.. -*- mode: rst -*-
.. vim:ft=rst

.. _changelog:

NiBabel Development Changelog
-----------------------------

NiBabel is the successor to the much-loved PyNifti package. Here we list the
releases for both packages.

The full VCS changelog is available here:

  http://github.com/nipy/nibabel/commits/master

Releases
~~~~~~~~

NiBabel
+++++++

Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
and Stephan Gerhard (SG).

References like "pr/298" refer to github pull request numbers.

* 2.0.1 (Saturday 27 June 2015)

  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 neuroimaging@python.org mailing list.

* 2.0.0 (Tuesday 9 December 2014)

  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 (Tuesday 11 September 2012)

  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 (Wednesday 27 June 2012)

  * 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.

* 1.2.1 (Wednesday 13 June 2012)

  Particular thanks to Yaroslav Halchecko for fixes and cleanups in this
  release.

  * Bugfix release
  * Make compatible with pydicom 0.9.7
  * Refactor, rename nifti diagnostic script to ``nib-nifti-dx``
  * Fix a bug causing an error when analyzing affines for orientation, when the
    affine contained all 0 columns
  * Add missing ``dicomfs`` script to installation list and rename to
    ``nib-dicomfs``

* 1.2.0 (Sunday 6 May 2012)

  This release had large contributions from Krish Subramaniam, Alexandre
  Gramfort, Cindee Madison, Félix C. Morency and Christian Haselgrove.

  * New feature and bugfix release
  * Freesurfer format support by Krish Subramaniam and Alexandre Gramfort.
  * ECAT read write support by Cindee Madison and Félix C. Morency.
  * A DICOM fuse filesystem by Christian Haselgrove.
  * Much work on making data scaling on read and write more robust to rounding
    error and overflow (MB).
  * Import of nipy functions for working with affine transformation matrices.
  * Added methods for working with nifti sform and qform fields by Bago
    Amirbekian and MB, with useful discussion by Brendan Moloney.
  * Fixes to read / write of RGB analyze images by Bago Amirbekian.
  * Extensions to ``concat_images`` by Yannick Schwartz.
  * A new ``nib-ls`` script to display information about neuroimaging files, and
    various other useful fixes by Yaroslav Halchenko.

* 1.1.0 (Thursday 28 April 2011)

  Special thanks to Chris Burns, Jarrod Millman and Yaroslav Halchenko.

  * New feature release
  * Python 3.2 support
  * Substantially enhanced gifti reading support (SG)
  * Refactoring of trackvis read / write to allow reading and writing of voxel
    points and mm points in tracks.  Deprecate use of negative voxel sizes;
    set voxel_order field in trackvis header.  Thanks to Chris Filo
    Gorgolewski for pointing out the problem and Ruopeng Wang in the trackvis
    forum for clarifying the coordinate system of trackvis files.
  * Added routine to give approximate array orientation in form such as 'RAS'
    or 'LPS'
  * Fix numpy dtype hash errors for numpy 1.2.1
  * Other bug fixes as for 1.0.2

* 1.0.2 (Thursday 14 April 2011)

  * Bugfix release
  * Make inference of data type more robust to changes in numpy dtype hashing
  * Fix incorrect thresholds in quaternion calculation (thanks to Yarik H for
    pointing this one out)
  * Make parrec2nii pass over errors more gracefully
  * More explicit checks for missing or None field in trackvis and other
    classes - thanks to Marc-Alexandre Cote
  * Make logging and error level work as expected - thanks to Yarik H
  * Loading an image does not change qform or sform - thanks to Yarik H
  * Allow 0 for nifti scaling as for spec - thanks to Yarik H
  * nifti1.save now correctly saves single or pair images

* 1.0.1 (Wednesday 23 Feb 2011)

  * Bugfix release
  * Fix bugs in tests for data package paths
  * Fix leaks of open filehandles when loading images (thanks to Gael
    Varoquaux for the report)
  * Skip rw tests for SPM images when scipy not installed
  * Fix various windows-specific file issues for tests
  * Fix incorrect reading of byte-swapped trackvis files
  * Workaround for odd numpy dtype comparisons leading to header errors for
    some loaded images (thanks to Cindee Madison for the report)

* 1.0.0 (Thursday, 13, Oct 2010)

  * This is the first public release of the NiBabel package.
