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.
For an overview of ITK 5 performance-related changes and the transition to modern C++, see the ITK 5 Alpha 1: Modern C++ and ITK 5 Alpha 2: Performance release announcements.
Python Interface
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.GetArrayFromImage(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
Performance Improvements
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.
- A new
itk::MultiThreaderBase::ParallelizeArrayfunction is available to quickly and easily dispatch C++11 lamda’s or std::function’s on linearly indexed containers, similar toitk::MultiThreaderBase::ParallelizeImageRegionfor operating on N-dimensional image regions. - A new
itk::MultiThreaderBase::ParallelizeImageRegionRestrictDirectionfunction is available to prevent splitting an image region over a given direction. -
SetNumberOfThreadshas been renamed toSetNumberOfWorkUnitsto 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
itk::ProgressTransformerclass. - A large corpus of code has been transitioned to ITK 5, and the process is now relatively straight forward and well documented. Please see the ITK 5 Migration Guide for more information.
Style changes
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.
New Classes
- 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.
- New, experimental ShapedImageNeighborhoodRange, HyperrectangularImageNeighborhoodShape classes are available, providing modern, C++ range operations and high performance.
- A new Simple Linear Iterative Clustering (SLIC) super-pixel segmentation filter is available. This implementation improves on 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, http://hdl.handle.net/1926/3596.
What’s Next
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): @blowekamp
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): @stnava
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): @dzenanz
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): @fbudin
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): @hjmjohnson
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): @ihnorton
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): @jcfr
BUG: Refactor itkFloatingPointExceptions to fix macOS support
Jon Haitz Legarreta Gorroño (5): @jhlegarreta
ENH: User initialization lists over direct assignment.
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): @matt.mccormick
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): @Niels_Dekker
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): @phcerdan
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): @seanm
COMP: Fixed warning about missing case label in public header
COMP: Fixed three misc clang warnings
Simon Rit (1): @simon.rit
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): @Vladimir_Fonov
MINC 2018-08-09 (ce4333ca)
Zlib Upstream (1):
zlib 2018-06-11 (355d8648)
Enjoy ITK!