ENH: Update to ITKv4.8rc2

$ git shortlog 38398fb..650d169 --no-merges

Alexander Hewer (1):
COMP: fixed error "Dunno about this gcc" for gcc 5.1

Arnaud Gelas (13):
ENH: add MinimalPathExtraction as a remote module
ENH: fix KWStyle errors for SubdivisionQuadEdgeMesh
COMP: fix warning with non default template parameter for OutputImage
COMP: missing ';' in itkSetClampMacro
STYLE: no need to expose internal type
DOC: add explanations about input and out filters
COMP: missing include in IterativeTriangleCellSubdivision
BUG: memory leaks when calling itk::Mesh::Graft
DOC: Improve documentation for ParameterizationQuadEdgeMeshFilter
BUG: not all combinations were actually test
ENH: add an exception in BorderQuadEdgeMeshFilter if no boundaries
COMP: fix CMake warning in ITKModuleHeaderTest
BUG: fix memory leaks in BorderQuadEdgeMeshFilter using itk::AutoPointer

Bill Lorensen (6):
ENH: Update to KWStyle conformant version
ENH: Add interpolate capability
ENH: WikiExamples QuickView Update
COMP: VTK AUTOINIT redefinition warnings
COMP: Compiler hidden visibility on Mac compiler
COMP: EventMacro backward compatibility

Brad King (24):
ENH: ExternalData: Allow local stores without any URL templates
ENH: ExternalData: Warn on missing file instead of failing
ENH: ExternalData: Add support for custom download scripts
ENH: ExternalData: Add support for custom algorithm-to-URL mapping
DOC: ExternalData: Update documentation to match CMake copy
ENH: Teach UpdateThirdPartyFromUpstream to support spaces in path
ENH: Improve UpdateThirdPartyFromUpstream for initial imports
ENH: Require CMake 2.8.9 or greater
ENH: Do not produce ITKGDCM library when using system GDCM
ENH: Drop gdcm source subtree to prepare for fresh import
ENH: Add script to update GDCM from upstream
STYLE: Tell Git not to check whitespace in GDCM
STYLE: Tell Git about larger files in GDCM
COMP: Configure GDCM to build inside ITK
COMP: Fix GDCM to handle older expat library
COMP: Cleanup CMP0022 warnings in GDCM module
COMP: Add missing include in GDCM source
COMP: Teach GDCM to honor ITK_DYNAMIC_LOADING option
ENH: KWSys: Tell Git not to export .gitattributes
COMP: Remove cmake_minimum_required calls from GDCM
COMP: Remove extra CMake policy settings in GDCM
COMP: Use more standard SSE intrinsics in GDCM copy of OpenJPEG
COMP: Fix GDCM std::accumulate initial value type
ENH: Update version of CastXML built for wrapper generation

Bradley Lowekamp (38):
PERF: Use ImageAlgorithm::Copy in ImageSeriesWriter
ENH: Refactor versor to matrix transform code
DOC: Clarify that Scale Skew Versor does addition
BUG: Correct Simularity3D Jacobian
BUG: Ensure OptimizerParameters doesn't leak its helper
PERF: Remove frequent dynamic allocations used with std::vector
BUG: Restore IO support for BSplineDeformableTransform
BUG: Replace std::cout message Warning marco
BUG: Correct ExtractImageFilters Type macro
DOC: Separately document IsNull and IsNotNull
ENH: Modularize KWStyleTests
BUG: Remove ExhaustiveOptimizer ivar which was unused
STYLE: Update IOFDF to address KWStyle issues
BUG: Fix undefined signed integer shift
BUG: Fix IOFDFInDoxygenGroup test
BUG: Update MGHImageIO for header guarder style
BUG: Fix itkFDFImageIOTest link error on windows
STYLE: Update SCIFIO for KWStyke failures
BUG: Use base's NumberOfIterations for stopping condition
PERF: Report progress for linear transform only at scanline completion
BUG: Avoid underflow in gradient range calculation
ENH: Use return by value for ImageAlgorithm::EnlargeRegionOverBox
BUG: No exception for 0 parameter transforms
COMP: Address conversion compilation warning
ENH: Use PrinSelfObjectMacro
BUG: Use module's libraries for linking header test.
ENH: Add export specifications to FFT library
COMP: Address conversion compilation warning
COMP: This patch address linking errors with WrapITK
DOC: Improving documentation for the names inputs of the ProcessObject
BUG: Isolate CannyEdgeDetection's internal filter from external
PERF: Refactor ExpandImageFilter loop
ENH: Add AtmoicInt class, use TimeStamp & LightObject
COMP: Address signed to unsigned comparison warning in AtomicInt Test
ENH: Move IsPrime and GreatestPrimeFactor to compiled cxx file
COMP: Add export missing export specifications
BUG: Fix reading HDF5 images into different dimension.
Revert selection "ENH: Add shared libraries for ITK libraries"

