[Neuroimaging] ANN: Nibabel release 2.3

Christopher Markiewicz markiewicz at stanford.edu
Tue Jun 12 14:06:01 EDT 2018

Hi all,

Nibabel 2.3 has been released just in time for OHBM. It's been published to PyPI and should be available on conda-forge within the next day.

Features to look out for in this release are a new image slicing interface and TRK/TCK conversion tools. There have also been a number of first-time contributors, which is always good to see.

As always, thanks to all contributors, reviewers and users.

Please cite using the Zenodo DOI: <https://doi.org/10.5281/zenodo.1011207> https://doi.org/10.5281/zenodo.1287921

The full changelog follows:

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)

* Simplify 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)

* 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
* Drop-in support for ``indexed_gzip < 0.7`` has been removed.



Chris Markiewicz

Center for Reproducible Neuroscience

Stanford University
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