07-epoch.py

import mne
import os.path as op
from config_AVTest import MEG_data_path,group_name,Ids,bids_root
from mne.preprocessing import read_ica
import numpy as np
import pandas as pd
from mne_bids import BIDSPath

task='AVTest'
day=200

for subject_id in Ids:
    
    subject = group_name+"%d" % subject_id
    print("processing subject: %s" % subject)
            
    fname=op.join(MEG_data_path,subject,task+'_%d'%(day+subject_id)+'_tsss_mc.fif')
    bids_path = BIDSPath(subject='%02d'%(subject_id), session='day2', task='AVTest', suffix='meg', datatype='meg', processing='tsss', extension='.fif', root=bids_root)
    raw_tsss_mc=mne.io.read_raw_fif(bids_path.fpath,preload=True)  
    
    raw_tsss_mc.filter(l_freq=0.1, h_freq=40.0,fir_design='firwin')  # low-pass filter data
    
    ica = read_ica(fname.replace("_tsss_mc", "-ica"))
    ica.exclude = np.load(fname.replace("tsss_mc.fif",'ICA_excludes_EOG_EKG.npy')).tolist()     #EOG_EKG
    raw_tsss_mc = ica.apply(raw_tsss_mc, exclude=ica.exclude)

    df=pd.read_csv(fname.replace('tsss_mc.fif','events_with_artifacts_marked.csv'))                
    df=df[df['artifacts']==False]
    
    events = df[["stim_onset", "button_press", "trigger_code"]].astype(int).values
    
    picks = mne.pick_types(raw_tsss_mc.info, meg=True, eeg=False, stim=False, eog=True,exclude='bads')
    epochs = mne.Epochs(raw_tsss_mc, events, event_id=None, tmin=-0.2, tmax=1.0, picks=picks, baseline=(None,0), preload=True,reject=None,proj=True,metadata=df)        

    # picks=mne.pick_channels(epochs.ch_names,[epochs.ch_names[0]]+epochs.ch_names[1::9]+epochs.ch_names[5::9]+epochs.ch_names[6::9])    
    # epochs.plot(n_channels=103,n_epochs=40,block = True,picks=picks, scalings='auto')
    
    epochs.save(fname.replace("_tsss_mc", "-epo"),overwrite=True)