ITK Release 5.0 Beta 1#
We are happy to announce the first beta release for ITK 5. This release features an additional, more Pythonic interface to filters. This interface is more familiar in Python and facilitates rapid prototyping. ITK 5.0 Beta 1 also includes many performance-related improvements, such as a pure C++11 thread pool by default, an HDF5 update to 1.10, new frequency domain iterators, new neighborhood range classes, and a new multi-dimensional, multi-component superpixel class.
The traditional, object-oriented interface to ITK’s Python classes allows the composition of filters in a pipeline. After setting up a chain of filters,
Update() is called at the end of the pipeline. This facilitates streaming of very large images that may exceed the system’s memory capacity. For example,
import itk input_image = itk.imread('input.nrrd') ImageType = type(input_image) radius = 2 median_filter = itk.MedianImageFilter[ImageType, ImageType].New() median_filter.SetInput(input_image) median_filter.SetRadius(radius) median_filter.Update() output_image = median_filter.GetOutput() itk.imwrite(output_image, 'output.nrrd')
While powerful, this interface is verbose.
A procedural interface is now available with PEP8-compliant snake case naming of all filters that inherit from
itk.ProcessObject. For example,
import itk input_image = itk.imread('input.nrrd') radius = 2 output_image = itk.median_image_filter(input_image, radius=radius) itk.imwrite(output_image, 'output.nrrd')
In this case, the type of the filter is implicitly determined by the input image type. Immediately, the filter is executed, and the result is directly returned. Object parameters defined by
Set* methods can be specified in the filter call with keyword arguments. The Pythonic, snake case form of these parameters can also be used.
PEP8 function naming has also been applied to the NumPy bridge.
array = itk.array_from_image(image)
array = itk.array_from_image(image)
Similar functions names are available when creating NumPy array views,
itk.Image’s from NumPy arrays, and converting VNL vector and matrices to NumPy arrays.
To test the 5.0 Beta 1 Python packages, run
python -m pip install --upgrade pip python -m pip install --upgrade --pre itk
Based on experiences since initial changes introduced in ITK 5 Alpha 2, many notable performance improvements have been made.
The default thread pool is now fully backed by C++11 threading primitives.
itk::MultiThreaderBase::ParallelizeArrayfunction is available to quickly and easily dispatch C++11 lamda’s or std::function’s on linearly indexed containers, similar to
itk::MultiThreaderBase::ParallelizeImageRegionfor operating on N-dimensional image regions.
itk::MultiThreaderBase::ParallelizeImageRegionRestrictDirectionfunction is available to prevent splitting an image region over a given direction.
SetNumberOfThreadshas been renamed to
SetNumberOfWorkUnitsto more accurately reflect configuration of work unit granularity, especially in the context of the Threading Building Blocks (TBB) backend.
Progress reporting with multiple parallel operations is enabled with a new
A large corpus of code has been transitioned ITK 5, and the process is now relatively straight forward and well documented. Please see the ITK 5 Migration Guide for more information.
Classes in the C++11 standard library are now preferred over ITK’s implementations. This includes atomic integers, mutex locks and related classes, and hash maps. For more information, please see the migration guide.
A set of new iterators and a band pass filter are available in a new ITKImageFrequency module. These classes help when operating in the dual domain and with the output of FFT’s. More details are available in this Insight Journal article.
A new Simple Linear Iterative Clustering (SLIC) super-pixel segmentation filter is available. This implementation improves or the original algorithm by supporting arbitrary dimensions, multi-component images, and a parallized implementation. More details are available in the Insight Journal article.
Visible Human superpixel segmentation. A 2D slice of 3D superpixel. For more information, see the Insight Journal article, Scalable Simple Linear Iterative Clustering (SSLIC) Using a Generic and Parallel Approach, Lowekamp, B et al, https://hdl.handle.net/1926/3596.
There are many more bug fixes and critical improvements not mentioned above. For more details, please see the change log below. Congratulations to everyone who contributed to this release.
