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Editor module - Change Label #1788
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jamesobutler
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Mar 13, 2021
…ools Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com> Slicer updates were made based on changes introduced in InsightSoftwareConsortium/ITK@076e990 ===================================================================== ITK: $ git shortlog --topo-order --no-merges v5.1.2..2b34388 Alex Domingo (1): BUG: fix python module definition in VtkGlue wrap Alexander Burchardt (1): DOC: fixes itkSoftwareGuide Slicer#146 Andreas Huber (1): BUG: Fix number encoding to use C locale (Slicer#2297) Antoine Robert (1): ENH: Use Numpy bridge with array of dimension 1 Atri Bhattacharya (2): Explicit libm linking for NrrdIO and libLBFGS. BUG: Use explicit libm linking only on UNIX. Baptiste Depalle (1): ENH: improve wrapping architecture Bernhard M. Wiedemann (1): BUG: Fix issue Slicer#1939: Use -mtune=generic Brad King (3): STYLE: Allow specific HDF5 sources to be larger than normal limit ENH: Update to newer third-party update script from CMake ENH: Convert VNL import script to use update-third-party.bash Brad T. Moore (3): BUG: WatershedImageFilter would crash with assert. BUG: Fix to ITKSetPython3Vars ignoring Python virtual environments (Slicer#2068). BUG: Add '_d' POSTFIX to Windows Python Debug (Slicer#2050) Bradley Lowekamp (34): ENH: Use named pipeline inputs for morphological reconstruction COMP: Add missing const qualifier BUG: Add StatisticsImageFilter::SetNumberOfStreamDivisions Python STYLE: remove extraneous semi-colon after bracket ENH: Add FunctionCommand with lambda support ENH: Add direct support for lambda command to Object class DOC: Update Object::AddObserver documentation COMP: Fix ~FunctionCommand implicit override warning COMP: Address no override keyword warning STYLE: Use defaulted constructor for event object macro BUG: Remove no output warning in ImageSink filters ENH: Bump SimpleITKFilters remote module ENH: PasteImageFilter input ND and constant value COMP: Update SimpleITKFilters remote module ENH: Add TernaryGeneratorImageFilter ENH: Change TernaryFunctor usage to TernaryGenerator ENH: Add GTest cases for TernaryGeneratorImageFilter DOC: Grammar fixes ENH: Update ternary filter wrapping for generator base class COMP: add missing parentheses COMP: Address unused other parameter in defaulted methods ENH: Moderinize ShiftScaleImageFilter ENH: remove redundant WriteImage overloads COMP: Address brace initializer warning BUG: Make OutputWindow instance a global singleton STYLE: Prefer function of direct access of output instance. ENH: Update ternary filter wrapping for generator base class BUG: Fix JPEG200Test6 file output clobbering ENH: Create ITK_DEFAULT_THREADER definition ENH: Add ITK_DEFAULT_THREADER as CMake configuration variable. COMP: Address gcc 4.8 compilation errors PERF: Replace thread index array with thread local storage BUG: Use graft of input to mini-pipeline ENH: Use dynamic threading model Bryn Lloyd (1): COMP: Fix warning in PointSetToPointSetMetricv4 (Slicer#1820) Charles Garraud (1): BUG: Fix BUILD_SHARED_LIBS state consistency for HDF5 Christina Rossmanith (5): STYLE: Remove blank before ::MemberName STYLE: Edited comments STYLE: New methods for translating Nifti datatypes to IOxxxxEnum BUG: read data arrays with intent NIFTI_INTENT_NONE for point or cell data STYLE: RGB comment Darren Thompson (1): ENH: Added itkPointSetToImageFilter.wrap David Thompson (1): ENH: Let gitlab-ci runners build with clang-tidy. Davis Vigneault (10): STYLE: Prefer Early Return ENH: Add Python Wrappers for Mesh Source Classes ENH: Review Cuberille Remote Module Compliance ENH: Assert in Debug Mode COMP: Address Wdeprecated-copy warnings in gcc9 STYLE: Call Superclass assignment operator ENH: Test Assignment and Copy of Spatial Objects COMP: Address Warnings in Vector and Map Container ENH: Test Map and Vector Iterators ENH: Add Missing Boolean Macros in QEFilters Dženan Zukić (34): ENH: updating remote modules to latest versions COMP: fix GPU compile errors when building as DLLs BUG: fix Statistics::Histogram::Mean calculation ENH: update remote modules DOC: restore LICENSE accidentally overwritten by a merge commit STYLE: rename libPNG's license to match the original one STYLE: remove duplicate item in a list ENH: progress reporting does not stall with PoolMultiThreader COMP: variable is uninitialized when passed as a const reference ENH: append properties instead of overwrite in HDF5 BUG: Filter inputs are erroneously released ENH: allow dependencies on remote modules DOC: add ComputeJacobianWithRespectToPosition change to migration guide DOC: hyperlink mentioned commits ENH: remove NumPy presence conditions from tests' CMakeLists.txt COMP: fix compilation with Python and tests enabled on Visual Studio ENH: add a convenience function WriteImage ENH: update remote modules COMP: externally built remote module libs went in /lib or C:/lib ENH: Python wrapping fixes ENH: updating remote modules using the script ENH: supporting multi-channel tensors as inputs and outputs in Python ENH: use master branch of GoogleTest until a stable version is released ENH: manually update minimum CMake version to 2.8.12 to avoid warning Revert "ENH: manually update minimum CMake version to 2.8.12 to avoid warning" Revert "ENH: use master branch of GoogleTest until a stable version is released" Revert "Merge branch 'upstream-googletest' into updateGTest" COMP: fix rename error from re-basing parallel branches ENH: make shared variables local to facilitate code reuse/parallelism ENH: reduce duplication in ContourExtractor2DImageFilter STYLE: review suggestions PERF: using constant boundary condition instead of filling the edge DOC: fix AtomicInt and MutexLock broken links in migration guide ENH: update remote modules using the script Eigen Upstream (1): Eigen3 2020-12-08 (b51eab5c) GCC-XML Upstream (1): ENH: pygccxml v2.0.1 (reduced) GDCM Upstream (2): GDCM 2020-06-30 (c0824c0a) GDCM 2020-12-10 (b380cbac) GoogleTest Upstream (1): GoogleTest 2021-02-05 (f3ef7e17) Gregory Lee (1): DOC: update references for recursive Gaussian filters HDF5 Maintainers (1): HDF5 2019-12-24 (5b9cf732) Hans J. Johnson (3): ENH: Prefer to use sform over qform when both are set VNL 2020-07-07 (4a5f1059) (Slicer#1916) ENH: Exercise converting Object::Pointer to Object::ConstPointer Hans Johnson (164): BUG: Double scaling introduced in refactoring ENH: Add test to monitor metric result value COMP: Missing defition of ITK_DISALLOW_COPY_AND_ASSIGN COMP: Resolve multi-line comment warning ENH: New test data for nifti qform/sform ENH: Add nifti sform read/write testing ENH: Do not pollute the global link_directories namespace BUG: Incomplete removal of ITK_INSTALL_NO_* variables COMP: Refine order of searching for header files BUG: itkhdf5 installed paths were incorrect with recent hdf5 versions ENH: Update building internal FFTW version BUG: Centos internal lib64 lib path BUG: Fix fftw linkage issue with system fftw STYLE: Use black formatting for python COMP: Ensure consistent ordering of list printed COMP: Local variable 's' might be referenced before assignment STYLE: Prefer fstrings for python 3.6+ BUG: snake case functions are erased STYLE: Missed conversions for new macro name BUG: Writing snake_files should not be appended BUG: Decoupled config files should not depend STYLE: Use consistent formatting for python files ENH: Move cmake config items into common itkConfig.py.in file ENH: Remove alias to 'object' variable name ENH: Extend dictionary with `update` not `add` ENH: Avoid bugs with mutable default arguments ENH: Use targeted import for element of sys COMP: Ambiguous 'range' function made explicit STYLE: Fix comment spelling errors. COMP: Avoid outscope variable shadowing COMP: Selective import of required components COMP: Avoid possible variable use before assignment. COMP: Remove redundant import. ENH: import modules at top of file COMP: Remove unneccessary HAVE_NUMPY conditionals STYLE: Apply consistent pep8 compatible indentation. COMP: Avoid reassigning parameters COMP: Too broad exception narrowed. STYLE: Prefer to use @staticmethod decorator. STYLE: Initial typehints added. ENH: Avoid poluting the global namespace STYLE: Avoid difficult to read anit-pattern STYLE: Remove python2 dictionary facade COMP: PEP 8: E722 do not use bare 'except' COMP: Address protected member warning COMP: Shadows name 'input_type','keys' from outer scope DOC: Spelling warnings removed. STYLE: Fix name and spelling issues COMP: Remove python2 dictionary compatibilties. COMP: Too broad exception clause fixed COMP: Method 'Stop' may be 'static' ENH: Remove unused variable warnings. STYLE: Applied recommend code refactorings COMP: Remove potential referenced before assignment COMP: Remove shadows name from outer scope. DOC: Improve variable name spelling COMP: Instance attributes should be defined in __init__ COMP: Remove shadow variable outer scope warnings. COMP: Remove difficult to debug use of global variable COMP: Avoid poluting the module namespace COMP: Remove unused local variables. STYLE: Use python preferred lower-snake-case variable names ENH: Prevent contaminating global namespace COMP: Keep local functions out of global namespace COMP: Use lowercase python compatible function name. COMP: Match variable names from itkBase. STYLE: pytype warning disabled. ENH: disable a false positive naming error from pytype. STYLE: Address shadow variable and python style issues COMP: Unresolved reference 'sqrt' STYLE: Remove pass through return of read-only values. ENH: Code review and simplified logic STYLE: Encapsulate initialization for keeping namespace clean. COMP: Simplify exposing elements from itk namespace. ENH: Remove circular module dependancy STYLE: Prefer to extend existing template ENH: Explicitly test the itkConfig.LazyLoad=False option ENH: Allow setting default behaviors with environment COMP: Allow type inference tracking with dynamic loading. ENH: Only copy __path__ __spec__ when needed STYLE: Reduce aliased object naming STYLE: Localize imports to minimum scope. BUG: Pickling of itk module was broken STYLE: Update to python3 compatible syntax. STYLE: Update python Test with `black` formatting DOC: Make variable name clarifications and type designations STYLE: Remove unused macro. COMP: Fix test for remote python module BUG: Must append the list itkConfig.path ENH: Avoid adding invalid path to the sys.path ENH: Add error checking for required paths STYLE: Prefer explicit check to nested try/catch COMP: Enforce name.strip() redundantly COMP: Provide full path to test script file STYLE: Only set paths necessary for current build STYLE: Fix spelling error interperter -> interpreter STYLE: Make self-contained module. ENH: Update minimum required version of ITK BUG: WRAPPER_LIBRARY_OUTPUT_DIR is needed before macro call STYLE: Prefer explicit in-package pathing STYLE: Improve relative pathing computations STYLE: Prefer explicit full module specification for __spec__ ENH: Use more standard symbol lifting into itk namespace COMP: Prefer static member function modify static instance vars STYLE: Remove duplicated content that was immediately overwritten STYLE: Update python Test with `black` formatting