ITK/Release 4.3 Changed From Previous

Andreas Schuh (1):

     DOC: Modify BSplineDeformableTransform comments.

Andriy Kot (1):

     ENH: Main filter for A2D2 PBNRR.

Arnaud Gelas (10):

     PERF: couple of performance improvements useful for mesh processing
     PERF: Minor performance improvement in KernelTransform
     BUG: Fix errors on MS Visual
     COMP: missing includes in itkVectorImageToImageMetricTraitsv4.h
     ENH: Add tests for iterator indices
     COMP: fix doxgen warnings
     COMP: fix warning about uninitialized value
     COMP: Fix compilation error (missing include).
     COMP: fix clang warning about unused parameter
     STYLE: Make CopyMeshToMesh a function just like the other Copy Container ones.

Baohua Wu (2):

     BUG: fixed a few bugs related to GPU Demons
     ENH: added suport for buffered region in GPU image

Bill Lorensen (11):

     COMP: Macro definition of None in X11 breaks enum
     BUG: ThirdParty should not depend on ITK
     ENH: Utility to find modules needed by an ITK app
     COMP: Incorrect test signature
     BUG: GDCMImageIO ignores ImagePositionPatient
     STYLE: Fix according to KWstyle
     BUG: DCMTKImageIOFactory has wrong class name
     COMP: Remove DCMTK from default modules
     COMP: add set methods for member variables where missing.
     BUG: Cannot read a 2 channel (gray, alpha) png file correctly
     COMP: Revert recent change to iterator that fails to compile

Brad King (11):

     MetaIO: Avoid NULL dereference in MetaOutput::GetUsername
     KWSys: Fix SystemInformation declaration order
     ENH: Allow ITK modules to export custom information
     ENH: ExternalData: Fix typo in unknown action error message
     COMP: Make module header tests depend on module libraries
     COMP: Make module header tests depend on module libraries
     STYLE: Replace write_file() with file(WRITE) and file(APPEND)
     STYLE: Replace make_directory() with file(MAKE_DIRECTORY)
     STYLE: Replace install_(files|programs|targets) with install command
     STYLE: Replace remove() with list(REMOVE_ITEM)
     STYLE: Remove unsed vxl source directory

Bradley Lowekamp (47):

     COMP: fixing error when instatiated with image of double
     COMP: fixing error when instatiated with image of double
     PERF: remove per sample allocation, use per-thread structure
     BUG: prevent static initialization fiasco during factory registration
     PERF: Avoid memcpy call per component for Nift
     BUG: Correct for divide by zero when first bin has zero frequency
     PERF: add alignment data attribute to per-thread structure
     BUG: fix writing a corrupt meta image header from unknow metadata
     PERF: remove per sample allocation, use per-thread structure
     BUG: prevent static initialization fiasco during factory registration
     BUG: fix writing a corrupt meta image header from unknow metadata
     BUG: fix for overlay functor for llvm optimization bug
     ENH: adding support for VectorImage output in LabelMapCountorOverlay
     BUG: Fix segfault when no inital means were set.
     BUG: verify sigma is a positive number for Recursive Gaussian
     COMP: fix exception specification warning
     BUG: Restore automatic loading of factories in ITK_AUTOLOAD_PATH
     BUG: Avoid warning by using ProcessObject::GetInput method
     COMP: add missing functional header for logic ops tests
     BUG: The incorrect auto_load path was specified in itkIOPluginTest
     BUG: Use path to configure NrrdIO.h for installation
     PERF: Replacing iterator copy with optimized ImageAgotithm::Copy
     BUG: Prevent segfault when logger not set for PatchedBasedDenoising
     BUG: Update uncrustify configuration with space before access spec
     ENH: Enabling support for system lib versions prior to TIFF 4.0.0
     STYLE: Fixed numerous style error in PatchBased denoising
     BUG: Internal factory must use RegisterFactoryInternal method
     BUG: Fix Wrapping FFTWComplexToComplex
     ENH: updating to libtif 4.0.3
     BUG: Fix compilation ofswig external project
     BUG: Fix segfault from integer overflow in NIFTI reader
     BUG: disable wrapping of Toboggan filter for win 64
     ENH: adding support for VectorImage to JoinSeries filter
     ENH: support for VectorImage output to GradientRecursiveGaussian
     BUG: Correcting wrapping CMakeList.txt for DCMTK
     ENH: Improve MRCImageIO support for VectorImages
     COMP: Adding Valgrind suppression for NRRD IO on RH6
     ENH: Convert the Modulus filter to standard binary filter
     BUG: unset environmental default number of threads
     COMP: Adding valgrid suppression file for RHEL6
     BUG: Remove NiftiBigIO Test add MEMORY_SIZE test lock
     COMP: Fix WrapITK warning in DCMTK
     BUG: Append FFTW dirs to ITK's in ITKConfig
     COMP: Fix link error with visibility-inlines-hidden
     BUG: ShrinkImageFilter marked as modified in SetShrinkFactor
     BUG: Prevent modulus by zero is Modulus functor
     BUG: Enable the rehash method to re-register internal factories.

