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  • v5.0.rc01 Changes

    February 05, 2019

    πŸš€ We are happy to announce the Insight Toolkit (ITK) Release Candidate 1! πŸŽ‰ As the first release candidate, the major advancements for ITK 5 have matured, and the community is encouraged to adopt the release candidate in ITK-based applications.

    πŸš€ This release improves Mesh support in Python though simplification and extension of Mesh and PointSet wrapping. In general, this release makes improvements to the modernization of the toolkit staged in ITK 5.
    The C++ range classes continue to advance, including the experimental itk::ImageBufferRange, itk::IndexRange, and itk::ShapedImageNeighborhoodRange. Our migration to GitHub was overwhelmingly successful, but it continues to improve. Pull requests now receive a helpful CDash build analysis GitHub Check.

    πŸ— GitHub CDash Build Analysis Check

    πŸš€ For an overview of ITK 5's transition to modern C++, performance-related changes, the new, Pythonic API, and the project's migration to GitHub, see the ITK 5 Alpha 1: Modern C++, ITK 5 Alpha 2: Performance, ITK 5 Beta 1: Pythonic Interface, and ITK 5 Beta 3: GitHub release announcements.

    🐎 Performance Improvements

    • N4BiasFieldCorrectionImageFilter accelerated through itk::ImageBufferRange and other optimizations.
    • 🚚 Various modern C++ improvements related to default constructors, move operations, etc.

    πŸ“š Documentation

    • ⚑️ ITK Software Guide PDF is now updated for ITK 5.
    • TransformIndexToPhysicalPoint notation is improved.


    • πŸ‘ Mesh IO classes, e.g. Gifti, OBJ, OFF, FreeSurfer, BYU, STL, are now split into separate modules for better modularity.
    • πŸ— A CDash build analysis summary and link is provided as a GitHub Check.
    • βž• Added new C++11 member functions from std::vector to itk::VectorContainer.

    Third Party

    • πŸ‘ DCMTK 3.6.4 is now supported.
    • CanRead is now faster for inspection of potential DICOM files, both with the GDCM and DCMTK DICOM backends.
    • ⚑️ Eigen updated to 3.3.7.
    • πŸ‘Œ Improved support for integration of a system Eigen.
    • πŸ‘Œ Improved compatibility with system HDF5.


    • Wrapping for Mesh and PointSet classes was simplified and extended.
    • BinaryMaskToNarrowBandPointSetFilter is now available in Python.
    • πŸ‘ Better itk.Image NumPy buffer management for advanced pipeline grafting.

    πŸš€ To install the 5.0 Release Candidate 1 Python packages, run

    python -m pip install --upgrade pip python -m pip install --upgrade --pre itk

    What's Next

    πŸš€ There are many more bug fixes and improvements not mentioned above. For more details, please see the change log below. Congratulations and thank you to everyone who contributed to this release.

    πŸ“š The ITK 5 Migration Guide is available to help transition a code base from ITK 4 to ITK 5. Please discuss your experiences on Discourse.

    πŸš€ We are approaching the 5.0.0 final release! The next release will be the second ITK 5 release candidate; it is scheduled for March.

    Enjoy ITK!

    Changes from v5.0b03 to v5.0rc01
    Bradley Lowekamp (2) @blowekamp:
          BUG: Use compatible ITKv4 computation
          BUG: Fix Ostu test to work with ITKv4 default options
    Dženan Zukić (9) @dzenanz:
          ENH: updating ITKMontage module
          DOC: trying to fix the doxygen warning
          ENH: Updating Visual Studio debug visualizer definitions
          DOC: removing long outdated comment
          ENH: updating Montage module
          STYLE: minor fixes to release notes
          COMP: a fix for system double-conversion build
          ENH: updating Montage: fix double-conversion include directory
          ENH: update ITKMontage: Fix crash when setting tiles from memory
    Eigen Upstream (1):
          Eigen3 2019-01-14 (16812519)
    Francois Budin (1) @fbudin69500:
          BUG: Missing ITK_WRAP_rgba_* variables in
    Hans Johnson (7) @hjmjohnson:
          STYLE: rm initializer list extra lines
          ENH: DCMTK 3.6.4 api changes accomodated
          ENH: Move default [con/de]strutor to .h
          COMP: Protected static function must be public
          PERF: GDCM & DCMTK CanRead fails very slowly for non-DICOM files.
          PERF: readability container size empty
          STYLE: Prefer = default to explicit constructor(){}
    Jon Haitz Legarreta GorroΓ±o (1) @jhlegarreta:
          DOC: Adjust the CoC Committee to the 01/09/2019 meeting decision.
    Matthew McCormick (31) @thewtex:
          ENH: Update Azure Pipelines CI testing cache to 5.0b03
          DOC: Releasing ITK updates for 5.0b03
          BUG: Exercise BinaryMaskToNarrowBandPointSetFilterTest
          BUG: BinaryMaskToNarrowBandPointSetFilter GenerateData protected
          BUG: Remove unused FixedDensityFunction in JensenHavrdaChatvatTsallis
          BUG: Do not build/use PoolMultiThreader without WinThreads or PThreads
          BUG: ShapeDetectionLevelSetFilter outputs
          BUG: ShapeDetectionLevelSetFilter outputFileName
          COMP: Remove itk::ThreadPool::GetGlobalDefaultNumberOfThreadsByPlatform
          DOC: Add 5.0 Beta 3 release notes
          DOC: Fix link to in
          ENH: Add wrapping for BinaryMaskToNarrowBandPointSetFilter
          COMP: Mark DCMTKImageIO::CanWriteFile argument as unused
          COMP: Fix Software Guide line length too long warnings
          COMP: Fix Software Guide line length too long warnings
          ENH: Use CompensatedSummation in point set metrics to improve robustness
          COMP: ShapedImageNeighborhoodRangeGTest array initialization
          ENH: Move Gifti Mesh IO into a separate module
          ENH: Consistency in wrapped mesh types
          PERF: Parallelize ManifoldParzenWidnowsPointSetFunction::SetInputPointSet
          ENH: Move OBJ Mesh IO into a separate module
          ENH: Migrate OFF IO into ITKIOMeshOFF
          ENH: Update IOSTL to 2019-01-16 master
          COMP: Do not use readNoPreambleDICOM with Emscripten
          BUG: Fix Azure Pipelines commit checkout
          BUG: Fix Azure Pipelines master checkout on Windows
          BUG: Default MeshIOBase PointDimension is 3
          ENH: Update IOMeshSTL remote module and update name
          ENH: Improve loading to help pyinstaller can analyze module dependencies
          COMP: Wrapping of VectorContainer and DefaultStaticMeshTraits
          ENH: Add legacy multi-frame DICOM MD5 content links
    Niels Dekker (19) @N-Dekker:
          DOC: issue #273: SyNImageRegistrationMethod default member initializers
          STYLE: Small improvements ImageBase constructor, SetRequestedRegion, '\'
          COMP: Fix "unreachable code" MakeOutput RegistrationMethods
          PERF: N4BiasFieldCorrectionImageFilter implementation using ImageRange
          STYLE: Renamed ImageRange to ImageBufferRange
          PERF: Remove SystemInformation data from ResourceProbe, fix issue #350
          STYLE: Remove dynamic_cast from CastToSTLContainer(), add noexcept
          PERF: N4BiasFieldCorrectionImageFilter adds points + weights ~20% faster
          PERF: Fast assign point data, weights BSplineScatteredData filter
          COMP: ImageBufferRange iterator same as const_iterator, for const image
          PERF: BSplineDecompositionImageFilter now calls ImageAlgorithm::Copy
          ENH: Add default-constructor and empty() to ShapedImageNeighborhoodRange
          ENH: Made ShapedImageNeighborhoodRange assignable and tested copy + move
          STYLE: C++ "Rule of Zero" for iterator classes of Range types
          PERF: Add fast noexcept move semantics to Neighborhood and its Allocator
          BUG: ResourceProbe::Reset() should set m_MaximumValue to lowest value
          BUG: Fixed MoveAssignedRangeHasSameIterators GTest of two range types
          STYLE: Move test utils default-constructed ranges to RangeGTestUtilities
          ENH: Add default-constructor and empty() to IndexRange
    Pablo Hernandez-Cerdan (14) @phcerdan:
          DOC: Fix doxygen in SymmetricEigenAnalysis
          ENH: Python, wrap complex in NumericTraits
          ENH: Update IsotropicWavelets module
          BUG: Fix failure of ITK_EIGEN macro expansion
          ENH: Add test checking noexcept moves in FixedArray
          STYLE: Change EXPECT_EQ to EXPECT_TRUE|FALSE in CommonTypeTraitGTest
          ENH: Add python wrapping for std::pair and other int containers
          ENH: Add internal/external eigen3 libraries
          ENH: Update IsotropicWavelets
          ENH: Add new c++11 member functions of std::vector to itk::VectorContainer
          ENH: Simplify specialization of NumericTraits<std::complex<TComponent>>
          BUG: itkMatrix: Use NumericTraits::Zero instead of literal 0
          DOC: SoftwareGuide: improve TransformIndexToPhysicalPoint notation
          COMP: Fix multi-line comment warning generated by latex notation
    Roman Grothausmann (1) @romangrothausmann:
          BUG: avoid overwriting output in 2nd run used for comparison in test:
    Simon Rit (1) @SimonRit:
          BUG: python itk.Image returned by GetImageFromArray now manages its own buffer
    @ihnorton (1):
          COMP: use HDF5 library names only to avoid abspaths w/ SYSTEM_HDF5
  • v5.0.b03 Changes

