InsightSoftwareConsortium/ITK: ITK 5.1.0
Creators
- Ibanez, Luis1
- Lorensen, Bill2
- McCormick, Matthew3
- King, Brad3
- Blezek, Daniel4
- Johnson, Hans5
- Lowekamp, Bradley
- Jomier, Julien6
- Miller, Jim
- Lehmann, Gaëtan
- Cates, Josh
- Ng, Lydia7
- Kim, Jisung
- Gelas, Arnaud
- Malaterre, Mathieu
- Krishnan, Karthik
- Hoffman, Bill
- Williams, Kent
- Budin, Francois
- Legarreta, Jon Haitz8
- Schroeder, Will
- R. Aylward, Stephen3
- Zukić, Dženan9
- Liu, Xiaoxiao
- Avants, Brian10
- Dekker, Niels
- Noe, Aljaz
- Popoff, Michka
- Hart, Gabe
- McBride, Sean
- Sundaram, Tessa
- Gouaillard, Alexandre
- Stauffer, Michael
- Enquobahrie, Andinet
- Tustison, Nick11
- Pathak, Sayan
- Cedilnik, Andy
- Chen, Ting
- Shelton, Damion
- Helba, Brian
- Quammen, Cory
- Jin, Yinpeng
- Padfield, Dirk
- Vercauteren, Tom
- Jae Kang, Hyun
- Turek, Matt
- Tamburo, Robert
- Audette, Michel
- Hernandez-Cerdan, Pablo
- Foskey, Mark
- Hughett, Paul
- Doria, David
- Kindlmann, Gordon
- Cole, David
- Fillion-Robin, Jean-Christophe3
- Turner, Wes
- Chen, Sophie
- S. FONOV, Vladimir
- Tasdizen, Tolga
- Duda, Jeffrey
- Galeotti, John
- BARRE, Sebastien
- Jaume, Sylvain
- Mosaliganti, Kishore
- Chandra, Parag
- Ghayoor, Ali
- Mackelfresh, Andrew
- Mullins, Christopher
- Zhuge, Ying
- Martin, Ken
- Xue, Xinwei
- Straing, Marius
- Estepar, Raul
- Squillacote, Amy
- Wyman, Brad
- Chang, Wilson
- Guyon, Jean-Philippe
- Botha, Charl
- Baghdadi, Leila
- maekclena
- Vigneault, Davis12
- P. Awate, Suyash
- Reynolds, Patrick
- Rit, Simon13
- Pincus, Zachary
- Finet, Julien
- Venkatram, Raghu
- Zygmunt, Kris
- Rondot, Pascale
- Davis, Brad
- Antiga, Luca
- Coursolle, Mathieu
- Roden, Mark
- Park, Sangwook
- Cheung, Ho
- Aaron Cois, C.
- Gandel, Lucas
- Kaucic, Robert
- Yaniv, Ziv
- D. Hanwell, Marcus
- Magnotta, Vincent
- Bertel, François
- Greer, Hastings
- Hipwell, John
- Chandrashekara, Raghavendra
- C. Bigler, Don
- Straing, Marius
- Styner, Martin
- Robbins, Steven
- Chalana, Vikram
- Le Poul, Yann
- Neundorf, Alexander
- Lamb, Peter
- Gerber, Samuel
- Williamson, Zach
- Braun-Jones, Taylor
- Wasem, Andrew
- Rannou, Nicolas
- Beare, Richard
- ITK Community Members
- 1. Google Inc, Kitware Inc, University of North Carolina at Chapel Hill, Université de Rennes 1, Universidad Industrial de Santander
- 2. GE Research
- 3. Kitware Inc
- 4. Mayo Clinic, Mayo Clinic Graduate School for Biomedical Sciences
- 5. University of Iowa
- 6. Kitware SAS, Kitware Inc
- 7. Allen Institute for Brain Science
- 8. Université de Sherbrooke
- 9. Kitware Inc, University of Siegen
- 10. University of Pennsylvania
- 11. University of California Irvine, University of Virginia, Washington University in Saint Louis, Brigham Young University
- 12. Tufts University School of Medicine
- 13. University of Lyon, CREATIS
Description
We are happy to announce the Insight Toolkit (ITK) 5.1.0! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration.
