[Neuroimaging] ANN: Nibabel release 2.3

paul mccarthy pauldmccarthy at gmail.com
Tue Jun 12 17:28:41 EDT 2018


Thanks for all the hard work Chris!

Paul

On 12 June 2018 at 21:37, Gael Varoquaux <gael.varoquaux at normalesup.org>
wrote:

> Congratulations! Thank you for keeping this crucial part of the ecosystem
> alive and kicking.
>
> On Tue, Jun 12, 2018 at 06:06:01PM +0000, Christopher Markiewicz wrote:
> > 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.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)
>
> > Enhancements
> > ------------
> > * 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)
>
> > 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.
>
>
>
> > Enjoy,
> --
>     Gael Varoquaux
>     Senior Researcher, INRIA Parietal
>     NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
>     Phone:  ++ 33-1-69-08-79-68
>     http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/neuroimaging/attachments/20180612/5c18ec25/attachment.html>


More information about the Neuroimaging mailing list