XDAWN Decoding From EEG data

ERP decoding with Xdawn ([1], [2]). For each event type, a set of spatial Xdawn filters are trained and applied on the signal. Channels are concatenated and rescaled to create features vectors that will be fed into a logistic regression.

References

[1]Rivet, B., Souloumiac, A., Attina, V., & Gibert, G. (2009). xDAWN algorithm to enhance evoked potentials: application to brain-computer interface. Biomedical Engineering, IEEE Transactions on, 56(8), 2035-2043.
[2]Rivet, B., Cecotti, H., Souloumiac, A., Maby, E., & Mattout, J. (2011, August). Theoretical analysis of xDAWN algorithm: application to an efficient sensor selection in a P300 BCI. In Signal Processing Conference, 2011 19th European (pp. 1382-1386). IEEE.
# Authors: Alexandre Barachant <alexandre.barachant@gmail.com>
#
# License: BSD (3-clause)

import numpy as np
import matplotlib.pyplot as plt

from sklearn.model_selection import StratifiedKFold
from sklearn.pipeline import make_pipeline
from sklearn.linear_model import LogisticRegression
from sklearn.metrics import classification_report, confusion_matrix
from sklearn.preprocessing import MinMaxScaler

from mne import io, pick_types, read_events, Epochs
from mne.datasets import sample
from mne.preprocessing import Xdawn
from mne.decoding import Vectorizer
from mne.viz import tight_layout


print(__doc__)

data_path = sample.data_path()

Out:

Successfully extracted to: [u'/home/ubuntu/mne_data/MNE-sample-data']

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 = -0.1, 0.3
event_id = dict(aud_l=1, aud_r=2, vis_l=3, vis_r=4)

# Setup for reading the raw data
raw = io.read_raw_fif(raw_fname, preload=True)
raw.filter(1, 20, fir_design='firwin')
events = read_events(event_fname)

picks = pick_types(raw.info, meg=False, eeg=True, stim=False, eog=False,
                   exclude='bads')

epochs = Epochs(raw, events, event_id, tmin, tmax, proj=False,
                picks=picks, baseline=None, preload=True,
                verbose=False)

# Create classification pipeline
clf = make_pipeline(Xdawn(n_components=3),
                    Vectorizer(),
                    MinMaxScaler(),
                    LogisticRegression(penalty='l1'))

# Get the labels
labels = epochs.events[:, -1]

# Cross validator
cv = StratifiedKFold(n_splits=10, shuffle=True, random_state=42)

# Do cross-validation
preds = np.empty(len(labels))
for train, test in cv.split(epochs, labels):
    clf.fit(epochs[train], labels[train])
    preds[test] = clf.predict(epochs[test])

# Classification report
target_names = ['aud_l', 'aud_r', 'vis_l', 'vis_r']
report = classification_report(labels, preds, target_names=target_names)
print(report)

# Normalized confusion matrix
cm = confusion_matrix(labels, preds)
cm_normalized = cm.astype(float) / cm.sum(axis=1)[:, np.newaxis]

# Plot confusion matrix
plt.imshow(cm_normalized, interpolation='nearest', cmap=plt.cm.Blues)
plt.title('Normalized Confusion matrix')
plt.colorbar()
tick_marks = np.arange(len(target_names))
plt.xticks(tick_marks, target_names, rotation=45)
plt.yticks(tick_marks, target_names)
tight_layout()
plt.ylabel('True label')
plt.xlabel('Predicted label')
plt.show()
../../_images/sphx_glr_plot_decoding_xdawn_eeg_001.png

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 band-pass filter from 1 - 20 Hz
l_trans_bandwidth chosen to be 1.0 Hz
h_trans_bandwidth chosen to be 5.0 Hz
Filter length of 496 samples (3.303 sec) selected
             precision    recall  f1-score   support

      aud_l       0.61      0.65      0.63        72
      aud_r       0.52      0.45      0.48        73
      vis_l       0.76      0.71      0.74        73
      vis_r       0.63      0.71      0.67        70

avg / total       0.63      0.63      0.63       288

Total running time of the script: ( 0 minutes 4.068 seconds)

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