ITK 5.0 Release Candidate 2: Spatial Object’s
We are happy to announce the Insight Toolkit (ITK) Release Candidate 2! This will be the final release candidate before the 5.0.0 release, and the community is encouraged to adopt 5.0 RC 2 in ITK-based applications.
ITK Python packages can be installed by running:
python -m pip install --upgrade pip python -m pip install --upgrade --pre itk
Unpack optional testing data in the same directory where the Library Source is unpacked.
Image denoising with the new ITKTotalVariation remote module. Left: Transmission electron microscopy image of pectin. Right: Denoised image.
This release features a major upgrade to the ITK Spatial Object framework, led by Stephen Aylward, with contributions from Hastings Greer, Forrest Lee, Niels Dekker, Dženan Zukić, and Hans Johnson. In ITK, a
itk::SpatialObject provides a representation of objects and the mechanism to specify their spatial relationship relative to other objects in a scene. Objects can be images but also abstract, parametric entities, such as a ellipse, box, or arrow, or point-based, such as a tube, contour, or surface. Objects can be organized into spatial hierarchies.
SpatialObjects are key for model-based registration, integration of segmentation results in multiple formats, conversions to and from images, and capturing spatial relationships between structures.
In ITK 5, the
SpatialObject framework was refactored to improve consistency in the the programming interface and simplify implementation and usage. As a result, incorrect or unexpected behaviors are avoided. Complexity and dependency were reduced by removing a dependency on the VNL tree data structures. Additionally, IndexSpace was removed from the API of all
SpatialObjects to prevent ambiguity while providing a consistent and intuitive interface. Only two reference spaces are consistently and explicitly available in the API: ObjectSpace and WorldSpace. ObjectSpace is the space local to each object, where the object’s parameters are defined. WorldSpace is the coordinate system defined by the top-level
SpatialObject in a hierachy, which is defined by parent-child object relationships. Only two transforms are now consistently and explicitly available in the API: ObjectToParent transform and ObjectToWorld transform. The ObjectToParent transform moves an object within its parent’s ObjectSpace. The ObjectToWorld transform is derived from component ObjectToParent transforms and is provided for convenience and to reduce redundant computations. The API is now more explicit regarding the space that an operation applies to. For instance,
IsInside(point) is now
IsInsideInWorldSpace(point). For more information on the
SpatialObjects changes, see the ITK 5 Migration Guide.
The Python package synchronization infrastructure for static global variables was refactored to support more variables and permit future additions to the singleton. This will prevent the need to rebuild remote module binary Python packages following future releases of ITK 5. However, current remote module Python packages that use ITK 5 should be rebuilt and republished for ITK 5.0 RC 2.
For an overview of ITK 5’s transition to modern C++, performance-related changes, the new, Pythonic API, the project’s migration to GitHub, and Mesh improvements, see the ITK 5 Alpha 1: Modern C++, ITK 5 Alpha 2: Performance, ITK 5 Beta 1: Pythonic Interface, ITK 5 Beta 3: GitHub and ITK 5 Release Candidate 1: Meshes release announcements.
Tomographic phantom reconstruction with the new Reconstruction Toolkit (RTK) remote module.
New Remote Modules
ITKIOScanco: read and write Scanco microCT .isq files.
ITKTotalVariation: total variation image denoising.
ITKRTK: the Reconstruction Toolkit provides high performance implementations of advanced tomographic image reconstruction algorithms.
ITKThickness3D: compute the skeleton and thickness transform from 3D images.
- Add MetaDataDictionary move support.
- MetaDataDictionary uses copy-on-write.
itk::Barrieris now deprecated: replace with the new multi-threading functions.
- Range-based for loops supported in
- Major performance improvements to TimeProbe, ResourceProbe constructor (issue #350).
- Repository README files were migrated to Markdown.
- Continuous code coverage builds from Azure Pipelines.
