ENH: Update ITK to v4.11.0 and SimpleITK to v1.0rc1
Tested-by: Andriy Fedorov <fedorov@bwh.harvard.edu>
Tested-by: Bradley Lowekamp <blowekamp@mail.nih.gov>
Tested-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Tested-by: Steve Pieper <pieper@bwh.harvard.edu>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
// ----------------------------------------------------------------------------
ITK changes:
git shortlog bd54ba1..71e441d --no-merges
Bill Lorensen (1):
ENH: Bump WikiExamples version
Bradley Lowekamp (36):
BUG: Enable VirtualDomain and FixedTransform in RegMethv4
ENH: Adding initial CircleCi configuration file
COMP: Fix float to unsigned integer conversion warnings
BUG: Include installed modules in ITK_MODULES_ENABLED
COMP: Address CMake error that ITKGPUCommon is not in export
COMP: Address wrong library types with VS and shared libraries
BUG: Ensure CreateImageIO is concurrent thread safe
ENH: Mark HDF5 CMake options as internal
COMP: Add template export declaration for ParametricPath
COMP: Correct TEMPLATE_EXPLICIT definition in Path module
ENH: Factor out common code in the TrasformFactoryBase registration
ENH: Add CMake variable for max transform dimension, defaults 4
ENH: Create CMake module to check for private RTTI compatibility
ENH: Improving setting of default ITK_TEMPATE_VISIBILITY_DEFAULT
COMP: Correct ifndef value to allow user defined ITK_TEMPLATE_EXPORT
BUG: Add explicit instantiate for ObjectToObjectOptimizerBase
COMP: Use add_definitions for CMake 2.8.9 compatibility
COMP: Add warning suppression for distcc warning
ENH: Explicitly instantiate the optimizer base over float
BUG: Use IsLinear to check if transform is "affine"
ENH: Remove unneeded includes of random iterator header
ENH: Improve thread-safety for Generator, and unique New sequence
ENH: Do not use global random generator
BUG: Update v3 registration metrics to use local seed
ENH: Prefer setting local seed over global in tests.
ENH: Update SWIG to latest 3.0.11 release
BUG: relax testing parameters for v3 translation registration
BUG: Restore baseline for debug registration
BUG: Remove unused SimpleImageRegistrationTest baselines
ENH: Expose GetNextSeed method in MersenneTwiseter Generator
BUG: Add option for fixed seed or wall clock seed for sampling
BUG: Use metric random seed in v3 examples
BUG: Prefer setting seed at algorithm in "v4" tests.
BUG: Add itk prefix to TIFF files in binary directory.
BUG: Remove ITK_DISALLOW_COPY_AND_ASSIGN as Doxygen private
BUG: First IterationEvent is at CurrentIteration==0
Caspar Goch (2):
BUG: Use printable type for RGBA pixel ostream for ITK-3501
STYLE: Remove extra space for ITK-3501
Davis Vigneault (1):
ENH: Add remote module DVMeshNoise
Dženan Zukić (5):
ENH: updating version of AnisotropicDiffusionLBR
ENH: adding UnsharpMaskingImageFilter
COMP: explicitly cast to output type
BUG: double call to update would cause empty output image
ENH: Updating RLEImage remote module. Change-log:
Francois Budin (26):
BUG: Supported extensions by PNG IO were not added in constructor.
DOC: Documentation in itkRBGAPixel and itkRGBPixel was incorrect.
ENH: Update SCIFIO to lastest (2016.12.01)
ENH: FixedPointInverseDisplacementField moved to InsightSoftwareConsortium
COMP: Remove compilation warnings
ENH: Improved support of ccache and distcc
BUG: GPUImage regression due to API change.
ENH: Update Bridge Numpy (2016.12.05)
ENH: Update VariationalRegistration to remove warnings during compilation
ENH: FindPythonLibs does not support both debug and release python libraries
ENH: Update VariationalRegistration
BUG: Missing ITK_TEMPLATE_EXPORT in forward declaration of itk::ImageBase
BUG: Missing ITK_TEMPLATE_EXPORT in itkOptimizerParametersHelper
BUG: Missing ITK_TEMPLATE_EXPORT in templated class
BUG: Remove linkage warnings on MacOS
BUG: HDF5 CMake installation directory variable had not been updated
BUG: Missing include header in AnisotropicDiffusionBLR remote module hxx files
COMP: Silencing unused variable warning in itkTimeStamp
STYLE: Improve style checking by using module ITKKWStyleOverwrite.txt
COMP: OS*Barrier functions are deprecated on MacOS 10.12
ENH: Update BridgeNumPy to latest version on 2017.01.08 to address ITK-3511
BUG: Extra \$ in doxygen comment
BUG: Binary include directory added only if enabled shared
ENH: Update SCIFIO to latest revision (2017.01.17)
ENH: Update SCIFIO to lastest commit (01.21.2017)
BUG: Alpha value created when converted image to RGBA is not always 1
Hans Johnson (3):
ENH: Provide mechanism for enhanced NIFTI support
BUG: Use NIFTI sform/qform conventions correctly
ENH: Remove ambiguity about sform/qform
Hastings Greer (1):
BUG: Add test demonstrating Python global timestamp issue
Jean-Christophe Fillion-Robin (1):
COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD
Jon Haitz Legarreta (54):
ENH: Get internal ImageIO via a const macro.
