ITK Release 4.1#

Announcement: ITK 4.1.0 has been released!

We are happy to announce the release of the InsightToolkit 4.1.0! Download links can be found at:

https://itk.org/ITK/resources/software.html

This release is the first since ITK 4.0.0 and includes a number of bug fixes and new features. Related to the transition to Git, it also is the first release to deviate from the even-only minor release number.

Notable changes:

  • A plethora of bug fixes.

  • VTK Bridge support improved ‚Äď currently requires VTK Git master.

  • A number of improvements to the Registrationv4 framework.

  • A new TimeVaryingBSplineVelocityFieldTransform.

  • New Deconvolution filtering module with a number of classes.

  • Performance improvements to the LevelSetsv4 framework.

  • Better WrapITK support.

  • A new video filtering module that includes a method to use standard filters in a video pipeline.

Some performance regressions were identified that were related to the use of GetInput() and GetOutput() in the inner loop of a filter. If you find similar behavior, please report it to the mailing list and issue tracker.

On the compiler front, CLang support continues to improve. Issues have been identified with parallel Visual Studio 10 builds. It appears that Visual Studio 10 has difficulty handling the many projects that result when BUILD_TESTING and BUILD_EXAMPLES are ON. The current workaround is to set

Tools>Options>Projects and Solutions>Build and Run>Maximum number of parallel project builds

to 1 or turn BUILD_TESTING or BUILD_EXAMPLES to OFF.

InsightApplications (from the ITKApps repository) has also seen a number of updates to ITKv4, mostly thanks to the work of Bill Lorenson and Arnaud Gelas. When building InsightApplications, it is recommended to use the ‚Äúsuperbuild‚ÄĚ by pointing CMake to the directory

 InsightApplications-4.1.1/Superbuild

as the target source directory.

New contributors with merged patches include

  • Andriy Kot

  • Felix Morency

In the upcoming 4.2 release, we will actively re-engage the community and will be seeking out new contributors.

Andriy Kot (1):

     ENH: itkMaskFeaturePointSelectionFilter: initial submission

Arnaud Gelas (9):

     DOC: fix doxygen warning
     DOC: Add formula for the curvature term
     DOC: update doxygen configuration file for Doxygen 1.6.1
     ENH: Possibility to provide a propagation image
     PERF: Minor speed improvement in LabelObject / LabelMap
     DOC: fix doxygen warnings
     ENH: Make use of types defined in Histogram to be able to handle 64 bit images
     ENH: Use types from itk::Histogram
     BUG: Lots of classes were undocumented cause of a __itkMacro_h was undefined

Baohua Wu (1):

     ENH: added convergence checking in itkGradientDescentOptimizerv4

Bill Lorensen (6):

     COMP: Unterminated string causes valgrind defect.
     BUG: Wrong size for parameters.
     BUG: Older versions of VTK do not define VTK_LIBRARIES
     BUG: Older version of VTK cannot be used with ITK
     BUG: zlib 1.2.6 API change
     BUG: CPack was not set up propery for ITKv4

Brad King (9):

     ENH: Teach ExternalData to expand DATA{} inside strings
¬†¬†¬†¬†¬†ENH:¬†ExternalData:¬†Add¬†‚Äú-stamp‚Ä̬†suffix¬†to¬†build¬†outputs
     ENH: ExternalData: Add option ExternalData_BINARY_ROOT
     ENH: Teach git-gerrit-(push|merge) to validate topic name
     ENH: Teach git-gerrit-merge to report topic name
     ENH: Simplify local Git hook chaining
     BUG: Fix ITK prepare-commit-msg hook to not erase branch name
     BUG: Fix ITK prepare-commit-msg hook for non-GNU sed
     MetaIO: Always use std:: streams for VTK

Bradley Lowekamp (26):

     COMP: Fixing compilation warning in the thresholding calculators
     DOC: Updated documentation for ThresholdMaximumConnectedComponents
     ENH: Adding support for VectorImages to LabelToRGBImageFilter
     ENH: VectorConnectedComponet filter to work with VectorImages
     BUG: Fixing UpperBoundary parameter in ThresholdMaxCC filter
     BUG: Fix mismatch in internal image types for IsolatedWatershed
     BUG: Some Set by scalar methods were not modifing the time of filter
     ENH: adding support to LabelOverlay for VectorImage output
     ENH: Adding Image::Rebind to support smoothing vector images
     ENH: Adding Image::Rebind to support smoothing vector images
     BUG: VotingBinary could not set output pixels before
     COMP: fix comparison between signed and unsigned with cast
     BUG: Restoring adaptor support to SmoothingRecursiveGaussian
     BUG: corrected libtiff to be confgured for big-endian system
     BUG: Adding tolerance to the VectorThreshold level-set test
     COMP: Address warnings in PreWarpTest
     BUG: Adding tolerance to ThresholdSegmentationLevelSetWhiteMatterTest
     COMP: attributes don't do anything in forward declarations
     COMP: fix warning of signed unsigned comparison
     BUG: Adjust intensity tolerance for SimpleImageRegistrationTest
     COMP: Use SizeValueType for indexing in Neighborhoods
     ENH: adding additional dart metric for image error statistics
     BUG: Corretly choose best baseline for difference image
     COMP: Fix warning in BalloonForceFilte about vd being unintialized
     BUG: prevent divide by zero in computing mean
     BUG: Set the number of components-per-pixel for SeriesReader

Brian Avants (5):

     ENH: adding a multi-start optimizer
     ENH: multi-optimizers w/registration tests
     ENH: fix jacobian wrt params + img-grad reorientation
     ENH: updates for algorithm correctness.
     BUG: cleaning up the tv field registration

Cory Quammen (5):

     STYLE: Fixed typo in test variable name
     COMP: Added undefined type
     ENH: Added Deconvolution module
     ENH: Added linear deconvolution filters
     DOC: Fixed indices in pad image filter diagrams

David Doria (1):

     DOC: Add Doxygen comments to some functions.

