[ITK-users] [ANNOUNCE] ITK 4.6.0 has been released!
Matt McCormick
matt.mccormick at kitware.com
Wed Jul 30 14:44:08 EDT 2014
On behalf of the Insight Toolkit community, we are proud to announce
that ITK 4.6.0 has been released!
Links to the Sourceforge.net tarballs can be found on the download page:
http://www.itk.org/ITK/resources/software.html
Outline
----------
1. Introduction
2. New Documentation
3 New Features
4. ITK Changelog
5. ITK Sphinx Examples Changelog
6. ITK Software Guide Changelog
Introduction
-------------------------
The 4.6 release is a major milestone that marks the hard work of many
outstanding community members.
Among the major contributions in this release are improved Remote
Module support with a number of exciting new Remote Modules. The
TransformToDisplacementField filter and a entire module of image noise
generation classes were migrated into the default build. A number of
new optimizers were added to the Registrationv4 framework, which also
experienced a number of performance improvements. Performance
improvements were a general theme as was improved code coverage.
Python wrapping underwent a huge cleanup.
Our documentation continues to improve with better examples, Doxygen
documentation, and guidance material. The Software Guide was split in
anticipation of the release of two new hard copy books.
Thanks to everyone for their hard work!
Enjoy ITK!
New Documentation
-------------------------
Our documentation continues to improve. Remote modules are now
grouped in the Doxygen Module page [1]. A number of new examples were
added to the Sphinx repository and the Wiki, which can now also be
built as Remote modules. The Software Guide was split into two books
and the ITK configure and build instructions were revised.
[1] http://www.itk.org/Doxygen/html/modules.html
New Features
------------------
* CMake improvements
- Improved Remote Module support
- Add ITK_FORBID_DOWNLOADS for package maintainers
- ITK_USE_SYSTEM_EXPAT available
* Filtering Improvements
- Moved TransformToDisplacementField out of Review
- An entire noise image generation module
- http://hdl.handle.net/10380/3158
- Better pipeline support for ResampleImageFilter
- Move MagnitudeAndPhaseToComplexImageFilter out of Review
- Setters for LabelMap overlay filters
- More consistent filter progress reporting
* ImageIO improvements
- Register the GE image formats by default
- More IO modules are built as shared libraries
- OpenFileForReading/Writing methods in ImageIO
- Support for system tiff 4.0.0-4.0.2 (e.g. some Ubuntu versions)
- Mangling to internal OpenJPEG
- SCIFIO improvements
* Infrastructure improvements
- MetaDataObject print specialization for common types
- Improvements to ResourceProbe and RealTimeClock
- More Solve methods for VNLSparseLUSolverTraits
- Output stream operator for LightObject exposed
- FFTW bump to 3.3.3
* New Remote Modules
- Skull stripper
- http://hdl.handle.net/10380/3353
- Wiki examples
- Sphinx examples
- Variational registration
- http://hdl.handle.net/10380/3460
- AnalyzeObjectMapIO
- http://hdl.handle.net/1926/593
- FDFImageIO
- SplitComponents
- http://hdl.handle.net/10380/320
* Registrationv4 improvements
- v4 regular step gradient descent optimizer
- v4 amoeba optimizer
- v4 exhaustive optimizer
- v4 Powell optimizer
- v4 one-plus-one-evolutionary optimizer
- v4 LBFGS optimizer improvements
- Use registration method classes as pipeline filters
* Performance improvements
- Registrationv4
- Histogram computation
- Improved SmartPointer copy
- CompositeTransform
- Registration Jacobian re-use
* Wrapping improvements
- pygccxml 1.0.0
- .pth symlink usable in a virtualenv
- Cleaner CMake configuration
- SWIG and PCRE updated to 3.0.2, 8.34
- Latest GCCXML, which works with GCC 4.9
- Sweeping wrapping generation cleanup
* Many style improvements -- ITK gets more stylish with every release!
* Improved code coverage -- some measures put us over 85%!
* *Lots* of important bug fixes
* And more! See details in the log below.
List of changes since v4.6rc03
--------------------------------------
Arnaud Gelas (1):
DOC: ThresholdBetween does not exist, it should be ThresholdOutside
Bradley Lowekamp (6):
BUG: Remove division in inner loop for otsu threshold calculator
COMP: Fix implicit conversion warnings
BUG: Print the histogram calculator for auto threshold filter
BUG: Use tolerant float compare when choosing better otsu threshold
BUG: Fix out of bounds access for image region size
BUG: Add export specification to DCMTKFileReader and utilities
Luis Ibanez (1):
BUG: Increased OtsuThreshold computation precision
Matthew McCormick (13):
COMP: Remove unused local typedef's.
COMP: Make Doxygen Modules group definition consistent.
STYLE: Improve readability and const correctness of ImageIORegion.
BUG: GDCM does not apply rescale slope / intercept on write.
COMP: Ignore itkIndex.h -Warray-bounds warnings on GCC 4.9.
COMP: Remove unused typedefs in ITKReview module.
COMP: Remove unused FFTW typedef's.
COMP: Remove unused typedefs from the Examples.
COMP: Remove unused typedefs in compatibility code.
BUG: Fix GDCM buffer size when written pixel type is different.
COMP: Disable array above bounds warnings in FixedArray for GCC 4.9.
BUG: Increase itkVoronoiPartitioningImageFilterTest1 for 32-bit builds.
