[pymvpa] How can I see the output of RFE?

life1994 at gmail.com life1994 at gmail.com
Mon Dec 29 21:10:34 UTC 2008


Dear pyMVPA experts,

I just ran the RFE by copying and pasting the code in the manual, but  
nothing pops up after it was run.
Is there any way to see the transfer error rate?
Below is the full code that I modified the one in the example.

Thanks,


--------------------------------------------------------
from mvpa.suite import *

#load nifti dataset
attr = SampleAttributes('label_25jun08MG.txt')
dataset = NiftiDataset(samples='wrbold_25jun08MG.nii.gz',  
labels=attr.labels,
chunks=attr.chunks, mask='mask.nii.gz')

#linearly detrend the data chunk-wise
detrend(dataset, perchunk=True, model="linear", polyord = 1)

# z-score the data relative to the baseline trials in each chunk:
zscore(dataset, perchunk=True, baselinelabels = [0], pervoxel = True,  
targetdtype = 'float64')


# define and run classifier

rfesvm_split = SplitClassifier(LinearCSVMC())
clf = \
FeatureSelectionClassifier(
clf = LinearCSVMC(),
# on features selected via RFE
feature_selection = RFE(
# based on sensitivity of a clf which does splitting internally
sensitivity_analyzer=rfesvm_split.getSensitivityAnalyzer(),
transfer_error=ConfusionBasedError(
rfesvm_split,
confusion_state="confusion"),
# and whose internal error we use
feature_selector=FractionTailSelector(
0.2, mode= 'discard', tail='lower'),
# remove 20% of features at each step
update_sensitivity=True),
# update sensitivity at each step
descr= 'LinSVM+RFE(splits_avg)')
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