ITK/Release 4.12 Changed From Previous
Changes from v4.12rc03 to v4.12.0
Bradley Lowekamp (1):
COMP: Inform Doxygen of ITK_FORCE_EXPORT_MACRO
Francois Budin (2):
BUG: Remove weak symbol warnings on MacOS in VNL template classes BUG: Replace class forward declaration attributes with ITK_FORWARD_EXPORT
Hans Johnson (2):
COMP: Remove unused boiler plate constants COMP: Incorrect scope resolution for typename
Jared Vicory (1):
BUG: Fix LBFGS crash when minimum is starting point.
Matthew McCormick (6):
COMP: Use ITK_TEMPLATE_EXPORT in explicit export forward declarations COMP: Suppress global weak symbol warnings for std::vector COMP: Linux explicitly instantiated build errors BUG: ITKIONIFTI DEPENDS on ITKNIFTI BUG: Remove duplicate VectorContainer integer wrapping BUG: Remove duplicate ImageSource Covariant Vector wrapping
Vladimir S. FONOV (1):
MINC 2017-05-28 (002d510c)
Changes from v4.12rc02 to v4.12rc03
Bradley Lowekamp (4):
BUG: include HDF5 config in ITK config BUG: Add fixed seed to registration tests ENH: Use scikit-ci-addons for CiricleCI CMake installation and junit BUG: Initialized the sampling seed for v3 registration test
Francois Budin (1):
ENH: Remove 'weak symbol' warning on MacOS
Matthew McCormick (5):
BUG: itk.ctype does not understand ints without signed BUG: Rename WrapITKBuildOptionsPython.py to itkBuildOptions.py DOC: Remove Doxygen note about GDCM version BUG: Bump Bridge NumPy to address Windows long sizes COMP: Suppress macOS std::string linker visibility warnings
Vladimir S. FONOV (1):
MINC 2017-05-19 (f6853a70)
Changes from v4.12rc01 to v4.12rc02
Christina Rossmanith (1):
BUG: calculate levelSetValue for IsoContourFilter with float precision
David T. Chen (1):
DOC: Fix Pysical Typo
Francois Budin (3):
BUG: Remove doxygen warnings 'Found unknown command \epsilon' ENH: Remove warning messages in GCC 5.1 due to ITK_TEMPLATE_EXPORT BUG: GCC 5.1 warnings 'type attributes ignored after type is already defined'
Jon Haitz Legarreta Gorroño (1):
DOC: Add use note to itkGridForwardWarpImageFilter.
Matthew McCormick (1):
BUG: Update the Strain remote module to 2017-05-05
Vladimir S. FONOV (3):
MINC 2017-04-28 (3d79acf3) MINC 2017-05-01 (4caf8f4c) MINC 2017-05-05 (cc682b52)
Changes from v4.11.0 to v4.12rc01
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 (2):
ENH: Introduce ITK_WRAP_PYTHON_LEGACY to exclude older Python package layout BUG: ITKPython: Do not install *.mdx files required only at generation time
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)
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
ITK Sphinx Examples Changes
Beatriz Paniagua (1):
ENH: Add FlipImageFilter
Dženan Zukić (3):
BUG: fixing misspelled directory name ENH: translating ImageReadExtractFilterInsertWrite into Python ENH: updating TODO list with recent patches
Francois Budin (4):
BUG: Reducing Windows path length was not consistent ENH: Import data into an ITK Image BUG: Move FlipImageFilter from src/Core/Common to src/Filtering/ImageGrid
Maeliss Jallais (1):
ENH: Add ReadWriteVectorImage
Matt McCormick (32):
BUG: Clean up ObserveAnEvent ENH: Add .sha512 content links ENH: Remove .md5 content links ENH: Update ExternalData_URL_TEMPLATES for sha512 resources ENH: Update the ITKExamples scripts to use the .sha512 content links ENH: Update CMake/ExternalData.cmake ENH: Remove Utilities/UploadBinaryData.py.in ENH: Remove Utilities/ArchiveBinaryData.py.in ENH: Remove pydas and related submodules ENH: Bump ITK to 2017-03-06 master ENH: Use GitHub for faster ITK repository downloads DOC: Update UploadBinaryData.rst DOC: Tweak content link usage with girder-cli DOC: Remove ContributeWithWebInterface.rst DOC: Swap WriteANewExample / ContributeWithGit order ENH: Do not build the Python wrapping in the Superbuild ENH: Enable ITKExamples_USE_WRAP_PYTHON by default ENH: Create itkpython virtualenv on Mac and Linux STYLE: Do not uses spaces after/before brackets in CMakeLists.txt ENH: Add the superbuild itkpython binary folder to FindSphinx BUG: CreateNewExample.py outputs template Code.py ENH: Download itkpython in the Windows superbuild DOC: Recommend cloning into a short directory on Windows ENH: Reduce Windows superbuild path length requirements BUG: Fix BoundingBoxOfAPointSetTestPython on Windows ENH: Add example image filenames in template figure directive ENH: Add Create An Image example BUG: CreateAImageRegion -> CreateAnImageRegion BUG: Fix CreateAnImageRegion output regex matching STYLE: Address spacing in CreateAnImage BUG: Update the Python package URL, nightly to latest DOC: How to run a Python example
Max Smolens (5):
BUG: Fix errors in generated Code.py ENH: Remove CannyEdgeDetectionImageFilter TODO items ENH: Add itk.RGBToLuminanceImageFilter Python example DOC: Fix typo in contribution documentation ENH: Add WarpImageFilter example
Neal Siekierski (1):
ENH: Add example of itk::Statistics::Histogram creation and access
Sam Horvath (2):
ENH: Add CreateAnImageOfVectors ENH: Add BlurringAnImageUsingABinomialKernel
ITK Software Guide Changes
Jon Haitz Legarreta (1):
DOC: Add testing section to SW guide.
Matt McCormick (6):
DOC: Document itk_module_add_library DOC: Modules without a src/ directory should not set ENABLE_SHARED Merge "DOC: Add testing section to SW guide." DOC: Update the Kitware BrainWeb data link BUG: Escape hash in Girder URL DOC: Add Python package installation instructions