ITK 5.1.0 is a feature release that improves and extends the major ITK 5.0 release. ITK 5.1.0 includes a NumPy and Xarray filter interface, clang-format enforced coding style, enhanced modern C++ range support, strongly-typed enum's, and much more.
A number of issues were addressed based on feedback from Release Candidate 3. Filters avoid extra copies when operating on NumPy arrays, and itk.Image
is now a NumPy array-like. Remote module CI testing infrastructure has been migrated to GitHub Actions for C++ tests, Python package builds, and automated Python package deployment.
Python Packages
Install ITK Python packages with:
pip install --upgrade itk
or:
conda -c conda-forge install itk
Guide and Textbook
Library Sources
Testing Data
Unpack optional testing data in the same directory where the Library Source is unpacked.
Checksums
FeaturesParabolic morphological filtering with the ITKParabolicMorphology remote module. To install the new Python package: pip install itk-parabolicmorphology
. Jupyter notebooks are provided as examples. For more information, see the Insight Journal article, Beare R. Morphology with parabolic structuring elements. The Insight Journal. January-June. 2008. http://www.insight-journal.org/browse/publication/228.
A GitHub Action configuration is available for ITK Remote Module continuous integration (CI) testing and Python packaging on Linux, macOS, and Windows. Continuous deployment (CD) is configured to upload packages to the Python Package Index (PyPI) when the repository is tagged. More information can be found in the ITK Python Package ReadTheDocs documentation.
Pass NumPy Array's or Xarray DataArray's to ITK Image FiltersThe Pythonic, functional-like interface to all ITK image-to-image-filters now directly supports operation on NumPy ndarray'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)
An itk.Image
is now more NumPy array-like: shape
, ndim
, and dtype
attributes are available; these correspond to the values when converted to a NumPy ndarray
. Basic NumPy functions can be called directly on an itk.Image
, i.e.,
min = np.min(image)
max = np.max(image)
mean = np.mean(image)
Similar, experimental support (subject to change) is also available for Xarray DataArray's. If an xarray.DataArray
is passed as an input, an xarray.DataArray
is returned as an output. Moreover, the operation preserves spatial and dimensional metadata. For example,
import xarray as xr
import itk
image = itk.imread('/path/to/image.tif')
da = itk.xarray_from_image(image)
smoothed = itk.median_image_filter(da, radius=3)
print(smoothed)
results in:
<xarray.DataArray (y: 288, x: 894)>
array([[255. , 255. , 255. , ..., 255. , 255. , 255. ],
[ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995],
[ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995],
...,
[ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995],
[ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995],
[ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995]],
dtype=float32)
Coordinates:
* x (x) float64 0.0 1.0 2.0 3.0 4.0 ... 889.0 890.0 891.0 892.0 893.0
* y (y) float64 0.0 1.0 2.0 3.0 4.0 ... 283.0 284.0 285.0 286.0 287.0
Attributes:
direction: [[1. 0.]\n [0. 1.]]
A round trip is possible with itk.image_from_xarray
.
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 available.
Python Package 64-bit Float SupportIn 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.
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.
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 ParallelismITK provides a powerful registration 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'sImprovements 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 now follow a consistent <Description>Enum
naming conversion, which results in a Python interface:
<Description>Enum_<EnumValue1>
<Description>Enum_<EnumValue2>
[...]
A guide for updating to the new enum's can be found in the Strongly Typed Enumerations section of the ITK 5 Migration Guide.
DICOM SupportITK'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 UpdatesNew remote module: TubeTK: An open-source toolkit, led by Kitware, Inc., for the segmentation, registration, and analysis of tubes and surfaces in images.
A new remote module grading system was added to help convey the quality compliance level for the 45 remote modules.
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.
Zenodo CitationITK has a Zenodo Citation:
This citation can be used to cite a specific version of the software. If you have contributed 10 or more patches to ITK, please add your ORCID iD to our .zenodo.json file for authorship association.
NumFOCUS Copyright TransferITK's copyright and the copyright of software held by the Insight Software Consortium have been transferred to NumFOCUS. CMake's copyright has been transferred to Kitware.
And MoreMany more improvements have been made. For details, see the changelogs for the release candidates and changelog below.
CongratulationsCongratulations and thank you to everyone who contributed to this release.
