Itk

ITK 5.0 brings dramatic improvements to ITK's API and performance. At the same time, there are minimal changes that break backwards compatibility.

This the first in a series of alpha releases to enable the community to test and improve these major changes.

In this first alpha release, we highlight ITK's adoption of and requirement for the **C++11 standard**. Prior to this release, a subset of C++11 functionality was utilized, when available, through backports and macros. ITKv5 deprecates or removes these macros (e.g. `ITK_NULLPTR`, `ITK_DELETED_FUNCTION`, ` ITK_NOEXCEPT`, `ITK_CONSTEXPR`) and directly uses C++11 keywords such as [`delete`](https://github.com/InsightSoftwareConsortium/ITK/commit/02128abbd0bf790deadc86a28c62c4a25e23518b), [`constexpr`](https://github.com/InsightSoftwareConsortium/ITK/commit/b8e41d0d1652a8f6ddb84328faef67b207e77430), [`nullptr`](https://github.com/InsightSoftwareConsortium/ITK/commit/3c6372b80ac2900e2e197899989c4cd151f1695f), [`override`](https://github.com/InsightSoftwareConsortium/ITK/commit/3ceacc0ad4ec699b094d96e23d33f9467c2a63c6), [`noexcept`](https://github.com/InsightSoftwareConsortium/ITK/commit/af4f65519abb32b59cebb2d72f0186a96efe3b4e). The keywords [`auto`](https://github.com/InsightSoftwareConsortium/ITK/commit/de713e7ac52f7815a35754de885795ff0a1c4981) and [`using`](https://github.com/InsightSoftwareConsortium/ITK/commit/66e5d6b3bcc28f1a85b702086b6cedc8cab6723b) as well as [range-based loops](https://github.com/InsightSoftwareConsortium/ITK/commit/48daed0751df99bcb5fd1077e78ceb1b47546ccc) are also now used heavily throughout ITK.

ITKv5 includes some API changes. Even though we tried to minimize backward compatibility issues, there will be a few (see below for important changes). These changes were discussed by the community on the ITK Discourse forum [[1]](https://discourse.itk.org/t/gearing-up-for-itk5/515)[[2]](https://discourse.itk.org/t/gearing-up-for-itk5/515/4)[[3]](https://discourse.itk.org/t/new-build-errors-on-cdash-1-24-18-drop-support-for-vs2013-in-itkv5/619/3)[[4]](https://discourse.itk.org/t/opinions-on-dropping-support-for-c-03/481/4). This ITK alpha release is purposefully created with the goal of helping developers to test their current software with this new ITK version, update their code if necessary, and report problems they encountered during this process.

ITK now [requires](https://github.com/InsightSoftwareConsortium/ITK/commit/3525bf45200bd9845259ea9a88f586684cc522db) CMake 3.9.5 for configuration and a compiler that supports C++11. This means that Visual Studio 2015 or later is required for Windows development with the Microsoft toolchain.

Important [changes in style](https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch13.html#x57-259000C) have also been integrated in ITK to match the C++11 best practices. This includes replacing `typedef` calls with the `using` keyword, the usage of the keyword `auto` when appropriate, and moving the macro `ITK_DISALLOW_COPY_AND_ASSIGN` from the private class section to the public class section. The [ITK Software Guide](https://itk.org/ITKSoftwareGuide/html/) has been updated to match these changes.

As shown below, toolkit has adopted the application of the `using` keyword for [type aliases](http://en.cppreference.com/w/cpp/language/type_alias), which many developers find easier to read and understand.

cpp
template< typename TInputImage, typename TOutputImage >
class ITK_TEMPLATE_EXPORT BoxImageFilter:
public ImageToImageFilter< TInputImage, TOutputImage >
{
public:
ITK_DISALLOW_COPY_AND_ASSIGN(BoxImageFilter);

/⋆⋆ Standard class type alias. ⋆/
using Self = BoxImageFilter;
using Superclass = ImageToImageFilter< TInputImage, TOutputImage >;

[...]

protected:
BoxImageFilter();
~BoxImageFilter() {}

void GenerateInputRequestedRegion() override;
void PrintSelf(std::ostream & os, Indent indent) const override;

private:
RadiusType m_Radius;
};

} // end namespace itk


For more information on style changes, see the [Coding Style Guide](https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch13.html#x57-259000C) found in the ITK Software Guide.

To test the 5.0 Alpha 1 Python packages, run

bash
python -m pip install --upgrade pip
python -m pip install --upgrade --pre itk


For a full list of the new features and changes in API, please review the log below. The community has been busy -- there have been **319 commits, 97,794 insertions, 152,791 deletions** since 4.13.0 was released in December!

Please discuss your experiences on [Discourse](https://discourse.itk.org/). The API is expected to change across alpha releases as we improve the library based on our experiences.


Changes from v4.13.0 to v5.0 Alpha1
------------------------------------------------

Bradley Lowekamp (49):
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
COMP: Use anonymous namespace for internal linkage
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
COMP: Update SimpleITKFilters for dependency issues
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
BUG: Add missing extensions to ImageIO
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

Bryce A Besler (1):
ENH: Move DiscreteGaussianDerivativeImageFilter from Review to ITKImageFeature

Dženan Zukić (27):
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

Francois Budin (17):
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
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

Gregory C. Sharp (1):
DOC: Fix misspelling of vertices

Hans Johnson (86):
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

Hastings Greer (1):
ENH: Add wrapping for Labeled PointSet to PointSet registration classes

Jean-Christophe Fillion-Robin (3):
BUG: Prevent gdcm "missing implementation" error on macOS
BUG: Prevent gdcm "missing implementation" error on macOS
STYLE: MeshIO: Introduce ITKIOMeshBase module. See 3393

Jon Haitz Legarreta (8):
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.

Jon Haitz Legarreta Gorroño (19):
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.
ENH: Add Python wrap file to itk::MultiResolutionPDEDeforableRegistration.
STYLE: Update the wrap files to match current CMake syntax.
DOC: Fix typo.

