[ITK-dev] [ANNOUNCE] ITK 4.7 Release Candidate 1 has been tagged!

Matt McCormick matt.mccormick at kitware.com
Mon Dec 8 23:44:31 EST 2014


On behalf of the Insight Toolkit community, we are proud to announce
that ITK 4.7.0 release candidate 1 has been tagged and is available
for testing!


To obtain the source code,

  git clone http://itk.org/ITK.git
  cd ITK
  git checkout -q --detach v4.7rc01

For more details, please see the Git documentation [1].


Please test the release candidate and share your experiences on the
mailing list, issue tracker, and Gerrit Code Review. Please help
identify issues submitting an Experimental build to the dashboard [2]
with:

  ctest -M Experimental  -T Configure -T Build -T Test -T Submit

and notifying the mailing list.  Testing your own applications against
the RC is also appreciated.


Congratulations and well done to everyone that has contributed to this
release. Release candidates are tagged every week.  The final release
is scheduled for December 18th.


[1] http://www.itk.org/Wiki/ITK/Git

[2] http://open.cdash.org/index.php?project=Insight



New Features
------------------
* Documentation Improvements
  - Update Software Guide registration examples to ITKv4 framework
  - Wiki and Sphinx examples are indexed in Doxygen
  - Clean Software Guide dashboard build

* Filtering Improvements
  - New Laplacian deformation filter’s for QuadEdgeMesh’s
    - IJ article: http://hdl.handle.net/10380/3410
 - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations

* ImageIO improvements
  - PNG sCAL unit support
  - TIFF IO performance greatly improved
  - TIFF tags read into Image MetaDataDictionary
  - MetaIO updated
  - Better support for system GDCM

* Infrastructure improvements
  - New method to erase a MetaDataDictionary entry
  - New global method to set physical space tolerance
  - New, experimental thread pool support
  - NumericTraits::Zero and ::One are deprecated in favor of
::ZeroValue() and ::OneValue()

* New Remote Modules
  - Higher Order Accurate Gradient
    - http://hdl.handle.net/10380/3231
  - IO Transform DCMTK
    - http://hdl.handle.net/10380/3468

* Registration improvements
  - LandmarkBasedTransformInitializer supports BSplineTransform
  - Transverse inverse consistency increased
  - Automatic initialization of the transform center for multi-stage
registrations
  - Sparse point B-spline field estimate

* Performance improvements
  - Faster recursive Gaussian on VectorImage
  - Mutual information faster, lower memory usage

* Wrapping improvements
  - Wrapping now builds without type warnings
  - pygccxml bumped to 1.6.2
  - Latest GCCXML
  - CMake wrapping infrastructure cleanup
  - Build with Ninja CMake generator
  - New GetTypes() and GetTypesAsList() methods
  - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake

* Many style improvements -- ITK gets more stylish with every release!

* Improved code coverage -- we are over 85%!

* *Lots* of important bug fixes

* And much more! See details in the log below.


List of changes since v4.5.0
--------------------------------------

Alexander Schmidt-Richberg (1):
      ENH: Updated Remote Module VariationalRegistration to new git tag

Ali Ghayoor (10):
      ENH: Make ITKv4 compatible with ITKSoftwareGuide
      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
      ENH: Convert three ImageRegistration Examples to ITKv4
      ENH: Add multi-Res and multistage registration Examples to ITKv4
      ENH: Convert DeformableReg examples to ITKv4 reg framework
      BUG: Expand a test to reflect multi-metric registration bug
      BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4
      ENH: Add direct initialization to SyN registration
      ENH: Direct initialization of SyN by restoring the state
      ENH: LandmarkBasedTransformInitializer supports BSplineTransformType

Arnaud Gelas (15):
      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
      ENH: Importing Laplacian Deformation for QuadEdgeMesh
      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified()
      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
      BUG: fix gdcm version in GDCMImageIO.
      COMP: missing cast when calling gdcm::DataElement::SetByteValue
      COMP: missing cast when calling gdcm::DataElement::SetByteValue
      ENH: increase LaplacianDeformation code coverage
      STYLE: use typedef rather than inheritance
      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false
      BUG: split include directories into appropriate cmake variables HDF5
      BUG: missing gdcm libraries when using system GDCM
      DOC: fix doxygen documentaiton for
itk::LaplacianDeformationQuadEdgeMeshFilter
      ENH: Add one method to erase a tag into MetaDataDictionary

Bill Lorensen (5):
      ENH: Specify required VTK modules
      COMP: Wiki examples require additional vtk modules
      ENH: Modify WikiExamples remote config
      COMP: Bad test signature
      COMP: Update tag for wiki examples

