Release ITK 5.4.0: ReadTheDocs Documentation · InsightSoftwareConsortium/ITK

We are happy to announce the Insight Toolkit (ITK) 5.4.0 is available for download! 🎉 🍻 🥳 ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration in a spatially-oriented architecture.

🔦 Highlights

We're excited to announce a transformation of ITK's documentation ecosystem in version 5.4.0. The documentation infrastructure has been modernized to provide a more accessible, maintainable, and user-friendly experience.

New Markdown-Based Documentation

Our documentation has undergone a complete migration from the traditional landing page and wiki to a modern, Markdown-based system hosted on ReadTheDocs. Experience our enhanced documentation at https://docs.itk.org.

ITK's new Markdown-based documentation, editable on GitHub and hosted on ReadTheDocs.

Enhanced API Documentation

The Doxygen documentation has been seamlessly integrated into ReadTheDocs, offering several key advantages:

Global CDN-powered access for fast, responsive performance worldwide
Complete archive of all previous API versions
Improved navigation and usability

ITK's Doxygen documentation, hosted on ReadTheDocs, provides easy access to all previous versions.

Unified Search Experience

Leveraging ReadTheDocs' subprojects architecture, we've implemented a powerful unified search system that:

Searches across all documentation sources simultaneously
Delivers fast, relevant results
Provides advanced search capabilities
Improves discovery of related content

ITK's unified search across documentation sources, hosted on ReadTheDocs.

These improvements represent our commitment to providing the best possible documentation experience for the ITK community. The new system not only enhances accessibility but also sets the foundation for future documentation innovations.

Elegant, Performance-optimized, Modern C++

This release candidate expands our support for elegant, performant, modern C++. For example, specializations of std::tuple_size and std::tuple_element for itk::ImageRegion in order to support C++17 structured bindings enable compile-time optimized statements to provide a multidimenional region's index and size:

auto [index, size] = image.GetRequestedRegion();

For more information on ITK 5.4's modern C++ support, see the Release Candidate 1 release notes.

Python 3.11 and Stable ABI Wheels

Moreover, this release candidate extends the toolkit's sustainability and Python support through Stable ABI Python wheels. This is made possible by upgrades to SWIG and scikit-build-core, the modern Python packaging standard evolution of scikit-build classic. Python 3.11 wheels will be recognized by pip and work with Python 3.11, 3.12, 3.13, 3.14, etc. While we also provide cross-platform wheels for Python 3.8-3.10, we can only use the Stable ABI with Python 3.11 because it is required for itk's NumPy support.

Remote Module Enhancements

ITK Remote Modules now also have GitHub Action-driven mac ARM / Apple Silicon Python wheel generation support. While a Remote Module setup.py file is still supported in ITK 5.4, migration to a scikit-build-core pyproject.toml file is encouraged. One important advantage is the generation of Stable ABI wheels for Python 3.11+. To migrate to scikit-build-core, use this pyproject.toml template and remove the setup.py file.

DICOM and Web3 Testing Data

For a summary of changes that continue our sustainability evolution with Web3 testing data, see the 5.4 Release Candidate 2 release notes. For a summary of DICOM improvements, including expanded support for additional modality features and crucial spatial metadata for Secondary Capture images, see the 5.4 Release Candidate 4 release notes.

💾 Download

Python Packages

Install ITK Python packages with:

pip install itk

Guide and Textbook

Library Sources

Testing Data

Unpack optional testing data in the same directory where the Library Source is unpacked.

Checksums and Signatures

✨ Features

Python

Wrapping for itk.PhasedArray3DSpecialCoordinatesImage
Better support for multi-component images in image_from_vtk_image
itk.imread supports a series_uid kwarg for DICOM series selection
TBB version updated to latest stable version, disabled on Intel macOS
Python binaries for 3.8-3.11 across platforms
Python 3.11 uses the Stable ABI -- works with Python 3.11+
Python 3.7 is no longer supported
Apple Silicon Remote Module GitHub Action wheels
Updated to the latest version of scikit-build-core
Import time improvements with torch
Add dict_from_polyline, polyline_from_dict
Add bufferedRegion to dict_from_image representation
Support passing a single transform to transformwrite

