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ITK 5.4 Release Candidate 2: Web3 Testing Data

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@thewtex thewtex released this 22 Jan 20:42
· 1170 commits to master since this release
v5.4rc02
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thewtex Matt McCormick
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We are happy to announce the Insight Toolkit (ITK) 5.4 Release Candidate 2 is available for testing! 🎉 ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration.

🔦 Highlights

ITK 5.4 marks a significant feature update aimed at bolstering the project's long-term sustainability. Specifically, this release harnesses the power of Web3 technology to enhance the process of contributing new data for collaborators, streamline software release management for quicker and more efficient rollouts, and facilitate decentralized, cost-efficient, and redundant data storage for extended distribution purposes.

Since every local Git repository contains a copy of the entire project history, it is important to avoid adding large binary files directly to the repository. Large binary files added and removed throughout a project's history will cause the repository to become bloated, take up too much disk space, require excessive time and bandwidth to download, etc.

A solution to this problem which has been adopted by ITK is to store binary files, such as images, in a separate location outside the Git repository, then download the files at build time with CMake.

A "content link" file contains an identifying cryptographic hash or Content Identifier (CID). The content link is stored in the Git repository at the path where the file would exist, but with a .cid extension appended to the file name. CMake will find these content link files at build time, download them from a list of server resources, and create symlinks or copies of the original files at the corresponding location in the build tree.

The CID is a self-describing hash following the multiformats standard created by the InterPlanetary Filesystem (IPFS) community. A file with a CID for its filename is content-verifiable. Locating files according to their CID makes content-addressed, as opposed to location-addressed, data exchange possible. This practice is the foundation of the decentralized web, also known as the dWeb or Web3. By adopting Web3, we gain:

  • Permissionless data uploads
  • Robust, redundant storage
  • Local and peer-to-peer storage
  • Scalability
  • Sustainability

Contributors to ITK can upload their data through a simple web app, (alt web3 link) that utilizes a free CID pinning service, web3.storage.

Data used in the ITK Git repository is periodically tracked in a dedicated Datalad repository, the ITKData DataLad repository. DataLad is a free and open source, Git-based distributed data management system that keeps track of data, ensures reproducibility, and supports collaboration. Versioned testing data trees can be browsed in a natural, nested directory / file layout, either via DataLad or IPFS's UnixFS storage.

The tracked data is stored across redundant locations so it can be retrieved from any of the following:

ITK testing data flow

Testing data workflow. Testing or example data is uploaded to IPFS via the content-link-upload.itk.org web app. This pins the data on multiple servers across the globe. At release time, the data is also pinned on multiple servers in the USA and France and community pinners. At release time, the data is also stored in the DataLad Git repository, served on an Apache HTTP server, and served on the GitHub Pages CDN. At test time an ITK build can pull the data from a local cache, archive tarball, the Apache HTTP server, GitHub Pages CDN, or multiple IPFS HTTP gateways.

For more information, see our testing data documentation.

ITK 5.4 contains many additional improvements; highlights can be found below along with a more detailed changelog. For a summary of changes that continues our modern C++ evolution see our 5.4 Release Candidate 1 release notes.

💾 Download

Python Packages

Install ITK Python packages with:

pip install --upgrade --pre itk

Guide and Textbook

Library Sources

Testing Data

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

Checksums

✨ 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 3.7-3.11 across platforms
  • This will be the last release with Python 3.7 suppport
  • Remote module GitHub action updated, Python 3.7 is not supported in Remote module builds
  • Updated to the latest version of scikit-build

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
  • Apply cmake-format for a consistent CMake style

Performance

  • Use index/point transforms without bounds checking
  • Improved SSE2 detection
  • Many improvements to how locks are handled

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

Remote module updates

Updated modules:

Third party library updates

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

🙏 Congratulations

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

Of the 43 authors who contributed since v5.3.0, we would like to specially recognize the new contributors:

Nicklas Larsson, huangjxbq, Sankhesh Jhaveri, adrinkwater, FabioLolix, Vaibhaw, Ningfei Li, Max Aehle, Noah Egnatis, Federico Zivolo, Patrick Linnane, LAURENDEAU Matthieu, Shreeraj Jadhav, Shengpeng YU, Fernando Bordignon, and Andras Lasso.

