Simpleitk

Announcement

Announcing the SimpleITK 2.4 Release Candidate 2!

This release was made with new infrastructure in Github Actions. 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/v2.4rc2


Please note that the binary distribution now contains wheels build on the Python 3.11 stable API ( see [PEP 384](https://peps.python.org/pep-0384/) ). These wheels contain "cp311-abi3" in the filename and should work with Python versions including and after 3.11.


<a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#2bd5931b60c8437551e710b25f1487c4"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#8d81514dde2f70f5fc82e4bc8a869fc5"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#56e810afac48dbe3dcaff2dba093a095"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp311-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#7f5a20fabc854f94f30db628d85fce1b"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp311-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#1b86c5c4fe69b2dfe7049c10c692532d"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#5ac06e3dbae05ebacbd143d6a0b5f51f"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#922a63ff090aafc8d13661b391ae5ff7"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#9bfee92ec8bdf0e911a102ba7acd93af"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp310-cp310-win_amd64.whl#72a8b73b13f57ed5d1bbcc853c7abff4"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp39-cp39-win_amd64.whl#6d57b8743dd3b76519c87e6a642b67ff"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp311-abi3-win_amd64.whl#8520256eca4d2b79d8b548a3d7f6b01a"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp38-cp38-win_amd64.whl#1029ff6c7930839008816492ab47aaef"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp311-abi3-macosx_10_9_x86_64.whl#79d025b2739d02b2e61ed9f64ada9cec"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp39-cp39-macosx_10_9_x86_64.whl#c04ab62b61fb8db37239aafd3f0365bf"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp38-cp38-macosx_10_9_x86_64.whl#6e2e2fde09ca5330c460d8cab8b2d355"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp310-cp310-macosx_10_9_x86_64.whl#5eb068e298ceee70a9526d35d1ce9813"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp310-cp310-macosx_11_0_arm64.whl#md5=b9309b8db297cb1987845ccb03c3cd0e" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp311-abi3-macosx_11_0_arm64.whl#md5=e5159d1087a41f165394ea1740722625" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp38-cp38-macosx_11_0_arm64.whl#md5=2c612a89d05292aa6595d0c08dd656a7" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.4rc2/SimpleITK-2.4.0rc2-cp39-cp39-macosx_11_0_arm64.whl#md5=f33f405da451f3b56c1d6b70eabb5e06" ></a>



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

New Features
------------
* Updated to ITK 5.4.0 [release](https://github.com/InsightSoftwareConsortium/ITK/releases) benefiting from all of the significant improvements in the underlying toolkit.
* Add `SimpleITK_PYTHON_USE_USE_LIMITED_API` CMake option.
* Build SimpleITK packages with limited Python API support for Python >=3.11.
* Add `ThresholdAbove`, `ThresholdBelow` and `OutsideValue` methods to `ThresholdImageFilter`.
* Add to Image readers `SpacingWarningRelThreshold` accessors.
* Use new `PathType` for file paths across toolkit.
* Improve Python support for `pathlib.Path` across the toolkit with custom conversion for new `PathType`.
* Add Image member functions `IsSameImageGeometryAs`, `IsCongruent`.
* Update Superbuild version of PCRE2 to 10.43
* Update Superbuild version of GTest to 1.14.0
* Update Superbuild SWIG to 4.2.1


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

* CenteredTransformInitializer now returns DowncastedTransform in Python.


Bug Fixes
---------

* Refactor `ImageViewer` class to fix initialization problems.
* Fix MD5 hash for CSharp ImageGetSetBuffer example.
* Use ITK's SizeGreatestPrimeFactor for `FFTPadImageFilter` , which is 5 for VNL and 13 for FFTW.


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

* Correct sphinx registration transform order in Registration Overview.
* Fix undeleted N4 filter in example.
* DICOM meta-data tags are lower case.
* Update documentation with Python version support policy.
* Add simplex delta documentation for Amoeba optimizer.
* Include a DICOM tag number with upper case letter in example.
* Fix math Latex notation for T_opt.
* Add FAQ entry for non-ASCII paths on windows.
* Added description of `LabelShapeStatisticFilter`'s bounding box.