BUG: Set output type to unsigned char when writing uchar in GDCMIO test.
Michka Popoff (3):
BUG: Fix GeodesicActiveContourImageFilterOutput7.png
STYLE: Threshold Segmentation LevelSet Image Filter Figure
ENH: Remove GeodesicActiveContourImageFilter.py example
List of changes since v4.6rc02
---------------------------------------
Ali Ghayoor (1):
ENH: Convert seven ImageRegistration examples to ITKv4
Bradley Lowekamp (2):
BUG: Remove multiple per-pixel allocations in Mahalanobis Membership
COMP: Fix unused-local-typedef warnings in the Registration
and Numeric
Hans Johnson (1):
ENH: Prepare for ITKv4 registration Examples
Matthew McCormick (5):
BUG: Improve module Group membership detection.
COMP: Fix unused-local-typedef warnings in Group Core.
BUG: Update TransformReadWrite example.
COMP: Fix unused-local-typedef warnings in the Filtering Group.
COMP: Remove unused typedefs.
Nick Tustison (1):
ENH: Missed spec for generic computation type.
List of changes since v4.6rc01
---------------------------------------
Bradley Lowekamp (3):
BUG: Do not ENABLED_SHARED for GDCMIO
DOC: Add break in brief description of Canny edge filter
BUG: Add additional MetaDataObject explicit instantiation.
Jean-Christophe Fillion-Robin (2):
COMP: Fix "unused-local-typedefs" warnings
COMP: Fix "unused-local-typedefs" warning in
LandmarkBasedTransformInitializer
Kent Williams (1):
COMP: Fix typo in ReflectiveImageRegionConstIterator.
Matthew McCormick (4):
DOC: CMake warning BRANWEB -> BRAINWEB.
BUG: Remove -Wno-unused-local-typedefs flag.
COMP: Fix IOSTL Doxygen group and Windows shared build.
BUG: Use Remote repository explicitly on git fetch.
Michka Popoff (6):
COMP: Move itkMatrixCoefficients wrapping to Filtering module
COMP: Fix wrapping with Core only
STYLE: Pep8 cleanup for generators
COMP: Fix default wrapping with all modules
ENH: Use open() instead of file() for python 3 compatibility
ENH: Allow to use methods which pass std::string by reference from python
Nick Tustison (1):
ENH: Adding generic computation type.
List of changes since v4.5.0
--------------------------------------
Alexander Schmidt-Richberg (1):
ENH: Added *.remote.cmake for remote module VariationalRegistration
Ali Ghayoor (22):
ENH: Add a registration test for LBFGS-B optimizer
ENH: Add versorTransformOptimizerv4 class to ITKv4
BUG: Fix Coverity defects for LBFGS-B tests
BUG: avoid division by zero in versorOptimizerv4
ENH: Add RegularStep gradient optimizer to ITKv4
DOC: The use of VersorTransformOptimizerv4 is deprecated.
ENH: [SG]et optimizable params ITKv4 registration
ENH: remove VersorTransformOptimizerv4 from ITKv4
ENH: Add AmoebaOptimizerv4 to ITKv4 registration
ENH: Add ExhaustiveOptimizerv4 to ITKv4 registration
ENH: Add PowellOptimizerv4 to ITKv4 registration
BUG: define the GetStopConditionDescription as a public member funciton
ENH: Add OnePlusOneEvolutionaryOptimizerv4 to ITKv4 registration
BUG: lbfgsb optimizer could not be used in unbounded mode
ENH: Add GetCurrentIteration to ExhaustiveOptimizerv4
ENH: Add currentIteration to the AmoebaOptimizerv4
PERF: Move the currentIteration to optimizersv4 base class
ENH: Move the NumberOfIterations to the Optimizersv4 base class
PERF: Change the parent class of RegularStepGradDescentv4 optimizer
ENH: Add currentIteration to LBFGSBOptimizerv4
BUG: Fix memory leak in LBFGSBOptimzierv4
ENH: Add distance vector to KdTree search API
Bill Lorensen (32):
BUG: Tiff compression was broken and untested
ENH: Add SetJPEGQuality method
COMP: Missing breaks in swithc
COMP: Uninitialized scalar field
COMP: Uninitialized scalar field
COMP: Unused pointer value
ENH: Add SkullStrip Remote Module
BUG: Tiff compression was broken and untested
COMP: Missing breaks in swithc
ENH: Improved message for missing IO factories
COMP: Remove vcl_time and vcl_clock
ENH: Remove vcl_math calls
COMP: std::abs integral overloads not always provided
COMP: Array versus singleton access
COMP: Failed to check dynamic_cast results
STYLE: Empty lines exceed 3
COMP: Uninitialized member data
BUG: Two tests try to write the same file
ENH: Uninitialized scalar field
COMP: Constructor initialize list improvement
COMP: Type warnings in constructors
BUG: Copy/paste error
COMP: Arguments of wrong type
BUG: Buffer not null terminated
BUG: Dereference after null check
BUG: Division or modulo by zero
ENH: Uninitialized scalar field
BUG: Uninitialized scalar field
BUG: Not restoring ostream format
ENH: Add an exception safe state restore class for streams
BUG: Not restoring ostream format
ENH: Add WikiExamples as a remote module
Brad King (4):
COMP: Remove extra calls to cmake_minimum_required
COMP: Fix cmake_minimum_required call order
COMP: Set CMake Policies CMP0025 and CMP0042 as necessary
