We are happy to announce that the Insight Toolkit (ITK) 5.1 Beta 1 is available for testing! 
ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration.
ITK 5.1 Beta 1 is a pre-release to enable testing of major improvements to ITK’s NumPy interface.
Python Packages
ITK Python packages can be installed by running:
pip install --upgrade --pre itk
The --pre flag will install the beta pre-release.
Library Sources
Testing Data
Unpack optional testing data in the same directory where the Library Source is unpacked.
Checksums
Pass NumPy Array’s to ITK Image Filters
The Pythonic, functional-like interface to all ITK image-to-image-filters now directly supports operation on NumPy array’s, i.e. numpy.ndarray. If a ndarray is passed as an input, a ndarray is returned as an output.
For example,
smoothed = itk.median_image_filter(array, radius=2)
Previously, explicit conversion to / from an itk.Image was required with itk.array_from_image and itk.image_from_array.
We can now also convert an itk.Image to a numpy.ndarray with the standard np.asarray call.
import numpy as np
import itk
image = itk.imread('/path/to/image.tif')
array = np.asarray(image)
Python 3 Only
ITK 5.1 will be the first Python 3-only release. Consistent with most scientific Python packages and CPython’s 2020 drop in support, Python 2 support and binaries will no longer be available.
clang-format enforced C++ coding style
ITK has adopted a .clang-format coding style configuration file so a consistent coding style can automatically be applied to C++ code with the clang-format binary. A consistent coding style is critical for readability and collaborative development.
clang-format has been applied to the entire codebase. The Whitesmiths style of brace indentation, previously part of the ITK Coding Style Guidelines, is not supported by clang-format, so it has been replaced by a brace style consistent with VTK’s current style.
A Git commit hook will automatically apply clang-format to changed C++ code. We are refining the related documentation and improving automated application of the style.
Point Set Registration Parallelism
ITK provides a powerful registration framework for point-set registration, offering information-theoretic similarity metrics, labeled point-set metrics, and spatial transformation models that range from affine to b-spline to dense displacement fields. ITK 5.1 features enhanced parallelism in point-set metric computation, leveraging the native thread-pool and Threading Building Blocks (TBB) enhancements in ITK 5.
ITK 5 Improvements
Many more improvements and refinements were added since the ITK 5.0.0 release, which are detailed in the change log below. For example, a number of improvements were made to the itk::SpatialObject’s.
Congratulations
Congratulations and thank you to everyone who contributed to this release. Of the 25 authors, we would like to specially recognize the new contributors: James Butler, Neslisah Torosdagli, Rinat Mukhometzianov, Genevieve Buckley, and yjcchen091.
What’s Next
Additional improvements ITK’s NumPy interface are planned for the next pre-release. Try out the current release, and take part in the community discussion at discourse.itk.org. Contribute with pull requests, code reviews, and issue discussions in our GitHub Organization.
Enjoy ITK!
Changes from 5.0.0 to 5.1 Beta 1
Bradley Lowekamp @blowekamp (32):
BUG: Use ProcessObject GetInput to obtain base pointer
BUG: Fix ProcessObject::RemoveOutput for null objects.
COMP: Address missing fftw include in CurvatureRegistrationFilter
BUG: Fix ProcessObject::RemoveOutput for null objects.