Please discuss your experiences on Discourse. The community has been quite active in testing and improving these changes for the next major release of ITK. Another beta release is planned for the October-November time period.
Changes from v5.0a02 to v5.0b01 ----------------------------------------------- Bradley Lowekamp (47): BUG: Prevent concurrent read/write in output image BUG: Handle case where output image is zero sized BUG: Add missing dependencies in Module testing ENH: Remove SPECIFIC_IMAGEIO_MODULE_TEST feature BUG: Fix name typo for ITK_GLOBAL_DEFAULT_THREADER BUG: Fix incorrect library variable for MeshIO test drivers ENH: Create TestKernel library COMP: Fix overflow in floating-point conversion warning ENH: Add SLIC segmentation to new Superpixel module COMP: Fix C++11 compatibility with assert in constexpr COMP: Use std::min over vnl_math_min BUG: Fix index type and and number of indexes BUG: Add alternate baseline itkSLICImageFilterTest1 test ENH: Update test output to include test name BUG: improve numeric consistency in linear algorithm COMP: Add missing overrride to virtual destructor ENH: TileImageFilter learns to use VectorImages COMP: Remove unused testing function and headers BUG: Finish updating to ScanlineIterator in nonlinear method ENH: Update SLIC filter to use new ITK threading model ENH: TileImageFilter learns to use VectorImages ENH: Update SimpleITKFilters remote modules COMP: remove duplicate declaration of TempImageType DOC: Add link to published Insight Journal paper ENH: Update CenteredTransformInitializer print self method PERF: Remove internal streaming in DiscreteGaussianImageFilter ENH: Update MinimumMaximumImageFilter to use dynamic threading ENH: Update StatisticsImageFiler to use DynamicThreadedGenerateData ENH: Add compensated summation to the StatisticsImageFitler BUG: Use pip to install cmake BUG: Use pip to install cmake for release PERF: Use the recursive Gaussian filter in registration method BUG: Add additional baseline for debug COMP: Length GTest discovery timeout BUG: Correct image used for debug SimpleImageRegistrationTest BUG: Add cxx suffix to specified source GTest code ENH: Consistently use default OutputWindow for messages BUG: Explicitly set sampled pointset in virtual domain ENH: Use std::enable_if and std::is_same in filters PERF: Memory alloc reduction in ComputeJacobianWithRespect PERF: Improve MatrixOffset Jacobian computation performance COMP: Address signed to unsigned comparison warning STYLE: Cleanup development comments PERF: perform matrix multiplication in-place for composite Jacobian ENH: Provide explicitly instantiated vnl_svd_fixed PERF: Change type of Jacobian w.r. position to vnl_matrix_fixed PERF: Change the purpose of the cache jacobian argument Brian Avants (1): PERF: Only throw exception if zero valid points Chao Wu (2): ENH: Enable writing scl_slope and scl_inter in NIfTI header BUG: Missing SetCPUBufferPointer in GPUImage<...>::SetPixelContainer(...) Dženan Zukić (45): STYLE: a more direct link (after PR has been merged) STYLE: update clang-format configuration ENH: adding ParallelizeArray method to MultiThreaderBase COMP: fixing warning in external module COMP: Address usage of deleted assignment operator ENH: more thorough removal of deprecated "multiple method" DOC: add compatibility warning to Barrier STYLE: initializing SingleMethod/SingleData in base class DOC: merging instructions from itkMultiThreader.h into migration guide ENH: rename NumberOfThreads into NumberOfWorkUnits in filters ENH: Add backwards compatibility for Get/SetNumberOfThreads ENH: renaming NumberOfThreads into NumberOfWorkUnits in MultiThreaderBase