def prepare_data(self, dataset, subjects):
"""Prepare data for classification."""
if len(dataset.event_id) < 3:
# multiclass, pick two first classes
raise (ValueError("Dataset %s only contains two classes" %
dataset.name))
event_id = dataset.event_id
epochs = self._epochs(dataset, subjects, event_id)
groups = []
full_epochs = []
for ii, epoch in enumerate(epochs):
epochs_list = [epoch[k] for k in event_id]
# equalize for accuracy
equalize_epoch_counts(epochs_list)
ep = concatenate_epochs(epochs_list)
groups.extend([ii] * len(ep))
full_epochs.append(ep)
epochs = concatenate_epochs(full_epochs)
X = epochs.get_data() * 1e6
y = epochs.events[:, -1]
groups = np.asarray(groups)
return X, y, groups
def load_subject_series_epochs(data_path,
subject_range,
series_range,
tmin=-0.2,
tmax=0.5,
baseline=(None, 0),
stim_channel=None):
all_epochs_list = []
for subject in subject_range:
subject_fname = data_path + '/subj{0}'.format(subject)
for series in series_range:
subject_series_fname = subject_fname + '_series{0}_data.csv'.format(
series)
subject_series = create_mne_raw_object(subject_series_fname)
subject_series_events = find_events(subject_series,
stim_channel=stim_channel,
verbose=False)
epochs = Epochs(subject_series,
subject_series_events,
tmin=tmin,
tmax=tmax,
baseline=baseline,
verbose=False)
all_epochs_list.append(epochs)
all_epochs = concatenate_epochs(all_epochs_list)
return all_epochs
def _get_data(tmin=-0.2, tmax=0.5, event_id=dict(aud_l=1, vis_l=3),
event_id_gen=dict(aud_l=2, vis_l=4), test_times=None):
"""Aux function for testing GAT viz."""
with warnings.catch_warnings(record=True): # deprecated
gat = GeneralizationAcrossTime()
raw = read_raw_fif(raw_fname)
raw.add_proj([], remove_existing=True)
events = read_events(event_name)
picks = pick_types(raw.info, meg='mag', stim=False, ecg=False,
eog=False, exclude='bads')
picks = picks[1:13:3]
decim = 30
# Test on time generalization within one condition
with warnings.catch_warnings(record=True):
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, decim=decim)
epochs_list = [epochs[k] for k in event_id]
equalize_epoch_counts(epochs_list)
epochs = concatenate_epochs(epochs_list)
# Test default running
with warnings.catch_warnings(record=True): # deprecated
gat = GeneralizationAcrossTime(test_times=test_times)
gat.fit(epochs)
gat.score(epochs)
return gat
def extract_data_from_cont(self, ep_list, event_id):
skip = False
event_epochs = dict(zip(event_id.keys(), [[]] * len(event_id)))
for epoch in ep_list:
for key in event_id.keys():
if key in epoch.event_id.keys():
event_epochs[key].append(epoch[key])
all_events = []
for key in event_id.keys():
if len(event_epochs[key]) > 0:
all_events.append(concatenate_epochs(event_epochs[key]))
# equalize for accuracy
if len(all_events) > 1:
equalize_epoch_counts(all_events)
ep = concatenate_epochs(all_events)
# previously multipled data by 1e6
X, y = (ep.get_data(), ep.events[:, -1])
return X, y
def prepare_data(self, subjects):
"""Prepare data for classification."""
event_id = dict(rest=1, left_hand=2, right_hand=3)
epochs = self._epochs(subjects, event_id)
# since we are using accuracy, we have to equalize the number of
# events
groups = []
full_epochs = []
for ii, epoch in enumerate(epochs):
epochs_list = [epoch[k] for k in event_id]
equalize_epoch_counts(epochs_list)
ep = concatenate_epochs(epochs_list)
groups.extend([ii] * len(ep))
full_epochs.append(ep)
epochs = concatenate_epochs(full_epochs)
X = epochs.get_data()*1e6
y = epochs.events[:, -1]
return X, y, groups
def prepare_data(self, subjects):
"""Prepare data for classification."""
event_id = dict(left_hand=2, right_hand=3)
epochs = self._epochs(subjects, event_id)
groups = []
for ii, ep in enumerate(epochs):
groups.extend([ii] * len(ep))
epochs = concatenate_epochs(epochs)
X = epochs.get_data()*1e6
y = epochs.events[:, -1] - 2
return X, y, groups
def prepare_data(self, dataset, subjects):
"""Prepare data for classification."""
