[Neuroimaging] ANN: NiBabel 3.0

[JB Poline]

This is great ! thanks so much
JB

On Wed, Dec 18, 2019 at 3:15 PM bthirion <bertrand.thirion at inria.fr> wrote:

> Congratulations and big thanks to the team !
>
> Best,
>
> Bertrand
>
> On 18/12/2019 18:23, Christopher Markiewicz wrote:
>
> Hi all,
>
> NiBabel 3.0 is out today! Thanks to everybody who tested the release
> candidates to help a smooth upgrade for users.
>
> The most consequential changes in this release are the removal of Python 2
> support and the deprecation of the img.get_data() accessor method to
> retrieve the image data block. The supported APIs for accessing data are
> img.get_fdata(), which always casts to float, and img.dataobj, which
> affords more control over the interpretation of the data object. The data
> object also now fully supports the numpy __array__ interface, which means
> it can be cast directly.
>
> Additionally, GIFTI images have a new agg_data() method that simplifies
> the retrieval of DataArrays from GIFTI files into usable numpy arrays.
> Most, if not all, filenames can now be passed as pathlib.Path objects. And
> there are significant updates to the streamlines package.
>
> Many thanks to everbody who took the time to investigate and report bugs,
> propose fixes, review pull requests and review the documentation, including
> first-time contributors Cameron Riddell, Hao-Ting Wang, Oscar Esteban,
> Dorota Jarecka, and Chris Gorgolewski.
>
> Full changelog follows.
>
> ----
>
> 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.
>
> 3.0.0 (Wednesday 18 December 2019)
> ==================================
>
> New features
> ------------
> * ArrayProxy ``__array__()`` now accepts a ``dtype`` parameter, allowing
>   ``numpy.array(dataobj, dtype=...)`` calls, as well as casting directly
>   with a dtype (for example, ``numpy.float32(dataobj)``) to control the
>   output type. Scale factors (slope, intercept) are applied, but may be
>   cast to narrower types, to control memory usage. This is now the basis
>   of ``img.get_fdata()``, which will scale data in single precision if
>   the output type is ``float32``. (pr/844) (CM, reviewed by Alejandro
>   de la Vega, 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
> ------------
> * Improve testing of data scaling in ArrayProxy API (pr/847) (CM, reviewed
>   by Alejandro de la Vega)
> * Document ``SpatialImage.slicer`` interface (pr/846) (CM)
> * ``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 ``Tractogram``s 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
> -----------
> * Remove replicated metadata for packaged data from MANIFEST.in (pr/845)
> (CM)
> * 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
> ----------------------------
> * Fully remove deprecated ``checkwarns`` and ``minc`` modules. (pr/852)
> (CM)
> * The ``keep_file_open`` argument to file load operations and
> ``ArrayProxy``s
>   no longer acccepts the value ``"auto"``, raising a ``ValueError``.
> (pr/852)
>   (CM)
> * 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)
>
>
> --
>
> Chris Markiewicz
>
> Center for Reproducible Neuroscience
>
> Stanford University
>
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