ITK 5.2 Release Candidate 1 available for testing

Announcements
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We are happy to announce the Insight Toolkit (ITK) 5.2 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 5.2 is a feature release that improves and extends interfaces to deep learning, artificial intelligence (AI) libraries, with an emphasis on Project MONAI, the Medical Open Network for AI. ITK 5.2 feature highlights include functional filter support for PyTorch tensors, Python dictionary interfaces to itk.Image metadata, NumPy-based pixel indexing, 4D Python image support, and improved multi-component image support.

Downloads

Python Packages

Install ITK pre-release binary 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

MONAI-compatible itk.Image metadata dict and NumPy-indexing pixel set/get Python interfaces.

  print(image['0008|0008'])
  image['origin'] = [4.0, 2.0, 2.0]

or a dictionary can be retrieved with:

  meta_dict = dict(image)

For example:

In [3]: dict(image)
Out[3]:
{'0008|0005': 'ISO IR 100',
 '0008|0008': 'ORIGINAL\\PRIMARY\\AXIAL',
 '0008|0016': '1.2.840.10008.5.1.4.1.1.2',
 '0008|0018': '1.3.12.2.1107.5.8.99.484849.834848.79844848.2001082217554549',
 '0008|0020': '20010822',

For non-string keys, they are passed to a NumPy array view so array views can be set and get with NumPy indexing syntax, e.g.

In [6]: image[0,:2,4] = [5,5]

In [7]: image[0,:4,4:6]
Out[7]:
NDArrayITKBase([[    5,  -997],
                [    5, -1003],
                [ -993,  -999],
                [ -996,  -994]], dtype=int16)

Provides a Python dictionary interface to image metadata, keys are
MetaDataDictionary entries along with ‘origin’, ‘spacing’, and
‘direction’ keys. The later reverse their order to be consistent with
the NumPy array index order resulting from array views of the image.

Python functional filter support for PyTorch tensors

Similar to functional filter support for NumPy ndarray-like images, i.e. a numpy.ndarray, Dask Array or xarray.DataArrays, all itk.Image filters now support execution on PyTorch Tensor's.

For example:

import itk
import torch
import numpy as np

a = np.random.rand(50,50)
t = torch.from_numpy(a)
r = itk.median_image_filter(t)

Pythonic enhancements

itk.Image now provides an astype() method for casting to a NumPy dtype or itk pixel type.

In addition to an image filename or an image filename stack in a Python list, pass in a directory to itk.imread containing a DICOM series to obtain the appropriately ordered 3D image.

itk.vtk_image_from_image() and itk.image_from_vtk_image() for working with VTK.

We now generate .pyi Python interface files, providing better feedback in integrated development environments (IDE)'s like PyCharm.

Python code was modernized for Python 3.6, including some typehints. We now use the black Python style.

An itk.set_nthreads() convenience function is available to set the default number of threads. Support is now available for use in the Python multiprocessing module.

Python package layout improvements

Python support module organization has been organized into the itk.support.* package.

Python development was added for multi-config CMake generators, e.g. Visual Studio or multi-config Ninja, with the limitation that it only works with the most recently built configuration. When developing ITK Python wrapping or ITK remote modules, copy the WrapITK.pth build tree file to your virtual environment or conda environment site-packages to experiment with the wrapping.

Python package advances

Improved VectorImage and multi-component image support is available in the ITK Python packages.

NumPy is now a required package dependency.

Python packages are now built with interprodedural optimizations (IPO). Linux Python packages are built with the manylinux2014 toolchain.

Python packages are available for Python 3.6 to 3.9. Following CPython deprecation schedule, this is the last release to support Python 3.6.

C++ interface improvements

A new itk::FunctionCommand class is available, an itk::Command subclass that calls a std::function objects or lambda functions.

New itk::ReadImage, itk::WriteImage convenience functions are available for reading and writing image files with minimal code.

An itk::Image now supports operator== and operator!=.

A new itk::TernaryGeneratorImageFilter class is now available.

Third party library updates

Updates were made for the third party libraries:

  • GDCM
  • HDF5
  • double-conversion
  • pygccxml
  • castxml
  • swig
  • VXL
  • KWIML
  • KWSys
  • MetaIO
  • cuFFTW

Remote Module Updates

We added a new adaptive denoising remote module.

Many remote modules were updated: AdaptiveDenoising, AnalyzeObjectLabelMap, AnisotropicDiffusionLBR, BSplineGradient, BioCell, BoneEnhancement, BoneMorphometry, Cuberille, FixedPointInverseDisplacementField, GenericLabelInterpolator, HigherOrderAccurateGradient, IOFDF, IOMeshSTL, IOOpenSlide, IOScanco, IOTransformDCMTK, IsotropicWavelets, LabelErodeDilate, LesionSizingToolkit, MGHIO, MeshNoise, MinimalPathExtraction, Montage, MorphologicalContourInterpolation, MultipleImageIterator, ParabolicMorphology, PerformanceBenchmarking, PhaseSymmetry, PolarTransform, PrincipalComponentsAnalysis, RLEImage, RTK, SCIFIO, SimpleITKFilters, SkullStrip, SmoothingRecursiveYvvGaussianFilter, SplitComponents, Strain, SubdivisionQuadEdgeMeshFilter, TextureFeatures, Thickness3D, TotalVariation, TubeTK, TwoProjectionRegistration, and VariationalRegistration.
Their updates are included in the detailed changelog below.

Support for cross-platform C++ testing, Python package generation, and PyPI deployment with GitHub Actions was added to almost all remote modules.

Test coverage and bug fixes

A multitude of test code coverage improvements were made – our code coverage is now 89.86% with 126,590 lines tested.

Many more bug fixes and improvements have been made. For details, see the changelog below.

Congratulations

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

Of the 51 authors who contributed since v5.1.0, we would like to specially recognize the new contributors:

Horea Christian, Baptiste Depalle, David Thompson, Pierre Wargnier, Darren Thompson, Sebastien Brousmiche, Alexander Burchardt, Marco Nolden, Michael Kuczynski, MrTzschr, Bernhard M. Wiedemann, Charles Garraud, Lee Newberg, Bryn Lloyd, Gregory Lee, justbennet, Kenji Tsumura, Zhiyuan Liu, Jonathan Daniel, Moritz Schaar, Atri Bhattacharya, and Mon-ius.

What’s Next

We anticipate at least one more release candidate following community testing before the 5.2.0 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 v5.1.0

Alexander Burchardt (1):

Documentation Updates

Antoine Robert (2):

Enhancements

  • Use Numpy bridge with array of dimension 1 (53ce90294b)

Atri Bhattacharya (2):

Bug Fixes

  • Use explicit libm linking only on UNIX. (0ba93de147)

Miscellaneous Changes

Baptiste Depalle (1):

Enhancements

Bernhard M. Wiedemann (1):

Bug Fixes

Brad King (1):

Style Changes

  • Allow specific HDF5 sources to be larger than normal limit (b9216207dc)

Brad T. Moore (3):

Bug Fixes

  • WatershedImageFilter would crash with assert. (6af6956d97)
  • Fix to ITKSetPython3Vars ignoring Python virtual environments (#2068). (38c39d8818)
  • Add ‘_d’ POSTFIX to Windows Python Debug (#2050) (e9fdf144f5)

Bradley Lowekamp (42):

Enhancements

  • Use named pipeline inputs for morphological reconstruction (9c45e84ace)
  • Add FunctionCommand with lambda support (b07b3cd319)
  • Add direct support for lambda command to Object class (b895526230)
  • Update GDCM to latest on the release-2.8 branch (90e6da1ff6)
  • Bump SimpleITKFilters remote module (50c23e0580)
  • PasteImageFilter input ND and constant value (498fee2173)
  • Add TernaryGeneratorImageFilter (d976b6f461)
  • Change TernaryFunctor usage to TernaryGenerator (cb5b726394)
  • Add GTest cases for TernaryGeneratorImageFilter (e0de7419c6)
  • Update ternary filter wrapping for generator base class (39b2c81b19)
  • Moderinize ShiftScaleImageFilter (5a8938c658)
  • remove redundant WriteImage overloads (d8af208642)

Documentation Updates

Platform Fixes

  • Add missing const qualifier (a7ffe5acad)
  • Address missing brace initializer warning (14a8919dfd)
  • Fix ~FunctionCommand implicit override warning (fd4c0f8e46)
  • Address no override keyword warning (34a414fbdb)
  • Update SimpleITKFilters remote module (459d798e43)
  • add missing parentheses (19969b4ef5)
  • Address unused other parameter in defaulted methods (6cedbbc261)
  • Address brace initializer warning (b1fc86afa6)

Bug Fixes

  • Add StatisticsImageFilter (b9ac060a53)
  • Disable dynamic threading in noise filter. (af780e8a03)
  • Add StatisticsImageFilter (43a8972077)
  • Fix segfault with empty CompositeTransforms (0300b63ddf)
  • Fix additional segmentation faults with empty Composite (7212dc719f)
  • Address memory leak in CastSpatialOpbjectTest (a243e9d9af)
  • Patch missing const qualifier to GDCM dircos_comp comparison (90ad651db4)
  • Address bug with small size in output of SliceImageFilter (7aac4a6748)
  • Update CI scripts from current ITK master (3213404416)
  • update CircleCI configuration with selections from master (08dc0116fe)
  • Don’t use InsertElement which modifies MTime (63d148715e)
  • Address buffer overflow with deprecated GDCM1 interface (5df152b4c3)
  • Remove no output warning in ImageSink filters (342098e460)
  • Address divide by zero error in SignedMaurerDistance (4fb2831d62)
  • Support MRC2014 mode 0 as signed 8-bit integer (f7d72576bf)

