nisl/tutorial — pull request #43 by pgervais (2013-04-08 12:40:39+00:00)
Title: API cleanup

This pull request clarifies and normalizes the API. Some optimizations have been implemented as well.

**This pull request breaks many things in the API**, hopefully for the best. Comments welcome.

Main change: orientation of input and output arrays has been inverted, to match scikit-learn's. Masked data (timeseries) are thus represented as an array with shape (number of time instants, number of masked voxels), instead of the inverse. It may remain some functions working the old way, I consider this as a bug. A consequence of this is that every "transpose" option has been removed. Porting old code may require adding a ".T" somewhere, but that's it.

The clean() function has been simplified and optimized. **Its output is slightly different from the previous state**. I find it clearer this way, but I need feedback on this matter. Some processing code may rely on a feature that I removed/changed. More specifically, the "shift_confounds" keyword argument has been removed, because its usage seemed rather obscure (and no documentation was available).

A lot of tests has been added/enhanced, including for technical functions like _standardize and _detrend. Documentation has been written/enhanced in many places.