- Better support for unicode in KWSys.
itksys::hash_setare deprecated in favor of
- New GitHub pull request templates and issue templates.
- New scripts added to update ITK remote modules.
itk::SpatialObjectframework refactored (see release notes introduction).
- Initial streaming support added to
itk::ResampleImageFilterfor linear transforms.
- Eigen 3 updated to the latest version.
- Better support for building against a system Eigen.
- GDCM updated to the latest version.
- HDF5 updated to 1.10.4.
- ITKVtkGlue support for VTK with
- KWSys updated to the latest version.
- MetaIO updated to the latest version.
- VXL updated to the latest version.
- MINC updated to the latest version.
- Static variable synchronization method refactored; ITK 5 remote module Python packages need to be rebuilt against 5.0 RC 2.
- Add wrapping for
- Docstrings added to snake case functions.
- Python tests should now be defined in /wrapping/test/CMakeLists.txt to exclude their definition when wrapping is not enabled.
- Conversion between ITK matrices and NumPy arrays is now supported.
- Additional wrapping types for
- Additional types supported for NumPy <-> ITK Image conversion.
- Additional wrapping and typemaps for
- Add wrapping for
- Add wrapping for
- Add wrapping for
To install the 5.0 Release Candidate 2 Python packages, run
python -m pip install --upgrade pip python -m pip install --upgrade --pre itk
There are many more improvements not mentioned above. For more details, please see the change log below. Congratulations and thank you to everyone who contributed to this release.
The ITK 5.0.0 final release is scheduled for May.
Bradley Lowekamp @blowekamp (14): ENH: Add move support to the MetaDataDictionary object PERF: Implement copy on write for MetaDataDictionary ENH: adding MetaDataDictionary GTests BUG: Do not modify MetaDataDictionary with operator const ENH: Improve ExposeMetaData efficiency 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 COMP: Address OSX Clang "direct access" linkage warnings ENH: Add Azure Pipelines script for coverage BUG: Fix Li threshold calculator for negative image values DOC: Correct documented Canny Segmentation filter example Dženan Zukić @dzenanz (18): ENH: add better support for Unicode by using UTF-8 by default in KWSys BUG: propagate ITK_LIBRARY_PROPERTIES into zlib COMP: fixing MSVC warning C4800 ENH: refactoring NarrowBandImageFilterBase to not use Barrier DOC: fixing code sample COMP: compile fixes for Visual Studio 2017 ENH: ModifiedTimeType uses 64 bits on Windows - it was 32 before ENH: refactor itkThreadPoolTest and rename into itkMultithreadingTest ENH: shuffling tests in ITKCommon to make the split more logical ENH: introduce a parameter to control level of output ENH: concentrating WaitForAll() in Iterate() ENH: ParallelSparseFieldLevelSetImageFilter no longer uses barrier ENH: moving Barrier into Deprecated module ENH: prevent false sharing between threads STYLE: declaration alignment ENH: replace itksys::hash_map and hash_set by std equivalents COMP: missing override for destructors Update ITK5MigrationGuide.md Eigen Upstream (3): Eigen3 2019-01-26 (e2c082bf) Eigen3 2019-03-05 (0805e8fd) Eigen3 2019-03-14 (8a3c2d91) Forrest Li @floryst (4): ENH: Update arrow spatial object ENH: Update EllipseSpatialObject ENH: Update box spatial object ENH: Update polygon SO and delete polygon group SO Francois Budin @fbudin69500 (25): BUG: Implement but hide MetaDataDictionary iterator methods BUG: Explicitly give Python library path to ITK Python targets for MSVC ENH: Wrap itkPCAShapeSignedDistanceFunction ENH: Synchronize factories across modules in Python ENH: Explicitly return `None` when calling `__call__`` if filter has no output ENH: Deprecated object call function and improve procedural call function ENH: Adds argument completion with procedural calls ENH: Add docstring to snake case functions BUG: Disable Python tests if `ITK_BUILD_DEFAULT_MODULES` is OFF BUG: Returns a copy of the VNL matrix instead of a reference ENH: Add helper functions to convert NumPy arrays to ITK matrices and back ENH: Add `ttype` keyword in New() function for Python templated classes ENH: `isinstance()` can be called without template parameters of classinfo BUG: Wrap itkImageDuplicator for all image types as it is used by NumPyBridge ENH: itkPCAShapeSignedDistanceFunction supports float images ENH: Add advanced CMake option `ITK_DO_NOT_BUILD_TESTDRIVERS` ENH: Move part of CI configuration into Azure YML files ENH: Move Python tests into wrapping subfolder BUG: Correct CMake variable name and move baseline files to appropriate folder ENH: Only run Python tests on Linux and Windows ENH: Adds wrapping for std::vector<itk::Image<...>::Pointer> and typemaps ENH: New test to verify that` ObjectFactoryBasePrivate` is destroyed correctly ENH: Enable forcing creating snake_case function for non-ProcessObject classes ENH: Add snake case method for non itkProcess derived class itkImageDuplicator BUG: itkObjectFactoryBasePrivateDestructor was not compiling with MSVC GDCM Upstream @malaterre (3): GDCM 2019-02-07 (8e1cfd05) GDCM 2018-10-23 (2e701ed7) GDCM 2019-02-08 (815caa81) HDF5 Maintainers (1): HDF5 2018-10-15 (545c5fb2) Hans J. Johnson (27): STYLE: Remove exact duplicate test code ENH: Improve by adding enhanced complexity to testing ENH: Add test for IsInsideInObjectSpace. DOC: Improve diagnostic message from ExtractImageFilter ENH: TransformIOBaseTemplate Must be explicitly instantiated STYLE: Instance variables should be private STYLE: Move default [con/de]strutor to .h (part 2) STYLE: Class derived from TransformBase need explicit instantiation STYLE: Remove functions that are not used ENH: Use member functions with default values COMP: Refactor to remove const_cast of void * STYLE: Fix spelling s/ranage/range/g in comment. ENH: Improve coverage for itk::FastMarchingImageFilterBase. COMP: Allow compiler option fixed in gcc 4.1.0 PERF: Allow overwriting ABI/Optimization & Warning flags DOC: Minor spelling corrections ENH: Improve test coverage of ImageMoments DOC: Expand GetAxisAlignedBoundingBoxRegion replacement code STYLE: Prefer using Update() for consistency ENH: Avoid deprecated SpatialObject function calls ENH: ProtectedComputeMyBoundingBox return not used ENH: Clean up tests to pass under new API COMP: Consolodate duplicate LogTester code COMP: Support ITK_LEGACY_REMOVE for SpatialObjects ENH: Add legacy interface to SpatialObjects BUG: Match return types for nullptr return values COMP: Remove compilation warning unmatched types Hastings Greer @HastingsGreer (6): BUG: ImageSpatialObject's BoundingBox was nonfunctional if not axis aligned BUG: ImageMaskSpatialObject::IsInside uses image cosines COMP: fix compilation errors COMP: Various compiler errors COMP: fixes to enable compilation with gcc COMP: Update tests Jerome Schmid @schmidje (1): COMP: VtkGlue module-Provide support for VTK new cmake targets Jon Haitz Legarreta Gorroño @jhlegarreta (29): ENH: Add a PrintHelper file to overload boolean and vector printing. ENH: Add a parameter to test to improve `itk::ResampleImageFilter` testing. ENH: