Changesets: Import 2017-06-07 23:51:09
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master 2bdc4529 2017-05-18 11:23:11 Details Diff |
STYLE: Buildsystem: Document variable Slicer_EXTENSION_SOURCE_DIRS git-svn-id: http://svn.slicer.org/Slicer4/trunk@26022 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 77a912a1 2017-05-18 11:23:09 Details Diff |
ENH: Buildsystem: Support packaging of existing extension install dirs Configuring Slicer using cmake -DSlicer_EXTENSION_INSTALL_DIRS:STRING=/path/to/ext1-install-tree;/path/to/ext2-install-tree ... will ensure the file found in each extension install directories are packaged with Slicer. Co-authored-by: Hina Shah <hina.shah@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@26021 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - CMake/SlicerBlockInstallExtensionPackages.cmake | Diff File | ||
| mod - CMake/SlicerCPack.cmake | Diff File | ||
| mod - SuperBuild.cmake | Diff File | ||
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master fb8f66fb 2017-05-18 11:23:07 Details Diff |
ENH: BuildSystem: Allow access to Slicer OS/Arch/bit vars in external project git-svn-id: http://svn.slicer.org/Slicer4/trunk@26020 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - CMakeLists.txt | Diff File | ||
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master a2fea914 2017-05-18 11:23:05 Details Diff |
STYLE: MIDASAPIUploadExtension: Fix typo git-svn-id: http://svn.slicer.org/Slicer4/trunk@26019 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Extensions/CMake/MIDASAPIUploadExtension.cmake | Diff File | ||
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master 169a602c 2017-05-17 22:18:46 Details Diff |
ENH: Made segmentations model export more robust In case there were errors in the subject hierarchy (SH), Segmentations module failed to export segments. Segmentations module is more robust now, if there are SH errors then it will just not place exported nodes in the same SH branch as the segmentation. git-svn-id: http://svn.slicer.org/Slicer4/trunk@26018 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Segmentations/qSlicerSegmentationsModuleWidget.cxx | Diff File | ||
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master 36c63aa7 2017-05-17 04:00:31 Details Diff |
COMP: Update ITKv4 to fix MINC build error using redhat devtoolset 2 This commit updates ITK and fix an error reported when building Slicer using redhat toolset 2 on CircleCI. Details: 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- commit Slicer/ITK@3cc1a24 Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> Date: Wed May 17 03:52:36 2017 -0400 COMP: libminc: Define _GNU_SOURCE to enable C99 extension during introspection This commit addresses failure to detect "round" function on compiler like g++ 4.8.2 provided by redhat devtoolset 2 [1]. More specifically, since the macro __USE_ISOC99 wasn't defined, function "round" declared in "mathcalls.h" (itself included from "math.h") wasn't found during introspection. Defining _GNU_SOURCE allows to enable c99. See features.h for more details. Error fixed by this commit is the following: /path/to/ITKv4/Modules/ThirdParty/MINC/src/libminc/libsrc2/hyper.c:64:1: error: redefinition of ‘round’ round(double x) ^ and it is reproducible using docker-centos-build [2]. CMake macro was adapated from python-cmake-buildsystem [3] [1] https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/2/html/2.0_Release_Notes/DTS2.0_Release.html [2] https://github.com/thewtex/docker-centos-build [3] https://github.com/python-cmake-buildsystem/python-cmake-buildsystem/blob/d0f47193837db6ad9e08bc99617276d4a24687c3/cmake/ConfigureChecks.cmake#L415 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- git-svn-id: http://svn.slicer.org/Slicer4/trunk@26017 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_ITKv4.cmake | Diff File | ||
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master a5525719 2017-05-16 21:38:13 Details Diff |
BUG: Segment editor widget layout issue fixed Most of the layout problems are solved. There are minor spaces between the widgets in certain rare cases, but there are no cramped widgets any more at all. git-svn-id: http://svn.slicer.org/Slicer4/trunk@26016 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Segmentations/Widgets/Resources/UI/qMRMLSegmentEditorWidget.ui | Diff File | ||
| mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx | Diff File | ||
| mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.h | Diff File | ||
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master 9f505633 2017-05-16 15:39:34 Details Diff |
ENH: Improved segment editor shortcuts Switch between last two effects using space bar (it can be used to quickly inactivate/reactivate scissors; switch between paint/erase; etc). Added shortcut for choosing more than 10+ effects by clicking shift+number (Shift+1, Shift+2, ...). git-svn-id: http://svn.slicer.org/Slicer4/trunk@26015 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx | Diff File | ||
| mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.h | Diff File | ||
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master 85676fa4 2017-05-16 04:53:16 Details Diff |