COMP: Add missing call to cmake_minimum_required
Bradley Lowekamp (91):
ENH: Removed non-work TCL Examples
DOC: Add missing const in Doxygen GetConstReferenceMacro
BUG: Correctly re-throw exception to restore AbortEvent, ProcessAborted
BUG: Emit StartEvent before a ProgressEvent
BUG: Do not throw exception in Probes with mis-matched Stop
BUG: Correctly re-throw exception to restore AbortEvent, ProcessAborted
BUG: Adding export specification to Exception objects
COMP: fix unused variable warning in abort test
BUG: Adding export specification to Exception objects
COMP: fix failing voronoi segmentation tests
COMP: Remove explicit typed exception specifications
ENH: Print Object name for observers of objects
ENH: Adding progress reporting to some filters
BUG: fixing grind peak progress to reach 1.0
COMP: use std::transform with static_cast to avoid conversion warning
BUG: disable ipa-cp-clone in GDCM
COMP: fix unused variable warning in abort test
BUG: Do not throw exception in Probes with mis-matched Stop
BUG: Address Shared Library issues with SCIFIO
COMP: fix failing voronoi segmentation tests
COMP: export required in explicitly defined NumbericTraits consts
DOC: Make comment the Doxygen brief
BUG: Adding missing raw data file to MINC test
BUG: Fix linkage for SmartPointerForwardReference for clang 4
BUG: Fixing missing char type and doc for Thresholding filters
BUG: Add support for system libtiff 4.0.0-4.0.2
BUG: remove second wrapping of BinShrink for scalars
BUG: Fix LabelStatistics and LabelOverlap to require same image size
PERF: Remove IncreaseFrequencyOfMeasurement from inner loops
STYLE: Save deference iterator mapped type to variable
PERF: switch to scanline and linear iterators
COMP: Fix checks for system libtiff
PERF: add namespace swap to SmartPoitners
PERF: Use stl iterator algorithm in Iterator Partitioner
BUG: Add mutex lock to MersenneTwister GetInstance
STYLE: MersenneTwister move methods to cxx, docs
STYLE: renaming files to standard ITK conventions
ENH: Improving Noise Simulation Filters
COMP: Explicitly make constant an unsigned int
BUG: Fix uninitialized ivar in NoiseBaseImageFilter
ENH: Make NoiseBaseImageFilter an abstract base class
COMP: remove extraneous cast to double
BUG: Same test function in different file causes conflict
ENH: Explicitly specify internal linkage for internal observer objects
ENH: Enable observed events to modify observers
BUG: Catch exception in DeleteEvent
STYLE: dynamic_cast to pointer does not throw
COMP: Fix GCC warning about unused typedef in ConceptChecking
COMP: Adding itkMacro.h for ITK_NULLPTR definition
ENH: Use DynamicCastInDebugMod for name input macros
BUG: Add support for signed char output
BUG: Use NewMacro for Clone with TimeVaryingVElocityFieldTransforms
ENH: Improve DataObjectDecorator with Modifiable, Graft ReleaseData
ENH: Improve Resample's use of pipeline inputs
ENH: Adding output of line and file on test failure
ENH: Add InitialTransform as pipelined input with inplace option
ENH: Use Transform base class as default template parameter
ENH: Use InitialTransform in deformation examples
COMP: add missing stl algorithm header for std::max
COMP: add missing stl algorithm header for std::max
Revert "ENH: Add Remote module group description to Doxygen."
COMP: Remove incorrect override declaration
ENH: Encapsulate expat header
ENH: Make IntialMoving and InitialFixed transforms decorated inputs
ENH: Update SimpleRegistration test
BUG: Don't create new Decorator in GenerateData
BUG: Use referenceImage for output information
ENH: Adding some ImageIO libraries as shared
ENH: Use TransformParametersAdaporBase on Transform base class
ENH: Removing const_casts from ImageRegistrationv4 tests
BUG: Add AllocateOutputs method to other v4 RegistrationMethods
ENH: Update v4 registration tests to set initial transform
BUG: Explicitly instantiate common MetaDataObjects
BUG: Disable explicit visibility with OSX gcc and llvm gcc 4.2
ENH: Register GE Image formats
COMP: Fix warning for overloading AllocateElements
COMP: Suppress warning for using extern template instantiation
PERF: Use shallow swap over deep assignment
ENH: Use LearingRate member variable for scaling gradient
ENH: support learning rate estimation for regular step optimizer
COMP: Add space between string literals
ENH: remove catch as dynamic_cast of pointers is nothrow
BUG: Use rounding in TestingStretchIntensity for portability
BUG: Warn if unsupported ITK_BRAINWEB_DATA_ROOT is being used
ENH: Use MultiResolutionIteration event for registration
ENH: Use exception safe copy-and-swap for assignment
BUG: Use DEPENDS for dependent files
STYLE: Add itkPrintSelfObjectMacro to improve indenting
BUG: Print missing member variables
ENH: Make more IO modules shared.