STYLE: Simplify writing template python code files COMP: Place python shared libs as subpackage of itk COMP: Unconditionally set wrapped shared lib directory ENH: Separate static components into base class DOC: Add autodoc request in swig .i files COMP: Add initial typing for itkExtras ENH: Adding function to help generate __init__.pyi STYLE: Use consistent formatting for python files BUG: Convert code to python3 compatible STYLE: Prefer fstrings for python 3.6+ BUG: Avoid itkConfig double import trap STYLE: Minimize cmake configured python files BUG: Limit ignore to build directories only COMP: Mypy signature mismatch fixed COMP: Adding typing for ITK manually. STYLE: Add typehints for the itkTypes STYLE: Prefer fstrings for readability. COMP: Add typehinting for support classes ENH: Exclude cvar from the testing. STYLE: Update processing of *Config.py files ENH: Update documentation for generation of itkTemplates. DOC: Make swig object registry more transparent STYLE: Re-enforce black formatting contraints STYLE: Remove duplicate module dependancy entries BUG: Explicit use of builtin set BUG: Add test exposing multiprocessing LazyLoad failure BUG: LazyLoading must be threadsafe ENH: Update to SWIG 4.0.2 ENH: Add swig doxygen and autodoc=2 formats BUG: Incorrect loop dimensions in untested code BUG: Do not wrap invalid template parameters COMP: Fix hidden overloaded-virtual warning ENH: Ignore huge file warning for HDF5 paths ENH: Remove python interface introspection ENH: Simplified multi-config generator wrapping ENH: HDF5 upstream now hosted on github Version 1.10.6 ENH: More closely match the 1.10.6 release hdf5 COMP: Avoid compiler warnings with IPO BUG: CASTXML fails with aggressive optimizer flags BUG: Missing output dependency shared/H5init.c BUG: New test for 3D support BUG: ASAN identified use after delete bug STYLE: Fix clang-format styling require macro ';' end COMP: Work around ghostflow-check-master warnings COMP: Set vxl minimum to 3.0.0 STYLE: Macros should respect an end-of line ; COMP: Use of uninitialzed variable warning ENH: Script for updating DoubleConversion library. ENH: Update Double-convert third-party ENH: Update remote modules to master branch COMP: Use ITK_MACROEND_NOOP_STATEMENT for GPU macro ending. STYLE: Make prototype match definition names STYLE: Throw expression should throw anonymous temporary values instead STYLE: Remove deprecated orientation enumeration codes COMP: Preserve const qualifier for variable ENH: Provide better failure diagnostics STYLE: Use default member initialization COMP: Prefer const pointer when value does not change Horea Christian (1): ENH: improved support for offline build James Butler (1): COMP: Fix OpenJPEG build error with Visual Studio 16.9 Jan Margeta (1): ENH: Support for non-compliant DICOM in itk-js Jon Haitz Legarreta Gorroño (78): STYLE: Transition `Testing/Data` `README` to Markdown DOC: Add NumFOCUS-related contents to README ENH: Update remote modules COMP: Fix SW Guide examples LaTeX block line start warnings ENH: Update `Montage` remote module COMP: Fix SW Guide examples multi-line comment warnings ENH: Improve `itk::ThresholdImageFilter` class coverage STYLE: Fix typo in `itkBinaryThresholdImageFilterTest` STYLE: Fix ivar print value in `itk::PolygonSpatialObject` ENH: Improve the `itk::VideoFileWriter` class coverage. COMP: Remove unnecessary inherited member re-definitions ENH: Improve `itk::DCMTKSeriesFileNames` class coverage ENH: Add `itk::GrayscaleGrindPeakImageFilter` class test STYLE: Avoid `try`/`catch` boilerplate code in updating writer DOC: Fix typos in DTI 3D reconstruction image filter example ENH: Add boolean macros to `SpatialObjects` module boolean ivars DOC: Fix typos in DTI module's anisotropy image filter classes ENH: Add the `PrintSelf` method to `itk::SpatialFunctionImageEvaluatorFilter` STYLE: Remove unnecessary comment lines ENH: Improve the DTI module classes coverage ENH: Improve coverage for `SpatialFunction` module classes COMP: Fix `itk::ContourSpatialObject` ivar initialization value type ENH: Improve coverage for `SpatialObjects` module classes. ENH: Improve TopHatImageFilter classes coverage DOC: Improve math morphology class documentation STYLE: Turn commented unnecessary commands into useful comments ENH: Use strongly typed enums for the `Algorithm` type in math morphology BUG: Fix math morphology strongly typed `enum` scope-resolution ENH: Test streaming math morphology `enum class` types COMP: Fix missing initialization braces warnings DOC: Fix link to NumFOCUS ITK project website in `README` DOC: Change the Insight Journal handle links to insight-journal links DOC: Fix verbatim block in `UpdatingThirdParty` doc file STYLE: Make indentation in `itk::ContourSpatialObject.h` conform to ITK ENH: Print all `itk::DCMTKSeriesFileNames` ivars in `PrintSelf` BUG: Fix `itk::DCMTKSeriesFileNames::GetOutputFileNames()` returned ivar ENH: Improve coverage for `itk::InverseDisplacementFieldImageFilter` class ENH: Improve coverage for `itk::RayCastInterpolateImageFunction` class ENH: Improve coverage for `itk::DCMTKSeriesFileNames` class ENH: Effectively test filename values causing exceptions ENH: Improve coverage for `MathematicalMorphology` module classes. STYLE: Improve `itk::ImageSeriesWriter` class test file style COMP: Fix `itk::DCMTKSeriesFileNames` compilation issues ENH: Improve coverage for `itk::GDCMSeriesFileNames` class ENH: Add test for `itk::MeshFileReader` class BUG: Fix `itkDCMTKSeriesREadImageWrite.cxx` test failures ENH: Increase `itk::ImageDuplicator` class coverage ENH: Increase `itk::ScaleLogarithmicTransform` class coverage BUG: Remove unnecessary IO member filter name of class print calls ENH: Increase `itk::BSplineControlPointImageFunction` class coverage COMP: Fix undeclared identifier ENH: Increase `itk::ObjectByObjectLabelMapFilter` class coverage STYLE: Use `itkBooleanMacro` to avoid boilerplate code ENH: Increase `ITKImageFeature` module classes coverage ENH: Increase `ITKImageGradient` module classes coverage COMP: Update legacy boolean ivar set method call to current API BUG: Use appropriate dimensionality for image and components weights ENH: Check input and output image dimensionality matches STYLE: Rename `ITK_EXERCISE_BASIC_OBJECT_METHODS` class names arguments STYLE: Provide default initialization to constructor in header file STYLE: Use single forward slashes in `CMakeLists.txt` data paths STYLE: Use the static `FixedArray::Filled` to initialize array ivars ENH: Use strongly typed enums for `itk::NiftiImageIO` readable formats BUG: Fix Superclass name in RTTI macro COMP: Remove duplicate include file ENH: Print all member variables. ENH: Use `itkBooleanMacro` for `ImageSpacing`, `InterpolateSurfaceLocation` ENH: Increase code coverage BUG: Fix `itkMultiphaseSparseFiniteDifferenceImageFilterTest` BUG: Fix Superclass name in RTTI macro BUG: Fix uninitialized variable use in `ANTS` neighborhood correlation metric BUG: Initialize member variables COMP: Fix deduced type initialization warning and operand mismatch error STYLE: Add missing source file extension to `Common` module tests COMP: Fix image pointer casting error STYLE: Move `DCMTK` test baselines to module's `Baseline` folder DOC: Remove duplicate `README` file from `Review` module test folder COMP: Fix missing initializer warning Jonathan Daniel (1): ENH: Added .vs to .gitignore KWIML Upstream (1): KWIML 2020-04-20 (4abfeaa7) KWSys Upstream (2): KWSys 2020-09-29 (4a19ed43) KWSys 2021-02-10 (dda7a943) Kenji Tsumura (1): BUG: Fix itkGPUDemonsRegistrationFilterTest fails Kris Thielemans (2): COMP: Fix linking problems with external HDF5 COMP: use HDF5 targets preferentially if using a system HDF5 LIBPNG Upstream (1): PNG 2020-05-24 (dbe3e0c4) Lee Newberg (26): ENH: Support additional pixel types in python wrapping for ShrinkImageFilter. BUG: Do not wrap signed distance map filters for integer image outputs BUG: Update associated test BUG: MinPriorityQueueElementWrapper constructor needs ZeroValue() BUG: MinPriorityQueueElementWrapper constructor needs default constructor ENH: WIP: Wrap CastImageFilter for VectorImage. ENH: Read DICOM directory with Python imread ENH: Support for VariableLengthVector in CastImageFilter ENH: Move ITKMeshToPolyData functionality into ITK ENH: Make Python Image.astype() work for more types ENH: Add tests for VectorImage.astype BUG: fix tests for VectorContainer and PyVectorContainerPython PERF: No need to check whether numpy is available COMP: Breaks Continuous test for Microsft OS; disable until debugged. ENH: Support `ttype` parameter for numpy<->ITK conversions ENH: ttype can be `ImageType` whenever `(ImageType,)` is accepted STYLE: Prevent CMake variable name collisions ENH: add additional assertions for `ttype` parameter COMP: remove warnings for template already defined COMP: remove CastImageFilter "template already defined" warnings ENH: Add "long long" support to itkVTKImageImport BUG: Fix crash of PythonExtrasTest when extra types are wrapped ENH: support multiple labels in ContourExtractor2DImageFilter COMP: type and const safety in ContourExtractor2DImageFilter PERF: Make loop over labels be multi-threaded ENH: Use (Shaped)RegionRange instead of (Shaped)RegionIterator. Mathew Seng (7): ENH: Update Remote Modules BUG: Missing end-of line macro changes BUG: Incorrect path for Sphinx Examples in Doxygen BUG: Invalid urls to outside sources ENH: Update SpatialObject and SpatialObjectPoint sphinx BUG: Incorrect syntax for doxygen code block DOC: Add Git upstreams for post-commit hook Mathieu Malaterre (1): STYLE: Teach git about GDCM oversize file Matt McCormick (73): COMP: itkResampleImageTest8 ~ProjectTransform mark as override ENH: Bump the ITK CMake version to 5.2.0 ENH: Add itk.vtk_image_from_image and itk.image_from_vtk_image BUG: Fetch full depth in apply-clang-format action DOC: Release process updates for 5.1.0 COMP: CurvesLevelSetImageFilter multi-line comment DOC: Add 5.1 Release Notes ENH: Bump CI ExternalData version to 5.1.0 COMP: Unused tc in SquaredEdgeLengthDecimationQuadEdgeMeshFilterTest DOC: Fix conda install command in ReleaseDownloadLinks.md COMP: Bump CastXML to 0.3.4 ENH: Add torch.Tensor input/output support for ITK filters DOC: Add pointers on how to browse and download testing data ENH: Add Label PR GitHub Action ENH: Add image.astype(pixel_type) for casting COMP: Add lxml to macOS CI environment ENH: Update UpdatepygccxmlFromUpstream.sh for pygccxml v2.0.1 COMP: Add missing itkMacro.h to itkSTLContainerAdapter.h DOC: Note content link update for bug fix releases ENH: Add Image dict and pixel set/get Python interfaces ENH: Wrap LabelOverlapMeasuresImageFilter ENH: Support Python debugging with Visual Studio ENH: WIP: Wrap CastImageFilter for VectorImage <-> Vector PERF: Add IPO flags to Python libraries COMP: Remove -fopenmp in castxml invocation COMP: Remove gold linker support COMP: Do not enable whole program optimization with MSVC COMP: Use CMake 3.18.4 in macOS CI builds ENH: Install dask for CI testing COMP: Set runtime output directory for Windows Python tests COMP: Only search for Python 3.6 and above DOC: Correct ITKExamples Python package testing command BUG: Python support module and __init__.py install location BUG: Prevent HDF5 from overwritting ITK library names ENH: Update GDCM upstream repository to GitHub