KWSys Upstream (1):
KWSys 2018-01-08 (f7990fc2)

Marcus D. Hanwell (1):
DOC: Add GitCheatSheet sources

Martino Pilia (2):
BUG: fix itkFormatWarning in Python wrapping
BUG: fix itkFormatWarning in Python wrapping

Matthew McCormick (46):
BUG: Remove ITKTubeTK remote
ENH: Add wrapping for BSplineTransformInitializer
ENH: Add PolarTransform remote module
COMP: Do not use absolute path to TestBigEndian.cmake in GDCM
COMP: Enable pthreads shim with Emscripten
COMP: Do not use absolute path to TestBigEndian.cmake in GDCM
COMP: Enable pthreads shim with Emscripten
BUG: Allow module examples to be enabled when built externally
ENH: Ensure external module examples get added to current build tree
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
COMP: Work around RegionGrow2DTest compiler error on ppc64le
BUG: Bump KWStyle for C++11 brace list initialization support
BUG: Fix MeshFileWriter export specification
BUG: Wrap long long instead of long
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

Niels Dekker (18):
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
COMP: Worked around endless VS2015 Release compilation on Math::Floor
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

Sean McBride (19):
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
STYLE: arranged/alphabetized things to make subsequent changes reviewable
COMP: Fixed some missing name mangling of libTIFF symbols
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: fixed crash on macOS under guardmalloc from RunOSCheck()
COMP: Mangle HDF5 symbol names
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

Simon Rit (1):
BUG: fix deadlock in FFTW for windows shared libs

Taylor Braun-Jones (1):
BUG: Handle single-component PLANARCONFIG_SEPARATE TIFF images (ITK-3518)

VXL Maintainers (3):
VNL 2018-01-25 (ed159d55)
VNL 2018-01-31 (39559d06)
VNL 2018-03-04 (09a097e6)

Ziv Yaniv (1):
ENH: Adding user set min and max values for noise.

------------------------------


Alexis Girault agirault (4):
ENH: Compare images converted from and to VTK in ITKVtkGlue tests
ENH: Pass directions in VTKImage import/export classes
ENH: Throw exception when necessary while importing a vtk image
BUG: Ignore calls to the direction APIs in VTK if lower than 8.90

Bradley Lowekamp blowekamp (46):
COMP: Address const char[] conversation warning
BUG: Fix leaking PNGIO resources during exception
BUG: Remove redundent fclose on PNG file pointer
ENH: Add Valgrind suppression file for Ubuntu 18.04 LTS
BUG: Update FEM test for new spatial objects
COMP: Correct continuous index type
BUG: Address valgrid defects related to the PointSpatialObject
BUG: Fix ownership of environment variable value
BUG: Fix leak in SpatialObject InternalClone method
ENH: Update a couple example to use the resample instead of warp
BUG: Set all component of 3D points
BUG: Add named output support to StreamingImageFilter
ENH: Deprecate VectorResampleImageFilter
ENH: Consolidating setting compression level interface to ImageIOBase
ENH: Implement InternalSetCompressor method in ImageIOs
DOC: Add compression documentation to ImageIOs
ENH: Use the empty string "" for the default compressor
ENH: Add compression level support to NRRD IO
ENH: Improve TIFF ImageIO compression testing
ENH: Add base class for generic streaming processes
ENH: Add ImageSink base filter class
ENH: Use streaming base class for LabelStatisticsImageFilter
ENH: Use named input in LabelStatisticsImageFilter
ENH: Add streaming support to StatisticsImageFilter
ENH: Add testing for streaming with StatisticsImageFilter
ENH: Remove output image, use standard decorator macros
ENH: Refactor min/max filter to use ImageSink
ENH: Add ImageSink::VerifyInputInformation
ENH: Add KWStyle override for ImageStatistics module
ENH: Use streaming sink base class for image to histogram filters
ENH: Deprecate ImageTransformer class
BUG: Update NormalizeImageFilter with double graft mini-pipeline
DOC: statistics filter changes for ITKv5
ENH: Add Python wrapping for streaming base classes
ENH: Add streaming testing of label statistics filter
COMP: Move deprecated VectorCastImageFilter wrapping to deprecated
BUG: Fix path for Brain Web data
BUG: Correct StreamingProcessObject's progress computation
STYLE: prefer variable-less catch re-throw
BUG: Set current request number back to -1 after stream execution
ENH: Expose streaming methods in MinimumMaximumImageFilter
ENH: Add streaming testing for min max filter
ENH: replace RGB adaptor with directly using CastImageFilter
ENH: Add cast support for per component conversion
ENH: Mark the Cast functor to be remove with legacy code
DOC: Update documentation for streaming statistics filters.

Dženan Zukić dzenanz (25):
ENH: make ITK_MAX_THREADS configurable
BUG: fix threading test bugs when ITK_DEFAULT_MAX_THREADS is over 256
COMP: compile GPU classes with legacies disabled
COMP: removing extraneous DLL specification from private member
COMP: follow-up on recent removal of METAIO_STL macro
COMP: add missing dependent module for ITKv3 examples
COMP: ResampleImageFilter does not have SetDisplacementField method
ENH: reduce default compression level for much faster compression
BUG: compression was accidentally disabled in NrrdImageIO
COMP: compile in ITK
STYLE: move ivar default values to header file
ENH: expose setting compression level in ImageFileWriter
ENH: expose compression level in MetaImageIO
BUG: the clang version check was overly strict on Apple platforms
COMP: fix build failures introduced by c76b193 (886)
ENH: cleaning up tests which are almost exact duplicates from MetaIO
ENH: updating remote modules
COMP: fix warning: 'return' will never be executed
COMP: fix export specification of Barrier class
COMP: follow up to 814419a (bounding box m_CornersContainer removal)
ENH: LevelSetsv4Visualization has moved to remote module ITKVtkGlue
ENH: run large image IO tests serially
ENH: enabling ResampleImage streaming test and updating baselines
ENH: enabling ResampleImage streaming test and updating baselines
ENH: exclude Eigen3 from the list of default modules

