ITK v5.0.0 Release Notes
Release Date: 2019-05-29 // almost 5 years ago-
π ITK 5.0.0 Release Notes
π± We are happy to announce the Insight Toolkit (ITK) 5.0.0! π ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration.
π ITK 5.0.0 is a major release that features an incredible number of improvements: This includes major enhancement in the development process, major code refactoring, addition of important features, improvement of ITK Python wrapping, and more.
π¦ Python Packages
π¦ ITK Python packages can be installed by running:
pip install itkπ¦ or to install the conda package, run:
conda install -c conda-forge itkSoftware Guide
Library Sources
β Testing Data
β Unpack optional testing data in the same directory where the Library Source is unpacked.
Checksums
- π MD5SUMS
- π SHA512SUMS
π Montaging for microscopy imaging files with the new ITKMontage remote module: High-Performance, Open-Source Microscopy Image Montaging. Matthew McCormick , DΕΎenan ZukiΔ , FranΓ§ois Budin , Michael Jackson, Dennis Dimiduk , David Rowenhorst , Sean Donegan, and Michael Groeber. WBIR 2018.ITK on GitHub
π An important step has been taken to faciliate participation of the community in the development of ITK: The official repository was moved to GitHub! This move includes ITK's main repository, as well as many other ITK projects such as the ITKExamples, and many ITK remote modules. It is now very easy for anyone to participate in the development of the library. This has already been a success with many new authors getting involved and submitting patches through the GitHub pull-request mechanism. This change also includes moving the issue tracker to the GitHub issue tracker where any problem encountered with ITK should be reported. ITK's GitHub migration was explained in more detail in ITK 5.0 Beta 3: GitHub. Finally, moving ITK to GitHub made it straightforward to use Microsoft Azure Pipeline Continuous Integration platform: Each pull-request is tested on all 3 major platforms (Windows, Linux, MacOS) and Python builds can be requested to ensure that a patch can be integrated.
C++11
Major C++ code refactoring brought dramatic improvements to ITK's API and performance (see ITK 5.0 Alpha 1: Modern C++ for more details). ITK now uses the C++11 standard allowing the developers full access to its new powerful features such as range-based loops, constexpr, lambda expressions, and uniform initialization syntax. Using C++ 11 also removes the necessity of many ITK macros (e.g.
ITK_NULLPTR,ITK_DELETED_FUNCTION) which have equivalents in the new standard. This also leads to changes in style to match the C++ 11 best practices. This includes replacingtypedefcalls with theusingkeyword to improve source code readability. ITK's C++ code is easier to read, understand, and maintain!Thread Pool
π This new release of ITK also integrates big performance improvements thanks to the refactoring of the multithreading infrastructure with a thread pool available by default, and the possible usage of the Intel Threading Building Blocks (TBB) threading backend (see ITK 5.0 Alpha 2: Performance for benchmarks).
Spatial Objects
β Additionally, a major upgrade of the ITK Spatial Object framework, which provides a representation of objects and the mechanism to specify their spatial relationship relative to other objects in a scene, was integrated in this new version of ITK. The new code improves consistency in the programming interface and simplifies implementation and usage (more details in ITK 5.0 Release Candidate 2: Spatial Objectβs.
π New Features
π Other new features in this ITK release include new algorithms, better mesh support (see ITK 5.0 Release Candidate 1: Meshes), new global variable model using one singleton, and better streaming capabilities.
Third Party Libraries
β‘οΈ Eigen, a C++ library for linear algebra, was integrated in ITK and gradual transition from VXL to Eigen for Linear algebra is planned. Many third party libraries were updated: VNL, DCMTK, GDCM, HDF5, KWSys, MetaIO, Zlib, GIFTI, nifti, pygccxml.
Remote Modules
π Remote modules, which allow easy integration of new image processing algorithm in ITK, were updated and new Python packages compatible with this new release of ITK were created. Four new remote modules were also added to ITK: PhaseSymmetry, IOOpenSlide, Montage, and BSplineGradient (description of the modules in ITK 5.0 Beta 3: GitHub).
