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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

Nibabel releases

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.

Upcoming Release

New features

  • CIFTI support (pr/249) (Satra Ghosh, Michiel Cottaar, BC, CM, Demian Wassermann, MB)

Enhancements

  • Support for alternative header field name variants in .PAR files (pr/507) (Gregory R. Lee)
  • Various enhancements to streamlines API by MC: support for reading TRK version 1 (pr/512); concatenation of tractograms using +/+= operators (pr/495); function to concatenate multiple ArraySequence objects (pr/494)
  • Support for numpy 1.12 (pr/500, pr/502) (MC, MB)
  • Allow dtype specifiers as fileslice input (pr/485) (MB)

Bug fixes

  • Miscellaneous MINC reader fixes (pr/493) (Robert D. Vincent, reviewed by CM, MB)

Maintenance

  • Documentation update (pr/514) (Ivan Gonzalez)
  • Update testing to use pre-release builds of dependencies (pr/509) (MB)
  • Better warnings when nibabel not on path (pr/503) (MB)

API changes and deprecations

2.1 (Monday 22 August 2016)

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 (Monday 23 November 2015)

  • 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 (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 releases

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)

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)

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.