP: Apply latest version of KWStyle >>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>> messages >>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>> messages >>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on Windows >>>>>>>>>> >> >> ENH: Update itkResourceProbe to calculate statistical >>>>>>>>>> data >>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on VS14 >>>>>>>>>> >> >> COMP: Fixed 'std::sqrt' : ambiguous call to overloaded >>>>>>>>>> function >>>>>>>>>> >> >> ENH: Update the Report() function of >>>>>>>>>> >> >> itkResourceProbesCollectorBase >>>>>>>>>> >> >> COMP: Fix data-conversion warning message on >>>>>>>>>> itkResourceProbe >>>>>>>>>> >> >> COMP: Fix additional warning messages of KWStyle >>>>>>>>>> >> >> COMP: Fix data-conversion warning messages >>>>>>>>>> >> >> >>>>>>>>>> >> >> Jon Haitz Legarreta (6): >>>>>>>>>> >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >>>>>>>>>> >> >> BUG: Fix compilation issues for >>>>>>>>>> StatisticsUniqueLabelMapFilterTest >>>>>>>>>> >> >> BUG: Fix comparison issues for >>>>>>>>>> itkStatisticsUniqueLabelMapFilter >>>>>>>>>> >> >> BUG: Test for StatisticsUniqueLabelMapFilter stability >>>>>>>>>> >> >> ENH: Add test for itkParametricStpaceToImageSpaceFilter >>>>>>>>>> >> >> ENH: Improve code coverage for >>>>>>>>>> >> >> itkParametricSpaceToImageSpaceMeshFilter >>>>>>>>>> >> >> >>>>>>>>>> >> >> Julien Michel (1): >>>>>>>>>> >> >> ENH: Support of VectorImage as template parameters for >>>>>>>>>> >> >> WarpImageFilter >>>>>>>>>> >> >> >>>>>>>>>> >> >> Junjie Bai (2): >>>>>>>>>> >> >> BUG: ConvertLabelMap with different LabelMapTypes >>>>>>>>>> >> >> BUG: LabelObject CopyAttribute support different >>>>>>>>>> LabelObject type >>>>>>>>>> >> >> >>>>>>>>>> >> >> KWSys Robot (4): >>>>>>>>>> >> >> KWSys 2015-07-10 (c9336bcf) >>>>>>>>>> >> >> KWSys 2015-07-30 (f63febb7) >>>>>>>>>> >> >> KWSys 2015-08-24 (cdaf522c) >>>>>>>>>> >> >> KWSys 2015-08-28 (dc3fdd7f) >>>>>>>>>> >> >> >>>>>>>>>> >> >> LIBPNG Upstream (2): >>>>>>>>>> >> >> PNG 2009-04-06 (e68f5a36) >>>>>>>>>> >> >> PNG 2014-02-05 (3e753eb8) >>>>>>>>>> >> >> >>>>>>>>>> >> >> Laurentiu Nicola (2): >>>>>>>>>> >> >> PERF: Avoid temporary smartptr in >>>>>>>>>> ProcessObject::GetInput >>>>>>>>>> >> >> PERF: Optimize WarpImageFilter by avoiding refcount >>>>>>>>>> bouncing >>>>>>>>>> >> >> >>>>>>>>>> >> >> Luc Hermitte (8): >>>>>>>>>> >> >> PERF: itk::Image::GetPixel() performance improvment. >>>>>>>>>> >> >> PERF: Performance enhancements on >>>>>>>>>> VariableLengthVectors 1/... >>>>>>>>>> >> >> ENH: Dependencies on itkVariableLengthVector.h reduced >>>>>>>>>> >> >> BUG: Error in VariableLengthVector Unit Tests >>>>>>>>>> >> >> PERF: Performance enhancements on VLV 2/... >>>>>>>>>> >> >> PERF: Performances enhancements on VLV 3/... >>>>>>>>>> >> >> COMP: Fix signed/unsigned warnings >>>>>>>>>> >> >> BUG: std::copy/fill on empty VLV >>>>>>>>>> >> >> >>>>>>>>>> >> >> Lucas Gandel (4): >>>>>>>>>> >> >> ENH: Move ImageToPathFilter from ITKReview to ITKPath >>>>>>>>>> module. >>>>>>>>>> >> >> BUG: Fixing ImageToPathFilter wrapping call from >>>>>>>>>> Review Module >>>>>>>>>> >> >> STYLE: Fix KWStyle dashboard errors >>>>>>>>>> >> >> BUG: Fix external module BUILD_SHARED_LIBS status >>>>>>>>>> >> >> >>>>>>>>>> >> >> Mathieu Malaterre (1): >>>>>>>>>> >> >> BUG: Name mangle the included expat third party >>>>>>>>>> library. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Matthew McCormick (94): >>>>>>>>>> >> >> ENH: Change itkSystemInformationTest to >>>>>>>>>> itkCMakeConfigurationTest. >>>>>>>>>> >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >>>>>>>>>> >> >> ENH: Bump ITK version to 4.9.0. >>>>>>>>>> >> >> BUG: Remove std::cout calls from classes. >>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>> >> >> BUG: Implement UpdateLargestPossibleRegion for >>>>>>>>>> >> >> ImageToVTKImageFilter. >>>>>>>>>> >> >> COMP: Add link interface specification for wrapping >>>>>>>>>> >> >> target_link_libraries. >>>>>>>>>> >> >> STYLE: Fix indentation in >>>>>>>>>> itkMINCTransformIOFactory.cxx. >>>>>>>>>> >> >> COMP: Fix MINCTransformIO factory registration. >>>>>>>>>> >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with >>>>>>>>>> Emscripten-1. >>>>>>>>>> >> >> COMP: Remove unknown doxygen command in >>>>>>>>>> AnisotropicDiffusionLBR. >>>>>>>>>> >> >> BUG: Initialize mutex for 32 bit AtomicInt. >>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>> Linux. >>>>>>>>>> >> >> STYLE: Rename gccxml -> castxml in {idx,igenerator}.py. >>>>>>>>>> >> >> COMP: Disable the gold linker for static builds on >>>>>>>>>> Ubuntu 14.04. >>>>>>>>>> >> >> ENH: Use Windows binaries for CastXML. >>>>>>>>>> >> >> ENH: Add better scoping in igenerator.py. >>>>>>>>>> >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + >>>>>>>>>> MSVC. >>>>>>>>>> >> >> BUG: LevelSetsv4 used signed char instead of char. >>>>>>>>>> >> >> ENH: Add better scoping to idx.py. >>>>>>>>>> >> >> COMP: Define newSize and oldSize in >>>>>>>>>> VariableLengthVector. >>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>> >> >> ENH: Add more progress information to >>>>>>>>>> IterativeClosestPoint2. >>>>>>>>>> >> >> BUG: Build BridgeNumPy with Visual Studio. >>>>>>>>>> >> >> ENH: Add ITKModuleExternal.cmake >>>>>>>>>> >> >> COMP: Wrap Image< bool, D > for FlatStructuringElement. >>>>>>>>>> >> >> BUG: Use CastXML binary built in Release. >>>>>>>>>> >> >> BUG: ContinuousIndex should not be templated over >>>>>>>>>> TCoordRep. >>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>> >> >> COMP: Address line length too long for Software Guide. >>>>>>>>>> >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >>>>>>>>>> >> >> BUG: Support Python 3 wrapping module initialization. >>>>>>>>>> >> >> BUG: Update itkTemplate.py for Python 3. >>>>>>>>>> >> >> BUG: Update itkExtras.py for Python 3. >>>>>>>>>> >> >> BUG: Prevent Python callback addition recursion. >>>>>>>>>> >> >> BUG: Fix test scripts for Python 3. >>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>> >> >> ENH: Allow projects to build against an external >>>>>>>>>> module. >>>>>>>>>> >> >> ENH: Replace CABLE_CONFIGURATION with >>>>>>>>>> ITK_WRAPPING_PARSER. >>>>>>>>>> >> >> ENH: Rename _cable_ to _wrappers_. >>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>> >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >>>>>>>>>> >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >>>>>>>>>> >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >>>>>>>>>> >> >> ENH: Bump CastXML version to 2015-30-29. >>>>>>>>>> >> >> ENH: Bump LLVM / Clang to 3.7.0. >>>>>>>>>> >> >> COMP: Avoid itklibminc linking with >>>>>>>>>> ITK_USE_SYSTEM_HDF5. >>>>>>>>>> >> >> COMP: Add missing ITKIOImageBase dependency for >>>>>>>>>> ITKTransformMINC. >>>>>>>>>> >> >> COMP: Use itkSimpleNewMacro in >>>>>>>>>> >> >> ThreadedIteratorRangePartitionerTest. >>>>>>>>>> >> >> ENH: Add wrapping support for building modules >>>>>>>>>> externally. >>>>>>>>>> >> >> BUG: Fix KWStyle test paths when building a module >>>>>>>>>> externally. >>>>>>>>>> >> >> ENH: Add Cuberille Remote module. >>>>>>>>>> >> >> COMP: Remove carriage returns from Cuberille remote. >>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>> >> >> ENH: Bump the MinimalPathExtraction Remote to >>>>>>>>>> 2015-10-20. >>>>>>>>>> >> >> COMP: Fix KernelTransform SetFixedParameters argument >>>>>>>>>> type. >>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>> sys.path >>>>>>>>>> >> >> Revert "COMP: Put vnl_export.h in the list of sources >>>>>>>>>> so it gets >>>>>>>>>> >> >> installed." >>>>>>>>>> >> >> BUG: Revert "BUG: ConvertLabelMap with different >>>>>>>>>> LabelMapTypes" >>>>>>>>>> >> >> ENH: Marking wrapping CMake configuration variables as >>>>>>>>>> advanced. >>>>>>>>>> >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >>>>>>>>>> >> >> COMP: Non-virtual copy attribute members in LabelMap >>>>>>>>>> cannot have >>>>>>>>>> >> >> override. >>>>>>>>>> >> >> COMP: Add wrapping for >>>>>>>>>> AdaptiveHistogramEqualizationImageFilter. >>>>>>>>>> >> >> COMP: Add itkMacro.h to itkPromoteType.h for >>>>>>>>>> ITK_EXCEPT. >>>>>>>>>> >> >> ENH: Remove CMake version check in >>>>>>>>>> ITKModuleHeaderTest.cmake >>>>>>>>>> >> >> BUG: Improve KWStyle ExternalProject utilization. >>>>>>>>>> >> >> ENH: Remove old KWStyle build script. >>>>>>>>>> >> >> COMP: Address VariableLengthVector Doxygen rhs @param >>>>>>>>>> not found. >>>>>>>>>> >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to >>>>>>>>>> WRAPPING_SUBMODULE_ORDER. >>>>>>>>>> >> >> ENH: Install Python bindings into site-packages. >>>>>>>>>> >> >> ENH: Improve readability of Python site-packages path >>>>>>>>>> detection. >>>>>>>>>> >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned >>>>>>>>>> expression >>>>>>>>>> >> >> warning. >>>>>>>>>> >> >> BUG: ITKCommon publically depends on >>>>>>>>>> ITKDoubleConversion. >>>>>>>>>> >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >>>>>>>>>> >> >> ENH: Improves names and export of module dependencies. >>>>>>>>>> >> >> STYLE: Improve namespace bracket style in >>>>>>>>>> itkIsConvertible. >>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>> >> >> BUG: Remove unused wrapping files. >>>>>>>>>> >> >> BUG: Do install install wrapping development files. >>>>>>>>>> >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >>>>>>>>>> >> >> BUG: Remove duplicate inclusion of wrapping submodules. >>>>>>>>>> >> >> COMP: Do not use C++ style comments for Doxygen cond. >>>>>>>>>> >> >> BUG: Fix detection of the gold linker. >>>>>>>>>> >> >> BUG: Update Python package installation locations. >>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >>>>>>>>>> >> >> ENH: Change BUILD_EXAMPLES default to OFF. >>>>>>>>>> >> >> BUG: Use 'from itk import ITKCommon' in module2module >>>>>>>>>> test. >>>>>>>>>> >> >> COMP: Link to VTK Python when built with Kits support. >>>>>>>>>> >> >> BUG: Install itk_minc2.h header. >>>>>>>>>> >> >> COMP: ITKIOMINC has a public dependency on >>>>>>>>>> ITKIOImageBase. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Michka Popoff (9): >>>>>>>>>> >> >> ENH: Update to swig 3.0.7 >>>>>>>>>> >> >> ENH: Do not link against specific Python library on OS >>>>>>>>>> X >>>>>>>>>> >> >> COMP: Fix wrapping warnings when building with >>>>>>>>>> >> >> ITK_WRAP_IMAGE_DIMS=2 >>>>>>>>>> >> >> COMP: Add missing wrapping for TransformBase >>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>> sys.path >>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python 3 >>>>>>>>>> wrapping >>>>>>>>>> >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>> >> >> module >>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python 3 >>>>>>>>>> wrapping >>>>>>>>>> >> >> ENH: Allow operations on Indexes and Offsets in Python >>>>>>>>>> >> >> >>>>>>>>>> >> >> Mikhail Isakov (1): >>>>>>>>>> >> >> BUG: DiffusionTensor3DReconstruction segfault if no >>>>>>>>>> baseline image >>>>>>>>>> >> >> >>>>>>>>>> >> >> Nick Tustison (5): >>>>>>>>>> >> >> BUG: Set a default b-spline epsilon. >>>>>>>>>> >> >> ENH: Adding testing for closed loop. >>>>>>>>>> >> >> BUG: Updating B-spline classes with the same epsilon >>>>>>>>>> strategy. >>>>>>>>>> >> >> PERF: Switch vnl_vectors for fixed arrays. >>>>>>>>>> >> >> ENH: Point-set registration with time-varying >>>>>>>>>> B-spline. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Olivier Commowick (3): >>>>>>>>>> >> >> BUG: Correct discrepancy in tridiagonal reduction wrt >>>>>>>>>> VNL eigen >>>>>>>>>> >> >> system >>>>>>>>>> >> >> BUG: Correct under/overflows in vnl_math_hypot (taken >>>>>>>>>> from pythag >>>>>>>>>> >> >> from V3P) >>>>>>>>>> >> >> BUG: Switch eigenvalues computation to double >>>>>>>>>> >> >> >>>>>>>>>> >> >> Pablo Hernandez-Cerdan (2): >>>>>>>>>> >> >> ENH: Help class for itkFlatStructuringElement with >>>>>>>>>> constructor >>>>>>>>>> >> >> from >>>>>>>>>> >> >> images. >>>>>>>>>> >> >> COMP: Fix test errors and warnings in >>>>>>>>>> FlatStructuringElement. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Seun Odutola (1): >>>>>>>>>> >> >> COMP: Fixed name clash with Apple header (check >>>>>>>>>> Macro), renamed >>>>>>>>>> >> >> check >>>>>>>>>> >> >> to Check >>>>>>>>>> >> >> >>>>>>>>>> >> >> Shawn Waldon (1): >>>>>>>>>> >> >> COMP: Set target OS X version in environment for tools >>>>>>>>>> using >>>>>>>>>> >> >> compiler >>>>>>>>>> >> >> >>>>>>>>>> >> >> Simon Alexander (1): >>>>>>>>>> >> >> BUG: incorrect closest point computation >>>>>>>>>> >> >> >>>>>>>>>> >> >> Tobias Wood (2): >>>>>>>>>> >> >> BUG: LBFGSB was printing messages even with debug >>>>>>>>>> switched off. >>>>>>>>>> >> >> BUG: Removed an unguarded print statement. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Vladimir S. FONOV (9): >>>>>>>>>> >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >>>>>>>>>> >> >> COMP: Changing the order of HDF5 library components >>>>>>>>>> >> >> COMP: Splitting up IOMINC module into two parts: MINC >>>>>>>>>> and >>>>>>>>>> >> >> Transform >>>>>>>>>> >> >> STYLE: updated comments to properly reference LIBMINC >>>>>>>>>> >> >> ENH: Add script to merge upstream MINC as a subtree >>>>>>>>>> >> >> MINC 2015-07-23 (c033d431) >>>>>>>>>> >> >> COMP: Update MINC CMake code >>>>>>>>>> >> >> MINC 2015-08-18 (6d7e3ba8) >>>>>>>>>> >> >> MINC 2015-09-13 (95cd5374) >>>>>>>>>> >> >> >>>>>>>>>> >> >> Xiaoxiao Liu (1): >>>>>>>>>> >> >> DOC: update email address for xiaoxiao. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Zach Williamson (10): >>>>>>>>>> >> >> BUG: Use correct libraries for ImageFusion tests >>>>>>>>>> >> >> ENH: Consolidate Library Dependencies >>>>>>>>>> >> >> COMP: Add a missing link to Review module >>>>>>>>>> >> >> COMP: Use correct linking macro in DCMTK >>>>>>>>>> >> >> BUG: Use correct libraries for TestKernel tests >>>>>>>>>> >> >> COMP: Fix inconsistant naming of >>>>>>>>>> GPUPDEDeformableRegistration >>>>>>>>>> >> >> ENH: Use new linking system macros >>>>>>>>>> >> >> PERF: Avoid searching private dependencies for include >>>>>>>>>> directories >>>>>>>>>> >> >> COMP: Recover missing dependencies >>>>>>>>>> >> >> ENH: use new linking macros in Filtering module >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> ----------------------------------------------------- >>>>>>>>>> >> >> Errors or omissions? Please fix them here: >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >>>>>>>>>> >> >> _____________________________________ >>>>>>>>>> >> >> Powered by www.kitware.com >>>>>>>>>> >> >> >>>>>>>>>> >> >> Visit other Kitware open-source projects at >>>>>>>>>> >> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >> >> >>>>>>>>>> >> >> Kitware offers ITK Training Courses, for more information >>>>>>>>>> visit: >>>>>>>>>> >> >> http://www.kitware.com/products/protraining.php >>>>>>>>>> >> >> >>>>>>>>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >> >> >>>>>>>>>> >> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>> >>>>>>>> >>>>>>>>> Powered by www.kitware.com >>>>>>>>> >>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>> >>>>>>>> http://kitware.com/products/protraining.php >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>> >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From skalexander at gmail.com Tue Dec 1 09:19:31 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 01 Dec 2015 14:19:31 +0000 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Hi Matt, So I pulled origin/master and rebuilt last night. I have different failures now, all by timeout: *Total Test time (real) = 6363.39 sec* *The following tests FAILED:* * 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo (Timeout)* * 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo (Timeout)* * 728 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout)* * 2025 - itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest (Timeout)* *Errors while running CTest* Any thoughts on what's going on there? On Mon, 30 Nov 2015 at 20:42 Matt McCormick wrote: > Hi Simon, > > I am returning from holiday, and also catching up on activity. > > > Hyun Jae has taken care of the KWStyle warnings and the data conversion > warning: > > http://review.source.kitware.com/#/c/20430/ > http://review.source.kitware.com/#/c/20446/ > > > And Dzenan and Bill have addressed Wiki examples errors: > > https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 > > > It is likely that the test failures on your build still remain. Did you > want to take them on? > > Thanks, > Matt > > On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? wrote: > >> Looking at the master branch is the right thing to do. I am not doing any >> active development regarding this right now. >> >> On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander >> wrote: >> >>> Hi All, >>> >>> I had hoped to be able to look at this over the weekend, but no such >>> luck. Is there somewhere useful I can help with it now? Not sure what >>> state we are in (or what branch). >>> >>> On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? wrote: >>> >>>> It turns out that all the compile errors were occurring in >>>> WikiExamples. I solved all except one: >>>> ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in >>>> file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line >>>> 23, but it should be judging from the comment on that line. >>>> >>>> For the rest, I created a pull request: >>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>>> >>>> On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander >>> > wrote: >>>> >>>>> Perfect. I'm under a deadline that is likely to eat the rest of the >>>>> week but if that clears up I'll try and jump in earlier. >>>>> >>>>> On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? wrote: >>>>> >>>>>> OK I will work on it for an hour or two now, and I will make a branch >>>>>> and push it to Gerrit so whoever wants can pick up from there and keep >>>>>> updating it. >>>>>> >>>>>> On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander < >>>>>> skalexander at gmail.com> wrote: >>>>>> >>>>>>> Makes sense. At this point I am unlikely to have time to look at >>>>>>> this until Saturday, but have hopes for a few free hours there. >>>>>>> >>>>>>> On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? wrote: >>>>>>> >>>>>>>> Building git master from Nov 23rd with examples and testing enabled >>>>>>>> I get 14 compile errors in VS2015 debug x64. Should we coordinate our >>>>>>>> efforts in fixing them? >>>>>>>> >>>>>>>> On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander < >>>>>>>> skalexander at gmail.com> wrote: >>>>>>>> >>>>>>>>> Two of the three failures look like truncation issues (like >>>>>>>>> https://open.cdash.org/testDetails.php?test=395263772&build=4117158 >>>>>>>>> ) >>>>>>>>> >>>>>>>>> The other ( >>>>>>>>> https://open.cdash.org/testDetails.php?test=395264938&build=4117158) >>>>>>>>> is less obvious. >>>>>>>>> >>>>>>>>> If I have time this evening I'll try and have a look at these. >>>>>>>>> >>>>>>>>> Is your standard test build in 32 bit ? That might explain the >>>>>>>>> difference if there are some underlying type assumptions, but not obvious >>>>>>>>> why 2015 would trigger but not 2013. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, 25 Nov 2015 at 11:01 Matt McCormick < >>>>>>>>> matt.mccormick at kitware.com> wrote: >>>>>>>>> >>>>>>>>>> Ah, cool! Here: >>>>>>>>>> >>>>>>>>>> https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 >>>>>>>>>> >>>>>>>>>> Could you please look into the test failures? >>>>>>>>>> >>>>>>>>>> @Hyun Jae, could you please look into the KWStyle warnings? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander < >>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>> > Sorry, if I wasn't clear - I submitted two builds yesterday >>>>>>>>>> from SIMON-LAP, >>>>>>>>>> > (actually 3 as I wasn't sure the config was right on the first >>>>>>>>>> one). VS2013 >>>>>>>>>> > was green, three failures on VS2015 (and 18 warnings). Looks >>>>>>>>>> like a >>>>>>>>>> > truncation problem on the resuts. >>>>>>>>>> > >>>>>>>>>> > On Wed, 25 Nov 2015 at 10:51 Matt McCormick < >>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>> > wrote: >>>>>>>>>> >> >>>>>>>>>> >> Hi Simon, >>>>>>>>>> >> >>>>>>>>>> >> Thanks for testing. >>>>>>>>>> >> >>>>>>>>>> >> We have a Visual Studio 2015 build on the dashboard that is >>>>>>>>>> green: >>>>>>>>>> >> >>>>>>>>>> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >>>>>>>>>> >> >>>>>>>>>> >> Are there any different flags? Could you please submit an >>>>>>>>>> Experimental >>>>>>>>>> >> build? >>>>>>>>>> >> >>>>>>>>>> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test -T >>>>>>>>>> Submit -C >>>>>>>>>> >> Release >>>>>>>>>> >> >>>>>>>>>> >> from a fresh build tree. >>>>>>>>>> >> >>>>>>>>>> >> Thanks, >>>>>>>>>> >> Matt >>>>>>>>>> >> >>>>>>>>>> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander < >>>>>>>>>> skalexander at gmail.com> >>>>>>>>>> >> wrote: >>>>>>>>>> >> > Looks like a few problems with x64 build on visual studio >>>>>>>>>> 2015 - do you >>>>>>>>>> >> > have >>>>>>>>>> >> > a test machine in this configuration? >>>>>>>>>> >> > >>>>>>>>>> >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick < >>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>> >> > wrote: >>>>>>>>>> >> >> >>>>>>>>>> >> >> On behalf of the Insight Toolkit community, we are proud to >>>>>>>>>> announce >>>>>>>>>> >> >> that >>>>>>>>>> >> >> ITK 4.9 release candidate 1 has been tagged and is >>>>>>>>>> available for >>>>>>>>>> >> >> testing! >>>>>>>>>> >> >> >>>>>>>>>> >> >> Please take this opportunity to test the new features in >>>>>>>>>> the release >>>>>>>>>> >> >> candidate. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> To obtain the source code, >>>>>>>>>> >> >> >>>>>>>>>> >> >> git clone http://itk.org/ITK.git >>>>>>>>>> >> >> cd ITK >>>>>>>>>> >> >> git checkout -q --detach v4.9rc01 >>>>>>>>>> >> >> >>>>>>>>>> >> >> For more details, please see the Git documentation [1]. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> A few selected highlights for this release: >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * New Remote modules: the Cuberille module for smooth >>>>>>>>>> generation of >>>>>>>>>> >> >> meshes >>>>>>>>>> >> >> from binary segmentation images, and the >>>>>>>>>> AnisotropicDiffusionLBR module >>>>>>>>>> >> >> improved edge-preserving smoothing. >>>>>>>>>> >> >> * Build your own ITK module outside the source tree, add >>>>>>>>>> continuous >>>>>>>>>> >> >> integration testing on GitHub, and easily add Python >>>>>>>>>> wrapping for your >>>>>>>>>> >> >> C++ >>>>>>>>>> >> >> algorithms. >>>>>>>>>> >> >> * Python wrapping, including Python 3, builds faster with a >>>>>>>>>> more >>>>>>>>>> >> >> standard >>>>>>>>>> >> >> installation >>>>>>>>>> >> >> * Improved performance of itk::Image::GetPixel and >>>>>>>>>> operations on >>>>>>>>>> >> >> itk::VariableLengthVector?s >>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>> private / >>>>>>>>>> >> >> compile / >>>>>>>>>> >> >> test >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Please test the release candidate and share your >>>>>>>>>> experiences on the >>>>>>>>>> >> >> mailing list, issue tracker, and Gerrit Code Review. The >>>>>>>>>> new module >>>>>>>>>> >> >> dependency specification mechanism may unearth missing >>>>>>>>>> dependencies for >>>>>>>>>> >> >> projects that use ITK COMPONENTS with the CMake >>>>>>>>>> find_package command. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> An Experimental build, which demonstrates how the test >>>>>>>>>> suite performs >>>>>>>>>> >> >> on >>>>>>>>>> >> >> your local build system, can be submitted to the dashboard >>>>>>>>>> [2] with: >>>>>>>>>> >> >> >>>>>>>>>> >> >> mkdir ../ITK-build >>>>>>>>>> >> >> cd ../ITK-build >>>>>>>>>> >> >> cmake ../ITK >>>>>>>>>> >> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test >>>>>>>>>> -T Submit >>>>>>>>>> >> >> >>>>>>>>>> >> >> Visual Studio builds must also add ?-C Release? to the >>>>>>>>>> ctest command. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Notify the mailing list if there are any unexpected >>>>>>>>>> failures. Testing >>>>>>>>>> >> >> your own applications against the RC is also appreciated. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Congratulations and well done to the 35 contributors to >>>>>>>>>> this release. >>>>>>>>>> >> >> We >>>>>>>>>> >> >> would especially like to recognize the new contributors: >>>>>>>>>> Mikhail >>>>>>>>>> >> >> Isakov, >>>>>>>>>> >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias >>>>>>>>>> Wood, Seun >>>>>>>>>> >> >> Odutola, >>>>>>>>>> >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo >>>>>>>>>> >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach >>>>>>>>>> Williamson, >>>>>>>>>> >> >> Luc >>>>>>>>>> >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> The final release is scheduled for mid-December. >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> [1] http://www.itk.org/Wiki/ITK/Git >>>>>>>>>> >> >> >>>>>>>>>> >> >> [2] http://open.cdash.org/index.php?project=Insight >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> New Features >>>>>>>>>> >> >> --------------------- >>>>>>>>>> >> >> >>>>>>>>>> >> >> Wrapping improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Python 3 supported >>>>>>>>>> >> >> * Wrapping builds much faster due to CastXML binaries >>>>>>>>>> >> >> * LandmarkBasedTransformInitializer now wrapped >>>>>>>>>> >> >> * NumPy bridge with VisualStudio >>>>>>>>>> >> >> * Wrapping for the MinimalPathExtraction module >>>>>>>>>> >> >> * Wrapping is now installed into Python?s site-packages >>>>>>>>>> directory in >>>>>>>>>> >> >> the >>>>>>>>>> >> >> ?itk? package >>>>>>>>>> >> >> * Wrapping package size is decreased >>>>>>>>>> >> >> * Better package portability on Mac OSX >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> New Remote Modules >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Cuberille >>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>> http://hdl.handle.net/10380/3186 >>>>>>>>>> >> >> * AnisotropicDiffusionLBR >>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>> http://hdl.handle.net/10380/3505 >>>>>>>>>> >> >> * Web browser reproducibility: >>>>>>>>>> >> >> http://www.kitware.com/blog/home/post/942 >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Core Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * External Modules can now be developed outside of the ITK >>>>>>>>>> source tree >>>>>>>>>> >> >> and >>>>>>>>>> >> >> on GitHub >>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/997 >>>>>>>>>> >> >> * New utilities in itk::Math: >>>>>>>>>> >> >> * AlmostEquals >>>>>>>>>> >> >> * NotAlmostEquals >>>>>>>>>> >> >> * ExactlyEquals >>>>>>>>>> >> >> * NotExactlyEquals >>>>>>>>>> >> >> * New itk::NumericTraits >>>>>>>>>> >> >> * IsInteger >>>>>>>>>> >> >> * IsSigned >>>>>>>>>> >> >> * Improved C++11 support >>>>>>>>>> >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >>>>>>>>>> >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >>>>>>>>>> >> >> * Improved capabilities of itk::ResourceProbe and >>>>>>>>>> >> >> itk::ResourceProbesCollectorBase >>>>>>>>>> >> >> * Improve numerical stability in VNL eigen system estimation >>>>>>>>>> >> >> * itksys_ios:: and itksys_stl:: have been remove (use std::) >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Filtering Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>> >> >> * WarpImageFilter support VectorImage?s >>>>>>>>>> >> >> * ConvertLabelMap supports different LabelMap types >>>>>>>>>> >> >> * ImageToPathFilter moved from the ITKReview to the ITKPath >>>>>>>>>> module >>>>>>>>>> >> >> * itk::MovingHistogramImageFilter moved to the >>>>>>>>>> ITKImageFilterBase >>>>>>>>>> >> >> module >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Registration Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Build Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>> private / >>>>>>>>>> >> >> compile / >>>>>>>>>> >> >> test >>>>>>>>>> >> >> * BUILD_EXAMPLES CMake option is now OFF by default >>>>>>>>>> >> >> * Option to export all library symbols on Windows: >>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/939 >>>>>>>>>> >> >> * Expat third party library is now name mangled >>>>>>>>>> >> >> * Many more modules can be built as shared libraries >>>>>>>>>> >> >> * KWStyle is automatically built and configured when tests >>>>>>>>>> are built >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Performance Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds >>>>>>>>>> members for >>>>>>>>>> >> >> metaprogramming >>>>>>>>>> >> >> * itk::mpl::{TrueType,FalseType} >>>>>>>>>> >> >> * itk::mpl::{If,Not,And,Or,Xor} >>>>>>>>>> >> >> * itk::mpl::EnableIf >>>>>>>>>> >> >> * itk::mpl::IsBaseOf >>>>>>>>>> >> >> * itk::mpl::IsConvertible >>>>>>>>>> >> >> * itk::mpl::IsNumber >>>>>>>>>> >> >> * itk::mpl::IsSame >>>>>>>>>> >> >> * itk::mpl::PromoteType >>>>>>>>>> >> >> * Image::GetPixel performance improvements >>>>>>>>>> >> >> * Many itk::VariableLengthVector performance improvements >>>>>>>>>> >> >> * AdaptiveHistogramEqualization uses a moving histogram >>>>>>>>>> >> >> * WarpImageFilter performance improvements >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Documentation Improvements >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx >>>>>>>>>> Examples >>>>>>>>>> >> >> * ITK Software Guide improvements >>>>>>>>>> >> >> * How to use Python wrapping >>>>>>>>>> >> >> * How to create an ITK module >>>>>>>>>> >> >> * Improvements to segmentation examples >>>>>>>>>> >> >> * Expanded Canny edge detection example >>>>>>>>>> >> >> * Expanded tree container example >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Third Party Library Updates >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * FFTW updated to latest upstream >>>>>>>>>> >> >> * Build with recent OpenCV 2 and 3 >>>>>>>>>> >> >> * Build with the latest VTK >>>>>>>>>> >> >> * PNG update to the latest upstream >>>>>>>>>> >> >> * GDCM updated to the latest upstream >>>>>>>>>> >> >> * KWSys updated to the latest upstream >>>>>>>>>> >> >> * MINC updated to the latest upstream >>>>>>>>>> >> >> * SWIG updated to the latest upstream >>>>>>>>>> >> >> * Third party PNG and MINC are now Git subtrees >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Style improvements -- ITK gets more stylish with every >>>>>>>>>> release! >>>>>>>>>> >> >> >>>>>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> * Private copy constructors and operator= use >>>>>>>>>> ITK_DELETE_FUNCTION >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Improved code coverage -- we are at 84.9%! >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> * *Lots* of important bug fixes >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> * And much more! See details in the log below. >>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Changes from v4.8.0..v4.9rc01 >>>>>>>>>> >> >> -------------------------------------------- >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> Abhishek Tiwari (1): >>>>>>>>>> >> >> BUG: "tmpImageIndex" not initialized to 0. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Adam Snyder (1): >>>>>>>>>> >> >> PERF: Reworked MMI Threading using a per-thread buffer >>>>>>>>>> >> >> >>>>>>>>>> >> >> Alexander Leinoff (6): >>>>>>>>>> >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >>>>>>>>>> >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be >>>>>>>>>> resolved. >>>>>>>>>> >> >> ENH: Adds ExactlyEquals and NotExactlyEquals functions >>>>>>>>>> to >>>>>>>>>> >> >> itkMath.h >>>>>>>>>> >> >> COMP: Removes floating-point equality checks >>>>>>>>>> >> >> ENH: COMP: Adds support for complex values to >>>>>>>>>> Math::AlmostEquals >>>>>>>>>> >> >> ENH: Updates fftw dependency >>>>>>>>>> >> >> >>>>>>>>>> >> >> Arnaud Gelas (5): >>>>>>>>>> >> >> COMP: fix warning (unused local typedef) >>>>>>>>>> >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >>>>>>>>>> >> >> DOC: add doxgen documentation for >>>>>>>>>> >> >> BinaryImageToLevelSetImageAdaptor >>>>>>>>>> >> >> ENH: add tests to exercise >>>>>>>>>> itk::ThreadedIteratorRangePartitioner >>>>>>>>>> >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >>>>>>>>>> >> >> >>>>>>>>>> >> >> Betsy McPhail (1): >>>>>>>>>> >> >> BUG: Improve buffer alignment in OctreeNode . >>>>>>>>>> >> >> >>>>>>>>>> >> >> Bill Hoffman (2): >>>>>>>>>> >> >> ENH: Use new CMake Windows export symbol dll feature. >>>>>>>>>> >> >> COMP: Put vnl_export.h in the list of sources so it >>>>>>>>>> gets >>>>>>>>>> >> >> installed. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Bill Lorensen (4): >>>>>>>>>> >> >> COMP: VTkGlue linker errors >>>>>>>>>> >> >> BUG: Inappropriate use of AlmostEquals >>>>>>>>>> >> >> ENH: Bump tag for wiki examples >>>>>>>>>> >> >> ENH: Better layout strategy >>>>>>>>>> >> >> >>>>>>>>>> >> >> Brad King (3): >>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>> itksys_ios::* >>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>> itksys_stl::* >>>>>>>>>> >> >> ENH: Update CMake Policy settings in >>>>>>>>>> Testing/TestExternal project >>>>>>>>>> >> >> >>>>>>>>>> >> >> Bradley Lowekamp (31): >>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>> construction >>>>>>>>>> >> >> ENH: Enable base classes for templates of landmark >>>>>>>>>> initializer >>>>>>>>>> >> >> STYLE: Use "Swap" for ITK member name >>>>>>>>>> >> >> BUG: Demonstrate Eigen analysis failure >>>>>>>>>> >> >> BUG: Fix computation of Eigen analysis >>>>>>>>>> >> >> ENH: Update DiscreteHessianGaussian Test baseline >>>>>>>>>> >> >> ENH: Correctly demonstrate float point Eigen failure >>>>>>>>>> >> >> ENH: compile vnl_math_hypot, and use at least double >>>>>>>>>> >> >> ENH: Adding initial update script from used libpng >>>>>>>>>> version. >>>>>>>>>> >> >> ENH: removing non-subtree files for itkpng >>>>>>>>>> >> >> ENH: Ported ITK changes for building to subtree merged >>>>>>>>>> code >>>>>>>>>> >> >> ENH: Update libpng update script for v1.6.9 >>>>>>>>>> >> >> BUG: Use ParameterValueType for computation of >>>>>>>>>> landmark affine >>>>>>>>>> >> >> ENH: Wrap LandmarkBasedTransformInitializer >>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>> itk::Object::UnRegister >>>>>>>>>> >> >> ENH: Update itkpng zlib, configuration, and rename >>>>>>>>>> >> >> ENH: Update itkpng name mangling >>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>> ReferenceImage >>>>>>>>>> >> >> ivar >>>>>>>>>> >> >> BUG: Increase tolerance for >>>>>>>>>> PhysicsBasedNonRigidRegistrationMethod >>>>>>>>>> >> >> BUG: Demonstrate side effect on registration due to >>>>>>>>>> BSplineScatter >>>>>>>>>> >> >> change >>>>>>>>>> >> >> ENH: Move MovingHistogramImageFilter base classes to >>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>> itk::Object::UnRegister >>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>> construction >>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>> ReferenceImage >>>>>>>>>> >> >> ivar >>>>>>>>>> >> >> ENH: Optimize AdaptiveHistogramEqualization with >>>>>>>>>> MovingHistogram >>>>>>>>>> >> >> base >>>>>>>>>> >> >> COMP: address sign unsigned comparison warning >>>>>>>>>> >> >> COMP: Address signed unsigned comparison warning >>>>>>>>>> >> >> COMP: Address unused member variable and methods in >>>>>>>>>> anonymous ns >>>>>>>>>> >> >> BUG: Fix segfault when with empty IsolatedWatershed >>>>>>>>>> Threshold >>>>>>>>>> >> >> range >>>>>>>>>> >> >> BUG: Adjust intensity tolerance for >>>>>>>>>> PhysicsBasedNonRigid test >>>>>>>>>> >> >> BUG: Reduce number of targets with MSVC >>>>>>>>>> >> >> >>>>>>>>>> >> >> Davis Vigneault (7): >>>>>>>>>> >> >> DOC: Minor improvements to segmentation examples. >>>>>>>>>> >> >> DOC: Expanded Canny Edge Detection Example >>>>>>>>>> >> >> DOC: Expanded TreeContainer Example >>>>>>>>>> >> >> COMP: Warnings in itkVTKImageExport when compiling >>>>>>>>>> with c++11 >>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>> c++11 >>>>>>>>>> >> >> COMP: Update Git Tag for Subdivision Module >>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>> c++11 >>>>>>>>>> >> >> >>>>>>>>>> >> >> D?enan Zuki? (1): >>>>>>>>>> >> >> STYLE: better formatting of the "usage" message >>>>>>>>>> >> >> >>>>>>>>>> >> >> Eugene Prilepin (1): >>>>>>>>>> >> >> BUG: Fix a template name formation in python wrappings >>>>>>>>>> >> >> >>>>>>>>>> >> >> Floris Berendsen (1): >>>>>>>>>> >> >> STYLE: Improve naming conventions in comments. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Hans Johnson (29): >>>>>>>>>> >> >> STYLE: Instrument for FixedParameters typedef >>>>>>>>>> >> >> BUG: Demonstrate DisplacementTransformFailure >>>>>>>>>> >> >> BUG: FixedParameters should be double precision >>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>> >> >> ENH: Provide consistent floating point comparisons >>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>> >> >> PERF: Remove floating point as sentinal value >>>>>>>>>> >> >> COMP: Const correctness needs to be maintained >>>>>>>>>> >> >> BUG: Preserve backwards compatibility >>>>>>>>>> >> >> DOC: Provide consistent naming in comments >>>>>>>>>> >> >> ENH: Conversion between transform type tolerance >>>>>>>>>> >> >> STYLE: Prefer initialization to assignment >>>>>>>>>> >> >> ENH: Missing ITK_OVERRIDE >>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>> >> >> COMP: Add missing ITK_OVERRIDE >>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>> >> >> ENH: C++11 allows for rigorous =delete >>>>>>>>>> >> >> COMP: Remove unnecessary failing assert test >>>>>>>>>> >> >> ENH: Ignore internal files for the Clion editor >>>>>>>>>> >> >> COMP: Fix VNL compilation for wider C++11 support >>>>>>>>>> >> >> BUG: In configuration test need to mirror code >>>>>>>>>> >> >> >>>>>>>>>> >> >> Hyun Jae Kang (27): >>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>> >> >> BUG: Avoid an unexpected output of static_cast >>>>>>>>>> >> >> BUG: Update python example codes for ImageRegistration >>>>>>>>>> >> >> BUG: Retrieve the missed wrap file >>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>> in VTK file >>>>>>>>>> >> >> header. >>>>>>>>>> >> >> BUG: Fix HDF5 CMake configuration with VS2015 >>>>>>>>>> >> >> BUG: Fix a compilation issue on ITK4 with FFTW and >>>>>>>>>> shared >>>>>>>>>> >> >> libraries >>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>> Mac OS X >>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>> in VTK file >>>>>>>>>> >> >> header. >>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>> >> >> ENH: Add automatic KWStyle build and configuration >>>>>>>>>> setup >>>>>>>>>> >> >> COMP: KWStyle shadow, format-nonliteral and >>>>>>>>>> autological-compare >>>>>>>>>> >> >> warning. >>>>>>>>>> >> >> COMP: Fixed the warning messages from itkGPU Module >>>>>>>>>> >> >> COMP: Fixed a warning message of unused-private-field >>>>>>>>>> >> >> COMP: Apply latest version of KWStyle >>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>> messages >>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>> messages >>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on Windows >>>>>>>>>> >> >> ENH: Update itkResourceProbe to calculate statistical >>>>>>>>>> data >>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on VS14 >>>>>>>>>> >> >> COMP: Fixed 'std::sqrt' : ambiguous call to overloaded >>>>>>>>>> function >>>>>>>>>> >> >> ENH: Update the Report() function of >>>>>>>>>> >> >> itkResourceProbesCollectorBase >>>>>>>>>> >> >> COMP: Fix data-conversion warning message on >>>>>>>>>> itkResourceProbe >>>>>>>>>> >> >> COMP: Fix additional warning messages of KWStyle >>>>>>>>>> >> >> COMP: Fix data-conversion warning messages >>>>>>>>>> >> >> >>>>>>>>>> >> >> Jon Haitz Legarreta (6): >>>>>>>>>> >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >>>>>>>>>> >> >> BUG: Fix compilation issues for >>>>>>>>>> StatisticsUniqueLabelMapFilterTest >>>>>>>>>> >> >> BUG: Fix comparison issues for >>>>>>>>>> itkStatisticsUniqueLabelMapFilter >>>>>>>>>> >> >> BUG: Test for StatisticsUniqueLabelMapFilter stability >>>>>>>>>> >> >> ENH: Add test for itkParametricStpaceToImageSpaceFilter >>>>>>>>>> >> >> ENH: Improve code coverage for >>>>>>>>>> >> >> itkParametricSpaceToImageSpaceMeshFilter >>>>>>>>>> >> >> >>>>>>>>>> >> >> Julien Michel (1): >>>>>>>>>> >> >> ENH: Support of VectorImage as template parameters for >>>>>>>>>> >> >> WarpImageFilter >>>>>>>>>> >> >> >>>>>>>>>> >> >> Junjie Bai (2): >>>>>>>>>> >> >> BUG: ConvertLabelMap with different LabelMapTypes >>>>>>>>>> >> >> BUG: LabelObject CopyAttribute support different >>>>>>>>>> LabelObject type >>>>>>>>>> >> >> >>>>>>>>>> >> >> KWSys Robot (4): >>>>>>>>>> >> >> KWSys 2015-07-10 (c9336bcf) >>>>>>>>>> >> >> KWSys 2015-07-30 (f63febb7) >>>>>>>>>> >> >> KWSys 2015-08-24 (cdaf522c) >>>>>>>>>> >> >> KWSys 2015-08-28 (dc3fdd7f) >>>>>>>>>> >> >> >>>>>>>>>> >> >> LIBPNG Upstream (2): >>>>>>>>>> >> >> PNG 2009-04-06 (e68f5a36) >>>>>>>>>> >> >> PNG 2014-02-05 (3e753eb8) >>>>>>>>>> >> >> >>>>>>>>>> >> >> Laurentiu Nicola (2): >>>>>>>>>> >> >> PERF: Avoid temporary smartptr in >>>>>>>>>> ProcessObject::GetInput >>>>>>>>>> >> >> PERF: Optimize WarpImageFilter by avoiding refcount >>>>>>>>>> bouncing >>>>>>>>>> >> >> >>>>>>>>>> >> >> Luc Hermitte (8): >>>>>>>>>> >> >> PERF: itk::Image::GetPixel() performance improvment. >>>>>>>>>> >> >> PERF: Performance enhancements on >>>>>>>>>> VariableLengthVectors 1/... >>>>>>>>>> >> >> ENH: Dependencies on itkVariableLengthVector.h reduced >>>>>>>>>> >> >> BUG: Error in VariableLengthVector Unit Tests >>>>>>>>>> >> >> PERF: Performance enhancements on VLV 2/... >>>>>>>>>> >> >> PERF: Performances enhancements on VLV 3/... >>>>>>>>>> >> >> COMP: Fix signed/unsigned warnings >>>>>>>>>> >> >> BUG: std::copy/fill on empty VLV >>>>>>>>>> >> >> >>>>>>>>>> >> >> Lucas Gandel (4): >>>>>>>>>> >> >> ENH: Move ImageToPathFilter from ITKReview to ITKPath >>>>>>>>>> module. >>>>>>>>>> >> >> BUG: Fixing ImageToPathFilter wrapping call from >>>>>>>>>> Review Module >>>>>>>>>> >> >> STYLE: Fix KWStyle dashboard errors >>>>>>>>>> >> >> BUG: Fix external module BUILD_SHARED_LIBS status >>>>>>>>>> >> >> >>>>>>>>>> >> >> Mathieu Malaterre (1): >>>>>>>>>> >> >> BUG: Name mangle the included expat third party >>>>>>>>>> library. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Matthew McCormick (94): >>>>>>>>>> >> >> ENH: Change itkSystemInformationTest to >>>>>>>>>> itkCMakeConfigurationTest. >>>>>>>>>> >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >>>>>>>>>> >> >> ENH: Bump ITK version to 4.9.0. >>>>>>>>>> >> >> BUG: Remove std::cout calls from classes. >>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>> >> >> BUG: Implement UpdateLargestPossibleRegion for >>>>>>>>>> >> >> ImageToVTKImageFilter. >>>>>>>>>> >> >> COMP: Add link interface specification for wrapping >>>>>>>>>> >> >> target_link_libraries. >>>>>>>>>> >> >> STYLE: Fix indentation in >>>>>>>>>> itkMINCTransformIOFactory.cxx. >>>>>>>>>> >> >> COMP: Fix MINCTransformIO factory registration. >>>>>>>>>> >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with >>>>>>>>>> Emscripten-1. >>>>>>>>>> >> >> COMP: Remove unknown doxygen command in >>>>>>>>>> AnisotropicDiffusionLBR. >>>>>>>>>> >> >> BUG: Initialize mutex for 32 bit AtomicInt. >>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>> Linux. >>>>>>>>>> >> >> STYLE: Rename gccxml -> castxml in {idx,igenerator}.py. >>>>>>>>>> >> >> COMP: Disable the gold linker for static builds on >>>>>>>>>> Ubuntu 14.04. >>>>>>>>>> >> >> ENH: Use Windows binaries for CastXML. >>>>>>>>>> >> >> ENH: Add better scoping in igenerator.py. >>>>>>>>>> >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + >>>>>>>>>> MSVC. >>>>>>>>>> >> >> BUG: LevelSetsv4 used signed char instead of char. >>>>>>>>>> >> >> ENH: Add better scoping to idx.py. >>>>>>>>>> >> >> COMP: Define newSize and oldSize in >>>>>>>>>> VariableLengthVector. >>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>> >> >> ENH: Add more progress information to >>>>>>>>>> IterativeClosestPoint2. >>>>>>>>>> >> >> BUG: Build BridgeNumPy with Visual Studio. >>>>>>>>>> >> >> ENH: Add ITKModuleExternal.cmake >>>>>>>>>> >> >> COMP: Wrap Image< bool, D > for FlatStructuringElement. >>>>>>>>>> >> >> BUG: Use CastXML binary built in Release. >>>>>>>>>> >> >> BUG: ContinuousIndex should not be templated over >>>>>>>>>> TCoordRep. >>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>> >> >> COMP: Address line length too long for Software Guide. >>>>>>>>>> >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >>>>>>>>>> >> >> BUG: Support Python 3 wrapping module initialization. >>>>>>>>>> >> >> BUG: Update itkTemplate.py for Python 3. >>>>>>>>>> >> >> BUG: Update itkExtras.py for Python 3. >>>>>>>>>> >> >> BUG: Prevent Python callback addition recursion. >>>>>>>>>> >> >> BUG: Fix test scripts for Python 3. >>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>> >> >> ENH: Allow projects to build against an external >>>>>>>>>> module. >>>>>>>>>> >> >> ENH: Replace CABLE_CONFIGURATION with >>>>>>>>>> ITK_WRAPPING_PARSER. >>>>>>>>>> >> >> ENH: Rename _cable_ to _wrappers_. >>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>> >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >>>>>>>>>> >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >>>>>>>>>> >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >>>>>>>>>> >> >> ENH: Bump CastXML version to 2015-30-29. >>>>>>>>>> >> >> ENH: Bump LLVM / Clang to 3.7.0. >>>>>>>>>> >> >> COMP: Avoid itklibminc linking with >>>>>>>>>> ITK_USE_SYSTEM_HDF5. >>>>>>>>>> >> >> COMP: Add missing ITKIOImageBase dependency for >>>>>>>>>> ITKTransformMINC. >>>>>>>>>> >> >> COMP: Use itkSimpleNewMacro in >>>>>>>>>> >> >> ThreadedIteratorRangePartitionerTest. >>>>>>>>>> >> >> ENH: Add wrapping support for building modules >>>>>>>>>> externally. >>>>>>>>>> >> >> BUG: Fix KWStyle test paths when building a module >>>>>>>>>> externally. >>>>>>>>>> >> >> ENH: Add Cuberille Remote module. >>>>>>>>>> >> >> COMP: Remove carriage returns from Cuberille remote. >>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>> >> >> ENH: Bump the MinimalPathExtraction Remote to >>>>>>>>>> 2015-10-20. >>>>>>>>>> >> >> COMP: Fix KernelTransform SetFixedParameters argument >>>>>>>>>> type. >>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>> sys.path >>>>>>>>>> >> >> Revert "COMP: Put vnl_export.h in the list of sources >>>>>>>>>> so it gets >>>>>>>>>> >> >> installed." >>>>>>>>>> >> >> BUG: Revert "BUG: ConvertLabelMap with different >>>>>>>>>> LabelMapTypes" >>>>>>>>>> >> >> ENH: Marking wrapping CMake configuration variables as >>>>>>>>>> advanced. >>>>>>>>>> >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >>>>>>>>>> >> >> COMP: Non-virtual copy attribute members in LabelMap >>>>>>>>>> cannot have >>>>>>>>>> >> >> override. >>>>>>>>>> >> >> COMP: Add wrapping for >>>>>>>>>> AdaptiveHistogramEqualizationImageFilter. >>>>>>>>>> >> >> COMP: Add itkMacro.h to itkPromoteType.h for >>>>>>>>>> ITK_EXCEPT. >>>>>>>>>> >> >> ENH: Remove CMake version check in >>>>>>>>>> ITKModuleHeaderTest.cmake >>>>>>>>>> >> >> BUG: Improve KWStyle ExternalProject utilization. >>>>>>>>>> >> >> ENH: Remove old KWStyle build script. >>>>>>>>>> >> >> COMP: Address VariableLengthVector Doxygen rhs @param >>>>>>>>>> not found. >>>>>>>>>> >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to >>>>>>>>>> WRAPPING_SUBMODULE_ORDER. >>>>>>>>>> >> >> ENH: Install Python bindings into site-packages. >>>>>>>>>> >> >> ENH: Improve readability of Python site-packages path >>>>>>>>>> detection. >>>>>>>>>> >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned >>>>>>>>>> expression >>>>>>>>>> >> >> warning. >>>>>>>>>> >> >> BUG: ITKCommon publically depends on >>>>>>>>>> ITKDoubleConversion. >>>>>>>>>> >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >>>>>>>>>> >> >> ENH: Improves names and export of module dependencies. >>>>>>>>>> >> >> STYLE: Improve namespace bracket style in >>>>>>>>>> itkIsConvertible. >>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>> >> >> BUG: Remove unused wrapping files. >>>>>>>>>> >> >> BUG: Do install install wrapping development files. >>>>>>>>>> >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >>>>>>>>>> >> >> BUG: Remove duplicate inclusion of wrapping submodules. >>>>>>>>>> >> >> COMP: Do not use C++ style comments for Doxygen cond. >>>>>>>>>> >> >> BUG: Fix detection of the gold linker. >>>>>>>>>> >> >> BUG: Update Python package installation locations. >>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >>>>>>>>>> >> >> ENH: Change BUILD_EXAMPLES default to OFF. >>>>>>>>>> >> >> BUG: Use 'from itk import ITKCommon' in module2module >>>>>>>>>> test. >>>>>>>>>> >> >> COMP: Link to VTK Python when built with Kits support. >>>>>>>>>> >> >> BUG: Install itk_minc2.h header. >>>>>>>>>> >> >> COMP: ITKIOMINC has a public dependency on >>>>>>>>>> ITKIOImageBase. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Michka Popoff (9): >>>>>>>>>> >> >> ENH: Update to swig 3.0.7 >>>>>>>>>> >> >> ENH: Do not link against specific Python library on OS >>>>>>>>>> X >>>>>>>>>> >> >> COMP: Fix wrapping warnings when building with >>>>>>>>>> >> >> ITK_WRAP_IMAGE_DIMS=2 >>>>>>>>>> >> >> COMP: Add missing wrapping for TransformBase >>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>> sys.path >>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python 3 >>>>>>>>>> wrapping >>>>>>>>>> >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>> >> >> module >>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python 3 >>>>>>>>>> wrapping >>>>>>>>>> >> >> ENH: Allow operations on Indexes and Offsets in Python >>>>>>>>>> >> >> >>>>>>>>>> >> >> Mikhail Isakov (1): >>>>>>>>>> >> >> BUG: DiffusionTensor3DReconstruction segfault if no >>>>>>>>>> baseline image >>>>>>>>>> >> >> >>>>>>>>>> >> >> Nick Tustison (5): >>>>>>>>>> >> >> BUG: Set a default b-spline epsilon. >>>>>>>>>> >> >> ENH: Adding testing for closed loop. >>>>>>>>>> >> >> BUG: Updating B-spline classes with the same epsilon >>>>>>>>>> strategy. >>>>>>>>>> >> >> PERF: Switch vnl_vectors for fixed arrays. >>>>>>>>>> >> >> ENH: Point-set registration with time-varying >>>>>>>>>> B-spline. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Olivier Commowick (3): >>>>>>>>>> >> >> BUG: Correct discrepancy in tridiagonal reduction wrt >>>>>>>>>> VNL eigen >>>>>>>>>> >> >> system >>>>>>>>>> >> >> BUG: Correct under/overflows in vnl_math_hypot (taken >>>>>>>>>> from pythag >>>>>>>>>> >> >> from V3P) >>>>>>>>>> >> >> BUG: Switch eigenvalues computation to double >>>>>>>>>> >> >> >>>>>>>>>> >> >> Pablo Hernandez-Cerdan (2): >>>>>>>>>> >> >> ENH: Help class for itkFlatStructuringElement with >>>>>>>>>> constructor >>>>>>>>>> >> >> from >>>>>>>>>> >> >> images. >>>>>>>>>> >> >> COMP: Fix test errors and warnings in >>>>>>>>>> FlatStructuringElement. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Seun Odutola (1): >>>>>>>>>> >> >> COMP: Fixed name clash with Apple header (check >>>>>>>>>> Macro), renamed >>>>>>>>>> >> >> check >>>>>>>>>> >> >> to Check >>>>>>>>>> >> >> >>>>>>>>>> >> >> Shawn Waldon (1): >>>>>>>>>> >> >> COMP: Set target OS X version in environment for tools >>>>>>>>>> using >>>>>>>>>> >> >> compiler >>>>>>>>>> >> >> >>>>>>>>>> >> >> Simon Alexander (1): >>>>>>>>>> >> >> BUG: incorrect closest point computation >>>>>>>>>> >> >> >>>>>>>>>> >> >> Tobias Wood (2): >>>>>>>>>> >> >> BUG: LBFGSB was printing messages even with debug >>>>>>>>>> switched off. >>>>>>>>>> >> >> BUG: Removed an unguarded print statement. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Vladimir S. FONOV (9): >>>>>>>>>> >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >>>>>>>>>> >> >> COMP: Changing the order of HDF5 library components >>>>>>>>>> >> >> COMP: Splitting up IOMINC module into two parts: MINC >>>>>>>>>> and >>>>>>>>>> >> >> Transform >>>>>>>>>> >> >> STYLE: updated comments to properly reference LIBMINC >>>>>>>>>> >> >> ENH: Add script to merge upstream MINC as a subtree >>>>>>>>>> >> >> MINC 2015-07-23 (c033d431) >>>>>>>>>> >> >> COMP: Update MINC CMake code >>>>>>>>>> >> >> MINC 2015-08-18 (6d7e3ba8) >>>>>>>>>> >> >> MINC 2015-09-13 (95cd5374) >>>>>>>>>> >> >> >>>>>>>>>> >> >> Xiaoxiao Liu (1): >>>>>>>>>> >> >> DOC: update email address for xiaoxiao. >>>>>>>>>> >> >> >>>>>>>>>> >> >> Zach Williamson (10): >>>>>>>>>> >> >> BUG: Use correct libraries for ImageFusion tests >>>>>>>>>> >> >> ENH: Consolidate Library Dependencies >>>>>>>>>> >> >> COMP: Add a missing link to Review module >>>>>>>>>> >> >> COMP: Use correct linking macro in DCMTK >>>>>>>>>> >> >> BUG: Use correct libraries for TestKernel tests >>>>>>>>>> >> >> COMP: Fix inconsistant naming of >>>>>>>>>> GPUPDEDeformableRegistration >>>>>>>>>> >> >> ENH: Use new linking system macros >>>>>>>>>> >> >> PERF: Avoid searching private dependencies for include >>>>>>>>>> directories >>>>>>>>>> >> >> COMP: Recover missing dependencies >>>>>>>>>> >> >> ENH: use new linking macros in Filtering module >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> ----------------------------------------------------- >>>>>>>>>> >> >> Errors or omissions? Please fix them here: >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> >> >> >>>>>>>>>> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >>>>>>>>>> >> >> _____________________________________ >>>>>>>>>> >> >> Powered by www.kitware.com >>>>>>>>>> >> >> >>>>>>>>>> >> >> Visit other Kitware open-source projects at >>>>>>>>>> >> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >> >> >>>>>>>>>> >> >> Kitware offers ITK Training Courses, for more information >>>>>>>>>> visit: >>>>>>>>>> >> >> http://www.kitware.com/products/protraining.php >>>>>>>>>> >> >> >>>>>>>>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >> >> >>>>>>>>>> >> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>> >>>>>>>> >>>>>>>>> Powered by www.kitware.com >>>>>>>>> >>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>> >>>>>>>> http://kitware.com/products/protraining.php >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>> >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Dec 1 09:21:50 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 1 Dec 2015 09:21:50 -0500 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: If you are running tests in debug, some of them are too slow and time out. On Tue, Dec 1, 2015 at 9:19 AM, Simon Alexander wrote: > Hi Matt, > > So I pulled origin/master and rebuilt last night. I have different > failures now, all by timeout: > > *Total Test time (real) = 6363.39 sec* > > *The following tests FAILED:* > * 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo > (Timeout)* > * 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo > (Timeout)* > * 728 - > itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout)* > * 2025 - itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest > (Timeout)* > *Errors while running CTest* > > > Any thoughts on what's going on there? > > > On Mon, 30 Nov 2015 at 20:42 Matt McCormick > wrote: > >> Hi Simon, >> >> I am returning from holiday, and also catching up on activity. >> >> >> Hyun Jae has taken care of the KWStyle warnings and the data conversion >> warning: >> >> http://review.source.kitware.com/#/c/20430/ >> http://review.source.kitware.com/#/c/20446/ >> >> >> And Dzenan and Bill have addressed Wiki examples errors: >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >> >> >> It is likely that the test failures on your build still remain. Did you >> want to take them on? >> >> Thanks, >> Matt >> >> On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? wrote: >> >>> Looking at the master branch is the right thing to do. I am not doing >>> any active development regarding this right now. >>> >>> On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander >>> wrote: >>> >>>> Hi All, >>>> >>>> I had hoped to be able to look at this over the weekend, but no such >>>> luck. Is there somewhere useful I can help with it now? Not sure what >>>> state we are in (or what branch). >>>> >>>> On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? wrote: >>>> >>>>> It turns out that all the compile errors were occurring in >>>>> WikiExamples. I solved all except one: >>>>> ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in >>>>> file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line >>>>> 23, but it should be judging from the comment on that line. >>>>> >>>>> For the rest, I created a pull request: >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>>>> >>>>> On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander < >>>>> skalexander at gmail.com> wrote: >>>>> >>>>>> Perfect. I'm under a deadline that is likely to eat the rest of the >>>>>> week but if that clears up I'll try and jump in earlier. >>>>>> >>>>>> On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? wrote: >>>>>> >>>>>>> OK I will work on it for an hour or two now, and I will make a >>>>>>> branch and push it to Gerrit so whoever wants can pick up from there and >>>>>>> keep updating it. >>>>>>> >>>>>>> On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander < >>>>>>> skalexander at gmail.com> wrote: >>>>>>> >>>>>>>> Makes sense. At this point I am unlikely to have time to look at >>>>>>>> this until Saturday, but have hopes for a few free hours there. >>>>>>>> >>>>>>>> On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Building git master from Nov 23rd with examples and testing >>>>>>>>> enabled I get 14 compile errors in VS2015 debug x64. Should we coordinate >>>>>>>>> our efforts in fixing them? >>>>>>>>> >>>>>>>>> On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander < >>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Two of the three failures look like truncation issues (like >>>>>>>>>> https://open.cdash.org/testDetails.php?test=395263772&build=4117158 >>>>>>>>>> ) >>>>>>>>>> >>>>>>>>>> The other ( >>>>>>>>>> https://open.cdash.org/testDetails.php?test=395264938&build=4117158) >>>>>>>>>> is less obvious. >>>>>>>>>> >>>>>>>>>> If I have time this evening I'll try and have a look at these. >>>>>>>>>> >>>>>>>>>> Is your standard test build in 32 bit ? That might explain the >>>>>>>>>> difference if there are some underlying type assumptions, but not obvious >>>>>>>>>> why 2015 would trigger but not 2013. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, 25 Nov 2015 at 11:01 Matt McCormick < >>>>>>>>>> matt.mccormick at kitware.com> wrote: >>>>>>>>>> >>>>>>>>>>> Ah, cool! Here: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 >>>>>>>>>>> >>>>>>>>>>> Could you please look into the test failures? >>>>>>>>>>> >>>>>>>>>>> @Hyun Jae, could you please look into the KWStyle warnings? >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander < >>>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>>> > Sorry, if I wasn't clear - I submitted two builds yesterday >>>>>>>>>>> from SIMON-LAP, >>>>>>>>>>> > (actually 3 as I wasn't sure the config was right on the first >>>>>>>>>>> one). VS2013 >>>>>>>>>>> > was green, three failures on VS2015 (and 18 warnings). Looks >>>>>>>>>>> like a >>>>>>>>>>> > truncation problem on the resuts. >>>>>>>>>>> > >>>>>>>>>>> > On Wed, 25 Nov 2015 at 10:51 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> Hi Simon, >>>>>>>>>>> >> >>>>>>>>>>> >> Thanks for testing. >>>>>>>>>>> >> >>>>>>>>>>> >> We have a Visual Studio 2015 build on the dashboard that is >>>>>>>>>>> green: >>>>>>>>>>> >> >>>>>>>>>>> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >>>>>>>>>>> >> >>>>>>>>>>> >> Are there any different flags? Could you please submit an >>>>>>>>>>> Experimental >>>>>>>>>>> >> build? >>>>>>>>>>> >> >>>>>>>>>>> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test >>>>>>>>>>> -T Submit -C >>>>>>>>>>> >> Release >>>>>>>>>>> >> >>>>>>>>>>> >> from a fresh build tree. >>>>>>>>>>> >> >>>>>>>>>>> >> Thanks, >>>>>>>>>>> >> Matt >>>>>>>>>>> >> >>>>>>>>>>> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander < >>>>>>>>>>> skalexander at gmail.com> >>>>>>>>>>> >> wrote: >>>>>>>>>>> >> > Looks like a few problems with x64 build on visual studio >>>>>>>>>>> 2015 - do you >>>>>>>>>>> >> > have >>>>>>>>>>> >> > a test machine in this configuration? >>>>>>>>>>> >> > >>>>>>>>>>> >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> On behalf of the Insight Toolkit community, we are proud >>>>>>>>>>> to announce >>>>>>>>>>> >> >> that >>>>>>>>>>> >> >> ITK 4.9 release candidate 1 has been tagged and is >>>>>>>>>>> available for >>>>>>>>>>> >> >> testing! >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please take this opportunity to test the new features in >>>>>>>>>>> the release >>>>>>>>>>> >> >> candidate. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> To obtain the source code, >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> git clone http://itk.org/ITK.git >>>>>>>>>>> >> >> cd ITK >>>>>>>>>>> >> >> git checkout -q --detach v4.9rc01 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> For more details, please see the Git documentation [1]. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> A few selected highlights for this release: >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * New Remote modules: the Cuberille module for smooth >>>>>>>>>>> generation of >>>>>>>>>>> >> >> meshes >>>>>>>>>>> >> >> from binary segmentation images, and the >>>>>>>>>>> AnisotropicDiffusionLBR module >>>>>>>>>>> >> >> improved edge-preserving smoothing. >>>>>>>>>>> >> >> * Build your own ITK module outside the source tree, add >>>>>>>>>>> continuous >>>>>>>>>>> >> >> integration testing on GitHub, and easily add Python >>>>>>>>>>> wrapping for your >>>>>>>>>>> >> >> C++ >>>>>>>>>>> >> >> algorithms. >>>>>>>>>>> >> >> * Python wrapping, including Python 3, builds faster with >>>>>>>>>>> a more >>>>>>>>>>> >> >> standard >>>>>>>>>>> >> >> installation >>>>>>>>>>> >> >> * Improved performance of itk::Image::GetPixel and >>>>>>>>>>> operations on >>>>>>>>>>> >> >> itk::VariableLengthVector?s >>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>> private / >>>>>>>>>>> >> >> compile / >>>>>>>>>>> >> >> test >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please test the release candidate and share your >>>>>>>>>>> experiences on the >>>>>>>>>>> >> >> mailing list, issue tracker, and Gerrit Code Review. The >>>>>>>>>>> new module >>>>>>>>>>> >> >> dependency specification mechanism may unearth missing >>>>>>>>>>> dependencies for >>>>>>>>>>> >> >> projects that use ITK COMPONENTS with the CMake >>>>>>>>>>> find_package command. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> An Experimental build, which demonstrates how the test >>>>>>>>>>> suite performs >>>>>>>>>>> >> >> on >>>>>>>>>>> >> >> your local build system, can be submitted to the dashboard >>>>>>>>>>> [2] with: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> mkdir ../ITK-build >>>>>>>>>>> >> >> cd ../ITK-build >>>>>>>>>>> >> >> cmake ../ITK >>>>>>>>>>> >> >> ctest -j 4 -M Experimental -T Configure -T Build -T >>>>>>>>>>> Test -T Submit >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Visual Studio builds must also add ?-C Release? to the >>>>>>>>>>> ctest command. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Notify the mailing list if there are any unexpected >>>>>>>>>>> failures. Testing >>>>>>>>>>> >> >> your own applications against the RC is also appreciated. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Congratulations and well done to the 35 contributors to >>>>>>>>>>> this release. >>>>>>>>>>> >> >> We >>>>>>>>>>> >> >> would especially like to recognize the new contributors: >>>>>>>>>>> Mikhail >>>>>>>>>>> >> >> Isakov, >>>>>>>>>>> >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias >>>>>>>>>>> Wood, Seun >>>>>>>>>>> >> >> Odutola, >>>>>>>>>>> >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo >>>>>>>>>>> >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach >>>>>>>>>>> Williamson, >>>>>>>>>>> >> >> Luc >>>>>>>>>>> >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> The final release is scheduled for mid-December. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> [1] http://www.itk.org/Wiki/ITK/Git >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> [2] http://open.cdash.org/index.php?project=Insight >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> New Features >>>>>>>>>>> >> >> --------------------- >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Wrapping improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Python 3 supported >>>>>>>>>>> >> >> * Wrapping builds much faster due to CastXML binaries >>>>>>>>>>> >> >> * LandmarkBasedTransformInitializer now wrapped >>>>>>>>>>> >> >> * NumPy bridge with VisualStudio >>>>>>>>>>> >> >> * Wrapping for the MinimalPathExtraction module >>>>>>>>>>> >> >> * Wrapping is now installed into Python?s site-packages >>>>>>>>>>> directory in >>>>>>>>>>> >> >> the >>>>>>>>>>> >> >> ?itk? package >>>>>>>>>>> >> >> * Wrapping package size is decreased >>>>>>>>>>> >> >> * Better package portability on Mac OSX >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> New Remote Modules >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Cuberille >>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>> http://hdl.handle.net/10380/3186 >>>>>>>>>>> >> >> * AnisotropicDiffusionLBR >>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>> http://hdl.handle.net/10380/3505 >>>>>>>>>>> >> >> * Web browser reproducibility: >>>>>>>>>>> >> >> http://www.kitware.com/blog/home/post/942 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Core Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * External Modules can now be developed outside of the ITK >>>>>>>>>>> source tree >>>>>>>>>>> >> >> and >>>>>>>>>>> >> >> on GitHub >>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/997 >>>>>>>>>>> >> >> * New utilities in itk::Math: >>>>>>>>>>> >> >> * AlmostEquals >>>>>>>>>>> >> >> * NotAlmostEquals >>>>>>>>>>> >> >> * ExactlyEquals >>>>>>>>>>> >> >> * NotExactlyEquals >>>>>>>>>>> >> >> * New itk::NumericTraits >>>>>>>>>>> >> >> * IsInteger >>>>>>>>>>> >> >> * IsSigned >>>>>>>>>>> >> >> * Improved C++11 support >>>>>>>>>>> >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >>>>>>>>>>> >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >>>>>>>>>>> >> >> * Improved capabilities of itk::ResourceProbe and >>>>>>>>>>> >> >> itk::ResourceProbesCollectorBase >>>>>>>>>>> >> >> * Improve numerical stability in VNL eigen system >>>>>>>>>>> estimation >>>>>>>>>>> >> >> * itksys_ios:: and itksys_stl:: have been remove (use >>>>>>>>>>> std::) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Filtering Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>> >> >> * WarpImageFilter support VectorImage?s >>>>>>>>>>> >> >> * ConvertLabelMap supports different LabelMap types >>>>>>>>>>> >> >> * ImageToPathFilter moved from the ITKReview to the >>>>>>>>>>> ITKPath module >>>>>>>>>>> >> >> * itk::MovingHistogramImageFilter moved to the >>>>>>>>>>> ITKImageFilterBase >>>>>>>>>>> >> >> module >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Registration Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Build Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>> private / >>>>>>>>>>> >> >> compile / >>>>>>>>>>> >> >> test >>>>>>>>>>> >> >> * BUILD_EXAMPLES CMake option is now OFF by default >>>>>>>>>>> >> >> * Option to export all library symbols on Windows: >>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/939 >>>>>>>>>>> >> >> * Expat third party library is now name mangled >>>>>>>>>>> >> >> * Many more modules can be built as shared libraries >>>>>>>>>>> >> >> * KWStyle is automatically built and configured when tests >>>>>>>>>>> are built >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Performance Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds >>>>>>>>>>> members for >>>>>>>>>>> >> >> metaprogramming >>>>>>>>>>> >> >> * itk::mpl::{TrueType,FalseType} >>>>>>>>>>> >> >> * itk::mpl::{If,Not,And,Or,Xor} >>>>>>>>>>> >> >> * itk::mpl::EnableIf >>>>>>>>>>> >> >> * itk::mpl::IsBaseOf >>>>>>>>>>> >> >> * itk::mpl::IsConvertible >>>>>>>>>>> >> >> * itk::mpl::IsNumber >>>>>>>>>>> >> >> * itk::mpl::IsSame >>>>>>>>>>> >> >> * itk::mpl::PromoteType >>>>>>>>>>> >> >> * Image::GetPixel performance improvements >>>>>>>>>>> >> >> * Many itk::VariableLengthVector performance improvements >>>>>>>>>>> >> >> * AdaptiveHistogramEqualization uses a moving histogram >>>>>>>>>>> >> >> * WarpImageFilter performance improvements >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Documentation Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx >>>>>>>>>>> Examples >>>>>>>>>>> >> >> * ITK Software Guide improvements >>>>>>>>>>> >> >> * How to use Python wrapping >>>>>>>>>>> >> >> * How to create an ITK module >>>>>>>>>>> >> >> * Improvements to segmentation examples >>>>>>>>>>> >> >> * Expanded Canny edge detection example >>>>>>>>>>> >> >> * Expanded tree container example >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Third Party Library Updates >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * FFTW updated to latest upstream >>>>>>>>>>> >> >> * Build with recent OpenCV 2 and 3 >>>>>>>>>>> >> >> * Build with the latest VTK >>>>>>>>>>> >> >> * PNG update to the latest upstream >>>>>>>>>>> >> >> * GDCM updated to the latest upstream >>>>>>>>>>> >> >> * KWSys updated to the latest upstream >>>>>>>>>>> >> >> * MINC updated to the latest upstream >>>>>>>>>>> >> >> * SWIG updated to the latest upstream >>>>>>>>>>> >> >> * Third party PNG and MINC are now Git subtrees >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Style improvements -- ITK gets more stylish with every >>>>>>>>>>> release! >>>>>>>>>>> >> >> >>>>>>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Private copy constructors and operator= use >>>>>>>>>>> ITK_DELETE_FUNCTION >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Improved code coverage -- we are at 84.9%! >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * *Lots* of important bug fixes >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * And much more! See details in the log below. >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Changes from v4.8.0..v4.9rc01 >>>>>>>>>>> >> >> -------------------------------------------- >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Abhishek Tiwari (1): >>>>>>>>>>> >> >> BUG: "tmpImageIndex" not initialized to 0. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Adam Snyder (1): >>>>>>>>>>> >> >> PERF: Reworked MMI Threading using a per-thread buffer >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Alexander Leinoff (6): >>>>>>>>>>> >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >>>>>>>>>>> >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be >>>>>>>>>>> resolved. >>>>>>>>>>> >> >> ENH: Adds ExactlyEquals and NotExactlyEquals >>>>>>>>>>> functions to >>>>>>>>>>> >> >> itkMath.h >>>>>>>>>>> >> >> COMP: Removes floating-point equality checks >>>>>>>>>>> >> >> ENH: COMP: Adds support for complex values to >>>>>>>>>>> Math::AlmostEquals >>>>>>>>>>> >> >> ENH: Updates fftw dependency >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Arnaud Gelas (5): >>>>>>>>>>> >> >> COMP: fix warning (unused local typedef) >>>>>>>>>>> >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >>>>>>>>>>> >> >> DOC: add doxgen documentation for >>>>>>>>>>> >> >> BinaryImageToLevelSetImageAdaptor >>>>>>>>>>> >> >> ENH: add tests to exercise >>>>>>>>>>> itk::ThreadedIteratorRangePartitioner >>>>>>>>>>> >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Betsy McPhail (1): >>>>>>>>>>> >> >> BUG: Improve buffer alignment in OctreeNode . >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bill Hoffman (2): >>>>>>>>>>> >> >> ENH: Use new CMake Windows export symbol dll feature. >>>>>>>>>>> >> >> COMP: Put vnl_export.h in the list of sources so it >>>>>>>>>>> gets >>>>>>>>>>> >> >> installed. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bill Lorensen (4): >>>>>>>>>>> >> >> COMP: VTkGlue linker errors >>>>>>>>>>> >> >> BUG: Inappropriate use of AlmostEquals >>>>>>>>>>> >> >> ENH: Bump tag for wiki examples >>>>>>>>>>> >> >> ENH: Better layout strategy >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Brad King (3): >>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>> itksys_ios::* >>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>> itksys_stl::* >>>>>>>>>>> >> >> ENH: Update CMake Policy settings in >>>>>>>>>>> Testing/TestExternal project >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bradley Lowekamp (31): >>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>> construction >>>>>>>>>>> >> >> ENH: Enable base classes for templates of landmark >>>>>>>>>>> initializer >>>>>>>>>>> >> >> STYLE: Use "Swap" for ITK member name >>>>>>>>>>> >> >> BUG: Demonstrate Eigen analysis failure >>>>>>>>>>> >> >> BUG: Fix computation of Eigen analysis >>>>>>>>>>> >> >> ENH: Update DiscreteHessianGaussian Test baseline >>>>>>>>>>> >> >> ENH: Correctly demonstrate float point Eigen failure >>>>>>>>>>> >> >> ENH: compile vnl_math_hypot, and use at least double >>>>>>>>>>> >> >> ENH: Adding initial update script from used libpng >>>>>>>>>>> version. >>>>>>>>>>> >> >> ENH: removing non-subtree files for itkpng >>>>>>>>>>> >> >> ENH: Ported ITK changes for building to subtree >>>>>>>>>>> merged code >>>>>>>>>>> >> >> ENH: Update libpng update script for v1.6.9 >>>>>>>>>>> >> >> BUG: Use ParameterValueType for computation of >>>>>>>>>>> landmark affine >>>>>>>>>>> >> >> ENH: Wrap LandmarkBasedTransformInitializer >>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>> >> >> ENH: Update itkpng zlib, configuration, and rename >>>>>>>>>>> >> >> ENH: Update itkpng name mangling >>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>> ReferenceImage >>>>>>>>>>> >> >> ivar >>>>>>>>>>> >> >> BUG: Increase tolerance for >>>>>>>>>>> PhysicsBasedNonRigidRegistrationMethod >>>>>>>>>>> >> >> BUG: Demonstrate side effect on registration due to >>>>>>>>>>> BSplineScatter >>>>>>>>>>> >> >> change >>>>>>>>>>> >> >> ENH: Move MovingHistogramImageFilter base classes to >>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>> construction >>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>> ReferenceImage >>>>>>>>>>> >> >> ivar >>>>>>>>>>> >> >> ENH: Optimize AdaptiveHistogramEqualization with >>>>>>>>>>> MovingHistogram >>>>>>>>>>> >> >> base >>>>>>>>>>> >> >> COMP: address sign unsigned comparison warning >>>>>>>>>>> >> >> COMP: Address signed unsigned comparison warning >>>>>>>>>>> >> >> COMP: Address unused member variable and methods in >>>>>>>>>>> anonymous ns >>>>>>>>>>> >> >> BUG: Fix segfault when with empty IsolatedWatershed >>>>>>>>>>> Threshold >>>>>>>>>>> >> >> range >>>>>>>>>>> >> >> BUG: Adjust intensity tolerance for >>>>>>>>>>> PhysicsBasedNonRigid test >>>>>>>>>>> >> >> BUG: Reduce number of targets with MSVC >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Davis Vigneault (7): >>>>>>>>>>> >> >> DOC: Minor improvements to segmentation examples. >>>>>>>>>>> >> >> DOC: Expanded Canny Edge Detection Example >>>>>>>>>>> >> >> DOC: Expanded TreeContainer Example >>>>>>>>>>> >> >> COMP: Warnings in itkVTKImageExport when compiling >>>>>>>>>>> with c++11 >>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>> c++11 >>>>>>>>>>> >> >> COMP: Update Git Tag for Subdivision Module >>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>> c++11 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> D?enan Zuki? (1): >>>>>>>>>>> >> >> STYLE: better formatting of the "usage" message >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Eugene Prilepin (1): >>>>>>>>>>> >> >> BUG: Fix a template name formation in python wrappings >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Floris Berendsen (1): >>>>>>>>>>> >> >> STYLE: Improve naming conventions in comments. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Hans Johnson (29): >>>>>>>>>>> >> >> STYLE: Instrument for FixedParameters typedef >>>>>>>>>>> >> >> BUG: Demonstrate DisplacementTransformFailure >>>>>>>>>>> >> >> BUG: FixedParameters should be double precision >>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>> >> >> ENH: Provide consistent floating point comparisons >>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>> >> >> PERF: Remove floating point as sentinal value >>>>>>>>>>> >> >> COMP: Const correctness needs to be maintained >>>>>>>>>>> >> >> BUG: Preserve backwards compatibility >>>>>>>>>>> >> >> DOC: Provide consistent naming in comments >>>>>>>>>>> >> >> ENH: Conversion between transform type tolerance >>>>>>>>>>> >> >> STYLE: Prefer initialization to assignment >>>>>>>>>>> >> >> ENH: Missing ITK_OVERRIDE >>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>> >> >> COMP: Add missing ITK_OVERRIDE >>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>> >> >> ENH: C++11 allows for rigorous =delete >>>>>>>>>>> >> >> COMP: Remove unnecessary failing assert test >>>>>>>>>>> >> >> ENH: Ignore internal files for the Clion editor >>>>>>>>>>> >> >> COMP: Fix VNL compilation for wider C++11 support >>>>>>>>>>> >> >> BUG: In configuration test need to mirror code >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Hyun Jae Kang (27): >>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>> >> >> BUG: Avoid an unexpected output of static_cast >>>>>>>>>>> >> >> BUG: Update python example codes for ImageRegistration >>>>>>>>>>> >> >> BUG: Retrieve the missed wrap file >>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>> in VTK file >>>>>>>>>>> >> >> header. >>>>>>>>>>> >> >> BUG: Fix HDF5 CMake configuration with VS2015 >>>>>>>>>>> >> >> BUG: Fix a compilation issue on ITK4 with FFTW and >>>>>>>>>>> shared >>>>>>>>>>> >> >> libraries >>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>> Mac OS X >>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>> in VTK file >>>>>>>>>>> >> >> header. >>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>> >> >> ENH: Add automatic KWStyle build and configuration >>>>>>>>>>> setup >>>>>>>>>>> >> >> COMP: KWStyle shadow, format-nonliteral and >>>>>>>>>>> autological-compare >>>>>>>>>>> >> >> warning. >>>>>>>>>>> >> >> COMP: Fixed the warning messages from itkGPU Module >>>>>>>>>>> >> >> COMP: Fixed a warning message of unused-private-field >>>>>>>>>>> >> >> COMP: Apply latest version of KWStyle >>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>> messages >>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>> messages >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on Windows >>>>>>>>>>> >> >> ENH: Update itkResourceProbe to calculate statistical >>>>>>>>>>> data >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on VS14 >>>>>>>>>>> >> >> COMP: Fixed 'std::sqrt' : ambiguous call to >>>>>>>>>>> overloaded function >>>>>>>>>>> >> >> ENH: Update the Report() function of >>>>>>>>>>> >> >> itkResourceProbesCollectorBase >>>>>>>>>>> >> >> COMP: Fix data-conversion warning message on >>>>>>>>>>> itkResourceProbe >>>>>>>>>>> >> >> COMP: Fix additional warning messages of KWStyle >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Jon Haitz Legarreta (6): >>>>>>>>>>> >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >>>>>>>>>>> >> >> BUG: Fix compilation issues for >>>>>>>>>>> StatisticsUniqueLabelMapFilterTest >>>>>>>>>>> >> >> BUG: Fix comparison issues for >>>>>>>>>>> itkStatisticsUniqueLabelMapFilter >>>>>>>>>>> >> >> BUG: Test for StatisticsUniqueLabelMapFilter stability >>>>>>>>>>> >> >> ENH: Add test for >>>>>>>>>>> itkParametricStpaceToImageSpaceFilter >>>>>>>>>>> >> >> ENH: Improve code coverage for >>>>>>>>>>> >> >> itkParametricSpaceToImageSpaceMeshFilter >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Julien Michel (1): >>>>>>>>>>> >> >> ENH: Support of VectorImage as template parameters for >>>>>>>>>>> >> >> WarpImageFilter >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Junjie Bai (2): >>>>>>>>>>> >> >> BUG: ConvertLabelMap with different LabelMapTypes >>>>>>>>>>> >> >> BUG: LabelObject CopyAttribute support different >>>>>>>>>>> LabelObject type >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> KWSys Robot (4): >>>>>>>>>>> >> >> KWSys 2015-07-10 (c9336bcf) >>>>>>>>>>> >> >> KWSys 2015-07-30 (f63febb7) >>>>>>>>>>> >> >> KWSys 2015-08-24 (cdaf522c) >>>>>>>>>>> >> >> KWSys 2015-08-28 (dc3fdd7f) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> LIBPNG Upstream (2): >>>>>>>>>>> >> >> PNG 2009-04-06 (e68f5a36) >>>>>>>>>>> >> >> PNG 2014-02-05 (3e753eb8) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Laurentiu Nicola (2): >>>>>>>>>>> >> >> PERF: Avoid temporary smartptr in >>>>>>>>>>> ProcessObject::GetInput >>>>>>>>>>> >> >> PERF: Optimize WarpImageFilter by avoiding refcount >>>>>>>>>>> bouncing >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Luc Hermitte (8): >>>>>>>>>>> >> >> PERF: itk::Image::GetPixel() performance improvment. >>>>>>>>>>> >> >> PERF: Performance enhancements on >>>>>>>>>>> VariableLengthVectors 1/... >>>>>>>>>>> >> >> ENH: Dependencies on itkVariableLengthVector.h reduced >>>>>>>>>>> >> >> BUG: Error in VariableLengthVector Unit Tests >>>>>>>>>>> >> >> PERF: Performance enhancements on VLV 2/... >>>>>>>>>>> >> >> PERF: Performances enhancements on VLV 3/... >>>>>>>>>>> >> >> COMP: Fix signed/unsigned warnings >>>>>>>>>>> >> >> BUG: std::copy/fill on empty VLV >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Lucas Gandel (4): >>>>>>>>>>> >> >> ENH: Move ImageToPathFilter from ITKReview to ITKPath >>>>>>>>>>> module. >>>>>>>>>>> >> >> BUG: Fixing ImageToPathFilter wrapping call from >>>>>>>>>>> Review Module >>>>>>>>>>> >> >> STYLE: Fix KWStyle dashboard errors >>>>>>>>>>> >> >> BUG: Fix external module BUILD_SHARED_LIBS status >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Mathieu Malaterre (1): >>>>>>>>>>> >> >> BUG: Name mangle the included expat third party >>>>>>>>>>> library. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Matthew McCormick (94): >>>>>>>>>>> >> >> ENH: Change itkSystemInformationTest to >>>>>>>>>>> itkCMakeConfigurationTest. >>>>>>>>>>> >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >>>>>>>>>>> >> >> ENH: Bump ITK version to 4.9.0. >>>>>>>>>>> >> >> BUG: Remove std::cout calls from classes. >>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>> >> >> BUG: Implement UpdateLargestPossibleRegion for >>>>>>>>>>> >> >> ImageToVTKImageFilter. >>>>>>>>>>> >> >> COMP: Add link interface specification for wrapping >>>>>>>>>>> >> >> target_link_libraries. >>>>>>>>>>> >> >> STYLE: Fix indentation in >>>>>>>>>>> itkMINCTransformIOFactory.cxx. >>>>>>>>>>> >> >> COMP: Fix MINCTransformIO factory registration. >>>>>>>>>>> >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with >>>>>>>>>>> Emscripten-1. >>>>>>>>>>> >> >> COMP: Remove unknown doxygen command in >>>>>>>>>>> AnisotropicDiffusionLBR. >>>>>>>>>>> >> >> BUG: Initialize mutex for 32 bit AtomicInt. >>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>> Linux. >>>>>>>>>>> >> >> STYLE: Rename gccxml -> castxml in >>>>>>>>>>> {idx,igenerator}.py. >>>>>>>>>>> >> >> COMP: Disable the gold linker for static builds on >>>>>>>>>>> Ubuntu 14.04. >>>>>>>>>>> >> >> ENH: Use Windows binaries for CastXML. >>>>>>>>>>> >> >> ENH: Add better scoping in igenerator.py. >>>>>>>>>>> >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + >>>>>>>>>>> MSVC. >>>>>>>>>>> >> >> BUG: LevelSetsv4 used signed char instead of char. >>>>>>>>>>> >> >> ENH: Add better scoping to idx.py. >>>>>>>>>>> >> >> COMP: Define newSize and oldSize in >>>>>>>>>>> VariableLengthVector. >>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>> >> >> ENH: Add more progress information to >>>>>>>>>>> IterativeClosestPoint2. >>>>>>>>>>> >> >> BUG: Build BridgeNumPy with Visual Studio. >>>>>>>>>>> >> >> ENH: Add ITKModuleExternal.cmake >>>>>>>>>>> >> >> COMP: Wrap Image< bool, D > for >>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>> >> >> BUG: Use CastXML binary built in Release. >>>>>>>>>>> >> >> BUG: ContinuousIndex should not be templated over >>>>>>>>>>> TCoordRep. >>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>> >> >> COMP: Address line length too long for Software Guide. >>>>>>>>>>> >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >>>>>>>>>>> >> >> BUG: Support Python 3 wrapping module initialization. >>>>>>>>>>> >> >> BUG: Update itkTemplate.py for Python 3. >>>>>>>>>>> >> >> BUG: Update itkExtras.py for Python 3. >>>>>>>>>>> >> >> BUG: Prevent Python callback addition recursion. >>>>>>>>>>> >> >> BUG: Fix test scripts for Python 3. >>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>> >> >> ENH: Allow projects to build against an external >>>>>>>>>>> module. >>>>>>>>>>> >> >> ENH: Replace CABLE_CONFIGURATION with >>>>>>>>>>> ITK_WRAPPING_PARSER. >>>>>>>>>>> >> >> ENH: Rename _cable_ to _wrappers_. >>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>> >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >>>>>>>>>>> >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >>>>>>>>>>> >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >>>>>>>>>>> >> >> ENH: Bump CastXML version to 2015-30-29. >>>>>>>>>>> >> >> ENH: Bump LLVM / Clang to 3.7.0. >>>>>>>>>>> >> >> COMP: Avoid itklibminc linking with >>>>>>>>>>> ITK_USE_SYSTEM_HDF5. >>>>>>>>>>> >> >> COMP: Add missing ITKIOImageBase dependency for >>>>>>>>>>> ITKTransformMINC. >>>>>>>>>>> >> >> COMP: Use itkSimpleNewMacro in >>>>>>>>>>> >> >> ThreadedIteratorRangePartitionerTest. >>>>>>>>>>> >> >> ENH: Add wrapping support for building modules >>>>>>>>>>> externally. >>>>>>>>>>> >> >> BUG: Fix KWStyle test paths when building a module >>>>>>>>>>> externally. >>>>>>>>>>> >> >> ENH: Add Cuberille Remote module. >>>>>>>>>>> >> >> COMP: Remove carriage returns from Cuberille remote. >>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>> >> >> ENH: Bump the MinimalPathExtraction Remote to >>>>>>>>>>> 2015-10-20. >>>>>>>>>>> >> >> COMP: Fix KernelTransform SetFixedParameters argument >>>>>>>>>>> type. >>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>> sys.path >>>>>>>>>>> >> >> Revert "COMP: Put vnl_export.h in the list of sources >>>>>>>>>>> so it gets >>>>>>>>>>> >> >> installed." >>>>>>>>>>> >> >> BUG: Revert "BUG: ConvertLabelMap with different >>>>>>>>>>> LabelMapTypes" >>>>>>>>>>> >> >> ENH: Marking wrapping CMake configuration variables >>>>>>>>>>> as advanced. >>>>>>>>>>> >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >>>>>>>>>>> >> >> COMP: Non-virtual copy attribute members in LabelMap >>>>>>>>>>> cannot have >>>>>>>>>>> >> >> override. >>>>>>>>>>> >> >> COMP: Add wrapping for >>>>>>>>>>> AdaptiveHistogramEqualizationImageFilter. >>>>>>>>>>> >> >> COMP: Add itkMacro.h to itkPromoteType.h for >>>>>>>>>>> ITK_EXCEPT. >>>>>>>>>>> >> >> ENH: Remove CMake version check in >>>>>>>>>>> ITKModuleHeaderTest.cmake >>>>>>>>>>> >> >> BUG: Improve KWStyle ExternalProject utilization. >>>>>>>>>>> >> >> ENH: Remove old KWStyle build script. >>>>>>>>>>> >> >> COMP: Address VariableLengthVector Doxygen rhs @param >>>>>>>>>>> not found. >>>>>>>>>>> >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to >>>>>>>>>>> WRAPPING_SUBMODULE_ORDER. >>>>>>>>>>> >> >> ENH: Install Python bindings into site-packages. >>>>>>>>>>> >> >> ENH: Improve readability of Python site-packages path >>>>>>>>>>> detection. >>>>>>>>>>> >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned >>>>>>>>>>> expression >>>>>>>>>>> >> >> warning. >>>>>>>>>>> >> >> BUG: ITKCommon publically depends on >>>>>>>>>>> ITKDoubleConversion. >>>>>>>>>>> >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >>>>>>>>>>> >> >> ENH: Improves names and export of module dependencies. >>>>>>>>>>> >> >> STYLE: Improve namespace bracket style in >>>>>>>>>>> itkIsConvertible. >>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>> >> >> BUG: Remove unused wrapping files. >>>>>>>>>>> >> >> BUG: Do install install wrapping development files. >>>>>>>>>>> >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >>>>>>>>>>> >> >> BUG: Remove duplicate inclusion of wrapping >>>>>>>>>>> submodules. >>>>>>>>>>> >> >> COMP: Do not use C++ style comments for Doxygen cond. >>>>>>>>>>> >> >> BUG: Fix detection of the gold linker. >>>>>>>>>>> >> >> BUG: Update Python package installation locations. >>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >>>>>>>>>>> >> >> ENH: Change BUILD_EXAMPLES default to OFF. >>>>>>>>>>> >> >> BUG: Use 'from itk import ITKCommon' in module2module >>>>>>>>>>> test. >>>>>>>>>>> >> >> COMP: Link to VTK Python when built with Kits support. >>>>>>>>>>> >> >> BUG: Install itk_minc2.h header. >>>>>>>>>>> >> >> COMP: ITKIOMINC has a public dependency on >>>>>>>>>>> ITKIOImageBase. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Michka Popoff (9): >>>>>>>>>>> >> >> ENH: Update to swig 3.0.7 >>>>>>>>>>> >> >> ENH: Do not link against specific Python library on >>>>>>>>>>> OS X >>>>>>>>>>> >> >> COMP: Fix wrapping warnings when building with >>>>>>>>>>> >> >> ITK_WRAP_IMAGE_DIMS=2 >>>>>>>>>>> >> >> COMP: Add missing wrapping for TransformBase >>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>> sys.path >>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>> 3 wrapping >>>>>>>>>>> >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>> >> >> module >>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>> 3 wrapping >>>>>>>>>>> >> >> ENH: Allow operations on Indexes and Offsets in Python >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Mikhail Isakov (1): >>>>>>>>>>> >> >> BUG: DiffusionTensor3DReconstruction segfault if no >>>>>>>>>>> baseline image >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Nick Tustison (5): >>>>>>>>>>> >> >> BUG: Set a default b-spline epsilon. >>>>>>>>>>> >> >> ENH: Adding testing for closed loop. >>>>>>>>>>> >> >> BUG: Updating B-spline classes with the same epsilon >>>>>>>>>>> strategy. >>>>>>>>>>> >> >> PERF: Switch vnl_vectors for fixed arrays. >>>>>>>>>>> >> >> ENH: Point-set registration with time-varying >>>>>>>>>>> B-spline. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Olivier Commowick (3): >>>>>>>>>>> >> >> BUG: Correct discrepancy in tridiagonal reduction wrt >>>>>>>>>>> VNL eigen >>>>>>>>>>> >> >> system >>>>>>>>>>> >> >> BUG: Correct under/overflows in vnl_math_hypot (taken >>>>>>>>>>> from pythag >>>>>>>>>>> >> >> from V3P) >>>>>>>>>>> >> >> BUG: Switch eigenvalues computation to double >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Pablo Hernandez-Cerdan (2): >>>>>>>>>>> >> >> ENH: Help class for itkFlatStructuringElement with >>>>>>>>>>> constructor >>>>>>>>>>> >> >> from >>>>>>>>>>> >> >> images. >>>>>>>>>>> >> >> COMP: Fix test errors and warnings in >>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Seun Odutola (1): >>>>>>>>>>> >> >> COMP: Fixed name clash with Apple header (check >>>>>>>>>>> Macro), renamed >>>>>>>>>>> >> >> check >>>>>>>>>>> >> >> to Check >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Shawn Waldon (1): >>>>>>>>>>> >> >> COMP: Set target OS X version in environment for >>>>>>>>>>> tools using >>>>>>>>>>> >> >> compiler >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Simon Alexander (1): >>>>>>>>>>> >> >> BUG: incorrect closest point computation >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Tobias Wood (2): >>>>>>>>>>> >> >> BUG: LBFGSB was printing messages even with debug >>>>>>>>>>> switched off. >>>>>>>>>>> >> >> BUG: Removed an unguarded print statement. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Vladimir S. FONOV (9): >>>>>>>>>>> >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >>>>>>>>>>> >> >> COMP: Changing the order of HDF5 library components >>>>>>>>>>> >> >> COMP: Splitting up IOMINC module into two parts: MINC >>>>>>>>>>> and >>>>>>>>>>> >> >> Transform >>>>>>>>>>> >> >> STYLE: updated comments to properly reference LIBMINC >>>>>>>>>>> >> >> ENH: Add script to merge upstream MINC as a subtree >>>>>>>>>>> >> >> MINC 2015-07-23 (c033d431) >>>>>>>>>>> >> >> COMP: Update MINC CMake code >>>>>>>>>>> >> >> MINC 2015-08-18 (6d7e3ba8) >>>>>>>>>>> >> >> MINC 2015-09-13 (95cd5374) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Xiaoxiao Liu (1): >>>>>>>>>>> >> >> DOC: update email address for xiaoxiao. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Zach Williamson (10): >>>>>>>>>>> >> >> BUG: Use correct libraries for ImageFusion tests >>>>>>>>>>> >> >> ENH: Consolidate Library Dependencies >>>>>>>>>>> >> >> COMP: Add a missing link to Review module >>>>>>>>>>> >> >> COMP: Use correct linking macro in DCMTK >>>>>>>>>>> >> >> BUG: Use correct libraries for TestKernel tests >>>>>>>>>>> >> >> COMP: Fix inconsistant naming of >>>>>>>>>>> GPUPDEDeformableRegistration >>>>>>>>>>> >> >> ENH: Use new linking system macros >>>>>>>>>>> >> >> PERF: Avoid searching private dependencies for >>>>>>>>>>> include directories >>>>>>>>>>> >> >> COMP: Recover missing dependencies >>>>>>>>>>> >> >> ENH: use new linking macros in Filtering module >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> ----------------------------------------------------- >>>>>>>>>>> >> >> Errors or omissions? Please fix them here: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >>>>>>>>>>> >> >> _____________________________________ >>>>>>>>>>> >> >> Powered by www.kitware.com >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Visit other Kitware open-source projects at >>>>>>>>>>> >> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Kitware offers ITK Training Courses, for more information >>>>>>>>>>> visit: >>>>>>>>>>> >> >> http://www.kitware.com/products/protraining.php >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> >>>>>>>>> >>>>>>>>>> Powered by www.kitware.com >>>>>>>>>> >>>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>>> >>>>>>>>> http://kitware.com/products/protraining.php >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>> >>>>> >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From dzenanz at gmail.com Tue Dec 1 09:21:50 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 1 Dec 2015 09:21:50 -0500 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: If you are running tests in debug, some of them are too slow and time out. On Tue, Dec 1, 2015 at 9:19 AM, Simon Alexander wrote: > Hi Matt, > > So I pulled origin/master and rebuilt last night. I have different > failures now, all by timeout: > > *Total Test time (real) = 6363.39 sec* > > *The following tests FAILED:* > * 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo > (Timeout)* > * 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo > (Timeout)* > * 728 - > itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout)* > * 2025 - itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest > (Timeout)* > *Errors while running CTest* > > > Any thoughts on what's going on there? > > > On Mon, 30 Nov 2015 at 20:42 Matt McCormick > wrote: > >> Hi Simon, >> >> I am returning from holiday, and also catching up on activity. >> >> >> Hyun Jae has taken care of the KWStyle warnings and the data conversion >> warning: >> >> http://review.source.kitware.com/#/c/20430/ >> http://review.source.kitware.com/#/c/20446/ >> >> >> And Dzenan and Bill have addressed Wiki examples errors: >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >> >> >> It is likely that the test failures on your build still remain. Did you >> want to take them on? >> >> Thanks, >> Matt >> >> On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? wrote: >> >>> Looking at the master branch is the right thing to do. I am not doing >>> any active development regarding this right now. >>> >>> On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander >>> wrote: >>> >>>> Hi All, >>>> >>>> I had hoped to be able to look at this over the weekend, but no such >>>> luck. Is there somewhere useful I can help with it now? Not sure what >>>> state we are in (or what branch). >>>> >>>> On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? wrote: >>>> >>>>> It turns out that all the compile errors were occurring in >>>>> WikiExamples. I solved all except one: >>>>> ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in >>>>> file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line >>>>> 23, but it should be judging from the comment on that line. >>>>> >>>>> For the rest, I created a pull request: >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>>>> >>>>> On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander < >>>>> skalexander at gmail.com> wrote: >>>>> >>>>>> Perfect. I'm under a deadline that is likely to eat the rest of the >>>>>> week but if that clears up I'll try and jump in earlier. >>>>>> >>>>>> On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? wrote: >>>>>> >>>>>>> OK I will work on it for an hour or two now, and I will make a >>>>>>> branch and push it to Gerrit so whoever wants can pick up from there and >>>>>>> keep updating it. >>>>>>> >>>>>>> On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander < >>>>>>> skalexander at gmail.com> wrote: >>>>>>> >>>>>>>> Makes sense. At this point I am unlikely to have time to look at >>>>>>>> this until Saturday, but have hopes for a few free hours there. >>>>>>>> >>>>>>>> On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Building git master from Nov 23rd with examples and testing >>>>>>>>> enabled I get 14 compile errors in VS2015 debug x64. Should we coordinate >>>>>>>>> our efforts in fixing them? >>>>>>>>> >>>>>>>>> On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander < >>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Two of the three failures look like truncation issues (like >>>>>>>>>> https://open.cdash.org/testDetails.php?test=395263772&build=4117158 >>>>>>>>>> ) >>>>>>>>>> >>>>>>>>>> The other ( >>>>>>>>>> https://open.cdash.org/testDetails.php?test=395264938&build=4117158) >>>>>>>>>> is less obvious. >>>>>>>>>> >>>>>>>>>> If I have time this evening I'll try and have a look at these. >>>>>>>>>> >>>>>>>>>> Is your standard test build in 32 bit ? That might explain the >>>>>>>>>> difference if there are some underlying type assumptions, but not obvious >>>>>>>>>> why 2015 would trigger but not 2013. