ITK 5.3 Release Candidate 1 Release Notes: Performance¶
We are happy to announce the Insight Toolkit (ITK) 5.3 Release Candidate 1 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.
Release Candidate 1 highlights performance improvements. For deformable image registration, b-spline sampling was improved by ~30%. Multi-threading in Python was improved by adding Threading Building Blocks (oneTBB) to the cross-platform binaries, which improves multi-threaded parallelism by ~5-10%. Compression time with zlib, used by common medical imaging file formats like NIFTI, NRRD, or MetaImage, was dramatically reduced through migration to zlib-ng.
name |
description |
zlib duration [ms] |
zlib C.Ratio |
zlib-ng duration [ms] |
zlib-ng C.Ratio |
zlib-ng Speed-up |
zlib-ng C. Ratio improvement |
---|---|---|---|---|---|---|---|
wbPET.mha |
whole body PET |
672 |
9.7% |
661 |
9.3% |
2% |
4% |
mra.nrrd |
MR angiography |
1300 |
49.0% |
1097 |
49.1% |
19% |
0% |
CBCT.nrrd |
ConeBeam CT |
11281 |
42.5% |
9486 |
41.3% |
19% |
3% |
input.nii |
brain MRI |
4818 |
57.6% |
3353 |
57.4% |
44% |
0% |
scan7.mha |
mouse ultrasound |
5939 |
45.4% |
4694 |
46.2% |
27% |
-2% |
TBR5_clinpet.nii |
label map |
782 |
0.5% |
91 |
0.5% |
759% |
-2% |
WhiteMatter.nii |
label map |
185 |
5.6% |
76 |
5.8% |
143% |
-4% |
Average |
145% |
0% |
Comparison of image compression with traditional zlib
library and the new zlib-ng
replacement introduced with ITK 5.3 using the default compression level.
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.
Initial Python wrapping is available for the Video modules.
TransformToDisplacementField
is now available in Python.
C++¶
C++14 is now required.
The minimum CMake version required is now 3.16.3.
New functions:
MakePoint
,MakeVector
,MakeIndex
,MakeSize
.
New filter¶
itk::TransformGeometryImageFilter
: applies a rigid transform to anImage
’s metadata.
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¶
gdcm
niftilib
zlib migrated to zlib-ng
hdf5
kwsys
metaio
googletest
vxl
Congratulations¶
Congratulations and thank you to everyone who contributed to this release.
Of the 32 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, and Philip Cook.
What’s Next¶
We anticipate an additional release candidate following community testing before the 5.3.0 release. The following release candidates 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 v5.2.0¶
Brad T. Moore (1):¶
Bug Fixes¶
fixed reference leak when SWIG passing tuples or lists (95ee15a07e)
Bradley Lowekamp (12):¶
Enhancements¶
Add additional testing for zero sized label object (bc95f51d9f)
StatisticsLabelMapFilter use improve integer histogram (daa2a20f4b)
Rename ResampleInPlaceImage to TransformGeometryImageFilter (9827449b4b)
Platform Fixes¶
Address braces around initializer warning. (dae904e3d9)
Use C99 int types over libtiff’s (f98f6a8920)
Bug Fixes¶
Register ComposeScaleSkewVersor3DTransform transform (8c7784d183)
Fix SpatialOrientationAdapter::FromDirectionCosines (8801247049)
Add tests demonstration current behavior of histogram based median (c6da8be54c)
Fix StatisticsLabelMap median for even number of pixels (208d7e32d7)
Fix HDF5 installation with cmake targets (4ecd711eab)
Propagate usage of HDF5 find_package NO_MODULE arg to install (f83a0ba9f4)
Add tests demonstration current behavior of histogram based median (55d0fdfafa)
Fix StatisticsLabelMap median for even number of pixels (3abace1991)
Correct stop condition description (362dd4c7cf)
Dave Chen (1):¶
Enhancements¶
add support for direction in VTK image (80bcb13d9b)
