PyPI · #3907 most downloaded on PyPI

simpleitk

2.5.61.1M downloads/moSimpleITK/SimpleITK ↗New releases in your daily digest, changelog included.

SimpleITK is a simplified interface to the Insight Toolkit (ITK) for image registration and segmentation

Last release 2 months ago
30 Jul 2026
Ships fairly regularly
a new release about every 4 months
Most releases are documented
notes for 30 of 40 stable releases
1 version withdrawn
withdrawn after publishing
12 years old
41 releases · first in 2014

Release timeline

41 releases since 2014

2014201620182020

Releases

2.5.630 Jul 2026Deprecated
CI: Migrate BatchBuild macOS jobs off deprecated macos-13 runner by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2653
To upgrade to this Python binary package run: pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.6

<a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp311-abi3-manylinux2014_aarch64.manylinux_2_17_aarch64.whl#md5=288eb3245a43117e72e62c612572aae4" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl#md5=dd8e7283b2a4bade62819cd15e72b665" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp39-cp39-manylinux2014_aarch64.manylinux_2_17_aarch64.whl#md5=14a7ca513063289153be6b5cbe8749e4" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl#md5=0f464a145dad8436f49b2170ccad4886" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl#md5=925d4220d43f5eac938e6d0b4ff75a04" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.whl#md5=62a2314daae7f75f8daa79771a305b55" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl#md5=258fa0df1795179b232bad27c4c9e5da" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl#md5=3251bcad7d9d62dfe2b3dc9ef105a698" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp311-abi3-win_amd64.whl#md5=49820312b896d5e8a18ea6a0c5df7b06" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp39-cp39-win_amd64.whl#md5=ff01111a758b0b353c86884d72317f48" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp310-cp310-win_amd64.whl#md5=a64472f849ecb5662d587bd25bd09656" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp314-cp314t-win_amd64.whl#md5=f51d9a3943fb3daa7ea22d4ca2785310" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp311-abi3-macosx_10_9_x86_64.whl#md5=0254d80dbc1ea26a7073de3cf4285644" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp39-cp39-macosx_10_9_x86_64.whl#md5=c550cae6ea2e13dbf49699fd6f456a36" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp314-cp314t-macosx_10_9_x86_64.whl#md5=b0d97c114b8ed0f40e5ca235f646b902" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp310-cp310-macosx_10_9_x86_64.whl#md5=e62d771d612079b24c3e437693e0942e" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp311-abi3-macosx_11_0_arm64.whl#md5=358f4e72314c7ea58a155c754d523e0e" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp314-cp314t-macosx_11_0_arm64.whl#md5=c9be28926fd578dc92ec47b7b0f8e247" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp39-cp39-macosx_11_0_arm64.whl#md5=9e9b207f600e7ab0e6d4786455ee84f9" ></a><a href="https://github.com/SimpleITK/SimpleITK/releases/download/v2.5.6/simpleitk-2.5.6-cp310-cp310-macosx_11_0_arm64.whl#md5=6c4f0d1abd5993fbbc4621e4c3659955" ></a>

What's Changed

Use reshape over setting ndarray shape by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2611

Update ITK version to 5.4.7 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2649

BUG: Remove copy=False kwarg from reshape in GetArrayViewFromImage by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2654

CI: Migrate BatchBuild macOS jobs off deprecated macos-13 runner by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2653

CI: Fix always-truthy if expression in BatchBuild.yml by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2658

BUG: Pin numpy <2.5 for manylinux2014 python test venv by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2659

Full Changelog: https://github.com/SimpleITK/SimpleITK/compare/v2.5.5...v2.5.6

2.5.513 May 2026

To upgrade to this Python binary package run: `pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/

To upgrade to this Python binary package run: pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.5

What's Changed

ENH: Add free-threaded Python (3.14t) packaging support - for release by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2580
ENH: Update macOS CI runner from macos-13 to macos-14 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2584
Fix R CLOENV - for release and master by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2585
BUG: Patch SWIG superbuild for R 4.6.0 API removals by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2587

Full Changelog: https://github.com/SimpleITK/SimpleITK/compare/v2.5.4...v2.5.5

Open source →

2.5.424 Apr 2026Deprecated

BUG: Replace deprecated macos-13 runner with macos-15-intel by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2553

To upgrade to this Python binary package run: pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.4

What's Changed

COMP: Update ITK to release-5.4 branch hash 2026-02-26 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2535
Separately backport gersemi CMake formatting for FindR.cmake by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2541
Update FindR to detect R.dll on windows. - for release by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2546
BUG: Replace deprecated macos-13 runner with macos-15-intel by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2553
Update ITK Superbuild version to 5.4.6 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2570

Full Changelog: https://github.com/SimpleITK/SimpleITK/compare/v2.5.3...v2.5.4

Open source →

2.5.321 Nov 2025Security

Addresses Out-of-Bounds vulnerability with a malformed DICOM file containing encapsulated PixelData fragments. The fix is contained in ITK 5.4.5.

To upgrade to this Python binary package run: pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.3

What's Changed

Use rossetta arch command to run python executable - for release by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2419
FOR RELEASE - Update docker based package builds to use external source by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2446
Fix generation of checksums - FOR RELEASE by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2450
Update superbuild ITK version to 5.4.5 release by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2449

Security Fixes

Addresses Out-of-Bounds vulnerability with a malformed DICOM file containing encapsulated PixelData fragments. The fix is contained in ITK 5.4.5.

Full Changelog: https://github.com/SimpleITK/SimpleITK/compare/v2.5.2...v2.5.3

Open source →

2.5.216 Jun 2025

To upgrade to this Python binary package run: `pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/

To upgrade to this Python binary package run: pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.2

What's Changed

Add ForceOrthogonalDirection and ReverseOrder options - for release by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2294
Fix Docker FromAsCasing error for Doxygen - for RELEASE by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2306
Update ITK Superbuild version to 5.4.4 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2319

Full Changelog: https://github.com/SimpleITK/SimpleITK/compare/v2.5.0...v2.5.2

Open source →

2.5.028 Apr 2025

Announcing the SimpleITK 2.5.0 Release!

Release Notes

Announcing the SimpleITK 2.5.0 Release!

The release includes critical bug fixes and compilation issues including an update to ITK v5.4.2.

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.

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 PyPI:
```
python -m pip install --upgrade pip
python -m pip install SimpleITK
```

NOTE: The Python package filename now follows the enforced name normalization on PyPI. That is the name of the file is now simpleitk....whl. PyPI is case insensitive with regards to names of packages. However, the name of the Python package when importing is still case and should be import SimpleITK.

The binary distribution contains wheels built on the Python 3.11 stable API ( see PEP 384 ) and should work with Python versions including and after 3.11.

Anaconda Binary Downloads

SimpleITK Conda binaries are available for the conda-forge ecosystem. To get started run the following command:

conda create --name sitk python=3.12 simpleitk --channel conda-forge --override-channels

Getting Started

To get started with pre-compiled Java or C# bindings, building the R binding via a devtools installer or building SimpleITK from source code see the Getting Started Guide.

Release Notes

New Features

Added support for up to 5D images in MinimumProjectionImageFilter.
Introduced wrapping for ReinitializeLevelSetImageFilter.
Enabled external ITK module LabelErodeDilate by default.

Updates

Removed packaging of Python 3.8 (EOL) in manylinux wheels and GitHub Actions.
Updated ITK to version 5.4.3.
Upgraded Superbuild components:
- PCRE2 to version 10.44.
- Lua to version 5.4.7.
- SWIG to version 4.3.0.
- GTest to version 1.15.2.

Bug Fixes

Resolved Valgrind issues in LabelErodeDilate module.
Fixed syntax warnings for Python 3.12 compatibility.

Documentation

Updated R documentation.
Conformed to Python package name normalization in documentation.
Fixed dead URLs in the read-the-docs documentation.

