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2.3rc1

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Announcement

Announcing the SimpleITK 2.3 Release Candidate 1!

Users and developers are encouraged to test the RC before the final release and report issues, bugs, and any compatibility problems.

Installing SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK [Read the Docs web page](https://simpleitk.readthedocs.io/en/master/index.html).

Python Binary Downloads

- Python binary wheels are available for download. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package from GitHub releases:

python -m pip install --upgrade pip
python -m pip install --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.3rc1


Release Notes
============


New Features
------------

In Python, add support for masked images to `__setitem__` as index parameter. The mask is considered a binary mask where assignment occurs. For example `img[img<0] = 0` can be used to remove negative numbers.
In Python, add `MinimumMaximum() -> Tuple[float, float]` procedure for `MinimumMaximumImageFilter`.
In Python, add `pathlib.Path` support to Transform IO methods.

Add `Clamp` boolean option to UnsharpMaskFilter.
Add `Image::ToVector` and `Image::ToScalar` methods to perform fast in-place conversion between vector pixel types (VectorImage), and high spatial dimension scalar images.
Add initial seed values to `FastMarchingBaseImageFilter` and `FastMarchingImageFilter`.
Add `KernelType` parameter `RankImageFilter` to support non box kernel shapes.
Wrap `MaskedAssignImageFilter`.
Add `AssignConstant` to `MaskedAssignImageFilter` and support for vector input images.
Internally replace `NPasteImageFilter` with `PasteImageFilter`.
Add to `N4BiasFieldCorrectionImageFilter` measurements of `CurrentLevel`, `ElapsedIterations`, and `CurrentConvergenceMeasurement` for observers.
Update `FFTNormalizedCorrelationImageFilter` to use named inputs.
Add missing `RequiredFractionOfOverlappingPixels` parameter to `FFTNormalizedCorrelationImageFilter`.
Various improvements to SimpleElastix integration and support.

Behavior Changes
------------------

Change `MaskImageFilter` and `MaskNegatedImageFilter to only support `sitkUInt8` pixel types for masked input. Previously, the filter erroneously expected both inputs to be of the same type.


Bug Fixes
---------

Fix already defined `GTest::Main` issue with using ITK out of a build tree.
Add an internal "Proxy" image to safely support exceptions with certain inplace operations in C++ and Python.
Fix `FastMarchingUpwindGradientImageFilter` setting target point before setting stopping criteria.
Test support of `LandmarkBasedInitialization` for `Similarity3DTransforms`.


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

Added to Sphinx generated documentation images and text output such as in [Fast Marching Segmentation](https://simpleitk.readthedocs.io/en/master/link_FastMarchingSegmentation_docs.html) and [Image Registration Method1](https://simpleitk.readthedocs.io/en/master/link_ImageRegistrationMethod1_docs.html) examples.
Fixed bug in example, working with DICOM tags.
Update JSON docs form ITK XML
Document specifying pixel type as part of reading.
Add information on dependency between GetGDCMSeriesIDs and GetGDCMSeriesFileNames.
In DicomTagsExample, included example run of DicomImagePrintTags code in the Sphinx docs.
Fix time date ordering in string in DicomSeriesFromArray.R example.


Compilation
-----------

Require C++17 for building SimpleITK.

2.2.1

The patch release includes bug fixes, and updates.


Installing SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK [Read the Docs web page](https://simpleitk.readthedocs.io/en/master/installation.html).

Python Binary Downloads

Python binary wheels are available for download from PyPI. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package:


python -m pip install --upgrade pip
python -m pip install SimpleITK



Anaconda Binary Downloads

SimpleITK packages are available for the _conda_ Python package manager as a monolithic package:


conda install -c simpleitk simpleitk


The packages are also on conda-forge with dependecies on the ecosystem:


conda install --channel conda-forge simpleitk



Release Notes
============


New Features
------------

Update ITK to 5.3.0 tagged release.
Add Python 3.11 binary packages.
Update LabelOverlapMeasures with ITK 5.3 changes: existing computation for FalsePositiveError was renamed to
FalseDiscoveryRate, and the computation for FPE corrected.


Bug Fixes
---------

Fix segmentation fault with exception in inplace operators, caused by invalid images after C++ move.
Fix viewer test to use system python executable.
Fix duplicate GTest CMake configuration from ITK
Support CMake DOWNLOAD_EXTRACT_TIMESTAMP option for correct SWIG and PCRE file timestamps.
Fix numpy character dtype conversion warning.
Fix error with itk::LabelOverlapMeasuresImageFilter::SetInput.


Compilation and CI
------------------

Update Github actions to fix warning.
Fix CircleCI Python 3.8 builds.