Of 73 authors since v5.0.0, we would like to specially recognize the 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, Brad T. Moore, Niklas Johansson, Flavien Bridault, Pradeep Garigipati, haaput, tabish, and Antoine Robert, Ben Wilson, Adam Rankin, PA Rodesch, Tabish Syed, vlibertiaux, Michael Jackson, Conrad Poelman, and muschellij2.
Enjoy ITK!
ITK Changes Since v5.1rc03 Bradley Lowekamp (3): Bug Fixes- Check if calculator is proper type (3e7307744e)
- Use one calculator in ItermodesThresholder (6dc4948017)
- Use GDCM as private dependency in ITKIOGDCM (ca1913cee6)
- Remove deprecated/removed std (7b2dfd28d4)
- add the .exe executable extension to clang-format on Windows (343cbf9236)
- efdd2cab95 (efdd2cab95)
- Remove use of deprecated, redundant interface (51792db03b)
- Prefer multiplication to division (50b91ab2cc)
- Variable names updated to better indicate their pupopse (5012b7e41f)
- Provide new baseline for ImageRegisration4Test (623bef5c10)
- Only compute log(fixedImageMarginalPDFValue once outside loop (e7ef06e39a)
- Avoid processing entire rows based on mathematical certainties (82730afa5c)
- Improve diagnostic message for exception (bebe1d6f4a)
- Fix missing \ingroup ITKIODCMTK (d7f8c463dc)
- Fix typo in comment User -> Uses (d87449620f)
- Suppress compiler warning about value trucation (9e137468bc)
- Unused variable warning (c40a494c79)
- TBB build requires consistent exception options (c4caa4cdbe)
- Pointer to temporary variable needs resetting to null. (b29dc9182e)
- Reorder commands for locallity of reference (8626163a48)
- Make alias variables to assist with clear documentation (56922b8d80)
- totalMassOfPDF == this->m_JointPDFSum by definition (982cfaec51)
- Fix -Wstrict-overflow warning in itkImageRegionConstIteratorWithIndex (93be179376)
- Improve Thresholding module filters' coverage. (e4507807e5)
- Change ivar name in `itk (e864411be3)
- Avoid duplicated code in `itk (4217cc08a3)
- Make the histogram generator set up method private (8f8b7ca7a4)
- Fix threshold variable type/value in histogram threshold calc classes (5c114fec35)
- Wrap unsigned long long for image reading writing (4febe70198)
- Improve is_vector identification in image_from_xarray (69b90001ed)
- Update CI testing virtual machine images (8463020847)
- Set Visual Studio toolset version in Python CI builds (8cd2bd66c7)
- ndim, shape, and dtype attributes for itk.Image (a1763524ff)
- Update testing data content links for 5.1.0 (d3286c9cc0)
- PyBuffer importImageFilterWillOwnTheBuffer is constexpr (a306f50eff)
- Update ITKBibliography.bib link (e401d14d76)
- Release process updates for v5.1rc03 (e4e08332db)
- Document how to handle operator<< link errors from enum libraries (bced49ef65)
- Update .zenodo (1865c357d9)
- Update CastXML binary for Visual Studio 2019 (ce5cf91651)
- Remove unused calls in itkHashTableTest (fc88c718ed)
- Silence discarding return value in GE5ImageIO (da78c29634)
- UnboundLocalError in _GetImageFromArray (97f281198c)
- Condition HDF5 HDopen on _MSC_VER definition (47a85f15a1)
- Correct image_view_from_array alias (26560ebc08)
- Reset m_Dimension in VideoFileWriter (136b8e462a)
- Return type for PyBuffer _GetImageViewFromArray with VectorImage (cd62423ed5)
- Keep a reference to the NumPy array passed to itk.image_view_from_array (60afb52f5b)
- Use linspace for coords in xarray_from_image (67ddcde911)
- Provide initial input_type value in itkTemplate (1cf6dd01b5)
- Keep itk.Image reference in NumPy array views (87bc23f723)
- Filters avoid extra copies when operating on NumPy arrays (8a8dfe5907)
- itk.CType to numpy.dtype types for Windows (7cd5889b1f)
- update remote module RTK (319799698c)
- remove warning when writing 1D, 4D, 5D and 6D images read from disk (8932e7ccb7)
- Upgrade version of TubeTK (3de18fcf2e)