BUG: Add casting for vector pixel types
STYLE: Use CTEST_TEST_TIMEOUT
ENH: Add testing for CastImageFilter for more type conversions
BUG: Restore support for Cast between explicitly cast-ed pixel type
BUG: Use ProcessObject GetInput to obtain base pointer
ENH: Add testing for CastImageFilter for more type conversions
BUG: Restore support for Cast between explicitly cast-ed pixel type
BUG: Add DataObject::New method
BUG: Install FFTW headers in same location as ITK
Revert "BUG: InterpolateImageFunction::GetRadius hidden in ITKV4_COMPATIBILITY"
BUG: Preserve Interpolate GetRadius behavior with ITKv4Compatibility
Revert "COMP: forgotten class for ITKV4_COMPATIBILITY in 2aae174"
BUG: HDF5 is clobbering ctest TIMEOUT variables
COMP: Fix not marked 'override' for ImageSink destructor
BUG: Use enable_if with SFINAE to dispatch
ENH: Add Vector constructor from C arrays with cast
COMP: Work around uninitialized value warnings
ENH: Update ITKv4 registration example to use resample over warp
BUG: Specify specific CircleCI docker image with platform
COMP: Address compilation warning with aggregate initializer
BUG: Specify specific CircleCI docker image with platform
ENH: Adding VS2019 v142, VS2017 v140 Azure Pipelines on merge
DOC: Tweak internal documentation in SliceImageFilter
BUG: Address bug with small size in output of SliceImageFilter
ENH: Add more test cases for the SliceImageFilter
COMP: Address internal compiler error on MSVC 19.0.24234.1 (v140)
ENH: Add check expected input in HistogramMatchingImageFilter
COMP: Add missing enum type_name from prior enum declaration style
Csaba Pinter @cpinter (2):
BUG: Fix loading of DICOM files with no preamble
ENH: Add test for DICOM without preamble for DCMTK and GDCM
Davis Vigneault @DVigneault (1):
BUG: Make BuildCellLinks method const
Dženan Zukić @dzenanz (32):
BUG: number of work units was greater than 1 even for 1 thread
BUG: fix a crash with ITK_DEFAULT_MAX_THREADS greater than 250
BUG: resample filter no longer triggers unnecessary exception
COMP: change export specification to template for un-specialized method
COMP: forgotten class for ITKV4_COMPATIBILITY in 2aae174
ENH: use double-conversion's CMake targets
COMP: fix warning about missing override in CastImageFilter
DOC: wrong class name for PlatformMultiThreader
COMP: get rid of MSVC's warning 4661
ENH: enable GaussianInterpolateImageFunction to work with streaming
STYLE: reduce space in ivar declarations
STYLE: ITK indentation style in test
STYLE: invert the name and internal logic of waiting for threads
BUG: ThreadPool::DoNotWaitForThreads did not work properly
STYLE: Add ITK prefix to testing macros in release branch
DOC: invocation of AddWork uses -> because instance is always a pointer
ENH: updating remote modules
ENH: PoolMultiThreader uses one less thread
ENH: documenting supported compilers
ENH: updating remote modules
STYLE: more consistent code formatting in test driver
BUG: offset was not updated after changing Euler angle order (ZYX)
Fix broken link in Data.md
ENH: support RGB image in windowed sinc interpolation
ENH: support RGB image in windowed sinc interpolation
ENH: updating remote modules
ENH: back-porting #1165 to support Visual Studio 2019
ENH: updating remote modules
COMP: fixed enum name error when legacy is OFF and ITK_USE_GPU is ON
ENH: removing deprecated Python functionality: imp
ENH: removing deprecated Python functionality: sys.version_info 2/3
ENH: removing deprecated Python functionality: import print_function
Francois Budin @fbudin69500 (4):
BUG: ImageBase regions and ImageRegion properties are returned as reference
DOC: Add ITK 5.0 release notes
BUG: m_NumberOfPointPixels was set equal to m_NumberOfPoints
ENH: Adds swig include directory to command line
GDCM Upstream (1):
GDCM 2019-05-22 (cc5358a1)
Genevieve Buckley @GenevieveBuckley (1):
BUG: All exceptions must be derived from python's BaseException class
Hans J. Johnson @hjmjohnson (64):
ENH: Update SphinxExamples to lastest master branch
COMP: Add attribute for large doxygen config file.
DOC: Remove ITK_FUTURE_LEGACY_REMOVE from documentation
ENH: Disable remote module processing when creating doxygen.
STYLE: Prevent double initialization
DOC: Purge outdated media wiki WikiExamples
BUG: Missed propagation of library dependancies
ENH: Deprecate Neuralnetwork module
Revert "Merge pull request #1039 from samuelgerber/MultithreadPointSetToPointSetMetricv4"
STYLE: Remove deprecated support for ITK_WRAP_PYTHON_LEGACY
DOC: Only warn when Module_NeuralNetworks is selected
ENH: Use consistent project name with module name
COMP: Fix clang-format nesting of empty macros
DOC: Deprecate https://itk.org/Wiki/ITK/Examples content.