C++

C++17 is now required
Many style improvements for modern C++ and consistency
GCC 13 support
Name mangling prefix for third party libraries is configurable
Update mangled 3rd-parties to use MANGLE_PREFIX CMake variable
Many improvements to code coverage
Enhanced NRRD and Nifti metadata support
CMake OPTIONAL_COMPONENTS support
Apply cmake-format for a consistent CMake style
get() member function to itk::SmartPointer
itk::Size::CalculateProductOfElements(), to compute number of pixels
Deref(T *), to ease dereferencing a pointer safely
itk::ShapedImageNeighborhoodRange support C-array of offsets (by C++17)
Add itk::Copy(const T & original), which simply returns a copy
Make itk::ImageRegion trivially copyable, remove inheritance (FUTURE)
itk::VTKPolyDataMeshIO support for reading VTK 5.1 format
Add ITK_DEFAULT_COPY_AND_MOVE(TypeName) macro definition
Replace (const std::string) casts with C++17 std::string_view
Replace SetSize/Index calls in tests with region{ index, size }
Optionally limit an ImageMask to a specific pixel value

Performance

Use index/point transforms without bounds checking
Improved SSE2 detection
Many improvements to how locks are handled
Major itk::SpatialObject performance improvements

Documentation

New GitHub Action to check spelling
Doxygen formatting cleanup
Doxygen spelling fixes
Doxygen Insight Journal links are consistent
Many Doxygen improvements to the content
Software Guide updated for style modernization
Change the Insight Journal handle links to insight-journal links
Replace itkTypeMacro with itkOverrideGetNameOfClassMacro
Cryptographic signatures are provided for release sources

Remote module updates

New modules:

FastBilateral - A Fast Approximation to the Bilateral Filter for ITK. Insight Journal article.

Updated modules:

Third party library updates

dcmtk
eigen
gdcm
googletest
kwsys
minc
meta-io
nifti
pygccxml
vxl
zlib-ng

🙏 Congratulations

Congratulations and thank you to everyone who contributed to this release.

Of the 60 authors who contributed since v5.3.0, we would like to specially recognize the new contributors:

Andrei Sandor, Nicklas Larsson, huangjxbq, Sankhesh Jhaveri, adrinkwater, FabioLolix, Vaibhaw, Ningfei Li, Max Aehle, Noah Egnatis, Federico Zivolo, Patrick Linnane, Shreeraj Jadhav, Shengpeng YU, Fernando Bordignon, Andras Lasso, Bernhard Froehler, Thomas BAUDIER, Matthieu LAURENDEAU, Fabian Wenzel, Mikhail Polkovnikov, Pritam Rungta, Florian de Gaulejac, Ramon Emiliani, Martin Hoßbach, Sadhana Ravikumar, and Gabriel Chartrand.

We extend our gratitude to all the ITK community members who have contributed to this release through code submissions, bug reports, and insightful discussions online.

🗣️ What's Next

ITK 5.4.0 represents a transformative milestone in our documentation journey. The finalization of 5.4.0 was delayed due to dependency issues in the example documentation's infrastructure. While these are addressed, we'll continue to refine the 5.4 series through patch releases. We're excited to eventually migrate the examples to a similar robust foundation in future innovations.

Looking ahead, we're thrilled to announce that ITK 6, our next major release, will showcase a substantial array of modernizations. The community has been hard at work implementing significant improvements that will elevate development with and on the toolkit. Watch for upcoming alpha and beta releases of ITK 6, which will run parallel to our 5.4 maintenance efforts.

This dual-track approach ensures both stability for current users and innovation for those ready to explore new features. Stay tuned for announcements about ITK 6's preview releases, which will demonstrate the exciting evolution of the Insight Toolkit.

Enjoy ITK!

ITK Changes Since v5.4rc04

Andrei Sandor (2):

Platform Fixes

Fixed Cpp Warnings (904c7c5838)
Remove \brief with nothing after (0fbb3bca2d)

Bradley Lowekamp (4):

Platform Fixes

Add testing of IsCongruentImageGeometry IsSameImageGeometryAs (7f1c584608)
Suppress LabelGeometryImageFilter deprecated warning (4f4110a275)

Bug Fixes

Mark LabelGeometryImageFilter as deprecated (eb8230c46b)

Style Changes

Improve style of Image.IsXGeometry (f383fe0a95)

Dženan Zukić (4):

Enhancements

Update Montage remote module (3235b3675c)
Update remote modules using a script (004fd7c066)
Update KWStyle [GCC 13.2 output buffer size truncation warnings] (a23e9a215a)

Documentation Updates

Add See Also entries for alternatives to LabelGeometryImageFilter (f408b77a57)

GDCM Upstream (1):

Miscellaneous Changes

GDCM 2024-05-03 (2eaae209) (a6240d348d)

Hans Johnson (13):

Enhancements

Add tests for known required size constraints (1540fa4ba4)

Performance Improvements

Prefer initialization to assignment (e64032ae75)

Platform Fixes

Avoid gcc13.2 compiler out-of-bounds index warnings (a0b816529c)
Avoid compiler false positive warning when assuming string processing (323e8217e1)
Fix uninialized variable warning (d9fcaa08e7)
Fix array bound warning for typecast initial value (462a874af2)
Fix gcc 13.2 compiler warning of large allocation size (6dcfb74e6b)
Fix gcc 13.2 compiler warnings (408cf0c7de)

