We are happy to announce the Insight Toolkit (ITK) 5.1 Release Candidate 1 is available for testing! 
ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration.
ITK 5.1 is a feature release that improves and extends the major ITK 5.0 release. ITK 5.1 includes a NumPy filter interface, clang-format enforced coding style, enhanced modern C++ range support, and much more.
Downloads
Python Packages
Install ITK pre-release binary Python packages with:
pip install --pre itk
Library Sources
Testing Data
Unpack optional testing data in the same directory where the Library Source is unpacked.
Checksums
Features
Tomographic sphere reconstruction with the RTK remote module. Reproduce this result by installing the RTK Python packages, pip install itk-rtk, and run the FirstReconstruction.py example.
Pass NumPy Array’s to ITK Image Filters
The Pythonic, functional-like interface to all ITK image-to-image-filters now directly supports operation on NumPy array’s, i.e. numpy.ndarray. If a ndarray is passed as an input, a ndarray is returned as an output.
For example,
smoothed = itk.median_image_filter(array, radius=2)
Previously, explicit conversion to / from an itk.Image was required with itk.array_from_image and itk.image_from_array.
We can now also convert an itk.Image to a numpy.ndarray with the standard np.asarray call.
import numpy as np
import itk
image = itk.imread('/path/to/image.tif')
array = np.asarray(image)
Python 3 Only
ITK 5.1 will be the first Python 3-only release. Consistent with most scientific Python packages and CPython’s 2020 drop in support, Python 2 support and binaries are no longer be available.
Python Package 64-bit Float Support
In addition to the many other pixel types supported, the itk binary Python packages now include support for the double pixel type, i.e. 64-bit IEEE floating-point pixels. This improves compatibility with scikit-image, which uses this pixel type as a default.
clang-format Enforced C++ Coding Style
ITK has adopted a .clang-format coding style configuration file so a consistent coding style can automatically be applied to C++ code with the clang-format binary. A consistent coding style is critical for readability and collaborative development.
clang-format has been applied to the entire codebase. The Whitesmiths style of brace indentation, previously part of the ITK Coding Style Guidelines, is not supported by clang-format, so it has been replaced by a brace style consistent with VTK’s current style.
A Git commit hook will automatically apply clang-format to changed C++ code.
Enhanced Modern C++ Range Support
In addition to the ImageBufferRange, ShapedImageNeighborhoodRange, and IndexRange classes introduced in ITK 5.0, ITK 5.1 adds an ImageRegionRange. These range classes conform to the Standard C++ Iterator requirements so they can be used in range-based for loop’s and passed to Standard C++ algorithms. Range-based for loops provide an elegant syntax for iteration. Moreover, they are often more performant than other iteration classes available.
For example, to add 42 to every pixel:
ImageBufferRange<ImageType> range{ *image };
for (auto&& pixel : range)
{
pixel = pixel + 42;
}
In ITK 5.1, adoption of the range classes was extended across the toolkit, which demonstrates their use and improves toolkit performance.
Point Set Registration Parallelism
ITK provides a powerful framework for point-set registration, offering information-theoretic similarity metrics, labeled point-set metrics, and spatial transformation models that range from affine to b-spline to dense displacement fields. ITK 5.1 features enhanced parallelism in point-set metric computation, leveraging the native thread-pool and Threading Building Blocks (TBB) enhancements in ITK 5.
SpatialObject’s and Strongly-Typed enum’s
Improvements and refinements were made to the ITK 5 itk::SpatialObject refactoring, and modern C++ interface. In particular, ITK 5.1 transitions enumerations to strongly-typed enumerations, which is flagged by modern compilers due to improved scoping and implicit conversions to int. Enum names are now follow a consistent <Description>Enum naming conversion, which results in a Python interface:
<Description>Enum_<EnumValue1>
<Description>Enum_<EnumValue2>
[...]
DICOM Support
ITK’s broadly adopted medical image support is hardened thanks to 20 years of testing and support from major open source DICOM library maintainers. In this release, many members of the community collaborated to further enhance ITK’s DICOM support for corner cases related to modality, pixel types, and vendor variations.
Remote Module Updates
Many remote modules were updated: AnalyzeObjectMapIO, AnisotropicDiffusionLBR, BSplineGradient, BioCell, BoneEnhancement, BoneMorphometry, Cuberille, FixedPointInverseDisplacementField, GenericLabelInterpolator, HigherOrderAccurateGradient, IOMeshSTL, IOOpenSlide, IOScanco, IOTransformDCMTK, IsotropicWavelets, LabelErodeDilate, LesionSizingToolkit, MinimalPathExtraction, Montage, MorphologicalContourInterpolation, ParabolicMorphology, PhaseSymmetry, RLEImage, RTK, SCIFIO, SimpleITKFilters, SkullStrip, SplitComponents, Strain, SubdivisionQuadEdgeMeshFilter, TextureFeatures, Thickness3D, TotalVariation, and TwoProjectionRegistration. Their updates are included in the detailed changelog below.
Congratulations
Congratulations and thank you to everyone who contributed to this release. Of the 50 authors, we would like to specially recognize the 20 new contributors: Mathew J. Seng, Zahil Shanis, yjcchen0913, PA Rodesch, Aurélien Coussat, yinkaola, Bryce Besler, Pierre Chatelier, Rinat Mukhometzianov, Ramraj Chandradevan, Hina Shah, Gordian Kabelitz, Genevieve Buckley, Aaron Bray, nslay, Antoine Robert, James Butler, Matthew Rocklin, Gina Helfrich, and Neslisah Torosdagli.
What’s Next
As we work towards the next release candidate, we will improve strongly typed enum adoption in the toolkit, consistent with the soft commitment to backwards compatibility to address any potential API or architectual issues until the 5.1.0 release. Please try out the current release candidate, and discuss your experiences at discourse.itk.org. Contribute with pull requests, code reviews, and issue discussions in our GitHub Organization.
Enjoy ITK!
ITK Changes Since v5.0.0
Aurélien Coussat (1):
ENH: wrap IterationReporter
Bradley Lowekamp (63):
BUG: Use ProcessObject GetInput to obtain base pointer
BUG: Fix ProcessObject::RemoveOutput for null objects.
COMP: Address missing fftw include in CurvatureRegistrationFilter
BUG: Fix ProcessObject::RemoveOutput for null objects.
