[pymvpa] Within-subject classification, getting each subject's scores averaged over number of runs
debian at onerussian.com
Fri Apr 22 12:38:43 UTC 2016
On Fri, 22 Apr 2016, Martin Sjøgård wrote:
> I'm running some within-subject classifications in pyMVPA (same as the
> example script on the site/in the manual in the hyperalignment section).
> Everything works fine, and I get the average within-subject classification
> scores. However, I also want to the classification scores for each
> The results are organized by the lines:
> wsc_results = [cv(sd) for sd in sd_all)
> wsc_results = vstack(wsc_results)
> If I type in:
> print wsc_results
> I get each subject's scores per run (7 runs), but I of course want to
> average the runs per subject. I've tried:
> wsc_results = [cv(sd)/nruns for sd in sd_all)
> But that doesn't work (TypeError: unsupported operand type(s) for /:
> 'Dataset' and 'int').
> Do you know how to get each subject's classification scores, averaged over
> number of runs?
even this would work
[np.mean(cv(sd)) for sd in sd_all]
but I would recommend to collect not just "mean scores" but all the
confusion matrices "just in case", e.g.
# enable_ca=['stats'] for your cv definion
cms = 
errors = 
for sd in sd_all:
then you can get all kinds of stats, e.g.
[cm.stats['ACC%'] for cm in cms]
would be your mean accuracies as well
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
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