  * NiBabel is a complete rewrite of the PyNifti package in pure python.  It was
    designed to make the code simpler and easier to work with. Like PyNifti,
    NiBabel has fairly comprehensive NIfTI read and write support.
  * Extended support for SPM Analyze images, including orientation affines from
    matlab ``.mat`` files.
  * Basic support for simple MINC 1.0 files (MB).  Please let us know if you
    have MINC files that we don't support well.
  * Support for reading and writing PAR/REC images (MH)
  * ``parrec2nii`` script to convert PAR/REC images to NIfTI format (MH)
  * Very preliminary, limited and highly experimental DICOM reading support (MB,
    Ian Nimmo Smith).
  * Some functions (`nibabel.funcs`) for basic image shape changes, including
    the ability to transform to the image with data closest to the cononical
    image orientation (first axis left-to-right, second back-to-front, third
    down-to-up) (MB, Jonathan Taylor)
  * Gifti format read and write support (preliminary) (Stephen Gerhard) 
  * Added utilities to use nipy-style data packages, by rip then edit of nipy
    data package code (MB)
  * Some improvements to release support (Jarrod Millman, MB, Fernando Perez)
  * Huge downward step in the quality and coverage by the docs, caused by MB,
    mostly fixed by a lot of good work by MH.
  * NiBabel will not work with Python < 2.5, and we haven't even tested it with
    Python 3.  We will get to it soon...

PyNifti
+++++++

Modifications are done by Michael Hanke, if not indicated otherwise. 'Closes'
statement IDs refer to the Debian bug tracking system and can be queried by
visiting the URL::

  http://bugs.debian.org/<bug id>

* 0.20100706.1 (Tue, 6 Jul 2010)

  * Bugfix: NiftiFormat.vx2s() used the qform not the sform. Thanks to Tom
    Holroyd for reporting.

* 0.20100412.1 (Mon, 12 Apr 2010)

  * Bugfix: Unfortunate interaction between Python garbage collection and C
    library caused memory problems. Thanks to Yaroslav Halchenko for the
    diagnose and fix.

* 0.20090303.1 (Tue, 3 Mar 2009)

  * Bugfix: Updating the NIfTI header from a dictionary was broken.
  * Bugfix: Removed left-over print statement in extension code.
  * Bugfix: Prevent saving of bogus 'None.nii' images when the filename
    was previously assign, before calling NiftiImage.save() (Closes: #517920).
  * Bugfix: Extension length was to short for all `edata` whos length matches
    n*16-8, for all integer n.

* 0.20090205.1 (Thu, 5 Feb 2009)

  * This release is the first in a series that aims stabilize the API and
    finally result in PyNIfTI 1.0 with full support of the NIfTI1 standard.
  * The whole package was restructured. The included renaming
    `nifti.nifti(image,format,clibs)` to `nifti.(image,format,clibs)`. Redirect
    modules make sure that existing user code will not break, but they will
    issue a DeprecationWarning and will be removed with the release of PyNIfTI
    1.0.
  * Added a special extension that can embed any serializable Python object
    into the NIfTI file header. The contents of this extension is
    automatically expanded upon request into the `.meta` attribute of each
    NiftiImage. When saving files to disk the content of the dictionary is also
    automatically dumped into this extension.
    Embedded meta data is not loaded automatically, since this has security
    implications, because code from the file header is actually executed.
    The documentation explicitely mentions this risk.
  * Added :class:`~nifti.extensions.NiftiExtensions`. This is a container-like
    handler to access and manipulate NIfTI1 header extensions.
  * Exposed :class:`~nifti.image.MemMappedNiftiImage` in the root module.
  * Moved :func:`~nifti.utils.cropImage` into the :mod:`~nifti.utils` module.
  * From now on Sphinx is used to generate the documentation. This includes a
    module reference that replaces that old API reference.
  * Added methods :meth:`~nifti.format.NiftiFormat.vx2q` and
    :meth:`~nifti.format.NiftiFormat.vx2s` to convert voxel indices into
    coordinates defined by qform or sform respectively.
  * Updating the `cal_min` and `cal_max` values in the NIfTI header when
    saving a file is now conditional, but remains enabled by default.