Brad King (6):
      COMP: Fix vxl_config_macros usage of CMake check macros
      ENH: Use if(DEFINED) to simplify conditions
      COMP: Fix vxl_config_macros checks broken by refactoring
      COMP: Fix one more vxl_config_macros check broken by refactoring
      BUG: Fix itk_module_config for repeated calls
      BUG: Fix itk_module_config for repeated calls

Bradley Lowekamp (52):
      ENH: Adding License file from upstream MetaIO
      ENH: Adding script to update MetaIO from upstream
      ENH: Remove ITK MetaIO to prepare for upstream import
      PERF: Remove dynamically allocated temporary in evaluate method
      COMP: Fix variable type for Set/Get macros
      BUG: Implement ITK Style Singleton design pattern
      ENH: Add no throw exception specification for UnRegister methods
      COMP: Must specify order as "noexcept override"
      BUG: Add GetInverse for IdentityTransform
      ENH: Adding SetIdentity method to base DisplacementField class
      BUG: Remove unused redefinition of NULL
      BUG: Don't print to std::cout in PrintSelf
      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit
      COMP: Fix signed to unsigned int comparison
      BUG: Fix overflows computing size of read tiff image
      ENH: Extract TiffReaderInternal to separate file
      ENH: Refactor ReadTwoSamplePerPixelImage into template function
      ENH: Refactor GenericReadImage into template function
      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO )
      ENH: Refactor method to convert RGBA image to output buffer
      ENH: Refactor duplicated code to read a page
      BUG: Fix right oriented tiff images
      BUG: Remove dead separated plannar code, add test
      STYLE: Fix minor kwstyle defects in test and test results
      BUG: Use array delete operator for array new allocations
      ENH: add arbitrary TIFF TAGs to meta-data dictionary
      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
      BUG: Address Coverity warning about null pointer dereferences
      ENH: Remove support for TIFF tile as 3D and dead code
      ENH: RGBA read images should stay unchanged.
      BUG: Override method to MakeOutput by name
      ENH: Refactor per pixel conversion function to per scan-line method
      PERF: Refactor color table lookup
      BUG: Adding missing parentheses around boolean expression
      ENH: adding TIFFImageIO test for RGB palette images
      PERF: Improve recursive Gaussian perfromance with VectorImages
      ENH: Query libtiff to determine compression support
      BUG: Support TIFF tiled image with TIFFReadRGBAImage
      BUG: Use SizeValueType for length of scanline
      PERF: Store causal results directly in output buffers
      COMP: Add explicit conversion to const char
      COMP: Explicitly add override to GetNameOfClass method
      COMP: Address internal segmentation fault with Intel compiler
      ENH: Adding method to set global physical space tolerance
      COMP: Explicitly add override to GetNameOfClass method
      BUG: Add new TypeMacro for non-overloaded classes
      BUG: Fix obscure race condition on access thread pool initialization
      BUG: Updating FDFImageIO remote module

Christopher Mullins (15):
      COMP: Allows latex to compile for ITKSoftwareGuide
      COMP: Allows latex to compile for ITKSoftwareGuide
      COMP: Wrap MeshBase templates
      COMP: Wrap MeshBase templates
      COMP: Fix warning in BlockMatchingImageFilter
      STYLE: Line lengths in examples should be no longer than 80 chars.
      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
      COMP: Fix LaTeX warnings.
      STYLE: Fix formatting/punctuation errors.
      STYLE: Formatting and punctuation fixes.
      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
      DOC: Edits for book 2 chapter 2.
      DOC: More chapter 2 edits
      DOC: Book 2 Chapter 3 edits (part 1)
      DOC: book 2 chapter 4 Segmentation edits

Danny Perry (2):
      BUG: adding test for vnl_sparse_matrix::mult()
      BUG: size of q buffer should actually be (this->rows())*pcols.

David T. Chen (1):
      DOC: Fixed HistogramThresholdImageFitler

Dirk Padfield (1):
      BUG: Corrected processing of last sigma

GCC-XML Upstream (1):
      ENH: pygccxml v1.6.2 (reduced)

Gert Wollny (1):
      COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)

Girish Mallya (1):
      BUG: Tests added for BinaryImageToLabelMapFilter for single-row images.

Hans Johnson (24):
      COMP: Add tolerance for comparing floating point
      PERF: Remove non-threadable algorithm components
      COMP: Add tolerance for comparing floating point
      PERF: Remove non-threadable algorithm components
      PERF: Remove large foot print of PDF derivatives.
      PERF: Revert Remove large foot print of PDF derivatives.
      STYLE: Test against almost equal for floating point values
      STYLE: Non-exact floating point testing
      PERF: Distribute initialization per thread buffers
      ENH: Remove unnecessary mutable qualifier.
      STYLE: Remove comment with no meaning.
      ENH: Moved accumlator logic to main MI class
      ENH: Allow staggering of accumulations per thread.
      PERF: Zero reset thread buffers during finalize
      BUG: Syntax error in comment
      PERF: Add non-blocking mutex locking.
      ENH: Use TryLock minimize thread stalls
      BUG: ThreadedIndexedContainerPartitioner is inclusive
      STYLE: Remove include_regular_expression from Examples
      BUG: Demonstrate Inv(Inv(T)) != T
      BUG: Ensure Inv(Inv(T)) == T for transforms
      COMP: Valgrind detects uninitialized memory read
      COMP: Missing required base class API component
      ENH: Expand interface for selecting threadpool

