Nibabel

==========================

Contributions from Egor Pafilov, Jath Palasubramaniam, Richard Nemec, and
Dave Allured.

Enhancements
------------
* Enable ``mmap``, ``keep_file_open`` options when loading any
``DataobjImage`` (pr/759) (CM, reviewed by PM)

Bug fixes
---------
* Ensure loaded GIFTI files expose writable data arrays (pr/750) (CM,
reviewed by PM)
* Safer warning registry manipulation when checking for overflows (pr/753)
(CM, reviewed by MB)
* Correctly write .annot files with duplicate labels (pr/763) (Richard Nemec
with CM)

Maintenance
-----------
* Fix typo in coordinate systems doc (pr/751) (Egor Panfilov, reviewed by
CM)
* Replace invalid MINC1 test file with fixed file (pr/754) (Dave Allured
with CM)
* Update Sphinx config to support recent Sphinx/numpydoc (pr/749) (CM,
reviewed by PM)
* Pacify ``FutureWarning`` and ``DeprecationWarning`` from h5py, numpy
(pr/760) (CM)
* Accommodate Python 3.8 deprecation of collections.MutableMapping
(pr/762) (Jath Palasubramaniam, reviewed by CM)

API changes and deprecations
----------------------------
* Deprecate ``keep_file_open == 'auto'`` (pr/761) (CM, reviewed by PM)

============================

New features
------------
* Alternative ``Axis``-based interface for manipulating CIFTI-2 headers
(pr/641) (Michiel Cottaar, reviewed by Demian Wassermann, CM, SG)

Enhancements
------------
* Accept TCK files produced by tools with other delimiter/EOF defaults
(pr/720) (Soichi Hayashi, reviewed by CM, MB, MC)
* Allow BrainModels or Parcels to contain a single vertex in CIFTI
(pr/739) (Michiel Cottaar, reviewed by CM)
* Support for ``NIFTI_XFORM_TEMPLATE_OTHER`` xform code (pr/743) (CM)

Bug fixes
---------
* Skip refcheck in ArraySequence construction/extension (pr/719) (Ariel
Rokem, reviewed by CM, MC)
* Use safe resizing for ArraySequence extension (pr/724) (CM, reviewed
by MC)
* Fix typo in error message (pr/726) (Jon Haitz Legarreta Gorroño,
reviewed by CM)
* Support DICOM slice sorting in Python 3 (pr/728) (Samir Reddigari,
reviewed by CM)
* Correctly reorient dim_info when reorienting NIfTI images
(Konstantinos Raktivan, CM, reviewed by CM)

Maintenance
-----------
* Import updates to reduce upstream deprecation warnings (pr/711,
pr/705, pr/738) (EL, YOH, reviewed by CM)
* Delay import of ``nibabel.testing``, ``nose`` and ``mock`` to speed up
import (pr/699) (CM)
* Increase coverage testing, drop coveralls (pr/722, pr/732) (CM)
* Add Zenodo metadata, sorted by commits (pr/732) (CM + others)
* Update author listing and copyrights (pr/742) (MB, reviewed by CM)

=================================

Maintenance
-----------
* Restore ``six`` dependency (pr/714) (CM, reviewed by Gael Varoquaux, MB)

================================

Enhancements
------------
* Enable toggling crosshair with ``Ctrl-x`` in ``OrthoSlicer3D`` viewer (pr/701)
(Miguel Estevan Moreno, reviewed by CM)

Bug fixes
---------
* Read .PAR files corresponding to ADC maps (pr/685) (Gregory R. Lee, reviewed
by CM)
* Increase maximum number of items read from Siemens CSA format (Igor Solovey,
reviewed by CM, MB)
* Check boolean dtypes with ``numpy.issubdtype(..., np.bool_)`` (pr/707)
(Jon Haitz Legarreta Gorroño, reviewed by CM)

Maintenance
-----------
* Fix small typos in parrec2nii help text (pr/682) (Thomas Roos, reviewed by
MB)
* Remove deprecated calls to ``numpy.asscalar`` (pr/686) (CM, reviewed by
Gregory R. Lee)
* Update QA directives to accommodate Flake8 3.6 (pr/695) (CM)
* Update DOI links to use ``https://doi.org`` (pr/703) (Katrin Leinweber,
reviewed by CM)
* Remove deprecated calls to ``numpy.fromstring`` (pr/700) (Ariel Rokem,
reviewed by CM, MB)
* Drop ``distutils`` support, require ``bz2file`` for Python 2.7 (pr/700)
(CM, reviewed by MB)
* Replace mutable ``bytes`` hack, disabled in numpy pre-release, with
``bytearray``/``readinto`` strategy (pr/700) (Ariel Rokem, CM, reviewed by
CM, MB)

API changes and deprecations
----------------------------
* Add ``Opener.readinto`` method to read file contents into pre-allocated buffers
(pr/700) (Ariel Rokem, reviewed by CM, MB)

===============================

New features
------------
* ``nib-diff`` command line tool for comparing image files (pr/617, pr/672,
pr/678) (CC, reviewed by YOH, Pradeep Raamana and CM)

Enhancements
------------
* Speed up reading of numeric arrays in CIFTI2 (pr/655) (Michiel Cottaar,
reviewed by CM)
* Add ``ndim`` property to ``ArrayProxy`` and ``DataobjImage`` (pr/674) (CM,
reviewed by MB)

Bug fixes
---------
* Deterministic deduction of slice ordering in degenerate cases (pr/647)
(YOH, reviewed by CM)
* Allow 0ms TR in MGH files (pr/653) (EL, reviewed by CM)
* Allow for PPC64 little-endian long doubles (pr/658) (MB, reviewed by CM)
* Correct construction of FreeSurfer annotation labels (pr/666) (CM, reviewed
by EL, Paul D. McCarthy)
* Fix logic for persisting filehandles with indexed-gzip (pr/679) (Paul D.
McCarthy, reviewed by CM)

Maintenance
-----------
* Fix semantic error in coordinate systems documentation (pr/646) (Ariel
Rokem, reviewed by CM, MB)
* Test on Python 3.7, minor associated fixes (pr/651) (CM, reviewed by Gregory
R. Lee, MB)

==========================

New features
------------
* TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM)
* Image slicing for SpatialImages (pr/550) (CM)

Enhancements
------------
* Simplfiy 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) (PM,
reviewed by CM, MB)
* Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves,
reviewed by CM, SG, 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) (PM, reviewed by CM, MB)

Bug fixes
---------
* Preserve first point of :py:class:`~nibabel.streamlines.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) (PM, 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.