Style Changes

  • remove extraneous semi-colon after bracket (c22e46b126)
  • Use defaulted constructor for event object macro (c24d5dd188)
  • Improve function types used in SignedMaurerDistanceMap (b706cf64c7)

Bryn Lloyd (2):

Platform Fixes

  • Fix warning in PointSetToPointSetMetricv4 (#1820) (0892462d78)

Charles Garraud (1):

Bug Fixes

  • Fix BUILD_SHARED_LIBS state consistency for HDF5 (8d9f078a3d)

Darren Thompson (1):

Enhancements

  • Added itkPointSetToImageFilter.wrap (75ed9591a5)

David Thompson (1):

Enhancements

  • Let gitlab-ci runners build with clang-tidy. (d97280f880)

Davis Vigneault (11):

Enhancements

  • Add Python Wrappers for Mesh Source Classes (a10f19eff8)
  • Review Cuberille Remote Module Compliance (f981de6829)
  • Assert in Debug Mode (128f58bc85)
  • Test Assignment and Copy of Spatial Objects (4afc284051)
  • Test Map and Vector Iterators (a2cb636777)
  • Add Missing Boolean Macros in QEFilters (d926647247)

Platform Fixes

  • Address Wdeprecated-copy warnings in gcc9 (4e0aea2092)

Bug Fixes

Style Changes

Dženan Zukić (27):

Enhancements

  • updating remote modules to latest versions (c9977356b6)
  • update remote modules (60207eec97)
  • use double-conversion’s CMake targets (3ee6f1e5c9)
  • back-porting #1165 to support Visual Studio 2019 (432dd1b9dc)
  • progress reporting does not stall with PoolMultiThreader (181171da21)
  • append properties instead of overwrite in HDF5 (ee249607e0)
  • allow dependencies on remote modules (fa1082b929)
  • remove NumPy presence conditions from tests’ CMakeLists.txt (71044d8495)
  • add a convenience function WriteImage (60b0984d41)
  • update remote modules (faec364cad)

Documentation Updates

  • restore LICENSE accidentally overwritten by a merge commit (a443c76bc5)
  • restore LICENSE accidentally overwritten by a merge commit (ed2a25db2c)
  • add ComputeJacobianWithRespectToPosition change to migration guide (e06776fea3)
  • hyperlink mentioned commits (8a17d4e611)

Platform Fixes

  • fix GPU compile errors when building as DLLs (5183490199)
  • a fix for non-system double-conversion build (a47c974f64)
  • update download location for pre-built ICU for Visual Studio (f360092423)
  • variable is uninitialized when passed as a const reference (c8ee1e55f9)
  • fix compilation with Python and tests enabled on Visual Studio (07382404bc)

Bug Fixes

Style Changes

  • make column limit more stringent in the examples (0b970d803d)
  • apply clang-format (d9e73e9a8b)
  • rename libPNG’s license to match the original one (e016512d77)
  • remove duplicate item in a list (481c31af68)
  • rename libPNG’s license to match the original one (5012917fb4)
  • remove duplicate item in a list (a8ba7686a5)

Eigen Upstream (1):

Miscellaneous Changes

GCC-XML Upstream (1):

Enhancements

GDCM Upstream (3):

Miscellaneous Changes

Gregory Lee (1):

Documentation Updates

  • update references for recursive Gaussian filters (1cf7142055)

HDF5 Maintainers (1):

Miscellaneous Changes

Hans J. Johnson (3):

Enhancements

  • Prefer to use sform over qform when both are set (34231b5702)
  • Exercise converting Object (d9e464c702)

Miscellaneous Changes

Hans Johnson (158):

Enhancements

  • Add test to monitor metric result value (d5549c93b0)
  • New test data for nifti qform/sform (616461fb62)
  • Add nifti sform read/write testing (8e2e52869e)
  • Do not pollute the global link_directories namespace (708c837788)
  • Update building internal FFTW version (7d033c2463)
  • Move cmake config items into common itkConfig.py.in file (a867b5e12e)
  • Remove alias to ‘object’ variable name (8223831a3c)
  • Extend dictionary with update not add (82b639b72f)
  • Avoid bugs with mutable default arguments (2b8e1e7919)
  • Use targeted import for element of sys (4f9b9918ea)
  • import modules at top of file (787c0b3c04)
  • Avoid poluting the global namespace (bb1c7b57ea)
  • Remove unused variable warnings. (1b1bf30d59)
  • Prevent contaminating global namespace (9f6cf0049b)
  • disable a false positive naming error from pytype. (3dd39f69e8)
  • Code review and simplified logic (b87caa1818)
  • Remove circular module dependancy (4606fb5aad)
  • Explicitly test the itkConfig.LazyLoad=False option (14873a246d)
  • Allow setting default behaviors with environment (6872aeaca0)
  • Only copy path spec when needed (30882f57c3)
  • Avoid adding invalid path to the sys.path (5be56ea461)
  • Add error checking for required paths (eb9d7ecb51)
  • Update minimum required version of ITK (ddf248309a)
  • Use more standard symbol lifting into itk namespace (be520e05fc)
  • Separate static components into base class (32185a5275)
  • Adding function to help generate init.pyi (82754b50fc)
  • Exclude cvar from the testing. (ba66340fe9)
  • Update documentation for generation of itkTemplates. (2884cb5fa3)
  • Update to SWIG 4.0.2 (46897c2fdf)
  • Add swig doxygen and autodoc=2 formats (1401fdbe4f)
  • Ignore huge file warning for HDF5 paths (f6dcbb9932)
  • Remove python interface introspection (693851bbc0)
  • Simplified multi-config generator wrapping (12e8d93a1c)
  • HDF5 upstream now hosted on github Version 1.10.6 (4726315a91)
  • More closely match the 1.10.6 release hdf5 (bbc7945343)
  • Script for updating DoubleConversion library. (7e50cec343)
  • Update Double-convert third-party (ee51ee18e6)
  • Update remote modules to master branch (4fec21155b)

Documentation Updates

  • Spelling warnings removed. (47fa99d824)
  • Improve variable name spelling (34e8618012)
  • Make variable name clarifications and type designations (18f1ca0a4c)
  • Add autodoc request in swig .i files (2b9324a58a)
  • Make swig object registry more transparent (7863da6db1)

Platform Fixes

  • Missing defition of ITK_DISALLOW_COPY_AND_ASSIGN (d933363875)
  • Resolve multi-line comment warning (7c6355841f)
  • Refine order of searching for header files (3192eb2975)
  • Ensure consistent ordering of list printed (362bf6b851)
  • Local variable ‘s’ might be referenced before assignment (80094567d7)
  • Ambiguous ‘range’ function made explicit (eeef5c82e6)
  • Avoid outscope variable shadowing (56be042274)
  • Selective import of required components (30dd1b5c12)
  • Avoid possible variable use before assignment. (183cb1db67)
  • Remove redundant import. (a5408c1ff4)
  • Remove unneccessary HAVE_NUMPY conditionals (8b65fc4bf6)
  • Avoid reassigning parameters (71830712eb)
  • Too broad exception narrowed. (ee452b875e)
  • PEP 8 (c7fb93c668)
  • Address protected member warning (cc1b39e514)
  • Shadows name ‘input_type’,‘keys’ from outer scope (db612aaf99)
  • Remove python2 dictionary compatibilties. (fade2565bb)
  • Too broad exception clause fixed (1f75a9a1fb)
  • Method ‘Stop’ may be ‘static’ (0c4269c551)
  • Remove potential referenced before assignment (af9526bdc7)
  • Remove shadows name from outer scope. (a94e0690c8)
  • Instance attributes should be defined in init (a8d0d06ac5)
  • Remove shadow variable outer scope warnings. (abd70cea64)
  • Remove difficult to debug use of global variable (35e625a7f9)
  • Avoid poluting the module namespace (cae100149c)
  • Remove unused local variables. (6c0c6ac468)
  • Keep local functions out of global namespace (05eef39b8c)
  • Use lowercase python compatible function name. (09b96dc67d)
  • Match variable names from itkBase. (d6c004d003)
  • Unresolved reference ‘sqrt’ (672d9cd4e0)
  • Simplify exposing elements from itk namespace. (92f4c11f56)
  • Allow type inference tracking with dynamic loading. (ba169e32c4)
  • Fix test for remote python module (523defbe78)
  • Enforce name.strip() redundantly (ab071e4e41)
  • Provide full path to test script file (305a09efd8)
  • Prefer static member function modify static instance vars (8cde96968f)
  • Place python shared libs as subpackage of itk (22998bd226)
  • Unconditionally set wrapped shared lib directory (0428956bce)
  • Add initial typing for itkExtras (f6c98a595e)
  • Mypy signature mismatch fixed (1a08df34b8)
  • Adding typing for ITK manually. (c635fc08f4)
  • Add typehinting for support classes (f7989935fb)
  • Fix hidden overloaded-virtual warning (ef8ffe5c6e)
  • Avoid compiler warnings with IPO (4b69a7141a)
  • Work around ghostflow-check-master warnings (5f96c9e279)
  • Set vxl minimum to 3.0.0 (a4ffdcf9b2)
  • Use of uninitialzed variable warning (4ea8d8a70c)