Brian Avants (2):

     COMP: The + operation was not registering on Win7-vc10-vce32rel
     BUG: InputImageDimension should be OutputImageDimension

Brian Helba (1):

     ENH: Update Remote/LesionSizingToolkit to newer commit

Cory Quammen (5):

     BUG: Added missing include <algorithm>
     BUG: Added missing include <algorithm>
     BUG: Propagate the spacing and meta-data in FFTWForwardFFT fitler.
     BUG: Added locking around fftw_destroy_plan
     DOC: Modify PasteImageFilter comments.

David Doria (6):

     ENH: Add a SetRegion function to all ImageIterators.
     ENH: Add SetRegion function to NeighborhoodIterators.
     ENH: Allow the ShapedNeighborhoodIterators to use SetRegion.
     COMP: Replace stdlib.h with cstdlib.
     STYLE: Replace dash character in comment.
     STYLE: Replace C Library headers with c[headername]

Dirk Padfield (3):

     PERF: Faster distance computation and fixed reflective iterator bug
     BUG: Corrected bug in SignedDanielssonDistanceMap and added regression tests.
     ENH: Templated MaskedFFTNormalizedCorr. over MaskType (#ITK-2940)

Fotis Drakopoulos (1):

     BUG: Variance and structure tensor fix

Gang Song (2):

     ENH: Add sparse threader for ANTS CC metric
     COMP: Remove deque header from metric class header

Gordon Kindlmann (5):

     ENH: updating ITK's NrrdIO to reflect state of Teem's NrrdIO, take 4
     ENH: re-enabling warnings for NrrdIO
     ENH: warning about idxIn in reorder.c; no trailing whitespace
     ENH: still trying to quash warning about idxIn in reorder.c
     BUG: tracking changes (hopefully the last) in Teem prior to its 1.11 release

Hans Johnson (35):

     ENH: Bump version to 4.3.0
     BUG: Test harness gave false positives
     BUG: Remove duplicate file in wrong place
     ENH: Allow removal of all Deprecated code
     COMP: Remove unnecessary const_cast.
     STYLE: Remove all references to StartRegistation
     BUG: Array overrun in LaplacianRecursiveGaussian
     COMP: Revert use of itkLegacyMacro
     ENH: Improve testing of GetInverse
     PERF:  Const correct optimize initialization.
     COMP: Fix data type for consistency
     ENH: Imaging data should not be in git
     BUG: Missing DisplacementFieldTransform IO
     COMP: Fix warning for propogating success status
     BUG: Make IsTransformQueueEmpty const
     STYLE: Convert CMake-language commands lower case
     STYLE: Remove CMake-language block-end arguments
     BUG: Reading composite transform error
     ENH: Update compiler fixes for fftw external
     BUG: Test harness gave false positives
     BUG: Remove duplicate file in wrong place
     COMP: Remove unnecessary const_cast.
     COMP: Unused variable warning with FFTW options
     ENH: Test always uncondintionally returned true
     STYLE: Add more files that need to be ignored
     STYLE: Fix typo in comment.
     PERF: Avoid costly redundant computations.
     BUG: Removed too stringent ConceptChecking
     PERF: Remove unnecessary function GetImageDimension
     STYLE: Remove dead code ITK_TEMPLATE_EXPLICIT
     STYLE: Made use of .hxx guards consistent
     DOC: Update space before access specification
     BUG: Allow backwards compatibilty for ITK_TEMPLATE_TXX
     STYLE: Make round consistent in ITK.
     BUG: Incorrect syntax for Intel optimize pragma

Ho Cheung (6):

     COMP: Add "#include <functional>" to classes for VS2012
     PERF: Fix usage of ElementAt in PolyLineParametricPath to use const version
     COMP: Add "#include <functional>" to classes for VS2012
     PERF: Fix usage of ElementAt in PolyLineParametricPath to use const version
     BUG: Make LaplRecurGauss filter set the number of threads on the subfilters
     COMP: Fix regression of name mangling for libtiff

ITK Migration V4 (3):

     DOC: Modify ComposeImageFilter comments.
     DOC: Modify VectorIndexSelectionCastImageFilter comments.
     DOC: Modify AnisotropicDiffusionFunction comments.

