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Published January 9, 2023 | Version 5.0.0
Software Open

nipy/nibabel: 5.0.0

Creators

  • 1. School of Psychology, University of Birmingham, Birmingham, UK
  • 2. Stanford University
  • 3. Otto-von-Guericke-University Magdeburg, Germany
  • 4. Microsoft Research, Montréal, Québec, Canada
  • 5. UC San Diego
  • 6. MIT
  • 7. Center for Open Neuroscience, Dartmouth College
  • 8. Dartmouth College: Hanover, NH, United States
  • 9. Wellcome Centre for Integrative Neuroimaging, University of Oxford, UK
  • 10. University of Washington: Seattle, WA, United States
  • 11. MIT, HMS
  • 12. Athena EPI, Inria Sophia-Antipolis
  • 13. Institute of Neuroinformatics, ETH/University of Zurich
  • 14. Deptartment of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH
  • 15. Harvard University - Psychology
  • 16. Department of Computer Science, Aalto University, Espoo, Finland and Department of Neuroscience, Imaging and Clinical Sciences, University G. D'Annunzio, Chieti, Italy
  • 17. The University of Washington eScience Institute
  • 18. CEA
  • 19. Montreal Neurological Institute and Hospital
  • 20. Department of Psychology, University of California Davis, CA, USA
  • 21. Berkeley Institute for Data Science, UC Berkeley
  • 22. CNRS LTCI, Telecom ParisTech, Université Paris-Saclay
  • 23. Center for Magnetic Resonance Research, University of Minnesota
  • 24. Google
  • 25. Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
  • 26. University of Geneva, Switzerland
  • 27. SRI International
  • 28. Department of Psychology, Stanford University, CA, USA
  • 29. University College London
  • 30. BrainSpec, Boston, MA
  • 31. INRIA
  • 32. Université de Sherbrooke
  • 33. Charite Universitatsmedizin Berlin, Germany
  • 34. McGill University
  • 35. University College London, London, UK
  • 36. University of California, San Francisco
  • 37. Department of Neuropsychiatry, University of Pennsylvania
  • 38. Hospital for Sick Children
  • 39. Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA
  • 40. TIB – Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany
  • 41. National Technical University of Athens, Greece
  • 42. Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
  • 43. National Institute of Mental Health and Neuro-Sciences, India

Description

New feature release in the 5.0.x series.

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

New features
  • SerializableImage now has to_stream() and from_stream() methods to read/write streams implementing the io.IOBase interface. A from_url() method enables loading images from URLs. (pr/1129) (CM, reviewed by MB)
  • TrkFile supports TRKv3, an undocumented but generally compatible variant of TRKv2. (pr/1125) (CM)
Enhancements
  • Support multiline header fields in TCKFile (pr/1175) (CM, reviewed by Matt Cieslak)
  • Make layout order an initialization parameter of ArrayProxy (pr/1131) (CM, reviewed by MB)
  • Initial support for type annotations. (pr/1115, pr/1178) (CM, reviewed by Zvi Baratz)
Bug fixes
  • Handle extension/file-format mismatches implemented incompletely in pr/1013 (pr/1138) (CM, reviewed by Thomas Phil)
  • Improve handling of invalid TCK files, which could sometimes cause an infinite loop (pr/1140) (Anibal Solon, reviewed by CM)
  • Clean up ECAT test case that left filehandle open and failed to use class variables (pr/1155) (Dimitri Papadopoulos, reviewed by CM)
Maintenance
  • Simplify TCK reading code by assuming files are open in binary mode (pr/1142) (Anibal Solon, reviewed by MC, CM)
  • Code support for tests covering deprecated functionality (pr/1159) (CM)
  • Miscellaneous code cleanups (pr/1148, pr/1149, pr/1153, pr/1154, pr/1156) (Dimitri Papadopoulos, reviewed by CM)
  • Update CI to build, test and deploy PyPI artifacts (pr/1134) (CM, reviewed by MB)
  • Transition from setup.cfg to pyproject.toml package configuration (pr/1133) (CM, reviewed by MB)
  • Addressed race conditions preventing running tests with pytest-xdist. (pr/1157, pr/1158) (CM, reviewed by Christian Haselgrove)
  • Apply blue and isort auto-formatters and provide pre-commit configuration to reduce human burden of style guidelines. (pr/1124, pr/1165, pr/1169) (CM and Zvi Baratz)
  • Manage versioning with setuptools_scm (pr/1171) (CM, reviewed by Zvi Baratz)
  • Reduce installed package size by excluding very large test file (pr/1176) (CM, reviewed by Zvi Baratz)
API changes and deprecations
  • Passing an int64 array to Nifti1Image without a header or dtype argument will raise a ValueError. (pr/1173) (CM)
  • tmpdirs.TemporaryDirectory is deprecated in favor of tempfile.TemporaryDirectory. (pr/1172) (CM, reviewed by Zvi Baratz)
  • The nisext package is deprecated and will be removed in NiBabel 6.0. (pr/1170) (CM, reviewed by MB)
  • Drop support for Python 3.7, Numpy < 1.19 (pr/1177) (CM)

  • The following deprecated functions and methods will now raise ExpiredDeprecationErrors

    • nibabel.loadsave.read_img_data
    • nibabel.dataobj_images.DataobjImage.get_data
    • nibabel.loadsave.guessed_image_type
    • nibabel.onetime.setattr_on_read
    • nibabel.orientations.flip_axis

  • Modules, classes and functions that expired at 4.0 were fully removed. ExpiredDeprecationError\s will now be AttributeError\s.

Files

nipy/nibabel-5.0.0.zip

Files (4.7 MB)

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Additional details

Related works

Is supplement to
https://github.com/nipy/nibabel/tree/5.0.0 (URL)