Dženan Zukić (50):¶
Enhancements¶
Add ResampleInPlaceImageFilter (53f8473c2d)
Update style and use the test of ResampleInPlaceImageFilter (e08395a7c0)
Add Transform::ApplyToImageMetadata method (510586750a)
Add support for long long pixel types to ImageDuplicator wrapping (18ae7502f0)
update remote modules using the maintenance script (c6f4685638)
Python wrapping reads VLV pixel type correctly (231ecb7d3d)
add HASI remote module (2798c2a85f)
Add GrowCut remote module (22524c5f71)
Remove WriteCompilerDetectionHeader (d3e151f09d)
Port GTest update script to update-third-party.bash (9661691ded)
Update GTest branch name to
master
in order to “Live at Head” (001cd1440b)fix Python multi-processing hang on unix (597a6dfe6f)
Python wrapping reads VLV pixel type correctly (4ae3749a61)
Add support for long long pixel types to ImageDuplicator wrapping (278ac68e40)
remove HDF5 customization to work with older versions of CMake (83bff5e537)
fix Windows Bitmap (BMP) channel order ABGR -> BGRA (29e60cdeca)
respect initial position in itkExhaustiveOptimizerv4 (7777908fe8)
Update remote modules using the script (1b16b76599)
Switch to modern maintained zlib-ng fork of zlib (f352883354)
Temporarily use a fork of zlib-ng until outstanding PRs are merged (ac071fa0f2)
Documentation Updates¶
Fix broken documentation in ResampleInPlaceImageFilter (047fa6934a)
Fix usage information in ImageReadExtractWrite example (c901eff21c)
document that 0 pixel count causes every chunk to report progress (aa36784239)
improve commands for updating mangling symbols on Windows for HDF5 (af1c73cad5)
Platform Fixes¶
Tests depend on GTest (e4a76a888b)
Use non-deprecated ITK_DISALLOW_COPY_AND_MOVE in ResampleInPlace (6500affdb5)
Update KWStyle to fix compile warnings on Ubuntu 20.04 (32501b4230)
Restore generation of static runtime library on MSVC (dbb34f96cc)
an explicit cast is required to convert itksys::Status into bool (b8ea8a11d4)
use WRAP_ITK_SCALAR instead of WRAP_ITK_REAL in mesh filters (4009370c61)
Update KWStyle’s version to avoid compile errors with C++23 (769981b974)
test fails to compile when legacy support is removed (041261e563)
directly use [[deprecated]] in itkLegacyMacro - C++14 allows that (196a4c8a69)
add ITK_ prefix in itkStochasticFractalDimensionImageFilterTest (dab652d279)
Update KWStyle’s version to avoid compile errors with C++23 (3d85fafc77)
use WRAP_ITK_SCALAR instead of WRAP_ITK_REAL in mesh filters (68944d52d7)
add Windows symbols to the mangling list (97105c3ae1)
add Linux and MacOS symbols to the mangling list (21cb724c2c)
a method should not return an integer instead of an std::string (f9f2ea833a)
update KWStyle (so it reports its version number) (581c4445ca)
modify zlib-ng to make it build within ITK (3bcc933052)
Bug Fixes¶
Fix wrong argument count comparison in ResampleImageFilter example (a652269b21)
add support for long long pixel types in PyBuffer (ae7079c4fd)
Style Changes¶
remove pixel count parameter which is no longer used (791534a99e)
enable git blame to use ignoreRevsFile by default (ce4fd8fe21)
remove uninformative comments in BMPImageIO (b6ccca64a6)
move initialization of iVars to itkExhaustiveOptimizerv4.h (9b2000ac21)
Miscellaneous Changes¶
Revert “COMP: Use CMake 3.18.4 in macOS CI builds” (ae01547bec)
Ebrahim Ebrahim (3):¶
Enhancements¶
Split Hausdorff distance test (ab15f0a343)
Simplify a directed Hausdorff distance test (3a63e79d17)
Style Changes¶
Make job piece naming consistent (03024da662)
GDCM Upstream (2):¶
Miscellaneous Changes¶
GDCM 2021-06-07 (4404b770) (aae9fdc684)
GDCM 2021-06-07 (4404b770) (47e97596b9)