BUG: Add casting for vector pixel types
STYLE: Use CTEST_TEST_TIMEOUT
ENH: Add testing for CastImageFilter for more type conversions
BUG: Restore support for Cast between explicitly cast-ed pixel type
BUG: Use ProcessObject GetInput to obtain base pointer
ENH: Add testing for CastImageFilter for more type conversions
BUG: Restore support for Cast between explicitly cast-ed pixel type
BUG: Add DataObject::New method
BUG: Install FFTW headers in same location as ITK
Revert "BUG: InterpolateImageFunction::GetRadius hidden in ITKV4_COMPATIBILITY"
BUG: Preserve Interpolate GetRadius behavior with ITKv4Compatibility
Revert "COMP: forgotten class for ITKV4_COMPATIBILITY in 2aae174"
BUG: HDF5 is clobbering ctest TIMEOUT variables
COMP: Fix not marked 'override' for ImageSink destructor
BUG: Use enable_if with SFINAE to dispatch
ENH: Add Vector constructor from C arrays with cast
COMP: Work around uninitialized value warnings
ENH: Update ITKv4 registration example to use resample over warp
BUG: Specify specific CircleCI docker image with platform
COMP: Address compilation warning with aggregate initializer
BUG: Specify specific CircleCI docker image with platform
ENH: Adding VS2019 v142, VS2017 v140 Azure Pipelines on merge
DOC: Tweak internal documentation in SliceImageFilter
BUG: Address bug with small size in output of SliceImageFilter
ENH: Add more test cases for the SliceImageFilter
COMP: Address internal compiler error on MSVC 19.0.24234.1 (v140)
ENH: Add check expected input in HistogramMatchingImageFilter
COMP: Add missing enum type_name from prior enum declaration style
ENH: Check physical location consistency after PermuteImageFilter
BUG: Address bug with small size in output of SliceImageFilter
COMP: Address internal compiler error on MSVC 19.0.24234.1 (v140)
COMP: Add missing include for VectorLinearInterpolateImageFunction
ENH: Move ImageToHistogram test to Statistics module
BUG: Fix outside buffered region exception in ImageToHistogramFilter
BUG: Fix ImageHistogram printing null inputs
ENH: Add basic object testing methods for ImageToHistogramFilter
ENH: Add testing for ImageToHistogram with AutoMinimumMaximum
ENH: Add missing boolean setter methods for AutoMinimumMaximum
BUG: Add valgrind suppression for zlib slide_hash
ENH: Add testing for OBB vertices and image with direction
BUG: Correct ShapeLabelObjectes OBB vertices
DOC: Update documentation for OBB vertices method
BUG: Add missing suppression name for zlib
BUG: Explicitly initialize CovariantVector in VectorImageTest
DOC: Adding migration guide for "vector" filters
BUG: Use default CircleCI resources
DOC: Grammar fixes in vector filter section of migration guide
ENH: Mark deprecated GDCM API as ITK legacy remove
ENH: Adding new test for GDCM ImageIO for different pixel types
BUG: Fix GDCMImageIO define order
BUG: Address buffer overflow with deprecated GDCM1 interface
BUG: Don't use InsertElement which modifies MTime
ENH: Update CircleCI docker image to python:3.7-stretch
ENH: Adding Valgrind suppression file for CentOS 7 system
BUG: Remove noisy cerr output when magic number fails
COMP: Address deprecated implicit vnl matrix conversions
BUG: Remove tiff from supported extensions for LSMImageIO
BUG: Wait for all threads when abort or exception occurs
BUG: Fix leaky dynamically allocated raw point
Csaba Pinter (2):
BUG: Fix loading of DICOM files with no preamble
ENH: Add test for DICOM without preamble for DCMTK and GDCM
Dave Chen (1):
Type fixing (#1233)
Davis Vigneault (1):
BUG: Make BuildCellLinks method const
Dženan Zukić (72):
BUG: number of work units was greater than 1 even for 1 thread
BUG: fix a crash with ITK_DEFAULT_MAX_THREADS greater than 250
BUG: resample filter no longer triggers unnecessary exception
COMP: change export specification to template for un-specialized method
COMP: forgotten class for ITKV4_COMPATIBILITY in 2aae174
ENH: use double-conversion's CMake targets
COMP: fix warning about missing override in CastImageFilter
DOC: wrong class name for PlatformMultiThreader
COMP: get rid of MSVC's warning 4661
ENH: enable GaussianInterpolateImageFunction to work with streaming
STYLE: reduce space in ivar declarations
STYLE: ITK indentation style in test
STYLE: invert the name and internal logic of waiting for threads
BUG: ThreadPool::DoNotWaitForThreads did not work properly
STYLE: Add ITK prefix to testing macros in release branch
DOC: invocation of AddWork uses -> because instance is always a pointer
ENH: updating remote modules
ENH: PoolMultiThreader uses one less thread
ENH: documenting supported compilers
ENH: updating remote modules
STYLE: more consistent code formatting in test driver
BUG: offset was not updated after changing Euler angle order (ZYX)
Fix broken link in Data.md
ENH: support RGB image in windowed sinc interpolation
ENH: support RGB image in windowed sinc interpolation
ENH: updating remote modules
ENH: back-porting #1165 to support Visual Studio 2019
ENH: updating remote modules
COMP: fixed enum name error when legacy is OFF and ITK_USE_GPU is ON
ENH: removing deprecated Python functionality: imp
ENH: removing deprecated Python functionality: sys.version_info 2/3
ENH: removing deprecated Python functionality: import print_function
ENH: update remote modules to comply with new enum class style
ENH: update Visual Studio debug visualizers
DOC: spelling correction in BSpline documentation
COMP: update VTKTetrahedralMeshReader to enum class
ENH: avoid repeated allocation of logSharpenedImage
ENH: publicly expose method ReconstructBiasField
BUG: wrong number of parameters was checked in itkTestDriverInclude
ENH: update OpenCV bridge
ENH: update tests' include files for OpenCV 4
ENH: add IsPositive() and friends to RGB's and RGBA's NumericTraits
ENH: updating remote modules
ENH: adding BoneEnhancement remote module
ENH: updating clang-format bash script to allow versions 8.0.x
STYLE: running clang-format
ENH: update PhaseSymmetry remote module
ENH: disable test whose failure is not reproducible
COMP: compile the test with legacy disabled
BUG: fix null deref in 'itkTreeContainerTest'. Closes #1358.
ENH: remove ivar m_End which is always equal to nullptr
ENH: adding JPEGBaseline1 DICOM reading test
ENH: update remote modules Montage and Examples
ENH: various DICOM compliance tests
ENH: DICOM compliance test for JPEG2000 YBR-RCT encoding
ENH: add regression test for conversion of MONOCHROME1 into MONOCHROME2
ENH: update KWStyle to fix potential buffer overflow
ENH: Updating remote modules
ENH: updating Cuberille and Montage remote modules
ENH: wrap StreamingImageFilter for all the dimensions
COMP: fixing a couple of VNL related linking errors
ENH: improving exception handling in PoolMultiThreader
ENH: stop this thread's work on first exception
ENH: update BoneEnhancement remote module
ENH: update remote modules
ENH: support testing multi-frame DICOMs (3D images)
BUG: avoid undefined behavior (dereferencing nullptr). Closes #1358
STYLE: Visual Studio static analysis fixes in MultiThreaders
STYLE: produce result directly in 64-bit precision (avoid a cast)
ENH: optionally write intermediate image in test
ENH: DiscreteGaussian filter is compatible with SmoothingRecursive one
ENH: update ITKExamples remote module version
Eigen Upstream (1):
Eigen3 2019-10-24 (5d8ba9ed)
Francois Budin (4):
BUG: ImageBase regions and ImageRegion properties are returned as reference
DOC: Add ITK 5.0 release notes
BUG: m_NumberOfPointPixels was set equal to m_NumberOfPoints
ENH: Adds swig include directory to command line
GDCM Upstream (5):
GDCM 2019-05-22 (cc5358a1)
GDCM 2019-10-08 (e470b82d)
GDCM 2019-10-23 (fcacc159)
GDCM 2019-10-24 (4b164b45)
GDCM 2019-11-04 (d11271f8)
Genevieve Buckley (1):
BUG: All exceptions must be derived from python's BaseException class
Gina Helfrich (1):
Create FUNDING.yml
Hans J. Johnson (75):
ENH: Update SphinxExamples to lastest master branch
COMP: Add attribute for large doxygen config file.
DOC: Remove ITK_FUTURE_LEGACY_REMOVE from documentation
ENH: Disable remote module processing when creating doxygen.
STYLE: Prevent double initialization
DOC: Purge outdated media wiki WikiExamples
BUG: Missed propagation of library dependancies
ENH: Deprecate Neuralnetwork module
Revert "Merge pull request #1039 from samuelgerber/MultithreadPointSetToPointSetMetricv4"
STYLE: Remove deprecated support for ITK_WRAP_PYTHON_LEGACY
DOC: Only warn when Module_NeuralNetworks is selected
ENH: Use consistent project name with module name
COMP: Fix clang-format nesting of empty macros
DOC: Deprecate https://itk.org/Wiki/ITK/Examples content.