2.2.0

The release includes new features, API changes, documentation updates and bug fixes.

A highlight of this release is the addition of SimpleElastix as a compile time option in SimpleITK.

<a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp310-cp310-macosx_10_9_x86_64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp310-cp310-macosx_11_0_arm64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp310-cp310-win_amd64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp37-cp37m-macosx_10_9_x86_64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp37-cp37m-win_amd64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp38-cp38-macosx_10_9_x86_64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp38-cp38-macosx_11_0_arm64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp38-cp38-win_amd64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp39-cp39-macosx_10_9_x86_64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp39-cp39-macosx_11_0_arm64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.2.0/SimpleITK-2.2.0-cp39-cp39-win_amd64.whl"></a>

Installing SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK [Read the Docs web page](https://simpleitk.readthedocs.io/en/master/installation.html).

Python Binary Downloads

Python binary wheels are available for download from PyPI. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package:


python -m pip install --upgrade pip
python -m pip install SimpleITK



Linux aarch64 Support

Included in this release are "manylinux2014_aarch64" wheels to provide support for the ARMv8-A (aarch64) on Linux.


Anaconda Binary Downloads

SimpleITK packages are available for the _conda_ Python package manager as a monolithic package:


conda install -c simpleitk simpleitk




Release Notes
============


Compatibility Changes
---------------------

* The string value of sitkBSpline changed to "sitkBSpline3".
* Update to CMake 3.16.3 requirements.
* SimpleITK libraries now require C++14
* Require SimpleITK_INT64_PIXELIDS for 64-bit builds.
* The Python ReadTransform method now returns a downcasted transform.
* Replace internal typelist meta-programming with typelist2::typelist utilizing variadic templates.



New Features
------------

* Add SimpleITK_USE_ELASTIX as a compile time option to incorporate SimpleElastix classes: ElastixImageFilter, TransformixImageFilter into the SimpleITK binary. By default, this option is disabled and the classes are not available in the SimpleITK binary distributions. To make these classes available you will need to [build SimpleITK from its source code](https://simpleitk.readthedocs.io/en/master/building.html) with the option turned on.
* Add wrapping of TransformGeometryImageFilter.
* Add EvaluateAtPhysicalPoint and EvaluateAtContinuousIndex methods to Image class.
* Improve Python GetImageFromArray performance.
* Add different orders for the BSpline interpolator.
* Downcast returned Transform objects to concrete class in Python.
* Add VectorDistanceMap results to Danielsson distance filters.
* Support max dimension in "projection" filters.
* Improved Python packaging type information (PEP 561).
* Improved types for manual Python procedural methods: Resample, GetArrayFromImage, GetImageFromArray, GetArrayViewFromImage, ReadImage, WriteImage, SmoothingRecursiveGaussian, DiscreteGaussian.
* Add missing GridImageSource::WhichDimensions method.
* Update ITK to 5.3rc04.




Bug Fixes
---------

* Fix unknown enum for smoothing DisplacementFieldTransforms.
* Change expected number of iterations for LBFGS2 test due to ITK changes.
* Additional baseline test image for AArch64/ARM64 systems.
* Fix test failure when system has more than 127 processors.
* Remove failing test with 32-bit pixel and JPEG file.
* On Apple OSX use .dylib extension for C native library.
* Fix setup.py to not loading SimpleITK native library.
* Fix Python resample procedure handling of unexpected keyword argument.
* Fix undefined test behavior expected in BasicFilters.Cast test.
* Fix GenericException assignment by using shared_ptr internally.
* Correct SinRegularizedHeviside option for ScalarChanAndVeseDenseLevelSetImageFilter.



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

* Add CSharp DicomSeriesReader example.
* Add section about the missing SimpleITK DLL in CSharp.
* Improve Doxygen documentation rendering with updated packages and improved efficiency of updates.
* Add C++ and C versions of N4 bias example.
* Add favicon to Sphinx docs.
* Update ImageGetSetBuffer.cs example.
* Doc page for the path length issue for Windows.
* Add documentation on registration reproducibility.
* Added FAQ entry: Why does my image appear to be empty / all black / blank when visualized?
* Update N4BiasFieldCorrection example to save full corrected image.
* Reformat Python example for flake8.
* Improve ImageSeriesReader documentation for determining pixel type.



