ENH: Update ITK to 4.12.0rc1

$ git shortlog 1619816..9c91cb6 --no-merges
Ben Boeckel (1):
ENH: Add a script to help update third-party sources

Brad King (5):
ENH: Update KWIML import script for new upstream URL
ENH: Teach update-third-party.bash to add a Change-Id
ENH: Port KWSys update script to update-third-party.bash
ENH: KWSys: Filter out unused attributes during import
ENH: KWSys: Apply attribute changes made upstream

Bradley Lowekamp (19):
COMP: Enable hidden visibility property with NIFTI static libraries
COMP: Enable hidden visibility property with GIFTI static libraries
BUG: Correct variable name used to check CXX version
BUG: Correct variable name used to check CXX version
COMP: Enable hidden visibility property with NIFTI static libraries
COMP: Enable hidden visibility property with GIFTI static libraries
BUG: Initialize ConvergenceValue in constructor
BUG: Initialize ConvergenceValue in constructor
ENH: Update CircleCi script to download latest binary tar-ball
BUG: Use CMAKE_DL_LIBS instead of explict "dl" library
COMP: Fix CircleCI ITK data download file name
ENH: Update CircleCI yaml file
BUG: Apply changes from MetaIO upstream to remove static variables
ENH: Update SWIG version to 3.0.12
ENH: Update PCRE version to 8.40
ENH: Add OrientedBoudingBox attributes to ShapeLabelMap
COMP: Use std::abs over vnl_math_abs
BUG: Initialize image data to 0
ENH: Fix clearing build tree error

David T. Chen (1):
BUG: Fixed quote style

Dženan Zukić (3):
STYLE: Simplify code by using TestingMacros
BUG: fixing wrong check for argument count
ENH: Add Strain as a remote module

Floris Berendsen (2):
COMP: Added missing png_get_uint_31 name mangling
COMP: Added missing png_get_uint_31 name mangling

Francois Budin (58):
STYLE: Typo corrections in itk*TopHatImageFilter.h
ENH: Prefer std::atomic over compiler specific implementation
BUG: Addresses 'ordered comparison between pointer and zero' error (clang-4)
BUG: Addresses InDoxygenGroup Test with Python 3.6 failures
BUG: BSplineScatteredDataPointSetToImageFilter output image is not generated
BUG: itk::RGBPixel<unsigned short> needs to be wrapped for itkTIFFImageIO
BUG: Usage of std::atomic was incorrectly used in itk::Detail::AtomicOps
ENH: Exposing functions to set real and imaginary part of complex numbers
BUG: ITK_OVERRIDE keyword for non-overriden funtion
BUG: 'typename' cannot be used outside of template declaration
BUG: Missing ITK_OVERRIDE
BUG: ITK_OVERRIDE keyword for non-overriden funtion
BUG: ITK_OVERRIDE keyword for non-overriden funtion
BUG: ITK_OVERRIDE keyword for non-overriden funtion
BUG: Missing ITK_OVERRIDE
