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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.

'Close gh-' statements refer to GitHub issues that are available at:

http://github.com/hanke/nibabel/issues

The full VCS changelog is available here:

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

Releases

NiBabel

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

  • 1.1.0 (Thursday 28 April 2011)
    • 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)
  • 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.