Update the ITKIOFDF remote module. ENH: Improve `itk::ResampleImageFilter` class coverage. BUG: Fix `ìtkResmapleImageTest2` test failing on 32-bit systems. DOC: Transition `Examples` folder `README` file to Markdown. DOC: Increase `VNL` ThirdParty module `README` information accuracy. ENH: Conform to GitHub PR and issue template guidelines. DOC: Transition the `Nonunit/Review` `README` to Markdown syntax. ENH: Bump the latest version of the `ITKThickness3D` remote. BUG: Fix GitHub community template syntax errors. STYLE: Transition GitHub community template filenames to lowercase. DOC: Change GitHub community template guidelines to HTML comment markup. ENH: Add new GitHub community issue templates. STYLE: Improve coverage issue template name wording. DOC: Fix PR template not being displayed. DOC: Add emojis to GitHub issue templates. ENH: Update a few remote modules to their latest commit versions. DOC: Improve the CONTRIBUTING guidelines document DOC: Fix typo. DOC: Add checklist to PR template. ENH: Add a script to update the remote module commit hashes ENH: Add a script to update the ITK tag as required in files ENH: Update the Remote module Python package version automatically STYLE: Rename remote module maintenance script DOC: Add Remote module PyPI update notice in Release guide ENH: Bump remote modules. ENH: Bump remote modules to latest commits ENH: Bump remote modules to their latest commits COMP: Fix Software Guide line length too long warnings KWSys Upstream @bradking (2): KWSys 2019-02-14 (e270ce9f) KWSys 2019-03-28 (e92bdbe8) Matthew McCormick @thewtex (51): ENH: Use HDF5 1.10.4 DOC: Updates to the README DOC: Use 'ITK: The Insight Toolkit' for README title ENH: Add legacy multi-frame DICOM MD5 content links COMP: Avoid duplicate wrapping of VectorContainer with unsigned short BUG: MeshIOBase ivars used for number points, cells, pixels STYLE: Keep ProjectObject methods protected in ResampleImageFilter STYLE: Remove unnecessary ResampleImageFilter input/output checks DOC: Updates to the Release documentation for 5.0 RC 1 ENH: Update CI ExternalDataVersion to 5.0rc01 DOC: Add ITK 5 Release Candidate 1 release notes ENH: Add regression test for reading legacy multi-frame DICOM ENH: Update itk_hdf5_mangle.h for HDF5 1.10.4 COMP: Re-apply HDF5 Emscripten clobbered by 1.10.4 update ENH: Add probot-stale GitHub bot configuration ENH: Add test result analysis to Azure Pipelines web interface COMP: Set CMP0083 for PIE flags COMP: HDF5 CMake does not have INTEGER cache type COMP: Do not also pass png_ptr twice to png_set_error_fn ENH: Wrap TriangleMeshToBinaryImageFilter PERF: Use constexpr in complex NumericTraits BUG: VTKPolyDataMeshIO CanReadFile returns false for non-PolyData COMP: Set CMP0083 for PIE flags BUG: Use VERSION_GREATER_EQUAL for PIE check ENH: Bump CMakeLists.txt version to 4.13.2 ENH: Add missing SHA512 content link ENH: Explicitly use Python 3.7 in Azure builds COMP: Prevent duplicate wrapping ouput file specification BUG: Add executable bit to prefer-type-alias-over-typedef.sh COMP: Specify type in LiThresholdCalculator min call ENH: Wrap ExtrapolateImageFunction ENH: Add Python wrapping for SymmetricEigenAnalysisImageFilter BUG: Add missing ITKImageGrid circle.png content links BUG: itkResampleImageTest2Streaming verification ENH: Add IOScanco remote module COMP: Add backwards compatible EnlargeRegionOverBox BUG: Set dashboard_do_coverage in Azure configuration COMP: Add export specification to ITKSpatialObjects BUG: Mark HDF5 CMake variables as advanced