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, 25 Nov 2015 at 11:01 Matt McCormick < >>>>>>>>>> matt.mccormick at kitware.com> wrote: >>>>>>>>>> >>>>>>>>>>> Ah, cool! Here: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 >>>>>>>>>>> >>>>>>>>>>> Could you please look into the test failures? >>>>>>>>>>> >>>>>>>>>>> @Hyun Jae, could you please look into the KWStyle warnings? >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander < >>>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>>> > Sorry, if I wasn't clear - I submitted two builds yesterday >>>>>>>>>>> from SIMON-LAP, >>>>>>>>>>> > (actually 3 as I wasn't sure the config was right on the first >>>>>>>>>>> one). VS2013 >>>>>>>>>>> > was green, three failures on VS2015 (and 18 warnings). Looks >>>>>>>>>>> like a >>>>>>>>>>> > truncation problem on the resuts. >>>>>>>>>>> > >>>>>>>>>>> > On Wed, 25 Nov 2015 at 10:51 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> Hi Simon, >>>>>>>>>>> >> >>>>>>>>>>> >> Thanks for testing. >>>>>>>>>>> >> >>>>>>>>>>> >> We have a Visual Studio 2015 build on the dashboard that is >>>>>>>>>>> green: >>>>>>>>>>> >> >>>>>>>>>>> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >>>>>>>>>>> >> >>>>>>>>>>> >> Are there any different flags? Could you please submit an >>>>>>>>>>> Experimental >>>>>>>>>>> >> build? >>>>>>>>>>> >> >>>>>>>>>>> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test >>>>>>>>>>> -T Submit -C >>>>>>>>>>> >> Release >>>>>>>>>>> >> >>>>>>>>>>> >> from a fresh build tree. >>>>>>>>>>> >> >>>>>>>>>>> >> Thanks, >>>>>>>>>>> >> Matt >>>>>>>>>>> >> >>>>>>>>>>> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander < >>>>>>>>>>> skalexander at gmail.com> >>>>>>>>>>> >> wrote: >>>>>>>>>>> >> > Looks like a few problems with x64 build on visual studio >>>>>>>>>>> 2015 - do you >>>>>>>>>>> >> > have >>>>>>>>>>> >> > a test machine in this configuration? >>>>>>>>>>> >> > >>>>>>>>>>> >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> On behalf of the Insight Toolkit community, we are proud >>>>>>>>>>> to announce >>>>>>>>>>> >> >> that >>>>>>>>>>> >> >> ITK 4.9 release candidate 1 has been tagged and is >>>>>>>>>>> available for >>>>>>>>>>> >> >> testing! >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please take this opportunity to test the new features in >>>>>>>>>>> the release >>>>>>>>>>> >> >> candidate. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> To obtain the source code, >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> git clone http://itk.org/ITK.git >>>>>>>>>>> >> >> cd ITK >>>>>>>>>>> >> >> git checkout -q --detach v4.9rc01 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> For more details, please see the Git documentation [1]. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> A few selected highlights for this release: >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * New Remote modules: the Cuberille module for smooth >>>>>>>>>>> generation of >>>>>>>>>>> >> >> meshes >>>>>>>>>>> >> >> from binary segmentation images, and the >>>>>>>>>>> AnisotropicDiffusionLBR module >>>>>>>>>>> >> >> improved edge-preserving smoothing. >>>>>>>>>>> >> >> * Build your own ITK module outside the source tree, add >>>>>>>>>>> continuous >>>>>>>>>>> >> >> integration testing on GitHub, and easily add Python >>>>>>>>>>> wrapping for your >>>>>>>>>>> >> >> C++ >>>>>>>>>>> >> >> algorithms. >>>>>>>>>>> >> >> * Python wrapping, including Python 3, builds faster with >>>>>>>>>>> a more >>>>>>>>>>> >> >> standard >>>>>>>>>>> >> >> installation >>>>>>>>>>> >> >> * Improved performance of itk::Image::GetPixel and >>>>>>>>>>> operations on >>>>>>>>>>> >> >> itk::VariableLengthVector?s >>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>> private / >>>>>>>>>>> >> >> compile / >>>>>>>>>>> >> >> test >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please test the release candidate and share your >>>>>>>>>>> experiences on the >>>>>>>>>>> >> >> mailing list, issue tracker, and Gerrit Code Review. The >>>>>>>>>>> new module >>>>>>>>>>> >> >> dependency specification mechanism may unearth missing >>>>>>>>>>> dependencies for >>>>>>>>>>> >> >> projects that use ITK COMPONENTS with the CMake >>>>>>>>>>> find_package command. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> An Experimental build, which demonstrates how the test >>>>>>>>>>> suite performs >>>>>>>>>>> >> >> on >>>>>>>>>>> >> >> your local build system, can be submitted to the dashboard >>>>>>>>>>> [2] with: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> mkdir ../ITK-build >>>>>>>>>>> >> >> cd ../ITK-build >>>>>>>>>>> >> >> cmake ../ITK >>>>>>>>>>> >> >> ctest -j 4 -M Experimental -T Configure -T Build -T >>>>>>>>>>> Test -T Submit >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Visual Studio builds must also add ?-C Release? to the >>>>>>>>>>> ctest command. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Notify the mailing list if there are any unexpected >>>>>>>>>>> failures. Testing >>>>>>>>>>> >> >> your own applications against the RC is also appreciated. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Congratulations and well done to the 35 contributors to >>>>>>>>>>> this release. >>>>>>>>>>> >> >> We >>>>>>>>>>> >> >> would especially like to recognize the new contributors: >>>>>>>>>>> Mikhail >>>>>>>>>>> >> >> Isakov, >>>>>>>>>>> >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias >>>>>>>>>>> Wood, Seun >>>>>>>>>>> >> >> Odutola, >>>>>>>>>>> >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo >>>>>>>>>>> >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach >>>>>>>>>>> Williamson, >>>>>>>>>>> >> >> Luc >>>>>>>>>>> >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> The final release is scheduled for mid-December. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> [1] http://www.itk.org/Wiki/ITK/Git >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> [2] http://open.cdash.org/index.php?project=Insight >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> New Features >>>>>>>>>>> >> >> --------------------- >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Wrapping improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Python 3 supported >>>>>>>>>>> >> >> * Wrapping builds much faster due to CastXML binaries >>>>>>>>>>> >> >> * LandmarkBasedTransformInitializer now wrapped >>>>>>>>>>> >> >> * NumPy bridge with VisualStudio >>>>>>>>>>> >> >> * Wrapping for the MinimalPathExtraction module >>>>>>>>>>> >> >> * Wrapping is now installed into Python?s site-packages >>>>>>>>>>> directory in >>>>>>>>>>> >> >> the >>>>>>>>>>> >> >> ?itk? package >>>>>>>>>>> >> >> * Wrapping package size is decreased >>>>>>>>>>> >> >> * Better package portability on Mac OSX >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> New Remote Modules >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Cuberille >>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>> http://hdl.handle.net/10380/3186 >>>>>>>>>>> >> >> * AnisotropicDiffusionLBR >>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>> http://hdl.handle.net/10380/3505 >>>>>>>>>>> >> >> * Web browser reproducibility: >>>>>>>>>>> >> >> http://www.kitware.com/blog/home/post/942 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Core Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * External Modules can now be developed outside of the ITK >>>>>>>>>>> source tree >>>>>>>>>>> >> >> and >>>>>>>>>>> >> >> on GitHub >>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/997 >>>>>>>>>>> >> >> * New utilities in itk::Math: >>>>>>>>>>> >> >> * AlmostEquals >>>>>>>>>>> >> >> * NotAlmostEquals >>>>>>>>>>> >> >> * ExactlyEquals >>>>>>>>>>> >> >> * NotExactlyEquals >>>>>>>>>>> >> >> * New itk::NumericTraits >>>>>>>>>>> >> >> * IsInteger >>>>>>>>>>> >> >> * IsSigned >>>>>>>>>>> >> >> * Improved C++11 support >>>>>>>>>>> >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >>>>>>>>>>> >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >>>>>>>>>>> >> >> * Improved capabilities of itk::ResourceProbe and >>>>>>>>>>> >> >> itk::ResourceProbesCollectorBase >>>>>>>>>>> >> >> * Improve numerical stability in VNL eigen system >>>>>>>>>>> estimation >>>>>>>>>>> >> >> * itksys_ios:: and itksys_stl:: have been remove (use >>>>>>>>>>> std::) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Filtering Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>> >> >> * WarpImageFilter support VectorImage?s >>>>>>>>>>> >> >> * ConvertLabelMap supports different LabelMap types >>>>>>>>>>> >> >> * ImageToPathFilter moved from the ITKReview to the >>>>>>>>>>> ITKPath module >>>>>>>>>>> >> >> * itk::MovingHistogramImageFilter moved to the >>>>>>>>>>> ITKImageFilterBase >>>>>>>>>>> >> >> module >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Registration Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Build Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>> private / >>>>>>>>>>> >> >> compile / >>>>>>>>>>> >> >> test >>>>>>>>>>> >> >> * BUILD_EXAMPLES CMake option is now OFF by default >>>>>>>>>>> >> >> * Option to export all library symbols on Windows: >>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/939 >>>>>>>>>>> >> >> * Expat third party library is now name mangled >>>>>>>>>>> >> >> * Many more modules can be built as shared libraries >>>>>>>>>>> >> >> * KWStyle is automatically built and configured when tests >>>>>>>>>>> are built >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Performance Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds >>>>>>>>>>> members for >>>>>>>>>>> >> >> metaprogramming >>>>>>>>>>> >> >> * itk::mpl::{TrueType,FalseType} >>>>>>>>>>> >> >> * itk::mpl::{If,Not,And,Or,Xor} >>>>>>>>>>> >> >> * itk::mpl::EnableIf >>>>>>>>>>> >> >> * itk::mpl::IsBaseOf >>>>>>>>>>> >> >> * itk::mpl::IsConvertible >>>>>>>>>>> >> >> * itk::mpl::IsNumber >>>>>>>>>>> >> >> * itk::mpl::IsSame >>>>>>>>>>> >> >> * itk::mpl::PromoteType >>>>>>>>>>> >> >> * Image::GetPixel performance improvements >>>>>>>>>>> >> >> * Many itk::VariableLengthVector performance improvements >>>>>>>>>>> >> >> * AdaptiveHistogramEqualization uses a moving histogram >>>>>>>>>>> >> >> * WarpImageFilter performance improvements >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Documentation Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx >>>>>>>>>>> Examples >>>>>>>>>>> >> >> * ITK Software Guide improvements >>>>>>>>>>> >> >> * How to use Python wrapping >>>>>>>>>>> >> >> * How to create an ITK module >>>>>>>>>>> >> >> * Improvements to segmentation examples >>>>>>>>>>> >> >> * Expanded Canny edge detection example >>>>>>>>>>> >> >> * Expanded tree container example >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Third Party Library Updates >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * FFTW updated to latest upstream >>>>>>>>>>> >> >> * Build with recent OpenCV 2 and 3 >>>>>>>>>>> >> >> * Build with the latest VTK >>>>>>>>>>> >> >> * PNG update to the latest upstream >>>>>>>>>>> >> >> * GDCM updated to the latest upstream >>>>>>>>>>> >> >> * KWSys updated to the latest upstream >>>>>>>>>>> >> >> * MINC updated to the latest upstream >>>>>>>>>>> >> >> * SWIG updated to the latest upstream >>>>>>>>>>> >> >> * Third party PNG and MINC are now Git subtrees >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Style improvements -- ITK gets more stylish with every >>>>>>>>>>> release! >>>>>>>>>>> >> >> >>>>>>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Private copy constructors and operator= use >>>>>>>>>>> ITK_DELETE_FUNCTION >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Improved code coverage -- we are at 84.9%! >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * *Lots* of important bug fixes >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * And much more! See details in the log below. >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Changes from v4.8.0..v4.9rc01 >>>>>>>>>>> >> >> -------------------------------------------- >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Abhishek Tiwari (1): >>>>>>>>>>> >> >> BUG: "tmpImageIndex" not initialized to 0. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Adam Snyder (1): >>>>>>>>>>> >> >> PERF: Reworked MMI Threading using a per-thread buffer >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Alexander Leinoff (6): >>>>>>>>>>> >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >>>>>>>>>>> >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be >>>>>>>>>>> resolved. >>>>>>>>>>> >> >> ENH: Adds ExactlyEquals and NotExactlyEquals >>>>>>>>>>> functions to >>>>>>>>>>> >> >> itkMath.h >>>>>>>>>>> >> >> COMP: Removes floating-point equality checks >>>>>>>>>>> >> >> ENH: COMP: Adds support for complex values to >>>>>>>>>>> Math::AlmostEquals >>>>>>>>>>> >> >> ENH: Updates fftw dependency >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Arnaud Gelas (5): >>>>>>>>>>> >> >> COMP: fix warning (unused local typedef) >>>>>>>>>>> >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >>>>>>>>>>> >> >> DOC: add doxgen documentation for >>>>>>>>>>> >> >> BinaryImageToLevelSetImageAdaptor >>>>>>>>>>> >> >> ENH: add tests to exercise >>>>>>>>>>> itk::ThreadedIteratorRangePartitioner >>>>>>>>>>> >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Betsy McPhail (1): >>>>>>>>>>> >> >> BUG: Improve buffer alignment in OctreeNode . >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bill Hoffman (2): >>>>>>>>>>> >> >> ENH: Use new CMake Windows export symbol dll feature. >>>>>>>>>>> >> >> COMP: Put vnl_export.h in the list of sources so it >>>>>>>>>>> gets >>>>>>>>>>> >> >> installed. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bill Lorensen (4): >>>>>>>>>>> >> >> COMP: VTkGlue linker errors >>>>>>>>>>> >> >> BUG: Inappropriate use of AlmostEquals >>>>>>>>>>> >> >> ENH: Bump tag for wiki examples >>>>>>>>>>> >> >> ENH: Better layout strategy >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Brad King (3): >>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>> itksys_ios::* >>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>> itksys_stl::* >>>>>>>>>>> >> >> ENH: Update CMake Policy settings in >>>>>>>>>>> Testing/TestExternal project >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bradley Lowekamp (31): >>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>> construction >>>>>>>>>>> >> >> ENH: Enable base classes for templates of landmark >>>>>>>>>>> initializer >>>>>>>>>>> >> >> STYLE: Use "Swap" for ITK member name >>>>>>>>>>> >> >> BUG: Demonstrate Eigen analysis failure >>>>>>>>>>> >> >> BUG: Fix computation of Eigen analysis >>>>>>>>>>> >> >> ENH: Update DiscreteHessianGaussian Test baseline >>>>>>>>>>> >> >> ENH: Correctly demonstrate float point Eigen failure >>>>>>>>>>> >> >> ENH: compile vnl_math_hypot, and use at least double >>>>>>>>>>> >> >> ENH: Adding initial update script from used libpng >>>>>>>>>>> version. >>>>>>>>>>> >> >> ENH: removing non-subtree files for itkpng >>>>>>>>>>> >> >> ENH: Ported ITK changes for building to subtree >>>>>>>>>>> merged code >>>>>>>>>>> >> >> ENH: Update libpng update script for v1.6.9 >>>>>>>>>>> >> >> BUG: Use ParameterValueType for computation of >>>>>>>>>>> landmark affine >>>>>>>>>>> >> >> ENH: Wrap LandmarkBasedTransformInitializer >>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>> >> >> ENH: Update itkpng zlib, configuration, and rename >>>>>>>>>>> >> >> ENH: Update itkpng name mangling >>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>> ReferenceImage >>>>>>>>>>> >> >> ivar >>>>>>>>>>> >> >> BUG: Increase tolerance for >>>>>>>>>>> PhysicsBasedNonRigidRegistrationMethod >>>>>>>>>>> >> >> BUG: Demonstrate side effect on registration due to >>>>>>>>>>> BSplineScatter >>>>>>>>>>> >> >> change >>>>>>>>>>> >> >> ENH: Move MovingHistogramImageFilter base classes to >>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>> construction >>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>> ReferenceImage >>>>>>>>>>> >> >> ivar >>>>>>>>>>> >> >> ENH: Optimize AdaptiveHistogramEqualization with >>>>>>>>>>> MovingHistogram >>>>>>>>>>> >> >> base >>>>>>>>>>> >> >> COMP: address sign unsigned comparison warning >>>>>>>>>>> >> >> COMP: Address signed unsigned comparison warning >>>>>>>>>>> >> >> COMP: Address unused member variable and methods in >>>>>>>>>>> anonymous ns >>>>>>>>>>> >> >> BUG: Fix segfault when with empty IsolatedWatershed >>>>>>>>>>> Threshold >>>>>>>>>>> >> >> range >>>>>>>>>>> >> >> BUG: Adjust intensity tolerance for >>>>>>>>>>> PhysicsBasedNonRigid test >>>>>>>>>>> >> >> BUG: Reduce number of targets with MSVC >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Davis Vigneault (7): >>>>>>>>>>> >> >> DOC: Minor improvements to segmentation examples. >>>>>>>>>>> >> >> DOC: Expanded Canny Edge Detection Example >>>>>>>>>>> >> >> DOC: Expanded TreeContainer Example >>>>>>>>>>> >> >> COMP: Warnings in itkVTKImageExport when compiling >>>>>>>>>>> with c++11 >>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>> c++11 >>>>>>>>>>> >> >> COMP: Update Git Tag for Subdivision Module >>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>> c++11 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> D?enan Zuki? (1): >>>>>>>>>>> >> >> STYLE: better formatting of the "usage" message >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Eugene Prilepin (1): >>>>>>>>>>> >> >> BUG: Fix a template name formation in python wrappings >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Floris Berendsen (1): >>>>>>>>>>> >> >> STYLE: Improve naming conventions in comments. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Hans Johnson (29): >>>>>>>>>>> >> >> STYLE: Instrument for FixedParameters typedef >>>>>>>>>>> >> >> BUG: Demonstrate DisplacementTransformFailure >>>>>>>>>>> >> >> BUG: FixedParameters should be double precision >>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>> >> >> ENH: Provide consistent floating point comparisons >>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>> >> >> PERF: Remove floating point as sentinal value >>>>>>>>>>> >> >> COMP: Const correctness needs to be maintained >>>>>>>>>>> >> >> BUG: Preserve backwards compatibility >>>>>>>>>>> >> >> DOC: Provide consistent naming in comments >>>>>>>>>>> >> >> ENH: Conversion between transform type tolerance >>>>>>>>>>> >> >> STYLE: Prefer initialization to assignment >>>>>>>>>>> >> >> ENH: Missing ITK_OVERRIDE >>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>> >> >> COMP: Add missing ITK_OVERRIDE >>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>> >> >> ENH: C++11 allows for rigorous =delete >>>>>>>>>>> >> >> COMP: Remove unnecessary failing assert test >>>>>>>>>>> >> >> ENH: Ignore internal files for the Clion editor >>>>>>>>>>> >> >> COMP: Fix VNL compilation for wider C++11 support >>>>>>>>>>> >> >> BUG: In configuration test need to mirror code >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Hyun Jae Kang (27): >>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>> >> >> BUG: Avoid an unexpected output of static_cast >>>>>>>>>>> >> >> BUG: Update python example codes for ImageRegistration >>>>>>>>>>> >> >> BUG: Retrieve the missed wrap file >>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>> in VTK file >>>>>>>>>>> >> >> header. >>>>>>>>>>> >> >> BUG: Fix HDF5 CMake configuration with VS2015 >>>>>>>>>>> >> >> BUG: Fix a compilation issue on ITK4 with FFTW and >>>>>>>>>>> shared >>>>>>>>>>> >> >> libraries >>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>> Mac OS X >>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>> in VTK file >>>>>>>>>>> >> >> header. >>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>> >> >> ENH: Add automatic KWStyle build and configuration >>>>>>>>>>> setup >>>>>>>>>>> >> >> COMP: KWStyle shadow, format-nonliteral and >>>>>>>>>>> autological-compare >>>>>>>>>>> >> >> warning. >>>>>>>>>>> >> >> COMP: Fixed the warning messages from itkGPU Module >>>>>>>>>>> >> >> COMP: Fixed a warning message of unused-private-field >>>>>>>>>>> >> >> COMP: Apply latest version of KWStyle >>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>> messages >>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>> messages >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on Windows >>>>>>>>>>> >> >> ENH: Update itkResourceProbe to calculate statistical >>>>>>>>>>> data >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on VS14 >>>>>>>>>>> >> >> COMP: Fixed 'std::sqrt' : ambiguous call to >>>>>>>>>>> overloaded function >>>>>>>>>>> >> >> ENH: Update the Report() function of >>>>>>>>>>> >> >> itkResourceProbesCollectorBase >>>>>>>>>>> >> >> COMP: Fix data-conversion warning message on >>>>>>>>>>> itkResourceProbe >>>>>>>>>>> >> >> COMP: Fix additional warning messages of KWStyle >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Jon Haitz Legarreta (6): >>>>>>>>>>> >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >>>>>>>>>>> >> >> BUG: Fix compilation issues for >>>>>>>>>>> StatisticsUniqueLabelMapFilterTest >>>>>>>>>>> >> >> BUG: Fix comparison issues for >>>>>>>>>>> itkStatisticsUniqueLabelMapFilter >>>>>>>>>>> >> >> BUG: Test for StatisticsUniqueLabelMapFilter stability >>>>>>>>>>> >> >> ENH: Add test for >>>>>>>>>>> itkParametricStpaceToImageSpaceFilter >>>>>>>>>>> >> >> ENH: Improve code coverage for >>>>>>>>>>> >> >> itkParametricSpaceToImageSpaceMeshFilter >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Julien Michel (1): >>>>>>>>>>> >> >> ENH: Support of VectorImage as template parameters for >>>>>>>>>>> >> >> WarpImageFilter >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Junjie Bai (2): >>>>>>>>>>> >> >> BUG: ConvertLabelMap with different LabelMapTypes >>>>>>>>>>> >> >> BUG: LabelObject CopyAttribute support different >>>>>>>>>>> LabelObject type >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> KWSys Robot (4): >>>>>>>>>>> >> >> KWSys 2015-07-10 (c9336bcf) >>>>>>>>>>> >> >> KWSys 2015-07-30 (f63febb7) >>>>>>>>>>> >> >> KWSys 2015-08-24 (cdaf522c) >>>>>>>>>>> >> >> KWSys 2015-08-28 (dc3fdd7f) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> LIBPNG Upstream (2): >>>>>>>>>>> >> >> PNG 2009-04-06 (e68f5a36) >>>>>>>>>>> >> >> PNG 2014-02-05 (3e753eb8) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Laurentiu Nicola (2): >>>>>>>>>>> >> >> PERF: Avoid temporary smartptr in >>>>>>>>>>> ProcessObject::GetInput >>>>>>>>>>> >> >> PERF: Optimize WarpImageFilter by avoiding refcount >>>>>>>>>>> bouncing >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Luc Hermitte (8): >>>>>>>>>>> >> >> PERF: itk::Image::GetPixel() performance improvment. >>>>>>>>>>> >> >> PERF: Performance enhancements on >>>>>>>>>>> VariableLengthVectors 1/... >>>>>>>>>>> >> >> ENH: Dependencies on itkVariableLengthVector.h reduced >>>>>>>>>>> >> >> BUG: Error in VariableLengthVector Unit Tests >>>>>>>>>>> >> >> PERF: Performance enhancements on VLV 2/... >>>>>>>>>>> >> >> PERF: Performances enhancements on VLV 3/... >>>>>>>>>>> >> >> COMP: Fix signed/unsigned warnings >>>>>>>>>>> >> >> BUG: std::copy/fill on empty VLV >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Lucas Gandel (4): >>>>>>>>>>> >> >> ENH: Move ImageToPathFilter from ITKReview to ITKPath >>>>>>>>>>> module. >>>>>>>>>>> >> >> BUG: Fixing ImageToPathFilter wrapping call from >>>>>>>>>>> Review Module >>>>>>>>>>> >> >> STYLE: Fix KWStyle dashboard errors >>>>>>>>>>> >> >> BUG: Fix external module BUILD_SHARED_LIBS status >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Mathieu Malaterre (1): >>>>>>>>>>> >> >> BUG: Name mangle the included expat third party >>>>>>>>>>> library. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Matthew McCormick (94): >>>>>>>>>>> >> >> ENH: Change itkSystemInformationTest to >>>>>>>>>>> itkCMakeConfigurationTest. >>>>>>>>>>> >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >>>>>>>>>>> >> >> ENH: Bump ITK version to 4.9.0. >>>>>>>>>>> >> >> BUG: Remove std::cout calls from classes. >>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>> >> >> BUG: Implement UpdateLargestPossibleRegion for >>>>>>>>>>> >> >> ImageToVTKImageFilter. >>>>>>>>>>> >> >> COMP: Add link interface specification for wrapping >>>>>>>>>>> >> >> target_link_libraries. >>>>>>>>>>> >> >> STYLE: Fix indentation in >>>>>>>>>>> itkMINCTransformIOFactory.cxx. >>>>>>>>>>> >> >> COMP: Fix MINCTransformIO factory registration. >>>>>>>>>>> >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with >>>>>>>>>>> Emscripten-1. >>>>>>>>>>> >> >> COMP: Remove unknown doxygen command in >>>>>>>>>>> AnisotropicDiffusionLBR. >>>>>>>>>>> >> >> BUG: Initialize mutex for 32 bit AtomicInt. >>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>> Linux. >>>>>>>>>>> >> >> STYLE: Rename gccxml -> castxml in >>>>>>>>>>> {idx,igenerator}.py. >>>>>>>>>>> >> >> COMP: Disable the gold linker for static builds on >>>>>>>>>>> Ubuntu 14.04. >>>>>>>>>>> >> >> ENH: Use Windows binaries for CastXML. >>>>>>>>>>> >> >> ENH: Add better scoping in igenerator.py. >>>>>>>>>>> >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + >>>>>>>>>>> MSVC. >>>>>>>>>>> >> >> BUG: LevelSetsv4 used signed char instead of char. >>>>>>>>>>> >> >> ENH: Add better scoping to idx.py. >>>>>>>>>>> >> >> COMP: Define newSize and oldSize in >>>>>>>>>>> VariableLengthVector. >>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>> >> >> ENH: Add more progress information to >>>>>>>>>>> IterativeClosestPoint2. >>>>>>>>>>> >> >> BUG: Build BridgeNumPy with Visual Studio. >>>>>>>>>>> >> >> ENH: Add ITKModuleExternal.cmake >>>>>>>>>>> >> >> COMP: Wrap Image< bool, D > for >>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>> >> >> BUG: Use CastXML binary built in Release. >>>>>>>>>>> >> >> BUG: ContinuousIndex should not be templated over >>>>>>>>>>> TCoordRep. >>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>> >> >> COMP: Address line length too long for Software Guide. >>>>>>>>>>> >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >>>>>>>>>>> >> >> BUG: Support Python 3 wrapping module initialization. >>>>>>>>>>> >> >> BUG: Update itkTemplate.py for Python 3. >>>>>>>>>>> >> >> BUG: Update itkExtras.py for Python 3. >>>>>>>>>>> >> >> BUG: Prevent Python callback addition recursion. >>>>>>>>>>> >> >> BUG: Fix test scripts for Python 3. >>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>> >> >> ENH: Allow projects to build against an external >>>>>>>>>>> module. >>>>>>>>>>> >> >> ENH: Replace CABLE_CONFIGURATION with >>>>>>>>>>> ITK_WRAPPING_PARSER. >>>>>>>>>>> >> >> ENH: Rename _cable_ to _wrappers_. >>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>> >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >>>>>>>>>>> >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >>>>>>>>>>> >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >>>>>>>>>>> >> >> ENH: Bump CastXML version to 2015-30-29. >>>>>>>>>>> >> >> ENH: Bump LLVM / Clang to 3.7.0. >>>>>>>>>>> >> >> COMP: Avoid itklibminc linking with >>>>>>>>>>> ITK_USE_SYSTEM_HDF5. >>>>>>>>>>> >> >> COMP: Add missing ITKIOImageBase dependency for >>>>>>>>>>> ITKTransformMINC. >>>>>>>>>>> >> >> COMP: Use itkSimpleNewMacro in >>>>>>>>>>> >> >> ThreadedIteratorRangePartitionerTest. >>>>>>>>>>> >> >> ENH: Add wrapping support for building modules >>>>>>>>>>> externally. >>>>>>>>>>> >> >> BUG: Fix KWStyle test paths when building a module >>>>>>>>>>> externally. >>>>>>>>>>> >> >> ENH: Add Cuberille Remote module. >>>>>>>>>>> >> >> COMP: Remove carriage returns from Cuberille remote. >>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>> >> >> ENH: Bump the MinimalPathExtraction Remote to >>>>>>>>>>> 2015-10-20. >>>>>>>>>>> >> >> COMP: Fix KernelTransform SetFixedParameters argument >>>>>>>>>>> type. >>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>> sys.path >>>>>>>>>>> >> >> Revert "COMP: Put vnl_export.h in the list of sources >>>>>>>>>>> so it gets >>>>>>>>>>> >> >> installed." >>>>>>>>>>> >> >> BUG: Revert "BUG: ConvertLabelMap with different >>>>>>>>>>> LabelMapTypes" >>>>>>>>>>> >> >> ENH: Marking wrapping CMake configuration variables >>>>>>>>>>> as advanced. >>>>>>>>>>> >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >>>>>>>>>>> >> >> COMP: Non-virtual copy attribute members in LabelMap >>>>>>>>>>> cannot have >>>>>>>>>>> >> >> override. >>>>>>>>>>> >> >> COMP: Add wrapping for >>>>>>>>>>> AdaptiveHistogramEqualizationImageFilter. >>>>>>>>>>> >> >> COMP: Add itkMacro.h to itkPromoteType.h for >>>>>>>>>>> ITK_EXCEPT. >>>>>>>>>>> >> >> ENH: Remove CMake version check in >>>>>>>>>>> ITKModuleHeaderTest.cmake >>>>>>>>>>> >> >> BUG: Improve KWStyle ExternalProject utilization. >>>>>>>>>>> >> >> ENH: Remove old KWStyle build script. >>>>>>>>>>> >> >> COMP: Address VariableLengthVector Doxygen rhs @param >>>>>>>>>>> not found. >>>>>>>>>>> >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to >>>>>>>>>>> WRAPPING_SUBMODULE_ORDER. >>>>>>>>>>> >> >> ENH: Install Python bindings into site-packages. >>>>>>>>>>> >> >> ENH: Improve readability of Python site-packages path >>>>>>>>>>> detection. >>>>>>>>>>> >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned >>>>>>>>>>> expression >>>>>>>>>>> >> >> warning. >>>>>>>>>>> >> >> BUG: ITKCommon publically depends on >>>>>>>>>>> ITKDoubleConversion. >>>>>>>>>>> >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >>>>>>>>>>> >> >> ENH: Improves names and export of module dependencies. >>>>>>>>>>> >> >> STYLE: Improve namespace bracket style in >>>>>>>>>>> itkIsConvertible. >>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>> >> >> BUG: Remove unused wrapping files. >>>>>>>>>>> >> >> BUG: Do install install wrapping development files. >>>>>>>>>>> >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >>>>>>>>>>> >> >> BUG: Remove duplicate inclusion of wrapping >>>>>>>>>>> submodules. >>>>>>>>>>> >> >> COMP: Do not use C++ style comments for Doxygen cond. >>>>>>>>>>> >> >> BUG: Fix detection of the gold linker. >>>>>>>>>>> >> >> BUG: Update Python package installation locations. >>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >>>>>>>>>>> >> >> ENH: Change BUILD_EXAMPLES default to OFF. >>>>>>>>>>> >> >> BUG: Use 'from itk import ITKCommon' in module2module >>>>>>>>>>> test. >>>>>>>>>>> >> >> COMP: Link to VTK Python when built with Kits support. >>>>>>>>>>> >> >> BUG: Install itk_minc2.h header. >>>>>>>>>>> >> >> COMP: ITKIOMINC has a public dependency on >>>>>>>>>>> ITKIOImageBase. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Michka Popoff (9): >>>>>>>>>>> >> >> ENH: Update to swig 3.0.7 >>>>>>>>>>> >> >> ENH: Do not link against specific Python library on >>>>>>>>>>> OS X >>>>>>>>>>> >> >> COMP: Fix wrapping warnings when building with >>>>>>>>>>> >> >> ITK_WRAP_IMAGE_DIMS=2 >>>>>>>>>>> >> >> COMP: Add missing wrapping for TransformBase >>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>> sys.path >>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>> 3 wrapping >>>>>>>>>>> >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>> >> >> module >>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>> 3 wrapping >>>>>>>>>>> >> >> ENH: Allow operations on Indexes and Offsets in Python >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Mikhail Isakov (1): >>>>>>>>>>> >> >> BUG: DiffusionTensor3DReconstruction segfault if no >>>>>>>>>>> baseline image >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Nick Tustison (5): >>>>>>>>>>> >> >> BUG: Set a default b-spline epsilon. >>>>>>>>>>> >> >> ENH: Adding testing for closed loop. >>>>>>>>>>> >> >> BUG: Updating B-spline classes with the same epsilon >>>>>>>>>>> strategy. >>>>>>>>>>> >> >> PERF: Switch vnl_vectors for fixed arrays. >>>>>>>>>>> >> >> ENH: Point-set registration with time-varying >>>>>>>>>>> B-spline. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Olivier Commowick (3): >>>>>>>>>>> >> >> BUG: Correct discrepancy in tridiagonal reduction wrt >>>>>>>>>>> VNL eigen >>>>>>>>>>> >> >> system >>>>>>>>>>> >> >> BUG: Correct under/overflows in vnl_math_hypot (taken >>>>>>>>>>> from pythag >>>>>>>>>>> >> >> from V3P) >>>>>>>>>>> >> >> BUG: Switch eigenvalues computation to double >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Pablo Hernandez-Cerdan (2): >>>>>>>>>>> >> >> ENH: Help class for itkFlatStructuringElement with >>>>>>>>>>> constructor >>>>>>>>>>> >> >> from >>>>>>>>>>> >> >> images. >>>>>>>>>>> >> >> COMP: Fix test errors and warnings in >>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Seun Odutola (1): >>>>>>>>>>> >> >> COMP: Fixed name clash with Apple header (check >>>>>>>>>>> Macro), renamed >>>>>>>>>>> >> >> check >>>>>>>>>>> >> >> to Check >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Shawn Waldon (1): >>>>>>>>>>> >> >> COMP: Set target OS X version in environment for >>>>>>>>>>> tools using >>>>>>>>>>> >> >> compiler >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Simon Alexander (1): >>>>>>>>>>> >> >> BUG: incorrect closest point computation >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Tobias Wood (2): >>>>>>>>>>> >> >> BUG: LBFGSB was printing messages even with debug >>>>>>>>>>> switched off. >>>>>>>>>>> >> >> BUG: Removed an unguarded print statement. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Vladimir S. FONOV (9): >>>>>>>>>>> >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >>>>>>>>>>> >> >> COMP: Changing the order of HDF5 library components >>>>>>>>>>> >> >> COMP: Splitting up IOMINC module into two parts: MINC >>>>>>>>>>> and >>>>>>>>>>> >> >> Transform >>>>>>>>>>> >> >> STYLE: updated comments to properly reference LIBMINC >>>>>>>>>>> >> >> ENH: Add script to merge upstream MINC as a subtree >>>>>>>>>>> >> >> MINC 2015-07-23 (c033d431) >>>>>>>>>>> >> >> COMP: Update MINC CMake code >>>>>>>>>>> >> >> MINC 2015-08-18 (6d7e3ba8) >>>>>>>>>>> >> >> MINC 2015-09-13 (95cd5374) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Xiaoxiao Liu (1): >>>>>>>>>>> >> >> DOC: update email address for xiaoxiao. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Zach Williamson (10): >>>>>>>>>>> >> >> BUG: Use correct libraries for ImageFusion tests >>>>>>>>>>> >> >> ENH: Consolidate Library Dependencies >>>>>>>>>>> >> >> COMP: Add a missing link to Review module >>>>>>>>>>> >> >> COMP: Use correct linking macro in DCMTK >>>>>>>>>>> >> >> BUG: Use correct libraries for TestKernel tests >>>>>>>>>>> >> >> COMP: Fix inconsistant naming of >>>>>>>>>>> GPUPDEDeformableRegistration >>>>>>>>>>> >> >> ENH: Use new linking system macros >>>>>>>>>>> >> >> PERF: Avoid searching private dependencies for >>>>>>>>>>> include directories >>>>>>>>>>> >> >> COMP: Recover missing dependencies >>>>>>>>>>> >> >> ENH: use new linking macros in Filtering module >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> ----------------------------------------------------- >>>>>>>>>>> >> >> Errors or omissions? Please fix them here: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >>>>>>>>>>> >> >> _____________________________________ >>>>>>>>>>> >> >> Powered by www.kitware.com >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Visit other Kitware open-source projects at >>>>>>>>>>> >> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Kitware offers ITK Training Courses, for more information >>>>>>>>>>> visit: >>>>>>>>>>> >> >> http://www.kitware.com/products/protraining.php >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> >>>>>>>>> >>>>>>>>>> Powered by www.kitware.com >>>>>>>>>> >>>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>>> >>>>>>>>> http://kitware.com/products/protraining.php >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>> >>>>> >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From skalexander at gmail.com Tue Dec 1 09:39:38 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 01 Dec 2015 14:39:38 +0000 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Ok, that makes sense. Would it be sensible to change the threshold for those on debug builds? On Tue, 1 Dec 2015 at 09:22 D?enan Zuki? wrote: > If you are running tests in debug, some of them are too slow and time out. > > On Tue, Dec 1, 2015 at 9:19 AM, Simon Alexander > wrote: > >> Hi Matt, >> >> So I pulled origin/master and rebuilt last night. I have different >> failures now, all by timeout: >> >> *Total Test time (real) = 6363.39 sec* >> >> *The following tests FAILED:* >> * 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo >> (Timeout)* >> * 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo >> (Timeout)* >> * 728 - >> itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout)* >> * 2025 - >> itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest (Timeout)* >> *Errors while running CTest* >> >> >> Any thoughts on what's going on there? >> >> >> On Mon, 30 Nov 2015 at 20:42 Matt McCormick >> wrote: >> >>> Hi Simon, >>> >>> I am returning from holiday, and also catching up on activity. >>> >>> >>> Hyun Jae has taken care of the KWStyle warnings and the data conversion >>> warning: >>> >>> http://review.source.kitware.com/#/c/20430/ >>> http://review.source.kitware.com/#/c/20446/ >>> >>> >>> And Dzenan and Bill have addressed Wiki examples errors: >>> >>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>> >>> >>> It is likely that the test failures on your build still remain. Did you >>> want to take them on? >>> >>> Thanks, >>> Matt >>> >>> On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? wrote: >>> >>>> Looking at the master branch is the right thing to do. I am not doing >>>> any active development regarding this right now. >>>> >>>> On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander >>> > wrote: >>>> >>>>> Hi All, >>>>> >>>>> I had hoped to be able to look at this over the weekend, but no such >>>>> luck. Is there somewhere useful I can help with it now? Not sure what >>>>> state we are in (or what branch). >>>>> >>>>> On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? wrote: >>>>> >>>>>> It turns out that all the compile errors were occurring in >>>>>> WikiExamples. I solved all except one: >>>>>> ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in >>>>>> file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line >>>>>> 23, but it should be judging from the comment on that line. >>>>>> >>>>>> For the rest, I created a pull request: >>>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>>>>> >>>>>> On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander < >>>>>> skalexander at gmail.com> wrote: >>>>>> >>>>>>> Perfect. I'm under a deadline that is likely to eat the rest of the >>>>>>> week but if that clears up I'll try and jump in earlier. >>>>>>> >>>>>>> On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? wrote: >>>>>>> >>>>>>>> OK I will work on it for an hour or two now, and I will make a >>>>>>>> branch and push it to Gerrit so whoever wants can pick up from there and >>>>>>>> keep updating it. >>>>>>>> >>>>>>>> On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander < >>>>>>>> skalexander at gmail.com> wrote: >>>>>>>> >>>>>>>>> Makes sense. At this point I am unlikely to have time to look at >>>>>>>>> this until Saturday, but have hopes for a few free hours there. >>>>>>>>> >>>>>>>>> On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Building git master from Nov 23rd with examples and testing >>>>>>>>>> enabled I get 14 compile errors in VS2015 debug x64. Should we coordinate >>>>>>>>>> our efforts in fixing them? >>>>>>>>>> >>>>>>>>>> On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander < >>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Two of the three failures look like truncation issues (like >>>>>>>>>>> https://open.cdash.org/testDetails.php?test=395263772&build=4117158 >>>>>>>>>>> ) >>>>>>>>>>> >>>>>>>>>>> The other ( >>>>>>>>>>> https://open.cdash.org/testDetails.php?test=395264938&build=4117158) >>>>>>>>>>> is less obvious. >>>>>>>>>>> >>>>>>>>>>> If I have time this evening I'll try and have a look at these. >>>>>>>>>>> >>>>>>>>>>> Is your standard test build in 32 bit ? That might explain the >>>>>>>>>>> difference if there are some underlying type assumptions, but not obvious >>>>>>>>>>> why 2015 would trigger but not 2013. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Wed, 25 Nov 2015 at 11:01 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Ah, cool! Here: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 >>>>>>>>>>>> >>>>>>>>>>>> Could you please look into the test failures? >>>>>>>>>>>> >>>>>>>>>>>> @Hyun Jae, could you please look into the KWStyle warnings? >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Matt >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander < >>>>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>>>> > Sorry, if I wasn't clear - I submitted two builds yesterday >>>>>>>>>>>> from SIMON-LAP, >>>>>>>>>>>> > (actually 3 as I wasn't sure the config was right on the >>>>>>>>>>>> first one). VS2013 >>>>>>>>>>>> > was green, three failures on VS2015 (and 18 warnings). >>>>>>>>>>>> Looks like a >>>>>>>>>>>> > truncation problem on the resuts. >>>>>>>>>>>> > >>>>>>>>>>>> > On Wed, 25 Nov 2015 at 10:51 Matt McCormick < >>>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>>> > wrote: >>>>>>>>>>>> >> >>>>>>>>>>>> >> Hi Simon, >>>>>>>>>>>> >> >>>>>>>>>>>> >> Thanks for testing. >>>>>>>>>>>> >> >>>>>>>>>>>> >> We have a Visual Studio 2015 build on the dashboard that is >>>>>>>>>>>> green: >>>>>>>>>>>> >> >>>>>>>>>>>> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >>>>>>>>>>>> >> >>>>>>>>>>>> >> Are there any different flags? Could you please submit an >>>>>>>>>>>> Experimental >>>>>>>>>>>> >> build? >>>>>>>>>>>> >> >>>>>>>>>>>> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test >>>>>>>>>>>> -T Submit -C >>>>>>>>>>>> >> Release >>>>>>>>>>>> >> >>>>>>>>>>>> >> from a fresh build tree. >>>>>>>>>>>> >> >>>>>>>>>>>> >> Thanks, >>>>>>>>>>>> >> Matt >>>>>>>>>>>> >> >>>>>>>>>>>> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander < >>>>>>>>>>>> skalexander at gmail.com> >>>>>>>>>>>> >> wrote: >>>>>>>>>>>> >> > Looks like a few problems with x64 build on visual studio >>>>>>>>>>>> 2015 - do you >>>>>>>>>>>> >> > have >>>>>>>>>>>> >> > a test machine in this configuration? >>>>>>>>>>>> >> > >>>>>>>>>>>> >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick < >>>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>>> >> > wrote: >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> On behalf of the Insight Toolkit community, we are proud >>>>>>>>>>>> to announce >>>>>>>>>>>> >> >> that >>>>>>>>>>>> >> >> ITK 4.9 release candidate 1 has been tagged and is >>>>>>>>>>>> available for >>>>>>>>>>>> >> >> testing! >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Please take this opportunity to test the new features in >>>>>>>>>>>> the release >>>>>>>>>>>> >> >> candidate. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> To obtain the source code, >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> git clone http://itk.org/ITK.git >>>>>>>>>>>> >> >> cd ITK >>>>>>>>>>>> >> >> git checkout -q --detach v4.9rc01 >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> For more details, please see the Git documentation [1]. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> A few selected highlights for this release: >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * New Remote modules: the Cuberille module for smooth >>>>>>>>>>>> generation of >>>>>>>>>>>> >> >> meshes >>>>>>>>>>>> >> >> from binary segmentation images, and the >>>>>>>>>>>> AnisotropicDiffusionLBR module >>>>>>>>>>>> >> >> improved edge-preserving smoothing. >>>>>>>>>>>> >> >> * Build your own ITK module outside the source tree, add >>>>>>>>>>>> continuous >>>>>>>>>>>> >> >> integration testing on GitHub, and easily add Python >>>>>>>>>>>> wrapping for your >>>>>>>>>>>> >> >> C++ >>>>>>>>>>>> >> >> algorithms. >>>>>>>>>>>> >> >> * Python wrapping, including Python 3, builds faster with >>>>>>>>>>>> a more >>>>>>>>>>>> >> >> standard >>>>>>>>>>>> >> >> installation >>>>>>>>>>>> >> >> * Improved performance of itk::Image::GetPixel and >>>>>>>>>>>> operations on >>>>>>>>>>>> >> >> itk::VariableLengthVector?s >>>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>>> private / >>>>>>>>>>>> >> >> compile / >>>>>>>>>>>> >> >> test >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Please test the release candidate and share your >>>>>>>>>>>> experiences on the >>>>>>>>>>>> >> >> mailing list, issue tracker, and Gerrit Code Review. The >>>>>>>>>>>> new module >>>>>>>>>>>> >> >> dependency specification mechanism may unearth missing >>>>>>>>>>>> dependencies for >>>>>>>>>>>> >> >> projects that use ITK COMPONENTS with the CMake >>>>>>>>>>>> find_package command. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> An Experimental build, which demonstrates how the test >>>>>>>>>>>> suite performs >>>>>>>>>>>> >> >> on >>>>>>>>>>>> >> >> your local build system, can be submitted to the >>>>>>>>>>>> dashboard [2] with: >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> mkdir ../ITK-build >>>>>>>>>>>> >> >> cd ../ITK-build >>>>>>>>>>>> >> >> cmake ../ITK >>>>>>>>>>>> >> >> ctest -j 4 -M Experimental -T Configure -T Build -T >>>>>>>>>>>> Test -T Submit >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Visual Studio builds must also add ?-C Release? to the >>>>>>>>>>>> ctest command. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Notify the mailing list if there are any unexpected >>>>>>>>>>>> failures. Testing >>>>>>>>>>>> >> >> your own applications against the RC is also appreciated. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Congratulations and well done to the 35 contributors to >>>>>>>>>>>> this release. >>>>>>>>>>>> >> >> We >>>>>>>>>>>> >> >> would especially like to recognize the new contributors: >>>>>>>>>>>> Mikhail >>>>>>>>>>>> >> >> Isakov, >>>>>>>>>>>> >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias >>>>>>>>>>>> Wood, Seun >>>>>>>>>>>> >> >> Odutola, >>>>>>>>>>>> >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, >>>>>>>>>>>> Pablo >>>>>>>>>>>> >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach >>>>>>>>>>>> Williamson, >>>>>>>>>>>> >> >> Luc >>>>>>>>>>>> >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> The final release is scheduled for mid-December. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> [1] http://www.itk.org/Wiki/ITK/Git >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> [2] http://open.cdash.org/index.php?project=Insight >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> New Features >>>>>>>>>>>> >> >> --------------------- >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Wrapping improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Python 3 supported >>>>>>>>>>>> >> >> * Wrapping builds much faster due to CastXML binaries >>>>>>>>>>>> >> >> * LandmarkBasedTransformInitializer now wrapped >>>>>>>>>>>> >> >> * NumPy bridge with VisualStudio >>>>>>>>>>>> >> >> * Wrapping for the MinimalPathExtraction module >>>>>>>>>>>> >> >> * Wrapping is now installed into Python?s site-packages >>>>>>>>>>>> directory in >>>>>>>>>>>> >> >> the >>>>>>>>>>>> >> >> ?itk? package >>>>>>>>>>>> >> >> * Wrapping package size is decreased >>>>>>>>>>>> >> >> * Better package portability on Mac OSX >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> New Remote Modules >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Cuberille >>>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>>> http://hdl.handle.net/10380/3186 >>>>>>>>>>>> >> >> * AnisotropicDiffusionLBR >>>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>>> http://hdl.handle.net/10380/3505 >>>>>>>>>>>> >> >> * Web browser reproducibility: >>>>>>>>>>>> >> >> http://www.kitware.com/blog/home/post/942 >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Core Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * External Modules can now be developed outside of the >>>>>>>>>>>> ITK source tree >>>>>>>>>>>> >> >> and >>>>>>>>>>>> >> >> on GitHub >>>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/997 >>>>>>>>>>>> >> >> * New utilities in itk::Math: >>>>>>>>>>>> >> >> * AlmostEquals >>>>>>>>>>>> >> >> * NotAlmostEquals >>>>>>>>>>>> >> >> * ExactlyEquals >>>>>>>>>>>> >> >> * NotExactlyEquals >>>>>>>>>>>> >> >> * New itk::NumericTraits >>>>>>>>>>>> >> >> * IsInteger >>>>>>>>>>>> >> >> * IsSigned >>>>>>>>>>>> >> >> * Improved C++11 support >>>>>>>>>>>> >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >>>>>>>>>>>> >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >>>>>>>>>>>> >> >> * Improved capabilities of itk::ResourceProbe and >>>>>>>>>>>> >> >> itk::ResourceProbesCollectorBase >>>>>>>>>>>> >> >> * Improve numerical stability in VNL eigen system >>>>>>>>>>>> estimation >>>>>>>>>>>> >> >> * itksys_ios:: and itksys_stl:: have been remove (use >>>>>>>>>>>> std::) >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Filtering Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>>> >> >> * WarpImageFilter support VectorImage?s >>>>>>>>>>>> >> >> * ConvertLabelMap supports different LabelMap types >>>>>>>>>>>> >> >> * ImageToPathFilter moved from the ITKReview to the >>>>>>>>>>>> ITKPath module >>>>>>>>>>>> >> >> * itk::MovingHistogramImageFilter moved to the >>>>>>>>>>>> ITKImageFilterBase >>>>>>>>>>>> >> >> module >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Registration Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Build Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>>> private / >>>>>>>>>>>> >> >> compile / >>>>>>>>>>>> >> >> test >>>>>>>>>>>> >> >> * BUILD_EXAMPLES CMake option is now OFF by default >>>>>>>>>>>> >> >> * Option to export all library symbols on Windows: >>>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/939 >>>>>>>>>>>> >> >> * Expat third party library is now name mangled >>>>>>>>>>>> >> >> * Many more modules can be built as shared libraries >>>>>>>>>>>> >> >> * KWStyle is automatically built and configured when >>>>>>>>>>>> tests are built >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Performance Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds >>>>>>>>>>>> members for >>>>>>>>>>>> >> >> metaprogramming >>>>>>>>>>>> >> >> * itk::mpl::{TrueType,FalseType} >>>>>>>>>>>> >> >> * itk::mpl::{If,Not,And,Or,Xor} >>>>>>>>>>>> >> >> * itk::mpl::EnableIf >>>>>>>>>>>> >> >> * itk::mpl::IsBaseOf >>>>>>>>>>>> >> >> * itk::mpl::IsConvertible >>>>>>>>>>>> >> >> * itk::mpl::IsNumber >>>>>>>>>>>> >> >> * itk::mpl::IsSame >>>>>>>>>>>> >> >> * itk::mpl::PromoteType >>>>>>>>>>>> >> >> * Image::GetPixel performance improvements >>>>>>>>>>>> >> >> * Many itk::VariableLengthVector performance improvements >>>>>>>>>>>> >> >> * AdaptiveHistogramEqualization uses a moving histogram >>>>>>>>>>>> >> >> * WarpImageFilter performance improvements >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Documentation Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx >>>>>>>>>>>> Examples >>>>>>>>>>>> >> >> * ITK Software Guide improvements >>>>>>>>>>>> >> >> * How to use Python wrapping >>>>>>>>>>>> >> >> * How to create an ITK module >>>>>>>>>>>> >> >> * Improvements to segmentation examples >>>>>>>>>>>> >> >> * Expanded Canny edge detection example >>>>>>>>>>>> >> >> * Expanded tree container example >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Third Party Library Updates >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * FFTW updated to latest upstream >>>>>>>>>>>> >> >> * Build with recent OpenCV 2 and 3 >>>>>>>>>>>> >> >> * Build with the latest VTK >>>>>>>>>>>> >> >> * PNG update to the latest upstream >>>>>>>>>>>> >> >> * GDCM updated to the latest upstream >>>>>>>>>>>> >> >> * KWSys updated to the latest upstream >>>>>>>>>>>> >> >> * MINC updated to the latest upstream >>>>>>>>>>>> >> >> * SWIG updated to the latest upstream >>>>>>>>>>>> >> >> * Third party PNG and MINC are now Git subtrees >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Style improvements -- ITK gets more stylish with every >>>>>>>>>>>> release! >>>>>>>>>>>> >> >> >>>>>>>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Private copy constructors and operator= use >>>>>>>>>>>> ITK_DELETE_FUNCTION >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Improved code coverage -- we are at 84.9%! >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * *Lots* of important bug fixes >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * And much more! See details in the log below. >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Changes from v4.8.0..v4.9rc01 >>>>>>>>>>>> >> >> -------------------------------------------- >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Abhishek Tiwari (1): >>>>>>>>>>>> >> >> BUG: "tmpImageIndex" not initialized to 0. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Adam Snyder (1): >>>>>>>>>>>> >> >> PERF: Reworked MMI Threading using a per-thread >>>>>>>>>>>> buffer >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Alexander Leinoff (6): >>>>>>>>>>>> >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >>>>>>>>>>>> >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be >>>>>>>>>>>> resolved. >>>>>>>>>>>> >> >> ENH: Adds ExactlyEquals and NotExactlyEquals >>>>>>>>>>>> functions to >>>>>>>>>>>> >> >> itkMath.h >>>>>>>>>>>> >> >> COMP: Removes floating-point equality checks >>>>>>>>>>>> >> >> ENH: COMP: Adds support for complex values to >>>>>>>>>>>> Math::AlmostEquals >>>>>>>>>>>> >> >> ENH: Updates fftw dependency >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Arnaud Gelas (5): >>>>>>>>>>>> >> >> COMP: fix warning (unused local typedef) >>>>>>>>>>>> >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >>>>>>>>>>>> >> >> DOC: add doxgen documentation for >>>>>>>>>>>> >> >> BinaryImageToLevelSetImageAdaptor >>>>>>>>>>>> >> >> ENH: add tests to exercise >>>>>>>>>>>> itk::ThreadedIteratorRangePartitioner >>>>>>>>>>>> >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Betsy McPhail (1): >>>>>>>>>>>> >> >> BUG: Improve buffer alignment in OctreeNode . >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Bill Hoffman (2): >>>>>>>>>>>> >> >> ENH: Use new CMake Windows export symbol dll feature. >>>>>>>>>>>> >> >> COMP: Put vnl_export.h in the list of sources so it >>>>>>>>>>>> gets >>>>>>>>>>>> >> >> installed. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Bill Lorensen (4): >>>>>>>>>>>> >> >> COMP: VTkGlue linker errors >>>>>>>>>>>> >> >> BUG: Inappropriate use of AlmostEquals >>>>>>>>>>>> >> >> ENH: Bump tag for wiki examples >>>>>>>>>>>> >> >> ENH: Better layout strategy >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Brad King (3): >>>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>>> itksys_ios::* >>>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>>> itksys_stl::* >>>>>>>>>>>> >> >> ENH: Update CMake Policy settings in >>>>>>>>>>>> Testing/TestExternal project >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Bradley Lowekamp (31): >>>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>>> construction >>>>>>>>>>>> >> >> ENH: Enable base classes for templates of landmark >>>>>>>>>>>> initializer >>>>>>>>>>>> >> >> STYLE: Use "Swap" for ITK member name >>>>>>>>>>>> >> >> BUG: Demonstrate Eigen analysis failure >>>>>>>>>>>> >> >> BUG: Fix computation of Eigen analysis >>>>>>>>>>>> >> >> ENH: Update DiscreteHessianGaussian Test baseline >>>>>>>>>>>> >> >> ENH: Correctly demonstrate float point Eigen failure >>>>>>>>>>>> >> >> ENH: compile vnl_math_hypot, and use at least double >>>>>>>>>>>> >> >> ENH: Adding initial update script from used libpng >>>>>>>>>>>> version. >>>>>>>>>>>> >> >> ENH: removing non-subtree files for itkpng >>>>>>>>>>>> >> >> ENH: Ported ITK changes for building to subtree >>>>>>>>>>>> merged code >>>>>>>>>>>> >> >> ENH: Update libpng update script for v1.6.9 >>>>>>>>>>>> >> >> BUG: Use ParameterValueType for computation of >>>>>>>>>>>> landmark affine >>>>>>>>>>>> >> >> ENH: Wrap LandmarkBasedTransformInitializer >>>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>>> >> >> ENH: Update itkpng zlib, configuration, and rename >>>>>>>>>>>> >> >> ENH: Update itkpng name mangling >>>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>>> ReferenceImage >>>>>>>>>>>> >> >> ivar >>>>>>>>>>>> >> >> BUG: Increase tolerance for >>>>>>>>>>>> PhysicsBasedNonRigidRegistrationMethod >>>>>>>>>>>> >> >> BUG: Demonstrate side effect on registration due to >>>>>>>>>>>> BSplineScatter >>>>>>>>>>>> >> >> change >>>>>>>>>>>> >> >> ENH: Move MovingHistogramImageFilter base classes to >>>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>>> construction >>>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>>> ReferenceImage >>>>>>>>>>>> >> >> ivar >>>>>>>>>>>> >> >> ENH: Optimize AdaptiveHistogramEqualization with >>>>>>>>>>>> MovingHistogram >>>>>>>>>>>> >> >> base >>>>>>>>>>>> >> >> COMP: address sign unsigned comparison warning >>>>>>>>>>>> >> >> COMP: Address signed unsigned comparison warning >>>>>>>>>>>> >> >> COMP: Address unused member variable and methods in >>>>>>>>>>>> anonymous ns >>>>>>>>>>>> >> >> BUG: Fix segfault when with empty IsolatedWatershed >>>>>>>>>>>> Threshold >>>>>>>>>>>> >> >> range >>>>>>>>>>>> >> >> BUG: Adjust intensity tolerance for >>>>>>>>>>>> PhysicsBasedNonRigid test >>>>>>>>>>>> >> >> BUG: Reduce number of targets with MSVC >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Davis Vigneault (7): >>>>>>>>>>>> >> >> DOC: Minor improvements to segmentation examples. >>>>>>>>>>>> >> >> DOC: Expanded Canny Edge Detection Example >>>>>>>>>>>> >> >> DOC: Expanded TreeContainer Example >>>>>>>>>>>> >> >> COMP: Warnings in itkVTKImageExport when compiling >>>>>>>>>>>> with c++11 >>>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>>> c++11 >>>>>>>>>>>> >> >> COMP: Update Git Tag for Subdivision Module >>>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>>> c++11 >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> D?enan Zuki? (1): >>>>>>>>>>>> >> >> STYLE: better formatting of the "usage" message >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Eugene Prilepin (1): >>>>>>>>>>>> >> >> BUG: Fix a template name formation in python >>>>>>>>>>>> wrappings >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Floris Berendsen (1): >>>>>>>>>>>> >> >> STYLE: Improve naming conventions in comments. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Hans Johnson (29): >>>>>>>>>>>> >> >> STYLE: Instrument for FixedParameters typedef >>>>>>>>>>>> >> >> BUG: Demonstrate DisplacementTransformFailure >>>>>>>>>>>> >> >> BUG: FixedParameters should be double precision >>>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>>> >> >> ENH: Provide consistent floating point comparisons >>>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>>> >> >> PERF: Remove floating point as sentinal value >>>>>>>>>>>> >> >> COMP: Const correctness needs to be maintained >>>>>>>>>>>> >> >> BUG: Preserve backwards compatibility >>>>>>>>>>>> >> >> DOC: Provide consistent naming in comments >>>>>>>>>>>> >> >> ENH: Conversion between transform type tolerance >>>>>>>>>>>> >> >> STYLE: Prefer initialization to assignment >>>>>>>>>>>> >> >> ENH: Missing ITK_OVERRIDE >>>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>>> >> >> COMP: Add missing ITK_OVERRIDE >>>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>>> >> >> ENH: C++11 allows for rigorous =delete >>>>>>>>>>>> >> >> COMP: Remove unnecessary failing assert test >>>>>>>>>>>> >> >> ENH: Ignore internal files for the Clion editor >>>>>>>>>>>> >> >> COMP: Fix VNL compilation for wider C++11 support >>>>>>>>>>>> >> >> BUG: In configuration test need to mirror code >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Hyun Jae Kang (27): >>>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>>> >> >> BUG: Avoid an unexpected output of static_cast >>>>>>>>>>>> >> >> BUG: Update python example codes for >>>>>>>>>>>> ImageRegistration >>>>>>>>>>>> >> >> BUG: Retrieve the missed wrap file >>>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>>> in VTK file >>>>>>>>>>>> >> >> header. >>>>>>>>>>>> >> >> BUG: Fix HDF5 CMake configuration with VS2015 >>>>>>>>>>>> >> >> BUG: Fix a compilation issue on ITK4 with FFTW and >>>>>>>>>>>> shared >>>>>>>>>>>> >> >> libraries >>>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>>> Mac OS X >>>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>>> in VTK file >>>>>>>>>>>> >> >> header. >>>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>>> >> >> ENH: Add automatic KWStyle build and configuration >>>>>>>>>>>> setup >>>>>>>>>>>> >> >> COMP: KWStyle shadow, format-nonliteral and >>>>>>>>>>>> autological-compare >>>>>>>>>>>> >> >> warning. >>>>>>>>>>>> >> >> COMP: Fixed the warning messages from itkGPU Module >>>>>>>>>>>> >> >> COMP: Fixed a warning message of unused-private-field >>>>>>>>>>>> >> >> COMP: Apply latest version of KWStyle >>>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>>> messages >>>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>>> messages >>>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on Windows >>>>>>>>>>>> >> >> ENH: Update itkResourceProbe to calculate >>>>>>>>>>>> statistical data >>>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on VS14 >>>>>>>>>>>> >> >> COMP: Fixed 'std::sqrt' : ambiguous call to >>>>>>>>>>>> overloaded function >>>>>>>>>>>> >> >> ENH: Update the Report() function of >>>>>>>>>>>> >> >> itkResourceProbesCollectorBase >>>>>>>>>>>> >> >> COMP: Fix data-conversion warning message on >>>>>>>>>>>> itkResourceProbe >>>>>>>>>>>> >> >> COMP: Fix additional warning messages of KWStyle >>>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Jon Haitz Legarreta (6): >>>>>>>>>>>> >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >>>>>>>>>>>> >> >> BUG: Fix compilation issues for >>>>>>>>>>>> StatisticsUniqueLabelMapFilterTest >>>>>>>>>>>> >> >> BUG: Fix comparison issues for >>>>>>>>>>>> itkStatisticsUniqueLabelMapFilter >>>>>>>>>>>> >> >> BUG: Test for StatisticsUniqueLabelMapFilter >>>>>>>>>>>> stability >>>>>>>>>>>> >> >> ENH: Add test for >>>>>>>>>>>> itkParametricStpaceToImageSpaceFilter >>>>>>>>>>>> >> >> ENH: Improve code coverage for >>>>>>>>>>>> >> >> itkParametricSpaceToImageSpaceMeshFilter >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Julien Michel (1): >>>>>>>>>>>> >> >> ENH: Support of VectorImage as template parameters >>>>>>>>>>>> for >>>>>>>>>>>> >> >> WarpImageFilter >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Junjie Bai (2): >>>>>>>>>>>> >> >> BUG: ConvertLabelMap with different LabelMapTypes >>>>>>>>>>>> >> >> BUG: LabelObject CopyAttribute support different >>>>>>>>>>>> LabelObject type >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> KWSys Robot (4): >>>>>>>>>>>> >> >> KWSys 2015-07-10 (c9336bcf) >>>>>>>>>>>> >> >> KWSys 2015-07-30 (f63febb7) >>>>>>>>>>>> >> >> KWSys 2015-08-24 (cdaf522c) >>>>>>>>>>>> >> >> KWSys 2015-08-28 (dc3fdd7f) >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> LIBPNG Upstream (2): >>>>>>>>>>>> >> >> PNG 2009-04-06 (e68f5a36) >>>>>>>>>>>> >> >> PNG 2014-02-05 (3e753eb8) >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Laurentiu Nicola (2): >>>>>>>>>>>> >> >> PERF: Avoid temporary smartptr in >>>>>>>>>>>> ProcessObject::GetInput >>>>>>>>>>>> >> >> PERF: Optimize WarpImageFilter by avoiding refcount >>>>>>>>>>>> bouncing >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Luc Hermitte (8): >>>>>>>>>>>> >> >> PERF: itk::Image::GetPixel() performance improvment. >>>>>>>>>>>> >> >> PERF: Performance enhancements on >>>>>>>>>>>> VariableLengthVectors 1/... >>>>>>>>>>>> >> >> ENH: Dependencies on itkVariableLengthVector.h >>>>>>>>>>>> reduced >>>>>>>>>>>> >> >> BUG: Error in VariableLengthVector Unit Tests >>>>>>>>>>>> >> >> PERF: Performance enhancements on VLV 2/... >>>>>>>>>>>> >> >> PERF: Performances enhancements on VLV 3/... >>>>>>>>>>>> >> >> COMP: Fix signed/unsigned warnings >>>>>>>>>>>> >> >> BUG: std::copy/fill on empty VLV >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Lucas Gandel (4): >>>>>>>>>>>> >> >> ENH: Move ImageToPathFilter from ITKReview to >>>>>>>>>>>> ITKPath module. >>>>>>>>>>>> >> >> BUG: Fixing ImageToPathFilter wrapping call from >>>>>>>>>>>> Review Module >>>>>>>>>>>> >> >> STYLE: Fix KWStyle dashboard errors >>>>>>>>>>>> >> >> BUG: Fix external module BUILD_SHARED_LIBS status >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Mathieu Malaterre (1): >>>>>>>>>>>> >> >> BUG: Name mangle the included expat third party >>>>>>>>>>>> library. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Matthew McCormick (94): >>>>>>>>>>>> >> >> ENH: Change itkSystemInformationTest to >>>>>>>>>>>> itkCMakeConfigurationTest. >>>>>>>>>>>> >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >>>>>>>>>>>> >> >> ENH: Bump ITK version to 4.9.0. >>>>>>>>>>>> >> >> BUG: Remove std::cout calls from classes. >>>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>>> >> >> BUG: Implement UpdateLargestPossibleRegion for >>>>>>>>>>>> >> >> ImageToVTKImageFilter. >>>>>>>>>>>> >> >> COMP: Add link interface specification for wrapping >>>>>>>>>>>> >> >> target_link_libraries. >>>>>>>>>>>> >> >> STYLE: Fix indentation in >>>>>>>>>>>> itkMINCTransformIOFactory.cxx. >>>>>>>>>>>> >> >> COMP: Fix MINCTransformIO factory registration. >>>>>>>>>>>> >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with >>>>>>>>>>>> Emscripten-1. >>>>>>>>>>>> >> >> COMP: Remove unknown doxygen command in >>>>>>>>>>>> AnisotropicDiffusionLBR. >>>>>>>>>>>> >> >> BUG: Initialize mutex for 32 bit AtomicInt. >>>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>>> Linux. >>>>>>>>>>>> >> >> STYLE: Rename gccxml -> castxml in >>>>>>>>>>>> {idx,igenerator}.py. >>>>>>>>>>>> >> >> COMP: Disable the gold linker for static builds on >>>>>>>>>>>> Ubuntu 14.04. >>>>>>>>>>>> >> >> ENH: Use Windows binaries for CastXML. >>>>>>>>>>>> >> >> ENH: Add better scoping in igenerator.py. >>>>>>>>>>>> >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja >>>>>>>>>>>> + MSVC. >>>>>>>>>>>> >> >> BUG: LevelSetsv4 used signed char instead of char. >>>>>>>>>>>> >> >> ENH: Add better scoping to idx.py. >>>>>>>>>>>> >> >> COMP: Define newSize and oldSize in >>>>>>>>>>>> VariableLengthVector. >>>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>>> >> >> ENH: Add more progress information to >>>>>>>>>>>> IterativeClosestPoint2. >>>>>>>>>>>> >> >> BUG: Build BridgeNumPy with Visual Studio. >>>>>>>>>>>> >> >> ENH: Add ITKModuleExternal.cmake >>>>>>>>>>>> >> >> COMP: Wrap Image< bool, D > for >>>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>>> >> >> BUG: Use CastXML binary built in Release. >>>>>>>>>>>> >> >> BUG: ContinuousIndex should not be templated over >>>>>>>>>>>> TCoordRep. >>>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>>> >> >> COMP: Address line length too long for Software >>>>>>>>>>>> Guide. >>>>>>>>>>>> >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >>>>>>>>>>>> >> >> BUG: Support Python 3 wrapping module initialization. >>>>>>>>>>>> >> >> BUG: Update itkTemplate.py for Python 3. >>>>>>>>>>>> >> >> BUG: Update itkExtras.py for Python 3. >>>>>>>>>>>> >> >> BUG: Prevent Python callback addition recursion. >>>>>>>>>>>> >> >> BUG: Fix test scripts for Python 3. >>>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>>> >> >> ENH: Allow projects to build against an external >>>>>>>>>>>> module. >>>>>>>>>>>> >> >> ENH: Replace CABLE_CONFIGURATION with >>>>>>>>>>>> ITK_WRAPPING_PARSER. >>>>>>>>>>>> >> >> ENH: Rename _cable_ to _wrappers_. >>>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>>> >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >>>>>>>>>>>> >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >>>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >>>>>>>>>>>> >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >>>>>>>>>>>> >> >> ENH: Bump CastXML version to 2015-30-29. >>>>>>>>>>>> >> >> ENH: Bump LLVM / Clang to 3.7.0. >>>>>>>>>>>> >> >> COMP: Avoid itklibminc linking with >>>>>>>>>>>> ITK_USE_SYSTEM_HDF5. >>>>>>>>>>>> >> >> COMP: Add missing ITKIOImageBase dependency for >>>>>>>>>>>> ITKTransformMINC. >>>>>>>>>>>> >> >> COMP: Use itkSimpleNewMacro in >>>>>>>>>>>> >> >> ThreadedIteratorRangePartitionerTest. >>>>>>>>>>>> >> >> ENH: Add wrapping support for building modules >>>>>>>>>>>> externally. >>>>>>>>>>>> >> >> BUG: Fix KWStyle test paths when building a module >>>>>>>>>>>> externally. >>>>>>>>>>>> >> >> ENH: Add Cuberille Remote module. >>>>>>>>>>>> >> >> COMP: Remove carriage returns from Cuberille remote. >>>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>>> >> >> ENH: Bump the MinimalPathExtraction Remote to >>>>>>>>>>>> 2015-10-20. >>>>>>>>>>>> >> >> COMP: Fix KernelTransform SetFixedParameters >>>>>>>>>>>> argument type. >>>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>>> sys.path >>>>>>>>>>>> >> >> Revert "COMP: Put vnl_export.h in the list of >>>>>>>>>>>> sources so it gets >>>>>>>>>>>> >> >> installed." >>>>>>>>>>>> >> >> BUG: Revert "BUG: ConvertLabelMap with different >>>>>>>>>>>> LabelMapTypes" >>>>>>>>>>>> >> >> ENH: Marking wrapping CMake configuration variables >>>>>>>>>>>> as advanced. >>>>>>>>>>>> >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >>>>>>>>>>>> >> >> COMP: Non-virtual copy attribute members in LabelMap >>>>>>>>>>>> cannot have >>>>>>>>>>>> >> >> override. >>>>>>>>>>>> >> >> COMP: Add wrapping for >>>>>>>>>>>> AdaptiveHistogramEqualizationImageFilter. >>>>>>>>>>>> >> >> COMP: Add itkMacro.h to itkPromoteType.h for >>>>>>>>>>>> ITK_EXCEPT. >>>>>>>>>>>> >> >> ENH: Remove CMake version check in >>>>>>>>>>>> ITKModuleHeaderTest.cmake >>>>>>>>>>>> >> >> BUG: Improve KWStyle ExternalProject utilization. >>>>>>>>>>>> >> >> ENH: Remove old KWStyle build script. >>>>>>>>>>>> >> >> COMP: Address VariableLengthVector Doxygen rhs >>>>>>>>>>>> @param not found. >>>>>>>>>>>> >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to >>>>>>>>>>>> WRAPPING_SUBMODULE_ORDER. >>>>>>>>>>>> >> >> ENH: Install Python bindings into site-packages. >>>>>>>>>>>> >> >> ENH: Improve readability of Python site-packages >>>>>>>>>>>> path detection. >>>>>>>>>>>> >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned >>>>>>>>>>>> expression >>>>>>>>>>>> >> >> warning. >>>>>>>>>>>> >> >> BUG: ITKCommon publically depends on >>>>>>>>>>>> ITKDoubleConversion. >>>>>>>>>>>> >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >>>>>>>>>>>> >> >> ENH: Improves names and export of module >>>>>>>>>>>> dependencies. >>>>>>>>>>>> >> >> STYLE: Improve namespace bracket style in >>>>>>>>>>>> itkIsConvertible. >>>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>>> >> >> BUG: Remove unused wrapping files. >>>>>>>>>>>> >> >> BUG: Do install install wrapping development files. >>>>>>>>>>>> >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >>>>>>>>>>>> >> >> BUG: Remove duplicate inclusion of wrapping >>>>>>>>>>>> submodules. >>>>>>>>>>>> >> >> COMP: Do not use C++ style comments for Doxygen cond. >>>>>>>>>>>> >> >> BUG: Fix detection of the gold linker. >>>>>>>>>>>> >> >> BUG: Update Python package installation locations. >>>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >>>>>>>>>>>> >> >> ENH: Change BUILD_EXAMPLES default to OFF. >>>>>>>>>>>> >> >> BUG: Use 'from itk import ITKCommon' in >>>>>>>>>>>> module2module test. >>>>>>>>>>>> >> >> COMP: Link to VTK Python when built with Kits >>>>>>>>>>>> support. >>>>>>>>>>>> >> >> BUG: Install itk_minc2.h header. >>>>>>>>>>>> >> >> COMP: ITKIOMINC has a public dependency on >>>>>>>>>>>> ITKIOImageBase. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Michka Popoff (9): >>>>>>>>>>>> >> >> ENH: Update to swig 3.0.7 >>>>>>>>>>>> >> >> ENH: Do not link against specific Python library on >>>>>>>>>>>> OS X >>>>>>>>>>>> >> >> COMP: Fix wrapping warnings when building with >>>>>>>>>>>> >> >> ITK_WRAP_IMAGE_DIMS=2 >>>>>>>>>>>> >> >> COMP: Add missing wrapping for TransformBase >>>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>>> sys.path >>>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>>> 3 wrapping >>>>>>>>>>>> >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >>>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>>> >> >> module >>>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>>> 3 wrapping >>>>>>>>>>>> >> >> ENH: Allow operations on Indexes and Offsets in >>>>>>>>>>>> Python >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Mikhail Isakov (1): >>>>>>>>>>>> >> >> BUG: DiffusionTensor3DReconstruction segfault if no >>>>>>>>>>>> baseline image >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Nick Tustison (5): >>>>>>>>>>>> >> >> BUG: Set a default b-spline epsilon. >>>>>>>>>>>> >> >> ENH: Adding testing for closed loop. >>>>>>>>>>>> >> >> BUG: Updating B-spline classes with the same >>>>>>>>>>>> epsilon strategy. >>>>>>>>>>>> >> >> PERF: Switch vnl_vectors for fixed arrays. >>>>>>>>>>>> >> >> ENH: Point-set registration with time-varying >>>>>>>>>>>> B-spline. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Olivier Commowick (3): >>>>>>>>>>>> >> >> BUG: Correct discrepancy in tridiagonal reduction >>>>>>>>>>>> wrt VNL eigen >>>>>>>>>>>> >> >> system >>>>>>>>>>>> >> >> BUG: Correct under/overflows in vnl_math_hypot >>>>>>>>>>>> (taken from pythag >>>>>>>>>>>> >> >> from V3P) >>>>>>>>>>>> >> >> BUG: Switch eigenvalues computation to double >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Pablo Hernandez-Cerdan (2): >>>>>>>>>>>> >> >> ENH: Help class for itkFlatStructuringElement with >>>>>>>>>>>> constructor >>>>>>>>>>>> >> >> from >>>>>>>>>>>> >> >> images. >>>>>>>>>>>> >> >> COMP: Fix test errors and warnings in >>>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Seun Odutola (1): >>>>>>>>>>>> >> >> COMP: Fixed name clash with Apple header (check >>>>>>>>>>>> Macro), renamed >>>>>>>>>>>> >> >> check >>>>>>>>>>>> >> >> to Check >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Shawn Waldon (1): >>>>>>>>>>>> >> >> COMP: Set target OS X version in environment for >>>>>>>>>>>> tools using >>>>>>>>>>>> >> >> compiler >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Simon Alexander (1): >>>>>>>>>>>> >> >> BUG: incorrect closest point computation >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Tobias Wood (2): >>>>>>>>>>>> >> >> BUG: LBFGSB was printing messages even with debug >>>>>>>>>>>> switched off. >>>>>>>>>>>> >> >> BUG: Removed an unguarded print statement. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Vladimir S. FONOV (9): >>>>>>>>>>>> >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >>>>>>>>>>>> >> >> COMP: Changing the order of HDF5 library components >>>>>>>>>>>> >> >> COMP: Splitting up IOMINC module into two parts: >>>>>>>>>>>> MINC and >>>>>>>>>>>> >> >> Transform >>>>>>>>>>>> >> >> STYLE: updated comments to properly reference LIBMINC >>>>>>>>>>>> >> >> ENH: Add script to merge upstream MINC as a subtree >>>>>>>>>>>> >> >> MINC 2015-07-23 (c033d431) >>>>>>>>>>>> >> >> COMP: Update MINC CMake code >>>>>>>>>>>> >> >> MINC 2015-08-18 (6d7e3ba8) >>>>>>>>>>>> >> >> MINC 2015-09-13 (95cd5374) >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Xiaoxiao Liu (1): >>>>>>>>>>>> >> >> DOC: update email address for xiaoxiao. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Zach Williamson (10): >>>>>>>>>>>> >> >> BUG: Use correct libraries for ImageFusion tests >>>>>>>>>>>> >> >> ENH: Consolidate Library Dependencies >>>>>>>>>>>> >> >> COMP: Add a missing link to Review module >>>>>>>>>>>> >> >> COMP: Use correct linking macro in DCMTK >>>>>>>>>>>> >> >> BUG: Use correct libraries for TestKernel tests >>>>>>>>>>>> >> >> COMP: Fix inconsistant naming of >>>>>>>>>>>> GPUPDEDeformableRegistration >>>>>>>>>>>> >> >> ENH: Use new linking system macros >>>>>>>>>>>> >> >> PERF: Avoid searching private dependencies for >>>>>>>>>>>> include directories >>>>>>>>>>>> >> >> COMP: Recover missing dependencies >>>>>>>>>>>> >> >> ENH: use new linking macros in Filtering module >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> ----------------------------------------------------- >>>>>>>>>>>> >> >> Errors or omissions? Please fix them here: >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >>>>>>>>>>>> >> >> _____________________________________ >>>>>>>>>>>> >> >> Powered by www.kitware.com >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Visit other Kitware open-source projects at >>>>>>>>>>>> >> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Kitware offers ITK Training Courses, for more information >>>>>>>>>>>> visit: >>>>>>>>>>>> >> >> http://www.kitware.com/products/protraining.php >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Powered by www.kitware.com >>>>>>>>>>> >>>>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>>>> >>>>>>>>>> http://kitware.com/products/protraining.php >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>> >>>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From skalexander at gmail.com Tue Dec 1 09:39:38 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 01 Dec 2015 14:39:38 +0000 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Ok, that makes sense. Would it be sensible to change the threshold for those on debug builds? On Tue, 1 Dec 2015 at 09:22 D?enan Zuki? wrote: > If you are running tests in debug, some of them are too slow and time out. > > On Tue, Dec 1, 2015 at 9:19 AM, Simon Alexander > wrote: > >> Hi Matt, >> >> So I pulled origin/master and rebuilt last night. I have different >> failures now, all by timeout: >> >> *Total Test time (real) = 6363.39 sec* >> >> *The following tests FAILED:* >> * 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo >> (Timeout)* >> * 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo >> (Timeout)* >> * 728 - >> itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout)* >> * 2025 - >> itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest (Timeout)* >> *Errors while running CTest* >> >> >> Any thoughts on what's going on there? >> >> >> On Mon, 30 Nov 2015 at 20:42 Matt McCormick >> wrote: >> >>> Hi Simon, >>> >>> I am returning from holiday, and also catching up on activity. >>> >>> >>> Hyun Jae has taken care of the KWStyle warnings and the data conversion >>> warning: >>> >>> http://review.source.kitware.com/#/c/20430/ >>> http://review.source.kitware.com/#/c/20446/ >>> >>> >>> And Dzenan and Bill have addressed Wiki examples errors: >>> >>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>> >>> >>> It is likely that the test failures on your build still remain. Did you >>> want to take them on? >>> >>> Thanks, >>> Matt >>> >>> On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? wrote: >>> >>>> Looking at the master branch is the right thing to do. I am not doing >>>> any active development regarding this right now. >>>> >>>> On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander >>> > wrote: >>>> >>>>> Hi All, >>>>> >>>>> I had hoped to be able to look at this over the weekend, but no such >>>>> luck. Is there somewhere useful I can help with it now? Not sure what >>>>> state we are in (or what branch). >>>>> >>>>> On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? wrote: >>>>> >>>>>> It turns out that all the compile errors were occurring in >>>>>> WikiExamples. I solved all except one: >>>>>> ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in >>>>>> file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line >>>>>> 23, but it should be judging from the comment on that line. >>>>>> >>>>>> For the rest, I created a pull request: >>>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>>>>> >>>>>> On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander < >>>>>> skalexander at gmail.com> wrote: >>>>>> >>>>>>> Perfect. I'm under a deadline that is likely to eat the rest of the >>>>>>> week but if that clears up I'll try and jump in earlier. >>>>>>> >>>>>>> On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? wrote: >>>>>>> >>>>>>>> OK I will work on it for an hour or two now, and I will make a >>>>>>>> branch and push it to Gerrit so whoever wants can pick up from there and >>>>>>>> keep updating it. >>>>>>>> >>>>>>>> On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander < >>>>>>>> skalexander at gmail.com> wrote: >>>>>>>> >>>>>>>>> Makes sense. At this point I am unlikely to have time to look at >>>>>>>>> this until Saturday, but have hopes for a few free hours there. >>>>>>>>> >>>>>>>>> On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Building git master from Nov 23rd with examples and testing >>>>>>>>>> enabled I get 14 compile errors in VS2015 debug x64. Should we coordinate >>>>>>>>>> our efforts in fixing them? >>>>>>>>>> >>>>>>>>>> On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander < >>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Two of the three failures look like truncation issues (like >>>>>>>>>>> https://open.cdash.org/testDetails.php?test=395263772&build=4117158 >>>>>>>>>>> ) >>>>>>>>>>> >>>>>>>>>>> The other ( >>>>>>>>>>> https://open.cdash.org/testDetails.php?test=395264938&build=4117158) >>>>>>>>>>> is less obvious. >>>>>>>>>>> >>>>>>>>>>> If I have time this evening I'll try and have a look at these. >>>>>>>>>>> >>>>>>>>>>> Is your standard test build in 32 bit ? That might explain the >>>>>>>>>>> difference if there are some underlying type assumptions, but not obvious >>>>>>>>>>> why 2015 would trigger but not 2013. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Wed, 25 Nov 2015 at 11:01 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Ah, cool! Here: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 >>>>>>>>>>>> >>>>>>>>>>>> Could you please look into the test failures? >>>>>>>>>>>> >>>>>>>>>>>> @Hyun Jae, could you please look into the KWStyle warnings? >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Matt >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander < >>>>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>>>> > Sorry, if I wasn't clear - I submitted two builds yesterday >>>>>>>>>>>> from SIMON-LAP, >>>>>>>>>>>> > (actually 3 as I wasn't sure the config was right on the >>>>>>>>>>>> first one). VS2013 >>>>>>>>>>>> > was green, three failures on VS2015 (and 18 warnings). >>>>>>>>>>>> Looks like a >>>>>>>>>>>> > truncation problem on the resuts. >>>>>>>>>>>> > >>>>>>>>>>>> > On Wed, 25 Nov 2015 at 10:51 Matt McCormick < >>>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>>> > wrote: >>>>>>>>>>>> >> >>>>>>>>>>>> >> Hi Simon, >>>>>>>>>>>> >> >>>>>>>>>>>> >> Thanks for testing. >>>>>>>>>>>> >> >>>>>>>>>>>> >> We have a Visual Studio 2015 build on the dashboard that is >>>>>>>>>>>> green: >>>>>>>>>>>> >> >>>>>>>>>>>> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >>>>>>>>>>>> >> >>>>>>>>>>>> >> Are there any different flags? Could you please submit an >>>>>>>>>>>> Experimental >>>>>>>>>>>> >> build? >>>>>>>>>>>> >> >>>>>>>>>>>> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test >>>>>>>>>>>> -T Submit -C >>>>>>>>>>>> >> Release >>>>>>>>>>>> >> >>>>>>>>>>>> >> from a fresh build tree. >>>>>>>>>>>> >> >>>>>>>>>>>> >> Thanks, >>>>>>>>>>>> >> Matt >>>>>>>>>>>> >> >>>>>>>>>>>> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander < >>>>>>>>>>>> skalexander at gmail.com> >>>>>>>>>>>> >> wrote: >>>>>>>>>>>> >> > Looks like a few problems with x64 build on visual studio >>>>>>>>>>>> 2015 - do you >>>>>>>>>>>> >> > have >>>>>>>>>>>> >> > a test machine in this configuration? >>>>>>>>>>>> >> > >>>>>>>>>>>> >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick < >>>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>>> >> > wrote: >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> On behalf of the Insight Toolkit community, we are proud >>>>>>>>>>>> to announce >>>>>>>>>>>> >> >> that >>>>>>>>>>>> >> >> ITK 4.9 release candidate 1 has been tagged and is >>>>>>>>>>>> available for >>>>>>>>>>>> >> >> testing! >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Please take this opportunity to test the new features in >>>>>>>>>>>> the release >>>>>>>>>>>> >> >> candidate. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> To obtain the source code, >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> git clone http://itk.org/ITK.git >>>>>>>>>>>> >> >> cd ITK >>>>>>>>>>>> >> >> git checkout -q --detach v4.9rc01 >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> For more details, please see the Git documentation [1]. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> A few selected highlights for this release: >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * New Remote modules: the Cuberille module for smooth >>>>>>>>>>>> generation of >>>>>>>>>>>> >> >> meshes >>>>>>>>>>>> >> >> from binary segmentation images, and the >>>>>>>>>>>> AnisotropicDiffusionLBR module >>>>>>>>>>>> >> >> improved edge-preserving smoothing. >>>>>>>>>>>> >> >> * Build your own ITK module outside the source tree, add >>>>>>>>>>>> continuous >>>>>>>>>>>> >> >> integration testing on GitHub, and easily add Python >>>>>>>>>>>> wrapping for your >>>>>>>>>>>> >> >> C++ >>>>>>>>>>>> >> >> algorithms. >>>>>>>>>>>> >> >> * Python wrapping, including Python 3, builds faster with >>>>>>>>>>>> a more >>>>>>>>>>>> >> >> standard >>>>>>>>>>>> >> >> installation >>>>>>>>>>>> >> >> * Improved performance of itk::Image::GetPixel and >>>>>>>>>>>> operations on >>>>>>>>>>>> >> >> itk::VariableLengthVector?s >>>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>>> private / >>>>>>>>>>>> >> >> compile / >>>>>>>>>>>> >> >> test >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Please test the release candidate and share your >>>>>>>>>>>> experiences on the >>>>>>>>>>>> >> >> mailing list, issue tracker, and Gerrit Code Review. The >>>>>>>>>>>> new module >>>>>>>>>>>> >> >> dependency specification mechanism may unearth missing >>>>>>>>>>>> dependencies for >>>>>>>>>>>> >> >> projects that use ITK COMPONENTS with the CMake >>>>>>>>>>>> find_package command. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> An Experimental build, which demonstrates how the test >>>>>>>>>>>> suite performs >>>>>>>>>>>> >> >> on >>>>>>>>>>>> >> >> your local build system, can be submitted to the >>>>>>>>>>>> dashboard [2] with: >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> mkdir ../ITK-build >>>>>>>>>>>> >> >> cd ../ITK-build >>>>>>>>>>>> >> >> cmake ../ITK >>>>>>>>>>>> >> >> ctest -j 4 -M Experimental -T Configure -T Build -T >>>>>>>>>>>> Test -T Submit >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Visual Studio builds must also add ?-C Release? to the >>>>>>>>>>>> ctest command. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Notify the mailing list if there are any unexpected >>>>>>>>>>>> failures. Testing >>>>>>>>>>>> >> >> your own applications against the RC is also appreciated. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Congratulations and well done to the 35 contributors to >>>>>>>>>>>> this release. >>>>>>>>>>>> >> >> We >>>>>>>>>>>> >> >> would especially like to recognize the new contributors: >>>>>>>>>>>> Mikhail >>>>>>>>>>>> >> >> Isakov, >>>>>>>>>>>> >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias >>>>>>>>>>>> Wood, Seun >>>>>>>>>>>> >> >> Odutola, >>>>>>>>>>>> >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, >>>>>>>>>>>> Pablo >>>>>>>>>>>> >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach >>>>>>>>>>>> Williamson, >>>>>>>>>>>> >> >> Luc >>>>>>>>>>>> >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> The final release is scheduled for mid-December. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> [1] http://www.itk.org/Wiki/ITK/Git >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> [2] http://open.cdash.org/index.php?project=Insight >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> New Features >>>>>>>>>>>> >> >> --------------------- >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Wrapping improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Python 3 supported >>>>>>>>>>>> >> >> * Wrapping builds much faster due to CastXML binaries >>>>>>>>>>>> >> >> * LandmarkBasedTransformInitializer now wrapped >>>>>>>>>>>> >> >> * NumPy bridge with VisualStudio >>>>>>>>>>>> >> >> * Wrapping for the MinimalPathExtraction module >>>>>>>>>>>> >> >> * Wrapping is now installed into Python?s site-packages >>>>>>>>>>>> directory in >>>>>>>>>>>> >> >> the >>>>>>>>>>>> >> >> ?itk? package >>>>>>>>>>>> >> >> * Wrapping package size is decreased >>>>>>>>>>>> >> >> * Better package portability on Mac OSX >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> New Remote Modules >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Cuberille >>>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>>> http://hdl.handle.net/10380/3186 >>>>>>>>>>>> >> >> * AnisotropicDiffusionLBR >>>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>>> http://hdl.handle.net/10380/3505 >>>>>>>>>>>> >> >> * Web browser reproducibility: >>>>>>>>>>>> >> >> http://www.kitware.com/blog/home/post/942 >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Core Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * External Modules can now be developed outside of the >>>>>>>>>>>> ITK source tree >>>>>>>>>>>> >> >> and >>>>>>>>>>>> >> >> on GitHub >>>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/997 >>>>>>>>>>>> >> >> * New utilities in itk::Math: >>>>>>>>>>>> >> >> * AlmostEquals >>>>>>>>>>>> >> >> * NotAlmostEquals >>>>>>>>>>>> >> >> * ExactlyEquals >>>>>>>>>>>> >> >> * NotExactlyEquals >>>>>>>>>>>> >> >> * New itk::NumericTraits >>>>>>>>>>>> >> >> * IsInteger >>>>>>>>>>>> >> >> * IsSigned >>>>>>>>>>>> >> >> * Improved C++11 support >>>>>>>>>>>> >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >>>>>>>>>>>> >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >>>>>>>>>>>> >> >> * Improved capabilities of itk::ResourceProbe and >>>>>>>>>>>> >> >> itk::ResourceProbesCollectorBase >>>>>>>>>>>> >> >> * Improve numerical stability in VNL eigen system >>>>>>>>>>>> estimation >>>>>>>>>>>> >> >> * itksys_ios:: and itksys_stl:: have been remove (use >>>>>>>>>>>> std::) >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Filtering Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>>> >> >> * WarpImageFilter support VectorImage?s >>>>>>>>>>>> >> >> * ConvertLabelMap supports different LabelMap types >>>>>>>>>>>> >> >> * ImageToPathFilter moved from the ITKReview to the >>>>>>>>>>>> ITKPath module >>>>>>>>>>>> >> >> * itk::MovingHistogramImageFilter moved to the >>>>>>>>>>>> ITKImageFilterBase >>>>>>>>>>>> >> >> module >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Registration Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Build Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>>> private / >>>>>>>>>>>> >> >> compile / >>>>>>>>>>>> >> >> test >>>>>>>>>>>> >> >> * BUILD_EXAMPLES CMake option is now OFF by default >>>>>>>>>>>> >> >> * Option to export all library symbols on Windows: >>>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/939 >>>>>>>>>>>> >> >> * Expat third party library is now name mangled >>>>>>>>>>>> >> >> * Many more modules can be built as shared libraries >>>>>>>>>>>> >> >> * KWStyle is automatically built and configured when >>>>>>>>>>>> tests are built >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Performance Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds >>>>>>>>>>>> members for >>>>>>>>>>>> >> >> metaprogramming >>>>>>>>>>>> >> >> * itk::mpl::{TrueType,FalseType} >>>>>>>>>>>> >> >> * itk::mpl::{If,Not,And,Or,Xor} >>>>>>>>>>>> >> >> * itk::mpl::EnableIf >>>>>>>>>>>> >> >> * itk::mpl::IsBaseOf >>>>>>>>>>>> >> >> * itk::mpl::IsConvertible >>>>>>>>>>>> >> >> * itk::mpl::IsNumber >>>>>>>>>>>> >> >> * itk::mpl::IsSame >>>>>>>>>>>> >> >> * itk::mpl::PromoteType >>>>>>>>>>>> >> >> * Image::GetPixel performance improvements >>>>>>>>>>>> >> >> * Many itk::VariableLengthVector performance improvements >>>>>>>>>>>> >> >> * AdaptiveHistogramEqualization uses a moving histogram >>>>>>>>>>>> >> >> * WarpImageFilter performance improvements >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Documentation Improvements >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx >>>>>>>>>>>> Examples >>>>>>>>>>>> >> >> * ITK Software Guide improvements >>>>>>>>>>>> >> >> * How to use Python wrapping >>>>>>>>>>>> >> >> * How to create an ITK module >>>>>>>>>>>> >> >> * Improvements to segmentation examples >>>>>>>>>>>> >> >> * Expanded Canny edge detection example >>>>>>>>>>>> >> >> * Expanded tree container example >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Third Party Library Updates >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * FFTW updated to latest upstream >>>>>>>>>>>> >> >> * Build with recent OpenCV 2 and 3 >>>>>>>>>>>> >> >> * Build with the latest VTK >>>>>>>>>>>> >> >> * PNG update to the latest upstream >>>>>>>>>>>> >> >> * GDCM updated to the latest upstream >>>>>>>>>>>> >> >> * KWSys updated to the latest upstream >>>>>>>>>>>> >> >> * MINC updated to the latest upstream >>>>>>>>>>>> >> >> * SWIG updated to the latest upstream >>>>>>>>>>>> >> >> * Third party PNG and MINC are now Git subtrees >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Style improvements -- ITK gets more stylish with every >>>>>>>>>>>> release! >>>>>>>>>>>> >> >> >>>>>>>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * Private copy constructors and operator= use >>>>>>>>>>>> ITK_DELETE_FUNCTION >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Improved code coverage -- we are at 84.9%! >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * *Lots* of important bug fixes >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> * And much more! See details in the log below. >>>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Changes from v4.8.0..v4.9rc01 >>>>>>>>>>>> >> >> -------------------------------------------- >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Abhishek Tiwari (1): >>>>>>>>>>>> >> >> BUG: "tmpImageIndex" not initialized to 0. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Adam Snyder (1): >>>>>>>>>>>> >> >> PERF: Reworked MMI Threading using a per-thread >>>>>>>>>>>> buffer >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Alexander Leinoff (6): >>>>>>>>>>>> >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >>>>>>>>>>>> >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be >>>>>>>>>>>> resolved. >>>>>>>>>>>> >> >> ENH: Adds ExactlyEquals and NotExactlyEquals >>>>>>>>>>>> functions to >>>>>>>>>>>> >> >> itkMath.h >>>>>>>>>>>> >> >> COMP: Removes floating-point equality checks >>>>>>>>>>>> >> >> ENH: COMP: Adds support for complex values to >>>>>>>>>>>> Math::AlmostEquals >>>>>>>>>>>> >> >> ENH: Updates fftw dependency >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Arnaud Gelas (5): >>>>>>>>>>>> >> >> COMP: fix warning (unused local typedef) >>>>>>>>>>>> >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >>>>>>>>>>>> >> >> DOC: add doxgen documentation for >>>>>>>>>>>> >> >> BinaryImageToLevelSetImageAdaptor >>>>>>>>>>>> >> >> ENH: add tests to exercise >>>>>>>>>>>> itk::ThreadedIteratorRangePartitioner >>>>>>>>>>>> >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Betsy McPhail (1): >>>>>>>>>>>> >> >> BUG: Improve buffer alignment in OctreeNode . >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Bill Hoffman (2): >>>>>>>>>>>> >> >> ENH: Use new CMake Windows export symbol dll feature. >>>>>>>>>>>> >> >> COMP: Put vnl_export.h in the list of sources so it >>>>>>>>>>>> gets >>>>>>>>>>>> >> >> installed. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Bill Lorensen (4): >>>>>>>>>>>> >> >> COMP: VTkGlue linker errors >>>>>>>>>>>> >> >> BUG: Inappropriate use of AlmostEquals >>>>>>>>>>>> >> >> ENH: Bump tag for wiki examples >>>>>>>>>>>> >> >> ENH: Better layout strategy >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Brad King (3): >>>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>>> itksys_ios::* >>>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>>> itksys_stl::* >>>>>>>>>>>> >> >> ENH: Update CMake Policy settings in >>>>>>>>>>>> Testing/TestExternal project >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Bradley Lowekamp (31): >>>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>>> construction >>>>>>>>>>>> >> >> ENH: Enable base classes for templates of landmark >>>>>>>>>>>> initializer >>>>>>>>>>>> >> >> STYLE: Use "Swap" for ITK member name >>>>>>>>>>>> >> >> BUG: Demonstrate Eigen analysis failure >>>>>>>>>>>> >> >> BUG: Fix computation of Eigen analysis >>>>>>>>>>>> >> >> ENH: Update DiscreteHessianGaussian Test baseline >>>>>>>>>>>> >> >> ENH: Correctly demonstrate float point Eigen failure >>>>>>>>>>>> >> >> ENH: compile vnl_math_hypot, and use at least double >>>>>>>>>>>> >> >> ENH: Adding initial update script from used libpng >>>>>>>>>>>> version. >>>>>>>>>>>> >> >> ENH: removing non-subtree files for itkpng >>>>>>>>>>>> >> >> ENH: Ported ITK changes for building to subtree >>>>>>>>>>>> merged code >>>>>>>>>>>> >> >> ENH: Update libpng update script for v1.6.9 >>>>>>>>>>>> >> >> BUG: Use ParameterValueType for computation of >>>>>>>>>>>> landmark affine >>>>>>>>>>>> >> >> ENH: Wrap LandmarkBasedTransformInitializer >>>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>>> >> >> ENH: Update itkpng zlib, configuration, and rename >>>>>>>>>>>> >> >> ENH: Update itkpng name mangling >>>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>>> ReferenceImage >>>>>>>>>>>> >> >> ivar >>>>>>>>>>>> >> >> BUG: Increase tolerance for >>>>>>>>>>>> PhysicsBasedNonRigidRegistrationMethod >>>>>>>>>>>> >> >> BUG: Demonstrate side effect on registration due to >>>>>>>>>>>> BSplineScatter >>>>>>>>>>>> >> >> change >>>>>>>>>>>> >> >> ENH: Move MovingHistogramImageFilter base classes to >>>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>>> construction >>>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>>> ReferenceImage >>>>>>>>>>>> >> >> ivar >>>>>>>>>>>> >> >> ENH: Optimize AdaptiveHistogramEqualization with >>>>>>>>>>>> MovingHistogram >>>>>>>>>>>> >> >> base >>>>>>>>>>>> >> >> COMP: address sign unsigned comparison warning >>>>>>>>>>>> >> >> COMP: Address signed unsigned comparison warning >>>>>>>>>>>> >> >> COMP: Address unused member variable and methods in >>>>>>>>>>>> anonymous ns >>>>>>>>>>>> >> >> BUG: Fix segfault when with empty IsolatedWatershed >>>>>>>>>>>> Threshold >>>>>>>>>>>> >> >> range >>>>>>>>>>>> >> >> BUG: Adjust intensity tolerance for >>>>>>>>>>>> PhysicsBasedNonRigid test >>>>>>>>>>>> >> >> BUG: Reduce number of targets with MSVC >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Davis Vigneault (7): >>>>>>>>>>>> >> >> DOC: Minor improvements to segmentation examples. >>>>>>>>>>>> >> >> DOC: Expanded Canny Edge Detection Example >>>>>>>>>>>> >> >> DOC: Expanded TreeContainer Example >>>>>>>>>>>> >> >> COMP: Warnings in itkVTKImageExport when compiling >>>>>>>>>>>> with c++11 >>>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>>> c++11 >>>>>>>>>>>> >> >> COMP: Update Git Tag for Subdivision Module >>>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>>> c++11 >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> D?enan Zuki? (1): >>>>>>>>>>>> >> >> STYLE: better formatting of the "usage" message >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Eugene Prilepin (1): >>>>>>>>>>>> >> >> BUG: Fix a template name formation in python >>>>>>>>>>>> wrappings >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Floris Berendsen (1): >>>>>>>>>>>> >> >> STYLE: Improve naming conventions in comments. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Hans Johnson (29): >>>>>>>>>>>> >> >> STYLE: Instrument for FixedParameters typedef >>>>>>>>>>>> >> >> BUG: Demonstrate DisplacementTransformFailure >>>>>>>>>>>> >> >> BUG: FixedParameters should be double precision >>>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>>> >> >> ENH: Provide consistent floating point comparisons >>>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>>> >> >> PERF: Remove floating point as sentinal value >>>>>>>>>>>> >> >> COMP: Const correctness needs to be maintained >>>>>>>>>>>> >> >> BUG: Preserve backwards compatibility >>>>>>>>>>>> >> >> DOC: Provide consistent naming in comments >>>>>>>>>>>> >> >> ENH: Conversion between transform type tolerance >>>>>>>>>>>> >> >> STYLE: Prefer initialization to assignment >>>>>>>>>>>> >> >> ENH: Missing ITK_OVERRIDE >>>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>>> >> >> COMP: Add missing ITK_OVERRIDE >>>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>>> >> >> ENH: C++11 allows for rigorous =delete >>>>>>>>>>>> >> >> COMP: Remove unnecessary failing assert test >>>>>>>>>>>> >> >> ENH: Ignore internal files for the Clion editor >>>>>>>>>>>> >> >> COMP: Fix VNL compilation for wider C++11 support >>>>>>>>>>>> >> >> BUG: In configuration test need to mirror code >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Hyun Jae Kang (27): >>>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>>> >> >> BUG: Avoid an unexpected output of static_cast >>>>>>>>>>>> >> >> BUG: Update python example codes for >>>>>>>>>>>> ImageRegistration >>>>>>>>>>>> >> >> BUG: Retrieve the missed wrap file >>>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>>> in VTK file >>>>>>>>>>>> >> >> header. >>>>>>>>>>>> >> >> BUG: Fix HDF5 CMake configuration with VS2015 >>>>>>>>>>>> >> >> BUG: Fix a compilation issue on ITK4 with FFTW and >>>>>>>>>>>> shared >>>>>>>>>>>> >> >> libraries >>>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>>> Mac OS X >>>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>>> in VTK file >>>>>>>>>>>> >> >> header. >>>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>>> >> >> ENH: Add automatic KWStyle build and configuration >>>>>>>>>>>> setup >>>>>>>>>>>> >> >> COMP: KWStyle shadow, format-nonliteral and >>>>>>>>>>>> autological-compare >>>>>>>>>>>> >> >> warning. >>>>>>>>>>>> >> >> COMP: Fixed the warning messages from itkGPU Module >>>>>>>>>>>> >> >> COMP: Fixed a warning message of unused-private-field >>>>>>>>>>>> >> >> COMP: Apply latest version of KWStyle >>>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>>> messages >>>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>>> messages >>>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on Windows >>>>>>>>>>>> >> >> ENH: Update itkResourceProbe to calculate >>>>>>>>>>>> statistical data >>>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on VS14 >>>>>>>>>>>> >> >> COMP: Fixed 'std::sqrt' : ambiguous call to >>>>>>>>>>>> overloaded function >>>>>>>>>>>> >> >> ENH: Update the Report() function of >>>>>>>>>>>> >> >> itkResourceProbesCollectorBase >>>>>>>>>>>> >> >> COMP: Fix data-conversion warning message on >>>>>>>>>>>> itkResourceProbe >>>>>>>>>>>> >> >> COMP: Fix additional warning messages of KWStyle >>>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Jon Haitz Legarreta (6): >>>>>>>>>>>> >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >>>>>>>>>>>> >> >> BUG: Fix compilation issues for >>>>>>>>>>>> StatisticsUniqueLabelMapFilterTest >>>>>>>>>>>> >> >> BUG: Fix comparison issues for >>>>>>>>>>>> itkStatisticsUniqueLabelMapFilter >>>>>>>>>>>> >> >> BUG: Test for StatisticsUniqueLabelMapFilter >>>>>>>>>>>> stability >>>>>>>>>>>> >> >> ENH: Add test for >>>>>>>>>>>> itkParametricStpaceToImageSpaceFilter >>>>>>>>>>>> >> >> ENH: Improve code coverage for >>>>>>>>>>>> >> >> itkParametricSpaceToImageSpaceMeshFilter >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Julien Michel (1): >>>>>>>>>>>> >> >> ENH: Support of VectorImage as template parameters >>>>>>>>>>>> for >>>>>>>>>>>> >> >> WarpImageFilter >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Junjie Bai (2): >>>>>>>>>>>> >> >> BUG: ConvertLabelMap with different LabelMapTypes >>>>>>>>>>>> >> >> BUG: LabelObject CopyAttribute support different >>>>>>>>>>>> LabelObject type >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> KWSys Robot (4): >>>>>>>>>>>> >> >> KWSys 2015-07-10 (c9336bcf) >>>>>>>>>>>> >> >> KWSys 2015-07-30 (f63febb7) >>>>>>>>>>>> >> >> KWSys 2015-08-24 (cdaf522c) >>>>>>>>>>>> >> >> KWSys 2015-08-28 (dc3fdd7f) >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> LIBPNG Upstream (2): >>>>>>>>>>>> >> >> PNG 2009-04-06 (e68f5a36) >>>>>>>>>>>> >> >> PNG 2014-02-05 (3e753eb8) >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Laurentiu Nicola (2): >>>>>>>>>>>> >> >> PERF: Avoid temporary smartptr in >>>>>>>>>>>> ProcessObject::GetInput >>>>>>>>>>>> >> >> PERF: Optimize WarpImageFilter by avoiding refcount >>>>>>>>>>>> bouncing >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Luc Hermitte (8): >>>>>>>>>>>> >> >> PERF: itk::Image::GetPixel() performance improvment. >>>>>>>>>>>> >> >> PERF: Performance enhancements on >>>>>>>>>>>> VariableLengthVectors 1/... >>>>>>>>>>>> >> >> ENH: Dependencies on itkVariableLengthVector.h >>>>>>>>>>>> reduced >>>>>>>>>>>> >> >> BUG: Error in VariableLengthVector Unit Tests >>>>>>>>>>>> >> >> PERF: Performance enhancements on VLV 2/... >>>>>>>>>>>> >> >> PERF: Performances enhancements on VLV 3/... >>>>>>>>>>>> >> >> COMP: Fix signed/unsigned warnings >>>>>>>>>>>> >> >> BUG: std::copy/fill on empty VLV >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Lucas Gandel (4): >>>>>>>>>>>> >> >> ENH: Move ImageToPathFilter from ITKReview to >>>>>>>>>>>> ITKPath module. >>>>>>>>>>>> >> >> BUG: Fixing ImageToPathFilter wrapping call from >>>>>>>>>>>> Review Module >>>>>>>>>>>> >> >> STYLE: Fix KWStyle dashboard errors >>>>>>>>>>>> >> >> BUG: Fix external module BUILD_SHARED_LIBS status >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Mathieu Malaterre (1): >>>>>>>>>>>> >> >> BUG: Name mangle the included expat third party >>>>>>>>>>>> library. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Matthew McCormick (94): >>>>>>>>>>>> >> >> ENH: Change itkSystemInformationTest to >>>>>>>>>>>> itkCMakeConfigurationTest. >>>>>>>>>>>> >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >>>>>>>>>>>> >> >> ENH: Bump ITK version to 4.9.0. >>>>>>>>>>>> >> >> BUG: Remove std::cout calls from classes. >>>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>>> >> >> BUG: Implement UpdateLargestPossibleRegion for >>>>>>>>>>>> >> >> ImageToVTKImageFilter. >>>>>>>>>>>> >> >> COMP: Add link interface specification for wrapping >>>>>>>>>>>> >> >> target_link_libraries. >>>>>>>>>>>> >> >> STYLE: Fix indentation in >>>>>>>>>>>> itkMINCTransformIOFactory.cxx. >>>>>>>>>>>> >> >> COMP: Fix MINCTransformIO factory registration. >>>>>>>>>>>> >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with >>>>>>>>>>>> Emscripten-1. >>>>>>>>>>>> >> >> COMP: Remove unknown doxygen command in >>>>>>>>>>>> AnisotropicDiffusionLBR. >>>>>>>>>>>> >> >> BUG: Initialize mutex for 32 bit AtomicInt. >>>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>>> Linux. >>>>>>>>>>>> >> >> STYLE: Rename gccxml -> castxml in >>>>>>>>>>>> {idx,igenerator}.py. >>>>>>>>>>>> >> >> COMP: Disable the gold linker for static builds on >>>>>>>>>>>> Ubuntu 14.04. >>>>>>>>>>>> >> >> ENH: Use Windows binaries for CastXML. >>>>>>>>>>>> >> >> ENH: Add better scoping in igenerator.py. >>>>>>>>>>>> >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja >>>>>>>>>>>> + MSVC. >>>>>>>>>>>> >> >> BUG: LevelSetsv4 used signed char instead of char. >>>>>>>>>>>> >> >> ENH: Add better scoping to idx.py. >>>>>>>>>>>> >> >> COMP: Define newSize and oldSize in >>>>>>>>>>>> VariableLengthVector. >>>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>>> >> >> ENH: Add more progress information to >>>>>>>>>>>> IterativeClosestPoint2. >>>>>>>>>>>> >> >> BUG: Build BridgeNumPy with Visual Studio. >>>>>>>>>>>> >> >> ENH: Add ITKModuleExternal.cmake >>>>>>>>>>>> >> >> COMP: Wrap Image< bool, D > for >>>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>>> >> >> BUG: Use CastXML binary built in Release. >>>>>>>>>>>> >> >> BUG: ContinuousIndex should not be templated over >>>>>>>>>>>> TCoordRep. >>>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>>> >> >> COMP: Address line length too long for Software >>>>>>>>>>>> Guide. >>>>>>>>>>>> >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >>>>>>>>>>>> >> >> BUG: Support Python 3 wrapping module initialization. >>>>>>>>>>>> >> >> BUG: Update itkTemplate.py for Python 3. >>>>>>>>>>>> >> >> BUG: Update itkExtras.py for Python 3. >>>>>>>>>>>> >> >> BUG: Prevent Python callback addition recursion. >>>>>>>>>>>> >> >> BUG: Fix test scripts for Python 3. >>>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>>> >> >> ENH: Allow projects to build against an external >>>>>>>>>>>> module. >>>>>>>>>>>> >> >> ENH: Replace CABLE_CONFIGURATION with >>>>>>>>>>>> ITK_WRAPPING_PARSER. >>>>>>>>>>>> >> >> ENH: Rename _cable_ to _wrappers_. >>>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>>> >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >>>>>>>>>>>> >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >>>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >>>>>>>>>>>> >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >>>>>>>>>>>> >> >> ENH: Bump CastXML version to 2015-30-29. >>>>>>>>>>>> >> >> ENH: Bump LLVM / Clang to 3.7.0. >>>>>>>>>>>> >> >> COMP: Avoid itklibminc linking with >>>>>>>>>>>> ITK_USE_SYSTEM_HDF5. >>>>>>>>>>>> >> >> COMP: Add missing ITKIOImageBase dependency for >>>>>>>>>>>> ITKTransformMINC. >>>>>>>>>>>> >> >> COMP: Use itkSimpleNewMacro in >>>>>>>>>>>> >> >> ThreadedIteratorRangePartitionerTest. >>>>>>>>>>>> >> >> ENH: Add wrapping support for building modules >>>>>>>>>>>> externally. >>>>>>>>>>>> >> >> BUG: Fix KWStyle test paths when building a module >>>>>>>>>>>> externally. >>>>>>>>>>>> >> >> ENH: Add Cuberille Remote module. >>>>>>>>>>>> >> >> COMP: Remove carriage returns from Cuberille remote. >>>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>>> >> >> ENH: Bump the MinimalPathExtraction Remote to >>>>>>>>>>>> 2015-10-20. >>>>>>>>>>>> >> >> COMP: Fix KernelTransform SetFixedParameters >>>>>>>>>>>> argument type. >>>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>>> sys.path >>>>>>>>>>>> >> >> Revert "COMP: Put vnl_export.h in the list of >>>>>>>>>>>> sources so it gets >>>>>>>>>>>> >> >> installed." >>>>>>>>>>>> >> >> BUG: Revert "BUG: ConvertLabelMap with different >>>>>>>>>>>> LabelMapTypes" >>>>>>>>>>>> >> >> ENH: Marking wrapping CMake configuration variables >>>>>>>>>>>> as advanced. >>>>>>>>>>>> >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >>>>>>>>>>>> >> >> COMP: Non-virtual copy attribute members in LabelMap >>>>>>>>>>>> cannot have >>>>>>>>>>>> >> >> override. >>>>>>>>>>>> >> >> COMP: Add wrapping for >>>>>>>>>>>> AdaptiveHistogramEqualizationImageFilter. >>>>>>>>>>>> >> >> COMP: Add itkMacro.h to itkPromoteType.h for >>>>>>>>>>>> ITK_EXCEPT. >>>>>>>>>>>> >> >> ENH: Remove CMake version check in >>>>>>>>>>>> ITKModuleHeaderTest.cmake >>>>>>>>>>>> >> >> BUG: Improve KWStyle ExternalProject utilization. >>>>>>>>>>>> >> >> ENH: Remove old KWStyle build script. >>>>>>>>>>>> >> >> COMP: Address VariableLengthVector Doxygen rhs >>>>>>>>>>>> @param not found. >>>>>>>>>>>> >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to >>>>>>>>>>>> WRAPPING_SUBMODULE_ORDER. >>>>>>>>>>>> >> >> ENH: Install Python bindings into site-packages. >>>>>>>>>>>> >> >> ENH: Improve readability of Python site-packages >>>>>>>>>>>> path detection. >>>>>>>>>>>> >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned >>>>>>>>>>>> expression >>>>>>>>>>>> >> >> warning. >>>>>>>>>>>> >> >> BUG: ITKCommon publically depends on >>>>>>>>>>>> ITKDoubleConversion. >>>>>>>>>>>> >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >>>>>>>>>>>> >> >> ENH: Improves names and export of module >>>>>>>>>>>> dependencies. >>>>>>>>>>>> >> >> STYLE: Improve namespace bracket style in >>>>>>>>>>>> itkIsConvertible. >>>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>>> >> >> BUG: Remove unused wrapping files. >>>>>>>>>>>> >> >> BUG: Do install install wrapping development files. >>>>>>>>>>>> >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >>>>>>>>>>>> >> >> BUG: Remove duplicate inclusion of wrapping >>>>>>>>>>>> submodules. >>>>>>>>>>>> >> >> COMP: Do not use C++ style comments for Doxygen cond. >>>>>>>>>>>> >> >> BUG: Fix detection of the gold linker. >>>>>>>>>>>> >> >> BUG: Update Python package installation locations. >>>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >>>>>>>>>>>> >> >> ENH: Change BUILD_EXAMPLES default to OFF. >>>>>>>>>>>> >> >> BUG: Use 'from itk import ITKCommon' in >>>>>>>>>>>> module2module test. >>>>>>>>>>>> >> >> COMP: Link to VTK Python when built with Kits >>>>>>>>>>>> support. >>>>>>>>>>>> >> >> BUG: Install itk_minc2.h header. >>>>>>>>>>>> >> >> COMP: ITKIOMINC has a public dependency on >>>>>>>>>>>> ITKIOImageBase. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Michka Popoff (9): >>>>>>>>>>>> >> >> ENH: Update to swig 3.0.7 >>>>>>>>>>>> >> >> ENH: Do not link against specific Python library on >>>>>>>>>>>> OS X >>>>>>>>>>>> >> >> COMP: Fix wrapping warnings when building with >>>>>>>>>>>> >> >> ITK_WRAP_IMAGE_DIMS=2 >>>>>>>>>>>> >> >> COMP: Add missing wrapping for TransformBase >>>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>>> sys.path >>>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>>> 3 wrapping >>>>>>>>>>>> >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >>>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>>> >> >> module >>>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>>> 3 wrapping >>>>>>>>>>>> >> >> ENH: Allow operations on Indexes and Offsets in >>>>>>>>>>>> Python >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Mikhail Isakov (1): >>>>>>>>>>>> >> >> BUG: DiffusionTensor3DReconstruction segfault if no >>>>>>>>>>>> baseline image >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Nick Tustison (5): >>>>>>>>>>>> >> >> BUG: Set a default b-spline epsilon. >>>>>>>>>>>> >> >> ENH: Adding testing for closed loop. >>>>>>>>>>>> >> >> BUG: Updating B-spline classes with the same >>>>>>>>>>>> epsilon strategy. >>>>>>>>>>>> >> >> PERF: Switch vnl_vectors for fixed arrays. >>>>>>>>>>>> >> >> ENH: Point-set registration with time-varying >>>>>>>>>>>> B-spline. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Olivier Commowick (3): >>>>>>>>>>>> >> >> BUG: Correct discrepancy in tridiagonal reduction >>>>>>>>>>>> wrt VNL eigen >>>>>>>>>>>> >> >> system >>>>>>>>>>>> >> >> BUG: Correct under/overflows in vnl_math_hypot >>>>>>>>>>>> (taken from pythag >>>>>>>>>>>> >> >> from V3P) >>>>>>>>>>>> >> >> BUG: Switch eigenvalues computation to double >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Pablo Hernandez-Cerdan (2): >>>>>>>>>>>> >> >> ENH: Help class for itkFlatStructuringElement with >>>>>>>>>>>> constructor >>>>>>>>>>>> >> >> from >>>>>>>>>>>> >> >> images. >>>>>>>>>>>> >> >> COMP: Fix test errors and warnings in >>>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Seun Odutola (1): >>>>>>>>>>>> >> >> COMP: Fixed name clash with Apple header (check >>>>>>>>>>>> Macro), renamed >>>>>>>>>>>> >> >> check >>>>>>>>>>>> >> >> to Check >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Shawn Waldon (1): >>>>>>>>>>>> >> >> COMP: Set target OS X version in environment for >>>>>>>>>>>> tools using >>>>>>>>>>>> >> >> compiler >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Simon Alexander (1): >>>>>>>>>>>> >> >> BUG: incorrect closest point computation >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Tobias Wood (2): >>>>>>>>>>>> >> >> BUG: LBFGSB was printing messages even with debug >>>>>>>>>>>> switched off. >>>>>>>>>>>> >> >> BUG: Removed an unguarded print statement. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Vladimir S. FONOV (9): >>>>>>>>>>>> >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >>>>>>>>>>>> >> >> COMP: Changing the order of HDF5 library components >>>>>>>>>>>> >> >> COMP: Splitting up IOMINC module into two parts: >>>>>>>>>>>> MINC and >>>>>>>>>>>> >> >> Transform >>>>>>>>>>>> >> >> STYLE: updated comments to properly reference LIBMINC >>>>>>>>>>>> >> >> ENH: Add script to merge upstream MINC as a subtree >>>>>>>>>>>> >> >> MINC 2015-07-23 (c033d431) >>>>>>>>>>>> >> >> COMP: Update MINC CMake code >>>>>>>>>>>> >> >> MINC 2015-08-18 (6d7e3ba8) >>>>>>>>>>>> >> >> MINC 2015-09-13 (95cd5374) >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Xiaoxiao Liu (1): >>>>>>>>>>>> >> >> DOC: update email address for xiaoxiao. >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Zach Williamson (10): >>>>>>>>>>>> >> >> BUG: Use correct libraries for ImageFusion tests >>>>>>>>>>>> >> >> ENH: Consolidate Library Dependencies >>>>>>>>>>>> >> >> COMP: Add a missing link to Review module >>>>>>>>>>>> >> >> COMP: Use correct linking macro in DCMTK >>>>>>>>>>>> >> >> BUG: Use correct libraries for TestKernel tests >>>>>>>>>>>> >> >> COMP: Fix inconsistant naming of >>>>>>>>>>>> GPUPDEDeformableRegistration >>>>>>>>>>>> >> >> ENH: Use new linking system macros >>>>>>>>>>>> >> >> PERF: Avoid searching private dependencies for >>>>>>>>>>>> include directories >>>>>>>>>>>> >> >> COMP: Recover missing dependencies >>>>>>>>>>>> >> >> ENH: use new linking macros in Filtering module >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> ----------------------------------------------------- >>>>>>>>>>>> >> >> Errors or omissions? Please fix them here: >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> >>>>>>>>>>>> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >>>>>>>>>>>> >> >> _____________________________________ >>>>>>>>>>>> >> >> Powered by www.kitware.com >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Visit other Kitware open-source projects at >>>>>>>>>>>> >> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Kitware offers ITK Training Courses, for more information >>>>>>>>>>>> visit: >>>>>>>>>>>> >> >> http://www.kitware.com/products/protraining.php >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>>> >> >> >>>>>>>>>>>> >> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Powered by www.kitware.com >>>>>>>>>>> >>>>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>>>> >>>>>>>>>> http://kitware.com/products/protraining.php >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>> >>>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Tue Dec 1 09:48:27 2015 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 1 Dec 2015 14:48:27 +0000 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: , Message-ID: If you compile on window in Debug mode, those tests are known to take a long time and time out. The options are to increase the timeout ( CTEST_TEST_TIMEOUT ) and/or exclude the ?RUNS_LONG? label from the tests run. Here is a ctest script which does this: https://open.cdash.org/viewNotes.php?buildid=4123585 HTH, Brad ________________________________ From: Simon Alexander [skalexander at gmail.com] Sent: Tuesday, December 01, 2015 9:19 AM To: Matt McCormick; D?enan Zuki? Cc: insight-users at itk.org; Hyun Jae Kang; ITK Subject: Re: [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! Hi Matt, So I pulled origin/master and rebuilt last night. I have different failures now, all by timeout: Total Test time (real) = 6363.39 sec The following tests FAILED: 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo (Timeout) 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo (Timeout) 728 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout) 2025 - itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest (Timeout) Errors while running CTest Any thoughts on what's going on there? On Mon, 30 Nov 2015 at 20:42 Matt McCormick > wrote: Hi Simon, I am returning from holiday, and also catching up on activity. Hyun Jae has taken care of the KWStyle warnings and the data conversion warning: http://review.source.kitware.com/#/c/20430/ http://review.source.kitware.com/#/c/20446/ And Dzenan and Bill have addressed Wiki examples errors: https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 It is likely that the test failures on your build still remain. Did you want to take them on? Thanks, Matt On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? > wrote: Looking at the master branch is the right thing to do. I am not doing any active development regarding this right now. On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander > wrote: Hi All, I had hoped to be able to look at this over the weekend, but no such luck. Is there somewhere useful I can help with it now? Not sure what state we are in (or what branch). On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? > wrote: It turns out that all the compile errors were occurring in WikiExamples. I solved all except one: ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line 23, but it should be judging from the comment on that line. For the rest, I created a pull request: https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander > wrote: Perfect. I'm under a deadline that is likely to eat the rest of the week but if that clears up I'll try and jump in earlier. On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? > wrote: OK I will work on it for an hour or two now, and I will make a branch and push it to Gerrit so whoever wants can pick up from there and keep updating it. On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander > wrote: Makes sense. At this point I am unlikely to have time to look at this until Saturday, but have hopes for a few free hours there. On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? > wrote: Building git master from Nov 23rd with examples and testing enabled I get 14 compile errors in VS2015 debug x64. Should we coordinate our efforts in fixing them? On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander > wrote: Two of the three failures look like truncation issues (like https://open.cdash.org/testDetails.php?test=395263772&build=4117158) The other (https://open.cdash.org/testDetails.php?test=395264938&build=4117158) is less obvious. If I have time this evening I'll try and have a look at these. Is your standard test build in 32 bit ? That might explain the difference if there are some underlying type assumptions, but not obvious why 2015 would trigger but not 2013. On Wed, 25 Nov 2015 at 11:01 Matt McCormick > wrote: Ah, cool! Here: https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 Could you please look into the test failures? @Hyun Jae, could you please look into the KWStyle warnings? Thanks, Matt On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander > wrote: > Sorry, if I wasn't clear - I submitted two builds yesterday from SIMON-LAP, > (actually 3 as I wasn't sure the config was right on the first one). VS2013 > was green, three failures on VS2015 (and 18 warnings). Looks like a > truncation problem on the resuts. > > On Wed, 25 Nov 2015 at 10:51 Matt McCormick > > wrote: >> >> Hi Simon, >> >> Thanks for testing. >> >> We have a Visual Studio 2015 build on the dashboard that is green: >> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >> >> Are there any different flags? Could you please submit an Experimental >> build? >> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit -C >> Release >> >> from a fresh build tree. >> >> Thanks, >> Matt >> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander > >> wrote: >> > Looks like a few problems with x64 build on visual studio 2015 - do you >> > have >> > a test machine in this configuration? >> > >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick > >> > wrote: >> >> >> >> On behalf of the Insight Toolkit community, we are proud to announce >> >> that >> >> ITK 4.9 release candidate 1 has been tagged and is available for >> >> testing! >> >> >> >> Please take this opportunity to test the new features in the release >> >> candidate. >> >> >> >> >> >> To obtain the source code, >> >> >> >> git clone http://itk.org/ITK.git >> >> cd ITK >> >> git checkout -q --detach v4.9rc01 >> >> >> >> For more details, please see the Git documentation [1]. >> >> >> >> >> >> A few selected highlights for this release: >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * New Remote modules: the Cuberille module for smooth generation of >> >> meshes >> >> from binary segmentation images, and the AnisotropicDiffusionLBR module >> >> improved edge-preserving smoothing. >> >> * Build your own ITK module outside the source tree, add continuous >> >> integration testing on GitHub, and easily add Python wrapping for your >> >> C++ >> >> algorithms. >> >> * Python wrapping, including Python 3, builds faster with a more >> >> standard >> >> installation >> >> * Improved performance of itk::Image::GetPixel and operations on >> >> itk::VariableLengthVector?s >> >> * Generate a FlatStructuringElement from an image >> >> * Point-set registration with time-varying B-splines >> >> * Module dependencies can now be specified as public / private / >> >> compile / >> >> test >> >> >> >> >> >> Please test the release candidate and share your experiences on the >> >> mailing list, issue tracker, and Gerrit Code Review. The new module >> >> dependency specification mechanism may unearth missing dependencies for >> >> projects that use ITK COMPONENTS with the CMake find_package command. >> >> >> >> >> >> An Experimental build, which demonstrates how the test suite performs >> >> on >> >> your local build system, can be submitted to the dashboard [2] with: >> >> >> >> mkdir ../ITK-build >> >> cd ../ITK-build >> >> cmake ../ITK >> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit >> >> >> >> Visual Studio builds must also add ?-C Release? to the ctest command. >> >> >> >> Notify the mailing list if there are any unexpected failures. Testing >> >> your own applications against the RC is also appreciated. >> >> >> >> >> >> Congratulations and well done to the 35 contributors to this release. >> >> We >> >> would especially like to recognize the new contributors: Mikhail >> >> Isakov, >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias Wood, Seun >> >> Odutola, >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach Williamson, >> >> Luc >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >> >> >> >> >> >> The final release is scheduled for mid-December. >> >> >> >> >> >> [1] http://www.itk.org/Wiki/ITK/Git >> >> >> >> [2] http://open.cdash.org/index.php?project=Insight >> >> >> >> >> >> >> >> New Features >> >> --------------------- >> >> >> >> Wrapping improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Python 3 supported >> >> * Wrapping builds much faster due to CastXML binaries >> >> * LandmarkBasedTransformInitializer now wrapped >> >> * NumPy bridge with VisualStudio >> >> * Wrapping for the MinimalPathExtraction module >> >> * Wrapping is now installed into Python?s site-packages directory in >> >> the >> >> ?itk? package >> >> * Wrapping package size is decreased >> >> * Better package portability on Mac OSX >> >> >> >> >> >> New Remote Modules >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Cuberille >> >> * Insight Journal Article: http://hdl.handle.net/10380/3186 >> >> * AnisotropicDiffusionLBR >> >> * Insight Journal Article: http://hdl.handle.net/10380/3505 >> >> * Web browser reproducibility: >> >> http://www.kitware.com/blog/home/post/942 >> >> >> >> >> >> Core Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * External Modules can now be developed outside of the ITK source tree >> >> and >> >> on GitHub >> >> * Details: http://www.kitware.com/blog/home/post/997 >> >> * New utilities in itk::Math: >> >> * AlmostEquals >> >> * NotAlmostEquals >> >> * ExactlyEquals >> >> * NotExactlyEquals >> >> * New itk::NumericTraits >> >> * IsInteger >> >> * IsSigned >> >> * Improved C++11 support >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >> >> * Improved capabilities of itk::ResourceProbe and >> >> itk::ResourceProbesCollectorBase >> >> * Improve numerical stability in VNL eigen system estimation >> >> * itksys_ios:: and itksys_stl:: have been remove (use std::) >> >> >> >> >> >> Filtering Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Generate a FlatStructuringElement from an image >> >> * WarpImageFilter support VectorImage?s >> >> * ConvertLabelMap supports different LabelMap types >> >> * ImageToPathFilter moved from the ITKReview to the ITKPath module >> >> * itk::MovingHistogramImageFilter moved to the ITKImageFilterBase >> >> module >> >> >> >> >> >> Registration Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Point-set registration with time-varying B-splines >> >> >> >> >> >> Build Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Module dependencies can now be specified as public / private / >> >> compile / >> >> test >> >> * BUILD_EXAMPLES CMake option is now OFF by default >> >> * Option to export all library symbols on Windows: >> >> * Details: http://www.kitware.com/blog/home/post/939 >> >> * Expat third party library is now name mangled >> >> * Many more modules can be built as shared libraries >> >> * KWStyle is automatically built and configured when tests are built >> >> >> >> >> >> Performance Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds members for >> >> metaprogramming >> >> * itk::mpl::{TrueType,FalseType} >> >> * itk::mpl::{If,Not,And,Or,Xor} >> >> * itk::mpl::EnableIf >> >> * itk::mpl::IsBaseOf >> >> * itk::mpl::IsConvertible >> >> * itk::mpl::IsNumber >> >> * itk::mpl::IsSame >> >> * itk::mpl::PromoteType >> >> * Image::GetPixel performance improvements >> >> * Many itk::VariableLengthVector performance improvements >> >> * AdaptiveHistogramEqualization uses a moving histogram >> >> * WarpImageFilter performance improvements >> >> >> >> >> >> Documentation Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples >> >> * ITK Software Guide improvements >> >> * How to use Python wrapping >> >> * How to create an ITK module >> >> * Improvements to segmentation examples >> >> * Expanded Canny edge detection example >> >> * Expanded tree container example >> >> >> >> >> >> Third Party Library Updates >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * FFTW updated to latest upstream >> >> * Build with recent OpenCV 2 and 3 >> >> * Build with the latest VTK >> >> * PNG update to the latest upstream >> >> * GDCM updated to the latest upstream >> >> * KWSys updated to the latest upstream >> >> * MINC updated to the latest upstream >> >> * SWIG updated to the latest upstream >> >> * Third party PNG and MINC are now Git subtrees >> >> >> >> >> >> Style improvements -- ITK gets more stylish with every release! >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Private copy constructors and operator= use ITK_DELETE_FUNCTION >> >> >> >> >> >> Improved code coverage -- we are at 84.9%! >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> >> >> * *Lots* of important bug fixes >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> >> >> * And much more! See details in the log below. >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> >> >> >> >> Changes from v4.8.0..v4.9rc01 >> >> -------------------------------------------- >> >> >> >> >> >> Abhishek Tiwari (1): >> >> BUG: "tmpImageIndex" not initialized to 0. >> >> >> >> Adam Snyder (1): >> >> PERF: Reworked MMI Threading using a per-thread buffer >> >> >> >> Alexander Leinoff (6): >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be resolved. >> >> ENH: Adds ExactlyEquals and NotExactlyEquals functions to >> >> itkMath.h >> >> COMP: Removes floating-point equality checks >> >> ENH: COMP: Adds support for complex values to Math::AlmostEquals >> >> ENH: Updates fftw dependency >> >> >> >> Arnaud Gelas (5): >> >> COMP: fix warning (unused local typedef) >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >> >> DOC: add doxgen documentation for >> >> BinaryImageToLevelSetImageAdaptor >> >> ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >> >> >> >> Betsy McPhail (1): >> >> BUG: Improve buffer alignment in OctreeNode . >> >> >> >> Bill Hoffman (2): >> >> ENH: Use new CMake Windows export symbol dll feature. >> >> COMP: Put vnl_export.h in the list of sources so it gets >> >> installed. >> >> >> >> Bill Lorensen (4): >> >> COMP: VTkGlue linker errors >> >> BUG: Inappropriate use of AlmostEquals >> >> ENH: Bump tag for wiki examples >> >> ENH: Better layout strategy >> >> >> >> Brad King (3): >> >> ENH: Remove use of include and itksys_ios::* >> >> ENH: Remove use of include and itksys_stl::* >> >> ENH: Update CMake Policy settings in Testing/TestExternal project >> >> >> >> Bradley Lowekamp (31): >> >> BUG: Avoid null deference in PrintSelf with default construction >> >> ENH: Enable base classes for templates of landmark initializer >> >> STYLE: Use "Swap" for ITK member name >> >> BUG: Demonstrate Eigen analysis failure >> >> BUG: Fix computation of Eigen analysis >> >> ENH: Update DiscreteHessianGaussian Test baseline >> >> ENH: Correctly demonstrate float point Eigen failure >> >> ENH: compile vnl_math_hypot, and use at least double >> >> ENH: Adding initial update script from used libpng version. >> >> ENH: removing non-subtree files for itkpng >> >> ENH: Ported ITK changes for building to subtree merged code >> >> ENH: Update libpng update script for v1.6.9 >> >> BUG: Use ParameterValueType for computation of landmark affine >> >> ENH: Wrap LandmarkBasedTransformInitializer >> >> BUG: Avoid potential exception in itk::Object::UnRegister >> >> ENH: Update itkpng zlib, configuration, and rename >> >> ENH: Update itkpng name mangling >> >> BUG: Use const pointer in Set method for constant ReferenceImage >> >> ivar >> >> BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod >> >> BUG: Demonstrate side effect on registration due to BSplineScatter >> >> change >> >> ENH: Move MovingHistogramImageFilter base classes to >> >> ImageFilterBase >> >> BUG: Avoid potential exception in itk::Object::UnRegister >> >> BUG: Avoid null deference in PrintSelf with default construction >> >> BUG: Use const pointer in Set method for constant ReferenceImage >> >> ivar >> >> ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram >> >> base >> >> COMP: address sign unsigned comparison warning >> >> COMP: Address signed unsigned comparison warning >> >> COMP: Address unused member variable and methods in anonymous ns >> >> BUG: Fix segfault when with empty IsolatedWatershed Threshold >> >> range >> >> BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test >> >> BUG: Reduce number of targets with MSVC >> >> >> >> Davis Vigneault (7): >> >> DOC: Minor improvements to segmentation examples. >> >> DOC: Expanded Canny Edge Detection Example >> >> DOC: Expanded TreeContainer Example >> >> COMP: Warnings in itkVTKImageExport when compiling with c++11 >> >> COMP: Warnings in FFTW Classes when compiling with c++11 >> >> COMP: Update Git Tag for Subdivision Module >> >> COMP: Warnings in FFTW Classes when compiling with c++11 >> >> >> >> D?enan Zuki? (1): >> >> STYLE: better formatting of the "usage" message >> >> >> >> Eugene Prilepin (1): >> >> BUG: Fix a template name formation in python wrappings >> >> >> >> Floris Berendsen (1): >> >> STYLE: Improve naming conventions in comments. >> >> >> >> Hans Johnson (29): >> >> STYLE: Instrument for FixedParameters typedef >> >> BUG: Demonstrate DisplacementTransformFailure >> >> BUG: FixedParameters should be double precision >> >> STYLE: Minor code style issues for MGHIO >> >> COMP: Update to version for WikiExamples >> >> ENH: Update Sphinx for ITK 4.8.0 >> >> ENH: Update MGHIO to be shared lib >> >> ENH: Provide consistent floating point comparisons >> >> BUG: Fix MGHIO to fix write failures >> >> PERF: Remove floating point as sentinal value >> >> COMP: Const correctness needs to be maintained >> >> BUG: Preserve backwards compatibility >> >> DOC: Provide consistent naming in comments >> >> ENH: Conversion between transform type tolerance >> >> STYLE: Prefer initialization to assignment >> >> ENH: Missing ITK_OVERRIDE >> >> COMP: Need to propagate ITKGDCM >> >> COMP: Need to propagate ITKGDCM >> >> COMP: Add missing ITK_OVERRIDE >> >> STYLE: Minor code style issues for MGHIO >> >> COMP: Update to version for WikiExamples >> >> ENH: Update Sphinx for ITK 4.8.0 >> >> ENH: Update MGHIO to be shared lib >> >> BUG: Fix MGHIO to fix write failures >> >> ENH: C++11 allows for rigorous =delete >> >> COMP: Remove unnecessary failing assert test >> >> ENH: Ignore internal files for the Clion editor >> >> COMP: Fix VNL compilation for wider C++11 support >> >> BUG: In configuration test need to mirror code >> >> >> >> Hyun Jae Kang (27): >> >> BUG: Remove std::cout calls from class >> >> BUG: Avoid an unexpected output of static_cast >> >> BUG: Update python example codes for ImageRegistration >> >> BUG: Retrieve the missed wrap file >> >> BUG: itkVTKImageIO class does not handle blank lines in VTK file >> >> header. >> >> BUG: Fix HDF5 CMake configuration with VS2015 >> >> BUG: Fix a compilation issue on ITK4 with FFTW and shared >> >> libraries >> >> BUG: Fixed older XCode linking error >> >> ENH: Use CastXML binaries when building with x86_64 Mac OS X >> >> BUG: Remove std::cout calls from class >> >> BUG: itkVTKImageIO class does not handle blank lines in VTK file >> >> header. >> >> BUG: Fixed older XCode linking error >> >> ENH: Add automatic KWStyle build and configuration setup >> >> COMP: KWStyle shadow, format-nonliteral and autological-compare >> >> warning. >> >> COMP: Fixed the warning messages from itkGPU Module >> >> COMP: Fixed a warning message of unused-private-field >> >> COMP: Apply latest version of KWStyle >> >> COMP: Update KWStyle to fix its additional warning messages >> >> COMP: Update KWStyle to fix its additional warning messages >> >> COMP: Fix data-conversion warning messages on Windows >> >> ENH: Update itkResourceProbe to calculate statistical data >> >> COMP: Fix data-conversion warning messages on VS14 >> >> COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function >> >> ENH: Update the Report() function of >> >> itkResourceProbesCollectorBase >> >> COMP: Fix data-conversion warning message on itkResourceProbe >> >> COMP: Fix additional warning messages of KWStyle >> >> COMP: Fix data-conversion warning messages >> >> >> >> Jon Haitz Legarreta (6): >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >> >> BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest >> >> BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter >> >> BUG: Test for StatisticsUniqueLabelMapFilter stability >> >> ENH: Add test for itkParametricStpaceToImageSpaceFilter >> >> ENH: Improve code coverage for >> >> itkParametricSpaceToImageSpaceMeshFilter >> >> >> >> Julien Michel (1): >> >> ENH: Support of VectorImage as template parameters for >> >> WarpImageFilter >> >> >> >> Junjie Bai (2): >> >> BUG: ConvertLabelMap with different LabelMapTypes >> >> BUG: LabelObject CopyAttribute support different LabelObject type >> >> >> >> KWSys Robot (4): >> >> KWSys 2015-07-10 (c9336bcf) >> >> KWSys 2015-07-30 (f63febb7) >> >> KWSys 2015-08-24 (cdaf522c) >> >> KWSys 2015-08-28 (dc3fdd7f) >> >> >> >> LIBPNG Upstream (2): >> >> PNG 2009-04-06 (e68f5a36) >> >> PNG 2014-02-05 (3e753eb8) >> >> >> >> Laurentiu Nicola (2): >> >> PERF: Avoid temporary smartptr in ProcessObject::GetInput >> >> PERF: Optimize WarpImageFilter by avoiding refcount bouncing >> >> >> >> Luc Hermitte (8): >> >> PERF: itk::Image::GetPixel() performance improvment. >> >> PERF: Performance enhancements on VariableLengthVectors 1/... >> >> ENH: Dependencies on itkVariableLengthVector.h reduced >> >> BUG: Error in VariableLengthVector Unit Tests >> >> PERF: Performance enhancements on VLV 2/... >> >> PERF: Performances enhancements on VLV 3/... >> >> COMP: Fix signed/unsigned warnings >> >> BUG: std::copy/fill on empty VLV >> >> >> >> Lucas Gandel (4): >> >> ENH: Move ImageToPathFilter from ITKReview to ITKPath module. >> >> BUG: Fixing ImageToPathFilter wrapping call from Review Module >> >> STYLE: Fix KWStyle dashboard errors >> >> BUG: Fix external module BUILD_SHARED_LIBS status >> >> >> >> Mathieu Malaterre (1): >> >> BUG: Name mangle the included expat third party library. >> >> >> >> Matthew McCormick (94): >> >> ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest. >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >> >> ENH: Bump ITK version to 4.9.0. >> >> BUG: Remove std::cout calls from classes. >> >> COMP: Remove unused argument in ConditionVariableNoThreads. >> >> BUG: Implement UpdateLargestPossibleRegion for >> >> ImageToVTKImageFilter. >> >> COMP: Add link interface specification for wrapping >> >> target_link_libraries. >> >> STYLE: Fix indentation in itkMINCTransformIOFactory.cxx. >> >> COMP: Fix MINCTransformIO factory registration. >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1. >> >> COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR. >> >> BUG: Initialize mutex for 32 bit AtomicInt. >> >> ENH: Use CastXML binaries when building with x86_64 Linux. >> >> STYLE: Rename gccxml -> castxml in {idx,igenerator}.py. >> >> COMP: Disable the gold linker for static builds on Ubuntu 14.04. >> >> ENH: Use Windows binaries for CastXML. >> >> ENH: Add better scoping in igenerator.py. >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC. >> >> BUG: LevelSetsv4 used signed char instead of char. >> >> ENH: Add better scoping to idx.py. >> >> COMP: Define newSize and oldSize in VariableLengthVector. >> >> STYLE: Use prefix increment operator in ImageBase. >> >> DOC: Correct spelling of Continuous. >> >> ENH: Add more progress information to IterativeClosestPoint2. >> >> BUG: Build BridgeNumPy with Visual Studio. >> >> ENH: Add ITKModuleExternal.cmake >> >> COMP: Wrap Image< bool, D > for FlatStructuringElement. >> >> BUG: Use CastXML binary built in Release. >> >> BUG: ContinuousIndex should not be templated over TCoordRep. >> >> COMP: Set CMP0054 to new. >> >> COMP: Address line length too long for Software Guide. >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >> >> BUG: Support Python 3 wrapping module initialization. >> >> BUG: Update itkTemplate.py for Python 3. >> >> BUG: Update itkExtras.py for Python 3. >> >> BUG: Prevent Python callback addition recursion. >> >> BUG: Fix test scripts for Python 3. >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >> >> ENH: Allow projects to build against an external module. >> >> ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER. >> >> ENH: Rename _cable_ to _wrappers_. >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >> >> ENH: Bump CastXML version to 2015-30-29. >> >> ENH: Bump LLVM / Clang to 3.7.0. >> >> COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5. >> >> COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC. >> >> COMP: Use itkSimpleNewMacro in >> >> ThreadedIteratorRangePartitionerTest. >> >> ENH: Add wrapping support for building modules externally. >> >> BUG: Fix KWStyle test paths when building a module externally. >> >> ENH: Add Cuberille Remote module. >> >> COMP: Remove carriage returns from Cuberille remote. >> >> COMP: Remove unused argument in ConditionVariableNoThreads. >> >> DOC: Correct spelling of Continuous. >> >> ENH: Bump the MinimalPathExtraction Remote to 2015-10-20. >> >> COMP: Fix KernelTransform SetFixedParameters argument type. >> >> STYLE: Use prefix increment operator in ImageBase. >> >> COMP: Use ITK's pygccxml by correctly setting up the sys.path >> >> Revert "COMP: Put vnl_export.h in the list of sources so it gets >> >> installed." >> >> BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes" >> >> ENH: Marking wrapping CMake configuration variables as advanced. >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >> >> COMP: Non-virtual copy attribute members in LabelMap cannot have >> >> override. >> >> COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter. >> >> COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT. >> >> ENH: Remove CMake version check in ITKModuleHeaderTest.cmake >> >> BUG: Improve KWStyle ExternalProject utilization. >> >> ENH: Remove old KWStyle build script. >> >> COMP: Address VariableLengthVector Doxygen rhs @param not found. >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER. >> >> ENH: Install Python bindings into site-packages. >> >> ENH: Improve readability of Python site-packages path detection. >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned expression >> >> warning. >> >> BUG: ITKCommon publically depends on ITKDoubleConversion. >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >> >> ENH: Improves names and export of module dependencies. >> >> STYLE: Improve namespace bracket style in itkIsConvertible. >> >> COMP: Set CMP0054 to new. >> >> BUG: Remove unused wrapping files. >> >> BUG: Do install install wrapping development files. >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >> >> BUG: Remove duplicate inclusion of wrapping submodules. >> >> COMP: Do not use C++ style comments for Doxygen cond. >> >> BUG: Fix detection of the gold linker. >> >> BUG: Update Python package installation locations. >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >> >> ENH: Change BUILD_EXAMPLES default to OFF. >> >> BUG: Use 'from itk import ITKCommon' in module2module test. >> >> COMP: Link to VTK Python when built with Kits support. >> >> BUG: Install itk_minc2.h header. >> >> COMP: ITKIOMINC has a public dependency on ITKIOImageBase. >> >> >> >> Michka Popoff (9): >> >> ENH: Update to swig 3.0.7 >> >> ENH: Do not link against specific Python library on OS X >> >> COMP: Fix wrapping warnings when building with >> >> ITK_WRAP_IMAGE_DIMS=2 >> >> COMP: Add missing wrapping for TransformBase >> >> COMP: Use ITK's pygccxml by correctly setting up the sys.path >> >> COMP: Disable incompatible modules when using Python 3 wrapping >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >> >> ImageFilterBase >> >> module >> >> COMP: Disable incompatible modules when using Python 3 wrapping >> >> ENH: Allow operations on Indexes and Offsets in Python >> >> >> >> Mikhail Isakov (1): >> >> BUG: DiffusionTensor3DReconstruction segfault if no baseline image >> >> >> >> Nick Tustison (5): >> >> BUG: Set a default b-spline epsilon. >> >> ENH: Adding testing for closed loop. >> >> BUG: Updating B-spline classes with the same epsilon strategy. >> >> PERF: Switch vnl_vectors for fixed arrays. >> >> ENH: Point-set registration with time-varying B-spline. >> >> >> >> Olivier Commowick (3): >> >> BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen >> >> system >> >> BUG: Correct under/overflows in vnl_math_hypot (taken from pythag >> >> from V3P) >> >> BUG: Switch eigenvalues computation to double >> >> >> >> Pablo Hernandez-Cerdan (2): >> >> ENH: Help class for itkFlatStructuringElement with constructor >> >> from >> >> images. >> >> COMP: Fix test errors and warnings in FlatStructuringElement. >> >> >> >> Seun Odutola (1): >> >> COMP: Fixed name clash with Apple header (check Macro), renamed >> >> check >> >> to Check >> >> >> >> Shawn Waldon (1): >> >> COMP: Set target OS X version in environment for tools using >> >> compiler >> >> >> >> Simon Alexander (1): >> >> BUG: incorrect closest point computation >> >> >> >> Tobias Wood (2): >> >> BUG: LBFGSB was printing messages even with debug switched off. >> >> BUG: Removed an unguarded print statement. >> >> >> >> Vladimir S. FONOV (9): >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >> >> COMP: Changing the order of HDF5 library components >> >> COMP: Splitting up IOMINC module into two parts: MINC and >> >> Transform >> >> STYLE: updated comments to properly reference LIBMINC >> >> ENH: Add script to merge upstream MINC as a subtree >> >> MINC 2015-07-23 (c033d431) >> >> COMP: Update MINC CMake code >> >> MINC 2015-08-18 (6d7e3ba8) >> >> MINC 2015-09-13 (95cd5374) >> >> >> >> Xiaoxiao Liu (1): >> >> DOC: update email address for xiaoxiao. >> >> >> >> Zach Williamson (10): >> >> BUG: Use correct libraries for ImageFusion tests >> >> ENH: Consolidate Library Dependencies >> >> COMP: Add a missing link to Review module >> >> COMP: Use correct linking macro in DCMTK >> >> BUG: Use correct libraries for TestKernel tests >> >> COMP: Fix inconsistant naming of GPUPDEDeformableRegistration >> >> ENH: Use new linking system macros >> >> PERF: Avoid searching private dependencies for include directories >> >> COMP: Recover missing dependencies >> >> ENH: use new linking macros in Filtering module >> >> >> >> >> >> >> >> ----------------------------------------------------- >> >> Errors or omissions? Please fix them here: >> >> >> >> >> >> >> >> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >> >> _____________________________________ >> >> Powered by www.kitware.com >> >> >> >> Visit other Kitware open-source projects at >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> http://www.kitware.com/products/protraining.php >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From blowekamp at mail.nih.gov Tue Dec 1 09:48:27 2015 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 1 Dec 2015 14:48:27 +0000 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: , Message-ID: If you compile on window in Debug mode, those tests are known to take a long time and time out. The options are to increase the timeout ( CTEST_TEST_TIMEOUT ) and/or exclude the ?RUNS_LONG? label from the tests run. Here is a ctest script which does this: https://open.cdash.org/viewNotes.php?buildid=4123585 HTH, Brad ________________________________ From: Simon Alexander [skalexander at gmail.com] Sent: Tuesday, December 01, 2015 9:19 AM To: Matt McCormick; D?enan Zuki? Cc: insight-users at itk.org; Hyun Jae Kang; ITK Subject: Re: [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! Hi Matt, So I pulled origin/master and rebuilt last night. I have different failures now, all by timeout: Total Test time (real) = 6363.39 sec The following tests FAILED: 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo (Timeout) 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo (Timeout) 728 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout) 2025 - itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest (Timeout) Errors while running CTest Any thoughts on what's going on there? On Mon, 30 Nov 2015 at 20:42 Matt McCormick > wrote: Hi Simon, I am returning from holiday, and also catching up on activity. Hyun Jae has taken care of the KWStyle warnings and the data conversion warning: http://review.source.kitware.com/#/c/20430/ http://review.source.kitware.com/#/c/20446/ And Dzenan and Bill have addressed Wiki examples errors: https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 It is likely that the test failures on your build still remain. Did you want to take them on? Thanks, Matt On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? > wrote: Looking at the master branch is the right thing to do. I am not doing any active development regarding this right now. On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander > wrote: Hi All, I had hoped to be able to look at this over the weekend, but no such luck. Is there somewhere useful I can help with it now? Not sure what state we are in (or what branch). On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? > wrote: It turns out that all the compile errors were occurring in WikiExamples. I solved all except one: ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line 23, but it should be judging from the comment on that line. For the rest, I created a pull request: https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander > wrote: Perfect. I'm under a deadline that is likely to eat the rest of the week but if that clears up I'll try and jump in earlier. On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? > wrote: OK I will work on it for an hour or two now, and I will make a branch and push it to Gerrit so whoever wants can pick up from there and keep updating it. On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander > wrote: Makes sense. At this point I am unlikely to have time to look at this until Saturday, but have hopes for a few free hours there. On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? > wrote: Building git master from Nov 23rd with examples and testing enabled I get 14 compile errors in VS2015 debug x64. Should we coordinate our efforts in fixing them? On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander > wrote: Two of the three failures look like truncation issues (like https://open.cdash.org/testDetails.php?test=395263772&build=4117158) The other (https://open.cdash.org/testDetails.php?test=395264938&build=4117158) is less obvious. If I have time this evening I'll try and have a look at these. Is your standard test build in 32 bit ? That might explain the difference if there are some underlying type assumptions, but not obvious why 2015 would trigger but not 2013. On Wed, 25 Nov 2015 at 11:01 Matt McCormick > wrote: Ah, cool! Here: https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 Could you please look into the test failures? @Hyun Jae, could you please look into the KWStyle warnings? Thanks, Matt On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander > wrote: > Sorry, if I wasn't clear - I submitted two builds yesterday from SIMON-LAP, > (actually 3 as I wasn't sure the config was right on the first one). VS2013 > was green, three failures on VS2015 (and 18 warnings). Looks like a > truncation problem on the resuts. > > On Wed, 25 Nov 2015 at 10:51 Matt McCormick > > wrote: >> >> Hi Simon, >> >> Thanks for testing. >> >> We have a Visual Studio 2015 build on the dashboard that is green: >> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >> >> Are there any different flags? Could you please submit an Experimental >> build? >> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit -C >> Release >> >> from a fresh build tree. >> >> Thanks, >> Matt >> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander > >> wrote: >> > Looks like a few problems with x64 build on visual studio 2015 - do you >> > have >> > a test machine in this configuration? >> > >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick > >> > wrote: >> >> >> >> On behalf of the Insight Toolkit community, we are proud to announce >> >> that >> >> ITK 4.9 release candidate 1 has been tagged and is available for >> >> testing! >> >> >> >> Please take this opportunity to test the new features in the release >> >> candidate. >> >> >> >> >> >> To obtain the source code, >> >> >> >> git clone http://itk.org/ITK.git >> >> cd ITK >> >> git checkout -q --detach v4.9rc01 >> >> >> >> For more details, please see the Git documentation [1]. >> >> >> >> >> >> A few selected highlights for this release: >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * New Remote modules: the Cuberille module for smooth generation of >> >> meshes >> >> from binary segmentation images, and the AnisotropicDiffusionLBR module >> >> improved edge-preserving smoothing. >> >> * Build your own ITK module outside the source tree, add continuous >> >> integration testing on GitHub, and easily add Python wrapping for your >> >> C++ >> >> algorithms. >> >> * Python wrapping, including Python 3, builds faster with a more >> >> standard >> >> installation >> >> * Improved performance of itk::Image::GetPixel and operations on >> >> itk::VariableLengthVector?s >> >> * Generate a FlatStructuringElement from an image >> >> * Point-set registration with time-varying B-splines >> >> * Module dependencies can now be specified as public / private / >> >> compile / >> >> test >> >> >> >> >> >> Please test the release candidate and share your experiences on the >> >> mailing list, issue tracker, and Gerrit Code Review. The new module >> >> dependency specification mechanism may unearth missing dependencies for >> >> projects that use ITK COMPONENTS with the CMake find_package command. >> >> >> >> >> >> An Experimental build, which demonstrates how the test suite performs >> >> on >> >> your local build system, can be submitted to the dashboard [2] with: >> >> >> >> mkdir ../ITK-build >> >> cd ../ITK-build >> >> cmake ../ITK >> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit >> >> >> >> Visual Studio builds must also add ?-C Release? to the ctest command. >> >> >> >> Notify the mailing list if there are any unexpected failures. Testing >> >> your own applications against the RC is also appreciated. >> >> >> >> >> >> Congratulations and well done to the 35 contributors to this release. >> >> We >> >> would especially like to recognize the new contributors: Mikhail >> >> Isakov, >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias Wood, Seun >> >> Odutola, >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach Williamson, >> >> Luc >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >> >> >> >> >> >> The final release is scheduled for mid-December. >> >> >> >> >> >> [1] http://www.itk.org/Wiki/ITK/Git >> >> >> >> [2] http://open.cdash.org/index.php?project=Insight >> >> >> >> >> >> >> >> New Features >> >> --------------------- >> >> >> >> Wrapping improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Python 3 supported >> >> * Wrapping builds much faster due to CastXML binaries >> >> * LandmarkBasedTransformInitializer now wrapped >> >> * NumPy bridge with VisualStudio >> >> * Wrapping for the MinimalPathExtraction module >> >> * Wrapping is now installed into Python?s site-packages directory in >> >> the >> >> ?itk? package >> >> * Wrapping package size is decreased >> >> * Better package portability on Mac OSX >> >> >> >> >> >> New Remote Modules >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Cuberille >> >> * Insight Journal Article: http://hdl.handle.net/10380/3186 >> >> * AnisotropicDiffusionLBR >> >> * Insight Journal Article: http://hdl.handle.net/10380/3505 >> >> * Web browser reproducibility: >> >> http://www.kitware.com/blog/home/post/942 >> >> >> >> >> >> Core Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * External Modules can now be developed outside of the ITK source tree >> >> and >> >> on GitHub >> >> * Details: http://www.kitware.com/blog/home/post/997 >> >> * New utilities in itk::Math: >> >> * AlmostEquals >> >> * NotAlmostEquals >> >> * ExactlyEquals >> >> * NotExactlyEquals >> >> * New itk::NumericTraits >> >> * IsInteger >> >> * IsSigned >> >> * Improved C++11 support >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >> >> * Improved capabilities of itk::ResourceProbe and >> >> itk::ResourceProbesCollectorBase >> >> * Improve numerical stability in VNL eigen system estimation >> >> * itksys_ios:: and itksys_stl:: have been remove (use std::) >> >> >> >> >> >> Filtering Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Generate a FlatStructuringElement from an image >> >> * WarpImageFilter support VectorImage?s >> >> * ConvertLabelMap supports different LabelMap types >> >> * ImageToPathFilter moved from the ITKReview to the ITKPath module >> >> * itk::MovingHistogramImageFilter moved to the ITKImageFilterBase >> >> module >> >> >> >> >> >> Registration Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Point-set registration with time-varying B-splines >> >> >> >> >> >> Build Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Module dependencies can now be specified as public / private / >> >> compile / >> >> test >> >> * BUILD_EXAMPLES CMake option is now OFF by default >> >> * Option to export all library symbols on Windows: >> >> * Details: http://www.kitware.com/blog/home/post/939 >> >> * Expat third party library is now name mangled >> >> * Many more modules can be built as shared libraries >> >> * KWStyle is automatically built and configured when tests are built >> >> >> >> >> >> Performance Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds members for >> >> metaprogramming >> >> * itk::mpl::{TrueType,FalseType} >> >> * itk::mpl::{If,Not,And,Or,Xor} >> >> * itk::mpl::EnableIf >> >> * itk::mpl::IsBaseOf >> >> * itk::mpl::IsConvertible >> >> * itk::mpl::IsNumber >> >> * itk::mpl::IsSame >> >> * itk::mpl::PromoteType >> >> * Image::GetPixel performance improvements >> >> * Many itk::VariableLengthVector performance improvements >> >> * AdaptiveHistogramEqualization uses a moving histogram >> >> * WarpImageFilter performance improvements >> >> >> >> >> >> Documentation Improvements >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples >> >> * ITK Software Guide improvements >> >> * How to use Python wrapping >> >> * How to create an ITK module >> >> * Improvements to segmentation examples >> >> * Expanded Canny edge detection example >> >> * Expanded tree container example >> >> >> >> >> >> Third Party Library Updates >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * FFTW updated to latest upstream >> >> * Build with recent OpenCV 2 and 3 >> >> * Build with the latest VTK >> >> * PNG update to the latest upstream >> >> * GDCM updated to the latest upstream >> >> * KWSys updated to the latest upstream >> >> * MINC updated to the latest upstream >> >> * SWIG updated to the latest upstream >> >> * Third party PNG and MINC are now Git subtrees >> >> >> >> >> >> Style improvements -- ITK gets more stylish with every release! >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> * Private copy constructors and operator= use ITK_DELETE_FUNCTION >> >> >> >> >> >> Improved code coverage -- we are at 84.9%! >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> >> >> * *Lots* of important bug fixes >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> >> >> * And much more! See details in the log below. >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> >> >> >> >> >> >> Changes from v4.8.0..v4.9rc01 >> >> -------------------------------------------- >> >> >> >> >> >> Abhishek Tiwari (1): >> >> BUG: "tmpImageIndex" not initialized to 0. >> >> >> >> Adam Snyder (1): >> >> PERF: Reworked MMI Threading using a per-thread buffer >> >> >> >> Alexander Leinoff (6): >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be resolved. >> >> ENH: Adds ExactlyEquals and NotExactlyEquals functions to >> >> itkMath.h >> >> COMP: Removes floating-point equality checks >> >> ENH: COMP: Adds support for complex values to Math::AlmostEquals >> >> ENH: Updates fftw dependency >> >> >> >> Arnaud Gelas (5): >> >> COMP: fix warning (unused local typedef) >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >> >> DOC: add doxgen documentation for >> >> BinaryImageToLevelSetImageAdaptor >> >> ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >> >> >> >> Betsy McPhail (1): >> >> BUG: Improve buffer alignment in OctreeNode . >> >> >> >> Bill Hoffman (2): >> >> ENH: Use new CMake Windows export symbol dll feature. >> >> COMP: Put vnl_export.h in the list of sources so it gets >> >> installed. >> >> >> >> Bill Lorensen (4): >> >> COMP: VTkGlue linker errors >> >> BUG: Inappropriate use of AlmostEquals >> >> ENH: Bump tag for wiki examples >> >> ENH: Better layout strategy >> >> >> >> Brad King (3): >> >> ENH: Remove use of include and itksys_ios::* >> >> ENH: Remove use of include and itksys_stl::* >> >> ENH: Update CMake Policy settings in Testing/TestExternal project >> >> >> >> Bradley Lowekamp (31): >> >> BUG: Avoid null deference in PrintSelf with default construction >> >> ENH: Enable base classes for templates of landmark initializer >> >> STYLE: Use "Swap" for ITK member name >> >> BUG: Demonstrate Eigen analysis failure >> >> BUG: Fix computation of Eigen analysis >> >> ENH: Update DiscreteHessianGaussian Test baseline >> >> ENH: Correctly demonstrate float point Eigen failure >> >> ENH: compile vnl_math_hypot, and use at least double >> >> ENH: Adding initial update script from used libpng version. >> >> ENH: removing non-subtree files for itkpng >> >> ENH: Ported ITK changes for building to subtree merged code >> >> ENH: Update libpng update script for v1.6.9 >> >> BUG: Use ParameterValueType for computation of landmark affine >> >> ENH: Wrap LandmarkBasedTransformInitializer >> >> BUG: Avoid potential exception in itk::Object::UnRegister >> >> ENH: Update itkpng zlib, configuration, and rename >> >> ENH: Update itkpng name mangling >> >> BUG: Use const pointer in Set method for constant ReferenceImage >> >> ivar >> >> BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod >> >> BUG: Demonstrate side effect on registration due to BSplineScatter >> >> change >> >> ENH: Move MovingHistogramImageFilter base classes to >> >> ImageFilterBase >> >> BUG: Avoid potential exception in itk::Object::UnRegister >> >> BUG: Avoid null deference in PrintSelf with default construction >> >> BUG: Use const pointer in Set method for constant ReferenceImage >> >> ivar >> >> ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram >> >> base >> >> COMP: address sign unsigned comparison warning >> >> COMP: Address signed unsigned comparison warning >> >> COMP: Address unused member variable and methods in anonymous ns >> >> BUG: Fix segfault when with empty IsolatedWatershed Threshold >> >> range >> >> BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test >> >> BUG: Reduce number of targets with MSVC >> >> >> >> Davis Vigneault (7): >> >> DOC: Minor improvements to segmentation examples. >> >> DOC: Expanded Canny Edge Detection Example >> >> DOC: Expanded TreeContainer Example >> >> COMP: Warnings in itkVTKImageExport when compiling with c++11 >> >> COMP: Warnings in FFTW Classes when compiling with c++11 >> >> COMP: Update Git Tag for Subdivision Module >> >> COMP: Warnings in FFTW Classes when compiling with c++11 >> >> >> >> D?enan Zuki? (1): >> >> STYLE: better formatting of the "usage" message >> >> >> >> Eugene Prilepin (1): >> >> BUG: Fix a template name formation in python wrappings >> >> >> >> Floris Berendsen (1): >> >> STYLE: Improve naming conventions in comments. >> >> >> >> Hans Johnson (29): >> >> STYLE: Instrument for FixedParameters typedef >> >> BUG: Demonstrate DisplacementTransformFailure >> >> BUG: FixedParameters should be double precision >> >> STYLE: Minor code style issues for MGHIO >> >> COMP: Update to version for WikiExamples >> >> ENH: Update Sphinx for ITK 4.8.0 >> >> ENH: Update MGHIO to be shared lib >> >> ENH: Provide consistent floating point comparisons >> >> BUG: Fix MGHIO to fix write failures >> >> PERF: Remove floating point as sentinal value >> >> COMP: Const correctness needs to be maintained >> >> BUG: Preserve backwards compatibility >> >> DOC: Provide consistent naming in comments >> >> ENH: Conversion between transform type tolerance >> >> STYLE: Prefer initialization to assignment >> >> ENH: Missing ITK_OVERRIDE >> >> COMP: Need to propagate ITKGDCM >> >> COMP: Need to propagate ITKGDCM >> >> COMP: Add missing ITK_OVERRIDE >> >> STYLE: Minor code style issues for MGHIO >> >> COMP: Update to version for WikiExamples >> >> ENH: Update Sphinx for ITK 4.8.0 >> >> ENH: Update MGHIO to be shared lib >> >> BUG: Fix MGHIO to fix write failures >> >> ENH: C++11 allows for rigorous =delete >> >> COMP: Remove unnecessary failing assert test >> >> ENH: Ignore internal files for the Clion editor >> >> COMP: Fix VNL compilation for wider C++11 support >> >> BUG: In configuration test need to mirror code >> >> >> >> Hyun Jae Kang (27): >> >> BUG: Remove std::cout calls from class >> >> BUG: Avoid an unexpected output of static_cast >> >> BUG: Update python example codes for ImageRegistration >> >> BUG: Retrieve the missed wrap file >> >> BUG: itkVTKImageIO class does not handle blank lines in VTK file >> >> header. >> >> BUG: Fix HDF5 CMake configuration with VS2015 >> >> BUG: Fix a compilation issue on ITK4 with FFTW and shared >> >> libraries >> >> BUG: Fixed older XCode linking error >> >> ENH: Use CastXML binaries when building with x86_64 Mac OS X >> >> BUG: Remove std::cout calls from class >> >> BUG: itkVTKImageIO class does not handle blank lines in VTK file >> >> header. >> >> BUG: Fixed older XCode linking error >> >> ENH: Add automatic KWStyle build and configuration setup >> >> COMP: KWStyle shadow, format-nonliteral and autological-compare >> >> warning. >> >> COMP: Fixed the warning messages from itkGPU Module >> >> COMP: Fixed a warning message of unused-private-field >> >> COMP: Apply latest version of KWStyle >> >> COMP: Update KWStyle to fix its additional warning messages >> >> COMP: Update KWStyle to fix its additional warning messages >> >> COMP: Fix data-conversion warning messages on Windows >> >> ENH: Update itkResourceProbe to calculate statistical data >> >> COMP: Fix data-conversion warning messages on VS14 >> >> COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function >> >> ENH: Update the Report() function of >> >> itkResourceProbesCollectorBase >> >> COMP: Fix data-conversion warning message on itkResourceProbe >> >> COMP: Fix additional warning messages of KWStyle >> >> COMP: Fix data-conversion warning messages >> >> >> >> Jon Haitz Legarreta (6): >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >> >> BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest >> >> BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter >> >> BUG: Test for StatisticsUniqueLabelMapFilter stability >> >> ENH: Add test for itkParametricStpaceToImageSpaceFilter >> >> ENH: Improve code coverage for >> >> itkParametricSpaceToImageSpaceMeshFilter >> >> >> >> Julien Michel (1): >> >> ENH: Support of VectorImage as template parameters for >> >> WarpImageFilter >> >> >> >> Junjie Bai (2): >> >> BUG: ConvertLabelMap with different LabelMapTypes >> >> BUG: LabelObject CopyAttribute support different LabelObject type >> >> >> >> KWSys Robot (4): >> >> KWSys 2015-07-10 (c9336bcf) >> >> KWSys 2015-07-30 (f63febb7) >> >> KWSys 2015-08-24 (cdaf522c) >> >> KWSys 2015-08-28 (dc3fdd7f) >> >> >> >> LIBPNG Upstream (2): >> >> PNG 2009-04-06 (e68f5a36) >> >> PNG 2014-02-05 (3e753eb8) >> >> >> >> Laurentiu Nicola (2): >> >> PERF: Avoid temporary smartptr in ProcessObject::GetInput >> >> PERF: Optimize WarpImageFilter by avoiding refcount bouncing >> >> >> >> Luc Hermitte (8): >> >> PERF: itk::Image::GetPixel() performance improvment. >> >> PERF: Performance enhancements on VariableLengthVectors 1/... >> >> ENH: Dependencies on itkVariableLengthVector.h reduced >> >> BUG: Error in VariableLengthVector Unit Tests >> >> PERF: Performance enhancements on VLV 2/... >> >> PERF: Performances enhancements on VLV 3/... >> >> COMP: Fix signed/unsigned warnings >> >> BUG: std::copy/fill on empty VLV >> >> >> >> Lucas Gandel (4): >> >> ENH: Move ImageToPathFilter from ITKReview to ITKPath module. >> >> BUG: Fixing ImageToPathFilter wrapping call from Review Module >> >> STYLE: Fix KWStyle dashboard errors >> >> BUG: Fix external module BUILD_SHARED_LIBS status >> >> >> >> Mathieu Malaterre (1): >> >> BUG: Name mangle the included expat third party library. >> >> >> >> Matthew McCormick (94): >> >> ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest. >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >> >> ENH: Bump ITK version to 4.9.0. >> >> BUG: Remove std::cout calls from classes. >> >> COMP: Remove unused argument in ConditionVariableNoThreads. >> >> BUG: Implement UpdateLargestPossibleRegion for >> >> ImageToVTKImageFilter. >> >> COMP: Add link interface specification for wrapping >> >> target_link_libraries. >> >> STYLE: Fix indentation in itkMINCTransformIOFactory.cxx. >> >> COMP: Fix MINCTransformIO factory registration. >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1. >> >> COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR. >> >> BUG: Initialize mutex for 32 bit AtomicInt. >> >> ENH: Use CastXML binaries when building with x86_64 Linux. >> >> STYLE: Rename gccxml -> castxml in {idx,igenerator}.py. >> >> COMP: Disable the gold linker for static builds on Ubuntu 14.04. >> >> ENH: Use Windows binaries for CastXML. >> >> ENH: Add better scoping in igenerator.py. >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC. >> >> BUG: LevelSetsv4 used signed char instead of char. >> >> ENH: Add better scoping to idx.py. >> >> COMP: Define newSize and oldSize in VariableLengthVector. >> >> STYLE: Use prefix increment operator in ImageBase. >> >> DOC: Correct spelling of Continuous. >> >> ENH: Add more progress information to IterativeClosestPoint2. >> >> BUG: Build BridgeNumPy with Visual Studio. >> >> ENH: Add ITKModuleExternal.cmake >> >> COMP: Wrap Image< bool, D > for FlatStructuringElement. >> >> BUG: Use CastXML binary built in Release. >> >> BUG: ContinuousIndex should not be templated over TCoordRep. >> >> COMP: Set CMP0054 to new. >> >> COMP: Address line length too long for Software Guide. >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >> >> BUG: Support Python 3 wrapping module initialization. >> >> BUG: Update itkTemplate.py for Python 3. >> >> BUG: Update itkExtras.py for Python 3. >> >> BUG: Prevent Python callback addition recursion. >> >> BUG: Fix test scripts for Python 3. >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >> >> ENH: Allow projects to build against an external module. >> >> ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER. >> >> ENH: Rename _cable_ to _wrappers_. >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >> >> ENH: Bump CastXML version to 2015-30-29. >> >> ENH: Bump LLVM / Clang to 3.7.0. >> >> COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5. >> >> COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC. >> >> COMP: Use itkSimpleNewMacro in >> >> ThreadedIteratorRangePartitionerTest. >> >> ENH: Add wrapping support for building modules externally. >> >> BUG: Fix KWStyle test paths when building a module externally. >> >> ENH: Add Cuberille Remote module. >> >> COMP: Remove carriage returns from Cuberille remote. >> >> COMP: Remove unused argument in ConditionVariableNoThreads. >> >> DOC: Correct spelling of Continuous. >> >> ENH: Bump the MinimalPathExtraction Remote to 2015-10-20. >> >> COMP: Fix KernelTransform SetFixedParameters argument type. >> >> STYLE: Use prefix increment operator in ImageBase. >> >> COMP: Use ITK's pygccxml by correctly setting up the sys.path >> >> Revert "COMP: Put vnl_export.h in the list of sources so it gets >> >> installed." >> >> BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes" >> >> ENH: Marking wrapping CMake configuration variables as advanced. >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >> >> COMP: Non-virtual copy attribute members in LabelMap cannot have >> >> override. >> >> COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter. >> >> COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT. >> >> ENH: Remove CMake version check in ITKModuleHeaderTest.cmake >> >> BUG: Improve KWStyle ExternalProject utilization. >> >> ENH: Remove old KWStyle build script. >> >> COMP: Address VariableLengthVector Doxygen rhs @param not found. >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER. >> >> ENH: Install Python bindings into site-packages. >> >> ENH: Improve readability of Python site-packages path detection. >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned expression >> >> warning. >> >> BUG: ITKCommon publically depends on ITKDoubleConversion. >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >> >> ENH: Improves names and export of module dependencies. >> >> STYLE: Improve namespace bracket style in itkIsConvertible. >> >> COMP: Set CMP0054 to new. >> >> BUG: Remove unused wrapping files. >> >> BUG: Do install install wrapping development files. >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >> >> BUG: Remove duplicate inclusion of wrapping submodules. >> >> COMP: Do not use C++ style comments for Doxygen cond. >> >> BUG: Fix detection of the gold linker. >> >> BUG: Update Python package installation locations. >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >> >> ENH: Change BUILD_EXAMPLES default to OFF. >> >> BUG: Use 'from itk import ITKCommon' in module2module test. >> >> COMP: Link to VTK Python when built with Kits support. >> >> BUG: Install itk_minc2.h header. >> >> COMP: ITKIOMINC has a public dependency on ITKIOImageBase. >> >> >> >> Michka Popoff (9): >> >> ENH: Update to swig 3.0.7 >> >> ENH: Do not link against specific Python library on OS X >> >> COMP: Fix wrapping warnings when building with >> >> ITK_WRAP_IMAGE_DIMS=2 >> >> COMP: Add missing wrapping for TransformBase >> >> COMP: Use ITK's pygccxml by correctly setting up the sys.path >> >> COMP: Disable incompatible modules when using Python 3 wrapping >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >> >> ImageFilterBase >> >> module >> >> COMP: Disable incompatible modules when using Python 3 wrapping >> >> ENH: Allow operations on Indexes and Offsets in Python >> >> >> >> Mikhail Isakov (1): >> >> BUG: DiffusionTensor3DReconstruction segfault if no baseline image >> >> >> >> Nick Tustison (5): >> >> BUG: Set a default b-spline epsilon. >> >> ENH: Adding testing for closed loop. >> >> BUG: Updating B-spline classes with the same epsilon strategy. >> >> PERF: Switch vnl_vectors for fixed arrays. >> >> ENH: Point-set registration with time-varying B-spline. >> >> >> >> Olivier Commowick (3): >> >> BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen >> >> system >> >> BUG: Correct under/overflows in vnl_math_hypot (taken from pythag >> >> from V3P) >> >> BUG: Switch eigenvalues computation to double >> >> >> >> Pablo Hernandez-Cerdan (2): >> >> ENH: Help class for itkFlatStructuringElement with constructor >> >> from >> >> images. >> >> COMP: Fix test errors and warnings in FlatStructuringElement. >> >> >> >> Seun Odutola (1): >> >> COMP: Fixed name clash with Apple header (check Macro), renamed >> >> check >> >> to Check >> >> >> >> Shawn Waldon (1): >> >> COMP: Set target OS X version in environment for tools using >> >> compiler >> >> >> >> Simon Alexander (1): >> >> BUG: incorrect closest point computation >> >> >> >> Tobias Wood (2): >> >> BUG: LBFGSB was printing messages even with debug switched off. >> >> BUG: Removed an unguarded print statement. >> >> >> >> Vladimir S. FONOV (9): >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >> >> COMP: Changing the order of HDF5 library components >> >> COMP: Splitting up IOMINC module into two parts: MINC and >> >> Transform >> >> STYLE: updated comments to properly reference LIBMINC >> >> ENH: Add script to merge upstream MINC as a subtree >> >> MINC 2015-07-23 (c033d431) >> >> COMP: Update MINC CMake code >> >> MINC 2015-08-18 (6d7e3ba8) >> >> MINC 2015-09-13 (95cd5374) >> >> >> >> Xiaoxiao Liu (1): >> >> DOC: update email address for xiaoxiao. >> >> >> >> Zach Williamson (10): >> >> BUG: Use correct libraries for ImageFusion tests >> >> ENH: Consolidate Library Dependencies >> >> COMP: Add a missing link to Review module >> >> COMP: Use correct linking macro in DCMTK >> >> BUG: Use correct libraries for TestKernel tests >> >> COMP: Fix inconsistant naming of GPUPDEDeformableRegistration >> >> ENH: Use new linking system macros >> >> PERF: Avoid searching private dependencies for include directories >> >> COMP: Recover missing dependencies >> >> ENH: use new linking macros in Filtering module >> >> >> >> >> >> >> >> ----------------------------------------------------- >> >> Errors or omissions? Please fix them here: >> >> >> >> >> >> >> >> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >> >> _____________________________________ >> >> Powered by www.kitware.com >> >> >> >> Visit other Kitware open-source projects at >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> http://www.kitware.com/products/protraining.php >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Dec 2 10:26:19 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 2 Dec 2015 10:26:19 -0500 Subject: [ITK] [ANN] ITK 4.9 Release Candidate 2 is ready for testing! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.9 release candidate 2 has been tagged and is available for testing! Please take this opportunity to test the new features in the release candidate. To obtain the source code, git clone http://itk.org/ITK.git cd ITK git checkout -q --detach v4.9rc02 For more details, please see the Git documentation [1]. A few selected highlights for this release: * New Remote modules: the Cuberille module for smooth generation of meshes from binary segmentation images, and the AnisotropicDiffusionLBR module improved edge-preserving smoothing. * Build your own ITK module outside the source tree, add continuous integration testing on GitHub, and easily add Python wrapping for your C++ algorithms. * Python wrapping, including Python 3, builds faster with a more standard installation * Improved performance of itk::Image::GetPixel and operations on itk::VariableLengthVector?s * Generate a FlatStructuringElement from an image * Point-set registration with time-varying B-splines * Module dependencies can now be specified as public / private / compile / test Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review. The new module dependency specification mechanism may unearth missing dependencies for projects that use ITK COMPONENTS with the CMake find_package command. An Experimental build, which demonstrates how the test suite performs on your local build system, can be submitted to the dashboard [2] with: mkdir ../ITK-build cd ../ITK-build cmake ../ITK ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit Visual Studio builds must also add ?-C Release? to the ctest command. Notify the mailing list if there are any unexpected failures. Testing your own applications against the RC is also appreciated. Congratulations and well done to the 35 contributors to this release. We would especially like to recognize the new contributors: Mikhail Isakov, Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias Wood, Seun Odutola, Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach Williamson, Luc Hermitte, Laurentiu Nicola, and Floris Berendsen. The final release is scheduled for mid-December. [1] http://www.itk.org/Wiki/ITK/Git [2] http://open.cdash.org/index.php?project=Insight New Features --------------------- * Wrapping improvements * Python 3 supported * Wrapping builds much faster due to CastXML binaries * LandmarkBasedTransformInitializer now wrapped * NumPy bridge with VisualStudio * Wrapping for the MinimalPathExtraction module * Wrapping is now installed into Python?s site-packages directory in the ?itk? package * Wrapping package size is decreased * Better package portability on Mac OSX * New Remote Modules * Cuberille * Insight Journal Article: http://hdl.handle.net/10380/3186 * AnisotropicDiffusionLBR * Insight Journal Article: http://hdl.handle.net/10380/3505 * Web browser reproducibility: http://www.kitware.com/blog/home/post/942 * Core Improvements * External Modules can now be developed outside of the ITK source tree and on GitHub * Details: http://www.kitware.com/blog/home/post/997 * New utilities in itk::Math: * AlmostEquals * NotAlmostEquals * ExactlyEquals * NotExactlyEquals * New itk::NumericTraits * IsInteger * IsSigned * Improved C++11 support * New ITK_DELETE_FUNCTION macro for ?=delete? * New ITK_NOEXCEPT macro for the ?noexcept? keyword * Improved capabilities of itk::ResourceProbe and itk::ResourceProbesCollectorBase * Improve numerical stability in VNL eigen system estimation * itksys_ios:: and itksys_stl:: have been remove (use std::) * Filtering Improvements * Generate a FlatStructuringElement from an image * WarpImageFilter support VectorImage?s * ConvertLabelMap supports different LabelMap types * ImageToPathFilter moved from the ITKReview to the ITKPath module * itk::MovingHistogramImageFilter moved to the ITKImageFilterBase module * Registration Improvements * Point-set registration with time-varying B-splines * Build Improvements * Module dependencies can now be specified as public / private / compile / test * BUILD_EXAMPLES CMake option is now OFF by default * Option to export all library symbols on Windows: * Details: http://www.kitware.com/blog/home/post/939 * Expat third party library is now name mangled * Many more modules can be built as shared libraries * KWStyle is automatically built and configured when tests are built * Performance Improvements * New MetaProgrammingLibrary namespace (itk::mpl) holds members for metaprogramming * itk::mpl::{TrueType,FalseType} * itk::mpl::{If,Not,And,Or,Xor} * itk::mpl::EnableIf * itk::mpl::IsBaseOf * itk::mpl::IsConvertible * itk::mpl::IsNumber * itk::mpl::IsSame * itk::mpl::PromoteType * Image::GetPixel performance improvements * Many itk::VariableLengthVector performance improvements * AdaptiveHistogramEqualization uses a moving histogram * WarpImageFilter performance improvements * Documentation Improvements * Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples * ITK Software Guide improvements * How to use Python wrapping * How to create an ITK module * Improvements to segmentation examples * Expanded Canny edge detection example * Expanded tree container example * Third Party Library Updates * FFTW updated to latest upstream * Build with recent OpenCV 2 and 3 * Build with the latest VTK * PNG update to the latest upstream * GDCM updated to the latest upstream * KWSys updated to the latest upstream * MINC updated to the latest upstream * SWIG updated to the latest upstream * Third party PNG and MINC are now Git subtrees * Style improvements -- ITK gets more stylish with every release! * Private copy constructors and operator= use ITK_DELETE_FUNCTION * Improved code coverage -- we are at 84.9%! * *Lots* of important bug fixes * And much more! See details in the log below. Changes from v4.9rc01..v4.9rc02 ------------------------------------------------ Bill Lorensen (1): BUG: Valgrind detected an invalid read Davis Vigneault (1): STYLE: Address some warnings when running cppcheck Hyun Jae Kang (2): COMP: Fixed a warning message of data-conversion on VS14 COMP: Update KWStyle to remove format-string warning message Matthew McCormick (3): DOC: Remove invalid wrapping example. BUG: Wrap AdaptiveEqualizationHistogram. COMP: Ignore Doxygen endcond warning in itkIsConvertible.h. Seun Odutola (1): COMP: Corrected minc2.h path installation from libsrc2/minc2.h to minc2.h Ziv Yaniv (2): BUG: Affine transformation was estimated without sufficient number of points. BUG: fixed BSpline initializer crash when reference image not set. ----------------------------------------------------- Errors or omissions? Please fix them here: https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Wed Dec 2 16:16:31 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 2 Dec 2015 16:16:31 -0500 Subject: [ITK] [ITK-dev] Additional valgrind option Message-ID: Brad, Can you add --track-fds=yes to CTEST_MEMORYCHECK_COMMAND_OPTIONS on your valgrind build. This tracks dangling file descriptors. I just spent some time tracking down a file descriptor leak. Thanks, Bill _______________________________________________ Powered by www.kitware.com 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 hobbsk at ohio.edu Wed Dec 2 14:49:37 2015 From: hobbsk at ohio.edu (Kevin H. Hobbs) Date: Wed, 2 Dec 2015 14:49:37 -0500 Subject: [ITK] [ITK-users] Radius in itkVectorGradientMagnitudeImageFilter Message-ID: <565F4B51.6090602@ohio.edu> For the attached program I see no difference in the output between radius[0] = 1; radius[1] = 1; radius[2] = 1; and radius[0] = 8; radius[1] = 8; radius[2] = 8; The RadiusType m_NeighborhoodRadius is set, printed, and used to expand the requested region but the gradient calculations use central differences only between pixels adjacent to the neighborhood center : d_phi_du[i][j] = ... it.GetNext(i)[j] - it.GetPrevious(i)[j]... Should these be : NeighborhoodIndexType ri = m_NeighborhoodRadius[i]; d_phi_du[i][j] = ... it.GetNext(i,ri)[j] - it.GetPrevious(i,ri)[j]... ? -------------- next part -------------- A non-text attachment was scrubbed... Name: RGBGradMag.cxx Type: text/x-c++src Size: 1240 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 173 bytes Desc: OpenPGP digital signature URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Dec 3 07:17:47 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 3 Dec 2015 07:17:47 -0500 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: here are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. Today, 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/u/1/events/cg2up31ai44ehm19vei2ccbntak On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/1/events/csr5b35n2rjptaou6n2ampnppv4 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! -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Thu Dec 3 08:29:53 2015 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 3 Dec 2015 14:29:53 +0100 Subject: [ITK] [ITK-users] Merge N slices In-Reply-To: <754010856.21635.1449148943243.JavaMail.administrator@mjim.nabble.com> References: <754010856.21635.1449148943243.JavaMail.administrator@mjim.nabble.com> Message-ID: <566043D1.4040104@gmail.com> Hi Dominik, I do not have access anymore to this code... Anyway, In my case the orientation of all images were the same... In your case, since it is really generic problem, I would recommend computing first the final image origin, orientation, spacing, and so on, allocating and fill the buffer. On the ith image, you iterate compute the world location of the pixel, from that you compute the corresponding index location on the final image, then set the pixel... HTH Arnaud On 03.12.2015 14:22, dominik.hofer at gmail.com wrote: > Dear Arnaud Gelas, > > I'm working on merging some slice volumes together into one volume (they do not overlap, are not parallel and have spacing in between slices) and I came across your thread where you write that you have found a solution for this. My question is if you would be so kind to share it. :) > > Link to thread: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-combining-N-images-tp7586088p7586104.html > > Cheers, > Dominik > > _____________________________________ > Sent from http://itk-insight-users.2283740.n2.nabble.com > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lasso at queensu.ca Thu Dec 3 09:19:27 2015 From: lasso at queensu.ca (Andras Lasso) Date: Thu, 3 Dec 2015 14:19:27 +0000 Subject: [ITK] [ITK-users] Merge N slices In-Reply-To: <566043D1.4040104@gmail.com> References: <754010856.21635.1449148943243.JavaMail.administrator@mjim.nabble.com> <566043D1.4040104@gmail.com> Message-ID: Volume reconstruction from arbitrarily oriented slices is not a trivial problem. It has a large literature but only a very few open-source implementations. One implementation is in the Plus toolkit (www.plustoolkit.org). It is fairly fast and supports clipping, hole filling (there are almost always holes between the slices), automatic output volume extent computation, etc. You can download the installation package and run the VolumeReconstructor command-line tool to build a volume from slices. Detailed description and sample data are available here: http://perk-software.cs.queensu.ca/plus/doc/nightly/user/ApplicationVolumeReconstructor.html You can also link PlusLib into your own project and call volume reconstructor algorithm from there. See for example how the algorithm is used in the VolumeReconstructor: https://www.assembla.com/spaces/plus/subversion/source/HEAD/trunk/PlusLib/src/VolumeReconstruction/Testing/VolumeReconstructor.cxx Andras -----Original Message----- From: Community [mailto:community-bounces at itk.org] On Behalf Of Arnaud Gelas Sent: December 3, 2015 8:30 AM To: dominik.hofer at gmail.com Cc: insight-users at itk.org Subject: Re: [ITK] [ITK-users] Merge N slices Hi Dominik, I do not have access anymore to this code... Anyway, In my case the orientation of all images were the same... In your case, since it is really generic problem, I would recommend computing first the final image origin, orientation, spacing, and so on, allocating and fill the buffer. On the ith image, you iterate compute the world location of the pixel, from that you compute the corresponding index location on the final image, then set the pixel... HTH Arnaud On 03.12.2015 14:22, dominik.hofer at gmail.com wrote: > Dear Arnaud Gelas, > > I'm working on merging some slice volumes together into one volume > (they do not overlap, are not parallel and have spacing in between > slices) and I came across your thread where you write that you have > found a solution for this. My question is if you would be so kind to > share it. :) > > Link to thread: > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-combining-N-i > mages-tp7586088p7586104.html > > Cheers, > Dominik > > _____________________________________ > Sent from http://itk-insight-users.2283740.n2.nabble.com > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Dec 3 17:40:23 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 3 Dec 2015 17:40:23 -0500 Subject: [ITK] [ITK-users] Radius in itkVectorGradientMagnitudeImageFilter In-Reply-To: <565F4B51.6090602@ohio.edu> References: <565F4B51.6090602@ohio.edu> Message-ID: Hi Kevin, Using an offset other than 1 makes little sense to me. Can you check what is done in regular (non-vector) gradient magnitude? Regards, D?enan On Wed, Dec 2, 2015 at 2:49 PM, Kevin H. Hobbs wrote: > For the attached program I see no difference in the output between > > radius[0] = 1; > radius[1] = 1; > radius[2] = 1; > > and > > radius[0] = 8; > radius[1] = 8; > radius[2] = 8; > > The RadiusType m_NeighborhoodRadius is set, printed, and used to expand > the requested region but the gradient calculations use central > differences only between pixels adjacent to the neighborhood center : > > d_phi_du[i][j] = ... it.GetNext(i)[j] - it.GetPrevious(i)[j]... > > Should these be : > > NeighborhoodIndexType ri = m_NeighborhoodRadius[i]; > d_phi_du[i][j] = ... it.GetNext(i,ri)[j] - it.GetPrevious(i,ri)[j]... > > ? > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From brad at lowekamp.net Thu Dec 3 20:56:30 2015 From: brad at lowekamp.net (Bradley Lowekamp) Date: Thu, 3 Dec 2015 20:56:30 -0500 Subject: [ITK] [ITK-users] Radius in itkVectorGradientMagnitudeImageFilter In-Reply-To: <565F4B51.6090602@ohio.edu> References: <565F4B51.6090602@ohio.edu> Message-ID: <00BABB34-ECB5-4D00-BC97-6095EF722DDA@mail.nih.gov> Kevin, I recall being stumped by this filter when I tried ( and apparently didn?t ) wrap this class for SimpleITK. There were several odd behaviors. Looking at the code, it does not look like the NeighborhoodRadius is actually used for the computation in the algorithm. Likely this filter was based on another, and never fully cleaned up. I think that the neighborhood parameter could just be removed and the code cleaned up without a problem. Brad > On Dec 2, 2015, at 2:49 PM, Kevin H. Hobbs wrote: > > For the attached program I see no difference in the output between > > radius[0] = 1; > radius[1] = 1; > radius[2] = 1; > > and > > radius[0] = 8; > radius[1] = 8; > radius[2] = 8; > > The RadiusType m_NeighborhoodRadius is set, printed, and used to expand > the requested region but the gradient calculations use central > differences only between pixels adjacent to the neighborhood center : > > d_phi_du[i][j] = ... it.GetNext(i)[j] - it.GetPrevious(i)[j]... > > Should these be : > > NeighborhoodIndexType ri = m_NeighborhoodRadius[i]; > d_phi_du[i][j] = ... it.GetNext(i,ri)[j] - it.GetPrevious(i,ri)[j]... > > ? > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From skalexander at gmail.com Fri Dec 4 09:31:17 2015 From: skalexander at gmail.com (Simon Alexander) Date: Fri, 04 Dec 2015 14:31:17 +0000 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Hi all, Apologies I haven't been able to put much time into this, ran into some interesting challenges with VS2015 itself (at least in my configuration) hanging permanently when changing from debug to release mode, or vice versa. It seems the generated project files are a bit of a challenge for it. At any rate, I have narrowed down part of the issue at least to being not in the interpolate filter itself, but rather in the test driver code ... somewhere in the nested loops incrementing the underlying array elements is behaving incorrectly in release mode. I'll try and have a closer look this weekend. On Tue, 1 Dec 2015 at 09:49 Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov> wrote: > If you compile on window in Debug mode, those tests are known to take a > long time and time out. > > The options are to increase the timeout ( CTEST_TEST_TIMEOUT ) and/or > exclude the ?RUNS_LONG? label from the tests run. > > Here is a ctest script which does this: > https://open.cdash.org/viewNotes.php?buildid=4123585 > > HTH, > Brad > ------------------------------ > *From:* Simon Alexander [skalexander at gmail.com] > *Sent:* Tuesday, December 01, 2015 9:19 AM > *To:* Matt McCormick; D?enan Zuki? > *Cc:* insight-users at itk.org; Hyun Jae Kang; ITK > *Subject:* Re: [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is > ready for testing! > > Hi Matt, > > So I pulled origin/master and rebuilt last night. I have different > failures now, all by timeout: > > *Total Test time (real) = 6363.39 sec* > > *The following tests FAILED:* > * 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo > (Timeout)* > * 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo > (Timeout)* > * 728 - > itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout)* > * 2025 - itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest > (Timeout)* > *Errors while running CTest* > > > Any thoughts on what's going on there? > > > On Mon, 30 Nov 2015 at 20:42 Matt McCormick > wrote: > >> Hi Simon, >> >> I am returning from holiday, and also catching up on activity. >> >> >> Hyun Jae has taken care of the KWStyle warnings and the data conversion >> warning: >> >> http://review.source.kitware.com/#/c/20430/ >> http://review.source.kitware.com/#/c/20446/ >> >> >> And Dzenan and Bill have addressed Wiki examples errors: >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >> >> >> It is likely that the test failures on your build still remain. Did you >> want to take them on? >> >> Thanks, >> Matt >> >> On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? wrote: >> >>> Looking at the master branch is the right thing to do. I am not doing >>> any active development regarding this right now. >>> >>> On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander >>> wrote: >>> >>>> Hi All, >>>> >>>> I had hoped to be able to look at this over the weekend, but no such >>>> luck. Is there somewhere useful I can help with it now? Not sure what >>>> state we are in (or what branch). >>>> >>>> On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? wrote: >>>> >>>>> It turns out that all the compile errors were occurring in >>>>> WikiExamples. I solved all except one: >>>>> ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in >>>>> file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line >>>>> 23, but it should be judging from the comment on that line. >>>>> >>>>> For the rest, I created a pull request: >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>>>> >>>>> On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander < >>>>> skalexander at gmail.com> wrote: >>>>> >>>>>> Perfect. I'm under a deadline that is likely to eat the rest of the >>>>>> week but if that clears up I'll try and jump in earlier. >>>>>> >>>>>> On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? wrote: >>>>>> >>>>>>> OK I will work on it for an hour or two now, and I will make a >>>>>>> branch and push it to Gerrit so whoever wants can pick up from there and >>>>>>> keep updating it. >>>>>>> >>>>>>> On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander < >>>>>>> skalexander at gmail.com> wrote: >>>>>>> >>>>>>>> Makes sense. At this point I am unlikely to have time to look at >>>>>>>> this until Saturday, but have hopes for a few free hours there. >>>>>>>> >>>>>>>> On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Building git master from Nov 23rd with examples and testing >>>>>>>>> enabled I get 14 compile errors in VS2015 debug x64. Should we coordinate >>>>>>>>> our efforts in fixing them? >>>>>>>>> >>>>>>>>> On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander < >>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Two of the three failures look like truncation issues (like >>>>>>>>>> https://open.cdash.org/testDetails.php?test=395263772&build=4117158) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The other ( >>>>>>>>>> https://open.cdash.org/testDetails.php?test=395264938&build=4117158) >>>>>>>>>> is less obvious. >>>>>>>>>> >>>>>>>>>> If I have time this evening I'll try and have a look at these. >>>>>>>>>> >>>>>>>>>> Is your standard test build in 32 bit ? That might explain the >>>>>>>>>> difference if there are some underlying type assumptions, but not obvious >>>>>>>>>> why 2015 would trigger but not 2013. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, 25 Nov 2015 at 11:01 Matt McCormick < >>>>>>>>>> matt.mccormick at kitware.com> wrote: >>>>>>>>>> >>>>>>>>>>> Ah, cool! Here: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 >>>>>>>>>>> >>>>>>>>>>> Could you please look into the test failures? >>>>>>>>>>> >>>>>>>>>>> @Hyun Jae, could you please look into the KWStyle warnings? >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander < >>>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>>> > Sorry, if I wasn't clear - I submitted two builds yesterday >>>>>>>>>>> from SIMON-LAP, >>>>>>>>>>> > (actually 3 as I wasn't sure the config was right on the first >>>>>>>>>>> one). VS2013 >>>>>>>>>>> > was green, three failures on VS2015 (and 18 warnings). Looks >>>>>>>>>>> like a >>>>>>>>>>> > truncation problem on the resuts. >>>>>>>>>>> > >>>>>>>>>>> > On Wed, 25 Nov 2015 at 10:51 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> Hi Simon, >>>>>>>>>>> >> >>>>>>>>>>> >> Thanks for testing. >>>>>>>>>>> >> >>>>>>>>>>> >> We have a Visual Studio 2015 build on the dashboard that is >>>>>>>>>>> green: >>>>>>>>>>> >> >>>>>>>>>>> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >>>>>>>>>>> >> >>>>>>>>>>> >> Are there any different flags? Could you please submit an >>>>>>>>>>> Experimental >>>>>>>>>>> >> build? >>>>>>>>>>> >> >>>>>>>>>>> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test >>>>>>>>>>> -T Submit -C >>>>>>>>>>> >> Release >>>>>>>>>>> >> >>>>>>>>>>> >> from a fresh build tree. >>>>>>>>>>> >> >>>>>>>>>>> >> Thanks, >>>>>>>>>>> >> Matt >>>>>>>>>>> >> >>>>>>>>>>> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander < >>>>>>>>>>> skalexander at gmail.com> >>>>>>>>>>> >> wrote: >>>>>>>>>>> >> > Looks like a few problems with x64 build on visual studio >>>>>>>>>>> 2015 - do you >>>>>>>>>>> >> > have >>>>>>>>>>> >> > a test machine in this configuration? >>>>>>>>>>> >> > >>>>>>>>>>> >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> On behalf of the Insight Toolkit community, we are proud >>>>>>>>>>> to announce >>>>>>>>>>> >> >> that >>>>>>>>>>> >> >> ITK 4.9 release candidate 1 has been tagged and is >>>>>>>>>>> available for >>>>>>>>>>> >> >> testing! >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please take this opportunity to test the new features in >>>>>>>>>>> the release >>>>>>>>>>> >> >> candidate. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> To obtain the source code, >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> git clone http://itk.org/ITK.git >>>>>>>>>>> >> >> cd ITK >>>>>>>>>>> >> >> git checkout -q --detach v4.9rc01 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> For more details, please see the Git documentation [1]. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> A few selected highlights for this release: >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * New Remote modules: the Cuberille module for smooth >>>>>>>>>>> generation of >>>>>>>>>>> >> >> meshes >>>>>>>>>>> >> >> from binary segmentation images, and the >>>>>>>>>>> AnisotropicDiffusionLBR module >>>>>>>>>>> >> >> improved edge-preserving smoothing. >>>>>>>>>>> >> >> * Build your own ITK module outside the source tree, add >>>>>>>>>>> continuous >>>>>>>>>>> >> >> integration testing on GitHub, and easily add Python >>>>>>>>>>> wrapping for your >>>>>>>>>>> >> >> C++ >>>>>>>>>>> >> >> algorithms. >>>>>>>>>>> >> >> * Python wrapping, including Python 3, builds faster with >>>>>>>>>>> a more >>>>>>>>>>> >> >> standard >>>>>>>>>>> >> >> installation >>>>>>>>>>> >> >> * Improved performance of itk::Image::GetPixel and >>>>>>>>>>> operations on >>>>>>>>>>> >> >> itk::VariableLengthVector?s >>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>> private / >>>>>>>>>>> >> >> compile / >>>>>>>>>>> >> >> test >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please test the release candidate and share your >>>>>>>>>>> experiences on the >>>>>>>>>>> >> >> mailing list, issue tracker, and Gerrit Code Review. The >>>>>>>>>>> new module >>>>>>>>>>> >> >> dependency specification mechanism may unearth missing >>>>>>>>>>> dependencies for >>>>>>>>>>> >> >> projects that use ITK COMPONENTS with the CMake >>>>>>>>>>> find_package command. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> An Experimental build, which demonstrates how the test >>>>>>>>>>> suite performs >>>>>>>>>>> >> >> on >>>>>>>>>>> >> >> your local build system, can be submitted to the dashboard >>>>>>>>>>> [2] with: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> mkdir ../ITK-build >>>>>>>>>>> >> >> cd ../ITK-build >>>>>>>>>>> >> >> cmake ../ITK >>>>>>>>>>> >> >> ctest -j 4 -M Experimental -T Configure -T Build -T >>>>>>>>>>> Test -T Submit >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Visual Studio builds must also add ?-C Release? to the >>>>>>>>>>> ctest command. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Notify the mailing list if there are any unexpected >>>>>>>>>>> failures. Testing >>>>>>>>>>> >> >> your own applications against the RC is also appreciated. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Congratulations and well done to the 35 contributors to >>>>>>>>>>> this release. >>>>>>>>>>> >> >> We >>>>>>>>>>> >> >> would especially like to recognize the new contributors: >>>>>>>>>>> Mikhail >>>>>>>>>>> >> >> Isakov, >>>>>>>>>>> >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias >>>>>>>>>>> Wood, Seun >>>>>>>>>>> >> >> Odutola, >>>>>>>>>>> >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo >>>>>>>>>>> >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach >>>>>>>>>>> Williamson, >>>>>>>>>>> >> >> Luc >>>>>>>>>>> >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> The final release is scheduled for mid-December. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> [1] http://www.itk.org/Wiki/ITK/Git >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> [2] http://open.cdash.org/index.php?project=Insight >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> New Features >>>>>>>>>>> >> >> --------------------- >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Wrapping improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Python 3 supported >>>>>>>>>>> >> >> * Wrapping builds much faster due to CastXML binaries >>>>>>>>>>> >> >> * LandmarkBasedTransformInitializer now wrapped >>>>>>>>>>> >> >> * NumPy bridge with VisualStudio >>>>>>>>>>> >> >> * Wrapping for the MinimalPathExtraction module >>>>>>>>>>> >> >> * Wrapping is now installed into Python?s site-packages >>>>>>>>>>> directory in >>>>>>>>>>> >> >> the >>>>>>>>>>> >> >> ?itk? package >>>>>>>>>>> >> >> * Wrapping package size is decreased >>>>>>>>>>> >> >> * Better package portability on Mac OSX >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> New Remote Modules >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Cuberille >>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>> http://hdl.handle.net/10380/3186 >>>>>>>>>>> >> >> * AnisotropicDiffusionLBR >>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>> http://hdl.handle.net/10380/3505 >>>>>>>>>>> >> >> * Web browser reproducibility: >>>>>>>>>>> >> >> http://www.kitware.com/blog/home/post/942 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Core Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * External Modules can now be developed outside of the ITK >>>>>>>>>>> source tree >>>>>>>>>>> >> >> and >>>>>>>>>>> >> >> on GitHub >>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/997 >>>>>>>>>>> >> >> * New utilities in itk::Math: >>>>>>>>>>> >> >> * AlmostEquals >>>>>>>>>>> >> >> * NotAlmostEquals >>>>>>>>>>> >> >> * ExactlyEquals >>>>>>>>>>> >> >> * NotExactlyEquals >>>>>>>>>>> >> >> * New itk::NumericTraits >>>>>>>>>>> >> >> * IsInteger >>>>>>>>>>> >> >> * IsSigned >>>>>>>>>>> >> >> * Improved C++11 support >>>>>>>>>>> >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >>>>>>>>>>> >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >>>>>>>>>>> >> >> * Improved capabilities of itk::ResourceProbe and >>>>>>>>>>> >> >> itk::ResourceProbesCollectorBase >>>>>>>>>>> >> >> * Improve numerical stability in VNL eigen system >>>>>>>>>>> estimation >>>>>>>>>>> >> >> * itksys_ios:: and itksys_stl:: have been remove (use >>>>>>>>>>> std::) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Filtering Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>> >> >> * WarpImageFilter support VectorImage?s >>>>>>>>>>> >> >> * ConvertLabelMap supports different LabelMap types >>>>>>>>>>> >> >> * ImageToPathFilter moved from the ITKReview to the >>>>>>>>>>> ITKPath module >>>>>>>>>>> >> >> * itk::MovingHistogramImageFilter moved to the >>>>>>>>>>> ITKImageFilterBase >>>>>>>>>>> >> >> module >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Registration Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Build Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>> private / >>>>>>>>>>> >> >> compile / >>>>>>>>>>> >> >> test >>>>>>>>>>> >> >> * BUILD_EXAMPLES CMake option is now OFF by default >>>>>>>>>>> >> >> * Option to export all library symbols on Windows: >>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/939 >>>>>>>>>>> >> >> * Expat third party library is now name mangled >>>>>>>>>>> >> >> * Many more modules can be built as shared libraries >>>>>>>>>>> >> >> * KWStyle is automatically built and configured when tests >>>>>>>>>>> are built >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Performance Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds >>>>>>>>>>> members for >>>>>>>>>>> >> >> metaprogramming >>>>>>>>>>> >> >> * itk::mpl::{TrueType,FalseType} >>>>>>>>>>> >> >> * itk::mpl::{If,Not,And,Or,Xor} >>>>>>>>>>> >> >> * itk::mpl::EnableIf >>>>>>>>>>> >> >> * itk::mpl::IsBaseOf >>>>>>>>>>> >> >> * itk::mpl::IsConvertible >>>>>>>>>>> >> >> * itk::mpl::IsNumber >>>>>>>>>>> >> >> * itk::mpl::IsSame >>>>>>>>>>> >> >> * itk::mpl::PromoteType >>>>>>>>>>> >> >> * Image::GetPixel performance improvements >>>>>>>>>>> >> >> * Many itk::VariableLengthVector performance improvements >>>>>>>>>>> >> >> * AdaptiveHistogramEqualization uses a moving histogram >>>>>>>>>>> >> >> * WarpImageFilter performance improvements >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Documentation Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx >>>>>>>>>>> Examples >>>>>>>>>>> >> >> * ITK Software Guide improvements >>>>>>>>>>> >> >> * How to use Python wrapping >>>>>>>>>>> >> >> * How to create an ITK module >>>>>>>>>>> >> >> * Improvements to segmentation examples >>>>>>>>>>> >> >> * Expanded Canny edge detection example >>>>>>>>>>> >> >> * Expanded tree container example >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Third Party Library Updates >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * FFTW updated to latest upstream >>>>>>>>>>> >> >> * Build with recent OpenCV 2 and 3 >>>>>>>>>>> >> >> * Build with the latest VTK >>>>>>>>>>> >> >> * PNG update to the latest upstream >>>>>>>>>>> >> >> * GDCM updated to the latest upstream >>>>>>>>>>> >> >> * KWSys updated to the latest upstream >>>>>>>>>>> >> >> * MINC updated to the latest upstream >>>>>>>>>>> >> >> * SWIG updated to the latest upstream >>>>>>>>>>> >> >> * Third party PNG and MINC are now Git subtrees >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Style improvements -- ITK gets more stylish with every >>>>>>>>>>> release! >>>>>>>>>>> >> >> >>>>>>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Private copy constructors and operator= use >>>>>>>>>>> ITK_DELETE_FUNCTION >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Improved code coverage -- we are at 84.9%! >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * *Lots* of important bug fixes >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * And much more! See details in the log below. >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Changes from v4.8.0..v4.9rc01 >>>>>>>>>>> >> >> -------------------------------------------- >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Abhishek Tiwari (1): >>>>>>>>>>> >> >> BUG: "tmpImageIndex" not initialized to 0. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Adam Snyder (1): >>>>>>>>>>> >> >> PERF: Reworked MMI Threading using a per-thread buffer >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Alexander Leinoff (6): >>>>>>>>>>> >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >>>>>>>>>>> >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be >>>>>>>>>>> resolved. >>>>>>>>>>> >> >> ENH: Adds ExactlyEquals and NotExactlyEquals >>>>>>>>>>> functions to >>>>>>>>>>> >> >> itkMath.h >>>>>>>>>>> >> >> COMP: Removes floating-point equality checks >>>>>>>>>>> >> >> ENH: COMP: Adds support for complex values to >>>>>>>>>>> Math::AlmostEquals >>>>>>>>>>> >> >> ENH: Updates fftw dependency >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Arnaud Gelas (5): >>>>>>>>>>> >> >> COMP: fix warning (unused local typedef) >>>>>>>>>>> >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >>>>>>>>>>> >> >> DOC: add doxgen documentation for >>>>>>>>>>> >> >> BinaryImageToLevelSetImageAdaptor >>>>>>>>>>> >> >> ENH: add tests to exercise >>>>>>>>>>> itk::ThreadedIteratorRangePartitioner >>>>>>>>>>> >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Betsy McPhail (1): >>>>>>>>>>> >> >> BUG: Improve buffer alignment in OctreeNode . >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bill Hoffman (2): >>>>>>>>>>> >> >> ENH: Use new CMake Windows export symbol dll feature. >>>>>>>>>>> >> >> COMP: Put vnl_export.h in the list of sources so it >>>>>>>>>>> gets >>>>>>>>>>> >> >> installed. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bill Lorensen (4): >>>>>>>>>>> >> >> COMP: VTkGlue linker errors >>>>>>>>>>> >> >> BUG: Inappropriate use of AlmostEquals >>>>>>>>>>> >> >> ENH: Bump tag for wiki examples >>>>>>>>>>> >> >> ENH: Better layout strategy >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Brad King (3): >>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>> itksys_ios::* >>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>> itksys_stl::* >>>>>>>>>>> >> >> ENH: Update CMake Policy settings in >>>>>>>>>>> Testing/TestExternal project >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bradley Lowekamp (31): >>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>> construction >>>>>>>>>>> >> >> ENH: Enable base classes for templates of landmark >>>>>>>>>>> initializer >>>>>>>>>>> >> >> STYLE: Use "Swap" for ITK member name >>>>>>>>>>> >> >> BUG: Demonstrate Eigen analysis failure >>>>>>>>>>> >> >> BUG: Fix computation of Eigen analysis >>>>>>>>>>> >> >> ENH: Update DiscreteHessianGaussian Test baseline >>>>>>>>>>> >> >> ENH: Correctly demonstrate float point Eigen failure >>>>>>>>>>> >> >> ENH: compile vnl_math_hypot, and use at least double >>>>>>>>>>> >> >> ENH: Adding initial update script from used libpng >>>>>>>>>>> version. >>>>>>>>>>> >> >> ENH: removing non-subtree files for itkpng >>>>>>>>>>> >> >> ENH: Ported ITK changes for building to subtree >>>>>>>>>>> merged code >>>>>>>>>>> >> >> ENH: Update libpng update script for v1.6.9 >>>>>>>>>>> >> >> BUG: Use ParameterValueType for computation of >>>>>>>>>>> landmark affine >>>>>>>>>>> >> >> ENH: Wrap LandmarkBasedTransformInitializer >>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>> >> >> ENH: Update itkpng zlib, configuration, and rename >>>>>>>>>>> >> >> ENH: Update itkpng name mangling >>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>> ReferenceImage >>>>>>>>>>> >> >> ivar >>>>>>>>>>> >> >> BUG: Increase tolerance for >>>>>>>>>>> PhysicsBasedNonRigidRegistrationMethod >>>>>>>>>>> >> >> BUG: Demonstrate side effect on registration due to >>>>>>>>>>> BSplineScatter >>>>>>>>>>> >> >> change >>>>>>>>>>> >> >> ENH: Move MovingHistogramImageFilter base classes to >>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>> construction >>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>> ReferenceImage >>>>>>>>>>> >> >> ivar >>>>>>>>>>> >> >> ENH: Optimize AdaptiveHistogramEqualization with >>>>>>>>>>> MovingHistogram >>>>>>>>>>> >> >> base >>>>>>>>>>> >> >> COMP: address sign unsigned comparison warning >>>>>>>>>>> >> >> COMP: Address signed unsigned comparison warning >>>>>>>>>>> >> >> COMP: Address unused member variable and methods in >>>>>>>>>>> anonymous ns >>>>>>>>>>> >> >> BUG: Fix segfault when with empty IsolatedWatershed >>>>>>>>>>> Threshold >>>>>>>>>>> >> >> range >>>>>>>>>>> >> >> BUG: Adjust intensity tolerance for >>>>>>>>>>> PhysicsBasedNonRigid test >>>>>>>>>>> >> >> BUG: Reduce number of targets with MSVC >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Davis Vigneault (7): >>>>>>>>>>> >> >> DOC: Minor improvements to segmentation examples. >>>>>>>>>>> >> >> DOC: Expanded Canny Edge Detection Example >>>>>>>>>>> >> >> DOC: Expanded TreeContainer Example >>>>>>>>>>> >> >> COMP: Warnings in itkVTKImageExport when compiling >>>>>>>>>>> with c++11 >>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>> c++11 >>>>>>>>>>> >> >> COMP: Update Git Tag for Subdivision Module >>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>> c++11 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> D?enan Zuki? (1): >>>>>>>>>>> >> >> STYLE: better formatting of the "usage" message >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Eugene Prilepin (1): >>>>>>>>>>> >> >> BUG: Fix a template name formation in python wrappings >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Floris Berendsen (1): >>>>>>>>>>> >> >> STYLE: Improve naming conventions in comments. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Hans Johnson (29): >>>>>>>>>>> >> >> STYLE: Instrument for FixedParameters typedef >>>>>>>>>>> >> >> BUG: Demonstrate DisplacementTransformFailure >>>>>>>>>>> >> >> BUG: FixedParameters should be double precision >>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>> >> >> ENH: Provide consistent floating point comparisons >>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>> >> >> PERF: Remove floating point as sentinal value >>>>>>>>>>> >> >> COMP: Const correctness needs to be maintained >>>>>>>>>>> >> >> BUG: Preserve backwards compatibility >>>>>>>>>>> >> >> DOC: Provide consistent naming in comments >>>>>>>>>>> >> >> ENH: Conversion between transform type tolerance >>>>>>>>>>> >> >> STYLE: Prefer initialization to assignment >>>>>>>>>>> >> >> ENH: Missing ITK_OVERRIDE >>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>> >> >> COMP: Add missing ITK_OVERRIDE >>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>> >> >> ENH: C++11 allows for rigorous =delete >>>>>>>>>>> >> >> COMP: Remove unnecessary failing assert test >>>>>>>>>>> >> >> ENH: Ignore internal files for the Clion editor >>>>>>>>>>> >> >> COMP: Fix VNL compilation for wider C++11 support >>>>>>>>>>> >> >> BUG: In configuration test need to mirror code >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Hyun Jae Kang (27): >>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>> >> >> BUG: Avoid an unexpected output of static_cast >>>>>>>>>>> >> >> BUG: Update python example codes for ImageRegistration >>>>>>>>>>> >> >> BUG: Retrieve the missed wrap file >>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>> in VTK file >>>>>>>>>>> >> >> header. >>>>>>>>>>> >> >> BUG: Fix HDF5 CMake configuration with VS2015 >>>>>>>>>>> >> >> BUG: Fix a compilation issue on ITK4 with FFTW and >>>>>>>>>>> shared >>>>>>>>>>> >> >> libraries >>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>> Mac OS X >>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>> in VTK file >>>>>>>>>>> >> >> header. >>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>> >> >> ENH: Add automatic KWStyle build and configuration >>>>>>>>>>> setup >>>>>>>>>>> >> >> COMP: KWStyle shadow, format-nonliteral and >>>>>>>>>>> autological-compare >>>>>>>>>>> >> >> warning. >>>>>>>>>>> >> >> COMP: Fixed the warning messages from itkGPU Module >>>>>>>>>>> >> >> COMP: Fixed a warning message of unused-private-field >>>>>>>>>>> >> >> COMP: Apply latest version of KWStyle >>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>> messages >>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>> messages >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on Windows >>>>>>>>>>> >> >> ENH: Update itkResourceProbe to calculate statistical >>>>>>>>>>> data >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on VS14 >>>>>>>>>>> >> >> COMP: Fixed 'std::sqrt' : ambiguous call to >>>>>>>>>>> overloaded function >>>>>>>>>>> >> >> ENH: Update the Report() function of >>>>>>>>>>> >> >> itkResourceProbesCollectorBase >>>>>>>>>>> >> >> COMP: Fix data-conversion warning message on >>>>>>>>>>> itkResourceProbe >>>>>>>>>>> >> >> COMP: Fix additional warning messages of KWStyle >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Jon Haitz Legarreta (6): >>>>>>>>>>> >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >>>>>>>>>>> >> >> BUG: Fix compilation issues for >>>>>>>>>>> StatisticsUniqueLabelMapFilterTest >>>>>>>>>>> >> >> BUG: Fix comparison issues for >>>>>>>>>>> itkStatisticsUniqueLabelMapFilter >>>>>>>>>>> >> >> BUG: Test for StatisticsUniqueLabelMapFilter stability >>>>>>>>>>> >> >> ENH: Add test for >>>>>>>>>>> itkParametricStpaceToImageSpaceFilter >>>>>>>>>>> >> >> ENH: Improve code coverage for >>>>>>>>>>> >> >> itkParametricSpaceToImageSpaceMeshFilter >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Julien Michel (1): >>>>>>>>>>> >> >> ENH: Support of VectorImage as template parameters for >>>>>>>>>>> >> >> WarpImageFilter >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Junjie Bai (2): >>>>>>>>>>> >> >> BUG: ConvertLabelMap with different LabelMapTypes >>>>>>>>>>> >> >> BUG: LabelObject CopyAttribute support different >>>>>>>>>>> LabelObject type >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> KWSys Robot (4): >>>>>>>>>>> >> >> KWSys 2015-07-10 (c9336bcf) >>>>>>>>>>> >> >> KWSys 2015-07-30 (f63febb7) >>>>>>>>>>> >> >> KWSys 2015-08-24 (cdaf522c) >>>>>>>>>>> >> >> KWSys 2015-08-28 (dc3fdd7f) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> LIBPNG Upstream (2): >>>>>>>>>>> >> >> PNG 2009-04-06 (e68f5a36) >>>>>>>>>>> >> >> PNG 2014-02-05 (3e753eb8) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Laurentiu Nicola (2): >>>>>>>>>>> >> >> PERF: Avoid temporary smartptr in >>>>>>>>>>> ProcessObject::GetInput >>>>>>>>>>> >> >> PERF: Optimize WarpImageFilter by avoiding refcount >>>>>>>>>>> bouncing >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Luc Hermitte (8): >>>>>>>>>>> >> >> PERF: itk::Image::GetPixel() performance improvment. >>>>>>>>>>> >> >> PERF: Performance enhancements on >>>>>>>>>>> VariableLengthVectors 1/... >>>>>>>>>>> >> >> ENH: Dependencies on itkVariableLengthVector.h reduced >>>>>>>>>>> >> >> BUG: Error in VariableLengthVector Unit Tests >>>>>>>>>>> >> >> PERF: Performance enhancements on VLV 2/... >>>>>>>>>>> >> >> PERF: Performances enhancements on VLV 3/... >>>>>>>>>>> >> >> COMP: Fix signed/unsigned warnings >>>>>>>>>>> >> >> BUG: std::copy/fill on empty VLV >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Lucas Gandel (4): >>>>>>>>>>> >> >> ENH: Move ImageToPathFilter from ITKReview to ITKPath >>>>>>>>>>> module. >>>>>>>>>>> >> >> BUG: Fixing ImageToPathFilter wrapping call from >>>>>>>>>>> Review Module >>>>>>>>>>> >> >> STYLE: Fix KWStyle dashboard errors >>>>>>>>>>> >> >> BUG: Fix external module BUILD_SHARED_LIBS status >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Mathieu Malaterre (1): >>>>>>>>>>> >> >> BUG: Name mangle the included expat third party >>>>>>>>>>> library. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Matthew McCormick (94): >>>>>>>>>>> >> >> ENH: Change itkSystemInformationTest to >>>>>>>>>>> itkCMakeConfigurationTest. >>>>>>>>>>> >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >>>>>>>>>>> >> >> ENH: Bump ITK version to 4.9.0. >>>>>>>>>>> >> >> BUG: Remove std::cout calls from classes. >>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>> >> >> BUG: Implement UpdateLargestPossibleRegion for >>>>>>>>>>> >> >> ImageToVTKImageFilter. >>>>>>>>>>> >> >> COMP: Add link interface specification for wrapping >>>>>>>>>>> >> >> target_link_libraries. >>>>>>>>>>> >> >> STYLE: Fix indentation in >>>>>>>>>>> itkMINCTransformIOFactory.cxx. >>>>>>>>>>> >> >> COMP: Fix MINCTransformIO factory registration. >>>>>>>>>>> >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with >>>>>>>>>>> Emscripten-1. >>>>>>>>>>> >> >> COMP: Remove unknown doxygen command in >>>>>>>>>>> AnisotropicDiffusionLBR. >>>>>>>>>>> >> >> BUG: Initialize mutex for 32 bit AtomicInt. >>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>> Linux. >>>>>>>>>>> >> >> STYLE: Rename gccxml -> castxml in >>>>>>>>>>> {idx,igenerator}.py. >>>>>>>>>>> >> >> COMP: Disable the gold linker for static builds on >>>>>>>>>>> Ubuntu 14.04. >>>>>>>>>>> >> >> ENH: Use Windows binaries for CastXML. >>>>>>>>>>> >> >> ENH: Add better scoping in igenerator.py. >>>>>>>>>>> >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + >>>>>>>>>>> MSVC. >>>>>>>>>>> >> >> BUG: LevelSetsv4 used signed char instead of char. >>>>>>>>>>> >> >> ENH: Add better scoping to idx.py. >>>>>>>>>>> >> >> COMP: Define newSize and oldSize in >>>>>>>>>>> VariableLengthVector. >>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>> >> >> ENH: Add more progress information to >>>>>>>>>>> IterativeClosestPoint2. >>>>>>>>>>> >> >> BUG: Build BridgeNumPy with Visual Studio. >>>>>>>>>>> >> >> ENH: Add ITKModuleExternal.cmake >>>>>>>>>>> >> >> COMP: Wrap Image< bool, D > for >>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>> >> >> BUG: Use CastXML binary built in Release. >>>>>>>>>>> >> >> BUG: ContinuousIndex should not be templated over >>>>>>>>>>> TCoordRep. >>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>> >> >> COMP: Address line length too long for Software Guide. >>>>>>>>>>> >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >>>>>>>>>>> >> >> BUG: Support Python 3 wrapping module initialization. >>>>>>>>>>> >> >> BUG: Update itkTemplate.py for Python 3. >>>>>>>>>>> >> >> BUG: Update itkExtras.py for Python 3. >>>>>>>>>>> >> >> BUG: Prevent Python callback addition recursion. >>>>>>>>>>> >> >> BUG: Fix test scripts for Python 3. >>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>> >> >> ENH: Allow projects to build against an external >>>>>>>>>>> module. >>>>>>>>>>> >> >> ENH: Replace CABLE_CONFIGURATION with >>>>>>>>>>> ITK_WRAPPING_PARSER. >>>>>>>>>>> >> >> ENH: Rename _cable_ to _wrappers_. >>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>> >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >>>>>>>>>>> >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >>>>>>>>>>> >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >>>>>>>>>>> >> >> ENH: Bump CastXML version to 2015-30-29. >>>>>>>>>>> >> >> ENH: Bump LLVM / Clang to 3.7.0. >>>>>>>>>>> >> >> COMP: Avoid itklibminc linking with >>>>>>>>>>> ITK_USE_SYSTEM_HDF5. >>>>>>>>>>> >> >> COMP: Add missing ITKIOImageBase dependency for >>>>>>>>>>> ITKTransformMINC. >>>>>>>>>>> >> >> COMP: Use itkSimpleNewMacro in >>>>>>>>>>> >> >> ThreadedIteratorRangePartitionerTest. >>>>>>>>>>> >> >> ENH: Add wrapping support for building modules >>>>>>>>>>> externally. >>>>>>>>>>> >> >> BUG: Fix KWStyle test paths when building a module >>>>>>>>>>> externally. >>>>>>>>>>> >> >> ENH: Add Cuberille Remote module. >>>>>>>>>>> >> >> COMP: Remove carriage returns from Cuberille remote. >>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>> >> >> ENH: Bump the MinimalPathExtraction Remote to >>>>>>>>>>> 2015-10-20. >>>>>>>>>>> >> >> COMP: Fix KernelTransform SetFixedParameters argument >>>>>>>>>>> type. >>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>> sys.path >>>>>>>>>>> >> >> Revert "COMP: Put vnl_export.h in the list of sources >>>>>>>>>>> so it gets >>>>>>>>>>> >> >> installed." >>>>>>>>>>> >> >> BUG: Revert "BUG: ConvertLabelMap with different >>>>>>>>>>> LabelMapTypes" >>>>>>>>>>> >> >> ENH: Marking wrapping CMake configuration variables >>>>>>>>>>> as advanced. >>>>>>>>>>> >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >>>>>>>>>>> >> >> COMP: Non-virtual copy attribute members in LabelMap >>>>>>>>>>> cannot have >>>>>>>>>>> >> >> override. >>>>>>>>>>> >> >> COMP: Add wrapping for >>>>>>>>>>> AdaptiveHistogramEqualizationImageFilter. >>>>>>>>>>> >> >> COMP: Add itkMacro.h to itkPromoteType.h for >>>>>>>>>>> ITK_EXCEPT. >>>>>>>>>>> >> >> ENH: Remove CMake version check in >>>>>>>>>>> ITKModuleHeaderTest.cmake >>>>>>>>>>> >> >> BUG: Improve KWStyle ExternalProject utilization. >>>>>>>>>>> >> >> ENH: Remove old KWStyle build script. >>>>>>>>>>> >> >> COMP: Address VariableLengthVector Doxygen rhs @param >>>>>>>>>>> not found. >>>>>>>>>>> >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to >>>>>>>>>>> WRAPPING_SUBMODULE_ORDER. >>>>>>>>>>> >> >> ENH: Install Python bindings into site-packages. >>>>>>>>>>> >> >> ENH: Improve readability of Python site-packages path >>>>>>>>>>> detection. >>>>>>>>>>> >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned >>>>>>>>>>> expression >>>>>>>>>>> >> >> warning. >>>>>>>>>>> >> >> BUG: ITKCommon publically depends on >>>>>>>>>>> ITKDoubleConversion. >>>>>>>>>>> >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >>>>>>>>>>> >> >> ENH: Improves names and export of module dependencies. >>>>>>>>>>> >> >> STYLE: Improve namespace bracket style in >>>>>>>>>>> itkIsConvertible. >>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>> >> >> BUG: Remove unused wrapping files. >>>>>>>>>>> >> >> BUG: Do install install wrapping development files. >>>>>>>>>>> >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >>>>>>>>>>> >> >> BUG: Remove duplicate inclusion of wrapping >>>>>>>>>>> submodules. >>>>>>>>>>> >> >> COMP: Do not use C++ style comments for Doxygen cond. >>>>>>>>>>> >> >> BUG: Fix detection of the gold linker. >>>>>>>>>>> >> >> BUG: Update Python package installation locations. >>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >>>>>>>>>>> >> >> ENH: Change BUILD_EXAMPLES default to OFF. >>>>>>>>>>> >> >> BUG: Use 'from itk import ITKCommon' in module2module >>>>>>>>>>> test. >>>>>>>>>>> >> >> COMP: Link to VTK Python when built with Kits support. >>>>>>>>>>> >> >> BUG: Install itk_minc2.h header. >>>>>>>>>>> >> >> COMP: ITKIOMINC has a public dependency on >>>>>>>>>>> ITKIOImageBase. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Michka Popoff (9): >>>>>>>>>>> >> >> ENH: Update to swig 3.0.7 >>>>>>>>>>> >> >> ENH: Do not link against specific Python library on >>>>>>>>>>> OS X >>>>>>>>>>> >> >> COMP: Fix wrapping warnings when building with >>>>>>>>>>> >> >> ITK_WRAP_IMAGE_DIMS=2 >>>>>>>>>>> >> >> COMP: Add missing wrapping for TransformBase >>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>> sys.path >>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>> 3 wrapping >>>>>>>>>>> >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>> >> >> module >>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>> 3 wrapping >>>>>>>>>>> >> >> ENH: Allow operations on Indexes and Offsets in Python >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Mikhail Isakov (1): >>>>>>>>>>> >> >> BUG: DiffusionTensor3DReconstruction segfault if no >>>>>>>>>>> baseline image >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Nick Tustison (5): >>>>>>>>>>> >> >> BUG: Set a default b-spline epsilon. >>>>>>>>>>> >> >> ENH: Adding testing for closed loop. >>>>>>>>>>> >> >> BUG: Updating B-spline classes with the same epsilon >>>>>>>>>>> strategy. >>>>>>>>>>> >> >> PERF: Switch vnl_vectors for fixed arrays. >>>>>>>>>>> >> >> ENH: Point-set registration with time-varying >>>>>>>>>>> B-spline. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Olivier Commowick (3): >>>>>>>>>>> >> >> BUG: Correct discrepancy in tridiagonal reduction wrt >>>>>>>>>>> VNL eigen >>>>>>>>>>> >> >> system >>>>>>>>>>> >> >> BUG: Correct under/overflows in vnl_math_hypot (taken >>>>>>>>>>> from pythag >>>>>>>>>>> >> >> from V3P) >>>>>>>>>>> >> >> BUG: Switch eigenvalues computation to double >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Pablo Hernandez-Cerdan (2): >>>>>>>>>>> >> >> ENH: Help class for itkFlatStructuringElement with >>>>>>>>>>> constructor >>>>>>>>>>> >> >> from >>>>>>>>>>> >> >> images. >>>>>>>>>>> >> >> COMP: Fix test errors and warnings in >>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Seun Odutola (1): >>>>>>>>>>> >> >> COMP: Fixed name clash with Apple header (check >>>>>>>>>>> Macro), renamed >>>>>>>>>>> >> >> check >>>>>>>>>>> >> >> to Check >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Shawn Waldon (1): >>>>>>>>>>> >> >> COMP: Set target OS X version in environment for >>>>>>>>>>> tools using >>>>>>>>>>> >> >> compiler >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Simon Alexander (1): >>>>>>>>>>> >> >> BUG: incorrect closest point computation >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Tobias Wood (2): >>>>>>>>>>> >> >> BUG: LBFGSB was printing messages even with debug >>>>>>>>>>> switched off. >>>>>>>>>>> >> >> BUG: Removed an unguarded print statement. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Vladimir S. FONOV (9): >>>>>>>>>>> >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >>>>>>>>>>> >> >> COMP: Changing the order of HDF5 library components >>>>>>>>>>> >> >> COMP: Splitting up IOMINC module into two parts: MINC >>>>>>>>>>> and >>>>>>>>>>> >> >> Transform >>>>>>>>>>> >> >> STYLE: updated comments to properly reference LIBMINC >>>>>>>>>>> >> >> ENH: Add script to merge upstream MINC as a subtree >>>>>>>>>>> >> >> MINC 2015-07-23 (c033d431) >>>>>>>>>>> >> >> COMP: Update MINC CMake code >>>>>>>>>>> >> >> MINC 2015-08-18 (6d7e3ba8) >>>>>>>>>>> >> >> MINC 2015-09-13 (95cd5374) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Xiaoxiao Liu (1): >>>>>>>>>>> >> >> DOC: update email address for xiaoxiao. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Zach Williamson (10): >>>>>>>>>>> >> >> BUG: Use correct libraries for ImageFusion tests >>>>>>>>>>> >> >> ENH: Consolidate Library Dependencies >>>>>>>>>>> >> >> COMP: Add a missing link to Review module >>>>>>>>>>> >> >> COMP: Use correct linking macro in DCMTK >>>>>>>>>>> >> >> BUG: Use correct libraries for TestKernel tests >>>>>>>>>>> >> >> COMP: Fix inconsistant naming of >>>>>>>>>>> GPUPDEDeformableRegistration >>>>>>>>>>> >> >> ENH: Use new linking system macros >>>>>>>>>>> >> >> PERF: Avoid searching private dependencies for >>>>>>>>>>> include directories >>>>>>>>>>> >> >> COMP: Recover missing dependencies >>>>>>>>>>> >> >> ENH: use new linking macros in Filtering module >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> ----------------------------------------------------- >>>>>>>>>>> >> >> Errors or omissions? Please fix them here: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >>>>>>>>>>> >> >> _____________________________________ >>>>>>>>>>> >> >> Powered by www.kitware.com >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Visit other Kitware open-source projects at >>>>>>>>>>> >> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Kitware offers ITK Training Courses, for more information >>>>>>>>>>> visit: >>>>>>>>>>> >> >> http://www.kitware.com/products/protraining.php >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> >>>>>>>>> >>>>>>>>>> Powered by www.kitware.com >>>>>>>>>> >>>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>>> >>>>>>>>> http://kitware.com/products/protraining.php >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>> >>>>> >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From skalexander at gmail.com Fri Dec 4 09:31:17 2015 From: skalexander at gmail.com (Simon Alexander) Date: Fri, 04 Dec 2015 14:31:17 +0000 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Hi all, Apologies I haven't been able to put much time into this, ran into some interesting challenges with VS2015 itself (at least in my configuration) hanging permanently when changing from debug to release mode, or vice versa. It seems the generated project files are a bit of a challenge for it. At any rate, I have narrowed down part of the issue at least to being not in the interpolate filter itself, but rather in the test driver code ... somewhere in the nested loops incrementing the underlying array elements is behaving incorrectly in release mode. I'll try and have a closer look this weekend. On Tue, 1 Dec 2015 at 09:49 Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov> wrote: > If you compile on window in Debug mode, those tests are known to take a > long time and time out. > > The options are to increase the timeout ( CTEST_TEST_TIMEOUT ) and/or > exclude the ?RUNS_LONG? label from the tests run. > > Here is a ctest script which does this: > https://open.cdash.org/viewNotes.php?buildid=4123585 > > HTH, > Brad > ------------------------------ > *From:* Simon Alexander [skalexander at gmail.com] > *Sent:* Tuesday, December 01, 2015 9:19 AM > *To:* Matt McCormick; D?enan Zuki? > *Cc:* insight-users at itk.org; Hyun Jae Kang; ITK > *Subject:* Re: [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is > ready for testing! > > Hi Matt, > > So I pulled origin/master and rebuilt last night. I have different > failures now, all by timeout: > > *Total Test time (real) = 6363.39 sec* > > *The following tests FAILED:* > * 726 - itkFastMarchingImageFilterTest_wm_multipleSeeds_NoTopo > (Timeout)* > * 727 - itkFastMarchingImageFilterTest_wm_multipleSeeds_StrictTopo > (Timeout)* > * 728 - > itkFastMarchingImageFilterTest_wm_multipleSeeds_NoHandlesTopo (Timeout)* > * 2025 - itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest > (Timeout)* > *Errors while running CTest* > > > Any thoughts on what's going on there? > > > On Mon, 30 Nov 2015 at 20:42 Matt McCormick > wrote: > >> Hi Simon, >> >> I am returning from holiday, and also catching up on activity. >> >> >> Hyun Jae has taken care of the KWStyle warnings and the data conversion >> warning: >> >> http://review.source.kitware.com/#/c/20430/ >> http://review.source.kitware.com/#/c/20446/ >> >> >> And Dzenan and Bill have addressed Wiki examples errors: >> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >> >> >> It is likely that the test failures on your build still remain. Did you >> want to take them on? >> >> Thanks, >> Matt >> >> On Mon, Nov 30, 2015 at 2:00 PM, D?enan Zuki? wrote: >> >>> Looking at the master branch is the right thing to do. I am not doing >>> any active development regarding this right now. >>> >>> On Mon, Nov 30, 2015 at 1:53 PM, Simon Alexander >>> wrote: >>> >>>> Hi All, >>>> >>>> I had hoped to be able to look at this over the weekend, but no such >>>> luck. Is there somewhere useful I can help with it now? Not sure what >>>> state we are in (or what branch). >>>> >>>> On Wed, 25 Nov 2015 at 16:41 D?enan Zuki? wrote: >>>> >>>>> It turns out that all the compile errors were occurring in >>>>> WikiExamples. I solved all except one: >>>>> ITK_FIXED_PARAMETERS_ARE_DOUBLE is not defined in >>>>> file ITK\Modules\Remote\WikiExamples\Utilities\FileOutputWindow.cxx line >>>>> 23, but it should be judging from the comment on that line. >>>>> >>>>> For the rest, I created a pull request: >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/pull/3 >>>>> >>>>> On Wed, Nov 25, 2015 at 4:08 PM, Simon Alexander < >>>>> skalexander at gmail.com> wrote: >>>>> >>>>>> Perfect. I'm under a deadline that is likely to eat the rest of the >>>>>> week but if that clears up I'll try and jump in earlier. >>>>>> >>>>>> On Wed, 25 Nov 2015 at 16:06 D?enan Zuki? wrote: >>>>>> >>>>>>> OK I will work on it for an hour or two now, and I will make a >>>>>>> branch and push it to Gerrit so whoever wants can pick up from there and >>>>>>> keep updating it. >>>>>>> >>>>>>> On Wed, Nov 25, 2015 at 4:02 PM, Simon Alexander < >>>>>>> skalexander at gmail.com> wrote: >>>>>>> >>>>>>>> Makes sense. At this point I am unlikely to have time to look at >>>>>>>> this until Saturday, but have hopes for a few free hours there. >>>>>>>> >>>>>>>> On Wed, 25 Nov 2015 at 15:58 D?enan Zuki? >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Building git master from Nov 23rd with examples and testing >>>>>>>>> enabled I get 14 compile errors in VS2015 debug x64. Should we coordinate >>>>>>>>> our efforts in fixing them? >>>>>>>>> >>>>>>>>> On Wed, Nov 25, 2015 at 11:29 AM, Simon Alexander < >>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Two of the three failures look like truncation issues (like >>>>>>>>>> https://open.cdash.org/testDetails.php?test=395263772&build=4117158) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The other ( >>>>>>>>>> https://open.cdash.org/testDetails.php?test=395264938&build=4117158) >>>>>>>>>> is less obvious. >>>>>>>>>> >>>>>>>>>> If I have time this evening I'll try and have a look at these. >>>>>>>>>> >>>>>>>>>> Is your standard test build in 32 bit ? That might explain the >>>>>>>>>> difference if there are some underlying type assumptions, but not obvious >>>>>>>>>> why 2015 would trigger but not 2013. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, 25 Nov 2015 at 11:01 Matt McCormick < >>>>>>>>>> matt.mccormick at kitware.com> wrote: >>>>>>>>>> >>>>>>>>>>> Ah, cool! Here: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://open.cdash.org/viewBuildError.php?type=1&buildid=4117158 >>>>>>>>>>> >>>>>>>>>>> Could you please look into the test failures? >>>>>>>>>>> >>>>>>>>>>> @Hyun Jae, could you please look into the KWStyle warnings? >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Matt >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Wed, Nov 25, 2015 at 10:55 AM, Simon Alexander < >>>>>>>>>>> skalexander at gmail.com> wrote: >>>>>>>>>>> > Sorry, if I wasn't clear - I submitted two builds yesterday >>>>>>>>>>> from SIMON-LAP, >>>>>>>>>>> > (actually 3 as I wasn't sure the config was right on the first >>>>>>>>>>> one). VS2013 >>>>>>>>>>> > was green, three failures on VS2015 (and 18 warnings). Looks >>>>>>>>>>> like a >>>>>>>>>>> > truncation problem on the resuts. >>>>>>>>>>> > >>>>>>>>>>> > On Wed, 25 Nov 2015 at 10:51 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>> > wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> Hi Simon, >>>>>>>>>>> >> >>>>>>>>>>> >> Thanks for testing. >>>>>>>>>>> >> >>>>>>>>>>> >> We have a Visual Studio 2015 build on the dashboard that is >>>>>>>>>>> green: >>>>>>>>>>> >> >>>>>>>>>>> >> https://open.cdash.org/buildSummary.php?buildid=4117955 >>>>>>>>>>> >> >>>>>>>>>>> >> Are there any different flags? Could you please submit an >>>>>>>>>>> Experimental >>>>>>>>>>> >> build? >>>>>>>>>>> >> >>>>>>>>>>> >> ctest -j 4 -M Experimental -T Configure -T Build -T Test >>>>>>>>>>> -T Submit -C >>>>>>>>>>> >> Release >>>>>>>>>>> >> >>>>>>>>>>> >> from a fresh build tree. >>>>>>>>>>> >> >>>>>>>>>>> >> Thanks, >>>>>>>>>>> >> Matt >>>>>>>>>>> >> >>>>>>>>>>> >> On Wed, Nov 25, 2015 at 9:07 AM, Simon Alexander < >>>>>>>>>>> skalexander at gmail.com> >>>>>>>>>>> >> wrote: >>>>>>>>>>> >> > Looks like a few problems with x64 build on visual studio >>>>>>>>>>> 2015 - do you >>>>>>>>>>> >> > have >>>>>>>>>>> >> > a test machine in this configuration? >>>>>>>>>>> >> > >>>>>>>>>>> >> > On Mon, 23 Nov 2015 at 17:53 Matt McCormick < >>>>>>>>>>> matt.mccormick at kitware.com> >>>>>>>>>>> >> > wrote: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> On behalf of the Insight Toolkit community, we are proud >>>>>>>>>>> to announce >>>>>>>>>>> >> >> that >>>>>>>>>>> >> >> ITK 4.9 release candidate 1 has been tagged and is >>>>>>>>>>> available for >>>>>>>>>>> >> >> testing! >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please take this opportunity to test the new features in >>>>>>>>>>> the release >>>>>>>>>>> >> >> candidate. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> To obtain the source code, >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> git clone http://itk.org/ITK.git >>>>>>>>>>> >> >> cd ITK >>>>>>>>>>> >> >> git checkout -q --detach v4.9rc01 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> For more details, please see the Git documentation [1]. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> A few selected highlights for this release: >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * New Remote modules: the Cuberille module for smooth >>>>>>>>>>> generation of >>>>>>>>>>> >> >> meshes >>>>>>>>>>> >> >> from binary segmentation images, and the >>>>>>>>>>> AnisotropicDiffusionLBR module >>>>>>>>>>> >> >> improved edge-preserving smoothing. >>>>>>>>>>> >> >> * Build your own ITK module outside the source tree, add >>>>>>>>>>> continuous >>>>>>>>>>> >> >> integration testing on GitHub, and easily add Python >>>>>>>>>>> wrapping for your >>>>>>>>>>> >> >> C++ >>>>>>>>>>> >> >> algorithms. >>>>>>>>>>> >> >> * Python wrapping, including Python 3, builds faster with >>>>>>>>>>> a more >>>>>>>>>>> >> >> standard >>>>>>>>>>> >> >> installation >>>>>>>>>>> >> >> * Improved performance of itk::Image::GetPixel and >>>>>>>>>>> operations on >>>>>>>>>>> >> >> itk::VariableLengthVector?s >>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>> private / >>>>>>>>>>> >> >> compile / >>>>>>>>>>> >> >> test >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please test the release candidate and share your >>>>>>>>>>> experiences on the >>>>>>>>>>> >> >> mailing list, issue tracker, and Gerrit Code Review. The >>>>>>>>>>> new module >>>>>>>>>>> >> >> dependency specification mechanism may unearth missing >>>>>>>>>>> dependencies for >>>>>>>>>>> >> >> projects that use ITK COMPONENTS with the CMake >>>>>>>>>>> find_package command. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> An Experimental build, which demonstrates how the test >>>>>>>>>>> suite performs >>>>>>>>>>> >> >> on >>>>>>>>>>> >> >> your local build system, can be submitted to the dashboard >>>>>>>>>>> [2] with: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> mkdir ../ITK-build >>>>>>>>>>> >> >> cd ../ITK-build >>>>>>>>>>> >> >> cmake ../ITK >>>>>>>>>>> >> >> ctest -j 4 -M Experimental -T Configure -T Build -T >>>>>>>>>>> Test -T Submit >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Visual Studio builds must also add ?-C Release? to the >>>>>>>>>>> ctest command. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Notify the mailing list if there are any unexpected >>>>>>>>>>> failures. Testing >>>>>>>>>>> >> >> your own applications against the RC is also appreciated. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Congratulations and well done to the 35 contributors to >>>>>>>>>>> this release. >>>>>>>>>>> >> >> We >>>>>>>>>>> >> >> would especially like to recognize the new contributors: >>>>>>>>>>> Mikhail >>>>>>>>>>> >> >> Isakov, >>>>>>>>>>> >> >> Betsy McPhail, Alexander Leinoff, Shawn Waldon, Tobias >>>>>>>>>>> Wood, Seun >>>>>>>>>>> >> >> Odutola, >>>>>>>>>>> >> >> Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Pablo >>>>>>>>>>> >> >> Hernandez-Cerdan, Abhishek Tiwari, Eugene Prilepin, Zach >>>>>>>>>>> Williamson, >>>>>>>>>>> >> >> Luc >>>>>>>>>>> >> >> Hermitte, Laurentiu Nicola, and Floris Berendsen. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> The final release is scheduled for mid-December. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> [1] http://www.itk.org/Wiki/ITK/Git >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> [2] http://open.cdash.org/index.php?project=Insight >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> New Features >>>>>>>>>>> >> >> --------------------- >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Wrapping improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Python 3 supported >>>>>>>>>>> >> >> * Wrapping builds much faster due to CastXML binaries >>>>>>>>>>> >> >> * LandmarkBasedTransformInitializer now wrapped >>>>>>>>>>> >> >> * NumPy bridge with VisualStudio >>>>>>>>>>> >> >> * Wrapping for the MinimalPathExtraction module >>>>>>>>>>> >> >> * Wrapping is now installed into Python?s site-packages >>>>>>>>>>> directory in >>>>>>>>>>> >> >> the >>>>>>>>>>> >> >> ?itk? package >>>>>>>>>>> >> >> * Wrapping package size is decreased >>>>>>>>>>> >> >> * Better package portability on Mac OSX >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> New Remote Modules >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Cuberille >>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>> http://hdl.handle.net/10380/3186 >>>>>>>>>>> >> >> * AnisotropicDiffusionLBR >>>>>>>>>>> >> >> * Insight Journal Article: >>>>>>>>>>> http://hdl.handle.net/10380/3505 >>>>>>>>>>> >> >> * Web browser reproducibility: >>>>>>>>>>> >> >> http://www.kitware.com/blog/home/post/942 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Core Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * External Modules can now be developed outside of the ITK >>>>>>>>>>> source tree >>>>>>>>>>> >> >> and >>>>>>>>>>> >> >> on GitHub >>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/997 >>>>>>>>>>> >> >> * New utilities in itk::Math: >>>>>>>>>>> >> >> * AlmostEquals >>>>>>>>>>> >> >> * NotAlmostEquals >>>>>>>>>>> >> >> * ExactlyEquals >>>>>>>>>>> >> >> * NotExactlyEquals >>>>>>>>>>> >> >> * New itk::NumericTraits >>>>>>>>>>> >> >> * IsInteger >>>>>>>>>>> >> >> * IsSigned >>>>>>>>>>> >> >> * Improved C++11 support >>>>>>>>>>> >> >> * New ITK_DELETE_FUNCTION macro for ?=delete? >>>>>>>>>>> >> >> * New ITK_NOEXCEPT macro for the ?noexcept? keyword >>>>>>>>>>> >> >> * Improved capabilities of itk::ResourceProbe and >>>>>>>>>>> >> >> itk::ResourceProbesCollectorBase >>>>>>>>>>> >> >> * Improve numerical stability in VNL eigen system >>>>>>>>>>> estimation >>>>>>>>>>> >> >> * itksys_ios:: and itksys_stl:: have been remove (use >>>>>>>>>>> std::) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Filtering Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Generate a FlatStructuringElement from an image >>>>>>>>>>> >> >> * WarpImageFilter support VectorImage?s >>>>>>>>>>> >> >> * ConvertLabelMap supports different LabelMap types >>>>>>>>>>> >> >> * ImageToPathFilter moved from the ITKReview to the >>>>>>>>>>> ITKPath module >>>>>>>>>>> >> >> * itk::MovingHistogramImageFilter moved to the >>>>>>>>>>> ITKImageFilterBase >>>>>>>>>>> >> >> module >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Registration Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Point-set registration with time-varying B-splines >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Build Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Module dependencies can now be specified as public / >>>>>>>>>>> private / >>>>>>>>>>> >> >> compile / >>>>>>>>>>> >> >> test >>>>>>>>>>> >> >> * BUILD_EXAMPLES CMake option is now OFF by default >>>>>>>>>>> >> >> * Option to export all library symbols on Windows: >>>>>>>>>>> >> >> * Details: http://www.kitware.com/blog/home/post/939 >>>>>>>>>>> >> >> * Expat third party library is now name mangled >>>>>>>>>>> >> >> * Many more modules can be built as shared libraries >>>>>>>>>>> >> >> * KWStyle is automatically built and configured when tests >>>>>>>>>>> are built >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Performance Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * New MetaProgrammingLibrary namespace (itk::mpl) holds >>>>>>>>>>> members for >>>>>>>>>>> >> >> metaprogramming >>>>>>>>>>> >> >> * itk::mpl::{TrueType,FalseType} >>>>>>>>>>> >> >> * itk::mpl::{If,Not,And,Or,Xor} >>>>>>>>>>> >> >> * itk::mpl::EnableIf >>>>>>>>>>> >> >> * itk::mpl::IsBaseOf >>>>>>>>>>> >> >> * itk::mpl::IsConvertible >>>>>>>>>>> >> >> * itk::mpl::IsNumber >>>>>>>>>>> >> >> * itk::mpl::IsSame >>>>>>>>>>> >> >> * itk::mpl::PromoteType >>>>>>>>>>> >> >> * Image::GetPixel performance improvements >>>>>>>>>>> >> >> * Many itk::VariableLengthVector performance improvements >>>>>>>>>>> >> >> * AdaptiveHistogramEqualization uses a moving histogram >>>>>>>>>>> >> >> * WarpImageFilter performance improvements >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Documentation Improvements >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Updates to the Software Guide, Doxygen, Wiki and Sphinx >>>>>>>>>>> Examples >>>>>>>>>>> >> >> * ITK Software Guide improvements >>>>>>>>>>> >> >> * How to use Python wrapping >>>>>>>>>>> >> >> * How to create an ITK module >>>>>>>>>>> >> >> * Improvements to segmentation examples >>>>>>>>>>> >> >> * Expanded Canny edge detection example >>>>>>>>>>> >> >> * Expanded tree container example >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Third Party Library Updates >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * FFTW updated to latest upstream >>>>>>>>>>> >> >> * Build with recent OpenCV 2 and 3 >>>>>>>>>>> >> >> * Build with the latest VTK >>>>>>>>>>> >> >> * PNG update to the latest upstream >>>>>>>>>>> >> >> * GDCM updated to the latest upstream >>>>>>>>>>> >> >> * KWSys updated to the latest upstream >>>>>>>>>>> >> >> * MINC updated to the latest upstream >>>>>>>>>>> >> >> * SWIG updated to the latest upstream >>>>>>>>>>> >> >> * Third party PNG and MINC are now Git subtrees >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Style improvements -- ITK gets more stylish with every >>>>>>>>>>> release! >>>>>>>>>>> >> >> >>>>>>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * Private copy constructors and operator= use >>>>>>>>>>> ITK_DELETE_FUNCTION >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Improved code coverage -- we are at 84.9%! >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * *Lots* of important bug fixes >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> * And much more! See details in the log below. >>>>>>>>>>> >> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Changes from v4.8.0..v4.9rc01 >>>>>>>>>>> >> >> -------------------------------------------- >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Abhishek Tiwari (1): >>>>>>>>>>> >> >> BUG: "tmpImageIndex" not initialized to 0. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Adam Snyder (1): >>>>>>>>>>> >> >> PERF: Reworked MMI Threading using a per-thread buffer >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Alexander Leinoff (6): >>>>>>>>>>> >> >> ENH: Adds IsInteger and IsSigned to NumericTraits. >>>>>>>>>>> >> >> COMP: Doxygen itkMath.h 'OneValue()' could not be >>>>>>>>>>> resolved. >>>>>>>>>>> >> >> ENH: Adds ExactlyEquals and NotExactlyEquals >>>>>>>>>>> functions to >>>>>>>>>>> >> >> itkMath.h >>>>>>>>>>> >> >> COMP: Removes floating-point equality checks >>>>>>>>>>> >> >> ENH: COMP: Adds support for complex values to >>>>>>>>>>> Math::AlmostEquals >>>>>>>>>>> >> >> ENH: Updates fftw dependency >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Arnaud Gelas (5): >>>>>>>>>>> >> >> COMP: fix warning (unused local typedef) >>>>>>>>>>> >> >> COMP: simplify ITKVideoBridgeOpenCV dependency >>>>>>>>>>> >> >> DOC: add doxgen documentation for >>>>>>>>>>> >> >> BinaryImageToLevelSetImageAdaptor >>>>>>>>>>> >> >> ENH: add tests to exercise >>>>>>>>>>> itk::ThreadedIteratorRangePartitioner >>>>>>>>>>> >> >> COMP: fix compilation error with OpenCV2 and OpenCV3 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Betsy McPhail (1): >>>>>>>>>>> >> >> BUG: Improve buffer alignment in OctreeNode . >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bill Hoffman (2): >>>>>>>>>>> >> >> ENH: Use new CMake Windows export symbol dll feature. >>>>>>>>>>> >> >> COMP: Put vnl_export.h in the list of sources so it >>>>>>>>>>> gets >>>>>>>>>>> >> >> installed. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bill Lorensen (4): >>>>>>>>>>> >> >> COMP: VTkGlue linker errors >>>>>>>>>>> >> >> BUG: Inappropriate use of AlmostEquals >>>>>>>>>>> >> >> ENH: Bump tag for wiki examples >>>>>>>>>>> >> >> ENH: Better layout strategy >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Brad King (3): >>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>> itksys_ios::* >>>>>>>>>>> >> >> ENH: Remove use of include and >>>>>>>>>>> itksys_stl::* >>>>>>>>>>> >> >> ENH: Update CMake Policy settings in >>>>>>>>>>> Testing/TestExternal project >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Bradley Lowekamp (31): >>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>> construction >>>>>>>>>>> >> >> ENH: Enable base classes for templates of landmark >>>>>>>>>>> initializer >>>>>>>>>>> >> >> STYLE: Use "Swap" for ITK member name >>>>>>>>>>> >> >> BUG: Demonstrate Eigen analysis failure >>>>>>>>>>> >> >> BUG: Fix computation of Eigen analysis >>>>>>>>>>> >> >> ENH: Update DiscreteHessianGaussian Test baseline >>>>>>>>>>> >> >> ENH: Correctly demonstrate float point Eigen failure >>>>>>>>>>> >> >> ENH: compile vnl_math_hypot, and use at least double >>>>>>>>>>> >> >> ENH: Adding initial update script from used libpng >>>>>>>>>>> version. >>>>>>>>>>> >> >> ENH: removing non-subtree files for itkpng >>>>>>>>>>> >> >> ENH: Ported ITK changes for building to subtree >>>>>>>>>>> merged code >>>>>>>>>>> >> >> ENH: Update libpng update script for v1.6.9 >>>>>>>>>>> >> >> BUG: Use ParameterValueType for computation of >>>>>>>>>>> landmark affine >>>>>>>>>>> >> >> ENH: Wrap LandmarkBasedTransformInitializer >>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>> >> >> ENH: Update itkpng zlib, configuration, and rename >>>>>>>>>>> >> >> ENH: Update itkpng name mangling >>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>> ReferenceImage >>>>>>>>>>> >> >> ivar >>>>>>>>>>> >> >> BUG: Increase tolerance for >>>>>>>>>>> PhysicsBasedNonRigidRegistrationMethod >>>>>>>>>>> >> >> BUG: Demonstrate side effect on registration due to >>>>>>>>>>> BSplineScatter >>>>>>>>>>> >> >> change >>>>>>>>>>> >> >> ENH: Move MovingHistogramImageFilter base classes to >>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>> >> >> BUG: Avoid potential exception in >>>>>>>>>>> itk::Object::UnRegister >>>>>>>>>>> >> >> BUG: Avoid null deference in PrintSelf with default >>>>>>>>>>> construction >>>>>>>>>>> >> >> BUG: Use const pointer in Set method for constant >>>>>>>>>>> ReferenceImage >>>>>>>>>>> >> >> ivar >>>>>>>>>>> >> >> ENH: Optimize AdaptiveHistogramEqualization with >>>>>>>>>>> MovingHistogram >>>>>>>>>>> >> >> base >>>>>>>>>>> >> >> COMP: address sign unsigned comparison warning >>>>>>>>>>> >> >> COMP: Address signed unsigned comparison warning >>>>>>>>>>> >> >> COMP: Address unused member variable and methods in >>>>>>>>>>> anonymous ns >>>>>>>>>>> >> >> BUG: Fix segfault when with empty IsolatedWatershed >>>>>>>>>>> Threshold >>>>>>>>>>> >> >> range >>>>>>>>>>> >> >> BUG: Adjust intensity tolerance for >>>>>>>>>>> PhysicsBasedNonRigid test >>>>>>>>>>> >> >> BUG: Reduce number of targets with MSVC >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Davis Vigneault (7): >>>>>>>>>>> >> >> DOC: Minor improvements to segmentation examples. >>>>>>>>>>> >> >> DOC: Expanded Canny Edge Detection Example >>>>>>>>>>> >> >> DOC: Expanded TreeContainer Example >>>>>>>>>>> >> >> COMP: Warnings in itkVTKImageExport when compiling >>>>>>>>>>> with c++11 >>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>> c++11 >>>>>>>>>>> >> >> COMP: Update Git Tag for Subdivision Module >>>>>>>>>>> >> >> COMP: Warnings in FFTW Classes when compiling with >>>>>>>>>>> c++11 >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> D?enan Zuki? (1): >>>>>>>>>>> >> >> STYLE: better formatting of the "usage" message >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Eugene Prilepin (1): >>>>>>>>>>> >> >> BUG: Fix a template name formation in python wrappings >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Floris Berendsen (1): >>>>>>>>>>> >> >> STYLE: Improve naming conventions in comments. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Hans Johnson (29): >>>>>>>>>>> >> >> STYLE: Instrument for FixedParameters typedef >>>>>>>>>>> >> >> BUG: Demonstrate DisplacementTransformFailure >>>>>>>>>>> >> >> BUG: FixedParameters should be double precision >>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>> >> >> ENH: Provide consistent floating point comparisons >>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>> >> >> PERF: Remove floating point as sentinal value >>>>>>>>>>> >> >> COMP: Const correctness needs to be maintained >>>>>>>>>>> >> >> BUG: Preserve backwards compatibility >>>>>>>>>>> >> >> DOC: Provide consistent naming in comments >>>>>>>>>>> >> >> ENH: Conversion between transform type tolerance >>>>>>>>>>> >> >> STYLE: Prefer initialization to assignment >>>>>>>>>>> >> >> ENH: Missing ITK_OVERRIDE >>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>> >> >> COMP: Need to propagate ITKGDCM >>>>>>>>>>> >> >> COMP: Add missing ITK_OVERRIDE >>>>>>>>>>> >> >> STYLE: Minor code style issues for MGHIO >>>>>>>>>>> >> >> COMP: Update to version for WikiExamples >>>>>>>>>>> >> >> ENH: Update Sphinx for ITK 4.8.0 >>>>>>>>>>> >> >> ENH: Update MGHIO to be shared lib >>>>>>>>>>> >> >> BUG: Fix MGHIO to fix write failures >>>>>>>>>>> >> >> ENH: C++11 allows for rigorous =delete >>>>>>>>>>> >> >> COMP: Remove unnecessary failing assert test >>>>>>>>>>> >> >> ENH: Ignore internal files for the Clion editor >>>>>>>>>>> >> >> COMP: Fix VNL compilation for wider C++11 support >>>>>>>>>>> >> >> BUG: In configuration test need to mirror code >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Hyun Jae Kang (27): >>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>> >> >> BUG: Avoid an unexpected output of static_cast >>>>>>>>>>> >> >> BUG: Update python example codes for ImageRegistration >>>>>>>>>>> >> >> BUG: Retrieve the missed wrap file >>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>> in VTK file >>>>>>>>>>> >> >> header. >>>>>>>>>>> >> >> BUG: Fix HDF5 CMake configuration with VS2015 >>>>>>>>>>> >> >> BUG: Fix a compilation issue on ITK4 with FFTW and >>>>>>>>>>> shared >>>>>>>>>>> >> >> libraries >>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>> Mac OS X >>>>>>>>>>> >> >> BUG: Remove std::cout calls from class >>>>>>>>>>> >> >> BUG: itkVTKImageIO class does not handle blank lines >>>>>>>>>>> in VTK file >>>>>>>>>>> >> >> header. >>>>>>>>>>> >> >> BUG: Fixed older XCode linking error >>>>>>>>>>> >> >> ENH: Add automatic KWStyle build and configuration >>>>>>>>>>> setup >>>>>>>>>>> >> >> COMP: KWStyle shadow, format-nonliteral and >>>>>>>>>>> autological-compare >>>>>>>>>>> >> >> warning. >>>>>>>>>>> >> >> COMP: Fixed the warning messages from itkGPU Module >>>>>>>>>>> >> >> COMP: Fixed a warning message of unused-private-field >>>>>>>>>>> >> >> COMP: Apply latest version of KWStyle >>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>> messages >>>>>>>>>>> >> >> COMP: Update KWStyle to fix its additional warning >>>>>>>>>>> messages >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on Windows >>>>>>>>>>> >> >> ENH: Update itkResourceProbe to calculate statistical >>>>>>>>>>> data >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages on VS14 >>>>>>>>>>> >> >> COMP: Fixed 'std::sqrt' : ambiguous call to >>>>>>>>>>> overloaded function >>>>>>>>>>> >> >> ENH: Update the Report() function of >>>>>>>>>>> >> >> itkResourceProbesCollectorBase >>>>>>>>>>> >> >> COMP: Fix data-conversion warning message on >>>>>>>>>>> itkResourceProbe >>>>>>>>>>> >> >> COMP: Fix additional warning messages of KWStyle >>>>>>>>>>> >> >> COMP: Fix data-conversion warning messages >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Jon Haitz Legarreta (6): >>>>>>>>>>> >> >> ENH: Add test for itkStatisticsUniqueLabelMapFilter >>>>>>>>>>> >> >> BUG: Fix compilation issues for >>>>>>>>>>> StatisticsUniqueLabelMapFilterTest >>>>>>>>>>> >> >> BUG: Fix comparison issues for >>>>>>>>>>> itkStatisticsUniqueLabelMapFilter >>>>>>>>>>> >> >> BUG: Test for StatisticsUniqueLabelMapFilter stability >>>>>>>>>>> >> >> ENH: Add test for >>>>>>>>>>> itkParametricStpaceToImageSpaceFilter >>>>>>>>>>> >> >> ENH: Improve code coverage for >>>>>>>>>>> >> >> itkParametricSpaceToImageSpaceMeshFilter >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Julien Michel (1): >>>>>>>>>>> >> >> ENH: Support of VectorImage as template parameters for >>>>>>>>>>> >> >> WarpImageFilter >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Junjie Bai (2): >>>>>>>>>>> >> >> BUG: ConvertLabelMap with different LabelMapTypes >>>>>>>>>>> >> >> BUG: LabelObject CopyAttribute support different >>>>>>>>>>> LabelObject type >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> KWSys Robot (4): >>>>>>>>>>> >> >> KWSys 2015-07-10 (c9336bcf) >>>>>>>>>>> >> >> KWSys 2015-07-30 (f63febb7) >>>>>>>>>>> >> >> KWSys 2015-08-24 (cdaf522c) >>>>>>>>>>> >> >> KWSys 2015-08-28 (dc3fdd7f) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> LIBPNG Upstream (2): >>>>>>>>>>> >> >> PNG 2009-04-06 (e68f5a36) >>>>>>>>>>> >> >> PNG 2014-02-05 (3e753eb8) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Laurentiu Nicola (2): >>>>>>>>>>> >> >> PERF: Avoid temporary smartptr in >>>>>>>>>>> ProcessObject::GetInput >>>>>>>>>>> >> >> PERF: Optimize WarpImageFilter by avoiding refcount >>>>>>>>>>> bouncing >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Luc Hermitte (8): >>>>>>>>>>> >> >> PERF: itk::Image::GetPixel() performance improvment. >>>>>>>>>>> >> >> PERF: Performance enhancements on >>>>>>>>>>> VariableLengthVectors 1/... >>>>>>>>>>> >> >> ENH: Dependencies on itkVariableLengthVector.h reduced >>>>>>>>>>> >> >> BUG: Error in VariableLengthVector Unit Tests >>>>>>>>>>> >> >> PERF: Performance enhancements on VLV 2/... >>>>>>>>>>> >> >> PERF: Performances enhancements on VLV 3/... >>>>>>>>>>> >> >> COMP: Fix signed/unsigned warnings >>>>>>>>>>> >> >> BUG: std::copy/fill on empty VLV >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Lucas Gandel (4): >>>>>>>>>>> >> >> ENH: Move ImageToPathFilter from ITKReview to ITKPath >>>>>>>>>>> module. >>>>>>>>>>> >> >> BUG: Fixing ImageToPathFilter wrapping call from >>>>>>>>>>> Review Module >>>>>>>>>>> >> >> STYLE: Fix KWStyle dashboard errors >>>>>>>>>>> >> >> BUG: Fix external module BUILD_SHARED_LIBS status >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Mathieu Malaterre (1): >>>>>>>>>>> >> >> BUG: Name mangle the included expat third party >>>>>>>>>>> library. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Matthew McCormick (94): >>>>>>>>>>> >> >> ENH: Change itkSystemInformationTest to >>>>>>>>>>> itkCMakeConfigurationTest. >>>>>>>>>>> >> >> ENH: Add AnisotropicDiffusionLBR Remote Module. >>>>>>>>>>> >> >> ENH: Bump ITK version to 4.9.0. >>>>>>>>>>> >> >> BUG: Remove std::cout calls from classes. >>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>> >> >> BUG: Implement UpdateLargestPossibleRegion for >>>>>>>>>>> >> >> ImageToVTKImageFilter. >>>>>>>>>>> >> >> COMP: Add link interface specification for wrapping >>>>>>>>>>> >> >> target_link_libraries. >>>>>>>>>>> >> >> STYLE: Fix indentation in >>>>>>>>>>> itkMINCTransformIOFactory.cxx. >>>>>>>>>>> >> >> COMP: Fix MINCTransformIO factory registration. >>>>>>>>>>> >> >> COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with >>>>>>>>>>> Emscripten-1. >>>>>>>>>>> >> >> COMP: Remove unknown doxygen command in >>>>>>>>>>> AnisotropicDiffusionLBR. >>>>>>>>>>> >> >> BUG: Initialize mutex for 32 bit AtomicInt. >>>>>>>>>>> >> >> ENH: Use CastXML binaries when building with x86_64 >>>>>>>>>>> Linux. >>>>>>>>>>> >> >> STYLE: Rename gccxml -> castxml in >>>>>>>>>>> {idx,igenerator}.py. >>>>>>>>>>> >> >> COMP: Disable the gold linker for static builds on >>>>>>>>>>> Ubuntu 14.04. >>>>>>>>>>> >> >> ENH: Use Windows binaries for CastXML. >>>>>>>>>>> >> >> ENH: Add better scoping in igenerator.py. >>>>>>>>>>> >> >> BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + >>>>>>>>>>> MSVC. >>>>>>>>>>> >> >> BUG: LevelSetsv4 used signed char instead of char. >>>>>>>>>>> >> >> ENH: Add better scoping to idx.py. >>>>>>>>>>> >> >> COMP: Define newSize and oldSize in >>>>>>>>>>> VariableLengthVector. >>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>> >> >> ENH: Add more progress information to >>>>>>>>>>> IterativeClosestPoint2. >>>>>>>>>>> >> >> BUG: Build BridgeNumPy with Visual Studio. >>>>>>>>>>> >> >> ENH: Add ITKModuleExternal.cmake >>>>>>>>>>> >> >> COMP: Wrap Image< bool, D > for >>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>> >> >> BUG: Use CastXML binary built in Release. >>>>>>>>>>> >> >> BUG: ContinuousIndex should not be templated over >>>>>>>>>>> TCoordRep. >>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>> >> >> COMP: Address line length too long for Software Guide. >>>>>>>>>>> >> >> COMP: Fix CannyEdgeDetectionImageFilter.cxx types. >>>>>>>>>>> >> >> BUG: Support Python 3 wrapping module initialization. >>>>>>>>>>> >> >> BUG: Update itkTemplate.py for Python 3. >>>>>>>>>>> >> >> BUG: Update itkExtras.py for Python 3. >>>>>>>>>>> >> >> BUG: Prevent Python callback addition recursion. >>>>>>>>>>> >> >> BUG: Fix test scripts for Python 3. >>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>> >> >> ENH: Allow projects to build against an external >>>>>>>>>>> module. >>>>>>>>>>> >> >> ENH: Replace CABLE_CONFIGURATION with >>>>>>>>>>> ITK_WRAPPING_PARSER. >>>>>>>>>>> >> >> ENH: Rename _cable_ to _wrappers_. >>>>>>>>>>> >> >> BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. >>>>>>>>>>> >> >> BUG: Define ITK_WRAPPING_PARSER when wrapping. >>>>>>>>>>> >> >> COMP: Do not use C++11 alignas in itkAlignedTypedef. >>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.1. >>>>>>>>>>> >> >> BUG: Pass the CMAKE_CXX_FLAGS to castxml. >>>>>>>>>>> >> >> ENH: Bump CastXML version to 2015-30-29. >>>>>>>>>>> >> >> ENH: Bump LLVM / Clang to 3.7.0. >>>>>>>>>>> >> >> COMP: Avoid itklibminc linking with >>>>>>>>>>> ITK_USE_SYSTEM_HDF5. >>>>>>>>>>> >> >> COMP: Add missing ITKIOImageBase dependency for >>>>>>>>>>> ITKTransformMINC. >>>>>>>>>>> >> >> COMP: Use itkSimpleNewMacro in >>>>>>>>>>> >> >> ThreadedIteratorRangePartitionerTest. >>>>>>>>>>> >> >> ENH: Add wrapping support for building modules >>>>>>>>>>> externally. >>>>>>>>>>> >> >> BUG: Fix KWStyle test paths when building a module >>>>>>>>>>> externally. >>>>>>>>>>> >> >> ENH: Add Cuberille Remote module. >>>>>>>>>>> >> >> COMP: Remove carriage returns from Cuberille remote. >>>>>>>>>>> >> >> COMP: Remove unused argument in >>>>>>>>>>> ConditionVariableNoThreads. >>>>>>>>>>> >> >> DOC: Correct spelling of Continuous. >>>>>>>>>>> >> >> ENH: Bump the MinimalPathExtraction Remote to >>>>>>>>>>> 2015-10-20. >>>>>>>>>>> >> >> COMP: Fix KernelTransform SetFixedParameters argument >>>>>>>>>>> type. >>>>>>>>>>> >> >> STYLE: Use prefix increment operator in ImageBase. >>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>> sys.path >>>>>>>>>>> >> >> Revert "COMP: Put vnl_export.h in the list of sources >>>>>>>>>>> so it gets >>>>>>>>>>> >> >> installed." >>>>>>>>>>> >> >> BUG: Revert "BUG: ConvertLabelMap with different >>>>>>>>>>> LabelMapTypes" >>>>>>>>>>> >> >> ENH: Marking wrapping CMake configuration variables >>>>>>>>>>> as advanced. >>>>>>>>>>> >> >> STYLE: Rename CASTXML to CASTXML_EXECUTABLE. >>>>>>>>>>> >> >> COMP: Non-virtual copy attribute members in LabelMap >>>>>>>>>>> cannot have >>>>>>>>>>> >> >> override. >>>>>>>>>>> >> >> COMP: Add wrapping for >>>>>>>>>>> AdaptiveHistogramEqualizationImageFilter. >>>>>>>>>>> >> >> COMP: Add itkMacro.h to itkPromoteType.h for >>>>>>>>>>> ITK_EXCEPT. >>>>>>>>>>> >> >> ENH: Remove CMake version check in >>>>>>>>>>> ITKModuleHeaderTest.cmake >>>>>>>>>>> >> >> BUG: Improve KWStyle ExternalProject utilization. >>>>>>>>>>> >> >> ENH: Remove old KWStyle build script. >>>>>>>>>>> >> >> COMP: Address VariableLengthVector Doxygen rhs @param >>>>>>>>>>> not found. >>>>>>>>>>> >> >> ENH: Rename WRAPPING_LIBRARY_GROUPS to >>>>>>>>>>> WRAPPING_SUBMODULE_ORDER. >>>>>>>>>>> >> >> ENH: Install Python bindings into site-packages. >>>>>>>>>>> >> >> ENH: Improve readability of Python site-packages path >>>>>>>>>>> detection. >>>>>>>>>>> >> >> COMP: DiscreteGaussianDerivativeImageFilter unsigned >>>>>>>>>>> expression >>>>>>>>>>> >> >> warning. >>>>>>>>>>> >> >> BUG: ITKCommon publically depends on >>>>>>>>>>> ITKDoubleConversion. >>>>>>>>>>> >> >> COMP: Improve scoping in CovariantVectorGeometryTest. >>>>>>>>>>> >> >> ENH: Improves names and export of module dependencies. >>>>>>>>>>> >> >> STYLE: Improve namespace bracket style in >>>>>>>>>>> itkIsConvertible. >>>>>>>>>>> >> >> COMP: Set CMP0054 to new. >>>>>>>>>>> >> >> BUG: Remove unused wrapping files. >>>>>>>>>>> >> >> BUG: Do install install wrapping development files. >>>>>>>>>>> >> >> ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. >>>>>>>>>>> >> >> BUG: Remove duplicate inclusion of wrapping >>>>>>>>>>> submodules. >>>>>>>>>>> >> >> COMP: Do not use C++ style comments for Doxygen cond. >>>>>>>>>>> >> >> BUG: Fix detection of the gold linker. >>>>>>>>>>> >> >> BUG: Update Python package installation locations. >>>>>>>>>>> >> >> ENH: Bump CMakeLists.txt version to 4.8.2. >>>>>>>>>>> >> >> ENH: Change BUILD_EXAMPLES default to OFF. >>>>>>>>>>> >> >> BUG: Use 'from itk import ITKCommon' in module2module >>>>>>>>>>> test. >>>>>>>>>>> >> >> COMP: Link to VTK Python when built with Kits support. >>>>>>>>>>> >> >> BUG: Install itk_minc2.h header. >>>>>>>>>>> >> >> COMP: ITKIOMINC has a public dependency on >>>>>>>>>>> ITKIOImageBase. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Michka Popoff (9): >>>>>>>>>>> >> >> ENH: Update to swig 3.0.7 >>>>>>>>>>> >> >> ENH: Do not link against specific Python library on >>>>>>>>>>> OS X >>>>>>>>>>> >> >> COMP: Fix wrapping warnings when building with >>>>>>>>>>> >> >> ITK_WRAP_IMAGE_DIMS=2 >>>>>>>>>>> >> >> COMP: Add missing wrapping for TransformBase >>>>>>>>>>> >> >> COMP: Use ITK's pygccxml by correctly setting up the >>>>>>>>>>> sys.path >>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>> 3 wrapping >>>>>>>>>>> >> >> COMP: Move MovingHistogramImageFilterBase wrapping to >>>>>>>>>>> >> >> ImageFilterBase >>>>>>>>>>> >> >> module >>>>>>>>>>> >> >> COMP: Disable incompatible modules when using Python >>>>>>>>>>> 3 wrapping >>>>>>>>>>> >> >> ENH: Allow operations on Indexes and Offsets in Python >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Mikhail Isakov (1): >>>>>>>>>>> >> >> BUG: DiffusionTensor3DReconstruction segfault if no >>>>>>>>>>> baseline image >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Nick Tustison (5): >>>>>>>>>>> >> >> BUG: Set a default b-spline epsilon. >>>>>>>>>>> >> >> ENH: Adding testing for closed loop. >>>>>>>>>>> >> >> BUG: Updating B-spline classes with the same epsilon >>>>>>>>>>> strategy. >>>>>>>>>>> >> >> PERF: Switch vnl_vectors for fixed arrays. >>>>>>>>>>> >> >> ENH: Point-set registration with time-varying >>>>>>>>>>> B-spline. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Olivier Commowick (3): >>>>>>>>>>> >> >> BUG: Correct discrepancy in tridiagonal reduction wrt >>>>>>>>>>> VNL eigen >>>>>>>>>>> >> >> system >>>>>>>>>>> >> >> BUG: Correct under/overflows in vnl_math_hypot (taken >>>>>>>>>>> from pythag >>>>>>>>>>> >> >> from V3P) >>>>>>>>>>> >> >> BUG: Switch eigenvalues computation to double >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Pablo Hernandez-Cerdan (2): >>>>>>>>>>> >> >> ENH: Help class for itkFlatStructuringElement with >>>>>>>>>>> constructor >>>>>>>>>>> >> >> from >>>>>>>>>>> >> >> images. >>>>>>>>>>> >> >> COMP: Fix test errors and warnings in >>>>>>>>>>> FlatStructuringElement. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Seun Odutola (1): >>>>>>>>>>> >> >> COMP: Fixed name clash with Apple header (check >>>>>>>>>>> Macro), renamed >>>>>>>>>>> >> >> check >>>>>>>>>>> >> >> to Check >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Shawn Waldon (1): >>>>>>>>>>> >> >> COMP: Set target OS X version in environment for >>>>>>>>>>> tools using >>>>>>>>>>> >> >> compiler >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Simon Alexander (1): >>>>>>>>>>> >> >> BUG: incorrect closest point computation >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Tobias Wood (2): >>>>>>>>>>> >> >> BUG: LBFGSB was printing messages even with debug >>>>>>>>>>> switched off. >>>>>>>>>>> >> >> BUG: Removed an unguarded print statement. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Vladimir S. FONOV (9): >>>>>>>>>>> >> >> BUG: Missing ITKIOMINC_EXPORT on __Private() >>>>>>>>>>> >> >> COMP: Changing the order of HDF5 library components >>>>>>>>>>> >> >> COMP: Splitting up IOMINC module into two parts: MINC >>>>>>>>>>> and >>>>>>>>>>> >> >> Transform >>>>>>>>>>> >> >> STYLE: updated comments to properly reference LIBMINC >>>>>>>>>>> >> >> ENH: Add script to merge upstream MINC as a subtree >>>>>>>>>>> >> >> MINC 2015-07-23 (c033d431) >>>>>>>>>>> >> >> COMP: Update MINC CMake code >>>>>>>>>>> >> >> MINC 2015-08-18 (6d7e3ba8) >>>>>>>>>>> >> >> MINC 2015-09-13 (95cd5374) >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Xiaoxiao Liu (1): >>>>>>>>>>> >> >> DOC: update email address for xiaoxiao. >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Zach Williamson (10): >>>>>>>>>>> >> >> BUG: Use correct libraries for ImageFusion tests >>>>>>>>>>> >> >> ENH: Consolidate Library Dependencies >>>>>>>>>>> >> >> COMP: Add a missing link to Review module >>>>>>>>>>> >> >> COMP: Use correct linking macro in DCMTK >>>>>>>>>>> >> >> BUG: Use correct libraries for TestKernel tests >>>>>>>>>>> >> >> COMP: Fix inconsistant naming of >>>>>>>>>>> GPUPDEDeformableRegistration >>>>>>>>>>> >> >> ENH: Use new linking system macros >>>>>>>>>>> >> >> PERF: Avoid searching private dependencies for >>>>>>>>>>> include directories >>>>>>>>>>> >> >> COMP: Recover missing dependencies >>>>>>>>>>> >> >> ENH: use new linking macros in Filtering module >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> ----------------------------------------------------- >>>>>>>>>>> >> >> Errors or omissions? Please fix them here: >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> >>>>>>>>>>> https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit >>>>>>>>>>> >> >> _____________________________________ >>>>>>>>>>> >> >> Powered by www.kitware.com >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Visit other Kitware open-source projects at >>>>>>>>>>> >> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Kitware offers ITK Training Courses, for more information >>>>>>>>>>> visit: >>>>>>>>>>> >> >> http://www.kitware.com/products/protraining.php >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> >> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >> >> >>>>>>>>>>> >> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> >>>>>>>>> >>>>>>>>>> Powered by www.kitware.com >>>>>>>>>> >>>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>>> >>>>>>>>> http://kitware.com/products/protraining.php >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>> >>>>> >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Dec 4 17:34:33 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 4 Dec 2015 17:34:33 -0500 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Hi Simon. Apologies I haven't been able to put much time into this, ran into some > interesting challenges with VS2015 itself (at least in my configuration) > hanging permanently when changing from debug to release mode, or vice > versa. It seems the generated project files are a bit of a challenge for > it. > Yes, Visual Studio has difficulty with large projects that have many build targets. With the 4.9 release, we addressed the behavior a bit by reducing the number of header tests and by turning BUILD_EXAMPLES OFF by default. By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be improved when focusing on development of a subset of modules. > At any rate, I have narrowed down part of the issue at least to being not > in the interpolate filter itself, but rather in the test driver code ... > somewhere in the nested loops incrementing the underlying array elements is > behaving incorrectly in release mode. I'll try and have a closer look > this weekend. > Thanks for taking a look at this! In the past, we ran into some issues with Visual Studio in Release mode where adding const or using a reference for the returned type avoided a faulty optimization. Bug reports to upstream Visual Studio have also helped resolve the issue in some cases, too. Thanks, Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Fri Dec 4 17:34:33 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 4 Dec 2015 17:34:33 -0500 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Hi Simon. Apologies I haven't been able to put much time into this, ran into some > interesting challenges with VS2015 itself (at least in my configuration) > hanging permanently when changing from debug to release mode, or vice > versa. It seems the generated project files are a bit of a challenge for > it. > Yes, Visual Studio has difficulty with large projects that have many build targets. With the 4.9 release, we addressed the behavior a bit by reducing the number of header tests and by turning BUILD_EXAMPLES OFF by default. By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be improved when focusing on development of a subset of modules. > At any rate, I have narrowed down part of the issue at least to being not > in the interpolate filter itself, but rather in the test driver code ... > somewhere in the nested loops incrementing the underlying array elements is > behaving incorrectly in release mode. I'll try and have a closer look > this weekend. > Thanks for taking a look at this! In the past, we ran into some issues with Visual Studio in Release mode where adding const or using a reference for the returned type avoided a faulty optimization. Bug reports to upstream Visual Studio have also helped resolve the issue in some cases, too. Thanks, Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Dec 4 18:38:27 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 4 Dec 2015 18:38:27 -0500 Subject: [ITK] [ITK-users] Own Transformation Class In-Reply-To: <1448963240154-7588226.post@n2.nabble.com> References: <1448627334852-7588218.post@n2.nabble.com> <1448963240154-7588226.post@n2.nabble.com> Message-ID: Hey Dominik, > A new transformation can often be avoided by calling SetWeights() on the > > optimizer as explained here [1]. This can be used to hold parameters > > constant for a given transform during the optimization process. > > > > However, it sounds like goal is to limit registration to information from > > a particular region in the image (the urethra). To achieve this goal, you > > may consider setting the Fixed and Moving image masks on the metric as > > described here [2]. > > I'm already using registration masks on the prostate itself to exclude the > surrounding tissue. However, the registration is always a bit off because > in > the result the urethras are not in the same place. In the histology the > urethra is more or less a point and in the MRI the urethra is like a vector > (well actually it is more like a curve). So I'd like the transformation to > edit it in a way that the point follows that curve. I hope my explanation > is > not too confusing :) > In this case, an approach that uses the corresponding fiducials with the LandmarkBasedTransformInitializer: http://www.itk.org/Doxygen/html/classitk_1_1LandmarkBasedTransformInitializer.html or a registration that combines a point set metric in a multi-metric may be helpful. http://www.itk.org/Doxygen/html/classitk_1_1PointSetToPointSetMetricv4.html http://www.itk.org/Doxygen/html/classitk_1_1ObjectToObjectMultiMetricv4.html > If every histology slice is registered independently, when they are merged > > together there will be gaps and overlap in the histology slice locations. > > Therefore, if a histology volume is desired, the histology slices could > be > > registered to each other first to generate a single histology slice > > volume, then that volume is registered to the MRI volume. > > The histology slices all have a certain distance to each other (and are not > even parallel I think), so I think gaps in the merged volume are desirable. > Therefore I can't just stack them. > As Andras mentioned in another thread, this is a hard problem. A basic first step could add images together generated with ResampleImageFilter. The volume reconstruction executable available in PlusLib is also nice. HTH, Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From mikhirev at gmail.com Sun Dec 6 15:09:48 2015 From: mikhirev at gmail.com (Dmitry Mikhirev) Date: Sun, 6 Dec 2015 23:09:48 +0300 Subject: [ITK] [ITK-dev] SimpleITK build failure on Fedora 23 Message-ID: <20151206230948.17650b7d@kafka> Hello! I'm trying to build SimpleITK package for Fedora. Unfortunately I'm unfamiliar with swig, and I need help in fixing build issue. I'm compiling SimpleITK 0.9.1 against Fedora's InsightToolkit 4.8.2 that is built with ITKv3 compatibility enabled. Here is the error message: [ 47%] Building CXX object Code/BasicFilters/src/CMakeFiles/SimpleITKBasicFilters6.dir/sitkHistogramMatchingImageFilter.cxx.o cd /builddir/build/BUILD/SimpleITK-0.9.1/build/Code/BasicFilters/src && /usr/lib64/ccache/c++ -DSITK_USE_EXPLICITITK -DSimpleITKBasicFilters6_EXPORTS -DSimpleITKBasicFilters_EXPORTS -DvtkRenderingCore_AUTOINIT="4(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingFreeTypeOpenGL,vtkRenderingOpenGL)" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fPIC -fPIC -I/usr/include/freetype2 -I/usr/include/vtk -I/usr/include/gdcm -I/usr/include/vxl/core -I/usr/include/vxl/vcl -I/usr/include/vxl/v3p/netlib -I/usr/include/InsightToolkit -I/builddir/build/BUILD/SimpleITK-0.9.1/Code/Common/include -I/builddir/build/BUILD/SimpleITK-0.9.1/Code/Registration/include -I/builddir/build/BUILD/SimpleITK-0.9.1/Code/BasicFilters/include -I/builddir/build/BUILD/SimpleITK-0.9.1/Code/IO/include -I/builddir/build/BUILD/SimpleITK-0.9.1/build/Code/BasicFilters/include -I/builddir/build/BUILD/SimpleITK-0.9.1/build/Code/Common/include -I/builddir/build/BUILD/SimpleITK-0.9.1/Code/Explicit/include -I/builddir/build/BUILD/SimpleITK-0.9.1/Code/BasicFilters/src -o CMakeFiles/SimpleITKBasicFilters6.dir/sitkHistogramMatchingImageFilter.cxx.o -c /builddir/build/BUILD/SimpleITK-0.9.1/build/Code/BasicFilters/src/sitkHistogramMatchingImageFilter.cxx <...> /usr/include/InsightToolkit/itkHistogram.h:285:8: error: 'bool itk::Statistics::Histogram::IncreaseFrequency(const MeasurementVectorType&, itk::Statistics::Histogram::AbsoluteFrequencyType) [with TMeasurement = long int; TFrequencyContainer = itk::Statistics::DenseFrequencyContainer2; itk::Statistics::Histogram::MeasurementVectorType = itk::Array; itk::Statistics::Histogram::AbsoluteFrequencyType = long unsigned int]' cannot be overloaded bool IncreaseFrequency( ^ /usr/include/InsightToolkit/itkHistogram.h:279:8: error: with 'bool itk::Statistics::Histogram::IncreaseFrequency(const IndexType&, itk::Statistics::Histogram::AbsoluteFrequencyType) [with TMeasurement = long int; TFrequencyContainer = itk::Statistics::DenseFrequencyContainer2; itk::Statistics::Histogram::IndexType = itk::Array; itk::Statistics::Histogram::AbsoluteFrequencyType = long unsigned int]' bool IncreaseFrequency(const IndexType & index, ^ The corresponding piese of code in itkHistogram.h is: #ifdef ITKV3_COMPATIBILITY //In ITKv4 the member functions are given unique names to dis-ambiguate //the intended behavior. Make aliases of the overloaded calls //for ITKv3 backwards compatibility. bool IncreaseFrequency(const IndexType & index, AbsoluteFrequencyType value) { return IncreaseFrequencyOfIndex(index,value); } bool IncreaseFrequency( const MeasurementVectorType & measurement, AbsoluteFrequencyType value) { return IncreaseFrequencyOfMeasurement(measurement,value); } #endif It is obvious that this error wouldn't occur if InsightToolkit was compiled without ITKv3 support, but I have to use Fedora's package. Is it possible to fix this issue with some simple patch or even configuration option for SimpleITK? Thank you! -- Regards, Dmitry Mikhirev _______________________________________________ Powered by www.kitware.com 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 mikhirev at gmail.com Sun Dec 6 15:31:28 2015 From: mikhirev at gmail.com (Dmitry Mikhirev) Date: Sun, 6 Dec 2015 23:31:28 +0300 Subject: [ITK] [ITK-dev] SimpleITK 0.9.1 tests failure Message-ID: <20151206233128.44f3af0f@kafka> Hello! That's me again. I also have another question about SimpleITK, so I ask it in separate thread. I recompiled Fedora's InsightToolkit 4.8.2 package without ITKv3 compatibility and built SimpleITK 0.9.1 against it. But some tests fail, and I can not determine is this a critical issue or not, and if yes, how to fix it. I would very appreciate any help. Below are the correspondent parts of build log. Sorry for long copy&paste. Last two errors (1255 and 1257) occurred because numpy was not installed on the build system, but I don't know how to deal with others. 148/1259 Test #148: Java.OrImageFilter .................................................. Passed 1.38 sec test 149 Start 149: BasicFilters.InverseDeconvolutionImageFilter 149: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver1 "--gtest_filter=BasicFilters.InverseDeconvolutionImageFilter:BasicFilters.InverseDeconvolutionImageFilter_*" 149: Test timeout computed to be: 1500 149: Note: Google Test filter = BasicFilters.InverseDeconvolutionImageFilter:BasicFilters.InverseDeconvolutionImageFilter_* 149: [==========] Running 2 tests from 1 test case. 149: [----------] Global test environment set-up. 149: [----------] 2 tests from BasicFilters 149: [ RUN ] BasicFilters.InverseDeconvolutionImageFilter 149: [ OK ] BasicFilters.InverseDeconvolutionImageFilter (34 ms) 149: [ RUN ] BasicFilters.InverseDeconvolutionImageFilter_defaults 149: Executing ITK filter: 149: InverseDeconvolutionImageFilter (0x55cab306f4e0) 149: RTTI typeinfo: itk::InverseDeconvolutionImageFilter, itk::Image, itk::Image, double> 149: Reference Count: 1 149: Modified Time: 2592 149: Debug: Off 149: Object Name: 149: Observers: 149: DeleteEvent(SimpleMemberCommand) 149: Inputs: 149: KernelImage: (0x55cab3070eb0) * 149: Primary: (0x55cab306cc70) * 149: Indexed Inputs: 149: 0: Primary (0x55cab306cc70) 149: Required Input Names: KernelImage, Primary 149: NumberOfRequiredInputs: 1 149: Outputs: 149: Primary: (0x55cab3070c30) 149: Indexed Outputs: 149: 0: Primary (0x55cab3070c30) 149: NumberOfRequiredOutputs: 1 149: Number Of Threads: 1 149: ReleaseDataFlag: Off 149: ReleaseDataBeforeUpdateFlag: Off 149: AbortGenerateData: Off 149: Progress: 0 149: Multithreader: 149: RTTI typeinfo: itk::MultiThreader 149: Reference Count: 1 149: Modified Time: 2558 149: Debug: Off 149: Object Name: 149: Observers: 149: none 149: Thread Count: 1 149: Global Maximum Number Of Threads: 128 149: Global Default Number Of Threads: 1 149: CoordinateTolerance: 1e-06 149: DirectionTolerance: 1e-06 149: Normalize: 1 149: BoundaryCondition: itkZeroFluxNeumannBoundaryCondition 149: OutputRegionMode: SAME 149: SizeGreatestPrimeFactor: 13 149: KernelZeroMagnitudeThreshold: 0.0001 149: Starting image compare on BasicFilters_InverseDeconvolutionImageFilter_defaults_ 149: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_InverseDeconvolutionImageFilter_defaults.nrrd 149: 10.7856 149: 0.0001 149: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Expected.png 149: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Actual.png 149: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Difference.png 149: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkInverseDeconvolutionImageFilterTest.cxx:144: Failure 149: Value of: imageCompare.compare( output, "", "" ) 149: Actual: false 149: Expected: true 149: ImageCompare: image Root Mean Square (RMS) difference was 10.7856 which exceeds the tolerance of 0.0001 149: 149: [ FAILED ] BasicFilters.InverseDeconvolutionImageFilter_defaults (185 ms) 149: [----------] 2 tests from BasicFilters (221 ms total) 149: 149: [----------] Global test environment tear-down 149: [==========] 2 tests from 1 test case ran. (222 ms total) 149: [ PASSED ] 1 test. 149: [ FAILED ] 1 test, listed below: 149: [ FAILED ] BasicFilters.InverseDeconvolutionImageFilter_defaults 149: 149: 1 FAILED TEST 149/1259 Test #149: BasicFilters.InverseDeconvolutionImageFilter ........................