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-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. 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-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. 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-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: 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-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: 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-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: 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-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: 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-users] [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 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-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: 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-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 > 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-users] [ITK] 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 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-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: 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-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 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-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: 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-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: 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-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: 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-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: 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-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. 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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. 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-users] [ITK] 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: 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-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: 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-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: 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-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 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-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: 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-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: 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-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: 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-users] 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-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 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-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. 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-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. 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-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. > 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-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. 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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: 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-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. 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-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: 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-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. 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-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: 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-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. 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-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: 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-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. 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-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: 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-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: 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-users] [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 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-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: 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-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: 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-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: 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-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: 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-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. 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-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: 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-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: 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-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: 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-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: 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-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. 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-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: 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-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. 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-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. 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-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 - 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