ITK 5.2.0 Release Notes We are happy to announce the release of Insight Toolkit (ITK) 5.2.0! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. ITK 5.2 is a feature release that improves and extends interfaces to deep learning, artificial intelligence (AI) libraries, with an emphasis on Project MONAI, the Medical Open Network for AI. ITK 5.2 feature highlights include functional filter support for PyTorch tensors, Python dictionary interfaces to itk.Image metadata, NumPy-based pixel indexing, 4D Python image support, and improved multi-component image support. Changes from Release Candidate 3 include an updated Python Quick Start Guide and many improvements to the ITK Sphinx Examples. Experimental pip-installable Python packages are available for ARMv8 on macOS for the Apple M1 Silicon processor, and Linux, also known as aarch64. For a scientific computing environment on these platforms, we recommend mini-forge. The pip-installable Python packages work with conda across all platforms. We are working to add native conda-forge packages in a future release. All Pythonic, functional filter interfaces have type annotations with common, standard types along with numpy.typing.ArrayLike and itk.support.types.ImageLike. Many other improvements were made since RC 3 based on community feedback. A full list can be found in the Changelog below. Downloads Python Packages Install ITK Python packages with: pip install --upgrade itk Guide and Textbook InsightSoftwareGuide-Book1-5.2.0.pdf InsightSoftwareGuide-Book2-5.2.0.pdf Library Sources InsightToolkit-5.2.0.tar.gz InsightToolkit-5.2.0.zip Testing Data Unpack optional testing data in the same directory where the Library Source is unpacked. InsightData-5.2.0.tar.gz InsightData-5.2.0.zip Checksums MD5SUMS SHA512SUMS Features MONAI-compatible itk.Image metadata dict and NumPy-indexing pixel set/get Python interfaces. print(image['0008|0008']) image['origin'] = [4.0, 2.0, 2.0] or a dictionary can be retrieved with: meta_dict = dict(image) For example: In [3]: dict(image) Out[3]: {'0008|0005': 'ISO IR 100', '0008|0008': 'ORIGINAL\\PRIMARY\\AXIAL', '0008|0016': '1.2.840.10008.5.1.4.1.1.2', '0008|0018': '1.3.12.2.1107.5.8.99.484849.834848.79844848.2001082217554549', '0008|0020': '20010822', For non-string keys, they are passed to the NumPy array view so array views can be set and get with NumPy indexing syntax, e.g. In [6]: image[0,:2,4] = [5,5] In [7]: image[0,:4,4:6] Out[7]: NDArrayITKBase([[ 5, -997], [ 5, -1003], [ -993, -999], [ -996, -994]], dtype=int16) Provides a Python dictionary interface to image metadata, keys are MetaDataDictionary entries along with 'origin', 'spacing', and *'direction' keys. The latter reverse their order to be consistent with the NumPy array index order resulting from array views of the image. The itk.xarray_from_image and itk.image_from_xarray functions gained support for transfer of itk MetaDataDictionary and xarray attrs along with support for ordering xarray DataArray dims. Pythonic enhancements Improved Xarray support was added in the functional filter support for NumPy ndarray-like images, i.e. a numpy.ndarray, Dask Array or xarray.DataArrays. itk.Image now provides an astype() method for casting to a NumPy dtype or itk pixel type. In addition to single files or an image stack in a Python list, a directory can be passed to itk.imread containing a DICOM series. A spatially ordered 3D image will be obtained. The conversion functions, itk.vtk_image_from_image() and itk.image_from_vtk_image() are directly available for working with VTK. We now generate .pyi Python interface files, providing better feedback in integrated development environments (IDE)'s like PyCharm. Python code was modernized for Python 3.6, including some typehints. We now use the black Python style. An itk.set_nthreads() convenience function is available to set the default number of threads. Support is now available for use in the Python multiprocessing module. In addition to itk.imread, itk.imwrite, itk.meshread, itk.meshwrite, spatial transformation IO functions are available, itk.transformread, itk.transformwrite. To provide an itk.ImageIOBase derived object to read a specific file format, itk.imread and itk.imwrite gained support for the imageio keyword argument. Python package layout improvements Python support module organization has been organized into the itk.support.