    January 04, 2019

    πŸš€ We are happy to announce the Insight Toolkit (ITK) version 5 Beta 3 release! πŸŽ‰ This release celebrates the community's migration to GitHub. :octocat: As a true open source project, community participation is a high priority. 🀝 Our migration to GitHub facilitates collaboration with the broader scientific open source community. πŸ”¬


    πŸš€ This release also includes major improvements in the areas of performance and third party libraries. A new, experimental ImageRange class enables iteration over an image's pixels in a modern, performant way. Fundamental ITK data structures were improved to enabled compiler optimizations for Plain Old Data objects. VXL was modernized to C++11, and Eigen is now available in the toolkit; ITK's gradual transition from VXL to Eigen for linear algebra has begun.

    πŸ“„ In addition, four new remote modules are available, FFT's can be computed on the GPU via cuFFTW, and ITK Python's itk.imread now supports image series. More information can be found in the feature summary below.

    πŸš€ For an overview of ITK 5's transition to modern C++, performance-related changes, and the new, Pythonic API, see the ITK 5 Alpha 1: Modern C++, ITK 5 Alpha 2: Performance, and ITK 5 Beta 1: Pythonic Interface release announcements.

    GitHub Migration

    GitHub now hosts the official ITK, ITKExamples, and ITKSoftwareGuide Git repositories:

    The InsightSoftwareConsortium GitHub Organization is currently home to 88 other ITK-related repositories. Many of these repositories are externally developed ITK modules. If you would like create a new repository or transfer a repository to the InsightSoftwareConsortium GitHub organization, let us know on ITK's Discourse discussion forum.

    Documentation on how to contribute has been updated and improved. Contribution documentation is available in the ITK Software Guide and as Markdown files in the source code repository, browsable in GitHub's web interface. Our file is a starting point for contributors. We also have a Git cheatsheet for quick reference.

    Our Code of Conduct describes our motivation to build impactful, open source image analysis software through a welcoming and productive community. The Code of Conduct also describes our values: to be open, welcoming, inclusive, civil and considerate, respectful, collaborative, careful in the words that we choose, responsible, and inquisitive. We expect community members to lead by example, but we also define a set of unacceptable behaviors and mechanisms to enforce conduct violations.

    To guide submission of pull requests and issues, we created templates used when issues and pull requests are opened. Release notes from previous releases were migrated from the Wiki; release notes can be browsed in repository Markdown files.

    πŸš€ Plans for upcoming releases can now be found in the project GitHub Milestones. Release artifacts will now be published on ITK's GitHub Releases as opposed to Sourceforge. Release artifact archives are now also available in the ITK Girder Collection.

    πŸ”§ The ./Utilities/ script now guides repository configuration for GitHub contributions. Git client-side hooks help submit a well-formatted commit message. Git aliases, review-push and pr, are provided to submit pull requests for review and download submitted pull requests for local testing.

    πŸ“š A new cross platform script, ITK/Utilities/, is available to upload binary testing data. This script, invoked directly or through the data-upload alias, performs an authenticated upload to and generates an ExternalData content link to avoid inflation of the source code repository's size. This script can be used to upload testing data for ITK or an externally developed module.

    A static archive of our previous code review system, the Gerrit Code Review instance, was created to preserve the code review discussions for nearly 24,000 changes on ITK and other Kitware supported projects.

    🍎 Continuous integration testing ensures the continued quality and productive development of the toolkit. CircleCI and Azure Pipelines CI testing run over 2,800 regression tests on Linux, macOS, and Windows for both C++ and Python builds. Pull requests content is checked by ghostflow-director to prevent integration of large files, etc.

    We now track issues in the repository's GitHub Issue Tracker. The legacy JIRA issue tracker is now read-only, and it will remain available for reference.

    🐎 Performance Improvements

    • A new, experimental ImageRange class provides range-based iteration over the pixels of an itk::Image.
    • The Rule of Five was applied to basic data structures like itk::FixedArray, itk::Point, itk::Vector so they satify std::is_trivial and std::is_standard_layout. This is now also tested. This enables compiler optimizations and moves.
    • ResampleImageFilter::CastPixelWithBoundsChecking is now faster.
    • Data copies in itk::BSplineTransform were reduced.
    • ⚑️ The number of evaluations in line search optimizer were reduced by half.

    ⚑️ Third Party Updates

    • 0️⃣ The Eigen linear algebra third party library is now available as an ITK module, and it is enabled by default.
    • ⚑️ VXL was updated to require C++11 and use modern C++ syntax
    • ⚑️ GDCM, Zlib and GIFTI were updated to the latest upstream.

    Remote Modules


    The result of phase symmetry filtration of a cardiac ultrasound B-mode volume. From Hatt C. "Multi-scale Steerable Phase-Symmetry Filters for ITK."
    The Insight Journal. July-December. 2011.

    πŸ†• New Remote Modules added:

    0️⃣ The itk::JPEG2000ImageIO class was migrated out the ITKReview module into its own module, ITKIOJPEG2000, and enabled by default.

    πŸ‘ Frequency Domain Support

    • βž• Added itk::HalfHermitianFrequencyIterator: iterate over images in the frequency domain generated with the itk::RealToHalfHermitianForwardFFTImageFilter
    • πŸ‘‰ Support for Fast Fourier Transforms (FFTs) computed on NVIDIA GPUs via cuFFTW: enable by setting ITK_USE_CUFFTW=ON.