Jean-Christophe Fillion-Robin (2):

     BUG: Prevent MetaIO vessel tube from getting stuck in while loop
     BUG: Add test for MetaIO vessel tube from getting stuck in while loop

Jeffrey Duda (1):

     ENH: Updates for multivariate metrics

Kent Williams (18):

     PERF: Pull expensive GetInput/GetOutput calls out of inner loops
     COMP: propogate compiler selection & flags to FFTW build
     STYLE: Remove superfluous static_cast
     PERF: Pull expensive GetInput/GetOutput calls out of inner loops
     STYLE: Refine usage of static_cast
     BUG: B.Lowenkamp's changes to detect empty fields in Meta files
     BUG: isblank is missing on Microsoft Visual Studio.
     COMP: propogate compiler selection & flags to FFTW build
     BUG: Added test to verify metadata gets copied on file write w/Nrrd
     BUG: Add regression test to try very long filename w/MetaIO
     ENH: Allow change of tolerance in ImageToImageFilter
     DOC: Document spacing/direction tolerance access methods.
     BUG: Orientation vector in FiniteCylinderFunction
     PERF: hoist computation of norm outside Evaluate method.
     ENH: Add DCMTKImageIO to ITK
     BUG: Origin was lost reading HDF5 format images.
     COMP: add new gdcm test for SeriesReader + MetaDataDictionary
     COMP: add set methods for member variables where missing.

Kris Zygmunt (6):

     PERF: Optimize patch-based denoiser tensor computations
     BUG: GPU tests sometimes fails
     BUG: GPU tests sometimes fails
     BUG: SymmetricEigenAnalysis OrderByMagnitude bug
     PERF: speed up patch-based denoising tests
     BUG: Denoising 3D patch weights incorrect

Luis Ibanez (1):

     BUG: MetaImage data file was missing path.

Marius Staring (1):

     ENH: Creating a typedef for the modified time

Matthew McCormick (65):