ENH: Improving usability in IPython
ENH: Update BridgeNumPy to most recent version (2017.02.24)
BUG: 3523 Even padding most value representations with space instead of '\0'
BUG: Remove extra space in chronometer command
DOC: Make it more explicit that 'push' authorization is not for everybody
BUG: 3523 Even padding most value representations with space instead of '\0'
BUG: 3519 KernelTransform WMatrix initialization
BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS
COMP: Do not expose functions to set real and img part of complex numbers
BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS
BUG: 3519 KernelTransform WMatrix initialization
DOC: Typo in itkNumberToString.h
BUG: Attribute names cannot start with a digit
BUG: Do not define deprecated function if ITK_LEGACY_REMOVE is selected
BUG: Wrap EllipseSpatialObject std::list in Python
ENH: Wrap itkN4BiasFieldCorrectionImageFilter in Python
BUG: itkStatisticsAlgorithmTest throwing exception on VS2015Update3 and VS2017
ENH: Skip generating export headers if module does not contain a target
BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review
ENH: Update BridgeNumPy to most recent version (2017.03.27)
BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review
BUG: Wrap EllipseSpatialObject std::list in Python
ENH: Improving usability in IPython
BUG: Attribute names cannot start with a digit
BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS
BUG: Do not export all symbols from third party libraries on Windows
ENH: Allows to call ImageFileWriter in Python with Input=Filter
BUG: Certain third party libraries need to export their symbols on Windows
BUG: Test if 'issubclass' only if 'isclass' is True
ENH: Add Python convenience function to read images
BUG: 3475 AccumulateImageFilter not setting direction cosines of output image
DOC: Removing typos in itkExtractImageFilter comments
BUG: ProjectionImageFilter did not copy direction cosine information to output
BUG: Test if 'issubclass' only if 'isclass' is True
BUG: 3475 AccumulateImageFilter not setting direction cosines of output image
BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS
BUG: Do not export all symbols from third party libraries on Windows
BUG: Certain third party libraries need to export their symbols on Windows
BUG: ProjectionImageFilter did not copy direction cosine information to output
ENH: Update BridgeNumPy (2016.04.28) and update itkExtras.py accordingly
BUG: Template type based input function parameter needs to be deterministic
ENH: Bump CMakeLists.txt version to 4.11.1
BUG: Problems due to ComputeOrientedBoundingBox in itkShapeLabelMapFilter