  * Full set of methods to query and modify axis units. This includes
    expanding the previous `xyzt_units` field in the header dictionary into
    editable `xyz_unit` and `time_unit` fields. The former `xyzt_units` field
    is no longer available. See:
    :meth:`~nifti.format.NiftiFormat.getXYZUnit`,
    :meth:`~nifti.format.NiftiFormat.setXYZUnit`,
    :meth:`~nifti.format.NiftiFormat.getTimeUnit`,
    :meth:`~nifti.format.NiftiFormat.setTimeUnit`,
    :attr:`~nifti.format.NiftiFormat.xyz_unit`,
    :attr:`~nifti.format.NiftiFormat.time_unit`
  * Full set of methods to query and manuipulate qform and sform codes. See:
    :meth:`~nifti.format.NiftiFormat.getQFormCode`,
    :meth:`~nifti.format.NiftiFormat.setQFormCode`,
    :meth:`~nifti.format.NiftiFormat.getSFormCode`,
    :meth:`~nifti.format.NiftiFormat.setSFormCode`,
    :attr:`~nifti.format.NiftiFormat.qform_code`,
    :attr:`~nifti.format.NiftiFormat.sform_code`
  * Each image instance is now able to generate a human-readable dump of its
    most important header information via `__str__()`.
  * :class:`~nifti.image.NiftiImage` objects can now be pickled.
  * Switched to NumPy's distutils for building the package. Cleaned and
    simplified the build procedure. Added optimization flags to SWIG call.
  * :attr:`nifti.image.NiftiImage.filename` can now also be used to assign a
    filename.
  * Introduced :data:`nifti.__version__` as canonical version string.
  * Removed `updateQFormFromQuarternion()` from the list of public methods of
    :class:`~nifti.format.NiftiFormat`. This is an internal method that
    should not be used in user code. However, a redirect to the new method
    will remain in-place until PyNIfTI 1.0.
  * Bugfix: :meth:`~nifti.image.NiftiImage.getScaledData` returns a
    unmodified data array if `slope` is set to zero (as required by the NIfTI
    standard). Thanks to Thomas Ross for reporting.
  * Bugfix: Unicode filenames are now handled properly, as long as they do not
    contain pure-unicode characters (since the NIfTI library does not support
    them). Thanks to Gaël Varoquaux for reporting this issue.

* 0.20081017.1 (Fri, 17 Oct 2008)

  * Updated included minimal copy of the nifticlibs to version 1.1.0.
  * Few changes to the Makefiles to enhance Posix compatibility. Thanks to
    Chris Burns.
  * When building on non-Debian systems, only add include and library paths
    pointing to the local nifticlibs copy, when it is actually built.
    On Debian system the local copy is still not used at all, as a proper
    nifticlibs package is guaranteed to be available.
  * Added minimal setup_egg.py for setuptools users. Thanks to Gaël Varoquaux.
  * PyNIfTI now does a proper wrapping of the image data with NumPy arrays,
    which no longer leads to accidental memory leaks, when accessing array
    data that has not been copied before (e.g. via the *data* property of
    NiftiImage). Thanks to Gaël Varoquaux for mentioning this possibility.

* 0.20080710.1 (Thu, 7 Jul 2008)

  * Bugfix: Pointer bug introduced by switch to new NumPy API in 0.20080624
    Thanks to Christopher Burns for fixing it.
  * Bugfix: Honored DeprecationWarning: sync() -> flush() for memory mapped
    arrays. Again thanks to Christopher Burns.
  * More unit tests and other improvements (e.g. fixed circular imports) done
    by Christopher Burns.

* 0.20080630.1 (Tue, 30 Jun 2008)

  * Bugfix: NiftiImage caused a memory leak by not calling the NiftiFormat
    destructor.
  * Bugfix: Merged bashism-removal patch from Debian packaging.


* 0.20080624.1 (Tue, 24 Jun 2008)

  * Converted all documentation (including docstrings) into the restructured
    text format.
  * Improved Makefile.
  * Included configuration and Makefile support for profiling, API doc
    generation (via epydoc) and code quality checks (with PyLint).
  * Consistently import NumPy as N.
  * Bugfix: Proper handling of [qs]form codes, which previously have not been
    handled at all. Thanks to Christopher Burns for pointing it out.
  * Bugfix: Make NiftiFormat work without setFilename(). Thanks to Benjamin
    Thyreau for reporting.
  * Bugfix: setPixDims() stored meaningless values.
  * Use new NumPy API and replace deprecated function calls
    (`PyArray_FromDimsAndData`).