Bug Fixes

  • Double scaling introduced in refactoring (d23cb9295e)
  • Double scaling introduced in refactoring (355c6cbda3)
  • Incomplete removal of ITK_INSTALL_NO_* variables (3adb25fd65)
  • itkhdf5 installed paths were incorrect with recent hdf5 versions (9e0d33cd1e)
  • Centos internal lib64 lib path (4026b5e4ba)
  • Fix fftw linkage issue with system fftw (85cb1d5860)
  • itkhdf5 installed paths were incorrect with recent hdf5 versions (fd4a438042)
  • snake case functions are erased (8a0a94041e)
  • Writing snake_files should not be appended (2504f43021)
  • Decoupled config files should not depend (4c3d376981)
  • Pickling of itk module was broken (e5208e54fb)
  • Must append the list itkConfig.path (0e0c9ababd)
  • WRAPPER_LIBRARY_OUTPUT_DIR is needed before macro call (008ea74e87)
  • Convert code to python3 compatible (fd74a79f8f)
  • Avoid itkConfig double import trap (1e334c9aab)
  • Limit ignore to build directories only (10a96a2b61)
  • Explicit use of builtin set (b978584a08)
  • Add test exposing multiprocessing LazyLoad failure (62916b2755)
  • LazyLoading must be threadsafe (2880b97c88)
  • Incorrect loop dimensions in untested code (43a3c6ac60)
  • Do not wrap invalid template parameters (57448a583d)
  • CASTXML fails with aggressive optimizer flags (cf39f4f871)
  • Missing output dependency shared/H5init.c (519f1bd65a)
  • New test for 3D support (bd7740cec7)
  • ASAN identified use after delete bug (ece02372ff)

Style Changes

  • Use black formatting for python (cf1095c835)
  • Prefer fstrings for python 3.6+ (3e797747dd)
  • Missed conversions for new macro name (bf30fc083c)
  • Use consistent formatting for python files (c7c0736e3d)
  • Fix comment spelling errors. (3a9a73c3ad)
  • Apply consistent pep8 compatible indentation. (425060c493)
  • Prefer to use @staticmethod decorator. (72e117da77)
  • Initial typehints added. (44083b64ba)
  • Avoid difficult to read anit-pattern (2e85876bae)
  • Remove python2 dictionary facade (5b5d79c04e)
  • Fix name and spelling issues (261bb0e152)
  • Applied recommend code refactorings (0a1b4a1658)
  • Use python preferred lower-snake-case variable names (065c7fd5f8)
  • pytype warning disabled. (93d479afb2)
  • Address shadow variable and python style issues (e7479f4306)
  • Remove pass through return of read-only values. (5e1c7c4277)
  • Encapsulate initialization for keeping namespace clean. (5a943bbead)
  • Prefer to extend existing template (e98a3010c8)
  • Reduce aliased object naming (17051ed75f)
  • Localize imports to minimum scope. (67459c3b28)
  • Update to python3 compatible syntax. (34ca41fbee)
  • Update python Test with black formatting (b3b7566b35)
  • Remove unused macro. (c59328a8d5)
  • Prefer explicit check to nested try/catch (213e3382c8)
  • Only set paths necessary for current build (c82803a767)
  • Fix spelling error interperter -> interpreter (6687482f48)
  • Make self-contained module. (97d506e23d)
  • Prefer explicit in-package pathing (d01deeb18c)
  • Improve relative pathing computations (2a628f2f43)
  • Prefer explicit full module specification for spec (bcf9afae3e)
  • Remove duplicated content that was immediately overwritten (d9de859473)
  • Update python Test with black formatting (70be2c1b8f)
  • Simplify writing template python code files (05a8362df9)
  • Use consistent formatting for python files (2f7c9a1837)
  • Prefer fstrings for python 3.6+ (b83ee83d9c)
  • Minimize cmake configured python files (98fe9d6205)
  • Add typehints for the itkTypes (83a662568a)
  • Prefer fstrings for readability. (cd3324726c)
  • Update processing of *Config.py files (53e4fe066f)
  • Re-enforce black formatting contraints (8e4a64b20a)
  • Remove duplicate module dependancy entries (102ce4f70d)
  • Fix clang-format styling require macro ‘;’ end (92b891d33a)
  • Macros should respect an end-of line ; (5a88436242)

Horea Christian (1):

Enhancements

Jan Margeta (1):

Enhancements

  • Support for non-compliant DICOM in itk-js (2810be637b)

Jerome Schmid (1):

Platform Fixes

  • VtkGlue module-Provide support for VTK new cmake targets (c2cfd2b6d1)

Jon Haitz Legarreta Gorroño (56):

Enhancements

Documentation Updates

  • Add NumFOCUS-related contents to README (79f4620757)
  • Fix typos in DTI 3D reconstruction image filter example (12f090deb2)
  • Fix typos in DTI module’s anisotropy image filter classes (b12ab31231)
  • Improve math morphology class documentation (6b58cb13eb)
  • Fix link to NumFOCUS ITK project website in README (f38b88fe95)
  • Change the Insight Journal handle links to insight-journal links (1fc01a7a8a)
  • Fix verbatim block in UpdatingThirdParty doc file (eca8e74d4a)

Platform Fixes

  • Fix SW Guide examples LaTeX block line start warnings (e95769af5b)
  • Fix SW Guide examples multi-line comment warnings (1ab9659e57)
  • Remove unnecessary inherited member re-definitions (a17edc6521)
  • Fix `itk (47617c2a6e)
  • Fix missing initialization braces warnings (698c936869)
  • Fix `itk (c0955f47b2)
  • Fix undeclared identifier (ca37e273cf)
  • Update legacy boolean ivar set method call to current API (0e18baab51)

Bug Fixes

  • Fix math morphology strongly typed enum scope-resolution (128e1d7373)
  • Fix `itk (7bdc54edb6)
  • Fix itkDCMTKSeriesREadImageWrite.cxx test failures (94154341cd)
  • Remove unnecessary IO member filter name of class print calls (fe8f991cb5)

Style Changes

  • Transition Testing/Data README to Markdown (3116466fa8)
  • Fix typo in itkBinaryThresholdImageFilterTest (f16dbf75d6)
  • Fix ivar print value in `itk (bdf5cab617)
  • Avoid try/catch boilerplate code in updating writer (96e8ecf665)
  • Remove unnecessary comment lines (d37d8b36df)
  • Turn commented unnecessary commands into useful comments (f05218b746)
  • Make indentation in `itk (9f6e623d7e)
  • Improve `itk (1ff221aea7)
  • Use itkBooleanMacro to avoid boilerplate code (532545a408)

Jonathan Daniel (3):

Enhancements

Bug Fixes

  • Accept TemplateTypeError with fallback_only (612a769660)

KWIML Upstream (1):

Miscellaneous Changes

KWSys Upstream (1):

Miscellaneous Changes

Kenji Tsumura (1):

Bug Fixes

  • Fix itkGPUDemonsRegistrationFilterTest fails (78e84e7c49)

LIBPNG Upstream (1):

Miscellaneous Changes

Lee Newberg (19):

Enhancements

  • Support additional pixel types in python wrapping for ShrinkImageFilter. (6b54a99207)
  • WIP (caf224974a)
  • Read DICOM directory with Python imread (e20335872f)
  • Support for VariableLengthVector in CastImageFilter (87c3fb1708)
  • Move ITKMeshToPolyData functionality into ITK (30da875f61)
  • Make Python Image.astype() work for more types (8f2a6c99fd)
  • Add tests for VectorImage.astype (1f5d3a4953)
  • Support ttype parameter for numpy<->ITK conversions (00e6785a6a)
  • ttype can be ImageType whenever (ImageType,) is accepted (5741f877be)
  • add additional assertions for ttype parameter (aac01f1179)

Performance Improvements

  • No need to check whether numpy is available (858792ab46)

Platform Fixes

  • Breaks Continuous test for Microsft OS; disable until debugged. (e749f3b781)

Bug Fixes

  • Do not wrap signed distance map filters for integer image outputs (076e990904)
  • Update associated test (0da293d648)
  • MinPriorityQueueElementWrapper constructor needs ZeroValue() (ce3444c652)
  • MinPriorityQueueElementWrapper constructor needs default constructor (fc37787a9e)
  • MinPriorityQueueElementWrapper constructor needs default constructor (b027780259)
  • fix tests for VectorContainer and PyVectorContainerPython (f24795b2e0)

Style Changes

  • Prevent CMake variable name collisions (623f466b0b)

Marco Nolden (1):

Platform Fixes

  • added vcl compiler detection for GCC 10.x (e53d1d94f0)

Mathew Seng (2):

Enhancements

Bug Fixes

Mathieu Malaterre (1):