DOC: Provide doxygen links for sphinx
DOC: Improve the documentation clarity for NormalizeImage.
DOC: Moved wiki examples to sphinx examples part2
ENH: itkObjectToObjectOptimizerBase Must be explicitly instantiated
COMP: Terminate conditional doxygen sections
DOC: Set class name for StreamingProcessObject doxygen
ENH: Update the DoxygenLayout.xml file
ENH: Update template files for Doxygen.
BUG: Patch submission scripts conflict with doxygen
COMP: Resolve 1000's of alias warnings in 1.8.15
DOC: Moved wiki pages to sphinx examples
BUG: Flawed logic for itkExceptionObject.h guards
STYLE: Use override statements for C++11
STYLE: Prefer c++11 'using' to 'typedef'
COMP: Another work around uninitialized value warnings
ENH: Prefer c++11 'using' to 'typedef' for structs
COMP: Update AnalyzeObjectMapIO remote for ITKv5.0
COMP: Suppress warning about file that is too large
STYLE: Use = default for trivial constructors
STYLE: For loops can have a space before ;
STYLE: Suppress longstanding kwstyle violations
STYLE: Use templated function over macro
ENH: Add LONGLONG & ULONGLONG types
STYLE: Remove unused protected ivar m_MyProduct
COMP: Isolate RAWIO non-templated code in cxx file
PERF: Byteswap only when request != system byte order
STYLE: Suppress longstanding kwstyle violations
STYLE: Define the .clang-format config file
ENH: Add script to assist with running clang-format on topic-branches
ENH: Update C++/C attributes for itk style conformance.
ENH: Add copy of git-clang-format from llvm binaries
ENH: Add cmake configuration for clang-format
ENH: Setup clang-format hooks for pre-commit-style
DOC: Add missing line separator for ingroup ITKCommon
DOC: Fix spelling typo VeriyInput -> VerifyInput
ENH: Refactor to allow ReferenceHistogram instead of ReferenceImage
COMP: Remove One Definition Rule conflict
COMP: Fix missing type specialization for `unsigned long long int`
STYLE: Convert 'enum' to 'enum class' objects with print enum function
ENH: Workaround MSVC preprocessor name conflict
STYLE: Prefer enum class definitions internally
STYLE: Prefer consistent capitalization of Colormap
ENH: Ignore wrapping warnings for `enum class`
BUG: Missing ImageAdapter function signatures
COMP: Change KWStyle to allow reformat to pass.
STYLE: No-space inside <> () []
STYLE: Change the packing of parameters.
STYLE: Use shorter column length for Software Guide.
STYLE: End of history preceeding clang-format-8.0 style
STYLE: Fix spelling error foramt -> format
ITK Maintainer (1):
STYLE: Enforce ITK style defined by .clang-format
James Butler @jamesobutler (1):
COMP: Add cmake_minimum_required to ITKNumericsFEM
Jean-Christophe Fillion-Robin @jcfr (1):
ENH: Support building ITKNumericsFEM as external module
Jon Haitz Legarreta Gorroño @jhlegarreta (4):
STYLE: Fix indentation in bash script
ENH: Add script to update ITK testing macros names
BUG: Fix remotes maintenance scripts
BUG: Fix wrong variable names
Matthew McCormick @thewtex (61):
ENH: Bump the ITK CMake version to 5.1.0
ENH: New content links for ITK 5.0.0
STYLE: DeformableRegistration2 line length warnings
COMP: SpatialObjectsHierarchy Software Guide newline
ENH: Bump CI ExternalDataVersion to 5.0.0
DOC: Release generation updates for ITK 5.0.0
DOC: Add a note about updating conda-forge for post wheels
ENH: Update Doxygen to 1.8.15
BUG: Add test/CMakeLists.txt stub to NumPy bridge
COMP: Provide NumericTraits<complex<T>>::ZeroValue() definition
COMP: Backwards compatibility testing macros without ITK_ prefix
BUG: Get latest tag in UpdateRequiredITKVersionInRemoteModules.sh