Francois Budin fbudin69500 (19):
ENH: Add `fallback_only` parameter to `imread()` Python function
ENH: Add suffix to Azure build running gcov to differentiate them
STYLE: Add display name to checkout step in AzurePipelineBatch.yml
ENH: Add JUnit test formatter to AzurePipelinesBatch.yml
STYLE: Add badge for Azure pipeline Linux code coverage build
ENH: Warning when trying to open in Python an image file that doesn't exist
BUG: Missing `ci_addons` to convert ctest results to JUnit format
BUG: Disable itkObjectFactoryBasePrivateDestructor test with -static link flag
ENH: Add Python function to print Python class name corresponding to C++ class
ENH: Python ImageFileReader error message improvement
ENH: Warning when trying to open in Python an image file that doesn't exist
ENH: Follow up commit to fix itkBoundingBox with LEGACY support
ENH: Follow up commit to fix itkBoundingBox with LEGACY support
BUG: std::list of `LineSpatialObject` needs to be wrapped
BUG: ITK could not find Eigen3::Eigen target when using system Eigen
BUG: Revert changing call to `Initialize()` with `clear()`
BUG: Corner positions were inserted at the end of a list that was initialized
BUG: Enforces consistent types
BUG: Remote modules Python files (*.so, *.py) were built in the wrong folder

GDCM Upstream (1):
GDCM 2019-05-16 (e405908e)

Hans J. Johnson hjmjohnson (20):
BUG: Usage name did not match file name.
STYLE: Minor indentation improvements.
ENH: Enable ITKV3_COMPATIBILITY option
STYLE: Remove outdated python examples
STYLE: Syncronize changes between RegistrationITKv[34]
STYLE: Remove RegistrationITKv3 duplicate examples
ENH: Remove ITKV3_COMPATIBILITY support from ITKv5.0
STYLE: Move deprecated Examples/RegistrationITKv3 to test
BUG: Explicit RegisterRequiredFactories needed as test
STYLE: Remove Software Guide tags from ITKv3 testing
DOC: Make use of checkboxes consistent with github
ENH: Add cmake override for GIT_TAG of remote modules
STYLE: Remove custom environmental override for WikiExamples
DOC: Fix spelling errors
ENH: Identify histogram min/max for UseSampledPointSet
BUG: itkConfigure.h defines ITK_DEFAULT_MAX_THREADS
COMP: Remove unused static variable warning
DOC: Remove documentation references to VectorResampleImageFilter
DOC: Remove VectorCastImage documentation references
ENH: Changes required for ITKv5 compatibility

Jon Haitz Legarreta Gorroño jhlegarreta (4):
STYLE: Remove tab.
DOC: Improve remote modules' maintenance scripts documentation
ENH: Add a script to apply another script to all remotes
DOC: Modify the CoC breach reporting procedure

Mathieu Malaterre malaterre (3):
STYLE: Teach git about GDCM oversize file
BUG: Do not include COPYING from a non existing directory
DOC: Fix old reference to Image Number

Matthew McCormick thewtex (23):
COMP: Wrap functions for WindowedSincInterpolateImageFunction
COMP: Wrapping windowed sinc function includes
COMP: Update for changes to VTK target names
DOC: Improve ease of release note command execution
DOC: Document generation of MD5SUMS and SHA512SUMS files for releases
DOC: Add More Information section to CONTRIBUTING
DOC: Add ITK 5.0 RC 2 release notes
BUG: PythonFindEmptyClasses test for windowed-sinc functions
BUG: Prevent ITKMesh README.md from installation as header
BUG: Fix identification of Clang major version
COMP: ImageMaskSpatialObjectGTest array initialization
COMP: ImageMaskSpatialObjectGTest add braces for initialization
ENH: Expand ResampleImageFilter requested region by interpolator domain
STYLE: Use typename instead of class in ImageSink
STYLE: override methods should not be marked virtual
BUG: ImageSink defines UpdateLargestPossibleRegion
STYLE: StreamingProcessingObject passing void with no arguments
BUG: {MinimumMaximum,StatisticsImageFilter} set PrimaryOutputName
BUG: Remove MinimumMaximumImageFilter from module2module test pipeline
BUG: InterpolateImageFunction::GetRadius hidden in ITKV4_COMPATIBILITY
BUG: Condition Eigen export code on ITK_BINARY_DIR
BUG: Fix ITKv3 registration test names for property setting
BUG: Remove CTEST_TEST_TIME debug message

MetaIO Maintainers (5):
MetaIO 2019-05-03 (7e16abe1)
MetaIO 2019-05-08 (dd5089a2)
MetaIO 2019-05-15 (bffb2ef1)
MetaIO 2019-05-16 (5010ab63)
MetaIO 2019-05-21 (368213e5)

Niels Dekker N-Dekker (21):
ENH: Add std style reverse iterators to FixedArray
ENH: Add ImageMaskSpatialObject::ComputeMyBoundingBoxInIndexSpace()
STYLE: SpatialObject() = default, const BoundingBox, Transform members
ENH: Added tests for ImageMaskSpatialObject::IsInside
ENH: Test ImageMaskSpatialObject::IsInside independent of distant pixels
BUG: Fix issue 785 removing BoundingBox check from ImageMask IsInside
PERF: Overload SpatialObject IsInsideInObjectSpace without name argument
BUG: Half a pixel margin ImageMaskSpatialObject::ComputeMyBoundingBox()
STYLE: Deprecated FixedArray member functions rBegin() and rEnd()
STYLE: Replace std::swap_ranges by C++11 std::swap of m_InternalArray
DOC: Use the term "object space" for ObjectSpace based member functions
STYLE: Replace unsigned short by unsigned int as FixedArray index type
STYLE: Explicitly defaulted default-constructors Vector Accessor classes
STYLE: Ensure that ContinuousIndex TCoordRep is a floating point type
ENH: Convenience overloads for ImageBase Transform member functions
ENH: Add NumberOfCorners and ComputeCorners() to BoundingBox
STYLE: Remove (deprecate) BoundingBox::GetCorners() + m_CornersContainer
COMP: Fixed GCC4 missing-field-initializers warning on `{}` in GTest
DOC: Fixed Doxygen description BoundingBox Get member functions
DOC: Fixed Doxygen description BoundingBox Get member functions
STYLE: Rename ITK macro EXPECT_VECTOR_NEAR to ITK_EXPECT_VECTOR_NEAR

Roman Grothausmann romangrothausmann (1):
ENH: Bump remote module ParabolicMorphology

Simon Rit SimonRit (4):
COMP: remove MSVC 14 C4800 (performance) warnings with FFTW
COMP: remove unused parameter warning with GCC 4.8.5
COMP: fix wrong GDCM library names for open jpeg
ENH: update RTK remote file with release tag v2.0.1

VXL Maintainers (1):
VNL 2019-05-08 (99697e67)

maekclena (8):
ENH: Update compiler macros (810)
BUG: Remove error prone test case
BUG: Fix reverse iterator increment return type
ENH: Add iterator increment operator return value test
BUG: Minor python wrapping fixes
ENH: Remove duplicate code
ENH: Use ResampleImageFilter for vectors
ENH: Deprecate VectorCastImageFilter (870)

We are happy to announce the Insight Toolkit (ITK) Release Candidate 2! :tada: This will be the final release candidate before the 5.0.0 release, and the community is encouraged to adopt 5.0 RC 2 in ITK-based applications.

