nibabel: 2.1.0

Abstract

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;