BUG: Further improvement of segment editor widget layout issue Still not perfect, but at least the layout is not completely cramped after changing modules and back git-svn-id: http://svn.slicer.org/Slicer4/trunk@26014 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx | Diff File | ||
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master e7e3de54 2017-05-15 12:07:56 Details Diff |
BUG: Fix warning message in extension wizard Fix warning message in extension wizard displayed when publishing from a Git branch other than master. Previously, the following error occurred when logging this warning message: TypeError: not all arguments converted during string formatting git-svn-id: http://svn.slicer.org/Slicer4/trunk@26013 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Utilities/Scripts/SlicerWizard/ExtensionWizard.py | Diff File | ||
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master 49e3a232 2017-05-15 12:07:52 Details Diff |
BUG: Remove explicit path to git executable for GitPython (Windows) On Windows, remove the explicit path to the git executable for GitPython. On modern versions of Git for Windows, the specified path (/bin/git) is not correct. This results in errors when running the command line extension wizard, for example when publishing an extension: $ slicerExtensionWizard --publish ~/Slicer-MyExtension/ ... git.exc.GitCommandNotFound: Cmd('C:/Program Files/Git/usr/bin/git') not found due to: WindowsError('[Error 2] The system cannot find the file specified') When the GIT_PYTHON_GIT_EXECUTABLE environment variable is not set, GitPython uses the git executable found in the path. Since the user is expected to run slicerExtensionWizard from Git Bash, it's reasonable to assume that the correct git executable is in the path. git-svn-id: http://svn.slicer.org/Slicer4/trunk@26012 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Utilities/Scripts/CMakeLists.txt | Diff File | ||
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master 837ff4bd 2017-05-15 11:46:24 Details Diff |
ENH: Add support for MINC image IO Issue 0004085 This enables MINC Image IO via ITK. This currently supports MINC version 2 (HDF5-based). Reviewed-by: Andriy Fedorov <fedorov@bwh.harvard.edu> Reviewed-by: Andras Lasso <lasso@queensu.ca> Reviewed-by: Johan Andruejol <johan.andruejol@kitware.com> Reviewed-by: Gabriel A. Devenyi <gdevenyi@gmail.com> Reviewed-by: Vladimir S. FONOV <vladimir.fonov@gmail.com> Tested-by: Andras Lasso <lasso@queensu.ca> Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> From: Matt McCormick <matt.mccormick@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@26011 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - Applications/SlicerApp/Data/Input/pd_z-_float_xyz.mnc.md5 | Diff File | ||
| mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt | Diff File | ||
| add - Base/Python/slicer/tests/test_slicer_minc.py | Diff File | ||
| mod - Libs/ITKFactoryRegistration/CMakeLists.txt | Diff File | ||
| mod - Libs/MRML/Core/vtkDataFileFormatHelper.cxx | Diff File | ||
| mod - Modules/Loadable/Volumes/qSlicerVolumesReader.cxx | Diff File | ||
| mod - SuperBuild/External_ITKv4.cmake | Diff File | ||
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master f77b8075 2017-05-15 10:44:24 Details Diff |
ENH: Update SimpleITK (Support for debug build) Fixes 0003816 Tested-by: Andras Lasso <lasso@queensu.ca> $ git shortlog v1.0rc1..6433028 Bradley Lowekamp (171): Update CircleCi CMake version to 2.7.2 Add CMake variable CMAKE_DL_LIBS to list for superbuild propagation Adding initially configured Sphinx documentation Add logo, title and under development note disable imgmath due to compatibility issues with readthedocs Merge topic 'AddInitialSphinxDocumentation' Use constant reference for FileName Merge topic 'IOFileNameByReference' Merge topic 'AddCMAKE_DL_LIBToSuperbuildPropagation' Merge topic 'UpdateCircleCiCMakeVersion' Replace 0 magic number with defined constant for WallClock Use namespace qualification for sitkWallClock Add RandomSeed header to wrap sitkWallClock enum Use sitkWallClock enum in test and examples Silence CMake message for CSharp targets Update ITK 4.11 along release branch Merge topic 'UpdateITK4.11-release' Merge topic 'SilenceCSharpTargets' Add clamping to optimizer's GetCurrentIteration method Use target definition over directory includes Remove required flags and replace with compile options property Adding CMake macro to migrate cache variable from SITK to SimpleITK Add missing library target to compile definitions Remove SITK_EXPRESS_INSTANTIATEDPIXELS option Migrate CMake options from SITK_ prefix to SimpleITK_ Migrate SITK_FORBID_DOWNLOADS option to SimpleITK_FORBID_DOWNLOADS Migrate option to SimpleITK_USE_VIRTUALENV from SITK prefix Migrate to SimpleITK_LUA_BUILD_EXECUTABLE CMake option Migrate to SimpleITK_GIT_PROTOCOL Migrate SITK_ prefix for LUA_EXECUTABLE to SimpleITK_ prefix Change internal variable to prefered SimpleITK_PYTHON project prefix Prefer SimpleITK over SIMPLEITK for CMake variables Merge topic 'AddressMSVCConversionWarning' Correct logic for running C++11 requirement Merge topic 'RemoveFontFromDoxygen' Merge topic 'UseCMakeTargetProperties' Merge topic 