Brian Helba (2):
ENH: Add scripts for automated updating of ThirdParty libraries
ENH: Make Vector construction from scalar value explicit

Christopher Mullins (10):
STYLE: Keep codesnippet lines under 80 characters.
STYLE: Fix Latex blocks in documentation to include newlines.
COMP: Fix clang warnings
DOC: Fix Latex underscore for SoftwareGuide
DOC: Use the dilated version of the FivePoints image
COMP: Use c++11 noexcept declarator.
COMP: Fix override warnings on clang with GPU module and MINC
COMP: Fix clang override warnings for Review module.
COMP: Fix more clang warnings in review module
COMP: Fix more clang override warnings in Review module.

Cyril Mory (3):
BUG: Fixed itkWarpImageFilter wrong result in some cases
ENH: Method to compute InputRequestedRegion in itkWarpImageFilter
ENH: Moved some of itkWarpFilter from private to protected

David Froger (2):
ENH: Check regions in HDF5 streaming test
BUG: Fix HDF5 write streaming test.

Davis Vigneault (5):
STYLE: Minor style and documentation changes to ITK examples.
DOC: Minor changes and clarifications to the registration chapter of Book 2.
STYLE: Minor wording and formatting changes to Software Guide Mesh examples.
COMP: Build failure using EuclideanDistancePointMetric with mismatched meshes.
STYLE: Minor typographical changes in ParameterizationQuadEdgeMeshFilter

Dženan Zukić (3):
ENH: adding reverse iteration test
ENH: using scanline iterator instead of linear iterator
DOC: Improve docs for ConnectedComponentImageFilter

GDCM Upstream (1):
GDCM 2015-04-29 (81e551fc)

Gary JIA (1):
BUG: Fix memory leak at GPUCommon

Gaëtan Lehmann (21):
BUG: fix extra carriage return in python callbacks
ENH: use castxml in wrapping
COMP: almost fix java build
ENH: use modern cmake list operations in wrapping
COMP: hide compiler warnings when building pcre and swig
COMP: fix the IOFDF module name used in wrapping
COMP: fix last python runtime warnings about unknown types
COMP: fix undefined __float128 type with gcc
BUG: reactivate PythonGetNameOfClass and fix the FDFImageIOFactory name
COMP: fix warnings due to double MultipleValuedCostFunction wrapper
BUG: fix ipython custom completion
BUG: fix runtime information for cross correlation filters
ENH: let the user choose the tradeoff between size and speed in fft operations
ENH: update progress in ImageFileReader
ENH: initialize the progress in ImageFileWriter
BUG: fix extra line return in terminal progress display
BUG: fix missing space before "done" in progress display
ENH: pass ActualXDimensionIsOdd through the pipeline
COMP: fixes for SizeGreatestPrimeFactor
ENH: Add itkFFTPadImageFilter
ENH: factorize shared code in itk::PadImageFilterBase