**Python Packages**

ITK Python packages can be installed by running:


python -m pip install --upgrade pip
python -m pip install --upgrade --pre itk


**Library Sources**

- [InsightToolkit-5.0rc02.tar.gz](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc02/InsightToolkit-5.0rc02.tar.gz)
- [InsightToolkit-5.0rc02.tar.xz](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc02/InsightData-5.0rc02.tar.xz)
- [InsightToolkit-5.0rc02.zip](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc02/InsightToolkit-5.0rc02.zip)

**Testing Data**

Unpack optional testing data in the same directory where the Library Source is unpacked.

- [InsightData-5.0rc02.tar.gz](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc02/InsightData-5.0rc02.tar.gz)
- [InsightData-5.0rc02.tar.xz](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc02/InsightData-5.0rc02.tar.xz)
- [InsightData-5.0rc02.zip](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc02/InsightData-5.0rc02.zip)

**Checksums**

- [MD5SUMS](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc02/MD5SUMS)
- [SHA512SUMS](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc02/SHA512SUMS)


*Image denoising with the new **ITKTotalVariation** remote module. Left: Transmission electron microscopy image of pectin. Right: Denoised image.*

This release features a major upgrade to the ITK *Spatial Object* framework, led by Stephen Aylward, with contributions from Hastings Greer, Forrest Lee, Niels Dekker, Dženan Zukić, and Hans Johnson. In ITK, a [`itk::SpatialObject`](https://itk.org/Doxygen/html/classitk_1_1SpatialObject.html) provides a representation of *objects* and the mechanism to specify their spatial relationship relative to other objects in a scene. Objects can be images but also abstract, parametric entities, such as a ellipse, box, or arrow, or point-based, such as a tube, contour, or surface. Objects can be organized into spatial hierarchies.`SpatialObject`s are key for model-based registration, integration of segmentation results in multiple formats, conversions to and from images, and capturing spatial relationships between structures.

In ITK 5, the `SpatialObject` framework was refactored to improve consistency in the the programming interface and simplify implementation and usage. As a result, incorrect or unexpected behaviors are avoided. Complexity and dependency were reduced by removing a dependency on the VNL tree data structures. Additionally, *IndexSpace* was removed from the API of all `SpatialObject`s to prevent ambiguity while providing a consistent and intuitive interface. Only two reference spaces are consistently and explicitly available in the API: *ObjectSpace* and *WorldSpace*. *ObjectSpace* is the space local to each object, where the object's parameters are defined. *WorldSpace* is the coordinate system defined by the top-level `SpatialObject` in a hierachy, which is defined by parent-child object relationships. Only two transforms are now consistently and explicitly available in the API: *ObjectToParent* transform and *ObjectToWorld* transform. The *ObjectToParent* transform moves an object within its parent's *ObjectSpace*. The *ObjectToWorld* transform is derived from component *ObjectToParent* transforms and is provided for convenience and to reduce redundant computations. The API is now more explicit regarding the space that an operation applies to. For instance, `IsInside(point)` is now `IsInsideInObjectSpace(point)` or `IsInsideInWorldSpace(point)`. For more information on the `SpatialObject`s changes, see the [ITK 5 Migration Guide](https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/ITK5MigrationGuide.md).

The Python package synchronization infrastructure for static global variables was refactored to support more variables and permit future additions to the singleton. This will prevent the need to rebuild remote module binary Python packages following future releases of ITK 5. However, current remote module Python packages that use ITK 5 should be rebuilt and republished for ITK 5.0 RC 2.

For an overview of ITK 5's transition to modern C++, performance-related changes, the new, Pythonic API, the project's migration to GitHub, and Mesh improvements, see the [ITK 5 Alpha 1: Modern C++](https://discourse.itk.org/t/itk-5-0-alpha-1-modern-c/843/7), [ITK 5 Alpha 2: Performance](https://discourse.itk.org/t/itk-5-0-alpha-2-performance/959), [ITK 5 Beta 1: Pythonic Interface](https://discourse.itk.org/t/itk-5-0-beta-1-pythonic-interface/1271), [ITK 5 Beta 3: GitHub](https://discourse.itk.org/t/itk-5-0-beta-3-github/1504) and [ITK 5 Release Candidate 1: Meshes](https://discourse.itk.org/t/itk-5-0-release-candidate-1-meshes/1576/3) release announcements.


*Tomographic phantom reconstruction with the new Reconstruction Toolkit (RTK) remote module.*

New Remote Modules
------------------

- [`ITKIOScanco`](https://github.com/KitwareMedical/ITKIOScanco): read and write Scanco microCT *.isq* files.
- [`ITKTotalVariation`](https://github.com/InsightSoftwareConsortium/ITKTotalVariation): total variation image denoising.
- [`ITKRTK`](https://github.com/SimonRit/RTK): the Reconstruction Toolkit provides high performance implementations of advanced tomographic image reconstruction algorithms.
- [`ITKThickness3D`](https://github.com/InsightSoftwareConsortium/ITKThickness3D): compute the skeleton and thickness transform from 3D images.

Performance Improvements
------------------------

- Add MetaDataDictionary move support.
- MetaDataDictionary uses copy-on-write.
- `itk::Barrier` is now deprecated: replace with the new multi-threading functions.
- Range-based for loops supported in `itk::FixedArray`.
- Major performance improvements to TimeProbe, ResourceProbe constructor (issue 350).