***Failed 0.89 sec test 150 Start 150: Lua.InverseDeconvolutionImageFilter 150: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver1 "--gtest_filter=Lua.InverseDeconvolutionImageFilter" 150: Test timeout computed to be: 1500 150: Note: Google Test filter = Lua.InverseDeconvolutionImageFilter 150: [==========] Running 1 test from 1 test case. 150: [----------] Global test environment set-up. 150: [----------] 1 test from Lua 150: [ RUN ] Lua.InverseDeconvolutionImageFilter 150: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKLua /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/LuaTests/InverseDeconvolutionImageFilterTest.lua defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Lua-InverseDeconvolutionImageFilter-defaults.nrrd ' 150: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 150: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd 150: 150: Starting image compare on BasicFilters_InverseDeconvolutionImageFilter_defaults 150: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_InverseDeconvolutionImageFilter_defaults.nrrd 150: 10.7856 150: 0.0001 150: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Expected.png 150: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Actual.png 150: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Difference.png 150: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkInverseDeconvolutionImageFilterTest.cxx:186: Failure 150: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 150: Actual: false 150: Expected: true 150: ImageCompare: image Root Mean Square (RMS) difference was 10.7856 which exceeds the tolerance of 0.0001 150: 150: [ FAILED ] Lua.InverseDeconvolutionImageFilter (693 ms) 150: [----------] 1 test from Lua (693 ms total) 150: 150: [----------] Global test environment tear-down 150: [==========] 1 test from 1 test case ran. (695 ms total) 150: [ PASSED ] 0 tests. 150: [ FAILED ] 1 test, listed below: 150: [ FAILED ] Lua.InverseDeconvolutionImageFilter 150: 150: 1 FAILED TEST 150/1259 Test #150: Lua.InverseDeconvolutionImageFilter .................................***Failed 1.35 sec test 151 Start 151: Python.InverseDeconvolutionImageFilter 151: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver1 "--gtest_filter=Python.InverseDeconvolutionImageFilter" 151: Test timeout computed to be: 1500 151: Note: Google Test filter = Python.InverseDeconvolutionImageFilter 151: [==========] Running 1 test from 1 test case. 151: [----------] Global test environment set-up. 151: [----------] 1 test from Python 151: [ RUN ] Python.InverseDeconvolutionImageFilter 151: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Installation/PythonVirtualenv/bin/python /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/PythonTests/InverseDeconvolutionImageFilterTest.py defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Python-InverseDeconvolutionImageFilter-defaults.nrrd ' 151: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 151: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd 151: 151: Starting image compare on BasicFilters_InverseDeconvolutionImageFilter_defaults 151: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_InverseDeconvolutionImageFilter_defaults.nrrd 151: 10.7856 151: 0.0001 151: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Expected.png 151: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Actual.png 151: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Difference.png 151: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkInverseDeconvolutionImageFilterTest.cxx:227: Failure 151: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 151: Actual: false 151: Expected: true 151: ImageCompare: image Root Mean Square (RMS) difference was 10.7856 which exceeds the tolerance of 0.0001 151: 151: [ FAILED ] Python.InverseDeconvolutionImageFilter (781 ms) 151: [----------] 1 test from Python (781 ms total) 151: 151: [----------] Global test environment tear-down 151: [==========] 1 test from 1 test case ran. (783 ms total) 151: [ PASSED ] 0 tests. 151: [ FAILED ] 1 test, listed below: 151: [ FAILED ] Python.InverseDeconvolutionImageFilter 151: 151: 1 FAILED TEST 151/1259 Test #151: Python.InverseDeconvolutionImageFilter ..............................***Failed 1.40 sec test 152 Start 152: Java.InverseDeconvolutionImageFilter 152: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver1 "--gtest_filter=Java.InverseDeconvolutionImageFilter" 152: Test timeout computed to be: 1500 152: Note: Google Test filter = Java.InverseDeconvolutionImageFilter 152: [==========] Running 1 test from 1 test case. 152: [----------] Global test environment set-up. 152: [----------] 1 test from Java 152: [ RUN ] Java.InverseDeconvolutionImageFilter 152: Running command: '/usr/bin/java -d64 -classpath /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/JavaTests:/builddir/build/BUILD/SimpleITK-0.9.1/build/Wrapping/simpleitk-0.9.1-gGIT-N.jar -Djava.library.path=/builddir/build/BUILD/SimpleITK-0.9.1/build/lib org.itk.simple.testing.InverseDeconvolutionImageFilterTest defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Java-InverseDeconvolutionImageFilter-defaults.nrrd ' 152: Starting image compare on BasicFilters_InverseDeconvolutionImageFilter_defaults 152: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_InverseDeconvolutionImageFilter_defaults.nrrd 152: 10.7856 152: 0.0001 152: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Expected.png 152: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Actual.png 152: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_InverseDeconvolutionImageFilter_defaults_Difference.png 152: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkInverseDeconvolutionImageFilterTest.cxx:366: Failure 152: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 152: Actual: false 152: Expected: true 152: ImageCompare: image Root Mean Square (RMS) difference was 10.7856 which exceeds the tolerance of 0.0001 152: 152: [ FAILED ] Java.InverseDeconvolutionImageFilter (800 ms) 152: [----------] 1 test from Java (801 ms total) 152: 152: [----------] Global test environment tear-down 152: [==========] 1 test from 1 test case ran. (802 ms total) 152: [ PASSED ] 0 tests. 152: [ FAILED ] 1 test, listed below: 152: [ FAILED ] Java.InverseDeconvolutionImageFilter 152: 152: 1 FAILED TEST 152/1259 Test #152: Java.InverseDeconvolutionImageFilter ................................***Failed 1.45 sec <...> test 177 Start 177: BasicFilters.WienerDeconvolutionImageFilter 177: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver1 "--gtest_filter=BasicFilters.WienerDeconvolutionImageFilter:BasicFilters.WienerDeconvolutionImageFilter_*" 177: Test timeout computed to be: 1500 177: Note: Google Test filter = BasicFilters.WienerDeconvolutionImageFilter:BasicFilters.WienerDeconvolutionImageFilter_* 177: [==========] Running 2 tests from 1 test case. 177: [----------] Global test environment set-up. 177: [----------] 2 tests from BasicFilters 177: [ RUN ] BasicFilters.WienerDeconvolutionImageFilter 177: [ OK ] BasicFilters.WienerDeconvolutionImageFilter (68 ms) 177: [ RUN ] BasicFilters.WienerDeconvolutionImageFilter_defaults 177: Executing ITK filter: 177: WienerDeconvolutionImageFilter (0x562191b754e0) 177: RTTI typeinfo: itk::WienerDeconvolutionImageFilter, itk::Image, itk::Image, double> 177: Reference Count: 1 177: Modified Time: 2592 177: Debug: Off 177: Object Name: 177: Observers: 177: DeleteEvent(SimpleMemberCommand) 177: Inputs: 177: KernelImage: (0x562191b76eb0) * 177: Primary: (0x562191b72c70) * 177: Indexed Inputs: 177: 0: Primary (0x562191b72c70) 177: Required Input Names: KernelImage, Primary 177: NumberOfRequiredInputs: 1 177: Outputs: 177: Primary: (0x562191b76c30) 177: Indexed Outputs: 177: 0: Primary (0x562191b76c30) 177: NumberOfRequiredOutputs: 1 177: Number Of Threads: 1 177: ReleaseDataFlag: Off 177: ReleaseDataBeforeUpdateFlag: Off 177: AbortGenerateData: Off 177: Progress: 0 177: Multithreader: 177: RTTI typeinfo: itk::MultiThreader 177: Reference Count: 1 177: Modified Time: 2558 177: Debug: Off 177: Object Name: 177: Observers: 177: none 177: Thread Count: 1 177: Global Maximum Number Of Threads: 128 177: Global Default Number Of Threads: 1 177: CoordinateTolerance: 1e-06 177: DirectionTolerance: 1e-06 177: Normalize: 1 177: BoundaryCondition: itkZeroFluxNeumannBoundaryCondition 177: OutputRegionMode: SAME 177: SizeGreatestPrimeFactor: 13 177: KernelZeroMagnitudeThreshold: 0.0001 177: NoiseVariance: 0 177: Starting image compare on BasicFilters_WienerDeconvolutionImageFilter_defaults_ 177: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_WienerDeconvolutionImageFilter_defaults.nrrd 177: 2.17091 177: 0.0001 177: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Expected.png 177: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Actual.png 177: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Difference.png 177: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkWienerDeconvolutionImageFilterTest.cxx:144: Failure 177: Value of: imageCompare.compare( output, "", "" ) 177: Actual: false 177: Expected: true 177: ImageCompare: image Root Mean Square (RMS) difference was 2.17091 which exceeds the tolerance of 0.0001 177: 177: [ FAILED ] BasicFilters.WienerDeconvolutionImageFilter_defaults (161 ms) 177: [----------] 2 tests from BasicFilters (231 ms total) 177: 177: [----------] Global test environment tear-down 177: [==========] 2 tests from 1 test case ran. (232 ms total) 177: [ PASSED ] 1 test. 177: [ FAILED ] 1 test, listed below: 177: [ FAILED ] BasicFilters.WienerDeconvolutionImageFilter_defaults 177: 177: 1 FAILED TEST 177/1259 Test #177: BasicFilters.WienerDeconvolutionImageFilter .........................***Failed 0.87 sec test 178 Start 178: Lua.WienerDeconvolutionImageFilter 178: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver1 "--gtest_filter=Lua.WienerDeconvolutionImageFilter" 178: Test timeout computed to be: 1500 178: Note: Google Test filter = Lua.WienerDeconvolutionImageFilter 178: [==========] Running 1 test from 1 test case. 178: [----------] Global test environment set-up. 178: [----------] 1 test from Lua 178: [ RUN ] Lua.WienerDeconvolutionImageFilter 178: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKLua /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/LuaTests/WienerDeconvolutionImageFilterTest.lua defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Lua-WienerDeconvolutionImageFilter-defaults.nrrd ' 178: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 178: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd 178: 178: Starting image compare on BasicFilters_WienerDeconvolutionImageFilter_defaults 178: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_WienerDeconvolutionImageFilter_defaults.nrrd 178: 2.17091 178: 0.0001 178: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Expected.png 178: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Actual.png 178: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Difference.png 178: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkWienerDeconvolutionImageFilterTest.cxx:186: Failure 178: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 178: Actual: false 178: Expected: true 178: ImageCompare: image Root Mean Square (RMS) difference was 2.17091 which exceeds the tolerance of 0.0001 178: 178: [ FAILED ] Lua.WienerDeconvolutionImageFilter (687 ms) 178: [----------] 1 test from Lua (687 ms total) 178: 178: [----------] Global test environment tear-down 178: [==========] 1 test from 1 test case ran. (689 ms total) 178: [ PASSED ] 0 tests. 178: [ FAILED ] 1 test, listed below: 178: [ FAILED ] Lua.WienerDeconvolutionImageFilter 178: 178: 1 FAILED TEST 178/1259 Test #178: Lua.WienerDeconvolutionImageFilter ..................................***Failed 1.34 sec test 179 Start 179: Python.WienerDeconvolutionImageFilter 179: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver1 "--gtest_filter=Python.WienerDeconvolutionImageFilter" 179: Test timeout computed to be: 1500 179: Note: Google Test filter = Python.WienerDeconvolutionImageFilter 179: [==========] Running 1 test from 1 test case. 179: [----------] Global test environment set-up. 179: [----------] 1 test from Python 179: [ RUN ] Python.WienerDeconvolutionImageFilter 179: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Installation/PythonVirtualenv/bin/python /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/PythonTests/WienerDeconvolutionImageFilterTest.py defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Python-WienerDeconvolutionImageFilter-defaults.nrrd ' 179: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 179: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd 179: 179: Starting image compare on BasicFilters_WienerDeconvolutionImageFilter_defaults 179: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_WienerDeconvolutionImageFilter_defaults.nrrd 179: 2.17091 179: 0.0001 179: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Expected.png 179: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Actual.png 179: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Difference.png 179: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkWienerDeconvolutionImageFilterTest.cxx:227: Failure 179: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 179: Actual: false 179: Expected: true 179: ImageCompare: image Root Mean Square (RMS) difference was 2.17091 which exceeds the tolerance of 0.0001 179: 179: [ FAILED ] Python.WienerDeconvolutionImageFilter (801 ms) 179: [----------] 1 test from Python (801 ms total) 179: 179: [----------] Global test environment tear-down 179: [==========] 1 test from 1 test case ran. (803 ms total) 179: [ PASSED ] 0 tests. 179: [ FAILED ] 1 test, listed below: 179: [ FAILED ] Python.WienerDeconvolutionImageFilter 179: 179: 1 FAILED TEST 179/1259 Test #179: Python.WienerDeconvolutionImageFilter ...............................***Failed 1.42 sec test 180 Start 180: Java.WienerDeconvolutionImageFilter 180: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver1 "--gtest_filter=Java.WienerDeconvolutionImageFilter" 180: Test timeout computed to be: 1500 180: Note: Google Test filter = Java.WienerDeconvolutionImageFilter 180: [==========] Running 1 test from 1 test case. 180: [----------] Global test environment set-up. 180: [----------] 1 test from Java 180: [ RUN ] Java.WienerDeconvolutionImageFilter 180: Running command: '/usr/bin/java -d64 -classpath /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/JavaTests:/builddir/build/BUILD/SimpleITK-0.9.1/build/Wrapping/simpleitk-0.9.1-gGIT-N.jar -Djava.library.path=/builddir/build/BUILD/SimpleITK-0.9.1/build/lib org.itk.simple.testing.WienerDeconvolutionImageFilterTest defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Java-WienerDeconvolutionImageFilter-defaults.nrrd ' 180: Starting image compare on BasicFilters_WienerDeconvolutionImageFilter_defaults 180: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_WienerDeconvolutionImageFilter_defaults.nrrd 180: 2.17091 180: 0.0001 180: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Expected.png 180: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Actual.png 180: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_WienerDeconvolutionImageFilter_defaults_Difference.png 180: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkWienerDeconvolutionImageFilterTest.cxx:366: Failure 180: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 180: Actual: false 180: Expected: true 180: ImageCompare: image Root Mean Square (RMS) difference was 2.17091 which exceeds the tolerance of 0.0001 180: 180: [ FAILED ] Java.WienerDeconvolutionImageFilter (774 ms) 180: [----------] 1 test from Java (774 ms total) 180: 180: [----------] Global test environment tear-down 180: [==========] 1 test from 1 test case ran. (776 ms total) 180: [ PASSED ] 0 tests. 180: [ FAILED ] 1 test, listed below: 180: [ FAILED ] Java.WienerDeconvolutionImageFilter 180: 180: 1 FAILED TEST 180/1259 Test #180: Java.WienerDeconvolutionImageFilter .................................***Failed 1.38 sec <...> test 729 Start 729: BasicFilters.TikhonovDeconvolutionImageFilter 729: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver4 "--gtest_filter=BasicFilters.TikhonovDeconvolutionImageFilter:BasicFilters.TikhonovDeconvolutionImageFilter_*" 729: Test timeout computed to be: 1500 729: Note: Google Test filter = BasicFilters.TikhonovDeconvolutionImageFilter:BasicFilters.TikhonovDeconvolutionImageFilter_* 729: [==========] Running 2 tests from 1 test case. 729: [----------] Global test environment set-up. 729: [----------] 2 tests from BasicFilters 729: [ RUN ] BasicFilters.TikhonovDeconvolutionImageFilter 729: [ OK ] BasicFilters.TikhonovDeconvolutionImageFilter (62 ms) 729: [ RUN ] BasicFilters.TikhonovDeconvolutionImageFilter_defaults 729: Executing ITK filter: 729: TikhonovDeconvolutionImageFilter (0x55e26c9cebb0) 729: RTTI typeinfo: itk::TikhonovDeconvolutionImageFilter, itk::Image, itk::Image, double> 729: Reference Count: 1 729: Modified Time: 2592 729: Debug: Off 729: Object Name: 729: Observers: 729: DeleteEvent(SimpleMemberCommand) 729: Inputs: 729: KernelImage: (0x55e26c9d0b80) * 729: Primary: (0x55e26c9cefd0) * 729: Indexed Inputs: 729: 0: Primary (0x55e26c9cefd0) 729: Required Input Names: KernelImage, Primary 729: NumberOfRequiredInputs: 1 729: Outputs: 729: Primary: (0x55e26c9d0900) 729: Indexed Outputs: 729: 0: Primary (0x55e26c9d0900) 729: NumberOfRequiredOutputs: 1 729: Number Of Threads: 1 729: ReleaseDataFlag: Off 729: ReleaseDataBeforeUpdateFlag: Off 729: AbortGenerateData: Off 729: Progress: 0 729: Multithreader: 729: RTTI typeinfo: itk::MultiThreader 729: Reference Count: 1 729: Modified Time: 2558 729: Debug: Off 729: Object Name: 729: Observers: 729: none 729: Thread Count: 1 729: Global Maximum Number Of Threads: 128 729: Global Default Number Of Threads: 1 729: CoordinateTolerance: 1e-06 729: DirectionTolerance: 1e-06 729: Normalize: 1 729: BoundaryCondition: itkZeroFluxNeumannBoundaryCondition 729: OutputRegionMode: SAME 729: SizeGreatestPrimeFactor: 13 729: KernelZeroMagnitudeThreshold: 0.0001 729: RegularizationConstant: 0 729: Starting image compare on BasicFilters_TikhonovDeconvolutionImageFilter_defaults_ 729: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_TikhonovDeconvolutionImageFilter_defaults.nrrd 729: 2.17091 729: 0.0001 729: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Expected.png 729: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Actual.png 729: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Difference.png 729: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkTikhonovDeconvolutionImageFilterTest.cxx:144: Failure 729: Value of: imageCompare.compare( output, "", "" ) 729: Actual: false 729: Expected: true 729: ImageCompare: image Root Mean Square (RMS) difference was 2.17091 which exceeds the tolerance of 0.0001 729: 729: [ FAILED ] BasicFilters.TikhonovDeconvolutionImageFilter_defaults (163 ms) 729: [----------] 2 tests from BasicFilters (226 ms total) 729: 729: [----------] Global test environment tear-down 729: [==========] 2 tests from 1 test case ran. (229 ms total) 729: [ PASSED ] 1 test. 729: [ FAILED ] 1 test, listed below: 729: [ FAILED ] BasicFilters.TikhonovDeconvolutionImageFilter_defaults 729: 729: 1 FAILED TEST 729/1259 Test #729: BasicFilters.TikhonovDeconvolutionImageFilter .......................***Failed 0.84 sec test 730 Start 730: Lua.TikhonovDeconvolutionImageFilter 730: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver4 "--gtest_filter=Lua.TikhonovDeconvolutionImageFilter" 730: Test timeout computed to be: 1500 730: Note: Google Test filter = Lua.TikhonovDeconvolutionImageFilter 730: [==========] Running 1 test from 1 test case. 730: [----------] Global test environment set-up. 730: [----------] 1 test from Lua 730: [ RUN ] Lua.TikhonovDeconvolutionImageFilter 730: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKLua /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/LuaTests/TikhonovDeconvolutionImageFilterTest.lua defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Lua-TikhonovDeconvolutionImageFilter-defaults.nrrd ' 730: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 730: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd 730: 730: Starting image compare on BasicFilters_TikhonovDeconvolutionImageFilter_defaults 730: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_TikhonovDeconvolutionImageFilter_defaults.nrrd 730: 2.17091 730: 0.0001 730: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Expected.png 730: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Actual.png 730: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Difference.png 730: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkTikhonovDeconvolutionImageFilterTest.cxx:186: Failure 730: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 730: Actual: false 730: Expected: true 730: ImageCompare: image Root Mean Square (RMS) difference was 2.17091 which exceeds the tolerance of 0.0001 730: 730: [ FAILED ] Lua.TikhonovDeconvolutionImageFilter (668 ms) 730: [----------] 1 test from Lua (668 ms total) 730: 730: [----------] Global test environment tear-down 730: [==========] 1 test from 1 test case ran. (668 ms total) 730: [ PASSED ] 0 tests. 730: [ FAILED ] 1 test, listed below: 730: [ FAILED ] Lua.TikhonovDeconvolutionImageFilter 730: 730: 1 FAILED TEST 730/1259 Test #730: Lua.TikhonovDeconvolutionImageFilter ................................***Failed 1.30 sec test 731 Start 731: Python.TikhonovDeconvolutionImageFilter 731: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver4 "--gtest_filter=Python.TikhonovDeconvolutionImageFilter" 731: Test timeout computed to be: 1500 731: Note: Google Test filter = Python.TikhonovDeconvolutionImageFilter 731: [==========] Running 1 test from 1 test case. 731: [----------] Global test environment set-up. 731: [----------] 1 test from Python 731: [ RUN ] Python.TikhonovDeconvolutionImageFilter 731: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Installation/PythonVirtualenv/bin/python /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/PythonTests/TikhonovDeconvolutionImageFilterTest.py defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Python-TikhonovDeconvolutionImageFilter-defaults.nrrd ' 731: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 731: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd 731: 731: Starting image compare on BasicFilters_TikhonovDeconvolutionImageFilter_defaults 731: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_TikhonovDeconvolutionImageFilter_defaults.nrrd 731: 2.17091 731: 0.0001 731: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Expected.png 731: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Actual.png 731: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Difference.png 731: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkTikhonovDeconvolutionImageFilterTest.cxx:227: Failure 731: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 731: Actual: false 731: Expected: true 731: ImageCompare: image Root Mean Square (RMS) difference was 2.17091 which exceeds the tolerance of 0.0001 731: 731: [ FAILED ] Python.TikhonovDeconvolutionImageFilter (756 ms) 731: [----------] 1 test from Python (756 ms total) 731: 731: [----------] Global test environment tear-down 731: [==========] 1 test from 1 test case ran. (758 ms total) 731: [ PASSED ] 0 tests. 731: [ FAILED ] 1 test, listed below: 731: [ FAILED ] Python.TikhonovDeconvolutionImageFilter 731: 731: 1 FAILED TEST 731/1259 Test #731: Python.TikhonovDeconvolutionImageFilter .............................***Failed 1.36 sec test 732 Start 732: Java.TikhonovDeconvolutionImageFilter 732: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver4 "--gtest_filter=Java.TikhonovDeconvolutionImageFilter" 732: Test timeout computed to be: 1500 732: Note: Google Test filter = Java.TikhonovDeconvolutionImageFilter 732: [==========] Running 1 test from 1 test case. 732: [----------] Global test environment set-up. 732: [----------] 1 test from Java 732: [ RUN ] Java.TikhonovDeconvolutionImageFilter 732: Running command: '/usr/bin/java -d64 -classpath /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/JavaTests:/builddir/build/BUILD/SimpleITK-0.9.1/build/Wrapping/simpleitk-0.9.1-gGIT-N.jar -Djava.library.path=/builddir/build/BUILD/SimpleITK-0.9.1/build/lib org.itk.simple.testing.TikhonovDeconvolutionImageFilterTest defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionKernel.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Java-TikhonovDeconvolutionImageFilter-defaults.nrrd ' 732: Starting image compare on BasicFilters_TikhonovDeconvolutionImageFilter_defaults 732: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_TikhonovDeconvolutionImageFilter_defaults.nrrd 732: 2.17091 732: 0.0001 732: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Expected.png 732: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Actual.png 732: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_TikhonovDeconvolutionImageFilter_defaults_Difference.png 732: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkTikhonovDeconvolutionImageFilterTest.cxx:366: Failure 732: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 732: Actual: false 732: Expected: true 732: ImageCompare: image Root Mean Square (RMS) difference was 2.17091 which exceeds the tolerance of 0.0001 732: 732: [ FAILED ] Java.TikhonovDeconvolutionImageFilter (795 ms) 732: [----------] 1 test from Java (796 ms total) 732: 732: [----------] Global test environment tear-down 732: [==========] 1 test from 1 test case ran. (797 ms total) 732: [ PASSED ] 0 tests. 732: [ FAILED ] 1 test, listed below: 732: [ FAILED ] Java.TikhonovDeconvolutionImageFilter 732: 732: 1 FAILED TEST 732/1259 Test #732: Java.TikhonovDeconvolutionImageFilter ...............................***Failed 1.40 sec <...> test 889 Start 889: BasicFilters.MaskedFFTNormalizedCorrelationImageFilter 889: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver5 "--gtest_filter=BasicFilters.MaskedFFTNormalizedCorrelationImageFilter:BasicFilters.MaskedFFTNormalizedCorrelationImageFilter_*" 889: Test timeout computed to be: 1500 889: Note: Google Test filter = BasicFilters.MaskedFFTNormalizedCorrelationImageFilter:BasicFilters.MaskedFFTNormalizedCorrelationImageFilter_* 889: [==========] Running 3 tests from 1 test case. 889: [----------] Global test environment set-up. 889: [----------] 3 tests from BasicFilters 889: [ RUN ] BasicFilters.MaskedFFTNormalizedCorrelationImageFilter 889: [ OK ] BasicFilters.MaskedFFTNormalizedCorrelationImageFilter (1 ms) 889: [ RUN ] BasicFilters.MaskedFFTNormalizedCorrelationImageFilter_defaults 889: Executing ITK filter: 889: MaskedFFTNormalizedCorrelationImageFilter (0x55af58f2e320) 889: RTTI typeinfo: itk::MaskedFFTNormalizedCorrelationImageFilter, itk::Image, itk::Image > 889: Reference Count: 1 889: Modified Time: 6222 889: Debug: Off 889: Object Name: 889: Observers: 889: DeleteEvent(SimpleMemberCommand) 889: Inputs: 889: Primary: (0x55af58f2dfd0) * 889: _1: (0x55af58f327d0) 889: _2: (0x55af58f33a50) 889: _3: (0x55af58f32d80) 889: Indexed Inputs: 889: 0: Primary (0x55af58f2dfd0) 889: 1: _1 (0x55af58f327d0) 889: 2: _2 (0x55af58f33a50) 889: 3: _3 (0x55af58f32d80) 889: Required Input Names: Primary 889: NumberOfRequiredInputs: 2 889: Outputs: 889: Primary: (0x55af58f34f90) 889: Indexed Outputs: 889: 0: Primary (0x55af58f34f90) 889: NumberOfRequiredOutputs: 1 889: Number Of Threads: 1 889: ReleaseDataFlag: Off 889: ReleaseDataBeforeUpdateFlag: Off 889: AbortGenerateData: Off 889: Progress: 0 889: Multithreader: 889: RTTI typeinfo: itk::MultiThreader 889: Reference Count: 1 889: Modified Time: 6204 889: Debug: Off 889: Object Name: 889: Observers: 889: none 889: Thread Count: 1 889: Global Maximum Number Of Threads: 128 889: Global Default Number Of Threads: 1 889: CoordinateTolerance: 1e-06 889: DirectionTolerance: 1e-06 889: Starting image compare on BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_ 889: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults.nrrd 889: 0.0100032 889: 0.01 889: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Expected.png 889: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Actual.png 889: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Difference.png 889: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkMaskedFFTNormalizedCorrelationImageFilterTest.cxx:124: Failure 889: Value of: imageCompare.compare( output, "", "" ) 889: Actual: false 889: Expected: true 889: ImageCompare: image Root Mean Square (RMS) difference was 0.0100032 which exceeds the tolerance of 0.01 889: 889: [ FAILED ] BasicFilters.MaskedFFTNormalizedCorrelationImageFilter_defaults (197 ms) 889: [ RUN ] BasicFilters.MaskedFFTNormalizedCorrelationImageFilter_3D 889: Executing ITK filter: 889: MaskedFFTNormalizedCorrelationImageFilter (0x55af58f2e940) 889: RTTI typeinfo: itk::MaskedFFTNormalizedCorrelationImageFilter, itk::Image, itk::Image > 889: Reference Count: 1 889: Modified Time: 15441 889: Debug: Off 889: Object Name: 889: Observers: 889: DeleteEvent(SimpleMemberCommand) 889: Inputs: 889: Primary: (0x55af58f2df20) * 889: _1: (0x55af58f2da20) 889: _2: (0x55af58f2e5b0) 889: _3: (0x55af58f32630) 889: Indexed Inputs: 889: 0: Primary (0x55af58f2df20) 889: 1: _1 (0x55af58f2da20) 889: 2: _2 (0x55af58f2e5b0) 889: 3: _3 (0x55af58f32630) 889: Required Input Names: Primary 889: NumberOfRequiredInputs: 2 889: Outputs: 889: Primary: (0x55af58f37840) 889: Indexed Outputs: 889: 0: Primary (0x55af58f37840) 889: NumberOfRequiredOutputs: 1 889: Number Of Threads: 1 889: ReleaseDataFlag: Off 889: ReleaseDataBeforeUpdateFlag: Off 889: AbortGenerateData: Off 889: Progress: 0 889: Multithreader: 889: RTTI typeinfo: itk::MultiThreader 889: Reference Count: 1 889: Modified Time: 15422 889: Debug: Off 889: Object Name: 889: Observers: 889: none 889: Thread Count: 1 889: Global Maximum Number Of Threads: 128 889: Global Default Number Of Threads: 1 889: CoordinateTolerance: 1e-06 889: DirectionTolerance: 1e-06 889: Starting image compare on BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D_ 889: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D.nrrd 889: [ OK ] BasicFilters.MaskedFFTNormalizedCorrelationImageFilter_3D (16455 ms) 889: [----------] 3 tests from BasicFilters (16653 ms total) 889: 889: [----------] Global test environment tear-down 889: [==========] 3 tests from 1 test case ran. (16655 ms total) 889: [ PASSED ] 2 tests. 889: [ FAILED ] 1 test, listed below: 889: [ FAILED ] BasicFilters.MaskedFFTNormalizedCorrelationImageFilter_defaults 889: 889: 1 FAILED TEST 889/1259 Test #889: BasicFilters.MaskedFFTNormalizedCorrelationImageFilter ..............***Failed 17.27 sec test 890 Start 890: Lua.MaskedFFTNormalizedCorrelationImageFilter 890: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver5 "--gtest_filter=Lua.MaskedFFTNormalizedCorrelationImageFilter" 890: Test timeout computed to be: 1500 890: Note: Google Test filter = Lua.MaskedFFTNormalizedCorrelationImageFilter 890: [==========] Running 1 test from 1 test case. 890: [----------] Global test environment set-up. 890: [----------] 1 test from Lua 890: [ RUN ] Lua.MaskedFFTNormalizedCorrelationImageFilter 890: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKLua /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/LuaTests/MaskedFFTNormalizedCorrelationImageFilterTest.lua defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Lua-MaskedFFTNormalizedCorrelationImageFilter-defaults.nrrd ' 890: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 890: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd 890: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 890: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd 890: 890: Starting image compare on BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults 890: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults.nrrd 890: 0.0100032 890: 0.01 890: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Expected.png 890: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Actual.png 890: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Difference.png 890: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkMaskedFFTNormalizedCorrelationImageFilterTest.cxx:232: Failure 890: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 890: Actual: false 890: Expected: true 890: ImageCompare: image Root Mean Square (RMS) difference was 0.0100032 which exceeds the tolerance of 0.01 890: 890: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKLua /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/LuaTests/MaskedFFTNormalizedCorrelationImageFilterTest.lua 3D /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Lua-MaskedFFTNormalizedCorrelationImageFilter-3D.nrrd ' 890: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd 890: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd 890: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd 890: reading.../builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd 890: 890: Starting image compare on BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D 890: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D.nrrd 890: [ FAILED ] Lua.MaskedFFTNormalizedCorrelationImageFilter (6759 ms) 890: [----------] 1 test from Lua (6760 ms total) 890: 890: [----------] Global test environment tear-down 890: [==========] 1 test from 1 test case ran. (6762 ms total) 890: [ PASSED ] 0 tests. 890: [ FAILED ] 1 test, listed below: 890: [ FAILED ] Lua.MaskedFFTNormalizedCorrelationImageFilter 890: 890: 1 FAILED TEST 890/1259 Test #890: Lua.MaskedFFTNormalizedCorrelationImageFilter .......................***Failed 9.58 sec test 891 Start 891: Python.MaskedFFTNormalizedCorrelationImageFilter 891: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver5 "--gtest_filter=Python.MaskedFFTNormalizedCorrelationImageFilter" 891: Test timeout computed to be: 1500 891: Note: Google Test filter = Python.MaskedFFTNormalizedCorrelationImageFilter 891: [==========] Running 1 test from 1 test case. 891: [----------] Global test environment set-up. 891: [----------] 1 test from Python 891: [ RUN ] Python.MaskedFFTNormalizedCorrelationImageFilter 891: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Installation/PythonVirtualenv/bin/python /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/PythonTests/MaskedFFTNormalizedCorrelationImageFilterTest.py defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Python-MaskedFFTNormalizedCorrelationImageFilter-defaults.nrrd ' 891: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 891: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd 891: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd 891: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd 891: 891: Starting image compare on BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults 891: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults.nrrd 891: 0.0100032 891: 0.01 891: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Expected.png 891: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Actual.png 891: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Difference.png 891: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkMaskedFFTNormalizedCorrelationImageFilterTest.cxx:308: Failure 891: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 891: Actual: false 891: Expected: true 891: ImageCompare: image Root Mean Square (RMS) difference was 0.0100032 which exceeds the tolerance of 0.01 891: 891: Running command: '/builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Installation/PythonVirtualenv/bin/python /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/PythonTests/MaskedFFTNormalizedCorrelationImageFilterTest.py 3D /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Python-MaskedFFTNormalizedCorrelationImageFilter-3D.nrrd ' 891: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd 891: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd 891: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd 891: reading /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd 891: 891: Starting image compare on BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D 891: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D.nrrd 891: [ FAILED ] Python.MaskedFFTNormalizedCorrelationImageFilter (6970 ms) 891: [----------] 1 test from Python (6971 ms total) 891: 891: [----------] Global test environment tear-down 891: [==========] 1 test from 1 test case ran. (6972 ms total) 891: [ PASSED ] 0 tests. 891: [ FAILED ] 1 test, listed below: 891: [ FAILED ] Python.MaskedFFTNormalizedCorrelationImageFilter 891: 891: 1 FAILED TEST 891/1259 Test #891: Python.MaskedFFTNormalizedCorrelationImageFilter ....................***Failed 7.57 sec test 892 Start 892: Java.MaskedFFTNormalizedCorrelationImageFilter 892: Test command: /builddir/build/BUILD/SimpleITK-0.9.1/build/bin/SimpleITKUnitTestDriver5 "--gtest_filter=Java.MaskedFFTNormalizedCorrelationImageFilter" 892: Test timeout computed to be: 1500 892: Note: Google Test filter = Java.MaskedFFTNormalizedCorrelationImageFilter 892: [==========] Running 1 test from 1 test case. 892: [----------] Global test environment set-up. 892: [----------] 1 test from Java 892: [ RUN ] Java.MaskedFFTNormalizedCorrelationImageFilter 892: Running command: '/usr/bin/java -d64 -classpath /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/JavaTests:/builddir/build/BUILD/SimpleITK-0.9.1/build/Wrapping/simpleitk-0.9.1-gGIT-N.jar -Djava.library.path=/builddir/build/BUILD/SimpleITK-0.9.1/build/lib org.itk.simple.testing.MaskedFFTNormalizedCorrelationImageFilterTest defaults /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/DeconvolutionInput.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/Gaussian_1.5.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Java-MaskedFFTNormalizedCorrelationImageFilter-defaults.nrrd ' 892: Starting image compare on BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults 892: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults.nrrd 892: 0.0100032 892: 0.01 892: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Expected.png 892: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Actual.png 892: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_defaults_Difference.png 892: /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/sitkMaskedFFTNormalizedCorrelationImageFilterTest.cxx:556: Failure 892: Value of: imageCompare.compare( output, "BasicFilters", "defaults" ) 892: Actual: false 892: Expected: true 892: ImageCompare: image Root Mean Square (RMS) difference was 0.0100032 which exceeds the tolerance of 0.01 892: 892: Running command: '/usr/bin/java -d64 -classpath /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Unit/JavaTests:/builddir/build/BUILD/SimpleITK-0.9.1/build/Wrapping/simpleitk-0.9.1-gGIT-N.jar -Djava.library.path=/builddir/build/BUILD/SimpleITK-0.9.1/build/lib org.itk.simple.testing.MaskedFFTNormalizedCorrelationImageFilterTest 3D /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd /builddir/build/BUILD/SimpleITK-0.9.1/build/Testing/Temporary/Java-MaskedFFTNormalizedCorrelationImageFilter-3D.nrrd ' 892: Starting image compare on BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D 892: Loading baseline /builddir/build/BUILD/SimpleITK-0.9.1/build/ExternalData/Testing/Data/Baseline/BasicFilters_MaskedFFTNormalizedCorrelationImageFilter_3D.nrrd 892: [ FAILED ] Java.MaskedFFTNormalizedCorrelationImageFilter (7119 ms) 892: [----------] 1 test from Java (7119 ms total) 892: 892: [----------] Global test environment tear-down 892: [==========] 1 test from 1 test case ran. (7121 ms total) 892: [ PASSED ] 0 tests. 892: [ FAILED ] 1 test, listed below: 892: [ FAILED ] Java.MaskedFFTNormalizedCorrelationImageFilter 892: 892: 1 FAILED TEST 892/1259 Test #892: Java.MaskedFFTNormalizedCorrelationImageFilter ......................***Failed 7.73 sec <...> 99% tests passed, 18 tests failed out of 1259 Total Test time (real) = 2266.01 sec The following tests FAILED: 149 - BasicFilters.InverseDeconvolutionImageFilter (Failed) 150 - Lua.InverseDeconvolutionImageFilter (Failed) 151 - Python.InverseDeconvolutionImageFilter (Failed) 152 - Java.InverseDeconvolutionImageFilter (Failed) 177 - BasicFilters.WienerDeconvolutionImageFilter (Failed) 178 - Lua.WienerDeconvolutionImageFilter (Failed) 179 - Python.WienerDeconvolutionImageFilter (Failed) 180 - Java.WienerDeconvolutionImageFilter (Failed) 729 - BasicFilters.TikhonovDeconvolutionImageFilter (Failed) 730 - Lua.TikhonovDeconvolutionImageFilter (Failed) 731 - Python.TikhonovDeconvolutionImageFilter (Failed) 732 - Java.TikhonovDeconvolutionImageFilter (Failed) 889 - BasicFilters.MaskedFFTNormalizedCorrelationImageFilter (Failed) 890 - Lua.MaskedFFTNormalizedCorrelationImageFilter (Failed) 891 - Python.MaskedFFTNormalizedCorrelationImageFilter (Failed) 892 - Java.MaskedFFTNormalizedCorrelationImageFilter (Failed) 1255 - Python.Test.ImageIndexing (Failed) 1257 - Python.Test.Numpy (Failed) Errors while running CTest -- Regards, Dmitry Mikhirev _______________________________________________ Powered by www.kitware.com 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 xi.chen at ultivue.com Sun Dec 6 17:07:13 2015 From: xi.chen at ultivue.com (Xi Chen) Date: Sun, 6 Dec 2015 17:07:13 -0500 Subject: [ITK] An exciting job opportunity awaits at Ultivue, Inc. Message-ID: Dear Colleagues, I?d like to announce an exciting job opportunity for imaging-related software engineers. Ultivue, the Cambridge, MA-based startup trying to democratize democratizing super-resolution imaging, is hiring an experienced software engineer to develop a user-friendly image-processing software to go along with their innovative reagent technologies. Here?s some press coverage of Ultivue: http://wyss.harvard.edu/viewpressrelease/223/ http://www.fiercebiotech.com/press-releases/ultivue-announces-515-million-series-financing http://www.fiercebiotech.com/story/wyss-spinout-bags-5m-one-nobel-prize-winning-tech/2015-10-13 And here?s the full job ad: Ultivue is an early stage life science tools company based in Cambridge, MA. We are looking for a software engineer to join our team to help develop transformative technologies in biological imaging applications. You will create software that has the potential to reach thousands of laboratories around the world. As a software engineer at Ultivue, you will work together with scientists to develop a cohesive hardware and software platform that will allow researchers and clinicians to see the molecular world with unprecedented clarity. Your efforts will drive new capabilities in molecular technology leading to advanced research opportunities, diagnostics, drug discovery, and much more. JOB DESCRIPTION You will build the first release-ready version of the software based on our previously developed prototypes and algorithms. You will create a robust software package with intuitive graphic user interface for both Mac and PC users. Cloud-based software is an option. Later on, you will lead the implementation of additional algorithms and features for advanced versions. You will be responsible for all aspects of the software including the architecture, algorithm implementation, memory management, GUI layout and system compatibility. You will also be expected to confer with alpha and beta testers as well as customers to make steady improvements on the usability and utility of the software. REQUIRED QUALIFICATIONS - BS or higher and cumulative 4+ years experience in Computer Science or related field. - Strong programming skills with object-oriented languages (C++, Java). - Advanced MATLAB programming. - Aptitude and passion for learning new programming languages, technologies, and algorithms. - 2+ years experience in production-quality software development. - Significant background in large-scale image processing applications. - Training and experience in designing and implementing UIs for standalone software (PC/Mac). - Strong technical learning and communication skills, especially with non-engineers. - Comfortable working independently and tackling large projects. PREFERRED QUALIFICATIONS - MS or higher in science or engineering field. - Experience with writing ImageJ plugins - Experience with server management, arduino, instrumentation hardware. - Familiarity with chemical and biological sciences. INTERESTED? Please send resume to xi.chen at ultivue.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikhirev at gmail.com Mon Dec 7 04:26:24 2015 From: mikhirev at gmail.com (Dmitry Mikhirev) Date: Mon, 7 Dec 2015 12:26:24 +0300 Subject: [ITK] [ITK-dev] SimpleITK build failure on Fedora 23 In-Reply-To: <4AE681D4-7789-4E2A-AECB-2AFB6455B6EC@mail.nih.gov> References: <20151206230948.17650b7d@kafka> <4AE681D4-7789-4E2A-AECB-2AFB6455B6EC@mail.nih.gov> Message-ID: <20151207122624.28955c17@dmikhirev.i.drweb.ru> ? Sun, 6 Dec 2015 20:28:07 -0500 Bradley Lowekamp ?????: > Hello Dmitry, Hello Brad! Thank you for your reply! > > SimpleITK is not built or tested against ITK with ITKv3 compatibility > turned on. And Most projects have this option turned off, so it?s not > as well tested as it used to be. > > This problem looks to be solely with ITK. It appears like the error > will happen just with the instantiation of: > > itk::Statistics::Histogram > > This issue looks fixable. I don?t know how many other errors will > occur when you get past this one. Well, most code is already compiled before this error occurs. So I guess there will not me much more. Can you give an advice what changes are needed to fix it? > > I?d recommend using the SimpleITK Superbuild by point CMake toward > the Superbuild subdirectory on the initial configuration. > > BTW, what is the reason you are ?required? to used the system ITK? I'm going to build a package for official Fedora repo. That's why I have to link to other libraries shipped by Fedora and not to bundle them. Of course, if the error were unfixable on SimpleITK side, I could send a bug report for InsigtToolkit package and ask maintainer to disable ITKv3 compatibility, but I afraid it can break some other packages. > > Brad > -- Regards, Dmitry Mikhirev _______________________________________________ Powered by www.kitware.com 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 ribaluigi at gmail.com Mon Dec 7 09:43:47 2015 From: ribaluigi at gmail.com (Luigi Riba) Date: Mon, 7 Dec 2015 15:43:47 +0100 Subject: [ITK] Metric NaN and multi resolution registration Message-ID: Dear ITK community, today I was trying to implement a multi-resolution registration process for 3d images. I started from the example in the tutorial. Unfortunately, I've received the following warning: > WARNING: In > f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, > line 529 > MeanSquaresImageToImageMetricv4 (000000006506C020): No valid points were > found during metric evaluation. For image metrics, verify that the images > overlap appropriately. For instance, you can align the image centers by > translation. For point-set metrics, verify that the fixed points, once > transformed into the virtual domain space, actually lie within the virtual > domain. These are the parameters I have used for the multi resolution process: > const unsigned int numberOfLevels = 3; > RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; > shrinkFactorsPerLevel.SetSize(numberOfLevels); > shrinkFactorsPerLevel[0] = 4; > shrinkFactorsPerLevel[1] = 2; > shrinkFactorsPerLevel[2] = 1; > RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; > smoothingSigmasPerLevel.SetSize(numberOfLevels); > smoothingSigmasPerLevel[0] = 2; > smoothingSigmasPerLevel[1] = 1; > smoothingSigmasPerLevel[2] = 0; > registration->SetNumberOfLevels(numberOfLevels); > registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); > registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); Could you please me explain what is the meaning of this warning? By the way, I am working with affine transformations and I have used the transform initializer. Best, Luigi -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Mon Dec 7 10:04:31 2015 From: matimontg at gmail.com (Matias Montroull) Date: Mon, 07 Dec 2015 15:04:31 +0000 Subject: [ITK] Metric NaN and multi resolution registration In-Reply-To: References: Message-ID: Hi Luigi, it could be for various reasons, mailny the transform initializer you use plus the number of samples and translationscale Try this code I have which I've done for MultiResolution and works fine for me: When you enter the parameters, try this: Relaxation: 0.99 Number of Bins: 50 Samples 3 (this is actually translated to 3% in my code as you will see below) maximum and minimum steplenght is not taken into account so you can put 0 and 0 translation scale 0.0001 #include "itkAffineTransform.h" #include "itkRegistrationParameterScalesFromPhysicalShift.h" #include "itkCenteredTransformInitializer.h" #include "itkLandmarkBasedTransformInitializer.h" #include "itkMultiResolutionImageRegistrationMethod.h" #include "itkMattesMutualInformationImageToImageMetric.h" #include "itkMeanSquaresImageToImageMetric.h" #include "itkRegularStepGradientDescentOptimizer.h" #include "itkRecursiveMultiResolutionPyramidImageFilter.h" #include "itkImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkResampleImageFilter.h" #include "itkCastImageFilter.h" #include "itkCheckerBoardImageFilter.h" #include "itkRescaleIntensityImageFilter.h" #include "itkNormalizeImageFilter.h" #include "itkCommand.h" class CommandIterationUpdate : public itk::Command { public: typedef CommandIterationUpdate Self; typedef itk::Command Superclass; typedef itk::SmartPointer Pointer; itkNewMacro(Self); protected: CommandIterationUpdate() : m_CumulativeIterationIndex(0) {}; public: typedef itk::RegularStepGradientDescentOptimizer OptimizerType; typedef const OptimizerType * OptimizerPointer; void Execute(itk::Object *caller, const itk::EventObject & event) ITK_OVERRIDE { Execute((const itk::Object *)caller, event); } void Execute(const itk::Object * object, const itk::EventObject & event) ITK_OVERRIDE { OptimizerPointer optimizer = static_cast(object); if (!(itk::IterationEvent().CheckEvent(&event))) { return; } std::cout << optimizer->GetCurrentIteration() << " "; std::cout << optimizer->GetValue() << " "; std::cout << optimizer->GetCurrentPosition() << " " << m_CumulativeIterationIndex++ << std::endl; } private: unsigned int m_CumulativeIterationIndex; }; template class RegistrationInterfaceCommand : public itk::Command { public: typedef RegistrationInterfaceCommand Self; typedef itk::Command Superclass; typedef itk::SmartPointer Pointer; itkNewMacro(Self); protected: RegistrationInterfaceCommand() {}; public: typedef TRegistration RegistrationType; typedef RegistrationType * RegistrationPointer; typedef itk::RegularStepGradientDescentOptimizer OptimizerType; typedef OptimizerType * OptimizerPointer; void Execute(itk::Object * object, const itk::EventObject & event) ITK_OVERRIDE { if (!(itk::IterationEvent().CheckEvent(&event))) { return; } RegistrationPointer registration = static_cast(object); OptimizerPointer optimizer = static_cast(registration->GetModifiableOptimizer()); std::cout << "-------------------------------------" << std::endl; std::cout << "MultiResolution Level : " << registration->GetCurrentLevel() << std::endl; std::cout << std::endl; if (registration->GetCurrentLevel() == 0) { optimizer->SetMaximumStepLength(1.0); optimizer->SetMinimumStepLength(0.001); } else { optimizer->SetMaximumStepLength(optimizer->GetMaximumStepLength() / 4.0); optimizer->SetMinimumStepLength(optimizer->GetMinimumStepLength() / 10.0); } } void Execute(const itk::Object *, const itk::EventObject &) ITK_OVERRIDE { return; } }; int main(int argc, char *argv[]) { if (argc < 10) { std::cerr << "Faltan Parametros " << std::endl; std::cerr << "Uso: " << argv[0]; std::cerr << " imagenfija imagenflotante "; std::cerr << " salida"; std::cerr << " Iteraciones Relaxation "; std::cerr << " NumeroBins Samples%(1/100) "; std::cerr << " StepMax(No Habilitado) StepMin(No Habilitado) TranslationFactor"; std::cerr << " " << std::endl; return EXIT_FAILURE; } const unsigned int Dimension = 3; typedef signed short PixelType; typedef itk::Image< PixelType, Dimension > FixedImageType; typedef itk::Image< PixelType, Dimension > MovingImageType; typedef float InternalPixelType; typedef itk::Image< InternalPixelType, Dimension > InternalImageType; typedef itk::AffineTransform< double, Dimension > TransformType; typedef itk::RegularStepGradientDescentOptimizer OptimizerType; typedef itk::LinearInterpolateImageFunction< InternalImageType, double > InterpolatorType; typedef itk::MattesMutualInformationImageToImageMetric< InternalImageType, InternalImageType > MetricType; typedef OptimizerType::ScalesType OptimizerScalesType; typedef itk::MultiResolutionImageRegistrationMethod< InternalImageType, InternalImageType > RegistrationType; OptimizerType::Pointer optimizer = OptimizerType::New(); InterpolatorType::Pointer interpolator = InterpolatorType::New(); RegistrationType::Pointer registration = RegistrationType::New(); MetricType::Pointer metric = MetricType::New(); TransformType::Pointer transform = TransformType::New(); registration->SetTransform(transform); typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType; typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType; FixedImageReaderType::Pointer fixedImageReader = FixedImageReaderType::New(); MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New(); fixedImageReader->SetFileName(argv[1]); movingImageReader->SetFileName(argv[2]); fixedImageReader->Update(); movingImageReader->Update(); typedef itk::CastImageFilter< FixedImageType, InternalImageType > FixedCastFilterType; typedef itk::CastImageFilter< MovingImageType, InternalImageType > MovingCastFilterType; FixedCastFilterType::Pointer fixedCaster = FixedCastFilterType::New(); MovingCastFilterType::Pointer movingCaster = MovingCastFilterType::New(); fixedCaster->SetInput(fixedImageReader->GetOutput()); movingCaster->SetInput(movingImageReader->GetOutput()); registration->SetFixedImage(fixedCaster->GetOutput()); registration->SetMovingImage(movingCaster->GetOutput()); fixedCaster->Update(); registration->SetFixedImageRegion(fixedCaster->GetOutput()->GetBufferedRegion()); typedef itk::CenteredTransformInitializer< TransformType, FixedImageType, MovingImageType > TransformInitializerType; TransformInitializerType::Pointer initializer = TransformInitializerType::New(); initializer->SetTransform(transform); initializer->SetFixedImage(fixedImageReader->GetOutput()); initializer->SetMovingImage(movingImageReader->GetOutput()); initializer->GeometryOn(); initializer->InitializeTransform(); typedef TransformType::ParametersType ParametersType; const unsigned int numberOfParameters = transform->GetNumberOfParameters(); ParametersType parameters(numberOfParameters); registration->SetInitialTransformParameters(transform->GetParameters()); OptimizerScalesType optimizerScales(transform->GetNumberOfParameters()); double translationScale = atof(argv[10]); optimizerScales[0] = 1.0; optimizerScales[1] = 1.0; optimizerScales[2] = 1.0; optimizerScales[3] = 1.0; optimizerScales[4] = 1.0; optimizerScales[5] = 1.0; optimizerScales[6] = 1.0; optimizerScales[7] = 1.0; optimizerScales[8] = 1.0; optimizerScales[9] = translationScale; optimizerScales[10] = translationScale; optimizerScales[11] = translationScale; optimizer->SetScales(optimizerScales); FixedImageType::RegionType fixedImageRegion = fixedCaster->GetOutput()->GetBufferedRegion(); const unsigned int numberOfPixels = fixedImageRegion.GetNumberOfPixels(); double porcentage_samples = atof(argv[7]); const unsigned int numberOfSamples = static_cast(numberOfPixels * porcentage_samples); optimizer->SetNumberOfIterations(atof(argv[4])); optimizer->SetRelaxationFactor(atof(argv[5])); metric->SetNumberOfHistogramBins(atof(argv[6])); metric->SetNumberOfSpatialSamples(numberOfSamples); optimizer->SetMaximumStepLength(atof(argv[8])); optimizer->SetMinimumStepLength(atof(argv[9])); optimizer->MinimizeOn(); CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New(); optimizer->AddObserver(itk::IterationEvent(), observer); typedef RegistrationInterfaceCommand CommandType; CommandType::Pointer command = CommandType::New(); registration->AddObserver(itk::IterationEvent(), command); registration->SetNumberOfLevels(1); registration->SetOptimizer(optimizer); registration->SetInterpolator(interpolator); registration->SetMetric(metric); FixedImageType::Pointer imagenfija = fixedImageReader->GetOutput(); MovingImageType::Pointer imagenflotante = movingImageReader->GetOutput(); typedef RegistrationType::ParametersType ParametersType; ParametersType InitialParameters = registration->GetInitialTransformParameters(); std::cout << "TranslationScale: " << translationScale << std::endl; std::cout << "MaximumStep: " << optimizer->GetMaximumStepLength() << std::endl; std::cout << "MinimunStep: " << optimizer->GetMinimumStepLength() << std::endl; std::cout << "Number of Bins: " << metric->GetNumberOfHistogramBins() << std::endl; std::cout << "Number of Samples: " << metric->GetNumberOfSpatialSamples() << std::endl; std::cout << "Iteraciones: " << optimizer->GetNumberOfIterations() << std::endl; std::cout << "Relaxation: " << optimizer->GetRelaxationFactor() << std::endl; std::cout << "Initial Parameters: " << InitialParameters << std::endl; std::cout << "Origen Fija: " << imagenfija->GetOrigin() << std::endl; std::cout << "Origen Flotante: " << imagenflotante->GetOrigin() << std::endl; std::cout << "Samples: " << numberOfSamples << std::endl; try { registration->Update(); std::cout << "Optimizer stop condition: " << registration->GetOptimizer()->GetStopConditionDescription() << std::endl; } catch (itk::ExceptionObject & err) { std::cout << "ExceptionObject caught !" << std::endl; std::cout << err << std::endl; return EXIT_FAILURE; } std::cout << "Optimizer Stopping Condition = " << optimizer->GetStopCondition() << std::endl; ParametersType finalParameters = registration->GetLastTransformParameters(); double TranslationAlongX = finalParameters[9]; double TranslationAlongY = finalParameters[10]; double TranslationAlongZ = finalParameters[11]; unsigned int numberOfIterations = optimizer->GetCurrentIteration(); double bestValue = optimizer->GetValue(); std::cout << "Resultado = " << std::endl; std::cout << " Traslacion X = " << TranslationAlongX << std::endl; std::cout << " Traslacion Y = " << TranslationAlongY << std::endl; std::cout << " Traslacion Z = " << TranslationAlongZ << std::endl; std::cout << " Iteraciones = " << numberOfIterations << std::endl; std::cout << " Metrica = " << bestValue << std::endl; typedef itk::ResampleImageFilter< MovingImageType, FixedImageType > ResampleFilterType; TransformType::Pointer finalTransform = TransformType::New(); finalTransform->SetParameters(finalParameters); finalTransform->SetFixedParameters(transform->GetFixedParameters()); ResampleFilterType::Pointer resample = ResampleFilterType::New(); resample->SetTransform(finalTransform); resample->SetInput(movingImageReader->GetOutput()); FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput(); PixelType backgroundGrayLevel = 0; //estaba en 100 resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize()); resample->SetOutputOrigin(fixedImage->GetOrigin()); resample->SetOutputSpacing(fixedImage->GetSpacing()); resample->SetOutputDirection(fixedImage->GetDirection()); resample->SetDefaultPixelValue(backgroundGrayLevel); typedef signed short OutputPixelType; typedef itk::Image< OutputPixelType, Dimension > OutputImageType; typedef itk::CastImageFilter< FixedImageType, OutputImageType > CastFilterType; typedef itk::ImageFileWriter< OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); CastFilterType::Pointer caster = CastFilterType::New(); writer->SetFileName(argv[3]); caster->SetInput(resample->GetOutput()); writer->SetInput(caster->GetOutput()); writer->Update(); Sleep(5000); /* typedef itk::CheckerBoardImageFilter< FixedImageType > CheckerBoardFilterType; CheckerBoardFilterType::Pointer checker = CheckerBoardFilterType::New(); checker->SetInput1(fixedImage); checker->SetInput2(resample->GetOutput()); caster->SetInput(checker->GetOutput()); writer->SetInput(caster->GetOutput()); resample->SetDefaultPixelValue(0); resample->SetTransform(finalTransform); if (argc > 10) { writer->SetFileName(argv[11]); writer->Update(); }*/ return EXIT_SUCCESS; } El lun., 7 de dic. de 2015 a la(s) 11:43, Luigi Riba escribi?: > Dear ITK community, > > today I was trying to implement a multi-resolution registration process > for 3d images. > > I started from the example in the tutorial. Unfortunately, I've received > the following warning: > >> WARNING: In >> f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, >> line 529 >> MeanSquaresImageToImageMetricv4 (000000006506C020): No valid points were >> found during metric evaluation. For image metrics, verify that the images >> overlap appropriately. For instance, you can align the image centers by >> translation. For point-set metrics, verify that the fixed points, once >> transformed into the virtual domain space, actually lie within the virtual >> domain. > > > These are the parameters I have used for the multi resolution process: >> const unsigned int numberOfLevels = 3; >> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >> shrinkFactorsPerLevel.SetSize(numberOfLevels); >> shrinkFactorsPerLevel[0] = 4; >> shrinkFactorsPerLevel[1] = 2; >> shrinkFactorsPerLevel[2] = 1; >> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >> smoothingSigmasPerLevel.SetSize(numberOfLevels); >> smoothingSigmasPerLevel[0] = 2; >> smoothingSigmasPerLevel[1] = 1; >> smoothingSigmasPerLevel[2] = 0; >> registration->SetNumberOfLevels(numberOfLevels); >> registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); >> registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); > > > Could you please me explain what is the meaning of this warning? > > By the way, I am working with affine transformations and I have used the > transform initializer. > > Best, > > Luigi > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Matias -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Mon Dec 7 10:06:35 2015 From: matimontg at gmail.com (Matias Montroull) Date: Mon, 07 Dec 2015 15:06:35 +0000 Subject: [ITK] Metric NaN and multi resolution registration In-Reply-To: References: Message-ID: Actually the min and max steplenght are taken into account, I use these: Min: 0.0001 Max: 0.1 El lun., 7 de dic. de 2015 a la(s) 12:04, Matias Montroull < matimontg at gmail.com> escribi?: > Hi Luigi, it could be for various reasons, mailny the transform > initializer you use plus the number of samples and translationscale > Try this code I have which I've done for MultiResolution and works fine > for me: > > When you enter the parameters, try this: > Relaxation: 0.99 > Number of Bins: 50 > Samples 3 (this is actually translated to 3% in my code as you will see > below) > maximum and minimum steplenght is not taken into account so you can put 0 > and 0 > translation scale 0.0001 > > #include "itkAffineTransform.h" > #include "itkRegistrationParameterScalesFromPhysicalShift.h" > #include "itkCenteredTransformInitializer.h" > #include "itkLandmarkBasedTransformInitializer.h" > #include "itkMultiResolutionImageRegistrationMethod.h" > #include "itkMattesMutualInformationImageToImageMetric.h" > #include "itkMeanSquaresImageToImageMetric.h" > #include "itkRegularStepGradientDescentOptimizer.h" > #include "itkRecursiveMultiResolutionPyramidImageFilter.h" > #include "itkImage.h" > #include "itkImageFileReader.h" > #include "itkImageFileWriter.h" > #include "itkResampleImageFilter.h" > #include "itkCastImageFilter.h" > #include "itkCheckerBoardImageFilter.h" > #include "itkRescaleIntensityImageFilter.h" > > #include "itkNormalizeImageFilter.h" > > #include "itkCommand.h" > class CommandIterationUpdate : public itk::Command > { > public: > typedef CommandIterationUpdate Self; > typedef itk::Command Superclass; > typedef itk::SmartPointer Pointer; > itkNewMacro(Self); > protected: > CommandIterationUpdate() : m_CumulativeIterationIndex(0) {}; > public: > typedef itk::RegularStepGradientDescentOptimizer OptimizerType; > typedef const OptimizerType * OptimizerPointer; > void Execute(itk::Object *caller, const itk::EventObject & event) > ITK_OVERRIDE > { > Execute((const itk::Object *)caller, event); > } > void Execute(const itk::Object * object, const itk::EventObject & event) > ITK_OVERRIDE > { > OptimizerPointer optimizer = static_cast(object); > if (!(itk::IterationEvent().CheckEvent(&event))) > { > return; > } > std::cout << optimizer->GetCurrentIteration() << " "; > std::cout << optimizer->GetValue() << " "; > std::cout << optimizer->GetCurrentPosition() << " " << > m_CumulativeIterationIndex++ << std::endl; > } > private: > unsigned int m_CumulativeIterationIndex; > }; > > template > class RegistrationInterfaceCommand : public itk::Command > { > public: > typedef RegistrationInterfaceCommand Self; > typedef itk::Command Superclass; > typedef itk::SmartPointer Pointer; > itkNewMacro(Self); > protected: > RegistrationInterfaceCommand() {}; > public: > typedef TRegistration RegistrationType; > typedef RegistrationType * RegistrationPointer; > typedef itk::RegularStepGradientDescentOptimizer OptimizerType; > typedef OptimizerType * OptimizerPointer; > void Execute(itk::Object * object, const itk::EventObject & event) > ITK_OVERRIDE > { > if (!(itk::IterationEvent().CheckEvent(&event))) > { > return; > } > RegistrationPointer registration = > static_cast(object); > OptimizerPointer optimizer = > static_cast(registration->GetModifiableOptimizer()); > std::cout << "-------------------------------------" << std::endl; > std::cout << "MultiResolution Level : " > << registration->GetCurrentLevel() << std::endl; > std::cout << std::endl; > if (registration->GetCurrentLevel() == 0) > { > optimizer->SetMaximumStepLength(1.0); > optimizer->SetMinimumStepLength(0.001); > } > else > { > optimizer->SetMaximumStepLength(optimizer->GetMaximumStepLength() / 4.0); > optimizer->SetMinimumStepLength(optimizer->GetMinimumStepLength() / 10.0); > } > } > void Execute(const itk::Object *, const itk::EventObject &) ITK_OVERRIDE > { return; } > }; > int main(int argc, char *argv[]) > { > if (argc < 10) > { > std::cerr << "Faltan Parametros " << std::endl; > std::cerr << "Uso: " << argv[0]; > std::cerr << " imagenfija imagenflotante "; > std::cerr << " salida"; > std::cerr << " Iteraciones Relaxation "; > std::cerr << " NumeroBins Samples%(1/100) "; > std::cerr << " StepMax(No Habilitado) StepMin(No Habilitado) > TranslationFactor"; > std::cerr << " " << std::endl; > > return EXIT_FAILURE; > } > > const unsigned int Dimension = 3; > typedef signed short PixelType; > typedef itk::Image< PixelType, Dimension > FixedImageType; > typedef itk::Image< PixelType, Dimension > MovingImageType; > typedef float InternalPixelType; > typedef itk::Image< InternalPixelType, Dimension > InternalImageType; > > typedef itk::AffineTransform< double, Dimension > TransformType; > > typedef itk::RegularStepGradientDescentOptimizer OptimizerType; > typedef itk::LinearInterpolateImageFunction< > InternalImageType, > double > InterpolatorType; > typedef itk::MattesMutualInformationImageToImageMetric< > InternalImageType, > InternalImageType > MetricType; > typedef OptimizerType::ScalesType OptimizerScalesType; > typedef itk::MultiResolutionImageRegistrationMethod< > InternalImageType, > InternalImageType > RegistrationType; > OptimizerType::Pointer optimizer = OptimizerType::New(); > InterpolatorType::Pointer interpolator = InterpolatorType::New(); > RegistrationType::Pointer registration = RegistrationType::New(); > MetricType::Pointer metric = MetricType::New(); > > > TransformType::Pointer transform = TransformType::New(); > registration->SetTransform(transform); > > typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType; > typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType; > FixedImageReaderType::Pointer fixedImageReader = > FixedImageReaderType::New(); > MovingImageReaderType::Pointer movingImageReader = > MovingImageReaderType::New(); > fixedImageReader->SetFileName(argv[1]); > movingImageReader->SetFileName(argv[2]); > > fixedImageReader->Update(); > movingImageReader->Update(); > > typedef itk::CastImageFilter< > FixedImageType, InternalImageType > FixedCastFilterType; > typedef itk::CastImageFilter< > MovingImageType, InternalImageType > MovingCastFilterType; > FixedCastFilterType::Pointer fixedCaster = FixedCastFilterType::New(); > MovingCastFilterType::Pointer movingCaster = MovingCastFilterType::New(); > fixedCaster->SetInput(fixedImageReader->GetOutput()); > movingCaster->SetInput(movingImageReader->GetOutput()); > > registration->SetFixedImage(fixedCaster->GetOutput()); > registration->SetMovingImage(movingCaster->GetOutput()); > fixedCaster->Update(); > > registration->SetFixedImageRegion(fixedCaster->GetOutput()->GetBufferedRegion()); > > typedef itk::CenteredTransformInitializer< > TransformType, FixedImageType, > MovingImageType > TransformInitializerType; > TransformInitializerType::Pointer initializer > = TransformInitializerType::New(); > initializer->SetTransform(transform); > initializer->SetFixedImage(fixedImageReader->GetOutput()); > initializer->SetMovingImage(movingImageReader->GetOutput()); > initializer->GeometryOn(); > initializer->InitializeTransform(); > > > typedef TransformType::ParametersType ParametersType; > const unsigned int numberOfParameters = transform->GetNumberOfParameters(); > ParametersType parameters(numberOfParameters); > registration->SetInitialTransformParameters(transform->GetParameters()); > > OptimizerScalesType optimizerScales(transform->GetNumberOfParameters()); > > double translationScale = atof(argv[10]); > optimizerScales[0] = 1.0; > optimizerScales[1] = 1.0; > optimizerScales[2] = 1.0; > optimizerScales[3] = 1.0; > optimizerScales[4] = 1.0; > optimizerScales[5] = 1.0; > optimizerScales[6] = 1.0; > optimizerScales[7] = 1.0; > optimizerScales[8] = 1.0; > optimizerScales[9] = translationScale; > optimizerScales[10] = translationScale; > optimizerScales[11] = translationScale; > > optimizer->SetScales(optimizerScales); > > FixedImageType::RegionType fixedImageRegion = > fixedCaster->GetOutput()->GetBufferedRegion(); > const unsigned int numberOfPixels = fixedImageRegion.GetNumberOfPixels(); > double porcentage_samples = atof(argv[7]); > const unsigned int numberOfSamples = static_cast int>(numberOfPixels * porcentage_samples); > > optimizer->SetNumberOfIterations(atof(argv[4])); > optimizer->SetRelaxationFactor(atof(argv[5])); > metric->SetNumberOfHistogramBins(atof(argv[6])); > metric->SetNumberOfSpatialSamples(numberOfSamples); > optimizer->SetMaximumStepLength(atof(argv[8])); > optimizer->SetMinimumStepLength(atof(argv[9])); > > > optimizer->MinimizeOn(); > CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New(); > optimizer->AddObserver(itk::IterationEvent(), observer); > > > typedef RegistrationInterfaceCommand CommandType; > CommandType::Pointer command = CommandType::New(); > registration->AddObserver(itk::IterationEvent(), command); > registration->SetNumberOfLevels(1); > registration->SetOptimizer(optimizer); > registration->SetInterpolator(interpolator); > registration->SetMetric(metric); > > FixedImageType::Pointer imagenfija = fixedImageReader->GetOutput(); > MovingImageType::Pointer imagenflotante = movingImageReader->GetOutput(); > > > typedef RegistrationType::ParametersType ParametersType; > ParametersType InitialParameters = > registration->GetInitialTransformParameters(); > std::cout << "TranslationScale: " << translationScale << std::endl; > std::cout << "MaximumStep: " << optimizer->GetMaximumStepLength() << > std::endl; > std::cout << "MinimunStep: " << optimizer->GetMinimumStepLength() << > std::endl; > std::cout << "Number of Bins: " << metric->GetNumberOfHistogramBins() << > std::endl; > std::cout << "Number of Samples: " << metric->GetNumberOfSpatialSamples() > << std::endl; > std::cout << "Iteraciones: " << optimizer->GetNumberOfIterations() << > std::endl; > std::cout << "Relaxation: " << optimizer->GetRelaxationFactor() << > std::endl; > std::cout << "Initial Parameters: " << InitialParameters << std::endl; > std::cout << "Origen Fija: " << imagenfija->GetOrigin() << std::endl; > std::cout << "Origen Flotante: " << imagenflotante->GetOrigin() << > std::endl; > std::cout << "Samples: " << numberOfSamples << std::endl; > > try > { > registration->Update(); > std::cout << "Optimizer stop condition: " > << registration->GetOptimizer()->GetStopConditionDescription() > << std::endl; > } > catch (itk::ExceptionObject & err) > { > std::cout << "ExceptionObject caught !" << std::endl; > std::cout << err << std::endl; > return EXIT_FAILURE; > } > std::cout << "Optimizer Stopping Condition = " > << optimizer->GetStopCondition() << std::endl; > > ParametersType finalParameters = > registration->GetLastTransformParameters(); > > double TranslationAlongX = finalParameters[9]; > double TranslationAlongY = finalParameters[10]; > double TranslationAlongZ = finalParameters[11]; > unsigned int numberOfIterations = optimizer->GetCurrentIteration(); > double bestValue = optimizer->GetValue(); > > std::cout << "Resultado = " << std::endl; > std::cout << " Traslacion X = " << TranslationAlongX << std::endl; > std::cout << " Traslacion Y = " << TranslationAlongY << std::endl; > std::cout << " Traslacion Z = " << TranslationAlongZ << std::endl; > std::cout << " Iteraciones = " << numberOfIterations << std::endl; > std::cout << " Metrica = " << bestValue << std::endl; > > > typedef itk::ResampleImageFilter< > MovingImageType, > FixedImageType > ResampleFilterType; > TransformType::Pointer finalTransform = TransformType::New(); > finalTransform->SetParameters(finalParameters); > finalTransform->SetFixedParameters(transform->GetFixedParameters()); > ResampleFilterType::Pointer resample = ResampleFilterType::New(); > resample->SetTransform(finalTransform); > resample->SetInput(movingImageReader->GetOutput()); > FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput(); > PixelType backgroundGrayLevel = 0; //estaba en 100 > > resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize()); > resample->SetOutputOrigin(fixedImage->GetOrigin()); > resample->SetOutputSpacing(fixedImage->GetSpacing()); > resample->SetOutputDirection(fixedImage->GetDirection()); > resample->SetDefaultPixelValue(backgroundGrayLevel); > typedef signed short OutputPixelType; > typedef itk::Image< OutputPixelType, Dimension > OutputImageType; > typedef itk::CastImageFilter< > FixedImageType, > OutputImageType > CastFilterType; > typedef itk::ImageFileWriter< OutputImageType > WriterType; > WriterType::Pointer writer = WriterType::New(); > CastFilterType::Pointer caster = CastFilterType::New(); > writer->SetFileName(argv[3]); > caster->SetInput(resample->GetOutput()); > writer->SetInput(caster->GetOutput()); > writer->Update(); > Sleep(5000); > /* > typedef itk::CheckerBoardImageFilter< FixedImageType > > CheckerBoardFilterType; > CheckerBoardFilterType::Pointer checker = CheckerBoardFilterType::New(); > checker->SetInput1(fixedImage); > checker->SetInput2(resample->GetOutput()); > caster->SetInput(checker->GetOutput()); > writer->SetInput(caster->GetOutput()); > resample->SetDefaultPixelValue(0); > > resample->SetTransform(finalTransform); > if (argc > 10) > { > writer->SetFileName(argv[11]); > writer->Update(); > }*/ > return EXIT_SUCCESS; > } > > > El lun., 7 de dic. de 2015 a la(s) 11:43, Luigi Riba > escribi?: > >> Dear ITK community, >> >> today I was trying to implement a multi-resolution registration process >> for 3d images. >> >> I started from the example in the tutorial. Unfortunately, I've received >> the following warning: >> >>> WARNING: In >>> f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, >>> line 529 >>> MeanSquaresImageToImageMetricv4 (000000006506C020): No valid points were >>> found during metric evaluation. For image metrics, verify that the images >>> overlap appropriately. For instance, you can align the image centers by >>> translation. For point-set metrics, verify that the fixed points, once >>> transformed into the virtual domain space, actually lie within the virtual >>> domain. >> >> >> These are the parameters I have used for the multi resolution process: >>> const unsigned int numberOfLevels = 3; >>> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >>> shrinkFactorsPerLevel.SetSize(numberOfLevels); >>> shrinkFactorsPerLevel[0] = 4; >>> shrinkFactorsPerLevel[1] = 2; >>> shrinkFactorsPerLevel[2] = 1; >>> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >>> smoothingSigmasPerLevel.SetSize(numberOfLevels); >>> smoothingSigmasPerLevel[0] = 2; >>> smoothingSigmasPerLevel[1] = 1; >>> smoothingSigmasPerLevel[2] = 0; >>> registration->SetNumberOfLevels(numberOfLevels); >>> registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); >>> registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); >> >> >> Could you please me explain what is the meaning of this warning? >> >> By the way, I am working with affine transformations and I have used the >> transform initializer. >> >> Best, >> >> Luigi >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > -- > Matias > -- Matias -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Mon Dec 7 11:06:17 2015 From: brad at lowekamp.net (Bradley Lowekamp) Date: Mon, 7 Dec 2015 11:06:17 -0500 Subject: [ITK] [ITK-dev] SimpleITK build failure on Fedora 23 In-Reply-To: <20151207122624.28955c17@dmikhirev.i.drweb.ru> References: <20151206230948.17650b7d@kafka> <4AE681D4-7789-4E2A-AECB-2AFB6455B6EC@mail.nih.gov> <20151207122624.28955c17@dmikhirev.i.drweb.ru> Message-ID: Hello, I uses SimpleITK?s Superbuild with -DITKV3_COMPATIBILITY:BOOL=ON -DITK_LEGACY_REMOVE=OFF, and got the same error. The good news is that this is the only error, and when it?s fixed it compiles. I have two solutions which I tested to suggest: First, is modifying SimpleITK so that the HistogramMatchingImageFilter is only instantiated with real number something like this: diff --git a/Code/BasicFilters/json/HistogramMatchingImageFilter.json b/Code/BasicFilters/json/HistogramMatchingImageFilter.json index a84dc83..89524fe 100644 --- a/Code/BasicFilters/json/HistogramMatchingImageFilter.json +++ b/Code/BasicFilters/json/HistogramMatchingImageFilter.json @@ -5,7 +5,7 @@ "filter_type" : "itk::HistogramMatchingImageFilter", "number_of_inputs" : 2, "doc" : "", - "pixel_types" : "BasicPixelIDTypeList", + "pixel_types" : "RealPixelIDTypeList", "members" : [ { "name" : "NumberOfHistogramLevels", @@ -41,6 +41,8 @@ "description" : "Simply run with default settings", "settings" : [], "tolerance" : "0.0001", + "inputA_cast" : "sitkFloat32", + "inputB_cast" : "sitkFloat32", "inputs" : [ "Input/Ramp-One-Zero-Float.nrrd", "Input/RA-Slice-Float.nrrd" @@ -63,6 +65,8 @@ } ], "md5hash" : "a963bd6a755b853103a2d195e01a50d3", + "inputA_cast" : "sitkFloat32", + "inputB_cast" : "sitkFloat32", "inputs" : [ "Input/RA-Short.nrrd", "Input/RA-Short.nrrd? This caused some minor testing problems[1]. And may cause some runtime compatibility issues with supported types for the filter with releases of SimpleITK. The other option is to remove that ITKv3 code block from the Histogram class. These legacy methods are problematic and using them cause case problems of the wrong method being called. With the ITK change and the Superbuild all the tests pass. I do have to restate that SimpleITK is not tested with the ITKv3_COMPATIBILITY flag. I don?t know if there are other implications for difference with the expected ITK configuration for building. Hope this helps, Brad [1] https://open.cdash.org/viewTest.php?onlyfailed&buildid=4136189 > On Dec 7, 2015, at 4:26 AM, Dmitry Mikhirev wrote: > > ? Sun, 6 Dec 2015 20:28:07 -0500 > Bradley Lowekamp ?????: > >> Hello Dmitry, > > Hello Brad! Thank you for your reply! >> >> SimpleITK is not built or tested against ITK with ITKv3 compatibility >> turned on. And Most projects have this option turned off, so it?s not >> as well tested as it used to be. >> >> This problem looks to be solely with ITK. It appears like the error >> will happen just with the instantiation of: >> >> itk::Statistics::Histogram >> >> This issue looks fixable. I don?t know how many other errors will >> occur when you get past this one. > > Well, most code is already compiled before this error occurs. So I > guess there will not me much more. Can you give an advice what changes > are needed to fix it? >> >> I?d recommend using the SimpleITK Superbuild by point CMake toward >> the Superbuild subdirectory on the initial configuration. >> >> BTW, what is the reason you are ?required? to used the system ITK? > > I'm going to build a package for official Fedora repo. That's why I > have to link to other libraries shipped by Fedora and not to bundle > them. Of course, if the error were unfixable on SimpleITK side, I could > send a bug report for InsigtToolkit package and ask maintainer to > disable ITKv3 compatibility, but I afraid it can break some other > packages. >> >> Brad >> > > -- > Regards, > Dmitry Mikhirev > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From skalexander at gmail.com Mon Dec 7 13:53:47 2015 From: skalexander at gmail.com (Simon Alexander) Date: Mon, 07 Dec 2015 18:53:47 +0000 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Hi Matt, Quick update: I've found two compiler bugs so far - not great. On hopefully better news, I've also found that update 1 has shipped. So I will configure that and run it against your RC2 to see if these things are resolved. If not I have workarounds, unsure of the wisdom of adding them. On Fri, 4 Dec 2015 at 17:34 Matt McCormick wrote: > Hi Simon. > > Apologies I haven't been able to put much time into this, ran into some >> interesting challenges with VS2015 itself (at least in my configuration) >> hanging permanently when changing from debug to release mode, or vice >> versa. It seems the generated project files are a bit of a challenge for >> it. >> > > Yes, Visual Studio has difficulty with large projects that have many build > targets. With the 4.9 release, we addressed the behavior a bit by reducing > the number of header tests and by turning BUILD_EXAMPLES OFF by default. > > By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be > improved when focusing on development of a subset of modules. > > > >> At any rate, I have narrowed down part of the issue at least to being not >> in the interpolate filter itself, but rather in the test driver code ... >> somewhere in the nested loops incrementing the underlying array elements is >> behaving incorrectly in release mode. I'll try and have a closer look >> this weekend. >> > > Thanks for taking a look at this! > > In the past, we ran into some issues with Visual Studio in Release mode > where adding const or using a reference for the returned type avoided a > faulty optimization. Bug reports to upstream Visual Studio have also helped > resolve the issue in some cases, too. > > Thanks, > Matt > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From skalexander at gmail.com Mon Dec 7 13:53:47 2015 From: skalexander at gmail.com (Simon Alexander) Date: Mon, 07 Dec 2015 18:53:47 +0000 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Hi Matt, Quick update: I've found two compiler bugs so far - not great. On hopefully better news, I've also found that update 1 has shipped. So I will configure that and run it against your RC2 to see if these things are resolved. If not I have workarounds, unsure of the wisdom of adding them. On Fri, 4 Dec 2015 at 17:34 Matt McCormick wrote: > Hi Simon. > > Apologies I haven't been able to put much time into this, ran into some >> interesting challenges with VS2015 itself (at least in my configuration) >> hanging permanently when changing from debug to release mode, or vice >> versa. It seems the generated project files are a bit of a challenge for >> it. >> > > Yes, Visual Studio has difficulty with large projects that have many build > targets. With the 4.9 release, we addressed the behavior a bit by reducing > the number of header tests and by turning BUILD_EXAMPLES OFF by default. > > By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be > improved when focusing on development of a subset of modules. > > > >> At any rate, I have narrowed down part of the issue at least to being not >> in the interpolate filter itself, but rather in the test driver code ... >> somewhere in the nested loops incrementing the underlying array elements is >> behaving incorrectly in release mode. I'll try and have a closer look >> this weekend. >> > > Thanks for taking a look at this! > > In the past, we ran into some issues with Visual Studio in Release mode > where adding const or using a reference for the returned type avoided a > faulty optimization. Bug reports to upstream Visual Studio have also helped > resolve the issue in some cases, too. > > Thanks, > Matt > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From mlt.khawla at gmail.com Tue Dec 8 05:04:28 2015 From: mlt.khawla at gmail.com (Daoued23) Date: Tue, 8 Dec 2015 03:04:28 -0700 (MST) Subject: [ITK] [ITK-users] How to split a volume into Suvolumes?? Message-ID: <1449569068146-36536.post@n7.nabble.com> Hello everyone, I want to split a volume into subvolumes. The subvolume in my case represents the voxel's neighborhood (size 9x9x9). I used the filter itk::ExtractImageFilter but it takes so long. Someone proposed that I use the Marching Cubes to divide my volume. Does anyone know how it works in this cas? If you have any suggestions, that would be really helpfull. Thank you Daoued23 -- View this message in context: http://itk-users.7.n7.nabble.com/How-to-split-a-volume-into-Suvolumes-tp36536.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hobbsk at ohio.edu Tue Dec 8 10:38:41 2015 From: hobbsk at ohio.edu (Kevin H. Hobbs) Date: Tue, 8 Dec 2015 10:38:41 -0500 Subject: [ITK] [ITK-users] Radius in itkVectorGradientMagnitudeImageFilter In-Reply-To: References: <565F4B51.6090602@ohio.edu> Message-ID: <5666F981.5080602@ohio.edu> On 12/03/2015 05:40 PM, D?enan Zuki? wrote: > Hi Kevin, > > Using an offset other than 1 makes little sense to me. I saw that the radius parameter was there, and used it to make the gradient calculation robust to noise on the small scale. I wanted to avoid filtering all the channels first. -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 173 bytes Desc: OpenPGP digital signature URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hobbsk at ohio.edu Tue Dec 8 10:41:46 2015 From: hobbsk at ohio.edu (Kevin H. Hobbs) Date: Tue, 8 Dec 2015 10:41:46 -0500 Subject: [ITK] [ITK-users] Radius in itkVectorGradientMagnitudeImageFilter In-Reply-To: <00BABB34-ECB5-4D00-BC97-6095EF722DDA@mail.nih.gov> References: <565F4B51.6090602@ohio.edu> <00BABB34-ECB5-4D00-BC97-6095EF722DDA@mail.nih.gov> Message-ID: <5666FA3A.3000607@ohio.edu> On 12/03/2015 08:56 PM, Bradley Lowekamp wrote: > I think that the neighborhood parameter could just be removed and the code cleaned up without a problem. I'll vote for that. -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 173 bytes Desc: OpenPGP digital signature URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Dec 8 11:26:51 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 8 Dec 2015 11:26:51 -0500 Subject: [ITK] [ITK-users] How to split a volume into Suvolumes?? In-Reply-To: <1449569068146-36536.post@n7.nabble.com> References: <1449569068146-36536.post@n7.nabble.com> Message-ID: Hi Daoued, if you want a sub-volume for each pixel, that would be a job for Neighborhood Iterator . If you want to split your image into 9x9x9 blocks, you could pre-create all of the images required, and then make one pass through the main image with an iterator and for each pixel calculate (by / and % operators on its index) in which of the sub-images it goes and into which location to copy it. Once that is finished, you could write the images or do something else with them. HTH, D?enan On Tue, Dec 8, 2015 at 5:04 AM, Daoued23 wrote: > Hello everyone, > > I want to split a volume into subvolumes. The subvolume in my case > represents the voxel's neighborhood (size 9x9x9). I used the filter > itk::ExtractImageFilter but it takes so long. > > Someone proposed that I use the Marching Cubes to divide my volume. Does > anyone know how it works in this cas? > > If you have any suggestions, that would be really helpfull. > > Thank you > > > Daoued23 > > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/How-to-split-a-volume-into-Suvolumes-tp36536.