Gabriel A. Devenyi (3):¶
Enhancements¶
Ignore more bulk changes for git blame (6b5578ceb1)
Prepare for update to NIFTILIB3.0.1 (68221fdd30)
Cleanup in preparation for zlib-ng (9bc41df7c7)
GoogleTest Upstream (3):¶
Miscellaneous Changes¶
GoogleTest 2019-10-03 (703bd9ca) (d685cc3ba5)
GoogleTest 2021-07-09 (8d51ffdf) (1b539548fc)
GoogleTest 2021-08-06 (aefb4546) (b73f9c3f95)
HDF5 Maintainers (1):¶
Miscellaneous Changes¶
HDF5 2020-10-16 (db30c2da) (044057f763)
Hans Johnson (6):¶
Enhancements¶
Run unexecuted NiftiImageIOTest12 (5b54be0b78)
Use language features directly without macro (2e8e4df315)
Platform Fixes¶
Fix compilation for ITK_FUTURE_LEGACY=ON (e88e234de1)
Bug Fixes¶
Missed wrapping of itkResampleInPlaceImageFilter (71e04b4fba)
Style Changes¶
Improve attribution by ignoring bulk formatting (3a969e556a)
utizes -> utilizes spelling fix (97945bc332)
Jon Haitz Legarreta Gorroño (23):¶
Enhancements¶
Improve
itk::ResampleInPlaceImageFilter
coverage (897351edfd)Add Python wrapping for
itk::ResampleInPlaceImageFilter
(3d492cfb85)Bump labeler action version (13b709360d)
Add further regexes to PR labeler config file (3bd6b6c715)
Add missing getter method to
itk::GaussianDerivativeOperator
ivar (d8856ebb1a)Add RTTI information to
itk::GaussianDerivativeOperator
(3a7bd3a328)Make
PixelType
alias bepublic
initk::AnnulusOperator
(8aacef9f1d)Add missing getter method to
itk::LaplacianOperator
ivar (d94d9ed8c8)Add RTTI information to
Common
operator classes (3f07584abd)Increase
Common
operators’ code coverage (71bb6a99fe)Increase
Review
module classes’ code coverage (230d319fde)
Documentation Updates¶
Improve
itk::ResampleInPlaceImageFilter
documentation (6fecdb5a57)Improve documentation in
Common
operator classes (fc822d75f7)Document members in header methods (67632ac0dc)
Fix enum class name in documentation (b4cb2d50cf)
Bug Fixes¶
Fix labeler action file regexes (#2516) (21793c61b1)
Fix Python wrapping labeler action regex (0c047d580d)
Initialize member in
itk::AttributeLabelObject
(ce012968d1)
Style Changes¶
Improve style in miscellaneous files (68d73baecb)
Make test style more consistent (8132e06fe0)
Prefer aliasing template pixel type in
common
operator classes (9f31b6a1c3)Prefer implicitly deriving array size in test (30e6e2b6c7)
Increase tests style consistency (16cadc05d0)
KWSys Upstream (1):¶
Miscellaneous Changes¶
KWSys 2021-07-08 (d5a1dc68) (12acc786e8)
Lee Newberg (9):¶
Enhancements¶
Propagate StatisticsLabelMapFilter’s default NumberOfBins (bb54bad693)
Wrap itkAdaptiveHistogramEqualizationImageFilter for Python. (974c63db99)
Platform Fixes¶
Change ::uint32_t to std::uint32_t, uint32 to uint32_t, etc. (12f7fede22)
Add ITK_TEMPLATE_EXPORT to some class declarations. (5efe8f3359)
Bug Fixes¶
Ellipsis is not iterable (ca0690069a)
Add run-time type information to FFT filter base classes (c693dbc830)
Style Changes¶
Apply “black -l 88” to format Python (fbbc7aa38c)
Add pyproject.toml to set default configuration for black Python format (935237cdf1)
Add recent Python-formatting commit’s hash to .git-blame-ignore-revs. (4705a3e692)
Matt McCormick (40):¶
Enhancements¶
Bump ITK version to 5.3.0 (0eacf4e96e)
Update CastXML source builds to v0.4.3, LLVM 11.1.0 (67fdd3067e)
Add CastXML binary for macOS arm64 (fde7fa6ce8)
Add Linux arm64 CastXML binaries (42aa3be3e4)
Updated CI cached testing ExternalData to 5.2.0 (356710288b)
Required VTK 8 or newer (9f88ad2007)
Bump the ITK CMake version to 5.1.0 (9f3fc5dd12)
Content link synchronization for ITK 5.2.1 (8be208ee1f)
Check for C++ standard after defaults applied (74fbb88ec4)