Gert Wollny (1):
COMP: defining ITK_USE_FLOAT_SPACE_PRECISION

Hans Johnson (40):
COMP: Add c++11 override designation
COMP: Identify null pointer assignments
STYLE: rm explicit void for parameterless function
STYLE: Use ITK_NULLPTR to utilize c++11 features
BUG: Incorrect addition of ITK_OVERRIDE
COMP: Use STREQUAL instead of MATCH
BUG: return type defaults to zero.
BUG: ImageType, CofficientImageArray types missing
DOC: Invalid doxygen return for void function.
COMP: _Pragma suppress fltpnt equality warnings
COMP: Allow exact floatpnt equality checks.
COMP: Avoid floatpnt equality check
COMP: Floatpnt equality for divisor
COMP: Avoid unnecessary float pnt equality checks.
PERF: Improve perf of ANTSNeighborhoodCorrelation
BUG: Test depending on itkMesh.h in Common
COMP: Make DCMTK header functions const
Revert "COMP: VTK AUTOINIT redefinition warnings"
COMP: VTK and ITK H5 build program collision
COMP: Create out-of-line virtual method defintions
COMP: Create out-of-line virtual method macros
DOC: Clarify strange syntax for itk::MetaEvent
COMP: Fix ENABLE_SHARED variable name
STYLE: Remove outdated cmake version support
STYLE: Move SymmetricEigenAnalysis to Deprecated
COMP: Prefer modern CMake visibility settings
STYLE: Use ITK_NOEXCEPTION macro
ENH: Continue to deprecate ::Zero and ::One
ENH: Avoid need for const_cast, ensure consistency
BUG: Incorrect function signature
COMP: Intel compiler warning suppression
ENH: Add shared libraries for ITK libraries
ENH: Remove unnecessary const_cast
STYLE: Move utility TransformIOHelper to cxx file
BUG: Missing ITKIOMINC_EXPORT on __Private()
STYLE: Fixed AnalyzeObjectMap header guard style.
COMP: Missing exports for templates
ENH: Update MGHIO for consistency with ITK.
BUG: Remove shared specifications from TransformIO
STYLE: Use consistent names in template parameters

Ivan Setiawan (2):
BUG: Fix initial ImageTrueMax to the most negative value.
BUG: Test case to verify fix of ImageTrueMax in MattesMI.

Jan Bergmeier (1):
DOC: Changed indices for steps in ExhaustiveOptimizer.

Jon Haitz Legarreta (9):
ENH: New test for the BinaryStatisticsKeepNObjectsImageFilter
ENH: New test for the itkLabelShapeKeepNObjectsImageFilter
ENH: Add test for itkShapeRelabelImageFilter
ENH: Add test for the itkLabelStatisticsKeepNObjectsImageFilter
ENH: Add test for itkBinaryShapeKeepNObjectsImageFilter
ENH: Add test for itkLabelStatisticsOpeningImageFilter
DOC: Correct documentation typo.
ENH: Increase code coverage for itkCustomColormapFunction
ENH: New test for the itkMetaGaussianConverter

Julien Jomier (1):
BUG: Output pointer origin is not set causing a memory access error.

KWSys Robot (3):
KWSys 2015-04-19 (4f39791b)
KWSys 2015-05-12 (b1d560a0)
KWSys 2015-05-18 (9a6b7c3f)

Kevin H. Hobbs (1):
COMP: new baseline for building against VTK master

Marius Staring (2):
BUG: workaround for 64bit VS2013 Release segfaults
COMP: workaround for 64bit VS2013 Release ICE