Félix C. Morency (1):

     ENH: Added itkVTKImageToImageFilter and Python wrapper to VtkGlue

Gang Song (3):

     BUG: return false if dividing by zero in ANTS CC
     ENH: Clean up the Normalized Cross Correlation in Metricv4
     ENH: add test for validating image gradients in metricv4

Ga√ętan Lehmann (9):

     ENH: Add required named inputs managements in ProcessObject
     BUG: fix module name in module2module.py
     ENH: add wrapping backward compatibility macros
     STYLE: fix InitializationBiasedParticleSwarmOptimizer doxygen name
     BUG: fix WRAP_ITK_INSTALL_PREFIX content
     BUG: remove SwigPyIterator/PySwigIterator
     COMP: global Clone() architecture compatible with java
     BUG: *InDoxygenGroup tests should be ignored by valgrind
     COMP: fix missing vtkImagingPythonD lib link

Hans Johnson (13):

     PERF: Updated lbfgsb to fix bug
     COMP: Be compliant with ANSI standard
     COMP: Removed clang compiler warnings.
     BUG: Remove uninitialized memory print.
     BUG: Virtual was missing on derived class
     COMP: Removed HDF5 unused types.
     COMP: Improve coverage of Kernel
     BUG: 32bit windows bug introduced
     DOC: Fixed documentation to match code behavior
     DOC:  Fixed minor documentation issues
     BUG: Added test to expose overlooked bug
     BUG: Propogated bug from ITKv3 Optimized BSplines
     COMP:  Mismatch array length traversal

ITK Migration V4 (3):

     DOC: Modify BinaryMorphologicalOpeningImageFilter comments.
     DOC: Modify ScalarImageToTextureFeaturesFilter comments.
     DOC: Modify IntensityWindowingImageFilter comments.

Kent Williams (3):

     COMP: cleanup based on CLang warnings
     COMP: Disable GNU extensions for CLang++
     ENH: Add Clone Method to transform hierarchy.

Luis Ibanez (1):

     ENH: Scripts to generate Git Statistics.

Marius Staring (1):

     PERF: Switched order of if-statement and for-loop in DetermineRegionOfSupport

Matthew McCormick (16):

     ENH: Bump CMakeLists.txt version to 4.1.0.
     DOC: Fix log_{10} e doxygen LaTeX formula.
     PERF: Thread Whitaker level set ComputeIteration.
     BUG: LevelSetDenseImage test recognize zero values.
     COMP: Fixing missing include in itkMaskFeaturePointSelectionFilter.
     BUG: Only add MRC to registration factories with ITK_USE_REVIEW ON.
     BUG: Check pthread_create return value.
     PERF: Thread LevelSetEvolution::ComputeIteration for multiple domains.
     ENH: Use compensated summation in  MutualInformationImageToImageMetric.
     STYLE: Fix KWStyle errors.
     BUG: Fix VideoFileReader memory leak.
     DOC: Fix typo in DifferenceImageFilter migration guide.
     COMP: Fix HDF5 build with Windows NMake JOM generator.
     BUG: Remove CTEST_MEMORYCHECK_SUPPRESSIONS_FILE from CTestCustom.cmake.in
     BUG: Add TimeVaryingBSplineVelocityFieldTransform to wrapping exclusion.
     COMP: Warn about VisualStudio parallel build issues.

Michael Stauffer (21):

     ENH: Add itkCompensatedSummationTest2
     BUG: Fix the mapping of sampled points in ImageToImageMetricv4.
     BUG: Fix itkCompensatedSummationTest2
     ENH: Add MattesMutualImageToImageMetricv4
     ENH: Add options for scales & learning rate estimation behavior
     BUG: Fix sampled point list creation in ImageToImageMetricv4
     BUG: Metricsv4: set default metric value to max
     PERF: itkTimeVaryingBSplineVelocityFieldImageRegistrationTest duration
     COMP: Fix warnings
     BUG: Remove zero-point assert in JointHistorgram metricv4
     BUG: Address valgrind errors in V4 registration framework.
     BUG: ANTSNeigh metric - check valid point & test non-overlapping
     BUG: MattesMutual v4 metric bug in number of points
     PERF: TimeVaryingVelocityField - Shorten test time
     BUG: Add debug info to SimpleImageRegistrationTest
     BUG: SimpleImageRegistrationTest - remove versions 2 & 3
     BUG: itkSimpleImageRegistrationTest - more debug changes
     BUG: itkSimpleImageRegistrationTest - still more debug changes
     BUG: ImageToImageMetricv4 - concept check for integer image
     BUG: Rename and fix v4 Demons metric to MeansSquares
     BUG: yet still more debugging for itkSimpleImageRegistrationTest

Nick Tustison (5):

     ENH:  Adding time-varying B-spline transform.
     ENH:  Adding SyN registration method.
     BUG: Assignment ordering was not correct.
     ENH:  Adding gaussian interpolators.
     BUG:  array subscript is out of bounds.

Richard Beare (2):

     ENH: Masking option for histogram thresholding
     BUG: Errors from dashboard

Sean McBride (1):

     BUG: disabled use of undefined signed overflow in nrrd test

Xiaoxiao Liu (2):

     ENH: Add a video filtering module.
     BUG: Fix OpenCVVideoIOTest windows compiling errors.