ITK Release 4.4#

We are excited to announce two new ImageIO modules available in the main repository. The MINC ImageIO module provides a bridge to the MINC file format, a powerful medical imaging format used by the MINC library, another open source library with many features similar to ITK. The new MINC module, which has Image IO and Transform IO capabilities, is considered experimental and must be enabled by turning Module_ITKIOMINC ON in CMake’s configuration. This will automatically build the MINC library, which is now available on Mac, Linux, and Windows. The HDF5-based MINC2 file format is supported, but support for the NetCDF-based MINC1 file format is not supported because NetCDF is not distributed with ITK.

Another new ImageIO module that expands the reach of ITK is the SCIFIO module. SCIFIO is a refactoring of the Bio-Formats library. This module provides access to a wide range of file formats encountered in life sciences/microscopy environments. This experimental feature is available a Remote module; to enable it, set the Fetch_SCIFIO CMake variable to ON. Many improvements and fixes are ongoing for this module; Git master is recommended for those interested in this module.

A number of improvements were also made to DCMTK ImageIO, but this module remains experimental on disabled by default. To try DCMTK ImageIO support, turn the CMake option Module_ITKIODCMTK ON. For Unix platforms, the supporting DCMTK library will automatically be built as a CMake ExternalProject. On Windows, the DCMTK library must be built independently of the ITK build system. Then, specify the location to the external build after setting the CMake option ITK_USE_SYSTEM_DCMTK ON.

A number of performance improvements were made to QuadEdgeMesh processing and memory copy functions. A new ImageScanlineIterator is available. This iterator can be used in many of the cases where an ImageRegionIterator is applied, but it has better performance.

The approach to split image regions for parallel processing is no longer hard coded to make multiple options available.

An API design change was started to improve the implied functionality of the GetObject methods. The non-const ‚ÄúGetObjectMacro‚ÄĚ has been replaced with a ‚ÄúGetModifiableObjectMacro‚ÄĚ that will result in a GetModifiableXXX method instead of a GetXXX method. This makes the non-const nature of the method and the circumvention of pipeline update semantics explicit for both the code author and those reading the class API. This was implemented in a backwards compatible way, and it will only be enforced if ITK_FUTURE_LEGACY_REMOVE is defined.

Support for the Google Double Conversion library was added to improve the reading and writing of double values as ASCII text with the intention to improve the precision of the text transform file format’s serialization.

It is now easier to identify filter inputs by both a string name or an integer index. The internal methods to store and retrieve inputs by either string or index was correspondingly refactored, and performance was also improved.

JPEG ImageIO now writes and reads image spacing in a manner similar to the TIFF ImageIO.

An extensive amount of code cruft was removed and coding style was made more consistent; ITK gets more stylish and classy with every release!

The ExternalData method to store large testing data outside of the Git repository is now in upstream CMake 2.8.11. Our internal version has been updated to the improved version in CMake.

The minimum CMake required version was bumped to 2.8.8 on Windows and 2.8.5 otherwise. This may be increased even higher in the near future to ensure all CMake features utilized operate correctly.

Known assertion failures occur when compiled under Visual Studio in the Debug configuration. This will be fixed in 4.4.1. If this has a significant negative impact on your work, please consider contributing a Nightly dashboard build under this configuration. As previously scheduled, Visual Studio 2005 is no longer be supported.

Support for building against system third party libraries continues to improve. Further improvements are expected for version 4.5.

All tests are now passing again on the Nightly big-endian dashboard system.

InsightApplications (ITKApps) has seen fixes in the FLTK superbuild and the TCL wrapped applications.