    πŸ“¦ To install the 5.0 Beta 3 Python packages, run

    python -m pip install --upgrade pip python -m pip install --upgrade --pre itk

    What's Next

    πŸš‘ There are many more bug fixes and critical improvements not mentioned above. For more details, please see the change log below. Congratulations and thank you to everyone who contributed to this release.

    πŸ“š The ITK 5 Migration Guide is available to help transition a code base from ITK 4 to ITK 5. Please discuss your experiences on Discourse. We are approaching the 5.0.0 final release! The next release will be the first ITK 5 release candidate; it is scheduled for the end of January.

    Enjoy ITK!

    Changes from v5.0b01 to v5.0b03
    Note: ITK v5.0b02 was skipped due to a build error with Visual Studio.
    Bai Shi (1):
          COMP: To fix compilation error of "cannot dynamic_cast 'x'
    Bradley Lowekamp (47):
          DOC: Improve Extract exception for region size mismatch
          BUG: Print ImageIOBase::m_Spacing
          BUG: Fix TIFFImageIO spacing for multi-page
          BUG: Support ITK transform files with corrected group names
          ENH: Only use one Work Unit in BSpline convergence checker
          BUG: Fix HDF5ImageIO reporting any HDF5 file is readable
          ENH: Improve N4BiasFieldCorrectionImageFilter
          ENH: Add extensions to HDF5ImageIO
          ENH: Add ImageIO methods to check name for file extensions
          BUG: Quiet HDF5-DIAG from H5File::isHdf5
          ENH: Update LabelStatistics to use dyanmic threading
          ENH: Move JPEG200 ImageIO into separate ImageIO module
          BUG: Update SCIOFIO to ITKv4.13 branch
          ENH: Make ProcessObject::VerifyInputInformation constant
          BUG: Handle boundary case with max metric
          PERF: Reduce number of evaluations in line search optimizer by half
          COMP: Fix unused argument warnings in SpatialObjectPoint::operator=
          BUG: Handle boundary case with max metric
          ENH: Update ImageToHistogram to use modern dynamic threading.
          PERF: implement concurrent histogram merge/reduce
          BUG: Fix move of histogram smart pointer
          BUG: Add parameter which stores the requested number of work units.
          BUG: use =default for default implementation of destructor
          BUG: Prevent square root of negative number
          BUG: Check all entries are not null
          STYLE: Prefer immediate exception over long if
          BUG: Fix sqrt of negative values
          BUG: Address valgrind leaks for classes which use ScanlineFilterCommon
          BUG: Limit number of threads used for testing ITK
          ENH: Replace centered transforms with non-centered versions
          BUG: Remove static member function variable
          DOC: Fix LBFBS2 typo
          BUG: Remove static member function variable
          BUG: Fix multi-resolution bspline registration example
          BUG: Adding updated baseline image for improved example
          DOC: Fix typos in LBFGS2 optimizer's error string
          ENH: On Azure DevOps only show test output on failure
          STYLE: Use GTest file name suffix for Google Test based tests
          BUG: Remove unused TRansfromDomainDirectionInverse IVAR
          BUG: Synchronize BSpline MeshDomain parameters from fixed params
          ENH: Adding GTest for BSplineTransform
          ENH: Create method to set transform domain params from coeff images
          BUG: Synchronize BSpline MeshDomain parameters from fixed params
          ENH: Refactor BSplineTransform
          DOC: Update the BSplineTransform class doxygen
          ENH: Update N4BiasField to utilized named positional inputs
          COMP: Addressed unused parameter warning in ImageRegion default
    Brian Helba (1) @brianhelba :
          BUG: Ensure that itkSampleToHistogramFilterTests fail on errors
    Dženan Zukić (50) @dzenanz :
          ENH: code simplification and more granular progress reporting
          ENH: return bin maximum as threshold
          STYLE: removing void if used in place of empty parameter list
          ENH: update remote module MorphologicalContourInterpolation
          BUG: nbOfThreads was bounded to GlobalMaximumNumber, but not work units
          ENH: Ignore current load in PoolMultiThreader
          COMP: missing ConstPointer declaration
          BUG: fix crash in RegionGrowingBenchmark
          ENH: reducing duplication in 4 scanline-based image filters
          ENH: use scanline iterators and clean up the code a little
          COMP: fix [-Wc++11-narrowing] in initializer list during Python wrapping
          ENH: refactor ConnectedComponent to not use Barrier. Also reduce duplication.
          STYLE: aligning macro continuation backslash
          COMP: fixing unused variable warning
          COMP: add Python wrapping for ScanlineFilterCommon
          ENH: updating remotes to their latest versions
          DOC: mentioning ITKV4_COMPATIBILITY in the migration guide
          COMP: minor fixes in preparation for deprecating atomic, mutex and friends
          ENH: updating remotes to latest versions
          ENH: using standard library's mutex primitives
          ENH: deprecating functionality which exist in C++11 standard library
          COMP: missing #include <condition_variable>
          BUG: clamp work units to ITK_MAX_THREADS in Platform and Pool MultiThreaders
          BUG: fix Python wrapping after deprecating MutexLock and friends
          ENH: adding new remote modules: Montage and BSplineGradient
          DOC: fixing copy-paste error about functor type
          ENH: improve precision of median calculation by default
          STYLE: minor space and line break improvements
          ENH: FrequencyBandImageFilter derives from UnaryFrequencyDomainFilter
          ENH: ITKv5_CONST macro for VerifyPreconditions() and VerifyInputInformation()
          ENH: ITKv5_CONST macro for VerifyPreconditions() and VerifyInputInformation()
          BUG: background label could be the same as one of the object labels
          COMP: fix compiler warning in itkIndexRange.h
          ENH: adding wrapping for UnaryFrequencyDomainFilter
          DOC: updating commit information for ITKv5_CONST in ITK 4.13.x
          ENH: commit message script uses GitHub issue referencing format.
          ENH: update Montage remote module
          BUG: test image was not properly initialized. Closes #207.
          COMP: fixing compile errors on Ubuntu 16.04 with GCC 5.4.0
          ENH: compile VNL in parallel on Visual Studio
          COMP: fix compile errors with CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS:BOOL=ON
          COMP: Remove VNL_EXPORT from header only class. Closes #191.
          COMP: fix link errors coming from undefined static constexpr member
          STYLE: rename template parameter TMatrixDimension into VDimension
          DOC: EigenValues parameter uses operator[], not operator[][]
          COMP: compile with Visual Studio in conformance mode AKA /permissive-
          COMP: moving the default constructor of vnl_matrix from .h into .hxx
          STYLE: removing empty lines between comments and constructors
          ENH: enable progress reporting with ITKV4_COMPATIBILITY. Closes #228.
    Eigen Upstream (1):
          Eigen3 2018-11-19 (493fa50e)
    Francois Budin (9) @fbudin69500 :
          BUG: THEADER instead of THREADER
          BUG: Disable using mkl_tbb_thread
          ENH: Adding IOOpenSlide ImageIO remote module to ITK
          BUG: WRAP_2 is a local variable, not a CACHE variable
          BUG: Wrong path to baseline images
          ENH: Allow selecting ImageIO in Python template code