BUG: Mark INSTALL_GTEST CMake variable as advanced STYLE: NIFTI CMake variable spacing BUG: Do not use CACHE variables for NIFTI when not required BUG: Mark TESTLIB_VCL_WHERE_ROOT_DIR_H as advanced BUG: Remove BUILD_* GDCM settings from the cache BUG: Remove ALLOW_UNSUPPORTED from the cache STYLE: C-style variable declarations in WindowedSinceInterpolateImageFunction ENH: Add wrapping for WindowedSincInterpolateImageFunction ENH: ITKVtkGlue only requires rendering libraries when needed COMP: GaussianInterpolateImageFunction test narrowing BUG: Allow Python tests in module test/CMakeLists.txt ENH: Add new content links for ITK 5.0 RC 2 MetaIO Maintainers (2): MetaIO 2019-01-15 (6efa2b32) MetaIO 2019-04-24 (9d2012d1) Mihail Isakov @issakomi (4): BUG: WhatModulesITK.py doesn't detect ITKMeshIO STYLE: header included twice, spelling BUG: index overflow in BinaryMask3DMeshSource BUG: changed to signed Niels Dekker @N-Dekker (28): PERF: Remove SystemInformation data from ResourceProbe, fix issue #350 COMP: Fix support itk::VectorContainer<TElementIdentifier, bool> COMP: Fix SymmetricEigenAnalysis support TMatrix = itk::Array2D<T> COMP: Trailing return types (reference, const_reference) VectorContainer STYLE: HoughTransform2DCircles, GaussianDerivativeImageFunc member init. COMP: Win32Header no longer disable MSVC warning C4800, C4290, C4786 COMP: Removed unreachable code, fixing VS2017 warning (level 4) C4702 STYLE: Removed '2' from GaussianDerivativeImageFunction::ImageDimension2 STYLE: Renamed SpatialFunction within GaussianDerivativeImageFunction BUG: Fixes crashes in unit tests when argv == nullptr STYLE: Removed InitializeConstShapedNeighborhoodIterator() STYLE: ImageFileReader uses std::unique_ptr<>, try-catch-throw removed STYLE: Renamed array of radii EllipseSpatialObject to RadiiInObjectSpace STYLE: Remove GetPixelTypeName() from both Image and Mesh SpatialObject ENH: GTest for ImageMaskSpatialObject::GetAxisAlignedBoundingBoxRegion() STYLE: Removed unused private EventObject::EventFactoryFunction type COMP: Support ITK_LEGACY_SILENT for ThreadInfoStruct STYLE: Removed five unused nested types from ImageSpatialObject ENH: Add static member function Size<VDimension>::Filled(SizeValueType) STYLE: Removed legacy-only ComputeMyBoundingBox() which was not in ITK4 STYLE: Renamed ProtectedComputeMyBoundingBox() to ComputeMyBoundingBox() STYLE: Remove const from SpatialObject::ComputeMyBoundingBox() BUG: Fix #734 Incorrect results GetAxisAlignedBoundingBoxRegion() for 2D ENH: Extend test ImageMaskSpatialObject::GetAxisAlignedBoundingBoxRegion STYLE: SpatialObject GetModifiableMyBoundingBoxInObjectSpace() non-const PERF: ImageMaskSpatialObject::GetAxisAlignedBoundingBoxRegion() faster ENH: Add explicit constructors Point and FixedArray for C++11 std::array ENH: Add begin() and end() to FixedArray, support range-based for-loops Pablo Hernandez-Cerdan @phcerdan (11): ENH: Add itk-module-init.cmake to Eigen3 COMP: Make ThirdParty Eigen3 COMPILE_DEPENDS COMP: Revert "COMP: Make ThirdParty Eigen3 COMPILE_DEPENDS" BUG: Fix Eigen3 INSTALL_DIR DOC: Update ITK5MigrationGuide BUG: Fix OFFIS_DMCTK_VERSION_NUMBER where wrunlock was introduced BUG: Fix export for ITKDeprecated classes BUG: Do no install any Eigen3 targets if ITK_USE_SYSTEM_EIGEN=ON ENH: Update Remote Module IsotropicWavelets ENH: Add COMPILE_DEFINITIONS to castxml ENH: Add remote module TotalVariation Roman Grothausmann @romangrothausmann (4): ENH: new tests to verify streaming capabilities of itkResampleImageFilter BUG: corrected logic for checking