SimpleITK 2.1 Release Candidate 1

Announcements
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Announcement

Announcing the SimpleITK 2.1 Release Candidate 1!

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

Installing SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK Read the Docs web page.

Python Binary Downloads

  • Python binary wheels are available for download. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package from GitHub releases:
python -m pip install --upgrade pip
python -m pip install --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.1rc1

Anaconda Binary Downloads

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

conda install -c simpleitk/label/dev simpleitk

Apple M1 ARM Support

SimpleITK v2.1rc1 has been successfully compiled and tested on Apple OS X running native M1 ARM. Thanks to the ITK development team for providing the foundation.

For the v2.1 .0 final release, we are currently only planning to release M1 ARM binaries for the conda-forge distribution.

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

Bug Fixes

  • The default ITK multi-threader is configured to be “Platform”. This addresssed issues with multi-processing and the Google Colaborratory environment.
  • Update expected results for Linux ppc64le in test ImageRegistrationMethodDisplacement1 and SLICImageFilter.
  • The GetPixelAsComplexFloat64 Image method in Python is correctly renamed to __GetPixelAsComplexFloat64__.

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.

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
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