🗣️ What's Next

Process improvements in this release will ensure more regular and frequent releases in the future. Listening to feedback from the community, we anticipate one additional 5.4 release candidate to enable testing of critical DICOM improvements. Our next release candidate will include improvements based on experiences with 5.4 RC 2. Please try out the current release candidate, and discuss your experiences at discourse.itk.org. Contribute with pull requests, code reviews, and issue discussions in our GitHub Organization.

Enjoy ITK!

ITK Changes Since v5.4rc01

Dave Chen (4):

Documentation Updates

  • Fixed spelling in itkRGBGibbsPriorFilter.h (a4a46ccf83)
  • spelling fixes for the new github action (55b5f46bab)
  • Spell out Computing for the checker (816d406fbb)

Bug Fixes

Dženan Zukić (7):

Enhancements

  • Add Python wrapping for itk::PhasedArray3DSpecialCoordinatesImage (4bfe66c762)
  • Better support for multi-component images in image_from_vtk_image (336be62d3d)
  • Improve warning messages (label numbers as ints instead of chars) (7b74fca444)

Performance Improvements

  • Use index/point transforms without bounds checking (6e5ccc7504)

Documentation Updates

  • Move detailed description to the top of class documentation page (afb5595d8f)
  • Update ITK version mentioned in download.md from 4.13.1 to 5.3.0 (80446b1c18)

Platform Fixes

  • Avoid CMake warning caused by feature test (5bdcb06679)

Gabriel A. Devenyi (1):

Bug Fixes

  • Fix incorrectly specified expected result in itkIOTransformMINCTest.cxx (279ffc9895)

Jean-Christophe Fillion-Robin (2):

Enhancements

  • Update mangled 3rd-parties to use MANGLE_PREFIX CMake variable (a3afcf6fcd)
  • Ensure 3D multi-components conversion in image_from_vtk_image is tested (abbab61c31)

Jon Haitz Legarreta Gorroño (104):

Enhancements

  • Increase coverage for miscellaneous classes (d6beb524a4)
  • Increase coverage for RegularStepGradientDescentBaseOptimizer (1312fca3d2)
  • Increase Optimizers classes coverage: get cost function derivate (bec6a42b7e)
  • Increase coverage for miscellaneous classes (99abf7b89b)
  • Increase coverage for miscellaneous classes (f7615d27ac)
  • Test the const point iterators in itk::QuadEdgeMeshPolygonCell (46c47e08b3)
  • Increase coverage for miscellaneous classes (fd873b7ecf)
  • Remove ivar memberless PrintSelf implementation (3a73368734)
  • Allow itkCellInterfaceTest to run as long as possible (e09713fbe9)
  • Print the superclass object in itk::MRFImageFilter::PrintSelf (a7a8254fe2)
  • Add boolean macro to itk::Statistics::Histogram::ClipBinsAtEnds (4179d83534)
  • Use itkPrintSelfObjectMacro to print smart pointers (20225e5b7a)
  • Add getter methods to itk::RGBGibbsPriorFilter ivars (d28311fb8e)

Documentation Updates

  • Change the Insight Journal handle links to insight-journal links (1d4d1ba198)
  • Remove class self reference in Doxygen \sa command (3ed75247e6)
  • Clean up itk::ConformalFlatteningMeshFilter Doxygen documentation (3a542d0d19)
  • Remove duplicate "type" in alias documentation (fabc102c52)
  • Document miscellaneous cell class methods in header files (291e618b24)
  • Avoid documenting ivar default values in SpatialFunction class (4418b97f56)
  • Make the RTTI method documentation consistent in module Video (a22d0a840f)
  • Add a note to the README about issues vs. questions (27f450358c)
  • Add a note to the first interaction workflow about its nature (b774fd5358)
  • Refer to ITK's discussion space in a consistent manner (c42a8a7d3f)
  • Reword the copyright holder sentence in the code of conduct (f2cec9b741)
  • Link the Creative Commons license page in the code of conduct (392b74dd30)
  • Improve consistency when referring to the issue tracker in README (66e933613c)
  • Fix MetaDataObject::EncapsulateMetaData empty return doc warning (68ab83372a)
  • Document MetaDataObject::EncapsulateMetaData parameters (0595670b96)
  • Document itk::Indent class methods in header file only (3eb8fd7cdf)
  • Improve MINC transform adapter exception message (a54062d23c)
  • Fix typo in itk::Math function parameter documentation (b87ed30059)
  • Use Doxygen math syntax for math notation in class documentation (365c547d9f)
  • Document RGBGibbsPriorFilter class methods in header file only (4e5be8334d)
  • Use proper Doxygen documentation style in RGBGibbsPriorFilter (309a0535de)
  • Improve comments in itkHistogramTest.cxx (657b793d97)
  • Remove François Budin from GPG key holder ITK maintainer's list (85072a41ee)
  • Remove updating ResearchGate ITK project from release tasks (4809e93798)
  • Explain better the release announcement in NumFOCUS newsletter (39138d78e6)
  • Remove unnecessary ITKIOTransformMINC README files (89e00d7ac8)
  • Improve ITKIOTransformMINC class documentation (7caf7e3c70)