ENH: Content link updates for ITK 5.2 RC 1 DOC: Update macOS Python package Release build instructions BUG: Set runtime output path for external module binaries COMP: Force runtime output with Visual Studio and Python wrapping ENH: Add ARM sources to libpng update from upstream script ENH: Add libpng ARM sources COMP: Add ARM sources to libpng build BUG: Do not assert module swig attribute for init_docstring BUG: init_docstring with filter instance from the current module ENH: Generate a list of remote modules changed for release notes BUG: Wrap MetaDataObject for Array and std::vector value types STYLE: Add SymmetricEigenAnalysisImageFilter::SetOrderEigenValuesBy ENH: Set default dimension for SymmetricEigenAnalysisImageFilter STYLE: Add SymmetricEigenAnalysisImageFilter::GetOrderEigenValuesBy BUG: Test SymmetricEigenAnalysisImageFilter::GetOrderEigenValuesBy ENH: Support alternate dim orders in image_from_xarray ENH: NumPy and XArray conversion for 4D images ENH: xarray_from_image "c" coords uint32 type ENH: Module configuration exec to import BUG: Remove Azure coverage CI build COMP: Remove invalid Emscripten HDF5 link flags COMP: Declare H5O__fsinfo_set_version COMP: Provide H5CX_set_apl declaration in H5Odeprec.c COMP: Provide H5CX_get_ohdr_flags declaration in H5Oint.c COMP: Declare H5CX_set_libver_bounds in H5Rint.c COMP: Add output redirection for H5Tinit.c, H5lib_settings.c generation BUG: Disable Emscripten exception for floating point exceptions COMP: Include stdio.h for printf BUG: SetPixelTypeInfo for VARIABLELENGTHVECTOR, ARRAY, VARIABLESIZEMATRIX ENH: Add itk.transformread, itk.transformwrite ENH: imageio kwarg for imread, imwrite STYLE: black formatting on itkExtras.py ENH: xarray_from_image .attr, image_from_xarray MetaDataDictionary support COMP: Migrate ITKVtkGlue library configuration to itk-module-init.cmake COMP: Include directories for CastXML when wrapping ITKVtkGlue ENH: Content link synchronization for v5.2rc03 ENH: Support 32 bit integer IO in wrapping BUG: Checkout full depths for clang-format-linter MetaIO Maintainers (4): MetaIO 2020-12-04 (1d5fb8c4) MetaIO 2020-12-23 (26d71aa2) MetaIO 2021-01-28 (ea2bb780) MetaIO 2021-02-12 (df6ad862) Michael Jackson (1): COMP: Detect Apple Silicon arch for Floating Point exceptions Mihail Isakov (3): ENH: GDCMImageIO SINGLEBIT image type DOC: Updated GDCMImageIO BUG: memory leak in LSMImageIOTest Mon ius (1): COMP: fix error on IBM POWER9 ppcle64 arch Moritz Schaar (1): BUG: Fix Python Wrapping with MSVC and CMake >= 3.18, Closes Slicer#2049 Nick Tustison (6): ENH: Add adaptive denoising module. DOC: Update description. ENH: Add criteria report, update git tag, and enhance description. ENH: Add test. ENH: Review. ENH: Add refactoring and more testing. Niels Dekker (51): STYLE: Move ITK5 ranges, shapes, policies out of Experimental namespace COMP: Fix arithmetic overflow MersenneTwisterRandomVariateGenerator STYLE: Allow conversion from nullptr to WeakPointer, not from zero STYLE: Add in-class default member initializer to SmartPointer m_Pointer DOC: Link region iterators to ImageRegionRange, ImageRegionIndexRange STYLE: Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE STYLE: Call ITK_DISALLOW_COPY_AND_MOVE, not ITK_DISALLOW_COPY_AND_ASSIGN DOC: Add Doxygen links from iterators to ShapedImageNeighborhoodRange STYLE: Remove C-style (const void *) casts STYLE: Remove space between class and member names in C++ source files STYLE: Remove "include guards" from cxx files STYLE: Use C++11 override and `= default` in itkWin32OutputWindow.h STYLE: Replace `container[container.size() - 1]` by `container.back()` ENH: Allow running various tests without arguments STYLE: Remove local possibleTransformIO from TransformIOFactoryTemplate STYLE: TxtTransformIO Read() no longer copy input file to data string STYLE: Declare OptimizerParameters::m_Helper as C++11 std::unique_ptr STYLE: Move OptimizerParameters implementation from .hxx to .h file STYLE: Replace `vnl_vector[vnl_vector.size() - 1]` by vnl_vector.back() BUG: Fix MatrixOffsetTransformBase SetFixedParameters if too few params COMP: Work around GCC-4.8 error converting to OptimizerParametersHelper COMP: Remove InvalidImageMomentsError from itkImageMomentsCalculator.hxx ENH: Test that MetaIO supports a string value of up to 32767 chars STYLE: Use the WriteImage convenience function in Core/Common/test BUG: DICOMParser should use `&&` instead of comma in for-loop condition STYLE: Use the WriteImage convenience function anywhere in Modules/Core BUG: Fix Euler3DTransform::SetFixedParameters crash when too few params ENH: Add operator== and operator!= to itk::Image ENH: Declare FixedArray::size() constexpr ENH: Add convenience function ReadImage ENH: Extend ITKWriteImageFunctionTest by reading the written image back ENH: Array, OptimizerParameters constructors with size and initial value ENH: Support calling a const NumberToString, add GoogleTest unit tests STYLE: Reduce buf size, remove builder.Reset() calls from NumberToString STYLE: Remove virtual from itkGPUKernelClassMacro, use C++11 `= delete` COMP: Fix itkGPUKernelClassMacro(kernel) backward compatibility STYLE: Remove dynamic_cast and GetPointer() from LightObject::Clone() STYLE: Remove 6 no-op dynamic_casts (casting T* to T*) from Modules/Core STYLE: Avoid "no-op" dynamic_cast from inside LightObject::New() STYLE: Remove 9 no-op dynamic_casts (casting T* to T*) ENH: Add explicit OptimizerParameters(inputData, dimension) constructor STYLE: Remove unintended extra space from destructors and operators STYLE: ExceptionObject may assume that std::string::c_str() never throws STYLE: Follow Rule of Zero and use std::shared_ptr in ExceptionObject BUG: Remove duplicate "itk::ERROR: itk::ERROR: " from itkExceptionMacro STYLE: C++11 inheriting constructors from ExceptionObject for 4 classes STYLE: Remove destructors ExceptionObject derived classes (Rule of Zero) BUG: Remove duplicate "itk::ERROR: " from itkSpecializedExceptionMacro STYLE: Use equal_to on pixel containers DenseFiniteDifferenceImageFilter COMP: Add virtual destructor to TestClass in ExceptionObject unit test STYLE: Replace "itk::ERROR" by "ITK ERROR" in description of exception Niklas Johansson (2): STYLE: Correct doc for ReadImageInformation ENH: Prevent segfault by failing fast in itkGDCMImageIO Pablo Hernandez-Cerdan (6): BUG: Use ITK_WRAP_IMAGE_DIMS in ViewImage.wrap ENH: Add data() and size() member functions to FixedArray COMP: Remove dynamic exception specifications in tests COMP: Avoid Dimension < 3 in FrustumSpatialFunction COMP: Fix warning -Wdeprecated-copy in itkQuadEdgeMeshBaseIterator COMP: Fix const-correctness of iterators in multiple classes Pierre Wargnier (2): BUG: Fix Mat to Image conversions for OpenCV 4.x; add support for int32 COMP: fix errors and warnings in OpenCV bridge Samuel Gerber (1): PERF: Avoid Superfluous PointsLocator Updates Sean McBride (13): COMP: Fixed link error with old versions of AppleClang COMP: Fixed compile error on old clang 7, prefixed ivar with this-> COMP: Remove prohibition against building Universal Binaries on macOS DOC: Removed obsolete readme info regarding updating HDF5 COMP: remove invalid double underscore usage COMP: ignore try_compile fenv_t results on macOS COMP: cherrypicked HDF5 upstream changes for macOS universal binary support COMP: Changed conditional include of emmintrin.h to use preprocessor ENH: changed CTEST_DROP_METHOD from http to https COMP: removed dead atomic operation checks ENH: fixed failing test with macOS Rosetta emulation by increasing buffer size COMP: remove try-compile for SSE2 detection COMP: cherrypick HDF5 commit that added C++11 override keywords Simon Rit (3): COMP: fix itk::ArrowSpatialObject warning when compling 1D wrappings DOC: fix description of Concept::SameDimensionOrMinusOne(OrTwo) COMP: export ITK_LIBRARY_BUILD_TYPE for external building of modules Stephen R. Aylward (18): BUG: CUFFTW paths were not being set and unnecessary FFTW files used BUG: CurvatureRegistrationFilter fix logic re: depends on FFTW (Slicer#1786) ENH: Bump TubeTK to support CUFFTW (Slicer#1788) ENH: Bump TubeTK to version that removes ArrayFire (replaced by cufft) ENH: ITKFFT library is now required, even if cufft is used. ENH: Bump MetaIO to address style and const params BUG: Frenet frame disrupted along tubes BUG: Bump TubeTK BUG: Update TubeTK to include version that addressed missing VTK files BUG: Bump TubeTK to isolate wrapping on vtk-dependent classes ENH: Bump MetaIO to use an enhanced MetaTubePoint (Slicer#1954) BUG: TubeSpatialObject normals not unit vectors (Slicer#1972) ENH: Bump TubeTK to version that works with updated Spatial Objects (Slicer#2002) ENH: Bump TubeTK to offer updated examples and improved tube seg COMP: Adds ComputeTangentAndNormals() function COMP: Adding itkLegacyMacro wrapping to ComputeTangentAndNormals() ENH: TubeTK release candidate for ITK v5.1.2 BUG: Update itkEventObjectTest to use new event macros Tom Birdsong (5): ENH: Python wrapping for v4 optimizers ENH: Relocate and test diff demons reg filter Python wrapping ENH: Wrap DisplacementFieldTransform for vector floats ENH: Wrap GradientDescentOptimizerv4 for Python ENH: Wrap CenteredTransformInitializer for template superclass VXL Maintainers (7): VNL 2020-10-05 (c45970ee) VNL 2020-10-07 (a302a89b) VNL 2020-11-20 (3d3e8683) VNL 2020-12-16 (a05ed916) VNL 2020-12-20 (85ae25b7) VXL 2020-12-16 (a05ed916) VXL 2021-02-15 (7edc7cd8) Zhiyuan Liu (2): DOC: improve helpers of itk.Filters. ENH: Add a convenient function to get/set the number of threads. justbennet (1): COMP: Fixing #include for itkExpectationMaximizationMixtureModelEstimator.h ===================================================================== SimpleITK: $ git shortlog --topo-order --no-merges v2.0.2..460f9c1 Bradley Lowekamp (78): Bumping version to 2.1 for development Add testing for concurrent reading of NIFTI files Enable the ITKIOTransformMINC module for xfm transform files Add testing for reading and writing transforms in Python Wrap Image's GetBuffer methods for Java Use "package_data" for SimpleITK documentation files. Add support to register single typelist to dual factory Add custom_register to DualDispatch template Add sitkUInt8 mask image support to MaskNegatedImageFilter Use dimension range member function registration method Add Python 3.9 to manylinux AZP CI packaging Add GetLogBiasFieldAsImage method to N4 filter Add testing for N4's GetLogBiasFieldAsImage method Update N4 example to use bias field at input resolution Add Image::GetSizeOfPixelComponent method Add testing for Image::GetSizeOfPixelComponent method Remove unused Java carray typemap Add to Java interface Image::GetBufferAsByteBuffer Add Python 3.9 to packaging pipeline AZP Mac Package explicit Python 3.6 version usage Exclude the "latest" branch from triggering packaging Update ITK Superbuild version along the ITK 5.2 development branch Update ITK along 5.2 development branch. Tweak manuylinux build scripts Add docker file for building manylinux2010 Python 2010 wheels Add manylinux2010 to AZP packaging Fix AZP Linux packaging to build configure.BuildHash Update ITK superbuild version to 5.2 rc1 Set CMake Policy version to 3.10 in Superbuild Suppress MSVC getenv security warning. Improve style with C++11 features Remove old TraviCI configuration Update CircleCCI