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Dec 8 12:31:23 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 8 Dec 2015 12:31:23 -0500 Subject: [ITK] [ITK-users] Radius in itkVectorGradientMagnitudeImageFilter In-Reply-To: <5666FA3A.3000607@ohio.edu> References: <565F4B51.6090602@ohio.edu> <00BABB34-ECB5-4D00-BC97-6095EF722DDA@mail.nih.gov> <5666FA3A.3000607@ohio.edu> Message-ID: Done: http://review.source.kitware.com/20517 On Tue, Dec 8, 2015 at 10:41 AM, Kevin H. Hobbs wrote: > On 12/03/2015 08:56 PM, Bradley Lowekamp wrote: > > > I think that the neighborhood parameter could just be removed and the > code cleaned up without a problem. > > I'll vote for that. > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From skalexander at gmail.com Tue Dec 8 16:31:15 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 08 Dec 2015 21:31:15 +0000 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: I've sent a patch set to gerrit, managed to screw it up somehow and generated 4 reviews instead of 1, whups. Matt, you're on them not sure who else should be. One of them is just a script modification so that my bash port likes your utilities script, just a proposal. The other three address each error. Two are a loop fusion issue where mixed type comparison is being generated incorrectly, changing the bound type fixes this. More concerning: the third change is an expansion issue with itk::Size<3> where it doesn't get the bound right for a .Fill call and never initializes the last element. Apologies for the delay, i'm hesitant to blame things on the compiler until I've convinced myself I know what is going on. TODO generate simplified versions to file with VS team. cheers, Simon On Mon, 7 Dec 2015 at 13:53 Simon Alexander wrote: > Hi Matt, > > Quick update: I've found two compiler bugs so far - not great. On > hopefully better news, I've also found that update 1 has shipped. So I > will configure that and run it against your RC2 to see if these things are > resolved. If not I have workarounds, unsure of the wisdom of adding them. > > > On Fri, 4 Dec 2015 at 17:34 Matt McCormick > wrote: > >> Hi Simon. >> >> Apologies I haven't been able to put much time into this, ran into some >>> interesting challenges with VS2015 itself (at least in my configuration) >>> hanging permanently when changing from debug to release mode, or vice >>> versa. It seems the generated project files are a bit of a challenge for >>> it. >>> >> >> Yes, Visual Studio has difficulty with large projects that have many >> build targets. With the 4.9 release, we addressed the behavior a bit by >> reducing the number of header tests and by turning BUILD_EXAMPLES OFF by >> default. >> >> By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be >> improved when focusing on development of a subset of modules. >> >> >> >>> At any rate, I have narrowed down part of the issue at least to being >>> not in the interpolate filter itself, but rather in the test driver code >>> ... somewhere in the nested loops incrementing the underlying array >>> elements is behaving incorrectly in release mode. I'll try and have a >>> closer look this weekend. >>> >> >> Thanks for taking a look at this! >> >> In the past, we ran into some issues with Visual Studio in Release mode >> where adding const or using a reference for the returned type avoided a >> faulty optimization. Bug reports to upstream Visual Studio have also helped >> resolve the issue in some cases, too. >> >> Thanks, >> Matt >> >> >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From skalexander at gmail.com Tue Dec 8 16:31:15 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 08 Dec 2015 21:31:15 +0000 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: I've sent a patch set to gerrit, managed to screw it up somehow and generated 4 reviews instead of 1, whups. Matt, you're on them not sure who else should be. One of them is just a script modification so that my bash port likes your utilities script, just a proposal. The other three address each error. Two are a loop fusion issue where mixed type comparison is being generated incorrectly, changing the bound type fixes this. More concerning: the third change is an expansion issue with itk::Size<3> where it doesn't get the bound right for a .Fill call and never initializes the last element. Apologies for the delay, i'm hesitant to blame things on the compiler until I've convinced myself I know what is going on. TODO generate simplified versions to file with VS team. cheers, Simon On Mon, 7 Dec 2015 at 13:53 Simon Alexander wrote: > Hi Matt, > > Quick update: I've found two compiler bugs so far - not great. On > hopefully better news, I've also found that update 1 has shipped. So I > will configure that and run it against your RC2 to see if these things are > resolved. If not I have workarounds, unsure of the wisdom of adding them. > > > On Fri, 4 Dec 2015 at 17:34 Matt McCormick > wrote: > >> Hi Simon. >> >> Apologies I haven't been able to put much time into this, ran into some >>> interesting challenges with VS2015 itself (at least in my configuration) >>> hanging permanently when changing from debug to release mode, or vice >>> versa. It seems the generated project files are a bit of a challenge for >>> it. >>> >> >> Yes, Visual Studio has difficulty with large projects that have many >> build targets. With the 4.9 release, we addressed the behavior a bit by >> reducing the number of header tests and by turning BUILD_EXAMPLES OFF by >> default. >> >> By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be >> improved when focusing on development of a subset of modules. >> >> >> >>> At any rate, I have narrowed down part of the issue at least to being >>> not in the interpolate filter itself, but rather in the test driver code >>> ... somewhere in the nested loops incrementing the underlying array >>> elements is behaving incorrectly in release mode. I'll try and have a >>> closer look this weekend. >>> >> >> Thanks for taking a look at this! >> >> In the past, we ran into some issues with Visual Studio in Release mode >> where adding const or using a reference for the returned type avoided a >> faulty optimization. Bug reports to upstream Visual Studio have also helped >> resolve the issue in some cases, too. >> >> Thanks, >> Matt >> >> >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Dec 8 16:45:09 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 8 Dec 2015 16:45:09 -0500 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Thanks Simon for getting to this. All changes look simple enough. You maybe needed to amend previous commits on the same topic to generate just one review. Regards, D?enan On Tue, Dec 8, 2015 at 4:31 PM, Simon Alexander wrote: > I've sent a patch set to gerrit, managed to screw it up somehow and > generated 4 reviews instead of 1, whups. Matt, you're on them not sure who > else should be. > > One of them is just a script modification so that my bash port likes your > utilities script, just a proposal. > > The other three address each error. Two are a loop fusion issue where > mixed type comparison is being generated incorrectly, changing the bound > type fixes this. > > More concerning: the third change is an expansion issue with itk::Size<3> > where it doesn't get the bound right for a .Fill call and never > initializes the last element. > > Apologies for the delay, i'm hesitant to blame things on the compiler > until I've convinced myself I know what is going on. TODO generate > simplified versions to file with VS team. > > cheers, > Simon > > On Mon, 7 Dec 2015 at 13:53 Simon Alexander wrote: > >> Hi Matt, >> >> Quick update: I've found two compiler bugs so far - not great. On >> hopefully better news, I've also found that update 1 has shipped. So I >> will configure that and run it against your RC2 to see if these things are >> resolved. If not I have workarounds, unsure of the wisdom of adding them. >> >> >> On Fri, 4 Dec 2015 at 17:34 Matt McCormick >> wrote: >> >>> Hi Simon. >>> >>> Apologies I haven't been able to put much time into this, ran into some >>>> interesting challenges with VS2015 itself (at least in my configuration) >>>> hanging permanently when changing from debug to release mode, or vice >>>> versa. It seems the generated project files are a bit of a challenge for >>>> it. >>>> >>> >>> Yes, Visual Studio has difficulty with large projects that have many >>> build targets. With the 4.9 release, we addressed the behavior a bit by >>> reducing the number of header tests and by turning BUILD_EXAMPLES OFF by >>> default. >>> >>> By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be >>> improved when focusing on development of a subset of modules. >>> >>> >>> >>>> At any rate, I have narrowed down part of the issue at least to being >>>> not in the interpolate filter itself, but rather in the test driver code >>>> ... somewhere in the nested loops incrementing the underlying array >>>> elements is behaving incorrectly in release mode. I'll try and have a >>>> closer look this weekend. >>>> >>> >>> Thanks for taking a look at this! >>> >>> In the past, we ran into some issues with Visual Studio in Release mode >>> where adding const or using a reference for the returned type avoided a >>> faulty optimization. Bug reports to upstream Visual Studio have also helped >>> resolve the issue in some cases, too. >>> >>> Thanks, >>> Matt >>> >>> >>> >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From dzenanz at gmail.com Tue Dec 8 16:45:09 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 8 Dec 2015 16:45:09 -0500 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Thanks Simon for getting to this. All changes look simple enough. You maybe needed to amend previous commits on the same topic to generate just one review. Regards, D?enan On Tue, Dec 8, 2015 at 4:31 PM, Simon Alexander wrote: > I've sent a patch set to gerrit, managed to screw it up somehow and > generated 4 reviews instead of 1, whups. Matt, you're on them not sure who > else should be. > > One of them is just a script modification so that my bash port likes your > utilities script, just a proposal. > > The other three address each error. Two are a loop fusion issue where > mixed type comparison is being generated incorrectly, changing the bound > type fixes this. > > More concerning: the third change is an expansion issue with itk::Size<3> > where it doesn't get the bound right for a .Fill call and never > initializes the last element. > > Apologies for the delay, i'm hesitant to blame things on the compiler > until I've convinced myself I know what is going on. TODO generate > simplified versions to file with VS team. > > cheers, > Simon > > On Mon, 7 Dec 2015 at 13:53 Simon Alexander wrote: > >> Hi Matt, >> >> Quick update: I've found two compiler bugs so far - not great. On >> hopefully better news, I've also found that update 1 has shipped. So I >> will configure that and run it against your RC2 to see if these things are >> resolved. If not I have workarounds, unsure of the wisdom of adding them. >> >> >> On Fri, 4 Dec 2015 at 17:34 Matt McCormick >> wrote: >> >>> Hi Simon. >>> >>> Apologies I haven't been able to put much time into this, ran into some >>>> interesting challenges with VS2015 itself (at least in my configuration) >>>> hanging permanently when changing from debug to release mode, or vice >>>> versa. It seems the generated project files are a bit of a challenge for >>>> it. >>>> >>> >>> Yes, Visual Studio has difficulty with large projects that have many >>> build targets. With the 4.9 release, we addressed the behavior a bit by >>> reducing the number of header tests and by turning BUILD_EXAMPLES OFF by >>> default. >>> >>> By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be >>> improved when focusing on development of a subset of modules. >>> >>> >>> >>>> At any rate, I have narrowed down part of the issue at least to being >>>> not in the interpolate filter itself, but rather in the test driver code >>>> ... somewhere in the nested loops incrementing the underlying array >>>> elements is behaving incorrectly in release mode. I'll try and have a >>>> closer look this weekend. >>>> >>> >>> Thanks for taking a look at this! >>> >>> In the past, we ran into some issues with Visual Studio in Release mode >>> where adding const or using a reference for the returned type avoided a >>> faulty optimization. Bug reports to upstream Visual Studio have also helped >>> resolve the issue in some cases, too. >>> >>> Thanks, >>> Matt >>> >>> >>> >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From skalexander at gmail.com Tue Dec 8 16:53:26 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 08 Dec 2015 21:53:26 +0000 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: No problem - only the template expansion one is worrying me about the compiler; I'm going to follow that up with the VS team as soon as I can generate as simpler example On Tue, 8 Dec 2015 at 16:45 D?enan Zuki? wrote: > Thanks Simon for getting to this. > > All changes look simple enough. You maybe needed to amend previous commits > on the same topic to generate just one review. > > Regards, > D?enan > > On Tue, Dec 8, 2015 at 4:31 PM, Simon Alexander > wrote: > >> I've sent a patch set to gerrit, managed to screw it up somehow and >> generated 4 reviews instead of 1, whups. Matt, you're on them not sure who >> else should be. >> >> One of them is just a script modification so that my bash port likes your >> utilities script, just a proposal. >> >> The other three address each error. Two are a loop fusion issue where >> mixed type comparison is being generated incorrectly, changing the bound >> type fixes this. >> >> More concerning: the third change is an expansion issue with itk::Size<3> >> where it doesn't get the bound right for a .Fill call and never >> initializes the last element. >> >> Apologies for the delay, i'm hesitant to blame things on the compiler >> until I've convinced myself I know what is going on. TODO generate >> simplified versions to file with VS team. >> >> cheers, >> Simon >> >> On Mon, 7 Dec 2015 at 13:53 Simon Alexander >> wrote: >> >>> Hi Matt, >>> >>> Quick update: I've found two compiler bugs so far - not great. On >>> hopefully better news, I've also found that update 1 has shipped. So I >>> will configure that and run it against your RC2 to see if these things are >>> resolved. If not I have workarounds, unsure of the wisdom of adding them. >>> >>> >>> On Fri, 4 Dec 2015 at 17:34 Matt McCormick >>> wrote: >>> >>>> Hi Simon. >>>> >>>> Apologies I haven't been able to put much time into this, ran into some >>>>> interesting challenges with VS2015 itself (at least in my configuration) >>>>> hanging permanently when changing from debug to release mode, or vice >>>>> versa. It seems the generated project files are a bit of a challenge for >>>>> it. >>>>> >>>> >>>> Yes, Visual Studio has difficulty with large projects that have many >>>> build targets. With the 4.9 release, we addressed the behavior a bit by >>>> reducing the number of header tests and by turning BUILD_EXAMPLES OFF by >>>> default. >>>> >>>> By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be >>>> improved when focusing on development of a subset of modules. >>>> >>>> >>>> >>>>> At any rate, I have narrowed down part of the issue at least to being >>>>> not in the interpolate filter itself, but rather in the test driver code >>>>> ... somewhere in the nested loops incrementing the underlying array >>>>> elements is behaving incorrectly in release mode. I'll try and have a >>>>> closer look this weekend. >>>>> >>>> >>>> Thanks for taking a look at this! >>>> >>>> In the past, we ran into some issues with Visual Studio in Release mode >>>> where adding const or using a reference for the returned type avoided a >>>> faulty optimization. Bug reports to upstream Visual Studio have also helped >>>> resolve the issue in some cases, too. >>>> >>>> Thanks, >>>> Matt >>>> >>>> >>>> >>>> >>>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From skalexander at gmail.com Tue Dec 8 16:53:26 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 08 Dec 2015 21:53:26 +0000 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: No problem - only the template expansion one is worrying me about the compiler; I'm going to follow that up with the VS team as soon as I can generate as simpler example On Tue, 8 Dec 2015 at 16:45 D?enan Zuki? wrote: > Thanks Simon for getting to this. > > All changes look simple enough. You maybe needed to amend previous commits > on the same topic to generate just one review. > > Regards, > D?enan > > On Tue, Dec 8, 2015 at 4:31 PM, Simon Alexander > wrote: > >> I've sent a patch set to gerrit, managed to screw it up somehow and >> generated 4 reviews instead of 1, whups. Matt, you're on them not sure who >> else should be. >> >> One of them is just a script modification so that my bash port likes your >> utilities script, just a proposal. >> >> The other three address each error. Two are a loop fusion issue where >> mixed type comparison is being generated incorrectly, changing the bound >> type fixes this. >> >> More concerning: the third change is an expansion issue with itk::Size<3> >> where it doesn't get the bound right for a .Fill call and never >> initializes the last element. >> >> Apologies for the delay, i'm hesitant to blame things on the compiler >> until I've convinced myself I know what is going on. TODO generate >> simplified versions to file with VS team. >> >> cheers, >> Simon >> >> On Mon, 7 Dec 2015 at 13:53 Simon Alexander >> wrote: >> >>> Hi Matt, >>> >>> Quick update: I've found two compiler bugs so far - not great. On >>> hopefully better news, I've also found that update 1 has shipped. So I >>> will configure that and run it against your RC2 to see if these things are >>> resolved. If not I have workarounds, unsure of the wisdom of adding them. >>> >>> >>> On Fri, 4 Dec 2015 at 17:34 Matt McCormick >>> wrote: >>> >>>> Hi Simon. >>>> >>>> Apologies I haven't been able to put much time into this, ran into some >>>>> interesting challenges with VS2015 itself (at least in my configuration) >>>>> hanging permanently when changing from debug to release mode, or vice >>>>> versa. It seems the generated project files are a bit of a challenge for >>>>> it. >>>>> >>>> >>>> Yes, Visual Studio has difficulty with large projects that have many >>>> build targets. With the 4.9 release, we addressed the behavior a bit by >>>> reducing the number of header tests and by turning BUILD_EXAMPLES OFF by >>>> default. >>>> >>>> By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be >>>> improved when focusing on development of a subset of modules. >>>> >>>> >>>> >>>>> At any rate, I have narrowed down part of the issue at least to being >>>>> not in the interpolate filter itself, but rather in the test driver code >>>>> ... somewhere in the nested loops incrementing the underlying array >>>>> elements is behaving incorrectly in release mode. I'll try and have a >>>>> closer look this weekend. >>>>> >>>> >>>> Thanks for taking a look at this! >>>> >>>> In the past, we ran into some issues with Visual Studio in Release mode >>>> where adding const or using a reference for the returned type avoided a >>>> faulty optimization. Bug reports to upstream Visual Studio have also helped >>>> resolve the issue in some cases, too. >>>> >>>> Thanks, >>>> Matt >>>> >>>> >>>> >>>> >>>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From skalexander at gmail.com Tue Dec 8 16:54:15 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 08 Dec 2015 21:54:15 +0000 Subject: [ITK] [ITK-users] [ITK-dev] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Oh, and I'm not sure how I managed to get gerrit to separate them, but I'll have a look at the aliases and figure that out. On Tue, 8 Dec 2015 at 16:53 Simon Alexander wrote: > No problem - only the template expansion one is worrying me about the > compiler; I'm going to follow that up with the VS team as soon as I can > generate as simpler example > > On Tue, 8 Dec 2015 at 16:45 D?enan Zuki? wrote: > >> Thanks Simon for getting to this. >> >> All changes look simple enough. You maybe needed to amend previous >> commits on the same topic to generate just one review. >> >> Regards, >> D?enan >> >> On Tue, Dec 8, 2015 at 4:31 PM, Simon Alexander >> wrote: >> >>> I've sent a patch set to gerrit, managed to screw it up somehow and >>> generated 4 reviews instead of 1, whups. Matt, you're on them not sure who >>> else should be. >>> >>> One of them is just a script modification so that my bash port likes >>> your utilities script, just a proposal. >>> >>> The other three address each error. Two are a loop fusion issue where >>> mixed type comparison is being generated incorrectly, changing the bound >>> type fixes this. >>> >>> More concerning: the third change is an expansion issue with >>> itk::Size<3> where it doesn't get the bound right for a .Fill call and >>> never initializes the last element. >>> >>> Apologies for the delay, i'm hesitant to blame things on the compiler >>> until I've convinced myself I know what is going on. TODO generate >>> simplified versions to file with VS team. >>> >>> cheers, >>> Simon >>> >>> On Mon, 7 Dec 2015 at 13:53 Simon Alexander >>> wrote: >>> >>>> Hi Matt, >>>> >>>> Quick update: I've found two compiler bugs so far - not great. On >>>> hopefully better news, I've also found that update 1 has shipped. So I >>>> will configure that and run it against your RC2 to see if these things are >>>> resolved. If not I have workarounds, unsure of the wisdom of adding them. >>>> >>>> >>>> On Fri, 4 Dec 2015 at 17:34 Matt McCormick >>>> wrote: >>>> >>>>> Hi Simon. >>>>> >>>>> Apologies I haven't been able to put much time into this, ran into >>>>>> some interesting challenges with VS2015 itself (at least in my >>>>>> configuration) hanging permanently when changing from debug to release >>>>>> mode, or vice versa. It seems the generated project files are a bit of a >>>>>> challenge for it. >>>>>> >>>>> >>>>> Yes, Visual Studio has difficulty with large projects that have many >>>>> build targets. With the 4.9 release, we addressed the behavior a bit by >>>>> reducing the number of header tests and by turning BUILD_EXAMPLES OFF by >>>>> default. >>>>> >>>>> By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be >>>>> improved when focusing on development of a subset of modules. >>>>> >>>>> >>>>> >>>>>> At any rate, I have narrowed down part of the issue at least to being >>>>>> not in the interpolate filter itself, but rather in the test driver code >>>>>> ... somewhere in the nested loops incrementing the underlying array >>>>>> elements is behaving incorrectly in release mode. I'll try and have a >>>>>> closer look this weekend. >>>>>> >>>>> >>>>> Thanks for taking a look at this! >>>>> >>>>> In the past, we ran into some issues with Visual Studio in Release >>>>> mode where adding const or using a reference for the returned type avoided >>>>> a faulty optimization. Bug reports to upstream Visual Studio have also >>>>> helped resolve the issue in some cases, too. >>>>> >>>>> Thanks, >>>>> Matt >>>>> >>>>> >>>>> >>>>> >>>>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From skalexander at gmail.com Tue Dec 8 16:54:15 2015 From: skalexander at gmail.com (Simon Alexander) Date: Tue, 08 Dec 2015 21:54:15 +0000 Subject: [ITK] [ITK-dev] [ITK-users] [ANN] ITK 4.9 Release Candidate 1 is ready for testing! In-Reply-To: References: Message-ID: Oh, and I'm not sure how I managed to get gerrit to separate them, but I'll have a look at the aliases and figure that out. On Tue, 8 Dec 2015 at 16:53 Simon Alexander wrote: > No problem - only the template expansion one is worrying me about the > compiler; I'm going to follow that up with the VS team as soon as I can > generate as simpler example > > On Tue, 8 Dec 2015 at 16:45 D?enan Zuki? wrote: > >> Thanks Simon for getting to this. >> >> All changes look simple enough. You maybe needed to amend previous >> commits on the same topic to generate just one review. >> >> Regards, >> D?enan >> >> On Tue, Dec 8, 2015 at 4:31 PM, Simon Alexander >> wrote: >> >>> I've sent a patch set to gerrit, managed to screw it up somehow and >>> generated 4 reviews instead of 1, whups. Matt, you're on them not sure who >>> else should be. >>> >>> One of them is just a script modification so that my bash port likes >>> your utilities script, just a proposal. >>> >>> The other three address each error. Two are a loop fusion issue where >>> mixed type comparison is being generated incorrectly, changing the bound >>> type fixes this. >>> >>> More concerning: the third change is an expansion issue with >>> itk::Size<3> where it doesn't get the bound right for a .Fill call and >>> never initializes the last element. >>> >>> Apologies for the delay, i'm hesitant to blame things on the compiler >>> until I've convinced myself I know what is going on. TODO generate >>> simplified versions to file with VS team. >>> >>> cheers, >>> Simon >>> >>> On Mon, 7 Dec 2015 at 13:53 Simon Alexander >>> wrote: >>> >>>> Hi Matt, >>>> >>>> Quick update: I've found two compiler bugs so far - not great. On >>>> hopefully better news, I've also found that update 1 has shipped. So I >>>> will configure that and run it against your RC2 to see if these things are >>>> resolved. If not I have workarounds, unsure of the wisdom of adding them. >>>> >>>> >>>> On Fri, 4 Dec 2015 at 17:34 Matt McCormick >>>> wrote: >>>> >>>>> Hi Simon. >>>>> >>>>> Apologies I haven't been able to put much time into this, ran into >>>>>> some interesting challenges with VS2015 itself (at least in my >>>>>> configuration) hanging permanently when changing from debug to release >>>>>> mode, or vice versa. It seems the generated project files are a bit of a >>>>>> challenge for it. >>>>>> >>>>> >>>>> Yes, Visual Studio has difficulty with large projects that have many >>>>> build targets. With the 4.9 release, we addressed the behavior a bit by >>>>> reducing the number of header tests and by turning BUILD_EXAMPLES OFF by >>>>> default. >>>>> >>>>> By setting ITK_BUILD_DEFAULT_MODULES to OFF, responsiveness can be >>>>> improved when focusing on development of a subset of modules. >>>>> >>>>> >>>>> >>>>>> At any rate, I have narrowed down part of the issue at least to being >>>>>> not in the interpolate filter itself, but rather in the test driver code >>>>>> ... somewhere in the nested loops incrementing the underlying array >>>>>> elements is behaving incorrectly in release mode. I'll try and have a >>>>>> closer look this weekend. >>>>>> >>>>> >>>>> Thanks for taking a look at this! >>>>> >>>>> In the past, we ran into some issues with Visual Studio in Release >>>>> mode where adding const or using a reference for the returned type avoided >>>>> a faulty optimization. Bug reports to upstream Visual Studio have also >>>>> helped resolve the issue in some cases, too. >>>>> >>>>> Thanks, >>>>> Matt >>>>> >>>>> >>>>> >>>>> >>>>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From zhuangming.shen at sphic.org.cn Tue Dec 8 19:47:35 2015 From: zhuangming.shen at sphic.org.cn (=?gb2312?B?yfLXr8P3?=) Date: Wed, 9 Dec 2015 00:47:35 +0000 Subject: [ITK] [ITK-users] Iterators for Python supported ITK Message-ID: <1449622055315.57210@sphic.org.cn> Hi all, Iterators are useful tools to sequential access of voxels in C++ supported ITK. I would like to know if the same tools are available in Python supported ITK? Could anyone give me an example? Thanks in advance. Regards, Zhuangming Shen -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dominik.hofer at gmail.com Wed Dec 9 07:14:27 2015 From: dominik.hofer at gmail.com (dominik) Date: Wed, 9 Dec 2015 05:14:27 -0700 (MST) Subject: [ITK] [ITK-users] Own Transformation Class In-Reply-To: References: <1448627334852-7588218.post@n2.nabble.com> <1448963240154-7588226.post@n2.nabble.com> Message-ID: <1449663267009-7588251.post@n2.nabble.com> Thanks for your answer. Now that I thought about it, maybe it would be better to write my own metric class, so that it's just the same as the Matte Mutual Information, but it just penalizes the cost the more the urethras are unaligned. So just add a sum of squared distances from the two urethras or so. Would that be possible? And more, if I want to use it in Slicer3D, is it possible to extend classes there or do I have to build my own ITK from the ground up? I also use SimpleITK in Slicer3D. Is all this possible in python? :) Cheers, Dominik -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Own-Transformation-Class-tp7588218p7588251.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lasso at queensu.ca Wed Dec 9 08:33:11 2015 From: lasso at queensu.ca (Andras Lasso) Date: Wed, 9 Dec 2015 13:33:11 +0000 Subject: [ITK] [ITK-users] Own Transformation Class Message-ID: If you don?t want to change any code then you might try to perform the registration in two steps: 1. Register the segmented prostate capsule with the urethra removed (doughnut shape) using binary image segmentation, with rigid transform. You can register binary images by computing distance transform and register those using a simple metric, see https://www.slicer.org/slicerWiki/index.php/Documentation/4.5/Modules/DistanceMapBasedRegistration 2. Perform bspline registration with limited control point motion (ITK supports this when you use L-BFGS-B optimizer) to account for local deformation Elastix can use multiple images for registration, so with that you may be able to perform the two stages simultaneously (image sets would be: 1. distance maps computed from the segmentations, 2. original grayscale volumes). Andras From: dominik Sent: December 9, 2015 07:14 To: insight-users at itk.org Subject: Re: [ITK] [ITK-users] Own Transformation Class Thanks for your answer. Now that I thought about it, maybe it would be better to write my own metric class, so that it's just the same as the Matte Mutual Information, but it just penalizes the cost the more the urethras are unaligned. So just add a sum of squared distances from the two urethras or so. Would that be possible? And more, if I want to use it in Slicer3D, is it possible to extend classes there or do I have to build my own ITK from the ground up? I also use SimpleITK in Slicer3D. Is all this possible in python? :) Cheers, Dominik -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Own-Transformation-Class-tp7588218p7588251.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jon.young at utexas.edu Wed Dec 9 13:18:10 2015 From: jon.young at utexas.edu (Jonathan Young) Date: Wed, 9 Dec 2015 12:18:10 -0600 Subject: [ITK] Geodesic active contour liver segmentation in 3D Message-ID: Hello all, I am trying to reconstruct a 3D model of the liver from an MRI of a patient with hepatocellular carcinoma. I have been able to obtain satisfactory segmentations using the geodesic active contour method in SimpleITK, but only when operating on a single slice at a time. When I tried extending the method to 3D by working with a series of image slices at once, the segmentation seems to fail. The initial level set propagates beyond the boundaries of the liver in a few slices, while in another slice it doesn't move at all. I did not have these issues in the 2D case. My work is done in an IPython notebook which can be found here: https://nbviewer.jupyter.org/github/jon-young/medicalimage/blob/master/Liver%20Segmentation%203D.ipynb At the bottom of the notebook, displaying the result of the segmentation shows the problems I described above. I don't think it is a matter of the number of iterations being run, as with fewer iterations the same issues occur. Could the problem stem from the way I've setup the initial level set? If anyone could take a look to see what I've done wrong, I would greatly appreciate it. Thanks, Jonathan -- Jonathan Young Graduate Research Assistant, Laboratory of Edward M. Marcotte Center for Systems and Synthetic Biology The University of Texas at Austin 2500 Speedway, MBB 3.128, Austin, TX 78712 (512) 232-3919 -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Dec 9 21:46:40 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 9 Dec 2015 21:46:40 -0500 Subject: [ITK] [ITK-users] Iterators for Python supported ITK In-Reply-To: <1449622055315.57210@sphic.org.cn> References: <1449622055315.57210@sphic.org.cn> Message-ID: Hi Zhuangming Shen, The Iterators are wrapped. However, when using Iterator's it is advisable to use C++ because Python will be slow. HTH, Matt On Tue, Dec 8, 2015 at 7:47 PM, ??? wrote: > Hi all, > > > *Iterators* are useful tools to sequential access of voxels in C++ > supported ITK. I would like to know if the same tools are available in > Python supported ITK? Could anyone give me an example? Thanks in advance. > > > Regards, > > > Zhuangming Shen > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From mikhirev at gmail.com Thu Dec 10 11:15:35 2015 From: mikhirev at gmail.com (Dmitry Mikhirev) Date: Thu, 10 Dec 2015 19:15:35 +0300 Subject: [ITK] [ITK-dev] SimpleITK 0.9.1 tests failure In-Reply-To: <470401C5-4002-4A66-B65B-2F02C1556E5A@mail.nih.gov> References: <20151206233128.44f3af0f@kafka> <470401C5-4002-4A66-B65B-2F02C1556E5A@mail.nih.gov> Message-ID: <20151210191535.33478748@dmikhirev.i.drweb.ru> Hello Brad! I'm sorry for long delay, I was a bit busy.. Here are test results: https://open.cdash.org/viewTest.php?onlyfailed&buildid=4137704 Please ignore java tests, they most probably failed because of misconfigured environment. The same tests passed successfully during package build. What do you think about BasicFilters ad Python tests results? Are they acceptable, or is it better to try fixing them (e. g. use another FFT library)? ? Sun, 6 Dec 2015 20:42:26 -0500 Bradley Lowekamp ?????: > Hello again, > > I don?t think these are critical, but they should be investigated. > > Missing numpy should have produced a warning during the build > process. If you have it installed in the system python it should get > copied over to the test environment. > > There other failures are with the following algorithms: > InverseDeconvolutionImageFilter > WienerDeconvolutionImageFilter > TikhonovDeconvolutionImageFilter > MaskedFFTNormalizedCorrelationImageFilter > > The all are failing with tolerance issues. Meaning that the results > are alittle different. These algorithms all use FFTs in the > computation. What FFT library is being used? FFTW? system VXL? ITK?s > VXL? > > The tests produce images for output including a difference image. > These should be inspected to see if it?s just noise or patterned > which may indicate something like a boundary condition issue. > > If you do a "ctest -D ExperimentalTest -D ExperimentalSubmit? the > results will be submitted to CDash so they can be better shared. > > Good luck, > Brad > -- Regards, Dmitry Mikhirev _______________________________________________ Powered by www.kitware.com 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 mikhirev at gmail.com Thu Dec 10 14:56:08 2015 From: mikhirev at gmail.com (Dmitry Mikhirev) Date: Thu, 10 Dec 2015 22:56:08 +0300 Subject: [ITK] [ITK-dev] SimpleITK build failure on Fedora 23 In-Reply-To: References: <20151206230948.17650b7d@kafka> <4AE681D4-7789-4E2A-AECB-2AFB6455B6EC@mail.nih.gov> <20151207122624.28955c17@dmikhirev.i.drweb.ru> Message-ID: <20151210225608.1995d2fe@kafka> Thank you again! I submitted a bug report for InsigtToolkit package in Fedora: https://bugzilla.redhat.com/show_bug.cgi?id=1290564 If maintainer will not disable ITKv3 compatibility, I will use your patch. ? Mon, 7 Dec 2015 11:06:17 -0500 Bradley Lowekamp ?????: > Hello, > > I uses SimpleITK?s Superbuild with -DITKV3_COMPATIBILITY:BOOL=ON > -DITK_LEGACY_REMOVE=OFF, and got the same error. > > The good news is that this is the only error, and when it?s fixed it > compiles. > > I have two solutions which I tested to suggest: > > First, is modifying SimpleITK so that the > HistogramMatchingImageFilter is only instantiated with real number > something like this: diff --git > a/Code/BasicFilters/json/HistogramMatchingImageFilter.json > b/Code/BasicFilters/json/HistogramMatchingImageFilter.json index > a84dc83..89524fe 100644 --- > a/Code/BasicFilters/json/HistogramMatchingImageFilter.json +++ > b/Code/BasicFilters/json/HistogramMatchingImageFilter.json @@ -5,7 > +5,7 @@ "filter_type" : > "itk::HistogramMatchingImageFilter", > "number_of_inputs" : 2, "doc" : "", > - "pixel_types" : "BasicPixelIDTypeList", > + "pixel_types" : "RealPixelIDTypeList", > "members" : [ > { > "name" : "NumberOfHistogramLevels", > @@ -41,6 +41,8 @@ > "description" : "Simply run with default settings", > "settings" : [], > "tolerance" : "0.0001", > + "inputA_cast" : "sitkFloat32", > + "inputB_cast" : "sitkFloat32", > "inputs" : [ > "Input/Ramp-One-Zero-Float.nrrd", > "Input/RA-Slice-Float.nrrd" > @@ -63,6 +65,8 @@ > } > ], > "md5hash" : "a963bd6a755b853103a2d195e01a50d3", > + "inputA_cast" : "sitkFloat32", > + "inputB_cast" : "sitkFloat32", > "inputs" : [ > "Input/RA-Short.nrrd", > "Input/RA-Short.nrrd? > > This caused some minor testing problems[1]. And may cause some > runtime compatibility issues with supported types for the filter with > releases of SimpleITK. > > > The other option is to remove that ITKv3 code block from the > Histogram class. These legacy methods are problematic and using them > cause case problems of the wrong method being called. > > With the ITK change and the Superbuild all the tests pass. > > I do have to restate that SimpleITK is not tested with the > ITKv3_COMPATIBILITY flag. I don?t know if there are other > implications for difference with the expected ITK configuration for > building. > > Hope this helps, > Brad > > > [1] https://open.cdash.org/viewTest.php?onlyfailed&buildid=4136189 > > > > On Dec 7, 2015, at 4:26 AM, Dmitry Mikhirev > > wrote: > > > > ? Sun, 6 Dec 2015 20:28:07 -0500 > > Bradley Lowekamp ?????: > > > >> Hello Dmitry, > > > > Hello Brad! Thank you for your reply! > >> > >> SimpleITK is not built or tested against ITK with ITKv3 > >> compatibility turned on. And Most projects have this option turned > >> off, so it?s not as well tested as it used to be. > >> > >> This problem looks to be solely with ITK. It appears like the error > >> will happen just with the instantiation of: > >> > >> itk::Statistics::Histogram > >> > >> This issue looks fixable. I don?t know how many other errors will > >> occur when you get past this one. > > > > Well, most code is already compiled before this error occurs. So I > > guess there will not me much more. Can you give an advice what > > changes are needed to fix it? > >> > >> I?d recommend using the SimpleITK Superbuild by point CMake toward > >> the Superbuild subdirectory on the initial configuration. > >> > >> BTW, what is the reason you are ?required? to used the system ITK? > > > > I'm going to build a package for official Fedora repo. That's why I > > have to link to other libraries shipped by Fedora and not to bundle > > them. Of course, if the error were unfixable on SimpleITK side, I > > could send a bug report for InsigtToolkit package and ask > > maintainer to disable ITKv3 compatibility, but I afraid it can > > break some other packages. > >> > >> Brad > >> > > > > -- > > Regards, > > Dmitry Mikhirev > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > -- Regards, Dmitry Mikhirev _______________________________________________ Powered by www.kitware.com 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 dzenanz at gmail.com Fri Dec 11 11:13:00 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 11 Dec 2015 11:13:00 -0500 Subject: [ITK] Deformable Model Simplex Mesh In-Reply-To: <565777825.46180.1449811002855.JavaMail.administrator@mtom.nabble.com> References: <565777825.46180.1449811002855.JavaMail.administrator@mtom.nabble.com> Message-ID: Hi Archie, if you are referring to DeformableSimplexMesh3DFilter , you should provide the code which is not working and then we might be able to help you. If you are referring to the ITK App , ITKApps have not been updated in a while and Matt can provide you with more information about its status. Regards, D?enan On Fri, Dec 11, 2015 at 1:01 AM, wrote: > Hello Mr. Zukic > > My name is Arthur Marques and I am a student of computer science at > Oakland University in MI, and I was wondering if you would be able to help > me with getting Deformable Model Simplex Mesh working. I was able to built > it in a ubuntu 14.04 64bits and I am able to load a metaimage (point to a > .raw file) into the application. However I am having quite a hard time > getting to plant the seed into the picture, as I understood I should from > the instructions. Whenever I create the mesh the red seed seems off the > picture and deforms incorrectly as expected. > > Also another error I receive on terminal the whole time the application is > running is "vtkStreamingDemandDrivenPipeline (0x1ce95f0): Input port 0 of > algorithm vtkOpenGLImageSliceMapper (0x16619a0) has 0 connections but is > not optional." I am not sure if this is an error corresponding to my > difficulty planting the seed, since I am quite unfamiliar with the whole > deformable model and vtk itself, or related to something else. I tried to > look into the code of those classes, none the less I feel more lost the > deeper I go. > > I truly appreciate any guidance you can assist me, > Archie. > > _____________________________________ > Sent from http://itk-users.7.n7.nabble.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Dec 11 12:22:05 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 11 Dec 2015 12:22:05 -0500 Subject: [ITK] [ITK-dev] itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest timeout Message-ID: Hi Nick, On some dashboard systems, itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest is taking a very long time, > 25 minutes, and timing out. Do you happen to recall any recent changes that might be related to this? Thanks, Matt PS. I created an issue to track this here: https://issues.itk.org/jira/browse/ITK-3399 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From ntustison at gmail.com Fri Dec 11 12:35:39 2015 From: ntustison at gmail.com (Nicholas Tustison) Date: Fri, 11 Dec 2015 09:35:39 -0800 Subject: [ITK] [ITK-dev] itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest timeout In-Reply-To: References: Message-ID: Hi Matt, I recently introduced that test with this patch http://review.source.kitware.com/#/c/20351/ I?m guessing we need to shrink it down. Nick > On Dec 11, 2015, at 9:22 AM, Matt McCormick wrote: > > Hi Nick, > > On some dashboard systems, itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest is taking a very long time, > 25 minutes, and timing out. Do you happen to recall any recent changes that might be related to this? > > Thanks, > Matt > > PS. I created an issue to track this here: > > https://issues.itk.org/jira/browse/ITK-3399 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From rick.avila at accumetra.com Fri Dec 11 13:03:14 2015 From: rick.avila at accumetra.com (Rick Avila) Date: Fri, 11 Dec 2015 13:03:14 -0500 Subject: [ITK] Free CT Scanner Image Quality Reports Message-ID: I would like to let you all know about a free and new CT image quality assessment service that we have launched as a resource to the imaging community. As we all know, it is important for image detection and measurement algorithms to understand and even adapt to the fundamental characteristics of an image (3D PSF, noise, ...) to achieve high performance and resilient results. If you have gone to the trouble of using traditional phantoms to estimate PSF and other image quality characteristics you also know it can be challenging to get hold of a phantom and enough CT scanner time to obtain these measurements for your projects. So we decided to make it as easy and inexpensive as possible to get some first order estimates and launched a free cloud based service to do this at RSNA last week. All you need to do is to zip up a single CT DICOM series of three rolls of 3M scotch tape, upload the data to our amazon cloud service, and we will email you back a report showing the fundamental characteristics of the scan from near isocenter out to the periphery. Once uploaded it generally takes around 15 minutes of processing time to calculate and send you back a report with fundamental image quality characteristics and estimates for the detection and measurement performance of different size lung nodules. Also keep in mind that the service will remain free and we would be delighted to collaborate with groups interested in extending this to other applications and measurements. You can find instructions for the service here: http://accumetra.com/solutions/free-ct-image-quality-reports/ I should also mention that we are working with multiple major hospitals and communities to build up a database CT scanner and protocol image quality and have collected data on the newest and most technically advanced CT scanner offerings from the major vendors (as well as older scanners). So in the future you we will also be able to tell you how your CT scan's performance stacks up to others and how much performance variability we are seeing out there. I encourage you all to give it a try and contact me if you have any questions or would like to see this extended to support additional features and functionality. If there is interest we can also set up a web conference to walk through the service and how to better access and use the information provided. - Rick -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Dec 11 16:31:29 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 11 Dec 2015 16:31:29 -0500 Subject: [ITK] [ITK-dev] itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest timeout In-Reply-To: References: Message-ID: Hi Nick, Thanks for the info. I talked with Hyun Jae, and he did some testing and found that on some systems it is taking over 4 hours (!) to run while on most it takes around 30 seconds. We will look for a bottleneck. Thanks, Matt On Fri, Dec 11, 2015 at 12:35 PM, Nicholas Tustison wrote: > Hi Matt, > > I recently introduced that test with this patch > > http://review.source.kitware.com/#/c/20351/ > > I?m guessing we need to shrink it down. > > Nick > > > > On Dec 11, 2015, at 9:22 AM, Matt McCormick > wrote: > > Hi Nick, > > On some dashboard > systems, itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest is > taking a very long time, > 25 minutes, and timing out. Do you happen to > recall any recent changes that might be related to this? > > Thanks, > Matt > > PS. I created an issue to track this here: > > https://issues.itk.org/jira/browse/ITK-3399 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From ntustison at gmail.com Fri Dec 11 16:52:08 2015 From: ntustison at gmail.com (Nicholas Tustison) Date: Fri, 11 Dec 2015 13:52:08 -0800 Subject: [ITK] [ITK-dev] itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest timeout In-Reply-To: References: Message-ID: Whoa, that?s quite the variation! Yeah, I?d love to know what?s going on. Thanks. > On Dec 11, 2015, at 1:31 PM, Matt McCormick wrote: > > Hi Nick, > > Thanks for the info. > > I talked with Hyun Jae, and he did some testing and found that on some systems it is taking over 4 hours (!) to run while on most it takes around 30 seconds. We will look for a bottleneck. > > Thanks, > Matt > > On Fri, Dec 11, 2015 at 12:35 PM, Nicholas Tustison > wrote: > Hi Matt, > > I recently introduced that test with this patch > > http://review.source.kitware.com/#/c/20351/ > > I?m guessing we need to shrink it down. > > Nick > > > >> On Dec 11, 2015, at 9:22 AM, Matt McCormick > wrote: >> >> Hi Nick, >> >> On some dashboard systems, itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest is taking a very long time, > 25 minutes, and timing out. Do you happen to recall any recent changes that might be related to this? >> >> Thanks, >> Matt >> >> PS. I created an issue to track this here: >> >> https://issues.itk.org/jira/browse/ITK-3399 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From Jared.Becksfort at STJUDE.ORG Mon Dec 14 01:48:33 2015 From: Jared.Becksfort at STJUDE.ORG (Becksfort, Jared) Date: Mon, 14 Dec 2015 06:48:33 +0000 Subject: [ITK] [ITK-users] RT Structure Files Have Negative Indexes Message-ID: Hello, I am trying to extract RT structure files into Niftii maps using the program found at http://www.insight-journal.org/browse/publication/887. I have compiled it, and it runs successfully with the test data, yielding correct masks. I then tried to run it on data given to me by a colleague. The output shows there are some negative slice indexes such as: Inserting region with 551 points into slice: -122 It also complains about contour points being outside the boundary, probably due to the negative indexes. I am attaching the output. I am not completely sure I can attach the RT file yet, as it is actual patient data. I can find out and do so if that helps. I don't know anything about RT structure files yet. Does anyone have ideas of what I can tell my colleague who generated the files? Thanks, Jared -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: dipg_itk_rt_output.txt URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From mohammedrashadkm at gmail.com Mon Dec 14 04:54:14 2015 From: mohammedrashadkm at gmail.com (Rashad Kanavath) Date: Mon, 14 Dec 2015 10:54:14 +0100 Subject: [ITK] [ITK-dev] error linking ITK with mingw 32bit Message-ID: Hello all, When I try to build with mingw32 bit, I am having a link error with itkTestDriver. Now the following patch fixes the problem for me. https://github.com/rashadkm/mxe/commit/fbc4075f5bdc41187908bc1b63fb4e9f49beb7a8 I am using MXE i686-shared cross compiler. For 64bit I dont have such issues. I got the above patch from itk's bug tracker. I don't remember the issue no. Before pushing the patch to mxe upstream, I would like to check with itk-developers about this. Thanks in advance. -- Regards, Rashad -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From Victor.Poughon at cnes.fr Mon Dec 14 10:40:48 2015 From: Victor.Poughon at cnes.fr (Poughon Victor) Date: Mon, 14 Dec 2015 15:40:48 +0000 Subject: [ITK] [ITK-users] Runtime dependent image iteration Message-ID: <3E55146A6A81B44A9CB69CAB65908CEA7B1C8B@TW-MBX-P01.cnesnet.ad.cnes.fr> Hello, I am trying to iterate over an image in a manner which depends on something only known at runtime. It seems like the iterator interface is not designed to handle this use case with polymorphism, because most methods are not virtual. I am thinking about writing that code into the iterator itself, but that's not so elegant because the iterator's code already has other responsibilities (iterating over the image in a specific way, etc.) Thanks for any help! Victor Poughon _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Dec 14 11:13:40 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 14 Dec 2015 11:13:40 -0500 Subject: [ITK] [ITK-dev] error linking ITK with mingw 32bit In-Reply-To: References: Message-ID: Hello Rashad, Thanks for discussing the issue. This has already been integrated in the current ITK 4.9 release candidate, so no further action is necessary. Thanks, Matt On Mon, Dec 14, 2015 at 4:54 AM, Rashad Kanavath wrote: > Hello all, > > When I try to build with mingw32 bit, I am having a link error with > itkTestDriver. > > Now the following patch fixes the problem for me. > > > https://github.com/rashadkm/mxe/commit/fbc4075f5bdc41187908bc1b63fb4e9f49beb7a8 > > I am using MXE i686-shared cross compiler. > > For 64bit I dont have such issues. I got the above patch from itk's bug > tracker. I don't remember the issue no. > > Before pushing the patch to mxe upstream, I would like to check with > itk-developers about this. > > Thanks in advance. > > > -- > Regards, > Rashad > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Dec 14 11:27:55 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 14 Dec 2015 11:27:55 -0500 Subject: [ITK] [ITK-users] Runtime dependent image iteration In-Reply-To: <3E55146A6A81B44A9CB69CAB65908CEA7B1C8B@TW-MBX-P01.cnesnet.ad.cnes.fr> References: <3E55146A6A81B44A9CB69CAB65908CEA7B1C8B@TW-MBX-P01.cnesnet.ad.cnes.fr> Message-ID: Hello Victor, This list of iterators is a good place to look for examples: http://www.itk.org/Doxygen/html/group__ImageIterators.html For instance, the itk::FloodFilledImageFunctionConditionalConstIterator may be of interest. The image iterators do not have many virtual methods, but that should not discourage the creation of new classes -- the methods are not virtual because of performance reasons. HTH, Matt On Mon, Dec 14, 2015 at 10:40 AM, Poughon Victor wrote: > > Hello, > > I am trying to iterate over an image in a manner which depends on > something only known at runtime. It seems like the iterator interface is > not designed to handle this use case with polymorphism, because most > methods are not virtual. > > I am thinking about writing that code into the iterator itself, but that's > not so elegant because the iterator's code already has other > responsibilities (iterating over the image in a specific way, etc.) > > Thanks for any help! > > Victor Poughon > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lasso at queensu.ca Mon Dec 14 11:59:04 2015 From: lasso at queensu.ca (Andras Lasso) Date: Mon, 14 Dec 2015 16:59:04 +0000 Subject: [ITK] [ITK-users] RT Structure Files Have Negative Indexes In-Reply-To: References: Message-ID: You might also use 3D Slicer with SlicerRT extension (www.slicerrt.org) to import all kinds of RT data - including structure sets - and save them as binary label maps or surfaces that are easy to load using ITK. Andras From: Community [mailto:community-bounces at itk.org] On Behalf Of Becksfort, Jared Sent: Monday, December 14, 2015 1:49 AM To: insight-users at itk.org; Jason.Dowling at csiro.au Subject: [ITK] [ITK-users] RT Structure Files Have Negative Indexes Hello, I am trying to extract RT structure files into Niftii maps using the program found at http://www.insight-journal.org/browse/publication/887. I have compiled it, and it runs successfully with the test data, yielding correct masks. I then tried to run it on data given to me by a colleague. The output shows there are some negative slice indexes such as: Inserting region with 551 points into slice: -122 It also complains about contour points being outside the boundary, probably due to the negative indexes. I am attaching the output. I am not completely sure I can attach the RT file yet, as it is actual patient data. I can find out and do so if that helps. I don't know anything about RT structure files yet. Does anyone have ideas of what I can tell my colleague who generated the files? Thanks, Jared -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From Jason.Dowling at csiro.au Mon Dec 14 20:06:31 2015 From: Jason.Dowling at csiro.au (Jason.Dowling at csiro.au) Date: Tue, 15 Dec 2015 01:06:31 +0000 Subject: [ITK] [ITK-users] RT Structure Files Have Negative Indexes In-Reply-To: References: Message-ID: <55F4C48F3D67D84ABD1C7A670EC51C801B63C883@exmbx03-cdc.nexus.csiro.au> Hi Jared, That's a bit strange. If you are able, feel free to send me the DICOM-RT files privately to test (and also let me know which TPS these contours were exported from?). If Slicer (or Plastimatch) extract the contours correctly could you also please let me know? All the best, Jason From: Andras Lasso [mailto:lasso at queensu.ca] Sent: Tuesday, 15 December 2015 2:59 AM To: Becksfort, Jared ; insight-users at itk.org; Dowling, Jason (H&B, Herston - RBWH) Subject: RE: RT Structure Files Have Negative Indexes You might also use 3D Slicer with SlicerRT extension (www.slicerrt.org) to import all kinds of RT data - including structure sets - and save them as binary label maps or surfaces that are easy to load using ITK. Andras From: Community [mailto:community-bounces at itk.org] On Behalf Of Becksfort, Jared Sent: Monday, December 14, 2015 1:49 AM To: insight-users at itk.org; Jason.Dowling at csiro.au Subject: [ITK] [ITK-users] RT Structure Files Have Negative Indexes Hello, I am trying to extract RT structure files into Niftii maps using the program found at http://www.insight-journal.org/browse/publication/887. I have compiled it, and it runs successfully with the test data, yielding correct masks. I then tried to run it on data given to me by a colleague. The output shows there are some negative slice indexes such as: Inserting region with 551 points into slice: -122 It also complains about contour points being outside the boundary, probably due to the negative indexes. I am attaching the output. I am not completely sure I can attach the RT file yet, as it is actual patient data. I can find out and do so if that helps. I don't know anything about RT structure files yet. Does anyone have ideas of what I can tell my colleague who generated the files? Thanks, Jared -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bakkari.abdelkhalek at hotmail.fr Mon Dec 14 20:43:03 2015 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Tue, 15 Dec 2015 02:43:03 +0100 Subject: [ITK] STATISTICAL FEATURES OF A 3D IMAGE Message-ID: Dear insight-users, How can I calculate the mean, variance, energy...etc of a 3D image and store them in an array as 3D images using ITK.The input 3D image is an output of VTK. Best regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Dec 15 10:48:19 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 15 Dec 2015 10:48:19 -0500 Subject: [ITK] [ITK-users] STATISTICAL FEATURES OF A 3D IMAGE In-Reply-To: References: Message-ID: Hi Abdelkhalek, if you are talking about GLCMs (gray level co-occurrence matrices), there was a discussion about it some time ago. If you are talking about something different, you need to explain better what you are trying to compute. Is that mean over some neighborhood region? How do you define energy? Regards, D?enan On Mon, Dec 14, 2015 at 8:43 PM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > > Dear insight-users, > > How can I calculate the mean, variance, energy...etc of a 3D image and > store them in an array as 3D images using ITK. > The input 3D image is an output of VTK. > > Best regards, > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.mo.burns at gmail.com Tue Dec 15 15:10:38 2015 From: david.mo.burns at gmail.com (David Burns) Date: Tue, 15 Dec 2015 15:10:38 -0500 Subject: [ITK] [ITK-dev] Linux c++11 build issue v4.8.2 Message-ID: <567073BE.80108@gmail.com> Dear Insight Developers I have compiled v4.8.2 on Ubuntu 14.04 successfully (g++ 4.8), however, I get compiler errors when building my own ITK applications with the following cmake flag set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11" I can compile ITK applications when not using this flag. I have tried using -fpermissive when building my application. I have also tried compiling ITK using -std=c++11 -fpermissive, individually and in combination. I always get the same errors. Any suggestions would be welcome. Thanks David Compiler errors /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:387:60: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::zero' of non-integral type [-fpermissive] static const float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:389:59: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::one' of non-integral type [-fpermissive] static const float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:391:62: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::maxval' of non-integral type [-fpermissive] static const float maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:410:61: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::zero' of non-integral type [-fpermissive] static const double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:412:60: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::one' of non-integral type [-fpermissive] static const double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:414:63: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::maxval' of non-integral type [-fpermissive] static const double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:433:66: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::zero' of non-integral type [-fpermissive] static const long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:435:65: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::one' of non-integral type [-fpermissive] static const long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:437:68: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::maxval' of non-integral type [-fpermissive] static const long double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From gabrielgimenez85 at gmail.com Tue Dec 15 15:25:11 2015 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Tue, 15 Dec 2015 13:25:11 -0700 (MST) Subject: [ITK] [ITK-users] Mattes Mutual Information can produce a false positive? Message-ID: <1450211111544-7588261.post@n2.nabble.com> Hi all, I hope you are well... My question is about a implementation of Mattes Mutual Information...is possible to produce a false positive ? at times it gives me a high metric value ... but the result of the recording is poor. We use it as a metric for two implementations of optimizers (PSO and Scatter search). Attached results of two executions, using scatter search: Moving image: mr_pd Fixed image: ct Images source: http://www.insight-journal.org/rire/download_data.php (patient_001) Thank you very much and I hope you can help me, regards. ct_mr_pd_incorrect_result.zip ct_mr_pd_accurate_result.zip -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-can-produce-a-false-positive-tp7588261.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hans-johnson at uiowa.edu Tue Dec 15 15:36:50 2015 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Tue, 15 Dec 2015 20:36:50 +0000 Subject: [ITK] [ITK-dev] Linux c++11 build issue v4.8.2 In-Reply-To: <567073BE.80108@gmail.com> References: <567073BE.80108@gmail.com> Message-ID: <0BFF7F7D-5861-43C9-BC1E-AF2E1391D5A5@uiowa.edu> This will be fixed when VXL is updated after the 4.9 release. Hans From: Insight-developers > on behalf of David Burns > Date: Tuesday, December 15, 2015 at 2:10 PM To: "insight-developers at itk.org" > Subject: [ITK-dev] Linux c++11 build issue v4.8.2 Dear Insight Developers I have compiled v4.8.2 on Ubuntu 14.04 successfully (g++ 4.8), however, I get compiler errors when building my own ITK applications with the following cmake flag set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11" I can compile ITK applications when not using this flag. I have tried using -fpermissive when building my application. I have also tried compiling ITK using -std=c++11 -fpermissive, individually and in combination. I always get the same errors. Any suggestions would be welcome. Thanks David Compiler errors /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:387:60: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::zero' of non-integral type [-fpermissive] static const float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:389:59: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::one' of non-integral type [-fpermissive] static const float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:391:62: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::maxval' of non-integral type [-fpermissive] static const float maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:410:61: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::zero' of non-integral type [-fpermissive] static const double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:412:60: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::one' of non-integral type [-fpermissive] static const double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:414:63: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::maxval' of non-integral type [-fpermissive] static const double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:433:66: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::zero' of non-integral type [-fpermissive] static const long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:435:65: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::one' of non-integral type [-fpermissive] static const long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:437:68: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::maxval' of non-integral type [-fpermissive] static const long double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); ^ /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x ^ ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From david.mo.burns at gmail.com Tue Dec 15 17:06:16 2015 From: david.mo.burns at gmail.com (David Burns) Date: Tue, 15 Dec 2015 17:06:16 -0500 Subject: [ITK] [ITK-dev] Linux c++11 build issue v4.8.2 In-Reply-To: <0BFF7F7D-5861-43C9-BC1E-AF2E1391D5A5@uiowa.edu> References: <567073BE.80108@gmail.com> <0BFF7F7D-5861-43C9-BC1E-AF2E1391D5A5@uiowa.edu> Message-ID: <56708ED8.8010005@gmail.com> Thanks Hans, based on the release schedule it looks like that will be out pretty soon. That's a big improvement to ITK to add c++11 support in my opinion. Thanks. David On 12/15/15 15:36, Johnson, Hans J wrote: > This will be fixed when VXL is updated after the 4.9 release. > > Hans > > > From: Insight-developers > on behalf of David Burns > > > Date: Tuesday, December 15, 2015 at 2:10 PM > To: "insight-developers at itk.org " > > > Subject: [ITK-dev] Linux c++11 build issue v4.8.2 > > Dear Insight Developers > > I have compiled v4.8.2 on Ubuntu 14.04 successfully (g++ 4.8), > however, I get compiler errors when building my own ITK applications > with the following cmake flag > > set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11" > > I can compile ITK applications when not using this flag. > > I have tried using -fpermissive when building my application. I have > also tried compiling ITK using -std=c++11 -fpermissive, individually > and in combination. I always get the same errors. > > Any suggestions would be welcome. Thanks > > David > > > > Compiler errors > > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:387:60: warning: > 'constexpr' needed for in-class initialization of static data member > 'const float vnl_numeric_traits::zero' of non-integral type > [-fpermissive] > static const float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:389:59: warning: > 'constexpr' needed for in-class initialization of static data member > 'const float vnl_numeric_traits::one' of non-integral type > [-fpermissive] > static const float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:391:62: warning: > 'constexpr' needed for in-class initialization of static data member > 'const float vnl_numeric_traits::maxval' of non-integral type > [-fpermissive] > static const float maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:410:61: warning: > 'constexpr' needed for in-class initialization of static data member > 'const double vnl_numeric_traits::zero' of non-integral type > [-fpermissive] > static const double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:412:60: warning: > 'constexpr' needed for in-class initialization of static data member > 'const double vnl_numeric_traits::one' of non-integral type > [-fpermissive] > static const double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:414:63: warning: > 'constexpr' needed for in-class initialization of static data member > 'const double vnl_numeric_traits::maxval' of non-integral type > [-fpermissive] > static const double maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:433:66: warning: > 'constexpr' needed for in-class initialization of static data member > 'const long double vnl_numeric_traits::zero' of > non-integral type [-fpermissive] > static const long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:435:65: warning: > 'constexpr' needed for in-class initialization of static data member > 'const long double vnl_numeric_traits::one' of > non-integral type [-fpermissive] > static const long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:437:68: warning: > 'constexpr' needed for in-class initialization of static data member > 'const long double vnl_numeric_traits::maxval' of > non-integral type [-fpermissive] > static const long double maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > > > ------------------------------------------------------------------------ > Notice: This UI Health Care e-mail (including attachments) is covered > by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is > confidential and may be legally privileged. If you are not the > intended recipient, you are hereby notified that any retention, > dissemination, distribution, or copying of this communication is > strictly prohibited. Please reply to the sender that you have > received the message in error, then delete it. Thank you. > ------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From itkhelpacc at gmail.com Wed Dec 16 03:02:13 2015 From: itkhelpacc at gmail.com (vishal) Date: Wed, 16 Dec 2015 01:02:13 -0700 (MST) Subject: [ITK] [ITK-users] Problem with building a journal paper Message-ID: <1450252933520-36557.post@n7.nabble.com> hi, I was trying to build the ITK journal paper "ITK-Based Implementation of Two-Projection 2D/3D Registration Method with an Application in Patient Setup for External Beam Radiotherapy" source code but it was showing the following error while configuring with CMake... 1) CMake Error at CMakeLists.txt:1 (INCLUDE): include could not find load file: D:/itk_example/Journal5ByWU/Source/images/IJMacros.txt 2) CMake Error at CMakeLists.txt:31 (LOADPACKAGE): Unknown CMake command "LOADPACKAGE". Configuring incomplete, errors occurred! See also "D:/itk_example/Journal5ByWU/Source/Build/CMakeFiles/CMakeOutput.log". As mentioned in the paper Im using Visual studio 2008, Cmake 2.8.12.2,ITK 3.20... please help me out.. Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Problem-with-building-a-journal-paper-tp36557.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From ribaluigi at gmail.com Wed Dec 16 04:24:18 2015 From: ribaluigi at gmail.com (Luigi Riba) Date: Wed, 16 Dec 2015 10:24:18 +0100 Subject: [ITK] Metric NaN and multi resolution registration In-Reply-To: References: Message-ID: Dear Matias and ITK community, thank you very much for your quick and detailed reply. I have tried a little bit of tinkering starting from your suggestion but I didn't overcome the errors. I am registering two images using the v4 framework with the following header #include #include #include I have initialized the transform with the transform initializer and computed the optimizer parameters with RegistratonParametersFromPhysicalShift and after a little of playing I left the relaxation factor to .5. *The registration process runs correctly at full resolution. * If I choose a multi resolution approach, like const unsigned int numberOfLevels = 3; > RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; > shrinkFactorsPerLevel.SetSize(numberOfLevels); > shrinkFactorsPerLevel[0] = 4; > shrinkFactorsPerLevel[1] = 2; > shrinkFactorsPerLevel[2] = 1; > RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; > smoothingSigmasPerLevel.SetSize(numberOfLevels); > smoothingSigmasPerLevel[0] = 2; > smoothingSigmasPerLevel[1] = 1; > smoothingSigmasPerLevel[2] = 0; the code stops working properly. In fact, I get the following warnings: - RegistrationParameterScalesFromPhysicalShift (00000000021F2630): Variation in any parameter won't change a voxel position. The default scales (1.0) are used to avoid division-by-zero. - WARNING: In f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, line 529 MeanSquaresImageToImageMetricv4 (00000000650FCB40): No valid points were found during metric evaluation. For image metrics, verify that the images overlap appropriately. For instance, you can align the image centers by translation. For point-set metrics, verify that the fixed points, once transformed into the virtual domain space, actually lie within the virtual domain. the metric is NaN and the registration process ends before its first step. Could you explain me the rationale behind this errors? I am probably overlooking something trivial. Best, Luigi 2015-12-07 16:06 GMT+01:00 Matias Montroull : > Actually the min and max steplenght are taken into account, I use these: > Min: 0.0001 > Max: 0.1 > > El lun., 7 de dic. de 2015 a la(s) 12:04, Matias Montroull < > matimontg at gmail.com> escribi?: > >> Hi Luigi, it could be for various reasons, mailny the transform >> initializer you use plus the number of samples and translationscale >> Try this code I have which I've done for MultiResolution and works fine >> for me: >> >> When you enter the parameters, try this: >> Relaxation: 0.99 >> Number of Bins: 50 >> Samples 3 (this is actually translated to 3% in my code as you will see >> below) >> maximum and minimum steplenght is not taken into account so you can put 0 >> and 0 >> translation scale 0.0001 >> >> #include "itkAffineTransform.h" >> #include "itkRegistrationParameterScalesFromPhysicalShift.h" >> #include "itkCenteredTransformInitializer.h" >> #include "itkLandmarkBasedTransformInitializer.h" >> #include "itkMultiResolutionImageRegistrationMethod.h" >> #include "itkMattesMutualInformationImageToImageMetric.h" >> #include "itkMeanSquaresImageToImageMetric.h" >> #include "itkRegularStepGradientDescentOptimizer.h" >> #include "itkRecursiveMultiResolutionPyramidImageFilter.h" >> #include "itkImage.h" >> #include "itkImageFileReader.h" >> #include "itkImageFileWriter.h" >> #include "itkResampleImageFilter.h" >> #include "itkCastImageFilter.h" >> #include "itkCheckerBoardImageFilter.h" >> #include "itkRescaleIntensityImageFilter.h" >> >> #include "itkNormalizeImageFilter.h" >> >> #include "itkCommand.h" >> class CommandIterationUpdate : public itk::Command >> { >> public: >> typedef CommandIterationUpdate Self; >> typedef itk::Command Superclass; >> typedef itk::SmartPointer Pointer; >> itkNewMacro(Self); >> protected: >> CommandIterationUpdate() : m_CumulativeIterationIndex(0) {}; >> public: >> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >> typedef const OptimizerType * OptimizerPointer; >> void Execute(itk::Object *caller, const itk::EventObject & event) >> ITK_OVERRIDE >> { >> Execute((const itk::Object *)caller, event); >> } >> void Execute(const itk::Object * object, const itk::EventObject & event) >> ITK_OVERRIDE >> { >> OptimizerPointer optimizer = static_cast(object); >> if (!(itk::IterationEvent().CheckEvent(&event))) >> { >> return; >> } >> std::cout << optimizer->GetCurrentIteration() << " "; >> std::cout << optimizer->GetValue() << " "; >> std::cout << optimizer->GetCurrentPosition() << " " << >> m_CumulativeIterationIndex++ << std::endl; >> } >> private: >> unsigned int m_CumulativeIterationIndex; >> }; >> >> template >> class RegistrationInterfaceCommand : public itk::Command >> { >> public: >> typedef RegistrationInterfaceCommand Self; >> typedef itk::Command Superclass; >> typedef itk::SmartPointer Pointer; >> itkNewMacro(Self); >> protected: >> RegistrationInterfaceCommand() {}; >> public: >> typedef TRegistration RegistrationType; >> typedef RegistrationType * RegistrationPointer; >> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >> typedef OptimizerType * OptimizerPointer; >> void Execute(itk::Object * object, const itk::EventObject & event) >> ITK_OVERRIDE >> { >> if (!(itk::IterationEvent().CheckEvent(&event))) >> { >> return; >> } >> RegistrationPointer registration = >> static_cast(object); >> OptimizerPointer optimizer = >> static_cast(registration->GetModifiableOptimizer()); >> std::cout << "-------------------------------------" << std::endl; >> std::cout << "MultiResolution Level : " >> << registration->GetCurrentLevel() << std::endl; >> std::cout << std::endl; >> if (registration->GetCurrentLevel() == 0) >> { >> optimizer->SetMaximumStepLength(1.0); >> optimizer->SetMinimumStepLength(0.001); >> } >> else >> { >> optimizer->SetMaximumStepLength(optimizer->GetMaximumStepLength() / 4.0); >> optimizer->SetMinimumStepLength(optimizer->GetMinimumStepLength() / 10.0); >> } >> } >> void Execute(const itk::Object *, const itk::EventObject &) ITK_OVERRIDE >> { return; } >> }; >> int main(int argc, char *argv[]) >> { >> if (argc < 10) >> { >> std::cerr << "Faltan Parametros " << std::endl; >> std::cerr << "Uso: " << argv[0]; >> std::cerr << " imagenfija imagenflotante "; >> std::cerr << " salida"; >> std::cerr << " Iteraciones Relaxation "; >> std::cerr << " NumeroBins Samples%(1/100) "; >> std::cerr << " StepMax(No Habilitado) StepMin(No Habilitado) >> TranslationFactor"; >> std::cerr << " " << std::endl; >> >> return EXIT_FAILURE; >> } >> >> const unsigned int Dimension = 3; >> typedef signed short PixelType; >> typedef itk::Image< PixelType, Dimension > FixedImageType; >> typedef itk::Image< PixelType, Dimension > MovingImageType; >> typedef float InternalPixelType; >> typedef itk::Image< InternalPixelType, Dimension > InternalImageType; >> >> typedef itk::AffineTransform< double, Dimension > TransformType; >> >> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >> typedef itk::LinearInterpolateImageFunction< >> InternalImageType, >> double > InterpolatorType; >> typedef itk::MattesMutualInformationImageToImageMetric< >> InternalImageType, >> InternalImageType > MetricType; >> typedef OptimizerType::ScalesType OptimizerScalesType; >> typedef itk::MultiResolutionImageRegistrationMethod< >> InternalImageType, >> InternalImageType > RegistrationType; >> OptimizerType::Pointer optimizer = OptimizerType::New(); >> InterpolatorType::Pointer interpolator = InterpolatorType::New(); >> RegistrationType::Pointer registration = RegistrationType::New(); >> MetricType::Pointer metric = MetricType::New(); >> >> >> TransformType::Pointer transform = TransformType::New(); >> registration->SetTransform(transform); >> >> typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType; >> typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType; >> FixedImageReaderType::Pointer fixedImageReader = >> FixedImageReaderType::New(); >> MovingImageReaderType::Pointer movingImageReader = >> MovingImageReaderType::New(); >> fixedImageReader->SetFileName(argv[1]); >> movingImageReader->SetFileName(argv[2]); >> >> fixedImageReader->Update(); >> movingImageReader->Update(); >> >> typedef itk::CastImageFilter< >> FixedImageType, InternalImageType > FixedCastFilterType; >> typedef itk::CastImageFilter< >> MovingImageType, InternalImageType > MovingCastFilterType; >> FixedCastFilterType::Pointer fixedCaster = FixedCastFilterType::New(); >> MovingCastFilterType::Pointer movingCaster = MovingCastFilterType::New(); >> fixedCaster->SetInput(fixedImageReader->GetOutput()); >> movingCaster->SetInput(movingImageReader->GetOutput()); >> >> registration->SetFixedImage(fixedCaster->GetOutput()); >> registration->SetMovingImage(movingCaster->GetOutput()); >> fixedCaster->Update(); >> >> registration->SetFixedImageRegion(fixedCaster->GetOutput()->GetBufferedRegion()); >> >> typedef itk::CenteredTransformInitializer< >> TransformType, FixedImageType, >> MovingImageType > TransformInitializerType; >> TransformInitializerType::Pointer initializer >> = TransformInitializerType::New(); >> initializer->SetTransform(transform); >> initializer->SetFixedImage(fixedImageReader->GetOutput()); >> initializer->SetMovingImage(movingImageReader->GetOutput()); >> initializer->GeometryOn(); >> initializer->InitializeTransform(); >> >> >> typedef TransformType::ParametersType ParametersType; >> const unsigned int numberOfParameters = >> transform->GetNumberOfParameters(); >> ParametersType parameters(numberOfParameters); >> registration->SetInitialTransformParameters(transform->GetParameters()); >> >> OptimizerScalesType optimizerScales(transform->GetNumberOfParameters()); >> >> double translationScale = atof(argv[10]); >> optimizerScales[0] = 1.0; >> optimizerScales[1] = 1.0; >> optimizerScales[2] = 1.0; >> optimizerScales[3] = 1.0; >> optimizerScales[4] = 1.0; >> optimizerScales[5] = 1.0; >> optimizerScales[6] = 1.0; >> optimizerScales[7] = 1.0; >> optimizerScales[8] = 1.0; >> optimizerScales[9] = translationScale; >> optimizerScales[10] = translationScale; >> optimizerScales[11] = translationScale; >> >> optimizer->SetScales(optimizerScales); >> >> FixedImageType::RegionType fixedImageRegion = >> fixedCaster->GetOutput()->GetBufferedRegion(); >> const unsigned int numberOfPixels = fixedImageRegion.GetNumberOfPixels(); >> double porcentage_samples = atof(argv[7]); >> const unsigned int numberOfSamples = static_cast> int>(numberOfPixels * porcentage_samples); >> >> optimizer->SetNumberOfIterations(atof(argv[4])); >> optimizer->SetRelaxationFactor(atof(argv[5])); >> metric->SetNumberOfHistogramBins(atof(argv[6])); >> metric->SetNumberOfSpatialSamples(numberOfSamples); >> optimizer->SetMaximumStepLength(atof(argv[8])); >> optimizer->SetMinimumStepLength(atof(argv[9])); >> >> >> optimizer->MinimizeOn(); >> CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New(); >> optimizer->AddObserver(itk::IterationEvent(), observer); >> >> >> typedef RegistrationInterfaceCommand CommandType; >> CommandType::Pointer command = CommandType::New(); >> registration->AddObserver(itk::IterationEvent(), command); >> registration->SetNumberOfLevels(1); >> registration->SetOptimizer(optimizer); >> registration->SetInterpolator(interpolator); >> registration->SetMetric(metric); >> >> FixedImageType::Pointer imagenfija = fixedImageReader->GetOutput(); >> MovingImageType::Pointer imagenflotante = movingImageReader->GetOutput(); >> >> >> typedef RegistrationType::ParametersType ParametersType; >> ParametersType InitialParameters = >> registration->GetInitialTransformParameters(); >> std::cout << "TranslationScale: " << translationScale << std::endl; >> std::cout << "MaximumStep: " << optimizer->GetMaximumStepLength() << >> std::endl; >> std::cout << "MinimunStep: " << optimizer->GetMinimumStepLength() << >> std::endl; >> std::cout << "Number of Bins: " << metric->GetNumberOfHistogramBins() << >> std::endl; >> std::cout << "Number of Samples: " << metric->GetNumberOfSpatialSamples() >> << std::endl; >> std::cout << "Iteraciones: " << optimizer->GetNumberOfIterations() << >> std::endl; >> std::cout << "Relaxation: " << optimizer->GetRelaxationFactor() << >> std::endl; >> std::cout << "Initial Parameters: " << InitialParameters << std::endl; >> std::cout << "Origen Fija: " << imagenfija->GetOrigin() << std::endl; >> std::cout << "Origen Flotante: " << imagenflotante->GetOrigin() << >> std::endl; >> std::cout << "Samples: " << numberOfSamples << std::endl; >> >> try >> { >> registration->Update(); >> std::cout << "Optimizer stop condition: " >> << registration->GetOptimizer()->GetStopConditionDescription() >> << std::endl; >> } >> catch (itk::ExceptionObject & err) >> { >> std::cout << "ExceptionObject caught !" << std::endl; >> std::cout << err << std::endl; >> return EXIT_FAILURE; >> } >> std::cout << "Optimizer Stopping Condition = " >> << optimizer->GetStopCondition() << std::endl; >> >> ParametersType finalParameters = >> registration->GetLastTransformParameters(); >> >> double TranslationAlongX = finalParameters[9]; >> double TranslationAlongY = finalParameters[10]; >> double TranslationAlongZ = finalParameters[11]; >> unsigned int numberOfIterations = optimizer->GetCurrentIteration(); >> double bestValue = optimizer->GetValue(); >> >> std::cout << "Resultado = " << std::endl; >> std::cout << " Traslacion X = " << TranslationAlongX << std::endl; >> std::cout << " Traslacion Y = " << TranslationAlongY << std::endl; >> std::cout << " Traslacion Z = " << TranslationAlongZ << std::endl; >> std::cout << " Iteraciones = " << numberOfIterations << std::endl; >> std::cout << " Metrica = " << bestValue << std::endl; >> >> >> typedef itk::ResampleImageFilter< >> MovingImageType, >> FixedImageType > ResampleFilterType; >> TransformType::Pointer finalTransform = TransformType::New(); >> finalTransform->SetParameters(finalParameters); >> finalTransform->SetFixedParameters(transform->GetFixedParameters()); >> ResampleFilterType::Pointer resample = ResampleFilterType::New(); >> resample->SetTransform(finalTransform); >> resample->SetInput(movingImageReader->GetOutput()); >> FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput(); >> PixelType backgroundGrayLevel = 0; //estaba en 100 >> >> resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize()); >> resample->SetOutputOrigin(fixedImage->GetOrigin()); >> resample->SetOutputSpacing(fixedImage->GetSpacing()); >> resample->SetOutputDirection(fixedImage->GetDirection()); >> resample->SetDefaultPixelValue(backgroundGrayLevel); >> typedef signed short OutputPixelType; >> typedef itk::Image< OutputPixelType, Dimension > OutputImageType; >> typedef itk::CastImageFilter< >> FixedImageType, >> OutputImageType > CastFilterType; >> typedef itk::ImageFileWriter< OutputImageType > WriterType; >> WriterType::Pointer writer = WriterType::New(); >> CastFilterType::Pointer caster = CastFilterType::New(); >> writer->SetFileName(argv[3]); >> caster->SetInput(resample->GetOutput()); >> writer->SetInput(caster->GetOutput()); >> writer->Update(); >> Sleep(5000); >> /* >> typedef itk::CheckerBoardImageFilter< FixedImageType > >> CheckerBoardFilterType; >> CheckerBoardFilterType::Pointer checker = CheckerBoardFilterType::New(); >> checker->SetInput1(fixedImage); >> checker->SetInput2(resample->GetOutput()); >> caster->SetInput(checker->GetOutput()); >> writer->SetInput(caster->GetOutput()); >> resample->SetDefaultPixelValue(0); >> >> resample->SetTransform(finalTransform); >> if (argc > 10) >> { >> writer->SetFileName(argv[11]); >> writer->Update(); >> }*/ >> return EXIT_SUCCESS; >> } >> >> >> El lun., 7 de dic. de 2015 a la(s) 11:43, Luigi Riba >> escribi?: >> >>> Dear ITK community, >>> >>> today I was trying to implement a multi-resolution registration process >>> for 3d images. >>> >>> I started from the example in the tutorial. Unfortunately, I've received >>> the following warning: >>> >>>> WARNING: In >>>> f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, >>>> line 529 >>>> MeanSquaresImageToImageMetricv4 (000000006506C020): No valid points >>>> were found during metric evaluation. For image metrics, verify that the >>>> images overlap appropriately. For instance, you can align the image centers >>>> by translation. For point-set metrics, verify that the fixed points, once >>>> transformed into the virtual domain space, actually lie within the virtual >>>> domain. >>> >>> >>> These are the parameters I have used for the multi resolution process: >>>> const unsigned int numberOfLevels = 3; >>>> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >>>> shrinkFactorsPerLevel.SetSize(numberOfLevels); >>>> shrinkFactorsPerLevel[0] = 4; >>>> shrinkFactorsPerLevel[1] = 2; >>>> shrinkFactorsPerLevel[2] = 1; >>>> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >>>> smoothingSigmasPerLevel.SetSize(numberOfLevels); >>>> smoothingSigmasPerLevel[0] = 2; >>>> smoothingSigmasPerLevel[1] = 1; >>>> smoothingSigmasPerLevel[2] = 0; >>>> registration->SetNumberOfLevels(numberOfLevels); >>>> registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); >>>> registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); >>> >>> >>> Could you please me explain what is the meaning of this warning? >>> >>> By the way, I am working with affine transformations and I have used the >>> transform initializer. >>> >>> Best, >>> >>> Luigi >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >> -- >> Matias >> > -- > Matias > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Wed Dec 16 09:35:39 2015 From: matimontg at gmail.com (Matias Montroull) Date: Wed, 16 Dec 2015 14:35:39 +0000 Subject: [ITK] Metric NaN and multi resolution registration In-Reply-To: References: Message-ID: The second warning looks like centers not aligned properly therefore the registration fails. Are you using CenteredTransformInitializer? El mi?., 16 de dic. de 2015 a la(s) 06:24, Luigi Riba escribi?: > Dear Matias and ITK community, > > thank you very much for your quick and detailed reply. > > I have tried a little bit of tinkering starting from your suggestion but I > didn't overcome the errors. > > I am registering two images using the v4 framework with the following > header > #include > #include > #include > > I have initialized the transform with the transform initializer and > computed the optimizer parameters with > RegistratonParametersFromPhysicalShift and after a little of playing I left > the relaxation factor to .5. > > *The registration process runs correctly at full resolution. * > > If I choose a multi resolution approach, like > > const unsigned int numberOfLevels = 3; >> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >> shrinkFactorsPerLevel.SetSize(numberOfLevels); >> shrinkFactorsPerLevel[0] = 4; >> shrinkFactorsPerLevel[1] = 2; >> shrinkFactorsPerLevel[2] = 1; >> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >> smoothingSigmasPerLevel.SetSize(numberOfLevels); >> smoothingSigmasPerLevel[0] = 2; >> smoothingSigmasPerLevel[1] = 1; >> smoothingSigmasPerLevel[2] = 0; > > > the code stops working properly. > > In fact, I get the following warnings: > > - RegistrationParameterScalesFromPhysicalShift (00000000021F2630): > Variation in any parameter won't change a voxel position. The default > scales (1.0) are used to avoid division-by-zero. > - WARNING: In > f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, > line 529 MeanSquaresImageToImageMetricv4 (00000000650FCB40): No valid > points were found during metric evaluation. For image metrics, verify that > the images overlap appropriately. For instance, you can align the image > centers by translation. For point-set metrics, verify that the fixed > points, once transformed into the virtual domain space, actually lie within > the virtual domain. > > the metric is NaN and the registration process ends before its first step. > > Could you explain me the rationale behind this errors? I am probably > overlooking something trivial. > > Best, > > Luigi > > > > 2015-12-07 16:06 GMT+01:00 Matias Montroull : > >> Actually the min and max steplenght are taken into account, I use these: >> Min: 0.0001 >> Max: 0.1 >> >> El lun., 7 de dic. de 2015 a la(s) 12:04, Matias Montroull < >> matimontg at gmail.com> escribi?: >> >>> Hi Luigi, it could be for various reasons, mailny the transform >>> initializer you use plus the number of samples and translationscale >>> Try this code I have which I've done for MultiResolution and works fine >>> for me: >>> >>> When you enter the parameters, try this: >>> Relaxation: 0.99 >>> Number of Bins: 50 >>> Samples 3 (this is actually translated to 3% in my code as you will see >>> below) >>> maximum and minimum steplenght is not taken into account so you can put >>> 0 and 0 >>> translation scale 0.0001 >>> >>> #include "itkAffineTransform.h" >>> #include "itkRegistrationParameterScalesFromPhysicalShift.h" >>> #include "itkCenteredTransformInitializer.h" >>> #include "itkLandmarkBasedTransformInitializer.h" >>> #include "itkMultiResolutionImageRegistrationMethod.h" >>> #include "itkMattesMutualInformationImageToImageMetric.h" >>> #include "itkMeanSquaresImageToImageMetric.h" >>> #include "itkRegularStepGradientDescentOptimizer.h" >>> #include "itkRecursiveMultiResolutionPyramidImageFilter.h" >>> #include "itkImage.h" >>> #include "itkImageFileReader.h" >>> #include "itkImageFileWriter.h" >>> #include "itkResampleImageFilter.h" >>> #include "itkCastImageFilter.h" >>> #include "itkCheckerBoardImageFilter.h" >>> #include "itkRescaleIntensityImageFilter.h" >>> >>> #include "itkNormalizeImageFilter.h" >>> >>> #include "itkCommand.h" >>> class CommandIterationUpdate : public itk::Command >>> { >>> public: >>> typedef CommandIterationUpdate Self; >>> typedef itk::Command Superclass; >>> typedef itk::SmartPointer Pointer; >>> itkNewMacro(Self); >>> protected: >>> CommandIterationUpdate() : m_CumulativeIterationIndex(0) {}; >>> public: >>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>> typedef const OptimizerType * OptimizerPointer; >>> void Execute(itk::Object *caller, const itk::EventObject & event) >>> ITK_OVERRIDE >>> { >>> Execute((const itk::Object *)caller, event); >>> } >>> void Execute(const itk::Object * object, const itk::EventObject & event) >>> ITK_OVERRIDE >>> { >>> OptimizerPointer optimizer = static_cast(object); >>> if (!(itk::IterationEvent().CheckEvent(&event))) >>> { >>> return; >>> } >>> std::cout << optimizer->GetCurrentIteration() << " "; >>> std::cout << optimizer->GetValue() << " "; >>> std::cout << optimizer->GetCurrentPosition() << " " << >>> m_CumulativeIterationIndex++ << std::endl; >>> } >>> private: >>> unsigned int m_CumulativeIterationIndex; >>> }; >>> >>> template >>> class RegistrationInterfaceCommand : public itk::Command >>> { >>> public: >>> typedef RegistrationInterfaceCommand Self; >>> typedef itk::Command Superclass; >>> typedef itk::SmartPointer Pointer; >>> itkNewMacro(Self); >>> protected: >>> RegistrationInterfaceCommand() {}; >>> public: >>> typedef TRegistration RegistrationType; >>> typedef RegistrationType * RegistrationPointer; >>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>> typedef OptimizerType * OptimizerPointer; >>> void Execute(itk::Object * object, const itk::EventObject & event) >>> ITK_OVERRIDE >>> { >>> if (!(itk::IterationEvent().CheckEvent(&event))) >>> { >>> return; >>> } >>> RegistrationPointer registration = >>> static_cast(object); >>> OptimizerPointer optimizer = >>> static_cast(registration->GetModifiableOptimizer()); >>> std::cout << "-------------------------------------" << std::endl; >>> std::cout << "MultiResolution Level : " >>> << registration->GetCurrentLevel() << std::endl; >>> std::cout << std::endl; >>> if (registration->GetCurrentLevel() == 0) >>> { >>> optimizer->SetMaximumStepLength(1.0); >>> optimizer->SetMinimumStepLength(0.001); >>> } >>> else >>> { >>> optimizer->SetMaximumStepLength(optimizer->GetMaximumStepLength() / 4.0); >>> optimizer->SetMinimumStepLength(optimizer->GetMinimumStepLength() / >>> 10.0); >>> } >>> } >>> void Execute(const itk::Object *, const itk::EventObject &) ITK_OVERRIDE >>> { return; } >>> }; >>> int main(int argc, char *argv[]) >>> { >>> if (argc < 10) >>> { >>> std::cerr << "Faltan Parametros " << std::endl; >>> std::cerr << "Uso: " << argv[0]; >>> std::cerr << " imagenfija imagenflotante "; >>> std::cerr << " salida"; >>> std::cerr << " Iteraciones Relaxation "; >>> std::cerr << " NumeroBins Samples%(1/100) "; >>> std::cerr << " StepMax(No Habilitado) StepMin(No Habilitado) >>> TranslationFactor"; >>> std::cerr << " " << std::endl; >>> >>> return EXIT_FAILURE; >>> } >>> >>> const unsigned int Dimension = 3; >>> typedef signed short PixelType; >>> typedef itk::Image< PixelType, Dimension > FixedImageType; >>> typedef itk::Image< PixelType, Dimension > MovingImageType; >>> typedef float InternalPixelType; >>> typedef itk::Image< InternalPixelType, Dimension > InternalImageType; >>> >>> typedef itk::AffineTransform< double, Dimension > TransformType; >>> >>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>> typedef itk::LinearInterpolateImageFunction< >>> InternalImageType, >>> double > InterpolatorType; >>> typedef itk::MattesMutualInformationImageToImageMetric< >>> InternalImageType, >>> InternalImageType > MetricType; >>> typedef OptimizerType::ScalesType OptimizerScalesType; >>> typedef itk::MultiResolutionImageRegistrationMethod< >>> InternalImageType, >>> InternalImageType > RegistrationType; >>> OptimizerType::Pointer optimizer = OptimizerType::New(); >>> InterpolatorType::Pointer interpolator = InterpolatorType::New(); >>> RegistrationType::Pointer registration = RegistrationType::New(); >>> MetricType::Pointer metric = MetricType::New(); >>> >>> >>> TransformType::Pointer transform = TransformType::New(); >>> registration->SetTransform(transform); >>> >>> typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType; >>> typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType; >>> FixedImageReaderType::Pointer fixedImageReader = >>> FixedImageReaderType::New(); >>> MovingImageReaderType::Pointer movingImageReader = >>> MovingImageReaderType::New(); >>> fixedImageReader->SetFileName(argv[1]); >>> movingImageReader->SetFileName(argv[2]); >>> >>> fixedImageReader->Update(); >>> movingImageReader->Update(); >>> >>> typedef itk::CastImageFilter< >>> FixedImageType, InternalImageType > FixedCastFilterType; >>> typedef itk::CastImageFilter< >>> MovingImageType, InternalImageType > MovingCastFilterType; >>> FixedCastFilterType::Pointer fixedCaster = FixedCastFilterType::New(); >>> MovingCastFilterType::Pointer movingCaster = MovingCastFilterType::New(); >>> fixedCaster->SetInput(fixedImageReader->GetOutput()); >>> movingCaster->SetInput(movingImageReader->GetOutput()); >>> >>> registration->SetFixedImage(fixedCaster->GetOutput()); >>> registration->SetMovingImage(movingCaster->GetOutput()); >>> fixedCaster->Update(); >>> >>> registration->SetFixedImageRegion(fixedCaster->GetOutput()->GetBufferedRegion()); >>> >>> typedef itk::CenteredTransformInitializer< >>> TransformType, FixedImageType, >>> MovingImageType > TransformInitializerType; >>> TransformInitializerType::Pointer initializer >>> = TransformInitializerType::New(); >>> initializer->SetTransform(transform); >>> initializer->SetFixedImage(fixedImageReader->GetOutput()); >>> initializer->SetMovingImage(movingImageReader->GetOutput()); >>> initializer->GeometryOn(); >>> initializer->InitializeTransform(); >>> >>> >>> typedef TransformType::ParametersType ParametersType; >>> const unsigned int numberOfParameters = >>> transform->GetNumberOfParameters(); >>> ParametersType parameters(numberOfParameters); >>> registration->SetInitialTransformParameters(transform->GetParameters()); >>> >>> OptimizerScalesType optimizerScales(transform->GetNumberOfParameters()); >>> >>> double translationScale = atof(argv[10]); >>> optimizerScales[0] = 1.0; >>> optimizerScales[1] = 1.0; >>> optimizerScales[2] = 1.0; >>> optimizerScales[3] = 1.0; >>> optimizerScales[4] = 1.0; >>> optimizerScales[5] = 1.0; >>> optimizerScales[6] = 1.0; >>> optimizerScales[7] = 1.0; >>> optimizerScales[8] = 1.0; >>> optimizerScales[9] = translationScale; >>> optimizerScales[10] = translationScale; >>> optimizerScales[11] = translationScale; >>> >>> optimizer->SetScales(optimizerScales); >>> >>> FixedImageType::RegionType fixedImageRegion = >>> fixedCaster->GetOutput()->GetBufferedRegion(); >>> const unsigned int numberOfPixels = fixedImageRegion.GetNumberOfPixels(); >>> double porcentage_samples = atof(argv[7]); >>> const unsigned int numberOfSamples = static_cast>> int>(numberOfPixels * porcentage_samples); >>> >>> optimizer->SetNumberOfIterations(atof(argv[4])); >>> optimizer->SetRelaxationFactor(atof(argv[5])); >>> metric->SetNumberOfHistogramBins(atof(argv[6])); >>> metric->SetNumberOfSpatialSamples(numberOfSamples); >>> optimizer->SetMaximumStepLength(atof(argv[8])); >>> optimizer->SetMinimumStepLength(atof(argv[9])); >>> >>> >>> optimizer->MinimizeOn(); >>> CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New(); >>> optimizer->AddObserver(itk::IterationEvent(), observer); >>> >>> >>> typedef RegistrationInterfaceCommand CommandType; >>> CommandType::Pointer command = CommandType::New(); >>> registration->AddObserver(itk::IterationEvent(), command); >>> registration->SetNumberOfLevels(1); >>> registration->SetOptimizer(optimizer); >>> registration->SetInterpolator(interpolator); >>> registration->SetMetric(metric); >>> >>> FixedImageType::Pointer imagenfija = fixedImageReader->GetOutput(); >>> MovingImageType::Pointer imagenflotante = movingImageReader->GetOutput(); >>> >>> >>> typedef RegistrationType::ParametersType ParametersType; >>> ParametersType InitialParameters = >>> registration->GetInitialTransformParameters(); >>> std::cout << "TranslationScale: " << translationScale << std::endl; >>> std::cout << "MaximumStep: " << optimizer->GetMaximumStepLength() << >>> std::endl; >>> std::cout << "MinimunStep: " << optimizer->GetMinimumStepLength() << >>> std::endl; >>> std::cout << "Number of Bins: " << metric->GetNumberOfHistogramBins() << >>> std::endl; >>> std::cout << "Number of Samples: " << >>> metric->GetNumberOfSpatialSamples() << std::endl; >>> std::cout << "Iteraciones: " << optimizer->GetNumberOfIterations() << >>> std::endl; >>> std::cout << "Relaxation: " << optimizer->GetRelaxationFactor() << >>> std::endl; >>> std::cout << "Initial Parameters: " << InitialParameters << std::endl; >>> std::cout << "Origen Fija: " << imagenfija->GetOrigin() << std::endl; >>> std::cout << "Origen Flotante: " << imagenflotante->GetOrigin() << >>> std::endl; >>> std::cout << "Samples: " << numberOfSamples << std::endl; >>> >>> try >>> { >>> registration->Update(); >>> std::cout << "Optimizer stop condition: " >>> << registration->GetOptimizer()->GetStopConditionDescription() >>> << std::endl; >>> } >>> catch (itk::ExceptionObject & err) >>> { >>> std::cout << "ExceptionObject caught !" << std::endl; >>> std::cout << err << std::endl; >>> return EXIT_FAILURE; >>> } >>> std::cout << "Optimizer Stopping Condition = " >>> << optimizer->GetStopCondition() << std::endl; >>> >>> ParametersType finalParameters = >>> registration->GetLastTransformParameters(); >>> >>> double TranslationAlongX = finalParameters[9]; >>> double TranslationAlongY = finalParameters[10]; >>> double TranslationAlongZ = finalParameters[11]; >>> unsigned int numberOfIterations = optimizer->GetCurrentIteration(); >>> double bestValue = optimizer->GetValue(); >>> >>> std::cout << "Resultado = " << std::endl; >>> std::cout << " Traslacion X = " << TranslationAlongX << std::endl; >>> std::cout << " Traslacion Y = " << TranslationAlongY << std::endl; >>> std::cout << " Traslacion Z = " << TranslationAlongZ << std::endl; >>> std::cout << " Iteraciones = " << numberOfIterations << std::endl; >>> std::cout << " Metrica = " << bestValue << std::endl; >>> >>> >>> typedef itk::ResampleImageFilter< >>> MovingImageType, >>> FixedImageType > ResampleFilterType; >>> TransformType::Pointer finalTransform = TransformType::New(); >>> finalTransform->SetParameters(finalParameters); >>> finalTransform->SetFixedParameters(transform->GetFixedParameters()); >>> ResampleFilterType::Pointer resample = ResampleFilterType::New(); >>> resample->SetTransform(finalTransform); >>> resample->SetInput(movingImageReader->GetOutput()); >>> FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput(); >>> PixelType backgroundGrayLevel = 0; //estaba en 100 >>> >>> resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize()); >>> resample->SetOutputOrigin(fixedImage->GetOrigin()); >>> resample->SetOutputSpacing(fixedImage->GetSpacing()); >>> resample->SetOutputDirection(fixedImage->GetDirection()); >>> resample->SetDefaultPixelValue(backgroundGrayLevel); >>> typedef signed short OutputPixelType; >>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType; >>> typedef itk::CastImageFilter< >>> FixedImageType, >>> OutputImageType > CastFilterType; >>> typedef itk::ImageFileWriter< OutputImageType > WriterType; >>> WriterType::Pointer writer = WriterType::New(); >>> CastFilterType::Pointer caster = CastFilterType::New(); >>> writer->SetFileName(argv[3]); >>> caster->SetInput(resample->GetOutput()); >>> writer->SetInput(caster->GetOutput()); >>> writer->Update(); >>> Sleep(5000); >>> /* >>> typedef itk::CheckerBoardImageFilter< FixedImageType > >>> CheckerBoardFilterType; >>> CheckerBoardFilterType::Pointer checker = CheckerBoardFilterType::New(); >>> checker->SetInput1(fixedImage); >>> checker->SetInput2(resample->GetOutput()); >>> caster->SetInput(checker->GetOutput()); >>> writer->SetInput(caster->GetOutput()); >>> resample->SetDefaultPixelValue(0); >>> >>> resample->SetTransform(finalTransform); >>> if (argc > 10) >>> { >>> writer->SetFileName(argv[11]); >>> writer->Update(); >>> }*/ >>> return EXIT_SUCCESS; >>> } >>> >>> >>> El lun., 7 de dic. de 2015 a la(s) 11:43, Luigi Riba < >>> ribaluigi at gmail.com> escribi?: >>> >>>> Dear ITK community, >>>> >>>> today I was trying to implement a multi-resolution registration process >>>> for 3d images. >>>> >>>> I started from the example in the tutorial. Unfortunately, I've >>>> received the following warning: >>>> >>>>> WARNING: In >>>>> f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, >>>>> line 529 >>>>> MeanSquaresImageToImageMetricv4 (000000006506C020): No valid points >>>>> were found during metric evaluation. For image metrics, verify that the >>>>> images overlap appropriately. For instance, you can align the image centers >>>>> by translation. For point-set metrics, verify that the fixed points, once >>>>> transformed into the virtual domain space, actually lie within the virtual >>>>> domain. >>>> >>>> >>>> These are the parameters I have used for the multi resolution process: >>>>> const unsigned int numberOfLevels = 3; >>>>> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >>>>> shrinkFactorsPerLevel.SetSize(numberOfLevels); >>>>> shrinkFactorsPerLevel[0] = 4; >>>>> shrinkFactorsPerLevel[1] = 2; >>>>> shrinkFactorsPerLevel[2] = 1; >>>>> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >>>>> smoothingSigmasPerLevel.SetSize(numberOfLevels); >>>>> smoothingSigmasPerLevel[0] = 2; >>>>> smoothingSigmasPerLevel[1] = 1; >>>>> smoothingSigmasPerLevel[2] = 0; >>>>> registration->SetNumberOfLevels(numberOfLevels); >>>>> registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); >>>>> registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); >>>> >>>> >>>> Could you please me explain what is the meaning of this warning? >>>> >>>> By the way, I am working with affine transformations and I have used >>>> the transform initializer. >>>> >>>> Best, >>>> >>>> Luigi >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >>> -- >>> Matias >>> >> -- >> Matias >> > > -- Matias -------------- next part -------------- An HTML attachment was scrubbed... URL: From ribaluigi at gmail.com Wed Dec 16 09:44:26 2015 From: ribaluigi at gmail.com (Luigi Riba) Date: Wed, 16 Dec 2015 15:44:26 +0100 Subject: [ITK] Metric NaN and multi resolution registration In-Reply-To: References: Message-ID: Hello, in fact I am surprised by this warning since I am using the CenteredTransformInitializer. This is the piece of code that involves the initialization of the transform: typedef itk::CenteredTransformInitializer ImageType> TransformInitializerType; > TransformInitializerType::Pointer transformInitializer = > TransformInitializerType::New(); > transformInitializer->SetTransform(transform); > transformInitializer->SetFixedImage(fixedReader->GetOutput()); > transformInitializer->SetMovingImage(movingReader->GetOutput()); > transformInitializer->GeometryOn(); > transformInitializer->InitializeTransform(); ... > registration->SetInitialTransform(transform); Thanks for the support, Luigi 2015-12-16 15:35 GMT+01:00 Matias Montroull : > The second warning looks like centers not aligned properly therefore the > registration fails. Are you using CenteredTransformInitializer? > > El mi?., 16 de dic. de 2015 a la(s) 06:24, Luigi Riba > escribi?: > >> Dear Matias and ITK community, >> >> thank you very much for your quick and detailed reply. >> >> I have tried a little bit of tinkering starting from your suggestion but >> I didn't overcome the errors. >> >> I am registering two images using the v4 framework with the following >> header >> #include >> #include >> #include >> >> I have initialized the transform with the transform initializer and >> computed the optimizer parameters with >> RegistratonParametersFromPhysicalShift and after a little of playing I left >> the relaxation factor to .5. >> >> *The registration process runs correctly at full resolution. * >> >> If I choose a multi resolution approach, like >> >> const unsigned int numberOfLevels = 3; >>> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >>> shrinkFactorsPerLevel.SetSize(numberOfLevels); >>> shrinkFactorsPerLevel[0] = 4; >>> shrinkFactorsPerLevel[1] = 2; >>> shrinkFactorsPerLevel[2] = 1; >>> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >>> smoothingSigmasPerLevel.SetSize(numberOfLevels); >>> smoothingSigmasPerLevel[0] = 2; >>> smoothingSigmasPerLevel[1] = 1; >>> smoothingSigmasPerLevel[2] = 0; >> >> >> the code stops working properly. >> >> In fact, I get the following warnings: >> >> - RegistrationParameterScalesFromPhysicalShift (00000000021F2630): >> Variation in any parameter won't change a voxel position. The default >> scales (1.0) are used to avoid division-by-zero. >> - WARNING: In >> f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, >> line 529 MeanSquaresImageToImageMetricv4 (00000000650FCB40): No valid >> points were found during metric evaluation. For image metrics, verify that >> the images overlap appropriately. For instance, you can align the image >> centers by translation. For point-set metrics, verify that the fixed >> points, once transformed into the virtual domain space, actually lie within >> the virtual domain. >> >> the metric is NaN and the registration process ends before its first step. >> >> Could you explain me the rationale behind this errors? I am probably >> overlooking something trivial. >> >> Best, >> >> Luigi >> >> >> >> 2015-12-07 16:06 GMT+01:00 Matias Montroull : >> >>> Actually the min and max steplenght are taken into account, I use these: >>> Min: 0.0001 >>> Max: 0.1 >>> >>> El lun., 7 de dic. de 2015 a la(s) 12:04, Matias Montroull < >>> matimontg at gmail.com> escribi?: >>> >>>> Hi Luigi, it could be for various reasons, mailny the transform >>>> initializer you use plus the number of samples and translationscale >>>> Try this code I have which I've done for MultiResolution and works fine >>>> for me: >>>> >>>> When you enter the parameters, try this: >>>> Relaxation: 0.99 >>>> Number of Bins: 50 >>>> Samples 3 (this is actually translated to 3% in my code as you will see >>>> below) >>>> maximum and minimum steplenght is not taken into account so you can put >>>> 0 and 0 >>>> translation scale 0.0001 >>>> >>>> #include "itkAffineTransform.h" >>>> #include "itkRegistrationParameterScalesFromPhysicalShift.h" >>>> #include "itkCenteredTransformInitializer.h" >>>> #include "itkLandmarkBasedTransformInitializer.h" >>>> #include "itkMultiResolutionImageRegistrationMethod.h" >>>> #include "itkMattesMutualInformationImageToImageMetric.h" >>>> #include "itkMeanSquaresImageToImageMetric.h" >>>> #include "itkRegularStepGradientDescentOptimizer.h" >>>> #include "itkRecursiveMultiResolutionPyramidImageFilter.h" >>>> #include "itkImage.h" >>>> #include "itkImageFileReader.h" >>>> #include "itkImageFileWriter.h" >>>> #include "itkResampleImageFilter.h" >>>> #include "itkCastImageFilter.h" >>>> #include "itkCheckerBoardImageFilter.h" >>>> #include "itkRescaleIntensityImageFilter.h" >>>> >>>> #include "itkNormalizeImageFilter.h" >>>> >>>> #include "itkCommand.h" >>>> class CommandIterationUpdate : public itk::Command >>>> { >>>> public: >>>> typedef CommandIterationUpdate Self; >>>> typedef itk::Command Superclass; >>>> typedef itk::SmartPointer Pointer; >>>> itkNewMacro(Self); >>>> protected: >>>> CommandIterationUpdate() : m_CumulativeIterationIndex(0) {}; >>>> public: >>>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>>> typedef const OptimizerType * OptimizerPointer; >>>> void Execute(itk::Object *caller, const itk::EventObject & event) >>>> ITK_OVERRIDE >>>> { >>>> Execute((const itk::Object *)caller, event); >>>> } >>>> void Execute(const itk::Object * object, const itk::EventObject & >>>> event) ITK_OVERRIDE >>>> { >>>> OptimizerPointer optimizer = static_cast(object); >>>> if (!