"""
===========================================================================
Motor imagery decoding from EEG data using the Common Spatial Pattern (CSP)
===========================================================================

Decoding of motor imagery applied to EEG data 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]

The EEGBCI dataset is documented in [2]
The data set is available at PhysioNet [3]

[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.

[2] Schalk, G., McFarland, D.J., Hinterberger, T., Birbaumer, N.,
    Wolpaw, J.R. (2004) BCI2000: A General-Purpose Brain-Computer Interface
    (BCI) System. IEEE TBME 51(6):1034-1043

[3] Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG,
    Mietus JE, Moody GB, Peng C-K, Stanley HE. (2000) PhysioBank,
    PhysioToolkit, and PhysioNet: Components of a New Research Resource for
    Complex Physiologic Signals. Circulation 101(23):e215-e220
"""
# Authors: Martin Billinger <martin.billinger@tugraz.at>
#
# License: BSD (3-clause)

print(__doc__)
import numpy as np
import matplotlib.pyplot as plt

from mne import Epochs, pick_types
from mne.io import concatenate_raws
from mne.io.edf import read_raw_edf
from mne.datasets import eegbci
from mne.event import find_events
from mne.decoding import CSP
from mne.layouts import read_layout

###############################################################################
## Set parameters and read data

# avoid classification of evoked responses by using epochs that start 1s after
# cue onset.
tmin, tmax = -1., 4.
event_id = dict(hands=2, feet=3)
subject = 1
runs = [6, 10, 14]  # motor imagery: hands vs feet

raw_fnames = eegbci.load_data(subject, runs)
raw_files = [read_raw_edf(f, tal_channel=-1, preload=True) for f in raw_fnames]
raw = concatenate_raws(raw_files)

# strip channel names
raw.info['ch_names'] = [chn.strip('.') for chn in raw.info['ch_names']]

# Apply band-pass filter
raw.filter(7., 30., method='iir')

events = find_events(raw, shortest_event=0, stim_channel='STI 014')

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

# Read epochs (train will be done only between 1 and 2s)
# Testing will be done with a running classifier
epochs = Epochs(raw, events, event_id, tmin, tmax, proj=True, picks=picks,
                baseline=None, preload=True, add_eeg_ref=False)
epochs_train = epochs.crop(tmin=1., tmax=2., copy=True)
labels = epochs.events[:, -1] - 2

###############################################################################
# Classification with linear discrimant analysis

from sklearn.lda import LDA
from sklearn.cross_validation import ShuffleSplit

# Assemble a classifier
svc = LDA()
csp = CSP(n_components=4, reg=None, log=True)

# 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()
epochs_data_train = epochs_train.get_data()

# Use scikit-learn Pipeline with cross_val_score function
from sklearn.pipeline import Pipeline
from sklearn.cross_validation import cross_val_score
clf = Pipeline([('CSP', csp), ('SVC', svc)])
scores = cross_val_score(clf, epochs_data_train, labels, cv=cv, n_jobs=1)

# 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))

# plot CSP patterns estimated on full data for visualization
csp.fit_transform(epochs_data, labels)

evoked = epochs.average()
evoked.data = csp.patterns_.T
evoked.times = np.arange(evoked.data.shape[0])

layout = read_layout('EEG1005')
evoked.plot_topomap(times=[0, 1, 2, 61, 62, 63], ch_type='eeg', layout=layout,
                    scale_time=1, time_format='%i', scale=1,
                    unit='Patterns (AU)', size=1.5)

###############################################################################
# Look at performance over time

sfreq = raw.info['sfreq']
w_length = int(sfreq * 0.5)   # running classifier: window length
w_step = int(sfreq * 0.1)  # running classifier: window step size
w_start = np.arange(0, epochs_data.shape[2] - w_length, w_step)

scores_windows = []

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[train_idx], y_train)
    X_test = csp.transform(epochs_data_train[test_idx])

    # fit classifier
    svc.fit(X_train, y_train)

    # running classifier: test classifier on sliding window
    score_this_window = []
    for n in w_start:
        X_test = csp.transform(epochs_data[test_idx][:, :, n:(n + w_length)])
        score_this_window.append(svc.score(X_test, y_test))
    scores_windows.append(score_this_window)

# Plot scores over time
w_times = (w_start + w_length / 2.) / sfreq + epochs.tmin
plt.plot(w_times, np.mean(scores_windows, 0), label='Score')
plt.axvline(0, linestyle='--', color='k', label='Onset')
plt.axhline(0.5, linestyle='-', color='k', label='Chance')
plt.xlabel('time (s)')
plt.ylabel('classification accuracy')
plt.title('Classification score over time')
plt.legend(loc='lower right')
plt.show()