          ENH: Support loading image series in itkTemplate.
          ENH: `itk.imread()` now supports image series
          ENH: Support for tuples passed as arguments through itkTemplate New() function
    GDCM Upstream (2) @malaterre :
          GDCM 2018-11-05 (3ffbf1ed)
          GDCM 2018-11-30 (ec82fb48)
    Gabriel A. Devenyi (1) @gdevenyi :
          PERF: Enable MINC internal compression by default
    Hans Johnson (58) @hjmjohnson :
          COMP: Prefer snprintf to avoid buffer overruns
          STYLE: Use modern C++11 =delete to indicate not implemented
          ENH: Update KWStyle hash to build latest updates
          STYLE: Prefer error checked std::stoi over atoi
          BUG: GE4IO atoi failures resulted in implicit 0 image slices
          BUG: Commandline arguments were not properly processed
          BUG: atoi failure => 0 hid processing failures
          BUG: Command line parsing silently failed
          STYLE: Prefer error checked std::stod over atof
          BUG: Failed conversion to float with uncaught failure
          STYLE: Pefer = default to explicitly trivial implementations
          COMP: Use nullptr instead of 0 or NULL
          STYLE: Replace defines with constexpr and using statements
          COMP: Fix VS2017 compilation regression
          COMP: Use static method from class directly
          STYLE: Remove support for pre 20160229 VXL_VERSION_DATE_FULL
          STYLE: Decouple matlab printing explicit instantiations
          ENH: Adding explicit instantiations for dimensions 1-10
          COMP: Remove duplicate explicit instantiations
          COMP: Remove unused variables.
          BUG: vidl_itk_istream does not override an ITK object
          ENH: Use C++11 override for overridden functions.
          STYLE: Remove unnecessary vcl_XXX.h headers
          ENH: Add scripts to assist with migrations
          ENH: Adding a few more clang tidy checks.
          BUG: Do not override user selection settings
          ENH: Update to require VXL 2.0.0 or later
          STYLE: Remove unused include headers
          ENH: Provide mechanism for changing git remote url
          COMP: Many of the remotes require updates for ITKv5
          STYLE: Remove VCL_INCLUDE_CXX_0X outdated reference.
          ENH: Add specification for -D __clang__ to clang-tidy
          PERF: emplace_back method results in potentially more efficient code
          STYLE: Replace integer literals which are cast to bool.
          ENH: Fetch upstream as part of setup.
          ENH: Stop abort on first failure.
          BUG: Default commit message fixed for =delete modernization
          ENH: Provide consistency with C++11 core guidelines
          BUG: Missing default argment override
          ENH: VXL 2.0.0 provides all instantiations needed by ITK
          ENH: Fix deficient itkCastImageFilter test
          STYLE: Minor variable naming and readability changes.
          COMP: Provide conversion range testing valid_static_cast function
          ENH: Increase minimum VXL version to 2.0.1 for wrapping
          ENH: REVERT compile VNL in parallel on Visual Studio
          ENH: Require VXL v2.0.2 release.
          ENH: Increase size attribute for large third party file.
          STYLE: Remove VXL_VERSION_DATE_FULL conditionals
          COMP: Remove duplicate explicit instantiation
          ENH: Provide range for non-warned cmake versions
          ENH: Update the GIFTI codebase
          DOC: Typo: @tparam -> @param fix doxygen generation
          DOC: Improved documentation for the migration guide
          ENH: Manually update nifti version from github
          ENH: Employ the `rule of zero` for aggregate types
          STYLE: Use default member initialization
          STYLE: Remove the register keyword
          ENH: NIFTI needs to be part of ITKTargets
    Hui Xie (1) @Hui-Xie :
          BUG: The Z spacing was set using thickness
    Isaiah Norton (1) @ihnorton :
          BUG: don't quote argument to URL_HASH for FFTW
    Jon Haitz Legarreta GorroΓ±o (14) @jhlegarreta :
          ENH: Improve itkEuclideanDistancePointMetric coverage.
          COMP: Use C++11 nullptr directly
          DOC: Fix incorrect class ref for Doxygen.
          ENH: Bump remote modules to their latest commits.
          ENH: Increase coverage for itk::GrayscaleFillholeFilterImage.
          DOC: Update the documentation concerning binary data.
          DOC: Format remote module documentation README to markdown.
          ENH: Update the SmoothingRecursiveYvvGaussianFilter remote module hash.
          DOC: Point to the ITK git cheat sheet in the repository.
          DOC: Fix the ITK Git cheat sheet file link.
          ENH: Add script to priviledge C++11 type alias over typedef.
          DOC: Advise users to delete the PR template in message.
          DOC: Move the issue and pull request templates to a specialized folder.
          ENH: Remove `FindITKPythonLibs.cmake` file.
          ENH: Follow remote repositories name changes.
    Matthew McCormick (77) @thewtex :
          ENH: Synchronize testing data content links
          DOC: Updates and improvements on the release process
          COMP: Address empty _FILE_OFFSET_BITS in tif_config.h with MinGW64
          BUG: Do not warn about FFTW GPL license when using Intel MKL
          DOC: Improve ITK_USE_MKL description
          BUG: Mark MKL CMake configuration options as advanced
          ENH: Add support for NVidia CUDA FFTs via cuFTTW
          COMP: Fix HDF5 itk_h5CX_set_apl implicit declaration
          COMP: Use the Platform Threader by default with Emscripten
          COMP: Set CMP0074 to NEW
          COMP: Fix HDF5TransformIO compatibility with HDF 1.8
          COMP: Set CMP0074 in third party libraries
          COMP: Do not mark itk::FloatingPointExceptions constructor as deleted
          COMP: Define TransformBaseTemplate constructor / destructor
          COMP: DataObject InvalidRequestedRegionError unused parameter
          COMP: Remove unused orig parameters in DataObject
          BUG: Remove unused itk_minc2 imported library statement
          BUG: Skip MINC static library build when building shared libraries
          COMP: Suppress undefined public symbol warnings in third party libs
          BUG: Remove duplicate ITK version number
          COMP: Do not install HDF5 static library with BUILD_SHARED_LIBS enabled
          COMP: Add override to TransformBaseTemplate destructor
          COMP: Avoid GCC 4.8 default destructor internal compiler error
          BUG: Import zlib1.rc from ZLib subtree
          BUG: Use GlobalDefaultNumberOfThreads for FFTW plans
          BUG: Simplify specification of greatest prime factor with cuFFTW
          ENH: Add Azure Pipelines configuration
          BUG: Remove ResampleImageFilter duplicate number of pixels check
          COMP: Avoid Intel compiler warning on unknown deprecated attribute
          ENH: Ensure that .sha512 content links have LF newlines
          ENH: Configure .gitattributes for ghostflow-director CheckSize
          DOC: Update ITK Git Reference for GitHub
          DOC: Update for GitHub
          COMP: Address ITKReview module wrapping following migration of ITKIOJPEG2000
          BUG: Migrate Python tests into their modules
          ENH: Use Release CMAKE_BUILD_TYPE for macOS Python CI builds
          BUG: Remove apt-get install's from macOS Azure Pipeline's configuration
          ENH: Update Git client side hooks for GitHub
          ENH: Add script
          COMP: Remove vcl_complex.h from Python builds
          BUG: Remove vcl_complex support from
          BUG: Disable PythonGetNameOfClass test
          BUG: Enable ITKIOJPEG2000 by default
