ITK/Release 4.4 Changed From Previous

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Changes in ITK from v4.3.0 to v4.4.0 from the Git log:

Ali Ghayoor (7):

       ENH: Get the internal transforms of SyN registration filter
       COMP: Fix all valid cppcheck warnings in "Module/Filtering" directory
       COMP: Fix all valid cppcheck warnings in "Module/Core" directory
       COMP: Fix all valid cppcheck warnings in "Module/Segmentation" directory
       COMP: Fix all valid cppcheck warnings in "Module/Registration" directory
       COMP: Fix all valid cppcheck warnings in ITK (last patch)
       COMP: Fix all valid cppcheck warnings in "ITK/Module" directory

Arnaud Gelas (4):

       PERF: improve performance of couple of methods of itk::QuadEdgeMesh
       PERF: couple of speed up improvements for QuadEdgeMesh processing
       PERF: avoid doing GetPoint and SetPoint for the same point
       ENH: Simplify template parameters in itk::PointsLocator

Bill Lorensen (20):

       ENH: Prevent duplicate loading of dynamic libraries
       COMP: Fix compile error in PhilipsRECImageIO
       COMP: Fix compile error in PhilipsRECImageIO
       BUG: Memory leak after failed RegisterFactory
       BUG: Warn on directories
       ENH: Refactor DoubleToString into NumberToString
       DOC: Escape hash in comment
       STYLE: Apply kwstyle to Modules/Core tests
       STYLE: Apply kwstyle to Modules/Filtering tests
       STYLE: Apply kwstyle to Modules/Segmentation tests
       STYLE: Apply kwstyle to Modules/IO tests
       STYLE: Apply kwstyle to Modules/Numerics tests
       STYLE: Apply kwstyle to Modules/Registration tests
       STYLE: Apply kwstyle to some tests
       BUG: Memory leak after failed RegisterFactory
       COMP: Remove copy_n wrapper for standard std::copy
       COMP: Make the test stable by removing random source
       COMP: More baselines
       COMP: Another baseline
       COMP: Missing return error after exception

Brad King (14):

       BUG: ExternalData: Do not match directory names when resolving DATA{}
       STYLE: ExternalData: Cleanup stray TODO and typo in comments
       STYLE: ExternalData: Remove unused private interface
       ENH: ExternalData: Improve series matching using an explicit syntax
       ENH: ExternalData: Allow ()-groups in series match regex
       ENH: ExternalData: Allow DATA{} syntax to reference directories
       ENH: Configure new ExternalData series parsing for ITK baselines
       BUG: ExternalData: Collapse ../ components in DATA{} paths
       BUG: Fix "git gerrit-push" for content links with spaces
       STYLE: Add detail to the vxl update instructions
       STYLE: Add more detail to the vxl update instructions
       ENH: ExternalData: Partly generalize hash algo/ext handling
       ENH: ExternalData: Attach download rules to content links in IDEs
       ENH: ExternalData: Preserve escaped semicolons during argument expansion

Bradley Lowekamp (78):

