ITK 5.4 Release Candidate 2: Web3 Testing Data¶
We are happy to announce the Insight Toolkit (ITK) 5.4 Release Candidate 2 is available for testing! :tada: 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:
Local IPFS nodes
Peer IPFS nodes
Kitware’s IPFS Server
ITKTestingData GitHub Pages CDN
Kitware’s Apache HTTP Server
Local testing data cache
Archive tarballs from GitHub Releases
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 aseries_uid
kwarg for DICOM series selectionTBB 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 variableMany 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
withitkOverrideGetNameOfClassMacro
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¶
Fixed BrainWeb link (61402981bb)
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 initk::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 inIOTransformMINC
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>
overstruct
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 inRGBGibbsPriorFilter
(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¶
Use full ::itk namespace in itkMacro.h (7fbe8880a9)
Remove pkg_resources import from base.py (b31c942bbe)
Encode the pygccxml version (1fec6af521)
Update w3 gateway CID identification (d7e6c200e2)
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¶
MetaIO 2023-07-16 (556864f5) (c42090c681)
Nicklas Larsson (1):¶
Bug Fixes¶
define SWIGPY_SLICEOBJECT (d2361b89fe)
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
withstd::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 passnullptr
to_beginthreadex
(2ee34dde73)Use
lock_guard<mutex>
inPlatformMultiThreader
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 useassert
inconstexpr
functions (e888f7bc2d)Use
insert_or_assign
in SingletonIndex SetGlobalInstancePrivate (5c14067e53)Let
SetGlobalInstancePrivate
returnvoid
, instead oftrue
(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
andSingleton
(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¶
VXL 2023-06-18 (4332fd74) (9c18c34119)
Zlib-ng Upstream (2):¶
Miscellaneous Changes¶
zlib-ng 2023-06-29 (cf89cf35) (2ab12b9807)
zlib-ng 2023-08-07 (73bbb54c) (68bc6c994e)
pygccxml Upstream (1):¶
Enhancements¶
pygccxml v2.4.0 (reduced) (6637e8709b)
ITK Sphinx Examples Changes Since v5.4rc01¶
Matt McCormick (5):¶
Enhancements¶
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¶
Style Changes¶
Finish coding style guideline item sentence with period (14aee41)
Matt McCormick (2):¶
Enhancements¶
Niels Dekker (1):¶
Documentation Updates¶
Replace
itkTypeMacro
withitkOverrideGetNameOfClassMacro
(5428594)