(itk::IterationEvent().CheckEvent(&event))) >>>> { >>>> return; >>>> } >>>> std::cout << optimizer->GetCurrentIteration() << " "; >>>> std::cout << optimizer->GetValue() << " "; >>>> std::cout << optimizer->GetCurrentPosition() << " " << >>>> m_CumulativeIterationIndex++ << std::endl; >>>> } >>>> private: >>>> unsigned int m_CumulativeIterationIndex; >>>> }; >>>> >>>> template >>>> class RegistrationInterfaceCommand : public itk::Command >>>> { >>>> public: >>>> typedef RegistrationInterfaceCommand Self; >>>> typedef itk::Command Superclass; >>>> typedef itk::SmartPointer Pointer; >>>> itkNewMacro(Self); >>>> protected: >>>> RegistrationInterfaceCommand() {}; >>>> public: >>>> typedef TRegistration RegistrationType; >>>> typedef RegistrationType * >>>> RegistrationPointer; >>>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>>> typedef OptimizerType * OptimizerPointer; >>>> void Execute(itk::Object * object, const itk::EventObject & event) >>>> ITK_OVERRIDE >>>> { >>>> if (!(itk::IterationEvent().CheckEvent(&event))) >>>> { >>>> return; >>>> } >>>> RegistrationPointer registration = >>>> static_cast(object); >>>> OptimizerPointer optimizer = >>>> static_cast(registration->GetModifiableOptimizer()); >>>> std::cout << "-------------------------------------" << std::endl; >>>> std::cout << "MultiResolution Level : " >>>> << registration->GetCurrentLevel() << std::endl; >>>> std::cout << std::endl; >>>> if (registration->GetCurrentLevel() == 0) >>>> { >>>> optimizer->SetMaximumStepLength(1.0); >>>> optimizer->SetMinimumStepLength(0.001); >>>> } >>>> else >>>> { >>>> optimizer->SetMaximumStepLength(optimizer->GetMaximumStepLength() / >>>> 4.0); >>>> optimizer->SetMinimumStepLength(optimizer->GetMinimumStepLength() / >>>> 10.0); >>>> } >>>> } >>>> void Execute(const itk::Object *, const itk::EventObject &) ITK_OVERRIDE >>>> { return; } >>>> }; >>>> int main(int argc, char *argv[]) >>>> { >>>> if (argc < 10) >>>> { >>>> std::cerr << "Faltan Parametros " << std::endl; >>>> std::cerr << "Uso: " << argv[0]; >>>> std::cerr << " imagenfija imagenflotante "; >>>> std::cerr << " salida"; >>>> std::cerr << " Iteraciones Relaxation "; >>>> std::cerr << " NumeroBins Samples%(1/100) "; >>>> std::cerr << " StepMax(No Habilitado) StepMin(No Habilitado) >>>> TranslationFactor"; >>>> std::cerr << " " << std::endl; >>>> >>>> return EXIT_FAILURE; >>>> } >>>> >>>> const unsigned int Dimension = 3; >>>> typedef signed short PixelType; >>>> typedef itk::Image< PixelType, Dimension > FixedImageType; >>>> typedef itk::Image< PixelType, Dimension > MovingImageType; >>>> typedef float InternalPixelType; >>>> typedef itk::Image< InternalPixelType, Dimension > InternalImageType; >>>> >>>> typedef itk::AffineTransform< double, Dimension > TransformType; >>>> >>>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>>> typedef itk::LinearInterpolateImageFunction< >>>> InternalImageType, >>>> double > InterpolatorType; >>>> typedef itk::MattesMutualInformationImageToImageMetric< >>>> InternalImageType, >>>> InternalImageType > MetricType; >>>> typedef OptimizerType::ScalesType OptimizerScalesType; >>>> typedef itk::MultiResolutionImageRegistrationMethod< >>>> InternalImageType, >>>> InternalImageType > RegistrationType; >>>> OptimizerType::Pointer optimizer = OptimizerType::New(); >>>> InterpolatorType::Pointer interpolator = InterpolatorType::New(); >>>> RegistrationType::Pointer registration = RegistrationType::New(); >>>> MetricType::Pointer metric = MetricType::New(); >>>> >>>> >>>> TransformType::Pointer transform = TransformType::New(); >>>> registration->SetTransform(transform); >>>> >>>> typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType; >>>> typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType; >>>> FixedImageReaderType::Pointer fixedImageReader = >>>> FixedImageReaderType::New(); >>>> MovingImageReaderType::Pointer movingImageReader = >>>> MovingImageReaderType::New(); >>>> fixedImageReader->SetFileName(argv[1]); >>>> movingImageReader->SetFileName(argv[2]); >>>> >>>> fixedImageReader->Update(); >>>> movingImageReader->Update(); >>>> >>>> typedef itk::CastImageFilter< >>>> FixedImageType, InternalImageType > FixedCastFilterType; >>>> typedef itk::CastImageFilter< >>>> MovingImageType, InternalImageType > MovingCastFilterType; >>>> FixedCastFilterType::Pointer fixedCaster = FixedCastFilterType::New(); >>>> MovingCastFilterType::Pointer movingCaster = >>>> MovingCastFilterType::New(); >>>> fixedCaster->SetInput(fixedImageReader->GetOutput()); >>>> movingCaster->SetInput(movingImageReader->GetOutput()); >>>> >>>> registration->SetFixedImage(fixedCaster->GetOutput()); >>>> registration->SetMovingImage(movingCaster->GetOutput()); >>>> fixedCaster->Update(); >>>> >>>> registration->SetFixedImageRegion(fixedCaster->GetOutput()->GetBufferedRegion()); >>>> >>>> typedef itk::CenteredTransformInitializer< >>>> TransformType, FixedImageType, >>>> MovingImageType > TransformInitializerType; >>>> TransformInitializerType::Pointer initializer >>>> = TransformInitializerType::New(); >>>> initializer->SetTransform(transform); >>>> initializer->SetFixedImage(fixedImageReader->GetOutput()); >>>> initializer->SetMovingImage(movingImageReader->GetOutput()); >>>> initializer->GeometryOn(); >>>> initializer->InitializeTransform(); >>>> >>>> >>>> typedef TransformType::ParametersType ParametersType; >>>> const unsigned int numberOfParameters = >>>> transform->GetNumberOfParameters(); >>>> ParametersType parameters(numberOfParameters); >>>> registration->SetInitialTransformParameters(transform->GetParameters()); >>>> >>>> OptimizerScalesType optimizerScales(transform->GetNumberOfParameters()); >>>> >>>> double translationScale = atof(argv[10]); >>>> optimizerScales[0] = 1.0; >>>> optimizerScales[1] = 1.0; >>>> optimizerScales[2] = 1.0; >>>> optimizerScales[3] = 1.0; >>>> optimizerScales[4] = 1.0; >>>> optimizerScales[5] = 1.0; >>>> optimizerScales[6] = 1.0; >>>> optimizerScales[7] = 1.0; >>>> optimizerScales[8] = 1.0; >>>> optimizerScales[9] = translationScale; >>>> optimizerScales[10] = translationScale; >>>> optimizerScales[11] = translationScale; >>>> >>>> optimizer->SetScales(optimizerScales); >>>> >>>> FixedImageType::RegionType fixedImageRegion = >>>> fixedCaster->GetOutput()->GetBufferedRegion(); >>>> const unsigned int numberOfPixels = >>>> fixedImageRegion.GetNumberOfPixels(); >>>> double porcentage_samples = atof(argv[7]); >>>> const unsigned int numberOfSamples = static_cast>>> int>(numberOfPixels * porcentage_samples); >>>> >>>> optimizer->SetNumberOfIterations(atof(argv[4])); >>>> optimizer->SetRelaxationFactor(atof(argv[5])); >>>> metric->SetNumberOfHistogramBins(atof(argv[6])); >>>> metric->SetNumberOfSpatialSamples(numberOfSamples); >>>> optimizer->SetMaximumStepLength(atof(argv[8])); >>>> optimizer->SetMinimumStepLength(atof(argv[9])); >>>> >>>> >>>> optimizer->MinimizeOn(); >>>> CommandIterationUpdate::Pointer observer = >>>> CommandIterationUpdate::New(); >>>> optimizer->AddObserver(itk::IterationEvent(), observer); >>>> >>>> >>>> typedef RegistrationInterfaceCommand CommandType; >>>> CommandType::Pointer command = CommandType::New(); >>>> registration->AddObserver(itk::IterationEvent(), command); >>>> registration->SetNumberOfLevels(1); >>>> registration->SetOptimizer(optimizer); >>>> registration->SetInterpolator(interpolator); >>>> registration->SetMetric(metric); >>>> >>>> FixedImageType::Pointer imagenfija = fixedImageReader->GetOutput(); >>>> MovingImageType::Pointer imagenflotante = >>>> movingImageReader->GetOutput(); >>>> >>>> >>>> typedef RegistrationType::ParametersType ParametersType; >>>> ParametersType InitialParameters = >>>> registration->GetInitialTransformParameters(); >>>> std::cout << "TranslationScale: " << translationScale << std::endl; >>>> std::cout << "MaximumStep: " << optimizer->GetMaximumStepLength() << >>>> std::endl; >>>> std::cout << "MinimunStep: " << optimizer->GetMinimumStepLength() << >>>> std::endl; >>>> std::cout << "Number of Bins: " << metric->GetNumberOfHistogramBins() >>>> << std::endl; >>>> std::cout << "Number of Samples: " << >>>> metric->GetNumberOfSpatialSamples() << std::endl; >>>> std::cout << "Iteraciones: " << optimizer->GetNumberOfIterations() << >>>> std::endl; >>>> std::cout << "Relaxation: " << optimizer->GetRelaxationFactor() << >>>> std::endl; >>>> std::cout << "Initial Parameters: " << InitialParameters << std::endl; >>>> std::cout << "Origen Fija: " << imagenfija->GetOrigin() << std::endl; >>>> std::cout << "Origen Flotante: " << imagenflotante->GetOrigin() << >>>> std::endl; >>>> std::cout << "Samples: " << numberOfSamples << std::endl; >>>> >>>> try >>>> { >>>> registration->Update(); >>>> std::cout << "Optimizer stop condition: " >>>> << registration->GetOptimizer()->GetStopConditionDescription() >>>> << std::endl; >>>> } >>>> catch (itk::ExceptionObject & err) >>>> { >>>> std::cout << "ExceptionObject caught !" << std::endl; >>>> std::cout << err << std::endl; >>>> return EXIT_FAILURE; >>>> } >>>> std::cout << "Optimizer Stopping Condition = " >>>> << optimizer->GetStopCondition() << std::endl; >>>> >>>> ParametersType finalParameters = >>>> registration->GetLastTransformParameters(); >>>> >>>> double TranslationAlongX = finalParameters[9]; >>>> double TranslationAlongY = finalParameters[10]; >>>> double TranslationAlongZ = finalParameters[11]; >>>> unsigned int numberOfIterations = optimizer->GetCurrentIteration(); >>>> double bestValue = optimizer->GetValue(); >>>> >>>> std::cout << "Resultado = " << std::endl; >>>> std::cout << " Traslacion X = " << TranslationAlongX << std::endl; >>>> std::cout << " Traslacion Y = " << TranslationAlongY << std::endl; >>>> std::cout << " Traslacion Z = " << TranslationAlongZ << std::endl; >>>> std::cout << " Iteraciones = " << numberOfIterations << std::endl; >>>> std::cout << " Metrica = " << bestValue << std::endl; >>>> >>>> >>>> typedef itk::ResampleImageFilter< >>>> MovingImageType, >>>> FixedImageType > ResampleFilterType; >>>> TransformType::Pointer finalTransform = TransformType::New(); >>>> finalTransform->SetParameters(finalParameters); >>>> finalTransform->SetFixedParameters(transform->GetFixedParameters()); >>>> ResampleFilterType::Pointer resample = ResampleFilterType::New(); >>>> resample->SetTransform(finalTransform); >>>> resample->SetInput(movingImageReader->GetOutput()); >>>> FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput(); >>>> PixelType backgroundGrayLevel = 0; //estaba en 100 >>>> >>>> resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize()); >>>> resample->SetOutputOrigin(fixedImage->GetOrigin()); >>>> resample->SetOutputSpacing(fixedImage->GetSpacing()); >>>> resample->SetOutputDirection(fixedImage->GetDirection()); >>>> resample->SetDefaultPixelValue(backgroundGrayLevel); >>>> typedef signed short OutputPixelType; >>>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType; >>>> typedef itk::CastImageFilter< >>>> FixedImageType, >>>> OutputImageType > CastFilterType; >>>> typedef itk::ImageFileWriter< OutputImageType > WriterType; >>>> WriterType::Pointer writer = WriterType::New(); >>>> CastFilterType::Pointer caster = CastFilterType::New(); >>>> writer->SetFileName(argv[3]); >>>> caster->SetInput(resample->GetOutput()); >>>> writer->SetInput(caster->GetOutput()); >>>> writer->Update(); >>>> Sleep(5000); >>>> /* >>>> typedef itk::CheckerBoardImageFilter< FixedImageType > >>>> CheckerBoardFilterType; >>>> CheckerBoardFilterType::Pointer checker = CheckerBoardFilterType::New(); >>>> checker->SetInput1(fixedImage); >>>> checker->SetInput2(resample->GetOutput()); >>>> caster->SetInput(checker->GetOutput()); >>>> writer->SetInput(caster->GetOutput()); >>>> resample->SetDefaultPixelValue(0); >>>> >>>> resample->SetTransform(finalTransform); >>>> if (argc > 10) >>>> { >>>> writer->SetFileName(argv[11]); >>>> writer->Update(); >>>> }*/ >>>> return EXIT_SUCCESS; >>>> } >>>> >>>> >>>> El lun., 7 de dic. de 2015 a la(s) 11:43, Luigi Riba < >>>> ribaluigi at gmail.com> escribi?: >>>> >>>>> Dear ITK community, >>>>> >>>>> today I was trying to implement a multi-resolution registration >>>>> process for 3d images. >>>>> >>>>> I started from the example in the tutorial. Unfortunately, I've >>>>> received the following warning: >>>>> >>>>>> WARNING: In >>>>>> f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, >>>>>> line 529 >>>>>> MeanSquaresImageToImageMetricv4 (000000006506C020): No valid points >>>>>> were found during metric evaluation. For image metrics, verify that the >>>>>> images overlap appropriately. For instance, you can align the image centers >>>>>> by translation. For point-set metrics, verify that the fixed points, once >>>>>> transformed into the virtual domain space, actually lie within the virtual >>>>>> domain. >>>>> >>>>> >>>>> These are the parameters I have used for the multi resolution process: >>>>>> const unsigned int numberOfLevels = 3; >>>>>> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >>>>>> shrinkFactorsPerLevel.SetSize(numberOfLevels); >>>>>> shrinkFactorsPerLevel[0] = 4; >>>>>> shrinkFactorsPerLevel[1] = 2; >>>>>> shrinkFactorsPerLevel[2] = 1; >>>>>> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >>>>>> smoothingSigmasPerLevel.SetSize(numberOfLevels); >>>>>> smoothingSigmasPerLevel[0] = 2; >>>>>> smoothingSigmasPerLevel[1] = 1; >>>>>> smoothingSigmasPerLevel[2] = 0; >>>>>> registration->SetNumberOfLevels(numberOfLevels); >>>>>> registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); >>>>>> registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); >>>>> >>>>> >>>>> Could you please me explain what is the meaning of this warning? >>>>> >>>>> By the way, I am working with affine transformations and I have used >>>>> the transform initializer. >>>>> >>>>> Best, >>>>> >>>>> Luigi >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>>> -- >>>> Matias >>>> >>> -- >>> Matias >>> >> >> -- > Matias > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Wed Dec 16 09:53:48 2015 From: matimontg at gmail.com (Matias Montroull) Date: Wed, 16 Dec 2015 14:53:48 +0000 Subject: [ITK] Metric NaN and multi resolution registration In-Reply-To: References: Message-ID: Try removing the GeometryOn() statement El mi?., 16 de dic. de 2015 a la(s) 11:44, Luigi Riba escribi?: > Hello, > > in fact I am surprised by this warning since I am using the > CenteredTransformInitializer. This is the piece of code that involves the > initialization of the transform: > > typedef itk::CenteredTransformInitializer> ImageType> TransformInitializerType; >> TransformInitializerType::Pointer transformInitializer = >> TransformInitializerType::New(); >> transformInitializer->SetTransform(transform); >> transformInitializer->SetFixedImage(fixedReader->GetOutput()); >> transformInitializer->SetMovingImage(movingReader->GetOutput()); >> transformInitializer->GeometryOn(); >> transformInitializer->InitializeTransform(); > > ... > >> registration->SetInitialTransform(transform); > > > Thanks for the support, > > Luigi > > 2015-12-16 15:35 GMT+01:00 Matias Montroull : > >> The second warning looks like centers not aligned properly therefore the >> registration fails. Are you using CenteredTransformInitializer? >> >> El mi?., 16 de dic. de 2015 a la(s) 06:24, Luigi Riba < >> ribaluigi at gmail.com> escribi?: >> >>> Dear Matias and ITK community, >>> >>> thank you very much for your quick and detailed reply. >>> >>> I have tried a little bit of tinkering starting from your suggestion but >>> I didn't overcome the errors. >>> >>> I am registering two images using the v4 framework with the following >>> header >>> #include >>> #include >>> #include >>> >>> I have initialized the transform with the transform initializer and >>> computed the optimizer parameters with >>> RegistratonParametersFromPhysicalShift and after a little of playing I left >>> the relaxation factor to .5. >>> >>> *The registration process runs correctly at full resolution. * >>> >>> If I choose a multi resolution approach, like >>> >>> const unsigned int numberOfLevels = 3; >>>> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >>>> shrinkFactorsPerLevel.SetSize(numberOfLevels); >>>> shrinkFactorsPerLevel[0] = 4; >>>> shrinkFactorsPerLevel[1] = 2; >>>> shrinkFactorsPerLevel[2] = 1; >>>> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >>>> smoothingSigmasPerLevel.SetSize(numberOfLevels); >>>> smoothingSigmasPerLevel[0] = 2; >>>> smoothingSigmasPerLevel[1] = 1; >>>> smoothingSigmasPerLevel[2] = 0; >>> >>> >>> the code stops working properly. >>> >>> In fact, I get the following warnings: >>> >>> - RegistrationParameterScalesFromPhysicalShift (00000000021F2630): >>> Variation in any parameter won't change a voxel position. The default >>> scales (1.0) are used to avoid division-by-zero. >>> - WARNING: In >>> f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, >>> line 529 MeanSquaresImageToImageMetricv4 (00000000650FCB40): No valid >>> points were found during metric evaluation. For image metrics, verify that >>> the images overlap appropriately. For instance, you can align the image >>> centers by translation. For point-set metrics, verify that the fixed >>> points, once transformed into the virtual domain space, actually lie within >>> the virtual domain. >>> >>> the metric is NaN and the registration process ends before its first >>> step. >>> >>> Could you explain me the rationale behind this errors? I am probably >>> overlooking something trivial. >>> >>> Best, >>> >>> Luigi >>> >>> >>> >>> 2015-12-07 16:06 GMT+01:00 Matias Montroull : >>> >>>> Actually the min and max steplenght are taken into account, I use these: >>>> Min: 0.0001 >>>> Max: 0.1 >>>> >>>> El lun., 7 de dic. de 2015 a la(s) 12:04, Matias Montroull < >>>> matimontg at gmail.com> escribi?: >>>> >>>>> Hi Luigi, it could be for various reasons, mailny the transform >>>>> initializer you use plus the number of samples and translationscale >>>>> Try this code I have which I've done for MultiResolution and works >>>>> fine for me: >>>>> >>>>> When you enter the parameters, try this: >>>>> Relaxation: 0.99 >>>>> Number of Bins: 50 >>>>> Samples 3 (this is actually translated to 3% in my code as you will >>>>> see below) >>>>> maximum and minimum steplenght is not taken into account so you can >>>>> put 0 and 0 >>>>> translation scale 0.0001 >>>>> >>>>> #include "itkAffineTransform.h" >>>>> #include "itkRegistrationParameterScalesFromPhysicalShift.h" >>>>> #include "itkCenteredTransformInitializer.h" >>>>> #include "itkLandmarkBasedTransformInitializer.h" >>>>> #include "itkMultiResolutionImageRegistrationMethod.h" >>>>> #include "itkMattesMutualInformationImageToImageMetric.h" >>>>> #include "itkMeanSquaresImageToImageMetric.h" >>>>> #include "itkRegularStepGradientDescentOptimizer.h" >>>>> #include "itkRecursiveMultiResolutionPyramidImageFilter.h" >>>>> #include "itkImage.h" >>>>> #include "itkImageFileReader.h" >>>>> #include "itkImageFileWriter.h" >>>>> #include "itkResampleImageFilter.h" >>>>> #include "itkCastImageFilter.h" >>>>> #include "itkCheckerBoardImageFilter.h" >>>>> #include "itkRescaleIntensityImageFilter.h" >>>>> >>>>> #include "itkNormalizeImageFilter.h" >>>>> >>>>> #include "itkCommand.h" >>>>> class CommandIterationUpdate : public itk::Command >>>>> { >>>>> public: >>>>> typedef CommandIterationUpdate Self; >>>>> typedef itk::Command Superclass; >>>>> typedef itk::SmartPointer Pointer; >>>>> itkNewMacro(Self); >>>>> protected: >>>>> CommandIterationUpdate() : m_CumulativeIterationIndex(0) {}; >>>>> public: >>>>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>>>> typedef const OptimizerType * OptimizerPointer; >>>>> void Execute(itk::Object *caller, const itk::EventObject & event) >>>>> ITK_OVERRIDE >>>>> { >>>>> Execute((const itk::Object *)caller, event); >>>>> } >>>>> void Execute(const itk::Object * object, const itk::EventObject & >>>>> event) ITK_OVERRIDE >>>>> { >>>>> OptimizerPointer optimizer = static_cast(object); >>>>> if (!(itk::IterationEvent().CheckEvent(&event))) >>>>> { >>>>> return; >>>>> } >>>>> std::cout << optimizer->GetCurrentIteration() << " "; >>>>> std::cout << optimizer->GetValue() << " "; >>>>> std::cout << optimizer->GetCurrentPosition() << " " << >>>>> m_CumulativeIterationIndex++ << std::endl; >>>>> } >>>>> private: >>>>> unsigned int m_CumulativeIterationIndex; >>>>> }; >>>>> >>>>> template >>>>> class RegistrationInterfaceCommand : public itk::Command >>>>> { >>>>> public: >>>>> typedef RegistrationInterfaceCommand Self; >>>>> typedef itk::Command Superclass; >>>>> typedef itk::SmartPointer Pointer; >>>>> itkNewMacro(Self); >>>>> protected: >>>>> RegistrationInterfaceCommand() {}; >>>>> public: >>>>> typedef TRegistration RegistrationType; >>>>> typedef RegistrationType * >>>>> RegistrationPointer; >>>>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>>>> typedef OptimizerType * OptimizerPointer; >>>>> void Execute(itk::Object * object, const itk::EventObject & event) >>>>> ITK_OVERRIDE >>>>> { >>>>> if (!(itk::IterationEvent().CheckEvent(&event))) >>>>> { >>>>> return; >>>>> } >>>>> RegistrationPointer registration = >>>>> static_cast(object); >>>>> OptimizerPointer optimizer = >>>>> static_cast(registration->GetModifiableOptimizer()); >>>>> std::cout << "-------------------------------------" << std::endl; >>>>> std::cout << "MultiResolution Level : " >>>>> << registration->GetCurrentLevel() << std::endl; >>>>> std::cout << std::endl; >>>>> if (registration->GetCurrentLevel() == 0) >>>>> { >>>>> optimizer->SetMaximumStepLength(1.0); >>>>> optimizer->SetMinimumStepLength(0.001); >>>>> } >>>>> else >>>>> { >>>>> optimizer->SetMaximumStepLength(optimizer->GetMaximumStepLength() / >>>>> 4.0); >>>>> optimizer->SetMinimumStepLength(optimizer->GetMinimumStepLength() / >>>>> 10.0); >>>>> } >>>>> } >>>>> void Execute(const itk::Object *, const itk::EventObject &) >>>>> ITK_OVERRIDE >>>>> { return; } >>>>> }; >>>>> int main(int argc, char *argv[]) >>>>> { >>>>> if (argc < 10) >>>>> { >>>>> std::cerr << "Faltan Parametros " << std::endl; >>>>> std::cerr << "Uso: " << argv[0]; >>>>> std::cerr << " imagenfija imagenflotante "; >>>>> std::cerr << " salida"; >>>>> std::cerr << " Iteraciones Relaxation "; >>>>> std::cerr << " NumeroBins Samples%(1/100) "; >>>>> std::cerr << " StepMax(No Habilitado) StepMin(No Habilitado) >>>>> TranslationFactor"; >>>>> std::cerr << " " << std::endl; >>>>> >>>>> return EXIT_FAILURE; >>>>> } >>>>> >>>>> const unsigned int Dimension = 3; >>>>> typedef signed short PixelType; >>>>> typedef itk::Image< PixelType, Dimension > FixedImageType; >>>>> typedef itk::Image< PixelType, Dimension > MovingImageType; >>>>> typedef float InternalPixelType; >>>>> typedef itk::Image< InternalPixelType, Dimension > InternalImageType; >>>>> >>>>> typedef itk::AffineTransform< double, Dimension > TransformType; >>>>> >>>>> typedef itk::RegularStepGradientDescentOptimizer OptimizerType; >>>>> typedef itk::LinearInterpolateImageFunction< >>>>> InternalImageType, >>>>> double > InterpolatorType; >>>>> typedef itk::MattesMutualInformationImageToImageMetric< >>>>> InternalImageType, >>>>> InternalImageType > MetricType; >>>>> typedef OptimizerType::ScalesType OptimizerScalesType; >>>>> typedef itk::MultiResolutionImageRegistrationMethod< >>>>> InternalImageType, >>>>> InternalImageType > RegistrationType; >>>>> OptimizerType::Pointer optimizer = OptimizerType::New(); >>>>> InterpolatorType::Pointer interpolator = InterpolatorType::New(); >>>>> RegistrationType::Pointer registration = RegistrationType::New(); >>>>> MetricType::Pointer metric = MetricType::New(); >>>>> >>>>> >>>>> TransformType::Pointer transform = TransformType::New(); >>>>> registration->SetTransform(transform); >>>>> >>>>> typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType; >>>>> typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType; >>>>> FixedImageReaderType::Pointer fixedImageReader = >>>>> FixedImageReaderType::New(); >>>>> MovingImageReaderType::Pointer movingImageReader = >>>>> MovingImageReaderType::New(); >>>>> fixedImageReader->SetFileName(argv[1]); >>>>> movingImageReader->SetFileName(argv[2]); >>>>> >>>>> fixedImageReader->Update(); >>>>> movingImageReader->Update(); >>>>> >>>>> typedef itk::CastImageFilter< >>>>> FixedImageType, InternalImageType > FixedCastFilterType; >>>>> typedef itk::CastImageFilter< >>>>> MovingImageType, InternalImageType > MovingCastFilterType; >>>>> FixedCastFilterType::Pointer fixedCaster = FixedCastFilterType::New(); >>>>> MovingCastFilterType::Pointer movingCaster = >>>>> MovingCastFilterType::New(); >>>>> fixedCaster->SetInput(fixedImageReader->GetOutput()); >>>>> movingCaster->SetInput(movingImageReader->GetOutput()); >>>>> >>>>> registration->SetFixedImage(fixedCaster->GetOutput()); >>>>> registration->SetMovingImage(movingCaster->GetOutput()); >>>>> fixedCaster->Update(); >>>>> >>>>> registration->SetFixedImageRegion(fixedCaster->GetOutput()->GetBufferedRegion()); >>>>> >>>>> typedef itk::CenteredTransformInitializer< >>>>> TransformType, FixedImageType, >>>>> MovingImageType > TransformInitializerType; >>>>> TransformInitializerType::Pointer initializer >>>>> = TransformInitializerType::New(); >>>>> initializer->SetTransform(transform); >>>>> initializer->SetFixedImage(fixedImageReader->GetOutput()); >>>>> initializer->SetMovingImage(movingImageReader->GetOutput()); >>>>> initializer->GeometryOn(); >>>>> initializer->InitializeTransform(); >>>>> >>>>> >>>>> typedef TransformType::ParametersType ParametersType; >>>>> const unsigned int numberOfParameters = >>>>> transform->GetNumberOfParameters(); >>>>> ParametersType parameters(numberOfParameters); >>>>> >>>>> registration->SetInitialTransformParameters(transform->GetParameters()); >>>>> >>>>> OptimizerScalesType >>>>> optimizerScales(transform->GetNumberOfParameters()); >>>>> >>>>> double translationScale = atof(argv[10]); >>>>> optimizerScales[0] = 1.0; >>>>> optimizerScales[1] = 1.0; >>>>> optimizerScales[2] = 1.0; >>>>> optimizerScales[3] = 1.0; >>>>> optimizerScales[4] = 1.0; >>>>> optimizerScales[5] = 1.0; >>>>> optimizerScales[6] = 1.0; >>>>> optimizerScales[7] = 1.0; >>>>> optimizerScales[8] = 1.0; >>>>> optimizerScales[9] = translationScale; >>>>> optimizerScales[10] = translationScale; >>>>> optimizerScales[11] = translationScale; >>>>> >>>>> optimizer->SetScales(optimizerScales); >>>>> >>>>> FixedImageType::RegionType fixedImageRegion = >>>>> fixedCaster->GetOutput()->GetBufferedRegion(); >>>>> const unsigned int numberOfPixels = >>>>> fixedImageRegion.GetNumberOfPixels(); >>>>> double porcentage_samples = atof(argv[7]); >>>>> const unsigned int numberOfSamples = static_cast>>>> int>(numberOfPixels * porcentage_samples); >>>>> >>>>> optimizer->SetNumberOfIterations(atof(argv[4])); >>>>> optimizer->SetRelaxationFactor(atof(argv[5])); >>>>> metric->SetNumberOfHistogramBins(atof(argv[6])); >>>>> metric->SetNumberOfSpatialSamples(numberOfSamples); >>>>> optimizer->SetMaximumStepLength(atof(argv[8])); >>>>> optimizer->SetMinimumStepLength(atof(argv[9])); >>>>> >>>>> >>>>> optimizer->MinimizeOn(); >>>>> CommandIterationUpdate::Pointer observer = >>>>> CommandIterationUpdate::New(); >>>>> optimizer->AddObserver(itk::IterationEvent(), observer); >>>>> >>>>> >>>>> typedef RegistrationInterfaceCommand CommandType; >>>>> CommandType::Pointer command = CommandType::New(); >>>>> registration->AddObserver(itk::IterationEvent(), command); >>>>> registration->SetNumberOfLevels(1); >>>>> registration->SetOptimizer(optimizer); >>>>> registration->SetInterpolator(interpolator); >>>>> registration->SetMetric(metric); >>>>> >>>>> FixedImageType::Pointer imagenfija = fixedImageReader->GetOutput(); >>>>> MovingImageType::Pointer imagenflotante = >>>>> movingImageReader->GetOutput(); >>>>> >>>>> >>>>> typedef RegistrationType::ParametersType ParametersType; >>>>> ParametersType InitialParameters = >>>>> registration->GetInitialTransformParameters(); >>>>> std::cout << "TranslationScale: " << translationScale << std::endl; >>>>> std::cout << "MaximumStep: " << optimizer->GetMaximumStepLength() << >>>>> std::endl; >>>>> std::cout << "MinimunStep: " << optimizer->GetMinimumStepLength() << >>>>> std::endl; >>>>> std::cout << "Number of Bins: " << metric->GetNumberOfHistogramBins() >>>>> << std::endl; >>>>> std::cout << "Number of Samples: " << >>>>> metric->GetNumberOfSpatialSamples() << std::endl; >>>>> std::cout << "Iteraciones: " << optimizer->GetNumberOfIterations() << >>>>> std::endl; >>>>> std::cout << "Relaxation: " << optimizer->GetRelaxationFactor() << >>>>> std::endl; >>>>> std::cout << "Initial Parameters: " << InitialParameters << std::endl; >>>>> std::cout << "Origen Fija: " << imagenfija->GetOrigin() << std::endl; >>>>> std::cout << "Origen Flotante: " << imagenflotante->GetOrigin() << >>>>> std::endl; >>>>> std::cout << "Samples: " << numberOfSamples << std::endl; >>>>> >>>>> try >>>>> { >>>>> registration->Update(); >>>>> std::cout << "Optimizer stop condition: " >>>>> << registration->GetOptimizer()->GetStopConditionDescription() >>>>> << std::endl; >>>>> } >>>>> catch (itk::ExceptionObject & err) >>>>> { >>>>> std::cout << "ExceptionObject caught !" << std::endl; >>>>> std::cout << err << std::endl; >>>>> return EXIT_FAILURE; >>>>> } >>>>> std::cout << "Optimizer Stopping Condition = " >>>>> << optimizer->GetStopCondition() << std::endl; >>>>> >>>>> ParametersType finalParameters = >>>>> registration->GetLastTransformParameters(); >>>>> >>>>> double TranslationAlongX = finalParameters[9]; >>>>> double TranslationAlongY = finalParameters[10]; >>>>> double TranslationAlongZ = finalParameters[11]; >>>>> unsigned int numberOfIterations = optimizer->GetCurrentIteration(); >>>>> double bestValue = optimizer->GetValue(); >>>>> >>>>> std::cout << "Resultado = " << std::endl; >>>>> std::cout << " Traslacion X = " << TranslationAlongX << std::endl; >>>>> std::cout << " Traslacion Y = " << TranslationAlongY << std::endl; >>>>> std::cout << " Traslacion Z = " << TranslationAlongZ << std::endl; >>>>> std::cout << " Iteraciones = " << numberOfIterations << std::endl; >>>>> std::cout << " Metrica = " << bestValue << std::endl; >>>>> >>>>> >>>>> typedef itk::ResampleImageFilter< >>>>> MovingImageType, >>>>> FixedImageType > ResampleFilterType; >>>>> TransformType::Pointer finalTransform = TransformType::New(); >>>>> finalTransform->SetParameters(finalParameters); >>>>> finalTransform->SetFixedParameters(transform->GetFixedParameters()); >>>>> ResampleFilterType::Pointer resample = ResampleFilterType::New(); >>>>> resample->SetTransform(finalTransform); >>>>> resample->SetInput(movingImageReader->GetOutput()); >>>>> FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput(); >>>>> PixelType backgroundGrayLevel = 0; //estaba en 100 >>>>> >>>>> resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize()); >>>>> resample->SetOutputOrigin(fixedImage->GetOrigin()); >>>>> resample->SetOutputSpacing(fixedImage->GetSpacing()); >>>>> resample->SetOutputDirection(fixedImage->GetDirection()); >>>>> resample->SetDefaultPixelValue(backgroundGrayLevel); >>>>> typedef signed short OutputPixelType; >>>>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType; >>>>> typedef itk::CastImageFilter< >>>>> FixedImageType, >>>>> OutputImageType > CastFilterType; >>>>> typedef itk::ImageFileWriter< OutputImageType > WriterType; >>>>> WriterType::Pointer writer = WriterType::New(); >>>>> CastFilterType::Pointer caster = CastFilterType::New(); >>>>> writer->SetFileName(argv[3]); >>>>> caster->SetInput(resample->GetOutput()); >>>>> writer->SetInput(caster->GetOutput()); >>>>> writer->Update(); >>>>> Sleep(5000); >>>>> /* >>>>> typedef itk::CheckerBoardImageFilter< FixedImageType > >>>>> CheckerBoardFilterType; >>>>> CheckerBoardFilterType::Pointer checker = >>>>> CheckerBoardFilterType::New(); >>>>> checker->SetInput1(fixedImage); >>>>> checker->SetInput2(resample->GetOutput()); >>>>> caster->SetInput(checker->GetOutput()); >>>>> writer->SetInput(caster->GetOutput()); >>>>> resample->SetDefaultPixelValue(0); >>>>> >>>>> resample->SetTransform(finalTransform); >>>>> if (argc > 10) >>>>> { >>>>> writer->SetFileName(argv[11]); >>>>> writer->Update(); >>>>> }*/ >>>>> return EXIT_SUCCESS; >>>>> } >>>>> >>>>> >>>>> El lun., 7 de dic. de 2015 a la(s) 11:43, Luigi Riba < >>>>> ribaluigi at gmail.com> escribi?: >>>>> >>>>>> Dear ITK community, >>>>>> >>>>>> today I was trying to implement a multi-resolution registration >>>>>> process for 3d images. >>>>>> >>>>>> I started from the example in the tutorial. Unfortunately, I've >>>>>> received the following warning: >>>>>> >>>>>>> WARNING: In >>>>>>> f:\libs\insighttoolkit-4.8.2\modules\numerics\optimizersv4\include\itkObjectToObjectMetric.hxx, >>>>>>> line 529 >>>>>>> MeanSquaresImageToImageMetricv4 (000000006506C020): No valid points >>>>>>> were found during metric evaluation. For image metrics, verify that the >>>>>>> images overlap appropriately. For instance, you can align the image centers >>>>>>> by translation. For point-set metrics, verify that the fixed points, once >>>>>>> transformed into the virtual domain space, actually lie within the virtual >>>>>>> domain. >>>>>> >>>>>> >>>>>> These are the parameters I have used for the multi resolution process: >>>>>>> const unsigned int numberOfLevels = 3; >>>>>>> RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; >>>>>>> shrinkFactorsPerLevel.SetSize(numberOfLevels); >>>>>>> shrinkFactorsPerLevel[0] = 4; >>>>>>> shrinkFactorsPerLevel[1] = 2; >>>>>>> shrinkFactorsPerLevel[2] = 1; >>>>>>> RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; >>>>>>> smoothingSigmasPerLevel.SetSize(numberOfLevels); >>>>>>> smoothingSigmasPerLevel[0] = 2; >>>>>>> smoothingSigmasPerLevel[1] = 1; >>>>>>> smoothingSigmasPerLevel[2] = 0; >>>>>>> registration->SetNumberOfLevels(numberOfLevels); >>>>>>> registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); >>>>>>> registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); >>>>>> >>>>>> >>>>>> Could you please me explain what is the meaning of this warning? >>>>>> >>>>>> By the way, I am working with affine transformations and I have used >>>>>> the transform initializer. >>>>>> >>>>>> Best, >>>>>> >>>>>> Luigi >>>>>> _______________________________________________ >>>>>> Community mailing list >>>>>> Community at itk.org >>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>> >>>>> -- >>>>> Matias >>>>> >>>> -- >>>> Matias >>>> >>> >>> -- >> Matias >> > > -- Matias -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.m.welch at gmail.com Wed Dec 16 12:55:39 2015 From: david.m.welch at gmail.com (David Welch) Date: Wed, 16 Dec 2015 11:55:39 -0600 Subject: [ITK] [ITK-users] Mattes Mutual Information can produce a false positive? In-Reply-To: <1450211111544-7588261.post@n2.nabble.com> References: <1450211111544-7588261.post@n2.nabble.com> Message-ID: <79DC6C6D-D325-48E3-8F34-3FE0F614ABF2@urthecast.com> Hi Gabriel, I?m a little rusty, so maybe someone else can correct my example. 1) Consider a circle with one half ?dark: and one half ?bright" with a gray background. 2) Then consider the inverted image (max() - image). 3) Rotate the inverted image randomly about the center. 4) Now register the two using Mattes?. Do you see the problem? Statistically, both pairings of bright->bright and bright->dark have the same entropy to Mattes?, so neither would be preferred and the algorithm would settle on which ever solution it reaches first and would give a false positive 50% of the time. So Mattes? CAN produce false positives depending on the underlying statistics for the image pairs. Cheers, Dave On 12/15/15, 2:25 PM, "Gabriel A. Gim?nez" wrote: >Hi all, I hope you are well... > >My question is about a implementation of Mattes Mutual Information...is >possible to produce a false positive ? at times it gives me a high metric >value ... but the result of the recording is poor. We use it as a metric for >two implementations of optimizers (PSO and Scatter search). > >Attached results of two executions, using scatter search: > >Moving image: mr_pd >Fixed image: ct >Images source: http://www.insight-journal.org/rire/download_data.php >(patient_001) > >Thank you very much and I hope you can help me, regards. > > >ct_mr_pd_incorrect_result.zip > >ct_mr_pd_accurate_result.zip > > > > >-- >View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Mattes-Mutual-Information-can-produce-a-false-positive-tp7588261.html >Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Dec 16 13:26:54 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 16 Dec 2015 13:26:54 -0500 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/u/1/events/cbhc4cnp61mrebvhtevhfr2st94 On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/1/events/cqneeprpkqv202klt1h14n0djlg 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! -------------- next part -------------- An HTML attachment was scrubbed... URL: From selwyn_hector at yahoo.com Wed Dec 16 22:37:59 2015 From: selwyn_hector at yahoo.com (Selwyn Hector) Date: Thu, 17 Dec 2015 03:37:59 +0000 (UTC) Subject: [ITK] CREATE 3D VOLUME References: <1253839382.31633.1450323479828.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1253839382.31633.1450323479828.JavaMail.yahoo@mail.yahoo.com> Dear ITK Community, I am high school senior extremely interested in programming and dedicated my graduating senior project to a SimpleITK program. I have basic understanding of computer science with skills in both python and Java.? I am basically trying to rewrite an ITK example,Create 3D Volume, into a SimpleITK program. Create 3D volume uses the TileImageFilter and DisconnectPipeline methods in order to merge multiple two dimensional images into a three dimensional image. If I follow the example on the site and use InputImageType as a parameter of InputImageType then I receive the error "wrong number or type of ?argument for overloaded function new_Image". I looked up the function .Image and rewrote the program in a way that fits all parameters. The program is below: from __future__ import print_function import SimpleITK as sitkimport sysimport osimport numpyimport matplotlib as plt if len(sys.argv) != 3:? ? print("Usage: " + sys.argv[0] + " ")? ? sys.exit(1) InputDimension = 2OutputDimension = 3 pixelType = sitk.sitkFloat32TInputImage = sitk.Image(32, 32, InputDimension)TOutputImage = sitk.Image(32, 32, OutputDimension) reader = sitk.ImageFileReader() tileFilter = sitk.TileImageFilter()? ??layout = [2, 2, 0]defaultvalue = 128 tileFilter.SetLayout(layout) for ii in range(1, len(sys.argv)-1):? ? reader.SetFileName(sys.argv[ii])? ? reader.Update() ? ? inputImage = sys.reader.GetOutput()? ? inputImage.DisconnectPipeline() ? ? tileFilter.SetInput(ii-1, inputImage) tileFilter.SetDefaultPixelValue(defaultvalue)tileFilter.Update() writer = sitk.ImageFileWriter(TOutputImage).New()writer.SetFileName(sys.argv[-1])writer.SetInput(TileFitler.GetOutput())writer.Update() This program is also based on the example but I doWhen i run this program through the command prompt along with images I am trying to import I receive the error "AttributeError; type object 'object' has no attribute '__getattr__'. I would love to complete this program and begin to work on future personal ITK projects so I would appreciate help on this. Please let me know If I have made any formatting mistakes or reached out in the wrong way. Thank you all so much! -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Thu Dec 17 03:17:16 2015 From: itkhelpacc at gmail.com (vishal) Date: Thu, 17 Dec 2015 01:17:16 -0700 (MST) Subject: [ITK] [ITK-users] itkvtkglue build error.. please help Message-ID: <1450340236770-36559.post@n7.nabble.com> hi Im using ITK 3.20, VTK 5.10, CMake 3.4.1 and Visual studio 2010... I have successfully build ITK as well as VTK... I need to combine both these libraries so i downloaded itkvtkglue package from Wiki examples Im getting the following error while build it in visual studio 2010... i have tried building it in Visual studio 2008 unfortunately it was still it was showing the same error:- 1> CMake does not need to re-run because C:/ItkVtkGlue/Build/CMakeFiles/generate.stamp is up-to-date. 1>FinalizeBuildStatus: 1> Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.unsuccessfulbuild". 1> Touching "x64\Debug\ZERO_CHECK\ZERO_CHECK.lastbuildstate". 1> 1>Build succeeded. 1> 1>Time Elapsed 00:00:00.48 2>------ Build started: Project: ItkVtkGlue, Configuration: Debug x64 ------ 2>Build started 12/17/2015 2:15:33 PM. 2>PrepareForBuild: 2> Creating directory "C:\ItkVtkGlue\Build\Debug\". 2>InitializeBuildStatus: 2> Creating "ItkVtkGlue.dir\Debug\ItkVtkGlue.unsuccessfulbuild" because "AlwaysCreate" was specified. 2>CustomBuild: 2> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt 2> CMake does not need to re-run because C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. 2>ClCompile: 2> QuickView.cxx 2>c:\itkvtkglue\QuickView.h(210): error C2039: 'IdentifierType' : is not a member of 'itk' 2>c:\itkvtkglue\QuickView.h(210): error C2146: syntax error : missing ';' before identifier 'm_Counter' 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - int assumed. Note: C++ does not support default-int 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - int assumed. Note: C++ does not support default-int 2>c:\itkvtkglue\QuickView.h(112): error C2065: 'm_Counter' : undeclared identifier 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : symbol cannot be used in a using-declaration 2> c:\itkvtkglue\itkImageToVTKImageFilter.h(94) : see reference to class template instantiation 'itk::ImageToVTKImageFilter' being compiled 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' : is not a member of 'itk::ProcessObject' 2> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) : see declaration of 'itk::ProcessObject' 2> ..\QuickView.cxx(254) : see reference to class template instantiation 'itk::ImageToVTKImageFilter' being compiled 2> with 2> [ 2> TInputImage=itk::Image 2> ] 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : symbol cannot be used in a using-declaration 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' : is not a member of 'itk::ProcessObject' 2> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) : see declaration of 'itk::ProcessObject' 2> ..\QuickView.cxx(255) : see reference to class template instantiation 'itk::ImageToVTKImageFilter' being compiled 2> with 2> [ 2> TInputImage=itk::Image,2> 2> ] 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : symbol cannot be used in a using-declaration 2>..\QuickView.cxx(423): error C2065: 'm_Counter' : undeclared identifier 2>..\QuickView.cxx(447): error C2065: 'm_Counter' : undeclared identifier 2> 2>Build FAILED. 2> 2>Time Elapsed 00:00:02.64 3>------ Build started: Project: ALL_BUILD, Configuration: Debug x64 ------ 3>Build started 12/17/2015 2:15:36 PM. 3>InitializeBuildStatus: 3> Creating "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild" because "AlwaysCreate" was specified. 3>CustomBuild: 3> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt 3> CMake does not need to re-run because C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. 3>FinalizeBuildStatus: 3> Deleting file "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild". 3> Touching "x64\Debug\ALL_BUILD\ALL_BUILD.lastbuildstate". 3> 3>Build succeeded. 3> 3>Time Elapsed 00:00:00.22 ========== Build: 2 succeeded, 1 failed, 0 up-to-date, 0 skipped ========== Im trying to write a code for 2D/3D registration so..I need to ITK 3.20 and VTK since im trying to build a journal paper [1] http://www.insight-journal.org/browse/publication/784 please help me out... Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/itkvtkglue-build-error-please-help-tp36559.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From suneezahanif02 at gmail.com Thu Dec 17 07:22:18 2015 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Thu, 17 Dec 2015 13:22:18 +0100 Subject: [ITK] [ITK-users] Question Message-ID: Hello Everyone, I have a question, Is it possible to pass certain image region for calculation of metric in registration process while registration is applied to whole image. Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Dec 17 09:16:17 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 17 Dec 2015 09:16:17 -0500 Subject: [ITK] CREATE 3D VOLUME In-Reply-To: <1253839382.31633.1450323479828.JavaMail.yahoo@mail.yahoo.com> References: <1253839382.31633.1450323479828.JavaMail.yahoo.ref@mail.yahoo.com> <1253839382.31633.1450323479828.JavaMail.yahoo@mail.yahoo.com> Message-ID: Hello Selwyn, It sounds like you have an exciting project. SimpleITK?s interface is a little different that native ITK. 1) There are no ?New? methods in SimpleITK. ITK?s is written for C++ and uses smart pointers with the ?New? method for memory allocations. On the other hand SimpleITK was designed for scripting languages where memory allocation and management happens automatically with in the language [1]. 2) SimpleITK?s filters have an Execute(input1, input2, etc..) method instead of ITK?s pipeline with methods like SetInput, Update, Disconnect, etc? SimpleITK?s uses the ?Execute" method for immediate execution which provide a simpler and some time more efficient execution model for image processing. 3) You may want to run through some of the SimpleITK Python Notebooks [2] for a tutorial. It will be well work the time to setup your Python environment to include Notebooks, so that you can interact with the Python interpreter command by command, and get inline help. HTH, Brad [1] https://en.wikipedia.org/wiki/Memory_management [2] https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks > On Dec 16, 2015, at 10:37 PM, Selwyn Hector via Community wrote: > > Dear ITK Community, > > I am high school senior extremely interested in programming and dedicated my graduating senior project to a SimpleITK program. I have basic understanding of computer science with skills in both python and Java. > > I am basically trying to rewrite an ITK example,Create 3D Volume , into a SimpleITK program. Create 3D volume uses the TileImageFilter and DisconnectPipeline methods in order to merge multiple two dimensional images into a three dimensional image. If I follow the example on the site and use InputImageType as a parameter of InputImageType then I receive the error "wrong number or type of argument for overloaded function new_Image". I looked up the function .Image and rewrote the program in a way that fits all parameters. The program is below: > > from __future__ import print_function > > import SimpleITK as sitk > import sys > import os > import numpy > import matplotlib as plt > > if len(sys.argv) != 3: > print("Usage: " + sys.argv[0] + " ") > sys.exit(1) > > InputDimension = 2 > OutputDimension = 3 > > pixelType = sitk.sitkFloat32 > TInputImage = sitk.Image(32, 32, InputDimension) > TOutputImage = sitk.Image(32, 32, OutputDimension) > > reader = sitk.ImageFileReader() > > tileFilter = sitk.TileImageFilter() > > layout = [2, 2, 0] > defaultvalue = 128 > > tileFilter.SetLayout(layout) > > for ii in range(1, len(sys.argv)-1): > reader.SetFileName(sys.argv[ii]) > reader.Update() > > inputImage = sys.reader.GetOutput() > inputImage.DisconnectPipeline() > > tileFilter.SetInput(ii-1, inputImage) > > tileFilter.SetDefaultPixelValue(defaultvalue) > tileFilter.Update() > > writer = sitk.ImageFileWriter(TOutputImage).New() > writer.SetFileName(sys.argv[-1]) > writer.SetInput(TileFitler.GetOutput()) > writer.Update() > > This program is also based on the example but I doWhen i run this program through the command prompt along with images I am trying to import I receive the error "AttributeError; type object 'object' has no attribute '__getattr__'. > > I would love to complete this program and begin to work on future personal ITK projects so I would appreciate help on this. Please let me know If I have made any formatting mistakes or reached out in the wrong way. Thank you all so much! > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Thu Dec 17 09:51:00 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 17 Dec 2015 09:51:00 -0500 Subject: [ITK] [ITK-users] itkvtkglue build error.. please help In-Reply-To: <1450340236770-36559.post@n7.nabble.com> References: <1450340236770-36559.post@n7.nabble.com> Message-ID: ?Hi Vishal, it looks like that version of itkVtkGlue is for a newer version of ITK.? Try this version: http://itk.org/gitweb?p=ITKApps.git;a=tree;f=Auxiliary/vtk;h=b6ae10b549c4ff60473b9069276a62fe1f7433bf;hb=2b5ec98662341c295f25da915afa4c0a8e794850 HTH, D?enan On Thu, Dec 17, 2015 at 3:17 AM, vishal wrote: > hi > Im using ITK 3.20, VTK 5.10, CMake 3.4.1 and Visual studio 2010... I have > successfully build ITK as well as VTK... I need to combine both these > libraries so i downloaded itkvtkglue package from Wiki examples Im getting > the following error while build it in visual studio 2010... i have tried > building it in Visual studio 2008 unfortunately it was still it was showing > the same error:- > > 1> CMake does not need to re-run because > C:/ItkVtkGlue/Build/CMakeFiles/generate.stamp is up-to-date. > 1>FinalizeBuildStatus: > 1> Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.unsuccessfulbuild". > 1> Touching "x64\Debug\ZERO_CHECK\ZERO_CHECK.lastbuildstate". > 1> > 1>Build succeeded. > 1> > 1>Time Elapsed 00:00:00.48 > 2>------ Build started: Project: ItkVtkGlue, Configuration: Debug x64 > ------ > 2>Build started 12/17/2015 2:15:33 PM. > 2>PrepareForBuild: > 2> Creating directory "C:\ItkVtkGlue\Build\Debug\". > 2>InitializeBuildStatus: > 2> Creating "ItkVtkGlue.dir\Debug\ItkVtkGlue.unsuccessfulbuild" because > "AlwaysCreate" was specified. > 2>CustomBuild: > 2> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt > 2> CMake does not need to re-run because > C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. > 2>ClCompile: > 2> QuickView.cxx > 2>c:\itkvtkglue\QuickView.h(210): error C2039: 'IdentifierType' : is not a > member of 'itk' > 2>c:\itkvtkglue\QuickView.h(210): error C2146: syntax error : missing ';' > before identifier 'm_Counter' > 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - int > assumed. Note: C++ does not support default-int > 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - int > assumed. Note: C++ does not support default-int > 2>c:\itkvtkglue\QuickView.h(112): error C2065: 'm_Counter' : undeclared > identifier > 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : > symbol cannot be used in a using-declaration > 2> c:\itkvtkglue\itkImageToVTKImageFilter.h(94) : see reference to > class template instantiation 'itk::ImageToVTKImageFilter' > being > compiled > 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' : > is > not a member of 'itk::ProcessObject' > 2> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) > : see declaration of 'itk::ProcessObject' > 2> ..\QuickView.cxx(254) : see reference to class template > instantiation 'itk::ImageToVTKImageFilter' being compiled > 2> with > 2> [ > 2> TInputImage=itk::Image > 2> ] > 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : > symbol cannot be used in a using-declaration > 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' : > is > not a member of 'itk::ProcessObject' > 2> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) > : see declaration of 'itk::ProcessObject' > 2> ..\QuickView.cxx(255) : see reference to class template > instantiation 'itk::ImageToVTKImageFilter' being compiled > 2> with > 2> [ > 2> TInputImage=itk::Image,2> > 2> ] > 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : > symbol cannot be used in a using-declaration > 2>..\QuickView.cxx(423): error C2065: 'm_Counter' : undeclared identifier > 2>..\QuickView.cxx(447): error C2065: 'm_Counter' : undeclared identifier > 2> > 2>Build FAILED. > 2> > 2>Time Elapsed 00:00:02.64 > 3>------ Build started: Project: ALL_BUILD, Configuration: Debug x64 ------ > 3>Build started 12/17/2015 2:15:36 PM. > 3>InitializeBuildStatus: > 3> Creating "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild" because > "AlwaysCreate" was specified. > 3>CustomBuild: > 3> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt > 3> CMake does not need to re-run because > C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. > 3>FinalizeBuildStatus: > 3> Deleting file "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild". > 3> Touching "x64\Debug\ALL_BUILD\ALL_BUILD.lastbuildstate". > 3> > 3>Build succeeded. > 3> > 3>Time Elapsed 00:00:00.22 > ========== Build: 2 succeeded, 1 failed, 0 up-to-date, 0 skipped ========== > > Im trying to write a code for 2D/3D registration so..I need to ITK 3.20 and > VTK since im trying to build a journal paper [1] > http://www.insight-journal.org/browse/publication/784 > please help me out... > Regards > Vishal > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/itkvtkglue-build-error-please-help-tp36559.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Dec 17 09:59:07 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 17 Dec 2015 09:59:07 -0500 Subject: [ITK] [ITK-users] Question In-Reply-To: References: Message-ID: Hi Suneeza, you can apply a spatial mask to indicate the region to be used by registration. If you are using affine, rigid or simpler transforms, those transforms will be valid for the entire image. Regards, D?enan On Thu, Dec 17, 2015 at 7:22 AM, suneeza hanif wrote: > Hello Everyone, > > I have a question, Is it possible to pass certain image region for > calculation of metric in registration process while registration is applied > to whole image. > > Best Regards > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Thu Dec 17 10:18:01 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 17 Dec 2015 10:18:01 -0500 Subject: [ITK] [ITK-dev] Linux c++11 build issue v4.8.2 In-Reply-To: <56708ED8.8010005@gmail.com> References: <567073BE.80108@gmail.com> <0BFF7F7D-5861-43C9-BC1E-AF2E1391D5A5@uiowa.edu> <56708ED8.8010005@gmail.com> Message-ID: <05C3001E-8C17-4C22-A2C4-4ADBFCCE21B4@mail.nih.gov> Hello, I thought we are requiring ITK to be built with C++11 if your application was going to be build with C++11. Is this saying we are going to support changing the C++ language after CMake configuration of ITK? I would think using the C++11 features of explicit constructor delete or default specifier may results is ABI compatibilities, among many other things. Thanks, Brad > On Dec 15, 2015, at 5:06 PM, David Burns wrote: > > Thanks Hans, based on the release schedule it looks like that will be out pretty soon. > > That's a big improvement to ITK to add c++11 support in my opinion. Thanks. > > David > > On 12/15/15 15:36, Johnson, Hans J wrote: >> This will be fixed when VXL is updated after the 4.9 release. >> >> Hans >> >> >> From: Insight-developers > on behalf of David Burns > >> Date: Tuesday, December 15, 2015 at 2:10 PM >> To: " insight-developers at itk.org " > >> Subject: [ITK-dev] Linux c++11 build issue v4.8.2 >> >> Dear Insight Developers >> >> I have compiled v4.8.2 on Ubuntu 14.04 successfully (g++ 4.8), however, I get compiler errors when building my own ITK applications with the following cmake flag >> >> set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11" >> >> I can compile ITK applications when not using this flag. >> >> I have tried using -fpermissive when building my application. I have also tried compiling ITK using -std=c++11 -fpermissive, individually and in combination. I always get the same errors. >> >> Any suggestions would be welcome. Thanks >> >> David >> >> >> >> Compiler errors >> >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:387:60: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::zero' of non-integral type [-fpermissive] >> static const float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:389:59: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::one' of non-integral type [-fpermissive] >> static const float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:391:62: warning: 'constexpr' needed for in-class initialization of static data member 'const float vnl_numeric_traits::maxval' of non-integral type [-fpermissive] >> static const float maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:410:61: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::zero' of non-integral type [-fpermissive] >> static const double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:412:60: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::one' of non-integral type [-fpermissive] >> static const double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:414:63: warning: 'constexpr' needed for in-class initialization of static data member 'const double vnl_numeric_traits::maxval' of non-integral type [-fpermissive] >> static const double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:433:66: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::zero' of non-integral type [-fpermissive] >> static const long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:435:65: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::one' of non-integral type [-fpermissive] >> static const long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:437:68: warning: 'constexpr' needed for in-class initialization of static data member 'const long double vnl_numeric_traits::maxval' of non-integral type [-fpermissive] >> static const long double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >> ^ >> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >> ^ >> >> >> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From david.mo.burns at gmail.com Thu Dec 17 10:37:01 2015 From: david.mo.burns at gmail.com (David Burns) Date: Thu, 17 Dec 2015 10:37:01 -0500 Subject: [ITK] [ITK-dev] Linux c++11 build issue v4.8.2 In-Reply-To: <05C3001E-8C17-4C22-A2C4-4ADBFCCE21B4@mail.nih.gov> References: <567073BE.80108@gmail.com> <0BFF7F7D-5861-43C9-BC1E-AF2E1391D5A5@uiowa.edu> <56708ED8.8010005@gmail.com> <05C3001E-8C17-4C22-A2C4-4ADBFCCE21B4@mail.nih.gov> Message-ID: <5672D69D.1050001@gmail.com> With 4.8.2 - I built ITK with C++11 (this required -fpermissive to complete) Despite doing that, I was still unable to built ITK applications with C++11 (even when also using -fpermissive). Let me know if you've had different results. I was hoping this would be resolved with 4.9. - David On 12/17/2015 10:18 AM, Bradley Lowekamp wrote: > Hello, > > I thought we are requiring ITK to be built with C++11 if your > application was going to be build with C++11. > > Is this saying we are going to support changing the C++ language after > CMake configuration of ITK? > > I would think using the C++11 features of explicit constructor delete > or default specifier may results is ABI compatibilities, among many > other things. > > Thanks, > Brad > > > >> On Dec 15, 2015, at 5:06 PM, David Burns > > wrote: >> >> Thanks Hans, based on the release schedule it looks like that will be >> out pretty soon. >> >> That's a big improvement to ITK to add c++11 support in my opinion. >> Thanks. >> >> David >> >> On 12/15/15 15:36, Johnson, Hans J wrote: >>> This will be fixed when VXL is updated after the 4.9 release. >>> >>> Hans >>> >>> >>> From: Insight-developers >> > on behalf of David >>> Burns > >>> Date: Tuesday, December 15, 2015 at 2:10 PM >>> To: "insight-developers at itk.org" >> > >>> Subject: [ITK-dev] Linux c++11 build issue v4.8.2 >>> >>> Dear Insight Developers >>> >>> I have compiled v4.8.2 on Ubuntu 14.04 successfully (g++ 4.8), >>> however, I get compiler errors when building my own ITK applications >>> with the following cmake flag >>> >>> set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11" >>> >>> I can compile ITK applications when not using this flag. >>> >>> I have tried using -fpermissive when building my application. I have >>> also tried compiling ITK using -std=c++11 -fpermissive, individually >>> and in combination. I always get the same errors. >>> >>> Any suggestions would be welcome. Thanks >>> >>> David >>> >>> >>> >>> Compiler errors >>> >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:387:60: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const float vnl_numeric_traits::zero' of non-integral type >>> [-fpermissive] >>> static const float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:389:59: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const float vnl_numeric_traits::one' of non-integral type >>> [-fpermissive] >>> static const float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:391:62: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const float vnl_numeric_traits::maxval' of non-integral type >>> [-fpermissive] >>> static const float maxval >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:410:61: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const double vnl_numeric_traits::zero' of non-integral type >>> [-fpermissive] >>> static const double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:412:60: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const double vnl_numeric_traits::one' of non-integral type >>> [-fpermissive] >>> static const double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:414:63: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const double vnl_numeric_traits::maxval' of non-integral >>> type [-fpermissive] >>> static const double maxval >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:433:66: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const long double vnl_numeric_traits::zero' of >>> non-integral type [-fpermissive] >>> static const long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:435:65: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const long double vnl_numeric_traits::one' of >>> non-integral type [-fpermissive] >>> static const long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:437:68: warning: >>> 'constexpr' needed for in-class initialization of static data member >>> 'const long double vnl_numeric_traits::maxval' of >>> non-integral type [-fpermissive] >>> static const long double maxval >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >>> ^ >>> /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in >>> definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' >>> # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x >>> ^ >>> >>> >>> ------------------------------------------------------------------------ >>> Notice: This UI Health Care e-mail (including attachments) is >>> covered by the Electronic Communications Privacy Act, 18 U.S.C. >>> 2510-2521, is confidential and may be legally privileged. If you >>> are not the intended recipient, you are hereby notified that any >>> retention, dissemination, distribution, or copying of this >>> communication is strictly prohibited. Please reply to the sender >>> that you have received the message in error, then delete it. Thank >>> you. >>> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From hyunjae.kang at kitware.com Thu Dec 17 11:12:26 2015 From: hyunjae.kang at kitware.com (Hyun Jae Kang) Date: Thu, 17 Dec 2015 11:12:26 -0500 Subject: [ITK] [ITK-dev] The timeout error of itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest Message-ID: Dear All, I am trying to fix the timeout error of itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest. ( https://open.cdash.org/testSummary.php?project=2&name=itkTimeVaryingBSplineVelocityFieldPointSetRegistrationTest&date=2015-12-17 ) >From my observation, the following function is a bottleneck of the whole pipeline: "template void TimeVaryingBSplineVelocityFieldImageRegistrationMethod ::GetMetricDerivativePointSetForAllTimePoints( VelocityFieldPointSetType *velocityFieldPointSet, WeightsContainerType *velocityFieldWeights )" ( https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/RegistrationMethodsv4/include/itkTimeVaryingBSplineVelocityFieldImageRegistrationMethod.hxx ) More specifically, the function call of " this->m_OutputTransform->IntegrateVelocityField();" from the following lines are slow. // Get the fixed transform. We need to duplicate the resulting // displacement field since it will be overwritten when we integrate // the velocity field to get the moving image transform. if( timePoint == 0 ) { this->m_OutputTransform->GetModifiableDisplacementField()->FillBuffer( zeroVector ); } else { this->m_OutputTransform->SetLowerTimeBound( t ); this->m_OutputTransform->SetUpperTimeBound( 0.0 ); this->m_OutputTransform->SetNumberOfIntegrationSteps( numberOfIntegrationSteps ); this->m_OutputTransform->IntegrateVelocityField(); } If you have any suggestion to solve the timeout error, please let me know. Thanks, Hyun Jae -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Dec 17 12:47:59 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 17 Dec 2015 12:47:59 -0500 Subject: [ITK] [ITK-dev] Linux c++11 build issue v4.8.2 In-Reply-To: <5672D69D.1050001@gmail.com> References: <567073BE.80108@gmail.com> <0BFF7F7D-5861-43C9-BC1E-AF2E1391D5A5@uiowa.edu> <56708ED8.8010005@gmail.com> <05C3001E-8C17-4C22-A2C4-4ADBFCCE21B4@mail.nih.gov> <5672D69D.1050001@gmail.com> Message-ID: ITK supports C++11 with GCC 4.8.2 -- we even have a a dashboard build with that configuration, and it has been clean for a long time: https://open.cdash.org/buildSummary.php?buildid=4150934 When configuring ITK (and other applications and libraries), make sure that the -std=c++11 flag is passed during the *initial* CMake configuration. There are CMake try_compiles that occur that assess the compiler, and their results are cached. FYI, there was a good recent post on C++ standard ABI compatibility with GCC here: https://developerblog.redhat.com/2015/02/05/gcc5-and-the-c11-abi/ A good general rule is to use the same standard for everything that is linked together. Regardless, the work Hans has been doing to improved and modernize VXL is very exciting, and it will be great to have that available. Matt On Thu, Dec 17, 2015 at 10:37 AM, David Burns wrote: > With 4.8.2 - I built ITK with C++11 (this required -fpermissive to > complete) > Despite doing that, I was still unable to built ITK applications with > C++11 (even when also using -fpermissive). > > Let me know if you've had different results. I was hoping this would be > resolved with 4.9. > > - David > > > On 12/17/2015 10:18 AM, Bradley Lowekamp wrote: > > Hello, > > I thought we are requiring ITK to be built with C++11 if your application > was going to be build with C++11. > > Is this saying we are going to support changing the C++ language after > CMake configuration of ITK? > > I would think using the C++11 features of explicit constructor delete or > default specifier may results is ABI compatibilities, among many other > things. > > Thanks, > Brad > > > > On Dec 15, 2015, at 5:06 PM, David Burns < > david.mo.burns at gmail.com> wrote: > > Thanks Hans, based on the release schedule it looks like that will be out > pretty soon. > > That's a big improvement to ITK to add c++11 support in my opinion. > Thanks. > > David > > On 12/15/15 15:36, Johnson, Hans J wrote: > > This will be fixed when VXL is updated after the 4.9 release. > > Hans > > > From: Insight-developers < > insight-developers-bounces at itk.org> on behalf of David Burns < > david.mo.burns at gmail.com> > Date: Tuesday, December 15, 2015 at 2:10 PM > To: " insight-developers at itk.org" < > insight-developers at itk.org> > Subject: [ITK-dev] Linux c++11 build issue v4.8.2 > > Dear Insight Developers > > I have compiled v4.8.2 on Ubuntu 14.04 successfully (g++ 4.8), however, I > get compiler errors when building my own ITK applications with the > following cmake flag > > set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11" > > I can compile ITK applications when not using this flag. > > I have tried using -fpermissive when building my application. I have also > tried compiling ITK using -std=c++11 -fpermissive, individually and in > combination. I always get the same errors. > > Any suggestions would be welcome. Thanks > > David > > > > Compiler errors > > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:387:60: warning: > 'constexpr' needed for in-class initialization of static data member 'const > float vnl_numeric_traits::zero' of non-integral type [-fpermissive] > static const float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:389:59: warning: > 'constexpr' needed for in-class initialization of static data member 'const > float vnl_numeric_traits::one' of non-integral type [-fpermissive] > static const float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:391:62: warning: > 'constexpr' needed for in-class initialization of static data member 'const > float vnl_numeric_traits::maxval' of non-integral type [-fpermissive] > static const float maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:410:61: warning: > 'constexpr' needed for in-class initialization of static data member 'const > double vnl_numeric_traits::zero' of non-integral type [-fpermissive] > static const double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:412:60: warning: > 'constexpr' needed for in-class initialization of static data member 'const > double vnl_numeric_traits::one' of non-integral type [-fpermissive] > static const double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:414:63: warning: > 'constexpr' needed for in-class initialization of static data member 'const > double vnl_numeric_traits::maxval' of non-integral type > [-fpermissive] > static const double maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:433:66: warning: > 'constexpr' needed for in-class initialization of static data member 'const > long double vnl_numeric_traits::zero' of non-integral type > [-fpermissive] > static const long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:435:65: warning: > 'constexpr' needed for in-class initialization of static data member 'const > long double vnl_numeric_traits::one' of non-integral type > [-fpermissive] > static const long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > /usr/local/include/ITK-4.8/vnl/vnl_numeric_traits.h:437:68: warning: > 'constexpr' needed for in-class initialization of static data member 'const > long double vnl_numeric_traits::maxval' of non-integral type > [-fpermissive] > static const long double maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); > ^ > /usr/local/include/ITK-4.8/vcl_config_compiler.h:152:48: note: in > definition of macro 'VCL_STATIC_CONST_INIT_FLOAT_DECL' > # define VCL_STATIC_CONST_INIT_FLOAT_DECL(x) = x > ^ > > > ------------------------------ > 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. 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Thank you. > ------------------------------ > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Dec 17 12:51:23 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 17 Dec 2015 12:51:23 -0500 Subject: [ITK] [ITK-users] itkvtkglue build error.. please help In-Reply-To: References: <1450340236770-36559.post@n7.nabble.com> Message-ID: Hi, The easiest to use and best maintained bridge between ITK and VTK is the ITKVtkGlue module, which is included in ITK. To use it, turn on Module_ITKVtkGlue in ITK's CMake configuration. http://www.itk.org/Insight/Doxygen/html/group__ITKVtkGlue.html HTH, Matt On Thu, Dec 17, 2015 at 9:51 AM, D?enan Zuki? wrote: > ?Hi Vishal, > > it looks like that version of itkVtkGlue is for a newer version of ITK.? > Try this version: > > http://itk.org/gitweb?p=ITKApps.git;a=tree;f=Auxiliary/vtk;h=b6ae10b549c4ff60473b9069276a62fe1f7433bf;hb=2b5ec98662341c295f25da915afa4c0a8e794850 > > HTH, > D?enan > > On Thu, Dec 17, 2015 at 3:17 AM, vishal wrote: > >> hi >> Im using ITK 3.20, VTK 5.10, CMake 3.4.1 and Visual studio 2010... I have >> successfully build ITK as well as VTK... I need to combine both these >> libraries so i downloaded itkvtkglue package from Wiki examples Im getting >> the following error while build it in visual studio 2010... i have tried >> building it in Visual studio 2008 unfortunately it was still it was >> showing >> the same error:- >> >> 1> CMake does not need to re-run because >> C:/ItkVtkGlue/Build/CMakeFiles/generate.stamp is up-to-date. >> 1>FinalizeBuildStatus: >> 1> Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.unsuccessfulbuild". >> 1> Touching "x64\Debug\ZERO_CHECK\ZERO_CHECK.lastbuildstate". >> 1> >> 1>Build succeeded. >> 1> >> 1>Time Elapsed 00:00:00.48 >> 2>------ Build started: Project: ItkVtkGlue, Configuration: Debug x64 >> ------ >> 2>Build started 12/17/2015 2:15:33 PM. >> 2>PrepareForBuild: >> 2> Creating directory "C:\ItkVtkGlue\Build\Debug\". >> 2>InitializeBuildStatus: >> 2> Creating "ItkVtkGlue.dir\Debug\ItkVtkGlue.unsuccessfulbuild" because >> "AlwaysCreate" was specified. >> 2>CustomBuild: >> 2> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt >> 2> CMake does not need to re-run because >> C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. >> 2>ClCompile: >> 2> QuickView.cxx >> 2>c:\itkvtkglue\QuickView.h(210): error C2039: 'IdentifierType' : is not a >> member of 'itk' >> 2>c:\itkvtkglue\QuickView.h(210): error C2146: syntax error : missing ';' >> before identifier 'm_Counter' >> 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - >> int >> assumed. Note: C++ does not support default-int >> 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - >> int >> assumed. Note: C++ does not support default-int >> 2>c:\itkvtkglue\QuickView.h(112): error C2065: 'm_Counter' : undeclared >> identifier >> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : >> symbol cannot be used in a using-declaration >> 2> c:\itkvtkglue\itkImageToVTKImageFilter.h(94) : see reference >> to >> class template instantiation 'itk::ImageToVTKImageFilter' >> being >> compiled >> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' : >> is >> not a member of 'itk::ProcessObject' >> 2> >> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) >> : see declaration of 'itk::ProcessObject' >> 2> ..\QuickView.cxx(254) : see reference to class template >> instantiation 'itk::ImageToVTKImageFilter' being compiled >> 2> with >> 2> [ >> 2> TInputImage=itk::Image >> 2> ] >> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : >> symbol cannot be used in a using-declaration >> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' : >> is >> not a member of 'itk::ProcessObject' >> 2> >> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) >> : see declaration of 'itk::ProcessObject' >> 2> ..\QuickView.cxx(255) : see reference to class template >> instantiation 'itk::ImageToVTKImageFilter' being compiled >> 2> with >> 2> [ >> 2> TInputImage=itk::Image,2> >> 2> ] >> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : >> symbol cannot be used in a using-declaration >> 2>..\QuickView.cxx(423): error C2065: 'm_Counter' : undeclared identifier >> 2>..\QuickView.cxx(447): error C2065: 'm_Counter' : undeclared identifier >> 2> >> 2>Build FAILED. >> 2> >> 2>Time Elapsed 00:00:02.64 >> 3>------ Build started: Project: ALL_BUILD, Configuration: Debug x64 >> ------ >> 3>Build started 12/17/2015 2:15:36 PM. >> 3>InitializeBuildStatus: >> 3> Creating "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild" because >> "AlwaysCreate" was specified. >> 3>CustomBuild: >> 3> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt >> 3> CMake does not need to re-run because >> C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. >> 3>FinalizeBuildStatus: >> 3> Deleting file "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild". >> 3> Touching "x64\Debug\ALL_BUILD\ALL_BUILD.lastbuildstate". >> 3> >> 3>Build succeeded. >> 3> >> 3>Time Elapsed 00:00:00.22 >> ========== Build: 2 succeeded, 1 failed, 0 up-to-date, 0 skipped >> ========== >> >> Im trying to write a code for 2D/3D registration so..I need to ITK 3.20 >> and >> VTK since im trying to build a journal paper [1] >> http://www.insight-journal.org/browse/publication/784 >> please help me out... >> Regards >> Vishal >> >> >> >> -- >> View this message in context: >> http://itk-users.7.n7.nabble.com/itkvtkglue-build-error-please-help-tp36559.html >> Sent from the ITK - Users mailing list archive at Nabble.com. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Dec 17 12:54:05 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 17 Dec 2015 12:54:05 -0500 Subject: [ITK] [ITK-users] Problem with building a journal paper In-Reply-To: <1450252933520-36557.post@n7.nabble.com> References: <1450252933520-36557.post@n7.nabble.com> Message-ID: Hi Vishal, A version of this Insight Journal article has been updated for ITKv4 here: https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration Please review this patch, which will make it available in ITK as a Remote module: https://open.cdash.org/viewTest.php?onlyfailed&buildid=4152230 Thanks, Matt On Wed, Dec 16, 2015 at 3:02 AM, vishal wrote: > hi, > I was trying to build the ITK journal paper "ITK-Based Implementation of > Two-Projection 2D/3D Registration Method with an Application in Patient > Setup for External Beam Radiotherapy" source code but it was showing the > following error while configuring with CMake... > > > 1) CMake Error at CMakeLists.txt:1 (INCLUDE): > include could not find load file: > > D:/itk_example/Journal5ByWU/Source/images/IJMacros.txt > 2) CMake Error at CMakeLists.txt:31 (LOADPACKAGE): > Unknown CMake command "LOADPACKAGE". > Configuring incomplete, errors occurred! > See also > "D:/itk_example/Journal5ByWU/Source/Build/CMakeFiles/CMakeOutput.log". > > > > As mentioned in the paper Im using Visual studio 2008, Cmake 2.8.12.2,ITK > 3.20... please help me out.. > Regards > Vishal > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Problem-with-building-a-journal-paper-tp36557.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Dec 17 13:45:24 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 17 Dec 2015 13:45:24 -0500 Subject: [ITK] [ITK-users] itkvtkglue build error.. please help In-Reply-To: References: <1450340236770-36559.post@n7.nabble.com> Message-ID: He is using ITK 3.20 with VTK 5.10. Where is itkVtkGlue for those versions? On Thu, Dec 17, 2015 at 12:51 PM, Matt McCormick wrote: > Hi, > > The easiest to use and best maintained bridge between ITK and VTK is the > ITKVtkGlue module, which is included in ITK. To use it, turn on > > Module_ITKVtkGlue > > in ITK's CMake configuration. > > http://www.itk.org/Insight/Doxygen/html/group__ITKVtkGlue.html > > HTH, > Matt > > On Thu, Dec 17, 2015 at 9:51 AM, D?enan Zuki? wrote: > >> ?Hi Vishal, >> >> it looks like that version of itkVtkGlue is for a newer version of ITK.? >> Try this version: >> >> http://itk.org/gitweb?p=ITKApps.git;a=tree;f=Auxiliary/vtk;h=b6ae10b549c4ff60473b9069276a62fe1f7433bf;hb=2b5ec98662341c295f25da915afa4c0a8e794850 >> >> HTH, >> D?enan >> >> On Thu, Dec 17, 2015 at 3:17 AM, vishal wrote: >> >>> hi >>> Im using ITK 3.20, VTK 5.10, CMake 3.4.1 and Visual studio 2010... I have >>> successfully build ITK as well as VTK... I need to combine both these >>> libraries so i downloaded itkvtkglue package from Wiki examples Im >>> getting >>> the following error while build it in visual studio 2010... i have tried >>> building it in Visual studio 2008 unfortunately it was still it was >>> showing >>> the same error:- >>> >>> 1> CMake does not need to re-run because >>> C:/ItkVtkGlue/Build/CMakeFiles/generate.stamp is up-to-date. >>> 1>FinalizeBuildStatus: >>> 1> Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.unsuccessfulbuild". >>> 1> Touching "x64\Debug\ZERO_CHECK\ZERO_CHECK.lastbuildstate". >>> 1> >>> 1>Build succeeded. >>> 1> >>> 1>Time Elapsed 00:00:00.48 >>> 2>------ Build started: Project: ItkVtkGlue, Configuration: Debug x64 >>> ------ >>> 2>Build started 12/17/2015 2:15:33 PM. >>> 2>PrepareForBuild: >>> 2> Creating directory "C:\ItkVtkGlue\Build\Debug\". >>> 2>InitializeBuildStatus: >>> 2> Creating "ItkVtkGlue.dir\Debug\ItkVtkGlue.unsuccessfulbuild" because >>> "AlwaysCreate" was specified. >>> 2>CustomBuild: >>> 2> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt >>> 2> CMake does not need to re-run because >>> C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. >>> 2>ClCompile: >>> 2> QuickView.cxx >>> 2>c:\itkvtkglue\QuickView.h(210): error C2039: 'IdentifierType' : is not >>> a >>> member of 'itk' >>> 2>c:\itkvtkglue\QuickView.h(210): error C2146: syntax error : missing ';' >>> before identifier 'm_Counter' >>> 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - >>> int >>> assumed. Note: C++ does not support default-int >>> 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - >>> int >>> assumed. Note: C++ does not support default-int >>> 2>c:\itkvtkglue\QuickView.h(112): error C2065: 'm_Counter' : undeclared >>> identifier >>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : >>> symbol cannot be used in a using-declaration >>> 2> c:\itkvtkglue\itkImageToVTKImageFilter.h(94) : see reference >>> to >>> class template instantiation 'itk::ImageToVTKImageFilter' >>> being >>> compiled >>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' >>> : is >>> not a member of 'itk::ProcessObject' >>> 2> >>> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) >>> : see declaration of 'itk::ProcessObject' >>> 2> ..\QuickView.cxx(254) : see reference to class template >>> instantiation 'itk::ImageToVTKImageFilter' being compiled >>> 2> with >>> 2> [ >>> 2> TInputImage=itk::Image >>> 2> ] >>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : >>> symbol cannot be used in a using-declaration >>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' >>> : is >>> not a member of 'itk::ProcessObject' >>> 2> >>> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) >>> : see declaration of 'itk::ProcessObject' >>> 2> ..\QuickView.cxx(255) : see reference to class template >>> instantiation 'itk::ImageToVTKImageFilter' being compiled >>> 2> with >>> 2> [ >>> 2> TInputImage=itk::Image,2> >>> 2> ] >>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' : >>> symbol cannot be used in a using-declaration >>> 2>..\QuickView.cxx(423): error C2065: 'm_Counter' : undeclared identifier >>> 2>..\QuickView.cxx(447): error C2065: 'm_Counter' : undeclared identifier >>> 2> >>> 2>Build FAILED. >>> 2> >>> 2>Time Elapsed 00:00:02.64 >>> 3>------ Build started: Project: ALL_BUILD, Configuration: Debug x64 >>> ------ >>> 3>Build started 12/17/2015 2:15:36 PM. >>> 3>InitializeBuildStatus: >>> 3> Creating "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild" because >>> "AlwaysCreate" was specified. >>> 3>CustomBuild: >>> 3> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt >>> 3> CMake does not need to re-run because >>> C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. >>> 3>FinalizeBuildStatus: >>> 3> Deleting file "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild". >>> 3> Touching "x64\Debug\ALL_BUILD\ALL_BUILD.lastbuildstate". >>> 3> >>> 3>Build succeeded. >>> 3> >>> 3>Time Elapsed 00:00:00.22 >>> ========== Build: 2 succeeded, 1 failed, 0 up-to-date, 0 skipped >>> ========== >>> >>> Im trying to write a code for 2D/3D registration so..I need to ITK 3.20 >>> and >>> VTK since im trying to build a journal paper [1] >>> http://www.insight-journal.org/browse/publication/784 >>> please help me out... >>> Regards >>> Vishal >>> >>> >>> >>> -- >>> View this message in context: >>> http://itk-users.7.n7.nabble.com/itkvtkglue-build-error-please-help-tp36559.html >>> Sent from the ITK - Users mailing list archive at Nabble.com. >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Dec 17 14:47:23 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 17 Dec 2015 14:47:23 -0500 Subject: [ITK] [ITK-users] itkvtkglue build error.. please help In-Reply-To: References: <1450340236770-36559.post@n7.nabble.com> Message-ID: The version of ITKVtkGlue that corresponds to ITK 3.20 can be found in the InsightApplications tarball for the corresponding version here: http://itk.org/ITK/resources/legacy_releases.html However, all new development for ITK should be done with ITKv4. There is an ITKv4 module for the Insight Journal article http://www.insight-journal.org/browse/publication/784 found here: https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration M On Thu, Dec 17, 2015 at 1:45 PM, D?enan Zuki? wrote: > He is using ITK 3.20 with VTK 5.10. Where is itkVtkGlue for those versions? > > On Thu, Dec 17, 2015 at 12:51 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> Hi, >> >> The easiest to use and best maintained bridge between ITK and VTK is the >> ITKVtkGlue module, which is included in ITK. To use it, turn on >> >> Module_ITKVtkGlue >> >> in ITK's CMake configuration. >> >> http://www.itk.org/Insight/Doxygen/html/group__ITKVtkGlue.html >> >> HTH, >> Matt >> >> On Thu, Dec 17, 2015 at 9:51 AM, D?enan Zuki? wrote: >> >>> ?Hi Vishal, >>> >>> it looks like that version of itkVtkGlue is for a newer version of ITK.? >>> Try this version: >>> >>> http://itk.org/gitweb?p=ITKApps.git;a=tree;f=Auxiliary/vtk;h=b6ae10b549c4ff60473b9069276a62fe1f7433bf;hb=2b5ec98662341c295f25da915afa4c0a8e794850 >>> >>> HTH, >>> D?enan >>> >>> On Thu, Dec 17, 2015 at 3:17 AM, vishal wrote: >>> >>>> hi >>>> Im using ITK 3.20, VTK 5.10, CMake 3.4.1 and Visual studio 2010... I >>>> have >>>> successfully build ITK as well as VTK... I need to combine both these >>>> libraries so i downloaded itkvtkglue package from Wiki examples Im >>>> getting >>>> the following error while build it in visual studio 2010... i have tried >>>> building it in Visual studio 2008 unfortunately it was still it was >>>> showing >>>> the same error:- >>>> >>>> 1> CMake does not need to re-run because >>>> C:/ItkVtkGlue/Build/CMakeFiles/generate.stamp is up-to-date. >>>> 1>FinalizeBuildStatus: >>>> 1> Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.unsuccessfulbuild". >>>> 1> Touching "x64\Debug\ZERO_CHECK\ZERO_CHECK.lastbuildstate". >>>> 1> >>>> 1>Build succeeded. >>>> 1> >>>> 1>Time Elapsed 00:00:00.48 >>>> 2>------ Build started: Project: ItkVtkGlue, Configuration: Debug x64 >>>> ------ >>>> 2>Build started 12/17/2015 2:15:33 PM. >>>> 2>PrepareForBuild: >>>> 2> Creating directory "C:\ItkVtkGlue\Build\Debug\". >>>> 2>InitializeBuildStatus: >>>> 2> Creating "ItkVtkGlue.dir\Debug\ItkVtkGlue.unsuccessfulbuild" because >>>> "AlwaysCreate" was specified. >>>> 2>CustomBuild: >>>> 2> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt >>>> 2> CMake does not need to re-run because >>>> C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. >>>> 2>ClCompile: >>>> 2> QuickView.cxx >>>> 2>c:\itkvtkglue\QuickView.h(210): error C2039: 'IdentifierType' : is >>>> not a >>>> member of 'itk' >>>> 2>c:\itkvtkglue\QuickView.h(210): error C2146: syntax error : missing >>>> ';' >>>> before identifier 'm_Counter' >>>> 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - >>>> int >>>> assumed. Note: C++ does not support default-int >>>> 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier - >>>> int >>>> assumed. Note: C++ does not support default-int >>>> 2>c:\itkvtkglue\QuickView.h(112): error C2065: 'm_Counter' : undeclared >>>> identifier >>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' >>>> : >>>> symbol cannot be used in a using-declaration >>>> 2> c:\itkvtkglue\itkImageToVTKImageFilter.h(94) : see >>>> reference to >>>> class template instantiation 'itk::ImageToVTKImageFilter' >>>> being >>>> compiled >>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' >>>> : is >>>> not a member of 'itk::ProcessObject' >>>> 2> >>>> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) >>>> : see declaration of 'itk::ProcessObject' >>>> 2> ..\QuickView.cxx(254) : see reference to class template >>>> instantiation 'itk::ImageToVTKImageFilter' being compiled >>>> 2> with >>>> 2> [ >>>> 2> TInputImage=itk::Image >>>> 2> ] >>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' >>>> : >>>> symbol cannot be used in a using-declaration >>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: 'SetInput' >>>> : is >>>> not a member of 'itk::ProcessObject' >>>> 2> >>>> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) >>>> : see declaration of 'itk::ProcessObject' >>>> 2> ..\QuickView.cxx(255) : see reference to class template >>>> instantiation 'itk::ImageToVTKImageFilter' being compiled >>>> 2> with >>>> 2> [ >>>> 2> TInputImage=itk::Image>>> char>,2> >>>> 2> ] >>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: 'SetInput' >>>> : >>>> symbol cannot be used in a using-declaration >>>> 2>..\QuickView.cxx(423): error C2065: 'm_Counter' : undeclared >>>> identifier >>>> 2>..\QuickView.cxx(447): error C2065: 'm_Counter' : undeclared >>>> identifier >>>> 2> >>>> 2>Build FAILED. >>>> 2> >>>> 2>Time Elapsed 00:00:02.64 >>>> 3>------ Build started: Project: ALL_BUILD, Configuration: Debug x64 >>>> ------ >>>> 3>Build started 12/17/2015 2:15:36 PM. >>>> 3>InitializeBuildStatus: >>>> 3> Creating "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild" because >>>> "AlwaysCreate" was specified. >>>> 3>CustomBuild: >>>> 3> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt >>>> 3> CMake does not need to re-run because >>>> C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. >>>> 3>FinalizeBuildStatus: >>>> 3> Deleting file "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild". >>>> 3> Touching "x64\Debug\ALL_BUILD\ALL_BUILD.lastbuildstate". >>>> 3> >>>> 3>Build succeeded. >>>> 3> >>>> 3>Time Elapsed 00:00:00.22 >>>> ========== Build: 2 succeeded, 1 failed, 0 up-to-date, 0 skipped >>>> ========== >>>> >>>> Im trying to write a code for 2D/3D registration so..I need to ITK 3.20 >>>> and >>>> VTK since im trying to build a journal paper [1] >>>> http://www.insight-journal.org/browse/publication/784 >>>> please help me out... >>>> Regards >>>> Vishal >>>> >>>> >>>> >>>> -- >>>> View this message in context: >>>> http://itk-users.7.n7.nabble.com/itkvtkglue-build-error-please-help-tp36559.html >>>> Sent from the ITK - Users mailing list archive at Nabble.com. >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From sklenarj at ohsu.edu Thu Dec 17 15:27:34 2015 From: sklenarj at ohsu.edu (Jiri Sklenar) Date: Thu, 17 Dec 2015 20:27:34 +0000 Subject: [ITK] [ITK-users] Problem compiling ITK for iOS Message-ID: <6BD26B18-34B0-4BC8-A5F0-5923777D04E7@ohsu.edu> I successfully compiled ITK 4.8.2 for OS X 10.10.5, but not for iOS 9.2, using Xcode 7.2. The error I?m getting is: ITK_bld_internal_H5make_libsettings "Target specifies product type 'com.apple.product-type.tool', but there's no such product type for the 'iphonesimulator? platform" [cid:3630B6DF-429E-4D9F-A015-AB5CC96F845E at ohsu.edu] Thanks for any help/suggestion. Jiri -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2015-12-17 at 12.21.40 PM.png Type: image/png Size: 16847 bytes Desc: Screen Shot 2015-12-17 at 12.21.40 PM.png URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Dec 17 16:00:05 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 17 Dec 2015 16:00:05 -0500 Subject: [ITK] [ITK-users] Problem compiling ITK for iOS In-Reply-To: <6BD26B18-34B0-4BC8-A5F0-5923777D04E7@ohsu.edu> References: <6BD26B18-34B0-4BC8-A5F0-5923777D04E7@ohsu.edu> Message-ID: Hi Jiri, Could you please list the steps you took to perform the build? Thanks, Matt On Thu, Dec 17, 2015 at 3:27 PM, Jiri Sklenar wrote: > I successfully compiled ITK 4.8.2 for OS X 10.10.5, but not for iOS 9.2, > using Xcode 7.2. > The error I?m getting is: > > ITK_bld_internal_H5make_libsettings > "Target specifies product type 'com.apple.product-type.tool', but there's > no such product type for the 'iphonesimulator? platform" > > > Thanks for any help/suggestion. > > Jiri > > > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2015-12-17 at 12.21.40 PM.png Type: image/png Size: 16847 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From sklenarj at ohsu.edu Thu Dec 17 17:03:51 2015 From: sklenarj at ohsu.edu (Jiri Sklenar) Date: Thu, 17 Dec 2015 22:03:51 +0000 Subject: [ITK] [ITK-users] Problem compiling ITK for iOS In-Reply-To: References: <6BD26B18-34B0-4BC8-A5F0-5923777D04E7@ohsu.edu> Message-ID: <439B65D2-4F5F-451C-A4AB-2587BD33A46E@ohsu.edu> Hi Matt, I followed the instructions from ?ITK on the iOS, Release 1.0" by Shabah et al -downloaded InsightToolkit 4.8.2 from Kitware website -downloaded and installed CMake App In CMakeLists.txt: - could not find lines 529 and 540 to comment out as instructed - took a chance and commented out lines 210 and 211 instead (guessing they serve the same purpose) -found the file vml_math.cxx (in a different directory then specified in the instructions), and added the line ?