What's Changed

Use SimpleITK_BUILD_DISTRIBUTE in Mac ARM build scrip by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2180
Remove CircleCI from readme by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2179
Instruct on creating isolated conda-forge ecosystem by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2182
Additional clarification on using conda-forge by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2183
STYLE: Fixes to the python examples for pylint by @dave3d in https://github.com/SimpleITK/SimpleITK/pull/2178
Update Superbuild GTest to 1.15.2 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2185
Update docs by @zivy in https://github.com/SimpleITK/SimpleITK/pull/2181
Add mac-arm64 to Build.yml by @jwj019 in https://github.com/SimpleITK/SimpleITK/pull/2158
DOC: Fixes for pylint by @dave3d in https://github.com/SimpleITK/SimpleITK/pull/2187
Fix SyntaxWarning in Python 3.12 by @fepegar in https://github.com/SimpleITK/SimpleITK/pull/2190
Update for 2.5.0 development by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2192
Remove Python 3.8 from GHA by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2194
BUG: Correct SITK_MAX_DIMENSION usage by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2193
Use constexpr statements over enable_if dispatched functions by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2196
Address unused variable warning related to constexpr by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2198
Use maybe_unused directive over Unsed function. by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2199
Use variadic template for function traits and bindings by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2197
Use SimpleITK_BUILD_STRIP for mac packages by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2201
Use protected member function for safe GetIndex method by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2204
ENH: Handle error strings in a way that doesn't produce compile warnings by @richardbeare in https://github.com/SimpleITK/SimpleITK/pull/2205
Update Superbuild to PCRE 10.44 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2210
Update to SWIG 4.3.0 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2208
Update Superbuild to lua 5.4.7 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2209
Remove legacy RUBY CMake variables by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2212
Separate SimpleITKFilters tests by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2211
Use Image::AllocateInitialized by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2213
Update along ITK release_5.4 branch by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2216
ENH: Add wrapping for ReinitializeLevelSetImageFilter by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2215
Use cmake_minimum_required with ...max_policy by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2217
Update ITK Superbuild version to 5.4.1 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2223
Update ITK to include vector image accessor patch by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2224
Use build-in xml package by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2219
Remove CircleCI configuration by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2150
Add dependabot to update github actions by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2228
Replace macos-12 batch builds by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2230
DOC: Update R documentation. by @zivy in https://github.com/SimpleITK/SimpleITK/pull/2232
Backport patches made in Slicer fork by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2137
Slicer backport for release by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2233
Enable external ITK module LabelErodeDilate by default by @dyollb in https://github.com/SimpleITK/SimpleITK/pull/2235
Add upto 5D support to MinimumProjectionImageFilter by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2236
Use loop and list for enabling ITK modules by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2237
Update clang format by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2238
Address Doxygen build issue with no python executable by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2242
Use pre-commit GHA action by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2240
Publish test pypi by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2231
Test using GHA host linux arm by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2239
Adress failing Doxygen builds in Packaging CI by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2243
Update CSVtoTable arguments in CMake by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2244
Add permissions to create release for publish action by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2246
Explicitly set OSX_ARCHITECTURES on osx java package by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2247
Bump pypa/gh-action-pypi-publish from 1.12.3 to 1.12.4 by @dependabot in https://github.com/SimpleITK/SimpleITK/pull/2245
Override LabelErodeDilate module hash to fix valgrind defect by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2249
Update ITK valgrind to include module used by simpleITK by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2250
Second attempt to resolve valgrind issues in LabelErodeDilate by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2253
Update Superbuild ITK version to v5.4.3 tag by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2256
BUG: Normalize Python package name to simpleitk by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2257
Image reader base dox by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2248
Make GHA packaging case insensitive for python wheels by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2258
Update documentation for python package name normalization by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2260
Normalize Python package name for latest release notes by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2262
Don't use head.sha for ci group by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2263
Replace self-hosted runners with GH hosted runners by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2259
Remove Python 3.8 from docker build script for manylinux wheels by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2267
BUG: Remove ">=" from command line requirements by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2270
DOC: Remove reference to kitware hosted wiki. by @zivy in https://github.com/SimpleITK/SimpleITK/pull/2273
DOC: Updated dead URLs in read-the-docs documentation. by @zivy in https://github.com/SimpleITK/SimpleITK/pull/2274

New Contributors

@fepegar made their first contribution in https://github.com/SimpleITK/SimpleITK/pull/2190
@dependabot made their first contribution in https://github.com/SimpleITK/SimpleITK/pull/2245

Full Changelog: https://github.com/SimpleITK/SimpleITK/compare/v2.4.1...v2.5.0

Open source →

2.4.113 Jan 2025

Announcing the SimpleITK 2.4.1 Release!

Release Notes

Announcing the SimpleITK 2.4.1 Release!

The release includes critical bug fixes and compilation issues including an update to ITK v5.4.2.

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.

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 PyPI:
```
python -m pip install --upgrade pip
python -m pip install SimpleITK
```

The binary distribution now contains wheels built on the Python 3.11 stable API ( see PEP 384 ) and should work with Python versions including and after 3.11.

Anaconda Binary Downloads

SimpleITK Conda binaries are available for the conda-forge ecosystem. To get started run the following command:

conda create --name sitk python=3.12 simpleitk --channel conda-forge --override-channels

Getting Started

To get started with pre-compiled Java or C# bindings, building the R binding via a devtools installer or building SimpleITK from source code see the Getting Started Guide.

Bug Fixes

For windows addresses issue with incorrect computation with image of vector pixel type larger than 4 gigabytes. #2220

To upgrade to the latest pre-release Python binary package run: pip install --upgrade --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.4.1

What's Changed

BUG: Correct SITK_MAX_DIMENSION usage - For Release by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2195
ENH: Use stderr in R, and modify string formatting to avoid compiler … by @richardbeare in https://github.com/SimpleITK/SimpleITK/pull/2207
Update ITK Superbuild version to 5.4.1 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2222
Update ITK superbuild to 5.4.2 by @blowekamp in https://github.com/SimpleITK/SimpleITK/pull/2227

Full Changelog: https://github.com/SimpleITK/SimpleITK/compare/v2.4.0...v2.4.1

Open source →

2.4.014 Aug 2024

Announcing the SimpleITK 2.4.0 Release!

Announcement

Announcing the SimpleITK 2.4.0 Release!

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.

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 PyPI:
```
python -m pip install --upgrade pip
python -m pip install SimpleITK
```

Please note that the binary distribution now contains wheels built on the Python 3.11 stable API ( see PEP 384 ). These wheels contain "cp311-abi3" in the filename and should work with Python versions including and after 3.11.

Anaconda Binary Downloads

SimpleITK Conda binaries are available for the conda-forge ecosystem. To get started run the following command:

conda create --name sitk python=3.11 simpleitk --channel conda-forge --override-channels

Getting Started

To get started with pre-compiled Java or C# bindings, building the R binding via a devtools installer or building SimpleITK from source code see the Getting Started Guide.

Release Notes

New Features

Updated to ITK 5.4.0 release 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.

Open source →

2.3.16 Nov 2023

Announcing the SimpleITK 2.3.1 Release!

Announcement

Announcing the SimpleITK 2.3.1 Release!

The release includes fixes to behavior regression, compilation issues, and support for Python 3.12.

Change Log

42ce27df Bump patch version to 2.3.1 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

Open source →

2.3.013 Sept 2023

Announcing the SimpleITK 2.3.0 Release!

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.

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.
- 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 and Image Registration Method1 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.

Open source →

2.2.18 Dec 2022

SimpleITK 2.2.1 has been released!

Release Notes

SimpleITK 2.2.1 has been released!

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.

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.

Open source →

2.2.029 Aug 2022

SimpleITK 2.2.0 has been released!

Announcement

SimpleITK 2.2.0 has been released!

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.

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.

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 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.

Open source →

2.1.023 Jul 2021

SimpleITK 2.1.0 has been released!

Announcement

SimpleITK 2.1.0 has been released!

The release includes new features, API changes, documentation updates and bug fixes. This is the first SimpleITK release to provide binaries for the new Apple M1 ARM.

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.

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

Apple M1 ARMv8 Support

Wheels with the platform tag "macxos-11_0_arm64" are available from PyPI, to provide initial support for the Apple M1 Silicon for Python 3.8 and 3.9.

Anaconda Binary Downloads

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

conda install -c simpleitk simpleitk

or integrated into the coda-forge package dependencies:

 conda install simpleitk --channel conda-forge

Release Notes

API Changes

Add Image::getBufferAsByteBuffer to Java interface, returns a type specific instance of java.nio.Buffer.
In Java add GetBufferAsNativePointer to Image class.
Add Image::GetSizeOfPixelComponent method.
Add N4BiasFieldCorrectionImageFilter::GetLogBiasFieldAsImage method.
Ignore constant Image::GetBufferAs... methods, in wrapped languages.

New Features

Update ITK superbuild version to v5.2.0.
Add new ComposeScaleSkewVersor3DTransform class.
In Python, add support for ellipsis ("...") indexing to the Image class.
In Python, add class dictionary like interface for the Image's meta-data dictionary. This includes implementations for __delitem__, __contains__, and __getitem__ with a string parameter.
Updating style in examples using modern Python, moving from 2.7 to 3.6+.
Add 4D ( and higher ) support for PermuteImageFilter.
New LoggerBase and ITKLogger classes to interface and override ITK's output messages.
Add output pixel type parameter to ShiftScaleImageFilter, to support arbitrary type conversion with intensity scaling.
Add sitkUInt8 mask image support to MaskNegatedImageFilter
Enable the ITKIOTransformMINC module for xfm transform files
Add ImageRegistrationMethod::StopRegistration method
Add StopRegistration method to Demons based registration filters
Update HistogramMatchingImageFilter to use named "referenceImage" input for second input image.

Bug Fixes

Set the default ITK multi-threader to "Platform" in Superbuild. This addressed issues with multi-processing and the Google Colaboratory environment.
Update expected results for Linux ppc64le in test ImageRegistrationMethodDisplacement1 and SLICImageFilter.
The GetPixelAsComplexFloat64 Image method in Python is correctly renamed to __GetPixelAsComplexFloat64__.
R calls to nonexistent methods are now handled gracefully
In BinaryMagnitudeImageFilter test, changed type from UInt32 to Int32 for defined C++ behavior, fixed Mac ARM testing failure.