* package. Python development was added for multi-config CMake generators, e.g. Visual Studio or multi-config Ninja, with the limitation that it only works with the most recently built configuration. When developing ITK Python wrapping or ITK remote modules, copy the WrapITK.pth build tree file to your virtual environment or conda environment site-packages to experiment with the wrapping. Python package advances Improved VectorImage and multi-component image support is available in the ITK Python packages. NumPy is now a required package dependency. Python packages are now built with interprodedural optimizations (IPO). Linux Python packages are built with the manylinux2014 toolchain. Binary Python packages are available for ARM on macOS and Linux. Python packages are available for Python 3.6 to 3.9. Following CPython deprecation schedule, this is the last release to support Python 3.6. C++ interface improvements A new itk::FunctionCommand class is available, an itk::Command subclass that calls std::function objects or lambda functions. New itk::ReadImage, itk::WriteImage convenience functions are available for reading and writing image files with minimal code. An itk::Image now supports operator== and operator!=. A new itk::TernaryGeneratorImageFilter class is now available. Third party library updates Updates were made for the third party libraries: GDCM HDF5 double-conversion pygccxml castxml swig VXL KWIML KWSys MetaIO cuFFTW Remote Module Updates We added a new adaptive denoising remote module. Many remote modules were updated: AdaptiveDenoising, AnalyzeObjectLabelMap, AnisotropicDiffusionLBR, BSplineGradient, BioCell, BoneEnhancement, BoneMorphometry, Cuberille, FixedPointInverseDisplacementField, GenericLabelInterpolator, HigherOrderAccurateGradient, IOFDF, IOMeshSTL, IOOpenSlide, IOScanco, IOTransformDCMTK, IsotropicWavelets, LabelErodeDilate, LesionSizingToolkit, MGHIO, MeshNoise, MinimalPathExtraction, Montage, MorphologicalContourInterpolation, MultipleImageIterator, ParabolicMorphology, PerformanceBenchmarking, PhaseSymmetry, PolarTransform, PrincipalComponentsAnalysis, RLEImage, RTK, SCIFIO, SimpleITKFilters, SkullStrip, SmoothingRecursiveYvvGaussianFilter, SplitComponents, Strain, SubdivisionQuadEdgeMeshFilter, TextureFeatures, Thickness3D, TotalVariation, TubeTK, TwoProjectionRegistration, and VariationalRegistration. Their updates are included in the detailed changelog below. Support for cross-platform C++ testing, Python package generation, and PyPI deployment with GitHub Actions was added to almost all remote modules. Test coverage and bug fixes A multitude of test code coverage improvements were made -- our code coverage is now 90.09% with 127,103 lines tested. Many more bug fixes and improvements have been made. For details, see the changelog below. Congratulations Congratulations and thank you to everyone who contributed to this release. Of the 63 authors who contributed since v5.1.0, we would like to specially recognize the new contributors: Horea Christian, Baptiste Depalle, David Thompson, Pierre Wargnier, Darren Thompson, Sebastien Brousmiche, Alexander Burchardt, Marco Nolden, Michael Kuczynski, MrTzschr, Bernhard M. Wiedemann, Charles Garraud, Lee Newberg, Bryn Lloyd, Gregory Lee, justbennet, Kenji Tsumura, Zhiyuan Liu, Jonathan Daniel, Moritz