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jcfr authored
To help extension developers transition their code base, a migration guide is also available on the wiki. See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/ITK4-to-ITK5 This commit implements the following changes * Compatibility with refactor of threading models in ITK: Fix compilation using ProcessingThreader class instead of PlatformMultiThreader. ITKv5 reorganized the multi-threading capabilities of ITK into a more modular organization and naming to support several modern parallelism paradigms. Note that these changes allow Slicer to compile with ITKv5, but does not take advantage of any enhancement supporting new threading models. ProcessingThreader is still the old-renamed PlatformMultiThreader. These changes were originally associated with PR https://github.com/Slicer/Slicer/pull/1057 * Fix compilation issue related to ComputeJacobianWithRespectToPosition parameter mismatch. ITKv5 change the argument of some transform functions from JacobianType to JacobianPositionType. This fixes the new signatures. These changes were originally associated with PR https://github.com/Slicer/Slicer/pull/1055 Co-authored-by: Pablo Hernandez-Cerdan <pablo.hernandez.cerdan@outlook.com> Co-authored-by: Hans Johnson <hans.j.johnson@gmail.com> Co-authored-by: Sam Horvath <sam.horvath@kitware.com> Co-authored-by: Jean-Christophe Fillion-Robin <jcfr@kitware.com> Highlighted changes ------------------- SimpleITK (v1.1 -> v1.2): * Compatibility with ITKv5 * New Filters: ObjectnessMeasuresImageFiler (Frangi's vesselness), IterativeInverseDisplacementFieldImageFilter, UnsharpMaskImageFilter, and RoundImageFilter. * Multi-resolution BSpline registration by adapting the BSplineTransform resolution in the ImageRegistrationMethod * Add support for multi-component images to ClampImageFilter, MeanProjectionImageFilter, SumProjectionImageFilter, and the TileImageFilter. * More information at: https://github.com/SimpleITK/SimpleITK/releases ITK (4.13 -> 5.0rc1): * Performance improvements: * N4BiasFieldCorrectionImageFilter accelerated through itk::ImageBufferRange and other optimizations. * Various modern C++ improvements related to default constructors and move operations. * ResampleImageFilter::CastPixelWithBoundsChecking is now faster. * Data copies in itk::BSplineTransform were reduced. * The number of evaluations in line search optimizer were reduced by half. * CanRead is now faster for inspection of potential DICOM files, both with the GDCM and DCMTK DICOM backends. * Add Frequency Domain Support for working with images in the dual domain, such as the output of FFT images. * A new Simple Linear Iterative Clustering (SLIC) super-pixel segmentation filter is available. * Completed transition to modern features introduced in c++11 * Third Parties updated and full support for new ones, such as DCMTK and Eigen3. * More information at: https://github.com/InsightSoftwareConsortium/ITK/releases BRAINSTools (v4.7.1 -> v5.0.0): * Completed transition to modern features introduced in c++11 * Bug fixes Complete list of changes ------------------------ List of ITK changes: ``` $ git shortlog 87f5d83..fec5de4 --no-merges Bai Shi (1): COMP: To fix compilation error of "cannot dynamic_cast 'x' Bradley Lowekamp (159): ENH: Adding more swap methods BUG: Respect Visibility Preset for initial template visibility COMP: Use explicit equality for boolean evaluation of real number BUG: Keep the SetSeed# methods in IsolatedConnectedImageFilter ENH: Use direct for loops for implementing image transformations ENH: Mark 2 template parameter ModulusTransform to be removed COMP: Remove legacy marking on definition of SetSeed methods STYLE: Use itk::v3 nested namespace for Rigid3DTransform BUG: Preserve option to use a "label value" mask and boolean mask ENH: update C+11 headers and try compile for headers ENH: Remove duplicated CMake module from upstream CMake COMP: Explicitly include the fixed width integer header before usage BUG: The CXX language must be enable to check compiler variables PERF: Support move semantics for ITK smart pointers ENH: Remove usage of SmartPointerForward reference ENH: Remove unneeded internal smart pointer type COMP: Require MSVC VS14 2015 for C++11 compatibility ENH: Use C++11 template alias for Image::Rebind STYLE: Use copy-swap idiom for SmartPointer ENH: Use std::unique_ptr over itk::AutoPointer DOC: Document additional MaskValue variable BUG: remove unused cmake CXX try compile file BUG: Remove un-configured and unused CMake configure define BUG: Improve Doxygen extraction with blank line ENH: Remove TEMPLATED_FRIEND macro and try compile ENH: Replace optional tr1 type_traits with c++11 standard ENH: Assume c++11, remove configure defines for optional TR1 features ENH: Only use std::atomic implementation for AtomicInt class ENH: Add direct SmartPointer conversions to match raw Pointers PERF: Use emplace when inserting into map for ProcessObject ENH: Create virtual interface for the MultiTheader ENH: Trying out the ThreadPool as a separate MultiThreader BUG: Fix uninitialized cross structuring element buffer BUG: Disable ThreadPools by default COMP: Add forward declaration of ExceptionObject in Macro.h COMP: Add forward declaration of ExceptionObject in Macro.h ENH: Use gtest_discover_tests if available DOC: Watershed filters is not stream-able COMP: Use nullptr over 0 for null pointer STYLE: Use SmartPointer direct conversion constructors Revert "BUG: Disable ThreadPools by default" BUG: Actually disable ThreadPools by default COMP: Suppress warning on CircleCI about itkIndex out of bounds ENH: Update CircleCI external data cache ENH: Address incorrect types with neighborhood iterator base class COMP: Make MirrorPadImageFilter::DelayBase a conventional parameter PERF: remove virtual methods in neighborhood iterators ENH: Add ITK_ITERATOR_FINAL ENH: Use named inputs for the PasteImageFilter PERF: Remove iterators stored as member variables BUG: Add specification of OutputImage Type for TobogganImageFilter ENH: Improve numerics of resampling for linear transform COMP: Fix gcc 4.8 initialize warning ENH: Add baseline image to sporadically failing test ENH: Adding Unary and Binary GeneratorImageFilter ENH: Convert functor based filters to generator ENH: Update internal filters to use BinaryGereratorImageFilter ENH: Updating Functor filter with parameters to the new Generator COMP: Address Generator filters destructors warning DOC: Fix BSplineDecompositionImageFilter Doxygen see also link ENH: reuse default splitter BUG: revert thread update to BSplineScatteredDataPointSetToImageFilter ENH: Update CircleCI CMake version to 3.11.2 BUG: Correct detection of most recent data file ENH: Improve numeric computation of linear interpolation for Resample ENH: Update baseline image for ResampleImageFilter3Test1 BUG: Add 4 pixel tolerance to ResampleImageFilter3Test1 BUG: Prevent concurrent read/write in output image BUG: Handle case where output image is zero sized BUG: Add missing dependencies in Module testing ENH: Remove SPECIFIC_IMAGEIO_MODULE_TEST feature BUG: Fix name typo for ITK_GLOBAL_DEFAULT_THREADER BUG: Fix incorrect library variable for MeshIO test drivers ENH: Create TestKernel library ENH: Add SLIC segmentation to new Superpixel module COMP: Fix C++11 compatibility with assert in constexpr COMP: Use std::min over vnl_math_min BUG: Fix index type and and number of indexes BUG: Add alternate baseline itkSLICImageFilterTest1 test ENH: Update test output to include test name BUG: improve numeric consistency in linear algorithm COMP: Add missing overrride to virtual destructor COMP: Remove unused testing function and headers BUG: Finish updating to ScanlineIterator in nonlinear method ENH: Update SLIC filter to use new ITK threading model ENH: TileImageFilter learns to use VectorImages COMP: remove duplicate declaration of TempImageType DOC: Add link to published Insight Journal paper ENH: Update CenteredTransformInitializer print self method PERF: Remove internal streaming in DiscreteGaussianImageFilter ENH: Update MinimumMaximumImageFilter to use dynamic threading ENH: Update StatisticsImageFiler to use DynamicThreadedGenerateData ENH: Add compensated summation to the StatisticsImageFitler BUG: Use pip to install cmake PERF: Use the recursive Gaussian filter in registration method BUG: Add additional baseline for debug COMP: Length GTest discovery timeout BUG: Correct image used for debug SimpleImageRegistrationTest BUG: Add cxx suffix to specified source GTest code ENH: Consistently use default OutputWindow for messages BUG: Explicitly set sampled pointset in virtual domain ENH: Use std::enable_if and std::is_same in filters PERF: Memory alloc reduction in ComputeJacobianWithRespect PERF: Improve MatrixOffset Jacobian computation performance COMP: Address signed to unsigned comparison warning STYLE: Cleanup development comments PERF: perform matrix multiplication in-place for composite Jacobian ENH: Provide explicitly instantiated vnl_svd_fixed PERF: Change type of Jacobian w.r. position to vnl_matrix_fixed PERF: Change the purpose of the cache jacobian argument DOC: Improve Extract exception for region size mismatch BUG: Print ImageIOBase::m_Spacing BUG: Fix TIFFImageIO spacing for multi-page BUG: Support ITK transform files with corrected group names ENH: Only use one Work Unit in BSpline convergence checker BUG: Fix HDF5ImageIO reporting any HDF5 file is readable ENH: Improve N4BiasFieldCorrectionImageFilter ENH: Add extensions to HDF5ImageIO ENH: Add ImageIO methods to check name for file extensions BUG: Quiet HDF5-DIAG from H5File::isHdf5 ENH: Update LabelStatistics to use dyanmic threading ENH: Move JPEG200 ImageIO into separate ImageIO module BUG: Update SCIOFIO to ITKv4.13 branch ENH: Make ProcessObject::VerifyInputInformation constant BUG: Handle boundary case with max metric PERF: Reduce number of evaluations in line search optimizer by half COMP: Fix unused argument warnings in SpatialObjectPoint::operator= BUG: Handle boundary case with max metric ENH: Update ImageToHistogram to use modern dynamic threading. PERF: implement concurrent histogram merge/reduce BUG: Fix move of histogram smart pointer