'DeprecateSITKCMakeOptionPrefix' Add missing EXPORTS define to BasicFilters1 library Merge topic 'UseCMakeTargetProperties' Organize json scipts into a directory Adding script to update json files with ITK module names Adding itk_module field to json files Separate BasicFilter library creation into function Add generated cxx file to list with ITK module names Create BasicFilter libraries corresponding to ITK modules Remove manual BasicFilters1 library Rename library by removing BasicFilters form ITK modular libraries. Update JSONValidate.py path for doxygen cmake code Include CMake legacy module when used Fix typeo in argument name for restoring LUA_EXECUTABLE cache variable Add required virutalenv version for producing wheels Add CMake option for --plat-name for distutils Merge topic 'DeprecateSITKCMakeOptionPrefix' Merge topic 'FixLuaExecutableCacheArgument' Merge topic 'UseITKModuleForLibraries' Merge topic 'RemoveDoubleBackticksForDoxygen' Adding comment to CMake function for building basic filter libraries Correct ITK Module some transform initializes belong to Fix basic filter source list to always remove modular sources Set target properties for using ITK modules instead of including use file Reduce the set of ITK modules required to build SimpleITK Do not process JSON filter if ITK modules is not enabled. Merge topic 'AddPythonPlatNameOption' Remove bad loop over ITK modules passed to sitk_target_use_itk Add library directories if needed when using an ITK module Use local variables for json file path Delete CMake all variables from cache for list of generated source Do not add examples as tests unless BUILD_TESTING is enabled Cast enum to uint32 to avoid signed integer conversion warning Add clamping to all optimizer's GetCurrentIteration wrapping Add CMake option for --plat-name for distutils Merge branch 'release' Up required Swig version to 3 in find_package command Merge topic 'UseEnumConstantForWallClockSentinel' Merge topic 'RefactorExampleIntoExampleDirectories' Merge topic 'AddressMSVCConversionWarning' Merge topic 'UseITKModulesToEnableLibraries' Merge topic 'RequireSwig3' Add error exception for pep425 wheel construction Merge topic 'gdcmSeriesFileNames' Update ITK Superbuild version along ITK 4.11 release Use CTest script to drive CircleCI builds Prefer CircleCI environment variables over repository specifics Merge topic 'UpdateITKOn4.11Release' Merge topic 'AddErrorExcpetionForPEP425Warning' Merge topic 'CircleCiUseCTest' Only install numpy into virtualenv when testing is enabled Fix correct syntax for CMake configuration variable substitution Set SITK_UNDEFINED_SYMBOLS_ALLOWED in language projects CircleCI builds on next branch should be the Continuous model Correct ctest to ingore pep425 error not warning Binary files were accidentally added and not md5 hash file Merge topic 'dicomTagsSpaceBug' Merge topic 'CMakeUndefVarName' Merge topic 'SetUndefinedSymbolsForLanguageProjects' Merge topic 'CircleCINextBuildAreContinuous' Merge topic 'FixBaselineBinaryAdded' Merge topic 'NumpyOnlyForTesting' Merge topic 'AddErrorExcpetionForPEP425Warning' Merge topic 'UpdateResampleDocumentation' Update CircleCI yaml to use ctest build flags Use CMake variable to execute cmake command Merge topic 'UpdateCircleCIWithCTestBuildFlags' Merge topic 'FixCMakeEchoCommand' Add sha512 hash data link files generated ContentLinkSynchronization Adding script to synchronize md5 and sha512 data link hashes Fix path to in source ExternalData with Superbuild Add Kitware's Girder as alternate download site for SHA512 data Fix the Doxygen mark up for the HashImageFilter Fix setting ITK Doxygen tag in configuration file Adding updated ExternalData module with support for multiple hashes Updating filter converge with ITK 4.11 release Merge topic 'FixHashFilterDocumentation' Merge topic 'bugExhaustiveOptimizer' Merge topic 'UpdateFilterConverage' Merge topic 'FixITKDoxygenTags' Add optional old_name to sitk_legacy_naming macro Rename Superbuild CMake variable to SimpleITK_USE_SYSTEM_* Remove code for old ITK_WRAPPING option. Merge topic 'AddSHA512ExternalDataSupport' Tweaks to R Documentation downloads Remove debugging message Merge topic 'FixSeeNodeIndentation' Merge topic 'RegeneratePythonDocstrings' Merge topic 'RDocFromMidas' Merge topic 'AddSHA512ExternalDataSupport' Rename git default variable to exclude from Superbuild propagation Merge topic 'UpdateSuperbuildUseSytemVariableNames' Merge topic 'RenameSimpleITKGitDefaultVar' Backport ExternalData.cmake for CMake version 3.0 Define RETURN_SELF macro to void when wrapping with SWIG Fix missing occurrence of rename CMake variable Only add version suffix and properties to libraries. Remove AnaconaBuild script Merge topic 'AddSHA512ExternalDataSupport' Merge topic 'RenameSimpleITKGitDefaultVar' Merge topic 'RemoveAnacondaBuildScript' Add exception for trying to write DICOM with ImageSeriesWriter Correct the CMake DATA syntax for using a series Must use a ImageSeriesReader to read a DICOM series Add Dockerfiles and script to build manylinux complaint wheels Merge topic 'AddPythonManyliunxDockerScripts' Merge topic 'OnlyVersionLibraries' Merge topic 'RDocEquationFixes' Merge topic 'AddExceptionForWritingDICOMWithSeriesWriter' Merge