Changes in ITK from v4.3.0 to v4.4.0 from the Git log:

Ali Ghayoor (7):

       ENH: Get the internal transforms of SyN registration filter
       COMP: Fix all valid cppcheck warnings in ITK (last patch)

Arnaud Gelas (4):

       PERF: improve performance of couple of methods of itk::QuadEdgeMesh
       PERF: couple of speed up improvements for QuadEdgeMesh processing
       PERF: avoid doing GetPoint and SetPoint for the same point
       ENH: Simplify template parameters in itk::PointsLocator

Bill Lorensen (20):

       ENH: Prevent duplicate loading of dynamic libraries
       COMP: Fix compile error in PhilipsRECImageIO
       COMP: Fix compile error in PhilipsRECImageIO
       BUG: Memory leak after failed RegisterFactory
       BUG: Warn on directories
       ENH: Refactor DoubleToString into NumberToString
       DOC: Escape hash in comment
       STYLE: Apply kwstyle to Modules/Core tests
       STYLE: Apply kwstyle to Modules/Filtering tests
       STYLE: Apply kwstyle to Modules/Segmentation tests
       STYLE: Apply kwstyle to Modules/IO tests
       STYLE: Apply kwstyle to Modules/Numerics tests
       STYLE: Apply kwstyle to Modules/Registration tests
       STYLE: Apply kwstyle to some tests
       BUG: Memory leak after failed RegisterFactory
       COMP: Remove copy_n wrapper for standard std::copy
       COMP: Make the test stable by removing random source
       COMP: More baselines
       COMP: Another baseline
       COMP: Missing return error after exception

Brad King (14):

       BUG: ExternalData: Do not match directory names when resolving DATA{}
       STYLE: ExternalData: Cleanup stray TODO and typo in comments
       STYLE: ExternalData: Remove unused private interface
       ENH: ExternalData: Improve series matching using an explicit syntax
       ENH: ExternalData: Allow ()-groups in series match regex
       ENH: ExternalData: Allow DATA{} syntax to reference directories
       ENH: Configure new ExternalData series parsing for ITK baselines
       BUG: ExternalData: Collapse ../ components in DATA{} paths
¬†¬†¬†¬†¬†¬†¬†BUG:¬†Fix¬†‚Äúgit`` ``gerrit-push‚Ä̬†for¬†content¬†links¬†with¬†spaces
       STYLE: Add detail to the vxl update instructions
       STYLE: Add more detail to the vxl update instructions
       ENH: ExternalData: Partly generalize hash algo/ext handling
       ENH: ExternalData: Attach download rules to content links in IDEs
       ENH: ExternalData: Preserve escaped semicolons during argument expansion

Bradley Lowekamp (78):