BUG: Add parameter which stores the requested number of work units. BUG: use =default for default implementation of destructor BUG: Prevent square root of negative number BUG: Check all entries are not null STYLE: Prefer immediate exception over long if BUG: Fix sqrt of negative values BUG: Address valgrind leaks for classes which use ScanlineFilterCommon BUG: Limit number of threads used for testing ITK ENH: Replace centered transforms with non-centered versions BUG: Remove static member function variable DOC: Fix LBFBS2 typo BUG: Remove static member function variable BUG: Fix multi-resolution bspline registration example BUG: Adding updated baseline image for improved example DOC: Fix typos in LBFGS2 optimizer's error string ENH: On Azure DevOps only show test output on failure STYLE: Use GTest file name suffix for Google Test based tests BUG: Remove unused TRansfromDomainDirectionInverse IVAR BUG: Synchronize BSpline MeshDomain parameters from fixed params ENH: Adding GTest for BSplineTransform ENH: Create method to set transform domain params from coeff images BUG: Synchronize BSpline MeshDomain parameters from fixed params ENH: Refactor BSplineTransform DOC: Update the BSplineTransform class doxygen ENH: Update N4BiasField to utilized named positional inputs COMP: Addressed unused parameter warning in ImageRegion default BUG: Use compatible ITKv4 computation BUG: Fix Ostu test to work with ITKv4 default options Brian Avants (1): PERF: Only throw exception if zero valid points Brian Helba (1): BUG: Ensure that itkSampleToHistogramFilterTests fail on errors Bryce A Besler (1): ENH: Move DiscreteGaussianDerivativeImageFilter from Review to ITKImageFeature Chao Wu (2): ENH: Enable writing scl_slope and scl_inter in NIfTI header BUG: Missing SetCPUBufferPointer in GPUImage<...>::SetPixelContainer(...) Dženan Zukić (169): ENH: updating SphinxExamples and pointing to GitHub COMP: Get rid of warning about registry key STYLE: minor fixes BUG: duplicator crashes if buffered region is smaller than largest region STYLE: reducing code duplication and cleaning up method documentation ENH: adding itkReviewPrintTest to tests. It existed but was not invoked. COMP: turn FEM off by default, as it takes a long time to build COMP: fixing compiler warnings ENH: making ITKBioCell and ITKNeuralNetworks remote modules COMP: fixing configure error COMP: long paths are not yet supported by all the tools in the build chain COMP: using ITK_DELETED_FUNCTION, and more consistent override specifier ENH: simplify code and properly support long long type COMP: fix compile warning STYLE: avoid redirect for repository address in DVMeshNoise ENH: update remote modules to require CMake 3.9.5 BUG: fixing crash in test ENH: Remove ITKFEMRegistration from default configuration ENH: Fixing error and improving examples' test ENH: Use MultiThreaderBase STYLE: reducing duplication and removing commented code in DistanceMap tests STYLE: fixing typo BUG: more reliably detect Windows+DLLs case ENH: enable thread pool by default ENH: adding exponential decay option to MirrorPadImageFilter BUG: Set/GetGlobalDefaultNumberOfThreads was forgotten in legacy #ifdef BUG: fixing Windows+DLL ThreadPool sporadic destructor hanging COMP: Using MultiThreaderBase, avoids legacy warning BUG: fixing null pointer dereference in PreOrderTreeIterator<>::Next() ENH: start migration guide document STYLE: increasing initial size of the debug window BUG: fixing null pointer dereference at the end of iteration COMP: reducing direct usage of MultiThreader BUG: remove observations in FilterWatcher's destructor ENH: support Unicode characters in class documentation BUG: fixing index computation in resample filter ENH: reducing code duplication in FilterWatcher ENH: refactoring MultiThreader infrastructure ENH: deciding which filters can use the new threading model ENH: reporting progress ENH: simplifying Canny filter by using new threading infrastructure STYLE: Renaming MultiThreader to PlatformMultiThreader ENH: use C++11 thread primitives instead of SpawnThread COMP: improve backwards compatibility by retaining the renamed header ENH: Add TBB-based multi-threader ENH: refactoring filters to avoid use of memory barrier ENH: reworking logic for determining default multi-threader COMP: fixing compile error on GCC 4.8.5 20150623 (Red Hat 4.8.5-28) STYLE: remove outdated and useless comments from VectorExpandImageFilter ENH: add a baseline for QuickViewTest.png (Win7x64+VS2017+VTK8.1OpenGL2) STYLE: reduce number of lines by removing unnecessary empty lines DOC: document FilterWatcher removal ENH: adding an .editorconfig file to aid IDE's code formatting options BUG: forgotten #ifdefs for ITK_LEGACY_REMOVE ENH: adding debugger help files for Visual Studio 2017 ENH: moving .clang-format file into the root folder, ENH: using the new threading mechanism for FFT module ENH: explicitly setting threading model in each multi-threaded filter ENH: support classic ThreadedGenerateData via ITK_CLASSIC_THREADING_MODEL BUG: fixing a test which has been failing since multi-threading refactoring ENH: updating baselines for itkBSplineScatteredDataPointSetToImageFilterTest* COMP: fixing 2 compile warnings STYLE: renaming migration guide document ENH: extending migration guide with threading refactoring instructions ENH: reducing redundancy in itkLandmarkBasedTransformInitializerTest ENH: eliminate CMake option ITK_CLASSIC_THREADING_MODEL STYLE: a more direct link (after PR has been merged) STYLE: update clang-format configuration ENH: adding ParallelizeArray method to MultiThreaderBase COMP: fixing warning in external module COMP: Address usage of deleted assignment operator ENH: more thorough removal of deprecated "multiple method" DOC: add compatibility warning to Barrier STYLE: initializing SingleMethod/SingleData in base class DOC: merging instructions from itkMultiThreader.h into migration guide ENH: rename NumberOfThreads into NumberOfWorkUnits in filters ENH: Add backwards compatibility for Get/SetNumberOfThreads ENH: renaming NumberOfThreads into NumberOfWorkUnits in MultiThreaderBase ENH: adding backwards compatibility for MultiThreaders ENH: default number of work units is greater than default number of threads COMP: fixing compile warning on GCC 4.8 ENH: rewriting thread pool to take advantage of C++11 ENH: implement Parallelize Array and ImageRegion in PoolMultiThreader COMP: SmoothingRecursiveYvvGaussianFilter compiles with new ITKv5 threading ENH: RGB/RGBA consistency, operator / and remove comments from implementation ENH: refactoring RecursiveSeparableImageFilter to use new threading ENH: updating MCI: adjusting to split between threads and work units in ITKv5 ENH: compute spacing using n-1 instead 2-1 in ImageSeriesReader BUG: updating the HDF5 symbol mangling ENH: fix reading of oblique image series BUG: fixing crash in ThreadPool's destructor COMP: fixing warning about shadowed global COMP: avoid warning with CMake 3.12 and newer regarding policy CMP0075 ENH: write format which is backwards-compatible with HDF5 version 1.8 ENH: refactoring BinaryImageToLabelMapFilter to use the new threading model ENH: adding ProgressTransformer ENH: proper backwards compatibility to HDF5 1.8 STYLE: fixing 'No new line at the end of file' ENH: adding short description of split between threads and work units ENH: rewriting BarrierTest to work with any MultiThreader ENH: cause compile error with HDF5 version 1.10.0 and 1.10.1 ENH: restore BeforeThreadedGenerateData method DOC: state that SetRecursive must be called before SetInputDirectory BUG: updating the symbol mangling list BUG: removing mangling of unversioned variant of versioned definitions ENH: update migration guide: prefer C++11 classes over ITK's ENH: cleaning up ProcessObject ENH: using progress transformer in recently refactored classes COMP: fixing LoggerBase to compile even when DEBUG is defined DOC: ProgressReporter should be replaced by ProgressTransformer ENH: code simplification and more granular progress reporting ENH: return bin maximum as threshold STYLE: removing void if used in place of empty parameter list ENH: update remote module MorphologicalContourInterpolation BUG: nbOfThreads was bounded to GlobalMaximumNumber, but not work units ENH: Ignore current load in PoolMultiThreader COMP: missing ConstPointer declaration BUG: fix crash in RegionGrowingBenchmark ENH: reducing duplication in 4 scanline-based image filters ENH: use scanline iterators and clean up the code a little COMP: fix [-Wc++11-narrowing] in initializer list during Python wrapping ENH: refactor ConnectedComponent to not use Barrier. Also reduce duplication. STYLE: aligning macro continuation backslash COMP: fixing unused variable warning COMP: add Python wrapping for ScanlineFilterCommon ENH: updating remotes to their latest versions DOC: mentioning ITKV4_COMPATIBILITY in the migration guide COMP: minor fixes in preparation for deprecating atomic, mutex and friends ENH: updating remotes to latest versions ENH: using standard library's mutex primitives ENH: deprecating functionality which exist in C++11 standard library COMP: missing #include <condition_variable> BUG: clamp work units to ITK_MAX_THREADS in Platform and Pool MultiThreaders BUG: fix Python wrapping after deprecating MutexLock and friends ENH: adding new remote modules: Montage and BSplineGradient DOC: fixing copy-paste error about functor type ENH: improve precision of median calculation by default STYLE: minor space and line break improvements ENH: FrequencyBandImageFilter derives from UnaryFrequencyDomainFilter ENH: ITKv5_CONST macro for VerifyPreconditions() and VerifyInputInformation() ENH: ITKv5_CONST macro for VerifyPreconditions() and VerifyInputInformation() BUG: background label could be the same as one of the object labels COMP: fix compiler warning in itkIndexRange.h ENH: adding wrapping for UnaryFrequencyDomainFilter DOC: updating commit information for ITKv5_CONST in ITK 4.13.x ENH: commit message script uses GitHub issue referencing format. ENH: update Montage remote module BUG: test image was not properly initialized. Closes #207. COMP: fixing compile errors on Ubuntu 16.04 with GCC 5.4.0 ENH: compile VNL in parallel on Visual