BUG: Filename vars in UpdateRequiredITKVersionInRemoteModules.sh
ENH: UpdateRequiredITKVersionInRemoteModules bump patch version
ENH: UpdateRequiredITKVersionInRemoteModules supports ITKPythonGitTag
BUG: Do not require PyBUF_WRITABLE in GetArrayViewFromImage
DOC: Update supported Python versions warning
ENH: Require Python 3.5 or newer on all platforms
BUG: ITKFixedPointInverseDisplacementField wrapping test config update
BUG: Remove VectorExpandImageFilter wrapping
BUG: Add PEP 366 __package__ support to ITKLazyModule
COMP: Remove HasNumericTraitsCheck from ExpandImageFilter
ENH: Wrap ExpandImageFilter with vector types
BUG: Release the Python Global Interpreter Lock (GIL) during execution
STYLE: Apply ITK Style Guidelines to itkPyCommand.cxx
BUG: itk::PyCommand ensures the GIL state
BUG: Support pickling LazyITKModule with cloudpickle
BUG: Add Pipeline name to Azure configuration
DOC: Update Azure Pipelines badge URL's
BUG: Add wrapping for TransformMeshFilter
ENH: Bump itkVersion.cmake for 5.0.1
ENH: CI testing uses Python 3
BUG: itkPyBufferTest: use bytes for Python 3 np.frombuffer
BUG: Remove NumberOfComponents check in _GetImageViewFromArray
BUG: Remove NumberOfComponents check in _GetImageViewFromArray
DOC: Update ITK.Linux.Python and ITK.Coverage README badges
BUG: Update SkullStrip module to address Doxygen configuration
BUG: Use ITK_BUILD_DOCUMENTATION to enable Doxygen builds
COMP: Update CastXML to 2019-07-15 master
DOC: Minor release documentation updates
ENH: Support numpy.asarray for itk.Image
ENH: Directly set an itk.ImageBase Direction with a NumPy Array
BUG: Ensure NumPy array is C-contiguous with matrix conversion
BUG: Enable ITKBridgeNumPy for Windows CI builds
DOC: AdaptiveHistogramEqualizationImageFilter default radius
BUG: Do not run itkPyBufferMemoryLeakTest on Windows
BUG: Remove Windows Python 2.7 hypot workaround
ENH: Support NumPy array-like inputs to image filters
DOC: Add Eigen license to NOTICE file
ENH: Download clang-format 8.0.1 executable
ENH: Add wrapping for LabelImageGaussianInterpolateImageFunction
DOC: 'weight' spelling in LabelImageGaussianInterpolateImageFunction
BUG: Add NumPy conversion for itk.Image[itk.Vector[itk.D,dim]]
BUG: Wrap WindowedSincInterpolateImageFunction SmartPointer
BUG: Do not apply style pre-commit hooks to ThirdParty code
BUG: Do not download clang-format with ITK_FORBID_DOWNLOADS enabled
BUG: Add missing KWStyle hook configuration
ENH: Update clang-format binary path configuration
BUG: Fix have_KWStyle detection when running clang-format hook
BUG: Improvements to pre-commit-style hook for clang-format
ENH: Check for required clang-format version in style hook
MetaIO Maintainers (1):
MetaIO 2019-05-22 (5f90075b)
Mihail Isakov (1):
ENH: added missing symbols to JPEG mangling header
Neslisah Torosdagli @neslimsah (2):
BUG: Regression in PolygonSpatialObject::IsInsideInObjectSpace #1082
BUG: Regression in PolygonSpatialObject::IsInsideInObjectSpace #1082
Niels Dekker @N-Dekker (22):
PERF: Replace mutex by atomic in MersenneTwisterRandomVariateGenerator
STYLE: Remove two duplicated #include <mutex> directives
STYLE: Add const to MersenneTwisterRandomVariateGenerator::GetSeed()
ENH: GTest MersenneTwisterRandomVariateGenerator::GetIntegerVariate()
STYLE: Use image->TransformPhysicalPointToIndex(point), returning index
ENH: ImageBase Transform-Vector single argument overloads more generic
STYLE: Use image->TransformVectorToVector(gradient), returning gradient
STYLE: Vector, CovariantVector(value) call base FixedArray(value)