Style Changes

Spelling Trasform->Transform fixes. (6324749c66)
Simplify code to remove unneeded dynamic_cast (6650d2ce90)
Make variable for magic number (fbe68ab5e2)
Remove dead code suppression of C++11 warnings (fdb94eddc5)
Make variables local scope (1155b5e99b)

Jon Haitz Legarreta Gorroño (4):

Platform Fixes

Suppress -Wformat-nonliteral warning in diff tensor example (abc789e834)
Use default copy and move construct and assign in itk::Region (ec2677f5a5)
Use default copy, move for construc, assign RealTimeStamp (9aff2101c1)
Fix implicit copy constructor definition deprecation warnings (d1ebdfaff6)

KWSys Upstream (2):

Miscellaneous Changes

KWSys 2024-03-08 (bc0706e7) (22754ed242)
KWSys 2024-03-08 (bc0706e7) (7e3f90d526)

Matt McCormick (19):

Enhancements

Add dict_from_polyline, polyline_from_dict (60f89eecbf)

Documentation Updates

Add 5.4 Release Candidate 4 release notes (57a6a66cc1)
ITK 5.4 RC 3 release documentation updates (d7b20b5931)
Update logo colors (54b7807e2a)

Platform Fixes

Add GDCM system version check for SetSecondaryCaptureImagePlaneModule (f4e9b0ba28)
Exclude itkPyBufferMemoryLeak test from macOS ARM CI (6df6b72557)
GCC 13 CastXML vector include workaround (ad6c58223d)

Bug Fixes

AuthorsChangesSince.py support both single and multiline (487da6d086)
Make dict_from_transform more consistent with other dict representations (5397f81b7f)
Add bufferedRegion to dict_from_image representation (c66b0466cd)
Support passing a single transform to transform write (36b3abec9a)
array_from_image shape for VectorImage with 1 component (2447a812b0)
Use unique filenames for Nifti tests (396d62f051)
ElementType with PolyLineParametricPath ContinuousIndex (db44bc8b9a)
VTKPolyDataMeshIO support for reading VTK 5.1 format (30a9409d89)
Mark GDCM macOS CMake variables as advanced (8e928a1cc0)
Mark Module_FastBilateral as advanced (f1c390a1e2)
Wrap SymmetricEigenAnalysisImageFilter with CovariantVector Image output (6e96da5956)

Style Changes

Apply clang-format to LabelGeometryImageFilter (ef9907597b)

Mihail Isakov (1):

Platform Fixes

Update GDCM system version check for SetSecondaryCaptureImagePlaneModule (6e14aadeff)

Niels Dekker (6):

Enhancements

Add ITK_DEFAULT_COPY_AND_MOVE(TypeName) macro definition (f65623be95)

Style Changes

Replace (const std::string) casts with C++17 std::string_view (2a1265d75f)
Replace SetSize/Index calls in tests with region{ index, size } (8f70ee7da1)
Replace SetIndex/Size calls in tests with region{ index, size } (3282875e7c)
Use ITK_DEFAULT_COPY_AND_MOVE for exceptions of Image and Mesh IO (16e6475260)
Use ITK_DEFAULT_COPY_AND_MOVE for RealTimeStamp and Region (4f42280e98)

Philip Cook (2):

Enhancements

Handle NIFTI space and time units more consistently (d9029dccb9)

Bug Fixes

Fix path to write itkNiftiImageIOTest14 data (21b74f0584)

Sean McBride (2):

Platform Fixes

Suppress some Wformat-nonliteral warnings (defa7129be)
restored old spelling of CLANG_SUPPRESS_Wfloat_equal (0c6782999b)

Simon Rit (1):

Enhancements

update remote module RTK (2132909781)

Stephen R. Aylward (3):

Enhancements

Optionally limit an ImageMask to a specific pixel value (c377692288)

Performance Improvements

Changed conditionals and use of const vars for speed (610de818c0)

Bug Fixes

Fix SpatialObjectProperties.GetTag*Value() to return values (ad25ca8900)

ITK Sphinx Examples Changes Since v5.4rc04

Hans J. Johnson (1):

Platform Fixes

Updating to find_package(Python3) (c84d33bc)

Hans Johnson (3):

Platform Fixes

Fix type comparison mismatch (00e2fad7)
Fix set but not used warnings (15820140)

Style Changes

One declaration per line for readability (a63e366a)

Jon Haitz Legarreta Gorroño (6):