Python versions to 3.6,3.9 ShiftScale supports output pixel type Add warning macro Create ObjectOwnedBase class Create ObjectOwnedBase class Move definition before HelloWorld target Add LoggerBase and ITKLogger classes Add wrapping for Logging classes Add Python Logger derivation support and example Fix implicit parent initialization Fix unable to load SWIG R wrapping due to abstract class Update Python pip before installation Add prose documentation for the Logging example Add Logging example to example index Add 4D ( and more ) support for PermuteImageFilter Discontinue packaging Python 3.5 Fix Logging example python code include link Replace virtualenv with venv Directly create CMake commands for creating venv and installing numpy Adding suppression of distutils unknow field warning. Update ITK version to after 5.2rc1 Use STEP_TARGETS option over EP Add_Step_Targets command Install wheel package to venv for packaging Update to support CMake Ruby module prefix AZP restore publishing of OSX and MS Windows Python packages Update CircleCI images to buster Correct setting of command ownership Add test to echo CMakeCache.txt CircleCI update cmake version to 3.18 Update ITK superbuild version to 5.2rc02 CMake fix detection of Ruby variables CMake prefer Ruby_EXECUTABLE Fix Doxygen style comment for grouping Remove unused VirtualEnv configuration variables Remove installation of numpy Remove numpy installation and unused virtualenv configuration Fix "..." in SWIG docstring causing parse error Revert removal of including PythonDoc.i file Remove old CentOS devtoolset 3,4 and 6 Set the default ITK Multithreader to Platform in Superbuild AZP On Windows separate the building of the core library and python AZP add Java build as separate step to Windows CI AZP To batch add osx 10.15 with newer xcode builds AZP Define env_file for all linux batch jobs AZP Add devtoolset-9 for linux batch jobs Address Python's pip upgrade warning Dave Chen (13): Spelling bugs I missed the first time around Update SetApplication docs added Linux example; some formatting tweaks Spell checking all the headers undoing fixes to TypeList.h BUG: unpack was moved to table.unpack for Lua 5.2 Fixed old,non-working Java HelloWorld example added SITK_NOSHOW check Run HelloWorld examples when testing convential -> conventional workflow to run spell checking changed pip to install from req.txt added IO examples for CSharp, C++, Java, Lua, Ruby and TCL. Ziv Yaniv (5): Correct grammar in displacementfield constructor error message. DOC: GetPixel example separated, dynamic and statically typed languages. BUG: The GetPixelAsComplexFloat64 in Python was not renamed. Updating to modern Python from 2.7 to 3.x. Fixed broken link in filters list. ===================================================================== BRAINSTools: $ git shortlog --topo-order --no-merges v5.2.0..590c371 Dave Welch (7): Create gh-pages branch via GitHub ENH: Added legal submodule Create gh-pages branch via GitHub Delete .gitmodules BUG: removed legal submodule dir Create gh-pages branch via GitHub Create gh-pages branch via GitHub Hans J. Johnson (112): ENH: Update to version 5.2.0 of BRAINSTools ENH: Fix error in GTRACT building requirements. ENH: Make TBB and FFTW conditional for simplifying windows builds. BUG: Double value passed as bool. ENH: Fix vxl version for ITK. ENH: Missing to_matrix call. ENH: Add starting code for reading slicer fiducials. ENH: Simplify ITK find_package. ENH: Fix ITK MI double scaling. ENH: Add Similarity3DTransform to LandmarkInitializer. ENH: Adding initial Similarity3D LMKInit ENH: Remove references to BRAINSCut from BAW. ENH: Remove BrainsCUT old files. DOC: Provide better diagnostic failure modes. ENH: Use exception failure for invalid cases. WIP: Fix version. STYLE: Spelling, organize,variable name changes for readability. STYLE: Add debugging, and cleanup variable names. ENH: Clarify names. BUG: Missing transform from msp->eyefixed->orig for RP point. DOC: Provide better diagnostics. BUG: Code used in debugging missed update step. BUG: Wrong variable name used for final result. ENH: Refine search region for eyes based on emperical data. ENH: Encapsulate ROI generation code. ENH: Restrict second eye location finding based on first eye location. COMP: Fix missing header error. COMP: Fix type narrowing warning. ENH: Allow versor rigid transforms for landmark moving. ENH: Allow output based temp file for fixing landmarks. BUG: Fix replace index counter variable mismatch for old/new strings ENH: Review script for fcsv files. ENH: Update ITK version. ENH: Update to version 5.3.0 for improved BCD performance. ENH: Allow any generic transform to be used for landmarks. ENH: Adding better fallthrough logic. ENH: Update version for latest tag version. ENH: Move useful functions to common library ENH: Use more robust computation for generating Tmsp ENH: Allow aligning to MSP from landmark points. ENH: Preserve original image pixel type. BUG: Restore deleted utility function ENH: Update test cases for minor numerical precision changes. COMP: Fix warning about shadow variable with missing return value ENH: Use ITK with sform preference. COMP: Better timeout and download behavior for large files. ENH: Update ANTs ENH: Remove tbb pre oneapi warnings by avoiding tbb.h ENH: Remove debugging code from standard runs. STYLE: Move build scripts together. ENH: Move old superbuild files out of the way. ENH: Enable building with shared libraries. ENH: Avoid polluting all the projects with build locations. BUG: Development installs needed for ITK BUG: SEM development install required. ENH: Provide installed version of libraries. ENH: Allow for shared libary builds of executables. ENH: Set default install prefix for builds. ENH: Update to fix shared library install of ITK. ENH: Remove outdated reference atlas files. ENH: Improve install path naming for BRAINSTools. ENH: Update to version 5.3.1 with installed shared libs. ENH: Update for fixed compilation of ANTS. COMP: Need extra flag to monitor built in default. ENH: Fixed zlib library extension for mac ENH: Fixed up FFTW installs. ENH: add BRAINSResample 'input' pixel type ENH: Provide linux relative pathing for shared libs BUG: Wrong tbb library search path given ENH: Use relative relocatable rpath for mac ENH: Allow both lmk and image base transforms. ENH: Fix for centos pathing of fftw. ENH: Adding debugging information for git tag. ENH: Updating version to v5.3.2 ENH: Explicitly set FPIC building. DOC: Add future interesting DCMTK option comment. COMP: Some systems use lib64 or lib32 for library directories BUG: Need to address the fact that slicer now write LPS landmarks STYLE: Remove errant cmake file. ENH: Update to install the Atlas reference files as well. ENH: Adding initial programs for defacing data. BUG: Can not write file to shared directory STYLE: Remove unused template parameter ENH: Add install commands STYLE: Remove duplicate code included in BRAINSCommonLib BUG: Fix template parameter to allow 2D and 3D ENH: Add implicit resampling to first image ENH: Adding simple generic transform for ImageCalculator. ENH: Add resampling to ImageCalculator ENH: Remove compiler warning unused variable. ENH: Deface with gradual blur ENH: Update versions to the latest versions. BUG: Output mask is not a debugging output. ENH: write mask image last as a sentinal file. ENH: Add passiveVolume processing BUG: Need to force out of FOV code ENH: Allow BCD to force any landmark location from input file STYLE: Make warning match variable name ENH: Improve the defacing algorithm to preserve regions above 80mm below AC point. ENH: Update the database to be read-only access. COMP: Add both ZLIB*DIR and ZLIB*DIRS variables DOC: Provide better documentation from XML for new version. ENH: Make SGEGraph only submit jobs that need running. ENH: Updating version tag to v5.4.0 ENH: Avoid incorrect typecasting of distance maps BUG: 2D images were not processed correctly ENH: Improve diagnostic for landmark comparison. ENH: Update ITK to 5.2rc2. Set theme jekyll-theme-modernist and migrate Page Generator content Update index.md ENH: Preparing for gh-pages in doc directory. BUG: Fix directory name fo gh-pages. Jean-Christophe Fillion-Robin (1): COMP: Fix windows compilation adding missing check_avx_flags function Kian Weimer (8): ENH: updated external packages to latest version Each external package was checked and updated to its latest version if needed. The following were updated: ANTs, ITK, OpenJPEG, VTK. The VTK component naming convention changes and required a few other files to be modified. BUG: Updated VTK utility names. Some VTK utility names were not changed after the recent External package update. This does not affect functionality but does cause CMake to throw an error in debug mode. These names have now been updated. DOC: Added markdown instructions for configuring CLion for BRAINSTools This includes several images. ENH: Swapped safe-to-replace local variable copies with a constant reference. In some code locations, local variables are created that simply represent a copy of another variable. For expensive to copy values, this can be inefficient. This commit converts such local variables whose contents are not modified to constant references. This implements a portion of the 'performance-unnecessary-copy-initialization' clang-tidy check. -"Local copy 'SET_DATA' of the variable 'strname' is never modified; consider avoiding the copy" STYLE: Applied clang-format style changes to entire BRAINSTools tree. ENH: Replaced string addition operations within loops to append operations. The append operation provided by `std::string` is more efficient than an addition. Large string addition operations within loops have been changed to append. This implements the 'performance-inefficient-string-concatenation' clang-tidy check. -"String concatenation results in allocation of unnecessary temporary strings; consider using 'operator+=' or 'string::append()' instead" ENH: Replaced single character string literals within find operations with characters. In several locations, a length 1 string is passed to `std::string::find()` or others. The character literal overload is more efficient so these values have been converted. This implements the 'performance-faster-string-find' clang-tidy check. -"'find' called with a string literal consisting of a single character; consider using the more effective overload accepting a character." ENH: Converted method parameters to pass by refrence. Constant method parameters are copied during each method invocation. These parameters have been changed to pass-by-reference to avoid unnecessary, expensive copies. This implements a portion of the 'performance-unnecessary-value-parm' clang-tidy check. -"The const qualified parameter 's' is copied for each invocation; consider making it a reference." abpwrs (10): ENH: mask lower 80mm more efficiently & pseudocode for apply mask ENH: adding flake and black configs STYLE: indentation change STYLE: pythonic if statement STYLE: fixing keyword naming `exit` to be exit_status ENH: adding diagnostic prints one exceptions ENH: BIDS style filename generation ENH: BIDS style file names can be generated automatically from a subject data dictionary ENH: adding assertion to bidsUtils_test.py FIX: correcting docs/comments + removed extra loop ENH: added noMaskApplication and inputMask falgs