topic 'dicomWrite' Merge topic 'RDocUpdateWarningsFixed' Merge topic 'DisableWrappedReturnSelf' Update setup.py classifiers Merge topic 'UpdatePythonAndJavaDocs' Merge topic 'UpdateSetup.pyClassifiers' Add variable options to manylinux docker builds Merge topic 'UpdateManyLinuxScripts' Fix the SimpleITK install directory used for superbuild SimpleITK Examples Use the install directory for include interface Merge branch 'FixSimpleITKVersionExampleSuperbuild-for-release' into release Merge branch 'FixIncludeInstallInterface-for-release' into release Use find_package for install and build path for build for ITK Pass ITK_DIR to the Examples Superbuild Updating Superbuild ITK version along release toward 4.11.1 Merge branch 'FixITKTargetsPathInConfig-for-release' into release Relax tolerance for DiscreteGaussianImageFilter_short test Merge branch 'RelaxShortDiscreteGaussianTestTolerance-for-release' into release Relax tolerance on MagnitudeAndPhaseToComplex from i686 results Release tolerance for LandmarkBasedInitialization for i686 Update to 4.11.1 tagged release Use exact reported version for required ITK version. Merge branch 'FixSimpleITKConfigITKVersion-for-release' into release Merge branch 'AdjustToleraceFori686Debug-for-release' into release Merge branch 'UpdateITK4.11.1-for-release' into release ENH: Support building debug SimpleITK against release Python Dave Chen (4): Removed font from Doxygen Fix the indentation of See nodes in the docs PythonDocstrings.i regenerated to update docs Update PythonDocstring.i and JavaDoc.i David T. Chen (2): Removed double backticks for Doxygen BUG: Check for undefined varName variable Richard Beare (3): Support for downloading archive of R documentation from midas Improved support for converting equations for R update R documentation md5 Ziv Yaniv (8): BUG: removed the loadPrivateTags parameter from GetGDCMSeriesFileNames. Improved documentation for GetGDCMSeriesFileNames. BUG: Comparison of image type tag (0008|0008) was incorrect. Corrected spelling mistake and added details for Resample functions. BUG: Wrong metric value returned from Exhaustive optimizer. Adding support for writing DICOM series. Example moved to new directory structure and added test. Adding forward declaration for smart pointer. From: Bradley Lowekamp <blowekamp@mail.nih.gov> git-svn-id: http://svn.slicer.org/Slicer4/trunk@26010 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild/External_SimpleITK.cmake | Diff File | ||
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master ccf66718 2017-05-10 13:24:19 Details Diff |
BUG: Attempt to fix Segment Editor layout issue The effect options widget was truncated and vertically pressed in some cases after changing the active effect. git-svn-id: http://svn.slicer.org/Slicer4/trunk@26009 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx | Diff File | ||
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master 4d4f1552 2017-05-09 18:19:29 Details Diff |
ENH: Update ITK to 4.12.0rc1 $ git shortlog 1619816..9c91cb6 --no-merges Ben Boeckel (1): ENH: Add a script to help update third-party sources Brad King (5): ENH: Update KWIML import script for new upstream URL ENH: Teach update-third-party.bash to add a Change-Id ENH: Port KWSys update script to update-third-party.bash ENH: KWSys: Filter out unused attributes during import ENH: KWSys: Apply attribute changes made upstream Bradley Lowekamp (19): COMP: Enable hidden visibility property with NIFTI static libraries COMP: Enable hidden visibility property with GIFTI static libraries BUG: Correct variable name used to check CXX version BUG: Correct variable name used to check CXX version COMP: Enable hidden visibility property with NIFTI static libraries COMP: Enable hidden visibility property with GIFTI static libraries BUG: Initialize ConvergenceValue in constructor BUG: Initialize ConvergenceValue in constructor ENH: Update CircleCi script to download latest binary tar-ball BUG: Use CMAKE_DL_LIBS instead of explict "dl" library COMP: Fix CircleCI ITK data download file name ENH: Update CircleCI yaml file BUG: Apply changes from MetaIO upstream to remove static variables ENH: Update SWIG version to 3.0.12 ENH: Update PCRE version to 8.40 ENH: Add OrientedBoudingBox attributes to ShapeLabelMap COMP: Use std::abs over vnl_math_abs BUG: Initialize image data to 0 ENH: Fix clearing build tree error David T. Chen (1): BUG: Fixed quote style Dženan Zukić (3): STYLE: Simplify code by using TestingMacros BUG: fixing wrong check for argument count ENH: Add Strain as a remote module Floris Berendsen (2): COMP: Added missing png_get_uint_31 name mangling COMP: Added missing png_get_uint_31 name mangling Francois Budin (58): STYLE: Typo corrections in itk*TopHatImageFilter.h ENH: Prefer std::atomic over compiler specific implementation BUG: Addresses 'ordered comparison between pointer and zero' error (clang-4) BUG: Addresses InDoxygenGroup Test with Python 3.6 failures BUG: BSplineScatteredDataPointSetToImageFilter output image is not generated BUG: itk::RGBPixel<unsigned short> needs to be wrapped for itkTIFFImageIO BUG: Usage of std::atomic was incorrectly used in itk::Detail::AtomicOps ENH: Exposing