ENH: Improve Boolean Algebra ImageFilters coverage.
STYLE: Improve the EuclideanDistancePointMetric style.
ENH: Improve itkSigmoidImageFilter coverage.
STYLE: Improve itkCropImageFilter style.
ENH: Improve itkCropImageFilter coverage.
ENH: Improve RGBToLuminanceImageFilter and Adaptor coverage.
ENH: Improve itkRescaleIntensityImageFilter coverage.
ENH: Improve the itkMatrixSelectionImageFilter coverage.
ENH: Improve itkTanImageFilter and Adaptor coverage.
ENH: Increase itkSqrtImageFilter and Adaptor coverage.
ENH: Increase itkTernaryOperatorImageFilter coverage.
ENH: Increase itkSymmetricEigenAnalysisImageFilter coverage.
STYLE: Improve itkScalarImagekmeansImageFilter style.
STYLE: Conform to TEST_SET_GET_VALUE definition.
BUG: Fix uninitialized variable due to dynamic analysis defect.
BUG: Fix uninitialized variable defect reported by valgrind.
ENH: Improve the itkPointSetToPointSetRegistrationTest.
ENH: Improve the itkPointSetToImageRegistrationTest.
ENH: Increas BinaryMagnitudeImageFilter coverage.
STYLE: Remove test name from std output.
ENH: Increase MagnitudeImageFilter coverage.
BUG: Fix uninitialized variable defect reported by valgrind.
BUG: Fix Superclass name in RTTI.
STYLE: Improve itkFrustumSpatialFunction style.
STYLE: Improve the itkConicShellInteriorExteriorSpatialFunction style.
BUG: Fix Superclass template argument list.
STYLE: Improve the itkTorusInteriorExteriorSpatialFunction style.
STYLE: Improve the itkCheckerBoardImageFilter class style.
ENH: Improve the itk::LabelVotingImageFilter coverage.
ENH: Improve itkCheckerBoardImageFilter coverage.
STYLE: Improve itk::LabelVotingImageFilter style.
STYLE: Improve the itkHoughTransform2DCirclesImageFilter style.
ENH: Add test for itk::FrustumSpatialFunction class.
ENH: Improve itkConnectedThresholdImageFilter coverage.
STYLE: Improve itkConnectedThresholdImageFilter style.
BUG: Fix FrustumSpatialFunction internal precision conversion.
COMP: Fix implicit conversion warning.
STYLE: Improve itkThresholdImageFilter style.
ENH: Add test for itk::TorusInteriorExteriorSpatialFunction.
BUG: Fix Superclass template argument list.
ENH: Improve itkUnsharpMaskingImageFilter implementation.
ENH: Improve the itkUnsharpMaskingImageFilter coverage.
ENH: Fix UnsharpMaskingImageFilter test inconsistencies.
BUG: Add missing itkTypeMacro.
DOC: Document the member variables.
BUG: Fix the itkImageSource RTTI class name,
DOC: Document itkLabelOverlapMeasuresImageFilter methods.
STYLE: Improve itkLabelImageGaussianInterpolateImageFunction style.
ENH: Finish itkGaussianInterpolateImageFunction PrintSelf.
STYLE: Improve itkLabelOverlapMeasurementImageFilter style.
DOC: Fix ITKImageNoise filters' doc TeX errors.
BUG: Fix uninitialized variables in itkGaussianInterpolateImageFunction.
BUG: Fix RTTI Superclass name in itkLabelMapMaskImageFilter.
KWSys Robot (3):
KWSys 2016-11-08 (2b3e2b1c)
KWSys 2016-11-09 (18c65411)
KWSys 2016-11-21 (cb55cf5a)
Matthew McCormick (21):
ENH: Wrap VectorImage with complex real pixel types
ENH: Bump PerformanceBenchmarking to 2016-11-07
BUG: Do not assume zero Index in ReinitializeLevelSetImageFilter
ENH: Create itk_module_add_library macro
BUG: Update computeCodeCoverageLocally.sh for KWStyle addition
COMP: Install a newer version of CMake on CircleCI
ENH: Use GitHub Pages as the first ExternalData resource
ENH: Add tests to demonstrate OSX dynamic_cast failure
BUG: Use random seed with for MersenneTwisterRandomVariateGenerator.