          DOC: Add Test a Topic to overview section
          DOC: Organize code of conduct sub-documents into a folder
          DOC: Update Documentation/ for GitHub migration
          DOC: Fix spelling of "individual" in
          DOC: Add CI status badges to the README
          COMP: Add missing mutex include to itkImageToHistogramFilter.h
          PERF: Use initializer list in ShapedImageNeighborhoodRange operator*
          DOC: Fix link
          BUG: Run apt-get update for Linux Azure configuration
          COMP: Wrap InPlaceImageFilter for complex float to complex double
          BUG: Do not gpg sign third party updates
          DOC: Note that a pull request has to be explicitly opened
          DOC: Suggest using 72 characters or less in commit hooks
          ENH: Ensure NumPy is available for Python tests
          BUG: Add missing export specification for XMLReader, XMLWriterBase
          BUG: Remove invalid ShapeDetectionLevelSetFilter arguments
          COMP: Remove Doxygen \ref, \copydetails commands
          STYLE: Improve readability of HexadedronCell::EvaluatePosition.
          COMP: Fix IsFloatingPoint concept check for VariableLengthVector
          BUG: Set up wrapping options for use in modules
          ENH: Add PhaseSymmetry remote module
          ENH: Download ExternalData cache for CI builds
          DOC: Remove the convention that release branches start with "release"
          ENH: Run content link synchronization script
          ENH: Add setup-girder-api-key Git Setup script
          BUG: Remove ExternalData MD5 content link generation
          ENH: Move FreeSurfer Mesh IO into a separate module
          DOC: Add missing link in
          ENH: Add regression test for reading legacy multi-frame DICOM
          COMP: Float narrowing conversion in BSpline class initialization
          DOC: Move maintainer documentation into Documentation/Maintenance
          DOC: Import release archive notes from the Wiki
          DOC: Improve 4.13, 5 release notes from GitHub Releases
    Niels Dekker (42) @N-Dekker :
          PERF: Made ResampleImageFilter::CastPixelWithBoundsChecking faster
          STYLE: NumericTraits::NonpositiveMin() using numeric_limits::lowest()
          BUG: Fixed casts to int64_t and double in ResampleImageFilter
          ENH: Tested ResampleImageFilter preserves 'double' and int64_t pixels
          STYLE: Replaced 'bool pre = 0' by 'bool pre = false'
          STYLE: Declared "IsAt" iterator member functions 'const'
          DOC: Replaced leading stars ('*') by spaces in Doxygen code blocks
          STYLE: Replaced "Hyperrect..." by "Rect..." in class + function names
          BUG: Removed underscores from GTest test names
          STYLE: Shortened itkShapedImageNeighborhoodRangeGTest test names
          STYLE: Declared VerifyPreconditions() member functions 'const'
          STYLE: Replaced star ('*') by space in front of Doxygen \code tags
          PERF: Made ConstNeighborhoodIterator::GetPixel(i) much faster
          ENH: Added GradientNormThreshold to HoughTransform2DCirclesImageFilter
          STYLE: Removed unused ShapedImageNeighborhoodRange::m_Image
          ENH: Added ConstShapedNeighborhoodIterator::ActivateOffsets(offsets)
          DOC: Replaced leading stars ('*') by spaces in indented Doxygen code
          ENH: Added GenerateConnectedImageNeighborhoodShapeOffsets()
          COMP: Fixed GDCM OpenJPEG name mangling
          ENH: Added ShapedImageNeighborhoodRange::SetLocation(index)
          COMP: Fixed GDCM OpenJPEG name mangling
          ENH: Added HoughTransform2DCirclesImageFilter::UseImageSpacing
          ENH: Added IndexRange for efficient region and grid space iteration
          COMP: Fixed IndexRange warnings -Wshadow -Wmissing-field-initializers
          PERF: unsharpenedImage iterator in N4Bias...Filter is now "WithIndex"
          BUG: Avoid premature GaussianDerivative kernel computation HoughCircles
          BUG: ShapedImageNeighborhoodRange should not try to avoid rvalue offsets
          ENH: Added policy for constant NeighborhoodRange values outside image
          STYLE: AccessorFunctor::SetPixelAccessor parameter reference to const
          PERF: Removed 'virtual' from Default Pixel Accessor destructors
          ENH: Added ImageRange: a range of iterators to the pixels of an image
          STYLE: ImageHelper now doing '+=' and using C++11 std::integral_constant
          BUG: Fixed ShapedImageNeighborhoodRange copying pixel access parameter
          COMP: Fixed ImageRange warning, passing object to variadic constructor
          DOC: Did #136 Update migration guide with Hough transform changes
          ENH: Added default-constructor and empty() to ImageRange
          ENH: ShapedImageNeighborhoodRange now supports any buffered region index
          PERF: Defining ImageRange iterator as raw pixel pointer, when possible
          ENH: Added Experimental::MakeImageRange(TImage*)
          PERF: Replaced postfix ++ calls on ITK iterators by the prefix ++ calls
          PERF: Small improvements to equality operators of Image Region classes
          PERF: Added C++11 final, noexcept, default, initializers to ImageRegion
    Pablo Hernandez-Cerdan (17) @phcerdan :
          COMP: Fix hdf5 warning missing perl script
          COMP: Fix HDF5 CMake warning policy CMP0075
          ENH: Tweak constructors, Ro5 in FixedArray, Point
          ENH: Add Ro5 to FixedArray and derived classes
          COMP: Fix warnings related to Ro5 changes in FixedArray
          ENH: Add Ro5 constructors to SymmetrySecondRankTensor
          ENH: Add Ro5 to classes derived from Point
          ENH: Initialize SecondRankTensor and RGBPixelType
          ENH: Print direction in ImageIOBase
          ENH: Add HalfHermitianFrequencyIterator
          ENH: Use variadic templates for SetPosition
          ENH: Add ThirdParty module Eigen3
          COMP: Add CONFIG to find_package(Eigen3)
          COMP: Add missing headers SymmetricEigenAnalysis
          COMP: Use the right constructors for fixed eigen3 matrix
          COMP: Reorder variables associated find_package in Eigen3
          ENH: Update external module ITKIsotropicWavelets
    Roman Grothausmann (2) @romangrothausmann :
          DOC: adjusted to fit more general case n != m
          DOC: corrected description of the output
    Sean McBride (3) @seanm :
          COMP: Added additional HDF5 symbols for mangling
          DOC: improved comments about HDF5 symbol mangling
          COMP: fixed some -Wunused-template warnings by adding private namespaces
    Simon Rit (2) @SimonRit :
          BUG: fix NumPy bridge for itk::Image with PixelType itk::Vector
          ENH: improve automatic Python ImageFileReader for non-scalar pixel types
    Tobias Wood (1) @spinicist :
          BUG: Swapped int to SizeType to prevent overflow errors
    VXL Maintainers (8):
          VNL 2018-11-04 (ea3a2cc9)
          VNL 2018-11-08 (88b72533)
          VNL 2018-11-14 (ee083096)
          VNL 2018-11-15 (4fe68119)
          VNL 2018-11-18 (fa7c7abd)
          VNL 2018-11-23 (cb6f5dcb)
          VNL 2018-11-29 (f6e20c3c)
          VNL 2018-12-15 (bb0d2eb6)
    Yann Le Poul (4) @YannLePoul :
          BUG: make sure the palette is empty when m_IsReadAsScalarPlusPalette is false
          DOC: fix rotation spelling issue in some versor related files
          STYLE: IsReadAsScalarPlusPalette already printed in parent class
          BUG: unnecessary call to GetExpandRGBPalette
    Zlib Upstream (1):
          zlib 2018-06-11 (355d8648)
    allywarner (1) @allywarner :
          BUG: CMake build errors
    pierre33 (1) @pierre33 :
          ENH: Update itkNaryFunctorImageFilter
  • v5.0.b02 Changes

