Decoding real-time data

Supervised machine learning applied to MEG data in sensor space. Here the classifier is updated every 5 trials and the decoding accuracy is plotted.

../../_images/sphx_glr_plot_compute_rt_decoder_001.png

Out:

Opening raw data file /home/circleci/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...
No baseline correction applied
Not setting metadata
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# Authors: Mainak Jas <mainak@neuro.hut.fi>
#
# License: BSD (3-clause)

import numpy as np
import matplotlib.pyplot as plt

from sklearn import preprocessing
from sklearn.linear_model import LogisticRegression
from sklearn.pipeline import Pipeline
from sklearn.model_selection import cross_val_score, ShuffleSplit
from mne.decoding import Vectorizer, FilterEstimator

import mne
from mne.realtime import MockRtClient, RtEpochs
from mne.datasets import sample

print(__doc__)

# Fiff file to simulate the realtime client
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
raw = mne.io.read_raw_fif(raw_fname, preload=True)

tmin, tmax = -0.2, 0.5
event_id = dict(aud_l=1, vis_l=3)

tr_percent = 60  # Training percentage
min_trials = 10  # minimum trials after which decoding should start

# select gradiometers
picks = mne.pick_types(raw.info, meg='grad', eeg=False, eog=True,
                       stim=True, exclude=raw.info['bads'])

# create the mock-client object
rt_client = MockRtClient(raw)

# create the real-time epochs object
rt_epochs = RtEpochs(rt_client, event_id, tmin, tmax, picks=picks, decim=1,
                     reject=dict(grad=4000e-13, eog=150e-6), baseline=None,
                     isi_max=4.)

# start the acquisition
rt_epochs.start()

# send raw buffers
rt_client.send_data(rt_epochs, picks, tmin=0, tmax=90, buffer_size=1000)

# Decoding in sensor space using a linear SVM
n_times = len(rt_epochs.times)

scores_x, scores, std_scores = [], [], []

# don't highpass filter because it's epoched data and the signal length
# is small
filt = FilterEstimator(rt_epochs.info, None, 40, fir_design='firwin')
scaler = preprocessing.StandardScaler()
vectorizer = Vectorizer()
clf = LogisticRegression(solver='lbfgs')

concat_classifier = Pipeline([('filter', filt), ('vector', vectorizer),
                              ('scaler', scaler), ('svm', clf)])

data_picks = mne.pick_types(rt_epochs.info, meg='grad', eeg=False, eog=False,
                            stim=False, exclude=raw.info['bads'])
ax = plt.subplot(111)
ax.set_xlabel('Trials')
ax.set_ylabel('Classification score (% correct)')
ax.set_title('Real-time decoding')
ax.set_xlim([min_trials, 50])
ax.set_ylim([30, 105])
plt.axhline(50, color='k', linestyle='--', label="Chance level")
plt.show(block=False)

for ev_num, ev in enumerate(rt_epochs.iter_evoked()):
    if ev_num >= 50:  # stop at 50
        break

    print("Just got epoch %d" % (ev_num + 1))

    if ev_num == 0:
        X = ev.data[np.newaxis, data_picks, :]
        y = int(ev.comment)  # the comment attribute contains the event_id
    else:
        X = np.concatenate((X, ev.data[np.newaxis, data_picks, :]), axis=0)
        y = np.append(y, int(ev.comment))

    if ev_num >= min_trials and ev_num % 5 == 0:
        cv = ShuffleSplit(5, test_size=0.2, random_state=42)  # 3 for speed
        scores_t = cross_val_score(concat_classifier, X, y, cv=cv,
                                   n_jobs=1) * 100

        std_scores.append(scores_t.std())
        scores.append(scores_t.mean())
        scores_x.append(ev_num)

        # Plot accuracy

        plt.plot(scores_x[-2:], scores[-2:], '-x', color='b',
                 label="Classif. score")
        ax.plot(scores_x[-1], scores[-1])

        hyp_limits = (np.asarray(scores) - np.asarray(std_scores),
                      np.asarray(scores) + np.asarray(std_scores))
        fill = plt.fill_between(scores_x, hyp_limits[0], y2=hyp_limits[1],
                                color='b', alpha=0.5)
        plt.pause(0.01)
        plt.draw()
        ax.collections.remove(fill)  # Remove old fill area

plt.fill_between(scores_x, hyp_limits[0], y2=hyp_limits[1], color='b',
                 alpha=0.5)
plt.draw()  # Final figure

Total running time of the script: ( 0 minutes 35.291 seconds)

Estimated memory usage: 129 MB

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