[pymvpa] Labels from permutation testing

Bill Broderick billbrod at gmail.com
Mon Jul 20 16:04:27 UTC 2015


Hi all,

I feel like this should be relatively simple, but I can't figure out how to
do it. Is it possible to get at the labels generated by
AttributePermutator? I would like to see what the individual permutations
look like, to make sure it's doing what I think it is, but other than
saving the whole dataset generated by CrossValidation, I can't see a way to
do it.

I'm trying to build a null distribution like the following, so I can save
each permutation, each searchlight separately (with how long the
permutation testing has been taking, I want to make sure there's constant
output in case something crashes and so I can monitor its progress, so I'm
not using MCNullDist).

    for i in searchlights:
        for j in permutations:
            permutator =
AttributePermutator('targets',limit={'partitions':1},count=1)
            nf =
NFoldPartitioner(attr=partition_attr,cvtype=leave_x_out,count=fold_num,selection_strategy=fold_select_strategy)
            null_cv =
CrossValidation(clf,ChainNode([nf,permutator],space=nf.get_space()),enable_ca='datasets',pass_attr=[('ca.datasets','fa')])
            sl_null = sphere_searchlight(null_cv,radius=3,center_ids=[i])
            null_dist.append(sl_null(ds))
            null_dist=hstack(null_dist)

So I would like to be able to check the permuted labels in order to
double-check that everything is working as I'd like.

Thanks,
Bill
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