COMP: Add missing header for EXIT_FAILURE
Brian Helba (66):
ENH: Disable tip to enable Uncrustify from SetupForDevelopment
STYLE: Rename TValueType template parameters to TValue
COMP: Fix compiler warnings with ITK_USE_SYSTEM_VXL
BUG: Make all specializations NumericTrails::SetLength re-zero contents
ENH: 3048, 3224: Refactor *SampleFilters to fix multiple issues
ENH: Re-enable the array-bounds warnings for GCC 4.7
DOC: Fix a bug with SquaredEdgeLengthDecimationQuadEdgeMeshFilter
DOC: Clean up comments in NiftiImageIO, for better Doxygen compatibility
STYLE: Remove unused typedefs from AlgorithmsPrintTests
BUG: Fix improper usage of VoronoiSegmentationRGBImageFilter
ENH: Move OpenFileForReading/Writing from StreamingImageIO to parent class
ENH: Improve OpenFileForReading/Writing logic and documentation
BUG: Prevent ObjectFactoryBase from possibly throwing an exception
STYLE: Make internal-use CMake variables lowercase in KWStyle.cmake
PERF: Prevent FindKWStyle.cmake from being called multiple times
BUG: Fix FindKWStyle crash when kwstyle returns empty version info
BUG: Fix Coverity issue 1081600: Use after free
BUG: Update SmoothingRecursiveYvvGaussianFilter to fix CMake warnings
ENH: Update ImageIO classes to use OpenFileForReading/Writing
COMP: Fix array subscript build warning
COMP: Except Git's status messages from CTest reporting
COMP: Suppress Coverity defect when Examples create an ITK object
BUG: Fix uninitialized variable in GradientRecursiveGaussianImageFilter
DOC: Fix documentation in VoronoiDiagram2DGenerator
BUG: Coverity 1081062: Fix big parameter passed by value
BUG: Update IOSTL to include new bug fixes upstream
DOC: Improve documentation for StatisticsAlgorithm functions
BUG: Coverity 1130670: Buffer not null terminated in GE4ImageIO
BUG: Coverity 1103200: Copy into fixed size buffer in GE5ImageIO
STYLE: Coverity 1080839: Dead default in switch in
QuadEdgeMeshEulerOperatorJoinVertexTest
STYLE: Coverity 1080963: Dereference after null check in TreeIteratorBase
BUG: Coverity 1081009: Missing break in switch in GiftiMeshIO
BUG: Coverity 1081422: Uninitialized pointer field in
QuadEdgeMeshFrontBaseIterator
STYLE: Coverity 1081140: Dereference before null check
BUG: Coverity 1081547: Uninitialized pointer field in
ConnectedRegionsMeshFilter
STYLE: Coverity 40ee44a9: Self assignment in
VoronoiSegmentationImageFilterTest
BUG: Coverity 1081129: Dereference before null check in itkIOCommonTest
COMP: Update libminc from upstream, fixing a compiler warning on OSX
BUG: Coverity 1081019: Improper use of negative value in StringTools
COMP: Fix downcast warnings
BUG: Coverity 1103189: Big parameter passed by value in FindSampleBound
COMP: Fix implicit conversion warning
COMP: Fix unused variable warning on Intel compilers
BUG: Fix uninitialized variable in GradientRecursiveGaussianImageFilter
BUG: Make all specializations NumericTrails::SetLength re-zero contents
BUG: Update SmoothingRecursiveYvvGaussianFilter remote module
BUG: Update SplitComponents remote module
COMP: Fix implicit conversion warning
BUG: Update SmoothingRecursiveYvvGaussianFilter remote module
COMP: Update LesionSizingToolkit remote module from upstream
STYLE: Coverity 1103618-1103620: Structurally dead code
STYLE: Coverity 1081585: Structurally dead code
STYLE: Coverity 1081584: Structurally dead code
STYLE: Coverity 1081583: Structurally dead code
STYLE: Coverity 1081580: Structurally dead code
STYLE: Coverity 1081570-1081578: Structurally dead code
STYLE: Coverity 1081566-1081568: Structurally dead code
STYLE: Coverity 1081564: Structurally dead code
STYLE: Coverity 1080826-1080827: Logically dead code
STYLE: Coverity 1080862: Logically dead code
STYLE: Coverity 1081598: Unused pointer value
BUG: Coverity 1103595: Uninitialized pointer field
BUG: Coverity 1081508: Uninitialized pointer field
BUG: Fix uninitialized pointer fields
BUG: Coverity 1081381: Uninitialized scalar field
STYLE: Coverity 1103107-1103116: Logically dead code
Constantine Zakkaroff (1):
DOC: HelloWorld Comments Edit for ITKSoftwareGuide
David Cole (2):
COMP: Eliminate some level 4 warnings
BUG: Add missing header files to enable try_run tests to run
without crashing
Dirk Padfield (2):
DOC: Improved comments and reorganized code for IsolatedConnected
DOC: Corrected documentation for threshold boundaries.
Eric Greveson (1):
ENH: Add setters for the overlay functor in labelmap overlay filters.
Fotis Drakopoulos (1):
ENH: Adding GetFEMFilter method to
PhysicsBasedNonRidgidRegistrationMethod.
GCC-XML Upstream (1):
pygccxml 1.0.0 (reduced)
Gaëtan Lehmann (1):
ENH: Importing files from Noise Simulation Article
Gib Bogle (1):
BUG: Windows BigTIFF errors: stat failure and lack of COMPRESSION_DEFLATE
Google double-conversion Maintainers (1):
COMP: Google double-conversion (reduced)
Guillaume Pasero (1):
ENH: Add mangling to internal OpenJpeg
Hans Johnson (40):
PERF: 15% speed improvement for registration
PERF: Simplify conditionals in loop
COMP: Conditional assert check warning unused var.
