ITK 5.3 Release Candidate 2 Release Notes: Grow Cuts¶
We are happy to announce the Insight Toolkit (ITK) 5.3 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.
ITK 5.3 is a feature release that accelerates performance, provides new segmentation and shape analysis algorithms, and makes over 200 more improvements. For more information about performance improvements, see the 5.3 RC 1 Release Notes.
ITK 5.3 RC 2 highlights a new remote module, ITKGrowCut, which segments a 3D image from user-provided seeds. This method was popularized by 3D Slicer and was improved for inclusion in Seg3D with support from the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) under grant numbers P41 GM103545 and R24 GM136986. This module can also be scripted in Python through a package installed with:
pip install itk-growcut
Seeds for ITKGrowCut module.
Results produced by ITKGrowCut module.
Download¶
Python Packages
Install ITK Python packages with:
pip install --upgrade --pre itk
Library Sources
Testing Data
Unpack optional testing data in the same directory where the Library Source is unpacked.
Checksums
Features¶
Python¶
Python packages now include oneTBB support for improved performance.
Following CPython’s deprecation schedule Python 3.6 is no longer supported.
Python packages added for Python 3.10
Initial Python wrapping is available for the Video modules.
TransformToDisplacementField
is now available in Python.Pythonic IO functions
itk.imread
understandspathlib.Path
’sNew
repr
foritk.Matrix
np.asarray
works onitk.Matrix
DCMTKImageIO
wrapping addressed
C++¶
C++14 is now required.
The minimum CMake version required is now 3.16.3.
New functions:
MakePoint
,MakeVector
,MakeIndex
,MakeSize
.Targets in Visual Studio and other IDE’s are now organize hierachically by ITK Group and Module
Most of
itk::mpl
meta-programming functions replaced by C++14 equivalentsPerformance accelerations for b-spline interpolation, Mattes mutual information metric computation
Improved modern C++ adoption, e.g. additional adoption of
constexpr
,auto
New filters¶
itk::TransformGeometryImageFilter
: applies a rigid transform to anImage
’s metadata.1D FFT classes
Interface classes for forward, inverse transformations, half-hermetian transformations
Vnl implementations
FFTW implementations
Remote module updates¶
New remote modules:
HASI: High-Throughput Applications for Skeletal Imaging
ITKGrowCut: segments a 3D image from user-provided foreground and background seeds
Updated modules: AdaptiveDenoising, AnisotropicDiffusionLBR, BSplineGradient, BoneEnhancement, BoneMorphometry, Cuberille, GrowCut, HASI, HigherOrderAccurateGradient, IOFDF, IOScanco, IsotropicWavelets, MinimalPathExtraction, Montage, MorphologicalContourInterpolation, RTK, SimpleITKFilters, SkullStrip, SplitComponents, Strain, TextureFeatures, Thickness3D, TotalVariation, TubeTK, and Ultrasound.
Third party library updates¶
expat
fftw
gdcm
googletest
hdf5
kwsys
metaio
niftilib
vxl
zlib migrated to zlib-ng
Congratulations¶
Congratulations and thank you to everyone who contributed to this release.
Of the 41 authors who contributed since v5.2.0, we would like to specially recognize the new contributors:
Pranjal Sahu, Darren Thompson, Tomoyuki SADAKANE, Oleksandr Zavalistyi, Jose Tascon, Kian Weimer, Michael Kuczynski, Ebrahim Ebrahim, Philip Cook, ambrozicc1, Jason Rudy, josempozo, Andreas Gravgaard Andersen, and Hastings Greer.
