NIPY Changelog

NIPY is not only a module for neuroimaing analysis but an umbrella for other Python neuroimaging-related projects -- see https://github.com/nipy and http://www.nipy.org for more information about their releases.

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

http://github.com/nipy/nipy/issues

The full VCS changelog is available here:

http://github.com/nipy/nipy/commits/master

Releases

Abbreviated authors are:

MB - Matthew Brett
BT - Bertrand Thirion
AR - Alexis Roche
GV - Gaël Varoquaux
YH - Yarik Halchenko
JBP - Jean-Baptiste Poline
JT - Jonathan Taylor
0.4.1 (Friday 10 February 2017)

Bugfix, refactoring and compatibility release.
- New discrete cosine transform functions for building basis sets;
- Fixes for compatibility with Python 3.6;
- Fixes for compatibility with Numpy 1.12 (1.12 no longer allows floating point values for indexing and other places where an integer value is required);
- Fixes for compatibility with Sympy 1.0;
- Drop compatibility with Python 2.6, 3.2, 3.3;
- Add ability to pass plotting arguments to plot_anat function (Matteo Visconti dOC);
- Some helpers for working with OpenFMRI datasets;
- Signal upcoming change in return shape from make_recarray when passing in an array for values. Allow user to select upcoming behavior with keyword argument;
- Bug fix for axis selection when using record arrays in numpies <= 1.7.1;
- Add flag to allow SpaceTimeRealign to read TR from image headers;
0.4.0 (Saturday 18 October 2015)

Bugfix, refactoring and compatibility release.
- Full port to Python 3 using single code-base;
- Various fixes for modern numpy, scipy, sympy, nibabel compatibility;
- Refactor space-time realignment (AR);
- Change in interface for slice-timing options in space-time realign (AR+MB);
- New nipy_4d_realign script to run space-time realign (Ariel Rokem);
- Drop requirement for BLAS / LAPACK external library at build-time (AR);
- Move much code out of nipy.labs into main tree (AR, BT);
- Deprecate remaining code in nipy.labs (AR, BT);
- Updates to landmark learning code including API (BT);
- Various fixes to design matrix machinery (BT, Michael Waskom);
- Fix to two-sample permutation test suggested by github user jwirsich (BF);
- Refactoring and fixes to design matrix drift calculations (JBP);
- Extending API of resampling code to allow more ndimage kwargs (JBP);
- Start of new example on OpenFMRI ds105 dataset (JT);
- New block_design function for designs with specified onsets (JT);
- New show_contrast function for reviewing contrasts (JT);
- Fix for bug in nipy_diagnose script / screens module giving incorrect PCA output;
- Added SPM HRF to other HRF options;
- Redesign concept of an image "space" with new image space modules, functions, classes;
- Various fixes for correct installation provided or suggested by YH;
- Some visualization changes by Elvis Dohmatob;
0.3.0 (Saturday 2 February 2013)

Bugfix, refactoring and compatibility release.
- Addition of EM algorithm for mixed effects analysis (BT)
- New high-level GLM class interface (BT)
- nipy diagnostic scripts save PCA and tsdifana vectors to npz file
- Python 3 compatibility through 3.3 (MB)
- Fixes for compatibility with upcoming Numpy 1.7
- Fixes to background and axis specification in visualization tools (GV, BT)
- Fixes and tests for installed nipy scripts (MB)
- Fix to optimization parameters for Realign4D - thanks to bpinsard
- Fix 0 in affine diagonal for TR=0 in affines by default (MB)
- Allow saving of nipy images loaded from nifti files that lack explicit affine (MB)
- Allow slice_order=None to FmriRealign4D when not doing time interpolation (AR); check for valid slice order specification (YH)
- Refactoring of quantile routine to move code out of C library (AR)
- Fix bug in resampling of unsigned int images (AR)
- Custom doctest machinery to work round differences of dtype repr on different platforms, and to skip doctests with optional dependencies (MB)
- Script to run examples for testing (MB)
- Fix for accidental integer division of frametimes in design matrix generation (Fabian Pedregosa)
- Various other fixes and refactorings with thanks from (AR, BT, MB, YH, Yannick Schwartz, Virgile Fritsch)
0.2.0 (Sunday 22 July 2012)

The first ever official release.
- > 30 contributors
- > 6 years in development
- 192 issues closed on github