Schaar, Atri Bhattacharya, Mon-ius, Michael Jackson, Tom Birdsong, Alex Domingo, Laurent Malka, Kris Thielemans, Andreas Huber, and Melvin Robinson. And the new contributors since v5.2rc03: Michael Kuczynski, Flanz, Robert, Adrien Boucaud, Tom Birdsong, and suryanshsangwan. What's Next Our next feature release, ITK 5.3, will follow a few patch releases. Remote module Python packages will be updated to leverage and work with itk-5.2.0.post3. Join the community discussion at discourse.itk.org. Contribute with pull requests, code reviews, and issue discussions in our GitHub Organization. Enjoy ITK! ITK Changes Since v5.2rc03 Bradley Lowekamp (6): Enhancements Use dynamic threading model (38dec0a2ce) Performance Improvements Replace thread index array with thread local storage (18f764f23a) Platform Fixes Address gcc 4.8 compilation errors (050172153c) Bug Fixes Use graft of input to mini-pipeline (6390ebf540) Initialize member variables (2819485a51) Style Changes Prefer in class initialization (46f9452491) Dženan Zukić (13): Enhancements update remote modules using the script (289564b5ff) update remote modules (b71b85f9cd) add Ultrasound remote module (04a661c78a) update remote modules by running the script (87de84a9b0) Performance Improvements using constant boundary condition instead of filling the edge (a3429dd18e) Documentation Updates fix AtomicInt and MutexLock broken links in migration guide (eb0e5a01fc) improve description of LBFGSERR_ROUNDING_ERROR stopping condition (3cff310b8c) Platform Fixes fix CMake Deprecation Warning (Compatibility with CMake < 2.8.12) (ff2643f37b) Fix CMake warning by setting policy 0120 to OLD (ce2efb1b9e) Disable CMake warning by setting policy 0120 to OLD (d9de577a7f) Bug Fixes Fix crash in itk.image_from_xarray if is_vector and Dimension==4 (3f2d117175) Style Changes mark ultrasound remote module enablement as advanced variable (2c660a404c) use ReadImage and WriteImage in PolygonSpatialObjectIsInsideTest (75adb9fa30) Flanz, Robert (1): Bug Fixes Fix regression in PolygonSpatialObject (e3bf8e9af8) James Butler (1): Platform Fixes Fix OpenJPEG build error with Visual Studio 16.9 (7cebc26dfa) Jon Haitz Legarreta Gorroño (11): Enhancements Label PRs on filenames (1db37989c2) Trigger PR labeler workflows from forks (3afcc781a0) Increase code coverage (f704b5f12c) Documentation Updates Remove duplicate README file from Review module test folder (c077bb3f62) Platform Fixes Fix deduced type initialization warning and operand mismatch error (25dea2f73d) Fix image pointer casting error (1c25350c93) Fix missing initializer warning (7548a390d7) Avoid creating a copy variable (6c352afd04) Fix unreachable code warning (4b8767b7c5) Style Changes Add missing source file extension to Common module tests (d5bfbef81c) Move DCMTK test baselines to module's Baseline folder (55a186f1d4) Lee Newberg (11): Enhancements Use (Shaped)RegionRange instead of (Shaped)RegionIterator. (ca23a2b2ad) Mark most CMake variables as advanced (4c785c2176) Support ArrayLike type with both numpy>=1.20 and numpy<1.20. (5c86c02178) Performance Improvements Make loop over labels be multi-threaded (b1ffefe79a) Use std (5e884ceb29) Platform Fixes type and const safety in ContourExtractor2DImageFilter (ad81939921) Fix gcc4.8 warnings + errors itkContourExtractor2DImageFilter.hxx (396c2a172e) Replace Type{} with Type() for gcc4. (22ca5dd83d) Address ContourExtractor2DImageFilter valgrind defects (be7c5fda7e) Bug Fixes Fix reference counts for HDF5 DataSet assignment operator (479b9424e8) Style Changes Mimic code that was reviewed for the upstream HDF5 source (090399dbf0) Matt McCormick (21): Enhancements Support 32 bit integer IO in wrapping (beb286c327) Bump KWStyle to 2021-03-17 master (541b779329) Add typehints for itk types to extras (22827a5e97) Add typehints for itk functional filters (ed1