Documentation
-------------

- Repository *README* files were migrated to Markdown.

Infrastructure
--------------

- Continuous code coverage builds from Azure Pipelines.
- Better support for unicode in KWSys.
- `itksys::hash_map` and `itksys::hash_set` are deprecated in favor of `std` equivalents.
- New GitHub pull request templates and issue templates.
- New scripts added to update ITK remote modules.

Core
----

- `itk::SpatialObject` framework refactored (see release notes introduction).
- Initial streaming support added to `itk::ResampleImageFilter` for linear transforms.

Third Party
-----------

- Eigen 3 updated to the latest version.
- Better support for building against a system Eigen.
- GDCM updated to the latest version.
- HDF5 updated to 1.10.4.
- ITKVtkGlue support for VTK with `VTK_RENDERING_BACKEND` set to `None`.
- KWSys updated to the latest version.
- MetaIO updated to the latest version.
- VXL updated to the latest version.
- MINC updated to the latest version.

Python
------

- Static variable synchronization method refactored; ITK 5 remote module Python packages need to be rebuilt against 5.0 RC 2.
- Add wrapping for `itk.PCAShapeSignedDistanceFunction`.
- Docstrings added to snake case functions.
- Python tests should now be defined in *<ITK-module>/wrapping/test/CMakeLists.txt* to exclude their definition when wrapping is not enabled.
- Conversion between ITK matrices and NumPy arrays is now supported.
- Additional wrapping types for `itk.ImageDuplicator`.
- Additional types supported for NumPy <-> ITK Image conversion.
- Additional wrapping and typemaps for `std::vector<itk::Image<...>::Pointer>`.
- Add wrapping for `itk.TriangleMeshToBinaryImageFilter`.
- Add wrapping for `itk.ExtrapolateImageFunction`.
- Add wrapping for `itk.WindowedSincInterpolateImageFunction`.

To install the 5.0 Release Candidate 2 Python packages, run

sh
python -m pip install --upgrade pip
python -m pip install --upgrade --pre itk


What's Next
-----------

There are many more improvements not mentioned above. For more details, please see the change log below. Congratulations and thank you to everyone who contributed to this release.

The [ITK 5 Migration Guide](https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/ITK5MigrationGuide.md) is available to help transition a code base from ITK 4 to ITK 5. Please discuss your experiences on [Discourse](https://discourse.itk.org).

The ITK 5.0.0 final release is [scheduled for May](https://github.com/InsightSoftwareConsortium/ITK/milestone/5).

**Enjoy ITK!**

Changes from 5.0 RC 1 to 5.0 RC 2
---------------------------------------------------


Bradley Lowekamp blowekamp (14):
ENH: Add move support to the MetaDataDictionary object
PERF: Implement copy on write for MetaDataDictionary
ENH: adding MetaDataDictionary GTests
BUG: Do not modify MetaDataDictionary with operator[] const
ENH: Improve ExposeMetaData efficiency
COMP: Address CMake policy warnings in ThirdParty libraries
ENH: Update AzurePipelines configuration from master
ENH: Explicitly set the XCode version used in Azure
COMP: Use CMP0048 new for wrapping
COMP: Set CMP0048 to new in ITK (Remote) Modules
COMP: Address OSX Clang "direct access" linkage warnings
ENH: Add Azure Pipelines script for coverage
BUG: Fix Li threshold calculator for negative image values
DOC: Correct documented Canny Segmentation filter example

Dženan Zukić dzenanz (18):
ENH: add better support for Unicode by using UTF-8 by default in KWSys
BUG: propagate ITK_LIBRARY_PROPERTIES into zlib
COMP: fixing MSVC warning C4800
ENH: refactoring NarrowBandImageFilterBase to not use Barrier
DOC: fixing code sample
COMP: compile fixes for Visual Studio 2017
ENH: ModifiedTimeType uses 64 bits on Windows - it was 32 before
ENH: refactor itkThreadPoolTest and rename into itkMultithreadingTest
ENH: shuffling tests in ITKCommon to make the split more logical
ENH: introduce a parameter to control level of output
ENH: concentrating WaitForAll() in Iterate()
ENH: ParallelSparseFieldLevelSetImageFilter no longer uses barrier
ENH: moving Barrier into Deprecated module
ENH: prevent false sharing between threads
STYLE: declaration alignment
ENH: replace itksys::hash_map and hash_set by std equivalents
COMP: missing override for destructors
Update ITK5MigrationGuide.md

Eigen Upstream (3):
Eigen3 2019-01-26 (e2c082bf)
Eigen3 2019-03-05 (0805e8fd)
Eigen3 2019-03-14 (8a3c2d91)

Forrest Li floryst (4):
ENH: Update arrow spatial object
ENH: Update EllipseSpatialObject
ENH: Update box spatial object
ENH: Update polygon SO and delete polygon group SO

Francois Budin fbudin69500 (25):
BUG: Implement but hide MetaDataDictionary iterator methods
BUG: Explicitly give Python library path to ITK Python targets for MSVC
ENH: Wrap itkPCAShapeSignedDistanceFunction
ENH: Synchronize factories across modules in Python
ENH: Explicitly return `None` when calling `__call__`` if filter has no output
ENH: Deprecated object call function and improve procedural call function
ENH: Adds argument completion with procedural calls
ENH: Add docstring to snake case functions
BUG: Disable Python tests if `ITK_BUILD_DEFAULT_MODULES` is OFF
BUG: Returns a copy of the VNL matrix instead of a reference
ENH: Add helper functions to convert NumPy arrays to ITK matrices and back
ENH: Add `ttype` keyword in New() function for Python templated classes
ENH: `isinstance()` can be called without template parameters of classinfo
BUG: Wrap itkImageDuplicator for all image types as it is used by NumPyBridge
ENH: itkPCAShapeSignedDistanceFunction supports float images
ENH: Add advanced CMake option `ITK_DO_NOT_BUILD_TESTDRIVERS`
ENH: Move part of CI configuration into Azure YML files
ENH: Move Python tests into wrapping subfolder
BUG: Correct CMake variable name and move baseline files to appropriate folder
ENH: Only run Python tests on Linux and Windows
ENH: Adds wrapping for std::vector<itk::Image<...>::Pointer> and typemaps
ENH: New test to verify that` ObjectFactoryBasePrivate` is destroyed correctly
ENH: Enable forcing creating snake_case function for non-ProcessObject classes
ENH: Add snake case method for non itkProcess derived class itkImageDuplicator
BUG: itkObjectFactoryBasePrivateDestructor was not compiling with MSVC