jamesobutler
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Mar 13, 2021
…ools Slicer updates were made based on changes introduced in InsightSoftwareConsortium/ITK@076e990 ===================================================================== ITK: $ git shortlog --topo-order --no-merges v5.1.2..2b34388 Alex Domingo (1): BUG: fix python module definition in VtkGlue wrap Alexander Burchardt (1): DOC: fixes itkSoftwareGuide Slicer#146 Andreas Huber (1): BUG: Fix number encoding to use C locale (Slicer#2297) Antoine Robert (1): ENH: Use Numpy bridge with array of dimension 1 Atri Bhattacharya (2): Explicit libm linking for NrrdIO and libLBFGS. BUG: Use explicit libm linking only on UNIX. Baptiste Depalle (1): ENH: improve wrapping architecture Bernhard M. Wiedemann (1): BUG: Fix issue Slicer#1939: Use -mtune=generic Brad King (3): STYLE: Allow specific HDF5 sources to be larger than normal limit ENH: Update to newer third-party update script from CMake ENH: Convert VNL import script to use update-third-party.bash Brad T. Moore (3): BUG: WatershedImageFilter would crash with assert. BUG: Fix to ITKSetPython3Vars ignoring Python virtual environments (Slicer#2068). BUG: Add '_d' POSTFIX to Windows Python Debug (Slicer#2050) Bradley Lowekamp (34): ENH: Use named pipeline inputs for morphological reconstruction COMP: Add missing const qualifier BUG: Add StatisticsImageFilter::SetNumberOfStreamDivisions Python STYLE: remove extraneous semi-colon after bracket ENH: Add FunctionCommand with lambda support ENH: Add direct support for lambda command to Object class DOC: Update Object::AddObserver documentation COMP: Fix ~FunctionCommand implicit override warning COMP: Address no override keyword warning STYLE: Use defaulted constructor for event object macro BUG: Remove no output warning in ImageSink filters ENH: Bump SimpleITKFilters remote module ENH: PasteImageFilter input ND and constant value COMP: Update SimpleITKFilters remote module ENH: Add TernaryGeneratorImageFilter ENH: Change TernaryFunctor usage to TernaryGenerator ENH: Add GTest cases for TernaryGeneratorImageFilter DOC: Grammar fixes ENH: Update ternary filter wrapping for generator base class COMP: add missing parentheses COMP: Address unused other parameter in defaulted methods ENH: Moderinize ShiftScaleImageFilter ENH: remove redundant WriteImage overloads COMP: Address brace initializer warning BUG: Make OutputWindow instance a global singleton STYLE: Prefer function of direct access of output instance. ENH: Update ternary filter wrapping for generator base class BUG: Fix JPEG200Test6 file output clobbering ENH: Create ITK_DEFAULT_THREADER definition ENH: Add ITK_DEFAULT_THREADER as CMake configuration variable. COMP: Address gcc 4.8 compilation errors PERF: Replace thread index array with thread local storage BUG: Use graft of input to mini-pipeline ENH: Use dynamic threading model Bryn Lloyd (1): COMP: Fix warning in PointSetToPointSetMetricv4 (Slicer#1820) Charles Garraud (1): BUG: Fix BUILD_SHARED_LIBS state consistency for HDF5 Christina Rossmanith (5): STYLE: Remove blank before ::MemberName STYLE: Edited comments STYLE: New methods for translating Nifti datatypes to IOxxxxEnum BUG: read data arrays with intent NIFTI_INTENT_NONE for point or cell data STYLE: RGB comment Darren Thompson (1): ENH: Added itkPointSetToImageFilter.wrap David Thompson (1): ENH: Let gitlab-ci runners build with clang-tidy. Davis Vigneault (10): STYLE: Prefer Early Return ENH: Add Python Wrappers for Mesh Source Classes ENH: Review Cuberille Remote Module Compliance ENH: Assert in Debug Mode COMP: Address Wdeprecated-copy warnings in gcc9 STYLE: Call Superclass assignment operator ENH: Test Assignment and Copy of Spatial Objects COMP: Address Warnings in Vector and Map Container ENH: Test Map and Vector Iterators ENH: Add Missing Boolean Macros in QEFilters Dženan Zukić (34): ENH: updating remote modules to latest versions COMP: fix GPU compile errors when building as DLLs BUG: fix Statistics::Histogram::Mean calculation ENH: update remote modules DOC: restore LICENSE accidentally overwritten by a merge commit STYLE: rename libPNG's license to match the original one STYLE: remove duplicate item in a list ENH: progress reporting does not stall with PoolMultiThreader COMP: variable is uninitialized when passed as a const reference ENH: append properties instead of overwrite in HDF5 BUG: Filter inputs are erroneously released ENH: allow dependencies on remote modules DOC: add ComputeJacobianWithRespectToPosition change to migration guide DOC: hyperlink mentioned commits ENH: remove NumPy presence conditions from tests' CMakeLists.txt COMP: fix compilation with Python and tests enabled on Visual Studio ENH: add a convenience function WriteImage ENH: update remote modules COMP: externally built remote module libs went in /lib or C:/lib ENH: Python wrapping fixes ENH: updating remote modules using the script ENH: supporting multi-channel tensors as inputs and outputs in Python ENH: use master branch of GoogleTest until a stable version is released ENH: manually update minimum CMake version to 2.8.12 to avoid warning Revert "ENH: manually update minimum CMake version to 2.8.12 to avoid warning" Revert "ENH: use master branch of GoogleTest until a stable version is released" Revert "Merge branch 'upstream-googletest' into updateGTest" COMP: fix rename error from re-basing parallel branches ENH: make shared variables local to facilitate code reuse/parallelism ENH: reduce duplication in ContourExtractor2DImageFilter STYLE: review suggestions PERF: using constant boundary condition instead of filling the edge DOC: fix AtomicInt and MutexLock broken links in migration guide ENH: update remote modules using the script Eigen Upstream (1): Eigen3 2020-12-08 (b51eab5c) GCC-XML Upstream (1): ENH: pygccxml v2.0.1 (reduced) GDCM Upstream (2): GDCM 2020-06-30 (c0824c0a) GDCM 2020-12-10 (b380cbac) GoogleTest Upstream (1): GoogleTest 2021-02-05 (f3ef7e17) Gregory Lee (1): DOC: update references for recursive Gaussian filters HDF5 Maintainers (1): HDF5 2019-12-24 (5b9cf732) Hans J. Johnson (3): ENH: Prefer to use sform over qform when both are set VNL 2020-07-07 (4a5f1059) (Slicer#1916) ENH: Exercise converting Object::Pointer to Object::ConstPointer Hans Johnson (164): BUG: Double scaling introduced in refactoring ENH: Add test to monitor metric result value COMP: Missing defition of ITK_DISALLOW_COPY_AND_ASSIGN COMP: Resolve multi-line comment warning ENH: New test data for nifti qform/sform ENH: Add nifti sform read/write testing ENH: Do not pollute the global link_directories namespace BUG: Incomplete removal of ITK_INSTALL_NO_* variables COMP: Refine order of searching for header files BUG: itkhdf5 installed paths were incorrect with recent hdf5 versions ENH: Update building internal FFTW version BUG: Centos internal lib64 lib path BUG: Fix fftw linkage issue with system fftw STYLE: Use black formatting for python COMP: Ensure consistent ordering of list printed COMP: Local variable 's' might be referenced before assignment STYLE: Prefer fstrings for python 3.6+ BUG: snake case functions are erased STYLE: Missed conversions for new macro name BUG: Writing snake_files should not be appended BUG: Decoupled config files should not depend STYLE: Use consistent formatting for python files ENH: Move cmake config items into common itkConfig.py.in file ENH: Remove alias to 'object' variable name ENH: Extend dictionary with `update` not `add` ENH: Avoid bugs with mutable default arguments ENH: Use targeted import for element of sys COMP: Ambiguous 'range' function made explicit STYLE: Fix comment spelling errors. COMP: Avoid outscope variable shadowing COMP: Selective import of required components COMP: Avoid possible variable use before assignment. COMP: Remove redundant import. ENH: import modules at top of file COMP: Remove unneccessary HAVE_NUMPY conditionals STYLE: Apply consistent pep8 compatible indentation. COMP: Avoid reassigning parameters COMP: Too broad exception narrowed. STYLE: Prefer to use @staticmethod decorator. STYLE: Initial typehints added. ENH: Avoid poluting the global namespace STYLE: Avoid difficult to read anit-pattern STYLE: Remove python2 dictionary facade COMP: PEP 8: E722 do not use bare 'except' COMP: Address protected member warning COMP: Shadows name 'input_type','keys' from outer scope DOC: Spelling warnings removed. STYLE: Fix name and spelling issues COMP: Remove python2 dictionary compatibilties. COMP: Too broad exception clause fixed COMP: Method 'Stop' may be 'static' ENH: Remove unused variable warnings. STYLE: Applied recommend code refactorings COMP: Remove potential referenced before assignment COMP: Remove shadows name from outer scope. DOC: Improve variable name spelling COMP: Instance attributes should be defined in __init__ COMP: Remove shadow variable outer scope warnings. COMP: Remove difficult to debug use of global variable COMP: Avoid poluting the module namespace COMP: Remove unused local variables. STYLE: Use python preferred lower-snake-case variable names ENH: Prevent contaminating global namespace COMP: Keep local functions out of global namespace COMP: Use lowercase python compatible function name. COMP: Match variable names from itkBase. STYLE: pytype warning disabled. ENH: disable a false positive naming error from pytype. STYLE: Address shadow variable and python style issues COMP: Unresolved reference 'sqrt' STYLE: Remove pass through return of read-only values. ENH: Code review and simplified logic STYLE: Encapsulate initialization for keeping namespace clean. COMP: Simplify exposing elements from itk namespace. ENH: Remove circular module dependancy STYLE: Prefer to extend existing template ENH: Explicitly test the itkConfig.LazyLoad=False option ENH: Allow setting default behaviors with environment COMP: Allow type inference tracking with dynamic loading. ENH: Only copy __path__ __spec__ when needed STYLE: Reduce aliased object naming STYLE: Localize imports to minimum scope. BUG: Pickling of itk module was broken STYLE: Update to python3 compatible syntax. STYLE: Update python Test with `black` formatting DOC: Make variable name clarifications and type designations STYLE: Remove unused macro. COMP: Fix test for remote python module BUG: Must append the list itkConfig.path ENH: Avoid adding invalid path to the sys.path ENH: Add error checking for required paths STYLE: Prefer explicit check to nested try/catch COMP: Enforce name.strip() redundantly COMP: Provide full path to test script file STYLE: Only set paths necessary for current build STYLE: Fix spelling error interperter -> interpreter STYLE: Make self-contained module. ENH: Update minimum required version of ITK BUG: WRAPPER_LIBRARY_OUTPUT_DIR is needed before macro call STYLE: Prefer explicit in-package pathing STYLE: Improve relative pathing computations STYLE: Prefer explicit full module specification for __spec__ ENH: Use more standard symbol lifting into itk namespace COMP: Prefer static member function modify static instance vars STYLE: Remove duplicated content that was immediately overwritten STYLE: Update python Test with `black` formatting STYLE: Simplify writing template python code files COMP: Place python shared libs as subpackage of itk COMP: Unconditionally set wrapped shared lib directory