Documentation

Add TCL, Ruby, Lua, R, Java, and C# languages for the Image and Transform IO example and documentation.
Add "Image Registration Optimizer Weights" example illustrating usage of optimizer weights.
Document details on naming conventions and object oriented, procedural interfaces.
Document importance of registration initialization and center of rotation docs.
Document ComposeScaleSkewVersorTransform in Sphinx overviews.
Fix broken link in filters list.
Add "IO Selection" examples for CSharp, C++, Java, Lua, Ruby and TCL.
Add example illustrating how to override ITK's messages with Python's logging module.
Separate the GetPixel example into dynamic and statically typed languages.
Update N4 example to use bias field at input resolution
Update ImageViewer::SetApplication docs.* Minor grammar and spelling changes to gettingStarted
Improve documentation for registration sampling strategies
Add example demonstration Java Image buffer interface
Add multiple language examples for ImageIOSelection
Added a Windows build page

Compilation

CMake use "Ruby" find package. The CMake variable related to Ruby changed from "RUBY" prefix to "Ruby".
Add test to echo CMakeCache.txt
Replace virtualenv with venv
Install wheel package to venv for packaging
Use STEP_TARGETS option over EP Add_Step_Targets command
Suppress MSVC getenv security warning.
Set CMake Policy version to 3.10 in Superbuild
Run HelloWorld examples when testing
Fix comparison between signed and unsigned integer compiler warning
Remove explicit instantiating of Image of deque of LabelObjectLine
Update SWIG to 4 require in CMake find_package

Open source →

2.0.022 Sept 2020Deprecated

Update ndarray.tostring to tobyte ( tostring deprecated in numpy 1.19.0 )

Announcement

SimpleITK 2.0 has been released! This major version update to SimpleITK includes updating to ITK version 5, significant code improvements, performance enhancements, and API changes.

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.

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

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

conda install -c simple simpleitk

2.0 Documentation

To learn more about SimpleITK go to simpleitk.org.

Highlights

Now using ITK version 5.1 with all the new improvements from ITKv5!
5D Image support for improved support of time series, and multi-channel images commonly used in microscopy.
- The default and distributed configurations now support image dimensions from 2 to 5 dimensions. The following filters are also instantiated in 4 and 5 dimensions: ExtractImageFilter, JoinSeriesImageFilter, PasteImageFilter, HashImageFilter, ImageFileReader, ImageFileWriter, ImageSeriesWriter.
Python's Image class has improved set item for assignment operations with a slice indexed sub-region on the left hand side. Also assignment of a constant value to a sub-region is supported.
- Please see the Slice by Slice example for details.
Python pickling of Image and Transform classes. Please note this is designed for operations such as interprocess communications; the standard ITK IO formats should be used as portable storage formats.
The Show procedure calls the ImageViewer class interface which utilizes the class's defaults and configuration.
Modernization of C++ code base with C++11, and clang tidy
In C++, temporary images or Rvalue References as arguments automatically enable filters to execute "in-place".
- Please see the In Place example for details.

Release Notes

API and Compatibility Changes

The environment variables related to the Show procedure are only checked once. The Show method now is a wrapper for the ImageViewer class, and the behavior changed. The SITK_SHOW_EXTENSION and SITK_SHOW_COMMAND environment variables if defined initialize the corresponding global defaults only the first time accessed. The environment variables SITK_COLOR_COMMAND and SITK_SHOW_3D_COMMAND are removed as the ImageViewer class allows for direct configuration of the command.
Remove from all filters the Execute method with filter parameters as arguments. The Execute method with the input images remains.
Remove AddTrialPoints and ClearTrialPoints methods from FastMarchingImageFilter due to consolidation of code generation templates.
With Java wrapped Vector types whose C++ element type is an unsigned integer, the wrapped element type changed to the next larger Java signed integer type ( see 618d89 ).
Removed procedural methods taking scalar radius from the following ( see 444f9a ):
- BinaryClosingByReconstruction
- BinaryDilate
- BinaryErode
- BinaryMorphologicalClosing
- BinaryMorphologicalOpening
- BinaryOpeningByReconstruction
- BlackTopHat
- ClosingByReconstruction
- DilateObjectMorphology
- ErodeObjectMorphology
- GrayscaleDilate
- GrayscaleErode
- GrayscaleMorphologicalClosing
- GrayscaleMorphologicalOpening
- MorphologicalGradient
- OpeningByReconstruction
- WhiteTopHat
Dropped Python 3.4 support due to end of life.
Remove the sitk::ImageFilter template parameter because it is no longer utilized.
The Python installation command using setup.py changed with the location of setup.py. To install see updated Sphinx documentation.
Remove Transform::AddTransform and Transform::FlattenTransform methods. Use the CompositeTransform class.

New Features

Rewrote Show to use ImageViewer class.
For ImageViewer add user's Application folder to search path.
Use NPasteImageFilter from the SimpleITKFilters remote ITK module to replace PasteImageFilter.
Add to SimpleITK's PasteImageFilter:
- DestinationSkipAxes parameter
- Support for pasting lower dimension to higher dimension image e.g 2D slice into 3D volume
- Ability to use a constant value as input instead of image
Add method to ImageFileReader::GetImageIOFromFileName get the ITK ImageIO automatically used for file.
Update superbuild Swig version to 4.0.2. SWIG >= 4 is now required.
Update ITK version to 5.1.1.
Disable ITK 4 legacy behaviors.
Add SignedDanielssonDistanceMapImageFilter::GetVoronoiMap method.
Add wrapping for CannySegmentationLevelSetImageFilter.
Update levelset segmentation filters to support named inputs.
Add 4D support toSliceImageFilter and to the Python slice indexing.
Add complex pixel support to Image::GetBufferAs... methods.
Add wrapping for BinaryPruningImageFilter.
Add per label measurements to LabelOverlapMeasuresImageFilter.
ResampleImageFilter add option to use nearest neighbor extrapolation.
Add ReturnBinMidPoint parameter to OtsuThresholdImageFilter. Defaults to false which may change results.
Add support to specify compression level and compression algorithm to ImageFileWriter and ImageSeriesWriter classes.
BSplineTransform Python support construction and SetCoefficientImage with list-like series of Images.
MeanImageFilter directly filters vector images, improving performance.
Add to LabelShapeStatisticsImageFilter per label method GetIndexes and GetRLEIndexes.
Add Image::IsUnique method.
Add wrapping for DICOMOrientImageFilter.
Add complex pixel type support to GetBufferAs methods.
Improve checking and error messages when Image inputs require the dimensions, sizes or pixel types to match.
Add LevelSetMotionRegistrationImageFilter::InitialDisplacementField method.
Refactor of the template code generation system to enable numerous new features and C++ style enhancements.
Add boolean in_place field to all JSON filter descriptions.
Add C++ automatic "in place" ITK filter execution with r-value image input.
Add C++ Image operators with automatic in-place filter execution with r-value Image classes.
Use native SWIG/R enumeration support.
Add named filter inputs to morphological reconstruction image filters.
Replace the CMake configuration option of "SimpleITK_4D_IMAGE" with "SimpleITK_MAX_DIMENSION"
Default configuration now include 5D Image support.
The following filters support up to "SimpleITK_MAX_DIMENSION":
- ExtractImageFilter
- JoinSeriesImageFilter
- PasteImageFilter
- HashImageFilter
- ImageFileReader
- ImageFileWriter and ImageSeriesWriter
Refactored MemberFunctionFactory's hashing function.
Add ExtractImageFilter support to extract an abitrary dimension e.g. 3D image from 5D image.
Add sitkScaleVersor enum.
Add Transform::GetTransfromEnum method.
Add CompositeTransform class.
Update to ITKv5 threading model behaviors for the following ProcessObject methods:
- SetGlobalDefaultThreader and GetGlobalDefaultThreader
- SetGlobalDefaultNumberOfThreads and GetGlobalDefaultNumberOfThreads
- SetNumberOfWorkUnits and GetNumberOfWorkUnits

Python

Add custom Python procedures for DiscreteGaussian, SmoothingRecursiveGaussian, ReadImage and WriteImage to support keyword arguments.
Add to the WriteImage Python procedure the keyword only arguments imageIO and compressor.
Add Python __setitem__ for [] operator support:
- assignment constant to a sliced indexed region

assignment of lower dimension image to matching sliced indexed region

Add Python support for complex pixels to GetArrayFromImage, GetImageFromArray and GetArrayViewFromImage methods.
Add Python deepcopy support to Image class, ensuring the copy is unique with lazy copying implementation.
Add Python pickling support for Image and Transform classes.
Add Python keyword argument support for Resample procedure.
Improve Python Image class's in-place operators to use C++ in-place operators.
Improve Python keyword arguments for procedural methods due to removal of overloaded methods.
Add Python slice indexing for arbitrary dimension extracting.
Add Python __setitem__ support for assigning sub-regions via the PasteImageFilter.
Refactor Python SWIG code to separate classes and add Python code as modules.
Add Python Transform.Downcast method.
Applied PEP 8 style to Python examples.