BUG: Enable program global timestamp
BUG: Set random number seed in Mattes metric test
BUG: Notify builder that ITK_DYNAMIC_LOADING is required with wrapping
BUG: Define ITK_DYNAMIC_LOADING before ITK_WRAP_PYTHON
BUG: Set random number seed mutual information metric tests
BUG: Wrap std::vector< itk.Point >
BUG: Fix wrapping of LandmarkBasedTransformInitializer
BUG: Rename UnsharpMaskingImageFilter to UnsharpMaskImageFilter
DOC: Add Dženan Zukić to .mailmap
BUG: Remove invalid ImageRegistration4Test.png.sha512
BUG: Fix cat/echo in ContentLinkSynchronization.sh
ENH: Add missing SHA512 content links
Max Smolens (1):
DOC: Fix itkUnsharpMaskImageFilter documentation typos
Mayeul Chassagnard (6):
ENH: Update add_library TO itk_module_add_library
COMP: Set Policy CMP0023 target_link_libraries for Modules/ThirdParty/VNLI...
BUG: Add ITK_TEMPLATE_EXPORT to template classes
BUG: Fix errors linked to dyn_cast merge
BUG: Restore old ITKModule_TEMPLATE_EXPORT specification for classes
BUG: dash3win7 dashboard build error unresolved external symbol
Richard Beare (1):
BUG: Fix precision issues with poly-line FlatStructuring element
Simon Rit (1):
BUG: ITK-based software was crasing when thread creation failed
Stephen Aylward (1):
BUG: Target file for modules moved to subdir Targets.
Taylor Braun-Jones (1):
COMP: Only include the headers for required OpenCV modules
// ----------------------------------------------------------------------------
SimpleITK changes:
$ git shortlog aeada7a..v1.0rc1 --no-merges
Bradley Lowekamp (135):
Update to development version of ITK 4.11
Remove duplication of transform being registered
Move ExpandTemplate code generator to separate directory
Moving template components under expand directory
Separate the json4lua module into separate file
Updating ITK along 4.11 development
Adding Transform IO tests to verify BSpline order
Add new baseline images for BSpline registration tests
Use the list of ITK modules as required components for ITK find
Mark integers as unsigned to avoid comparison warnings.
Add Colormap option to LabelMapToRGB filter.
ENH: adding methods and tests for Virtual image
Remove extraneous print statements.
Adding registration test with multi-levels and virtual image
Use correct triple slash doxygen mark up for enum
Adding documentation for EstimateLearningRate enum
Adding check for virtual domain parameters
Update ITK along master branch
Use shared libraries on CircleCi to reduce memory required for linkage
Set the displacement field interpolator for inverse too
address signed to unsigned integer comparison warning
Update Superbuild ITK version
Fix the CMake type for visibility preset variables
Adding test for concurrent file reading
Update python virtualenv to 15.1.0
Update tests to not use the "no_return_image" value.
Use void return type when no_return_image is set to true.
Adding lua JSONQuery script to get a json field
Pass ExternalData_OBJECT_STORES to SimpleITK sub-project
Correct version of virtualenv currently used
Fix another signed to unsigned comparison warning
Only use USESTERMINAL when cmake is of sufficient version
Only use TERMINAL feature with supported CMake version
Use CMAKE<LANG>_COMPILER_LAUNCHER in superbuild propagation variables
Adding warning for CMAKE_CXX_COMPILERARG1 usage.
Update example to use Enum over Value types for pixel Ids
Update tests to use Enum over pixel Value Type
Remove legacy CastImageFilter set output pixel id by value
Fix Java enum does not not used construction, but value
Updating Java example to use PixelID enum over value
Improve error checking for memoryView creation
Only return a memoryview for a bufferobject, rename internal method
Reduce duplicate code in GetArray methods
Fix unsuported Xdoclint option being used
Fix incorrect variable used to detect if javadoc support Xdoclint option
Update Documentation of get array methods.
Fix detection of javadoc doclint option
Add "sitk" prefix to functions
Use CMake method to set SITK_UNDEFINED_SYMBOLS_ALLOWED
Address CMP0054 warning with "unused" string/variable
Remove writable view option
Due to change to use memoryview object Python 2.7 is now required
Correct Java std::vector wrapping to rename push_back to add
Enable NLM's midas server as download
Update to SWIG 3.0.11
Update SWIG version string
Updating ITK Superbuild to 4.11 release candidate.