Studio COMP: fix compile errors with CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS:BOOL=ON COMP: Remove VNL_EXPORT from header only class. Closes #191. COMP: fix CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS COMP: fix link errors coming from undefined static constexpr member STYLE: rename template parameter TMatrixDimension into VDimension DOC: EigenValues parameter uses operator[], not operator[][] COMP: compile with Visual Studio in conformance mode AKA /permissive- COMP: moving the default constructor of vnl_matrix from .h into .hxx STYLE: removing empty lines between comments and constructors ENH: enable progress reporting with ITKV4_COMPATIBILITY. Closes #228. ENH: updating ITKMontage module DOC: trying to fix the doxygen warning ENH: Updating Visual Studio debug visualizer definitions DOC: removing long outdated comment ENH: updating Montage module STYLE: minor fixes to release notes COMP: a fix for system double-conversion build ENH: updating Montage: fix double-conversion include directory ENH: update ITKMontage: Fix crash when setting tiles from memory Eigen Upstream (2): Eigen3 2018-11-19 (493fa50e) Eigen3 2019-01-14 (16812519) Francois Budin (30): BUG: Update ITK test files SHA and debug ContentLinkSynchronization.sh ENH: Bump ITK version to 5.0.0. ENH: lifting path length limitation on Windows 10 version 1607+ BUG: Remove bad guards stopping inclusion of necessary hxx file BUG: Remove extern "C" call to include <cstring> BUG: Initializes CMAKE_DEBUG_POSTFIX to be empty DOC: Remove CMake comments mentioning CMake 3.4 DOC: ITK_CONSTEXPR* and ITK_HAS_CXX11_RVREF are deprecated BUG: DCMTK builds fails with ICU ON on Linux and Mac BUG: LabelErodeDilate remote module repositories are out of sync BUG: Projects could not link to DCMTK on Windows and MacOS DOC: Add missing documentation for `github_compare` option ENH: Update CMake code to use IN_LIST (CMake >= 3.3) BUG: Update LabelErodeDilate ENH: Compile ITK with MKL (FFTW) installed on system BUG: Update ParabolicMorphology remote module ENH: Sync ThreadPool and MultiThreaderBase global variables across modules BUG: Add function to not wait for threads when destroying thread pool BUG: Improvements to ITK NumPyBridge DOC: Improve exception message to precise what image sizes can be processed BUG: THEADER instead of THREADER BUG: Disable using mkl_tbb_thread ENH: Adding IOOpenSlide ImageIO remote module to ITK BUG: WRAP_2 is a local variable, not a CACHE variable BUG: Wrong path to baseline images ENH: Allow selecting ImageIO in Python template code ENH: Support loading image series in itkTemplate. ENH: `itk.imread()` now supports image series ENH: Support for tuples passed as arguments through itkTemplate New() function BUG: Missing ITK_WRAP_rgba_* variables in WrapITKConfig.cmake.in GCC-XML Upstream (1): ENH: pygccxml develop (reduced) GDCM Upstream (3): GDCM 2018-05-23 (69cb71a4) GDCM 2018-11-05 (3ffbf1ed) GDCM 2018-11-30 (ec82fb48) Gabriel A. Devenyi (1): PERF: Enable MINC internal compression by default Gregory C. Sharp (1): DOC: Fix misspelling of vertices HDF5 Maintainers (3): HDF5 2016-05-10 (7453bbef) HDF5 2018-07-20 (bed5b207) HDF5 2018-08-22 (08d77e43) Hans Johnson (164): ENH: Update Wiki examples for latest code changes COMP: Remove override warnings ENH: Cuberille future compilation deprecations ENH: Strain future compilation deprecations COMP: TwoProjectionRegistration Future proof code COMP: LevelSetsv4 used deprecated api COMP: N4 remove testing of deprecated SetMaskLabel BUG: Provide consistent GetOutput behavior BUG: GetModifiableTransformList needs to always be available BUG: Restore backwards compatibility DOC: Remove ITKv3 to ITKv4 migration documentation. COMP: Provide migration documentation old macros STYLE: Remove deprecated code directory contents STYLE: Remove all vestiges of ITKv3 code STYLE: Remove legacy code for ITKv5 starting ENH: Revert to include itkv3::Rigid3DTransform STYLE: Move Future deprecated to deprecated BUG: Restored testing for long HistorgramMatching COMP: Remove unnecessary conditional tests COMP: Force using lower deployment targert for fftw COMP: Use C++ headers over C headers COMP: Set ITK_VERSION_MAJOR to 5 STYLE: Fix header guard format COMP: Remove ITK_USE_STRICT_CONCEPT_CHECKING flag ENH: Set cmake Minimums to 3.9.5 COMP: Change min cmake version to 3.9.5 for circleci COMP: Directly use cmake compiler_detection.h STYLE: Fix typo requireing -> requiring COMP: Consistently set use of CMake 3.9.5 and options COMP: Enforce building ITK with C++11 COMP: Modularize cmake config like VTK. COMP: Use C++ headers over C headers (part 2) ENH: Scripts used during ITKv5 migration STYLE: Remove conditional version 201103L code COMP: Need to match type for different threaders COMP: Preparing for ITKv5 by adding override COMP: Use C++11 override directly STYLE: Use override statements for C++11 COMP: Use C++11 ITK_NULLPTR directly COMP: Use nullptr instead of 0 or NULL STYLE: Prefer nullptr for C++11 COMP: Use C++11 nullptr directly BUG: VXL visibility must match ITK visibility COMP: Use C++11 = delete directly COMP: Use C++11 constexpr directly STYLE: ITK_COMPILER_CXX_CONSTEXPR is always true BUG: Missing external linkage options for float and double. COMP: Remove deprecated C++ 11 features ENH: ReplaceitkGetObjectMacro.sh used during ITKv5 migration ENH: Update SeveralRemotes to latest version. COMP: Suppress invalid warning STYLE: Remove outdated conditional code STYLE: Remove unnecessary old CMakeCode ENH: Remote for SmoothingRecursiveYvvGaussianFilter STYLE: Prefer C++11 type alias over typedef BUG: Type alias errent typo in name BUG: ConceptChecking type matching failed. STYLE: Remove ITK_HAS variables that should not be defined COMP: Allow using cmake 3.9.5 default for RPATH setting STYLE: Replace itkStaticConstMacro with static constexpr BUG: Propagate C++11 requirements to external project STYLE: Prefer constexpr for const numeric literals STYLE: Use range-based loops from C++11 PERF: Allow compiler to choose best way to construct a copy PERF: Replace explicit return calls of constructor STYLE: Use auto for variable creation BUG: Restore ITK.kws.xml preferences ENH: Provide advanced development mode for writing GTests COMP: Use C++11 noexcept directly ENH: Use simplified/natural conversion to const pointer ENH: Use natural ConstPointer conversion STYLE: Use override statements for C++11 COMP: Use C++11 noexcept directly ENH: Add google test for itkIndex.h ENH: Make const operator[] conform to standards STYLE: Change aggregate classes to mirror std::array ENH: Update all remote modules with C++11 conformance BUG: New SmartPointer conversion ambiguity BUG: Error in ITK_VERSION construction ENH: Add introspection into the build process COMP: Silence warning of mismatched signs. ENH: Bring in C++11 updates for ITKBridgeNumPy STYLE: Do not use itkGetStaticConstMacro in ITK COMP: Make member name match kwstyle requirements. BUG: Add ability to construct SmartPointer with NULL BUG: Update NULL pointer patch with final fixes COMP: std::bind2nd deprecated C++11, remove C++17 COMP: Improve variable naming for m_DerivativeOperator STYLE: Use C++11 override keyword directly STYLE: Use C++11 override keyword directly ENH: Add compression option for Transform files COMP: Address type mis-match compiler warning COMP: Remove unused variable warning ENH: HDF5 moved from svn to git ENH: Update HDF5 import script for 1.10.2 ENH: Remove svn version of hdf5 files not added by import from git STYLE: Consistently name for ITK conventions BUG: Fixing the HDF5 internal path names tests COMP: Fix const assignment error in testing COMP: Prefer snprintf to avoid buffer overruns STYLE: Use modern C++11 =delete to indicate not implemented ENH: Update KWStyle hash to build latest updates STYLE: Prefer error checked std::stoi over atoi BUG: GE4IO atoi failures resulted in implicit 0 image slices BUG: Commandline arguments were not properly processed BUG: atoi failure => 0 hid processing failures BUG: Command line parsing silently failed STYLE: Prefer error checked std::stod over atof BUG: Failed conversion to float with uncaught failure STYLE: Pefer = default to explicitly trivial implementations COMP: Use nullptr instead of 0 or NULL STYLE: Replace defines with constexpr and using statements COMP: Fix VS2017 compilation regression COMP: Use static method from class directly STYLE: Remove support for pre 20160229 VXL_VERSION_DATE_FULL STYLE: Decouple matlab printing explicit instantiations ENH: Adding explicit instantiations for dimensions 1-10 COMP: Remove duplicate explicit instantiations COMP: Remove unused variables. BUG: vidl_itk_istream does not override an ITK object ENH: Use C++11 override for overridden functions. STYLE: Remove unnecessary vcl_XXX.h headers ENH: Add scripts to assist with migrations ENH: Adding a few more clang tidy checks. BUG: Do not override user selection settings ENH: Update to require VXL 2.0.0 or later STYLE: Remove unused include headers ENH: Provide mechanism for changing git remote url COMP: Many of the remotes require updates for ITKv5 STYLE: Remove VCL_INCLUDE_CXX_0X outdated reference. ENH: Add specification for -D__clang__ to clang-tidy PERF: emplace_back method results in potentially more efficient code STYLE: Replace integer literals which are cast to bool. ENH: Fetch upstream as part of setup. ENH: Stop abort on first failure. BUG: Default commit message fixed for =delete modernization ENH: Provide consistency with C++11 core guidelines BUG: Missing default argment override ENH: VXL 2.0.0 provides all instantiations needed by ITK ENH: Fix deficient itkCastImageFilter test STYLE: Minor variable naming and readability changes. COMP: Provide conversion range testing valid_static_cast function ENH: Increase minimum VXL version to 2.0.1 for wrapping ENH: REVERT compile VNL in parallel on Visual Studio ENH: Require VXL v2.0.2 release. ENH: Increase size attribute for large third party file. STYLE: Remove VXL_VERSION_DATE_FULL conditionals COMP: Remove duplicate explicit instantiation ENH: Provide range for non-warned cmake versions ENH: Update the GIFTI codebase DOC: Typo: @tparam -> @param fix doxygen generation DOC: Improved