COMP: SimpleITK linkage failure
BUG: Missing Modified() call
COMP: SimpleITK linkage failure
BUG: Element numbers 1053, 1052 not hex
BUG: Remove valgrind reported leak
BUG: Add missing transform types to factory
BUG: Missing Modified() call
PERF: Reviewing code for facilitating compiler optimizations
COMP: Fix const constructor for const arrays
ENH: Add LBFGOptimizerv4(for BSPline registration)
COMP: Test failure from numerical precision
BUG: Memory leak introduced.
COMP: Remove deprecated 'register' keyword
ENH: Ignore autocompletion clang helper files
ENH: Move to latest remote module tag
STYLE: Improve testing of member Get/Set functions
COMP: Update AnalyzeObjectMapIO replacing deprecated
DOC: Fixed documentation regarding multi-threading
DOC: Improved Image Representation
PERF: Minimize redundant function calls
PERF: Pull loop termination constants out of loop
ENH: Refactoring the CompositeTransform class
STYLE: Explicitly declare virtual for derived class member functions
STYLE: Explicitly recognize virtual functions
STYLE: Add ITK_NULLPTR supporting c++11 checks
BUG: Missing parentheses for logic comparison
STYLE: Explicitly declare virtual (cont. of 1c8609)
STYLE: Consistency of threadID and threadId
BUG: FFTConvolutionImageFilter outputs incorrect
STYLE: GetStopConditionDescription abstract method
PERF: Re-use jacobian rather than instantiation
ENH: Improve test in preparation for performance testing
PERF: Code simplifications for performance testing
BUG: Missed an API change for Allocate
STYLE: Remove unnecessary comments.
BUG: Expose unusable functions
BUG: Incomplete refactoring of member variable name
Jean-Christophe Fillion-Robin (1):
COMP: Fix "unused-local-typedefs" warnings
Jens Wetzl (2):
BUG: Fix race conditions in itkInvertDisplacementFieldImageFilter
STYLE: Incorporated reviewer suggestions
Jon Haitz Legarreta (8):
ENH: New test for itkSigmoidTransferFunction.
COMP: Fix type casting build warning.
ENH: New test for itkLogSigmoidTransferFunction
ENH: Added call to Print() method
STYLE: Changed LogSigmoidTransferFunction template argument names.
ENH: Added StatisticsRelabelImageFilterTest to testing
BUG: Fix issues with the BinaryStatisticsOpeningImageFilter test
COMP: Test for itkCustomColormapFunction
Kent Williams (13):
ENH: Add remote module for AnalyzeObjectMapIO
BUG: incorrect loop var increment
COMP: Update the DoubleConversion library upstream update script.
ENH: Turn off DCMTK Logger messages by default
COMP: fixed license test command in UpdateDoubleConversionFromGoogle.sh
ENH: Add FDFImageIO as a remote module.
PERF: replace image allocate followed by fillbuffer with allocate(true)
COMP: Add test to verify Slope/Intercept handling
BUG: GDCM reporting wrong spacing for some Media Types
ENH: Add test for itkTestingStretchIntensityImageFilter
COMP: Fix misplaced closing brace
ENH: Remove try/catch exception handling around dynamic_catch
ENH: Disallow vector multiply by itself
Liza Shrestha (1):
COMP: Added new unit tests for increasing code coverage
Luis Ibanez (11):
ENH: Add STLMeshIO remote module.
BUG: Fixed module name IOSTL.
COMP: Fixing instantiation of templated functions.
BUG: Fixed Affine test 32bits. Precision checks.
PERF: Accelerate initialize via selective testing.
COMP: ShapeUniqueLabelMapFilter test was missing.
STYLE: Coverity 1103119: Logically dead code
BUG: itkLoggerThreadWrapper test was disabled.
BUG: No DiscreteHessianGaussianImageFunctionTest.
BUG: DiffusionTensorReconstruction lacked Progress
BUG: TestingExtractSliceImageFilter lacked test.
Luke Bloy (4):
BUG: Fixes itkBoxSpatialObject part of issue ITK-3153
BUG: Fixes itkImageMaskSpatialObject part of issue ITK-3153
BUG: Fixes itkBoxSpatialObject part of issue ITK-3153
BUG: Fixes itkImageMaskSpatialObject part of issue ITK-3153
Marius Staring (2):
ENH: add reset function to resource probe
ENH: adding handle to RealTimeClock
Mark Hiner (1):
ENH: bump to latest scifio-imageio
Martin Steghöfer (1):
BUG: Match behavior of SimpleFastMutexLock on different
platforms (#ITK-3248)
Matthew McCormick (93):
ENH: Bump CMakeLists.txt to version 4.6.0.
BUG: Remove unused itkAffineTransformXX.txt content links.
BUG: Avoid SimpleImageRegistration{Float,Double}Test output clobbering.
BUG: Prevent MINC transform tests outputs from clobbering.
BUG: Add random number generator seed for vnl_algo_test_sparse_lm.
COMP: Update libminc to latest version.
ENH: Only build tests for modules explicitly enabled.
BUG: Remove unused forward declarations in RegistrationMethodsv4.
COMP: Update libminc to latest version.
ENH: Add REQUIRES_DISPLAY CTest label.
ENH: Add SplitComponents Remote Module.