CSharp

Add C# constant image buffer access methods of the form GetConstBufferAs....

Bug Fixes

Fix the ImageRegistrationMethod exception to use GetPixelIDTypeAsString
Update ndarray.tostring to tobyte ( tostring deprecated in numpy 1.19.0 )
Add missing deepcopy implementation for Image with RLE "Label" pixel types.
Fixed Python pickling for missed transform classes.
Refactored GetImageFromVector method to retain reference to original container with a command object. Fixing image buffer aliasing with BSplineTransform and DisplacementFieldTransform.
Make TranslationTransform conversion constructor explicit.
Remove implicit conversion from Image to Transform class.
Update StatisticsImageFilter input convention for ITKv5.
Remove WarpImageFilter matching image size requirement.
The results of the LiThresholdImageFilter changes with ITK, baseline test results were updated. ( See ITK commit e3ce37 for details. )
Add additional baseline images for registration results, due to change in ImageRegistration's smoothing algorithm. ( See ITK commit 569a47 for details. )
Correct LabelShapeStatistics baseline for OrientedBoundingBoxVertices results. ( See ITK commit 50c695 for details. )
Fix potential double memory free of pixel container in results from internal image to vector image conversions.
Fix RelabelComponentImageFilter incorrect object size computation with sorting enabled. ( See ITK commit 162101 for details. )
Fix potential ITK pipeline execution error when a filter execute on a vector image by per component.
Add C++11 move semantics support to the Image class.
Add direct support for C++11 lambda command to the ProcessObject class.
Add GetBufferAsVoid method to the Image class.
Add Decay parameter to the MirrorPadImageFilter.

Documentation

Update doc strings for Python and JAVA from JSON filter descriptions.
Update examples to use slice based assignment instead of PasteImageFilter.
Update the tutorials page.
Update FAQ.
Improve WriteImage Doxygen documentation.
Update RTD Show procedure documentation.
Add custom HTML Doxygen header with dynamic timestamp insertion, and privacy policy.
Add procedural example to IO page.
Updating the main Doxygen page.
Update Sphinx filter list.
Add example for reading raw image files.
Add DICOM series writing example with floating point pixels.
Add FAQ entry for the differences between ITK and SimpleITK.
Rename Sphinx "installation" page to "getting started".
Update examples from using scalar radius to vector.
Use Doxygen interactive SVG output, and enable client side MathJax for Latex rendering.
Add C++ CMake example for using SimpleITK.
Update examples to use CompositeTransform.
Update copyright to NumFOCUS.
Add casting to N4BiasFieldCorrection example.
Typo fixes.
Create Docker images for generating Doxygen.
Add C# ConnectedThresholdSegmentation example.
Remove references to next branch in documentation.
Update R installation instructions.
Add C# ImageReistrationMethod2 example.
Add multi-lingual examples for FastMarchingSegmentationImageFilter.
Uset stopping time parameter in FastMarchingSegmentation examples.
Add C# CannySegmentationLevelSetImageFilter example.
Improve documentation to GetImageFromArray about isVector parameter.
Update referenced tutorials.
Add acknowledgment section to readme.
Update Java and CSharp installation instructions.
Move Doxygen pages to Sphinx documents, remove other out dated pages.
Move Sphinx documentation to docs directory.

Compilation

Address signed to unsigned comparison compiler warnings.
Fix PYTHON_EXECUTABLE being undefined in CMake for Doxygen.
Add Doxygen MathJAX URL as CMake option.
Continue to address compilation warnings.
Pin Sphinx version for Read-The-Docs.
Remove EXPORT specification for static member function declaration.
Support pass TBB_DIR to ITK in the Superbuild.
Require C++11 standard for compilation.
Replace C++ tr1 usage with standard C++11 classes.
Replace compiler depended defines with C++11 keywords.
Prefer using C++11 lambda over std::bind when std::placeholders are not needed.
Improve support on OSX for isysroot flag and CMAKE_OSX_SYSROOT variable.
Support additional CMAKE_GENERATOR_*, CMAKE_VS_PLATFORM_TOOLSET_* variables is superbuild.
Added AWS S3 buckets for data mirroring.
Use SHA512 hash files as index for downloaded source code.
Use CMake for creating zip archives.
Improve finding of Lua interpreter.
Update Lua superbuild version to 5.3.5, require Lua version 5.2 or 5.3 for code generation.
Update PCRE superbuild version to 8.43.
Add USE_CCACHE cmake option to automatically use ccache as launcher if available.
Enable GNU gold linker by default if available.
Update GTest vesrion to 1.10.0 in superbuild.
Fix incorrect version of virtualenv detected.

Miscellaneous

Update SimpleITK logo.
Test the ImageViewer class and Show procedure.
Update and add more testing for Python ImageRead and ImageWrite procedures.
Prefer using absolute imports in Python.
Updates to manylinux Dockerfile including updating CMake and openssl versions.
Write testing output with compression enabled.
Use C++11 nullptr over NULL.
Update classes to use C++11 inline class initializaton.
Use C++11 default class constructors.
Use C++11 type alias over typedefs.
Use clang-tidy to improve code with:
- modernize-redundant-void-arg
- modernize-use-equals-default
- modernize-use-override
- modernize-use-emplace
- readability-container-size-empty
Continuing updates and improvements to the testing, build and packaging infrastructure.
Update set parameter methods to use std::vector by value with C++ std::move internally.
Add CI for running flake8.
Continuing updates and improvements to the testing, build and packaging infrastructure.
Add tolerance for testing BSpline domains.
Update setup for development scripts to support github workflows.
Add Insight Software Consortium Code of Conduct.
Archive SHA512 in distributed data archive.
Disable ITK's automatic advanced architecture compilation settings in packaging builds.

Open source →

1.2.08 Jan 2019

We are pleased to announce the SimpleITK 1.2 Release!

Announcement

We are pleased to announce the SimpleITK 1.2 Release!

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 (http://simpleitk.readthedocs.io/en/release/Documentation/docs/source/installation.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 form PyPI:
```
python -m pip install --upgrade pip
python -m pip install SimpleITK
```
- Conda packages are available from Anaconda Cloud on the SimpleITK channel. These can be installed with:
```
conda install -c simpleitk simpleitk
```
A complete available set of compiled binaries, including select CSharp and Java distributions, along with source and data tar-balls are available on Source Forge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.2.0/).

Release Notes

Improvements
- New look for ReadTheDocs, along with more examples and documentation. (http://simpleitk.readthedocs.io/en/master/)
- Support for stream reading regions from files. The ImageFileReader adds the option to specify an image region to extract while reading from disk. (https://simpleitk.readthedocs.io/en/master/Examples/AdvancedImageReading/Documentation.html)
- Option to specify the ITK ImageIO used in the ImageFileReader class or ReadImage procedure. (https://simpleitk.readthedocs.io/en/master/Examples/ImageIOSelection/Documentation.html)
- Multi-resolution BSpline registration by adapting the BSplineTransform resolution in the ImageRegistrationMethod. (https://simpleitk.readthedocs.io/en/master/Examples/ImageRegistrationMethodBSpline3/Documentation.html)
- Added BSplineDecompositionImageFilter , and new BSplineTransform initialization from coefficient images.
- Added ImageRegistrationMethod method GetMetricSamplingPercentage to get the number of samples used after each iteration.
- Wrapping of the SLICImageFilter ( http://hdl.handle.net/10380/3596 ).
- New ImageViewer class to support state-full parameters while providing the behavior supported by the Show procedure.
- Added support for multi-component images to ClampImageFilter, MeanProjectionImageFilter, SumProjectionImageFilter, and the TileImageFilter.
- Improvements to the R interface and packaging.
- Fix 4D Image support in the Python GetArrayFromImage and GetArrayViewFromImage procedures.
- Added Transform FlattenTransform method, to combine nested composite transforms.
- ITKv5 compatibility enables SimpleITK to be compiled against ITKv5 betas.
- The default and binaries are built against the proven ITK 4.13.1 release branch. Comprehensive SimpleITK testing has lead to improvements in upstream ITK. (https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v4.13.1)
- Miscellaneous build and documentation fixes.

Open source →

1.1.026 Mar 2018

We are pleased to announce the SimpleITK 1.1 Release!

Announcement

We are pleased to announce the SimpleITK 1.1 Release!

Installing SimpleITK

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 form PyPI:
```
python -m pip install --upgrade pip
python -m pip install SimpleITK
```
- Many Conda packages have been upload to Anaconda Cloud on the SimpleITK channel. These can be installed with:
```
conda install -c simpleitk simpleitk
```
A complete available set of compiled binaries, including select CSharp and Java distributions, along with source and data tar-balls are available on Source Forge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.1.0/).