DOC: Provide doxygen links for sphinx
DOC: Improve the documentation clarity for NormalizeImage.
DOC: Moved wiki examples to sphinx examples part2
ENH: itkObjectToObjectOptimizerBase Must be explicitly instantiated
COMP: Terminate conditional doxygen sections
DOC: Set class name for StreamingProcessObject doxygen
ENH: Update the DoxygenLayout.xml file
ENH: Update template files for Doxygen.
BUG: Patch submission scripts conflict with doxygen
COMP: Resolve 1000's of alias warnings in 1.8.15
DOC: Moved wiki pages to sphinx examples
BUG: Flawed logic for itkExceptionObject.h guards
STYLE: Use override statements for C++11
STYLE: Prefer c++11 'using' to 'typedef'
COMP: Another work around uninitialized value warnings
ENH: Prefer c++11 'using' to 'typedef' for structs
COMP: Update AnalyzeObjectMapIO remote for ITKv5.0
COMP: Suppress warning about file that is too large
STYLE: Use = default for trivial constructors
STYLE: For loops can have a space before ;
STYLE: Suppress longstanding kwstyle violations
STYLE: Use templated function over macro
ENH: Add LONGLONG & ULONGLONG types
STYLE: Remove unused protected ivar m_MyProduct
COMP: Isolate RAWIO non-templated code in cxx file
PERF: Byteswap only when request != system byte order
STYLE: Suppress longstanding kwstyle violations
STYLE: Define the .clang-format config file
ENH: Add script to assist with running clang-format on topic-branches
ENH: Update C++/C attributes for itk style conformance.
ENH: Add copy of git-clang-format from llvm binaries
ENH: Add cmake configuration for clang-format
ENH: Setup clang-format hooks for pre-commit-style
DOC: Add missing line separator for ingroup ITKCommon
DOC: Fix spelling typo VeriyInput -> VerifyInput
ENH: Refactor to allow ReferenceHistogram instead of ReferenceImage
COMP: Remove One Definition Rule conflict
COMP: Fix missing type specialization for `unsigned long long int`
STYLE: Convert 'enum' to 'enum class' objects with print enum function
ENH: Workaround MSVC preprocessor name conflict
STYLE: Prefer enum class definitions internally
STYLE: Prefer consistent capitalization of Colormap
ENH: Ignore wrapping warnings for `enum class`
BUG: Missing ImageAdapter function signatures
COMP: Change KWStyle to allow reformat to pass.
STYLE: No-space inside <> () []
STYLE: Change the packing of parameters.
STYLE: Use shorter column length for Software Guide.
STYLE: End of history preceeding clang-format-8.0 style
STYLE: Fix spelling error foramt -> format
ENH: Prefer explicit casting over implicit casting for vxl
STYLE: Only python > 3.5 is supported
BUG: castxml fails with C++11 'enum class'
ENH: Clarify the use and interaction of LEGACY Reporting
ENH: Run larger memory tests if supported
PERF: Provide hints regarding test timing
BUG: Warning macros for ITK_LEGACY_SILENT are wrong
ENH: Improve diagnostic warnings for ResampleImage misuse
DOC: More clearly describe foreground/background
ENH: Avoid alias names for [Fore|Back]groundValue
ENH: Shadowed typedef warnings removed
ITK Maintainer (1):
STYLE: Enforce ITK style defined by .clang-format
James Butler (1):
COMP: Add cmake_minimum_required to ITKNumericsFEM
Jean-Christophe Fillion-Robin (3):
ENH: Support building ITKNumericsFEM as external module
COMP: Disable CMake user registry lookup by find_package.
COMP: Support disabling CMake user registry lookup for CMake >= 3.16
Jon Haitz Legarreta Gorroño (4):
STYLE: Fix indentation in bash script
ENH: Add script to update ITK testing macros names
BUG: Fix remotes maintenance scripts
BUG: Fix wrong variable names
Marian Klymov (3):
BUG: BMP can't be read without proper extension
BUG: Workaround for segfault in itkStatisticsAlgorithmTest (v140)
STYLE: Add additional braces around initialization of subobject
Mathieu Malaterre (6):
ENH: Remove Utilities/C99 from GDCM sync script
STYLE: Teach git about GDCM oversize file
BUG: Always convert YBR_FULL to RGB
ENH: Decompress the Pixel Data buffer when needed
ENH: Make sure to check the return value of filters
ENH: Properly convert MONOCHROME1 into MONOCHROME2
Matt McCormick (108):
ENH: Bump the ITK CMake version to 5.1.0
ENH: New content links for ITK 5.0.0
STYLE: DeformableRegistration2 line length warnings
COMP: SpatialObjectsHierarchy Software Guide newline
ENH: Bump CI ExternalDataVersion to 5.0.0
DOC: Release generation updates for ITK 5.0.0
DOC: Add a note about updating conda-forge for post wheels
ENH: Update Doxygen to 1.8.15
BUG: Add test/CMakeLists.txt stub to NumPy bridge
COMP: Provide NumericTraits<complex<T>>::ZeroValue() definition
COMP: Backwards compatibility testing macros without ITK_ prefix
BUG: Get latest tag in UpdateRequiredITKVersionInRemoteModules.sh
BUG: Filename vars in UpdateRequiredITKVersionInRemoteModules.sh
ENH: UpdateRequiredITKVersionInRemoteModules bump patch version
ENH: UpdateRequiredITKVersionInRemoteModules supports ITKPythonGitTag
BUG: Do not require PyBUF_WRITABLE in GetArrayViewFromImage
DOC: Update supported Python versions warning
ENH: Require Python 3.5 or newer on all platforms
BUG: ITKFixedPointInverseDisplacementField wrapping test config update
BUG: Remove VectorExpandImageFilter wrapping
BUG: Add PEP 366 __package__ support to ITKLazyModule
COMP: Remove HasNumericTraitsCheck from ExpandImageFilter
ENH: Wrap ExpandImageFilter with vector types
BUG: Release the Python Global Interpreter Lock (GIL) during execution
STYLE: Apply ITK Style Guidelines to itkPyCommand.cxx
BUG: itk::PyCommand ensures the GIL state
BUG: Support pickling LazyITKModule with cloudpickle
BUG: Add Pipeline name to Azure configuration
DOC: Update Azure Pipelines badge URL's
BUG: Add wrapping for TransformMeshFilter
ENH: Bump itkVersion.cmake for 5.0.1
ENH: CI testing uses Python 3
BUG: itkPyBufferTest: use bytes for Python 3 np.frombuffer
BUG: Remove NumberOfComponents check in _GetImageViewFromArray
BUG: Remove NumberOfComponents check in _GetImageViewFromArray
DOC: Update ITK.Linux.Python and ITK.Coverage README badges
BUG: Update SkullStrip module to address Doxygen configuration
BUG: Use ITK_BUILD_DOCUMENTATION to enable Doxygen builds
COMP: Update CastXML to 2019-07-15 master
DOC: Minor release documentation updates
ENH: Support numpy.asarray for itk.Image
ENH: Directly set an itk.ImageBase Direction with a NumPy Array
BUG: Ensure NumPy array is C-contiguous with matrix conversion
BUG: Enable ITKBridgeNumPy for Windows CI builds
DOC: AdaptiveHistogramEqualizationImageFilter default radius
BUG: Do not run itkPyBufferMemoryLeakTest on Windows
BUG: Remove Windows Python 2.7 hypot workaround
ENH: Support NumPy array-like inputs to image filters