DOC: Suggest MeshFileReader instead VTKPolyDataReader.
DOC: Add itkSetGetDecoratedInputMacro definition for Doxygen.
COMP: Bump DCMTK to fix warning.
BUG: Wrap TransformFileReader, TransformFileWriter.
BUG: Remove unused itkAffineTransformXX.txt content links.
COMP: Wrap OptimizerParameterScalesEstimatorTemplate.
COMP: CommandIterationUpdate has field whose type uses anonymous
namespace.
COMP: Do not use -fno-ipa-cp-clone with clang.
ENH: Move TransformToDisplacementFieldSource out of Review.
ENH: Bump ITK version to 4.5.1.
COMP: ImageRegistrationHistogramPlotter Clone never referenced.
ENH: Add the ITK_INSTALL_LIBRARY_DIR to WrapITK.pth.
ENH: Bump SCIFIO to add wrapping.
COMP: ImageRegistrationHistogramPlotter unchecked dynamic_cast.
BUG: Fix Array memory leaks with non-const construction.
BUG: Prevent ambiguous Array construction methods.
COMP: HDF5 library version variables contain '@'.
COMP: Remove add_custom_command(SOURCE...
COMP: Wrap OptimizerParameterScalesEstimatorTemplate.
BUG: Wrap TransformFileReader, TransformFileWriter.
COMP: Add missing itkVerson.h header.
COMP: LBFGSOptimizerBasev4 explicit Doxygen link request.
ENH: Bump FFTW to 3.3.3.
COMP: Duplicated VectorContainer wrapping for real types.
BUG: Increase tolerance for itkFEMC0TriangularElement-NodalLoads-BCs
STYLE: Add missing "Test" to GDCM test names and filenames.
DOC: No ReferenceImage members in TransformToDisplacementFieldSource.
COMP: Bump LesionSizingToolkit for Doxygen warnings.
BUG: GDCM Series does not write z-spacing.
COMP: Remove unreachable return statements.
ENH: Add ITK_FORBID_DOWNLOADS option. ITK-3239
COMP: Bump SplitComponents Remote for Doxygen warnings.
COMP: return will never be executed after exception thrown.
BUG: Invalid read during ImageIOBase SetDirection.
COMP: Fix failed itkTIFFImageIOCompressionTest merge.
ENH: Bump version to 4.5.2.
COMP: return will never be executed after exception thrown.
COMP: SigmoidTransferFunction conversion from double.
BUG: BoxImageFilter GenerateInputRequestRegion public -> protected.
DOC: KernelImageFilter does not reimplement GenerateInputRequestedRegion.
STYLE: Remove SigmoidTransferFunction .hxx doxy comments.
BUG: Clean up Python module2module test.
BUG: TestingExtractSliceImageFilterTest v3 direction strategy.
STYLE: Remove duplicated TestingExtractSliceImageFilter doxygen.
COMP: Use latex formula for HoughTransform doxygen.
COMP: SigmoidTransferFunction members Alpha, Beta real type.
STYLE: Fix SigmoidTransformFunction template argument names.
COMP: BuildHeaderTest.py print_function import.
BUG: Fix print function errors in pygccxml.
BUG: Fix print functions in igenerator.py.
ENH: Add Remote module group description to Doxygen.
STYLE: Clean up MetaDataObjectBase.
STYLE: Clean up MetaDataObject.
ENH: Add unit test for MetaDataObject.
ENH: Add MetaDataObject Print specialization for common types.
STYLE: Fix template statements in SigmoidTransformFunction.
BUG: Remove public MetaDataObject constructors.
BUG: Add missing private copy constructors to MetaDataObject.
BUG: Remove FEMRegistrationFilter debug code.
DOC: Improve documentation and types for SplitRequestedRegion.
Revert "Revert "ENH: Add Remote module group description to Doxygen.""
DOC: Remove errant "+" in Remote_documentation.
ENH: For shared libraries when wrapping.
ENH: Collect all wrapping configuration checks in one place.
ENH: Better CMake defaults with wrapping.
ENH: Replace CSWIG preprocessor definition with ITK_WRAPPING.
BUG: Remove old itkSampleBuildTest.cmake.in file.
ENH: Move MagnitudeAndPhaseToComplexImageFilter out of Review.
COMP: Fix Doxygen warnings in itkMetaDataObject.h.
BUG: Exclude Remote Modules the default ON Group values.
COMP: Documentation CMake target must come before add_custom_command.
BUG: Assign Remote modules to groups more robustly.
BUG: Remove MagnitudeAndPhaseWriteComplexImageFilter test from
Review Module.
BUG: Remove old tests from Review for classes that have been removed.
DOC: Fix Software Guide LaTeX syntax errors in the examples.
COMP: Define ITKCommon_EXPORT_EXPLICIT for Doxygen.
COMP: Remove itkImageReadComplexWriteMagnitudeAndPhaseTest.cxx from list.
BUG: Move MagnitudeAndPhaseToComplexImageFilter to the
ImageIntensity module.
COMP: StdStreamStateSave Doxygen include.
ENH: Add Sphinx examples as a Remote Module.
BUG: Remove ITK_INSTALL_NO_LIBRARIES and ITK_INSTALL_NO_DEVELOPMENT.
ENH: Make ITK_WRAPPING INTERNAL.