    December 19, 2018

    πŸš€ This release was superseded by ITK 5.0 Beta 3 due to Visual Studio build errors.

  • v5.0.b01 Changes

    September 11, 2018

    πŸš€ 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.

    πŸš€ 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 = 2median\_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 = 2output\_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.

    πŸ“¦ 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.

    • 0️⃣ The default thread pool is now fully backed by C++11 threading primitives.
    • A new itk::MultiThreaderBase::ParallelizeArray function is available to quickly and easily dispatch C++11 lamda's or std::function's on linearly indexed containers, similar to itk::MultiThreaderBase::ParallelizeImageRegion for operating on N-dimensional image regions.
    • A new itk::MultiThreaderBase::ParallelizeImageRegionRestrictDirection function is available to prevent splitting an image region over a given direction.
    • πŸ— SetNumberOfThreads has been renamed to SetNumberOfWorkUnits to 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::ProgressTransformer class.
    • πŸ“š 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.

    πŸ’… Style changes

    πŸ“š 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.

    πŸ†• New Classes

    πŸ‘€ 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,

    What's Next

    πŸš‘ 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.

    πŸš€ 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 GorroΓ±o (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 to
          ENH: Remove itkzlib in preparation for subtree update
          ENH: Add ZLIB
          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.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
          BUG: Use manylinux to build CastXML linux executable
          BUG: Avoid symlink issues in
          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)

    Enjoy ITK!

  • v5.0.a02 Changes

    May 28, 2018

    🐎 Major improvements in ITK 5.0 include a switch to C++11 language standard, improved performance, and cleanup of legacy code. More information about the C++11 transition, spearheaded by Hans Johnson, can be read in the ITK 5.0 Alpha 1 announcement.

    🐎 ITK 5.0 Alpha 2 emphasizes performance improvements: 1) A refactored multithreading infrastructure, 2) in ITK 5, a thread pool is available by default, 3) an Intel Threading Building Blocks (TBB) threading backend with dynamic region splitting, 4) improved image iterator performance, 5) simple APIs to execute functions in parallel, 6) simple construction of unary and binary generator image filters filters, and 7) new, experimental C++11 range classes for iteration in range-based for loops.

    There are now two multi-threaded "GenerateData" method signatures. The classic one, ThreadedGenerateData, is kept when a filter needs to know in advance the number of pieces into which the requested region will be split. This information was previously used by some filters to allocate intermediate, thread-local data. The new dynamic signature, DynamicThreadedGenerateData, allows the region to be split dynamically in response to data content and multi-processor load to achieve load balancing. Presently, only the TBB backend performs dynamic splitting. More information can be found in the Multi-Threading section of in The ITK Software Guide. Instructions that describe changes required to leverage dynamic parallelism in external filters can be found in the migration guide. Most existing ITK-based codes will build with minimal to no modifications required.

    An itk::PoolMultiThreader is the default in ITK 5, which provides a thread pool for platform native threads. The itk::PlatformMultiThreader is also available, which behaves like the previous itk::MultiThreader class.

    Our multi-threading refactoring enables better load balancing for filters with variable per-pixel computation cost. As TBB is one of the best open source libraries for load-balanced threading, it was an easy choice. The itk::TBBMultiThreader can be enabled by setting Module_ITKTBB to ON in ITK's CMake configuration.

    🐎 Most methods in neighborhood iterators were virtual, but this was a rarely-used feature. That virtualization is now a configure-time parameter, and it is off by default. This significantly improves performance of filters which utilize neighborhood iterators. More information can be found in the Discourse discussion.

    πŸ“š A ParallelizeImageRegion method allows multi-threaded processing without writing a full-blown filter class. As evident in this example, multiple parallelized operations of arbitrary complexity can now be concisely specified and executed with C++11 lamda's or std::function's.

    The new itk::UnaryGeneratorImageFilter and itk::BinaryGeneratorImageFilter's allow per-pixel operations to be specified in several ways: 1) traditional "Functor", with operator(), 2) C++11 lambda functions, with closures, 3) C++11 std::function 4) C-style function pointers.

    New, experimental classes for C++11 iteration in range-based for loops, e.g. itk::Experimental::ShapedImageNeighborhoodRange, provide a modern, convenient syntax for image pixel iteration, and dramatic performance improvements.

    Furthmore, ITK 5 improves performance by leveraging Rvalue references to implement move semantics and perfect forwarding.

    🐎 ITK 5 Performance Benchmarks
    🐎 ITK 5 Performance Benchmark Improvements ITK Performance Benchmarks, lower is better, for ITK 4.13.0, ITK 5.0 Alpha 2 with the platform thread pool, and ITK 5.0 Alpha 2 with TBB. ITK 5.0 advances performance in general, especially with the TBB threading backend.

    Thanks to everyone who contributed to the major advancements made in the ITK 5 performance refactoring. Special recognition goes to Dženan Zukić, Kitware, who lead the refactoring effort. Contributions were also made by Jared Vicory, Robert Maynard, Francois Budin, Matt McCormick, Pablo Hernandez-Cerdan, Kitware, Jonathan Lefman, formerly of Intel, Bradley Lowekamp, associated with the National Library of Medicine, Hans Johnson, the University of Iowa, Simon Warfield, Benoit Scherrer, Rene-Paul Debroize, Amir Jaberzadeh, and Etienne St-Onge, Boston's Children's Hospital. The TBB-refactoring was inspired by the TBBImageToImageFilter, which was supported in part by the Intel Parallel Computing Center at the Computational Radiology Laboratory, Boston Children's Hospital. Bradley Lowekamp contributed the itk::UnaryGeneratorImageFilter and itk::BinaryGeneratorImageFilter filters. Neils Dekker, Leiden University Medical Center, contributed the new range classes.

    πŸ›  There were many other improvements and bug fixes since 5.0 Alpha 1. For example, addition of .editorconfig, prominent placement of .clang-format, addition of ITK-specific debug visualizers for Visual Studio versions 2012-2017 improve editing and debugging experience in Visual Studio.

    πŸ“¦ To test the ITK 5.0 Alpha 2 Python packages, run

    python -m pip install --upgrade pip python -m pip install --upgrade --pre itk

    πŸš€ Note: there are a few warnings that appear when using the wrapping. These will be addressed with the next release.

    πŸš€ The next planned release, ITK 5.0 RC1, will focus on the transition of code review process to GitHub.