Style Changes

Matt McCormick (59):

Enhancements

  • Bump the ITK CMake version to 5.2.0 (13f6310924)
  • Add itk.vtk_image_from_image and itk.image_from_vtk_image (f13e760be2)
  • Bump CI ExternalData version to 5.1.0 (c444993267)
  • Add torch.Tensor input/output support for ITK filters (b9deb4743e)
  • Add Label PR GitHub Action (28d2289399)
  • Add image.astype(pixel_type) for casting (5f6aecf652)
  • Bump CMakeLists.txt version to 4.13.3 (f7ac08b4c9)
  • Update UpdatepygccxmlFromUpstream.sh for pygccxml v2.0.1 (8430295f67)
  • Add testing data content links for ITK 5.1.1 (866ee013a1)
  • Update ITK CMake version for 5.1.1 (3ecf6c87d1)
  • Add Image dict and pixel set/get Python interfaces (d8086fad34)
  • Wrap LabelOverlapMeasuresImageFilter (c39ea2f1b4)
  • Support Python debugging with Visual Studio (6837c58908)
  • WIP (58661ec04d)
  • Update ITK CMake version for 5.1.2 (39d9b1712f)
  • Add int.tiff.md5 content link for 5.1.2 release (a0125aa894)
  • Install dask for CI testing (8a89d1f7a2)
  • Update GDCM upstream repository to GitHub (6d35c93c95)
  • Content link updates for ITK 5.2 RC 1 (be70e83f91)

Performance Improvements

Documentation Updates

  • Release process updates for 5.1.0 (dec528a777)
  • Add 5.1 Release Notes (9f79ab220d)
  • Fix conda install command in ReleaseDownloadLinks.md (b7af5ee6bc)
  • Add pointers on how to browse and download testing data (3adc97511a)
  • Note content link update for bug fix releases (b2dcce79bb)
  • Correct ITKExamples Python package testing command (8e45514502)

Platform Fixes

  • itkResampleImageTest8 ~ProjectTransform mark as override (deb5f46f2c)
  • Duplicate ImageToImageFilter wrapping of ULL (e747b0a946)
  • CurvesLevelSetImageFilter multi-line comment (c66679392c)
  • Unused tc in SquaredEdgeLengthDecimationQuadEdgeMeshFilterTest (419b92403c)
  • Bump CastXML to 0.3.4 (795bbd9a27)
  • Avoid duplicate itk.PointSetD3 wrapping (bea2a7906e)
  • Do not reference FE_DIVBYZERO FE_INVALID with Emscripten (b05b007a63)
  • Add VXL support for GCC 9 (9825d546c4)
  • Add lxml to macOS CI environment (7c230e02e6)
  • Add lxml to macOS CI environment (1919eaa95b)
  • Add missing itkMacro.h to itkSTLContainerAdapter.h (db4a897729)
  • Remove -fopenmp in castxml invocation (45f13f04cf)
  • Remove gold linker support (214328cae7)
  • Do not enable whole program optimization with MSVC (ae44277a03)
  • Use CMake 3.18.4 in macOS CI builds (414d4c0502)
  • Set runtime output directory for Windows Python tests (ea617e3521)
  • Only search for Python 3.6 and above (93986e0e6c)

Bug Fixes

  • Fetch full depth in apply-clang-format action (01d2e08deb)
  • Specify itk package in SWIG Python modules (98fc085a9d)
  • Simplify itk.BlockMatchingImageFilter feature points PointSet mangling (2e2b3332cd)
  • Import C module from Python submodule (a6a5140f4d)
  • ITKModuleExternal CMAKE_LIBRARY_OUTPUT_DIRECTORY when wrapping (eb97b5aa4a)
  • Wrap ExtractImageFilter for UL (972a89c228)
  • Support casting unsigned long pixel types in Python (530e61eedf)
  • Remove netnlib triangle classes (7f95961fa7)
  • Remove License incompatible netlib files from vxl updates (d1066224e3)
  • Empty image support in image_from_xarray (3da4926531)
  • Add missing enumerate with multi-ndarray-output itk filters (c7595ff794)
  • Do not wrap unsigned char for connected component output (f3e328657f)
  • Add TIFFImageIO support for unsigned int and int pixel types (241953dd23)
  • Python support module and init.py install location (5bcfac618b)
  • Prevent HDF5 from overwritting ITK library names (700eb96f6b)

Style Changes

  • ITK_WRAP_PYTHON_PROCCESS to ITK_WRAP_PYTHON_PROCESS (166be4d32b)

MetaIO Maintainers (2):

Miscellaneous Changes

Mihail Isakov (2):

Enhancements

Documentation Updates

Mon ius (1):

Platform Fixes

  • fix error on IBM POWER9 ppcle64 arch (9b7a28032e)

Moritz Schaar (1):

Bug Fixes

  • Fix Python Wrapping with MSVC and CMake >= 3.18, Closes #2049 (4f6fc719bd)

Nick Tustison (6):

Enhancements

Documentation Updates

Niels Dekker (33):

Enhancements

  • Allow running various tests without arguments (5d02fac6bd)
  • Test that MetaIO supports a string value of up to 32767 chars (7e9934a5e4)
  • Add operator== and operator!= to itk (7f3337d27e)
  • Declare FixedArray (c5aa259a0d)
  • Add convenience function ReadImage (aeea88b192)
  • Extend ITKWriteImageFunctionTest by reading the written image back (21cf6485e6)

Documentation Updates

  • Link region iterators to ImageRegionRange, ImageRegionIndexRange (ddca18b894)
  • Add Doxygen links from iterators to ShapedImageNeighborhoodRange (2b92d3973c)

Platform Fixes

  • Fix arithmetic overflow MersenneTwisterRandomVariateGenerator (e632d97ffc)
  • Work around GCC-4.8 error converting to OptimizerParametersHelper (ee78a176b8)
  • Remove InvalidImageMomentsError from itkImageMomentsCalculator.hxx (7332fa8c40)

Bug Fixes

  • Fix issue #1950, ImageMaskSpatialObject access outside image buffer (ceb157d634)
  • Fix MatrixOffsetTransformBase SetFixedParameters if too few params (fcb85b3a1e)
  • Fix MatrixOffsetTransformBase SetFixedParameters if too few params (33e9e6bdba)
  • DICOMParser should use && instead of comma in for-loop condition (c90bfa4f47)
  • Fix Euler3DTransform (4d5b1a535f)

Style Changes

  • Move ITK5 ranges, shapes, policies out of Experimental namespace (e50b279bcb)
  • Allow conversion from nullptr to WeakPointer, not from zero (03ce742132)
  • Add in-class default member initializer to SmartPointer m_Pointer (1ab9a173dd)
  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE (7d177ca0c7)
  • Call ITK_DISALLOW_COPY_AND_MOVE, not ITK_DISALLOW_COPY_AND_ASSIGN (4c0982ddec)
  • Remove C-style (const void *) casts (077b1232de)
  • Remove space between class and member names in C++ source files (734d6f84d7)
  • Remove “include guards” from cxx files (94218d38bf)
  • Use C++11 override and = default in itkWin32OutputWindow.h (bc66259dcb)
  • Replace container[container.size() - 1] by container.back() (5eb4697298)
  • Remove local possibleTransformIO from TransformIOFactoryTemplate (d262349111)
  • TxtTransformIO Read() no longer copy input file to data string (99093d4f02)
  • Declare OptimizerParameters (5e692d171b)
  • Move OptimizerParameters implementation from .hxx to .h file (4812f18f6f)
  • Replace vnl_vector[vnl_vector.size() - 1] by vnl_vector.back() (bff1ce86ab)
  • Use the WriteImage convenience function in Core/Common/test (4e87206392)
  • Use the WriteImage convenience function anywhere in Modules/Core (91418de61e)

Niklas Johansson (2):

Enhancements

  • Prevent segfault by failing fast in itkGDCMImageIO (7f34bba177)

Style Changes

  • Correct doc for ReadImageInformation (5b5a771d58)

Pablo Hernandez-Cerdan (6):

Enhancements

  • Add data() and size() member functions to FixedArray (38939ff86d)

Platform Fixes

  • Remove dynamic exception specifications in tests (840f22feb3)
  • Avoid Dimension < 3 in FrustumSpatialFunction (4427477a5e)
  • Fix warning -Wdeprecated-copy in itkQuadEdgeMeshBaseIterator (90b1128df6)
  • Fix const-correctness of iterators in multiple classes (d8d726ecf0)

Bug Fixes

  • Use ITK_WRAP_IMAGE_DIMS in ViewImage.wrap (680f10f8a4)

Pierre Wargnier (2):

Platform Fixes

  • fix errors and warnings in OpenCV bridge (1331c92e30)

Bug Fixes

  • Fix Mat to Image conversions for OpenCV 4.x; add support for int32 (abb177865f)

Sean McBride (2):

Platform Fixes

  • Fixed link error with old versions of AppleClang (1bb185a073)
  • Fixed compile error on old clang 7, prefixed ivar with this-> (469a8b3981)

Simon Rit (3):

Documentation Updates

Platform Fixes

Stephen R. Aylward (19):