Release Notes

Improvements:

Enabled 4D Images for IO, ExtractImageFilter, and output of JoinSeriesImageFilter.
Enabled MINC IO by default.
New Filters: ObjectnessMeasuresImageFiler (Frangi's vesselness), IterativeInverseDisplacementFieldImageFilter, UnsharpMaskImageFilter, and RoundImageFilter.
Added LBFGS2 optimizer to ImageRegistrationMethod.
Improved Show search path for FIJI now includes home directories.
Improved ITK Modular awareness, including ImageIOs.
Superbuild update PCRE 8.40, SWIG 3.0.12, ITK 4.13.
Many bug fixes and a couple segmentation fault issues addressed.
The build system is better and more robust then ever! Many new improvements and features!
Migrating examples, miscellaneous documentation and Wiki to Read the Docs: http://simpleitk.readthedocs.io/en/master/
Improved reading and writing of 64-bit integer images across platforms (except python 2.7 on Windows).
Added optional wrapping of the CoherenceEnahancingDiffusionImageFilter (not enabled in binary distributions).
Added and improved examples related to DICOM reading, writing and manipulating the meta-data dictionary.

API Changes:

Added ImageFileReader::ReadImageInformation.
- This adds support to read meta-data from any supported image file format with any dimension without reading the bulk pixel data.
Added ImageReaderBase::GetRegisteredImageIOs method to obtain list of loaded ITK ImageIO modules.
Added Version::ITKModulesEnabled method to obtain a list of ITK enabled modules when SimpleITK was built.
Added BinaryImageToLabelMap::GetNumberOfObjects.
Added optional MaskImage input to ConnectedComponentImageFilter.
Added SignedMaurerDistanceMapImageFilter::BackgroundValue paramater.
WarpImageFilter now uses named inputs.
Convolution filters use named inputs.
Added optional OrientedBoundingBox to LabelShapeStatisticsImageFilter.
Added missing features to RelabelComponentImageFilter including SortByObjectSize parameter and NumberOfObjects, SizeOfObjectsInPhysicalUnits measurements.
Added LabelStatisticsImageFilter::GetRegion.
Added MetaDataDictionaries to the ImageSeriesReader.

Compatibility:

DiscreteGaussianImageFilter, SmoothingRecursiveGaussianImageFilter now optionally take a vector argument for variance and sigma respectfully.
In Python the procedural methods, DiscreteGaussian and SmoothingRecursiveGaussian may not work with named arguments due to limitation with SWIG and overloaded functions.
N4BiasFiledCorrectionImageFilter now only takes uint8 pixel types for mask image input.

Open source →

1.0.17 Aug 2017

The SimpleITK Development Team and the Insight Software Consortium are announcing the release of version 1.0.1 of SimpleITK.

Announcement

The SimpleITK Development Team and the Insight Software Consortium are announcing the release of version 1.0.1 of SimpleITK.

SimpleITK is available for the following programing languages: Python, R, Java, C#, C++, Lua, Ruby, and TCL. Binary versions of the toolkit are available for the GNU Linux, Apple OS X, and Microsoft Windows operating systems. All of the source code is freely available on Github under an Apache-2.0 license.

We are in the process of migrating the old SimpleITK Wiki (https://itk.org/Wiki/SimpleITK), to Read The Docs (http://simpleitk.readthedocs.io/en/latest/).

Downloading SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries can be found on Read The Docs (http://simpleitk.readthedocs.io/en/latest/Documentation/docs/source/installation.html).

Python Binary Downloads
- Python binary wheels are available for download. It is important to have the latest version of pip to ensure correct wheel compatibility and installation. To install the latest SimpleITK package form PyPI:
```
python -m pip install --upgrade pip
python -m pip install SimpleITK
```
- Many Conda package have been upload to Anaconda Cloud on the SimpleITK. These can be installed with:
```
conda install -c simpleitk simpleitk
```
A complete available set of compiled binaries, including select CSharp and Java distributions, along with source and data tar-balls are available on Source Forge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/).
SimpleITK has a robust Superbuild CMake system which minimized the dependencies needed to build SimpleITK from scratch. Complete compilation instructions can be found on Read the Docs (http://simpleitk.readthedocs.io/en/latest/Documentation/docs/source/building.html).

Release Notes

Improvements
- Uses ITK 4.11.1, tested for compatibility with ITK 4.12
- Improved error reporting for sitk.Show
- Improved search paths for sitk.Show
- Updated documentation from ITK and corrected spelling mistakes
Bug Fixes
- Numerous compilation issues related to R and mingw
- Fix CMake searching for Lua and Python
- Fix enabling SITK_4D_IMAGE
- Fix SimpleITKConfig.cmake.in compatibility for installed ITK
- Fix Superbuild issues with the Example directory as a project
- Fix out of bound array access in Image4D.ExtractImageFilter test
- Fixes to Python's setup.py for build_ext