GDCM Upstream malaterre (3):
GDCM 2019-02-07 (8e1cfd05)
GDCM 2018-10-23 (2e701ed7)
GDCM 2019-02-08 (815caa81)

HDF5 Maintainers (1):
HDF5 2018-10-15 (545c5fb2)

Hans J. Johnson (27):
STYLE: Remove exact duplicate test code
ENH: Improve by adding enhanced complexity to testing
ENH: Add test for IsInsideInObjectSpace.
DOC: Improve diagnostic message from ExtractImageFilter
ENH: TransformIOBaseTemplate Must be explicitly instantiated
STYLE: Instance variables should be private
STYLE: Move default [con/de]strutor to .h (part 2)
STYLE: Class derived from TransformBase need explicit instantiation
STYLE: Remove functions that are not used
ENH: Use member functions with default values
COMP: Refactor to remove const_cast of void *
STYLE: Fix spelling s/ranage/range/g in comment.
ENH: Improve coverage for itk::FastMarchingImageFilterBase.
COMP: Allow compiler option fixed in gcc 4.1.0
PERF: Allow overwriting ABI/Optimization & Warning flags
DOC: Minor spelling corrections
ENH: Improve test coverage of ImageMoments
DOC: Expand GetAxisAlignedBoundingBoxRegion replacement code
STYLE: Prefer using Update() for consistency
ENH: Avoid deprecated SpatialObject function calls
ENH: ProtectedComputeMyBoundingBox return not used
ENH: Clean up tests to pass under new API
COMP: Consolodate duplicate LogTester code
COMP: Support ITK_LEGACY_REMOVE for SpatialObjects
ENH: Add legacy interface to SpatialObjects
BUG: Match return types for nullptr return values
COMP: Remove compilation warning unmatched types

Hastings Greer HastingsGreer (6):
BUG: ImageSpatialObject's BoundingBox was nonfunctional if not axis aligned
BUG: ImageMaskSpatialObject::IsInside uses image cosines
COMP: fix compilation errors
COMP: Various compiler errors
COMP: fixes to enable compilation with gcc
COMP: Update tests

Jerome Schmid schmidje (1):
COMP: VtkGlue module-Provide support for VTK new cmake targets

Jon Haitz Legarreta Gorroño jhlegarreta (29):
ENH: Add a PrintHelper file to overload boolean and vector printing.
ENH: Add a parameter to test to improve `itk::ResampleImageFilter` testing.
ENH: Update the ITKIOFDF remote module.
ENH: Improve `itk::ResampleImageFilter` class coverage.
BUG: Fix `ìtkResmapleImageTest2` test failing on 32-bit systems.
DOC: Transition `Examples` folder `README` file to Markdown.
DOC: Increase `VNL` ThirdParty module `README` information accuracy.
ENH: Conform to GitHub PR and issue template guidelines.
DOC: Transition the `Nonunit/Review` `README` to Markdown syntax.
ENH: Bump the latest version of the `ITKThickness3D` remote.
BUG: Fix GitHub community template syntax errors.
STYLE: Transition GitHub community template filenames to lowercase.
DOC: Change GitHub community template guidelines to HTML comment markup.
ENH: Add new GitHub community issue templates.
STYLE: Improve coverage issue template name wording.
DOC: Fix PR template not being displayed.
DOC: Add emojis to GitHub issue templates.
ENH: Update a few remote modules to their latest commit versions.
DOC: Improve the CONTRIBUTING guidelines document
DOC: Fix typo.
DOC: Add checklist to PR template.
ENH: Add a script to update the remote module commit hashes
ENH: Add a script to update the ITK tag as required in files
ENH: Update the Remote module Python package version automatically
STYLE: Rename remote module maintenance script
DOC: Add Remote module PyPI update notice in Release guide
ENH: Bump remote modules.
ENH: Bump remote modules to latest commits
ENH: Bump remote modules to their latest commits
COMP: Fix Software Guide line length too long warnings

KWSys Upstream bradking (2):
KWSys 2019-02-14 (e270ce9f)
KWSys 2019-03-28 (e92bdbe8)

Matthew McCormick thewtex (51):
ENH: Use HDF5 1.10.4
DOC: Updates to the README
DOC: Use 'ITK: The Insight Toolkit' for README title
ENH: Add legacy multi-frame DICOM MD5 content links
COMP: Avoid duplicate wrapping of VectorContainer with unsigned short
BUG: MeshIOBase ivars used for number points, cells, pixels
STYLE: Keep ProjectObject methods protected in ResampleImageFilter
STYLE: Remove unnecessary ResampleImageFilter input/output checks
DOC: Updates to the Release documentation for 5.0 RC 1
ENH: Update CI ExternalDataVersion to 5.0rc01
DOC: Add ITK 5 Release Candidate 1 release notes
ENH: Add regression test for reading legacy multi-frame DICOM
ENH: Update itk_hdf5_mangle.h for HDF5 1.10.4
COMP: Re-apply HDF5 Emscripten clobbered by 1.10.4 update
ENH: Add probot-stale GitHub bot configuration
ENH: Add test result analysis to Azure Pipelines web interface
COMP: Set CMP0083 for PIE flags
COMP: HDF5 CMake does not have INTEGER cache type
COMP: Do not also pass png_ptr twice to png_set_error_fn
ENH: Wrap TriangleMeshToBinaryImageFilter
PERF: Use constexpr in complex NumericTraits
BUG: VTKPolyDataMeshIO CanReadFile returns false for non-PolyData
COMP: Set CMP0083 for PIE flags
BUG: Use VERSION_GREATER_EQUAL for PIE check
ENH: Bump CMakeLists.txt version to 4.13.2
ENH: Add missing SHA512 content link
ENH: Explicitly use Python 3.7 in Azure builds
COMP: Prevent duplicate wrapping ouput file specification
BUG: Add executable bit to prefer-type-alias-over-typedef.sh
COMP: Specify type in LiThresholdCalculator min call
ENH: Wrap ExtrapolateImageFunction
ENH: Add Python wrapping for SymmetricEigenAnalysisImageFilter
BUG: Add missing ITKImageGrid circle.png content links
BUG: itkResampleImageTest2Streaming verification
ENH: Add IOScanco remote module
COMP: Add backwards compatible EnlargeRegionOverBox
BUG: Set dashboard_do_coverage in Azure configuration
COMP: Add export specification to ITKSpatialObjects
BUG: Mark HDF5 CMake variables as advanced
BUG: Mark INSTALL_GTEST CMake variable as advanced
STYLE: NIFTI CMake variable spacing
BUG: Do not use CACHE variables for NIFTI when not required
BUG: Mark TESTLIB_VCL_WHERE_ROOT_DIR_H as advanced
BUG: Remove BUILD_* GDCM settings from the cache
BUG: Remove ALLOW_UNSUPPORTED from the cache
STYLE: C-style variable declarations in WindowedSinceInterpolateImageFunction
ENH: Add wrapping for WindowedSincInterpolateImageFunction
ENH: ITKVtkGlue only requires rendering libraries when needed
COMP: GaussianInterpolateImageFunction test narrowing
BUG: Allow Python tests in module test/CMakeLists.txt
ENH: Add new content links for ITK 5.0 RC 2