Matthew Woehlke (1):
COMP: Fix egregious -Wcast-qual warnings
Michka Popoff (53):
BUG: Fix for the WrapITK.pth destination path
COMP: Fixes the Python wrapping under OS 10.8.5
STYLE: Removed itkExtras folder
BUG: Fix for the WrapITK.pth destination path
COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
STYLE: 4 space indentation for python files
COMP: Fixed itkGradientDescentOptimizerv4 wrapping warnings
STYLE: Removed deprecated itk functions
STYLE: Removed unused and misplaced python tests
STYLE: Removed legacy python importing
STYLE: Pep8 cleanup for the python files
STYLE: Remove deprecated python strel function
COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
COMP: Fixed itkGradientDescentOptimizerv4 wrapping warnings
ENH: Use python warnings module for template warnings
COMP: Duplicated wrapping for double in Array2D
COMP: Update SWIG to 2.0.12
COMP: Require at least Python 2.6 for Python wrapping
ENH: Remove python dl dependency
ENH: Remove psyco import
COMP: Update PCRE to 8.34
ENH: Update Swig to 3.0.0
STYLE: Remove WrapITK versions
COMP: Remove cmp0011 in wrapping
COMP: Remove unused code in ConfigureWrapping.cmake
COMP: Remove clrLine in itkExtras
COMP: Fix the python import and progress callbacks
STYLE: Remove reference to CableSwig
STYLE: Clean up BinaryThresholdImageFilter (python)
COMP: Fix the Python ResampleImageFilter test
ENH: Bump SCIFIO for OS X installation
ENH: Bump SCIFIO for OS X installation
COMP: Update PCRE to 8.35
STYLE: Remove unused compile all code for Python Wrapping
ENH: Replace python print with print() function
STYLE: Remove deprecated Python wrapping macros
COMP: Fix failing header test
COMP: Fix the writing of .idx files
COMP: Fix python print import for .pth file creation
COMP: Fix print import statement in itkExtras.py
STYLE: Refactor swig call and code cleanup
COMP: Fix for wrapping warnings (RealTimeClock and SimpleFastMutexLock)
STYLE: Remove old Python examples
COMP: Update gccxml
ENH: Use pygccxml snapshot.
ENH: Update to swig 3.0.2
DOC: Update commit instructions for JIRA bugtracker
ENH: Update GCCXML
BUG: Fix wrapping with dimension 2 only
COMP: Temporarily hide pygccxml warnings
BUG: Do not wrap BinaryMask3DMeshSource when building with 2D only
COMP: Move itkMatrixCoefficients wrapping to Filtering module
COMP: Fix wrapping with Core only
Miguel Algaba (1):
ENH: Added further Solve methods to VNLSparseLUSolverTraits
Nick Tustison (2):
BUG: Ignored the case for exceeding iteration limit.
ENH: Preparing point set metrics for use with registration.
Rashad M (1):
STYLE: Allow system installed expat library with ITK_USE_SYSTEM_EXPAT=ON
Sean McBride (6):
BUG: initialize m_SmallBlock ivar in ctor; fixes garbage read
BUG: changed some variables involved in shifting to unsigned
COMP: Updated libminc to a78661bb592359ab86f417cc0c298299e593d808
BUG: initialize m_SmallBlock ivar in ctor; fixes garbage read
PERF: Mark ImageRegistration8Test with RUNS_LONG
COMP: workaround clang -Windent warnings by fixing indentation
Sebastian Pölsterl (1):
BUG: Return null pointer if class label does not exist (#3235)
Taylor Braun-Jones (1):
ENH: Expose the output stream operator for LightObject
Vladimir Chalupecky (1):
DOC: Fix description of SpatialObject::GetBoundingBox()
Vladimir S. FONOV (3):
COMP: Fixed libminc to build on Windows
COMP: Updated libminc, hopefully reducing number of warnings
COMP: Improved MINCIOTransform tests
Wei Liu (1):
BUG: Fixed a bug in ExpectationMaximiationMixtureModelEstimator.
Yves Frederix (1):
ENH: GeodesicActiveContourShapePrior deals with DerivativeSigma
equal to zero
ITK Sphinx Examples Changelog
-----------------------------------------
Arnaud Gelas (25):
remove annonying messages about include folders not used with Clang
ENH: Add one example for LabelMapMakImageFilter
upgrade breathe to 1.2.0
add documentation for ITKLabelMap
ENH: Add one example to convert a triangular mesh to binary image
ENH: Add example for itk::AccumulateImageFilter
read an unknown image type
add example to generate mesh from binary image
ENH: Add one example for ExpNegativeImageFilter
add one example for ThresholdImageFilter
Add one example to translate one itk::Mesh
add Iterative hole filling example
wrong directory name
fix link to c++ code
link to the wrong folder for canny edge detection example
Resample scalar image (with identity transform)
fix command line for cloning in README
COMP: Fix for failing ApplyAccumulateImageFilter baseline comparison test
add one example to translate one itk::Image
add PasteImageFilter example
fix path in ArchiveBinaryData.py.in
BUG: error when TEST_IMAGE_PREFIX was used
fix broken links as detected by linkcheck
add example for PermuteAxesImageFilter
Add one example to apply an affine transform given homogeneous matrix
Brian Helba (3):
ENH: Support ExternalData_OBJECT_STORES being set with a Superbuild
ENH: Allow ExternalData path to be set by environment on dashboards
BUG: Set correct URL scheme in dashboard common script
Matt McCormick (21):
ENH: DilateABinaryImage uses FlatStructuringElement.
