Created
May 2, 2016 15:59
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EEG files save in GDF are convert in Matlab format with BioSig. This code convert the .mat files in pickled gzip and FIF files, ready to be used in Python with MNE.
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| from __future__ import print_function | |
| from scipy.io import loadmat | |
| from os import listdir | |
| from numpy import nan_to_num | |
| import pickle | |
| import gzip | |
| import sys | |
| import mne | |
| def convert_to_pz(fname): | |
| """Open and convert EEG mat file to pickled gzip file. | |
| Parameters | |
| ---------- | |
| fname : string, name of the mat file, without the .mat | |
| Returns | |
| ------- | |
| s : ndarray, shape(time samples, channels) | |
| The EEG signal | |
| """ | |
| print ("Loading"+fname+".mat file: ") | |
| o = loadmat(fname+'.mat', struct_as_record=True) | |
| print ('Done') | |
| s = nan_to_num(o['s']) | |
| sample_rate = o['SampleRate'] | |
| channels_name = o['label'] | |
| print ('Writing '+fname+'.pz file: ') | |
| with gzip.open(fname+'_raw.pz', 'wb') as f: | |
| p = {'raw_signal': s, 'sample_rate': sample_rate, | |
| 'channels_name': channels_name} | |
| pickle.dump(p, f) | |
| print ('done') | |
| return s | |
| def convert_to_fif(fname, s, id): | |
| """Convert a signal and save it under fname.fif | |
| Parameters | |
| ---------- | |
| fname : string, name of the mat file, without the .mat | |
| s : ndarray, shape(time samples, channels) | |
| The EEG signal | |
| id : int, subject identifier | |
| """ | |
| print ('Warning: the channels name are harcoded, change if needed!') | |
| channel_names = ['Oz', 'C1', 'Pz', 'C2', 'P2', 'EOG1', 'P4', 'Cz'] | |
| channel_types = 5 * ['eeg'] + ['eog'] + 2*['eeg'] | |
| sfreq = 256 | |
| montage = 'standard_1020' | |
| info = mne.create_info(channel_names, sfreq, channel_types, montage) | |
| raw = mne.io.RawArray(s.T, info) | |
| raw.info['description'] = 'Tests for Ellis car' | |
| raw.info['experimenter'] = 'Julian Devaux Cindric et Babacar Diankha' | |
| raw.info['subject_info'] = {'id':id, 'his_id':'S'+str(id)} | |
| raw.info['line_freq'] = 50. | |
| raw.info['custom_ref_applied'] = True | |
| print ('Writing '+fname+'.fif file: ', end='') | |
| raw.save(fname+'.fif', overwrite=True) | |
| print ('done') | |
| if __name__ == '__main__': | |
| if len(sys.argv) != 2: | |
| print ('Usage: ' + sys.argv[0] + ' filename') | |
| sys.exit(1) | |
| fname = sys.argv[1] | |
| s = convert_to_pz(fname) | |
| convert_to_fif(fname, s, 2) | |
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