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ENH: fsl.load_stats to load cope/zstat etc from .feat directories #603

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  • assigns targets to correspond to description of each contrast
  • assigns indexes to the index of the contrast as known to FSL
  • can take keyword args to pass into fmri_dataset
  • removes any time_ sa upon loading
  • can load arbitrary set of stats, by default only "cope" is loaded

Example:

openfmri/ds000107[tags/1.0.0^0]sub026/model/model001/task001_run001.feat
$> PYTHONPATH=/home/yoh/proj/pymvpa/pymvpa python -c 'from mvpa2.misc.fsl import load_stats; print(load_stats(".", ["cope", "tstat"]))'
... pruned irrelevant warnings ...
 * Please note: warnings are printed only once, but underlying problem might occur many times *
<Dataset: 14x143360@float32, <sa: indexes,stats,targets>, <fa: voxel_indices>>

TODOs:

  • test(s)
  • remove restriction for having real = orig, @yarikoptic just forgot the details already

Optional TODOs:

  • autodetection of the file extension. ATM defaults to .nii.gz and has an option to override

@coveralls
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Coverage Status

Coverage increased (+0.01%) to 80.29% when pulling 1112938 on yarikoptic:enh-fsl-load_stats into aa18b0e on PyMVPA:master.

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codecov-io commented Mar 20, 2019

Codecov Report

Merging #603 into master will increase coverage by <.01%.
The diff coverage is 8.69%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #603      +/-   ##
==========================================
+ Coverage   75.77%   75.78%   +<.01%     
==========================================
  Files         366      366              
  Lines       41914    41937      +23     
  Branches     6750     6754       +4     
==========================================
+ Hits        31759    31780      +21     
+ Misses       8270     8269       -1     
- Partials     1885     1888       +3
Impacted Files Coverage Δ
mvpa2/misc/fsl/base.py 48.46% <8.69%> (-8.55%) ⬇️
mvpa2/clfs/stats.py 71.91% <0%> (-0.81%) ⬇️
mvpa2/tests/test_searchlight.py 93.03% <0%> (-0.25%) ⬇️
mvpa2/tests/test_searchlight_hyperalignment.py 97.11% <0%> (+0.41%) ⬆️
mvpa2/base/dochelpers.py 82.68% <0%> (+0.7%) ⬆️
mvpa2/testing/sweep.py 82.5% <0%> (+26.25%) ⬆️

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