Compilation and Infrastructure
-----------

* Use GitHub Actions for packing and CI, removing Azure Pipelines.
* Fix build dependency on option ITK GenericLabelInterpolator module.
* Apply clang tidy modernize-concat-nested-namespaces, modernize-avoid-bind, modernize-make-unique.
* Code improvements for modern C++17.
* Get CommentSpellCheck from PyPI.
* Format Python files per Black.
* Use pre-commit for black, yaml, json checks and other linting.
* In R, remove overloaded AddCommand method.
* Restrict SWIGWORDSIZE64 definition to required SWIG versions.
* Use optional components feature when finding ITK.
* Directly use fold expression in TypeListHasPixelIDValue.
* Package Java and CSharp on Linux.
* Use new CMP0156 to address duplicate library warnings.

da780800 Explicitly install setuptools in environment
ad198eb3 Add Python 3.12 packaging support
0ca94ef6 Address missing Generic Label Interpolator
27112d21 Fix undeleted N4 filter in example
0b0a492e Use reusable MockLogger to capture warning messages
72ee8bf3 Restore and depricate MaskImageFilter support for mask input types

<a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp311-cp311-macosx_10_9_x86_64.whl#3314ff839fdc358a13495bd8d0ded6cb"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl#ff53ba7e6c3a92e0a45654c810ba7216"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp310-cp310-macosx_10_9_x86_64.whl#3773b41affc15948cc8db98c2cbfec2b"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp39-cp39-win_amd64.whl#9cb76e131e80f507abd0d8c004a4b540"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp312-cp312-macosx_10_9_x86_64.whl#0b757640efde05a1fb3686418d5b63f4"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp310-cp310-win_amd64.whl#554174888beaea248489f8bf62657b5c"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp312-cp312-win_amd64.whl#5d0fe0e463d58e7d3210146c223930e0"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#03f39942801267ef6e8aca0e48e134e4"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#7f9182da06577c67261218663f96b81f"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp38-cp38-macosx_10_9_x86_64.whl#f15e23e18c9a082669e5cdf3634978d5"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#93633c8c00d70362a3f4660c4d45ceef"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#6a83296612cd4bd875c93414d94fc40d"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#23dc6a6b62a741a9b6163ac3da97cc81"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp39-cp39-macosx_10_9_x86_64.whl#005de609b106aed4d89000e666161cbf"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp38-cp38-win_amd64.whl#33361421474552c70ab8528ea7e2c70e"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp310-cp310-macosx_11_0_arm64.whl#5eb873169f2179c49e07322af4e1d3bd"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp311-cp311-macosx_11_0_arm64.whl#e1173c4fc867a7bac21d08077bd0be0a"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp312-cp312-macosx_11_0_arm64.whl#e10b8b304c6f105c9929455edb136640"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp38-cp38-macosx_11_0_arm64.whl#de5a8cf882f780a45fce4ca420be74f3"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp39-cp39-macosx_11_0_arm64.whl#65d8cb505ea4d7e081c00a4d271329d1"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#06c37f1c60e8d98a4e6d92b5c9ad0068"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#73abbb3e2982e23d670ec8b687e064ff"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#1e4de7b1019c9d1062ba15e003bd0803"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#84c5f281745e1cb38de8934af79c6c58"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3.1/SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#20c125c221ff86fddc3217fd041ec356"></a>

Announcement

Announcing the SimpleITK 2.3.0 Release!

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


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/gettingStarted.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


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


conda install --channel conda-forge simpleitk


Starting with SimpleITK 2.3.0, binary packages will *no longer be available* in the "simpleitk" anaconda channel. Older versions continue to be available in that channel.


Contributors

Thank you to all contributors to SimpleITK and ITK. The new contributors to SimpleITK include mbopfNIH kaspermarstal umasehs caolonghao wbzyl.