Content link synchronization for ITK 5.3 RC 1 (6dd08e6a55)
Documentation Updates¶
Add a pointer to good first issues (ca39327b60)
Remove indication NarrowBandCurvesLevelSetImageFilter not wrapped (f7e67070d5)
Add Professional Services section to the README (88085c0177)
Improve Apple Clang error to include C++14 requirement (6e3d31d138)
Platform Fixes¶
Backport CastXML arm64 Eigen support (a3996fe99a)
Do not add IPO to Python wrapping if not supported (3d2e898400)
Only use np.float128 when available (1237a57a3d)
Make floating point exceptions a no-op with MUSL, Linux, ARMv8 (0afa3f06a1)
Replace np.bool with np.bool8 (5c5e679675)
Require Python 3.7 or newer (dfa43f3837)
Use Python 3.9 in macOS.Python CI build (a654bc0317)
Remove MultiThreaderBase pixelCount (e086988337)
Use numpy==1.20.3 for CI testing (b667ce4d25)
Provide default values for floating point macros (26b2a2fb4d)
Do not enable remote module examples when building Doxygen docs (c754b5d010)
Use mallinfo2 when available (54fe14a568)
Revert “COMP: Use numpy==1.20.3 for CI testing” (04fd61e3e0)
Add missing template exports to ResampleInPlace,N4Bias,Py ImageFilters (cafb5ff591)
Add missing template export macro to SLICImageFilter (c3e40927f8)
Bump KWStyle to address Boost warnings with GCC 11.2 (a2aab1bb9c)
Bug Fixes¶
Add vnl_vector_from_array to extras all (3f8b14be54)
Do not create global multiprocessing RLock (cfdb5023a8)
Support double colons in Changelog commit summary (62804d09e9)
Use consistent ITK_USE_CLANG_FORMAT variable name (8ecdebad1e)
Ignore ImageToVTKImageFilter in VerifyGetOutputAPIConsistency test (b085d40c02)
Initialize C++ standard for remote modules (9ef180e254)
Remove slicer.kitware.com as a content link server (453fc6be24)
Improve dimension-dependent BSplineInterpolationWeightFunction wrapping (61f98c7fff)
Style Changes¶
Apply black to AuthorsChangesSince.py script (7504f6e45c)
Use CLANG_FORMAT in CMake variable names (90398b4aad)
MetaIO Maintainers (1):¶
Miscellaneous Changes¶
MetaIO 2021-06-24 (3f37ad78) (8131832530)
NIFTI Upstream (1):¶
Miscellaneous Changes¶
nifti 2020-08-07 (96b9954f) (9c2c9fa9b8)
Niels Dekker (49):¶
Enhancements¶
Overload
PhasedArray3DSpecialCoordinatesImage
Transform functions (3d7b84e6ed)Add explicit
itk::Vector(const std::array &)
constructor (4ce3383a46)Add operator==, operator!= to MetaDataObject and MetaDataDictionary (694bbc0a1f)
Upgrade ITK from C++11 to C++14 (daec0fdd70)
Add numbers to the three
itkPyBufferMemoryLeakTest
print messages (8d2de7122a)Add
ITK_UNEQUAL_OPERATOR_MEMBER_FUNCTION
, definingoperator!=
(5efdd93749)Add
NthElementPixelAccessor::operator==
(c97191e6f6)Add
ITK_EXPERIMENTAL_CXX20_REWRITTEN_UNEQUAL_OPERATOR
macro (2e5ffc8bd4)Add MakePoint, MakeVector, MakeIndex, MakeSize function templates (8aed68490b)
Declare Filled and operator[] of Index, Size, FixedArray constexpr (829bb066a0)
Replace GetNumberOfWeights() by static constexpr
NumberOfWeights
(34f3db8d8a)Replace BSpline GetSupportSize() by static constexpr
SupportSize
(c178324e39)Add static member function
BSplineKernelFunction::FastEvaluate(u)
(99f04d7df4)
Performance Improvements¶
Make
ResampleImageFilter::LinearThreadedGenerateData
faster (c64a58d42a)Use FixedArray for BSplineInterpolationWeightFunction OutputType (9bf745bda5)
Use FixedArray for BSplineBaseTransform ParameterIndexArrayType (bc7c5dff2d)
Remove BSplineInterpolationWeightFunction Kernel, use FastEvaluate (c23944ba54)
Platform Fixes¶
Require compiler versions that support C++14 (4e812d6074)
Adjust CMAKE_CXX…_COMPILE_OPTION for _castxml_cc_flags to C++14 (577ba4380a)