Matthew McCormick (142):
ENH: Add BridgeNumPy Remote Module.
COMP: Bump AnalyzeObjectMapIO to fix doxygen warning.
STYLE: Style changes for itkGaussianDerivativeImageFunctionTest.
ENH: Test GaussianDerivativeImageFunction with unsigned short.
DOC: Add C++11 macros to doxygen configuration.
ENH: Remove FindNUMARRAY.cmake.
STYLE: Too many spaces before semi-colon in PCAShapeSignedDistanceFunction.
COMP: Bump Wiki Examples revision to fix Doxygen warnings.
COMP: Fix ITK_OVERRIDE update DebugMacro build errors.
DOC: Updates to GettingStarted.txt.
BUG: Remove Testing/Temporary/CTestCostData.txt.
ENH: Update doxygen.config for Doxygen 1.8.9.1.
ENH: Bump CMakeLists.txt version to 4.8.0.
DOC: Rename duplicate doxygen section.
Revert Doxygen version 1.8.9.1 to 1.8.5 config to clean up dashboard
DOC: Fix Doxygen override, nullptr, noexcept definitions.
DOC: Note that push access is not required to get patches merged.
DOC: Clean up some wrapping comments.
STYLE: Clean up inter-definition space for Image,ImageBase,ProcessObject.
ENH: Fetch source tarball external data from midas3.kitware.com.
BUG: Fix BridgeNumPy signed / unsigned short correspondance.
DOC: Improve ImageScanlineIterator documentation.
ENH: Add missing {Set,Get}Element methods to Array2D.
BUG: Fix linking SmoothingRecursiveYvvGaussianFilter with install tree.
BUG: Add CMake export code for ITK_USE_SYSTEM_GDCM.
ENH: Pass CMAKE_GENERATOR to ExternalProject's.
ENH: Update LLVM/Clang ExternalProject to 3.6.0.
ENH: Update MetaIO License from Upstream.
ENH: Bump MetaIO to latest upstream.
COMP: Do not include tests/ directory in clang tarball.
ENH: Add Azure Storage as ExternalData source.
STYLE: Update SplitComponents module for KWStyle fixes.
STYLE: Style fixes for LevelSetsv4 and related classes.
BUG: Move MagnitudeAndPhaseToComplex filter wrapping to ITKImageIntensity.
ENH: Document testModules.sh and move to Utilities/Maintenance
BUG: Fix Python tests on Windows with Ninja generator.
STYLE: Update IOSTL module for KWStyle test.
BUG: Suppress wrapping type conversions warnings with MSVC.
COMP: Address quoted MSVC variable in GDCM.
BUG: WrapITK.pth should contain the lib/ directory with VS.
COMP: Suppress swig build configure warning.
ENH: Use CMAKE_CROSSCOMPILING_EMULATOR to run HDF5 detection.
BUG: Do not use EXECUTABLE_OUTPUT_PATH for vcl tests.
BUG: Do not enable floating point exceptions in tests with MinGW.
DOC: Update KWStyle location.
BUG: Add QuickViewTest baseline for Mac.
ENH: MetaIO use UpdateThirdPartyFromUpstream.sh
ENH: Arrange MetaIO sources for UpdateThirdPartyFromUpstream.sh.
ENH: Add root snapshot commit support to UpdateThirdPartyFromUpstream.sh
COMP: Do not try to generate tiff_fax3sm.c when cross compiling.
COMP: Android does not currently have posix_memalign.
COMP: The Android pwd.h passwd struct does not have a pw_gecos entry.
COMP: Android does not have pthread_setcancelstate.
COMP: Do not do __errno_location workaround on Android.
COMP: Removed unused parameters in itkThreadPoolTest.
BUG: Address detection of TransformReadWriteTest as executable.
ENH: Set CMP0056 to NEW.
COMP: Work around test file too big with x64_64-w64-mingw32.
COMP: Increase itkMattesMutualInformationImageToIMageMetricv4Test tolerance.
COMP: Address NumericTraits warning related to POWER8 char.
BUG: Add new ResampleImageFilter9Test baseline for MinGW.
BUG: Add MinGW baseline for VoronoiPartitioningImageFilterTest1.
COMP: Fix vnl_sample.cxx for srand48 but no drand48.
ENH: Add ITK_DYNAMIC_LOADING CMake option.
COMP: Support S_IRUSR and S_IWUSR.
COMP: Do not log swig configure output.
BUG: NumericTraits< char > does not have Self typedef.
ENH: Do not use TestBigEndian from CMAKE_ROOT.
COMP: Use sizeof(void *) instead of sizeof(size_t) for address model.
COMP: Do not use GCC demangling with emscripten.
