[ITK-dev] [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.


More information about the Insight-developers mailing list