Open source →

1.0.010 Apr 2017

``` .''. :_\/_: . .''.: /\ : _\(/_ :_\/_:'.:::. /)\*''* : /\ : ::::: '*_\/_* '..' ':::' * /\ *

       .''.             
      :_\/_:   .    
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      *          *..* 
 _____  _                    _       _____  _____  _   __    __     _____ 
/  ___|(_)                  | |     |_   _||_   _|| | / /   /  |   |  _  |
\ `--.  _  _ __ ___   _ __  | |  ___  | |    | |  | |/ /    `| |   | |/' |
 `--. \| || '_ ` _ \ | '_ \ | | / _ \ | |    | |  |    \     | |   |  /| |
/\__/ /| || | | | | || |_) || ||  __/_| |_   | |  | |\  \   _| |_ _\ |_/ /
\____/ |_||_| |_| |_|| .__/ |_| \___|\___/   \_/  \_| \_/   \___/(_)\___/ 
                     | |                                                  
                     |_|                                                  
                                                              .''.             
                                                             :_\/_:   .     
                                                         .''.: /\ : _\(/_  
                                                        :_\/_:'.:::. /)\*''* 
                                                        : /\ : :::::  '*_\/_*
                                                         '..'  ':::'   * /\ *
                                                                        *..*

Announcement

The SimpleITK Development Team and the Insight Software Consortium are proud to announce the first major release of SimpleITK.

SimpleITK is a simplified multi-language interface to the National Library of Medicine’s Insight Segmentation and Registration Toolkit (ITK). Providing an easy to use interface to ITK.

SimpleITK is intended to broaden the use of ITK to researchers and domain scientist who are novice software developers, enabling them to benefit from the image-analysis power of ITK. For experienced software developers, the toolkit enables rapid prototyping of image segmentation and registration frameworks and facilitates evaluation of the effects algorithmic parameter settings have on results with minimal programming effort. In the educational setting SimpleITK's concise interface allows students to experiment with well known algorithms, enhancing their understanding of algorithm performance without the need for advanced software engineering skills.

The toolkit development process follows best software engineering practices including code reviews and continuous integration testing, with results displayed online allowing everyone to gauge the status of the current code and any code that is under consideration for incorporation into the toolkit. User support is available through a dedicated mailing list and the project’s Wiki. SimpleITK is available for the following programing languages: Python, R, Java, C#, C++, Lua, Ruby, and TCL. Binary versions of the toolkit are available for the GNU Linux, Apple OS X, and Microsoft Windows operating systems. All of the source code is freely available on github under an Apache-2.0 license.

Downloading SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK Wiki (https://itk.org/Wiki/SimpleITK/GettingStarted).

Python Binary Downloads
- Python binary wheels are available for download. It is important to have the latest version of pip to ensure correct wheel compatibility and installation. To install the latest SimpleITK package form PyPI:
```
pip install --upgrade pip
pip install SimpleITK
```
- Many Conda package have been upload to Anaconda Cloud on the SimpleITK. These can be installed with:
```
conda install -c simpleitk simpleitk
```
A complete available set of compiled binaries, including select CSharp and Java distributions, along with source and data tar-balls are available on Source Forge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/).

Release Notes

Key Improvements:
- Improved Python data bridge
  - New Python method GetArrayViewFromImage provides copy free read-only access
  - Updated Python data structures to use memory view objects
- New language specific building SimpleITK front-ends
  - R devtools based installer (https://github.com/SimpleITK/SimpleITKRInstaller).
  - Python: scripts for building wheels (https://github.com/SimpleITK/SimpleITKPythonPackage) and a Conda recipe (https://github.com/SimpleITK/SimpleITKCondaRecipe).
- Improved writing DICOM tags when writing a slice, and disabled writing a DICOM series with the ImageSeriesWriter
- Support use of virtual image domain in the ImageRegistrationMethod
- OnePlusOneOptimizer added to registration framework
- Improved support for R: propogating C++ exceptions into R, additional R tests
- Additional tests for Java
- Python and R notebooks repository illustrating the basics and more advanced functionality of SimpleITK (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks)
- Added continous integration via CircleCI
- Updated version and improved integration of Google Test
- Updated ITK version to 4.11.0+
- Updated minimal required CMake version to 3.0, and numerous CMake changes to support various build configurations
- Fix, "pip install" works for Apple Mac OS X.
- Updated to usage of SWIG 3.0.11 ( using the latest SIWG is strongly recommended for R )
- Reorganized examples directory into example based sub-directories with multiple languages
- Improvements to documentation transmogrification scripts
- Many bug fixes and improvement to the build system!
Additional Improvements:
- Added multi-hash ExternalData support for sha512
- Added R Documentation files
- Update Python and Java documentation strings files
- Fix allowing undefined symbols when building standalone language wrapping
- Reorganized examples directory
- Reorganized filter libraries to match ITK modules
- Improved compilation with more specific ITK module usage
- Now using modern CMake 3 style properties for exported libraries
API Changes
- Replaced return Self with void for wrapped languages, to address memory and segmentation fault issue.
- Depricated CMake variables with "SITK" prefix, now consistenly using the "SimpleITK" prefix for configurable CMake variables
- Removed ImageSeriesReader::GetGDCMSeriesFileNames parameter loadPrivateTags parameter. This removes an overloaded version of the class method.
- Added sitkWallClock enum for a sentinel value for random number seed to indicate initialization from the clock
- New method Image::GetNumberOfPixels
- New method LabelMapContourOverlayImageFilter::SetColormap
- New method LabelMapToRGBImageFilter::SetColormap
- New method ImageRegistrationMethod::SetVirtualDomain
- New method ImageRegistrationMethod::SetVirtualDomainFromImage
- New seed parameter to ImageRegistrationMethod::AddMetricSamplingSeed method
- CastImageFilter::SetOutputPixelType method no longer accepts the pixel ID by value, uses only enumerated type

Open source →

0.10.028 Jul 2016

We are pleased to announce the release of SimpleITK 0.10.0!

Announcement

We are pleased to announce the release of SimpleITK 0.10.0!

As with all SimpleITK releases, we have a variety of binaries available. This includes fresh Python Wheels for MS Windows, GNU Linux and Apple OS X, along with Java and CSharp binaries for MS Windows. Additionally, binaries for the Python distribution Anaconda are available.

This release features major improvements to the build infrastructure, improved support for R, better downloads with pip and many new features!

Information on how to get started and download the binaries: https://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries

Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/

Release Doxygen Documentation: https://www.itk.org/SimpleITKDoxygen010/html/index.html

Key Improvements

The R language bindings have received extensive improvements and bug fixes.
Added Image::SetMetaData method
Added LandmarkBasedTransformInitializer
Added MultiLableSTAPLEImageFilter
Show now prefers Fiji over the basic ImageJ
Refactored Wrapping directory into separate languages (paths have changed!)
Separated Lua, GTest, and virtualenv into SuperBuild dependencies
Added SITK_FORBID_DOWNLOADS option
Enabled each language wrapping to be an independent project dependent on the SimpleITK C++ interface and libraries.
Many CMake build improvements to default configurations such as visibility, and link library interfaces
Support for gcc 6.1 and compatibility with c++14
CMake version 3.3 is now required

Python

Update your pip version!
Added manylinux1 wheels (PEP 513)
SimpleITK_PYTHON_THREADS enabled by default to better support multi-threading in Python
No egg binary distributions, wheels fully support the standard platforms
Python 2.7 is no longer packaged for 64-bit windows
Avoid linking against libpython.so to improve compatibility and portability

Lua

Lua languages bindings now compile as a loadable module
Created Lua rockspec builder (https://github.com/SimpleITK/SimpleITKLuaRock)
Can be used in Lua Torch

Fix issues with the bracket operator preserving physical location
Created script to generate R man pages
Disabled return Self value from functions
Create simplified R Installer (https://github.com/SimpleITK/SimpleITKRInstaller)

Open source →

0.9.128 Sept 2015

We are pleased to announce the release of SimpleITK 0.9.1!

Announcement

We are pleased to announce the release of SimpleITK 0.9.1!

As with all SimpleITK releases, we have a variety of binaries available. This includes fresh Python Wheels and Eggs, along with Java, and CSharp binaries. Additionally, new binaries for Anaconda have been made improving the dependency requirements.

This is a patch release and includes an update to the ITK version from 4.7.2+ to 4.8.1. Additional updates include: improved formatting for python documentation, fixes to the transform interfaces, improved ImageIO exceptions and build improvements.

Information on how to get started and download the binaries: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries

Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/

Release Doxygen Documentation: http://www.itk.org/SimpleITKDoxygen09/html/index.html

Commits

* db0ce5d Updating SimpleITK to 0.9.1 version for release
*   aa2c3ff Merge branch 'UpdateITKTo4.8.1' into release
|\
| * fee435f Update ITK superbuild to 4.8.1 release
* |   6c3b4f0 Merge branch 'AddMissingJavaCMakeVariables' into release
|\ \
| * | cec0b39 Add missing Java variables to the language options files
|/ /
* |   1c5f9b4 Merge branch 'UpdateITKTo4.8.1' into release
|\ \
| |/
| * c027978 Updating ITK superbuild towards v4.8.1 pending release