What’s Next¶
We anticipate an additional release candidate following community testing before the 5.3.0 release. The following release candidate(s) will improve related documentation and make further improvements. 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 v5.3rc01¶
Aaron Bray (1):¶
Enhancements¶
Create an IDE folder structure (#2791) (569f96529e)
Andreas Gravgaard Andersen (4):¶
Enhancements¶
Update expat files (9e337d3a23)
Update expat CMake config (95ab3c2a3d)
Update exported symbols for expat (ea54bc77d7)
re-apply ITK symbol export definitions (0e9afe968a)
Brad King (3):¶
Enhancements¶
Update to newer third-party update script (28bf772844)
Convert MetaIO import script to use update-third-party.bash (b59cfe70d3)
Update to newer third-party update script (19155f3996)
Bradley Lowekamp (6):¶
Enhancements¶
Refactor TransformGeometryImageFilter pipeline i/o (2de73abe37)
Use InPlaceImageFilter for base class, run in-place by default (4379b75c2a)
Support generic linear Transform (978bc5b9f5)
Bug Fixes¶
Use GenerateOutputInformation and pipeline isolation (374940a1c6)
Fix ImageRegionSplitters with zero sized image (63f4ab7dd8)
Install ITKInitializeCXXStandard.cmake (98f0f5c5ed)
Bryn Lloyd (2):¶
Bug Fixes¶
pythonic itk should understand pathlib.Path (051ad61e26)
failing test - only pythonic api knows PathLike paths (0178cf01af)
Dženan Zukić (14):¶
Enhancements¶
use std::enable_if instead of itk::mpl::EnableIf (6b58ee8fce)
deprecate itk::EnableIf and the header which implements it (9f3a6243bf)
replace instances of mpl::IsSame by std::is_same (c28930c90f)
deprecate itk::IsSame and the header which implements it (342845e644)
replace itkStaticAssert by STL’s static_assert (cd43985eba)
fully cover the logical test cases in MetaProgrammingLibraryTest (dcd7dfd469)
replace usage of IsBaseOf by std::is_base_of (e90519eeed)
deprecate mpl::IsBaseOf and the header which implements it (d458298bdd)
Deprecated mpl::IsConvertible and the header which implements it (2f29c8d2d0)
switch to zlib-ng official repository (dcaecbe147)
Platform Fixes¶
remove a workaround for a bug in Visual Studio 2015 (2f732c0f05)
fix VS2017 compile error in itkFEMElementStd.h (182d302823)
Style Changes¶
nifti_installed_targets message is gray instead of default red (83a51e21c6)
remove unnecessary parentheses around logical conditions (e092a3df47)
Hans Johnson (3):¶
Enhancements¶
Update FFTW to 3.3.10 (03338d41c9)
Bug Fixes¶
Wrong superclass identified for child class. (e64795cee5)
Style Changes¶
Avoid repeating parent aliases (4f309803b9)
Hastings Greer (1):¶
Enhancements¶
Make representation match repr(itkVector) (5210cc23ab)
HastingsGreer (1):¶
Enhancements¶
Add a useful repr for itkMatrix (152ed0028f)
Jason Rudy (1):¶
Platform Fixes¶
Fix Python wrapping of DCMTKImageIO. Closes #2762. (40235a57b4)
Jon Haitz Legarreta Gorroño (25):¶
Enhancements¶
Add further regexes for the issue/PR labeler (bffcf331db)
Improve KLCompareHistogramImageToImageMetric coverage (77fc43ba1b)
Improve KLCompareHistogramImageToImageMetric coverage (eec8c4dd2a)
Increase forward/inverse 1D FFT filters’ coverage (89837f6b80)
Increase code coverage (c4a359cc98)
Platform Fixes¶
Fix missing initialization braces warning (c7641fc000)
Fix missing initialization braces warning (33d1d0d3cc)
Fix missing initialization braces warning (c19cdcdf4e)
Fix undeclared identifier error (94dfea440b)