ENH: adding backwards compatibility for MultiThreaders ENH: default number of work units is greater than default number of threads COMP: fixing compile warning on GCC 4.8 ENH: rewriting thread pool to take advantage of C++11 ENH: implement Parallelize Array and ImageRegion in PoolMultiThreader COMP: SmoothingRecursiveYvvGaussianFilter compiles with new ITKv5 threading ENH: RGB/RGBA consistency, operator / and remove comments from implementation ENH: refactoring RecursiveSeparableImageFilter to use new threading ENH: updating MCI: adjusting to split between threads and work units in ITKv5 ENH: compute spacing using n-1 instead 2-1 in ImageSeriesReader BUG: updating the HDF5 symbol mangling ENH: fix reading of oblique image series BUG: fixing crash in ThreadPool's destructor COMP: fixing warning about shadowed global COMP: avoid warning with CMake 3.12 and newer regarding policy CMP0075 ENH: write format which is backwards-compatible with HDF5 version 1.8 ENH: refactoring BinaryImageToLabelMapFilter to use the new threading model ENH: adding ProgressTransformer ENH: proper backwards compatibility to HDF5 1.8 STYLE: fixing 'No new line at the end of file' ENH: adding short description of split between threads and work units ENH: rewriting BarrierTest to work with any MultiThreader ENH: cause compile error with HDF5 version 1.10.0 and 1.10.1 STYLE: fixing 'No new line at the end of file' ENH: restore BeforeThreadedGenerateData method DOC: state that SetRecursive must be called before SetInputDirectory BUG: updating the symbol mangling list BUG: removing mangling of unversioned variant of versioned definitions ENH: update migration guide: prefer C++11 classes over ITK's ENH: cleaning up ProcessObject ENH: using progress transformer in recently refactored classes COMP: fixing LoggerBase to compile even when DEBUG is defined DOC: ProgressReporter should be replaced by ProgressTransformer Francois Budin (3): BUG: Improvements to ITK NumPyBridge DOC: Improve exception message to precise what image sizes can be processed BUG: Improvements to ITK NumPyBridge GCC-XML Upstream (1): ENH: pygccxml develop (reduced) GDCM Upstream (1): GDCM 2018-05-23 (69cb71a4) HDF5 Maintainers (3): HDF5 2016-05-10 (7453bbef) HDF5 2018-07-20 (bed5b207) HDF5 2018-08-22 (08d77e43) Hans Johnson (6): ENH: HDF5 moved from svn to git ENH: Update HDF5 import script for 1.10.2 ENH: Remove svn version of hdf5 files not added by import from git STYLE: Consistently name for ITK conventions BUG: Fixing the HDF5 internal path names tests COMP: Fix const assignment error in testing Isaiah Norton (3): BUG: prevent segfault when transform reader fails to load .mat PERF: improve DCMTKFileReader::CanReadFile perf BUG: prevent segfault when transform reader fails to load .mat Jean-Christophe Fillion-Robin (1): BUG: Refactor itkFloatingPointExceptions to fix macOS support Jon Haitz Legarreta (1): ENH: User initialization lists over direct assignment. Jon Haitz Legarreta Gorroño (4): ENH: Add the ITK BoneMorphometry module as a remote. COMP: Bump remote modules versions. ENH: Clean up itkGrayscaleMorphologyImageFilter tests. ENH: Increase itk::OtsuMultipleThresholdsImageFilter coverage. KWSys Upstream (1): KWSys 2018-06-01 (8ef62b28) Kwame Kutten (2): BUG: Removed quotes from fftwf and fftwd hashes ENH: Make StatisticsImageFilter returns Sum Of Squares Marian Klymov (1): ENH: Mark copy constructor of ExceptionObject and derived classes noexcept. Matthew McCormick (39): COMP: Reduce example line lengths for inclusion in the SG COMP: Remove duplicate InPlaceImageFilter wrapping for RGB -> UC BUG: Do not copy workbox files when BUILD_DOCUMENTATION is OFF COMP: Remove duplicate BinaryGeneratorImageFilter class wrapping BUG: Migrate midas3.kitware.com to data.kitware.com ENH: Remove itkzlib in preparation for subtree update ENH: Add ZLIB UpdateFromUpstream.sh BUG: Do not use P-threads with Emscripten COMP: Remove extra argument from HoughTransform3DCircles wrapping ENH: Update testing data content links BUG: Correct Windows and macOS CastXML hashes BUG: Fix SLICImageFilter wrapping BUG: Improve backwards compatibility of BoxUtilities functions BUG: Remove commented, unused Python wrapping configuration BUG: Remove deprecated GetPointer wrapping method ENH: Python snake case functions BUG: Remove deprecated itk.write function BUG: Remove unmaintained itk.show, itk.show2D ENH: Add snake case function aliases for NumPy conversions DOC: ITK 5 now requires CMake 3.10.2 BUG: Bump SplitComponents remote module to 2018-07-18 BUG: Remove TBBImageToImageFilter remote module BUG: Correct Windows and macOS CastXML hashes COMP: Set CMake project command VERSION COMP: Do not wrap itk::ThreadJob COMP: Set CMake project command VERSION ENH: Add ParallelizeImageRegionRestrictDirection COMP: Bump CastXML for Visual Studio 2017 support ENH: Bump pygccxml hash to 2018-08-07 develop branch ENH: Update pygccxml git subtree version BUG: Remove ArchiveTestingDataOnMidas.py BUG: Use manylinux to build CastXML linux executable BUG: Avoid symlink issues in UpdateThirdPartyFromUpstream.sh DOC: Additional information and updates on bug fix release process COMP: Prevent duplicate wrapping ouput file specification COMP: Support instantiation of a 1D TranslationTransform DOC: Update how to reference a GitHub issue in the commit-msg hook DOC: ITK 5 Migration Guide grammar tweaks ENH: PEP8 for itk.Extras arguments MetaIO Maintainers (1): MetaIO 2018-07-17 (6328f544) Niels Dekker (14): DOC: Fixed \code sections ShapedImageNeighborhoodRange and added \author STYLE: Renamed RelativeIndices to ShapeOffsets in ShapedImageNeighborhoodRange ENH: Added ConnectedImageNeighborhoodShape, for N-connected neighborhoods ENH: Added operator to ShapedImageNeighborhoodRange ENH: Documented + tested order offsets ConnectedImageNeighborhoodShape COMP: Fixed conversion to PDFValueType in MattesMutualInfo...Threader ENH: Added reverse iterators to ShapedImageNeighborhoodRange STYLE: Removed HoughTransform2DCircles default for TRadiusPixelType ENH: Changed type float data members HoughTransform filters to double ENH: Added Functor::CoLexicographicCompare ENH: Made Functor::LexicographicCompare more generic and easier to use BUG: Added default-constructor iterator ShapedImageNeighborhoodRange ENH: Added ImageNeighborhoodPixelAccessPolicy for custom border extrapolation STYLE: Removed LinearInterpolateImageFunction::m_Neighbors Pablo Hernandez-Cerdan (11): COMP: Remove ignored const qualifier in template. COMP: Fix warnings -Wcatch-value ENH: Update isotropic wavelets module. ENH: Add frequency iterators and band pass filter. COMP: Update IsotropicWavelets, remove FrequencyIterators STYLE: Remove comment in ITKImageFrequency cmake BUG: Fixes generating floating point exceptions COMP: Fix warnings in cdash introduced after FPE. DOC: Add example using std::atomic for multithreading. STYLE: Mark CMAKE_DEBUG_POSTFIX as advanced. COMP: Avoid extra point copy in MetaTube Sean McBride (2): COMP: Fixed warning about missing case label in public header COMP: Fixed three misc clang warnings Simon Rit (1): ENH: allow wrapping of XML writers VXL Maintainers (3): VNL 2018-07-26 (2a77e40b) VNL 2018-08-04 (3dafea87) VNL 2018-09-05 (fc0c9043) Vladimir S. FONOV (1): MINC 2018-08-09 (ce4333ca) Zlib Upstream (1): zlib 2018-06-11 (355d8648)