    Changes from v5.0 Alpha 1 to v5.0 Alpha 2
    Bradley Lowekamp (22):
          PERF: remove virtual methods in neighborhood iterators
          ENH: Use named inputs for the PasteImageFilter
          PERF: Remove iterators stored as member variables
          BUG: Add specification of OutputImage Type for TobogganImageFilter
          BUG: Add specification of OutputImage Type for TobogganImageFilter
          ENH: Improve numerics of resampling for linear transform
          COMP: Fix gcc 4.8 initialize warning
          ENH: Add baseline image to sporadically failing test
          ENH: Adding Unary and Binary GeneratorImageFilter
          ENH: Convert functor based filters to generator
          ENH: Update internal filters to use BinaryGereratorImageFilter
          ENH: Updating Functor filter with parameters to the new Generator
          COMP: Address Generator filters destructors warning
          DOC: Fix BSplineDecompositionImageFilter Doxygen see also link
          ENH: reuse default splitter
          BUG: revert thread update to BSplineScatteredDataPointSetToImageFilter
          ENH: Update CircleCI CMake version to 3.11.2
          BUG: Correct detection of most recent data file
          ENH: Improve numeric computation of linear interpolation for Resample
          ENH: Update baseline image for ResampleImageFilter3Test1
          BUG: Add 4 pixel tolerance to ResampleImageFilter3Test1
    Dženan Zukić (37):
          ENH: start migration guide document
          STYLE: increasing initial size of the debug window
          BUG: fixing null pointer dereference at the end of iteration
          COMP: reducing direct usage of MultiThreader
          BUG: remove observations in FilterWatcher's destructor
          ENH: support Unicode characters in class documentation
          BUG: fixing index computation in resample filter
          ENH: reducing code duplication in FilterWatcher
          ENH: refactoring MultiThreader infrastructure
          ENH: deciding which filters can use the new threading model
          ENH: reporting progress
          ENH: simplifying Canny filter by using new threading infrastructure
          STYLE: Renaming MultiThreader to PlatformMultiThreader
          ENH: use C++11 thread primitives instead of SpawnThread
          COMP: improve backwards compatibility by retaining the renamed header
          ENH: Add TBB-based multi-threader
          ENH: refactoring filters to avoid use of memory barrier
          ENH: reworking logic for determining default multi-threader
          COMP: fixing compile error on GCC 4.8.5 20150623 (Red Hat 4.8.5-28)
          STYLE: remove outdated and useless comments from VectorExpandImageFilter
          ENH: add a baseline for QuickViewTest.png (Win7x64+VS2017+VTK8.1OpenGL2)
          STYLE: reduce number of lines by removing unnecessary empty lines
          DOC: document FilterWatcher removal
          ENH: adding an .editorconfig file to aid IDE's code formatting options
          BUG: forgotten #ifdefs for ITK_LEGACY_REMOVE
          ENH: adding debugger help files for Visual Studio 2017
          ENH: moving .clang-format file into the root folder,
          ENH: using the new threading mechanism for FFT module
          ENH: explicitly setting threading model in each multi-threaded filter
          ENH: support classic ThreadedGenerateData via ITK_CLASSIC_THREADING_MODEL
          BUG: fixing a test which has been failing since multi-threading refactoring
          ENH: updating baselines for itkBSplineScatteredDataPointSetToImageFilterTest*
          COMP: fixing 2 compile warnings
          STYLE: renaming migration guide document
          ENH: extending migration guide with threading refactoring instructions
          ENH: reducing redundancy in itkLandmarkBasedTransformInitializerTest
          ENH: eliminate CMake option ITK_CLASSIC_THREADING_MODEL
    Hans Johnson (5):
          STYLE: Use C++11 override keyword directly
          STYLE: Use C++11 override keyword directly
          ENH: Add compression option for Transform files
          COMP: Address type mis-match compiler warning
          COMP: Remove unused variable warning
    Jon Haitz Legarreta GorroΓ±o (10):
          COMP: Use and move ITK_DISALLOW_COPY_AND_ASSIGN calls to public section.
          ENH: Update the WikiExamples remote module commit hash.
          COMP: Bump the remote modules' versions.
          DOC: Fix miscellaneous typos.
          DOC: Update the ITK logo files in `Documentation` folder.
          DOC: Remove PSD files containing old ITK logo.
          BUG: Address use of CMake variables in CMakeLists.txt.
          COMP: Set the minimum required CMake version to 3.10.2.
          STYLE: Stick to the ITK style guidelines.
          COMP: Bump the remote modules' versions after the CMake ver update.
    Lucas Gandel (2):
          ENH: include WrapITKConfig for external module
          ENH: Allow for itk::ImageSource wrapping override
    Matthew McCormick (17):
          ENH: Support Python snake case keyword arguments in object initializion
          PERF: Avoid extra condition check in
          COMP: Detect Linux in itkMemoryUsageObserver.h on Alpine Linux
          COMP: Define ITK_DELETE_FUNCTION for backwards compatibility
          BUG: Fix bugs in ITKV4_COMPATIBILITY definition
          COMP: Wrap MultiResolutionPDEDeformableRegistration for Pyramid filter types
          COMP: Do not disallow constructors in Python classes
          DOC: Add Mathieu Malaterre to GDCM copyright holders in NOTICE
          COMP: Address array initialization in itkShapedImageNeighborhoodRangeGTest
          COMP: ShapeImageNeighborhoodRange signed unsigned comparison
          COMP: Add missing itkViewImage.h include to itkViewImage.hxx
          COMP: Initialize CovariantVector in DeformableSimplexMesh3DFilter
          COMP: Update Unary and Binary filters for new generator class base
          COMP: Initialize DeformableSimpleMesh3DFilter displacement
          COMP: Suppress maybe-uninitialized in SimpleDataObjectDecorator Component
          COMP: Do not include itkMultiThreader.h in the header tests
          COMP: Fix Python wrapping of MultiThreaderBase
    Niels Dekker (11):
          ENH: Added Compute member functions to NeighborhoodInnerProduct
          STYLE: Added DISALLOW_COPY_AND_ASSIGN(GaussianDerivativeImageFunction), etc.
          ENH: Added ShapedImageNeighborhoodRange for modern C++ style iteration
          STYLE: Removed '&' from pixelPointer param of NeighborhoodAccessorFunctor::Set
          PERF: Removed virtual ~NeighborhoodAccessorFunctor() and made class final
          COMP: Fixed ShapedImageNeighborhoodRange doxygen + signed/unsigned warning
          BUG: Dropped OffsetTable assumptions from ShapedImageNeighborhoodRange
          PERF: Made HoughTransform2DCircles GaussianDerivative call non-virtual
          COMP: Workaround Clang range-loop-analysis warning NeigborhoodRange test
          ENH: Added class to create offsets for a hyperrectangular neighborhood shape
          ENH: Random access support for ShapedImageNeighborhoodRange iterators
    Pablo Hernandez-Cerdan (4):
          ENH: Add stateless viewer ViewImage with Python wrap.
          DOC: Add docs to ViewImage.
          COMP: Fix catch by value warning in SpatialObject.
          COMP: Fix VNL to compile with gcc8.
    Rashad Kanavath (1):
          COMP: fix linking on OpenBSD
    Sean McBride (4):
          COMP: -Wunused-template & -Winconsistent-missing-destructor-override warnings
          BUG: removed illegal int to enum conversion
          COMP: fix warning about implicit double to bool conversion
          COMP: fix warning about implicit double to bool conversion
    Simon Rit (1):
          COMP: missing include path for FFTW
    Taylor Braun-Jones (1):
          COMP: Fix clang diagnostic: case value cannot be narrowed
    VXL Maintainers (1):
          VNL 2018-05-16 (26628604)

    Enjoy ITK!

  • v4.13.3 Changes

    August 03, 2020

    πŸš€ On behalf of the Insight Toolkit (ITK) Community, we are happy to announce the release of ITK 4.13.3! ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration.

    πŸš€ Release files can be downloaded from

    πŸš€ This purpose of this release is to provide updated compiler support as projects continue the transition to ITK 5. Only updated source code and testing data tarballs are provided in this release.

    πŸš€ This release includes fixes for GCC 9, 10, Visual Studio 2019 and fixes in GDCM for improved DICOM support. For more details, please see the log below.

    πŸ“š This is the last anticipated release in the ITK 4 series. Projects are encourage to migrate to ITK 5 following the migration guide.

    Enjoy ITK!