Compilation and CI
------------------

* Update superbuild version PCRE to 8.45.
* Update superbuild googletest version to 1.11.
* Add dockerfile to build manylinux2014 on AZP for packaging.
* Fix unused type alias warning.
* Make CreateInterpolator methods with hidden linkage.
* Remove Nightly Doxygen on CircleCI.
* Merge Lint and Spell workflows.
* Address clang lambda capture warning.
* AZP Packaging use macos-10.15.
* Remove old manylinux1 builds.
* Dockerfile to build on linux-aarch64.
* Update CircleCI configuration.
* Various CI maintenance update including updating OS images used and tool versions.
* Add CSharp building and packaging in AZP for Mac OSX.
* Update MacOSX version.
* Build with SimpleITK_USE_ELASTIX on Github Actions.

2.2rc4

Announcing the SimpleITK 2.2 Release Candidate 4!

Users and developers are encouraged to test the RC before the final release and report issues, bugs, and any compatibility problems. This is the final RC before the 2.2 final release.

In collaboration with the [Elastix](https://github.com/SuperElastix/elastix) team, the addition of [SimpleElastix](https://simpleelastix.github.io) as a compile time option is the highlight of this release. Please download the SimpleITK source and compile with the CMake SimpleITK_USE_ELASTIX option enabled to try out this experimental feature.

Installing SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK [Read the Docs web page](https://simpleitk.readthedocs.io/en/master/index.html).

Python Binary Downloads

* Python binary wheels are available for download. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package from GitHub releases:

python -m pip install --upgrade pip
python -m pip install --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.2rc4



Release Notes
=============

New Features
--------------

* Add SimpleITK_USE_ELASTIX as a compile time option for [SimpleElastix](https://github.com/SuperElastix/SimpleElastix) classes: ElastixImageFilter, TransformixImageFilter. This option is currently disabled by default.
* Update ITK to 5.3rc04

Bug Fixes
----------

* Fix undefined behavior in BasicFilters.Cast test
* Fix GenericException assignment by using shared_ptr internally
* Correct SinRegularizedHeaviside option for ScalarChanAndVeseDenseLevelSetImageFilter


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

* Reformat Python example for flake8
* Improve ImageSeriesReader documentation for method used to determining pixel type.

Compilation
------------

* Update MacOSX version in CI
* Build with SimpleITK_USE_ELASTIX enabled on Github Actions.

2.2rc3

Announcement

Announcing the SimpleITK 2.2 Release Candidate 3!

Users and developers are encouraged to test the RC before the final release and report issues, bugs, and any compatibility problems. The SimpleITK 2.2.0 final is planned to be published shortly after the next ITK tag, either v5.3rc04 or v5.3.0.

Installing SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK [Read the Docs web page](https://simpleitk.readthedocs.io/en/master/index.html).

Python Binary Downloads

* Python binary wheels are available for download. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package from GitHub releases:

python -m pip install --upgrade pip
python -m pip install --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.2rc3


Anaconda Binary Downloads

Conda packages are available from Anaconda Cloud on the `SimpleITK` channel. These can be installed with:

conda install -c simpleitk/label/dev simpleitk


Note that pre-release packages with the "dev" channel may be deleted in the future after the releases are made.

Release Notes

API Changes/Compatibility Changes
---------------------------------

* Replace internal typelist meta-programming with typelist2::typelist utilizing variadic template.

New Features
------------

* Update ITK superbuild version to ITK hash ee664da6bb1a83cdf82e2582126e65119a4de1a4.
* Add missing GridImageSource::WhichDimensions method.

Bug Fixes
---------

* On Apple OSX use .dylib extension for C native library
* Fix setup.py to not load SimpleITK native library.
* Fix Python resample procedure handling of unexpected keyword argument.

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

* Added FAQ entry: Why does my image appear to be empty / all black / blank when visualized?
* Update N4BiasFieldCorrection example to save full corrected image.

Compilation
-----------

* Update CircleCI configure
* Various CI maintenance update including updating OS images used and tool versions.
* Add CSharp building and packaging in AZP for Mac OSX.

2.2rc2

Announcement

Tagged on 2/2/2022 we are happy to announce SimpleITK 2.2 Release Candidate 2!

Users and developers are encouraged to test the RC before the final release and report issues, bugs, and any compatibility problems.


Installing SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK [Read the Docs web page](https://simpleitk.readthedocs.io/en/master/index.html).

Python Binary Downloads

- Python binary wheels are available for download. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package from GitHub releases:

python -m pip install --upgrade pip
python -m pip install --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.2rc2

Anaconda Binary Downloads

Conda packages are available from Anaconda Cloud on the `SimpleITK` channel. These can be installed with:

conda install -c simpleitk/label/dev simpleitk



Release Notes
============

Compatibility Changes
---------------------

Require SimpleITK_INT64_PIXELIDS for 64-bit builds.
The Python ReadTransform method now returns a downcasted transform.


New Features
------------

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