documentation for the migration guide ENH: Manually update nifti version from github ENH: Employ the `rule of zero` for aggregate types STYLE: Use default member initialization STYLE: Remove the register keyword ENH: NIFTI needs to be part of ITKTargets STYLE: rm initializer list extra lines ENH: DCMTK 3.6.4 api changes accomodated ENH: Move default [con/de]strutor to .h COMP: Protected static function must be public PERF: GDCM & DCMTK CanRead fails very slowly for non-DICOM files. PERF: readability container size empty STYLE: Prefer = default to explicit constructor(){} Hastings Greer (1): ENH: Add wrapping for Labeled PointSet to PointSet registration classes Hui Xie (1): BUG: The Z spacing was set using thickness Isaiah Norton (3): PERF: improve DCMTKFileReader::CanReadFile perf BUG: prevent segfault when transform reader fails to load .mat BUG: don't quote argument to URL_HASH for FFTW Jean-Christophe Fillion-Robin (3): BUG: Prevent gdcm "missing implementation" error on macOS STYLE: MeshIO: Introduce ITKIOMeshBase module. See #3393 BUG: Refactor itkFloatingPointExceptions to fix macOS support Jon Haitz Legarreta (16): STYLE: Fix typo in itk::VariableLengthVector struct name. ENH: Set the InsightSoftwareConsortium repo as the remote. STYLE: Improve itkHoughTransform2DLinesImageFilter style. DOC: Add different GitHub badges to the `README.md` file. DOC: Change the ITK Git tips wiki page reference for Git scm website. DOC: Add commands in a `Review` section to the ITK Git cheat sheet. DOC: Change the `ITKGitCheatSheet.tex` file tittle. DOC: Make references to ITK issue tracking system consistent. DOC: Update the ITK logo files in `Documentation` folder. DOC: Remove PSD files containing old ITK logo. BUG: Address use of CMake variables in CMakeLists.txt. COMP: Set the minimum required CMake version to 3.10.2. STYLE: Stick to the ITK style guidelines. COMP: Bump the remote modules' versions after the CMake ver update. ENH: User initialization lists over direct assignment. ENH: Improve itkEuclideanDistancePointMetric coverage. Jon Haitz Legarreta Gorroño (41): BUG: Fix bug in class LaTeX documentation Doxygen link. BUG: Fix unnecessary explicit itk namespace mention in Doxygen link. DOC: Remove redundant ellipsis after "etc." in LaTeX doc. DOC: Remove unnecessary EOF comments. DOC: Make namespace closing bracket comments consistent. DOC: Fix typo: substract to subtract. DOC: Remove unnecessary ifdef and class ending comments in FEM. DOC: Remove non-existing namespace comment. ENH: Add a code of conduct to the ITK project. ENH: Bump latest version of the ITKSplitComponents remote module. DOC: Remove unnecessary Doxygen \ref keyword in module crossrefs. DOC: Remove crossrefs to non-existing classes. DOC: Improve the ISSUE_TEMPLATE.md markdown file contents. DOC: Change the term `mailing list` in README.md. DOC: Fix syntax mistake in `Sharing Data` section of CoC. DOC: Fix typos in class doc. STYLE: Update the wrap files to match current CMake syntax. DOC: Fix typo. COMP: Use and move ITK_DISALLOW_COPY_AND_ASSIGN calls to public section. ENH: Update the WikiExamples remote module commit hash. COMP: Bump the remote modules' versions. DOC: Fix miscellaneous typos. ENH: Add the ITK BoneMorphometry module as a remote. COMP: Bump remote modules versions. ENH: Clean up itkGrayscaleMorphologyImageFilter tests. ENH: Increase itk::OtsuMultipleThresholdsImageFilter coverage. COMP: Use C++11 nullptr directly DOC: Fix incorrect class ref for Doxygen. ENH: Bump remote modules to their latest commits. ENH: Increase coverage for itk::GrayscaleFillholeFilterImage. DOC: Update the documentation concerning binary data. DOC: Format remote module documentation README to markdown. ENH: Update the SmoothingRecursiveYvvGaussianFilter remote module hash. DOC: Point to the ITK git cheat sheet in the repository. DOC: Fix the ITK Git cheat sheet file link. ENH: Add script to priviledge C++11 type alias over typedef. DOC: Advise users to delete the PR template in message. DOC: Move the issue and pull request templates to a specialized folder. ENH: Remove `FindITKPythonLibs.cmake` file. ENH: Follow remote repositories name changes. DOC: Adjust the CoC Committe to the 01/09/2019 meeting decision. KWSys Upstream (2): KWSys 2018-01-08 (f7990fc2) KWSys 2018-06-01 (8ef62b28) Kwame Kutten (2): BUG: Removed quotes from fftwf and fftwd hashes ENH: Make StatisticsImageFilter returns Sum Of Squares Lucas Gandel (2): ENH: include WrapITKConfig for external module ENH: Allow for itk::ImageSource wrapping override Marcus D. Hanwell (1): DOC: Add GitCheatSheet sources Marian Klymov (1): ENH: Mark copy constructor of ExceptionObject and derived classes noexcept. Martino Pilia (1): BUG: fix itkFormatWarning in Python wrapping Matthew McCormick (197): BUG: Remove ITKTubeTK remote ENH: Add PolarTransform remote module COMP: Do not use absolute path to TestBigEndian.cmake in GDCM COMP: Enable pthreads shim with Emscripten COMP: Specify OutputImageType for boundary conditions in FFTPadImageFilter COMP: Update DCMTK to 2018.01.16 and support Emscripten COMP: Fix cross compiling DCMTK BUG: Do not set DCMTK_WITH_XML to ON in DCMTK configuration COMP: itk::Math perfect forward return type BUG: Do not segfault when trying to use PDEDeformableRegistrationFilter COMP: Ensure CastXML uses C++11 with GCC or Clang COMP: Remove legacy BackTransform methods from Rigid3DTransform COMP: Explicitly add NumericTraits::max to the API COMP: Address SG line length warnings in DataRepresentation, Filtering DOC: Update README Software Guide link DOC: Update Discussion link in the README ENH: Add banner to the README COMP: Bump KWStyle to 2018-02-22 master COMP: Add missing wrapping for MultiThreaderBase COMP: Do not wrap methods with ?unknown? type COMP: Add missing itkSimpleFastMutexLock headers ENH: Import the ITKBridgeNumPy module BUG: GetArrayFromImage calls UpdateLargestPossibleRegion BUG: Add missing wrapping for PoolMultiThreader BUG: Exclude MultiThreaderBase from GetNameOfClass test COMP: Add SimpleFastMutexLock include to ESMDemonsRegistrationFunction BUG: Cast to correct iterator type in PeriodicBoundaryCondition BUG: Fix casting in PeriodicBoundaryCondition BUG: Bump KWStyle for C++11 brace list initialization support BUG: Fix MeshFileWriter export specification ENH: Create ITKIOMeshVTK module COMP: ExceptionObject declaration must come before usage ENH: Migrate BYU IO into ITKIOMeshBYU COMP: Bump ParabolicMorphology for MultiThreaderChanges COMP: Remove SmartPointer NULL initialization compatibility code DOC: Use http for issues.itk.org ENH: Migrate MultiScaleHessianBasedMeasureImageFilter out of ITKReview ENH: Move ContourExtractor2DImageFilter out of ITKReview DOC: Avoid Voronoi term when referring to the pixel center COMP: Wrap MultiResolutionPDEDeformableRegistration for Pyramid filter types ENH: Support Python snake case keyword arguments in object initializion PERF: Avoid extra condition check in itkBase.py COMP: Define ITK_DELETE_FUNCTION for backwards compatibility BUG: Fix bugs in ITKV4_COMPATIBILITY definition COMP: Do not disallow constructors in Python classes DOC: Add Mathieu Malaterre to GDCM copyright holders in NOTICE COMP: Address array initialization in itkShapedImageNeighborhoodRangeGTest COMP: ShapeImageNeighborhoodRange signed unsigned comparison COMP: Add missing itkViewImage.h include to itkViewImage.hxx COMP: Initialize CovariantVector in DeformableSimplexMesh3DFilter COMP: Update Unary and Binary filters for new generator class base COMP: Initialize DeformableSimpleMesh3DFilter displacement COMP: Suppress maybe-uninitialized in SimpleDataObjectDecorator Component COMP: Do not include itkMultiThreader.h in the header tests COMP: Fix Python wrapping of MultiThreaderBase COMP: Reduce example line lengths for inclusion in the SG COMP: Remove duplicate InPlaceImageFilter wrapping for RGB -> UC BUG: Do not copy workbox files when BUILD_DOCUMENTATION is OFF COMP: Remove duplicate BinaryGeneratorImageFilter class wrapping ENH: Remove itkzlib in preparation for subtree update ENH: Add ZLIB UpdateFromUpstream.sh BUG: Do not use P-threads with Emscripten COMP: Remove extra argument from HoughTransform3DCircles wrapping ENH: Update testing data content links BUG: Correct Windows and macOS CastXML hashes BUG: Fix SLICImageFilter wrapping BUG: Improve backwards compatibility of BoxUtilities functions BUG: Remove commented, unused Python wrapping configuration BUG: Remove deprecated GetPointer wrapping method ENH: Python snake case functions BUG: Remove deprecated itk.write function BUG: Remove unmaintained itk.show, itk.show2D ENH: Add snake case function aliases for NumPy conversions DOC: ITK 5 now requires CMake 3.10.2 BUG: Bump SplitComponents remote module to 2018-07-18 BUG: Remove TBBImageToImageFilter remote module COMP: Set CMake project command VERSION COMP: Do not wrap itk::ThreadJob ENH: Add ParallelizeImageRegionRestrictDirection ENH: Bump pygccxml hash to 2018-08-07 develop branch ENH: Update pygccxml git subtree version BUG: Remove ArchiveTestingDataOnMidas.py BUG: Avoid symlink issues in UpdateThirdPartyFromUpstream.sh DOC: Additional information and updates on bug fix release process COMP: Prevent duplicate wrapping ouput file specification COMP: Support instantiation of a 1D TranslationTransform DOC: Update how to reference a GitHub issue in the commit-msg hook DOC: ITK 5 Migration Guide grammar tweaks ENH: PEP8 for itk.Extras arguments ENH: Synchronize testing data content links DOC: Updates and improvements on the release process COMP: Address empty _FILE_OFFSET_BITS in tif_config.h with MinGW64 BUG: Do not warn about FFTW GPL license when using Intel MKL DOC: Improve ITK_USE_MKL description BUG: Mark MKL CMake configuration options as advanced ENH: Add support for NVidia CUDA FFTs via cuFTTW COMP: Fix HDF5 CMAKE_CROSSCOMPILING_EMULATOR support COMP: Fix HDF5 itk_h5CX_set_apl implicit declaration COMP: Use the Platform Threader by default with Emscripten COMP: Set CMP0074 to NEW COMP: Fix HDF5TransformIO compatibility with HDF 1.8 COMP: Set CMP0074 in third party libraries COMP: Do not mark itk::FloatingPointExceptions constructor as deleted COMP: Define TransformBaseTemplate constructor / destructor