functions to set real and imaginary part of complex numbers BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: 'typename' cannot be used outside of template declaration BUG: Missing ITK_OVERRIDE BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: Missing ITK_OVERRIDE ENH: Improving usability in IPython ENH: Update BridgeNumPy to most recent version (2017.02.24) BUG: 3523 Even padding most value representations with space instead of '\0' BUG: Remove extra space in chronometer command DOC: Make it more explicit that 'push' authorization is not for everybody BUG: 3523 Even padding most value representations with space instead of '\0' BUG: 3519 KernelTransform WMatrix initialization BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS COMP: Do not expose functions to set real and img part of complex numbers BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS BUG: 3519 KernelTransform WMatrix initialization DOC: Typo in itkNumberToString.h BUG: Attribute names cannot start with a digit BUG: Do not define deprecated function if ITK_LEGACY_REMOVE is selected BUG: Wrap EllipseSpatialObject std::list in Python ENH: Wrap itkN4BiasFieldCorrectionImageFilter in Python BUG: itkStatisticsAlgorithmTest throwing exception on VS2015Update3 and VS2017 ENH: Skip generating export headers if module does not contain a target BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review ENH: Update BridgeNumPy to most recent version (2017.03.27) BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review BUG: Wrap EllipseSpatialObject std::list in Python ENH: Improving usability in IPython BUG: Attribute names cannot start with a digit BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS BUG: Do not export all symbols from third party libraries on Windows ENH: Allows to call ImageFileWriter in Python with Input=Filter BUG: Certain third party libraries need to export their symbols on Windows BUG: Test if 'issubclass' only if 'isclass' is True ENH: Add Python convenience function to read images BUG: 3475 AccumulateImageFilter not setting direction cosines of output image DOC: Removing typos in itkExtractImageFilter comments BUG: ProjectionImageFilter did not copy direction cosine information to output BUG: Test if 'issubclass' only if 'isclass' is True BUG: 3475 AccumulateImageFilter not setting direction cosines of output image BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS BUG: Do not export all symbols from third party libraries on Windows BUG: Certain third party libraries need to export their symbols on Windows BUG: ProjectionImageFilter did not copy direction cosine information to output ENH: Update BridgeNumPy (2016.04.28) and update itkExtras.py accordingly BUG: Template type based input function parameter needs to be deterministic ENH: Bump CMakeLists.txt version to 4.11.1 BUG: Problems due to ComputeOrientedBoundingBox in itkShapeLabelMapFilter Jean-Baptiste VIMORT (1): PERF: Improvement of the itkHistogram class in order to make it faster Jean-Christophe Fillion-Robin (3): ENH: Introduce ITK_WRAP_PYTHON_LEGACY to exclude older Python package layout BUG: ITKPython: Do not install *.mdx files required only at generation time COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD Johan Andruejol (1): ENH: Add wrapping for PathToImageFilter Jon Haitz Legarreta (131): ENH: Improve the itkFileListVideoIO coverage. STYLE: Improve the BSplineScatteredDataPointSetToImageFilter style, ENH: Improve the itkBSplineScatteredDataPointSetToImageFilter coverage. ENH: Add missing ivars in function PrintSelf. STYLE: Improve ImageNoise filters' style. STYLE: Improve the ImageNoise filters tests' style. STYLE: Improve ITKImageSources module filters' style. STYLE: Improve the itkLinearInterpolateImageFunction style. ENH: Improve the itkLabelOverlapMeasuresImageFilter coverage. STYLE: Improve itkAdaptiveHistogramEqualizationImageFilter style. ENH: Improve itkAdaptiveHistogramEqualizationImageFilter coverage. STYLE: Improve itkKappaStatisticImageToImageMetric style. ENH: Improve the itkKappaStatisticImageToImageMetric coverage. STYLE: Improve itkBinaryGrindPeakImageFilter style. STYLE: Improve the itkCannyEdgeDetectionImageFilter style. ENH: Improve itkCannyEdgeDetectionImageFilter coverage. ENH: Improve itkBarrier class coverage. STYLE: Improve itkFlipImageFilterStyle. STYLE: Improve itkSpatialObjectToPointSetFilter style. STYLE: Improve itkStretchIntensityImageFilter style. ENH: Print all ivars for itkStretchIntensityImageFilter. ENH: Improve itkPhysicalPointImageSource class coverage. ENH: Add missing ivars to LabelMapMaskImageFilter PrintSelf. ENH: Improve itkRealTimeClock coverage. STYLE: Improve the itkRealTimeClock style. ENH: Improve itkBsplineDecompositionImageFilter coverage. ENH: Improve itkTestingStretchIntensityImageFilter coverage. STYLE: Improve itkPathToChainCodePathFilter style. ENH: Add a Get method for itkPathToChainCodePathFilter ivar. ENH: Add specific testing macro for boolean members. STYLE: Improve itkLabelMapMaskImageFilter style. STYLE: Improve BSplineDecompositionImageFilter style. ENH: Finish itkAdaptiveHistogramEqualizationImageFilter PrintSelf. COMP: Fix ImageGrid tests compiler warnings. ENH: Finish