Mark class destructors with
override
(1daf2182f8)Mark class destructors with
override
(7ef2496a26)
Bug Fixes¶
Provide missing template parameter to superclass (280c43e6a2)
Style Changes¶
Avoid repeating parent aliases in operator classes (babece933d)
Improve
itk::SimilarityIndexImageFilter
class test file style (ada00b5a00)Sort the infrastructure regexes in labeler dictionary (8225a45cad)
Remove unnecessary implementation file manual instantiation guard (36bb69db44)
Improve the ivar printing in
PrintSelf
methods (286fca2694)Make
itkLabelImageToLabelMapFilterTest
style consistent (014c08fc68)Improve the ivar printing in
PrintSelf
methods (ef5a73456a)Make
IODCMTK
module test style consistent (9cf28765c8)Make
FFT
module test style consistent (59f16e7094)Make style consistent in miscellaneous tests (5ce113f95b)
Prefer = default to explicitly trivial implementations (85e80f1fb0)
Prefer = default to explicitly trivial implementations (9b7464014d)
Make CMake flag help text third-party toolkit names consistent (867bf80e16)
KWSys Upstream (1):¶
Miscellaneous Changes¶
KWSys 2021-10-08 (b8c734ba) (bdbe89864e)
Lee Newberg (1):¶
Bug Fixes¶
Correct extra reference count from ObjectFactory
::Create() (d8742f00b8)
Matt McCormick (11):¶
Enhancements¶
Support np.asarray on itk.Matrix (76fa38c13f)
Add MD5 content links for ITK 5.3RC2 (b218281460)
Documentation Updates¶
Recommend GitHub CLI (5e0a11483f)
Document Linux ARM Python package builds (509a66e176)
Software Guide link to GeodesicActiveContourShapePriorLevelSetImageFilter (911430821c)
Platform Fixes¶
Avoid Superclass type alias GCC compile errors (230be6be26)
Update CircleCI image to cimg/python:3.9 (b9e51f1c0d)
Initialize CXX standard in ITK_USE_FILE (9233ef9a7d)
Update KWStyle for macOS unknown -Wdeprecated-copy (0cc6867f37)
Bug Fixes¶
Improve dimension-dependent BSplineInterpolationWeightFunction wrapping (61f98c7fff)
Remove unused FFT1D testing data content links (ae983e8170)
MetaIO Maintainers (2):¶
Miscellaneous Changes¶
MetaIO 2021-06-24 (3f37ad78) (f3adb4ec2e)
MetaIO 2021-09-28 (5e87f062) (9b85a2fe1a)
Niels Dekker (24):¶
Enhancements¶
Add static
FastEvaluate(u)
toBSplineDerivativeKernelFunction
(760ae1246c)Add
RegisterInternalFactoryOnce<TFactory>()
to ObjectFactoryBase (9f29a52d6c)Improve thread-safety of registration of internal IO factories (fb47ffaf62)
Performance Improvements¶
Use FixedArray for table within BSplineInterpolationWeightFunction (974540982b)
Use FastEvaluate in MattesMutualInformationImageToImageMetric + v4 (9961ccd672)
Remove unnecessary
IdentityTransform::m_ZeroJacobian
(eec9fe6705)Remove protected
itk::Transform
data memberm_DirectionChange
(0539a2c4dd)
Platform Fixes¶
Copy BSplineInterpolationWeightFunction::SupportSize within lambda (27e4815bb8)
Workaround VS2017 error C2653/C2886 using-declaration compiler bug (066ddb8859)
Use trailing return type instead of
typename
+ dependent type (c54ad6715a)Fix KWStyle check errors from cxx files Modules/Core/Common/CMake (809f14958a)
Declare
IOFactoryRegisterManager
constructorsexplicit
(72782b8f01)Remove pointer-to-bool conversions from
IOFactoryRegisterManager
(49c910a1fe)Add “const” to
IOFactoryRegisterManager
implementations (f56cc7ef17)Fix error: constexpr variable ‘ImageIOFactoryRegisterRegisterList’ (3ad34a16e8)
Style Changes¶
Use modern C++
TRealValueType{ x }