ENH: Use try_run to determine if double correction required.
COMP: Suppress Swig configure output.
COMP: Set CMP0058 to NEW.
COMP: Add missing InternalLabelType.
BUG: Specify absolute path to double-conversion-configure.h for install.
DOC: Clarify the UpdateThirdPartyFromUpstream.sh commit message.
COMP: Pass --quiet to swig's configure script.
STYLE: Update HigherOrderAccurateGradient module for style fixes.
ENH: Mark ITK_DYNAMIC_LOADING as an advanced CMake variable.
COMP: Ignore swig-prefix warnings.
BUG: GDCM set default ultrasound spacing when not found.
COMP: Initialize arrays in itkCurvatureFlowFunction.
COMP: Add itkIntTypes.h header for SizeValueType in itkVnlFFTCommon.h
STYLE: Style fixes for RayCastHelper::CalcRayIntercepts
COMP: Run the SWIG configure step in a CMake script.
STYLE: Bump IOFDF module for style and cleanup.
BUG: Fix DoxygenInGroup test from .zip release files.
COMP: Do not wrap exotic QuadEdgeMesh CellInterface types.
COMP: Remove FFTWGlobalConfiguration param doxygen keyword.
COMP: Do not reference ::MetaEvent in itkMetaEvent.h docs.
DOC: itkSymmetricEigenSystem is now in the ITKDeprecated module.
BUG: Fix TestDriver executable for itkSymmetricEigenSystemTest.
BUG: Use consistent SizeGreatestPrimeFactor in deconvolution tests.
COMP: Use signed char in ImageToImageMetricv4 test.
COMP: Do not include itkDynamicLoader in header tests.
COMP: Include byteswap.h for Android in GDCM.
COMP: Use signal.h instead of sys/signal.h in GDCM.
COMP: Not all versions of Android have posix_memalign.
COMP: Initialize variable in PointSetToListSampleAdaptorTest.
COMP: Suppress getpwnam warning with static executables.
COMP: Tighten LandmarkWarping2 lines for Software Guide.
ENH: Allow skip of FloatPointExceptions implementation for absent fenv.h.
COMP: Define feenableexcept for Emscripten.
BUG: HDF5 do not force CMake CheckTypeSize on include.
STYLE: Style fixes to itkVideoStream.e
COMP: Ignore build warnings for libs unfound by emscripten.
BUG: Run HDF5 H5detect in working directory with the executable.
BUG: HDF5 use CMAKE_EXECUTABLE_SUFFIX.
COMP: Work around Emscripten internal compiler crash in VideoStream.
COMP: Use byteswap.h with GDCM with Emscripten.
COMP: Recognize Emscripten in socket++.
BUG: Remove HDF5's own internal CheckTypeSize.cmake.
ENH: Enable cross-compiling of the wrapping.
COMP: Missing semi-colon in FFT Hermitian filters.
ENH: Add ExternalData_NO_SYMLINKS option.
ENH: Mount local filesystem in the test driver for Emscripten.
BUG: Do not install wrapping with CMAKE_PREFIX_PATH.
ENH: Define CPACK_PACKAGE_CONTACT.
ENH: Add post-commit hook for third party library patches.
ENH: Pass the CastXML flags directly.
STYLE: Rename GCC-XML references to CastXML.
ENH: Send an error when CMAKE_CXX_COMPILER_TARGET is not set.
ENH: Bump CastXML version for cross-compiling target fix.
BUG: Use STRING type for PY_SITE_PACKAGES_PATH.
BUG: Continue when IPython.get_ipython throws an AttributeError.
ENH: Add ITK_USE_SYSTEM_LIBRARIES
STYLE: Fix indentation in ITKSetStandardCompilerFlags.cmake.
COMP: Do not enable ITK_HAVE_SYNC_BUILTINS with Emscripten.
COMP: Fix MinGW ITK_HAVE_SYNC_BUILTINS detection.
ENH: Split testing data tarball form source tarball.
COMP: Do not use ITK_NULLPTR as sentinel.
ENH: Use gold linker on Linux with GCC.
COMP: Add try_compile check for gold linker.
COMP: Do not build dsrc2c.c with -fvisibility-inlines-hidden.
BUG: Remove shared specifications from IOTransformBase.
BUG: Required GCC version for gold linker is 4.8.3.
BUG: Fix ITKIOMINCExport.h capitalization.
BUG: Add missing include directory required after MINC update.
BUG: Bring in IOFDF license updates.
COMP: Add missing HDF5 include for MINC.
COMP: Add missing HDF5 include directory for ITKIOMINC.
COMP: Fix itkVTKImageExport.h header name in VtkGlue.i.