DOC: Add Eigen license to NOTICE file
ENH: Download clang-format 8.0.1 executable
ENH: Add wrapping for LabelImageGaussianInterpolateImageFunction
DOC: 'weight' spelling in LabelImageGaussianInterpolateImageFunction
BUG: Add NumPy conversion for itk.Image[itk.Vector[itk.D,dim]]
BUG: Wrap WindowedSincInterpolateImageFunction SmartPointer
BUG: Do not apply style pre-commit hooks to ThirdParty code
BUG: Do not download clang-format with ITK_FORBID_DOWNLOADS enabled
BUG: Add missing KWStyle hook configuration
ENH: Update clang-format binary path configuration
BUG: Fix have_KWStyle detection when running clang-format hook
BUG: Improvements to pre-commit-style hook for clang-format
ENH: Check for required clang-format version in style hook
BUG: Use castxml binary compatible with CentOS 5
BUG: Use https for GitSetup hooks checkout
DOC: Consistent naming for 'Insight Toolkit (ITK)'
BUG: Update IsotropicWavelets module for Doxygen build
DOC: Extend Doxygen main page toolkit description
DOC: Update Examples/README.md
BUG: Implicit Python filter type selection uses second template param
BUG: Remove WrapITK external project initialization
STYLE: More Pythonic style in itkExtra's test
ENH: Add itk.meshread
ENH: Add itk.meshwrite
ENH: Add itk.__version__
DOC: Update PhaseSymmetry for Doxygen configuration
DOC: Add note on ISC board approval of Apache 2.0 license
BUG: Set the __spec__ attribute on the itk package
DOC: Add HDF5 copyright to NOTICE file
DOC: Note that KWStyle is built when ITK is built
BUG: Only require clang-format major.minor version in hook check
DOC: Note that clang-format is downloaded when ITK is built
ENH: Update CI ExternalDataVersion to 5.0.1
ENH: Add new content links
BUG: Wrap new enum classes
DOC: Add release download links cookiecutter
ENH: Wrap ConnectedRegionsMeshFilter
BUG: Add missing itkTypeMacro to ConnectedRegionsMeshFilter
ENH: Wrap KdTree classes
ENH: Enable building ITKGPUCommon externally
ENH: Enable building ITKGPUFiniteDifference externally
COMP: Define CL_TARGET_OPENCL_VERSION
ENH: Add GPUCommon wrapping
ENH: Add GPUFiniteDifference wrapping
ENH: Add wrapping for GPUImageFilterBase
ENH: Enable building ITKGPUImageFilterBase externally
ENH: Wrap GPUAnisotropicSmoothing module
ENH: Add ITKGPUSmoothing Python wrapping
STYLE: Avoid repeated sizeof calles in GPUKernelManager SetKernelArg
COMP: Update SWIG to 4.0.1 for Windows build
ENH: Enable ITK_LEGACY_REMOVE when wrapping is enabled
COMP: Do not avoid legacy enum definitions when wrapping
BUG: Fix wrapping for TransformBaseTemplate class
BUG: Use itk.array_from_image for __array__
ENH: Gracefully convert non-contiguous NumPy arrays
BUG: ITK_LEGACY_REMOVE cmake_dependent_option logic
ENH: Consistent use of typed enums, naming
COMP: Use SWIG 3.0.12 on Unix
BUG: Install itkBase.py
BUG: TransformBaseTemplate wrapping warning
Matthew Rocklin (1):
BUG: Support Numpy inputs in keywords that include "image"
MetaIO Maintainers (4):
MetaIO 2019-05-22 (5f90075b)
MetaIO 2019-09-16 (7b46b9a7)
MetaIO 2019-09-16 (7b46b9a7)
MetaIO 2019-10-02 (177df110)
Mihail Isakov (4):
ENH: added missing symbols to JPEG mangling header
BUG: GDCMIO crash if bits allocated 16, stored 8
STYLE: remove unused code from 168c457 in GDCM IO
ENH: Better reading of Y'CbCR DICOM files
Neslisah Torosdagli (1):
BUG: Regression in PolygonSpatialObject::IsInsideInObjectSpace #1082
Niels Dekker (63):
PERF: Replace mutex by atomic in MersenneTwisterRandomVariateGenerator
STYLE: Remove two duplicated #include <mutex> directives
STYLE: Add const to MersenneTwisterRandomVariateGenerator::GetSeed()
ENH: GTest MersenneTwisterRandomVariateGenerator::GetIntegerVariate()
STYLE: Use image->TransformPhysicalPointToIndex(point), returning index
ENH: ImageBase Transform-Vector single argument overloads more generic
STYLE: Use image->TransformVectorToVector(gradient), returning gradient
STYLE: Vector, CovariantVector(value) call base FixedArray(value)
STYLE: FastMarching replace FixedArray Begin(), End() by range-based for
STYLE: Replace FixedArray Begin(), End() by cbegin(), cend()
STYLE: itkFixedArray.hxx using std::equal, and C++11 fill_n and copy_n
STYLE: Add const to SetStartingShrinkFactors parameter
STYLE: Replace std::copy(input, input + n, output) by C++11 std::copy_n
ENH: Add ImageRegionRange, to iterate over the pixels of an image region
COMP: No longer disable obsolete MSVC warning C4231 on 'extern' template
STYLE: Order #pragma warning directives in itkWin32Header.h
COMP: No longer disable obsolete MSVC warning C4231 in VNL/vxl/vcl
BUG: Fix possible loss of data on type conversion
COMP: QuadEdgeMesh::SetCell avoid assignment in conditional expression
COMP: Remove (char) casts of hexadecimal int literals from UnicodeIOTest
COMP: ImageRegionRangeGTest issue #1147 Unused function template warning
COMP: Fix loss of data ProcessObject GetNumberOfValidRequiredInputs()
STYLE: Remove reinterpret_cast's from void to non-void pointer
STYLE: Use C++11 nullptr in itkDynamicCastInDebugMode
STYLE: Use nullptr for isSpecialCoordinatesImage in ResampleImageFilter
STYLE: Remove redundant code from operator<< for enum's, using lambda's
STYLE: Replace 0 by nullptr when appropriate
ENH: Add data() member functions to NeighborhoodAllocator
ENH: Add unit tests for NeighborhoodAllocator Allocate and Deallocate
STYLE: Modernize NeighborhoodAllocator data management, using unique_ptr
STYLE: For a const image, iterator and const_iterator should be the same
PERF: Use ShapedImageNeighborhoodRange in ConfidenceConnectedImageFilter
PERF: Use ShapedImageNeighborhoodRange in SumOfSquaresImageFunction
PERF: Use ImageBufferRange in ImageKernelOperator GenerateCoefficients()
PERF: Use IndexRange in BSplineInterpolationWeightFunction constructor
ENH: Add GoogleTest for SumOfSquaresImageFunction
PERF: Call FillBuffer in watershed Segmenter::InitializeBoundary()
PERF: Use ShapedImageNeighborhoodRange in MeanImageFunction
PERF: Use ImageBufferRange in Testing::StretchIntensityImageFilter
PERF: Use ShapedImageNeighborhoodRange in MedianImageFunction
ENH: Add BufferedImageNeighborhoodPixelAccessPolicy for faster access
PERF: Use ShapedImageNeighborhoodRange in MeanImageFilter
ENH: Add GoogleTests for MeanImageFilter and MedianImageFilter
ENH: Separate boundary/non-boundary regions ImageBoundaryFacesCalculator
COMP: Fix GTest gcc4.6, Mac10.10 error VNumberOfExpectedPixels deduction
PERF: Use ShapedImageNeighborhoodRange in MedianImageFilter
COMP: Range-based for-loops on BoundaryFaces should use reference
STYLE: Remove repeated GetBufferedRegion() calls from ImageBoundaryFaces
BUG: Fix IndexRange for itk::Size that has both zero's and non-zero's