ENH: Separate static components into base class DOC: Add autodoc request in swig .i files COMP: Add initial typing for itkExtras ENH: Adding function to help generate __init__.pyi STYLE: Use consistent formatting for python files BUG: Convert code to python3 compatible STYLE: Prefer fstrings for python 3.6+ BUG: Avoid itkConfig double import trap STYLE: Minimize cmake configured python files BUG: Limit ignore to build directories only COMP: Mypy signature mismatch fixed COMP: Adding typing for ITK manually. STYLE: Add typehints for the itkTypes STYLE: Prefer fstrings for readability. COMP: Add typehinting for support classes ENH: Exclude cvar from the testing. STYLE: Update processing of *Config.py files ENH: Update documentation for generation of itkTemplates. DOC: Make swig object registry more transparent STYLE: Re-enforce black formatting contraints STYLE: Remove duplicate module dependancy entries BUG: Explicit use of builtin set BUG: Add test exposing multiprocessing LazyLoad failure BUG: LazyLoading must be threadsafe ENH: Update to SWIG 4.0.2 ENH: Add swig doxygen and autodoc=2 formats BUG: Incorrect loop dimensions in untested code BUG: Do not wrap invalid template parameters COMP: Fix hidden overloaded-virtual warning ENH: Ignore huge file warning for HDF5 paths ENH: Remove python interface introspection ENH: Simplified multi-config generator wrapping ENH: HDF5 upstream now hosted on github Version 1.10.6 ENH: More closely match the 1.10.6 release hdf5 COMP: Avoid compiler warnings with IPO BUG: CASTXML fails with aggressive optimizer flags BUG: Missing output dependency shared/H5init.c BUG: New test for 3D support BUG: ASAN identified use after delete bug STYLE: Fix clang-format styling require macro ';' end COMP: Work around ghostflow-check-master warnings COMP: Set vxl minimum to 3.0.0 STYLE: Macros should respect an end-of line ; COMP: Use of uninitialzed variable warning ENH: Script for updating DoubleConversion library. ENH: Update Double-convert third-party ENH: Update remote modules to master branch COMP: Use ITK_MACROEND_NOOP_STATEMENT for GPU macro ending. STYLE: Make prototype match definition names STYLE: Throw expression should throw anonymous temporary values instead STYLE: Remove deprecated orientation enumeration codes COMP: Preserve const qualifier for variable ENH: Provide better failure diagnostics STYLE: Use default member initialization COMP: Prefer const pointer when value does not change Horea Christian (1): ENH: improved support for offline build James Butler (1): COMP: Fix OpenJPEG build error with Visual Studio 16.9 Jan Margeta (1): ENH: Support for non-compliant DICOM in itk-js Jon Haitz Legarreta Gorroño (78): STYLE: Transition `Testing/Data` `README` to Markdown DOC: Add NumFOCUS-related contents to README ENH: Update remote modules COMP: Fix SW Guide examples LaTeX block line start warnings ENH: Update `Montage` remote module COMP: Fix SW Guide examples multi-line comment warnings ENH: Improve `itk::ThresholdImageFilter` class coverage STYLE: Fix typo in `itkBinaryThresholdImageFilterTest` STYLE: Fix ivar print value in `itk::PolygonSpatialObject` ENH: Improve the `itk::VideoFileWriter` class coverage. COMP: Remove unnecessary inherited member re-definitions ENH: Improve `itk::DCMTKSeriesFileNames` class coverage ENH: Add `itk::GrayscaleGrindPeakImageFilter` class test STYLE: Avoid `try`/`catch` boilerplate code in updating writer DOC: Fix typos in DTI 3D reconstruction image filter example ENH: Add boolean macros to `SpatialObjects` module boolean ivars DOC: Fix typos in DTI module's anisotropy image filter classes ENH: Add the `PrintSelf` method to `itk::SpatialFunctionImageEvaluatorFilter` STYLE: Remove unnecessary comment lines ENH: Improve the DTI module classes coverage ENH: Improve coverage for `SpatialFunction` module classes COMP: Fix `itk::ContourSpatialObject` ivar initialization value type ENH: Improve coverage for `SpatialObjects` module classes. ENH: Improve TopHatImageFilter classes coverage DOC: Improve math morphology class documentation STYLE: Turn commented unnecessary commands into useful comments ENH: Use strongly typed enums for the `Algorithm` type in math morphology BUG: Fix math morphology strongly typed `enum` scope-resolution ENH: Test streaming math morphology `enum class` types COMP: Fix missing initialization braces warnings DOC: Fix link to NumFOCUS ITK project website in `README` DOC: Change the Insight Journal handle links to insight-journal links DOC: Fix verbatim block in `UpdatingThirdParty` doc file STYLE: Make indentation in `itk::ContourSpatialObject.h` conform to ITK ENH: Print all `itk::DCMTKSeriesFileNames` ivars in `PrintSelf` BUG: Fix `itk::DCMTKSeriesFileNames::GetOutputFileNames()` returned ivar ENH: Improve coverage for `itk::InverseDisplacementFieldImageFilter` class ENH: Improve coverage for `itk::RayCastInterpolateImageFunction` class ENH: Improve coverage for `itk::DCMTKSeriesFileNames` class ENH: Effectively test filename values causing exceptions ENH: Improve coverage for `MathematicalMorphology` module classes. STYLE: Improve `itk::ImageSeriesWriter` class test file style COMP: Fix `itk::DCMTKSeriesFileNames` compilation issues ENH: Improve coverage for `itk::GDCMSeriesFileNames` class ENH: Add test for `itk::MeshFileReader` class BUG: Fix `itkDCMTKSeriesREadImageWrite.cxx` test failures ENH: Increase `itk::ImageDuplicator` class coverage ENH: Increase `itk::ScaleLogarithmicTransform` class coverage BUG: Remove unnecessary IO member filter name of class print calls ENH: Increase `itk::BSplineControlPointImageFunction` class coverage COMP: Fix undeclared identifier ENH: Increase `itk::ObjectByObjectLabelMapFilter` class coverage STYLE: Use `itkBooleanMacro` to avoid boilerplate code ENH: Increase `ITKImageFeature` module classes coverage ENH: Increase `ITKImageGradient` module classes coverage COMP: Update legacy boolean ivar set method call to current API BUG: Use appropriate dimensionality for image and components weights ENH: Check input and output image dimensionality matches STYLE: Rename `ITK_EXERCISE_BASIC_OBJECT_METHODS` class names arguments STYLE: Provide default initialization to constructor in header file STYLE: Use single forward slashes in `CMakeLists.txt` data paths STYLE: Use the static `FixedArray::Filled` to initialize array ivars ENH: Use strongly typed enums for `itk::NiftiImageIO` readable formats BUG: Fix Superclass name in RTTI macro COMP: Remove duplicate include file ENH: Print all member variables. ENH: Use `itkBooleanMacro` for `ImageSpacing`, `InterpolateSurfaceLocation` ENH: Increase code coverage BUG: Fix `itkMultiphaseSparseFiniteDifferenceImageFilterTest` BUG: Fix Superclass name in RTTI macro BUG: Fix uninitialized variable use in `ANTS` neighborhood correlation metric BUG: Initialize member variables COMP: Fix deduced type initialization warning and operand mismatch error STYLE: Add missing source file extension to `Common` module tests COMP: Fix image pointer casting error STYLE: Move `DCMTK` test baselines to module's `Baseline` folder DOC: Remove duplicate `README` file from `Review` module test folder COMP: Fix missing initializer warning Jonathan Daniel (1): ENH: Added .vs to .gitignore KWIML Upstream (1): KWIML 2020-04-20 (4abfeaa7) KWSys Upstream (2): KWSys 2020-09-29 (4a19ed43) KWSys 2021-02-10 (dda7a943) Kenji Tsumura (1): BUG: Fix itkGPUDemonsRegistrationFilterTest fails Kris Thielemans (2): COMP: Fix linking problems with external HDF5 COMP: use HDF5 targets preferentially if using a system HDF5 LIBPNG Upstream (1): PNG 2020-05-24 (dbe3e0c4) Lee Newberg (26): ENH: Support additional pixel types in python wrapping for ShrinkImageFilter. BUG: Do not wrap signed distance map filters for integer image outputs BUG: Update associated test BUG: MinPriorityQueueElementWrapper constructor needs ZeroValue() BUG: MinPriorityQueueElementWrapper constructor needs default constructor ENH: WIP: Wrap CastImageFilter for VectorImage. ENH: Read DICOM directory with Python imread ENH: Support for VariableLengthVector in CastImageFilter ENH: Move ITKMeshToPolyData functionality into ITK ENH: Make Python Image.astype() work for more types ENH: Add tests for VectorImage.astype BUG: fix tests for VectorContainer and PyVectorContainerPython PERF: No need to check whether numpy is available COMP: Breaks Continuous test for Microsft OS; disable until debugged. ENH: Support `ttype` parameter for numpy<->ITK conversions ENH: ttype can be `ImageType` whenever `(ImageType,)` is accepted STYLE: Prevent CMake variable name collisions ENH: add additional assertions for `ttype` parameter COMP: remove warnings for template already defined COMP: remove CastImageFilter "template already defined" warnings ENH: Add "long long" support to itkVTKImageImport BUG: Fix crash of PythonExtrasTest when extra types are wrapped ENH: support multiple labels in ContourExtractor2DImageFilter COMP: type and const safety in ContourExtractor2DImageFilter PERF: Make loop over labels be multi-threaded ENH: Use (Shaped)RegionRange instead of (Shaped)RegionIterator. Mathew Seng (7): ENH: Update Remote Modules BUG: Missing end-of line macro changes BUG: Incorrect path for Sphinx Examples in Doxygen BUG: Invalid urls to outside sources ENH: Update SpatialObject and SpatialObjectPoint sphinx BUG: Incorrect syntax for doxygen code block DOC: Add Git upstreams for post-commit hook Mathieu Malaterre (1): STYLE: Teach git about GDCM oversize file Matt McCormick (73): COMP: itkResampleImageTest8 ~ProjectTransform mark as override ENH: Bump the ITK CMake version to 5.2.0 ENH: Add itk.vtk_image_from_image and itk.image_from_vtk_image BUG: Fetch full depth in apply-clang-format action DOC: Release process updates for 5.1.0 COMP: CurvesLevelSetImageFilter multi-line comment DOC: Add 5.1 Release Notes ENH: Bump CI ExternalData version to 5.1.0 COMP: Unused tc in SquaredEdgeLengthDecimationQuadEdgeMeshFilterTest DOC: Fix conda install command in ReleaseDownloadLinks.md COMP: Bump CastXML to 0.3.4 ENH: Add torch.Tensor input/output support for ITK filters DOC: Add pointers on how to browse and download testing data ENH: Add Label PR GitHub Action ENH: Add image.astype(pixel_type) for casting COMP: Add lxml to macOS CI environment ENH: Update UpdatepygccxmlFromUpstream.sh for pygccxml v2.0.1 COMP: Add missing itkMacro.h to itkSTLContainerAdapter.h DOC: Note content link update for bug fix releases ENH: Add Image dict and pixel set/get Python interfaces ENH: Wrap LabelOverlapMeasuresImageFilter ENH: Support Python debugging with Visual Studio ENH: WIP: Wrap CastImageFilter for VectorImage <-> Vector PERF: Add IPO flags to Python libraries COMP: Remove -fopenmp in castxml invocation COMP: Remove gold linker support COMP: Do not enable whole program optimization with MSVC COMP: Use CMake 3.18.4 in macOS CI builds ENH: Install dask for CI testing COMP: Set runtime output directory for Windows Python tests COMP: Only search for Python 3.6 and above DOC: Correct ITKExamples Python package testing command BUG: Python support module and __init__.py install location BUG: Prevent HDF5 from overwritting ITK library names ENH: Update GDCM upstream repository to GitHub ENH: Content link updates for ITK 5.2 RC 1 DOC: Update macOS Python package Release build instructions BUG: Set runtime output path for external module binaries