     ENH: Allow custom name for ProcessObject Primary Input/Output.
     DOC: Clarify ProcessObject NumberOfRequiredInputs.
     STYLE: Fix style in itkBlockMatchingImageFilterTest.
     BUG: Fix BlockMatchingImageFilter for pipeline updating.
     DOC: Use one column in the Doxygen alphabetical class index.
     BUG: Fix GCC_XML and SWIG ExternalProject dependencies.
     BUG: Fix GCC_XML and SWIG ExternalProject dependencies.
     BUG: Fix multi-object MetaIO reading for ASCII MetaVesselTube.
     STYLE: Improve readability and debugability in MetaScene.
     BUG: Fix multi-object MetaIO reading for ASCII MetaVesselTube.
     COMP: Fix QuadEdgeMesh doxygen warnings.
     ENH: Wrap new exponential Transform classes.
     STYLE: Use typedefs in TreeNode.
     STYLE: Use more descriptive names in itkSceneSpatialObject.hxx.
     STYLE: Cleanup WrapITK comments.
     BUG: Fix WrapITK GCCXML ExternalProject dependency.
     COMP: Make sure the VC script gets executed after gccxml installation.
     ENH: Use tarball for gccxml ExternalProject build.
     PERF: Use GetPrimaryOutput in ImageSource GetOutput.
     COMP: Add missing deque header for ANTSNeighborhoodCorrelation metric.
     BUG: Fix WrapITK GCCXML ExternalProject dependency.
     COMP: Make sure the VC script gets executed after gccxml installation.
     BUG: Fix multi-object MetaIO reading for ASCII MetaVesselTube.
     ENH: Bump release branch CMakeLists.txt version to 4.2.1.
     DOC: Update Doxygen config's for 1.8.2.
     DOC: Remove out-of-date files in Documentation/
     STYLE: Use EXIT_SUCCESS in itkQuadEdgeMeshPolygonCellTest.
     DOC: Improve Doxygen HTML layout.
     STYLE: Improve style in itkGaussianImageSourceTest.
     COMP: GaussianImageSource unsigned comparison always false.
     BUG: Fix VelocityFieldTransform classes wrapping.
     ENH: Support Vector scalar product with CovariantVector.
     MetaIO: Remove the executable bit from metaFEMObject.{h,cxx}.
     MetaIO: Fix invalid memory dereference with empty Meta field.
     COMP: Fix invalid unsigned comparison with 1D instantiation.
     ENH: Archive testing data in Midas.
     BUG: FixedArray wrapping for 4D wrapping.
     ENH: Add operator=( FloatType & rhs ) to CompensatedSummation.
     BUG: Improve robustness of RayCastInterpolateImageFunction.
     BUG: VTKPolyDataMeshIO for Meshes with Tensor Pixels. #2961
     COMP: Do not wrap WatershedImageFilter on Windows.
     BUG: Set the third-party libtiff VERSION to the correct value.
     COMP: Build with ITK_USE_SYSTEM_TIFF. #2967
     COMP: Fix wrapping of itkNarrowBandCurvesLevelSetImageFilter. #2970.
     COMP: Do not run itkSampleToHistogramFilterTest4 with VC.
     COMP: Fix 1D wrapping of itkImageToVTKImageFilter.
     MetaIO: Prevent vessel tube from getting stuck in while loop
     MetaIO: Fix error in metaVesselTube ASCII reader.
     COMP: Disable DCMTK for MinGW.
     COMP: Ignore DCMTK build warnings.
     BUG: Use HTTP protocol by default for Git pull URLs.
     COMP: Better identification of MSVC90.
     STYLE: Fix style of BorderQuadEdgeMeshFilter.
     STYLE: Fix style of CleanQuadEdgeMeshFilter.
     STYLE: Rename itkMultiTransformBase to itkMultiTransform.
     COMP: Wrap MultiTransform.
     STYLE: Fix style in MultiTransform.
     COMP: Disabling the VideoStreamTest.
     COMP: Suppress fftw ExternalProject warnings.
     COMP: LabelImageInterpolateImageFunctionTest type conversion.
     COMP: Add include directory for ITK_USE_SYSTEM_HDF5.
     COMP: itkLabelImageGaussianInterpolateImageFunctionTest signed unsigned.
     COMP: Fix Doxygen warnings.
     COMP: Ignore libtool FFTW warnings with quote.
     COMP: Fix HDF5IO with ITK_USE_64BITS_IDS on Windows.

Matthias Seise (2):

     COMP: Compile wrapITK for python2.7,64bit on windows
     COMP: Compile wrapITK for python2.7,64bit on windows

Michael Stauffer (6):

     PERF: Optimize GetValue in v4 image metrics.
     ENH: Add "WithOnlyIndex" iterators.
     PERF: improve speed of ImageToImageMetricv4 and derived metrics
     ENH: Add parameter weighting option to Optimizersv4
     ENH: Add MultiTransformBase
     DOC: Fix to ObjectToObjectOptimizerBase documentation

Nick Tustison (20):

     ENH: Expanding HasLocalSupport to transform categories.
     ENH:  Adding ability to prepend transform queue.
     ENH: Adding labeled point set metric.
     ENH:  Add GetTransformCategory() to translation transform.
     ENH: Adding exponential transforms.
     ENH:  Adding common transforms to be registered.
     BUG:  Voxel size scaling needed
     ENH:  Enable inverse for exponential transforms.
     ENH:  BSpline automated scales estimation.
     BUG: Fix resampling of constant velocity field.
     BUG:  Uninitialized variable.
     ENH:  Reorganization of vel. field transforms.
     BUG:  Control point grid origin wasn't set correctly.
     ENH:  Adding option to permit voxel-based smoothing.
     ENH:  Adding Multiple label STAPLE.
     BUG:  Disp. field xfrm inverse not set correctly.
     ENH: Multiple metrics in registration methods.
     BUG:  Incomplete dynamic casting.
     BUG: Correcting valgrind error.
     BUG:  Set correct images in update field.

Paul Novotny (1):

     COMP: Fix Spatial Object Test Segfaults

Richard Beare (1):

     ENH: Functors for logic operations

Willi Huber (2):

     COMP: WrapITK generates non-unique typedefs in FFT submodule
     COMP: Fix the wrapping for some modules

Xiaoxiao Liu (3):

     ENH: Update LSTK version.
     BUG: Update LSTK version to sync with VTK 6.0.
     BUG: Fix ffmpeg VideoStream failing tests.