STYLE: MeanImageFilter use vector<Offset>, range-based-for on IndexRange
ENH: Add static member function itk::Index::Filled(IndexValueType)
STYLE: Fix small inconsistency between IndexRange constructors
STYLE: Remove run-time estimation of operator radius in gradient filters
STYLE: Simplify Neighborhood::ComputeNeighborhoodStrideTable()
STYLE: C++ Rule of Zero for Neighborhood Operators, support nothrow move
STYLE: Move #include "itk_H5Cpp.h" from itkHDF5TransformIO.h to cxx file
PERF: Do not allocate buffer in HDF5TransformIOTemplate::WriteParameters
ENH: Allow copy and noexcept move of BackwardDifferenceOperator objects
STYLE: Replace macro's in PoolMultiThreader by ExceptionHandling class
PERF: Do not allocate buffer in HDF5ImageIO WriteVector and ReadVector
ENH: Add UnsignedPower(base, exp) and UnsignedProduct(a, b) to itk::Math
STYLE: Improve ImageIORegion special member functions, move-semantics
COMP: Workaround Clang 3.8 -Wundefined-inline warning Math UnsignedPower
Pablo Hernandez-Cerdan (2):
BUG: Fix COMPILE_DEFINITIONS of castxml
COMP: Update Eigen3 to top of branch 3.3
Pierre Chatelier (4):
ENH: MultiResolutionPDEDeformableRegistration supports more RegistrationFilter
BUG: more template parameters
STYLE: enforce ITK style defined by clang-format
BUG: fix template parameters
Rinat Mukhometzianov (3):
COMP: MSVC AVX flag fix
COMP: Fix SSE for MSVC x86
COMP: Replace legacy ITK_Check...Flag.cmake with check_..._flag cmake function
Samuel Gerber (5):
PERF: Remove Temporary Variable in GetMeasurementVector
ENH: Add Multithreading to PointSetToPointSetMetricv4
Revert "Revert "Merge pull request #1039 from samuelgerber/MultithreadPointSetToPointSetMetricv4""
BUG: Fix PointSetToPointSetMetric Thread Safety
BUG: Fix CompositeTransform ThreadSafety
Sean McBride (7):
COMP: Fixed -Wshadow warnings by renaming method parameter
COMP: Fixed the only -Wmissing-braces warning
COMP: Removed check for old __sync builtins, since they're no longer used
BUG: integer division by zero is undefined behaviour, no point in testing it
COMP: Remove workarounds for old MS compilers
COMP: fixed compilation with AppleClang 7 and 8.
BUG: Fixed signed overflow in float ULP comparisons
Simon Rit (4):
BUG: test for AVX compatibility to set MSVC optimization flags
BUG: sign memory probe to detect freed memory
BUG: origin was not accounted for correctly in RayCastInterpolateImageFunction
ENH: use RTK v2.1.0 (remote module)
Stephen Aylward (21):
ENH: Updated Spatial Object tex to match ITKv5
BUG: Fixed spelling mistakes and use of plural member functions
BUG: Fixed spelling mistakes and use of plural member functions
BUG: Fix grammar and naming mistakes in SpatialObject documentation
DOC: Fixed expected output of examples and documentation
BUG: Fix grammar and naming mistakes in SpatialObject documentation
DOC: Fixed expected output of examples and documentation
BUG: Use AddPoint() for PointBasedSpatialObjects to set SO
ENH: Replace ExceptionObjects with itkExceptionMacro.
ENH: Converted TubeSpatialObject ComputeTangentsAndNormals to frenet
BUG: Resolve corner case bug in ComputeTangentsAndNormals in TubeSO
ENH: Improved IsInside computation (speed and accuracy) of tube
ENH: Updating TubeSO test to match assumption that default is EndRounded
BUG: operator= defined in [tube|*]SpatialObjectPoint incomplete
BUG: Fixes bugs in SpatialObject to MetaIO conversion
ENH: Only create extra SO group on read if needed.
BUG: Duplicate typedef declarations in itkMetaSceneConverter
COMP: Update MinimalPathExtraction to remove warnings
BUG: MetaIO format for spatial objects updated to use elementspacing
COMP: Remove debugging cout statements from itkMetaVesselConverter
BUG: Missing typename keyword for variable declarations
Steve Pieper (1):
DOC: ITK5 SpatialObject Scene to Group change
VXL Maintainers (4):
VNL 2019-08-15 (7cc97a62)
VNL 2019-11-18 (13735a37)
VNL 2019-11-20 (3d5fbcdf)
VNL 2019-11-24 (5f5d5dc3)
Vladimir S. FONOV (9):
ENH: included new file in libminc MODULE
MINC 2019-10-03 (592dd487)
BUG: fixed composite transform writing to .xfm
ENH: Restored behaviour of depricated Analyze reader w.r.t orientation code
COMP: Fixing autodeduction of type for old clang compiler
COMP: Fixed itkWarningMacro and itkDebugMacro to confirm to PRE10-C
ENH: Added code to detect non-uniform sampling in ImageSeriesReader
ENH: Preserving information about auto-flipped negative steps in metadata
ENH: added metadata flag to contain maximum deviation in series reader
Yann Le Poul (5):
BUG: 256 colors of tiff palette were read, only correct for 8bit images
ENH: Palette image write support for TIFF and PNG. (#1219)
BUG: Wrong component type for non supported tiff with USHORT palette
BUG: solve memory leak when allocating png palette for writing
COMP: remove old style casting and use correct integer type if possible
Ziv Yaniv (2):
DOC: Correcting some grammer and updating the toolkit name. (#980)
ENH: Adding support for writing aux_file in Nifti.
maekclena (11):
STYLE: Add ITK prefix to testing macros
BUG: Fix BSplineGradient configuration
ENH: Mark VectorExpandImageFilter as deprecated
ENH: Deprecate VectorCentralDifferenceImageFilter
ENH: Remove VectorExpandImageFilter when ITK_LEGACY_REMOVE is on
BUG: add required method for Pickling
BUG: Fix GaussianInterpolateImageFunction with streaming
BUG: Avoid buffer overwriting in DCMTKImageIO
ENH: Disable itkDCMTKImageIOMultiFrameImageTest
BUG: Mitigate overflow in DCMTKImageIO::Read
BUG: Re-implement is_static_castable to be compatible with gcc 8 (#1227)
yjcchen0913 (1):
BUG: Ensure strict weak ordering in HessianToObjectnessMeasure's sort
ITK Examples Changes Since v5.0.0
Aaron Bray (1):
BUG: Move error handling exit to correct location
Bradley Lowekamp (1):
BUG: Relax adaptive histogram example with an intensity tolerance 1
Dženan Zukić (8):
ENH: update the super-build tag to ITKv5.0.0
ENH: Updating baselines for SegmentWithWatershedImageFilter
ENH: updating baselines for AdaptiveHistogramEqualizationImageFilter
COMP: fixing compile error
BUG: make it run with ITK 5 and legacy disabled
ENH: use DynamicThreadedGenerateData
ENH: support non-identity metadata in GeodesicActiveContour
DOC: updating comments to reflect actual behavior
Hans J. Johnson (16):
BUG: pngmath deprecated for sphinx >= 1.4
ENH: Move to v4.13.0.post0 version of breath
ENH: Update sphinx-bootstrap-theme to v0.7.1
ENH: Update gitstats to latest master branch version.
COMP: Must remove incomplete ITKDoxygenTAG_DIR
ENH: Change url from http: to https: for kitware sites
DOC: Prefer http: to https: for web addresses.
