[Neuroimaging] Nibabel release 2.1

Jan Schreiber j.schreiber at fz-juelich.de
Wed Aug 24 07:42:48 EDT 2016

NiBabel is awesome :-)


On 08/23/16 05:40, Matthew Brett wrote:
> Hi,
> Welcome to the new 2.1 release of nibabel, the result of six months of
> hard work.
> Many thanks in particular to Ben, Marc-Alexandre Côté, Chris
> Markiewicz, Eric Larson, Gregory Lee and Erik Kastman for their large
> contributions to this release.
> A special shout-out to those of you doing code-reviews, it's essential
> work, and not enough rewarded.  A special-special shout-out to Chris,
> Eric and Ben, and much thanks to Jean-Christophe Houde, Bago
> Amirbekian, Eleftherios Garyfallidis, Samuel St-Jean for their work
> reviewing Marc-Alexandre Côté's huge streamline format PR (see below).
> Here's the Changelog for your viewing pleasure:
> 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.
> 2.1 (Monday 22 August 2016)
> ===========================
> New features
> ------------
> * New API for managing streamlines and their different file formats. This
>    adds a new module ``nibabel.streamlines`` that will eventually deprecate
>    the current trackvis reader found in ``nibabel.trackvis`` (pr/391) (MC,
>    reviewed by Jean-Christophe Houde, Bago Amirbekian, Eleftherios
>    Garyfallidis, Samuel St-Jean, MB);
> * A prototype image viewer using matplotlib (pr/404) (EL, based on a
>    proto-prototype by Paul Ivanov) (Reviewed by Gregory R. Lee, MB);
> * Functions for image resampling and smoothing using scipy ndimage (pr/255)
>    (MB, reviewed by EL, BC);
> * Add ability to write FreeSurfer morphology data (pr/414) (CM, BC, reviewed
>    by BC);
> * Read and write support for DICOM tags in NIfTI Extended Header using
>    pydicom (pr/296) (Eric Kastman).
> Enhancements
> ------------
> * Extensions to FreeSurfer module to fix reading and writing of FreeSurfer
>    geometry data (pr/460) (Alexandre Gramfort, Jaakko Leppäkangas, reviewed
>    by EL, CM, MB);
> * Various improvements to PAR / REC handling by Gregory R. Lee: supporting
>    multiple TR values (pr/429); output of volume labels (pr/427); fix for
>    some diffusion files (pr/426); option for more sophisticated sorting of
>    volumes (pr/409);
> * Original trackvis reader will now allow final streamline to have fewer
>    points than the number declared in the header, with ``strict=False``
>    argument to ``read`` function;
> * Helper function to return voxel sizes from an affine matrix (pr/413);
> * Fixes to DICOM multiframe reading to avoid assumptions on the position of
>    the multiframe index (pr/439) (Eric M. Baker);
> * More robust handling of "CSA" private information in DICOM files (pr/393)
>    (Brendan Moloney);
> * More explicit error when trying to read image from non-existent file
>    (pr/455) (Ariel Rokem);
> * Extension to `nib-ls` command to show image statistics (pr/437) and other
>    header files (pr/348) (Yarik Halchenko).
> Bug fixes
> ---------
> * Fixes to rotation order to generate affine matrices of PAR / REC files (MB,
>    Gregory R Lee).
> Maintenance
> -----------
> * Dropped support for Pythons 2.6 and 3.2;
> * Comprehensive refactor and generalization of surface / GIFTI file support
>    with improved API and extended tests (pr/352-355, pr/360, pr/365, pr/403)
>    (BC, reviewed by CM, MB);
> * Refactor of image classes (pr/328, pr/329) (BC, reviewed by CM);
> * Better Appveyor testing on new Python versions (pr/446) (Ariel Rokem);
> * Fix shebang lines in scripts for correct install into virtualenvs via pip
>    (pr/434);
> * Various fixes for numpy, matplotlib, and PIL / Pillow compatibility (CM,
>    Ariel Rokem, MB);
> * Improved test framework for warnings (pr/345) (BC, reviewed by CM, MB);
> * New decorator to specify start and end versions for deprecation warnings
>    (MB, reviewed by CM);
> * Write qform affine matrix to NIfTI images output by ``parrec2nii`` (pr/478)
>    (Jasper J.F. van den Bosch, reviewed by Gregory R. Lee, MB).
> API changes and deprecations
> ----------------------------
> * Minor API breakage in original (rather than new) trackvis reader. We are now
>    raising a ``DataError`` if there are too few streamlines in the file,
>    instead of a ``HeaderError``.  We are raising a ``DataError`` if the track
>    is truncated when ``strict=True`` (the default), rather than a ``TypeError``
>    when trying to create the points array.
> * Change sform code that ``parrec2nii`` script writes to NIfTI images; change
>    from 2 ("aligned") to 1 ("scanner");
> * Deprecation of ``get_header``, ``get_affine`` method of image objects for
>    removal in version 4.0;
> * Removed broken ``from_filespec`` method from image objects, and deprecated
>    ``from_filespec`` method of ECAT image objects for removal in 4.0;
> * Deprecation of ``class_map`` instance in ``imageclasses`` module in favor of
>    new image class attributes, for removal in 4.0;
> * Deprecation of ``ext_map`` instance in ``imageclasses`` module in favor of
>    new image loading API, for removal in 4.0;
> * Deprecation of ``Header`` class in favor of ``SpatialHeader``, for removal
>    in 4.0;
> * Deprecation of ``BinOpener`` class in favor of more generic ``Opener``
>    class, for removal in 4.0;
> * Deprecation of ``GiftiMetadata`` methods ``get_metadata`` and ``get_rgba``;
>    ``GiftiDataArray`` methods ``get_metadata``, ``get_labeltable``,
>    ``set_labeltable``; ``GiftiImage`` methods ``get_meta``, ``set_meta``.  All
>    these deprecated in favor of corresponding properties, for removal in 4.0;
> * Deprecation of ``giftiio`` ``read`` and ``write`` functions in favor of
>    nibabel ``load`` and ``save`` functions, for removal in 4.0;
> * Deprecation of ``gifti.data_tag`` function, for removal in 4.0;
> * Deprecation of write-access to ``GiftiDataArray.num_dim``, and new error
>    when trying to set invalid values for ``num_dim``.  We will remove
>    write-access in 4.0;
> * Deprecation of ``GiftiDataArray.from_array`` in favor of ``GiftiDataArray``
>    constructor, for removal in 4.0;
> * Deprecation of ``GiftiDataArray`` ``to_xml_open, to_xml_close`` methods in
>    favor of ``to_xml`` method, for removal in 4.0;
> * Deprecation of ``parse_gifti_fast.Outputter`` class in favor of
>    ``GiftiImageParser``, for removal in 4.0;
> * Deprecation of ``parse_gifti_fast.parse_gifti_file`` function in favor of
>    ``GiftiImageParser.parse`` method, for removal in 4.0;
> * Deprecation of ``loadsave`` functions ``guessed_image_type`` and
>    ``which_analyze_type``, in favor of new API where each image class tests the
>    file for compatibility during load, for removal in 4.0;
> NGUNS, on behalf of all Nibabelers,
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

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