Nibabel

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

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)
* Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
by CM)
* 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 accepts 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)

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

Bug-fix release in the 2.5.x series. This is an extended-support series,
providing bug fixes for Python 2.7 and 3.4.

This and all future releases in the 2.5.x series will be incompatible with
Python 3.9. The last compatible series of numpy and scipy are 1.16.x and
1.2.x, respectively.

If you are able to upgrade to Python 3, it is recommended to upgrade to
NiBabel 3.

Bug fixes
---------
* Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
by CM)
* Re-import externals/netcdf.py from scipy to resolve numpy deprecation
(pr/821) (CM)

Maintenance
-----------
* Set maximum numpy to 1.16.x, maximum scipy to 1.2.x (pr/901) (CM)

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

Enhancements
------------
* Ignore endianness in ``nib-diff`` if values match (pr/799) (YOH, reviewed
by CM)

Bug fixes
---------
* Correctly handle Philips DICOMs w/ derived volume (pr/795) (Mathias
Goncalves, reviewed by CM)
* Raise CSA tag limit to 1000, parametrize for future relaxing (pr/798,
backported to 2.5.x in pr/800) (Henry Braun, reviewed by CM, MB)
* Coerce data types to match NIfTI intent codes when writing GIFTI data
arrays (pr/806) (CM, reported by Tom Holroyd)

Maintenance
-----------
* Require h5py 2.10 for Windows + Python < 3.6 to resolve unexpected dtypes
in Minc2 data (pr/804) (CM, reviewed by YOH)

API changes and deprecations
----------------------------
* Deprecate ``nicom.dicomwrappers.Wrapper.get_affine()`` in favor of ``affine``
property; final removal in nibabel 4.0 (pr/796) (YOH, reviewed by CM)

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

The 2.5.x series is the last with support for either Python 2 or Python 3.4.
Extended support for this series 2.5 will last through December 2020.

Thanks for the test ECAT file and fix provided by Andrew Crabb.

Enhancements
------------
* Add SerializableImage class with to/from_bytes methods (pr/644) (CM,
reviewed by MB)
* Check CIFTI-2 data shape matches shape described by header (pr/774)
(Michiel Cottaar, reviewed by CM)

Bug fixes
---------
* Handle stricter numpy casting rules in tests (pr/768) (CM)
reviewed by PM)
* TRK header fields flipped in files written on big-endian systems
(pr/782) (CM, reviewed by YOH, MB)
* Load multiframe ECAT images with Python 3 (CM and Andrew Crabb)

Maintenance
-----------
* Fix CodeCov paths on Appveyor for more accurate coverage (pr/769) (CM)
* Move to setuptools and reduce use ``nisext`` functions (pr/764) (CM,
reviewed by YOH)
* Better handle test setup/teardown (pr/785) (CM, reviewed by YOH)

API changes and deprecations
----------------------------
* Effect threatened warnings and set some deprecation timelines (pr/755) (CM)
* Trackvis methods now default to v2 formats
* ``nibabel.trackvis`` scheduled for removal in nibabel 4.0
* ``nibabel.minc`` and ``nibabel.MincImage`` will be removed in nibabel 3.0

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

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)