|/
* aa33380 Do not pass unneeded language arguments on the command line
* 7b83998 Require libraries when a wrapping for a language is enabled
* 5b1c3b5 Regenerated the .i files
* 0399fb6 Updated space_parse with a noLeadingSpace flag
* 792c306 Fix leading space problem in doxy2swig.py
* 8754ca5 Add unsigned int specifier
* 92fee75 Adding ObjectCount measurement to ConnectedComponents filter
* 1ac4872 WIP: Adding local transform fixes
*   a389ca0 Merge branch 'SIMPLEITK-638_ImproveImageReadException' into release
|\
| * a55f6b0 Improve exception when unable to create ImageIO
* 706b697 Merge branch 'SIMPLEITK-639_PatchRevisionDescription' into release
* fd06d0b Replace tabs with spaces.
* 13c0d41 GetGitRevisionDescription: Fix issue referencing project source

Open source →

0.9.015 May 2015

We are pleased to announce the release of SimpleITK 0.9!

Announcement

We are pleased to announce the release of SimpleITK 0.9!

NOW WITH REGISTRATION

Here is a quick overview of the ITKv4's registration in SimpleITK via IPython/Jupiter notebook: http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/60_RegistrationIntroduction.html

This release features the ImageRegistrationMethod which brings a SimpleITK style interface to the modular ITKv4 registration framework. This adds support for a variety of transforms including rigid, affine, b-spline, and deformation fields. The metrics supported include correlation, means squares, ANTS neighborhood correlation, and mutual information. A variety of optimizers are available along with scales estimators for the optimized transformation parameters and built in multi-scale registration support.

Additionally, a number of registration filters have been added: DemonsRegistrationFilter, DiffeomorphicDemonsRegistrationFilter, FastSymmetricForcesDemonsRegistrationFilter, LevelSetMotionRegistrationFilter and SymmetricForcesDemonsRegistrationFilter.

Several examples can be found in the examples directory to help you get started. These examples include Affine registration, BSpline, Demons and Displacement fields. http://www.itk.org/SimpleITKDoxygen/html/examples.html

We have also added the following filters: AdditiveGaussianNoiseImageFilter, AggregateLabelMapFilter, BinaryImageToLabelMapFilter, ChangeLabelLabelMapFilter, CollidingFrontsImageFilter, DisplacementFieldJacobianDeterminantFilter, FastMarchingBaseImageFilter, FastMarchingUpwindGradientImageFilter, InverseDisplacementFieldImageFilter, InvertDisplacementFieldImageFilter, LabelImageToLabelMapFilter, LabelShapeStatisticsImageFilter, LabelStatisticsImageFilter, LabelUniqueLabelMapFilter, MergeLabelMapFilter, RelabelLabelMapFilter, SaltAndPepperNoiseImageFilter, ShotNoiseImageFilter, SpeckleNoiseImageFilter and TransformToDisplacementFieldFilter

Information on how to get started and download the binaries: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries

Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9rc1/

Release Doxygen Documentation: http://www.itk.org/SimpleITKDoxygen09/html/index.html

Additional Release Notes: http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release

Sub-task

SIMPLEITK-426 - Wrap Image registration filters
SIMPLEITK-521 - Add initial RegistrationMethod class with basic components
SIMPLEITK-522 - Add support for active optimizing transform.
SIMPLEITK-536 - Create Infrastructure to support testing registration
SIMPLEITK-537 - Add support for Displacement fields
SIMPLEITK-538 - Add support for B-Splines Transforms
SIMPLEITK-549 - Add initial Implementation of ImageRegistrationMethodv4
SIMPLEITK-558 - Add support for fixed and moving image masks.
SIMPLEITK-560 - Comprehensive coverage testing of the registration framework is needed.
SIMPLEITK-561 - Handle copy on write for the InitialTransform input to the ImageRegistrationMethod
SIMPLEITK-562 - Write documentation for the transform and registration method classes.
SIMPLEITK-563 - Wrap CenteredVersorTransformInitaizalizer
SIMPLEITK-564 - Refactor ImageRegistrationMethodv4 ivar for components
SIMPLEITK-574 - Add ImageRegistrationMethodv4 methods to set all transforms
SIMPLEITK-575 - Add access to the estimated optimizer scales
SIMPLEITK-595 - Add DisplacementField specific interface
SIMPLEITK-608 - Add Evaluate metod to the ImageRegistrationMethod
SIMPLEITK-609 - Remove Transform's polymorphism cast/conversion

Bug

SIMPLEITK-393 - Does not write correct type for Int8
SIMPLEITK-525 - Enable deletion of command while an filter exists.
SIMPLEITK-526 - Fix CreateInterpolator guarder define miss match
SIMPLEITK-565 - The filters with multiple named inputs are not being checked if the image's type and dimension match.
SIMPLEITK-582 - Unable to load certain DICOM series by seriesID
SIMPLEITK-590 - Fix PNG sCal issue in master
SIMPLEITK-598 - CMake BUILD_EXAMPLES SuperBuild flag not propogated correctly
SIMPLEITK-616 - Using the ImageSeriesWriter with VectorImages does not work.
SIMPLEITK-617 - Check if the LBFGSB optimizer respects the number of iteration parameters. This may be an ITK bug.
SIMPLEITK-622 - LevelSetMotionRegistrationFilter documentation
SIMPLEITK-624 - Linking is running out of memory on windows with the monolithic build for distrubutions
SIMPLEITK-626 - When printing transform the reported ITK reference count is 2.
SIMPLEITK-629 - VS11 has compilation error with std::bind
SIMPLEITK-632 - Intermettent build failure of SimpleITK
SIMPLEITK-633 - invoking execute method without setting initial transform segfaults

Epic

SIMPLEITK-1 - Develop registration framework for ITKv4 Framework
SIMPLEITK-571 - Add More Registration Examples

Improvement

SIMPLEITK-378 - The Readme.md file is not particularly user friendly for Windows

users. Could it be renamed for the C# package to say "Readme.txt"?

SIMPLEITK-490 - Update Measurements to be tr1::function calls to the base ITK object.
SIMPLEITK-512 - Add basic LabelMap Filters for manipulating labels.
SIMPLEITK-586 - Enforcing System ITK Module dependencies
SIMPLEITK-596 - Update SimpleITK Doxygen doxygen.config
SIMPLEITK-611 - request for transform constructors

New Feature

SIMPLEITK-298 - MergeLabelMapFilter
SIMPLEITK-345 - The Image readers should have a cast or read as option
SIMPLEITK-429 - Some filter have optional inputs. This include PDE registration and masked thresholding. The needs to be added to the JSON.
SIMPLEITK-533 - Develop the Interface for the ImageRegistrationMethodv4 based on the ITKv4 registration framework.
SIMPLEITK-541 - The Demons registration based filters need an optional input for the initial deformation field.
SIMPLEITK-542 - Add the filter from the ImageNoise module
SIMPLEITK-543 - Update ITK towards version 4.6
SIMPLEITK-550 - Add TransfromToDisplacementField filter.
SIMPLEITK-555 - Refactor Transforms to allow specific interface for different transformation types
SIMPLEITK-567 - Add wrapping for the ScaleSkewVersor
SIMPLEITK-573 - Add missing methods to the transform interfaces
SIMPLEITK-588 - Add access to the GlobalPhysicalSpaceTolerance variable.
SIMPLEITK-603 - Add transform adaptor support for the ImageRegistration method
SIMPLEITK-605 - Add ScaleTransform
SIMPLEITK-607 - Missing methods to the ImageRegistrationMethod class
SIMPLEITK-612 - For Image and Transform class make public and rename MakeUniqueForWrite to MakeUnique
SIMPLEITK-613 - Add FastMarchingUpwindGradient and CollidingFronts filters
SIMPLEITK-623 - Add optimizer weights to image registration method

Task

SIMPLEITK-438 - add method to use a VectorImage as a Image of Vectors for displacement fields.
SIMPLEITK-530 - Test and validate useful and correct functionality of the components in the ImageRegistrationMethods
SIMPLEITK-531 - Use SimpleITK's Registration to perform a complete neuro-imaging registration sequence.
SIMPLEITK-544 - Update SWIG to 3.0.2
SIMPLEITK-545 - Upgrade PCRE to latest version.
SIMPLEITK-591 - run script that propagates doxygen documentation to python docstring
SIMPLEITK-599 - Update SWIG to 3.0.4 and PCRE to 8.36
SIMPLEITK-610 - Fix Dashboard warnings and failing tests.
SIMPLEITK-614 - Address CMake CMP0054 policy warnings.
SIMPLEITK-618 - Update ITK super build version to 4.7.1
SIMPLEITK-619 - Update SWIG doc strings.
SIMPLEITK-630 - Reduce dashboard warnings.
SIMPLEITK-634 - Update ITK super build toward 4.7.2
SIMPLEITK-636 - Update SimpleITK Doxygen documentation form ITK and update the SWIG documentation.
SIMPLEITK-637 - Why are there no symbols in the Doxygen?

Open source →

0.8.122 Dec 2014

We are pleased to announce the SimpleITK 0.8.1 Release.

Announcement

We are pleased to announce the SimpleITK 0.8.1 Release.

SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education and interpreted languages. SimpleITK provides binaries for several wrapped languages to enable users to rapidly get started using ITK.

Information on how to get started and download the binaries: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries

This patch release updates the ITK version to the newly released 4.7.0. Additionally, this patch contains improved support for CMake 3.0, fixes for compilation issues, the addition of the LabelOverlapMeasures filter, and a fix for the ClampCast filter.

Also, we are now compiling for Python 3.4, and have stopped compiling for Python 3.2. Lastly, we are providing some binaries for the Anaconda Python distribution on Binstar.

Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.1/

Release Doxygen Documentation: http://www.itk.org/SimpleITKDoxygen08/html/index.html

Sub-task

SIMPLEITK-583 - Don't always use ez_setup which downloads setup tools

Bug

SIMPLEITK-513 - The R package has version 0.5-1 for SimpleITK
SIMPLEITK-514 - Off by one error in CMake code for splitting the basic filters library, can result in missing link dependencies.
SIMPLEITK-517 - Associate installation of all headers with "Development" component
SIMPLEITK-518 - Version variable not set after "find_package(SimpleITK)
SIMPLEITK-526 - Fix CreateInterpolator guarder define miss match
SIMPLEITK-529 - Minor Help Documentation bug
SIMPLEITK-546 - SimpleITK Java bindings fail to compile
SIMPLEITK-551 - Clamp cast filter is not setting correct bounds.
SIMPLEITK-552 - CMake 3.0 warning - Do not use LOCATION property in Wrapping/CMakeLists.txt
SIMPLEITK-553 - CMake 3.0 warning - sitkConfigureFileBuildtime - non-existent target in get_target_property
SIMPLEITK-554 - CMake 3.0 Waring - TARGET SimpleITKBasicFilters does not exist
SIMPLEITK-568 - In Doxygen coming from ITK, there are missing spaces before and after some reference links