ENH: Address documentation build warnings
COMP: Resolve search for ITKVtkGlue status
ENH: Avoid contaminating Remote module builds with ITK_DIR
STYLE: Use range-based loops from C++11
STYLE: Use auto for variable type
STYLE: Pefer = default to explicitly trivial implementations
STYLE: Pefer = delete to explicitly trivial implementations
ENH: Fix signature of override function.
BUG: Fix many failing tests for the Sphinx Examples
Hans Johnson (21):
ENH: VTK 8.2.0 as a requirement for SphinxExamples
COMP: Update CMAKE_CXX_STANDARD settings to match ITKv5 settings
DOC: Update build instructions with greater detail.
ENH: Adding media wiki examples to sphinx examples
BUG: Unsigned char SetAlpha must be on scale of 0-255
COMP: Remove unused variables and set override.
COMP: Use std::sqrt instead of vcl_sqrt.
ENH: Only build ITKV4 examples with when selected in ITK.
ENH: Add support files from media wiki examples
COMP: Fix VTK 8.2.0 build issues.
DOC: Improved results and indexing. Addition changes mentioned in pull request.
ENH: Improve documentation images
ENH: Remove outdated CreateNewExample.py.in reference
ENH: Require building with VTK support
ENH: Require ITK version 5.0.0 or greater
STYLE: Remove outdated todo file for WikiExamples.
ENH: Allow building without VTK support
BUG: Fix failing tests and build errors of SphinxExamples
ENH: Update to latest version of ITK to support enum-classes
STYLE: Enforce ITK style defined by .clang-format
DOC: Improve example to provide more complete usage
Hina Shah (3):
BUG: Fix path for GitSetup.git
BUG: Fix minor issues with create new example script
ENH: adding new example for reading and printing dicom image tags
Jon Haitz Legarreta Gorroño (4):
STYLE: Fix typo in example name
STYLE: Prefer error checked std::sto[id] over ato[if]
ENH: Add a cookiecutter template to create new examples
BUG: Fix new example script cookiecutter
Mathew J. Seng (1):
BUG: TODO added for examples containing errors from original wiki.
Matt McCormick (10):
DOC: Update required ITK and Python versions in README
BUG: Do not enable Module_ITKLevelSetsv4Visualization
BUG: Use sphinx-build executable from Superbuild
BUG: Transparency.png was a TIFF file
DOC: Remove invalid FilterImageWithoutCopying input / output
DOC: Fix figure input filenames
ENH: Add SetDefaultNumberOfThreads
DOC: Update ContributeWithGit for cookiecutter script
DOC: Remove Gerrit reference and improve link location
ENH: Point GitSetup to ITK repository
ITK Software Guide Changes Since v5.0.0
Bradley Lowekamp (1):
ENH: Add VerifyPreconditions and VerifyInputInformation
Francois Budin (2):
COMP: Correct typo that made ITKSoftwareGuide compilation fail
STYLE: Page size and page numbers of the Guide front page were updated
Hans Johnson (2):
DOC: Add commentary about the coding style used.
COMP: Exceptions should be caught by constant reference
Jon Haitz Legarreta Gorroño (3):
COMP: Fix too long line lengths
DOC: Update ITK testing macros names
DOC: Fix testing macro name
Matt McCormick (9):
ENH: Update ITK ExternalProject version for 5.0.0.
COMP: Bump ITK to address line length warnings
DOC: Update supported Visual Studio versions
ENH: Bump ITK version to v5.0.1
ENH: Use https for GitSetup hooks checkout
BUG: Remove CircleCI resource_class specification
ENH: Point GitSetup to ITK repository
DOC: Update history to ITK 5
ENH: Bump ITK version to v5.1rc01
Stephen Aylward (5):
ENH: Updated tex for SpatialObjects to match ITKv5
ENH: Added details on use of TubeSpatialObjects.
BUG: Fixed spelling mistake
ENH: Added details on use of TubeSpatialObjects.
Enh: Clarify that GroupSO replaces SceneSO
Remote Module Changes Since v5.0.0
AnalyzeObjectMapIO:
Hans Johnson (2):
COMP: Do not include itkExceptionObject.h directly
COMP: Fix refactoring to enhanced for loop structure
AnisotropicDiffusionLBR:
Hans J. Johnson (1):
ENH: Fix spelling error s/tropci/tropic/g
Mathew J. Seng (1):
STYLE: Change enum to new enum class definition
Matt McCormick (3):
ENH: Add Azure Pipelines configuration
ENH: Python package for ITK 5.0.0
DOC: Add Azure Pipelines, PyPI, License badges
BSplineGradient:
Matt McCormick (5):
ENH: Add Azure Pipelines configuration
DOC: Add Azure Pipelines status badge
ENH: Update ImageToPointSetFilter wrapping for ITK 5 types
ENH: Add wrapping for BSplineGradientImageFilter
DOC: Add installation instructions
BioCell:
Mathew J. Seng (1):
COMP: Change enum to new enum class definitions
BoneEnhancement:
Bryce Besler (35):
ENH: Implemented HessianGaussianImageFilter with streaming
ENH: Implemented itkEigenToMeasureParameterEstimationFilter
ENH: Implemented DescoteauxEigenToMeasureParameterEstimationFilter
DOC: Fixed naming for DescoteauxEigenToMeasureParameterFunctor
BUG: Fixed initialization bug in HessianGaussianImageFilter
ENH: Added EigenToMeasureImageFilter and DescoteauxEigenToMeasureImageFilter
DOC: Added documentation to MaximumAbsoluteValue Functor
ENH: Added ITKReview
ENH: Descoteaux implementation
ENH: Move itkMultiScaleHessianEnhancementImageFilterStaticMethodsTest to GTest
ENH: Move itkMaximumAbsoluteValueImageFilterTest to GTest
ENH: Move itkHessianGaussianImageFilterTest to GTest
ENH: Update Descoteaux filter to ITKv5 DynamicThreadedGenerateData
ENH: Implement Krcah parameter estimation filter and unit test
STYLE: Updated to CI table
ENH: Implemented HessianGaussianImageFilter with streaming
ENH: Implemented itkEigenToMeasureParameterEstimationFilter
ENH: Implemented DescoteauxEigenToMeasureParameterEstimationFilter
DOC: Fixed naming for DescoteauxEigenToMeasureParameterFunctor
BUG: Fixed initialization bug in HessianGaussianImageFilter
ENH: Added EigenToMeasureImageFilter and DescoteauxEigenToMeasureImageFilter
DOC: Added documentation to MaximumAbsoluteValue Functor
ENH: Added ITKReview
ENH: Descoteaux implementation
ENH: Move itkMultiScaleHessianEnhancementImageFilterStaticMethodsTest to GTest
ENH: Move itkMaximumAbsoluteValueImageFilterTest to GTest
ENH: Move itkHessianGaussianImageFilterTest to GTest
ENH: Remove ITKReview module
ENH: Update Descoteaux filter to ITKv5 DynamicThreadedGenerateData
ENH: Implement Krcah parameter estimation filter and unit test
STYLE: Prefer C++11 type alias over typedef.
