nipy/nibabel 2.3.0

on GitHub

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.