ITK 4.12 Release Candidate 1 is ready for testing!
On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.12 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, use the links:
https://github.com/Kitware/ITK/archive/v4.12rc01.zip
https://github.com/Kitware/ITK/archive/v4.12rc01.tar.gz
Morphological watershed segmentation of a CT head slice. From “The watershed transform in ITK – discussion and new developments”, Richard Beare and Gaëtan Lehmann. The Insight Journal. http://hdl.handle.net/1926/202. These contributions have been moved into the ITKWatersheds module in the 4.12 release.
A few selected highlights for this release:
– Strain remote module added to ITK. Strain quantifies local deformation of a solid body. In medical imaging, it can be used to quantify growth or atrophy of tissue. The module contains filters to compute a strain tensor image from a displacement field image or a general spatial transform. In both cases, infinitesimal, Green-Lagrangian, or Eulerian-Almansi strain can be generated.
– Many improvements in ITK Python wrapping: convenient functions to read and write images, better integration in Jupyter Notebook, new filters wrapped, build support for Microsoft Visual C++ Compiler for Python 2.7
– Better compilation support for Microsoft Visual Studio 2017, Clang 4, GCC7
– Filters moved out of Review modules: Morphological Watersheds, and itkHessianToObjectnessMeasureImageFilter
– Improvement of palette image support for PNG TIFF and BMP: The user can now choose whether or not to expand the palette image to true color.
– Performance improvements for some ITK filters: itkHistogram (increase speed), itkImagePCAShapeModelEstimator (decrease memory usage).
Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review.
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 to the 23 contributors to this release. We would especially like to recognize the new contributors: Sam Horvath, Shusil Dangi, Ben Boeckel, Yann Le Poul, Jean-Baptiste Vimort, and Samuel Gerber.
The 4.12.0 final release is scheduled for May 24th.
New Features
* Wrapping Improvements
– Enable BridgeNumPy by default with Python wrapping
– Build support for Microsoft Visual C++ Compiler for Python 2.7
– BridgeNumpy integrates new pairs of functions. GetArrayViewFromImage() and GetImageViewFromArray() return views on the source object given as a parameter to the function. Memory is shared among input and output objects and the source object still manages pixel buffer memory. The existing functions GetArrayFromImage() and GetImageFromArray() perform a deep copy of the source object.
– Similar NumPy bridge functions have been created for VNL matrices and VNL vectors.
– Convenience functions imread() and imwrite() have been added to the Python itk namespace. These functions facilitate respectively reading and writing images using ITK without having to specify the input or output image component type. The naming of these functions follows the convention used in several other Python project such as scikit-learn and scipy.
– Better integration in Jupyter Notebook: addressed tab completion bug for IPython >= 5.0.0, replaced underscore with ‘x’ to name attributes that start with a digit to show attributes when trying to autocomplete in IPython.
– Wrap itkN4BiasFieldCorrectionImageFilter, NormalVariateGenerator, and PathToImageFilter.
– Allows calling ImageFileWriter in Python with an ITK filter as input image argument.
– Build Python wrapping with hidden visibility
* New Remote Modules
– Strain: Filters to estimate a strain tensor field from a displacement field or a spatial transformation (http://hdl.handle.net/10380/3573)
* Core Improvements
– Enable hidden visibility property with NIFTI and GIFTI static libraries
– Fix clearing build tree error
– Add examples and doc build flag support for external modules
– Support for recent Clang in FreeBSD
– Improved support for Visual Studio 2017
– Prefer std::atomic over compiler specific implementation
* Filtering Improvements
– Add OrientedBoudingBox attributes to ShapeLabelMap
– Prefer std::atomic over compiler specific implementation
– Skip generating export headers if module does not contain a target
– Introduce ITK_WRAP_PYTHON_LEGACY to exclude older Python package layout
– Move morphological watersheds out of ITKReview
– Add SetReferenceImage to GenerateImageSource
– Reduce memory usage of itkImagePCAShapeModelEstimator
– Improvement of itkHistogram in order to make it faster
– Better compatibility with OpenCVImageBridge
* IO Improvements
– Improvement of palette image support for PNG, TIFF and BMP
* Documentation Improvements
– Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples
* Remote Module Updates
– BridgeNumPy updated to latest upstream (04.28.2017)
* Third Party Library Updates
– Update SWIG version to 3.0.12
– Update PCRE version to 8.40
– MetaIO updated to latest upstream (04.08.2017)
– KWSys updated to latest upstream (04.20.2017)
– KWIML updated to latest upstream (02.27.2017)
– VNL updated to latest upstream (02.01.2017)
* Improved Code Coverage — we are at 85.7%
– Jon Haitz-Legarreta’s extensive code coverage improvements
* *Lots* of important bug fixes
* And much more! See details in the log below.
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 (57):
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
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 (133):
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.
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