STYLE: Use "typename" for template parameters
BUG: Fix Krcah implementation
ENH: Remove SpatialObject parameterization
BUG: Follow templating of itkStreamableImageFilter for wrapping
Dženan Zukić (10):
ENH: Build both examples
COMP: fix compile error and warning
ENH: remove unused command-line parameter
COMP: make it compile after the big merge
BUG: fix Python wrapping
COMP: support running with legacy removed
ENH: removing unused files
ENH: parallelizing EigenToMeasureParameterEstimation filters
ENH: parallelize EigenToMeasure filter
ENH: adding current ITK code style definition files
Pablo Hernandez-Cerdan (1):
COMP: Remove deprecated throw specification
BoneMorphometry:
Dženan Zukić (1):
COMP: itksys::hash_map has been removed in ITKv5
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
Matt McCormick (4):
ENH: Add Azure Pipelines configuration
DOC: Add Azure pipelines badge
DOC: Add PyPI and license badge
BUG: Bump ITK Python required version to 5.0.1
Cuberille:
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
Matt McCormick (9):
ENH: Move Azure Pipelines configuration to test/ directory
ENH: Support ITKPythonGitTag in Azure Pipelines configuration
ENH: Update ITK version in Azure Pipeline configuration to 5.0.0
ENH: Wrap for all scalar pixel types
ENH: Build against ITK 5.0.1
DOC: Fix Azure badge link
ENH: Enable the use of a different interpolator in wrapping
STYLE: class -> typename
ENH: Bump Python package version
FixedPointInverseDisplacementField:
matt.mccormick@kitware.com (1):
STYLE: Move Python test to wrapping/test/CMakeLists.txt
GenericLabelInterpolator:
Dženan Zukić (1):
STYLE: replacing MD5 hashes by SHA512 hashes
yinkaola (2):
Update itkLabelImageGenericInterpolateImageFunction.h
Update itkLabelImageGenericInterpolateImageFunction.hxx
HigherOrderAccurateGradient:
Matt McCormick (4):
ENH: Build against ITK 5.0.0
ENH: Build Python packages against v5.0.0.post1
ENH: Improve Azure specification of ITK versions
DOC: Fix build spelling in C++ build documentation
IOMeshSTL:
Dženan Zukić (2):
COMP: fix link errors
ENH: require ITK 5.0.1
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
IOOpenSlide:
Mathew J. Seng (1):
STYLE: Change to enum to new enum class definitions
IOScanco:
Dženan Zukić (1):
ENH: update version numbers
Jon Haitz Legarreta Gorroño (2):
STYLE: Add ITK prefix to testing macros
ENH: Improve tests
IOTransformDCMTK:
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
IsotropicWavelets:
Matt McCormick (3):
COMP: Wrap GaussianImageSource for StructureTensor
BUG: Move Python tests to wrapping/test/CMakeLists.txt
ENH: Build against ITK 5.0.1 and bump Python package version
Ramraj (1):
ENH: Implemented composite filters for phase analysis
Ramraj Chandradevan (2):
ENH: Build against ITK 5.0.0
ENH: Update setup.py
LabelErodeDilate:
Mathew J. Seng (1):
ENH: Change to enum to new enum class definitions
LesionSizingToolkit:
Jon Haitz Legarreta Gorroño (1):
COMP: Fix unused type alias warnings
MinimalPathExtraction:
Matt McCormick (12):
ENH: CI builds with ITK 5.0.0.post1
STYLE: Indentation in the example
ENH: Example: check command line arguments
STYLE: Example: Run clang-format
DOC: SpeedFunctionToPathFilter update
STYLE: SpeedFunctionToPathFilter improvements
BUG: Use ITK_TEMPLATE_EXPORT with templated classes
STYLE: Update license header
ENH: Add Python test
STYLE: Use const_cast instead of C cast
STYLE: Use itkNotUsed
ENH: DSA example notebook
Stephen Aylward (3):
BUG: Replace include of itkExceptionObject.h with itkMacro.h
BUG: Replace itkExceptionObject.h with itkMacro.h
COMP: C++11 has deprecated the "throw" function declaration decorator
Montage:
Dzenan Zukic (4):
BUG: read CRLF line endings without crashing
COMP: adding a few missing typenames
COMP: fixing example compile warnings on GCC 5.4.0
COMP: fixing warnings
Dženan Zukić (100):
COMP: double-conversion is only a private dependency, not a public one
ENH: tests now handle image spacing correctly
BUG: fix spacing support
ENH: replace pixels by physical units in file pairs test parameters
DOC: expose transform writing in usage
BUG: with peak merging enabled a peak can have a brighter pixel nearby
ENH: Build against ITK 5.0.0 and bump Python package version
ENH: do not require unnecessary maxima
BUG: cosine interpolation avoids NaNs for additional candidates
STYLE: rename directory of Ti7Al test case
ENH: adding Ti7/Region1_10_Mosaic36 and Ti7/Region1_10_Mosaic180 tests
ENH: Adding Medium Carbon Steel 1701701_000000 test (UES corporation)
ENH: adding 05MAR09_run2_64-Raw test data from CMU
ENH: add the problematic region of S200 as a standalone test case
BUG: correctly offset translations by position of tile 0
BUG: fix calculation of average tile displacement error
ENH: account for accumulation of errors
ENH: Ti64 tests are no longer failing
ENH: reorganizing test names and output locations
ENH: expose allowing accumulation of errors (drift) in tests
ENH: global optimization with outlier detection and removal
ENH: increase test success threshold from 1.0 to 1.2 pixels
ENH: update examples to support non-unit spacing
STYLE: remove empty space in example
ENH: use translation offsets instead of transforms internally
ENH: move more test to expected to pass category
STYLE: review suggestions
BUG: fix re-ordering of peak maxima during zero suppression
ENH: expose position precision in TileMontage class
ENH: rewrite position tolerance to be expressed in pixels
ENH: use tile position tolerance in tests. Closes #105.
ENH: reduce evaluations of exp function
ENH: write input images after FFT band-pass filtering
ENH: crop images to overlapping portion for cross-correlation
ENH: expand the cropping region
BUG: fix wrong test parameters
ENH: allow drift for MNML5
ENH: adding first registration pair of 10-129-C_2 as a separate test
BUG: I forgot to update sheet/line zero suppression formula
ENH: do zero suppression only if needed
ENH: make zero suppression more consistent and less pronounced
ENH: prevent translations being rejected simply for being large
ENH: more informative outlier reporting
ENH: adding problematic S200 pairs as separate tests
BUG: better message for wrong number of parameters
BUG: merge peak distance was not respected (1 was always used)
BUG: fix and slightly optimize zero suppression
ENH: allow more low frequencies to pass by default
STYLE: simplifying type specification
ENH: allowing specification of real type used in FFTs
BUG: residuals were not properly divided by spacing
ENH: use registration confidence in equations and cost
ENH: more granular progress reporting (per pair, not per tile)
ENH: output indication of failing tile and average error to TSV file
STYLE: avoid specifying ITK namespace when already inside it
ENH: only two tests still fail
ENH: change parameters of large tests to reduce peak memory use
ENH: the stitched mosaic does not have to be written
ENH: all tests write their result except S200
ENH: adding github.io as an alternative source for testing data
COMP: ITK testing macros have ITK_ prefix since version 5.0+
Reduce majority of duplication in synthetic tests
ENH: parallel generation of synthetic sphere image
ENH: increase parallelism and cache tiles
ENH: checking whether interpolation is needed
COMP: fix unused variable warning
BUG: Old .bmp named file was a TIFF
ENH: adding ground truth creator. Closes #108.
ENH: WindowedSincInterpolateImageFunction for better resampling quality
ENH: update ITK to support RGB in WindowedSinc interpolator
BUG: file opening was not checked for success. Closes #122.
BUG: conversion from linear to nD index was wrong for 3D montages
ENH: add 3D ground truth case
STYLE: update clang-format style to follow recent ITK change
STYLE: applying new ITK style
STYLE: fixing KWStyle error
STYLE: manual fix of KWSTyle alignment error
STYLE: rename itkParseTileConfiguration into itkTileConfiguration
STYLE: converting README.rst into README.md. Closes #128.
ENH: support multi-dimensional tile configuration. Closes #127.