MetaIO Maintainers (2):
MetaIO 2015-04-12 (b7969294)
MetaIO 2015-04-21 (dc4f7d16)

Michka Popoff (20):
COMP: Use c++ style comments in pyBase.i
ENH: Update to swig 3.0.3
STYLE: Cleanup up cmake files (if, endif, foreach, endforeach).
ENH: Update to SWIG 3.0.5
COMP: Fix PythonReadDicomTagTest on OS X
ENH: Improve wrapping for Vector image types
ENH: Cleanup itkComposeImageFilter wrapping
ENH: Setup correct wrapping of GradientRecursiveGaussianImageFilter
ENH: Add Get/SetSigmaArray to GradientRecursiveGaussianImageFilter
ENH: Add checks for base types when wrapping more complex types
COMP: Fix DiffeomorphicDemonsRegistration Wrapping
STYLE: Rename ITK_WRAP_DIMS to ITK_WRAP_IMAGE_DIMS
ENH: Add ITK_WRAP_VECTOR_COMPONENTS option
STYLE: Replace GCCXML by CASTXML
BUG: Wrap FixedArray sizes also for vector components
ENH: Wrap MersenneTwisterRandomVariateGenerator
ENH: Wrap CustomColormapFunction
ENH: Update to PCRE 8.37
ENH: Enable wrapping of 4 dimensional vectors
ENH: Remove inline namespace fix for Wrapping

Nick Tustison (11):
ENH: Adding point set reg. capabilities for SyN.
PERF: Tolerance for testing needs to be increased.
BUG: Coverity divide by zero complaint.
BUG: Metric evaluation had an incorrect sign.
ENH: Making the point set type visible.
BUG: Need to check if maxNorm == 0.
BUG: Pixel type shouldn't be initialized with scalar.
ENH: Cleaning up point set reg. in BSplineSyN
ENH: Adding tangent space calculation for SyN methods.
BUG: Added sampling only within the specified mask.
BUG: Added sampling only within the specified mask.

Niels Dekker (2):
BUG: workaround for 64bit VS2013 Release segfault
COMP: Fixed MSVC warnings, "warning D9025: overriding '/W1' with '/w'"

Richard Beare (3):
ENH: LabelErodeDilate as a remote module
ENH: remote.cmake for parabolic morphology
ENH: Use SHA for LabelErodeDilate module.

Rolf Eike Beer (2):
STYLE: ExternalData: Replace MATCHES with STREQUAL where possible
STYLE: ExternalData: Clean up duplicate regex matches with CMAKEMATCH<n>

Sean McBride (14):
COMP: Changed KWStyle check for header include guard names
COMP: Remove double underscore in header guards (.h & itk_h form)
COMP: Remove double underscore in header guards (.hxx & __itk_h form)
COMP: Remove double underscore in header guards (.in & itk*_h form)
COMP: Remove remaining double underscore in header guards (itk form)
COMP: Remove unnecessary header guards in .cxx files
COMP: Manually search for "itk" and clean up double underscore usage
COMP: fixed clang -Wkeyword-macro warning by removing invalid #undef
COMP: Suppress clang -Wdocumentation-unknown-command false positive
COMP: properly escape @ char in doxygen comments
COMP: Escaped @ character in doxygen comments
BUG: updated libminc SHA to newest
COMP: Update MINC to upstream 85145dca36
BUG: updated MINC to a77da29

Ziv Yaniv (1):
BUG: Versor initialized with null axis (0,0,0) did not throw exception.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24360 3bd1e089-480b-0410-8dfb-8563597acbee