Platform Fixes

  • Fix method parameter bound mismatch warning in itk::VertexCell (2338bdc487)
  • Fix method parameter bound mismatch warning in misc cell classes (a66bc7dc48)
  • Add missing semicolon to macro statement end in tests (1801209574)

Bug Fixes

  • Return exit failure when insufficient test arguments are provided (3b7078fdb4)
  • Fix dynamically allocated memory management (edd6051ae3)

Style Changes

  • Increase itk::LabelStatisticsImageFilter::PrintSelf consistency (20124626ae)
  • Use macros in tests (84769233ee)
  • Improve ivar printing style (4ca8106ef7)
  • Conform to ITK comment style for within code in OpenCVVideoCapture (1d4cc7ab36)
  • Increase consistency in test argument check message (3e41b8213d)
  • Honor FastIncrementalBinaryDilateImageFilter class in test name (ae3ee1de82)
  • Improve style across miscellaneous tests (424f25800e)
  • Conform to ITK SWG style guidelines adding a test ending message (19ae34f628)
  • Conform to ITK style guidelines in miscellaneous test comments (be8e4f6020)
  • Remove empty comment lines in itk::TriangleCell implementation (16f42267a0)
  • Prefer using the ITK_TRY_EXPECT macros in test (eacd1d24fa)
  • Conform to ITK style guidelines in test (b3c935159b)
  • Conform to ITK SWG style guidelines in test ending message (5c8f982e34)
  • Use the itkNameOfTestExecutableMacro macro in tests (395c8f44ea)
  • Use exception checking macros in tests (2038fd7695)
  • Remove test input argument checking if no argument is required (2596ea22b8)
  • Fix ITK coding style inconsistency linter error (18dd3e693f)
  • Honor the filter name in source code filename (c3ae51517e)
  • Increase consistency in test argument check message (5ca4f3b02a)
  • Conform to ITK style guidelines in test ending message (cfb8ae114d)
  • Conform to ITK comment style for within-code comments (tests) (35b85b15bf)
  • Remove empty comment lines in tests (7a316c9c12)
  • Remove uninformative standard output messages in tests (05a0e03c31)
  • Do not allow lonely std output endl statements in misc tests (f795943d61)
  • Improve printed message style across miscellaneous tests (83c1c48c95)
  • Declare variables close to where they are used in tests (8a1d3d7420)
  • Declare and use test image dimensionality as constexpr (8bc48815e5)
  • Do not declare a test status variable that is only used once (e388b79fdd)
  • Use exception checking macros in itkVectorExpandImageFilterTest (6e8a2600d1)
  • Prefer setting the input once all ivars have been set in test (bb3d6d1696)
  • Use ITK_TRY_EXPECT_NO_EXCEPTION macro in IOTransformMINC test (204d23a7e8)
  • Prefer using ITK_TEST_EXPECT_EQUAL lh and rh comparison macro (56bd332807)
  • Prefer using itk::Math::FloatAlmostEqual in comparisons (93d3d88c76)
  • Add vertical space for readability in itkIOTransformMINCTest (47df4f3567)
  • Use macros in tests (c313059069)
  • Honor itk::RGBGibbsPriorFilter classname in its test filename (86e2e937c0)
  • Use an unsigned integer to store the number of poles (6807db4845)
  • Prefer using setter macro for itk::RGBGibbsPriorFilter ivar (452cb3f971)
  • Use standard return codes in example (2535192fb3)
  • Increase consistency in example argument check message (5707df8d3e)
  • Make non-macro comparison conditional blocks consistent in tests (67d18e4715)
  • Increase consistency in test argument check message (c2688765c2)
  • Conform to ITK style guidelines in test ending message (dfc9fcd32f)
  • Prefer using constexpr <type> over struct for image dimension (eaf25ef26b)
  • Conform to ITK comment style for within-code comments (tests) (488ac833aa)
  • Remove empty comment lines in tests (e4643c59f0)
  • Remove uninformative standard output message in itkHistogramTest (41ad697626)
  • Remove uninformative comments in tests (b9b530f620)
  • Do not allow lonely std output endl statements in misc tests (f9f3078385)
  • Increase consistency in newline character use in tests (154938d8ca)
  • Remove blank lines in excess in miscellaneous tests (603b67d7b9)
  • Prefer using macros for itk::SLICImageFilter basic methods (df51b3ffa2)
  • Use standard exit return code in itk::SLICImagetFilter test (8930ed2da3)
  • Conform to ITK SWG style guidelines in test ending message (d9f0d5e66a)
  • Do not use superclass template parameters in itk::fem RTTI (9f1d99077f)
  • Prefer double forward slashes for within-method body comments (8d3df523ff)
  • Use testing macros in itkHistogramTest.cxx (397278f75f)
  • Make non-macro comparison blocks consistent in itkHistogramTest (d6111f2edb)
  • Use this to address self methods in RGBGibbsPriorFilter (034cd067bb)

