[Neuroimaging] Nibabel release 2.1

Wed Aug 24 06:48:58 EDT 2016

Congrats!

On Aug 24, 2016 4:52 AM, "JB Poline" <jbpoline at gmail.com> wrote:

> Thanks a lot for this
> JB
>
> On 22 August 2016 at 20:40, Matthew Brett <matthew.brett at gmail.com> 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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