[pymvpa] Surface searchlight taking 6 to 8 hours

[John Baublitz]

Hi all,
I have been battling with a surface searchlight that has been taking 6 to 8
hours for a small dataset. It outputs a usable analysis but the time it
takes is concerning given that our lab is looking to use even higher
resolution fMRI datasets in the future. I profiled the searchlight call and
it looks like approximately 90% of those hours is spent mapping in the
function from feature IDs to linear voxel IDs (the
function feature_id2linear_voxel_ids). I looked into the source code and it
appears that it is using the in keyword on a list which has to search
through every element of the list for each iteration of the list
comprehension and then calls that function for each feature. This might
account for the slowdown. I'm wondering if there is a way to work around
this or speed it up.

Thanks,
John
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