SIMPLEITK-581 - For the Superbuild have a way so specify the paths which are searched for system libraries.
SIMPLEITK-584 - Address compilation warning on the CDash package release section.
SIMPLEITK-589 - Update png test images with an sCal of METER.

Improvement

SIMPLEITK-489 - Wrap the LabelOverlapMeasures filter
SIMPLEITK-510 - LabelStatisticsImageFilter needs the option to turn off using histograms.
SIMPLEITK-577 - On Windows add support to build SimpleITK shared but use release Python libraries.
SIMPLEITK-585 - Upgrade ITK Superbuild version to 4.7
SIMPLEITK-569 - Upgrade 0.8 to use ITK 4.6

Task

SIMPLEITK-503 - Update a the visual guide for building on Linux, change to debian, and update packages needed.
SIMPLEITK-511 - Update to ITK 4.5.2
SIMPLEITK-523 - Update the SWIG .i documentation files for the new LabelOverlap filter.
SIMPLEITK-578 - Update To ITK 4.6.1
SIMPLEITK-587 - Update JSON Doxygen strings with latest from ITK 4.7

Open source →

0.8.015 Jul 2014Deprecated

The KernelEnum types as an object member has been deprecated.

Announcement

We are happy to announce the SimpleITK 0.8.0 Release.

SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education and interpreted languages. SimpleITK provide binaries for several wrapped languages to enable users to rapidly get started using ITK.

Information on how to get started and download the binaries: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries

Improvements:

Support for events and command call-backs. More information can be found here: http://www.itk.org/SimpleITKDoxygen/html/CommandPage.html
Includes lambdas for Python, and derived delegate classes for CSharp, Java, Ruby and Python.
Support for compiling OSX Mavericks, by enabling C+11 automatically.
Improved support for C++11
Improved support for setting dimensional vector parameters as scalars in the OOP interface
Improved ProcessObject base class features in OOP interface
Swig 2.0.12
Wrapping for R will automatically be enabled if detected due to increased stability with SWIG update.
Improved printing of enum types.
Automatically enabling >4GB image on windows.
Newly wrapped filters BinShrinkImageFilter, CyclicShiftImageFilter, DiscreteGaussianDerivativeImageFilter, LabelVotingImageFilter, and WarpImageFilter.
Threshold measurement available in automatic thresholding filters
Experimental Support for generating Python wheels
ITK 4.5.1

Compatibility:

The operator "~" was incorrectly implemented as a logical not. This has been corrected to be a bitwise not operator for images.
The KernelEnum types as an object member has been deprecated.
In-favor of namespace enum: http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a38998f2c7b469b1ad8e337a0c6c0697b

Updated Documentation:

http://www.itk.org/Wiki/SimpleITK/GettingStarted/Visual_guide_to_building_on_Linux
http://www.itk.org/Wiki/SimpleITK/GettingStarted/A_visual_guide_to_SimpleITK_with_CSharp
http://simpleitk.github.io/SimpleITK-Notebooks/41_Progress.html

Binary distribution for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.0/

Release Doxygen Documentation: http://www.itk.org/SimpleITKDoxygen08/html/index.html

Sub-task

SIMPLEITK-391 - Correct overloaded operator to use Bitwise filter for bitwise operators
SIMPLEITK-476 - Check if the custom std_vector.i file for R is still needed
SIMPLEITK-477 - Latest R installs require a NAMESPACE file

Bug

SIMPLEITK-445 - `GLIBC_2.14' not found
SIMPLEITK-451 - The C++ Examples are not being tested.
SIMPLEITK-453 - CLang 5.0 OS X 10.9 std::tr1 namespace doesn't exist
SIMPLEITK-478 - Test Java Command Delegate
SIMPLEITK-480 - Automatically add -std=c++11 flag for clang 5.0 on mavericks.
SIMPLEITK-482 - Fix CMake configuration warning about linking to ourselves.
SIMPLEITK-495 - Update virtualenv version, not compatible with Ubuntu 13.10, or Debian testing
SIMPLEITK-496 - On Maverick with c++11 SWIG is failing with Java and std::vector<bool>
SIMPLEITK-507 - The Examples in the "Segmentation" sub-directory are not being run and need to be updated.
SIMPLEITK-508 - The Python PEP386 version should not have a '.' before the release candidate suffix.

Improvement

SIMPLEITK-430 - The InterpolatorEnums are print as integers, this should be strings.
SIMPLEITK-431 - The enums for morphology filters are local to each filter, they should be moved to common location with the sitk prefix.
SIMPLEITK-432 - upgrade toward ITK 4.5
SIMPLEITK-433 - Add Warp ImageFilter
SIMPLEITK-434 - Add BinShrink filter
SIMPLEITK-436 - Expose the hidden CMake Variable as advanced options.
SIMPLEITK-450 - Break compilation of LabelStatisticsImageFilter into 2 file for compilation speed.
SIMPLEITK-457 - Add CSharp example and test for GetBuffer methods.
SIMPLEITK-467 - Update super ITK build version towards 4.5.1.
SIMPLEITK-472 - make using 64 integers default for windows 64
SIMPLEITK-473 - Turn on R by default if detected.
SIMPLEITK-491 - Move WRAPITK option to advanced.
SIMPLEITK-494 - Reduce time taken for lengthy tests.
SIMPLEITK-501 - An optional stripping of symbols needs to be done on OSX for the distributed libraries. This reduces the size of the libraries by ~100 Megabytes.

New Feature

SIMPLEITK-372 - When testing is disabled Python eggs are not created by the "dist" target.
SIMPLEITK-410 - Add BUILD_EXAMPLES option to SimpleITK actual build.
SIMPLEITK-422 - Add missing connectivity to threshold connected image filter
SIMPLEITK-423 - adding missing resulting measurements to confidence connected filter.
SIMPLEITK-435 - Add basic access to Image's Meta Data Dictionary
SIMPLEITK-440 - Add option to dim_vec to set as a scalar for all components.
SIMPLEITK-441 - Create Prototype for progress reporting and call backs from filters.
SIMPLEITK-443 - add DiscreteGaussianDerivative Filter
SIMPLEITK-444 - Add additional procedure which take dim_vec as scalars if first parameter.
SIMPLEITK-447 - Refactor ImageFilter to include ProcessObject base class
SIMPLEITK-449 - There are some basic missing matrix based transforms that are missing such as Euler and Versor transforms.
SIMPLEITK-454 - Add call-back events and progress reporting form ITK process objects.
SIMPLEITK-456 - Add support to transform continuous index to physical point.
SIMPLEITK-462 - Add SWIG Delegate Support for Command Class
SIMPLEITK-463 - Add direct lambda support to ProcessObject::AddCommand in Python
SIMPLEITK-468 - Add output operator support for KernelEnums
SIMPLEITK-469 - Add output operator to PixelIDTypeEnum
SIMPLEITK-493 - Add script to upload data to midas.
SIMPLEITK-505 - Add threshold value as measurement to auto thresholding filters.
SIMPLEITK-506 - Add support for generating python wheel to enable pip to download binaries.

Task

SIMPLEITK-437 - Add more Filters.
SIMPLEITK-452 - Add const correctness to Get member functions.
SIMPLEITK-455 - Update to SWIG version 2.0.11
SIMPLEITK-466 - Add Doxygen page describing commands, and events in process objects.
SIMPLEITK-479 - Remove SWIG patch step and just patch the downloaded source
SIMPLEITK-481 - Update the Wrapping.dox Doxygen page
SIMPLEITK-485 - Update to SWIG 2.0.12
SIMPLEITK-486 - Update the JSON doxygen from the ITK XML.
SIMPLEITK-487 - Update the SWIG docs files from the update SimpleITK JSON.
SIMPLEITK-488 - Update the Filter Coverage
SIMPLEITK-492 - Reduce warnings on the dashboard.
SIMPLEITK-502 - Create Visual guide for using SimpleITK with CSharp on Windows.
SIMPLEITK-504 - Add the SimpleITK Notebook page on progress reporting to the master.

Open source →

0.7.0

We are pleased to announce the release of SimpleITK 0.7.0!

Announcement

We are pleased to announce the release of SimpleITK 0.7.0!

The release's binary built distributions are available for many languages and platforms. They are available for download:

http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.7.0/

There are numerous binaries available for download for Python via setuptools' easy_install. Additionally, we have select binary distributions for C# and Java. Information on downloading and getting started can be found here:

http://www.itk.org/Wiki/SimpleITK/GettingStarted#Downloading_the_binaries

Notable improvement:

Based on ITK 4.4.2 with enhanced performance for operators
New filters including: Clamp, PatchedBasedDenoising, ScalarChanAndVese, BitwiseNot
Support for 64-bit integer Pixels ( not enable with windows VS9, nor packaged )
Add Debug flag for filters to print ITK filter
Bug fixes.
And Many more!

CSharp:

Additional image overloaded operators

Doxygen for this release can be found here: http://itk.org/SimpleITKDoxygen07/html/pages.html

Sub-task

SIMPLEITK-359 - Look into integration of ExternalData.cmake

Bug

SIMPLEITK-210 - Use printable types for ToString methods
SIMPLEITK-371 - SetPixel test is failing on windows in debug mode
SIMPLEITK-387 - CSharp version is invalid causing compilation error.
SIMPLEITK-398 - CSharp is missing the Image::GetBufferAs... methods
SIMPLEITK-401 - Verify TR1 error checking for logic
SIMPLEITK-405 - Fix some dashboard warnings
SIMPLEITK-406 - Can not convert image >4GB to numpy array
SIMPLEITK-408 - Swig build error on windows64 when ITK is not installed, due to excessive path length.
SIMPLEITK-417 - LabelStatisticsImageFilter does not reset internal measurements for each execution.

Improvement

SIMPLEITK-389 - Overload image operators for C# wrappers
SIMPLEITK-390 - Add BitwiseNot functor filter
SIMPLEITK-392 - Improve scanning time of JSON files.
SIMPLEITK-399 - Update to ITK patch release 4.3.2
SIMPLEITK-400 - Update towards ITK 4.4
SIMPLEITK-409 - There is an unneeded dependency of many of the BasicFilter libraries on the previous on. This should be removed.

New Feature

SIMPLEITK-330 - Add PatchBaseDenoising filter
SIMPLEITK-411 - Add new json field type for enums.
SIMPLEITK-415 - Add ClampImageFilter

Task

SIMPLEITK-352 - Have separate versions of SimpleITK doxygen for each version or tag
SIMPLEITK-355 - Add CMake file to use Midas and MD5 files for data.
SIMPLEITK-356 - Migrate the data from the data submodule to the Midas md5 download system.
SIMPLEITK-366 - System ITK with Superbuild.
SIMPLEITK-367 - Move WIki pages to version directories.
SIMPLEITK-375 - Update SimpleITK Wiki and FAQ, including compiler support and FAQ entries.
SIMPLEITK-407 - Update the style of SWIG and PCRE.
SIMPLEITK-412 - Fix dashboard issues
SIMPLEITK-416 - Update Source Tarball script for midas data.
SIMPLEITK-418 - The size of the monolithic test driver is too big on windows. This should be broken up

Open source →