  * Initial support for memory mapped access to uncompressed NIfTI files
    (`MemMappedNiftiImage`).
  * Add a proper Makefile and setup.cfg for compiling PyNIfTI under Windows
    with MinGW.
  * Include a minimal copy of the most recent nifticlibs (just libniftiio and
    znzlib; version 1.0), to lower the threshold to build PyNIfTI on systems
    that do not provide a developer package for those libraries.


* 0.20070930.1 (Sun, 30 Sep 2007)

  * Relicense under the MIT license, to be compatible with SciPy license.
    http://www.opensource.org/licenses/mit-license.php
  * Updated documentation.


* 0.20070917.1 (Mon, 17 Sep 2007)

  * Bugfix: Can now update NIfTI header data when no filename is set
    (Closes: #442175).
  * Unloading of image data without a filename set is no checked and prevented
    as it would damage data integrity and the image data could not be
    recovered.
  * Added 'pixdim' property (Yaroslav Halchenko).


* 0.20070905.1  (Wed, 5 Sep 2007)

  * Fixed a bug in the qform/quaternion handling that caused changes to the
    qform to vanish when saving to file (Yaroslav Halchenko).
  * Added more unit tests.
  * 'dim' vector in the NIfTI header is now guaranteed to only contain
    non-zero elements. This caused problems with some applications.


* 0.20070803.1 (Fri, 3 Aug 2007)

  * Does not depend on SciPy anymore.
  * Initial steps towards a unittest suite.
  * pynifti_pst can now print the peristimulus signal matrix for a single
    voxel (onsets x time) for easier processing of this information in
    external applications.
  * utils.getPeristimulusTimeseries() can now be used to compute mean and
    variance of the signal (among others).
  * pynifti_pst is able to compute more than just the mean peristimulus
    timeseries (e.g. variance and standard deviation).
  * Set default image description when saving a file if none is present.
  * Improved documentation.


* 0.20070425.1 (Wed, 25 Apr 2007)

  * Improved documentation. Added note about the special usage of the header
    property. Also added notes about the relevant properties in the docstring
    of the corresponding accessor methods.
  * Added property and accessor methods to access/modify the repetition time
    of timeseries (dt).
  * Added functions to manipulate the pixdim values.
  * Added utils.py with some utility functions.
  * Added functions/property to determine the bounding box of an image.
  * Fixed a bug that caused a corrupted sform matrix when converting a NumPy
    array and a header dictionary into a NIfTI image.
  * Added script to compute peristimulus timeseries (pynifti_pst).
  * Package now depends on python-scipy.


* 0.20070315.1 (Thu, 15 Mar 2007)

  * Removed functionality for "NiftiImage.save() raises an IOError
    exception when writing the image file fails." (Yaroslav Halchenko)
  * Added ability to force a filetype when setting the filename or saving 
    a file.
  * Reverse the order of the 'header' and 'load' argument in the NiftiImage
    constructor. 'header' is now first as it seems to be used more often.
  * Improved the source code documentation.
  * Added getScaledData() method to NiftiImage that returns a copy of the data
    array that is scaled with the slope and intercept stored in the NIfTI
    header.


* 0.20070301.2 (Thu, 1 Mar 2007)

  * Fixed wrong link to the source tarball in README.html. 


* 0.20070301.1 (Thu, 1 Mar 2007)

  * Initial upload to the Debian archive. (Closes: #413049)
  * NiftiImage.save() raises an IOError exception when writing the image file
    fails.
  * Added extent, volextent, and timepoints properties to NiftiImage
    class (Yaroslav Halchenko).


* 0.20070220.1 (Tue, 20 Feb 2007)

  * NiftiFile class is renamed to NiftiImage.
  * SWIG-wrapped libniftiio functions are no available in the nifticlib
    module.
  * Fixed broken NiftiImage from Numpy array constructor.
  * Added initial documentation in README.html.
  * Fulfilled a number of Yarik's wishes ;)


* 0.20070214.1 (Wed, 14 Feb 2007)

  * Does not depend on libfslio anymore.
  * Up to seven-dimensional dataset are supported (as much as NIfTI can do).
  * The complete NIfTI header dataset is modifiable.
  * Most image properties are accessable via class attributes and accessor
    methods.
  * Improved documentation (but still a long way to go).


* 0.20061114 (Tue, 14 Nov 2006)

  * Initial release.
