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5.2rc03

5.2rc02

5.2rc01

5.1.2

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

Bradley Lowekamp (4):

Platform Fixes

- Updating ITKSimpleITKFilters remote module ([e3ba060fe5](https://github.com/InsightSoftwareConsortium/ITK/commit/e3ba060fe5))

Bug Fixes

- Address divide by zero error in SignedMaurerDistance ([4fb2831d62](https://github.com/InsightSoftwareConsortium/ITK/commit/4fb2831d62))
- Support MRC2014 mode 0 as signed 8-bit integer ([f7d72576bf](https://github.com/InsightSoftwareConsortium/ITK/commit/f7d72576bf))

Style Changes

- Improve function types used in SignedMaurerDistanceMap ([b706cf64c7](https://github.com/InsightSoftwareConsortium/ITK/commit/b706cf64c7))


Hans Johnson (1):

Bug Fixes

- itkhdf5 installed paths were incorrect with recent hdf5 versions ([fd4a438042](https://github.com/InsightSoftwareConsortium/ITK/commit/fd4a438042))


Lee Newberg (1):

Bug Fixes

- MinPriorityQueueElementWrapper constructor needs default constructor ([b027780259](https://github.com/InsightSoftwareConsortium/ITK/commit/b027780259))


Matt McCormick (3):

Enhancements

- Update ITK CMake version for 5.1.2 ([39d9b1712f](https://github.com/InsightSoftwareConsortium/ITK/commit/39d9b1712f))
- Add int.tiff.md5 content link for 5.1.2 release ([a0125aa894](https://github.com/InsightSoftwareConsortium/ITK/commit/a0125aa894))

Bug Fixes

- Add TIFFImageIO support for unsigned int and int pixel types ([241953dd23](https://github.com/InsightSoftwareConsortium/ITK/commit/241953dd23))


Niels Dekker (1):

Bug Fixes

- Fix MatrixOffsetTransformBase SetFixedParameters if too few params ([33e9e6bdba](https://github.com/InsightSoftwareConsortium/ITK/commit/33e9e6bdba))

5.1.1

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


Antoine Robert (1):

Enhancements

- Use Numpy bridge with array of dimension 1 ([caae21695f](https://github.com/InsightSoftwareConsortium/ITK/commit/caae21695f))


Bradley Lowekamp (14):

Enhancements

- Update GDCM to latest on the release-2.8 branch ([90e6da1ff6](https://github.com/InsightSoftwareConsortium/ITK/commit/90e6da1ff6))

Platform Fixes

- Add missing const qualifier ([8c4d3da09d](https://github.com/InsightSoftwareConsortium/ITK/commit/8c4d3da09d))
- Address missing brace initializer warning ([14a8919dfd](https://github.com/InsightSoftwareConsortium/ITK/commit/14a8919dfd))

Bug Fixes

- Disable dynamic threading in noise filter. ([af780e8a03](https://github.com/InsightSoftwareConsortium/ITK/commit/af780e8a03))
- Add StatisticsImageFilter ([43a8972077](https://github.com/InsightSoftwareConsortium/ITK/commit/43a8972077))
- Fix segfault with empty CompositeTransforms ([0300b63ddf](https://github.com/InsightSoftwareConsortium/ITK/commit/0300b63ddf))
- Fix additional segmentation faults with empty Composite ([7212dc719f](https://github.com/InsightSoftwareConsortium/ITK/commit/7212dc719f))
- Address memory leak in CastSpatialOpbjectTest ([a243e9d9af](https://github.com/InsightSoftwareConsortium/ITK/commit/a243e9d9af))
- Patch missing const qualifier to GDCM dircos_comp comparison ([90ad651db4](https://github.com/InsightSoftwareConsortium/ITK/commit/90ad651db4))
- Address bug with small size in output of SliceImageFilter ([7aac4a6748](https://github.com/InsightSoftwareConsortium/ITK/commit/7aac4a6748))
- Update CI scripts from current ITK master ([3213404416](https://github.com/InsightSoftwareConsortium/ITK/commit/3213404416))
- update CircleCI configuration with selections from master ([08dc0116fe](https://github.com/InsightSoftwareConsortium/ITK/commit/08dc0116fe))
- Don't use InsertElement which modifies MTime ([63d148715e](https://github.com/InsightSoftwareConsortium/ITK/commit/63d148715e))
- Address buffer overflow with deprecated GDCM1 interface ([5df152b4c3](https://github.com/InsightSoftwareConsortium/ITK/commit/5df152b4c3))