COMP: DataObject InvalidRequestedRegionError unused parameter COMP: Remove unused orig parameters in DataObject BUG: Remove unused itk_minc2 imported library statement BUG: Skip MINC static library build when building shared libraries COMP: Suppress undefined public symbol warnings in third party libs BUG: Remove duplicate ITK version number COMP: Do not install HDF5 static library with BUILD_SHARED_LIBS enabled COMP: Add override to TransformBaseTemplate destructor COMP: Avoid GCC 4.8 default destructor internal compiler error BUG: Import zlib1.rc from ZLib subtree BUG: Use GlobalDefaultNumberOfThreads for FFTW plans BUG: Simplify specification of greatest prime factor with cuFFTW ENH: Add Azure Pipelines configuration BUG: Remove ResampleImageFilter duplicate number of pixels check COMP: Avoid Intel compiler warning on unknown deprecated attribute ENH: Ensure that .sha512 content links have LF newlines ENH: Configure .gitattributes for ghostflow-director CheckSize DOC: Update ITK Git Reference for GitHub DOC: Update CONTRIBUTING.md for GitHub COMP: Address ITKReview module wrapping following migration of ITKIOJPEG2000 BUG: Migrate Python tests into their modules ENH: Use Release CMAKE_BUILD_TYPE for macOS Python CI builds BUG: Remove apt-get install's from macOS Azure Pipeline's configuration ENH: Update Git client side hooks for GitHub ENH: Add UploadBinaryData.sh script COMP: Remove vcl_complex.h from Python builds BUG: Remove vcl_complex support from itkTemplate.py BUG: Disable PythonGetNameOfClass test BUG: Enable ITKIOJPEG2000 by default DOC: Add Test a Topic to overview section DOC: Organize code of conduct sub-documents into a folder DOC: Update Documentation/Introduction.md for GitHub migration DOC: Fix spelling of "individual" in CONTRIBUTING.md DOC: Add CI status badges to the README COMP: Add missing mutex include to itkImageToHistogramFilter.h PERF: Use initializer list in ShapedImageNeighborhoodRange operator* DOC: Fix UploadBinaryData.sh link BUG: Run apt-get update for Linux Azure configuration COMP: Wrap InPlaceImageFilter for complex float to complex double BUG: Do not gpg sign third party updates DOC: Note that a pull request has to be explicitly opened DOC: Suggest using 72 characters or less in commit hooks ENH: Ensure NumPy is available for Python tests BUG: Add missing export specification for XMLReader, XMLWriterBase BUG: Remove invalid ShapeDetectionLevelSetFilter arguments COMP: Remove Doxygen \ref, \copydetails commands STYLE: Improve readability of HexadedronCell::EvaluatePosition. COMP: Fix IsFloatingPoint concept check for VariableLengthVector BUG: Set up wrapping options for use in modules ENH: Add PhaseSymmetry remote module ENH: Download ExternalData cache for CI builds DOC: Remove the convention that release branches start with "release" ENH: Run content link synchronization script ENH: Add setup-girder-api-key Git Setup script BUG: Remove ExternalData MD5 content link generation ENH: Move FreeSurfer Mesh IO into a separate module DOC: Add missing CONTRIBUTING.md link in UploadBinaryData.md ENH: Add regression test for reading legacy multi-frame DICOM COMP: Float narrowing conversion in BSpline class initialization DOC: Move maintainer documentation into Documentation/Maintenance DOC: Import release archive notes from the Wiki DOC: Improve 4.13, 5 release notes from GitHub Releases ENH: Update Azure Pipelines CI testing cache to 5.0b03 DOC: Releasing ITK updates for 5.0b03 BUG: Exercise BinaryMaskToNarrowBandPointSetFilterTest BUG: BinaryMaskToNarrowBandPointSetFilter GenerateData protected BUG: Remove unused FixedDensityFunction in JensenHavrdaChatvatTsallis BUG: Do not build/use PoolMultiThreader without WinThreads or PThreads BUG: ShapeDetectionLevelSetFilter outputs BUG: ShapeDetectionLevelSetFilter outputFileName COMP: Remove itk::ThreadPool::GetGlobalDefaultNumberOfThreadsByPlatform DOC: Add 5.0 Beta 3 release notes DOC: Fix link to UpdatingThirdParty.md in CONTRIBUTING.md ENH: Add wrapping for BinaryMaskToNarrowBandPointSetFilter COMP: Mark DCMTKImageIO::CanWriteFile argument as unused COMP: Fix Software Guide line length too long warnings COMP: Fix Software Guide line length too long warnings ENH: Use CompensatedSummation in point set metrics to improve robustness COMP: ShapedImageNeighborhoodRangeGTest array initialization ENH: Move Gifti Mesh IO into a separate module ENH: Consistency in wrapped mesh types PERF: Parallelize ManifoldParzenWidnowsPointSetFunction::SetInputPointSet ENH: Move OBJ Mesh IO into a separate module ENH: Migrate OFF IO into ITKIOMeshOFF ENH: Update IOSTL to 2019-01-16 master COMP: Do not use readNoPreambleDICOM with Emscripten BUG: Fix Azure Pipelines commit checkout BUG: Fix Azure Pipelines master checkout on Windows BUG: Default MeshIOBase PointDimension is 3 ENH: Update IOMeshSTL remote module and update name ENH: Improve loading to help pyinstaller can analyze module dependencies COMP: Wrapping of VectorContainer and DefaultStaticMeshTraits ENH: Add legacy multi-frame DICOM MD5 content links MetaIO Maintainers (1): MetaIO 2018-07-17 (6328f544) Niels Dekker (103): PERF: Improved speed of copying and resizing NeighborhoodAllocator STYLE: Removed 'char(255)' casts from NumericTraits min() and max() STYLE: Removed assignments from Neighborhood copy constructor BUG: Fixed semantics NeighborhoodAllocator operator== and operator!= BUG: GaussianDerivativeImageFunction should use image spacing consistently PERF: NeighborhoodOperatorImageFunction avoids copy ConstNeighborhoodIterator PERF: Removed blurring from GaussianDerivativeImageFunction ENH: Added GetCenterPoint and SetCenterPoint to EllipseSpatialObject DOC: Explained calling GetCenterPoint() when using Hough filter->GetCircles() ENH: IsInside(point) made easier, especially for HoughTransform circles STYLE: Using C++11 auto in HoughTransform2DCirclesImageFilter PERF: GaussianDerivativeImageFunction now reuses NeighborhoodIterator objects PERF: GaussianDerivativeImageFunction constructor, RecomputeGaussianKernel() COMP: ITK_DISALLOW_COPY_AND_ASSIGN now unconditionally does '= delete' COMP: Moved ITK_DISALLOW_COPY_AND_ASSIGN calls to public section COMP: Manually moved ITK_DISALLOW_COPY_AND_ASSIGN calls to public section COMP: Moved ITK_DISALLOW_COPY_AND_ASSIGN calls in *.cxx to public section ENH: Added Compute member functions to NeighborhoodInnerProduct STYLE: Added DISALLOW_COPY_AND_ASSIGN(GaussianDerivativeImageFunction), etc. ENH: Added ShapedImageNeighborhoodRange for modern C++ style iteration STYLE: Removed '&' from pixelPointer param of NeighborhoodAccessorFunctor::Set PERF: Removed virtual ~NeighborhoodAccessorFunctor() and made class final COMP: Fixed ShapedImageNeighborhoodRange doxygen + signed/unsigned warning BUG: Dropped OffsetTable assumptions from ShapedImageNeighborhoodRange PERF: Made HoughTransform2DCircles GaussianDerivative call non-virtual COMP: Workaround Clang range-loop-analysis warning NeigborhoodRange test ENH: Added class to create offsets for a hyperrectangular neighborhood shape ENH: Random access support for ShapedImageNeighborhoodRange iterators DOC: Fixed \code sections ShapedImageNeighborhoodRange and added \author STYLE: Renamed RelativeIndices to ShapeOffsets in ShapedImageNeighborhoodRange ENH: Added ConnectedImageNeighborhoodShape, for N-connected neighborhoods ENH: Added operator[] to ShapedImageNeighborhoodRange ENH: Documented + tested order offsets ConnectedImageNeighborhoodShape COMP: Fixed conversion to PDFValueType in MattesMutualInfo...Threader ENH: Added reverse iterators to ShapedImageNeighborhoodRange STYLE: Removed HoughTransform2DCircles default for TRadiusPixelType ENH: Changed type float data members HoughTransform filters to double ENH: Added Functor::CoLexicographicCompare ENH: Made Functor::LexicographicCompare more generic and easier to use BUG: Added default-constructor iterator ShapedImageNeighborhoodRange ENH: Added ImageNeighborhoodPixelAccessPolicy for custom border extrapolation STYLE: Removed LinearInterpolateImageFunction::m_Neighbors PERF: Made ResampleImageFilter::CastPixelWithBoundsChecking faster STYLE: NumericTraits::NonpositiveMin() using numeric_limits::lowest() BUG: Fixed casts to int64_t and double in ResampleImageFilter ENH: Tested ResampleImageFilter preserves 'double' and int64_t pixels STYLE: Replaced 'bool pre = 0' by 'bool pre = false' STYLE: Declared "IsAt" iterator member functions 'const' DOC: Replaced leading stars ('*') by spaces in Doxygen code blocks STYLE: Replaced "Hyperrect..." by "Rect..." in class + function names BUG: Removed underscores from GTest test names STYLE: Shortened itkShapedImageNeighborhoodRangeGTest test names STYLE: Declared VerifyPreconditions() member functions 'const' STYLE: Replaced star ('*') by space in front of Doxygen \code tags PERF: Made ConstNeighborhoodIterator::GetPixel(i) much faster ENH: Added GradientNormThreshold to HoughTransform2DCirclesImageFilter STYLE: Removed unused ShapedImageNeighborhoodRange::m_Image ENH: Added ConstShapedNeighborhoodIterator::ActivateOffsets(offsets) DOC: Replaced leading stars ('*') by spaces in indented Doxygen code ENH: Added GenerateConnectedImageNeighborhoodShapeOffsets() COMP: Fixed GDCM OpenJPEG name mangling ENH: Added ShapedImageNeighborhoodRange::SetLocation(index) COMP: Fixed GDCM OpenJPEG name mangling ENH: Added HoughTransform2DCirclesImageFilter::UseImageSpacing ENH: Added IndexRange for efficient region and grid space iteration COMP: Fixed IndexRange warnings -Wshadow -Wmissing-field-initializers PERF: unsharpenedImage iterator in N4Bias...Filter is now "WithIndex" BUG: Avoid premature GaussianDerivative kernel computation HoughCircles BUG: ShapedImageNeighborhoodRange should not try to avoid rvalue offsets ENH: Added policy for constant NeighborhoodRange values outside image STYLE: AccessorFunctor::SetPixelAccessor parameter reference to const PERF: Removed 'virtual' from Default Pixel Accessor destructors ENH: Added ImageRange: a range of iterators to the pixels of an image STYLE: ImageHelper now doing '+=' and using C++11 std::integral_constant BUG: Fixed ShapedImageNeighborhoodRange copying pixel access parameter COMP: Fixed ImageRange warning, passing object to variadic