BSplineDecompositionImageFilter PrintSelf. BUG: Fix Uninitialized Memory errors reported by Valgrind. ENH: Improve itkLabelMapMaskImageFilter coverage. ENH: Improve itkBinaryGrindPeakImageFilter coverage. ENH: Improve itkPathToChainCodePathFilter coverage. ENH: Move LabelMap module test baselines. ENH: Move BinaryMathMorphology test baselines out of review. ENH: Move ImageFusion test baselines out of review. ENH: Improve itkAutoCropLabelMapFilter tests. ENH: Improve itkSpatialObjectToPointSetFilter coverage. ENH: Move ImageLabel test baselines out of Review. ENH: Move ImageGrid test baselines out of review. STYLE: Improve itkGaussianSpatialFunction class' style. ENH: Improve the ITKPath module classes coverage. BUG: Fix BSplineDecompositionImageFilter Valgrind defects. STYLE: Improve itkColorTable style. ENH: Improve itkHoughTransform2DLinesImageFilter coverage. ENH: Improve itkHoughTransform2DCirclesImageFilter coverage. BUG: Address uninitialized variable defects. STYLE: Improve itk::HistogramThresholdImageFilter style. DOC: Fix a typo in the term "threshold". STYLE: Imporve itkContourSpatialObjectPoint style. ENH: Print all HoughTransform2DLinesImageFilter ivars. STYLE: Fix type in Optimizersv4 and Metricsv4 modules. ENH: Add PhiLattice regression baseline. ENH: Print all itkVoronoiDiagram2DGenerator ivars. ENH: Improve itkColorTable coverage. ENH: Improve the itk::GradientDescentOptimizerv4 style. ENH: Improve the itkImageSources module's filters' coverage. ENH: Add PhiLattice regression baseline. ENH: Add a new test for itk::ContourSpatialObjectPoint. BUG: Fix bug in itkContourSpatialObjectPointTest test. STYLE: Improve the itkGaussianSpatialFunctionTest style. ENH: Improve itkVotingBinaryHoleFillingImageFilter coverage. BUG: Fix precision issues in itkGaborKernelFunctionTest. BUG: Relax tolerance in itkGaborKernelFunctionTest. DOC: Fix minor typo in itkHistogramThresholdImageFilter doc. ENH: Print all ivars in GradientDescentOptimizer base classes. STYLE: Improve TIFFImageIO tests. ENH: Add Get methods for itk::BSplineDecompositionImageFilter ivars. BUG: Fix TimeProbes name in itkLargeTIFFImageWriteReadTest. BUG: Fix memory leaks in BMP and PNG tests. COMP: Fix signed/unsigned mismatch warning. COMP: Fix signed/unsigned mismatch warning. BUG: Fix Superclass for ITKThresholding calculators. BUG: Make the number of filters be an integer. ENH: Honor the itkBooleanMacro for boolean class members. ENH: Improve the Watershed module code coverage. COMP: Fix double to unsigned int cast warning. ENH: Improve coverage for MorphologicalWatersheds filters. STYLE: Improve the Denoising module style. BUG: Fix the itkPatchBasedDenoisingImageFilter RTTI Superclass name. COMP: Fix unsigned char from double conversion warning. ENH: Improve itkWatershedMiniPipelineProgressCommand coverage. ENH: Improve the itkRegionalMin/Max filters member print types. ENH: Improve the itkMorphologicalWatershedFromMarkers coverage. ENH: Improve the itkIsolatedWatershedImageFilter coverage. STYLE: Improve the Denoisinig module style. STYLE: Improve the FEMRegistration module files style. DOC: Fix itkOrientImageFilter UseImageDirection method doc typo. STYLE: Improve the ITKThresholding module classes style. BUG: Fix itkIsolatedWatershedImageFilterTest valgrind errors. STYLE: Improve the itkApproximateSignedDistanceMapImageFilter style. ENH: Improve Denoising module filters' coverage. ENH: Improve the FEMRegistration module coverage. STYLE: Improve the itkDisplacementFieldTransform class style. STYLE: Limit itkFlipImageFilter methods' loops variables' scope. ENH: Improve itkFlipImageFilter coverage. COMP: Fix itkPhysicsBasedNonRigidRegistrationMethodTest cast warning. STYLE: Improve the HessianToObjectnessMeasureImageFilter style. ENH: Improve coverage for HessianToObjectnessMeasureImageFilter. ENH: Improve DiscreteGaussianImage operators review classes' coverage. ENH: Add test for itk::ConicShellInteriorExteriorSpatialFunction. ENH: Print all itkHoughTransform2DCirclesImageFilter ivars. ENH: Improve coverage for itk::DisplacementFieldTransform. STYLE: Make itkPatchBasedDenoisingBaseImageFilter ivars private. STYLE: Improve the itkRobustAutomaticThreshold classes style. COMP: Fix itkDisplacementFieldTransformTest compiler warning. STYLE: Improve the itkGridForwardWarpImageFilter style. ENH: Improve coverage for itkGridForwardWarpImageFilter. ENH: Improve coverage for itkRobustAutomaticThreshold classes. ENH: Remove duplicate test files in Review. DOC: Fix itkDivideByConstantImageFilter doc error. STYLE: Improve exception message. STYLE: Improve ImageIntensity module image arithm op tests' style. STYLE: Improve HConc/Conv HMaxima/HMinima image filters' style. ENH: Improve the HConc/HConv HMaxima/HMinima filters' coverage. ENH: Improve DiscreteGaussianImage operators review classes' coverage. ENH: Change the URL for the PCA remote module repo. STYLE: Make flow control variables have a local scope. ENH: Add examples and doc build flag support for external modules. DOC: Remove wrong group tag for itk::QuadEdgeMeshExtendedTraits. BUG: Fix itk::FastMarchingImageFilter RTTI superclass name. STYLE: Improve the itk::NodePair class style. STYLE: Use the ITK_MANUAL_INSTANTIATION