Support non-EqualityComparable pixels Image template instantiation (a293c03b46)
Require Apple Clang 7.0.2 as minimum in itkCompilerChecks.cmake (ae4c0ab756)
Add missing
#include <iostream>
to Deprecated module test (2a7f5ed199)Remove comparison to FixedArray in MatrixOffsetTransformBase GTest (feb845afb1)
Bug Fixes¶
Avoid crash TranslationTransform::SetParameters when too few params (deb0af73c0)
Remove unused virtual operator!=, operator== from ColormapFunction (384fc45b0c)
Similarity3DTransform::SetScale
should recomputem_Offset
(53bb498ba4)Similarity3DTransform::SetScale
should recomputem_Offset
(dd893faf8a)BSplineInterpolationWeightFunction should not print NumberOfWeights (8dba2bdefe)
Style Changes¶
Replace postfix by prefix increment in
for
loops in Core/Common (f81578bbb6)Replace postfix by prefix increment in
for
loops in ITK/Modules (971aef211c)Replace postfix by prefix increment in
for
loops in Examples (878fa6f435)Matrix constructors vnl_matrix/vnl_matrix_fixed explicit/implicit (7f5f3360a2)
Combine code
MatrixOffsetTransformBase
constructors (e6f5f96975)Remove obsolete FixedArray::operator[] workaround for Visual C++ (fc100111c4)
Replace
new
by C++14std::make_unique
(22bce725ae)Use C++14 <type_traits> template aliases instead of nested types (0f139ccfff)
Use C++14
make_reverse_iterator
insideCoLexicographicCompare
(4ed1cf4035)C++14 auto return type for ConnectedImageNeighborhoodShapeOffsets (6ccf7bc3e0)
Use
ITK_UNEQUAL_OPERATOR_MEMBER_FUNCTION
in Core/Common (0ad6ef1b55)Use
ITK_UNEQUAL_OPERATOR_MEMBER_FUNCTION
in Modules/Core (27f26685cc)ITK_UNEQUAL_OPERATOR_MEMBER_FUNCTION when
==
just returns true (f820eef7a5)Use ITK_UNEQUAL_OPERATOR_MEMBER_FUNCTION in Modules/Filtering (647efb8507)
Use ITK_UNEQUAL_OPERATOR_MEMBER_FUNCTION in Numerics, …, Video (29da972077)
Make operator!= of UnsharpMaskingFunctor and SliceIterator const (be45faec96)
Add TanHelper::operator== + ITK_UNEQUAL_OPERATOR_MEMBER_FUNCTION (16607aa7b7)
Add default member initializer
true
tom_LetArrayManageMemory
(67d4cf7cfe)Use MakePoint, MakeVector, MakeIndex, MakeSize from itk namespace (5ac7407986)
Remove
Make
functions from itk::GTest::TypedefsAndConstructors (558ea67a35)TransformInitializers constructors = default; default-member-init (d2548ce321)
Oleksandr Zavalistyi (1):¶
Bug Fixes¶
Fix initializing FixedImageMarginalPDF with garbage (0de9cfe31d)
Pablo Hernandez-Cerdan (2):¶
Enhancements¶
Increase hook-max-size for next GDCM update (e25fbbffc2)
Platform Fixes¶
CastXML, ITKVtkGlue, include only when property exists (0c31aa688e)
Philip Cook (1):¶
Bug Fixes¶
Fix matrix check rejecting NIFTI sform for small voxels (6278c4171f)
Samuel Gerber (1):¶
Enhancements¶
Adapt LBFGS2Optimizerv4 to inherit from GradientDescentOptimizerV4 (c34fb54e10)
Sean McBride (3):¶
Enhancements¶
Updated HDF5 update script’s HDF5 git tag from 1.10.6 to 1.10.7 (15f1e33e8c)
Made a few slow tests run serially, so they won’t timeout (d794791c7e)
Platform Fixes¶
Increased min cmake from 3.10.2 to 3.16.3 (0c3b8cbf9b)
Stephen R. Aylward (8):¶
Enhancements¶
Bump TubeTK to TubeTK 0.9.0 rc1 (b8d95b7cad)
Bump TubeTK to version the fixes linux CI (e230e6d322)
Updated SpatialObject wrapping to support CONST_POINTER (28cb8507fd)
Documentation Updates¶
Fix description of SpatialObjectToImage registration (11c2977314)
Platform Fixes¶
Update SpatialObjects to correct const-ness (903f7c152e)
Bug Fixes¶
SpatialObject writes object color (3bf34f6cc5)
TubeSpatialObject missing CopyInformation (3060a6d1e5)
TubeSpatialObject didn’t preserver Artery flag (2c3d27c9ee)