       STYLE: Use ITK_ prefix for FFTW cmake variables and defines
       BUG: Change default boundary condition to ZeroFlux
       ENH: wrapping itkImageSeriesWriter
       BUG: incorrect CMake variable for system jpeg include
       DOC: Correct description of Bitwise binary filters
       BUG: incorrect CMake variable for system jpeg include
       COMP: GetTimeVaryingVelocityField methods did not compile
       ENH: Creating templateless region splitter classes
       ENH: Adding image region splitter for separable filtering
       PERF: Do not spawn threads that will not be used.
       ENH: ImageIO's now use ImageRegionSplitter base
       COMP: Specify export for Specialized Array output operators
       ENH: making old ImageRegionSplitter compatible with new splitter
       BUG: initials Direction IVAR
       STYLE: never a space before;
       COMP: Address unused parameter warning in GPU code
       BUG: Do not create static initialized ITK objects
       ENH: Converted Multidimensional splitter to new base class
       ENH: moving old ImageRegionSplitter to Deprecated Module
       BUG: Only thread 0 should report progress.
       PERF: Use std::fill for image filling
       BUG: Only thread 0 should report progress in LabelMapFilters
       COMP: Adding missing header
       BUG: Using CMake variable in external builds with autoconf environment
       BUG: initialize InverseCovariance size with degenerate matrix
       ENH: Adding numeric_traits specializations for "long long"
       ENH: instantiate vnl types with "long long" on all platforms
       Revert "ENH: Use named inputs in BinaryReconstruction filters."
       BUG: initialize InverseCovariance size with degenerate matrix
       BUG: Using CMake variable in external builds with autoconf environment
       COMP: Address unused parameter warning in GPU code
       BUG: Only thread 0 should report progress in LabelMapFilters
       BUG: Only thread 0 should report progress.
       COMP: Adding missing header
       ENH: Adding support for instantiating long long pixel types
       BUG: VerifyPreconditions checks required named inputs
       PERF: Adding performance oriented ScanlineIterator
       COMP: Remove copy_n wrapper for standard std::copy
       COMP: Missing ProgressReporter header
       COMP: Suppress linker warning from fftw external project
       COMP: Add missing ImageRegionIterator header in test
       BUG: Don't allocate empty names in Get I/O Names methods
       COMP: Make GPUFunctorBase destructor virtual
       PERF: Changing filters to use ImageScanlineInterator
       COMP: GCC_XML external project does not use BUILD_EXAMPLES
       BUG: Scanline iterator in STAPLE filter not advanced to next line
       PERF: Use ImageScanlineIterator in ImageAlgorithm::Copy
       PERF: Use iterators into name map for index inputs
       ENH: index can be associated with required input
       PERF: Add global variable of index names in ProcessObject
       COMP: fix unused result warning in ProcessObject
       ENH: Remove names inputs specialized comparison
       DOC: Updated input methods doxygen
       PERF: Use ImageAlgorithm::Copy in JoinSeries filter
       PERF: Change default index i/o prefix to just "_"
       PERF: Use ImageAlgorithm::Copy in CastImageFilter
       COMP: Fix failing implicit conversion from NULL
       BUG: restore gnu aligned attribute
       PERF: ImageAlgorithm::copy to use std::copy for conversion
       PERF: Store indexed outputs in array for constant time access
       COMP: GCC_XML compilation error with type_traits
       BUG: Add unsigned int concept check to LabelVoting filter
       COMP: Disable conversion warning for std::copy in ImageAlgorithm
       BUG: Use correct types for TIFF Tags and buff math
       BUG: Use local var for TIFF va_list parameter
       BUG: Use correct bytes for BigEndian magic number
       COMP: Fix int to char narrowing error and warning
       COMP: Fix int to char narrowing error and warning
       COMP: Fix scanf conversion specification to %u
       COMP: Fix scanf conversion specification for id types
       BUG: Remove extraneous print statement in tiffio
       BUG: Incorrect va_arg type used in TIFF and LSM
       BUG: JPEG2000 bool type in C is now unsigned char
       BUG: add a test to demonstrate ThreadedIteratorPartitioner bug
       BUG: Fix written other magic number in FreeSurferBinaryMeshIO
       COMP: Fix assert in LSM, = in err of ==
       BUG: IteratorPartitioner extra thread don't advance
       BUG: C++ bool is 4 bytes on osx ppc

Brian Helba (11):

       STYLE: Ensure documentation \author tags are parsed
       STYLE: Remove unnecessary overloads in favor of implicit conversion
       PERF: Replace deep copy with const const signature
       ENH: Re-enable LoadPrivateTags option in GDCMImageIO
       STYLE: Slightly refactor ImageFileWriter::Write to simplify logic
       ENH: Always enable Get*FromTag methods in GDCMImageIO
       DOC: Fix misspelling in MorphologyImageFilter
       DOC: Fix misspelling in ObjectMorphologyImageFilter
       STYLE: Remove unnecessary function call in GDCMImageIO
       STYLE: Remove calls to deprecated functionality from DICOM Examples / Tests
       ENH: Allow Get*FromTag to accept uppercase hex

Cory Quammen (1):

       COMP: Bumped up minimum required CMake version

Cyrille Faucheux (2):

       ENH: allow the ClampImageFilter to use user-defined bounds (#3016).
       ENH: Move the ClampImageFilter to the ImageIntensity module (#3016).