Jean-Baptiste VIMORT (1):
PERF: Improvement of the itkHistogram class in order to make it faster

Jean-Christophe Fillion-Robin (3):
ENH: Introduce ITK_WRAP_PYTHON_LEGACY to exclude older Python package layout
BUG: ITKPython: Do not install *.mdx files required only at generation time
COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Johan Andruejol (1):
ENH: Add wrapping for PathToImageFilter

Jon Haitz Legarreta (131):
ENH: Improve the itkFileListVideoIO coverage.
STYLE: Improve the BSplineScatteredDataPointSetToImageFilter style,
ENH: Improve the itkBSplineScatteredDataPointSetToImageFilter coverage.
ENH: Add missing ivars in function PrintSelf.
STYLE: Improve ImageNoise filters' style.
STYLE: Improve the ImageNoise filters tests' style.
STYLE: Improve ITKImageSources module filters' style.
STYLE: Improve the itkLinearInterpolateImageFunction style.
ENH: Improve the itkLabelOverlapMeasuresImageFilter coverage.
STYLE: Improve itkAdaptiveHistogramEqualizationImageFilter style.
ENH: Improve itkAdaptiveHistogramEqualizationImageFilter coverage.
STYLE: Improve itkKappaStatisticImageToImageMetric style.
ENH: Improve the itkKappaStatisticImageToImageMetric coverage.
STYLE: Improve itkBinaryGrindPeakImageFilter style.
STYLE: Improve the itkCannyEdgeDetectionImageFilter style.
ENH: Improve itkCannyEdgeDetectionImageFilter coverage.
ENH: Improve itkBarrier class coverage.
STYLE: Improve itkFlipImageFilterStyle.
STYLE: Improve itkSpatialObjectToPointSetFilter style.
STYLE: Improve itkStretchIntensityImageFilter style.
ENH: Print all ivars for itkStretchIntensityImageFilter.
ENH: Improve itkPhysicalPointImageSource class coverage.
ENH: Add missing ivars to LabelMapMaskImageFilter PrintSelf.
ENH: Improve itkRealTimeClock coverage.
STYLE: Improve the itkRealTimeClock style.
ENH: Improve itkBsplineDecompositionImageFilter coverage.
ENH: Improve itkTestingStretchIntensityImageFilter coverage.
STYLE: Improve itkPathToChainCodePathFilter style.
ENH: Add a Get method for itkPathToChainCodePathFilter ivar.
ENH: Add specific testing macro for boolean members.
STYLE: Improve itkLabelMapMaskImageFilter style.
STYLE: Improve BSplineDecompositionImageFilter style.
ENH: Finish itkAdaptiveHistogramEqualizationImageFilter PrintSelf.
COMP: Fix ImageGrid tests compiler warnings.
ENH: Finish BSplineDecompositionImageFilter PrintSelf.
BUG: Fix Uninitialized Memory errors reported by Valgrind.
ENH: Improve itkLabelMapMaskImageFilter coverage.
ENH: Improve itkBinaryGrindPeakImageFilter coverage.
ENH: Improve itkPathToChainCodePathFilter coverage.
ENH: Move LabelMap module test baselines.
ENH: Move BinaryMathMorphology test baselines out of review.
ENH: Move ImageFusion test baselines out of review.
ENH: Improve itkAutoCropLabelMapFilter tests.
ENH: Improve itkSpatialObjectToPointSetFilter coverage.
ENH: Move ImageLabel test baselines out of Review.
ENH: Move ImageGrid test baselines out of review.
STYLE: Improve itkGaussianSpatialFunction class' style.
ENH: Improve the ITKPath module classes coverage.
BUG: Fix BSplineDecompositionImageFilter Valgrind defects.
STYLE: Improve itkColorTable style.
ENH: Improve itkHoughTransform2DLinesImageFilter coverage.
ENH: Improve itkHoughTransform2DCirclesImageFilter coverage.
BUG: Address uninitialized variable defects.
STYLE: Improve itk::HistogramThresholdImageFilter style.
DOC: Fix a typo in the term "threshold".
STYLE: Imporve itkContourSpatialObjectPoint style.
ENH: Print all HoughTransform2DLinesImageFilter ivars.
STYLE: Fix type in Optimizersv4 and Metricsv4 modules.
ENH: Add PhiLattice regression baseline.
ENH: Print all itkVoronoiDiagram2DGenerator ivars.
ENH: Improve itkColorTable coverage.
ENH: Improve the itk::GradientDescentOptimizerv4 style.
ENH: Improve the itkImageSources module's filters' coverage.
ENH: Add PhiLattice regression baseline.