Bryn Lloyd (1):

Platform Fixes

- Fix warning in PointSetToPointSetMetricv4 (1820) ([567764e1ae](https://github.com/InsightSoftwareConsortium/ITK/commit/567764e1ae))


Davis Vigneault (1):

Bug Fixes

- Fix Segfault in Delaunay Filter ([e72fd012a4](https://github.com/InsightSoftwareConsortium/ITK/commit/e72fd012a4))


Dženan Zukić (9):

Enhancements

- use double-conversion's CMake targets ([3ee6f1e5c9](https://github.com/InsightSoftwareConsortium/ITK/commit/3ee6f1e5c9))
- back-porting 1165 to support Visual Studio 2019 ([432dd1b9dc](https://github.com/InsightSoftwareConsortium/ITK/commit/432dd1b9dc))

Documentation Updates

- restore LICENSE accidentally overwritten by a merge commit ([ed2a25db2c](https://github.com/InsightSoftwareConsortium/ITK/commit/ed2a25db2c))

Platform Fixes

- a fix for non-system double-conversion build ([a47c974f64](https://github.com/InsightSoftwareConsortium/ITK/commit/a47c974f64))
- update download location for pre-built ICU for Visual Studio ([f360092423](https://github.com/InsightSoftwareConsortium/ITK/commit/f360092423))

Style Changes

- make column limit more stringent in the examples ([0b970d803d](https://github.com/InsightSoftwareConsortium/ITK/commit/0b970d803d))
- apply clang-format ([d9e73e9a8b](https://github.com/InsightSoftwareConsortium/ITK/commit/d9e73e9a8b))
- rename libPNG's license to match the original one ([5012917fb4](https://github.com/InsightSoftwareConsortium/ITK/commit/5012917fb4))
- remove duplicate item in a list ([a8ba7686a5](https://github.com/InsightSoftwareConsortium/ITK/commit/a8ba7686a5))


GDCM Upstream (1):

Miscellaneous Changes

- 0353bb40ed ([0353bb40ed](https://github.com/InsightSoftwareConsortium/ITK/commit/0353bb40ed))


Hans Johnson (1):

Bug Fixes

- Double scaling introduced in refactoring ([355c6cbda3](https://github.com/InsightSoftwareConsortium/ITK/commit/355c6cbda3))


Jerome Schmid (1):

Platform Fixes

- VtkGlue module-Provide support for VTK new cmake targets ([c2cfd2b6d1](https://github.com/InsightSoftwareConsortium/ITK/commit/c2cfd2b6d1))


Jonathan Daniel (2):

Enhancements

- Added .vs to .gitignore ([e4f20e2580](https://github.com/InsightSoftwareConsortium/ITK/commit/e4f20e2580))

Bug Fixes

- Accept TemplateTypeError with fallback_only ([612a769660](https://github.com/InsightSoftwareConsortium/ITK/commit/612a769660))


Marco Nolden (1):

Platform Fixes

- added vcl compiler detection for GCC 10.x ([e53d1d94f0](https://github.com/InsightSoftwareConsortium/ITK/commit/e53d1d94f0))


Matt McCormick (20):

Enhancements

- Bump CMakeLists.txt version to 4.13.3 ([f7ac08b4c9](https://github.com/InsightSoftwareConsortium/ITK/commit/f7ac08b4c9))
- Add testing data content links for ITK 5.1.1 ([866ee013a1](https://github.com/InsightSoftwareConsortium/ITK/commit/866ee013a1))
- Update ITK CMake version for 5.1.1 ([3ecf6c87d1](https://github.com/InsightSoftwareConsortium/ITK/commit/3ecf6c87d1))