STYLE: FastMarching replace FixedArray Begin(), End() by range-based for
STYLE: Replace FixedArray Begin(), End() by cbegin(), cend()
STYLE: itkFixedArray.hxx using std::equal, and C++11 fill_n and copy_n
STYLE: Add const to SetStartingShrinkFactors parameter
STYLE: Replace std::copy(input, input + n, output) by C++11 std::copy_n
ENH: Add ImageRegionRange, to iterate over the pixels of an image region
COMP: No longer disable obsolete MSVC warning C4231 on 'extern' template
STYLE: Order #pragma warning directives in itkWin32Header.h
COMP: No longer disable obsolete MSVC warning C4231 in VNL/vxl/vcl
BUG: Fix possible loss of data on type conversion
COMP: QuadEdgeMesh::SetCell avoid assignment in conditional expression
COMP: Remove (char) casts of hexadecimal int literals from UnicodeIOTest
COMP: ImageRegionRangeGTest issue #1147 Unused function template warning
COMP: Fix loss of data ProcessObject GetNumberOfValidRequiredInputs()
Pablo Hernandez-Cerdan @phcerdan (1):
BUG: Fix COMPILE_DEFINITIONS of castxml
Rinat Mukhometzianov @rmukh (3):
COMP: MSVC AVX flag fix
COMP: Fix SSE for MSVC x86
COMP: Replace legacy ITK_Check...Flag.cmake with check_..._flag cmake function
Samuel Gerber @samuelgerber (7):
PERF: Remove Temporary Variable in GetMeasurementVector
ENH: Add Multithreading to PointSetToPointSetMetricv4
ENH: Add Multithreading to PointSetToPointSetMetricv4
ENH: Add Multithreading to PointSetToPointSetMetricv4
Revert "Revert "Merge pull request #1039 from samuelgerber/MultithreadPointSetToPointSetMetricv4""
BUG: Fix PointSetToPointSetMetric Thread Safety
BUG: Fix CompositeTransform ThreadSafety
Stephen Aylward @aylward (17):
ENH: Updated Spatial Object tex to match ITKv5
BUG: Fixed spelling mistakes and use of plural member functions
ENH: Updated Spatial Object tex to match ITKv5
BUG: Fixed spelling mistakes and use of plural member functions
BUG: Fix grammar and naming mistakes in SpatialObject documentation
DOC: Fixed expected output of examples and documentation
BUG: Fix grammar and naming mistakes in SpatialObject documentation
DOC: Fixed expected output of examples and documentation
BUG: Use AddPoint() for PointBasedSpatialObjects to set SO
ENH: Replace ExceptionObjects with itkExceptionMacro.
BUG: Use AddPoint() for PointBasedSpatialObjects to set SO
ENH: Replace ExceptionObjects with itkExceptionMacro.
ENH: Converted TubeSpatialObject ComputeTangentsAndNormals to frenet
BUG: Resolve corner case bug in ComputeTangentsAndNormals in TubeSO
ENH: Improved IsInside computation (speed and accuracy) of tube
ENH: Updating TubeSO test to match assumption that default is EndRounded
BUG: operator= defined in [tube|*]SpatialObjectPoint incomplete
Steve Pieper @pieper (1):
DOC: ITK5 SpatialObject Scene to Group change
VXL Maintainers (1):
VNL 2019-08-15 (7cc97a62)
Ziv Yaniv @zivy (1):
DOC: Correcting some grammer and updating the toolkit name. (#980)
@maekclena (10):
STYLE: Add ITK prefix to testing macros
BUG: Fix BSplineGradient configuration
ENH: Mark VectorExpandImageFilter as deprecated
ENH: Deprecate VectorCentralDifferenceImageFilter
ENH: Remove VectorExpandImageFilter when ITK_LEGACY_REMOVE is on
BUG: add required method for Pickling
BUG: Fix GaussianInterpolateImageFunction with streaming
BUG: Avoid buffer overwriting in DCMTKImageIO
ENH: Disable itkDCMTKImageIOMultiFrameImageTest
BUG: Mitigate overflow in DCMTKImageIO::Read
@yjcchen0913 (1):
BUG: Ensure strict weak ordering in HessianToObjectnessMeasure's sort
– we are working towards that with a 