ENH: Add a new test for itk::ContourSpatialObjectPoint.
BUG: Fix bug in itkContourSpatialObjectPointTest test.
STYLE: Improve the itkGaussianSpatialFunctionTest style.
ENH: Improve itkVotingBinaryHoleFillingImageFilter coverage.
BUG: Fix precision issues in itkGaborKernelFunctionTest.
BUG: Relax tolerance in itkGaborKernelFunctionTest.
DOC: Fix minor typo in itkHistogramThresholdImageFilter doc.
ENH: Print all ivars in GradientDescentOptimizer base classes.
STYLE: Improve TIFFImageIO tests.
ENH: Add Get methods for itk::BSplineDecompositionImageFilter ivars.
BUG: Fix TimeProbes name in itkLargeTIFFImageWriteReadTest.
BUG: Fix memory leaks in BMP and PNG tests.
COMP: Fix signed/unsigned mismatch warning.
COMP: Fix signed/unsigned mismatch warning.
BUG: Fix Superclass for ITKThresholding calculators.
BUG: Make the number of filters be an integer.
ENH: Honor the itkBooleanMacro for boolean class members.
ENH: Improve the Watershed module code coverage.
COMP: Fix double to unsigned int cast warning.
ENH: Improve coverage for MorphologicalWatersheds filters.
STYLE: Improve the Denoising module style.
BUG: Fix the itkPatchBasedDenoisingImageFilter RTTI Superclass name.
COMP: Fix unsigned char from double conversion warning.
ENH: Improve itkWatershedMiniPipelineProgressCommand coverage.
ENH: Improve the itkRegionalMin/Max filters member print types.
ENH: Improve the itkMorphologicalWatershedFromMarkers coverage.
ENH: Improve the itkIsolatedWatershedImageFilter coverage.
STYLE: Improve the Denoisinig module style.
STYLE: Improve the FEMRegistration module files style.
DOC: Fix itkOrientImageFilter UseImageDirection method doc typo.
STYLE: Improve the ITKThresholding module classes style.
BUG: Fix itkIsolatedWatershedImageFilterTest valgrind errors.
STYLE: Improve the itkApproximateSignedDistanceMapImageFilter style.
ENH: Improve Denoising module filters' coverage.
ENH: Improve the FEMRegistration module coverage.
STYLE: Improve the itkDisplacementFieldTransform class style.
STYLE: Limit itkFlipImageFilter methods' loops variables' scope.
ENH: Improve itkFlipImageFilter coverage.
COMP: Fix itkPhysicsBasedNonRigidRegistrationMethodTest cast warning.
STYLE: Improve the HessianToObjectnessMeasureImageFilter style.
ENH: Improve coverage for HessianToObjectnessMeasureImageFilter.
ENH: Improve DiscreteGaussianImage operators review classes' coverage.
ENH: Add test for itk::ConicShellInteriorExteriorSpatialFunction.
ENH: Print all itkHoughTransform2DCirclesImageFilter ivars.
ENH: Improve coverage for itk::DisplacementFieldTransform.
STYLE: Make itkPatchBasedDenoisingBaseImageFilter ivars private.
STYLE: Improve the itkRobustAutomaticThreshold classes style.
COMP: Fix itkDisplacementFieldTransformTest compiler warning.
STYLE: Improve the itkGridForwardWarpImageFilter style.
ENH: Improve coverage for itkGridForwardWarpImageFilter.
ENH: Improve coverage for itkRobustAutomaticThreshold classes.
ENH: Remove duplicate test files in Review.
DOC: Fix itkDivideByConstantImageFilter doc error.
STYLE: Improve exception message.
STYLE: Improve ImageIntensity module image arithm op tests' style.
STYLE: Improve HConc/Conv HMaxima/HMinima image filters' style.
ENH: Improve the HConc/HConv HMaxima/HMinima filters' coverage.
ENH: Improve DiscreteGaussianImage operators review classes' coverage.
ENH: Change the URL for the PCA remote module repo.
STYLE: Make flow control variables have a local scope.
ENH: Add examples and doc build flag support for external modules.
DOC: Remove wrong group tag for itk::QuadEdgeMeshExtendedTraits.
BUG: Fix itk::FastMarchingImageFilter RTTI superclass name.
STYLE: Improve the itk::NodePair class style.
STYLE: Use the ITK_MANUAL_INSTANTIATION macro consistently.
STYLE: Delete FastMarching module classes methods consistently.
DOC: Fix typo in the "implementation" word across the code.