Platform Fixes

- Duplicate ImageToImageFilter wrapping of ULL ([e747b0a946](https://github.com/InsightSoftwareConsortium/ITK/commit/e747b0a946))
- Avoid duplicate itk.PointSetD3 wrapping ([bea2a7906e](https://github.com/InsightSoftwareConsortium/ITK/commit/bea2a7906e))
- Do not reference FE_DIVBYZERO FE_INVALID with Emscripten ([b05b007a63](https://github.com/InsightSoftwareConsortium/ITK/commit/b05b007a63))
- Add VXL support for GCC 9 ([9825d546c4](https://github.com/InsightSoftwareConsortium/ITK/commit/9825d546c4))
- Add lxml to macOS CI environment ([1919eaa95b](https://github.com/InsightSoftwareConsortium/ITK/commit/1919eaa95b))

Bug Fixes

- Specify itk package in SWIG Python modules ([98fc085a9d](https://github.com/InsightSoftwareConsortium/ITK/commit/98fc085a9d))
- Simplify itk.BlockMatchingImageFilter feature points PointSet mangling ([2e2b3332cd](https://github.com/InsightSoftwareConsortium/ITK/commit/2e2b3332cd))
- Import C module from Python submodule ([a6a5140f4d](https://github.com/InsightSoftwareConsortium/ITK/commit/a6a5140f4d))
- ITKModuleExternal CMAKE_LIBRARY_OUTPUT_DIRECTORY when wrapping ([eb97b5aa4a](https://github.com/InsightSoftwareConsortium/ITK/commit/eb97b5aa4a))
- Wrap ExtractImageFilter for UL ([972a89c228](https://github.com/InsightSoftwareConsortium/ITK/commit/972a89c228))
- Support casting unsigned long pixel types in Python ([530e61eedf](https://github.com/InsightSoftwareConsortium/ITK/commit/530e61eedf))
- Remove netnlib triangle classes ([7f95961fa7](https://github.com/InsightSoftwareConsortium/ITK/commit/7f95961fa7))
- Remove License incompatible netlib files from vxl updates ([d1066224e3](https://github.com/InsightSoftwareConsortium/ITK/commit/d1066224e3))
- Empty image support in image_from_xarray ([3da4926531](https://github.com/InsightSoftwareConsortium/ITK/commit/3da4926531))
- Add missing enumerate with multi-ndarray-output itk filters ([c7595ff794](https://github.com/InsightSoftwareConsortium/ITK/commit/c7595ff794))
- Do not wrap unsigned char for connected component output ([f3e328657f](https://github.com/InsightSoftwareConsortium/ITK/commit/f3e328657f))

Style Changes

- ITK_WRAP_PYTHON_PROCCESS to ITK_WRAP_PYTHON_PROCESS ([166be4d32b](https://github.com/InsightSoftwareConsortium/ITK/commit/166be4d32b))


Niels Dekker (1):

Bug Fixes

- Fix issue 1950, ImageMaskSpatialObject access outside image buffer ([ceb157d634](https://github.com/InsightSoftwareConsortium/ITK/commit/ceb157d634))


Stephen R. Aylward (1):

Bug Fixes

- CUFFTW paths were not being set and unnecessary FFTW files used ([449c571897](https://github.com/InsightSoftwareConsortium/ITK/commit/449c571897))


Zhiyuan Liu (2):

Documentation Updates

- improve helpers of itk.Filters. ([7818607b62](https://github.com/InsightSoftwareConsortium/ITK/commit/7818607b62))

Bug Fixes

- Register Dask serialization functions for NDArrayITKBase ([27fe268d9d](https://github.com/InsightSoftwareConsortium/ITK/commit/27fe268d9d))

5.1

**Python Packages**

ITK Python packages can be installed by running:


pip install --upgrade --pre itk


The `--pre` flag will install the beta pre-release.

