Decoding in sensor space data using the Common Spatial Pattern (CSP)

Decoding applied to MEG data in sensor space decomposed using CSP. Here the classifier is applied to features extracted on CSP filtered signals.

See http://en.wikipedia.org/wiki/Common_spatial_pattern and [1].

References

[1]Zoltan J. Koles. The quantitative extraction and topographic mapping of the abnormal components in the clinical EEG. Electroencephalography and Clinical Neurophysiology, 79(6):440–447, December 1991.
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#          Romain Trachel <romain.trachel@inria.fr>
#
# License: BSD (3-clause)

import numpy as np
import matplotlib.pyplot as plt

import mne
from mne import io
from mne.datasets import sample

print(__doc__)

data_path = sample.data_path()

Set parameters and read data

raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
tmin, tmax = -0.2, 0.5
event_id = dict(aud_l=1, vis_l=3)

# Setup for reading the raw data
raw = io.read_raw_fif(raw_fname, preload=True)
raw.filter(2, None)  # replace baselining with high-pass
events = mne.read_events(event_fname)

raw.info['bads'] = ['MEG 2443']  # set bad channels
picks = mne.pick_types(raw.info, meg='grad', eeg=False, stim=False, eog=False,
                       exclude='bads')

# Read epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
                    picks=picks, baseline=None, preload=True)

labels = epochs.events[:, -1]
evoked = epochs.average()

Out:

Opening raw data file /home/ubuntu/mne_data/MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw.fif...
    Read a total of 4 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
        Average EEG reference (1 x 60)  idle
    Range : 6450 ... 48149 =     42.956 ...   320.665 secs
Ready.
Current compensation grade : 0
Reading 0 ... 41699  =      0.000 ...   277.709 secs...
Setting up high-pass filter at 2 Hz
l_trans_bandwidth chosen to be 2.0 Hz
Filter length of 496 samples (3.303 sec) selected
145 matching events found
4 projection items activated
Loading data for 145 events and 106 original time points ...
0 bad epochs dropped

Decoding in sensor space using a linear SVM

from sklearn.svm import SVC  # noqa
from sklearn.cross_validation import ShuffleSplit  # noqa
from mne.decoding import CSP  # noqa

n_components = 3  # pick some components
svc = SVC(C=1, kernel='linear')
csp = CSP(n_components=n_components)

# Define a monte-carlo cross-validation generator (reduce variance):
cv = ShuffleSplit(len(labels), 10, test_size=0.2, random_state=42)
scores = []
epochs_data = epochs.get_data()

for train_idx, test_idx in cv:
    y_train, y_test = labels[train_idx], labels[test_idx]

    X_train = csp.fit_transform(epochs_data[train_idx], y_train)
    X_test = csp.transform(epochs_data[test_idx])

    # fit classifier
    svc.fit(X_train, y_train)

    scores.append(svc.score(X_test, y_test))

# Printing the results
class_balance = np.mean(labels == labels[0])
class_balance = max(class_balance, 1. - class_balance)
print("Classification accuracy: %f / Chance level: %f" % (np.mean(scores),
                                                          class_balance))

# Or use much more convenient scikit-learn cross_val_score function using
# a Pipeline
from sklearn.pipeline import Pipeline  # noqa
from sklearn.cross_validation import cross_val_score  # noqa
cv = ShuffleSplit(len(labels), 10, test_size=0.2, random_state=42)
clf = Pipeline([('CSP', csp), ('SVC', svc)])
scores = cross_val_score(clf, epochs_data, labels, cv=cv, n_jobs=1)
print(scores.mean())  # should match results above

# And using reuglarized csp with Ledoit-Wolf estimator
csp = CSP(n_components=n_components, reg='ledoit_wolf')
clf = Pipeline([('CSP', csp), ('SVC', svc)])
scores = cross_val_score(clf, epochs_data, labels, cv=cv, n_jobs=1)
print(scores.mean())  # should get better results than above

# plot CSP patterns estimated on full data for visualization
csp.fit_transform(epochs_data, labels)
data = csp.patterns_
fig, axes = plt.subplots(1, 4)
for idx in range(4):
    mne.viz.plot_topomap(data[idx], evoked.info, axes=axes[idx], show=False)
fig.suptitle('CSP patterns')
fig.tight_layout()
fig.show()
../../_images/sphx_glr_plot_decoding_csp_space_001.png

Out:

Classification accuracy: 0.934483 / Chance level: 0.503448
0.934482758621
0.944827586207

Total running time of the script: ( 0 minutes 9.388 seconds)

Generated by Sphinx-Gallery