       STYLE: Use ITK_ prefix for FFTW cmake variables and defines
       BUG: Change default boundary condition to ZeroFlux
       ENH: wrapping itkImageSeriesWriter
       BUG: incorrect CMake variable for system jpeg include
       DOC: Correct description of Bitwise binary filters
       BUG: incorrect CMake variable for system jpeg include
       COMP: GetTimeVaryingVelocityField methods did not compile
       ENH: Creating templateless region splitter classes
       ENH: Adding image region splitter for separable filtering
       PERF: Do not spawn threads that will not be used.
       ENH: ImageIO's now use ImageRegionSplitter base
       COMP: Specify export for Specialized Array output operators
       ENH: making old ImageRegionSplitter compatible with new splitter
       BUG: initials Direction IVAR
       STYLE: never a space before;
       COMP: Address unused parameter warning in GPU code
       BUG: Do not create static initialized ITK objects
       ENH: Converted Multidimensional splitter to new base class
       ENH: moving old ImageRegionSplitter to Deprecated Module
       BUG: Only thread 0 should report progress.
       PERF: Use std::fill for image filling
       BUG: Only thread 0 should report progress in LabelMapFilters
       COMP: Adding missing header
       BUG: Using CMake variable in external builds with autoconf environment
       BUG: initialize InverseCovariance size with degenerate matrix
¬†¬†¬†¬†¬†¬†¬†ENH:¬†Adding¬†numeric_traits¬†specializations¬†for¬†‚Äúlong`` ``long‚ÄĚ
¬†¬†¬†¬†¬†¬†¬†ENH:¬†instantiate¬†vnl¬†types¬†with¬†‚Äúlong`` ``long‚Ä̬†on¬†all¬†platforms
¬†¬†¬†¬†¬†¬†¬†Revert¬†‚ÄúENH:`` ``Use`` ``named`` ``inputs`` ``in`` ``BinaryReconstruction`` ``filters.‚ÄĚ
       BUG: initialize InverseCovariance size with degenerate matrix
       BUG: Using CMake variable in external builds with autoconf environment
       COMP: Address unused parameter warning in GPU code
       BUG: Only thread 0 should report progress in LabelMapFilters
       BUG: Only thread 0 should report progress.
       COMP: Adding missing header
       ENH: Adding support for instantiating long long pixel types
       BUG: VerifyPreconditions checks required named inputs
       PERF: Adding performance oriented ScanlineIterator
       COMP: Remove copy_n wrapper for standard std::copy
       COMP: Missing ProgressReporter header
       COMP: Suppress linker warning from fftw external project
       COMP: Add missing ImageRegionIterator header in test
       BUG: Don't allocate empty names in Get I/O Names methods
       COMP: Make GPUFunctorBase destructor virtual
       PERF: Changing filters to use ImageScanlineInterator
       COMP: GCC_XML external project does not use BUILD_EXAMPLES
       BUG: Scanline iterator in STAPLE filter not advanced to next line
       PERF: Use ImageScanlineIterator in ImageAlgorithm::Copy
       PERF: Use iterators into name map for index inputs
       ENH: index can be associated with required input
       PERF: Add global variable of index names in ProcessObject
       COMP: fix unused result warning in ProcessObject
       ENH: Remove names inputs specialized comparison
       DOC: Updated input methods doxygen
       PERF: Use ImageAlgorithm::Copy in JoinSeries filter
       PERF: Use ImageAlgorithm::Copy in CastImageFilter
       COMP: Fix failing implicit conversion from NULL
       BUG: restore gnu aligned attribute
       PERF: ImageAlgorithm::copy to use std::copy for conversion
       PERF: Store indexed outputs in array for constant time access
       COMP: GCC_XML compilation error with type_traits
       BUG: Add unsigned int concept check to LabelVoting filter
       COMP: Disable conversion warning for std::copy in ImageAlgorithm
       BUG: Use correct types for TIFF Tags and buff math
       BUG: Use local var for TIFF va_list parameter
       BUG: Use correct bytes for BigEndian magic number
       COMP: Fix int to char narrowing error and warning
       COMP: Fix int to char narrowing error and warning
       COMP: Fix scanf conversion specification to %u
       COMP: Fix scanf conversion specification for id types
       BUG: Remove extraneous print statement in tiffio
       BUG: Incorrect va_arg type used in TIFF and LSM
       BUG: JPEG2000 bool type in C is now unsigned char
       BUG: add a test to demonstrate ThreadedIteratorPartitioner bug
       BUG: Fix written other magic number in FreeSurferBinaryMeshIO
       COMP: Fix assert in LSM, = in err of ==
       BUG: IteratorPartitioner extra thread don't advance
       BUG: C++ bool is 4 bytes on osx ppc

Brian Helba (11):

       STYLE: Ensure documentation \author tags are parsed
       STYLE: Remove unnecessary overloads in favor of implicit conversion
       PERF: Replace deep copy with const const signature
       ENH: Re-enable LoadPrivateTags option in GDCMImageIO
       STYLE: Slightly refactor ImageFileWriter::Write to simplify logic
       ENH: Always enable Get*FromTag methods in GDCMImageIO
       DOC: Fix misspelling in MorphologyImageFilter
       DOC: Fix misspelling in ObjectMorphologyImageFilter
       STYLE: Remove unnecessary function call in GDCMImageIO
       STYLE: Remove calls to deprecated functionality from DICOM Examples / Tests
       ENH: Allow Get*FromTag to accept uppercase hex

Cory Quammen (1):

       COMP: Bumped up minimum required CMake version

Cyrille Faucheux (2):

       ENH: allow the ClampImageFilter to use user-defined bounds (#3016).
       ENH: Move the ClampImageFilter to the ImageIntensity module (#3016).