Python
π Traditionally, ITK in Python had to be used through an object-oriented interface. In this new release, we have added a functional interface which is more Pythonic and should be more familiar to Python programmers. Examples on how to use this new procedural interface are available in ITK 5.0 Beta 1: Pythonic Interface.
Congratulations
π Congratulations and thank you to everyone who contributed to this release. Of the 49 authors, we would like to specially recognize the new contributors, Isaiah Norton, maekclena, Rashad Kanavath, Bai Shi, Hui Xie, Martino Pilia, Ally Warner, pierre33, Chao Wu, Gregory C. Sharp, Bryce A Besler, Kwame Kutten, Mihail Isakov, Jerome Schmid, Roman Grothausmann, Alexis Girault, Gabriel A. Devenyi, Marian Klymov, Thomas Janvier, and Forrest Li.
Migration to ITKv5
π 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.
What's Next
Join us in the creation of advanced, open source scientific image analysis tools. Get started with the ITK examples. Take part in the community discussion at discourse.itk.org. Contribute with pull requests, code reviews, and issue discussions in our GitHub Organization.
π We have a soft commitment to backwards compatibility to address any potential API or architectual issues until the next feature release. Stay tuned for upcoming announcements on ITK's integration with modern web technologies and improved support for Remote Module development on GitHub.
Enjoy ITK!
π Changes from 5.0 RC 2 to 5.0.0
Alexis Girault @agirault (4): ENH: Compare images converted from and to VTK in ITKVtkGlue tests ENH: Pass directions in VTKImage import/export classes ENH: Throw exception when necessary while importing a vtk image BUG: Ignore calls to the direction APIs in VTK if lower than 8.90 Bradley Lowekamp @blowekamp (46): COMP: Address const char[] conversation warning BUG: Fix leaking PNGIO resources during exception BUG: Remove redundent fclose on PNG file pointer ENH: Add Valgrind suppression file for Ubuntu 18.04 LTS BUG: Update FEM test for new spatial objects COMP: Correct continuous index type BUG: Address valgrid defects related to the PointSpatialObject BUG: Fix ownership of environment variable value BUG: Fix leak in SpatialObject InternalClone method ENH: Update a couple example to use the resample instead of warp BUG: Set all component of 3D points BUG: Add named output support to StreamingImageFilter ENH: Deprecate VectorResampleImageFilter ENH: Consolidating setting compression level interface to ImageIOBase ENH: Implement InternalSetCompressor method in ImageIOs DOC: Add compression documentation to ImageIOs ENH: Use the empty string "" for the default compressor ENH: Add compression level support to NRRD IO ENH: Improve TIFF ImageIO compression testing ENH: Add base class for generic streaming processes ENH: Add ImageSink base filter class ENH: Use streaming base class for LabelStatisticsImageFilter ENH: Use named input in LabelStatisticsImageFilter ENH: Add streaming support to StatisticsImageFilter ENH: Add testing for streaming with StatisticsImageFilter ENH: Remove output image, use standard decorator macros ENH: Refactor min/max filter to use ImageSink ENH: Add ImageSink::VerifyInputInformation ENH: Add KWStyle override for ImageStatistics module ENH: Use streaming sink base class for image to histogram filters ENH: Deprecate ImageTransformer class BUG: Update NormalizeImageFilter with double graft mini-pipeline DOC: statistics filter changes for ITKv5 ENH: Add Python wrapping for streaming base classes ENH: Add streaming testing of label statistics filter COMP: Move deprecated VectorCastImageFilter wrapping to deprecated BUG: Fix path for Brain Web data BUG: Correct StreamingProcessObject's progress computation STYLE: prefer variable-less catch re-throw BUG: Set current request number back to -1 after stream execution ENH: Expose streaming methods in MinimumMaximumImageFilter ENH: Add streaming testing for min max filter ENH: replace RGB adaptor with directly