2.1.0

New feature release for the 2.1 series.

Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan
Gerhard (SG) and Eric Larson (EL).

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

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 [email protected] 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.

1.2.1

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: DOC: fix broken rst link in main info

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

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

• 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