Enhancements

  • Bump TubeTK to support CUFFTW (#1788) (68a5b65357)
  • Bump TubeTK to version that removes ArrayFire (replaced by cufft) (15c287ef70)
  • ITKFFT library is now required, even if cufft is used. (656878aaa2)
  • Bump MetaIO to address style and const params (c3d645c8d9)
  • Bump MetaIO to use an enhanced MetaTubePoint (#1954) (4bdc38ca9b)
  • Bump TubeTK to version that works with updated Spatial Objects (#2002) (631aeaebf8)
  • Bump TubeTK to offer updated examples and improved tube seg (75ca90fc98)
  • TubeTK release candidate for ITK v5.1.2 (7daaa13217)

Platform Fixes

  • Adds ComputeTangentAndNormals() function (1435bf57e8)
  • Adding itkLegacyMacro wrapping to ComputeTangentAndNormals() (229fa4424d)

Bug Fixes

  • CUFFTW paths were not being set and unnecessary FFTW files used (0f47aae052)
  • CurvatureRegistrationFilter fix logic re (9ab4c1f45a)
  • CUFFTW paths were not being set and unnecessary FFTW files used (449c571897)
  • Frenet frame disrupted along tubes (25bb5cac00)
  • Bump TubeTK (9d33b08766)
  • Update TubeTK to include version that addressed missing VTK files (e5ab67d198)
  • Bump TubeTK to isolate wrapping on vtk-dependent classes (36e5c27312)
  • TubeSpatialObject normals not unit vectors (#1972) (bc0d6ad9ab)
  • Update itkEventObjectTest to use new event macros (48768c45c0)

VXL Maintainers (5):

Miscellaneous Changes

Zhiyuan Liu (4):

Enhancements

  • Add a convenient function to get/set the number of threads. (bc162de3dd)

Documentation Updates

Bug Fixes

  • Register Dask serialization functions for NDArrayITKBase (27fe268d9d)

justbennet (1):

Platform Fixes

  • Fixing #include for itkExpectationMaximizationMixtureModelEstimator.h (880a932fce)

Remote Module Changes Since v5.1.0

AdaptiveDenoising:

Hans Johnson (2):

Platform Fixes

  • Update to new ITK_DISALLOW_COPY_AND_MOVE macro (b3c1a47)
  • Add missing ‘;’ at end of macro (6aff4c8)

Jon Haitz Legarreta Gorroño (3):

Enhancements

  • Use strongly typed enums (ffa3bcc)
  • Test the similarity metric (48e4599)

Platform Fixes

  • Use and move ITK_DISALLOW_COPY_AND_ASSIGN calls to public section. (7f214f2)

Nick Tustison (3):

Enhancements

AnalyzeObjectLabelMap:

Mathew Seng (5):

Enhancements

  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (f52174d)

Platform Fixes

  • Update ITK Python Package to 5.1.0.post2 in setup.py (dcc1639)

Bug Fixes

  • Allow module to find older versions of ITK Removing 5.1 allows the module to locate older versions of ITK (i.e. 5.0) that can be compatible with the module (c581299)

Style Changes

  • Fixes clang errors caused by clang-format-linter.yml (99fba4c)
  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (7a0cd1a)

AnisotropicDiffusionLBR:

Hans Johnson (1):

Platform Fixes

  • Update to new ITK_DISALLOW_COPY_AND_MOVE macro (b5724f9)

Mathew Seng (9):

Enhancements

  • Update ITK package to version 5.1rc03 (5f4c4e1)
  • Remove old ci testing to fit ITKModuleTemplate (1eff30f)
  • Remove Azure pipeline testing and update README.rst (5854833)
  • Update python package version from 5.1.0 to 5.1.0.post2 This required changing the ITK Python Package to 5.1.0.post2 in setup.py. Because we are updating the package, we must incremement the itk-anisotropicdiffusionlbr version from 1.1.1 to 1.1.2. (7a9ad68)
  • Bump ITK version to 5.1.1 and ITK python version to 5.1.1.post1 This will bump the ITK version in the GitHub Actions build and setup.py. In addition, the package version has been updated from 1.1.2 to 1.1.3 in setup.py. (57a0041)
  • Update supported Python versions for package builds The minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. (ba2790e)
  • Update python package version for modules This will bump the package version in setup.py from 1.1.6 to 1.2.0 (beff186)

Bug Fixes

  • Fix failing examples test I have included a Data subdirectory in AnisotropicDiffusionLBR/examples/Data and upload the raw png file used for the example’s test. In addition, the image was not being properly read, so I required the ITKIOImageBase module be imported for proper reading. (649ceb2)
  • ITK runtime directory in PATH for Windows not specified (c371130)

Matt McCormick (8):

Enhancements

  • Add Clang-format GitHub Actions (cbb320c)
  • Add Build, test, package GitHub Action (919fead)
  • Update Python package version to 1.1.0 (5ccd97b)
  • Update Python package version to 1.1.1 (3ae027a)

Documentation Updates

  • Add Build, test package GitHub Action badge (f9eae6d)
  • Remove old CI badges (62ec87a)

Bug Fixes

  • Download packages for PyPI upload on Linux (b5d8105)
  • Add CI builds for pull requests (4a2b68f)

BSplineGradient:

Mathew Seng (11):

Enhancements

  • Delete old ci testing for new GitHub Actions Removing existing ci-testing that has already been depracated. This includes AppVeyor, Travis and CircleCI testing. (96d99b5)
  • Update ITK python package to 5.1.0.post2 in setup.py (355e64f)
  • Configure new GitHub Actions ci testing Using the GitHub’s Action testing, we can allow users to generate their own ci testing through GitHub. This can be done without the use of an admin. These changes are based off the ITKModuleTemplate’s GitHub Actions. (256a654)
  • Remove Azure Pipeline testing for new GitHub Actions (0eb86ec)
  • Bump ITK version to 5.1.1 and ITK python version to 5.1.1.post1 This will bump the ITK version in the GitHub Actions build and setup.py. In addition, the package version has been updated from 0.2.0 to 0.2.1 in setup.py (5cc2176)
  • Update supported Python versions for package builds The minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. (eff9bf7)
  • Update package version from 0.2.1 to 0.2.2 (3298978)

Bug Fixes

  • Fix compiler warning for ITKv5.1 and clang 11. When compiled against ITKv5.1 and clang 11, an overloaded virtual function warning is thrown. By being more explicit and declaring (d1284ef)
  • ITK runtime directory in PATH for Windows not specified (b493bd8)
  • Incorrect CI referenced in README.rst This references azurepipelines when it should GitHub Actions (1b12a23)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (d4bf474)

Matt McCormick (1):

Enhancements

  • Bump Python package version to 0.2.1 (024bfed)

BioCell:

Mathew Seng (7):

Enhancements

  • Update setup.py’s ITK Python Package to v5.1.0.post2 (94e7a96)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. Also, the README was updated. (bafb684)
  • Remove CircleCI for new GitHub Actions (a8daee3)
  • Bump ITK version to 5.1.1 in GitHub Actions (345746e)

Bug Fixes

  • Fix failing tests for examples Replaced ITKIONRRD with ITKIOPNG and ITKIOMeta, because the examples were trying to build the png and mha images as nrrd, thus throwing an error. (a913422)
  • ITK runtime directory in PATH for Windows not specified (7869027)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (804d397)

BoneEnhancement:

Mathew Seng (7):

Enhancements

  • Incorporate clang-format-linter.yml from ITKModuleTemplate This workflow will verify the proposed changes adhere to the clang style (d33bded)
  • Bump ITK version to 5.1.1 and ITK Python package version to 5.1.1.post1 (3deab7c)
  • Update supported Python versions for package builds This minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. In order to enable this, the ITK version has been bumped to 5.1.1 in setup.py (0f83f36)
  • Update python package version for modules This will bump the package version in setup.py from 0.3.1 to 0.4.0 (e0f0644)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (f662d80)

Style Changes

  • Adjust to clang format This fixes clang errors thrown from running the newly integrated clang-format-linter.yml (e1b4449)
  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (c218246)

Matt McCormick (9):

Enhancements

  • Add GitHub Actions configuration (bb013c5)

Documentation Updates

  • Add missing Doxygen \ingroup BoneEnhancement (9ee81bc)
  • Add Python package installation instructions (e0c078f)
  • Add Python package description (0ca9446)

Platform Fixes

  • Update GTest TYPED_TEST_CASE to TYPED_TEST_SUITE (686045e)
  • Update EigenValueOrder enum using declaration (3978d94)

Bug Fixes

  • Remove ald Azure Pipelines configuration (c7bf485)
  • Double parallelism in EigenToMeasureImageFilter (568b16f)
  • Retain previous EigenToMeasureImageFilter (be145aa)

BoneMorphometry:

Mathew Seng (1):

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (39b2718)

Matt McCormick (4):

Enhancements

  • Add GitHub Actions configuration (f38526d)
  • Bump Python package version to 1.2.0 (202c3c7)

Documentation Updates

  • Replace Azure Pipelines with GitHub Action badge (67df662)

Bug Fixes

  • Remove old CI configuration files (72c8bb3)

Cuberille:

Davis Marc Vigneault (1):

Bug Fixes

  • Fix Incorrect Indexing in Case 231 (0c4f3f8)