using CastImageFilter ENH: Add cast support for per component conversion ENH: Mark the Cast functor to be remove with legacy code DOC: Update documentation for streaming statistics filters. DΕΎenan ZukiΔ @dzenanz (25): ENH: make ITK_MAX_THREADS configurable BUG: fix threading test bugs when ITK_DEFAULT_MAX_THREADS is over 256 COMP: compile GPU classes with legacies disabled COMP: removing extraneous DLL specification from private member COMP: follow-up on recent removal of METAIO_STL macro COMP: add missing dependent module for ITKv3 examples COMP: ResampleImageFilter does not have SetDisplacementField method ENH: reduce default compression level for much faster compression BUG: compression was accidentally disabled in NrrdImageIO COMP: compile in ITK STYLE: move ivar default values to header file ENH: expose setting compression level in ImageFileWriter ENH: expose compression level in MetaImageIO BUG: the clang version check was overly strict on Apple platforms COMP: fix build failures introduced by c76b193 (#886) ENH: cleaning up tests which are almost exact duplicates from MetaIO ENH: updating remote modules COMP: fix warning: 'return' will never be executed COMP: fix export specification of Barrier class COMP: follow up to 814419a (bounding box m_CornersContainer removal) ENH: LevelSetsv4Visualization has moved to remote module ITKVtkGlue ENH: run large image IO tests serially ENH: enabling ResampleImage streaming test and updating baselines ENH: enabling ResampleImage streaming test and updating baselines ENH: exclude Eigen3 from the list of default modules Francois Budin @fbudin69500 (19): ENH: Add `fallback_only` parameter to `imread()` Python function ENH: Add suffix to Azure build running gcov to differentiate them STYLE: Add display name to checkout step in AzurePipelineBatch.yml ENH: Add JUnit test formatter to AzurePipelinesBatch.yml STYLE: Add badge for Azure pipeline Linux code coverage build ENH: Warning when trying to open in Python an image file that doesn't exist BUG: Missing `ci_addons` to convert ctest results to JUnit format BUG: Disable itkObjectFactoryBasePrivateDestructor test with -static link flag ENH: Add Python function to print Python class name corresponding to C++ class ENH: Python ImageFileReader error message improvement ENH: Warning when trying to open in Python an image file that doesn't exist ENH: Follow up commit to fix itkBoundingBox with LEGACY support ENH: Follow up commit to fix itkBoundingBox with LEGACY support BUG: std::list of `LineSpatialObject` needs to be wrapped BUG: ITK could not find Eigen3::Eigen target when using system Eigen BUG: Revert changing call to `Initialize()` with `clear()` BUG: Corner positions were inserted at the end of a list that was initialized BUG: Enforces consistent types BUG: Remote modules Python files (*.so, *.py) were built in the wrong folder GDCM Upstream (1): GDCM 2019-05-16 (e405908e) Hans J. Johnson @hjmjohnson (20): BUG: Usage name did not match file name. STYLE: Minor indentation improvements. ENH: Enable ITKV3_COMPATIBILITY option STYLE: Remove outdated python examples STYLE: Syncronize changes between RegistrationITKv[34] STYLE: Remove RegistrationITKv3 duplicate examples ENH: Remove ITKV3_COMPATIBILITY support from ITKv5.0 STYLE: Move deprecated Examples/RegistrationITKv3 to test BUG: Explicit RegisterRequiredFactories needed as test STYLE: Remove Software Guide tags from ITKv3 testing DOC: Make use of checkboxes consistent with github ENH: Add cmake override for GIT_TAG of remote modules STYLE: Remove custom environmental override for WikiExamples DOC: Fix spelling errors ENH: Identify histogram min/max for UseSampledPointSet BUG: itkConfigure.h defines ITK_DEFAULT_MAX_THREADS COMP: Remove unused static variable warning DOC: Remove documentation references to VectorResampleImageFilter DOC: Remove VectorCastImage documentation references ENH: Changes required for ITKv5 compatibility Jon Haitz Legarreta GorroΓ±o @jhlegarreta (4): STYLE: Remove