MetaIO Maintainers (2):
MetaIO 2019-01-15 (6efa2b32)
MetaIO 2019-04-24 (9d2012d1)

Mihail Isakov issakomi (4):
BUG: WhatModulesITK.py doesn't detect ITKMeshIO
STYLE: header included twice, spelling
BUG: index overflow in BinaryMask3DMeshSource
BUG: changed to signed

Niels Dekker N-Dekker (28):
PERF: Remove SystemInformation data from ResourceProbe, fix issue 350
COMP: Fix support itk::VectorContainer<TElementIdentifier, bool>
COMP: Fix SymmetricEigenAnalysis support TMatrix = itk::Array2D<T>
COMP: Trailing return types (reference, const_reference) VectorContainer
STYLE: HoughTransform2DCircles, GaussianDerivativeImageFunc member init.
COMP: Win32Header no longer disable MSVC warning C4800, C4290, C4786
COMP: Removed unreachable code, fixing VS2017 warning (level 4) C4702
STYLE: Removed '2' from GaussianDerivativeImageFunction::ImageDimension2
STYLE: Renamed SpatialFunction within GaussianDerivativeImageFunction
BUG: Fixes crashes in unit tests when argv[0] == nullptr
STYLE: Removed InitializeConstShapedNeighborhoodIterator()
STYLE: ImageFileReader uses std::unique_ptr<[]>, try-catch-throw removed
STYLE: Renamed array of radii EllipseSpatialObject to RadiiInObjectSpace
STYLE: Remove GetPixelTypeName() from both Image and Mesh SpatialObject
ENH: GTest for ImageMaskSpatialObject::GetAxisAlignedBoundingBoxRegion()
STYLE: Removed unused private EventObject::EventFactoryFunction type
COMP: Support ITK_LEGACY_SILENT for ThreadInfoStruct
STYLE: Removed five unused nested types from ImageSpatialObject
ENH: Add static member function Size<VDimension>::Filled(SizeValueType)
STYLE: Removed legacy-only ComputeMyBoundingBox() which was not in ITK4
STYLE: Renamed ProtectedComputeMyBoundingBox() to ComputeMyBoundingBox()
STYLE: Remove const from SpatialObject::ComputeMyBoundingBox()
BUG: Fix 734 Incorrect results GetAxisAlignedBoundingBoxRegion() for 2D
ENH: Extend test ImageMaskSpatialObject::GetAxisAlignedBoundingBoxRegion
STYLE: SpatialObject GetModifiableMyBoundingBoxInObjectSpace() non-const
PERF: ImageMaskSpatialObject::GetAxisAlignedBoundingBoxRegion() faster
ENH: Add explicit constructors Point and FixedArray for C++11 std::array
ENH: Add begin() and end() to FixedArray, support range-based for-loops

Pablo Hernandez-Cerdan phcerdan (11):
ENH: Add itk-module-init.cmake to Eigen3
COMP: Make ThirdParty Eigen3 COMPILE_DEPENDS
COMP: Revert "COMP: Make ThirdParty Eigen3 COMPILE_DEPENDS"
BUG: Fix Eigen3 INSTALL_DIR
DOC: Update ITK5MigrationGuide
BUG: Fix OFFIS_DMCTK_VERSION_NUMBER where wrunlock was introduced
BUG: Fix export for ITKDeprecated classes
BUG: Do no install any Eigen3 targets if ITK_USE_SYSTEM_EIGEN=ON
ENH: Update Remote Module IsotropicWavelets
ENH: Add COMPILE_DEFINITIONS to castxml
ENH: Add remote module TotalVariation

Roman Grothausmann romangrothausmann (4):
ENH: new tests to verify streaming capabilities of itkResampleImageFilter
BUG: corrected logic for checking that streaming was not used
ENH: compare outputs of itkResampleImageTest2Streaming to determine success:
ENH: Stream ResampleImageFilter for linear transforms

Simon Rit SimonRit (2):
ENH: add RTK as a remote module
ENH: added test to check that Matrix returns a copy of the vnl matrix