David Cole (4):

       BUG: Avoid using def file when BUILD_SHARED_LIBS is off
       BUG: Do not undefine _WIN32_WINNT
       BUG: Avoid using def file when BUILD_SHARED_LIBS is off
       BUG: Do not undefine _WIN32_WINNT

David Fuentes (2):

       ENH: Allow block matching on diff size images
       ENH: wrapping itkMaskFeaturePointSelectionFilter itkBlockMatchingImageFilter

Dirk Padfield (6):

       BUG: CSVFileReader was reading all values as NaN
       DOC: Made AnisotropicDiffusion documentation consistent with code
       ENH: Enable MetaIO to read filenames with spaces using regex
       BUG: CSVFileReader was reading all values as NaN
       ENH: Added m_RequiredFractionOfOverlappingPixels to MaskedFFTNCC
       BUG: SignedMaurerDistanceMap in 4D

Google double-conversion Maintainers (1):

       Google double-conversion (reduced)

Hans Johnson (21):

       COMP: Remove unnecessary BORLAND code
       COMP: Make type conversions explicit/consistent
       PERF: Optimize loop index computations
       COMP: Remove unnecessary BORLAND code
       COMP: Incomplete variable name change.
       COMP: Incorrect warning presented for cppcheck
       STYLE: The FFTW libs should be co-located with ITK
       COMP: Fix robustness of DCMTK internal builds
       ENH: Get function accessible from const objects
       COMP: Missing patch for ITK_FUTURE_LEGACY_REMOVE
       STYLE: Reduce redundant code identified by cpd
       BUG: Return a modifiable object or provide const
       STYLE: Improve SoftwareGuide documentation
       COMP: Type mis-match for comparison operator
       STYLE: Enforce using ITK macros when available
       COMP: Type mis-match for comparison operator
       BUG: ITK_FUTURE_LEGACY_REMOVE must cmake configured
       BUG: Expose BSplineInterpolateImageFunction test
       COMP: Linkage ITK_ABI_EXPORT to ITKCommon_EXPORT
       BUG: itk_tiff.h should not be in itkTIFFImageIO.h
       DOC: Fix line length issues for the SoftwareGuide

Ho Cheung (7):

       BUG: GradientVectorFlow should calculate timestep based on image dimension
       STYLE: GradientVectorFlow - Add const correctness
       STYLE: GradientVectorFlow
       PERF: GradientVectorFlow - Remove redundant initializations
       BUG: itkPolyLineParametricPath infinite loop for degenerate paths
       BUG: Fix ITK Path test failures
       BUG: ITK unable to detect number of threads under Unix in recent glibc.

ITK Migration V4 (4):

       DOC: Modify ContourMeanDistanceImageFilter comments.
       DOC: Modify MattesMutualInformationImageToImageMetric comments.
       DOC: Modify MaskImageFilter comments.
       DOC: Modify BSplineTransformInitializer comments.