Enhancements

Bump macOS version to 10.13 in GHA build, test, publish (540f1852)
Use specific XCode version for GHA macOS 13 build (a88dee79)
Bump macOS version for notebook build, test GHA action step (e7af6630)
Bump checkout and setup-python GitHub actions versions (3df5ef36)
Bump super-linter GitHub action version (38d345a5)
Bump upload-artifact actions version to v4 (f0bd2af9)

Matt McCormick (4):

Documentation Updates

Update Doxygen XML for ITK 5.3.0 (94e4144f)

Platform Fixes

Bump itkwdigets version 1.0a51 (75bef2a0)

Style Changes

Specify ReadTheDocs custom domain configuration (be8dcfc3)
Remove extra spaces in CMake/Doxygen* (dfb07dae)

Niels Dekker (4):

Platform Fixes

Replace itkTypeMacro calls with itkOverrideGetNameOfClassMacro (3b20b544)

Style Changes

Replace Fill(0) on local variables with {} initialization (f5ca3d30)
Replace Size var; var.Fill with auto var = Size::Filled (fe7bd2ae)
Replace Index var; var.Fill with auto var = Index::Filled (6fac7f27)

Pablo Hernandez-Cerdan (1):

Enhancements

Bump ITK to 5.4.0 release (f6c8b9c8)

Tom Birdsong (2):

Enhancements

Modify test macro with option for Python baseline test only (64c20ec1)
Add 1D FFT Example (8b7f38dd)

ITK Software Guide Changes Since v5.4rc04

Dženan Zukić (2):

Documentation Updates

Fix a typo in CreateAModule chapter (1d04a60)
Update supported compiler version information (95b46fe)

Matt McCormick (6):

Enhancements

Bump ITK Superbuild version to 5.4 RC 4 (f37b396)
Improve Actions PDF artifact name (dd86548)
Bump ITK version to v5.4.0 (c722c6a)

Documentation Updates

Update ITK logo (d341bad)
Update single PDF cover page for ITK 5.4.0 (0e3ae9e)

Platform Fixes

Bump actions versions (7af04df)

Niels Dekker (2):

Enhancements

Add section "Initializing variables of fixed size array types" (f10846c)

Platform Fixes

Replace backticks with \code{} in Initialization and Assignment (5246e64)

Remote Module Changes Since v5.4rc04

MeshToPolyData:

Matt McCormick (3):

Enhancements

Build against ITK 5.4 RC 3 (fbb5cf4)
Transition to scikit-build-core, pyproject.toml (6885961)
Build macOS ARM wheels (498b40e)

dependabot[bot] (1):

Miscellaneous Changes

Bump vite from 4.5.2 to 4.5.3 (4d706a8)

Montage:

Dženan Zukić (7):

Enhancements

Compute and expose per-tile registration reliability (b354335)
Update CI for ITK 5.4 RC 04 (c000499)
Switch to SciKit build core (fb14158)
Use updated remote module action which includes notebook fix (91eccc5)
Enable unit tests which are no longer failing (801bf31)
Add per-test regression intensity tolerance (06cacd6)

Documentation Updates

Improve class description and documentation of parameters (0070c46)

MorphologicalContourInterpolation:

Matt McCormick (3):

Enhancements

Add 4D support to wasm (1f5f597)
Bump itk-wasm to 1.0.0-b.173 (bb38356)
Bump CI configuration for ITK 5.4rc03 (6fb73c0)

Stephen Aylward (5):

Enhancements

Bump setup.py and CI to use ITK v5.4 rc2 (edb76bb)
Eliminate old compiler requirements (b38c10a)
Update CI build to macos-12 from macos-11 (c69fce0)
Specify XCode on MacOS (a5f0fcb)

Bug Fixes

Tag is v5.4rc02 - adding missing 0 (5464e2e)

RTK:

Simon Rit (11):

Enhancements

Remove CUDA code for compute capability 1 (4dfa4890)
Replace texture references by objects for CUDA 12 compatibility (5361f69a)
Rename lp_solve library according to ITK's conventions (938aa33a)
Use 64-bit cublas for CUDA 12 (74d25e0a)
Avoid single component intermediate CUDA array for scalar images (bfdca5b6)

Platform Fixes

Display deprecation CUDA messages (902db67f)
Fix ramp filter redefinition of itkSetMacro (4e8331f8)
Remove deprecated inclusion of CUDA's math_functions.h (4c2a3b57)

Bug Fixes

Use size_t to compute CUDA memory length (0a1a8ca8)

Style Changes

Refactor function for preparing texture objects for vector images (f109868a)
Cleanup useless code after CUDA function calls (1a2ca55e)

TubeTK:

Stephen Aylward (1):

Bug Fixes

Incorrect class specification for InverseIntensityImageFilter (ddeae653)

WebAssemblyInterface:

Many. Removed for size constraints.