There is a newer version of the record available.

Published October 8, 2024 | Version 5.3.0
Software Open

nipy/nibabel: 5.3.0

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

Description

Release notes

This release primarily adds support for Python 3.13 and Numpy 2.0.

NiBabel 6.0 will drop support for Numpy 1.x.

New features

  • Update NIfTI extension protocol to include .content : bytes, .text : str and .json : dict properties for accessing extension contents. Exceptions will be raised on .text and .json if conversion fails. (#1336) (CM)

Enhancements

  • Ability to read data from many multiframe DICOM files that previously generated errors (#1340) (Brendan Moloney, reviewed by CM)
  • nib-nifti-dx now supports NIfTI-2 files with a --nifti2 flag (#1323) (CM)
  • Update nibabel.streamlines.tractogram to support ragged arrays. (#1291) (Serge Koudoro, reviewed by CM)
  • Filter numpy UserWarning on np.finfo(np.longdouble). This can occur on Windows systems, but it's done in the context of checking for the problem that is being warned against, so there's no need to be noisy. (#1310) (Joshua Newton, reviewed by CM)
  • Improve error message for for dicomwrapper errors in shape calculation (#1302) (YOH, reviewed by CM)
  • Support "flat" ASCII-encoded GIFTI DataArrays (#1298) (PM, reviewed by CM)

Bug fixes

  • Fix location initialization/update in OrthoSlicer3D for permuted axes (#1319, #1350) (Guillaume Becq, reviewed by CM)
  • Fix DICOM scaling, making frame filtering explicit (#1342) (Brendan Moloney, reviewed by CM)
  • Fixed multiframe DICOM issue where data could be flipped along slice dimension relative to the affine (#1340) (Brendan Moloney, reviewed by CM)
  • Fixed multiframe DICOM issue where image_position and the translation component in the affine could be incorrect (#1340) (Brendan Moloney, reviewed by CM)

Maintenance

  • Numpy 2.0 compatibility and addressing deprecations in numpy API (#1304, #1330, #1331, #1334, #1337) (Jon Haitz Legarreta Gorroño, CM)
  • Python 3.13 compatibility (#1315) (Sandro from the Fedora Project, reviewed by CM)
  • Testing on Python 3.13 with free-threading (#1339) (CM)
  • Testing on ARM64 Mac OS runners (#1320) (CM)
  • Proactively address deprecations in coming Python versions (#1329, #1332, #1333) (Jon Haitz Legarreta Gorroño, reviewed by CM)
  • Replace nose-era setup() and teardown() functions with pytest equivalents (#1325) (Sandro from the Fedora Project, reviewed by Étienne Mollier and CM)
  • Transitioned from blue/isort/flake8 to ruff. (#1289) (Dimitri Papadopoulos, reviewed by CM)
  • Vetted and added various rules to the ruff configuration for auto-formatting and style guide enforcement. (#1321, #1351, #1352, #1353, #1354, #1355, #1357, #1358, #1359, #1360, #1361, #1362, #1363, #1364, #1368, #1369) (Dimitri Papadopoulos, reviewed by CM)
  • Fixing typos when found. (#1313, #1370) (MB, Dimitri Papadopoulos)
  • Applied Repo-Review suggestions (Dimitri Papadopoulos, reviewed by CM)

API changes and deprecations

New Contributors

  • @joshuacwnewton made their first contribution in https://github.com/nipy/nibabel/pull/1310
  • @gjpcbecq made their first contribution in https://github.com/nipy/nibabel/pull/1319

Full Changelog: https://github.com/nipy/nibabel/compare/5.2.1...5.3.0

Files

nipy/nibabel-5.3.0.zip

Files (4.7 MB)

Name Size Download all
md5:b6daea29e6fe2ee24dc00fd2b0536664
4.7 MB Preview Download

Additional details

Related works

Is supplement to
Software: https://github.com/nipy/nibabel/tree/5.3.0 (URL)