that streaming was not used ENH: compare outputs of itkResampleImageTest2Streaming to determine success: ENH: Stream ResampleImageFilter for linear transforms Simon Rit @SimonRit (2): ENH: add RTK as a remote module ENH: added test to check that Matrix returns a copy of the vnl matrix Stephen R.Aylward @aylward (47): ENH: Refactor of SpatialObject top-level class ENH: Remove itkAffineGeometryFrame file ENH: Update ArrowSpatialObject ENH: Children name match using string.find (i.e., any substring) ENH: Refined SpatialObject base class and organized .h. Refactoring. ENH: Refactor Line and Landmark Spatial Objects ENH: Refactor Mesh and fix bugs found in previous refactorings BUG: Remove itkPlaneSpatialObject because it implemented a boxSO ENH: Refactor itkPolygon[Group]SpatialObject ENH: Refactor Scene to be a Group and refine base SpatialObject ENH: Refactoring the SpatialObject to be more intuitive ENH: SpatialObjects have "MyBoundingBox" and "FamilyBoundingBox" ENH: Resolved SpatialObject member function and variable names ENH: Updated subclasses to match SpatialObjectAPI ENH: SpatialObjectPoint and Properties updated ENH: Removed unwanted TreeNode classes ENH: Removing outdated source files COMP: SpatialObjectProperties now a cxx file that compiles ENH: Refactor SpatialObjectPoints and TubeSpatialObjectPoints ENH: Update PolygonGroup IO to use new spatial object classes ENH: Refactoring for IO ENH: Renamed functions to make coordinate system explicit ENH: Refactoring Meta*Converter classes ENH: Update to tests to fit new SO API BUG: Fixed bugs on windows for tests ENH: Updated wrapping and examples to compile SpatialObjects ENH: Updated itkGetObjectMcro to itkGetModifiableObjectMacro ENH: Updates to fix failing tests ENH: Fix two more tests BUG: Fix bug in ImageMaskSO bounding box ENH: Making tests pass...one bug at a time... BUG: Missing center computation in isInside function for Ellipse ENH: Adding support for Clone member function to perform a deep copy BUG: Last spatial-object-specific tests now pass. BUG: Fix const issues regarding My/Family Bounding Box BUG: Fix warnings and other minor things ENH: Fixing PolygonSpatialObject ENH: Made ContourSO and PolygonSO more consistent in logic BUG: Fix IsInsideObjectSpace function in PolygonSpatialObject BUG: Fix multiple bugs in refactoring of spatial objects DOC: SpatialObject docs in migration guide (#630) DOC: Detail function change in ImageMaskSpatialObject DOC: Specify ITK class alternatives to removed SO member functions BUG: Adds RemovePoint() to PointBasedSpatialObjects (#693) DOC: PointBasedSpatialObject's PointListType migration docs provided (#652) BUG: Adding a consistent Clear() to SpatialObjects (#700) DOC: Update recommendation for computing a Boundoing Region in IndexSpace (#699) Thomas Janvier @T4mmi (1): ENH: Add Thickness3D Remote module. VXL Maintainers (3): VNL 2019-03-04 (1e8a027f) VNL 2019-03-11 (3d183906) VNL 2019-03-22 (d0ff9f72) Vladimir S. FONOV @vfonov (2): MINC 2019-04-23 (44fae20d) ENH: fixed build script Ziv Yaniv @zivy (1): BUG: PNGImageIO segfaults on corrupt png. @maekclena (13): BUG: Initialize array with expected number of elements BUG: Disable TIFF predictor BUG: Python3 compatibility ENH: Cleanup python wrapping tests ENH: Address review comments ENH: Update maintenance script BUG: Replace sed by ex for portability ENH: fix inconsistencies and clearer output ENH: Update remote modules BUG: fix gaussian interpolate test BUG: Ignore comment lines STYLE: Visually indent array BUG: Remove outdated class declaration