**Library Sources**

- [InsightToolkit-5.1b01.tar.gz](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1b01/InsightToolkit-5.1b01.tar.gz)
- [InsightToolkit-5.1b01.zip](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1b01/InsightToolkit-5.1b01.zip)

**Testing Data**

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

- [InsightData-5.1b01.tar.gz](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1b01/InsightData-5.1b01.tar.gz)
- [InsightData-5.1b01.zip](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1b01/InsightData-5.1b01.zip)

**Checksums**

- [MD5SUMS](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1b01/MD5SUMS)
- [SHA512SUMS](https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1b01/SHA512SUMS)

Pass NumPy Array's to ITK Image Filters
---------------------------------------

The [Pythonic, functional-like interface](https://discourse.itk.org/t/itk-5-0-beta-1-pythonic-interface/1271) to all ITK image-to-image-filters now directly supports operation on [NumPy array's](https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html), i.e. `numpy.ndarray`. If a `ndarray` is passed as an input, a `ndarray` is returned as an output.

For example,


smoothed = itk.median_image_filter(array, radius=2)


Previously, explicit conversion to / from an `itk.Image` was required with `itk.array_from_image` and `itk.image_from_array`.

We can now also convert an `itk.Image` to a `numpy.ndarray` with the standard `np.asarray` call.


import numpy as np
import itk

image = itk.imread('/path/to/image.tif')
array = np.asarray(image)


Python 3 Only
-------------

ITK 5.1 will be the first Python 3-only release. Consistent with most scientific Python packages and [CPython's 2020 drop in support](https://pythonclock.org), Python 2 support and binaries will no longer be available.

clang-format enforced C++ coding style
--------------------------------------

ITK has adopted a [*.clang-format*](https://github.com/InsightSoftwareConsortium/ITK/blob/master/.clang-format) coding style configuration file so a consistent coding style can automatically be applied to C++ code with the [`clang-format`](http://releases.llvm.org/download.html) binary. A consistent coding style is critical for readability and collaborative development.

`clang-format` has been applied to the entire codebase. The Whitesmiths style of brace indentation, previously part of the [ITK Coding Style Guidelines](https://itk.org/ItkSoftwareGuide.pdf), is not supported by clang-format, so it has been replaced by a brace style consistent with VTK's current style.

A Git commit hook will automatically apply `clang-format` to changed C++ code. We are refining the related documentation and improving automated application of the style.

Point Set Registration Parallelism
----------------------------------

ITK provides a powerful registration framework for point-set registration, offering information-theoretic similarity metrics, labeled point-set metrics, and spatial transformation models that range from affine to b-spline to dense displacement fields. ITK 5.1 features enhanced parallelism in point-set metric computation, leveraging the [native thread-pool and Threading Building Blocks (TBB)](https://discourse.itk.org/t/itk-5-0-alpha-2-performance/959) enhancements in ITK 5.

ITK 5 Improvements
------------------

Many more improvements and refinements were added since the ITK 5.0.0 release, which are detailed in the change log below. For example, a number of improvements were made to the *itk::SpatialObject's*.

Congratulations
---------------

Congratulations and **thank you** to everyone who contributed to this release. Of the 25 authors, we would like to specially recognize the new contributors: James Butler, Neslisah Torosdagli, Rinat Mukhometzianov, Genevieve Buckley, and yjcchen091.

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

Additional improvements ITK's NumPy interface are [planned for the next pre-release](https://github.com/InsightSoftwareConsortium/ITK/milestone/11). Try out the current release, and take part in the community discussion at [discourse.itk.org](https://discourse.itk.org). Contribute with pull requests, code reviews, and issue discussions in our [GitHub Organization](https://github.com/InsightSoftwareConsortium).