- Added jacobian computation to ComposeScaleSkewVersorTransform (#1755) (2f38debfe3)
- 21e619bf69 (21e619bf69)
- Add CMAKE_SH definition for Eigen ExternalProject (b21c5f6001)
- Fix HDF5 HDopen definition for MinGW (d997cb288f)
- update usage for ResampleAnImage (433c158a)
- Add python testing and I/O moved to Girder Python testing is now configured for this module. (dbe29b80)
- Test expects failure, removing EXIT_FAILURE allows test to continue (fbe2eaaf)
- Change python enums to new v5 enum structure (de6e33be)
- Add exception for invalid keys that cannot be processed at runtime. (a2fc2fbe)
- Invalid vtk image being processed. Changed to use mushroom.vtk taken ITK test. (779409a4)
- Prefer making deleted functions public Deleting a function affects fundamental aspects of the client interface of a class, and hiding them in private as if they were implementation details is unhelpful. (881346ff)
- Bump ITK External Project version to v5.1.0 (df2a71e2)
- Update Sphinx date, copyright assignment (d41321f7)
- Update links to Sphinx (7644858a)
- Remove invalid label map article link (fdd95a86)
- Update breathe for Sphinx compatibility (2216fcbe)
- Update pyparsing for Python 3 (8032f868)
- Update doxylink for recent Sphinx (1426ac93)
- Update breathelink for recent Sphinx (f8d6c7b0)
- Correct ReadAndPrintDICOMTags output (880cee9c)
- Disable AdaptiveHistogramEqualization Python tests (7c0f4999)
- Add missing table borders in
How To Create A Module
chapter (7fd0894) - Add section about tests for Wrapping files (fbb8615)
- Miscellaneous fixes in introduction and installation (a5f9673)
- Bump ITK ExternalProject version to v5.1.0 (8d41ce7)
- Add GitHub Action to build and publish Guide PDFs (68e2f9f)
- Remove CircleCI configuration (5e18abd)
- wrap image file reader and writer for dimension 1 (0832018a)
- wrap NumpyBridge for dimension 1 (72ed4dfb)
- Add quadratic penalization to OSEM algorithm (b806c7e6)
- Fix wrapping when building ITK with dimension 1 (3a02b74f)
- Use real image type as input of Hilbert filter (0d135b4d)
- Change member type from float to double in Zeng projectors (adb8061f)
- ProgressReporter for FDK reconstruction (4b2b1fd8)
- filters check whether their geometry is set (40c0565d)
- default projectors for all iterative filters (2c8ae75f)
- set division threshold for SART (a0e604c7)
- reduced size of application tests (40f49ecc)
- solve memory leak in rtkcheckimagequality (2a3eb595)
- fixed format in rtkIterationCommands.h (324f0609)
- Add rtkSimulatedGeometry python application (1edbc560)
- Add ITK clang-format linter check (1a888880)
- Apply clang-format to PR with tag action (974eb598)
- Set latest available itk version in setup.py (a6437840)
- Exclude gengetopt and lpsolve folders from clang formatting (590cf8f5)
- change CMake variable name for RTK git tag (eeac6312)
- remove MacOS and Windows self-hosted Cuda python packages (df54c6f7)
- fix wrong header guard for rtkProgressCommands.h (e7e4c8d1)
- fix missing ITKGDCM dependency (957d049e)
- remove warnings due to unhandled enum value (69b08d8e)
- minimize disk space in Linux Azure pipelines to avoid saturation (fed8944a)
- wrong target libraries in FirstReconstruction examples (cf776249)
- fix wrappings for 1D and double (b36a0442)
- remove unused kernel parameter in Cuda forward projection (dcb015ee)
- fix ITK clang-format to a few RTK source files (bbcc5802)
- fix ITK clang-format (84a0611c)
- remove unused examples/CMakeLists.txt (a90d7738)
- Make find_package(ITK) dependent (NOT ITK_SOURCE) (#4) (892a43bc)
- Make find_package(ITK) dependent (NOT ITK_SOURCE) (#5) (30a909d2)
- 077e4a93 (077e4a93)
Files
InsightSoftwareConsortium/ITK-v5.1.0.zip
Files
(33.0 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/InsightSoftwareConsortium/ITK/tree/v5.1.0 (URL)