ENH: Update InMemoryMontageTest to use nD structure
STYLE: remove 2D from example names
ENH: add TileConfiguration comparison tool
ENH: add ImageCompareCommand.cxx from ITKExamples
ENH: add 2D sample data to examples (from ground truth creator)
ENH: add 3D sample data to examples (from ground truth creator)
ENH: updating examples to work with nD montages
ENH: Removing Parse/Write TileConfiguration2D
ENH: read images just once
ENH: adding bias field correction to the complete example
ENH: write bias-corrected images
ENH: add 3D test for CompleteMontage
ENH: resolving TODOs
ENH: add noise reduction step to the complete example
ENH: add calculation of systematic translation bias to pair-wise test
COMP: fixing in-source build of the examples
BUG: fix buffer overflow on float to string conversion
BUG: 1701701_000000_Fused is in TIF format
ENH: better exception reporting in test
ENH: better error reporting in GroundTruthCreator
Jon Haitz Legarreta Gorroño (1):
COMP: Fix unused variable warning
Mathew J. Seng (1):
COMP: Change to enum to new enum class definitions
Matt McCormick (9):
ENH: Update CI Build to build against 5.0.0.post1
DOC: Update Azure pipeline badge
ENH: Update Azure Pipelines configuration to support ITKPythonGitTag
ENH: Remove Travis config
ENH: Support arbitrary ITK C++ Git commit in Azure
ENH: Bump CI ITK Git commit to 2019-07-23 master
ENH: Bump Python package version to 0.4.0
ENH: Build Python package against ITK 5.0.1
DOC: Document installation
MorphologicalContourInterpolation:
Mathew J. Seng (1):
STYLE: Change to enum to new enum class definitions
NeuralNetworks:
Hans J. Johnson (1):
DOC: Explicitly specify that these methods are outdated
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
ParabolicMorphology:
Jon Haitz Legarreta Gorroño (1):
STYLE: Use "typename" for template parameters.
PhaseSymmetry:
Dženan Zukić (4):
ENH: allow finding ITK via configuration file
COMP: build with legacy disabled
ENH: use ITKImageIO and ITKTransformIO in examples' CMakeLists.txt
BUG: maintain image direction in internal filters. Closes #23.
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
Matt McCormick (5):
ENH: Add Azure pipelines configuration
COMP: Address signed / unsigned integer comparison warnings
COMP: Remove unused variable
DOC: Add Azure badge and C++ installation to README
BUG: Disable the module examples since they require SEM
Zahil Shanis (2):
BUG: Reverted Flip output
Removed itkFlipImageFilter from header
RLEImage:
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
Mathew J. Seng (1):
ENH: Change to enum to new enum class definitions
RTK:
Antoine Robert (1):
ENH: Wrapped TotalVariationDenoisingBPDQImageFilter
Gordian Kabelitz (2):
COMP: Remove dependency from std::unary_function
FIX Change frpm std::random_shuffle to std::shuffle
Lucas GANDEL (1):
ENH: Setup azure pipelines
Lucas Gandel (1):
COMP: Set RTK target properties
PA Rodesch (2):
One-step two materials
ENH: Wrapping for rtkMechlemOneStepSpectralReconstructionFilter with 2 or 3 materials
Simon Rit (33):
DOC: fixed image types in dot graph
ENH: improve backprojection speed for cylindrical detector with atan2
BUG: detector offsets badly accounted for with cylindrical detector in backprojection
COMP: fix new itkReadRawBytesAfterSwappingMacro format
FIX: exception for parallel geometry was not thrown
DOC: first version of the installation instructions
FIX: remove HelloWorld code (fully overlaps with FirstReconstruction)
DOC: add missing consortium members in LICENSE.TXT
COMP: adapt to enum class objects
COMP: remove nvcc-check.cmake, rely on system configuration.
BUG: part of the CUDA data manager was not thread safe
FIX: remove nvcc-check.cmake from install (deleted by 0fe32a6)
FIX: replace CudaInPlaceImageFilter with CudaImageToImageFilter where required
ENH: made rtkspectralonestep compatible with 2 or 3 materials
STYLE: remove unused code
ENH: New itk::CudaMemoryProbe
ENH: modified time probing with time + (cuda) memory probing
ENH: process projections one by one in Mechlem's one step
COMP: missing Windows dll export in itk::CudaMemoryProbe
ENH: new option in spectral one step to use spatially varying regularization
FIX: wrapping warning
ENH: add possibility to add clip planes to geometric phantom
ENH: add Attenuation member to convex shapes for exponential line integral
DOC: remove doxygen warnings caused by multiple group definitions
COMP: fix errors introduced by InsightSoftwareConsortium@0f23472
FIX: add exception for wrong file name in ProjectionsReader
COMP: remove vnl warnings caused by InsightSoftwareConsortium/ITK#1422
COMP: avoid brew install cmake in TravisCI OSX, seems usesless and harmful now
STYLE: add ; after macros
STYLE: use newer version of ReadRawBytesAfterSwapping
STYLE: split lines longer than 120 characters in digraph
STYLE: apply ITK's clang-format
Release of RTK v2.1.0
SCIFIO:
Dzenan Zukic (1):
COMP: fix direct inclusion of itkExceptionObject
SimpleITKFilters:
Bradley Lowekamp (4):
BUG: Removing comment out use of ITK test macro
ENH: Update CI to use Azure pipeline
BUG: Update to new ITK_ prefixed testing macros
Update README with Azure Pipeline badges
SkullStrip:
Jon Haitz Legarreta Gorroño (2):
ENH: Transition the example to the ITK testing framework.
BUG: Fix wrapping.
Matt McCormick (1):
BUG: Use ITK_TEMPLATE_EXPORT macro for StripTsImageFilter
SplitComponents:
Jon Haitz Legarreta Gorroño (1):
STYLE: Prefer = default to explicitly trivial implementations
Matt McCormick (1):
ENH: Bump ITK package dependency to 5.0.0.post1
Strain:
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
Matt McCormick (5):
ENH: Add Azure Pipelines configuration
DOC: Add Azure Pipelines badge
DOC: Add Python package installation
BUG: Do not wrap ImageToImageFilter scalar to covariant vector
ENH: Bump Python package version to 0.2.0
SubdivisionQuadEdgeMeshFilter:
Jon Haitz Legarreta Gorroño (1):
ENH: Add CI.
TextureFeatures:
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
Matt McCormick (2):
ENH: Update Python package for ITK 5.0.0.post1
COMP: Bump ITK C++ testing Git tag to 2019-06-21 master
Thickness3D:
Matt McCormick (2):
BUG: Prevent segfault in MedialThickness constructor (#24)
ENH: Build Python package against ITK 5.0.0.post1 (#25)
Thomas Janvier (3):
BUG: fix tests after PR#24 (#26)
REL: update version after tests validation (#27)
Update README.rst
TotalVariation:
Dženan Zukić (1):
ENH: Build against ITK 5.0.0
Jon Haitz Legarreta Gorroño (1):
STYLE: Add ITK prefix to testing macros
Matt McCormick (5):
BUG: Require ITK 5.0.1 for the Python package build
BUG: Remove old Azure configuration
ENH: Update Azure configuration to use ITK 5.0.1
BUG: Run Window Python package build as administrator
Revert "BUG: Run Window Python package build as administrator"
Samuel Gerber (1):
FIX: Image Axes Change
TwoProjectionRegistration:
Dženan Zukić (1):
COMP: do not #include "itkExceptionObject.h" directly
Matt McCormick (8):
ENH: Bump tests with Release CMAKE_BUILD_TYPE
ENH: Bump setup.py version to 1.0.1
ENH: Bump Azure ITK version for ITK 5.0.0
COMP: Add SiddonJacobRayCastInterpolateImageFunction for ITK 5
COMP: Remove GetMTime method
COMP: Use SpatialObject explicit IsInsideWorldSpace API for ITK 5
DOC: Add Python installation instructions
DOC: Fix Python package installation formatting