COMP: Force runtime output with Visual Studio and Python wrapping ENH: Add ARM sources to libpng update from upstream script ENH: Add libpng ARM sources COMP: Add ARM sources to libpng build BUG: Do not assert module swig attribute for init_docstring BUG: init_docstring with filter instance from the current module ENH: Generate a list of remote modules changed for release notes BUG: Wrap MetaDataObject for Array and std::vector value types STYLE: Add SymmetricEigenAnalysisImageFilter::SetOrderEigenValuesBy ENH: Set default dimension for SymmetricEigenAnalysisImageFilter STYLE: Add SymmetricEigenAnalysisImageFilter::GetOrderEigenValuesBy BUG: Test SymmetricEigenAnalysisImageFilter::GetOrderEigenValuesBy ENH: Support alternate dim orders in image_from_xarray ENH: NumPy and XArray conversion for 4D images ENH: xarray_from_image "c" coords uint32 type ENH: Module configuration exec to import BUG: Remove Azure coverage CI build COMP: Remove invalid Emscripten HDF5 link flags COMP: Declare H5O__fsinfo_set_version COMP: Provide H5CX_set_apl declaration in H5Odeprec.c COMP: Provide H5CX_get_ohdr_flags declaration in H5Oint.c COMP: Declare H5CX_set_libver_bounds in H5Rint.c COMP: Add output redirection for H5Tinit.c, H5lib_settings.c generation BUG: Disable Emscripten exception for floating point exceptions COMP: Include stdio.h for printf BUG: SetPixelTypeInfo for VARIABLELENGTHVECTOR, ARRAY, VARIABLESIZEMATRIX ENH: Add itk.transformread, itk.transformwrite ENH: imageio kwarg for imread, imwrite STYLE: black formatting on itkExtras.py ENH: xarray_from_image .attr, image_from_xarray MetaDataDictionary support COMP: Migrate ITKVtkGlue library configuration to itk-module-init.cmake COMP: Include directories for CastXML when wrapping ITKVtkGlue ENH: Content link synchronization for v5.2rc03 ENH: Support 32 bit integer IO in wrapping BUG: Checkout full depths for clang-format-linter MetaIO Maintainers (4): MetaIO 2020-12-04 (1d5fb8c4) MetaIO 2020-12-23 (26d71aa2) MetaIO 2021-01-28 (ea2bb780) MetaIO 2021-02-12 (df6ad862) Michael Jackson (1): COMP: Detect Apple Silicon arch for Floating Point exceptions Mihail Isakov (3): ENH: GDCMImageIO SINGLEBIT image type DOC: Updated GDCMImageIO BUG: memory leak in LSMImageIOTest Mon ius (1): COMP: fix error on IBM POWER9 ppcle64 arch Moritz Schaar (1): BUG: Fix Python Wrapping with MSVC and CMake >= 3.18, Closes Slicer#2049 Nick Tustison (6): ENH: Add adaptive denoising module. DOC: Update description. ENH: Add criteria report, update git tag, and enhance description. ENH: Add test. ENH: Review. ENH: Add refactoring and more testing. Niels Dekker (51): STYLE: Move ITK5 ranges, shapes, policies out of Experimental namespace COMP: Fix arithmetic overflow MersenneTwisterRandomVariateGenerator STYLE: Allow conversion from nullptr to WeakPointer, not from zero STYLE: Add in-class default member initializer to SmartPointer m_Pointer DOC: Link region iterators to ImageRegionRange, ImageRegionIndexRange STYLE: Rename ITK_DISALLOW_COPY_AND_ASSIGN to ITK_DISALLOW_COPY_AND_MOVE STYLE: Call ITK_DISALLOW_COPY_AND_MOVE, not ITK_DISALLOW_COPY_AND_ASSIGN DOC: Add Doxygen links from iterators to ShapedImageNeighborhoodRange STYLE: Remove C-style (const void *) casts STYLE: Remove space between class and member names in C++ source files STYLE: Remove "include guards" from cxx files STYLE: Use C++11 override and `= default` in itkWin32OutputWindow.h STYLE: Replace `container[container.size() - 1]` by `container.back()` ENH: Allow running various tests without arguments STYLE: Remove local possibleTransformIO from TransformIOFactoryTemplate STYLE: TxtTransformIO Read() no longer copy input file to data string STYLE: Declare OptimizerParameters::m_Helper as C++11 std::unique_ptr STYLE: Move OptimizerParameters implementation from .hxx to .h file STYLE: Replace `vnl_vector[vnl_vector.size() - 1]` by vnl_vector.back() BUG: Fix MatrixOffsetTransformBase SetFixedParameters if too few params COMP: Work around GCC-4.8 error converting to OptimizerParametersHelper COMP: Remove InvalidImageMomentsError from itkImageMomentsCalculator.hxx ENH: Test that MetaIO supports a string value of up to 32767 chars STYLE: Use the WriteImage convenience function in Core/Common/test BUG: DICOMParser should use `&&` instead of comma in for-loop condition STYLE: Use the WriteImage convenience function anywhere in Modules/Core BUG: Fix Euler3DTransform::SetFixedParameters crash when too few params ENH: Add operator== and operator!= to itk::Image ENH: Declare FixedArray::size() constexpr ENH: Add convenience function ReadImage ENH: Extend ITKWriteImageFunctionTest by reading the written image back ENH: Array, OptimizerParameters constructors with size and initial value ENH: Support calling a const NumberToString, add GoogleTest unit tests STYLE: Reduce buf size, remove builder.Reset() calls from NumberToString STYLE: Remove virtual from itkGPUKernelClassMacro, use C++11 `= delete` COMP: Fix itkGPUKernelClassMacro(kernel) backward compatibility STYLE: Remove dynamic_cast and GetPointer() from LightObject::Clone() STYLE: Remove 6 no-op dynamic_casts (casting T* to T*) from Modules/Core STYLE: Avoid "no-op" dynamic_cast from inside LightObject::New() STYLE: Remove 9 no-op dynamic_casts (casting T* to T*) ENH: Add explicit OptimizerParameters(inputData, dimension) constructor STYLE: Remove unintended extra space from destructors and operators STYLE: ExceptionObject may assume that std::string::c_str() never throws STYLE: Follow Rule of Zero and use std::shared_ptr in ExceptionObject BUG: Remove duplicate "itk::ERROR: itk::ERROR: " from itkExceptionMacro STYLE: C++11 inheriting constructors from ExceptionObject for 4 classes STYLE: Remove destructors ExceptionObject derived classes (Rule of Zero) BUG: Remove duplicate "itk::ERROR: " from itkSpecializedExceptionMacro STYLE: Use equal_to on pixel containers DenseFiniteDifferenceImageFilter COMP: Add virtual destructor to TestClass in ExceptionObject unit test STYLE: Replace "itk::ERROR" by "ITK ERROR" in description of exception Niklas Johansson (2): STYLE: Correct doc for ReadImageInformation ENH: Prevent segfault by failing fast in itkGDCMImageIO Pablo Hernandez-Cerdan (6): BUG: Use ITK_WRAP_IMAGE_DIMS in ViewImage.wrap ENH: Add data() and size() member functions to FixedArray COMP: Remove dynamic exception specifications in tests COMP: Avoid Dimension < 3 in FrustumSpatialFunction COMP: Fix warning -Wdeprecated-copy in itkQuadEdgeMeshBaseIterator COMP: Fix const-correctness of iterators in multiple classes Pierre Wargnier (2): BUG: Fix Mat to Image conversions for OpenCV 4.x; add support for int32 COMP: fix errors and warnings in OpenCV bridge Samuel Gerber (1): PERF: Avoid Superfluous PointsLocator Updates Sean McBride (13): COMP: Fixed link error with old versions of AppleClang COMP: Fixed compile error on old clang 7, prefixed ivar with this-> COMP: Remove prohibition against building Universal Binaries on macOS DOC: Removed obsolete readme info regarding updating HDF5 COMP: remove invalid double underscore usage COMP: ignore try_compile fenv_t results on macOS COMP: cherrypicked HDF5 upstream changes for macOS universal binary support COMP: Changed conditional include of emmintrin.h to use preprocessor ENH: changed CTEST_DROP_METHOD from http to https COMP: removed dead atomic operation checks ENH: fixed failing test with macOS Rosetta emulation by increasing buffer size COMP: remove try-compile for SSE2 detection COMP: cherrypick HDF5 commit that added C++11 override keywords Simon Rit (3): COMP: fix itk::ArrowSpatialObject warning when compling 1D wrappings DOC: fix description of Concept::SameDimensionOrMinusOne(OrTwo) COMP: export ITK_LIBRARY_BUILD_TYPE for external building of modules Stephen R. Aylward (18): BUG: CUFFTW paths were not being set and unnecessary FFTW files used BUG: CurvatureRegistrationFilter fix logic re: depends on FFTW (Slicer#1786) ENH: Bump TubeTK to support CUFFTW (Slicer#1788) ENH: Bump TubeTK to version that removes ArrayFire (replaced by cufft) ENH: ITKFFT library is now required, even if cufft is used. ENH: Bump MetaIO to address style and const params BUG: Frenet frame disrupted along tubes BUG: Bump TubeTK BUG: Update TubeTK to include version that addressed missing VTK files BUG: Bump TubeTK to isolate wrapping on vtk-dependent classes ENH: Bump MetaIO to use an enhanced MetaTubePoint (Slicer#1954) BUG: TubeSpatialObject normals not unit vectors (Slicer#1972) ENH: Bump TubeTK to version that works with updated Spatial Objects (Slicer#2002) ENH: Bump TubeTK to offer updated examples and improved tube seg COMP: Adds ComputeTangentAndNormals() function COMP: Adding itkLegacyMacro wrapping to ComputeTangentAndNormals() ENH: TubeTK release candidate for ITK v5.1.2 BUG: Update itkEventObjectTest to use new event macros Tom Birdsong (5): ENH: Python wrapping for v4 optimizers ENH: Relocate and test diff demons reg filter Python wrapping ENH: Wrap DisplacementFieldTransform for vector floats ENH: Wrap GradientDescentOptimizerv4 for Python ENH: Wrap CenteredTransformInitializer for template superclass VXL Maintainers (7): VNL 2020-10-05 (c45970ee) VNL 2020-10-07 (a302a89b) VNL 2020-11-20 (3d3e8683) VNL 2020-12-16 (a05ed916) VNL 2020-12-20 (85ae25b7) VXL 2020-12-16 (a05ed916) VXL 2021-02-15 (7edc7cd8) Zhiyuan Liu (2): DOC: improve helpers of itk.Filters. ENH: Add a convenient function to get/set the number of threads. justbennet (1): COMP: Fixing #include for itkExpectationMaximizationMixtureModelEstimator.h ===================================================================== SimpleITK: $ git shortlog --topo-order --no-merges v2.0.2..460f9c1 Bradley Lowekamp (78): Bumping version to 2.1 for development Add testing for concurrent reading of NIFTI files Enable the ITKIOTransformMINC module for xfm transform files Add testing for reading and writing transforms in Python Wrap Image's GetBuffer methods for Java Use "package_data" for SimpleITK documentation files. Add support to register single typelist to dual factory Add custom_register to DualDispatch template Add sitkUInt8 mask image support to MaskNegatedImageFilter Use dimension range member function registration method Add Python 3.9 to manylinux AZP CI packaging Add GetLogBiasFieldAsImage method to N4 filter Add testing for N4's GetLogBiasFieldAsImage method Update N4 example to use bias field at input resolution Add Image::GetSizeOfPixelComponent method Add testing for Image::GetSizeOfPixelComponent method Remove unused Java carray typemap Add to Java interface Image::GetBufferAsByteBuffer Add Python 3.9 to packaging pipeline AZP Mac Package explicit Python 3.6 version usage Exclude the "latest" branch from triggering packaging Update ITK Superbuild version along the ITK 5.2 development branch Update ITK along 5.2 development branch. Tweak manuylinux build scripts Add docker file for building manylinux2010 Python 2010 wheels Add manylinux2010 to AZP packaging Fix AZP Linux packaging to build configure.BuildHash Update ITK superbuild version to 5.2 rc1 Set CMake Policy version to 3.10 in Superbuild Suppress MSVC getenv security warning. Improve style with C++11 features Remove old TraviCI configuration Update CircleCCI Python versions to 3.6,3.9 ShiftScale supports output pixel type Add warning macro Create ObjectOwnedBase class Create ObjectOwnedBase class Move