constructor DOC: Did #136 Update migration guide with Hough transform changes ENH: Added default-constructor and empty() to ImageRange ENH: ShapedImageNeighborhoodRange now supports any buffered region index PERF: Defining ImageRange iterator as raw pixel pointer, when possible ENH: Added Experimental::MakeImageRange(TImage*) PERF: Replaced postfix ++ calls on ITK iterators by the prefix ++ calls PERF: Small improvements to equality operators of Image Region classes PERF: Added C++11 final, noexcept, default, initializers to ImageRegion DOC: issue #273: SyNImageRegistrationMethod default member initializers STYLE: Small improvements ImageBase constructor, SetRequestedRegion, '\' COMP: Fix "unreachable code" MakeOutput RegistrationMethods PERF: N4BiasFieldCorrectionImageFilter implementation using ImageRange STYLE: Renamed ImageRange to ImageBufferRange PERF: Remove SystemInformation data from ResourceProbe, fix issue #350 STYLE: Remove dynamic_cast from CastToSTLContainer(), add noexcept PERF: N4BiasFieldCorrectionImageFilter adds points + weights ~20% faster PERF: Fast assign point data, weights BSplineScatteredData filter COMP: ImageBufferRange iterator same as const_iterator, for const image PERF: BSplineDecompositionImageFilter now calls ImageAlgorithm::Copy ENH: Add default-constructor and empty() to ShapedImageNeighborhoodRange ENH: Made ShapedImageNeighborhoodRange assignable and tested copy + move STYLE: C++ "Rule of Zero" for iterator classes of Range types PERF: Add fast noexcept move semantics to Neighborhood and its Allocator BUG: ResourceProbe::Reset() should set m_MaximumValue to lowest value BUG: Fixed MoveAssignedRangeHasSameIterators GTest of two range types STYLE: Move test utils default-constructed ranges to RangeGTestUtilities ENH: Add default-constructor and empty() to IndexRange Pablo Hernandez-Cerdan (47): STYLE: Add script Move_DISALLOW_COPY_to_public ENH: Add stateless viewer ViewImage with Python wrap. DOC: Add docs to ViewImage. COMP: Fix catch by value warning in SpatialObject. COMP: Remove ignored const qualifier in template. COMP: Fix warnings -Wcatch-value ENH: Update isotropic wavelets module. ENH: Add frequency iterators and band pass filter. COMP: Update IsotropicWavelets, remove FrequencyIterators STYLE: Remove comment in ITKImageFrequency cmake BUG: Fixes generating floating point exceptions COMP: Fix warnings in cdash introduced after FPE. DOC: Add example using std::atomic for multithreading. COMP: Avoid extra point copy in MetaTube COMP: Fix hdf5 warning missing perl script COMP: Fix HDF5 CMake warning policy CMP0075 ENH: Tweak constructors, Ro5 in FixedArray, Point ENH: Add Ro5 to FixedArray and derived classes COMP: Fix warnings related to Ro5 changes in FixedArray ENH: Add Ro5 constructors to SymmetrySecondRankTensor ENH: Add Ro5 to classes derived from Point ENH: Initialize SecondRankTensor and RGBPixelType ENH: Print direction in ImageIOBase ENH: Add HalfHermitianFrequencyIterator ENH: Use variadic templates for SetPosition ENH: Add ThirdParty module Eigen3 COMP: Add CONFIG to find_package(Eigen3) COMP: Add missing headers SymmetricEigenAnalysis COMP: Use the right constructors for fixed eigen3 matrix COMP: Reorder variables associated find_package in Eigen3 ENH: Update external module ITKIsotropicWavelets DOC: Fix doxygen in SymmetricEigenAnalysis ENH: Python, wrap complex in NumericTraits ENH: Update IsotropicWavelets module BUG: Fix failure of ITK_EIGEN macro expansion ENH: Add test checking noexcept moves in FixedArray STYLE: Change EXPECT_EQ to EXPECT_TRUE|FALSE in CommonTypeTraitGTest ENH: Add python wrapping for std::pair and other int containers ENH: Add internal/external eigen3 libraries ENH: Update IsotropicWavelets ENH: Add new c++11 member functions of std::vector to itk::VectorContainer ENH: Simplify specialization of NumericTraits<std::complex<TComponent>> BUG: itkMatrix: Use NumericTraits::Zero instead of literal 0 DOC: SoftwareGuide: improve TransformIndexToPhysicalPoint notation COMP: Fix multi-line comment warning generated by latex notation [Backport] BUG: Fix OFFIS_DMCTK_VERSION_NUMBER where wrunlock was introduced [Backport] BUG: Fix export for ITKDeprecated classes Rashad Kanavath (1): COMP: fix linking on OpenBSD Roman Grothausmann (3): DOC: adjusted to fit more general case n != m DOC: corrected description of the output BUG: avoid overwriting output in 2nd run used for comparison in test: Sean McBride (29): STYLE: Fixed up confusion between base 2 and base 10 prefixes STYLE: arranged/alphabetized things to make subsequent changes reviewable COMP: Fixed some missing name mangling of libTIFF symbols BUG: fixed crash on macOS under guardmalloc from RunOSCheck() BUG: don't use double underscore, which is reserved in C++ STYLE: fixed some spelling, spacing, and comments DOC: Fixed comment about LegacyAnalyze75Mode default value BUG: Some minor cleanup and improvement after itkNiftiImageIO code review BUG: Analyze 7.5 fixes/improvements COMP: Mangle HDF5 symbol names COMP: Fixed clang Wrange-loop-analysis warnings DOC: fixed minor typo in comment BUG: Revert part of f38b1dd4, which caused a regression ENH: Added new DetermineFileType() API to NiftiImageIO COMP: fixed clang warning about unnecessary copy in for loop COMP: -Wunused-template & -Winconsistent-missing-destructor-override warnings COMP: Exercise dead code, fixing -Wunused-template COMP: Removed dead code, fixing -Wunused-template COMP: Fixed -Winconsistent-missing-destructor-override warnings BUG: Don't force GDCM_USE_COREFOUNDATION_LIBRARY to OFF COMP: Suppress some warnings in ThirdParty/DoubleConversion BUG: fixed null access found by UBSan BUG: removed illegal int to enum conversion COMP: fix warning about implicit double to bool conversion COMP: Fixed warning about missing case label in public header COMP: Fixed three misc clang warnings COMP: Added additional HDF5 symbols for mangling DOC: improved comments about HDF5 symbol mangling COMP: fixed some -Wunused-template warnings by adding private namespaces Simon Rit (6): BUG: fix deadlock in FFTW for windows shared libs COMP: missing include path for FFTW ENH: allow wrapping of XML writers BUG: fix NumPy bridge for itk::Image with PixelType itk::Vector ENH: improve automatic Python ImageFileReader for non-scalar pixel types BUG: python itk.Image returned by GetImageFromArray now manages its own buffer Taylor Braun-Jones (2): BUG: Handle single-component PLANARCONFIG_SEPARATE TIFF images (#ITK-3518) COMP: Fix clang diagnostic: case value cannot be narrowed Tobias Wood (1): BUG: Swapped int to SizeType to prevent overflow errors VXL Maintainers (15): VNL 2018-01-25 (ed159d55) VNL 2018-01-31 (39559d06) VNL 2018-03-04 (09a097e6) VNL 2018-05-16 (26628604) VNL 2018-07-26 (2a77e40b) VNL 2018-08-04 (3dafea87) VNL 2018-09-05 (fc0c9043) VNL 2018-11-04 (ea3a2cc9) VNL 2018-11-08 (88b72533) VNL 2018-11-14 (ee083096) VNL 2018-11-15 (4fe68119) VNL 2018-11-18 (fa7c7abd) VNL 2018-11-23 (cb6f5dcb) VNL 2018-11-29 (f6e20c3c) VNL 2018-12-15 (bb0d2eb6) Vladimir S. FONOV (1): MINC 2018-08-09 (ce4333ca) Yann Le Poul (4): BUG: make sure the palette is empty when m_IsReadAsScalarPlusPalette is false DOC: fix rotation spelling issue in some versor related files STYLE: IsReadAsScalarPlusPalette already printed in parent class BUG: unnecessary call to GetExpandRGBPalette Ziv Yaniv (1): ENH: Adding user set min and max values for noise. Zlib Upstream (2): zlib 2018-06-11 (355d8648) zlib 2018-06-11 (355d8648) allywarner (1): BUG: CMake build errors ihnorton (1): COMP: use HDF5 library names only to avoid abspaths w/ SYSTEM_HDF5 pierre33 (1): ENH: Update itkNaryFunctorImageFilter ``` List of BRAINSTools changes: ``` $ git shortlog --no-merges b045970..ac4dafaa Alexander Leinoff (1): COMP: Allow cmake generation on OSX without XCode David Ellis (2): ENH: Adds logismosb interfaces and workflows ENH: Nipype recon-all workflow added Hans J. Johnson (196): ENH: Prefer to build everything as static to avoid libary dependancies. ENH: Force the NO_MODULE for RTK. ENH: Resyncronized with Slicer packages. ENH: Update Opencv ENH: Propagate CXX settings to all sub-projects ENH: ITK Intermediate update. STYLE: Name ITKv5 as target name for dependancies ENH: Turn off ITK_LEGACY to prep for ITKv5 ENH: Update ANTS,RTK and SlicerExecutionModel checkout tags COMP: Set VTK version identifier. ENH: Updated VTK with C++11 override instrumentation. BUG: UseImageSpacing should be defaulted to On ENH: Add github templates for PR and ISSUES COMP: Disable floating point exceptions checking BUG: New ITK enhanced random needs consistency in test. ENH: Set random number generated to historical ITK values COMP: Make tests pass BUG: Fix incorrect DATA{} syntax. ENH: Fix pre-mature exit when writing debug image STYLE: Minor code organization ENH: Setting min cmake version number. STYLE: Remove CMake-language block-end command arguments STYLE: Convert CMake-language commands to lower case COMP: Use recommended const interfaces ENH: Explicitly use parameters instead of defaults. ENH: Instrument to identify test failures COMP: Link to correct version of zlib COMP: Use C++11 nullptr directly COMP: Identify null pointer assignments COMP: Use C++11 override directly STYLE: Setting override for overriden member functions. BUG: Missing data dependancies for test suite COMP: Remove compiler warnings from cnpy COMP: BRAINSSurfaceTools are not compiling currently. COMP: Remove outdated policies for CMP0017. STYLE: Use override statements for C++11 ENH: Change to https from git download. ENH: Set BRAINSABC to always build. COMP: Update to new version of tbb ENH: Use C++ headers instead of C headers. COMP: Missing dependancy on ITKv5 ENH: Setting deployment target to 10.9 for mac ENH: Put BRAINSSuperResolution code together. COMP: Attempt to build BRAINSTools for redistribution. STYLE: Push parts of codebase into an ARCHIVE dir BUG: Provide mechanism to move some modules to the ARCHIVAL status. COMP: Remove outdated cmake policy behavior ENH: Move old programs to an archive directory COMP: Remove shadowed typedefs by using explit namespaces ENH: Move BRAINSTalairach to the ARCHIVE Directory. ENH: Move BRAINSRefacer to the archive directory. ENH: Set ARHIVE