SimpleITK Release v0.9.0

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?