Ismael Belghiti (1):
      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter

Jim Miller (1):
      STYLE: Removing what appears to be a temporary file

Johan Andruejol (1):
      ENH: Fix normalization for null vectors and return the norm

Jon Haitz Legarreta (1):
      ENH: New test for itkLabelShapeOpeningImageFilter

Kent Williams (9):
      COMP: use find_package(VTK COMPONENTS) to specify just needed
VTK Components
      BUG: ImageSources/test/CMakeLists.txt incorrect library var reference
      COMP: Fix coverity defects related to RegistrationV4 examples
      COMP: silence warning of vnl_vector_fixed_ref::assert_size
      COMP: Fix various Coverity warnings
      COMP: Fix a typo in an error message print statement.
      COMP: itk::Command-derived class used pointless dynamic_cast.
      PERF: Don't recompute InternalInverse repeatedly
      COMP: Correct orientation/spacing for Philips MultiFrame

Mark Hiner (2):
      ENH: Update SCIFIO remote module hash
      BUG: Fix duplicate variables in Windows

Matthew McCormick (105):
      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
      ENH: Move FFTComplexToComplexImageFilter out of Review.
      ENH: Add VnlComplexToComplexFFTImageFilter.
      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
      ENH: Bump CMakeLists.txt version to 4.7.0.
      BUG: ArchiveTestingData.py future imports must occur at the beginning.
      BUG: Do not run vnl_test_na with broken libc++.
      DOC: Remove Image2.cxx reference from Book 2.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.
      DOC: Remove references to Book 1 sections from Book 2.
      DOC: Make BinaryThresholdImageFilter not floating.
      DOC: Fix Software Guide figure caption for FlipImageFilter.
      DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.
      DOC: Remove duplicate figure in
LaplacianRecursiveGaussianImageFilter2.cxx.
      DOC: ImageRandomConstIteratorWithIndex table reference.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
      BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter.
      BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.
      STYLE: Fix style in VoronoiDiagram2D.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      BUG: Bump GCCXML to 2014-08-06.
      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
      BUG: Fix Win MultiThreader check for successful process creation.
      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
      DOC: itk::statistics -> itk::Statistics.
      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      COMP: Improve const correctness of GradientRecursiveGaussianImageFilter.
      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
      COMP: ThreadJob NULL not defined.
      BUG: Fix alpha assignment for RGBA TIFF.
      COMP: Remove unused typedefs in LevelSetsv4Visualization.
      COMP: Remove unused typedef's in VtkGlue.
      ENH: Mark BSplineWarping2Test as RUNS_LONG.
      BUG: Fix Nifti IO read with large images.
      COMP: Remove call for non-existent variable in Nifti debugging.
      BUG: Close the file on Read and Write in HDF5TransformIO.
      BUG: Remove InsightLegacy test code from TransformHDF5Test.
      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
      ENH: Allow specification of orthogonality tolerance in rigid transforms.
      BUG: TransformFileReader does not clear its TransformList.
      BUG: Prevent dangling pointer in HDF5TransformIO.
      COMP: Do not use _stat64 with MinGW-32.
      BUG: Improve thread-safety and performance of
PCAShapeSignedDistanceFunction.
      DOC: itk::statistics -> itk::Statistics.
      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
      COMP: Address LaplacianDeformation Doxygen warnings.
      BUG: TransformFileReader does not clear its TransformList.
      BUG: Prevent dangling pointer in HDF5TransformIO.
      COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
      BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform
      COMP: Do not wrap the FixedArray of Image SmartPointer's.
      COMP: Add missing wrapping for TransformIOBaseTemplate.
      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
      STYLE: Improve style in BinaryImageToLabelMapFilter.
      BUG: Fix BinaryImageToLabelMapFilter on 1D image.
      ENH: Improve precision of the joint PDF sum
      BUG: Fix BinShrinkImageFilter for different input/output image types.
      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
      BUG: Use -py3 when building wrapping for Python 3.
      COMP: Add missing wrapping for TransformIOBaseTemplate.
      DOC: Improve ImageRegistration4 grammar.
      ENH: Add IOTransformDCMTK Remote module.
      BUG: gdcm::StringFilter recognizes backslash delimiter.
      DOC: Add migration guide for GDCM Rescale slope intercept apply on write.
      COMP: Remove unused typedef's in GPU code.
      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
      COMP: Use ConceptChecking for IterativeInverse dimension check.
      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
      COMP: Add warning exceptions for third party pcre, swig, gccxml.
      ENH: Bump ITK version to 4.6.1.
      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
      BUG: Remove GaussianImageSource members shadowing GenerateImageSource.
      STYLE: Style fixes to ITKImageSources module.
      BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType.
      BUG: Do not perform itk_download_attempt_check when not building ITK.
      DOC: Update GDCMImageIO rescale slope intercept doc.
      BUG: Only register requestion IO COMPONENT modules.
      BUG: Fix wrapping .i, .idx CMake dependencies.
      COMP: Add VTK Python module when wrapping ITKVtkGlue.
      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef.
      COMP: Add missing VTK module dependency for LevelSetsv4Visualization.
      BUG: By default, do not create any fixed parameters.
      STYLE: Remove trivial method comments in itkTransform.hxx.
      BUG: PolylineMask Filter's GenerateData is protected / virtual.
      ENH: Add HigherOrderAccurateGradient Module.
      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal.
      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
      STYLE: Style fixes for Transform classes.
      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
      DOC: Index Wiki examples with Doxygen.
      COMP: Bump SphinxExamples remote module.
      DOC: Index Sphinx examples in Doxygen.
      COMP: Remove old java examples.
      COMP: Remove duplicate DiffusionTensor3DReconstruction example reference.
      COMP: Address GradientAnisotropicDiffusionImageFilter example settings.
      COMP: Bump Sphinx Examples remote.
      COMP: Bump WikiExamples remote.