syntax (c9b05ab2f9)Improve const-correctness of protected CompositeTransform members (a4693b5074)
Do not use itkGetStaticConstMacro in ITK/Modules/Filtering (4408bd4b72)
Replace itkStaticConstMacro ImageSink, BinaryGeneratorImageFilter (f4e12a0b4b)
FUTURE_LEGACY_REMOVE itkStaticConstMacro, itkGetStaticConstMacro (bb217ca4a7)
clang-format AlignEscapedNewlines Left (for macro definitions) (7829ef68ad)
git blame should ignore “clang-format AlignEscapedNewlines Left” (b3bceaf2b8)
Use
auto
for declaration of variables initialized byNew()
(828453d1bf)Remove redundant overrides of Get and Set member functions (5b155aec50)
Philip Cook (1):¶
Enhancements¶
Test NIFTI I/O with small voxels (6fc6164252)
Sean McBride (6):¶
Enhancements¶
make BSplineWarping2Test run serially, as it’s quite slow (0836c79324)
Platform Fixes¶
fixed compile errors due to incorrect superclass identification (9e2b8841ef)
modified several sed invocations to be BSD compatible (b76ff2cfe5)
fixed various Wunused-but-set-variable warnings from Clang 13 (b85f24600a)
Bug Fixes¶
fixed various threading errors in logging code, found by TSan (9599fc6cc0)
Style Changes¶
fixed repeated spelling mistake/typo (54731ef592)
Simon Rit (3):¶
Enhancements¶
test exception handling in multithreading (24c3ad91db)
Bug Fixes¶
fix exception handling in itk::PoolMultiThreader (ec43890e1a)
fix installation of the generated file expat_config.h (9b74f7b38b)
Stephen R. Aylward (3):¶
Enhancements¶
Bump TubeTK (6c82281a35)
Bump TubeTK to v1.0.0 (04a50e4cd6)
Use v1.0.0 for tag (fc3178008f)
Tom Birdsong (8):¶
Enhancements¶
Add ITKShape as a remote module (fdd52cecc4)
Add 1D FFT classes from ITKUltrasound (0487709dc6)
Platform Fixes¶
Replace itkStaticConstMacro with constexpr in 1D FFT classes (cb25661a12)
Bug Fixes¶
Respect UseImageSpacing flag in LaplacianImageFilter (8f7a832b14)
Fixups for adding 1D FFT classes from ITKUltrasound to ITK (9332084028)
Replace deprecated macro in 1D FFT classes (2c2a48494c)
Style Changes¶
Use itkGetConstMacro for getting 1D FFT direction (d88c631d98)
Mark FFTW 1D FFT class destructors with
override
(eb6001490b)
Ziv Yaniv (1):¶
Bug Fixes¶
VersorTransform did not update offset in SetParameters (fb64eb2a89)
Zlib-ng Upstream (1):¶
Miscellaneous Changes¶
zlib-ng 2021-10-13 (a7b77369) (394fd57aff)
ambrozicc1 (1):¶
Bug Fixes¶
Disable all floating point exceptions (cd3f05eb0b)
josempozo (1):¶
Style Changes¶
itkTimeVaryingBSplineVelocityFieldImageRegistrationMethod.hxx (#2722) (52477f353f)
ITK Sphinx Examples Changes Since v5.3rc01¶
Dženan Zukić (1):¶
Bug Fixes¶
filling the buffer was forgotten in CreateImage (fc491a42)
Hans Johnson (3):¶
Platform Fixes¶
Bug Fixes¶
Missed setting file from command line. (3930982d)
Jon Haitz Legarreta Gorroño (1):¶
Enhancements¶
Add labeler workflow (3f8d0a2b)
Mathew Seng (1):¶
Enhancements¶
BinaryMathematicalMorphology baseline testing (a91c350b)
ITK Software Guide Changes Since v5.3rc01¶
Jon Haitz Legarreta Gorroño (1):¶
Enhancements¶
Add labeler workflow (1fca7b9)
Niels Dekker (4):¶
Platform Fixes¶
Fix compile errors from *.cxx files in SoftwareGuide/Cover/Source (ca70c18)
Bug Fixes¶
Replace “assigment” with “initialization” in the
auto
section (fb9eb1e)
Style Changes¶
Remote Module Changes Since v5.3rc01¶
Shape:¶
TubeTK:¶
Stephen R. Aylward (9):¶
Enhancements¶
Bug Fixes¶
Miscellaneous Changes¶
Fix dashboards (#83) (e6a435c7)