Jon Haitz Legarreta Gorroño (2):
STYLE: Improve itkWarpHarmonicEnergyCalculator style.
DOC: Add a notice to let users know about related implementations.

KWIML Upstream (1):
KWIML 2017-02-27 (aa3a7733)

KWSys Upstream (3):
KWSys 2016-11-21 (cb55cf5a)
KWSys 2017-03-28 (34999b6a)
KWSys 2017-04-20 (8785f84f)

Matthew McCormick (40):
COMP: Add missing headers in OpenCVImageBridge
COMP: Use double for gradient calculations in MinMaxCurvatureFlow
ENH: Bump ITK version to 4.12.0.
COMP: Add VCL support for GCC 7
COMP: Define ITK_FALLTHROUGH for GCC 7
COMP: Add missing ITK_FALLTHROUGH in TiffImageIO
COMP: Avoid -Warray-bounds in FixedArray with GCC 7
COMP: Add ProcessObject include in itkLevelSetBase.hxx
ENH: Exclude Kitware Robot from third party update commit messages
BUG: Address tab completion with IPython >= 5.0.0
BUG: Do not use terminal_progress with the Jupyter Notebook
ENH: Enable BridgeNumPy with Python wrapping
COMP: Do not require numeric_traits::has_infinity
BUG: Fix passing _NO_TR1 definition with VS9 and Python
BUG: Do not tests that require NumPy when it is not available
ENH: Build Python wrapping with hidden visibility
ENH: Move morphological watersheds out of ITKReview
BUG: Do not upload top level folder in ArchiveTestingDataOnGirder.py
BUG: Remove unused content links from PNG test additions
ENH: Add .sha512 content links for IO pallette test data
BUG: Add missing export macros for SpatialObject forward declarations
BUG: Always wrap basic type RGBUC
COMP: Do not add Visual Studio numeric_traits workarounds with MinGWPy
COMP: Increase gold linker requirement to GCC 4.9.0
COMP: Detect Windows with _WIN32 in socket++/fork.cpp
BUG: Revert "BUG: Include installed modules in ITK_MODULES_ENABLED"
BUG: Set ${itk-module}_ENABLE_SHARED in ITKModuleExternal
BUG: PolyLineParametricPath must be loaded before PathToImageFilter
COMP: Address Python 2.7 Windows _hypot build errors
COMP: Undefine Py_hash_t when wrapping VtkGlue
ENH: Update BridgeNumPy to most recent version (2017.03.05)
BUG: Improve itkTemplate New compatibility with Python 3
ENH: Bump CastXML to 2017-04-18
STYLE: Remove empty or erroreous comments in ImageToImageFilter
ENH: Use itk.imread and itk.imwrite as standard function names
BUG: Correct size specification in ImportImageFilter::SetImportPointer
BUG: Improve large file support in MetaIO
ENH: Wrap itk::IdentifierType for ScalarToRGBColormapImageFilter
BUG: LevelSetNeighborhoodExtractor uses spacing
BUG: Fix PCRE 8.40 download URL

MetaIO Maintainers (1):
MetaIO 2017-04-08 (dead6687)

Olivier Commowick (1):
BUG: Correct ITK eigen system (was producing NaN or different values than VNL)

Pablo Hernandez-Cerdan (4):
ENH: Add SetReferenceImage to GenerateImageSource.
ENH: Change the metadata of all outputs in GenerateImageSource.
BUG: Fix Normalization kernel step of ConvolutionImageFilter.
BUG: Remove call to Superclass::GenerateOutputInformation.

Richard Beare (1):
DOC: PrincipleComponent flag incorrectly reported by PrintSelf

Sam Horvath (1):
PERF: reduce memory usage of itkImagePCAShapeModelEstimator

Samuel Gerber (2):
DOC: Added description to itkLBFGSOptimizerv4.h
DOC: LBFGSOptimizer doc update

Shusil Dangi (2):
ENH: Ignores MacOS .DS_Store file
ENH: Wrap NormalVariateGenerator in the Statistics Module

Simon Rit (2):
BUG: memory leak in ITK_USE_THREADPOOL
BUG: Join threads when using thread pool (ITK_USE_THREADPOOL)

Taylor Braun-Jones (1):
COMP: Only include the headers for required OpenCV modules (fixup)

VXL Maintainers (2):
VNL 2017-02-01 (ae6eff5e)
VNL 2017-02-08 (ae8eef13)

Vladimir S. FONOV (3):
MINC 2017-04-28 (3d79acf3)
MINC 2017-05-01 (4caf8f4c)
MINC 2017-05-05 (cc682b52)

Yann Le Poul (4):
ENH: improvement of palette image support for PNG TIFF and BMP.
STYLE: Misleading IsReadAsScalarPlusPalette Printing string
STYLE: ReadAsScalarPlusPalette info already printed in itkImageIOBase
BUG: ExpandRGBPalette used instead of IsReadAsScalarPlusPalette

git-svn-id: http://svn.slicer.org/Slicer4/trunk@26008 3bd1e089-480b-0410-8dfb-8563597acbee