PyNIfTI Development Changelog

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>

The full VCS changelog is available here:

Unreleased changes

Changes described here are not yet released, but available from VCS repository.

None yet.

Releases

  • 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 a integer n.

  • 0.20090205.1 (Thu, 5 Feb 2009)

    • This release is the first in a series that aims stabilize the API and finally result in PyNIfTI 1.0 with full support of the NIfTI1 standard.
    • The whole package was restructured. The included renaming nifti.nifti(image,format,clibs) to nifti.(image,format,clibs). Redirect modules make sure that existing user code will not break, but they will issue a DeprecationWarning and will be removed with the release of PyNIfTI 1.0.
    • Added a special extension that can embed any serializable Python object into the NIfTI file header. The contents of this extension is automatically expanded upon request into the .meta attribute of each NiftiImage. When saving files to disk the content of the dictionary is also automatically dumped into this extension. Embedded meta data is not loaded automatically, since this has security implications, because code from the file header is actually executed. The documentation explicitely mentions this risk.
    • Added NiftiExtensions. This is a container-like handler to access and manipulate NIfTI1 header extensions.
    • Exposed MemMappedNiftiImage in the root module.
    • Moved cropImage() into the utils module.
    • From now on Sphinx is used to generate the documentation. This includes a module reference that replaces that old API reference.
    • Added methods vx2q() and vx2s() to convert voxel indices into coordinates defined by qform or sform respectively.
    • Updating the cal_min and cal_max values in the NIfTI header when saving a file is now conditional, but remains enabled by default.
    • Full set of methods to query and modify axis units. This includes expanding the previous xyzt_units field in the header dictionary into editable xyz_unit and time_unit fields. The former xyzt_units field is no longer available. See: getXYZUnit(), setXYZUnit(), getTimeUnit(), setTimeUnit(), xyz_unit, time_unit
    • Full set of methods to query and manuipulate qform and sform codes. See: getQFormCode(), setQFormCode(), getSFormCode(), setSFormCode(), qform_code, sform_code
    • Each image instance is now able to generate a human-readable dump of its most important header information via __str__().
    • NiftiImage objects can now be pickled.
    • Switched to NumPy’s distutils for building the package. Cleaned and simplified the build procedure. Added optimization flags to SWIG call.
    • nifti.image.NiftiImage.filename can now also be used to assign a filename.
    • Introduced nifti.__version__ as canonical version string.
    • Removed updateQFormFromQuarternion() from the list of public methods of NiftiFormat. This is an internal method that should not be used in user code. However, a redirect to the new method will remain in-place until PyNIfTI 1.0.
    • Bugfix: getScaledData() returns a unmodified data array if slope is set to zero (as required by the NIfTI standard). Thanks to Thomas Ross for reporting.
    • Bugfix: Unicode filenames are now handled properly, as long as they do not contain pure-unicode characters (since the NIfTI library does not support them). Thanks to Gaël Varoquaux for reporting this issue.

  • 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.