Davis Vigneault (5):

Enhancements

  • Improve Code Coverage (483aeec)
  • Add Clang Format Linter to Github Actions (5f3b5c9)

Platform Fixes

  • Address Wmissing-braces Warnings (60783ab)

Bug Fixes

  • Fix URL in License File (f485520)
  • Handle Non-Manifold Geometry (5cdccb1)

Mathew Seng (6):

Enhancements

  • Remove Azure pipeline testing and update README (978cdbd)
  • Bump ITK version to 5.1.1 and ITK Python version to 5.1.1.post1 This will bump the versions in the GitHub Actions build-test-package.yml (d731745)
  • Update supported Python versions for package builds This minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. In order to enable this, the ITK version has been bumped to 5.1.1 in setup.py (38782ec)
  • Update python package version for modules This will bump the package version in setup.py from 2.3.0 to 2.4.0 (35f5197)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (5f7a83f)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (bc07c58)

Matt McCormick (5):

Enhancements

  • Bump itk version to 5.1.0 (8130b57)
  • Add Build, test package GitHub Action (cf8b9ce)
  • Add Build, test, package GitHub Action configuration (45b1ec4)
  • Build against itk 5.1.0.post2 (e06622c)

Bug Fixes

  • CI configuration updates (bb3ac00)

FixedPointInverseDisplacementField:

Mathew Seng (3):

Enhancements

  • Update ITK Python Package version to v5.1.1 (9055b25)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (92fb91c)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (f11d994)

Matt McCormick (2):

Documentation Updates

  • Remove old badges (47d6472)
  • Fix Python package installation formatting (bf939af)

GenericLabelInterpolator:

Davis Vigneault (3):

Enhancements

  • Add GitHub Actions Configuration (9d803a2)

Platform Fixes

Bug Fixes

  • Remove Old CI Service Configurations (08d48c6)

Mathew Seng (5):

Enhancements

  • Bump ITK version to 5.1.1 and ITK Python version to 5.1.1.post1 This will bump the versions in the GitHub Actions build-test-package.yml (4f59ea2)
  • Update supported Python versions for package builds This minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. In order to enable this, the ITK version has been bumped to 5.1.1 in setup.py (7592ace)
  • Update python package version for modules This will bump the package version in setup.py from 1.0.0 to 1.1.0 (0567c80)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (f7cac06)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (9304d52)

Matt McCormick (1):

Enhancements

  • Update CI build for ITK v5.1.0.post3 (62f5534)

HigherOrderAccurateGradient:

Mathew Seng (8):

Enhancements

  • Update ITK Python Package version to v5.1.0.post2 in setup.py (996adbf)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (f3530a4)
  • Bump ITK version to 5.1.1 and ITK Python version to 5.1.1.post1 (1bdce83)
  • Update supported Python versions for package builds The minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. (169ae94)
  • Update python package version for modules This will bump the package version in setup.py from 1.0.6 to 1.0.7 (61bb1c5)

Platform Fixes

  • Add missing ‘;’ at end of macro A ‘;’ is required at the end of macros in a future version of ITK (d093c10)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (48502a1)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (fee20ca)

Matt McCormick (2):

Enhancements

  • Remove CircleCI, AppVeyor, TravisCI configurations (5287682)

Documentation Updates

  • Remove Azure Pipelines badge (129e280)

IOFDF:

Mathew Seng (3):

Enhancements

  • Update ITK Python Package to 5.1.1 in setup.py (cf03ecd)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (2832bdd)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (1f5c55e)

Matt McCormick (1):

Documentation Updates

IOMeshSTL:

Davis Vigneault (2):

Enhancements

  • Add Clang Format Linter to Github Actions (348276e)

Bug Fixes

  • Fix 404 in License File URL (656cc3b)

Mathew Seng (5):

Enhancements

  • Bump ITK version to 5.1.1 and ITK Python version to 5.1.1.post1 This will bump the ITK version to 5.1.1 and the ITK Python version to 5.1.1.post1 (8a7b04f)
  • Update supported Python versions for package builds This minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. In order to enable this, the ITK version has been bumped to 5.1.1 in setup.py. (f42c7a0)
  • Update python package version for modules This will bump the package version in setup.py from 2.1.0 to 2.2.0 (bdee146)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (7a912fa)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (97fb257)

Matt McCormick (3):

Enhancements

  • Add Build, test, package GitHub Actions (e4d7235)
  • Bump Python package version to 2.1.0 (8ee8e72)

Bug Fixes

  • Remove old TravisCI, CircleCI, Appveyor configurations (a024fa9)

IOOpenSlide:

Mathew Seng (2):

Bug Fixes

  • Incorrect Enum reference After the addition of the strongly typed enumerations, the path for many of them changes. This defines the new enumeration IOFileModeEnum (fb65455)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (1c40759)

IOScanco:

Mathew Seng (9):

Enhancements

  • Bump ITK Python version to v5.1.0.post2 (7f2077b)
  • Bump ITK version to 5.1.1 and ITK Python version to 5.1.1.post1 (1aad4a4)
  • Update supported Python versions for package builds This minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. In order to enable this, the ITK version has been bumped to 5.1.1 in setup.py (79bb4eb)
  • Include clang-format.yml from the ITKModuleTemplate (8ec410e)
  • Update python package version for modules This will bump the package version in setup.py from 0.6.1 to 0.7.0 (f9d9ad5)

Platform Fixes

  • Add missing ‘;’ at end of macro A ‘;’ is required at the end of macros in a future version of ITK. (3835e20)

Bug Fixes

  • Remove azure-pipelines.yml for new GitHub Actions (0ac2c38)
  • ITK runtime directory in PATH for Windows not specified (35b4501)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (be7410f)

Matt McCormick (7):

Enhancements

  • Add Build, test, package, GitHub Actions (7a6794e)
  • Expose CreationDate and ModificationDate in the API (96aed93)
  • Update Python package version to 0.5.0 (835370c)
  • Bump Python package version to 0.6.0 (5ca9656)
  • Bump package version to 0.6.1 (c452b8c)

Documentation Updates

  • Remove Azure badge, fix GitHub Actions badge (e438297)

Platform Fixes

  • Update GitHub Actions for v5.1.2, macOS 10.15 image updates (7e8b089)

Michael Kuczynski (1):

Bug Fixes

  • Fix ReadAIMHeader to work with short images (#36) (67b64cc)

IOTransformDCMTK:

Mathew Seng (1):

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (dc3d569)

IsotropicWavelets:

Mathew Seng (5):

Enhancements

  • Bump ITK Python Package to 5.1.1 in setup.py (2e2b737)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. Also, the README was updated. (47650d6)

Platform Fixes

  • Add missing ‘;’ at end of macro A ‘;’ is required at the end of macros in a future version of ITK. (26bac2f)
  • Rename old macro definitions This will place an ITK_ infront of all the ITK testing macros used in this module. (086541b)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (06f3448)

LabelErodeDilate:

Mathew Seng (8):

Enhancements

  • Update ITK Python Package to 5.1.1 in setup.py (398719c)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (3d4b8b0)
  • Bump ITK version to 5.1.2 This will bump all versions of ITK in setup.py and the GitHub Actions to 5.1.2 (96c94fe)

Bug Fixes

  • Change dim to Dim to support KWStyle test (9926299)
  • Fix test errors resulting from incorrect multi-threading format. The filters were originlly setup to utilize the new Multi-threader format. However, these filters utilize a custom region splitter that requires the classic multi-threader. The changes required changing (1779487)
  • Remove deprecated CI As the GitHub Actions have been integrated, there is no need for the previous CI for this module. This specifically removes CircleCI, Appveyor and Travis CI. (f396898)

Style Changes

  • Adjust several scripts to adhere to clang format (ef01cad)
  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (eafe0c5)

Matt McCormick (1):

Documentation Updates

LesionSizingToolkit:

Mathew Seng (4):

Bug Fixes

  • Incorrect classe references for EXERCISE_BASIC_OBJECT_METHODS. (bfc4cc3)
  • Incorrect comparison of Float values. Originally, FloatAlmostEqual was comparing our percent error with .1% to check if the estimation was within that range. However, we actually want to compare the percent error and 0.0%. Using the absolute value of their difference, we can check if they are within the allowedVolumePercentageError. (ef6db4e)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (b88c50e)
  • Rename old macro definitions This will place an ITK_ infront of all the ITK testing macros allowing them to be up-to date with the current defintions in ITK master." (c4f607b)

MGHIO:

Mathew Seng (7):

Enhancements

  • Configure new Github Actions ci testing Using the GitHub’s Action testing, we can allow users to generate their own ci testing through GitHub. This can be done without the use of an admin. These changes are based off the ITKModuleTemplate’s GitHub Actions. (992be3f)
  • Implement CTestConfig.cmake to publish ctest results to cdash (b05cbf2)
  • Bump ITK version to 5.1.1 and ITK Python version to 5.1.1.post1 These versions are bumped in the GitHub Actions build-test-package.yml (277fa58)
  • Update supported Python versions for package builds This minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. In order to enable this, the ITK version has been bumped to 5.1.1 in setup.py (cffff89)
  • Update python package version for modules This will bump the package version in setup.py from 1.0.0 to 1.1.0. In addition, this commit must be tagged and pushed to GitHub. (fbdf13b)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (de5a211)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (49956e9)