Jan Margeta (1):

       COMP: Added missing header  in itkAnchorCloseImageFilter.h

Julien Finet (2):

       ENH: Add unit test to itkThresholdImageFilterTest
       ENH: Add MaskingValue to MaskImageFilter

Julien Malik (2):

       BUG: Remove itkLoad definition in JPEG2000ImageIOFactory
       ENH: Add missing NumericTraits for complex

Julien Michel (2):

       BUG: Fix InverseDisplacementFieldImageFilter bug
       BUG: Fix InverseDisplacementFieldImageFilter bug

Kent Williams (21):

       COMP: Turn on -fpic in options for DCMTK External Project
       BUG: using InputPixelType to hold label count can overflow.
       COMP: Update DCMTK version to incorporate new fixes.
       COMP: Use portable method to find source dir & find DCMTK headers
       COMP: Start using ITKConsortium github to retrieve DCMTK.
       BUG: Regressions with respect to building DCMTK
       COMP: Added patch from Dirk Padfield
       ENH: use find_package(DCMTK NO_MODULE)
       ENH: Add double-conversion library for precise Float output
       COMP: replace in-line access methods with itk Macros
       COMP: The install path for DoubleConversion lib was wrong.
       COMP: removed warnings on Windows due to generic vs excp obj throw.
       COMP: check for this == &rhs as much as possible.
       COMP: Replace memcpy with std::copy in ImportImageContainer.
       COMP: Replace memcpy calls with std::copy
       COMP: Further changes to the use of std::copy_n
       COMP: Add preprocessor symbols to double-conversion for OS X PPC
       COMP: Add DoubleConversion merge from upstream documentation
       BUG: Return of NaN by DiffusionTensor3D::GetFractionalAnisotropy
       BUG: Dicom method for Dir Cosines made non-orthogonal directions
       COMP: Install openjpgDllConfig.h

Kris Zygmunt (1):

       PERF: Provide better default config for patch-based denoiser

Luis Ibanez (1):

       ENH: Maurer for Danielsson in Surface Distance.

Manuel Grizonnet (4):

       BUG: Inconsistency detected by due to static const string
       BUG: Inconsistency detected by due to static const string
       BUG: Inconsistency detected by due to static const string
       BUG: Inconsistency detected by due to static const string

Marco Feuerstein (1):

       ENH: JPEG IO now writes and reads spacing, similar to the TIFF IO (ITK-3023)

Marius Staring (3):

       ENH: expose parameter in Bilateral filter
       PERF: Replace fill and copy with std alternatives
       BUG: B-spline interpolator should use direction

Mark Hiner (1):

       ENH: Add SCIFIOImageIO.

Matthew McCormick (47):

       COMP: Fix wrapping configuration warnings about itkMeshBase, etc.
       COMP: Fix HDF5 unused function for long long on Unix.
       ENH: Bump CMake version numbers to 4.4.0.
       BUG: Remove unused metric test content link.
       COMP: Add DLL to PATH for Python tests on Visual Studio.
       BUG: Do not nullify the DCMTK ExternalProject UPDATE_COMMAND.
       BUG: Fix DCMTK lib_prefix identification.
       COMP: Fix HDF5 unused function for long long on Unix.
       BUG: Remove unused metric test content link.
       COMP: Add DLL to PATH for Python tests on Visual Studio.
       ENH: Bump CMakeLists.txt ITK version to 4.3.1.
       STYLE: Fix errors detected by KWStyleCodeTest.
       COMP: VectorIndexSelectionCastImageFilter extra itk namespace.
       STYLE: Fix alignment in itkMask{Image,Negated}ImageFilter.h
       ENH: Doxygen configuration update to
       BUG: Fix FFTW install paths in ITKConfig.cmake (ITK-2995).
       DOC: Doxygen detection of DirectionTolerance as private.
       ENH: Get Direction and CoordinateTolerance are const methods.
       BUG: Add missing header to the third party TIFF install.
       COMP: More fixes to mesh wrapping warnings.
       BUG: Temporarily disable Python utility tests.
       COMP: Avoid explicit instantiation and specialization for Array.
       ENH: Add utility script to create JRE tarballs.
       ENH: Use named inputs in BinaryReconstruction filters.
       STYLE: Remove redundant itk namespace.
       DOC: CreateTestDriver srcs should have the .cxx extension.
       COMP: Must reinterpret the pointers to match
       COMP: Fix project linking against ITK that does not use VtkGlue.
       COMP: Fix project linking against ITK that does not use VtkGlue.
       BUG: Fix FFTW install paths in ITKConfig.cmake (ITK-2995).
       ENH: Bump version in CMakeLists.txt to 4.3.2.
       DOC: Doxygen expansion of itkGetModifiableObjectMacro.
       ENH: Remove unused wrapping code. ITK-3032.
       ENH: Use named inputs in BinaryReconstruction filters.
       COMP: Distance maps filters cannot wrap 1D.
       DOC: Remove reference to MeanDistanceImageFilter.
       STYLE: Fix KWStyle errors.
       STYLE: Remove entries from the old MINC2ImageIO.
       BUG: Remove MINCIO from the default registered modules.
       BUG: Add EXCLUDE_FROM_ALL to ThirdParty/MINC.
       BUG: Include SCIFIO in the auto-registered factories if the module