David Cole (4):

       BUG: Avoid using def file when BUILD_SHARED_LIBS is off
       BUG: Do not undefine _WIN32_WINNT
       BUG: Avoid using def file when BUILD_SHARED_LIBS is off
       BUG: Do not undefine _WIN32_WINNT

David Fuentes (2):

       ENH: Allow block matching on diff size images
       ENH: wrapping itkMaskFeaturePointSelectionFilter itkBlockMatchingImageFilter

Dirk Padfield (6):

       BUG: CSVFileReader was reading all values as NaN
       DOC: Made AnisotropicDiffusion documentation consistent with code
       ENH: Enable MetaIO to read filenames with spaces using regex
       BUG: CSVFileReader was reading all values as NaN
       ENH: Added m_RequiredFractionOfOverlappingPixels to MaskedFFTNCC
       BUG: SignedMaurerDistanceMap in 4D

Google double-conversion Maintainers (1):

       Google double-conversion (reduced)

Hans Johnson (21):

       COMP: Remove unnecessary BORLAND code
       COMP: Make type conversions explicit/consistent
       PERF: Optimize loop index computations
       COMP: Remove unnecessary BORLAND code
       COMP: Incomplete variable name change.
       COMP: Incorrect warning presented for cppcheck
       STYLE: The FFTW libs should be co-located with ITK
       COMP: Fix robustness of DCMTK internal builds
       ENH: Get function accessible from const objects
       COMP: Missing patch for ITK_FUTURE_LEGACY_REMOVE
       STYLE: Reduce redundant code identified by cpd
       BUG: Return a modifiable object or provide const
       STYLE: Improve SoftwareGuide documentation
       COMP: Type mis-match for comparison operator
       STYLE: Enforce using ITK macros when available
       COMP: Type mis-match for comparison operator
       BUG: ITK_FUTURE_LEGACY_REMOVE must cmake configured
       BUG: Expose BSplineInterpolateImageFunction test
       COMP: Linkage ITK_ABI_EXPORT to ITKCommon_EXPORT
       BUG: itk_tiff.h should not be in itkTIFFImageIO.h
       DOC: Fix line length issues for the SoftwareGuide

Ho Cheung (7):

       BUG: GradientVectorFlow should calculate timestep based on image dimension
       STYLE: GradientVectorFlow - Add const correctness
       STYLE: GradientVectorFlow
       PERF: GradientVectorFlow - Remove redundant initializations
       BUG: itkPolyLineParametricPath infinite loop for degenerate paths
       BUG: Fix ITK Path test failures
       BUG: ITK unable to detect number of threads under Unix in recent glibc.

ITK Migration V4 (4):

       DOC: Modify ContourMeanDistanceImageFilter comments.
       DOC: Modify MattesMutualInformationImageToImageMetric comments.
       DOC: Modify MaskImageFilter comments.
       DOC: Modify BSplineTransformInitializer comments.