tab. DOC: Improve remote modules' maintenance scripts documentation ENH: Add a script to apply another script to all remotes DOC: Modify the CoC breach reporting procedure Mathieu Malaterre @malaterre (3): STYLE: Teach git about GDCM oversize file BUG: Do not include COPYING from a non existing directory DOC: Fix old reference to Image Number Matthew McCormick @thewtex (23): COMP: Wrap functions for WindowedSincInterpolateImageFunction COMP: Wrapping windowed sinc function includes COMP: Update for changes to VTK target names DOC: Improve ease of release note command execution DOC: Document generation of MD5SUMS and SHA512SUMS files for releases DOC: Add More Information section to CONTRIBUTING DOC: Add ITK 5.0 RC 2 release notes BUG: PythonFindEmptyClasses test for windowed-sinc functions BUG: Prevent ITKMesh README.md from installation as header BUG: Fix identification of Clang major version COMP: ImageMaskSpatialObjectGTest array initialization COMP: ImageMaskSpatialObjectGTest add braces for initialization ENH: Expand ResampleImageFilter requested region by interpolator domain STYLE: Use typename instead of class in ImageSink STYLE: override methods should not be marked virtual BUG: ImageSink defines UpdateLargestPossibleRegion STYLE: StreamingProcessingObject passing void with no arguments BUG: {MinimumMaximum,StatisticsImageFilter} set PrimaryOutputName BUG: Remove MinimumMaximumImageFilter from module2module test pipeline BUG: InterpolateImageFunction::GetRadius hidden in ITKV4_COMPATIBILITY BUG: Condition Eigen export code on ITK_BINARY_DIR BUG: Fix ITKv3 registration test names for property setting BUG: Remove CTEST_TEST_TIME debug message MetaIO Maintainers (5): MetaIO 2019-05-03 (7e16abe1) MetaIO 2019-05-08 (dd5089a2) MetaIO 2019-05-15 (bffb2ef1) MetaIO 2019-05-16 (5010ab63) MetaIO 2019-05-21 (368213e5) Niels Dekker @N-Dekker (21): ENH: Add std style reverse iterators to FixedArray ENH: Add ImageMaskSpatialObject::ComputeMyBoundingBoxInIndexSpace() STYLE: SpatialObject() = default, const BoundingBox, Transform members ENH: Added tests for ImageMaskSpatialObject::IsInside ENH: Test ImageMaskSpatialObject::IsInside independent of distant pixels BUG: Fix issue #785 removing BoundingBox check from ImageMask IsInside PERF: Overload SpatialObject IsInsideInObjectSpace without name argument BUG: Half a pixel margin ImageMaskSpatialObject::ComputeMyBoundingBox() STYLE: Deprecated FixedArray member functions rBegin() and rEnd() STYLE: Replace std::swap_ranges by C++11 std::swap of m_InternalArray DOC: Use the term "object space" for ObjectSpace based member functions STYLE: Replace unsigned short by unsigned int as FixedArray index type STYLE: Explicitly defaulted default-constructors Vector Accessor classes STYLE: Ensure that ContinuousIndex TCoordRep is a floating point type ENH: Convenience overloads for ImageBase Transform member functions ENH: Add NumberOfCorners and ComputeCorners() to BoundingBox STYLE: Remove (deprecate) BoundingBox::GetCorners() + m_CornersContainer COMP: Fixed GCC4 missing-field-initializers warning on `{}` in GTest DOC: Fixed Doxygen description BoundingBox Get member functions DOC: Fixed Doxygen description BoundingBox Get member functions STYLE: Rename ITK macro EXPECT_VECTOR_NEAR to ITK_EXPECT_VECTOR_NEAR Roman Grothausmann @romangrothausmann (1): ENH: Bump remote module ParabolicMorphology Simon Rit @SimonRit (4): COMP: remove MSVC 14 C4800 (performance) warnings with FFTW COMP: remove unused parameter warning with GCC 4.8.5 COMP: fix wrong GDCM library names for open jpeg ENH: update RTK remote file with release tag v2.0.1 VXL Maintainers (1): VNL 2019-05-08 (99697e67) @maekclena (8): ENH: Update compiler macros (#810) BUG: Remove error prone test case BUG: Fix reverse iterator increment return type ENH: Add iterator increment operator return value test BUG: Minor python wrapping fixes ENH: Remove duplicate code ENH: Use ResampleImageFilter for vectors ENH: Deprecate VectorCastImageFilter (#870)