ENH: Add DilateABinaryImage.py.
ENH: ErodeABinaryImage uses FlatStructuringElement.
ENH: Add ErodeABinaryImage.py.
ENH: Use Git email as default when uploading binary data.
BUG: ITKIOImageBase module directory not included.
BUG: MaskOneImageGivenLabelMap test name for baseline comparison.
ENH: Add Register IO Factories example.
ENH: Add documentation upload to common CDash script.
ENH: Add ApplyExpNegativeImageFilter.py.
BUG: Remove non-existent Sphinx example entry.
DOC: Give an example call to UploadBinaryData.py.
COMP: Fix Doxygen link to LevelSets visualization classes.
ENH: Rename module to follow Remote Module convention.
COMP: QUIET initial find_package( ITK ).
ENH: Bump ITK Superbuild tag to 4.6.0.
BUG: Fix ConvertAnITKGrayScaleImageToCVMat compare_to_baseline.
COMP: Remove breathe link to ConstantPadImageFilter.
BUG: Fix figure path for Iterative Hole Filling.
BUG: Evolution.gif needs to be ..only:: html
COMP: Content not permitted in image:: directive.
Michka Popoff (29):
ENH: Add examples for grayscale image dilation/erosion
ENH: Add BinaryThresholdImageFilter example
COMP: Fix for cmake 3.0 compatibility
ENH: Clean up ThresholdAnImageUsingOtsu
ENH: Add missing python documentation call for binarythreshold example
STYLE: Fix Python subtitles
ENH: Add CannyEdgeDetectionImageFilter example
COMP: Add cmake_minimum_required back
STYLE: Cleanup include( ${ITK_USE_FILE} ) and minor alignements
COMP: Fix for Canny Edge example
ENH: Add CastImageFilter.py and code cleanup
ENH: Add ComputeCurvatureAnisotropicDiffusion example
ENH: Add GradientAnisotropicDiffusionImageFilter example
ENH: Add ComputeGradientMagnitudeRecursiveGaussian python example
ENH: Add CurvatureFlowImageFilter example
STYLE: Clean up pipeline and uniformize error catching
ENH: Add mean and median filters
ENH: Add Laplacian filter example
ENH: Add an example of image resampling
COMP: Fix two documentation warnings
STYLE: Update sys.argv len() checks
ENH: Add example for Sigmoid computation
STYLE: Rename python examples to Code.py
ENH: Fix the git URL
ENH: Add python code for ThresholdAnImage
ENH: Add example for SmoothWithRecursiveGaussianImageFilter
COMP: Fix failing setup of SegmentBloodVessels example
STYLE: Update title for Apply Affine Transform example
ENH: Add GeodesicActiveContourLevelSetImageFilter example
ITK Software Guide Changelog
---------------------------------------
Brad King (3):
SoftwareGuideCover: Port to VTK >= 5
SoftwareGuideCover: Re-order code to simplify non-interactive run
SoftwareGuideCover: Adjust colors and camera position for new cover
Bradley Lowekamp (1):
Fix spelling of Lowekamp
Constantine Zakkaroff (1):
ENH: Revise Configure and Build Instructions
Hans Johnson (4):
ENH: Reorder IO and filtering chapters.
STYLE: Remove end of line spaces.
COMP: File name change needed
DOC: Added Direction to the figure
Matt McCormick (39):
ENH: Improve Hello World directions.
BUG: Remove extra configuration of SoftwareGuideConfiguration.tex.
ENH: Update the printed SoftwareGuide authors.
BUG: Updates to PrintedPreamble.
BUG: Update the cover sources location.
STYLE: Update CMake style in SoftwareGuide/Latex/CMakeLists.txt
ENH: Split into two books.
BUG: Build resolving citations.
BUG: Update build process description in SoftwareGuide/README.txt.
BUG: Remove SoftwareGuide/Latex/00-SoftwareGuide.tex.
DOC: Move build instructions to top level README.
ENH: Update funding acknowledgement.
DOC: Remove minipage about VTK/CMake books.
STYLE: Improve spacing after preamble year.
BUG: Update Cover VWSegmentation CMakeLists.txt.
COMP: Fix compilation of ModerBasedSegmentation.cxx.
STYLE: Strip trailing whitespace from SoftwareGuide sources.
COMP: Add -dUseCIEColor when building Printer quality.
BUG: o -> % in comment.
ENH: Update the Kitware logo.
ENH: Update copyright notice.
STYLE: Place the appendix before \backmatter.
BUG: Remove commentted content.
ENH: Matt -> Matthew.
ENH: Add Ali Ghayoor to contributors.
ENH: Add contributors for covers.
BUG: Update participants URL.
BUG: Move build configuration to PrintedPreamble-Common.
ENH: Add description for book cover 2.
BUG: Update index generation.
BUG: Remove wrapping Tcl entry.
BUG: Remove old comments.
ENH: Bump ITK to v4.6.0.
ENH: Pass PDF_QUALITY_LEVEL in superbuild.
BUG: Remove unused RunExamples.py imports.
ENH: Reduce verbosity of RunExamples.py.
BUG: Do not include RegistrationITKv4 example sources in the build.
BUG: Fix caption on Confidence Connectened on BrainWeb figures.
BUG: Bump the ITK superbuild for LaTeX fixes.
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