**Enjoy ITK!**

Changes from 5.0.0 to 5.1 Beta 1
--------------------------------


Bradley Lowekamp blowekamp (32):
BUG: Use ProcessObject GetInput to obtain base pointer
BUG: Fix ProcessObject::RemoveOutput for null objects.
COMP: Address missing fftw include in CurvatureRegistrationFilter
BUG: Fix ProcessObject::RemoveOutput for null objects.
BUG: Add casting for vector pixel types
STYLE: Use CTEST_TEST_TIMEOUT
ENH: Add testing for CastImageFilter for more type conversions
BUG: Restore support for Cast between explicitly cast-ed pixel type
BUG: Use ProcessObject GetInput to obtain base pointer
ENH: Add testing for CastImageFilter for more type conversions
BUG: Restore support for Cast between explicitly cast-ed pixel type
BUG: Add DataObject::New method
BUG: Install FFTW headers in same location as ITK
Revert "BUG: InterpolateImageFunction::GetRadius hidden in ITKV4_COMPATIBILITY"
BUG: Preserve Interpolate GetRadius behavior with ITKv4Compatibility
Revert "COMP: forgotten class for ITKV4_COMPATIBILITY in 2aae174"
BUG: HDF5 is clobbering ctest TIMEOUT variables
COMP: Fix not marked 'override' for ImageSink destructor
BUG: Use enable_if with SFINAE to dispatch
ENH: Add Vector constructor from C arrays with cast
COMP: Work around uninitialized value warnings
ENH: Update ITKv4 registration example to use resample over warp
BUG: Specify specific CircleCI docker image with platform
COMP: Address compilation warning with aggregate initializer
BUG: Specify specific CircleCI docker image with platform
ENH: Adding VS2019 v142, VS2017 v140 Azure Pipelines on merge
DOC: Tweak internal documentation in SliceImageFilter
BUG: Address bug with small size in output of SliceImageFilter
ENH: Add more test cases for the SliceImageFilter
COMP: Address internal compiler error on MSVC 19.0.24234.1 (v140)
ENH: Add check expected input in HistogramMatchingImageFilter
COMP: Add missing enum type_name from prior enum declaration style

Csaba Pinter cpinter (2):
BUG: Fix loading of DICOM files with no preamble
ENH: Add test for DICOM without preamble for DCMTK and GDCM

Davis Vigneault DVigneault (1):
BUG: Make BuildCellLinks method const

Dženan Zukić dzenanz (32):
BUG: number of work units was greater than 1 even for 1 thread
BUG: fix a crash with ITK_DEFAULT_MAX_THREADS greater than 250
BUG: resample filter no longer triggers unnecessary exception
COMP: change export specification to template for un-specialized method
COMP: forgotten class for ITKV4_COMPATIBILITY in 2aae174
ENH: use double-conversion's CMake targets
COMP: fix warning about missing override in CastImageFilter
DOC: wrong class name for PlatformMultiThreader
COMP: get rid of MSVC's warning 4661
ENH: enable GaussianInterpolateImageFunction to work with streaming
STYLE: reduce space in ivar declarations
STYLE: ITK indentation style in test
STYLE: invert the name and internal logic of waiting for threads
BUG: ThreadPool::DoNotWaitForThreads did not work properly
STYLE: Add ITK prefix to testing macros in release branch
DOC: invocation of AddWork uses -> because instance is always a pointer
ENH: updating remote modules
ENH: PoolMultiThreader uses one less thread
ENH: documenting supported compilers
ENH: updating remote modules
STYLE: more consistent code formatting in test driver
BUG: offset was not updated after changing Euler angle order (ZYX)
Fix broken link in Data.md
ENH: support RGB image in windowed sinc interpolation
ENH: support RGB image in windowed sinc interpolation
ENH: updating remote modules
ENH: back-porting 1165 to support Visual Studio 2019
ENH: updating remote modules
COMP: fixed enum name error when legacy is OFF and ITK_USE_GPU is ON
ENH: removing deprecated Python functionality: imp
ENH: removing deprecated Python functionality: sys.version_info 2/3
ENH: removing deprecated Python functionality: import print_function

Francois Budin fbudin69500 (4):
BUG: ImageBase regions and ImageRegion properties are returned as reference
DOC: Add ITK 5.0 release notes
BUG: m_NumberOfPointPixels was set equal to m_NumberOfPoints
ENH: Adds swig include directory to command line

GDCM Upstream (1):
GDCM 2019-05-22 (cc5358a1)

Genevieve Buckley GenevieveBuckley (1):
BUG: All exceptions must be derived from python's BaseException class