Disable building of KWStyle with ITK
Update Parameter Estimator test for ITK change
Fix output pixel type for TransformToDisplacementFieldFilter
Update ITK Superbuild version to 4.11rc2
Adding missing connection for optimizer scales measurement.
Adding test for scales callback for optimizers
Adding OnePlusOneOptimizer to registration framework
Update ITK superbuild version
Adding change in header order.
No longer return Self in Transform::AddTransform
Separate legacy Python packaging into a separate file
Fix path of SimpleITK documents files with language build
Pass SKBUILD to ExternalProjects
Using seed parameter for 1+1 optimizer
Update to the SimpleITK 4.11.0 release!
Remove options to compile ITK Wrapping along side SimpleITK
Add seed parameter for registration point set generation
Address signed to unsigned comparison warning
Add missing time header for Visual Studio
The next release of SimpleITK will be 1.0
Fix failure to pass CMake visibility options to ITK
Address new ITK template visibility feature
Correct DYNAMICLOOKUP cache type to STRING
Explicitly make pimple classes hidden
Explicitly make typelist meta-programming structures hidden
Propagate ITKV3COMPATIBILITY to the ITK sub-build
Add advanced CMake variable to determine default value of WRAP
Update GoogleTest to 1.8.0 release
Update FindGTest to latest CMake version
Update GTest usage to use targets instead of CMake variables
Correct local FindGTest to use system include file.
Only use Threads target when it exists.
Fallback to variable based library for link dependency on threads
Only download GTest in Superbuild
We require a recent version of Swig 3
Add support for GTEST_ROOT as source directory.
Fix checking if a variable is defined before adding to cache
Remove SwigWin version from path
Change to target_include_directories
Rely on exported properties instead if SimpleITK Use file
Remove stdint.h utility header
Use target based include directories for languages
Extract gtest_add_tests macro into separate file
Update CircleCi
Update the superbuild ITK version along the 4.11 release branch
Correct CircleCi to use shared libraries
Enable Python wrapping
Adding libpython-dev for Python.h
Move using Google Test as subdirectory
Add casting to GetCurrentIteration in registration
Adding Github pages as an external data download repository.
Adding SimpleITK libraries to runtime path for Python testing
Disable stripping post build step if CMAKE_STRIP is empty
Install numpy for CircleCI via pip
Explicitly add bigobj for MSVC in standalone languages
Update ITK version to include valgrind defect patch
Remove unused superbuild definition and MSVC bigobj flag
Add test to verify randomness for seeds being set
Update along ITK 4.11+ release branch
Ran SwigDocUpdate.sh to update Java and Python Swig docstring files
Improve Optimizer_ScalesEstimator test
Revert "Remove stdint.h utility header"
Remove direct include of stdint.h
Add stdint alternative as public target include directory
Compile the Explicit library with default visibility
Move two example for multiple languages into the same directory
Consolidate DicomSeriesReader examples into single directory
Consolidate FilterProgressReporting examples
Refactoring Demons and Method2 registration example directory
Consolidate BSpline and Displacement registration examples
Remove Java example subdirectory
Removing Lua example subdirectory
Move DicomImagePrintTags examples to one directory
FIXUP.......
Moving Python registration related examples to separate directories
Adding cmake file for N4 Example
Adding missing CMakeLists.txt files for example subdirectories
Only add test property when language is enabled.
Dave Chen (2):
Enforce SITK_FORBID_DOWNLOADS
Updated JSON files
David T. Chen (4):
Added some error handling to JSONQuery.lua
Initial checkin of GenerateDoc.py
Removed all groovy usage
Delete GenerateDocumentation.groovy
Ghislain Antony Vaillant (1):
Derive default package dir from library dir.
Hyun Jae Kang (2):
ENH: Add new functionality to NumPy bridge methods for array views
Copy Numpy Array test to test arrayview option
Jean-Christophe Fillion-Robin (4):
ENH: Update external project to display build output with Ninja generator
ENH: Update custom command to display build output with Ninja generator
Adding .ExternalSource to gitignore
targetLinkLibrariesWithDynamicLookup: Backport module from scikit-build
Richard Beare (2):
Propogate C++ exceptions into R.
Added a missing typemap for vectors of strings
Ziv Yaniv (4):
Adding a test for R Translation Transform GetOffset method.
Adding test for Composite transform AddTransform method.
Adding test for returning vector of strings.
Updated the documentation for the ReadImage procedural interfaces.
From: Bradley Lowekamp <blowekamp@mail.nih.gov>
git-svn-id: http://svn.slicer.org/Slicer4/trunk@25719 3bd1e089-480b-0410-8dfb-8563597acbee |
