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Published November 16, 2019 | Version 3.0.0rc1
Software Open

nipy/nibabel: 3.0.0rc1

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

Description

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, and Stephan Gerhard.

References like "pr/298" refer to github pull request numbers.

3.0.0rc1 (Saturday 16 November 2019)

Release candidate for NiBabel 3.0, initiating a minimum one-month testing window.

Downstream projects are requested to test against the release candidate by installing with pip install --pre nibabel.

New features
  • ArrayProxy method get_scaled() scales data with a dtype of a specified precision, promoting as necessary to avoid overflow. This is to used in img.get_fdata() to control memory usage. (pr/833) (CM, reviewed by Ross Markello)
  • GiftiImage method agg_data() to return usable data arrays (pr/793) (Hao-Ting Wang, reviewed by CM)
  • Accept os.PathLike objects in place of filenames (pr/610) (Cameron Riddell, reviewed by MB, CM)
  • Function to calculate obliquity of affines (pr/815) (Oscar Esteban, reviewed by MB)
Enhancements
  • get_fdata(dtype=np.float32) will attempt to avoid casting data to np.float64 when scaling parameters would otherwise promote the data type unnecessarily. (pr/833) (CM, reviewed by Ross Markello)
  • ArraySequence now supports a large set of Python operators to combine or update in-place. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Warn, rather than fail, on DICOMs with unreadable Siemens CSA tags (pr/818) (Henry Braun, reviewed by CM)
  • Improve clarity of coordinate system tutorial (pr/823) (Egor Panfilov, reviewed by MB)
Bug fixes
  • Sliced Tractograms no longer apply_affine to the original Tractogram's streamlines. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Re-import externals/netcdf.py from scipy to resolve numpy deprecation (pr/821) (CM)
Maintenance
  • Support Python >=3.5.1, including Python 3.8.0 (pr/787) (CM)
  • Manage versioning with slightly customized Versioneer (pr/786) (CM)
  • Reference Nipy Community Code and Nibabel Developer Guidelines in GitHub community documents (pr/778) (CM, reviewed by MB)
API changes and deprecations
  • Deprecate ArraySequence.data in favor of ArraySequence.get_data(), which will return a copy. ArraySequence.data now returns a read-only view. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
  • Deprecate DataobjImage.get_data() API, to be removed in nibabel 5.0 (pr/794, pr/809) (CM, reviewed by MB)

Files

nipy/nibabel-3.0.0rc1.zip

Files (4.5 MB)

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Additional details

Related works

Is supplement to
https://github.com/nipy/nibabel/tree/3.0.0rc1 (URL)