Stephen R.Aylward aylward (47):
ENH: Refactor of SpatialObject top-level class
ENH: Remove itkAffineGeometryFrame file
ENH: Update ArrowSpatialObject
ENH: Children name match using string.find (i.e., any substring)
ENH: Refined SpatialObject base class and organized .h. Refactoring.
ENH: Refactor Line and Landmark Spatial Objects
ENH: Refactor Mesh and fix bugs found in previous refactorings
BUG: Remove itkPlaneSpatialObject because it implemented a boxSO
ENH: Refactor itkPolygon[Group]SpatialObject
ENH: Refactor Scene to be a Group and refine base SpatialObject
ENH: Refactoring the SpatialObject to be more intuitive
ENH: SpatialObjects have "MyBoundingBox" and "FamilyBoundingBox"
ENH: Resolved SpatialObject member function and variable names
ENH: Updated subclasses to match SpatialObjectAPI
ENH: SpatialObjectPoint and Properties updated
ENH: Removed unwanted TreeNode classes
ENH: Removing outdated source files
COMP: SpatialObjectProperties now a cxx file that compiles
ENH: Refactor SpatialObjectPoints and TubeSpatialObjectPoints
ENH: Update PolygonGroup IO to use new spatial object classes
ENH: Refactoring for IO
ENH: Renamed functions to make coordinate system explicit
ENH: Refactoring Meta*Converter classes
ENH: Update to tests to fit new SO API
BUG: Fixed bugs on windows for tests
ENH: Updated wrapping and examples to compile SpatialObjects
ENH: Updated itkGetObjectMcro to itkGetModifiableObjectMacro
ENH: Updates to fix failing tests
ENH: Fix two more tests
BUG: Fix bug in ImageMaskSO bounding box
ENH: Making tests pass...one bug at a time...
BUG: Missing center computation in isInside function for Ellipse
ENH: Adding support for Clone member function to perform a deep copy
BUG: Last spatial-object-specific tests now pass.
BUG: Fix const issues regarding My/Family Bounding Box
BUG: Fix warnings and other minor things
ENH: Fixing PolygonSpatialObject
ENH: Made ContourSO and PolygonSO more consistent in logic
BUG: Fix IsInsideObjectSpace function in PolygonSpatialObject
BUG: Fix multiple bugs in refactoring of spatial objects
DOC: SpatialObject docs in migration guide (630)
DOC: Detail function change in ImageMaskSpatialObject
DOC: Specify ITK class alternatives to removed SO member functions
BUG: Adds RemovePoint() to PointBasedSpatialObjects (693)
DOC: PointBasedSpatialObject's PointListType migration docs provided (652)
BUG: Adding a consistent Clear() to SpatialObjects (700)
DOC: Update recommendation for computing a Boundoing Region in IndexSpace (699)

Thomas Janvier T4mmi (1):
ENH: Add Thickness3D Remote module.

VXL Maintainers (3):
VNL 2019-03-04 (1e8a027f)
VNL 2019-03-11 (3d183906)
VNL 2019-03-22 (d0ff9f72)

Vladimir S. FONOV vfonov (2):
MINC 2019-04-23 (44fae20d)
ENH: fixed build script

Ziv Yaniv zivy (1):
BUG: PNGImageIO segfaults on corrupt png.

maekclena (13):
BUG: Initialize array with expected number of elements
BUG: Disable TIFF predictor
BUG: Python3 compatibility
ENH: Cleanup python wrapping tests
ENH: Address review comments
ENH: Update maintenance script
BUG: Replace sed by ex for portability
ENH: fix inconsistencies and clearer output
ENH: Update remote modules
BUG: fix gaussian interpolate test
BUG: Ignore comment lines
STYLE: Visually indent array
BUG: Remove outdated class declaration

-----------------------------------------------

Bradley Lowekamp (2) blowekamp:
BUG: Use compatible ITKv4 computation
BUG: Fix Ostu test to work with ITKv4 default options

Dženan Zukić (9) dzenanz:
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 (1):
Eigen3 2019-01-14 (16812519)

Francois Budin (1) fbudin69500:
BUG: Missing ITK_WRAP_rgba_* variables in WrapITKConfig.cmake.in

Hans Johnson (7) hjmjohnson:
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(){}

Jon Haitz Legarreta Gorroño (1) jhlegarreta:
DOC: Adjust the CoC Committee to the 01/09/2019 meeting decision.

Matthew McCormick (31) thewtex:
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

Niels Dekker (19) N-Dekker:
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 (14) phcerdan:
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

Roman Grothausmann (1) romangrothausmann:
BUG: avoid overwriting output in 2nd run used for comparison in test:

Simon Rit (1) SimonRit:
BUG: python itk.Image returned by GetImageFromArray now manages its own buffer

ihnorton (1):
COMP: use HDF5 library names only to avoid abspaths w/ SYSTEM_HDF5

-----------------------------------------------

Note: ITK v5.0b02 was skipped due to a build error with Visual Studio.

Bai Shi (1):
COMP: To fix compilation error of "cannot dynamic_cast 'x'

Bradley Lowekamp (47):
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

Brian Helba (1) brianhelba :
BUG: Ensure that itkSampleToHistogramFilterTests fail on errors

Dženan Zukić (50) dzenanz :
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.

Eigen Upstream (1):
Eigen3 2018-11-19 (493fa50e)

Francois Budin (9) fbudin69500 :
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

GDCM Upstream (2) malaterre :
GDCM 2018-11-05 (3ffbf1ed)
GDCM 2018-11-30 (ec82fb48)

Gabriel A. Devenyi (1) gdevenyi :
PERF: Enable MINC internal compression by default

Hans Johnson (58) hjmjohnson :
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

Hui Xie (1) Hui-Xie :
BUG: The Z spacing was set using thickness

Isaiah Norton (1) ihnorton :
BUG: don't quote argument to URL_HASH for FFTW

Jon Haitz Legarreta Gorroño (14) jhlegarreta :
ENH: Improve itkEuclideanDistancePointMetric 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.

Matthew McCormick (77) thewtex :
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

Niels Dekker (42) N-Dekker :
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

Pablo Hernandez-Cerdan (17) phcerdan :
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

Roman Grothausmann (2) romangrothausmann :
DOC: adjusted to fit more general case n != m
DOC: corrected description of the output

Sean McBride (3) seanm :
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 (2) SimonRit :
BUG: fix NumPy bridge for itk::Image with PixelType itk::Vector
ENH: improve automatic Python ImageFileReader for non-scalar pixel types

Tobias Wood (1) spinicist :
BUG: Swapped int to SizeType to prevent overflow errors

VXL Maintainers (8):
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)

Yann Le Poul (4) YannLePoul :
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

Zlib Upstream (1):
zlib 2018-06-11 (355d8648)

allywarner (1) allywarner :
BUG: CMake build errors

pierre33 (1) pierre33 :
ENH: Update itkNaryFunctorImageFilter

This release was superseded by ITK 5.0 Beta 3 due to Visual Studio build errors.