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


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

* Added `sitkLabelLinear` interpolator for multi-label images. The implementation is the `LabelImageGenericInterpolateImageFunction` class from GenericLabelInterpolator ITK remote module. ( Contributed by dyollb )
* 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 to CMake FindPython module for configuration of the python build environment. CMake configuration variable such as "PYTHON_EXECUTABLE" are now changed to "Python_EXECUTABLE". Additionally, the new CMake module uses "modern" logic for detecting which python executable to use, and the "Python_EXECUTABLE" CMake variable may need to be set to ensure the correct python environment is used.
* Change `MaskImageFilter` and `MaskNegatedImageFilter` to only support `sitkUInt8` pixel types for masked input. This unifies the supported mask image types between these two filters and the `MaskedAssignedImageFilter` to match SimpleITK's [common conventions for mask images](https://simpleitk.readthedocs.io/en/master/conventions.html#mask-image-types-and-default-values).
* For the `MaskImageFilter` it is recommended to update to casting the mask input parameter to `sitkUInt8` pixel type. This is compatible with versions before SimpleITK 2.0.
* The `MaskNegatedImageFilter` old behavior erroneously expected both inputs to be of the same type. The new behavior expects the inputs to be of `sitkUInt8`
* Removed Python 3.7 packaging.
* Restore functions for static members like ImageSeriesReader_GetGDCMSeriesIDs (restores 2.2 behavior).
SWIG 4.1.0 changed behavior to removing flattened static methods for objects. The compatible behavior can be restored by adding `-flatstaticmethod` argument to SWIG. The SimpleITK_PYTHON_FLATSTATICMETHOD CMake variable has been added to control the usage of this flag. It is currently enabled by default and is planned to default to OFF in future releases.


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 in place 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.
* Update GTest Superbuild version to 1.13.0
* Update Swig Superbuild version to 4.1.1
* Various C++17 modernization in testing include more usage of initializer lists, and namespaces.
* Change PimpleImageBase to return unique_ptr over raw.
* Address unused return value in image transform point methods and in transform tests.
* Use unique_ptr for Transform interface.
* Remove references to legacy SITK_4D_IMAGES definition.
* Enable ITK_LEGACY_REMOVE by default in SuperBuild.
* Update ITK enum to remove legacy enums type.
* Update to CSharp DotNet version 4 by default.
* Update SimpleITK Superbuild Lua to 5.4.4 and enable usage of Lua 5.4.
* Remove disutils and setupegg.py from Python packaging fallback.
* Add pyproject.toml to address wheel dependency warning.
* Add baseline images for `LaplacianSharpening` to update for ITK v5.4 changes.
* Update SuperBuild Lua version to 5.4.6.
* Many continuous integration improvements.

Announcement

Announcing the SimpleITK 2.3 Release Candidate 2!

This is expected to be the final RC before the 2.3.0 release. 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/v2.3rc2


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

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

* Removed Python 3.7 packaging.
* Restore functions for static members like ImageSeriesReader_GetGDCMSeriesIDs (restores 2.2 behavior).

SWIG 4.1.0 change behavior to removing flattened static methods for objects. The compatible behavior can be restored by adding `-flatstaticmethod` argument to SWIG. The SimpleITK_PYTHON_FLATSTATICMETHOD CMake variable has been added to control the usage of this flag. It is currently enabled by default and is planned to default to OFF in future releases.

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

* Add baseline images for `LaplacianSharpening` to update for ITK v5.4 changes.
* Update Superbuild Lua version to 5.4.6
* Additional CI changes.

<a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3rc1/SimpleITK-2.3.0rc1-cp310-cp310-macosx_10_9_x86_64.whl#"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3rc1/SimpleITK-2.3.0rc1-cp310-cp310-macosx_11_0_arm64.whl#"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3rc1/SimpleITK-2.3.0rc1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3rc1/SimpleITK-2.3.0rc1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3rc1/SimpleITK-2.3.0rc1-cp310-cp310-win_amd64.whl#"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3rc1/SimpleITK-2.3.0rc1-cp311-cp311-macosx_10_9_x86_64.whl#"></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.3rc1/SimpleITK-2.3.0rc1-cp311-cp311-macosx_11_0_arm64.whl#"></a><a 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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.

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.