    ITK changes from v4.13.2 to v4.13.3:

    Bradley Lowekamp (7):
          BUG: Patch missing const qualifier to GDCM dircos_comp comparison
          BUG: Address bug with small size in output of SliceImageFilter
          BUG: Update CI scripts from current ITK master
          ENH: Update GDCM to latest on the release-2.8 branch
          BUG: update CircleCI configuration with selections from master
          BUG: Don't use InsertElement which modifies MTime
          BUG: Address buffer overflow with deprecated GDCM1 interface
    Dženan Zukić (4):
          ENH: use double-conversion's CMake targets
          COMP: a fix for non-system double-conversion build
          ENH: back-porting #1165 to support Visual Studio 2019
          COMP: update download location for pre-built ICU for Visual Studio
    GDCM Upstream (1):
          GDCM 2019-11-04 (7e3be76f)
    Jerome Schmid (1):
          COMP: VtkGlue module-Provide support for VTK new cmake targets
    Marco Nolden (1):
          COMP: added vcl compiler detection for GCC 10.x
    Matthew McCormick (3):
          COMP: Prevent duplicate wrapping ouput file specification
          COMP: Add VXL support for GCC 9
          ENH: Bump CMakeLists.txt version to 4.13.3
  • v4.13.2 Changes

    March 22, 2019

    πŸš€ On behalf of the Insight Toolkit (ITK) Community, we are happy to announce the release of ITK 4.13.2!

    ITK is an open-source, cross-platform library for multidimensional image analysis.

    πŸš€ Release files can be downloaded from

    ⬆️ To install or upgrade Python packages with pip:

    python -m pip install --upgrade pip python -m pip install --upgrade itk

    πŸ“š This is a patch release that fixes critical issues, regressions, documentation, and compiler support. This release includes a number of fixes for GDCM for improved DICOM support. The build system is updated for compatibility with newer CMake. Continuous integration testing is also improved following our migration to GitHub.

    πŸš€ The next feature pre-release for ITK 5, ITK 5 Release Candidate 2, is anticipated in a few weeks.

    Enjoy ITK!

    ITK changes from v4.13.1 to v4.13.2:

    Bai Shi (1):
          COMP: To fix compilation error of "cannot dynamic_cast 'x'
    Bradley Lowekamp @blowekamp (10):
          BUG: Support ITK transform files with corrected group names
          BUG: Update SCIOFIO to ITKv4.13 branch
          BUG: Handle boundary case with max metric
          BUG: Remove static member function variable
          BUG: Synchronize BSpline MeshDomain parameters from fixed params
          COMP: Address CMake policy warnings in ThirdParty libraries
          ENH: Update AzurePipelines configuration from master
          ENH: Explicitly set the XCode version used in Azure
          COMP: Use CMP0048 new for wrapping
          COMP: Set CMP0048 to new in ITK (Remote) Modules
    Dženan Zukić @dzenanz (2):
          STYLE: fixing 'No new line at the end of file'
          ENH: ITKv5_CONST macro for VerifyPreconditions() and VerifyInputInformation()
    Francois Budin @fbudin69500 (1):
          BUG: Disable Python tests if `ITK_BUILD_DEFAULT_MODULES` is OFF
    GDCM Upstream @malaterre (3):
          GDCM 2019-02-07 (8e1cfd05)
          GDCM 2018-10-23 (2e701ed7)
          GDCM 2019-02-08 (815caa81)
    Isaiah Norton @ihnorton (2):
          BUG: prevent segfault when transform reader fails to load .mat
          BUG: don't quote argument to URL_HASH for FFTW
    Matthew McCormick @thewtex (9):
          BUG: Use manylinux to build CastXML linux executable
          COMP: Address empty _FILE_OFFSET_BITS in tif_config.h with MinGW64
          BUG: Remove duplicate ITK version number
          ENH: Add Azure Pipelines configuration
          ENH: Add regression test for reading legacy multi-frame DICOM
          COMP: Set CMP0083 for PIE flags
          ENH: Bump CMakeLists.txt version to 4.13.2
          ENH: Add missing SHA512 content link
          ENH: Explicitly use Python 3.7 in Azure builds
    Niels Dekker @N-Dekker (2):
          COMP: Fixed GDCM OpenJPEG name mangling
          PERF: Remove SystemInformation data from ResourceProbe, fix issue #350
  • v4.13.1 Changes

    August 09, 2018

    πŸš€ On behalf of the Insight Segmentation and Registration Toolkit (ITK) Community, we are happy to announce the release of ITK 4.13.1!

    ITK is an open-source, cross-platform library for multidimensional image analysis.

    πŸš€ Release files can be downloaded from

    ⬆️ To install or upgrade Python packages with pip:

    python -m pip install --upgrade pip
    python -m pip install --upgrade --upgrade-strategy eager itk

    πŸ“¦ To install packages with conda:

    conda install -c conda-forge itk

    This is a patch release that fixes critical issues, regressions, documentation, and compiler support. This release includes the addition of symbol name mangling for HDF5 and fixes to the name mangling for libtiff. A number of fixes were added to the NumPy bridge along with miscellaneous improvements. For more details, see the log below.

    πŸš€ This release is also the first time packages are available for Python 3.7.

    πŸš€ The next feature pre-release for ITK 5, ITK 5 Beta 1, is anticipated within the next few weeks.

    Enjoy ITK!

    ITK changes from v4.13.0 to v4.13.1:

    Bradley Lowekamp (10):
          COMP: Use anonymous namespace for internal linkage
          COMP: Update SimpleITKFilters for dependency issues
          BUG: Add missing extensions to ImageIO
          BUG: Add specification of OutputImage Type for TobogganImageFilter
          BUG: Prevent concurrent read/write in output image
          BUG: Handle case where output image is zero sized
          COMP: Fix overflow in floating-point conversion warning
          ENH: TileImageFilter learns to use VectorImages
          ENH: Update SimpleITKFilters remote modules
          BUG: Use pip to install cmake for release
    Francois Budin (2):
          BUG: Initializes CMAKE_DEBUG_POSTFIX to be empty
          BUG: Improvements to ITK NumPyBridge
    Jean-Christophe Fillion-Robin (1):
          BUG: Prevent gdcm "missing implementation" error on macOS
    Jon Haitz Legarreta GorroΓ±o (1):
          ENH: Add Python wrap file to itk::MultiResolutionPDEDeforableRegistration.
    Martino Pilia (1):
          BUG: fix itkFormatWarning in Python wrapping
    Matthew McCormick (13):
          ENH: Add wrapping for BSplineTransformInitializer
          COMP: Do not use absolute path to TestBigEndian.cmake in GDCM
          COMP: Enable pthreads shim with Emscripten
          BUG: Allow module examples to be enabled when built externally
          ENH: Ensure external module examples get added to current build tree
          COMP: Work around RegionGrow2DTest compiler error on ppc64le
          BUG: Wrap long long instead of long
          COMP: Detect Linux in itkMemoryUsageObserver.h on Alpine Linux
          COMP: Wrap MultiResolutionPDEDeformableRegistration for Pyramid filter types
          BUG: Migrate to
          BUG: Correct Windows and macOS CastXML hashes
          COMP: Set CMake project command VERSION
          COMP: Bump CastXML for Visual Studio 2017 support
    Niels Dekker (1):
          COMP: Worked around endless VS2015 Release compilation on Math::Floor
    Pablo Hernandez-Cerdan (2):
          COMP: Fix VNL to compile with gcc8.
          STYLE: Mark CMAKE_DEBUG_POSTFIX as advanced.
    Sean McBride (5):
          STYLE: arranged/alphabetized things to make subsequent changes reviewable
          COMP: Fixed some missing name mangling of libTIFF symbols
          BUG: fixed crash on macOS under guardmalloc from RunOSCheck()
          COMP: Mangle HDF5 symbol names
          COMP: fix warning about implicit double to bool conversion