Matt McCormick (22):

Enhancements

  • Bump pygccxml to v2.4.0 (b1f03a845c)
  • Migrate content links from .md5, .sha512 to .cid (f3899ce8c6)
  • Add cmake-format config and script (788fbc4858)
  • Remove setup-girder-api-key GitSetup script (31597d4fac)
  • Remove UploadBinaryData.sh script (2916886bfb)

Documentation Updates

  • Release documentation updates for ITK 5.4 RC 01 (779afebce0)
  • Update testing data upload docs for CID transition (53fddd33c6)
  • Update .git-blame-ignore-revs for cmake-format, .cid content links (9442dcdcec)
  • Update content link upload documention in GitCheatSheet.pdf (caedb38830)
  • Add Sphinx Documentation rendering (effb802abd)

Platform Fixes

Bug Fixes

  • GetGlobalDefaultSplitter to a global singleton (94344fd0b5)
  • Update pygccxml source code path in update script (886b5243b1)
  • Fix xarray compute value check (ff64d3c3ff)
  • Remove extra space in CppcheckTargets VERBATIM (078db2e1bc)
  • Fix ITKGroup identification with multiline itk_module (6384cd067a)

Style Changes

  • Separate \ingroup for MultiThreaded with AddImageFilter, PowImageFilter (1ec8df840a)
  • Initial run of cmake-format (efa749515d)
  • Lower case for function name in ITKModuleEnablement (3568eeec2b)

MetaIO Maintainers (1):

Miscellaneous Changes

Nicklas Larsson (1):

Bug Fixes

Niels Dekker (41):

Enhancements

  • Add TEST(ObjectFactoryBase, CreatedInstanceHasReferenceCountOfTwo) (47bcc5081e)
  • Make VectorContainer::size_type public, test nested vector types (dc641cd7d7)
  • Add MersenneTwisterRandomVariateGenerator::ResetNextSeed() (ecd7bdae82)

Documentation Updates

  • Note that object returned by CreateInstance has reference count 2 (f981aae69d)
  • itkGetObjectMacro member functions return a raw (not smart) pointer (eb97e952c2)
  • Document that SetGlobalInstance always returns true (9da299b85c)

Platform Fixes

  • Adjust check that all arguments of MakePoint/Vector have same type (89d3c3c015)

Bug Fixes

  • ImageRandomIteratorWithIndex should not assign data in constructor (997ff54d59)
  • Use lock_guard<mutex> in FFT configuration to deal with exception (a00eb3914d)
  • Use lock_guard<mutex> in FEMFactoryBase to deal with exception (c1e15a36d0)