Jan Margeta (1):

       COMP: Added missing header <functional> in itkAnchorCloseImageFilter.h

Julien Finet (2):

       ENH: Add unit test to itkThresholdImageFilterTest
       ENH: Add MaskingValue to MaskImageFilter

Julien Malik (2):

       BUG: Remove itkLoad definition in JPEG2000ImageIOFactory
       ENH: Add missing NumericTraits for complex

Julien Michel (2):

       BUG: Fix InverseDisplacementFieldImageFilter bug
       BUG: Fix InverseDisplacementFieldImageFilter bug

Kent Williams (21):

       COMP: Turn on -fpic in options for DCMTK External Project
       BUG: using InputPixelType to hold label count can overflow.
       COMP: Update DCMTK version to incorporate new fixes.
       COMP: Use portable method to find source dir & find DCMTK headers
       COMP: Start using ITKConsortium github to retrieve DCMTK.
       BUG: Regressions with respect to building DCMTK
       COMP: Added patch from Dirk Padfield
       ENH: use find_package(DCMTK NO_MODULE)
       ENH: Add double-conversion library for precise Float output
       COMP: replace in-line access methods with itk Macros
       COMP: The install path for DoubleConversion lib was wrong.
       COMP: removed warnings on Windows due to generic vs excp obj throw.
       COMP: check for this == &rhs as much as possible.
       COMP: Replace memcpy with std::copy in ImportImageContainer.
       COMP: Replace memcpy calls with std::copy
       COMP: Further changes to the use of std::copy_n
       COMP: Add preprocessor symbols to double-conversion for OS X PPC
       COMP: Add DoubleConversion merge from upstream documentation
       BUG: Return of NaN by DiffusionTensor3D::GetFractionalAnisotropy
       BUG: Dicom method for Dir Cosines made non-orthogonal directions
       COMP: Install openjpgDllConfig.h

Kris Zygmunt (1):

       PERF: Provide better default config for patch-based denoiser

Luis Ibanez (1):

       ENH: Maurer for Danielsson in Surface Distance.

Manuel Grizonnet (4):

       BUG: Inconsistency detected by ld.so due to static const string
       BUG: Inconsistency detected by ld.so due to static const string
       BUG: Inconsistency detected by ld.so due to static const string
       BUG: Inconsistency detected by ld.so due to static const string

Marco Feuerstein (1):

       ENH: JPEG IO now writes and reads spacing, similar to the TIFF IO (ITK-3023)

Marius Staring (3):

       ENH: expose parameter in Bilateral filter
       PERF: Replace fill and copy with std alternatives
       BUG: B-spline interpolator should use direction

Mark Hiner (1):

       ENH: Add SCIFIOImageIO.

Matthew McCormick (47):

       COMP: Fix wrapping configuration warnings about itkMeshBase, etc.
       COMP: Fix HDF5 unused function for long long on Unix.
       ENH: Bump CMake version numbers to 4.4.0.
       BUG: Remove unused metric test content link.
       COMP: Add DLL to PATH for Python tests on Visual Studio.
       BUG: Do not nullify the DCMTK ExternalProject UPDATE_COMMAND.
       BUG: Fix DCMTK lib_prefix identification.
       COMP: Fix HDF5 unused function for long long on Unix.
       BUG: Remove unused metric test content link.
       COMP: Add DLL to PATH for Python tests on Visual Studio.
       ENH: Bump CMakeLists.txt ITK version to 4.3.1.
       STYLE: Fix errors detected by KWStyleCodeTest.
       COMP: VectorIndexSelectionCastImageFilter extra itk namespace.
       STYLE: Fix alignment in itkMask{Image,Negated}ImageFilter.h
       ENH: Doxygen configuration update to 1.8.3.1.
       BUG: Fix FFTW install paths in ITKConfig.cmake (ITK-2995).
       DOC: Doxygen detection of DirectionTolerance as private.
       ENH: Get Direction and CoordinateTolerance are const methods.
       BUG: Add missing header to the third party TIFF install.
       COMP: More fixes to mesh wrapping warnings.
       BUG: Temporarily disable Python utility tests.
       COMP: Avoid explicit instantiation and specialization for Array.
       ENH: Add utility script to create JRE tarballs.
       ENH: Use named inputs in BinaryReconstruction filters.
       STYLE: Remove redundant itk namespace.
       DOC: CreateTestDriver srcs should have the .cxx extension.
       COMP: Must reinterpret the pointers to match
       COMP: Fix project linking against ITK that does not use VtkGlue.
       COMP: Fix project linking against ITK that does not use VtkGlue.
       BUG: Fix FFTW install paths in ITKConfig.cmake (ITK-2995).
       ENH: Bump version in CMakeLists.txt to 4.3.2.
       DOC: Doxygen expansion of itkGetModifiableObjectMacro.
       ENH: Remove unused wrapping code. ITK-3032.
       ENH: Use named inputs in BinaryReconstruction filters.
       COMP: Distance maps filters cannot wrap 1D.
       DOC: Remove reference to MeanDistanceImageFilter.
       STYLE: Fix KWStyle errors.
       STYLE: Remove entries from the old MINC2ImageIO.
       BUG: Remove MINCIO from the default registered modules.
       BUG: Add EXCLUDE_FROM_ALL to ThirdParty/MINC.
       BUG: Include SCIFIO in the auto-registered factories if the module