Matt McCormick (3):

Enhancements

Documentation Updates

  • Add GitHub Actions, PyPI badges (18c8709)

Bug Fixes

  • Correct GitHub Actions Python CI configuration (3ef19fa)

MeshNoise:

Davis Marc Vigneault (3):

Enhancements

  • Add GitHub Actions Configuration (b87dac3)

Bug Fixes

  • Remove old CI service configurations (3907936)

Style Changes

Davis Vigneault (1):

Platform Fixes

Jon Haitz Legarreta Gorroño (1):

Style Changes

  • Add ITK prefix to testing macros (541aa10)

Mathew Seng (5):

Enhancements

  • Bump ITK version to 5.1.1 and ITK Python Package version to 5.1.1.post1 (3311a84)
  • Update supported Python versions for package builds This minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. In order to enable this, the ITK version has been bumped to 5.1.1 in setup.py (80d6b80)
  • Update python package version for modules This will bump the package version in setup.py from 0.0.1 to 0.1.0 (bdc5dac)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (0eb6f99)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (1d2a3c6)

MinimalPathExtraction:

Mathew Seng (2):

Bug Fixes

  • Remove old CI for new GitHub Actions GitHub Actions has already been added, thus travis, circleci, appveyor, and azurepipelines ci testing must be deprecated. Also, README.rst had it’s azurepipelines badge removed. (ea89894)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (fad8f17)

Matt McCormick (8):

Enhancements

  • Azure Pipelines build against ITK v5.1rc03 (f59d5a5)
  • Bump Python package version to 1.1rc1 (204d276)
  • Update to most recent ITKModuleTemplate Azure Pipelines config (4d1eeee)
  • Add Python Packages GitHub Action (20d44a7)
  • Bump builds and Python package to use ITK 5.1.0 (8286c7f)
  • Add Build, test, package GitHub Actions (6f47210)

Bug Fixes

  • Remove old Python packages GitHub Action configuration (72a89da)
  • Build against itk 5.1.0.post2 (68683be)

Montage:

Dženan Zukić (25):

Enhancements

  • rename EnableFailingTests option for better grouping (9b2557e)
  • adding public release numbers for MNML datasets (fdeae44)
  • adding blending explanation montage from paper (6efd6b8)
  • add ostream operator for printing padding method enumeration (9af0805)
  • updating reference montages using Fiji 1.52p (931bad2)
  • adding more ground truth test cases (40177e0)
  • less strict ground truth testing (23cf88a)
  • use a different split into tiles to avoid a single pair’s failure (b986471)
  • tile configuration comparison tool can save results to a .tsv file (fbb69c8)
  • write ground truth to a different file (e776118)
  • run ground truth tests with just the default set of parameters (14defcf)
  • reduce number of tiles in 3D ground truth test (b1e41dd)
  • add a concept check to make sure we are not instantiated with bool (87499d7)
  • updating CI configuration based on current ModuleTemplate (019c1bd)
  • build examples as part of CI testing (8b62c9e)

Documentation Updates

  • number of steps clarified (5a29130)

Platform Fixes

  • change ordinary setter into enum setter (46c409f)
  • apply recent refactoring to examples (b7c1626)
  • use built-in ReadImage and WriteImage convenience functions (bb9055a)

Bug Fixes

  • iteration over peak methods was not working properly (a488145)
  • requesting to try all peak methods works around the issue (0b4fbca)

Style Changes

  • remove debugging output (67b8459)
  • improve console output for padding method (bb898e4)

Miscellaneous Changes

  • trying to force enum values to be sequential in Release mode (bad9687)
  • using master branch until v5.2.0 is released (652d0fb)

Hans Johnson (2):

Style Changes

  • Force semi-colon at end of macros (846f00f)
  • 2nd attempt to force semi-colon at end of macros (b8d4942)

Jon Haitz Legarreta Gorroño (1):

Platform Fixes

  • Fix variable shadowing and unused variable warnings (70c206a)

Mathew Seng (7):

Enhancements

  • Bump ITK version to 5.1.1 and ITK Python version to 5.1.1.post1 (5793b4b)
  • Update supported Python versions for package builds The minimum version has been bumped from 3.5 to 3.6. The maximum has been bumped from 3.8 to 3.9. Lastly, itk-core, itk-filtering, and itk-io versions in setup.py have been bumped to 5.1.1. (bbb08da)
  • Update python package version for modules This will bump the package version in setup.py from 0.6.0 to 0.7.0 (74e6f69)

Bug Fixes

  • Remove already deprecated appveyor ci This module has appveyor testing disabled, but the script appveyor.yml has not been removed. (eca1207)
  • ITK runtime directory in PATH for Windows not specified (ac9fce4)

Style Changes

  • Fix clang format (8f05ef2)
  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (d8a8921)

Matt McCormick (31):

Enhancements

  • Add GitHub Actions Build, Test, Package action (f699c76)
  • Bump Azure Pipelines ITK version to v5.1.0 (d757297)
  • Update CI for v5.1.0.post3 (843e2af)
  • Factor output SamplePeakCorrelationOptimizer (e988f0c)
  • Use correlation image for peak interpolation (ee382f6)
  • PhaseFrequencyCorrelationOptimizer initial addition (cef7549)
  • Move PeakInterpolationMethodEnum to PhaseCorrelationOptimizer (64b0287)
  • Add PhaseCorrelationOptimizer (9013900)
  • Iterate all supported interpolation methods in PairwiseTestHelper (105d439)
  • Add PeakInterpolationMethod (bc4b141)
  • PhaseCorrelationOptimizer class consolidation (5056c32)
  • Bump Python package version to 0.6.0 (4db6143)
  • Improve test output formatting (a0e07a7)

Performance Improvements

  • Avoid AdjustedImage memory reallocation (fc75c5e)

Documentation Updates

  • Update copyright assignment to NumFOCUS (ed355f3)
  • Correct badge URLs (a1d7d0f)

Platform Fixes

  • GetSamplePeakOptimizer -> GetModifiableSamplePeakOptimizer (14d20a9)
  • constexpr std (b9d65ad)

Bug Fixes

  • Remove Azure Pipelines configuration (764d352)
  • Update Python package dependency versions (f7c42fe)
  • Remove patched igenerator.py (e3e2b69)
  • Add numpy Python package dependency (29c3e37)
  • itkMontageTestHelper peak interpolation method selection (3dc1b39)
  • Remove AppVeyor configuration (741130e)
  • Update wrapping of itkPhaseCorrelationOptimizer (805e2ce)

Style Changes

  • Remove trailing whitespace in test/CMakeLists.txt (374afbc)
  • Using static constexpr for ImageDimension (7f9d94e)
  • PeakInterpolationMethod -> PeakInterpolationMethodEnum (d89a4f3)
  • PaddingMethod -> PaddingMethodEnum (bdd01bf)
  • Run clang-format (d30b5e5)
  • Run clang-format (21f7113)

MorphologicalContourInterpolation:

Dženan Zukić (1):

Enhancements

  • enable remote module RLEImage in ITK’s build (63aa88d)

Mathew Seng (1):

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (3e4f655)

Matt McCormick (2):

Enhancements

  • Add GitHub Actions CI configuration (0e0d8f9)

Bug Fixes

  • Remove old CI configurations (a83850a)

MultipleImageIterator:

Mathew Seng (6):

Enhancements

  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. Also, the README was updated. (e771184)
  • Configure CTestConfig.cmake to allow cdash submission of ctest results (20ff486)
  • Include LICENSE incorporated from ITKModuleTemplate (8a2595b)
  • Bump ITK version to 5.1.1 This bumps the ITK version to v5.1.1 from v5.1.0. (f37a531)

Documentation Updates

  • Create README.rst for the module (d363669)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (e0c195e)

ParabolicMorphology:

Mathew Seng (3):

Bug Fixes

  • Fix test errors resulting from incorrect multi-threading format. The filters were originlly setup to utilize the new Multi-threader format. However, these filters utilize a custom region splitter that requires the classic multi-threader. The changes required changing (78b3384)
  • Fix failing KWStyle check. Changed parameter doOpen to DoOpen to fit template (71afc97)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (e9a9c49)

Matt McCormick (8):

Enhancements

  • Remove old CI configurations (a4c9fd7)
  • Add GitHub Actions Build, Test, Package configuration (83cfec9)
  • Add wrapping for MorphologicalSharpeningImageFilter (984a679)

Documentation Updates

  • Add Python package installation instructions (ab37877)
  • Add an example Jupyter notebook on cthead1 image (f785e21)

Platform Fixes

  • Remove deprecated dynamic exception specification (fd619fb)
  • Replace ITK_EXPORT with ITK_TEMPLATE_EXPORT (d3c11aa)

Bug Fixes

  • Update Python package builds for itk 5.1.0.post2 (0d38c60)

Richard Beare (1):

Platform Fixes

  • Include version tags in python setup.py (5552148)

PerformanceBenchmarking:

Hans Johnson (1):

Enhancements

  • Update jsonxx package to remove compiler warnings (95698a3)

Mathew Seng (6):