project to on if ARCHIVE builds choosen. ENH: Add old DicomSignature program to archive COMP: Fix building against new GDCM version. Update NOTICE ENH: Use file introspection to determine BVec file format ENH: Remove unnecessary manual read file type flag ENH: Add thicknes from spacing when converting from FSL to NRRD. ENH: use constant scale factor initialization BUG: ITK_VERSION_MAJOR version checking ENH: Remove redundant ExternalData.cmake that overrode CMake version. STYLE: Prefer constexpr for const numeric literals STYLE: Replace itkStaticConstMacro with static constexpr STYLE: Prefer constexpr for const numeric literals STYLE: Do not use itkGetStaticConstMacro in ITK ENH: Update to ITKv5 with using over typedefs. ENH: Update dependancies for BRAINSTools. COMP: Wrong name specified for target_properties. BUG: regex substitution failure for const COMP: Silence build warning about unused CMAKE_EXPORT_COMPILE_COMMANDS COMP: Cleanup build options for BRAINSTools ENH: Organized for project name setting. ENH: Improve CXX_STANDARDS checking logic ENH: Remove outdated ITKv3 configuration checking. ENH: Set GENERATECLP_USE_MD5 unconditionally. STYLE: Organize build default settings. ENH: Use explicit named mark_as_superbuild parameters. ENH: Add better debugging to version checking. ENH: Improve version settings for BRAINSTools ENH: Use MultiThreaderBase to get GlobalVariables. ENH: Provide new baseline for BRAINSFitTest_RigidRotGeomNoMasks ENH: Prevent constant changes as patches are added BUG: Prevent constant changes as patches are added ENH: Fixed tests failures due to incorrect testing environments ENH: Syncronized external superbuilds with Slicer. ENH: Convert BRAINSCut python to python 3 ENH: Convert all python code to python 3 conformance ENH: Version 5.0.0 of BRAINSTools ENH: Allow for compressed transform files. ENH: Reorganize python code to be compliant with Python3 modules BUG: New versions of ANTs have slightly different options BUG: Fix new nipype behavior of data sink with missing values. ENH: Consolodate duplicate functions ENH: Fix simple itk usage failure. STYLE: Update comments. BUG: Nipype needs OrderedDict for hash consistency ENH: Passing dict() or OrderedDict() through pipeline causes hashing issues BUG: Incorrect debugging option retained for None images ENH: Allow for possiblility of compiling with ITKv4 ENH: Update ITKv5 to version with UseCompression for transforms. ENH: Update to latest version of boost. BUG: Fix bug in mark_as_superbuild PROJECT->PROJECTS BUG: Error in caused mark_as_superbuild items to be missed ENH: Sync with slicer mark_as_superbuild options. ENH: Re-organize build option settings STYLE: Reviewed and cleaned up superbuild ENH: Updated static version string setting. COMP: Add quick -march=native compiler flag adding ENH: Remove unnecessary build code for superbuild. ENH: Syncronized with NAMICExternalProjects build. ENH: Propogate default /lib /bin directories to all projects BUG: Bad hash for scan3Mask1.nii.gz.md5. ENH: Unlink ITK from VTK GUI build. COMP: HD5 changed API for printing Errors. COMP: Remove unused variables. COMP: ITKv5 updates for JPEG2000. ENH: Updated packages for improved C++11. ENH: Add azure testing scripts. COMP: Fix KWStyle compilation fixes. BUG: Mismatch type for CovariantVector initialization. COMP: virtual designation is redundant with override designation. COMP: ITKv5 multi-threading model compatibility. COMP: ITKv5 uses std::mutex directly. COMP: Only configure inner BRAINSTools COMP: Fix function signature for override COMP: Future proof vnl_math_XXX function usage. COMP: Replace vcl_XXX items with std::XXX COMP: Remove unused variable. ENH: ITKv5 itkMultiThreader.h -> itkMultiThreaderBase.h STYLE: Replace itkStaticConstMacro with static constexpr STYLE: Use "typename" for template parameters STYLE: Prefer error checked std::sto[id] over ato[if] COMP: Prefer C++ headers to C99 headers. COMP: Use C++11 nullptr directly COMP: Use and move ITK_DISALLOW_COPY_AND_ASSIGN calls to public section. ENH: Update external packages C++11 compliance ENH: ITKv5 Threading Model changes needed for testing STYLE: Prefer C++11 type alias over typedef DOC: Add documentation for newer OS versions. ENH: Comment out tests that do not work due to missing data ENH: Disable building of BRAINSSurfaceTools COMP: Remove compiler warnings. COMP: Make VerifyInputInformation a const function (ITKv5) ENH: Update to 2019_U2 to fix TBB issues with mac min version compilations. ENH: Propagate MAC_OS_X_VERSION_MIN_REQUIRED to TBB build. ENH: Improve TBB versioning selection. COMP: Update new reference data after VXL ITKv5 updates. ENH: Updated BCD baselines for ITKv5 COMP: ITKv5 backward compatibility fixess. ENH: Update BRAINSFit baselines for ITKv5 ENH: Try to make random number generation consistent. ENH: Update ANTs and ITKv5 for more test coverage. ENH: Update data regression. COMP: Remove compiler warnings. ENH: Duplicate names for testing BUG: Failing test updated after visual review COMP: Cleanup compiler warnings. ENH: UPdate ITK to include vxl explicit instantiations. COMP: Remove deprecated SetUseFixedSampledPointSet COMP: SetNumberOfThreads -> SetNumberOfWorkUnits ENH: Update reference data to sha512 on new data source. ENH: Remove duplicate md5 signatures. BUG: Failed uploads fixed for sha512 COMP: Valgrind un-initialized memory reads STYLE: Prefer error checked std::sto[id] over ato[if] ENH: Adding an editor config for BRAINSTools. ENH: Add extra landmark Eye sanity checking for BCD. ENH: Add component testing for valid values to workflow running. STYLE: Remove trailing whitespace from files COMP: Add missing iostream header. STYLE: Remove unused file and directory ExternalSources. ENH: Fix dependency ordering for new project() syntax. ENH: Use range of new CMake features. ENH: Update to latest TBB build 2019_U3 for 10.14 compatibility. ENH: Update to latest version of packages ENH: Temporary ITK branch for dcmtk api compatibility. ENH: Add Travis pull request builds. ENH: Add helper file for configuring BRAINSTools for IDE. COMP: Errors with VTK TBB building in superbuild mode. STYLE: Fix naming of variables for DWIConverter class. ENH: Force clean ITKv5 building, remove legacy modes. ENH: ITKv5 const fix for duplicater image filter. ENH: ITKv5 fix for duplicater image filter. COMP: Allow building with C++ > 11 ENH: Fix failing CI .travis.yml syntax. ENH: Add diagnostics for failed TBB download. ENH: Test for extra long test times. COMP: Moved my.cdash.org only supports https now. ENH: The maximum cmake version is only for policies ENH: Fix backward compatibility with OpenCV4. COMP: Match types for loops. BUG: Python set inclusion syntax error fixed. ENH: The maximum cmake version is only for policies ENH: Update wts reference file to have comment line. ENH: Wts file has header line to be ignored. BUG: Simple ITK does not currently expose SetNumberOfWorkUnits Hui-Xie (6): COMP: change VTK min version ENH: Add support for r/w Dicom, FSL, Nrrd formats BUG: erase unnecessary cmake config BUG: erase unnecessary lib in CMake file ENH: add DWI file convert utility interfaces BUG: stat uses ITK KWSys wrapper interface Isaiah Norton (4): BUG: DWIConverter hard-coded transpose/FSLBy3Rows setting ENH: don't allow matching bvec and bval file names ENH: DWIConvert, Philips: also check supplement 49 b value field Bump ITK to v5b1 to resolve FFTW broken download Jean-Christophe Fillion-Robin (4): Add License file STYLE: Add Notice file ENH: Improve build targets organization in IDE that support folders ENH: Use a single data management target and support customizing its name Johan Andruejol (1): BUG: Add try/catch around BrainsFitHelper update Regina EY Kim (2): BUG: Add a missing header ENH: fix the probabilityMap RegistrationToSubject option azure-pipelines[bot] (1): Set up CI with Azure Pipelines ``` List of SimpleITK changes: ``` $ git shortlog --no-merges v1.1.0..dc5c1a1d ASVBPREAUBV github_user (1): Update DicomSeriesReadModifySeriesWrite.R Bradley Lowekamp (164): Bumping version to 1.2 for development Adding Python wheel downloads for v1.1.0 from SourceForge Fix template generator custom method with multiple parameters Add docs for set methods Add SetRegionOfInterest method Document conventions for Image Regions Add GetRegion method to LabelMap based statistics filters Correct RegionOfInterest doxygen from proper ITK class Adding wrapping for filters from remote LabelErodeDilate module Use named inputs for the paste image filter Adding wrapping for StochasticFractalDimensionImageFilter Add names inputs for FFTConvolutionImageFilter Update JSON python scripts to end files with newline Add ExternalData step to building Sphinx documentation Adding Readme for Sphinx images directory Adding Readme to white list of files Correct code-block indentation Add overflow and underflow count to ShiftScaleImageFilter Adding wrapping for the BSplineDecompositionImageFilter Add interpolator enum for the BSplineResampleImageFunction Fix documentation for GetCoefficientImages method Adding test for resampling with the BSplineResampler iterpolator Add specification of ITK ImageIO used to read image Use return self macro Adding testing for setting ImageIO Adding baseline hash for LabelSetErode filter Update require CMake version to 3.10 Remove CMake version checks for version before required version Remove local CMake GTest module, use gtest_discover_tests Set pointer to null after deleting Correct interpolate for ruby bspline_resample test Only label unstable on apple systems Correct capitalization style for ruby enum Update SimpleITK Version in Sphinx Adding support for ImageBase types to ImageTypeToPixelIDValue Add a descriptive error message for image casting failure Add propagation of CMake job pool variables in Superbuild Remove deprecated midas3 from external download URLs Remove unused variable value Remove imported CMake ExternalData module Update referenced json Update name field and reference script used for doc fields Add doc for itk_module json field Adding R language to CircleCI testing Only add R dependencies for R job Adding R Unit tests when R is built as a project Add junit test formatting for python and R Make and