macro consistently. STYLE: Delete FastMarching module classes methods consistently. DOC: Fix typo in the "implementation" word across the code. Jon Haitz Legarreta Gorroño (2): STYLE: Improve itkWarpHarmonicEnergyCalculator style. DOC: Add a notice to let users know about related implementations. KWIML Upstream (1): KWIML 2017-02-27 (aa3a7733) KWSys Upstream (3): KWSys 2016-11-21 (cb55cf5a) KWSys 2017-03-28 (34999b6a) KWSys 2017-04-20 (8785f84f) Matthew McCormick (40): COMP: Add missing headers in OpenCVImageBridge COMP: Use double for gradient calculations in MinMaxCurvatureFlow ENH: Bump ITK version to 4.12.0. COMP: Add VCL support for GCC 7 COMP: Define ITK_FALLTHROUGH for GCC 7 COMP: Add missing ITK_FALLTHROUGH in TiffImageIO COMP: Avoid -Warray-bounds in FixedArray with GCC 7 COMP: Add ProcessObject include in itkLevelSetBase.hxx ENH: Exclude Kitware Robot from third party update commit messages BUG: Address tab completion with IPython >= 5.0.0 BUG: Do not use terminal_progress with the Jupyter Notebook ENH: Enable BridgeNumPy with Python wrapping COMP: Do not require numeric_traits::has_infinity BUG: Fix passing _NO_TR1 definition with VS9 and Python BUG: Do not tests that require NumPy when it is not available ENH: Build Python wrapping with hidden visibility ENH: Move morphological watersheds out of ITKReview BUG: Do not upload top level folder in ArchiveTestingDataOnGirder.py BUG: Remove unused content links from PNG test additions ENH: Add .sha512 content links for IO pallette test data BUG: Add missing export macros for SpatialObject forward declarations BUG: Always wrap basic type RGBUC COMP: Do not add Visual Studio numeric_traits workarounds with MinGWPy COMP: Increase gold linker requirement to GCC 4.9.0 COMP: Detect Windows with _WIN32 in socket++/fork.cpp BUG: Revert "BUG: Include installed modules in ITK_MODULES_ENABLED" BUG: Set ${itk-module}_ENABLE_SHARED in ITKModuleExternal BUG: PolyLineParametricPath must be loaded before PathToImageFilter COMP: Address Python 2.7 Windows _hypot build errors COMP: Undefine Py_hash_t when wrapping VtkGlue ENH: Update BridgeNumPy to most recent version (2017.03.05) BUG: Improve itkTemplate New compatibility with Python 3 ENH: Bump CastXML to 2017-04-18 STYLE: Remove empty or erroreous comments in ImageToImageFilter ENH: Use itk.imread and itk.imwrite as standard function names BUG: Correct size specification in ImportImageFilter::SetImportPointer BUG: Improve large file support in MetaIO ENH: Wrap itk::IdentifierType for ScalarToRGBColormapImageFilter BUG: LevelSetNeighborhoodExtractor uses spacing BUG: Fix PCRE 8.40 download URL MetaIO Maintainers (1): MetaIO 2017-04-08 (dead6687) Olivier Commowick (1): BUG: Correct ITK eigen system (was producing NaN or different values than VNL) Pablo Hernandez-Cerdan (4): ENH: Add SetReferenceImage to GenerateImageSource. ENH: Change the metadata of all outputs in GenerateImageSource. BUG: Fix Normalization kernel step of ConvolutionImageFilter. BUG: Remove call to Superclass::GenerateOutputInformation. Richard Beare (1): DOC: PrincipleComponent flag incorrectly reported by PrintSelf Sam Horvath (1): PERF: reduce memory usage of itkImagePCAShapeModelEstimator Samuel Gerber (2): DOC: Added description to itkLBFGSOptimizerv4.h DOC: LBFGSOptimizer doc update Shusil Dangi (2): ENH: Ignores MacOS .DS_Store file ENH: Wrap NormalVariateGenerator in the Statistics Module Simon Rit (2): BUG: memory leak in ITK_USE_THREADPOOL BUG: Join threads when using thread pool (ITK_USE_THREADPOOL) Taylor Braun-Jones (1): COMP: Only include the headers for required OpenCV modules (fixup) VXL Maintainers (2): VNL 2017-02-01 (ae6eff5e) VNL 2017-02-08 (ae8eef13) Vladimir S. FONOV (3): MINC 2017-04-28 (3d79acf3) MINC 2017-05-01 (4caf8f4c) MINC 2017-05-05 (cc682b52) Yann Le Poul (4): ENH: improvement of palette image support for PNG TIFF and BMP. STYLE: Misleading IsReadAsScalarPlusPalette Printing string STYLE: ReadAsScalarPlusPalette info already printed in itkImageIOBase BUG: ExpandRGBPalette used instead of IsReadAsScalarPlusPalette git-svn-id: http://svn.slicer.org/Slicer4/trunk@26008 3bd1e089-480b-0410-8dfb-8563597acbee |
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master aba8928c 2017-05-06 15:01:05 Details Diff |
COMP: Update CTK and fix warnings $ git shortlog a63253f..7129bb0 --no-merges Jean-Christophe Fillion-Robin (2): Update QtTesting to fix overload warnings COMP: ctkErrorLogFDMessageHandler: Fix "unused-result" warning git-svn-id: http://svn.slicer.org/Slicer4/trunk@26007 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/QTCLI/qSlicerCLIModuleWidgetEventPlayer.h | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLCheckableNodeComboBoxEventPlayer.h | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLNodeComboBoxEventPlayer.h | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLNodeComboBoxEventTranslator.h | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLTreeViewEventPlayer.h | Diff File | ||
| mod - Libs/MRML/Widgets/qMRMLTreeViewEventTranslator.h | Diff File | ||
| mod - SuperBuild/External_CTK.cmake | Diff File | ||
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master 67b25be0 2017-05-06 00:52:23 Details Diff |