is enabled.

       BUG: Visual Studio itkClampImageFilterTest failures.
       STYLE: itkClampImageFilter.hxx in the wrong module.
       COMP: Add _CRT_NO_SECURE_WARNINGS when building GCCXML.
       COMP: Prevent ITK_USE_64BITS_IDS with Wrapping on Windows.
       STYLE: Too many blank lines in itkCastImageFilterTest.cxx.
       COMP: Bump MINC third party to fix warnings.

Nick Tustison (4):

       ENH:  Adding masking capabilities with confidence mask option.
       BUG:  Masks need to be warped.
       ENH:  Permitting access to shrinking per dimension.
       BUG: Valgrind error.

Nicolas Rey (1):

       STYLE: Minor style fixes

Paul Novotny (3):

       COMP: Fix TIFF on big endian systems
       COMP: Build fails with ITK_USE_SYSTEM_TIFF
       COMP: Fix TIFF on big endian systems

Prathamesh Kulkarni (1):

       COMP: QuickViewTest new baseline.

Sean McBride (4):

       STYLE: fixed minor spelling: XCode -> Xcode
       COMP: fixed clang warning about NULL to bool conversion
       BUG: Handle missing Analyze 7.5 flipped directions
       COMP: Handle missing Analyze 7.5 flipped directions

Tim Allman (3):

       DOC: Modify BSplineTransform comments.
       DOC: Modify JointHistogramMutualInformationImageToImageMetricv4 comments.
       DOC: Modify JointHistogramMutualInformationImageToImageMetricv4 comments.

Tom Vercauteren (2):


Vladimir S. FONOV (2):

       ENH: Adding libminc and updating MINC IO support.
       BUG: Making 2D Minc IO work properly

Xiaoxiao Liu (2):

       ENH: Sync python scripts with python3.
       ENH: Sync python scripts with python3.

Yan Xu (1):

       COMP: static cast unsigned int to int

Changes in ITKapps from v4.3.0-apps to v4.4.0-apps:

Bill Lorensen (3):

       COMP: VTK6 API change
       ENH: Add TCL Wrapped examples
       BUG: Missing includes for ITK4.4

Hans Johnson (1):

       COMP: Mac 10.8 fixes were incorporated in FLTK

Jamie Snape (1):

       BUG: Propagate build, linker, and OSX settings to external projects

Matt McCormick (6):

       COMP: Re-add the FLTK patch for some Macs.
       BUG: ITK External build only depends on VTK if being built.
       COMP: Update FLTK SVN configuration.
       ENH: Bump VTK ExternalProject to 5.10.1.
       COMP: Use FLTK zip file stored on Midas3.
       ENH: Bump ITK superbuild version to 4.4.0.

Roland Kwitt (1):

       COMP: Shadowing warning in GLSliceView.h

Stephen R. Aylward (1):

       COMP: Fix FLTK build error on Mac/Clang.

Xiaoxiao Liu (1):

       ENH: Print out accurate image IO error message.