ITK 5.0.0
ITK 5.0.0 Release Notes
We are happy to announce the Insight Toolkit (ITK) 5.0.0! 🎉 ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration.
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.
Python Packages
ITK Python packages can be installed by running:
pip install itk
or to install the conda package, run:
conda install -c conda-forge itk
Software Guide
Library Sources
Testing Data
Unpack optional testing data in the same directory where the Library Source is unpacked.
Checksums
Montaging for microscopy imaging files with the new ITKMontage remote module: High-Performance, Open-Source Microscopy Image Montaging. Matthew McCormick , Dženan Zukić , François Budin , Michael Jackson, Dennis Dimiduk , David Rowenhorst , Sean Donegan, and Michael Groeber. WBIR 2018.
ITK on GitHub
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 replacing typedef calls with the using keyword to improve source code readability. ITK's C++ code is easier to read, understand, and maintain!
Thread Pool
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
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 Object’s.
New Features
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
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
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
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
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
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.
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!
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.
Dženan Zukić @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 Gorroño @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)