is enabled.

       BUG: Visual Studio itkClampImageFilterTest failures.
       STYLE: itkClampImageFilter.hxx in the wrong module.
       COMP: Add _CRT_NO_SECURE_WARNINGS when building GCCXML.
       COMP: Prevent ITK_USE_64BITS_IDS with Wrapping on Windows.
       STYLE: Too many blank lines in itkCastImageFilterTest.cxx.
       COMP: Bump MINC third party to fix warnings.

Nick Tustison (4):

       ENH:  Adding masking capabilities with confidence mask option.
       BUG:  Masks need to be warped.
       ENH:  Permitting access to shrinking per dimension.
       BUG: Valgrind error.

Nicolas Rey (1):

       STYLE: Minor style fixes

Paul Novotny (3):

       COMP: Fix TIFF on big endian systems
       COMP: Build fails with ITK_USE_SYSTEM_TIFF
       COMP: Fix TIFF on big endian systems

Prathamesh Kulkarni (1):

       COMP: QuickViewTest new baseline.

Sean McBride (4):

       STYLE: fixed minor spelling: XCode -> Xcode
       COMP: fixed clang warning about NULL to bool conversion
       BUG: Handle missing Analyze 7.5 flipped directions
       COMP: Handle missing Analyze 7.5 flipped directions

Tim Allman (3):

       DOC: Modify BSplineTransform comments.
       DOC: Modify JointHistogramMutualInformationImageToImageMetricv4 comments.
       DOC: Modify JointHistogramMutualInformationImageToImageMetricv4 comments.

Tom Vercauteren (2):

       COMP: GPUPDEDeformableRegistrationFilter.cl fails to "compile".
       COMP: GPUPDEDeformableRegistrationFilter.cl fails to "compile".

Vladimir S. FONOV (2):

       ENH: Adding libminc and updating MINC IO support.
       BUG: Making 2D Minc IO work properly

Xiaoxiao Liu (2):

       ENH: Sync python scripts with python3.
       ENH: Sync python scripts with python3.

Yan Xu (1):

       COMP: static cast unsigned int to int



Changes in ITKapps from v4.3.0-apps to v4.4.0-apps:

Bill Lorensen (3):

       COMP: VTK6 API change
       ENH: Add TCL Wrapped examples
       BUG: Missing includes for ITK4.4

Hans Johnson (1):

       COMP: Mac 10.8 fixes were incorporated in FLTK

Jamie Snape (1):

       BUG: Propagate build, linker, and OSX settings to external projects

Matt McCormick (6):

       COMP: Re-add the FLTK patch for some Macs.
       BUG: ITK External build only depends on VTK if being built.
       COMP: Update FLTK SVN configuration.
       ENH: Bump VTK ExternalProject to 5.10.1.
       COMP: Use FLTK zip file stored on Midas3.
       ENH: Bump ITK superbuild version to 4.4.0.

Roland Kwitt (1):

       COMP: Shadowing warning in GLSliceView.h

Stephen R. Aylward (1):

       COMP: Fix FLTK build error on Mac/Clang.

Xiaoxiao Liu (1):

       ENH: Print out accurate image IO error message.