nipy/nibabel 2.1.0

on GitHub

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;