Convert epochs to stc and save as array for use in Blender.

epochsToNpy.py

"""
epochsToStc

@author:wronk

Convert epochs to stc and save as array for use in Blender.
"""

import mne
import numpy as np
from mne.minimum_norm import apply_inverse as inv_evoked
from os import path as op
from os import environ
import fnmatch
import os

subj_list = ['fsaverage']

subj_info_dir = op.join(environ['CODE_ROOT'], 'switchBCIFiles')
subjListFName = op.join(subj_info_dir, 'SoP_MEG.txt')

struct_dir = op.join(environ['SUBJECTS_DIR'])

subj_d = []

stc_dir = '/media/Toshiba/Blender/Ross_AudVis/stcs/'
save_dir = '/media/Toshiba/Blender/Ross_AudVis/'

##############################################################################
### Load inverse, forward, and epochs
print 'Reading stcs'

f_names = ['Masker', 'Target']#, 'Visual']
#f_names = ['Visual']
stc_list = []

for fi, f_name in enumerate(f_names):
    print '\t' + f_name,
    temp_stc = mne.read_source_estimate(op.join(stc_dir, f_name),
                                        subject=subj_list[0])
    temp_stc.tmin += 0.050
    temp_stc.crop(-0.050, None)
    temp_stc = temp_stc.morph('fsaverage', grade=None, smooth=10)
    stc_list.append(temp_stc)

    print ' ...  Done'

##############################################################################
### Calculate inverse and save as array
print 'Saving stcs to npy for:'
for si, stc in enumerate(stc_list):
    print '\t' + f_names[si],

    # Morph to fill the entire surface
    #s_d['stc'] = temp_stc.morph(s_d['name'], grade=None, smooth=5)

    # Save arrays with the stc data
    # Data for both hemispheres is saved in each
    np.save(op.join(save_dir, 'stcs/data', f_names[si] + '-lh'), stc.lh_data)
    np.save(op.join(save_dir, 'stcs/data', f_names[si] + '-rh'), stc.rh_data)
    np.save(op.join(save_dir, 'stcs/vertices', f_names[si] + '-lh'),
            stc.vertices[0])
    np.save(op.join(save_dir, 'stcs/vertices', f_names[si] + '-rh'),
            stc.vertices[1])

    #stc_data = np.load(op.join(save_dir, 'stcs/data', 'Visual-lh.npy'))

    print ' ...  Done'

#stc = mne.read_source_estimate(op.join(save_dir, 'stcs/data', f_names[0] + 'debug'))