Nibabel

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2.1

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

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.

2.0.2

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

* Fix for integer overflow on large images (pr/325) (MB);
* Fix for Freesurfer nifti files with unusual dimensions (pr/332) (Chris
Markiewicz);
* Fix typos on benchmarks and tests (pr/336, pr/340, pr/347) (Chris
Markiewicz);
* Fix Windows install script (pr/339) (MB);
* Support for Python 3.5 (pr/363) (MB) and numpy 1.10 (pr/358) (Chris
Markiewicz);
* Update pydicom imports to permit version 1.0 (pr/379) (Chris Markiewicz);
* Workaround for Python 3.5.0 gzip regression (pr/383) (Ben Cipollini).
* tripwire.TripWire object now raises subclass of AttributeError when trying
to get an attribute, rather than a direct subclass of Exception. This
prevents Python 3.5 triggering the tripwire when doing inspection prior to
running doctests.
* Minor API change for tripwire.TripWire object; code that checked for
AttributeError will now also catch TripWireError.

2.0.1

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

Contributions from Ben Cipollini, Chris Markiewicz, Alexandre Gramfort,
Clemens Bauer, github user freec84.

* Bugfix release with minor new features;
* Added ``axis`` parameter to ``concat_images`` (pr/298) (Ben Cipollini);
* Fix for unsigned integer data types in ECAT images (pr/302) (MB, test data
and issue report from Github user freec84);
* Added new ECAT and Freesurfer data files to automated testing;
* Fix for Freesurfer labels error on early numpies (pr/307) (Alexandre
Gramfort);
* Fixes for PAR / REC header parsing (pr/312) (MB, issue reporting and test
data by Clemens C. C. Bauer);
* Workaround for reading Freesurfer ico7 surface files (pr/315) (Chris
Markiewicz);
* Changed to github pages for doc hosting;
* Changed docs to point to neuroimagingpython.org mailing list.

2.0.0

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

This release had large contributions from Eric Larson, Brendan Moloney,
Nolan Nichols, Basile Pinsard, Chris Johnson and Nikolaas N. Oosterhof.

* New feature, bugfix release with minor API breakage;
* Minor API breakage: default write of NIfTI / Analyze image data offset
value. The data offset is the number of bytes from the beginning of file
to skip before reading the image data. Nibabel behavior changed from
keeping the value as read from file, to setting the offset to zero on
read, and setting the offset when writing the header. The value of the
offset will now be the minimum value necessary to make room for the header
and any extensions when writing the file. You can override the default
offset by setting value explicitly to some value other than zero. To read
the original data offset as read from the header, use the ``offset``
property of the image ``dataobj`` attribute;
* Minor API breakage: data scaling in NIfTI / Analyze now set to NaN when
reading images. Data scaling refers to the data intercept and slope
values in the NIfTI / Analyze header. To read the original data scaling
you need to look at the ``slope`` and ``inter`` properties of the image
``dataobj`` attribute. You can set scaling explicitly by setting the
slope and intercept values in the header to values other than NaN;
* New API for managing image caching; images have an ``in_memory`` property
that is true if the image data has been loaded into cache, or is already
an array in memory; ``get_data`` has new keyword argument ``caching`` to
specify whether the cache should be filled by ``get_data``;
* Images now have properties ``dataobj``, ``affine``, ``header``. We will
slowly phase out the ``get_affine`` and ``get_header`` image methods;
* The image ``dataobj`` can be sliced using an efficient algorithm to avoid
reading unnecessary data from disk. This makes it possible to do very
efficient reads of single volumes from a time series;
* NIfTI2 read / write support;
* Read support for MINC2;
* Much extended read support for PAR / REC, largely due to work from Eric
Larson and Gregory R. Lee on new code, advice and code review. Thanks also
to Jeff Stevenson and Bennett Landman for helpful discussion;
* ``parrec2nii`` script outputs images in LAS voxel orientation, which
appears to be necessary for compatibility with FSL ``dtifit`` /
``fslview`` diffusion analysis pipeline;
* Preliminary support for Philips multiframe DICOM images (thanks to Nolan
Nichols, Ly Nguyen and Brendan Moloney);
* New function to save Freesurfer annotation files (by Github user ohinds);
* Method to return MGH format ``vox2ras_tkr`` affine (Eric Larson);
* A new API for reading unscaled data from NIfTI and other images, using
``img.dataobj.get_unscaled()``. Deprecate previous way of doing this,
which was to read data with the ``read_img_data`` function;
* Fix for bug when replacing NaN values with zero when writing floating
point data as integers. If the input floating point data range did not
include zero, then NaN would not get written to a value corresponding to
zero in the output;
* Improvements and bug fixes to image orientation calculation and DICOM
wrappers by Brendan Moloney;
* Bug fixes writing GIfTI files. We were using a base64 encoding that didn't
match the spec, and the wrong field name for the endian code. Thanks to
Basile Pinsard and Russ Poldrack for diagnosis and fixes;
* Bug fix in ``freesurfer.read_annot`` with ``orig_ids=False`` when annot
contains vertices with no label (Alexandre Gramfort);
* More tutorials in the documentation, including introductory tutorial on
DICOM, and on coordinate systems;
* Lots of code refactoring, including moving to common code-base for Python
2 and Python 3;
* New mechanism to add images for tests via git submodules.

1.3.0

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

Special thanks to Chris Johnson, Brendan Moloney and JB Poline.

* New feature and bugfix release
* Add ability to write Freesurfer triangle files (Chris Johnson)
* Relax threshold for detecting rank deficient affines in orientation
detection (JB Poline)
* Fix for DICOM slice normal numerical error (issue 137) (Brendan Moloney)
* Fix for Python 3 error when writing zero bytes for offset padding

1.2.2

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

* Bugfix release
* Fix longdouble tests for Debian PPC (thanks to Yaroslav Halchecko for
finding and diagnosing these errors)
* Generalize longdouble tests in the hope of making them more robust
* Disable saving of float128 nifti type unless platform has real IEEE
binary128 longdouble type.

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