[pymvpa] ERNiftiDataset working slowly

[Jonas Kubilius]

Hey all,

I have been trying to use ERNiftiDataset but it seems to be working very
slowly, by which I mean one minute to read in a single nifti file (shape =
(168, 50, 69, 57)) as compared to an almost instant behavior of
NiftiDataset. (My computer is a new Dell Optiplex 760 with Intel Core Quad
running Vista; mvpa version is 0.4.2.)

The code I'm trying to run is trivial:

nim = ERNiftiDataset(samples = 'niftiFile.nii', events = myEvents),

where myEvents is a list with 168 dictionary entries like this:

{'chunk': 0, 'duration': 4, 'label': 0, onset: 0.0}

(If I reduce duration to 1, the time drops to 15 sec.)

This seems very slow to me, especially since NiftiDataset is so fast. In
principle, I could use NiftiDataset with 168 labels and that would match my
current example with duration 1 in ERNiftiDataset, is that true? Yet the
NiftiDataset makes it, again, almost instantly. Am I doing something wrong
here or is this the expected behavior?

Thanks!
Jonas
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