definition before HelloWorld target Add LoggerBase and ITKLogger classes Add wrapping for Logging classes Add Python Logger derivation support and example Fix implicit parent initialization Fix unable to load SWIG R wrapping due to abstract class Update Python pip before installation Add prose documentation for the Logging example Add Logging example to example index Add 4D ( and more ) support for PermuteImageFilter Discontinue packaging Python 3.5 Fix Logging example python code include link Replace virtualenv with venv Directly create CMake commands for creating venv and installing numpy Adding suppression of distutils unknow field warning. Update ITK version to after 5.2rc1 Use STEP_TARGETS option over EP Add_Step_Targets command Install wheel package to venv for packaging Update to support CMake Ruby module prefix AZP restore publishing of OSX and MS Windows Python packages Update CircleCI images to buster Correct setting of command ownership Add test to echo CMakeCache.txt CircleCI update cmake version to 3.18 Update ITK superbuild version to 5.2rc02 CMake fix detection of Ruby variables CMake prefer Ruby_EXECUTABLE Fix Doxygen style comment for grouping Remove unused VirtualEnv configuration variables Remove installation of numpy Remove numpy installation and unused virtualenv configuration Fix "..." in SWIG docstring causing parse error Revert removal of including PythonDoc.i file Remove old CentOS devtoolset 3,4 and 6 Set the default ITK Multithreader to Platform in Superbuild AZP On Windows separate the building of the core library and python AZP add Java build as separate step to Windows CI AZP To batch add osx 10.15 with newer xcode builds AZP Define env_file for all linux batch jobs AZP Add devtoolset-9 for linux batch jobs Address Python's pip upgrade warning Dave Chen (13): Spelling bugs I missed the first time around Update SetApplication docs added Linux example; some formatting tweaks Spell checking all the headers undoing fixes to TypeList.h BUG: unpack was moved to table.unpack for Lua 5.2 Fixed old,non-working Java HelloWorld example added SITK_NOSHOW check Run HelloWorld examples when testing convential -> conventional workflow to run spell checking changed pip to install from req.txt added IO examples for CSharp, C++, Java, Lua, Ruby and TCL. Ziv Yaniv (5): Correct grammar in displacementfield constructor error message. DOC: GetPixel example separated, dynamic and statically typed languages. BUG: The GetPixelAsComplexFloat64 in Python was not renamed. Updating to modern Python from 2.7 to 3.x. Fixed broken link in filters list. ===================================================================== BRAINSTools: $ git shortlog --topo-order --no-merges v5.2.0..590c371 Dave Welch (7): Create gh-pages branch via GitHub ENH: Added legal submodule Create gh-pages branch via GitHub Delete .gitmodules BUG: removed legal submodule dir Create gh-pages branch via GitHub Create gh-pages branch via GitHub Hans J. Johnson (112): ENH: Update to version 5.2.0 of BRAINSTools ENH: Fix error in GTRACT building requirements. ENH: Make TBB and FFTW conditional for simplifying windows builds. BUG: Double value passed as bool. ENH: Fix vxl version for ITK. ENH: Missing to_matrix call. ENH: Add starting code for reading slicer fiducials. ENH: Simplify ITK find_package. ENH: Fix ITK MI double scaling. ENH: Add Similarity3DTransform to LandmarkInitializer. ENH: Adding initial Similarity3D LMKInit ENH: Remove references to BRAINSCut from BAW. ENH: Remove BrainsCUT old files. DOC: Provide better diagnostic failure modes. ENH: Use exception failure for invalid cases. WIP: Fix version. STYLE: Spelling, organize,variable name changes for readability. STYLE: Add debugging, and cleanup variable names. ENH: Clarify names. BUG: Missing transform from msp->eyefixed->orig for RP point. DOC: Provide better diagnostics. BUG: Code used in debugging missed update step. BUG: Wrong variable name used for final result. ENH: Refine search region for eyes based on emperical data. ENH: Encapsulate ROI generation code. ENH: Restrict second eye location finding based on first eye location. COMP: Fix missing header error. COMP: Fix type narrowing warning. ENH: Allow versor rigid transforms for landmark moving. ENH: Allow output based temp file for fixing landmarks. BUG: Fix replace index counter variable mismatch for old/new strings ENH: Review script for fcsv files. ENH: Update ITK version. ENH: Update to version 5.3.0 for improved BCD performance. ENH: Allow any generic transform to be used for landmarks. ENH: Adding better fallthrough logic. ENH: Update version for latest tag version. ENH: Move useful functions to common library ENH: Use more robust computation for generating Tmsp ENH: Allow aligning to MSP from landmark points. ENH: Preserve original image pixel type. BUG: Restore deleted utility function ENH: Update test cases for minor numerical precision changes. COMP: Fix warning about shadow variable with missing return value ENH: Use ITK with sform preference. COMP: Better timeout and download behavior for large files. ENH: Update ANTs ENH: Remove tbb pre oneapi warnings by avoiding tbb.h ENH: Remove debugging code from standard runs. STYLE: Move build scripts together. ENH: Move old superbuild files out of the way. ENH: Enable building with shared libraries. ENH: Avoid polluting all the projects with build locations. BUG: Development installs needed for ITK BUG: SEM development install required. ENH: Provide installed version of libraries. ENH: Allow for shared libary builds of executables. ENH: Set default install prefix for builds. ENH: Update to fix shared library install of ITK. ENH: Remove outdated reference atlas files. ENH: Improve install path naming for BRAINSTools. ENH: Update to version 5.3.1 with installed shared libs. ENH: Update for fixed compilation of ANTS. COMP: Need extra flag to monitor built in default. ENH: Fixed zlib library extension for mac ENH: Fixed up FFTW installs. ENH: add BRAINSResample 'input' pixel type ENH: Provide linux relative pathing for shared libs BUG: Wrong tbb library search path given ENH: Use relative relocatable rpath for mac ENH: Allow both lmk and image base transforms. ENH: Fix for centos pathing of fftw. ENH: Adding debugging information for git tag. ENH: Updating version to v5.3.2 ENH: Explicitly set FPIC building. DOC: Add future interesting DCMTK option comment. COMP: Some systems use lib64 or lib32 for library directories BUG: Need to address the fact that slicer now write LPS landmarks STYLE: Remove errant cmake file. ENH: Update to install the Atlas reference files as well. ENH: Adding initial programs for defacing data. BUG: Can not write file to shared directory STYLE: Remove unused template parameter ENH: Add install commands STYLE: Remove duplicate code included in BRAINSCommonLib BUG: Fix template parameter to allow 2D and 3D ENH: Add implicit resampling to first image ENH: Adding simple generic transform for ImageCalculator. ENH: Add resampling to ImageCalculator ENH: Remove compiler warning unused variable. ENH: Deface with gradual blur ENH: Update versions to the latest versions. BUG: Output mask is not a debugging output. ENH: write mask image last as a sentinal file. ENH: Add passiveVolume processing BUG: Need to force out of FOV code ENH: Allow BCD to force any landmark location from input file STYLE: Make warning match variable name ENH: Improve the defacing algorithm to preserve regions above 80mm below AC point. ENH: Update the database to be read-only access. COMP: Add both ZLIB*DIR and ZLIB*DIRS variables DOC: Provide better documentation from XML for new version. ENH: Make SGEGraph only submit jobs that need running. ENH: Updating version tag to v5.4.0 ENH: Avoid incorrect typecasting of distance maps BUG: 2D images were not processed correctly ENH: Improve diagnostic for landmark comparison. ENH: Update ITK to 5.2rc2. Set theme jekyll-theme-modernist and migrate Page Generator content Update index.md ENH: Preparing for gh-pages in doc directory. BUG: Fix directory name fo gh-pages. Jean-Christophe Fillion-Robin (1): COMP: Fix windows compilation adding missing check_avx_flags function Kian Weimer (8): ENH: updated external packages to latest version Each external package was checked and updated to its latest version if needed. The following were updated: ANTs, ITK, OpenJPEG, VTK. The VTK component naming convention changes and required a few other files to be modified. BUG: Updated VTK utility names. Some VTK utility names were not changed after the recent External package update. This does not affect functionality but does cause CMake to throw an error in debug mode. These names have now been updated. DOC: Added markdown instructions for configuring CLion for BRAINSTools This includes several images. ENH: Swapped safe-to-replace local variable copies with a constant reference. In some code locations, local variables are created that simply represent a copy of another variable. For expensive to copy values, this can be inefficient. This commit converts such local variables whose contents are not modified to constant references. This implements a portion of the 'performance-unnecessary-copy-initialization' clang-tidy check. -"Local copy 'SET_DATA' of the variable 'strname' is never modified; consider avoiding the copy" STYLE: Applied clang-format style changes to entire BRAINSTools tree. ENH: Replaced string addition operations within loops to append operations. The append operation provided by `std::string` is more efficient than an addition. Large string addition operations within loops have been changed to append. This implements the 'performance-inefficient-string-concatenation' clang-tidy check. -"String concatenation results in allocation of unnecessary temporary strings; consider using 'operator+=' or 'string::append()' instead" ENH: Replaced single character string literals within find operations with characters. In several locations, a length 1 string is passed to `std::string::find()` or others. The character literal overload is more efficient so these values have been converted. This implements the 'performance-faster-string-find' clang-tidy check. -"'find' called with a string literal consisting of a single character; consider using the more effective overload accepting a character." ENH: Converted method parameters to pass by refrence. Constant method parameters are copied during each method invocation. These parameters have been changed to pass-by-reference to avoid unnecessary, expensive copies. This implements a portion of the 'performance-unnecessary-value-parm' clang-tidy check. -"The const qualified parameter 's' is copied for each invocation; consider making it a reference." abpwrs (10): ENH: mask lower 80mm more efficiently & pseudocode for apply mask ENH: adding flake and black configs STYLE: indentation change STYLE: pythonic if statement STYLE: fixing keyword naming `exit` to be exit_status ENH: adding diagnostic prints one exceptions ENH: BIDS style filename generation ENH: BIDS style file names can be generated automatically from a subject data dictionary ENH: adding assertion to bidsUtils_test.py FIX: correcting docs/comments + removed extra loop ENH: added noMaskApplication and inputMask falgs Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com>
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