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Published June 12, 2018 | Version 2.3.0
Software Open

nipy/nibabel: 2.3.0

Authors/Creators

  • 1. University of Birmingham
  • 2. Stanford University
  • 3. MIT
  • 4. INRIA
  • 5. Dartmouth College, @Debian, @DataLad, @PyMVPA, @fail2ban
  • 6. University of Washington
  • 7. Cincinnati Children's Hospital Medical Center
  • 8. Harvard University
  • 9. Imeka
  • 10. The University of Washington eScience Institute
  • 11. FMRIB, University of Oxford
  • 12. UC Berkeley
  • 13. McGill University
  • 14. Dartmouth College
  • 15. Inria
  • 16. University of Toronto
  • 17. Genentech

Description

New feature release for the 2.3 series.

Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH) Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan Gerhard (SG) and Eric Larson (EL).

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

New features
  • TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM)
  • Image slicing for SpatialImages (pr/550) (CM)
Enhancements
  • Simplfiy MGHImage and add footer fields (pr/569) (CM, reviewed by MB)
  • Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul McCarthy, reviewed by MB, CM)
  • Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy, reviewed by CM, MB)
  • Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves, reviewed by CM, Satra Ghosh, MB, Tim Coalson)
  • Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed by CM, MB)
  • Accept degenerate filenames such as .nii (pr/621) (Dimitri Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko)
  • Take advantage of IndexedGzipFile drop_handles flag to release filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB)
Bug fixes
  • Preserve first point of LazyTractogram (pr/588) (MC, reviewed by Nil Goyette, CM, MB)
  • Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by CM, MB)
  • Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan, MB, reviewed by MB, MC, CM)
  • Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB)
  • Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro, reviewed by MC, MB, Eleftherios Garyfallidis, CM)
  • Resolve UnboundLocalError in Python 3 (pr/607) (Jakub Kaczmarzyk, reviewed by MB, CM)
  • Do not crash on non-ImportError failures in optional imports (pr/618) (Yaroslav Halchenko, reviewed by CM)
  • Return original array from get_fdata for array image, if no cast required (pr/638, MB, reviewed by CM)
Maintenance
  • Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB)
  • Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM)
  • Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM)
  • Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by Yaroslav Halchenko, MB)
  • Move nib-ls and other programs to a new cmdline module (pr/601, pr/615) (Chris Cheng, reviewed by MB, Yaroslav Halchenko)
  • Remove deprecated numpy indexing (EL, reviewed by CM)
  • Update documentation to encourage get_fdata over get_data (pr/637, MB, reviewed by CM)
API changes and deprecations
  • Support for keep_file_open = 'auto' as a parameter to Opener() will be deprecated in 2.4, for removal in 3.0. Accordingly, support for openers.KEEP_FILE_OPEN_DEFAULT = 'auto' will be dropped on the same schedule.
  • Drop-in support for indexed_gzip < 0.7 has been removed.

Files

nipy/nibabel-2.3.0.zip

Files (4.4 MB)

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md5:0411ed000d58e8b4fc5915433ab2b394
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Additional details

Related works

Is supplement to
https://github.com/nipy/nibabel/tree/2.3.0 (URL)