SimpleITK/ReleaseNotes

SimpleITK - Version 0.9 beta 1 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-527]] - Test which transform is active during registration
• [[SIMPLEITK-536]] - Create Infrastructure to support testing registration
• [[SIMPLEITK-537]] - Add support for Displacement fields
• [[SIMPLEITK-538]] - Add support for B-Splines Transforms
• [[SIMPLEITK-548]] - Enable Python test to run via the system Python
• [[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 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-535]] - When compiled against HDF5 system library we can not write out and HDF5 transform.
• [[SIMPLEITK-559]] - Gradient descent based optimizer don't converge at optimal position with MattesMutualInformation.
• [[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-594]] - The sitkDisplacementFieldTransform::GetDisplacementField method returns an sitkImage which can modify the internal displacement field, this should use a copy on write mechanism.
• [[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.

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-524]] - Add Wrapping of LabelGeometryImageFilter
• [[SIMPLEITK-533]] - Develop the Interface for the ImageRegistrationMethodv4 based on the ITKv4 registration framework.
• [[SIMPLEITK-540]] - Add a cmake option to forbid downloads during the build
• [[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

Task

• [[SIMPLEITK-361]] - Adding testing for threading in Python
• [[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-534]] - Verify the correct functionality and feature completeness of B-Spline transformations and deformation fields in SimpleITK.
• [[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 - Version 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

Additional Release Notes: http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.8.1_Release

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

SimpleITK - Version 0.8.0 Release

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

Additional Release Note: http://www.itk.org/Wiki/index.php?title=SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.8.0_Release

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.

SimpleITK - Version 0.7.1 Release

Bug

• [SIMPLEITK-419] - Fix numpy conversion warning on windows.
• [SIMPLEITK-420] - Fix numpy conversion warning on windows.
• [SIMPLEITK-421] - Documentation for Statistics image filter bounding box needs to be corrected.
• [SIMPLEITK-424] - Unable to convert 4GB+ numpy array to sitkImage

SimpleITK - Version 0.7.0 Release

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