#define finite(x) __inline_isfinited((double)x)? after line 77 Downloaded Xcode 7.2 Started CMake and specified the source and binary directories for ITK ran configuration once disabled ?BUILD_EXAMPLES? did not change anything else ran configuration again ran generation Opened XCode project in the ITK binary directory, and built successfully for OSX, Then it became little more complicated: 1. changed to Base SDK to ?Latest iOS (iOS 9.2) -> this resulted in ?Standard architectures (armv7, arm64) (? is this the problem, the instructions speciified armv6 and armv7) 2. Removed dependancies for the ALL_BUILT target on itkmkg3states and itkTestDriver 3. removed dependancy of the target itktiff on itkmkg3states 4. compiled with error message related to ITK_bld_internal_H5make_libsettings XCode changed a bit since the Shabah?s paper was last published, I could not follow the instructions literally to accomplish required tasks. Thank you for your help, Jiri Jiri Sklenar, Ph.D. Research Associate Professor Knight Cardiovascular Institute Oregon Health & Science University Portland, Oregon 97239 [cid:2AD48BF8-B86A-49ED-90D6-46A29E8DAB46 at ohsu.edu] On Dec 17, 2015, at 1:00 PM, Matt McCormick > wrote: Hi Jiri, Could you please list the steps you took to perform the build? Thanks, Matt On Thu, Dec 17, 2015 at 3:27 PM, Jiri Sklenar > wrote: I successfully compiled ITK 4.8.2 for OS X 10.10.5, but not for iOS 9.2, using Xcode 7.2. The error I?m getting is: ITK_bld_internal_H5make_libsettings "Target specifies product type 'com.apple.product-type.tool', but there's no such product type for the 'iphonesimulator? platform" Thanks for any help/suggestion. Jiri _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 6791 bytes Desc: image003.jpg URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From abenchaaben at histalim.com Fri Dec 18 02:54:27 2015 From: abenchaaben at histalim.com (abenchaaben) Date: Fri, 18 Dec 2015 00:54:27 -0700 (MST) Subject: [ITK] [ITK-users] SCIFIO ImageIO plugin Message-ID: <1450425267798-7588276.post@n2.nabble.com> Hi, I build ITK with the SCIFIO ImageIO plugin. I did exactly what was marked her : https://github.com/scifio/scifio-imageio. The problem is that when i run the example i have this error : Any help please. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/SCIFIO-ImageIO-plugin-tp7588276.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Dec 18 10:35:50 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 18 Dec 2015 10:35:50 -0500 Subject: [ITK] [ITK-users] SCIFIO ImageIO plugin In-Reply-To: <1450425267798-7588276.post@n2.nabble.com> References: <1450425267798-7588276.post@n2.nabble.com> Message-ID: Hi, Could you please provide more information: - the version of ITK - the input data file - the compiler version Thanks, Matt On Fri, Dec 18, 2015 at 2:54 AM, abenchaaben wrote: > Hi, > > I build ITK with the SCIFIO ImageIO plugin. I did exactly what was marked > her : https://github.com/scifio/scifio-imageio. > > The problem is that when i run the example i have this error : > > < > http://itk-insight-users.2283740.n2.nabble.com/file/n7588276/Sans_titre.png > > > > Any help please. > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/SCIFIO-ImageIO-plugin-tp7588276.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From abenchaaben at histalim.com Fri Dec 18 11:34:39 2015 From: abenchaaben at histalim.com (abenchaaben) Date: Fri, 18 Dec 2015 09:34:39 -0700 (MST) Subject: [ITK] [ITK-users] SCIFIO ImageIO plugin In-Reply-To: References: <1450425267798-7588276.post@n2.nabble.com> Message-ID: <1450456479657-7588278.post@n2.nabble.com> Hi Matt McCormick-2, I use ITK 4.7.2 build with cmake and Visual studio 2012 x64. The file extension is a czi zeiss file. her is the information of the file (take it by imagej) (Fiji Is Just) ImageJ 2.0.0-rc-43/1.50e; Java 1.8.0_60 [64-bit]; Windows 7 6.1; 75MB of 4539MB (1%) Title: Image1.czi Width: 607.2801 microns (1024) Height: 607.2801 microns (1024) Depth: 400 microns (40) Size: 40MB Resolution: 1.6862 pixels per micron Voxel size: 0.5930x0.5930x10 micron^3 ID: -4 Bits per pixel: 8 (grayscale LUT) Display range: 0-255 Image: 1/40 (z:1/40 - Image 1 #1) No threshold Magnification: 0.75 Uncalibrated Thanks for help -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/SCIFIO-ImageIO-plugin-tp7588276p7588278.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Dec 18 14:34:16 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 18 Dec 2015 14:34:16 -0500 Subject: [ITK] [ITK-users] SCIFIO ImageIO plugin In-Reply-To: <1450456479657-7588278.post@n2.nabble.com> References: <1450425267798-7588276.post@n2.nabble.com> <1450456479657-7588278.post@n2.nabble.com> Message-ID: Thanks for the information. Could you please try with ITK 4.9RC2? On Fri, Dec 18, 2015 at 11:34 AM, abenchaaben wrote: > Hi Matt McCormick-2, > > I use ITK 4.7.2 build with cmake and Visual studio 2012 x64. The file > extension is a czi zeiss file. her is the information of the file (take it > by imagej) > > (Fiji Is Just) ImageJ 2.0.0-rc-43/1.50e; Java 1.8.0_60 [64-bit]; Windows 7 > 6.1; 75MB of 4539MB (1%) > > Title: Image1.czi > Width: 607.2801 microns (1024) > Height: 607.2801 microns (1024) > Depth: 400 microns (40) > Size: 40MB > Resolution: 1.6862 pixels per micron > Voxel size: 0.5930x0.5930x10 micron^3 > ID: -4 > Bits per pixel: 8 (grayscale LUT) > Display range: 0-255 > Image: 1/40 (z:1/40 - Image 1 #1) > No threshold > Magnification: 0.75 > Uncalibrated > > > Thanks for help > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/SCIFIO-ImageIO-plugin-tp7588276p7588278.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Dec 18 18:32:59 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 18 Dec 2015 18:32:59 -0500 Subject: [ITK] [ITK-dev] ITKExamples OpenCV related link errors In-Reply-To: References: Message-ID: Patch: http://review.source.kitware.com/#/c/20575/ On Fri, Oct 2, 2015 at 3:10 PM, Matt McCormick wrote: > Hi Arnaud, > > This means that OpenCV's *Targets.cmake file is not read. This file > informs CMake of all the imported library targets' full paths. > > To ensure this file is read, 'find_package(OpenCV)' should be called. > This reads in the OpenCVConfig.cmake file, which should read in the > OpenCVTargets.cmake file (I have not checked if these files have these > exact names, but that is the idea). > > To make this happen, > > Modules/Video/BridgeOpenCV/CMakeLists.txt > > should set ITKVideoBridgeOpenCV_EXPORT_CODE_BUILD and > ITKVideoBridgeOpen_EXPORT_CODE_INSTALL to strings that contain > > set(OpenCV_DIR \"${OpenCV_DIR}\") > find_package(OpenCV REQUIRED) > > The contents of these variable are added to a module's CMake > information file, which is loaded when the module is loaded. > > The file > > Modules/ThirdParty/DCMTK/CMakeLists.txt > > serves as a good example. > > HTH, > Matt > > On Thu, Oct 1, 2015 at 9:39 AM, Arnaud Gelas > wrote: > > Hi all, > > > > I have built ITK with BridgeOpenCV turned ON and when I compile > ITKExamples, > > I get the following linking errors: > > > > FAILED: : && /usr/lib/ccache/c++ -msse2 -g > > src/CMakeFiles/ImageCompareCommand.dir/ImageCompareCommand.cxx.o -o > > bin/ImageCompareCommand -rdynamic > > /home/arnaud/install/lib/libITKIOBMP-4.9.so.1 -lexpat -lz > > /home/arnaud/install/lib/libITKIOGDCM-4.9.so.1 > > /home/arnaud/install/lib/libITKIOGIPL-4.9.so.1 -ljpeg > > /home/arnaud/install/lib/libITKIOJPEG-4.9.so.1 > > /home/arnaud/install/lib/libITKIOMeta-4.9.so.1 > > /home/arnaud/install/lib/libITKIONIFTI-4.9.so.1 > > /home/arnaud/install/lib/libITKIONRRD-4.9.so.1 -lpng > > /home/arnaud/install/lib/libITKIOPNG-4.9.so.1 -ltiff > > /home/arnaud/install/lib/libITKIOVTK-4.9.so.1 > > /home/arnaud/install/lib/libITKLabelMap-4.9.so.1 > > /home/arnaud/install/lib/libITKQuadEdgeMesh-4.9.so.1 > > /home/arnaud/install/lib/libITKPolynomials-4.9.so.1 > > /home/arnaud/install/lib/libITKBiasCorrection-4.9.so.1 > > /home/arnaud/install/lib/libITKBioCell-4.9.so.1 > > /home/arnaud/install/lib/libITKDICOMParser-4.9.so.1 > > /home/arnaud/install/lib/libITKIOSpatialObjects-4.9.so.1 > > /home/arnaud/install/lib/libITKFEM-4.9.so.1 > > /home/arnaud/install/lib/libITKIOMesh-4.9.so.1 > > /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5_cpp.so > > /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so -lpthread -ldl -lm > > /home/arnaud/install/lib/libITKIOBioRad-4.9.so.1 > > /home/arnaud/install/lib/libITKIOCSV-4.9.so.1 > > /home/arnaud/install/lib/libITKIOGE-4.9.so.1 > > /home/arnaud/install/lib/libITKIOSiemens-4.9.so.1 > > /home/arnaud/install/lib/libITKIOHDF5-4.9.so.1 > > /home/arnaud/install/lib/libITKIOLSM-4.9.so.1 > > /home/arnaud/install/lib/libITKIOMRC-4.9.so.1 > > /home/arnaud/install/lib/libITKIOStimulate-4.9.so.1 > > /home/arnaud/install/lib/libITKIOTransformHDF5-4.9.so.1 > > /home/arnaud/install/lib/libITKIOTransformInsightLegacy-4.9.so.1 > > /home/arnaud/install/lib/libITKIOTransformMatlab-4.9.so.1 > > /home/arnaud/install/lib/libITKKLMRegionGrowing-4.9.so.1 > > /home/arnaud/install/lib/libITKWatersheds-4.9.so.1 > > /home/arnaud/install/lib/libITKOptimizersv4-4.9.so.1 > > /home/arnaud/install/lib/libITKVideoBridgeOpenCV-4.9.so.1 > > /home/arnaud/install/lib/libITKVtkGlue-4.9.so.1 > > /home/arnaud/install/lib/libitkgdcmMSFF-4.9.so.1 > > /home/arnaud/install/lib/libitkgdcmDICT-4.9.so.1 > > /home/arnaud/install/lib/libitkgdcmIOD-4.9.so.1 > > /home/arnaud/install/lib/libitkgdcmDSED-4.9.so.1 > > /home/arnaud/install/lib/libitkgdcmCommon-4.9.so.1 > > /home/arnaud/install/lib/libITKNrrdIO-4.9.so.1 > > /home/arnaud/install/lib/libITKIOXML-4.9.so.1 > > /home/arnaud/install/lib/libITKMetaIO-4.9.so.1 > > /home/arnaud/install/lib/libITKgiftiio-4.9.so.1 -lexpat > > /home/arnaud/install/lib/libITKniftiio-4.9.so.1 > > /home/arnaud/install/lib/libITKznz-4.9.so.1 > > /home/arnaud/install/lib/libITKIOIPL-4.9.so.1 > > /home/arnaud/install/lib/libITKIOTIFF-4.9.so.1 > > /home/arnaud/install/lib/libITKIOTransformBase-4.9.so.1 > > /home/arnaud/install/lib/libITKSpatialObjects-4.9.so.1 > > /home/arnaud/install/lib/libITKMesh-4.9.so.1 > > /home/arnaud/install/lib/libITKPath-4.9.so.1 > > /home/arnaud/install/lib/libITKOptimizers-4.9.so.1 > > /home/arnaud/install/lib/libITKStatistics-4.9.so.1 > > /home/arnaud/install/lib/libitkNetlibSlatec-4.9.so.1 > > /home/arnaud/install/lib/libITKVideoIO-4.9.so.1 > > /home/arnaud/install/lib/libITKIOImageBase-4.9.so.1 > > /home/arnaud/install/lib/libITKVideoCore-4.9.so.1 -lopencv_videostab > > -lopencv_video -lopencv_ts -lopencv_superres -lopencv_stitching > > -lopencv_photo -lopencv_ocl -lopencv_objdetect -lopencv_nonfree > -lopencv_ml > > -lopencv_legacy -lopencv_imgproc -lopencv_highgui -lopencv_gpu > > -lopencv_flann -lopencv_features2d -lopencv_core -lopencv_contrib > > -lopencv_calib3d -ljpeg -lpng -ltiff > > /home/arnaud/install/lib/libITKVTK-4.9.so.1 > > /home/arnaud/install/lib/libITKCommon-4.9.so.1 > > /home/arnaud/install/lib/libitkdouble-conversion-4.9.so.1 > > /home/arnaud/install/lib/libitksys-4.9.so.1 > > /home/arnaud/install/lib/libITKVNLInstantiation-4.9.so.1 > > /home/arnaud/install/lib/libitkvnl_algo-4.9.so.1 > > /home/arnaud/install/lib/libitkv3p_lsqr-4.9.so.1 > > /home/arnaud/install/lib/libitkvnl-4.9.so.1 > > /home/arnaud/install/lib/libitkvcl-4.9.so.1 > > /home/arnaud/install/lib/libitkv3p_netlib-4.9.so.1 -lm -lpthread -lm > > /home/arnaud/install/lib/libvtkRenderingOpenGL-6.3.so.1 -lGLU -lSM -lICE > > -lX11 -lXext -lSM -lICE -lX11 -lXext -lXt > > /home/arnaud/install/lib/libvtkImagingHybrid-6.3.so.1 > > /home/arnaud/install/lib/libvtkIOImage-6.3.so.1 > > /home/arnaud/install/lib/libvtkDICOMParser-6.3.so.1 > > /home/arnaud/install/lib/libvtkIOCore-6.3.so.1 > > /home/arnaud/install/lib/libvtkmetaio-6.3.so.1 -lz > > /home/arnaud/install/lib/libvtkRenderingFreeType-6.3.so.1 > > /home/arnaud/install/lib/libvtkftgl-6.3.so.1 -lfreetype -lGL > > /home/arnaud/install/lib/libvtkInteractionStyle-6.3.so.1 > > /home/arnaud/install/lib/libvtkRenderingCore-6.3.so.1 > > /home/arnaud/install/lib/libvtkCommonColor-6.3.so.1 > > /home/arnaud/install/lib/libvtkFiltersGeometry-6.3.so.1 > > /home/arnaud/install/lib/libvtkFiltersExtraction-6.3.so.1 > > /home/arnaud/install/lib/libvtkFiltersStatistics-6.3.so.1 > > /home/arnaud/install/lib/libvtkImagingFourier-6.3.so.1 > > /home/arnaud/install/lib/libvtkalglib-6.3.so.1 > > /home/arnaud/install/lib/libvtkFiltersSources-6.3.so.1 > > /home/arnaud/install/lib/libvtkFiltersGeneral-6.3.so.1 > > /home/arnaud/install/lib/libvtkFiltersCore-6.3.so.1 > > /home/arnaud/install/lib/libvtkCommonComputationalGeometry-6.3.so.1 > > /home/arnaud/install/lib/libvtkImagingSources-6.3.so.1 > > /home/arnaud/install/lib/libvtkImagingCore-6.3.so.1 > > /home/arnaud/install/lib/libvtkCommonExecutionModel-6.3.so.1 > > /home/arnaud/install/lib/libvtkCommonDataModel-6.3.so.1 > > /home/arnaud/install/lib/libvtkCommonMisc-6.3.so.1 > > /home/arnaud/install/lib/libvtkCommonSystem-6.3.so.1 > > /home/arnaud/install/lib/libvtksys-6.3.so.1 -ldl > > /home/arnaud/install/lib/libvtkCommonTransforms-6.3.so.1 > > /home/arnaud/install/lib/libvtkCommonMath-6.3.so.1 > > /home/arnaud/install/lib/libvtkCommonCore-6.3.so.1 > > > -Wl,-rpath,/home/arnaud/install/lib:/usr/lib/x86_64-linux-gnu/hdf5/serial/lib > > -Wl,-rpath-link,/home/arnaud/install/lib && : > > /usr/bin/ld: cannot find -lopencv_videostab > > /usr/bin/ld: cannot find -lopencv_video > > /usr/bin/ld: cannot find -lopencv_ts > > /usr/bin/ld: cannot find -lopencv_superres > > /usr/bin/ld: cannot find -lopencv_stitching > > /usr/bin/ld: cannot find -lopencv_photo > > /usr/bin/ld: cannot find -lopencv_ocl > > /usr/bin/ld: cannot find -lopencv_objdetect > > /usr/bin/ld: cannot find -lopencv_nonfree > > /usr/bin/ld: cannot find -lopencv_ml > > /usr/bin/ld: cannot find -lopencv_legacy > > /usr/bin/ld: cannot find -lopencv_imgproc > > /usr/bin/ld: cannot find -lopencv_highgui > > /usr/bin/ld: cannot find -lopencv_gpu > > /usr/bin/ld: cannot find -lopencv_flann > > /usr/bin/ld: cannot find -lopencv_features2d > > /usr/bin/ld: cannot find -lopencv_core > > /usr/bin/ld: cannot find -lopencv_contrib > > /usr/bin/ld: cannot find -lopencv_calib3d > > collect2: error: ld returned 1 exit status > > [14/255] Building CXX object > > src/Core/Common/ObserveAnEvent/CMakeFiles/ObserveAnEvent.dir/Code.cxx.o > > > > > > It actually occurs for all executables... > > > > ${ITK_LIBRARIES} does not contain ${OpenCV_LIBS}, leading to this error. > > Correct? > > > > What would be the best/correct way to fix this error? > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From itkhelpacc at gmail.com Sat Dec 19 01:39:54 2015 From: itkhelpacc at gmail.com (vishal) Date: Fri, 18 Dec 2015 23:39:54 -0700 (MST) Subject: [ITK] [ITK-users] Problem with building a journal paper In-Reply-To: References: <1450252933520-36557.post@n7.nabble.com> Message-ID: <1450507194690-36574.post@n7.nabble.com> hi Matt, I downloaded the zip file from the site u suggested... while configuring the following errors occur.. The C compiler identification is MSVC 17.0.50727.1 The CXX compiler identification is MSVC 17.0.50727.1 Check for working C compiler using: Visual Studio 11 2012 Win64 Check for working C compiler using: Visual Studio 11 2012 Win64 -- works Detecting C compiler ABI info Detecting C compiler ABI info - done Check for working CXX compiler using: Visual Studio 11 2012 Win64 Check for working CXX compiler using: Visual Studio 11 2012 Win64 -- works Detecting CXX compiler ABI info Detecting CXX compiler ABI info - done Detecting CXX compile features Detecting CXX compile features - done CMake Error at CMakeLists.txt:7 (include): include could not find load file: ITKModuleExternal please suggest what should i do next? Regards Vishal Configuring incomplete, errors occurred! See also "C:/itk2d3d/ITKTwoProjectionRegistration-master/build/CMakeFiles/CMakeOutput.log". -- View this message in context: http://itk-users.7.n7.nabble.com/Problem-with-building-a-journal-paper-tp36557p36574.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sat Dec 19 12:09:56 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 19 Dec 2015 12:09:56 -0500 Subject: [ITK] [ITK-users] Problem with building a journal paper In-Reply-To: <1450507194690-36574.post@n7.nabble.com> References: <1450252933520-36557.post@n7.nabble.com> <1450507194690-36574.post@n7.nabble.com> Message-ID: Hi Vishal, Please try building against the latest ITK 4.9 release candidate. Thanks, Matt On Sat, Dec 19, 2015 at 1:39 AM, vishal wrote: > hi Matt, > I downloaded the zip file from the site u suggested... while configuring > the > following errors occur.. > > The C compiler identification is MSVC 17.0.50727.1 > The CXX compiler identification is MSVC 17.0.50727.1 > Check for working C compiler using: Visual Studio 11 2012 Win64 > Check for working C compiler using: Visual Studio 11 2012 Win64 -- works > Detecting C compiler ABI info > Detecting C compiler ABI info - done > Check for working CXX compiler using: Visual Studio 11 2012 Win64 > Check for working CXX compiler using: Visual Studio 11 2012 Win64 -- works > Detecting CXX compiler ABI info > Detecting CXX compiler ABI info - done > Detecting CXX compile features > Detecting CXX compile features - done > CMake Error at CMakeLists.txt:7 (include): > include could not find load file: > > ITKModuleExternal > > > please suggest what should i do next? > Regards > Vishal > > > Configuring incomplete, errors occurred! > See also > > "C:/itk2d3d/ITKTwoProjectionRegistration-master/build/CMakeFiles/CMakeOutput.log". > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Problem-with-building-a-journal-paper-tp36557p36574.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From abenchaaben at histalim.com Mon Dec 21 10:19:05 2015 From: abenchaaben at histalim.com (abenchaaben) Date: Mon, 21 Dec 2015 08:19:05 -0700 (MST) Subject: [ITK] [ITK-users] SCIFIO ImageIO plugin In-Reply-To: References: <1450425267798-7588276.post@n2.nabble.com> <1450456479657-7588278.post@n2.nabble.com> Message-ID: <1450711145889-7588282.post@n2.nabble.com> Hi Matt McCormick-2, I tried ITK 4.9RC2 but i got the same error. The problem is this is the testing program. Normally, it's has to work without problem?? Regards. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/SCIFIO-ImageIO-plugin-tp7588276p7588282.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From suneezahanif02 at gmail.com Tue Dec 22 10:47:40 2015 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Tue, 22 Dec 2015 16:47:40 +0100 Subject: [ITK] [ITK-users] Question In-Reply-To: References: Message-ID: Hello D?enan, Thanks a lot for your help. :) I have one more question. When I applied spatial mask I got this warning and registration was not performed. *" WARNING: In ..\....\itkObjectToObjectMetric.hxx, line 529MeanSquaresImageToImageMetricv4 (00FDCC00): No valid points were found during metric evaluation. For image metrics, verify that the images overlap appropriately. For instance, you can align the image centers by translation. For point-set metrics, verify that the fixed points, once transformed into the virtual domain space, actually lie within the virtual domain."* For spatial mask is it necessary that both mask and image have same number of bits? Regards, Suneeza -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Dec 22 11:40:23 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 22 Dec 2015 11:40:23 -0500 Subject: [ITK] [ITK-users] Question In-Reply-To: References: Message-ID: On Tue, Dec 22, 2015 at 10:47 AM, suneeza hanif wrote: > Hello D?enan, > > Thanks a lot for your help. :) > > I have one more question. When I applied spatial mask I got this warning > and registration was not performed. > > > *" WARNING: In ..\....\itkObjectToObjectMetric.hxx, line > 529MeanSquaresImageToImageMetricv4 (00FDCC00): No valid points were found > during metric evaluation. For image metrics, verify that the images overlap > appropriately. For instance, you can align the image centers by > translation. For point-set metrics, verify that the fixed points, once > transformed into the virtual domain space, actually lie within the virtual > domain."* > ?You need to give initial transform which transforms the moving image so there is some overlap.? ?Mathematical formulation: l ?Local optimization methods need a to have a starting point which is inside the domain of the cost function. ? ?Take a look at this example , ?which is also included with ITK's source code. > > For spatial mask is it necessary that both mask and image have same number > of bits? > ?It is not necessary.? > > Regards, > Suneeza > > ?HTH? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Dec 22 18:57:04 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 22 Dec 2015 18:57:04 -0500 Subject: [ITK] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.9 release candidate 3 has been tagged and is available for testing! Please take this opportunity to test the new features in the release candidate. To obtain the source code, git clone http://itk.org/ITK.git cd ITK git checkout -q --detach v4.9rc03 For more details, please see the Git documentation [1]. A few selected highlights for this release: * New Remote modules: the Cuberille module for smooth generation of meshes from binary segmentation images, and the AnisotropicDiffusionLBR module improved edge-preserving smoothing. * Build your own ITK module outside the source tree, add continuous integration testing on GitHub, and easily add Python wrapping for your C++ algorithms. * Python wrapping, including Python 3, builds faster with a more standard installation * Improved performance of itk::Image::GetPixel and operations on itk::VariableLengthVector?s * Generate a FlatStructuringElement from an image * Point-set registration with time-varying B-splines * Module dependencies can now be specified as public / private / compile / test Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review. The new module dependency specification mechanism may unearth missing dependencies for projects that use ITK COMPONENTS with the CMake find_package command. An Experimental build, which demonstrates how the test suite performs on your local build system, can be submitted to the dashboard [2] with: mkdir ../ITK-build cd ../ITK-build cmake ../ITK ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit Visual Studio builds must also add ?-C Release? to the ctest command. Notify the mailing list if there are any unexpected failures. Testing your own applications against the RC is also appreciated. Congratulations and well done to the 43 contributors to this release. We would especially like to recognize the new contributors: Mikhail Isakov, Betsy McPhail, Luc Hermitte, Shawn Waldon, Tobias Wood, Ricardo Ortiz, Sreekanth Arikatla, Hyun Jae Kang, Lucas Gandel, Adam Snyder, Junjie Bai, Seun Odutola, Abhishek Tiwari, Eugene Prilepin, Zach Williamson, Alexander Leinoff, Alexis Girault, Laurentiu Nicola, Floris Berendsen, Max Smolens, and Pablo Hernandez-Cerdan. Many community members stepped up to contribute fixes for this release candidate. To allow testing and accommodate the upcoming holiday, the final release is re-scheduled for mid-January. Known issues in this release candidate, to be fixed before the final release: * TransformReadWriteTest fails on Mac OSX with shared libraries. * Mac OSX 10.6 has build errors. [1] http://www.itk.org/Wiki/ITK/Git [2] http://open.cdash.org/index.php?project=Insight New Features --------------------- * Wrapping improvements * Python 3 supported * Wrapping builds much faster due to CastXML binaries * LandmarkBasedTransformInitializer now wrapped * NumPy bridge with VisualStudio * Wrapping for the MinimalPathExtraction module * Wrapping is now installed into Python?s site-packages directory in the ?itk? package * Wrapping package size is decreased * Better package portability on Mac OSX * New Remote Modules * Cuberille * Insight Journal Article: http://hdl.handle.net/10380/3186 * AnisotropicDiffusionLBR * Insight Journal Article: http://hdl.handle.net/10380/3505 * Web browser reproducibility: http://www.kitware.com/blog/home/post/942 * Core Improvements * External Modules can now be developed outside of the ITK source tree and on GitHub * Details: http://www.kitware.com/blog/home/post/997 * New utilities in itk::Math: * AlmostEquals * NotAlmostEquals * ExactlyEquals * NotExactlyEquals * New itk::NumericTraits * IsInteger * IsSigned * Improved C++11 support * New ITK_DELETE_FUNCTION macro for ?=delete? * New ITK_NOEXCEPT macro for the ?noexcept? keyword * Improved capabilities of itk::ResourceProbe and itk::ResourceProbesCollectorBase * Improve numerical stability in VNL eigen system estimation * itksys_ios:: and itksys_stl:: have been remove (use std::) * Filtering Improvements * Generate a FlatStructuringElement from an image * WarpImageFilter support VectorImage?s * ConvertLabelMap supports different LabelMap types * ImageToPathFilter moved from the ITKReview to the ITKPath module * itk::MovingHistogramImageFilter moved to the ITKImageFilterBase module * Registration Improvements * Point-set registration with time-varying B-splines * Build Improvements * Module dependencies can now be specified as public / private / compile / test * BUILD_EXAMPLES CMake option is now OFF by default * Option to export all library symbols on Windows: * Details: http://www.kitware.com/blog/home/post/939 * Expat third party library is now name mangled * Many more modules can be built as shared libraries * KWStyle is automatically built and configured when tests are built * Performance Improvements * New MetaProgrammingLibrary namespace (itk::mpl) holds members for metaprogramming * itk::mpl::{TrueType,FalseType} * itk::mpl::{If,Not,And,Or,Xor} * itk::mpl::EnableIf * itk::mpl::IsBaseOf * itk::mpl::IsConvertible * itk::mpl::IsNumber * itk::mpl::IsSame * itk::mpl::PromoteType * Image::GetPixel performance improvements * Many itk::VariableLengthVector performance improvements * AdaptiveHistogramEqualization uses a moving histogram * WarpImageFilter performance improvements * Documentation Improvements * Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples * ITK Software Guide improvements * How to use Python wrapping * How to create an ITK module * Improvements to segmentation examples * Expanded Canny edge detection example * Expanded tree container example * Third Party Library Updates * FFTW updated to latest upstream * Build with recent OpenCV 2 and 3 * Build with the latest VTK * PNG update to the latest upstream * GDCM updated to the latest upstream * KWSys updated to the latest upstream * MINC updated to the latest upstream * SWIG updated to the latest upstream * Third party PNG and MINC are now Git subtrees * Style improvements -- ITK gets more stylish with every release! * Private copy constructors and operator= use ITK_DELETE_FUNCTION * Improved code coverage -- we are at 84.9%! * *Lots* of important bug fixes * And much more! See details in the log below. Changes from v4.9rc02..v4.9rc03 ------------------------------------------------ Alexis Girault (1): BUG: Implement SetAutoMinimumMaximum in itkScalarImageToHistogramGenerator Bill Lorensen (1): BUG: nifti_read_subregion_image was leaking file pointers Brad King (7): ENH: Teach ITK module macros to support independent header-only modules ENH: Add script to import KWIML library source code ENH: Add `ITKKWIML` module to provide external KWIML library ENH: Port TIFF integer types from KWSys to KWIML ENH: Port LSM integer types from KWSys to KWIML ENH: Port itkIntTypes.h from KWSys to KWIML ENH: Drop KWSys FundamentalType component Bradley Lowekamp (1): ENH: Add option to choose scheme for git download Davis Vigneault (1): STYLE: Use cstdlib return macros in ITK examples D?enan Zuki? (3): BUG: do not pass 0,0,0 to Versor.Set() STYLE: Removing the unused NeighborhoodRadius property ENH: Write out transform in DeformableRegistration15 Gert Wollny (1): BUG: Remove double-conversion from public interface, use system. Hyun Jae Kang (8): ENH: Use a data struct to export the system information of a probe. ENH: Create a test for the SpawnThread function ( ITK-3317) STYLE: Remove an unnecessary file (-w) from source code BUG: Fixed the failed case of itkStdStreamStateSaveTest on OS X 10.8 BUG: Fixed the failed test case of itkThreadPoolTest on OS X 10.8 BUG: Fixed a failed test of ITKDistanceMapTestDriver BUG: Fixed the failed test VideoSourceTest PERF: Improve the performance of a test of ITKRegistrationMethodsv4TestDriver COMP: Fixed the compiler error of itkDisplacementFieldToBSplineImageFilterTest Jean-Christophe Fillion-Robin (25): BUG: Build ITKIOTransformHDF5 as shared library. See #3393 BUG: Build ITKIOTransformMINC as shared library. See #3393 BUG: Build ITKIOTransformMatlab as shared library. See #3393 BUG: Build ITKIOTransformInsightLegacy as shared library. See #3393 STYLE: TransformIOFactory: Remove obsolete declaration. See #3393 COMP: TransformIOFactory: Add missing ctor/dtor from hxx file. See #3393 COMP: TransformFileWriter: Remove method "OpenStream()" without definition COMP: TransformFileReaderTemplate: Remove undefined method "CreateTransform()" ENH: Update ITKIOPhilipsREC to allow static initialization. See #3393 ENH: Update ITKIOTransformMINC to allow static initialization. See #3393 COMP: MINC: Fix VS2008 "unknown round" build error. See #3393 COMP: MINC: Fix VS2008 "unknown arpa/inet.h" build error. See #3393 COMP: Configure ENABLE_SHARED into .cmake file. See #3393 COMP: Fix configuration of IOFactory header. See #3393 STYLE: UseITK: Removed redundant code setting ImageIO factory name. See #3393 STYLE: UseITK: Re-factor introducing _configure_IOFactoryRegisterManager STYLE: UseITK: Set TransformIO factory and module name using convention. BUG: Ensure Image IO factories are registered once. See #3393 BUG: Ensure Transform IO factories are registered once. COMP: ITKIOXML: Fix VS11 "already defined std::string" link error. See #3393 BUG: TransformIO: Implement explicit template instantiation using "extern". COMP: TransformIO: Fix VS build errors removing extra EXPORT COMP: TransformIO: Handle compiler not supporting "pragma diagnostic". COMP: TransformIO: TransformFile(Reader|Writer) still need to be exported. COMP: TransformIO: Fix explicit instantiation approach Johan Andruejol (1): ENH: Add ITK_RUNTIME_LIBRARY_DIRS for external projects KWIML Upstream (1): KWIML 2015-12-09 (43f9f8d0) Lucas Gandel (1): BUG: PhysicsBasedNonRigidRegistrationMethod test failure on Debian 32bit Matthew McCormick (16): COMP: Fix PointDimension reference in AzimuthElevationToCartesian test. STYLE: Improve scoping in AzimuthElevationToCartesian test. STYLE: Explicitly mark the ProcessObject methods virtual in SignedMaurer. BUG: Do not try to install targets that do not exist when building externally. BUG: ITKIOMeta needs a public dependency on ITKMetaIO. COMP: Update LesionSizingToolkit for external build and style test failures. BUG: Add CMake OpenCV export code to ITKVideoBridgeOpenCV. COMP: Improve compatibility with OpenCV 3. DOC: Fix class references in StatisticsLabelMapFilter. STYLE: Improved readability of itkStatisticsUniqueLabelMapFilterTest1. DOC: Correct ReverseOrdering description in ShapeUniqueLabelMapFilter. STYLE: Add own copy of GenerateExportHeader COMP: Create _TEMPLATE_EXPORT macros. COMP: TransformIOBaseTemplate must be explicitly instantiated. BUG: Do not use dynamic_cast for DisplacementFieldType in HDF5 test. COMP: Do not use string(MAKE_C_IDENTIFIER with CMake < 2.8.12 Max Smolens (1): BUG: VoronoiSegmentationRGBImageFilter: add pixel dimension check Mikhail Isakov (1): DOC: correction in DiffusionTensor3D Reconstruction Ricardo Ortiz (1): BUG: Set itkBinaryImageTo*LabelMapFilter foreground/background values Seun Odutola (1): BUG: absolute value of tolerance taken to cater for negative spacing Shawn Waldon (1): COMP: OSX set deployment target when building fftw Simon Alexander (4): STYLE: Change to make git bash on windows happy with the function name COMP: fixes for visual studio 2015update1 x86 in release mode COMP: fixes for visual studio 2015update1 x86 in release mode COMP: fixes for visual studio 2015update1 x86 in release mode Sreekanth Arikatla (2): BUG: Resolved const correctness in itkMatrix.h ENH: Fixes the symmetry of AzimuthElevationToCartesianTransform and adds tests Changes from v4.9rc01..v4.9rc02 ------------------------------------------------ Bill Lorensen (1): BUG: Valgrind detected an invalid read Davis Vigneault (1): STYLE: Address some warnings when running cppcheck Hyun Jae Kang (2): COMP: Fixed a warning message of data-conversion on VS14 COMP: Update KWStyle to remove format-string warning message Matthew McCormick (3): DOC: Remove invalid wrapping example. BUG: Wrap AdaptiveEqualizationHistogram. COMP: Ignore Doxygen endcond warning in itkIsConvertible.h. Seun Odutola (1): COMP: Corrected minc2.h path installation from libsrc2/minc2.h to minc2.h Ziv Yaniv (2): BUG: Affine transformation was estimated without sufficient number of points. BUG: fixed BSpline initializer crash when reference image not set. Changes from v4.8.0..v4.9rc01 -------------------------------------------- Abhishek Tiwari (1): BUG: "tmpImageIndex" not initialized to 0. Adam Snyder (1): PERF: Reworked MMI Threading using a per-thread buffer Alexander Leinoff (6): ENH: Adds IsInteger and IsSigned to NumericTraits. COMP: Doxygen itkMath.h 'OneValue()' could not be resolved. ENH: Adds ExactlyEquals and NotExactlyEquals functions to itkMath.h COMP: Removes floating-point equality checks ENH: COMP: Adds support for complex values to Math::AlmostEquals ENH: Updates fftw dependency Arnaud Gelas (5): COMP: fix warning (unused local typedef) COMP: simplify ITKVideoBridgeOpenCV dependency DOC: add doxgen documentation for BinaryImageToLevelSetImageAdaptor ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner COMP: fix compilation error with OpenCV2 and OpenCV3 Betsy McPhail (1): BUG: Improve buffer alignment in OctreeNode . Bill Hoffman (2): ENH: Use new CMake Windows export symbol dll feature. COMP: Put vnl_export.h in the list of sources so it gets installed. Bill Lorensen (4): COMP: VTkGlue linker errors BUG: Inappropriate use of AlmostEquals ENH: Bump tag for wiki examples ENH: Better layout strategy Brad King (3): ENH: Remove use of include and itksys_ios::* ENH: Remove use of include and itksys_stl::* ENH: Update CMake Policy settings in Testing/TestExternal project Bradley Lowekamp (31): BUG: Avoid null deference in PrintSelf with default construction ENH: Enable base classes for templates of landmark initializer STYLE: Use "Swap" for ITK member name BUG: Demonstrate Eigen analysis failure BUG: Fix computation of Eigen analysis ENH: Update DiscreteHessianGaussian Test baseline ENH: Correctly demonstrate float point Eigen failure ENH: compile vnl_math_hypot, and use at least double ENH: Adding initial update script from used libpng version. ENH: removing non-subtree files for itkpng ENH: Ported ITK changes for building to subtree merged code ENH: Update libpng update script for v1.6.9 BUG: Use ParameterValueType for computation of landmark affine ENH: Wrap LandmarkBasedTransformInitializer BUG: Avoid potential exception in itk::Object::UnRegister ENH: Update itkpng zlib, configuration, and rename ENH: Update itkpng name mangling BUG: Use const pointer in Set method for constant ReferenceImage ivar BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod BUG: Demonstrate side effect on registration due to BSplineScatter change ENH: Move MovingHistogramImageFilter base classes to ImageFilterBase BUG: Avoid potential exception in itk::Object::UnRegister BUG: Avoid null deference in PrintSelf with default construction BUG: Use const pointer in Set method for constant ReferenceImage ivar ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram base COMP: address sign unsigned comparison warning COMP: Address signed unsigned comparison warning COMP: Address unused member variable and methods in anonymous ns BUG: Fix segfault when with empty IsolatedWatershed Threshold range BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test BUG: Reduce number of targets with MSVC Davis Vigneault (7): DOC: Minor improvements to segmentation examples. DOC: Expanded Canny Edge Detection Example DOC: Expanded TreeContainer Example COMP: Warnings in itkVTKImageExport when compiling with c++11 COMP: Warnings in FFTW Classes when compiling with c++11 COMP: Update Git Tag for Subdivision Module COMP: Warnings in FFTW Classes when compiling with c++11 D?enan Zuki? (1): STYLE: better formatting of the "usage" message Eugene Prilepin (1): BUG: Fix a template name formation in python wrappings Floris Berendsen (1): STYLE: Improve naming conventions in comments. Hans Johnson (29): STYLE: Instrument for FixedParameters typedef BUG: Demonstrate DisplacementTransformFailure BUG: FixedParameters should be double precision STYLE: Minor code style issues for MGHIO COMP: Update to version for WikiExamples ENH: Update Sphinx for ITK 4.8.0 ENH: Update MGHIO to be shared lib ENH: Provide consistent floating point comparisons BUG: Fix MGHIO to fix write failures PERF: Remove floating point as sentinal value COMP: Const correctness needs to be maintained BUG: Preserve backwards compatibility DOC: Provide consistent naming in comments ENH: Conversion between transform type tolerance STYLE: Prefer initialization to assignment ENH: Missing ITK_OVERRIDE COMP: Need to propagate ITKGDCM COMP: Need to propagate ITKGDCM COMP: Add missing ITK_OVERRIDE STYLE: Minor code style issues for MGHIO COMP: Update to version for WikiExamples ENH: Update Sphinx for ITK 4.8.0 ENH: Update MGHIO to be shared lib BUG: Fix MGHIO to fix write failures ENH: C++11 allows for rigorous =delete COMP: Remove unnecessary failing assert test ENH: Ignore internal files for the Clion editor COMP: Fix VNL compilation for wider C++11 support BUG: In configuration test need to mirror code Hyun Jae Kang (27): BUG: Remove std::cout calls from class BUG: Avoid an unexpected output of static_cast BUG: Update python example codes for ImageRegistration BUG: Retrieve the missed wrap file BUG: itkVTKImageIO class does not handle blank lines in VTK file header. BUG: Fix HDF5 CMake configuration with VS2015 BUG: Fix a compilation issue on ITK4 with FFTW and shared libraries BUG: Fixed older XCode linking error ENH: Use CastXML binaries when building with x86_64 Mac OS X BUG: Remove std::cout calls from class BUG: itkVTKImageIO class does not handle blank lines in VTK file header. BUG: Fixed older XCode linking error ENH: Add automatic KWStyle build and configuration setup COMP: KWStyle shadow, format-nonliteral and autological-compare warning. COMP: Fixed the warning messages from itkGPU Module COMP: Fixed a warning message of unused-private-field COMP: Apply latest version of KWStyle COMP: Update KWStyle to fix its additional warning messages COMP: Update KWStyle to fix its additional warning messages COMP: Fix data-conversion warning messages on Windows ENH: Update itkResourceProbe to calculate statistical data COMP: Fix data-conversion warning messages on VS14 COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function ENH: Update the Report() function of itkResourceProbesCollectorBase COMP: Fix data-conversion warning message on itkResourceProbe COMP: Fix additional warning messages of KWStyle COMP: Fix data-conversion warning messages Jon Haitz Legarreta (6): ENH: Add test for itkStatisticsUniqueLabelMapFilter BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter BUG: Test for StatisticsUniqueLabelMapFilter stability ENH: Add test for itkParametricStpaceToImageSpaceFilter ENH: Improve code coverage for itkParametricSpaceToImageSpaceMeshFilter Julien Michel (1): ENH: Support of VectorImage as template parameters for WarpImageFilter Junjie Bai (2): BUG: ConvertLabelMap with different LabelMapTypes BUG: LabelObject CopyAttribute support different LabelObject type KWSys Robot (4): KWSys 2015-07-10 (c9336bcf) KWSys 2015-07-30 (f63febb7) KWSys 2015-08-24 (cdaf522c) KWSys 2015-08-28 (dc3fdd7f) LIBPNG Upstream (2): PNG 2009-04-06 (e68f5a36) PNG 2014-02-05 (3e753eb8) Laurentiu Nicola (2): PERF: Avoid temporary smartptr in ProcessObject::GetInput PERF: Optimize WarpImageFilter by avoiding refcount bouncing Luc Hermitte (8): PERF: itk::Image::GetPixel() performance improvment. PERF: Performance enhancements on VariableLengthVectors 1/... ENH: Dependencies on itkVariableLengthVector.h reduced BUG: Error in VariableLengthVector Unit Tests PERF: Performance enhancements on VLV 2/... PERF: Performances enhancements on VLV 3/... COMP: Fix signed/unsigned warnings BUG: std::copy/fill on empty VLV Lucas Gandel (4): ENH: Move ImageToPathFilter from ITKReview to ITKPath module. BUG: Fixing ImageToPathFilter wrapping call from Review Module STYLE: Fix KWStyle dashboard errors BUG: Fix external module BUILD_SHARED_LIBS status Mathieu Malaterre (1): BUG: Name mangle the included expat third party library. Matthew McCormick (94): ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest. ENH: Add AnisotropicDiffusionLBR Remote Module. ENH: Bump ITK version to 4.9.0. BUG: Remove std::cout calls from classes. COMP: Remove unused argument in ConditionVariableNoThreads. BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. COMP: Add link interface specification for wrapping target_link_libraries. STYLE: Fix indentation in itkMINCTransformIOFactory.cxx. COMP: Fix MINCTransformIO factory registration. COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1. COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR. BUG: Initialize mutex for 32 bit AtomicInt. ENH: Use CastXML binaries when building with x86_64 Linux. STYLE: Rename gccxml -> castxml in {idx,igenerator}.py. COMP: Disable the gold linker for static builds on Ubuntu 14.04. ENH: Use Windows binaries for CastXML. ENH: Add better scoping in igenerator.py. BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC. BUG: LevelSetsv4 used signed char instead of char. ENH: Add better scoping to idx.py. COMP: Define newSize and oldSize in VariableLengthVector. STYLE: Use prefix increment operator in ImageBase. DOC: Correct spelling of Continuous. ENH: Add more progress information to IterativeClosestPoint2. BUG: Build BridgeNumPy with Visual Studio. ENH: Add ITKModuleExternal.cmake COMP: Wrap Image< bool, D > for FlatStructuringElement. BUG: Use CastXML binary built in Release. BUG: ContinuousIndex should not be templated over TCoordRep. COMP: Set CMP0054 to new. COMP: Address line length too long for Software Guide. COMP: Fix CannyEdgeDetectionImageFilter.cxx types. BUG: Support Python 3 wrapping module initialization. BUG: Update itkTemplate.py for Python 3. BUG: Update itkExtras.py for Python 3. BUG: Prevent Python callback addition recursion. BUG: Fix test scripts for Python 3. BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. ENH: Allow projects to build against an external module. ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER. ENH: Rename _cable_ to _wrappers_. BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. BUG: Define ITK_WRAPPING_PARSER when wrapping. COMP: Do not use C++11 alignas in itkAlignedTypedef. ENH: Bump CMakeLists.txt version to 4.8.1. BUG: Pass the CMAKE_CXX_FLAGS to castxml. ENH: Bump CastXML version to 2015-30-29. ENH: Bump LLVM / Clang to 3.7.0. COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5. COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC. COMP: Use itkSimpleNewMacro in ThreadedIteratorRangePartitionerTest. ENH: Add wrapping support for building modules externally. BUG: Fix KWStyle test paths when building a module externally. ENH: Add Cuberille Remote module. COMP: Remove carriage returns from Cuberille remote. COMP: Remove unused argument in ConditionVariableNoThreads. DOC: Correct spelling of Continuous. ENH: Bump the MinimalPathExtraction Remote to 2015-10-20. COMP: Fix KernelTransform SetFixedParameters argument type. STYLE: Use prefix increment operator in ImageBase. COMP: Use ITK's pygccxml by correctly setting up the sys.path Revert "COMP: Put vnl_export.h in the list of sources so it gets installed." BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes" ENH: Marking wrapping CMake configuration variables as advanced. STYLE: Rename CASTXML to CASTXML_EXECUTABLE. COMP: Non-virtual copy attribute members in LabelMap cannot have override. COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter. COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT. ENH: Remove CMake version check in ITKModuleHeaderTest.cmake BUG: Improve KWStyle ExternalProject utilization. ENH: Remove old KWStyle build script. COMP: Address VariableLengthVector Doxygen rhs @param not found. ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER. ENH: Install Python bindings into site-packages. ENH: Improve readability of Python site-packages path detection. COMP: DiscreteGaussianDerivativeImageFilter unsigned expression warning. BUG: ITKCommon publically depends on ITKDoubleConversion. COMP: Improve scoping in CovariantVectorGeometryTest. ENH: Improves names and export of module dependencies. STYLE: Improve namespace bracket style in itkIsConvertible. COMP: Set CMP0054 to new. BUG: Remove unused wrapping files. BUG: Do install install wrapping development files. ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. BUG: Remove duplicate inclusion of wrapping submodules. COMP: Do not use C++ style comments for Doxygen cond. BUG: Fix detection of the gold linker. BUG: Update Python package installation locations. ENH: Bump CMakeLists.txt version to 4.8.2. ENH: Change BUILD_EXAMPLES default to OFF. BUG: Use 'from itk import ITKCommon' in module2module test. COMP: Link to VTK Python when built with Kits support. BUG: Install itk_minc2.h header. COMP: ITKIOMINC has a public dependency on ITKIOImageBase. Michka Popoff (9): ENH: Update to swig 3.0.7 ENH: Do not link against specific Python library on OS X COMP: Fix wrapping warnings when building with ITK_WRAP_IMAGE_DIMS=2 COMP: Add missing wrapping for TransformBase COMP: Use ITK's pygccxml by correctly setting up the sys.path COMP: Disable incompatible modules when using Python 3 wrapping COMP: Move MovingHistogramImageFilterBase wrapping to ImageFilterBase module COMP: Disable incompatible modules when using Python 3 wrapping ENH: Allow operations on Indexes and Offsets in Python Mikhail Isakov (1): BUG: DiffusionTensor3DReconstruction segfault if no baseline image Nick Tustison (5): BUG: Set a default b-spline epsilon. ENH: Adding testing for closed loop. BUG: Updating B-spline classes with the same epsilon strategy. PERF: Switch vnl_vectors for fixed arrays. ENH: Point-set registration with time-varying B-spline. Olivier Commowick (3): BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen system BUG: Correct under/overflows in vnl_math_hypot (taken from pythag from V3P) BUG: Switch eigenvalues computation to double Pablo Hernandez-Cerdan (2): ENH: Help class for itkFlatStructuringElement with constructor from images. COMP: Fix test errors and warnings in FlatStructuringElement. Seun Odutola (1): COMP: Fixed name clash with Apple header (check Macro), renamed check to Check Shawn Waldon (1): COMP: Set target OS X version in environment for tools using compiler Simon Alexander (1): BUG: incorrect closest point computation Tobias Wood (2): BUG: LBFGSB was printing messages even with debug switched off. BUG: Removed an unguarded print statement. Vladimir S. FONOV (9): BUG: Missing ITKIOMINC_EXPORT on __Private() COMP: Changing the order of HDF5 library components COMP: Splitting up IOMINC module into two parts: MINC and Transform STYLE: updated comments to properly reference LIBMINC ENH: Add script to merge upstream MINC as a subtree MINC 2015-07-23 (c033d431) COMP: Update MINC CMake code MINC 2015-08-18 (6d7e3ba8) MINC 2015-09-13 (95cd5374) Xiaoxiao Liu (1): DOC: update email address for xiaoxiao. Zach Williamson (10): BUG: Use correct libraries for ImageFusion tests ENH: Consolidate Library Dependencies COMP: Add a missing link to Review module COMP: Use correct linking macro in DCMTK BUG: Use correct libraries for TestKernel tests COMP: Fix inconsistant naming of GPUPDEDeformableRegistration ENH: Use new linking system macros PERF: Avoid searching private dependencies for include directories COMP: Recover missing dependencies ENH: use new linking macros in Filtering module ----------------------------------------------------- Errors or omissions? Please fix them here: https://docs.google.com/document/d/1j3IAZFfi0ToO8N6hTr0fVTTMmHIMkXAxx0AsAajsYuM/edit From matt.mccormick at kitware.com Tue Dec 22 19:53:03 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 22 Dec 2015 19:53:03 -0500 Subject: [ITK] [ITK-dev] Merging to ITK master for 4.10 Message-ID: Hi folks, Thanks to everyone who helped clean up the dashboard for the 4.9 release. We are getting back to our "happy place" -- the land of green dashboard wonderfulness. There were many of fixes for 4.9RC3. Unfortunately, we did not make the target release date. However, the dashboard is in good enough condition to confidently make the final release, apart from a few outstanding issues. I have collected known issues in the issue tracker with the tag "20151214_ITKv4.9.0_FINAL": https://issues.itk.org/jira/issues/?jql=fixVersion%20%3D%20%2220151214_ITKv4.9.0_FINAL%22%20AND%20project%20%3D%20ITK%20AND%20resolution%20%3D%20Unresolved%20ORDER%20BY%20priority%20DESC If there are other issues to address, please add them there. Since the dashboard is getting back into shape, we should be able to merge enhancements for 4.10. Please branch fixes for 4.9 off the release branch and make a note in Gerrit so they can be merged into the release branch. As always, please help keep the dashboard in a clean state so regressions do not progressively accumulate. Thanks, Matt _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From zhuangming.shen at sphic.org.cn Tue Dec 22 20:41:04 2015 From: zhuangming.shen at sphic.org.cn (=?utf-8?B?5rKI5bqE5piO?=) Date: Wed, 23 Dec 2015 01:41:04 +0000 Subject: [ITK] [ITK-users] Strange situation when ITK writes DICOM file Message-ID: <1450834862664.8600@sphic.org.cn> Hi all, I met a very strange situation when I used ITK 4.8.1. I'd like to read a DICOM series, write it to a DICOM file (i.e. save the volume created by the DICOM series to a .dcm file), and read the DICOM file. Theoretically, the DICOM series and the DCM file should have the same information, e.g origin, spacing, size. However, My results show me that the information has been changed. When I use other ITK-support file format (e.g. nii, nrrd), the information has not been changed. It seems a bug. My code and results are listed as below. Has anyone met the same situation? Regards, Zhuangming Shen ? ================ My code ================= import itk input_dir = "/home/zshen/workspace/Data/testDCM/bbb" output_filename = "/home/zshen/workspace/Data/bbb2.dcm" # read DICOM series dicom_io = itk.GDCMImageIO.New() reader = itk.ImageSeriesReader[itk.Image.SS3].New() reader.SetImageIO(dicom_io) name_generator = itk.GDCMSeriesFileNames.New() name_generator.SetUseSeriesDetails(True) name_generator.SetDirectory(input_dir) series_uid = name_generator.GetSeriesUIDs() series_identifier = series_uid[0] file_names = name_generator.GetFileNames(series_identifier) reader.SetFileNames(file_names) reader.Update() print("**** series DICOM information: *****") print("size: "+str(reader.GetOutput().GetLargestPossibleRegion().GetSize())) print("origin: "+str(reader.GetOutput().GetOrigin())) print("spacing: "+str(reader.GetOutput().GetSpacing())) writer = itk.ImageFileWriter[itk.Image.SS3].New() writer.SetInput(reader.GetOutput()) writer.SetFileName(output_filename) writer.Update() # read again reader2 = itk.ImageFileReader[itk.Image.SS3].New() reader2.SetFileName(output_filename) reader2.Update() print("**** DICOM information: *****") print("size: "+str(reader2.GetOutput().GetLargestPossibleRegion().GetSize())) print("origin: "+str(reader2.GetOutput().GetOrigin())) print("spacing: "+str(reader2.GetOutput().GetSpacing())) ================= My results ==================== **** series DICOM information: ***** size: itkSize3 ([512, 512, 118]) origin: itkPointD3 ([-229.5, -96.5, -553]) spacing: itkVectorD3 ([0.896484, 0.896484, 3]) **** DICOM information: ***** size: itkSize3 ([512, 512, 118]) origin: itkPointD3 ([0, 0, 0]) spacing: itkVectorD3 ([0.896484, 0.896484, 1]) -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From Victor.Poughon at cnes.fr Wed Dec 23 05:47:32 2015 From: Victor.Poughon at cnes.fr (Poughon Victor) Date: Wed, 23 Dec 2015 10:47:32 +0000 Subject: [ITK] [ITK-users] iterator IsAtBegin method not const Message-ID: <3E55146A6A81B44A9CB69CAB65908CEA0D951501@TW-MBX-P01.cnesnet.ad.cnes.fr> Hello all, I am working with iterators currently, and I am wondering if there is a reason why in itk::ImageReverseConstIterator the IsAtBegin() and IsAtEnd() methods are not const? Because they are in other iterators, for example itk::ImageConstIterator. Thanks, Victor Poughon -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From marco.dev.open at gmail.com Wed Dec 23 09:30:25 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Wed, 23 Dec 2015 18:00:25 +0330 Subject: [ITK] [ITK-dev] itk and vtk for NDK Message-ID: Hi, is there any reference or example source code for building itk and vtk for Android with NDK ? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check 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 suneezahanif02 at gmail.com Wed Dec 23 09:39:50 2015 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Wed, 23 Dec 2015 15:39:50 +0100 Subject: [ITK] [ITK-users] Image Registration Message-ID: Hello Everyone, I want to monitor my registration process. I want to extract transformation parameters after each iteration and use them to create intermediate image. I don't know how to use these parameter generated through command/observer method by calling *"optimizer->GetCurrentPosition()". * Is there any way that I can get transformation parameters and use them further after each iteration? Thank you. Best Regards, Suneeza -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From suneezahanif02 at gmail.com Wed Dec 23 09:45:31 2015 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Wed, 23 Dec 2015 15:45:31 +0100 Subject: [ITK] [ITK-users] Question In-Reply-To: References: Message-ID: Hello D?enan, The problem was that my images were in float and the mask I generated was in unsigned char. So in registration process, no overlapping region was found. When I changed my image type and mask type to unsigned short it worked then. Best Regards, Suneeza On Wed, Dec 23, 2015 at 3:27 PM, D?enan Zuki? wrote: > Hi Suneeza, > > maybe you should explain what was the problem, so if someone else comes > across this thread it can help him. > > Regards > > On Wed, Dec 23, 2015 at 6:07 AM, suneeza hanif > wrote: > >> Hello D?enan, >> >> Finally It worked. I am really grateful for your help. >> >> Best Regards, >> Suneeza >> >> On Wed, Dec 23, 2015 at 11:05 AM, suneeza hanif > > wrote: >> >>> Hello D?enan, >>> >>> I have three images fixed image , mask image and moving image. If I >>> remove mask image and perform registration it works fine. But if add mask >>> image it generates this sort of warning and does not perform registration. >>> So I need to align mask image with moving image or fixed image? >>> >>> Secondly If I run same code with images (.png) provided in the example >>> it works fine. Images I am using are dicom images and in this case it does >>> not work. >>> >>> Thanks in advance. >>> >>> Best Regards, >>> Suneeza >>> >>> On Tue, Dec 22, 2015 at 5:40 PM, D?enan Zuki? wrote: >>> >>>> >>>> On Tue, Dec 22, 2015 at 10:47 AM, suneeza hanif < >>>> suneezahanif02 at gmail.com> wrote: >>>> >>>>> Hello D?enan, >>>>> >>>>> Thanks a lot for your help. :) >>>>> >>>>> I have one more question. When I applied spatial mask I got this >>>>> warning and registration was not performed. >>>>> >>>>> >>>>> *" WARNING: In ..\....\itkObjectToObjectMetric.hxx, line >>>>> 529MeanSquaresImageToImageMetricv4 (00FDCC00): No valid points were found >>>>> during metric evaluation. For image metrics, verify that the images overlap >>>>> appropriately. For instance, you can align the image centers by >>>>> translation. For point-set metrics, verify that the fixed points, once >>>>> transformed into the virtual domain space, actually lie within the virtual >>>>> domain."* >>>>> >>>> ?You need to give initial transform which transforms the moving image >>>> so there is some overlap.? >>>> >>>> ?Mathematical formulation: l >>>> ?Local optimization methods need a to have a starting point which is >>>> inside the domain of the cost function. ? >>>> ?Take a look at this example >>>> , >>>> ?which is also included with ITK's source code. >>>> >>>>> >>>>> For spatial mask is it necessary that both mask and image have same >>>>> number of bits? >>>>> >>>> ?It is not necessary.? >>>> >>>>> >>>>> Regards, >>>>> Suneeza >>>>> >>>>> >>>> ?HTH? >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From itkhelpacc at gmail.com Thu Dec 24 02:12:57 2015 From: itkhelpacc at gmail.com (vishal) Date: Thu, 24 Dec 2015 00:12:57 -0700 (MST) Subject: [ITK] [ITK-users] Problem with building a journal paper In-Reply-To: References: <1450252933520-36557.post@n7.nabble.com> <1450507194690-36574.post@n7.nabble.com> Message-ID: <1450941177578-36584.post@n7.nabble.com> Hi Matt, Thank you for helping me out.. ur advice help me a lot... I have tried a way that allows me to run the code [1] https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration in ITK 4.6. i followed the steps given in this site [2]http://www.itk.org/Wiki/ITK/Release_4/Modularization/Add_an_external_module_(external_module) I going to explain the process so that it help anyone else who is having a similar problem... step1) download the zip file from [1] step2) extract and paste it into it source file directory C:\ITK\Source\InsightToolkit-4.6.0\Modules\External step3) then run cmake gui..paste the source directory path and build directory path as usual step4) click configure.. once configure is complete... in advanced..search for the Module_ITKTwoProjectionRegistration-master and CHECK it... step 5) then on the same process as for build itk (click generate, all build) after one should be able to build the code in [1] *BUT im having a DOUBT.*.. when running the code i found that it takes a long time abt 1 hour to completer the registration.. is this normal? Im going to try it with ITK 4.9 once.. before that anyone please clarify my doubt..?? regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Problem-with-building-a-journal-paper-tp36557p36584.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hanacherif62 at gmail.com Thu Dec 24 09:21:53 2015 From: hanacherif62 at gmail.com (Hana Cherif) Date: Thu, 24 Dec 2015 15:21:53 +0100 Subject: [ITK] [ITK-users] RGB D images Message-ID: Hello all,, How can i manipulate rgb d images in itk please !! Best regards -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Dec 24 11:42:08 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 24 Dec 2015 11:42:08 -0500 Subject: [ITK] [ITK-users] RGB D images In-Reply-To: References: Message-ID: Hi Hana, have you tried using RGBA pixel type and treating alpha as depth? You could also use 4-dimensional covariant vector as pixel type for an itk::Image. An example usage can be found here: http://www.itk.org/Wiki/ITK/Examples/SimpleOperations/Transparency HTH, D?enan On Thu, Dec 24, 2015 at 9:21 AM, Hana Cherif wrote: > Hello all,, > > How can i manipulate rgb d images in itk please !! > > Best regards > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Dec 24 11:44:17 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 24 Dec 2015 11:44:17 -0500 Subject: [ITK] [ITK-users] Image Registration In-Reply-To: References: Message-ID: Hi Suneeza, doesn't transform->SetParameters() do what you want? HTH, D?enan On Wed, Dec 23, 2015 at 9:39 AM, suneeza hanif wrote: > Hello Everyone, > > I want to monitor my registration process. I want to extract > transformation parameters after each iteration and use them to create > intermediate image. I don't know how to use these parameter generated > through command/observer method by calling *"optimizer->GetCurrentPosition()". > * > > Is there any way that I can get transformation parameters and use them > further after each iteration? > > Thank you. > > Best Regards, > Suneeza > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Fri Dec 25 12:44:41 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 25 Dec 2015 12:44:41 -0500 Subject: [ITK] [ITK-users] Strange situation when ITK writes DICOM file In-Reply-To: <1450834862664.8600@sphic.org.cn> References: <1450834862664.8600@sphic.org.cn> Message-ID: ?I have confirmed this bug and entered it into tracker along with a DICOM series which reproduces it.? Thanks Shen On Tue, Dec 22, 2015 at 8:41 PM, ??? wrote: > Hi all, > > > I met a very strange situation when I used ITK 4.8.1. I'd like to read a > DICOM series, write it to a DICOM file (i.e. save the volume created by the > DICOM series to a .dcm file), and read the DICOM file. Theoretically, the > DICOM series and the DCM file should have the same information, e.g origin, > spacing, size. However, My results show me that the information has been > changed. When I use other ITK-support file format (e.g. nii, nrrd), the > information has not been changed. It seems a bug. My code and results are > listed as below. Has anyone met the same situation? > > > Regards, > > > Zhuangming Shen > > > > ? > > ================ My code ================= > > > import itk > > input_dir = "/home/zshen/workspace/Data/testDCM/bbb" > output_filename = "/home/zshen/workspace/Data/bbb2.dcm" > > # read DICOM series > dicom_io = itk.GDCMImageIO.New() > > reader = itk.ImageSeriesReader[itk.Image.SS3].New() > reader.SetImageIO(dicom_io) > > name_generator = itk.GDCMSeriesFileNames.New() > name_generator.SetUseSeriesDetails(True) > name_generator.SetDirectory(input_dir) > > series_uid = name_generator.GetSeriesUIDs() > > series_identifier = series_uid[0] > > file_names = name_generator.GetFileNames(series_identifier) > > reader.SetFileNames(file_names) > reader.Update() > > print("**** series DICOM information: *****") > print("size: > "+str(reader.GetOutput().GetLargestPossibleRegion().GetSize())) > print("origin: "+str(reader.GetOutput().GetOrigin())) > print("spacing: "+str(reader.GetOutput().GetSpacing())) > > writer = itk.ImageFileWriter[itk.Image.SS3].New() > writer.SetInput(reader.GetOutput()) > writer.SetFileName(output_filename) > writer.Update() > > # read again > reader2 = itk.ImageFileReader[itk.Image.SS3].New() > reader2.SetFileName(output_filename) > reader2.Update() > > print("**** DICOM information: *****") > print("size: > "+str(reader2.GetOutput().GetLargestPossibleRegion().GetSize())) > print("origin: "+str(reader2.GetOutput().GetOrigin())) > print("spacing: "+str(reader2.GetOutput().GetSpacing())) > > > ================= My results ==================== > **** series DICOM information: ***** > size: itkSize3 ([512, 512, 118]) > origin: itkPointD3 ([-229.5, -96.5, -553]) > spacing: itkVectorD3 ([0.896484, 0.896484, 3]) > **** DICOM information: ***** > size: itkSize3 ([512, 512, 118]) > origin: itkPointD3 ([0, 0, 0]) > spacing: itkVectorD3 ([0.896484, 0.896484, 1]) > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jan.witowski at student.uj.edu.pl Sun Dec 27 10:20:38 2015 From: jan.witowski at student.uj.edu.pl (Jan Witowski) Date: Sun, 27 Dec 2015 15:20:38 +0000 Subject: [ITK] CT liver segmentation Message-ID: Hello, I am working with CT abdomen images and trying to segmentate the liver (liver itself, vessels and the HCC tumor). I managed to do it using OsiriX which was rather manual segmentation, and now I am working to do the same using more accurate and semi-automatic algorithms with usage of SimpleITK. I don?t really have much experience with ITK and image manipulation which is why I ask you guys for some help. Currently, I want to try the watershed method. I loaded my DICOM series, ran the GradientMagnitude filter and proceeded with MorphologicalWatershed (using arg Level=17, value chosen manually). I got pretty nice output image, I guess: http://jwitowski.com/content/images/2015/12/WSsegmentation-4469-0.jpg But now, the question is - how do I take that liver out of the image above? My best guess is, I should run a region growing segmentation. I tried to do that, but - no matter what parameters I choose - I always get the all-black image as an output. The whole image is black. I tried different thresholds and other starting seeds, but? no result. Here is a gist of my segmentation part: https://gist.github.com/jwitos/4b953b3ef873fee3965c I would really appreciate any help or tip Best, Jan Witowski Collegium Medicum Jagiellonian University in Krakow -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Sun Dec 27 11:35:02 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sun, 27 Dec 2015 11:35:02 -0500 Subject: [ITK] CT liver segmentation In-Reply-To: References: Message-ID: Hi Jan, that sounds like some silly simple mistake. If you provided a short compilable example with the accompanying input, somebody will probably be able to point out the problem. Regards, D?enan On Sun, Dec 27, 2015 at 10:20 AM, Jan Witowski < jan.witowski at student.uj.edu.pl> wrote: > Hello, > > I am working with CT abdomen images and trying to segmentate the liver > (liver itself, vessels and the HCC tumor). I managed to do it using OsiriX > which was rather manual segmentation, and now I am working to do the same > using more accurate and semi-automatic algorithms with usage of SimpleITK. > I don?t really have much experience with ITK and image manipulation which > is why I ask you guys for some help. > > Currently, I want to try the watershed method. I loaded my DICOM series, > ran the GradientMagnitude filter and proceeded with MorphologicalWatershed > (using arg Level=17, value chosen manually). I got pretty nice output > image, I guess: > http://jwitowski.com/content/images/2015/12/WSsegmentation-4469-0.jpg > > But now, the question is - how do I take that liver out of the image > above? My best guess is, I should run a region growing segmentation. > I tried to do that, but - no matter what parameters I choose - I always > get the all-black image as an output. The whole image is black. I tried > different thresholds and other starting seeds, but? no result. > Here is a gist of my segmentation part: > https://gist.github.com/jwitos/4b953b3ef873fee3965c > > I would really appreciate any help or tip > > > Best, > Jan Witowski > Collegium Medicum Jagiellonian University in Krakow > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.witowski at student.uj.edu.pl Sun Dec 27 16:49:27 2015 From: jan.witowski at student.uj.edu.pl (Jan Witowski) Date: Sun, 27 Dec 2015 21:49:27 +0000 Subject: [ITK] CT liver segmentation In-Reply-To: References: Message-ID: Hello D?enan, Thanks for your assistance. Full code of my example is located here: https://gist.github.com/jwitos/9abe7124e28ce2e31b6e I?ve also uploaded the DICOMs I?ve been using (30~MB, 152 .dcms inside) if you want to test them out: http://cm-uj.pl/files/cleaned.zip Best, Jan On 27 grudnia 2015 at 17:35:24, D?enan Zuki? (dzenanz at gmail.com) wrote: Hi Jan, that sounds like some silly simple mistake. If you provided a short compilable example with the accompanying input, somebody will probably be able to point out the problem. Regards, D?enan On Sun, Dec 27, 2015 at 10:20 AM, Jan Witowski > wrote: Hello, I am working with CT abdomen images and trying to segmentate the liver (liver itself, vessels and the HCC tumor). I managed to do it using OsiriX which was rather manual segmentation, and now I am working to do the same using more accurate and semi-automatic algorithms with usage of SimpleITK. I don?t really have much experience with ITK and image manipulation which is why I ask you guys for some help. Currently, I want to try the watershed method. I loaded my DICOM series, ran the GradientMagnitude filter and proceeded with MorphologicalWatershed (using arg Level=17, value chosen manually). I got pretty nice output image, I guess: http://jwitowski.com/content/images/2015/12/WSsegmentation-4469-0.jpg But now, the question is - how do I take that liver out of the image above? My best guess is, I should run a region growing segmentation. I tried to do that, but - no matter what parameters I choose - I always get the all-black image as an output. The whole image is black. I tried different thresholds and other starting seeds, but? no result. Here is a gist of my segmentation part: https://gist.github.com/jwitos/4b953b3ef873fee3965c I would really appreciate any help or tip Best, Jan Witowski Collegium Medicum Jagiellonian University in Krakow _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Sun Dec 27 23:42:38 2015 From: itkhelpacc at gmail.com (vishal) Date: Sun, 27 Dec 2015 21:42:38 -0700 (MST) Subject: [ITK] [ITK-users] Visualize Intermediate result of ITK registration in vtk Message-ID: <1451277758067-36590.post@n7.nabble.com> hi, Im trying to write a code that will visualize the Intermediate registration results (result after every iterations) in vtk. Im running the registration example code ImageResgistration2.cxx in ITK and I want to apply the output (translation parameters) to an image in VTK after the every iteration... Could anyone please help me out...(i have tested ItkVtkglue and it is working fine)...any advice is appreciated. Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Visualize-Intermediate-result-of-ITK-registration-in-vtk-tp36590.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Mon Dec 28 11:07:32 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 28 Dec 2015 11:07:32 -0500 Subject: [ITK] CT liver segmentation In-Reply-To: References: Message-ID: Hi Jan, the code was fine, you missed to match the seed position to the value coming out of the watershed filter (imgWS) in that location. As you were feeding the output of the watershed filter to the segmentation filter, you needed to give the thresholds related to the values of that image and not the original input image (imgSeries). My modification is attached. ImageJ connection did not work out of the box for me so I wrote intermediate images to disk in order to inspect them. Regards, D?enan On Sun, Dec 27, 2015 at 4:49 PM, Jan Witowski < jan.witowski at student.uj.edu.pl> wrote: > Hello D?enan, > > Thanks for your assistance. > Full code of my example is located here: > https://gist.github.com/jwitos/9abe7124e28ce2e31b6e > I?ve also uploaded the DICOMs I?ve been using (30~MB, 152 .dcms inside) if > you want to test them out: http://cm-uj.pl/files/cleaned.zip > > Best, > Jan > > On 27 grudnia 2015 at 17:35:24, D?enan Zuki? (dzenanz at gmail.com) wrote: > > Hi Jan, > > that sounds like some silly simple mistake. If you provided a short > compilable example with the accompanying input, somebody will probably be > able to point out the problem. > > Regards, > D?enan > > On Sun, Dec 27, 2015 at 10:20 AM, Jan Witowski < > jan.witowski at student.uj.edu.pl> wrote: > >> Hello, >> >> I am working with CT abdomen images and trying to segmentate the liver >> (liver itself, vessels and the HCC tumor). I managed to do it using OsiriX >> which was rather manual segmentation, and now I am working to do the same >> using more accurate and semi-automatic algorithms with usage of SimpleITK. >> I don?t really have much experience with ITK and image manipulation which >> is why I ask you guys for some help. >> >> Currently, I want to try the watershed method. I loaded my DICOM series, >> ran the GradientMagnitude filter and proceeded with MorphologicalWatershed >> (using arg Level=17, value chosen manually). I got pretty nice output >> image, I guess: >> http://jwitowski.com/content/images/2015/12/WSsegmentation-4469-0.jpg >> >> But now, the question is - how do I take that liver out of the image >> above? My best guess is, I should run a region growing segmentation. >> I tried to do that, but - no matter what parameters I choose - I always >> get the all-black image as an output. The whole image is black. I tried >> different thresholds and other starting seeds, but? no result. >> Here is a gist of my segmentation part: >> https://gist.github.com/jwitos/4b953b3ef873fee3965c >> >> I would really appreciate any help or tip >> >> >> Best, >> Jan Witowski >> Collegium Medicum Jagiellonian University in Krakow >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: watershed.py Type: application/octet-stream Size: 2199 bytes Desc: not available URL: From dzenanz at gmail.com Mon Dec 28 11:11:49 2015 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 28 Dec 2015 11:11:49 -0500 Subject: [ITK] [ITK-users] Visualize Intermediate result of ITK registration in vtk In-Reply-To: <1451277758067-36590.post@n7.nabble.com> References: <1451277758067-36590.post@n7.nabble.com> Message-ID: Hi Vishal, you could pass those parameters to VTK and apply them as a user transform to the image being displayed: http://www.vtk.org/doc/nightly/html/classvtkProp3D.html#aac7f621f0a3666a29d21b5087919797a HTH, D?enan On Sun, Dec 27, 2015 at 11:42 PM, vishal wrote: > hi, > Im trying to write a code that will visualize the Intermediate registration > results (result after every iterations) in vtk. Im running the registration > example code ImageResgistration2.cxx in ITK and I want to apply the output > (translation parameters) to an image in VTK after the every iteration... > Could anyone please help me out...(i have tested ItkVtkglue and it is > working fine)...any advice is appreciated. > Regards > Vishal > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Visualize-Intermediate-result-of-ITK-registration-in-vtk-tp36590.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jan.witowski at student.uj.edu.pl Mon Dec 28 11:30:35 2015 From: jan.witowski at student.uj.edu.pl (Jan Witowski) Date: Mon, 28 Dec 2015 16:30:35 +0000 Subject: [ITK] CT liver segmentation In-Reply-To: References: Message-ID: Hi D?enan, Thank you very much for your reply. I really appreciate that. I can definitely see my mistakes right now: 1) When I was looking at the output of the watershed filter, I passed it through LabelToRGB() - don?t really know why. That?s the reason why I?ve been using wrong thresholds. 2) Also, I am using Fiji (I had some issues running ImageJ with latest Java+OSX El Capitan) to display my images, and the axis there are marked in microns instead of pixels. That also caused some trouble, because it made me place wrong seed locations. Once again, thanks a lot for your kindness. Code after your modifications works flawlessly. :) Best regards, Jan On 28 grudnia 2015 at 17:07:55, D?enan Zuki? (dzenanz at gmail.com) wrote: Hi Jan, the code was fine, you missed to match the seed position to the value coming out of the watershed filter (imgWS) in that location. As you were feeding the output of the watershed filter to the segmentation filter, you needed to give the thresholds related to the values of that image and not the original input image (imgSeries). My modification is attached. ImageJ connection did not work out of the box for me so I wrote intermediate images to disk in order to inspect them. Regards, D?enan On Sun, Dec 27, 2015 at 4:49 PM, Jan Witowski > wrote: Hello D?enan, Thanks for your assistance. Full code of my example is located here: https://gist.github.com/jwitos/9abe7124e28ce2e31b6e I?ve also uploaded the DICOMs I?ve been using (30~MB, 152 .dcms inside) if you want to test them out: http://cm-uj.pl/files/cleaned.zip Best, Jan On 27 grudnia 2015 at 17:35:24, D?enan Zuki? (dzenanz at gmail.com) wrote: Hi Jan, that sounds like some silly simple mistake. If you provided a short compilable example with the accompanying input, somebody will probably be able to point out the problem. Regards, D?enan On Sun, Dec 27, 2015 at 10:20 AM, Jan Witowski > wrote: Hello, I am working with CT abdomen images and trying to segmentate the liver (liver itself, vessels and the HCC tumor). I managed to do it using OsiriX which was rather manual segmentation, and now I am working to do the same using more accurate and semi-automatic algorithms with usage of SimpleITK. I don?t really have much experience with ITK and image manipulation which is why I ask you guys for some help. Currently, I want to try the watershed method. I loaded my DICOM series, ran the GradientMagnitude filter and proceeded with MorphologicalWatershed (using arg Level=17, value chosen manually). I got pretty nice output image, I guess: http://jwitowski.com/content/images/2015/12/WSsegmentation-4469-0.jpg But now, the question is - how do I take that liver out of the image above? My best guess is, I should run a region growing segmentation. I tried to do that, but - no matter what parameters I choose - I always get the all-black image as an output. The whole image is black. I tried different thresholds and other starting seeds, but? no result. Here is a gist of my segmentation part: https://gist.github.com/jwitos/4b953b3ef873fee3965c I would really appreciate any help or tip Best, Jan Witowski Collegium Medicum Jagiellonian University in Krakow _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From goretzki.imre at gmail.com Tue Dec 29 06:02:19 2015 From: goretzki.imre at gmail.com (Imre Goretzki) Date: Tue, 29 Dec 2015 12:02:19 +0100 Subject: [ITK] method to extract regions In-Reply-To: <5681B9CB.9070502@gmail.com> References: <5681B9CB.9070502@gmail.com> Message-ID: <5682683B.1000905@gmail.com> Is there an easier way in ITK? Thanks Imre Am 28.12.2015 um 23:38 schrieb Imre Goretzki: > Hey guys, > > I use the vtkPolyDataConnectivityFilter from polydata to extract > several different and more or less unknown regions. > My problem is that I want to extract regions from this filter, but if > I do this, the update process for all regions takes up to 10minutes: > > filter->SetExtractionModeToAllRegions(); > filter->Update(); > ... > > for (int i = 0; i < filter->GetNumberOfExtractedRegions(); i++) > { > extractFilter->InitializeSpecifiedRegionList(); > extractFilter->AddSpecifiedRegion(i); > extractFilter->Modified(); > extractFilter->Update(); > extractRegionData->DeepCopy(extractFilter->GetOutput()); > } > extractFilter->InitializeSpecifiedRegionList(); > > Background for this: I want to use the points of each region to check > whether they lie within an object in my binary > mask image. So the pipeline would be like this: > > 1) Get all Regions > 2) get region /i/ > 3) get points of region /i/ > 4) check if point /j/ lies within the binary mask /B/ > (/B/_/j/ == 255) > 4a) if true then add region to the extractFilter and > break (-> next region /i/) > 4b) if false then continue with next point /j/ > 5) Mark all regions red (done easily) > 6) Mark some regions green that are above a specific size (can be > accessed with filter->GetRegionSizes() ) > 7) Mark some regions yellow (the regions that are extracted during > step 1-4a) > > I do not know if the PolyDataConnectivityFilter is the right class for > this, I think it is. > If I store the extractRegionData in a vector, all regions have the > same number of points (which is kind of strange) but different number > of cells (region size == number of cells is correct). > > I would now try to get the points from the cells and check the binary > mask, because the > > vtkPolyData->GetNumberOfPoints() > > and > > vtkPolyData->GetPoint(pointCounter, point); > > are not working correctly in this scenario (all regions are extracted > because every single region has every point? > i did not verify my guess but I think there would be the problem) > > The binary mask is a vtkImageData, that could be transformed to > vtkPolyData. > The input image (already filtered with vtkMarchingCubes) and the > binary mask have the same dimensions (x,y,z). > > I hope you can imagine what I'm trying to do and have some tips for > me, if my approach is correct. > > Regards > Imre -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicole at bwh.harvard.edu Tue Dec 29 11:34:37 2015 From: nicole at bwh.harvard.edu (Aucoin, Nicole) Date: Tue, 29 Dec 2015 16:34:37 +0000 Subject: [ITK] Building BridgeOpenCV outside of ITK Message-ID: Hello, I?m working inside the context of creating an extension for a larger package (Slicer) that builds against ITK - the default package doesn?t enable the BridgeOpenCV module, but my extension will include OpenCV and I want to provide the capability of bridging it to ITK. I had started by pointing my code?s CMakeLists.txt to the Slicer checkout of ITK via an ExternalProject_Add command and reconfiguring that ITK source dir to set OpenCV_DIR to my built OpenCV, and Module_ITKVideoBridgeOpenCV set to ON. But the eventual goal is to extract the new module libraries and include them with the binary extension for distribution through the automated build system on the Slicer factory machines - it?s not going to work to reconfigure the factory?s ITK to include OpenCV. I found some hints in the mailing list archives on building ITK Snap outside of the ITK tree: http://itk-users.7.n7.nabble.com/Problems-building-ITK-Snap-outside-the-Ins ight-Applications-tree-td14733.html And will be trying that method. I wanted to check in with the community to see if there are any updates to that method or generally on building ITK modules (specifically Modules/Video) outside of ITK, since the post is from 2008. Thanks, Nicole The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From blowekamp at mail.nih.gov Tue Dec 29 16:02:51 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 29 Dec 2015 16:02:51 -0500 Subject: [ITK] Building BridgeOpenCV outside of ITK In-Reply-To: References: Message-ID: Hello Nicole, With the upcoming 4.9 release these is expanded support to build external ITK modules as a separate project. You can see an example of that here: https://github.com/InsightSoftwareConsortium/ITKIOTransformDCMTK/blob/master/CMakeLists.txt It should be possible to make some minor changes to the module to get it to build similar to an external project like the IOTransformDCMTK module. HTH, Brad > On Dec 29, 2015, at 11:34 AM, Aucoin, Nicole wrote: > > Hello, > > I?m working inside the context of creating an extension for a larger > package (Slicer) that builds against ITK - the default package doesn?t > enable the BridgeOpenCV module, but my extension will include OpenCV and I > want to provide the capability of bridging it to ITK. > > I had started by pointing my code?s CMakeLists.txt to the Slicer checkout > of ITK via an ExternalProject_Add command and reconfiguring that ITK > source dir to set OpenCV_DIR to my built OpenCV, and > Module_ITKVideoBridgeOpenCV set to ON. But the eventual goal is to extract > the new module libraries and include them with the binary extension for > distribution through the automated build system on the Slicer factory > machines - it?s not going to work to reconfigure the factory?s ITK to > include OpenCV. > > I found some hints in the mailing list archives on building ITK Snap > outside of the ITK tree: > http://itk-users.7.n7.nabble.com/Problems-building-ITK-Snap-outside-the-Ins > ight-Applications-tree-td14733.html > And will be trying that method. I wanted to check in with the community to > see if there are any updates to that method or generally on building ITK > modules (specifically Modules/Video) outside of ITK, since the post is > from 2008. > > Thanks, > Nicole > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From itkhelpacc at gmail.com Tue Dec 29 23:34:58 2015 From: itkhelpacc at gmail.com (vishal) Date: Tue, 29 Dec 2015 21:34:58 -0700 (MST) Subject: [ITK] [ITK-users] Visualize Intermediate result of ITK registration in vtk In-Reply-To: References: <1451277758067-36590.post@n7.nabble.com> Message-ID: <1451450098542-36592.post@n7.nabble.com> hi D?enan, thank you for ur help...But i have another doubt.. In the registration algorithms in ITK in order to print the optimizer result, the optimizer object is passed to the Execute() callback function.. to my understanding only one object and one event object can be send to Execute()... inorder to update my VTK render window il have to pass two objects (one ITK optimizer and VTK renderer object) as argument to Execute()...get the transform from the optimizer parameter and apply transform as you have suggested to the VTK object... This is where im having confusion.. How to achieve this? Is my understanding about the registration algorithm correct? Please help me out... Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Visualize-Intermediate-result-of-ITK-registration-in-vtk-tp36590p36592.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From rphellan2210 at gmail.com Wed Dec 30 02:30:35 2015 From: rphellan2210 at gmail.com (Renzo Ph) Date: Wed, 30 Dec 2015 02:30:35 -0500 Subject: [ITK] WhiteTopImageFilter Message-ID: Hi, I'm having some issues with the itkWhiteTopImageFilter ( http://www.itk.org/Doxygen/html/classitk_1_1WhiteTopHatImageFilter.html) I have a 512 x 512 x120 pixels image. Its intensity values go from 0 to 966. I've read and written the image declaring its pixel values as int and unsigned int. However, when I apply the WhiteTopImageFilter, the result presents negative values (range from -200 to 725) if the image pixel type is declared as int. If the pixel type is declared as unsigned int, values range from 0 to 725. I'm worried about losing information or applying the filter in the wrong way. Any suggestions, please? Renzo -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Wed Dec 30 23:34:48 2015 From: itkhelpacc at gmail.com (vishal) Date: Wed, 30 Dec 2015 21:34:48 -0700 (MST) Subject: [ITK] [ITK-users] Bug in ITK 4.8.2 Message-ID: <1451536488731-36593.post@n7.nabble.com> hi itk-users, I recently switched from ITK 4.6 to ITK 4.8.2... In ITK 4.6 had no problems when I was executing the DicomSeriesReadImageWrite2.cxx and DigitallyReconstructedRadiograph1... But after switching to ITK 4.8.2 it is showing the error as shown in the screenshots attached with this message... Even thought the error is present* I get the expected result *but I would like to solve this error.. could anyone please help me out?? regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Bug-in-ITK-4-8-2-tp36593.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From itkhelpacc at gmail.com Thu Dec 31 03:45:44 2015 From: itkhelpacc at gmail.com (vishal) Date: Thu, 31 Dec 2015 01:45:44 -0700 (MST) Subject: [ITK] [ITK-users] itkvtkglue build error.. please help In-Reply-To: References: <1450340236770-36559.post@n7.nabble.com> Message-ID: hi, Thank u all for the reply.. it helped me alot Regards Vishal On Fri, Dec 18, 2015 at 12:32 AM, Matt McCormick-3 [via ITK - Users] < ml-node+s7n36566h31 at n7.nabble.com> wrote: > The version of ITKVtkGlue that corresponds to ITK 3.20 can be found in the > InsightApplications tarball for the corresponding version here: > > http://itk.org/ITK/resources/legacy_releases.html > > However, all new development for ITK should be done with ITKv4. There is > an ITKv4 module for the Insight Journal article > http://www.insight-journal.org/browse/publication/784 found here: > > > https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration > > M > > On Thu, Dec 17, 2015 at 1:45 PM, D?enan Zuki? <[hidden email] > > wrote: > >> He is using ITK 3.20 with VTK 5.10. Where is itkVtkGlue for those >> versions? >> >> On Thu, Dec 17, 2015 at 12:51 PM, Matt McCormick <[hidden email] >> > wrote: >> >>> Hi, >>> >>> The easiest to use and best maintained bridge between ITK and VTK is the >>> ITKVtkGlue module, which is included in ITK. To use it, turn on >>> >>> Module_ITKVtkGlue >>> >>> in ITK's CMake configuration. >>> >>> http://www.itk.org/Insight/Doxygen/html/group__ITKVtkGlue.html >>> >>> HTH, >>> Matt >>> >>> On Thu, Dec 17, 2015 at 9:51 AM, D?enan Zuki? <[hidden email] >>> > wrote: >>> >>>> ?Hi Vishal, >>>> >>>> it looks like that version of itkVtkGlue is for a newer version of >>>> ITK.? Try this version: >>>> >>>> http://itk.org/gitweb?p=ITKApps.git;a=tree;f=Auxiliary/vtk;h=b6ae10b549c4ff60473b9069276a62fe1f7433bf;hb=2b5ec98662341c295f25da915afa4c0a8e794850 >>>> >>>> HTH, >>>> D?enan >>>> >>>> On Thu, Dec 17, 2015 at 3:17 AM, vishal <[hidden email] >>>> > wrote: >>>> >>>>> hi >>>>> Im using ITK 3.20, VTK 5.10, CMake 3.4.1 and Visual studio 2010... I >>>>> have >>>>> successfully build ITK as well as VTK... I need to combine both these >>>>> libraries so i downloaded itkvtkglue package from Wiki examples Im >>>>> getting >>>>> the following error while build it in visual studio 2010... i have >>>>> tried >>>>> building it in Visual studio 2008 unfortunately it was still it was >>>>> showing >>>>> the same error:- >>>>> >>>>> 1> CMake does not need to re-run because >>>>> C:/ItkVtkGlue/Build/CMakeFiles/generate.stamp is up-to-date. >>>>> 1>FinalizeBuildStatus: >>>>> 1> Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.unsuccessfulbuild". >>>>> 1> Touching "x64\Debug\ZERO_CHECK\ZERO_CHECK.lastbuildstate". >>>>> 1> >>>>> 1>Build succeeded. >>>>> 1> >>>>> 1>Time Elapsed 00:00:00.48 >>>>> 2>------ Build started: Project: ItkVtkGlue, Configuration: Debug x64 >>>>> ------ >>>>> 2>Build started 12/17/2015 2:15:33 PM. >>>>> 2>PrepareForBuild: >>>>> 2> Creating directory "C:\ItkVtkGlue\Build\Debug\". >>>>> 2>InitializeBuildStatus: >>>>> 2> Creating "ItkVtkGlue.dir\Debug\ItkVtkGlue.unsuccessfulbuild" >>>>> because >>>>> "AlwaysCreate" was specified. >>>>> 2>CustomBuild: >>>>> 2> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt >>>>> 2> CMake does not need to re-run because >>>>> C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. >>>>> 2>ClCompile: >>>>> 2> QuickView.cxx >>>>> 2>c:\itkvtkglue\QuickView.h(210): error C2039: 'IdentifierType' : is >>>>> not a >>>>> member of 'itk' >>>>> 2>c:\itkvtkglue\QuickView.h(210): error C2146: syntax error : missing >>>>> ';' >>>>> before identifier 'm_Counter' >>>>> 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier >>>>> - int >>>>> assumed. Note: C++ does not support default-int >>>>> 2>c:\itkvtkglue\QuickView.h(210): error C4430: missing type specifier >>>>> - int >>>>> assumed. Note: C++ does not support default-int >>>>> 2>c:\itkvtkglue\QuickView.h(112): error C2065: 'm_Counter' : undeclared >>>>> identifier >>>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: >>>>> 'SetInput' : >>>>> symbol cannot be used in a using-declaration >>>>> 2> c:\itkvtkglue\itkImageToVTKImageFilter.h(94) : see >>>>> reference to >>>>> class template instantiation 'itk::ImageToVTKImageFilter' >>>>> being >>>>> compiled >>>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: >>>>> 'SetInput' : is >>>>> not a member of 'itk::ProcessObject' >>>>> 2> >>>>> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) >>>>> : see declaration of 'itk::ProcessObject' >>>>> 2> ..\QuickView.cxx(254) : see reference to class template >>>>> instantiation 'itk::ImageToVTKImageFilter' being compiled >>>>> 2> with >>>>> 2> [ >>>>> 2> TInputImage=itk::Image >>>>> 2> ] >>>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: >>>>> 'SetInput' : >>>>> symbol cannot be used in a using-declaration >>>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2039: >>>>> 'SetInput' : is >>>>> not a member of 'itk::ProcessObject' >>>>> 2> >>>>> C:\ITK\InsightToolkit-3.20.1\Code\Common\itkProcessObject.h(87) >>>>> : see declaration of 'itk::ProcessObject' >>>>> 2> ..\QuickView.cxx(255) : see reference to class template >>>>> instantiation 'itk::ImageToVTKImageFilter' being compiled >>>>> 2> with >>>>> 2> [ >>>>> 2> TInputImage=itk::Image>>>> char>,2> >>>>> 2> ] >>>>> 2>c:\itkvtkglue\itkImageToVTKImageFilter.h(68): error C2873: >>>>> 'SetInput' : >>>>> symbol cannot be used in a using-declaration >>>>> 2>..\QuickView.cxx(423): error C2065: 'm_Counter' : undeclared >>>>> identifier >>>>> 2>..\QuickView.cxx(447): error C2065: 'm_Counter' : undeclared >>>>> identifier >>>>> 2> >>>>> 2>Build FAILED. >>>>> 2> >>>>> 2>Time Elapsed 00:00:02.64 >>>>> 3>------ Build started: Project: ALL_BUILD, Configuration: Debug x64 >>>>> ------ >>>>> 3>Build started 12/17/2015 2:15:36 PM. >>>>> 3>InitializeBuildStatus: >>>>> 3> Creating "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild" because >>>>> "AlwaysCreate" was specified. >>>>> 3>CustomBuild: >>>>> 3> Building Custom Rule C:/ItkVtkGlue/CMakeLists.txt >>>>> 3> CMake does not need to re-run because >>>>> C:\ItkVtkGlue\Build\CMakeFiles\generate.stamp is up-to-date. >>>>> 3>FinalizeBuildStatus: >>>>> 3> Deleting file "x64\Debug\ALL_BUILD\ALL_BUILD.unsuccessfulbuild". >>>>> 3> Touching "x64\Debug\ALL_BUILD\ALL_BUILD.lastbuildstate". >>>>> 3> >>>>> 3>Build succeeded. >>>>> 3> >>>>> 3>Time Elapsed 00:00:00.22 >>>>> ========== Build: 2 succeeded, 1 failed, 0 up-to-date, 0 skipped >>>>> ========== >>>>> >>>>> Im trying to write a code for 2D/3D registration so..I need to ITK >>>>> 3.20 and >>>>> VTK since im trying to build a journal paper [1] >>>>> http://www.insight-journal.org/browse/publication/784 >>>>> please help me out... >>>>> Regards >>>>> Vishal >>>>> >>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://itk-users.7.n7.nabble.com/itkvtkglue-build-error-please-help-tp36559.html >>>>> Sent from the ITK - Users mailing list archive at Nabble.com. >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-users.7.n7.nabble.com/itkvtkglue-build-error-please-help-tp36559p36566.html > To unsubscribe from itkvtkglue build error.. please help, click here > > . > NAML > > -- View this message in context: http://itk-users.7.n7.nabble.com/itkvtkglue-build-error-please-help-tp36559p36594.html Sent from the ITK - Users mailing list archive at Nabble.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From ribaluigi at gmail.com Tue Dec 15 10:32:41 2015 From: ribaluigi at gmail.com (Luigi Riba) Date: Tue, 15 Dec 2015 15:32:41 -0000 Subject: [ITK] [ITK-users] STATISTICAL FEATURES OF A 3D IMAGE In-Reply-To: References: Message-ID: Dear Abdelkhalek Bakkari, to compute a bunch of statistical data about your image you could use: itkStatisticsImageFilter . I have attached at this mail a minimal working example for 2d images. Since you are dealing with VTK images you should probably use itkVTKToImageFilter to get an ITK image from a VTK one. I am sorry, but I haven't quite understood the part regarding storing the mean, the variance, etc as a 3D image. Anyhow, you can always build an empty image and change its values pixel by pixel using an image iterator. Best, Luigi 2015-12-15 2:43 GMT+01:00 Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr>: > > Dear insight-users, > > How can I calculate the mean, variance, energy...etc of a 3D image and > store them in an array as 3D images using ITK. > The input 3D image is an output of VTK. > > Best regards, > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- project(statistics) cmake_minimum_required(VERSION 2.8) #ITK find_package(ITK REQUIRED) include(${ITK_USE_FILE}) add_executable(${PROJECT_NAME} ${PROJECT_NAME}.cxx) target_link_libraries(${PROJECT_NAME} ${ITK_LIBRARIES}) -------------- next part -------------- A non-text attachment was scrubbed... Name: lena512.bmp Type: image/bmp Size: 263222 bytes Desc: not available URL: -------------- next part -------------- // Statistics // Author: Luigi Riba, ribaluigi (at) gmail (dot) com // Date: 20th December 2015 // INPUTS [OPTIONAL] // inputImage, lena512.bmp in this case // OUTPUTS [OPTIONAL] // a bunch of statistics on the image #include #include int main(int argc, char *argv[]) { const unsigned int Dimension = 2; typedef float PixelType; typedef itk::Image ImageType; // read your image, in this case lena512.bmp typedef itk::ImageFileReader ImageReaderType; ImageReaderType::Pointer reader = ImageReaderType::New(); reader->SetFileName("lena512.bmp"); typedef itk::StatisticsImageFilter StatisticsFilterType; StatisticsFilterType::Pointer statistics = StatisticsFilterType::New(); statistics->SetInput(reader->GetOutput()); statistics->Update(); // you can now get access to the computed values via the GetSomething method // for example: double mean = statistics->GetMean(); // or you can just print all the computed values calling the Print method // of the object itself: statistics.Print(std::cout); system("pause"); return EXIT_SUCCESS; }