Nibabel

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

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.

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

Bug fixes
---------

* Set L/R labels in orthoview correctly (pr/564) (CM)
* Defer use of ufunc / memmap test - allows "freezing" (pr/572) (MB, reviewed
by SG)
* Fix doctest failures with pre-release numpy (pr/582) (MB, reviewed by CM)

Maintenance
-----------

* Update documentation around NIfTI qform/sform codes (pr/576) (PM,
reviewed by MB, CM) + (pr/580) (Bennet Fauber, reviewed by PM)
* Skip precision test on macOS, newer numpy (pr/583) (MB, reviewed by CM)
* Simplify AppVeyor script, removing conda (pr/584) (MB, reviewed by CM)

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

New features
------------

* CIFTI support (pr/249) (SG, Michiel Cottaar, BC, CM, Demian Wassermann, MB)
* Support for MRtrix TCK streamlines file format (pr/486) (MC, reviewed by
MB, Arnaud Bore, J-Donald Tournier, Jean-Christophe Houde)
* Added ``get_fdata()`` as default method to retrieve scaled floating point
data from ``DataobjImage``\s (pr/551) (MB, reviewed by CM, SG)

Enhancements
------------

* Support for alternative header field name variants in .PAR files
(pr/507) (Gregory R. Lee)
* Various enhancements to streamlines API by MC: support for reading TRK
version 1 (pr/512); concatenation of tractograms using ``+``/``+=`` operators
(pr/495); function to concatenate multiple ArraySequence objects (pr/494)
* Support for numpy 1.12 (pr/500, pr/502) (MC, MB)
* Allow dtype specifiers as fileslice input (pr/485) (MB)
* Support "headerless" ArrayProxy specification, enabling memory-efficient
ArrayProxy reshaping (pr/521) (CM)
* Allow unknown NIfTI intent codes, add FSL codes (pr/528) (PM)
* Improve error handling for ``img.__getitem__`` (pr/533) (Ariel Rokem)
* Delegate reorientation to SpatialImage classes (pr/544) (Mark Hymers, CM,
reviewed by MB)
* Enable using ``indexed_gzip`` to reduce memory usage when reading from
gzipped NIfTI and MGH files (pr/552) (PM, reviewed by MB, CM)

Bug fixes
---------

* Miscellaneous MINC reader fixes (pr/493) (Robert D. Vincent, reviewed by CM,
MB)
* Fix corner case in ``wrapstruct.get`` (pr/516) (PM, reviewed by
CM, MB)

Maintenance
-----------

* Fix documentation errors (pr/517, pr/536) (Fernando Perez, Venky Reddy)
* Documentation update (pr/514) (Ivan Gonzalez)
* Update testing to use pre-release builds of dependencies (pr/509) (MB)
* Better warnings when nibabel not on path (pr/503) (MB)

API changes and deprecations
----------------------------

* ``header`` argument to ``ArrayProxy.__init__`` is renamed to ``spec``
* Deprecation of ``header`` property of ``ArrayProxy`` object, for removal in
3.0
* ``wrapstruct.get`` now returns entries evaluating ``False``, instead of ``None``
* ``DataobjImage.get_data`` to be deprecated April 2018, scheduled for removal
April 2020