MetaIO Maintainers (1):
      MetaIO (reduced)

Michka Popoff (40):
      ENH: Fixes for python 3 support
      BUG: Add VTK_VERSION for older VTK versions
      BUG: Improve SWIG version check
      COMP: Add wrapping for ThreadPool and ThreadJob
      COMP: Remove unimplemented DestroyPool method
      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
      COMP: Do not hide pygccxml warnings
      ENH: Update links in readme file
      BUG: Improve SWIG version check
      BUG: Add VTK_VERSION for older VTK versions
      STYLE: Remove trailing whitespaces
      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
      BUG: Fix memory leak in MetaImageIO after exception
      ENH: Add script to update pygccxml from upstream
      BUG: Update VTK minimum version (for release)
      BUG: Fix memory leak in MetaImageIO after exception
      ENH: Remove Sun OS compatibility for the wrappings
      COMP: Fix for conversion to non-pointer like type warning
      STYLE: LabelObject style
      DOC: Remove broken link from LabelObject class description
      ENH: Do not setup the python tests if not asked
      ENH: Add new GetTypes() and GetTypesAsList() methods to the template class
      COMP: Fix CMP0054 warnings in wrappings
      STYLE: Remove old cmake < 2.8.4 specific code
      STYLE: Remove old cmake < 2.8.5 specific code
      ENH: Update to PCRE 8.36
      COMP: Refactor Wrapping setup and fix legacy warnings
      ENH: Add wrapping configuration to ITKConfig.cmake
      STYLE: Some minor code cleanup in the wrapping setup
      DOC: Fix typo in RelabelComponentImageFilter
      ENH: Deprecate VectorResampleImageFilter
      DOC: Add migration guide for ::Zero and ::One
      ENH: Deprecate ::Zero and ::One
      ENH: Add option to disable sorting by size in
itkRelabelComponentImageFilter
      ENH: Add Vector and RGB wrapping to linear interpolator
      STYLE: Remove SORT macro in wrappings
      COMP: Fix warning for InterpolateImageFunction wrapping
      COMP: Add a check for Blocks in GPU module
      COMP: Bump SCIFIO to fix test build warnings
      COMP: Fix wrapping of itkImageFunctionBase

Nick Tustison (7):
      BUG:  Need to explicitly specify spline order.
      ENH:  Initializing the transform center.
      BUG:  Need to check the dynamic cast before any calls.
      ENH:  Adding modifications for point set metrics.
      BUG:  Need to specify TInternalComputationValueType for default metric.
      ENH:  Adding sparse points to B-spline field estimate.
      BUG:  Uninitialized variables.

Richard Beare (1):
      ENH: Include TIFF tags in the MetaDataDictionary

Taylor Braun-Jones (1):
      BUG: Fix SliceBySliceImageFilter doesn't propagate information internally

Umang B (1):
      ENH: Use thread pool to dispatch multithreading tasks

Vivien Delmon (2):
      BUG: ExtractImageFilter::CollapseToSubMatrix fix
      ENH: Add a test on extracted directions in CollapseToSubMatrix mode

Vladimir S. FONOV (1):
      BUG: Fixing incorrect MINC style inverse transform



-----------------------------------------------------
Errors or omissions? Please fix them here:

https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing


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