BUG: Update EMSegment: Fix "comparison of pointer with integer zero" warning This commit is similar to r24685 but applies to vtkLevelSets instead vtkImageLevelSets EMSegment updates: ------------------------------------------------------------------------ r17129 | jcfr | 2017-05-06 00:48:04 -0400 (Sat, 06 May 2017) | 1 line COMP: vtkLevelSets: Removed variable to fix unused-but-set-variable warning ------------------------------------------------------------------------ r17128 | jcfr | 2017-05-06 00:43:27 -0400 (Sat, 06 May 2017) | 21 lines BUG: vtkLevelSets: Fix logic error in vtkLevelSets::CheckConvergence This commit fixes logic error reported as "-Wextra" warning. It integrates fix similar to r17108 that was specific to vtkImageLevelSets.h 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- /path/to/EMSegment/AMF/vtkLevelSets.cxx: In member function ‘unsigned char vtkLevelSets::CheckConvergence()’: /path/to/EMSegment/AMF/vtkLevelSets.cxx:1279:24: warning: ordered comparison of pointer with integer zero [-Wextra] if (this->u[p] <= 0) total++; ^ /path/to/EMSegment/AMF/vtkLevelSets.cxx:1284:65: warning: ordered comparison of pointer with integer zero [-Wextra] if ((this->stored_seg[p] == ON_STORED) && (this->u[p] > 0)) ^ /path/to/EMSegment/AMF/vtkLevelSets.cxx:1287:66: warning: ordered comparison of pointer with integer zero [-Wextra] if ((this->stored_seg[p] == OFF_STORED) && (this->u[p] <= 0)) ^ /path/to/EMSegment/AMF/vtkLevelSets.cxx:1291:24: warning: ordered comparison of pointer with integer zero [-Wextra] if (this->u[p] <= 0) ^ 8<---8<---8<---8<---8<---8<---8<---8<---8<---8<--- git-svn-id: http://svn.slicer.org/Slicer4/trunk@26006 3bd1e089-480b-0410-8dfb-8563597acbee |
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master ffa442b8 2017-05-06 00:52:22 Details Diff |
STYLE: qMRMLSegmentEditorWidget: Fix unused variable and reorder warnings git-svn-id: http://svn.slicer.org/Slicer4/trunk@26005 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx | Diff File | ||
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master ff890408 2017-05-06 00:52:20 Details Diff |
STYLE: SHDiffusionTensorVolumesPlugin: Fix unused variable warnings git-svn-id: http://svn.slicer.org/Slicer4/trunk@26004 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyDiffusionTensorVolumesPlugin.cxx | Diff File | ||
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master 89278ced 2017-05-06 00:52:18 Details Diff |
STYLE: vtkMRMLSegmentationNode: Fix "unused parameters" warnings git-svn-id: http://svn.slicer.org/Slicer4/trunk@26003 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLSegmentationNode.cxx | Diff File | ||
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master c9b4644e 2017-05-06 00:52:16 Details Diff |
STYLE: vtkMRMLScalarVolumeDisplayNode: Fix "narrowing conversion" warning git-svn-id: http://svn.slicer.org/Slicer4/trunk@26002 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLScalarVolumeDisplayNode.cxx | Diff File | ||
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master f6df62e8 2017-05-05 23:53:44 Details Diff |
ENH: Ensure node loaded by volume logic respect default nodes To that effect, this commit introduces the new method "vtkMRMLScene::AddNewNodeByClass()". It allows to: (1) easily create a node by className, optionally set its name and then add it to the scene. (2) ensure properties of loaded node are initialized considering default nodes. Suggested-by: Andras Lasso <lasso@queensu.ca> Reviewed-by: Andras Lasso <lasso@queensu.ca> Thanks: Andras Lasso <lasso@queensu.ca> git-svn-id: http://svn.slicer.org/Slicer4/trunk@26001 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/MRML/Core/vtkMRMLScene.cxx | Diff File | ||
| mod - Libs/MRML/Core/vtkMRMLScene.h | Diff File | ||
| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx | Diff File | ||
| mod - Modules/Loadable/Volumes/Testing/Cxx/vtkSlicerVolumesLogicTest1.cxx | Diff File | ||
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master 50f6752f 2017-05-05 23:53:41 Details Diff |
BUG: Update Volume loading to consider LabelMap DisplayNode default properties This commit enables customization of the LabelMapVolumeDisplayNode attributes by ensuring the custom properties set on the corresponding default node are effectively re-used. git-svn-id: http://svn.slicer.org/Slicer4/trunk@26000 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx | Diff File | ||
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master 7345cd30 2017-05-05 14:37:10 Details Diff |
BUG: Fixed crash when sending node via OpenIGTLink Updated to OpenIGTLinkIF version that contains the fix (recent regression). git-svn-id: http://svn.slicer.org/Slicer4/trunk@25999 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - SuperBuild.cmake | Diff File | ||
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master 84f11249 2017-05-04 16:20:39 Details Diff |
BUG: Use segment ID in AddEmptySegment Even if segment ID was specified, that argument was not used, and the segment name became the actual segment ID. git-svn-id: http://svn.slicer.org/Slicer4/trunk@25998 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Libs/vtkSegmentationCore/vtkSegmentation.cxx | Diff File | ||