Tabish Syed (1):¶
Bug Fixes¶
Call Specialized Curvature Computation for 3D (faccaa9681)
Thompson, Darren (IM&T, Clayton) (2):¶
Platform Fixes¶
Removed constructor template parameters from the VNL library (103ffa4372)
Removed constructor template parameters from itkSmapsFileParser (867dda0585)
Tom Birdsong (8):¶
Enhancements¶
Add ITKVideoCore Python wrapping (b31c5d4b73)
Add
float
wrappings for itkSymmetricSecondRankTensor (11fbc6ecce)Add wrappings for video IO (ad6e718858)
Add ImageToVideoFilter and accompanying wrappings (546ba05c37)
Add vector image support to VideoStream and ImageToVideoFilter (9125fca8f8)
Add
float
wrappings for itkSymmetricSecondRankTensor (5378dae447)Wrap TransformToDisplacementField for Python (f87c9bdaee)
Bug Fixes¶
Resolve warnings with MakeIndex and MakePoint (7f1469270a)
VXL Maintainers (2):¶
Miscellaneous Changes¶
VXL 2021-07-15 (d8888fd5) (afa97fa43b)
VXL 2021-07-19 (22f874db) (82e8027330)
Zlib-ng Upstream (1):¶
Miscellaneous Changes¶
zlib-ng 2021-09-07 (547e8bc1) (f0790950ed)
ITK Sphinx Examples Changes Since v5.2.0¶
Brad T. Moore (2):¶
Enhancements¶
Dženan Zukić (2):¶
Enhancements¶
Update build-test-documentation to use v5.2.0 (59473cb3)
Style Changes¶
Switch to the new code order: Python before C++ (5db4da31)
Jose Tascon (5):¶
Style Changes¶
Use itk::WriteImage in ScaleAnImage (fe75959c)
Use itk::ReadImage and itk::WriteImage in src/Core examples (9ab36963)
Use itk::ReadImage and itk::WriteImage in src/Filtering examples (6fa7e3c9)
Use itk::ReadImage and itk::WriteImage in src/ Reg., Seg., Num. (7ab88a63)
Use itk::ReadImage and itk::WriteImage in remaining modules (367b6b56)
Kian Weimer (12):¶
Enhancements¶
Added ThinImage Python script (c1ca53f6)
Added WriteAnImage Python script (ce855854)
Added RescaleIntensity Python script (62407af0)
Added ApplyKernelToEveryPixel Python script (473c1c27)
Added missing Python licensing files (8d0cf11e)
Added ReadAnImage Python script (35ca99d7)
Added CombineTwoImagesWithCheckerBoardPattern Python script (1a6ddb3f)
Added CreateAListOfFileNames Python script (6918c50b)
Added ComputeInverseFFTOfImage Python script (1c1318bc)
Added SobelEdgeDetectionImageFilter Python script (5e4adf5c)
Added LaplacianRecursiveGaussianImageFilter Python script (38987907)
Modified most Python examples to make use of
argparse
. (29857829)
Lee Newberg (5):¶
Documentation Updates¶
Indicate how to adjust resolution in ResampleAnImage (896d48e2)
Add details for running CreateNewExample.py (532ca008)
RescaleAnImage -> RescaleIntensity to clarify that it’s not about size. (a732d546)
Bug Fixes¶
Fix continuous integration failure of ResampleAnImage (66b8d2f0)
Style Changes¶
Reformat Jupyter labs using jblack. (6fb0e9c8)
Matt McCormick (15):¶
Enhancements¶
Documentation Updates¶
Install titlecase package for CreateNewExample.py script (7489cce3)
Update example Download link instructions (c17864d3)
Update build instructions for example .zip files (249b93e9)
Platform Fixes¶
Make the Sphinx linkcheck optional (7eae01a1)
Bug Fixes¶
Require itk>=5.2.0.post2 for notebook tests (97c6e553)
Tarball html output path when not built as a remote module (f76dc431)
Fix download links (635cbc75)
Add ipython to Python environment for documentation build (f6cbeb76)
Correct MutualInformationAffine output (f5e029f2)
Transform SVG files in Sphinx (0e0de5fb)
Fix epub output path link in documentation (0ca83aa3)
Style Changes¶
Only output downloadable .zip archives for examples (567b01c6)
Stephen Aylward (4):¶
Bug Fixes¶
CreateTarball assumes /src/ is unique in path (37da5d6c)