use separate environment anchor Update documented CMake required version Add wrapping for Toboggan filter Update ITK superbuild version along ITK v41.3 release Make variables, functions, and structs local scope Add support for VectorImages to the Tile filter Specifying Toboggan output types as uint32_t for portability Just link the SimpleITK on Sourceforge, not the versioned sub-directory. Reduce CircleCI dependencies, and use system SWIG Correcting link to Java visual guide Improve doxygen documentation for the Image class Fix tense per code review Use standard find_package for ITK in SimpleITK Config Use modern CMake IN_LIST if operator Remove legacy BasicFiltersN loop code Correct variable name used to disable building documentation Update Superbuild ITK version along 4.13 release branch Set CircleCI to use Github for ITK repo Add wrapping for SLICImageFilter from SimpleITKFilters module Correct Github ITK repo in CircleCI CMake configuration Specify data root as SimpleITK root project Add BUILD_EXAMPLES option to standalone language builds Enable CircleCI testing of examples when language is built ENH: Support passing ITKV4_COMPATIBILITY to ITK superbuild Enable ITK_LEGACY_REMOVE to be overridden Explicitly specify stretch docker image add python 3.6 for testing Explicitly use python to invoke pip, print python version COMP: Lengthen GTest discovery timeout Adding Java build to CircleCI Add testing for Java stand-alone project No CI for languages on next branch Remove BUILD_DOCUMENTS CMake option Exclude files leading with a '.' from globs Add Update data link for R man documents Add TransformVector method to Transform class Update Superbuild ITK version to 4.13.1 This data file hash is neither used nor does it exit Update links for downloads in tarball generation Adding data links from ContentLinkSynchronization.sh execution If ITKv5 map number of threads to number of "Work Units" Add access to number of valid point used during registration Fix Python index test with empty comparison Fix recursive option with GetGDCMSeriesFileNames Adding Transform method to flatten composites transforms Add mirror of SimpleITK External Data repository Documentation tweaks Remove dimension limitations form GetImageFromNumpy Improve exception for unsupported Image size Use baseline images for testing Set the default CMake policy to 3.10 Adding request of IO region to ImageFileReader Adding testing for reading an extraction region Update ITK superbuild along 4.13 release branch Adding vector image support to Mean and Sum projection image filters Improve documentation for SetExtractSize Add new 5d test image Add IO extract direction matrix behavior documentation Add IO extraction test with 5d file Fix size shortening warning Remove uint64 to uint copy to avoid warnings Add Doxygen grouping to ImageReaderBase::Set/GetImageIO Create common method to create ImageIO by string name Fix indentation in ImageFileWriter Add SetImageIO method to ImageFileWriter Add option to set ImageIO to the series writer Add debugging information to ReadInformation Remove typename outside of template Add support for vector images to the clamp image filter Improve documentation of some RegistrationMethod methods. Add method to access the metric's sampling percentage. Add testing for GetMetricSamplingPercentagePerLevel method ITK superbuild version along the 4.13 release branch Address implicit conversion warnings from float to double Adding construction of BSpline transform from coefficient images Add testing of constructing BSpline Transform from images Add methods to transform class to get number of parameters Improve image registration per level documentation Add registration support for multi-resolution bspline transform Add unit testing of BSpline parameters Fix reassigning initial transform issue Adding testing of BSplineTransform registration in place Update the ITK superbuild version along release-4.13 ENH: Adding example of multi-resolution bspline registration Adding prose document to BSpline3 example Adding C++ BSpline3 example Add labels to docs referenced from BSpline3 Quote function name and remove extraneous prose fragment. Use the official ITK Github repo Restore needed storage option to increase default size Update manylinux to use CMake 3.11.4 Update manylinux openssl to 1.0.2q Create wheel even when tests fail Update JSON documentation from ITK release-4.13 Updating Java and Python docstrings from current build Updating ITK version with BSpline mesh parameter fix Add test for BSplineTransform copy on write Add multi-resolution BSpline registration test non-inplace Adding option to procedure ReadImage to specify the ImageIO Sort the json descriptions to maintain order Update Sphinx filter descriptions via script. Fix conversion warning Update the FAQ Fix up in wording in FAQ Update SwigDocStrings for Python and Java Update R documentation files Add missing parameter documentation to the ReadImage method Update from SwigDocUpdate.sh with latest changes Update R documentation archive Change broken quote to bash code block. Update R Rd document files with manual fix Applied correction to escape % in R documentation. Apply escape sequence to all occurrences of % Add isysroot as require flag in non-cmake superbuild projects Don't use CMAKE_OSX_SYSROOT is empty string Update ITK Superbuild version along 4.13 release branch Remove extraneous CMake message statement Adding Azure Pipelines configuration from master branch Dave Chen (11): Large refactor of GenerateDoc.py Ran JSONBeautify.py Ran new GenerateDoc.py on JSON files GenerateDoc.py fixed to handle Unicode input Added test of default ResampleImageFilter params Fixed wrong method. Missing '&' on Windows Fixed memory leak Improved testing of the ImageViewer class Modified test to improve code coverage Fix for hang in Show function on Windows David T. Chen (19): Fixed some formatting, adjusted a few other things. Use TextOutput for OutputWindow Fix string comparison bug ENH: Initial check-in of the ImageViewer class Use ImageViewer class Fix for ITK code style More code fixes Print more defaults it ToString Added SetGlobalDefaultDebugOn/Off methods Fix type warning on Windows Added 'command' param to SetApplication. Fix for Show w/o ImageJ or Fiji Improve test coverage for ImageViewer class. Removed ImageJ stuff from Installation doc Updated the building.rst doc A few small fixes Updated for Python 3 Re-run for SimpleITK v1.2rc1 Fix R documentation warning Jean-Christophe Fillion-Robin (2): circleci: Fix and simplify install of CMake circleci: Install scikit-ci-addons to ensure ctest_junit_formatter is available Kasper Marstal (2): ENH: Use return instead of raising StopIteration (PEP 479) ENH: Add empty image Python indexing test Richard Beare (25): Vignette update R package DESCRIPTION update moved methods import to namespace and referenced the dll Modified generation of namespace file R version check during configuration Installation of R from CRAN for circleci testing R package rules don't allow non standard file formats in the data directory. Add index entry to latex preamble of vignette Update formatting of license field in R DESCRIPTION file use Rd note section instead of usage as the latter requires R code Formulas processed to avoid breaking latex after conversion place holders in empty sections for procedural interface tidied up testing for missing fields importFrom for utils package in NAMESPACE file updated instructions for documentation Add as.image to index entry Add text to empty fields and allow additional sectiondef Modified creation of filenames of R documentation Add documentation file for S4 methods. Add replacement R functions. Add better support for R namespaces and documentation Fix: spurious bracket in script ENH: Improving formatting of DESCRIPTION file according to --as-cran checks Fix: C++11 style init causing problems with RTools(windows) c++ Modified functions exported by R package. Seungkyoon Bong (24): Updated tutorial link for SimpleITK Translated the common conventions page from the Doxygen Deleted the .rst change Added hyperlinks and inline markups for code Created a page with SimpleITK Filters Changed the HTML template of the documentation Added Relevant Resources and link to paper to index.rst Corrected LaTeX notation in Registration Overview Create image and transformation IO page Translate and Update Page for Eclipse Set Up Translate and Update Visual Studio Set Up Convert pngs to web-optimized jpgs Restore simpleitk_logo.png.md5 Translate N4BiasFieldCorrection R Example Create filter and slicing operator comparison Translate DemonsRegistration1 R Example Translate DemonsRegistration2 R Example Translate DicomSeriesFromArray R Example Translate ImageRegistrationMethodBSpline1-2 R Example Fix spelling error in N4BiasFieldCorrection Translate 2 ImageRegistrationMethod R Examples Translate ImageRegistrationMethod2-4 R Example Remove internal function in ImageRegistrationMethod1 Remove internal functions in DemonsRegistration1-2 Ziv Yaniv (18): Adding support for vector images in as.image conversion. Adding test to the patch (moving between R array 2 image 2 R array). Adding read the docs sphinx fundamental concepts documentation. Adding concepts of channels and resampling. Adding section on resampling and updating the images location. Adding reference to image md5 for download. Typo in example, comma instead of bar in the specification of Instance Number. ImageJ not found in expected location FAQ information. Updatind publication citation list. Adding the tutorials and course page to the documentation. Adding introductory information with respect to tutorials. Corrected backslash not visible in documentation of windows path. Renamed the example to reflect its content. Adding image viewing example. ENH: Adding new example illustrating new SimpleITK IO. ENH: separated the example in two based on code review. Upadated readme file to match our current state (rc1.2). Adding the SPIE course to the tutorials' list. ``` From: Hans Johnson <hans.j.johnson@gmail.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@28016 3bd1e089-480b-0410-8dfb-8563597acbee
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