Hans J. Johnson hjmjohnson (64):
ENH: Update SphinxExamples to lastest master branch
COMP: Add attribute for large doxygen config file.
DOC: Remove ITK_FUTURE_LEGACY_REMOVE from documentation
ENH: Disable remote module processing when creating doxygen.
STYLE: Prevent double initialization
DOC: Purge outdated media wiki WikiExamples
BUG: Missed propagation of library dependancies
ENH: Deprecate Neuralnetwork module
Revert "Merge pull request 1039 from samuelgerber/MultithreadPointSetToPointSetMetricv4"
STYLE: Remove deprecated support for ITK_WRAP_PYTHON_LEGACY
DOC: Only warn when Module_NeuralNetworks is selected
ENH: Use consistent project name with module name
COMP: Fix clang-format nesting of empty macros
DOC: Deprecate https://itk.org/Wiki/ITK/Examples content.
DOC: Provide doxygen links for sphinx
DOC: Improve the documentation clarity for NormalizeImage.
DOC: Moved wiki examples to sphinx examples part2
ENH: itkObjectToObjectOptimizerBase Must be explicitly instantiated
COMP: Terminate conditional doxygen sections
DOC: Set class name for StreamingProcessObject doxygen
ENH: Update the DoxygenLayout.xml file
ENH: Update template files for Doxygen.
BUG: Patch submission scripts conflict with doxygen
COMP: Resolve 1000's of alias warnings in 1.8.15
DOC: Moved wiki pages to sphinx examples
BUG: Flawed logic for itkExceptionObject.h guards
STYLE: Use override statements for C++11
STYLE: Prefer c++11 'using' to 'typedef'
COMP: Another work around uninitialized value warnings
ENH: Prefer c++11 'using' to 'typedef' for structs
COMP: Update AnalyzeObjectMapIO remote for ITKv5.0
COMP: Suppress warning about file that is too large
STYLE: Use = default for trivial constructors
STYLE: For loops can have a space before ;
STYLE: Suppress longstanding kwstyle violations
STYLE: Use templated function over macro
ENH: Add LONGLONG & ULONGLONG types
STYLE: Remove unused protected ivar m_MyProduct
COMP: Isolate RAWIO non-templated code in cxx file
PERF: Byteswap only when request != system byte order
STYLE: Suppress longstanding kwstyle violations
STYLE: Define the .clang-format config file
ENH: Add script to assist with running clang-format on topic-branches
ENH: Update C++/C attributes for itk style conformance.
ENH: Add copy of git-clang-format from llvm binaries
ENH: Add cmake configuration for clang-format
ENH: Setup clang-format hooks for pre-commit-style
DOC: Add missing line separator for ingroup ITKCommon
DOC: Fix spelling typo VeriyInput -> VerifyInput
ENH: Refactor to allow ReferenceHistogram instead of ReferenceImage
COMP: Remove One Definition Rule conflict
COMP: Fix missing type specialization for `unsigned long long int`
STYLE: Convert 'enum' to 'enum class' objects with print enum function
ENH: Workaround MSVC preprocessor name conflict
STYLE: Prefer enum class definitions internally
STYLE: Prefer consistent capitalization of Colormap
ENH: Ignore wrapping warnings for `enum class`
BUG: Missing ImageAdapter function signatures
COMP: Change KWStyle to allow reformat to pass.
STYLE: No-space inside <> () []
STYLE: Change the packing of parameters.
STYLE: Use shorter column length for Software Guide.
STYLE: End of history preceeding clang-format-8.0 style
STYLE: Fix spelling error foramt -> format

ITK Maintainer (1):
STYLE: Enforce ITK style defined by .clang-format

James Butler jamesobutler (1):
COMP: Add cmake_minimum_required to ITKNumericsFEM

Jean-Christophe Fillion-Robin jcfr (1):
ENH: Support building ITKNumericsFEM as external module

Jon Haitz Legarreta Gorroño jhlegarreta (4):
STYLE: Fix indentation in bash script
ENH: Add script to update ITK testing macros names
BUG: Fix remotes maintenance scripts
BUG: Fix wrong variable names

Matthew McCormick thewtex (61):
ENH: Bump the ITK CMake version to 5.1.0
ENH: New content links for ITK 5.0.0
STYLE: DeformableRegistration2 line length warnings
COMP: SpatialObjectsHierarchy Software Guide newline
ENH: Bump CI ExternalDataVersion to 5.0.0

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