Style Changes¶
Reformatting CreateTarball.py to match lint (e706163a)
Additional lint changes to CreateTarball.py (d19ecc34)
Miscellaneous Changes¶
Style: Fix remaining lint issues (94d58947)
ITK Software Guide Changes Since v5.2.0¶
Jon Haitz Legarreta Gorroño (3):¶
Documentation Updates¶
Style Changes¶
Use
itkNameOfTestExecutableMacro
macro for test names (e116243)
Matt McCormick (3):¶
Enhancements¶
Documentation Updates¶
Correct signed long mangling and C++ variables (1481a04)
Niels Dekker (2):¶
Enhancements¶
Remote Module Changes Since v5.2.0¶
AdaptiveDenoising:¶
Hans Johnson (1):¶
Platform Fixes¶
Replace SetUseImageSpacingOn() with SetUseImageSpacing(true) (a31fc7d)
AnisotropicDiffusionLBR:¶
Matt McCormick (1):¶
Enhancements¶
Update package for itk-5.2.0.post2 (690cfa5)
BSplineGradient:¶
Dženan Zukić (1):¶
Enhancements¶
Update CI to 5.2 (85e38ff)
Matt McCormick (1):¶
Enhancements¶
Update package for itk-5.2.0.post2 (a93687b)
Tom Birdsong (1):¶
Enhancements¶
Update Python CI for ITK v5.2.0.post2 (11e7430)
BoneEnhancement:¶
Dženan Zukić (7):¶
Enhancements¶
update CI to 5.2.0 (b21721f)
Platform Fixes¶
Tests depend on GTest (1b8f2b4)
Bug Fixes¶
disable unit tests which fail on CI but not locally (0faa86d)
Style Changes¶
update style in the reverted code (91217df)
Miscellaneous Changes¶
Mathew Seng (1):¶
Platform Fixes¶
updating CI to ITKv5.2RC3+ (ece9d47)
Tom Birdsong (1):¶
Enhancements¶
Bump for ITK Python v5.2.0.post2 (a36ab2f)
BoneMorphometry:¶
Matt McCormick (1):¶
Enhancements¶
Update package for itk-5.2.0.post2 (10d3eb2)
Cuberille:¶
Matt McCormick (1):¶
Enhancements¶
Update CI for ITK v5.2.0 (023878d)
GrowCut:¶
Dženan Zukić (6):¶
Enhancements¶
Bug Fixes¶
re-introduce region padding radius (e6e978a)
HASI:¶
HigherOrderAccurateGradient:¶
Dženan Zukić (1):¶
Enhancements¶
Update CI to 5.2.0 (c816e46)
Matt McCormick (1):¶
Enhancements¶
Update package for itk-5.2.0.post2 (03d1753)
Tom Birdsong (1):¶
Enhancements¶
Update Python CI for ITK v5.2.0.post2 (64ff5e5)
IOFDF:¶
Matt McCormick (1):¶
Enhancements¶
Update package for itk-5.2.0.post3 (90e0ad6)
IOScanco:¶
Dženan Zukić (5):¶
Enhancements¶
Bug Fixes¶
fix Windows packages CI path (505976e)
Style Changes¶
initialize the header fields in the order of declaration (69e6de6)
Matt McCormick (11):¶
Enhancements¶
Documentation Updates¶
Bug Fixes¶
Update itk package requirement to 5.2.0 (957ac6d)
Style Changes¶
Move binder/ to .binder/ (fb7c12f)
Michael Kuczynski (1):¶
Enhancements¶
Apply rescaling to compressed images (#56) (e585671)
IsotropicWavelets:¶
Dženan Zukić (3):¶
Enhancements¶
Pablo Hernandez-Cerdan (5):¶
Enhancements¶
Miscellaneous Changes¶
Style: Rename itkStructureTensor to itkStructureTensorImageFilter (1c28ed0)
pranjal.sahu@kitware.com (3):¶
Miscellaneous Changes¶
MinimalPathExtraction:¶
Matt McCormick (1):¶
Enhancements¶
Update CI for ITK 5.2.0 (2dc7ed8)
Montage:¶
Dženan Zukić (1):¶
Enhancements¶
Update CI to 5.2.0 (e2039b9)
MorphologicalContourInterpolation:¶
Dženan Zukić (1):¶
Enhancements¶
Update CI to v5.2.0.post3 (44854a4)
RTK:¶
Antoine Robert (2):¶
Bug Fixes¶
Lucas Gandel (1):¶
Platform Fixes¶
Fix hardcoded path in RTK install (42f0c5fc)
Simon Rit (16):¶
Enhancements¶
Platform Fixes¶
Install newer Python for cookiecutter testing (fe0d1f3d)
remove warnings due to unused type and lambda capture (835d4e3b)
remove warnings due to the use of deprecated CUDA declarations (184d0cad)
fix CMake CMP0106 witk RTK_BUILD_DOXYGEN (6399e12a)
do not set C++ standard manually, use cmake property (f66e98ac)
clean and modernize CMake handling of CUDA compilation (642ad254)