Style Changes

  • Call GetTransformTypeAsString() just once, in TransformFactory (9baa34b699)
  • Remove redundant GetPrimaryOutput() calls from ProcessObject (997aa169a2)
  • Remove redundant checks in ProcessObject::VerifyPreconditions() (c3ee320bf8)
  • ImageSourceCommonGlobals default member initializer, Rule of Zero (c6690b9209)
  • Replace std::unique_lock with std::lock_guard in ThreadPool (1094cdde9a)
  • Replace std::unique_lock with std::lock_guard in Filter.hxx files (3335e69433)
  • Remove duplicate assignment from itkPlatformMultiThreaderPosix (1dc9deb15c)
  • Remove unused threadId, just pass nullptr to _beginthreadex (2ee34dde73)
  • Use lock_guard<mutex> in PlatformMultiThreader classes (c4c3710d5f)
  • Use lock_guard<mutex> in PlatformMultiThreader::TerminateThread (e56c7bdf20)
  • Use lock_guard<mutex> in ParallelSparseFieldLevelSetImageFilter (5e1f0cf1c0)
  • Use lock_guard<mutex> in PDEDeformable Registration classes (873a724b92)
  • Replace std::min, std::max in MultiThreaderBase with std::clamp (0c31b223ed)
  • Remove ITK_X_ASSERT, just use assert in constexpr functions (e888f7bc2d)
  • Use insert_or_assign in SingletonIndex SetGlobalInstancePrivate (5c14067e53)
  • Let SetGlobalInstancePrivate return void, instead of true (eadc465c3f)
  • Let Singleton assume that SetGlobalInstance always returns true (6ec6328ed2)
  • SingletonIndex does not need to store the unused func parameter (6d1c4c7ab7)
  • Remove unused parameter from SetGlobalInstance and Singleton (8598841db5)
  • Replace Registration/Metricsv4 "LockPtr" with "MutexPtr" (8149ba9651)
  • Rename private and internal data members from "Lock" to "Mutex" (0150e46924)
  • Code cleanup ImageRandomConstIteratorWith(Only)Index RandomJump() (d92dc14c7f)
  • Rename local std::lock_guard variables "lockGuard" (04100e62e0)
  • Default constructors VectorContainer, Iterator, ConstIterator (ff47f5cf84)
  • Remove private ObjectFactoryBase member InitializeFactoryList() (82d7060408)
  • Replace std::bind in ThreadPool::AddWork with lambda expression (75b99671a8)
  • Simply assign factories, in ObjectFactoryBase::RegisterInternal() (2859d67cda)
  • Remove private ObjectFactoryBase member RegisterInternal() (427972e600)
  • Remove lock MersenneTwisterRandomVariateGenerator ResetNextSeed (1ce107fc42)
  • Disallow copy/move, default constructor MersenneTwisterGlobals (89d4735e05)
  • Add using-declaration MersenneTwisterRandomVariateGenerator GTest (bdcb9e33cb)

Sean McBride (1):

Bug Fixes

  • Use atomic bool to fix race found by thread sanitizer (c3a8eab2ad)

VXL Maintainers (1):

Miscellaneous Changes

Zlib-ng Upstream (2):

Miscellaneous Changes

pygccxml Upstream (1):

Enhancements

ITK Sphinx Examples Changes Since v5.4rc01

Matt McCormick (5):

Enhancements

  • Update to ITK 5.4 RC 01 (0b4ca644)
  • Bump ITK to 5.4 Release Candidate 2 (e404022a)
  • Add PASS_REGULAR_EXPRESION to ConvertImageWithLabelsToShapeLabelMap (84fb315d)

Platform Fixes

  • pandoc version for docs build (3370d2ae)

Bug Fixes

  • Disable ConvertImageWithLabelsToShapeLabelMapTest on Windows (db481ba1)

ITK Software Guide Changes Since v5.4rc01

Jon Haitz Legarreta Gorroño (5):

Documentation Updates

  • Avoid documenting ivar default values (6a2861a)
  • Avoid using initialization lists in coding style snippets (35a15c2)
  • Use non-boolean, built-in type ivars to illustrate PrintSelf (8f61111)
  • Do not encourage using empty comment lines (278366c)

Style Changes

  • Finish coding style guideline item sentence with period (14aee41)

Matt McCormick (2):

Enhancements

  • Bump ITK Superbuild version to 5.4 RC 1 (381c84c)
  • Bump ITK Superbuild version to 5.4 RC 2 (3b541a4)

Niels Dekker (1):

Documentation Updates

  • Replace itkTypeMacro with itkOverrideGetNameOfClassMacro (5428594)
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