Enhancements

  • Configure new GitHub Actions ci testing These changes required implementing GitHub Actions copied from the ITKModuleTemplate. In addition, this required updating the README.rst (f9e2feb)
  • Remove azure-pipelines.yml and update README for new GitHub Actions (455b36e)
  • Bump ITK version to 5.1.1 This bumps the ITK version in GitHub Actions from 5.1.0 to 5.1.1 (26c9c9f)

Bug Fixes

  • C++11 deprecation warning fix by changing to new std (ac6baa2)
  • ITK runtime directory in PATH for Windows not specified (39b4c0c)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (c56106e)

PhaseSymmetry:

Mathew Seng (3):

Enhancements

  • Bump ITK Python Package to 5.1.1 in setup.py (a732a86)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (6e28a8a)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (e156479)

Matt McCormick (2):

Enhancements

  • Bump Python package version to 1.0.4 (df6240d)

Documentation Updates

PolarTransform:

Mathew Seng (5):

Enhancements

  • Bump itk-core to 5.1.1 in setup.py (0f27262)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (afde9bb)
  • Bump ITK version to 5.1.2 This will bump all versions of ITK in setup.py and the GitHub Actions to 5.1.2 (d66d676)

Bug Fixes

  • Remove deprecated CI As the GitHub Actions have been integrated, there is no need for the previous CI for this module. This specifically removes CircleCI, Appveyor, Azure, and Travis CI. (f2fa772)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (0f9fa99)

Matt McCormick (2):

Enhancements

  • Bump Python package to 1.1.2 (061ff94)

Documentation Updates

PrincipalComponentsAnalysis:

Mathew Seng (4):

Enhancements

  • Bump ITK Python Package version to 5.1.1 in setup.py (8f2c71c)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (8b42ce6)

Style Changes

  • Adjust several scripts to adhere to clang format (550af55)
  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (ae01070)

Matt McCormick (1):

Documentation Updates

  • Remove old CI badges, Python package installation (f19cbd4)

RLEImage:

Mathew Seng (2):

Bug Fixes

  • Fix ‘test not run’ error thrown when built as ITK remote. When ITK builds ITKRLEImage as an interal remote module, and BUILD_SHARED_LIBS = OFF, a ‘test not run’ error is thrown. Changing the names of tests and adding them to the TestDriver allows them to run with BUILD_SHARED_LIB = OFF and not throw any sort of error. (c8941e6)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (66ef01f)

RTK:

Antoine Robert (5):

Enhancements

  • Compute the backprojection of ones only once in OSEM (68e11211)
  • Improve center of volume computation (2cca14c1)

Bug Fixes

  • Fix attenuation correction in zengBackProjectionImageFilter (887ebab8)
  • Take into account the direction of the projections (07c14734)

Miscellaneous Changes

  • Rename InputSpaceDimension to InputImageDimension (c40cd024)

Aurélien Coussat (2):

Enhancements

  • progress reporting for ramp filter (bf59d23b)
  • one-line iteration reporting (e09780d4)

Julien Finet (7):

Enhancements

  • Configure out pixel value in FieldOfViewImageFilter (b8f28d39)

Documentation Updates

Platform Fixes

  • Support multiple find_package(Gengetopt) (fcd012aa)
  • Fix CMake module include typo (f3c15f2e)
  • Declare lpsolve55 as an IMPORTED library in ITKTargets.cmake (214b1375)
  • Prevent RTK from overwriting CMAKE_MODULE_PATH (1ce1a4f5)
  • Support if(… IN_LIST…) with CMake old projects (c8aca0e8)

Lucas Gandel (4):

Enhancements

  • Update pre-commit hook to force run style checks (60223ad6)
  • Include PyBuffer.i at a submodule level (5aef6eeb)
  • Use ITK PyBuffer swig files (e81224f0)

Platform Fixes

  • Fix Multiple KWStyle and ClangFormat downloads (13045f18)

MrTzschr (1):

Documentation Updates

  • Fixed typo in rtkDaubechiesWaveletsConvolutionImageFilter (d0262808)

Sebastien Brousmiche (1):

Bug Fixes

  • Fixed detector offset initialization (40822608)

Simon Rit (36):

Enhancements

  • update Azure pipeline images (5b35c46e)
  • upgrade ITK minimal version to v5.1 (28d2d7e8)
  • add Azure package for linux and Python 3.8 (29e79c02)
  • wrap rtk (78d7b39b)
  • add Build-Test-Package github action (0524d9c2)
  • upgrade CI for python packages to 5.1.2 (2ffafe0e)

Documentation Updates

  • fix homepage badge for workflow Build, Test, Package (9641ad9b)

Platform Fixes

  • add missing verbose flag for RTK_PROBE_EACH_FILTER (96212492)
  • add missing include of itkProgressReporter.h (170ac8ac)
  • split Windows python package per python version on Azure (86f25837)
  • remove wrapping of Cuda double images, incompatible with Cuda code (0babff4d)
  • keep only Azure for the CI, remove CircleCI and TravisCI (ef18f74b)
  • fix warnings triggered by unused variables (f046c337)
  • fix one more warning triggered by unused variable (96c49e75)
  • only keep compute capabilities 3.0 for Cuda 9 and 10 (4fc1222e)
  • add missing include (33a4b199)
  • disable loading of external libraries (51973d42)
  • Use CMake 3.18.3 (91dc70e0)
  • Install specific XCode version for Python packages (f54bf5ad)
  • missing definition of ITK_LIBRARY_BUILD_TYPE for external build (ddced642)

Bug Fixes

  • correct itkTypeMacro parameters where needed (1c204a4d)
  • process projections one by one in convolution instead of doing 3D FFT (a719d891)
  • pre-commit and bash scripts must be executable (37f40637)
  • projection filtering should also be allowed for 4D and 5D images (84d20145)
  • fix iteration reporting for 4D conjugate gradient (5292bde7)
  • fix backprojection computation of requested region in projections (840b18a3)
  • fix projections convolution for 4D projections (fcb53079)
  • inconsistencies between CPU and GPU in Parker weighting (b5c41fb7)
  • fix rtk (a82c1343)
  • add ITK runtime path to Windows CI for RTK tests (23dd65af)
  • progress event attached to wrong ramp filter with cuda (6be65bc4)

Style Changes

  • remove backward compatibility with ITK v5.0.1 (1e2bccbd)
  • fix KWStyle issues (ba811801)
  • Call ITK_DISALLOW_COPY_AND_MOVE, not ITK_DISALLOW_COPY_AND_ASSIGN (8ac7f0b2)
  • keep only github-actions CI (f6c22c24)
  • Macros should respect an end-of line ; (772bf18b)

SCIFIO:

Mathew Seng (5):

Enhancements

  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. Also, the README was updated. (52a19d0)
  • Bump ITK version from 5.1.0 to 5.1.1. (22d3cd6)
  • Disable azure-pipelines.yml for new GitHub Actions This also updates the README.md (250dbde)

Bug Fixes

  • ITK runtime directory in PATH for Windows not specified (b2194bf)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (2c35556)

SimpleITKFilters:

Bradley Lowekamp (12):

Enhancements

  • CI build against ITK 5.1.0 (043d96d)
  • Add NPasteImageFilter (37ce190)

Documentation Updates

  • tweak NPaste documentation (4415840)

Platform Fixes

  • fix compilation error with SetDesiredCoordinateOrientation (e383bad)

Bug Fixes

  • Safely return INVALID in GetAsString (c0cc6e4)

Miscellaneous Changes

Hans Johnson (2):

Enhancements

  • Adding missing macro end of line semi-colon (49bb41d)

Style Changes

  • Match clang-format style for ITK (7dadf89)

Mathew Seng (3):

Enhancements

  • Update ITK Python Package to 5.1.0.post2 in setup.py (e3dbeea)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (6a17aa5)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (7f969cb)

Matt McCormick (1):

Bug Fixes

  • Remove old Azure Pipelines configuration (a7a7f66)

SkullStrip:

Mathew Seng (6):

Enhancements

  • Bump ITK Python Package to 5.1.1 in setup.py (033d3bf)
  • Incorporate GitHub Actions from ITKModuleTemplate This requires the incorporation of 2 yml scripts that will test the module under various configurations for Windows, Linux and MacOS. These scripts were copied from the ITKModuleTemplate. (e222631)
  • Bump ITK version to 5.1.2 This will bump all versions of ITK in setup.py and the GitHub Actions to 5.1.2 (d934bb9)

Platform Fixes

  • Rename ITK macros to up-to-date name conventions This includes changing TRY_EXPECT_NO_EXCEPTION to ITK_TRY_EXPECT_NO_EXCEPTION. Also it changes EXERCISE_BASIC_OBJECT_METHODS to ITK_EXERCISE_BASIC_OBJECT_METHODS. (9f7c907)

Bug Fixes

  • Remove deprecated CI As the GitHub Actions have been integrated, there is no need for the previous CI for this module. This specifically removes CircleCI, Appveyor and Travis CI. (632ded2)

Style Changes

  • Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE Fixes changes made in #2053. ITK_DISALLOW_COPY_AND_ASSIGN will be used if ITK_FUTURE_LEGACY_REMOVE=OFF. (f879274)

Matt McCormick (1):

Documentation Updates

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