add missing depedency of lib RTK to lib ITKCudaCommon (4d288a55)
Bug Fixes¶
Tomoyuki SADAKANE (1):¶
Platform Fixes¶
Fix compilation error with VS 2019 (16.9.5) and CUDA 11.1 (3bd80190)
SimpleITKFilters:¶
Bradley Lowekamp (8):¶
Miscellaneous Changes¶
Update checkout version 2 (83cc86d)
Update to ITK tag v5.20 (9450615)
Update Ubuntu 20.04 (4cd0a63)
Update used python version in setup (8a7586c)
Add test case for report matrix with an INVALID orientation (0a6d1bf)
Update to greedy algorithm for determining closes orientation (a728f6d)
Fix CI to use Ubuntu 18.04 (432d457)
Mathew Seng (2):¶
Platform Fixes¶
Update GitHub Actions from ITKModuleTemplate (6917415)
Bug Fixes¶
Incorrect expectations for tests (be21024)
SkullStrip:¶
Matt McCormick (2):¶
Enhancements¶
Update package for itk-5.2.0.post2 (51fc9be)
Documentation Updates¶
Add PyPI, License badges (fcb84ce)
SplitComponents:¶
Dženan Zukić (1):¶
Enhancements¶
Update CI to 5.2.0 (ff8b58d)
Matt McCormick (1):¶
Enhancements¶
Update Python package for itk-5.2.0.post2 (faea2f4)
Tom Birdsong (1):¶
Enhancements¶
Update Python CI for ITK v5.2.0.post2 (58bde35)
Strain:¶
Dženan Zukić (2):¶
Enhancements¶
Matt McCormick (1):¶
Enhancements¶
Update package version for itk-5.2.0.post2 (892c54d)
Tom Birdsong (1):¶
Enhancements¶
Update Python CI for ITK v5.2.0.post2 (b09e3bd)
TextureFeatures:¶
Matt McCormick (2):¶
Enhancements¶
Thickness3D:¶
Dženan Zukić (1):¶
Enhancements¶
Update package versions to v5.2.0.post3 (4f29b73)
TotalVariation:¶
Matt McCormick (1):¶
Enhancements¶
Update package for itk-5.2.0.post2 (9ac40a6)
TubeTK:¶
Matt McCormick (1):¶
Enhancements¶
Update for ITK 5.2.0.post2 (#56) (9a93871e)
Pablo Hernandez-Cerdan (1):¶
Documentation Updates¶
Fix links and small typo in README (#53) (ce024a88)
Stephen Aylward (6):¶
Enhancements¶
Bug Fixes¶
Stephen R. Aylward (17):¶
Enhancements¶
Tube path interpolation uses stepsize (max dist between interp pnts) (#61) (f5524ca3)
Add sphinx_autodoc_typehints (e0cecfa0)
require sphinx_rtd_theme (cf4e4fc5)
Upgrade readthedocs to use cpython3 (#73) (59622ce2)
Add apt-get update to remove stale repos (1ad63f72)
Reduce list in requirements.txt to essential top-level (ca5f67d9)
Platform Fixes¶
Removed shadowed typedefs from tubeTubeMathFilters.hxx (#60) (0abd1cfe)
Bug Fixes¶
Style Changes¶
Remove year from copyright notice (3be3736a)
Miscellaneous Changes¶
Ultrasound:¶
Dženan Zukić (8):¶
Enhancements¶
update CI to ITK v5.2.0 (260de1d)
replace VectorResampleIdentityNeumann by ordinary Resample filter (343afab)
remove ResampleIdentityNeumannImageFilter (7de39b3)
Example notebook for Spectral generation and visualization (2e4918c)
add symbolic link to requirements.txt in .binder directory (29937ee)
Set a longer cell execution timeout (8ee4f97)
Cover all (Continuous)Index<->PhysicalPoint conversion signatures (d5d9f41)
Platform Fixes¶
Fix CI. Closes #143. (8c2a21f)
Lee Newberg (1):¶
Style Changes¶
Add semicolons at end of macro invocations. (1f3a06f)
Matt McCormick (4):¶
Enhancements¶
Bug Fixes¶
Update Binder requirement to itk-ultrasound>=0.3.2 (b4b30e0)
Tom Birdsong (7):¶
Enhancements¶
Add wrapping files for forward and inverse 1D FFT filter (581e97d)
Add analytic filter wrappings (5429066)
Add example for generating power spectral distribution plot (3c8be0a)
Add descriptive comments to spectra filter files (067677e)
Add example notebook for BMode image generation steps (a664fa3)
Fix frequency axis in PlotPowerSpectra example notebook (2f0a6f0)
Add SRAD denoising filter with data and testing (e1bcd9b)