event_id = dataset.event_id
epochs = self._epochs(dataset, subjects, event_id)
groups = []
full_epochs = []
for ii, epoch in enumerate(epochs):
epochs_list = [epoch[k] for k in event_id]
# equalize for accuracy
equalize_epoch_counts(epochs_list)
ep = concatenate_epochs(epochs_list)
groups.extend([ii] * len(ep))
full_epochs.append(ep)
epochs = concatenate_epochs(full_epochs)
#X = epochs.get_data()*1e6
X = epochs.get_data()
y = epochs.events[:, -1]
groups = np.asarray(groups)
return X, y, groups
def csp_training(raw, picks, nfilters):
""" Implement CSP training
:param raw: Raw data
:return: The csp filter
"""
epochs_tot = []
y = []
# get event position corresponding to Replace
events = find_events(raw, stim_channel='HandStart', verbose=False)
# epochs signal for 1.5 second before the movement
epochs = Epochs(raw, events, {'during': 1}, 0, 2, proj=False,
picks=picks, baseline=None, preload=True,
add_eeg_ref=False, verbose=False)
epochs_tot.append(epochs)
y.extend([1] * len(epochs))
# epochs signal for 1.5 second after the movement, this correspond to the
# rest period.
epochs_rest = Epochs(raw, events, {'before': 1}, -2, 0, proj=False,
picks=picks, baseline=None, preload=True,
add_eeg_ref=False, verbose=False)
# Workaround to be able to concatenate epochs with MNE
epochs_rest.times = epochs.times
y.extend([-1] * len(epochs_rest))
epochs_tot.append(epochs_rest)
# Concatenate all epochs
epochs = concatenate_epochs(epochs_tot)
# get data
X = epochs.get_data()
y = np.array(y)
# train CSP
csp = CSP(n_components=nfilters, reg='lws')
csp.fit(X, y)
return csp
def prepare_data(self, dataset, subjects):
"""Prepare data for classification."""
if len(dataset.event_id) > 2:
# multiclass, pick two first classes
raise (ValueError("Dataset %s contain more than two classes" %
dataset.name))
event_id = dataset.event_id
epochs = self._epochs(dataset, subjects, event_id)
groups = []
for ii, ep in enumerate(epochs):
groups.extend([ii] * len(ep))
epochs = concatenate_epochs(epochs)
X = epochs.get_data() * 1e6
y = epochs.events[:, -1]
y = np.asarray(y == np.max(y), dtype=np.int32)
groups = np.asarray(groups)
return X, y, groups
def _get_data(tmin=-0.2,
tmax=0.5,
event_id=dict(aud_l=1, vis_l=3),
event_id_gen=dict(aud_l=2, vis_l=4),
test_times=None):
"""Aux function for testing GAT viz"""
gat = GeneralizationAcrossTime()
raw = read_raw_fif(raw_fname, preload=False, add_eeg_ref=False)
raw.add_proj([], remove_existing=True)
events = read_events(event_name)
picks = pick_types(raw.info,
meg='mag',
stim=False,
ecg=False,
eog=False,
exclude='bads')
picks = picks[1:13:3]
decim = 30
# Test on time generalization within one condition
with warnings.catch_warnings(record=True):
epochs = Epochs(raw,
events,
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0),
preload=True,
decim=decim,
add_eeg_ref=False)
epochs_list = [epochs[k] for k in event_id]
equalize_epoch_counts(epochs_list)
epochs = concatenate_epochs(epochs_list)
# Test default running
gat = GeneralizationAcrossTime(test_times=test_times)
gat.fit(epochs)
gat.score(epochs)
return gat
def compute_transform(subj_id, nfilters=4):
freqs = [7, 30]
b, a = butter(5, np.array(freqs) / 250.0, btype='bandpass')
epochs_tot = []
y = []
fnames = glob('data/train/subj%d_series*_data.csv' % (subj_id))
train_raw = concatenate_raws(
[create_mne_raw_object(fname) for fname in fnames])
picks = pick_types(train_raw.info, eeg=True)
train_raw._data[picks] = lfilter(b, a, train_raw._data[picks])
events = find_events(train_raw, stim_channel='Replace', verbose=False)
epochs = Epochs(train_raw,
events, {'during': 1},
-2,
-0.5,
proj=False,
picks=picks,
baseline=None,
preload=True,
add_eeg_ref=False,
verbose=False)
epochs_tot.append(epochs)
y.extend([1] * len(epochs))
epochs_rest = Epochs(train_raw,
events, {'after': 1},
0.5,
2,
proj=False,
picks=picks,
baseline=None,
preload=True,
add_eeg_ref=False,
verbose=False)
epochs_rest.times = epochs.times
y.extend([-1] * len(epochs_rest))
epochs_tot.append(epochs_rest)
# Concatenate all epochs
epochs = concatenate_epochs(epochs_tot)
# get data
X = epochs.get_data()
y = np.array(y)
# train CSP
csp = CSP(n_components=nfilters, reg='lws')
csp.fit(X, y)
#from pyriemann.spatialfilters import Xdawn
#xdawn = Xdawn(nfilter=nfilters / 2)
#xdawn.fit(X, y)
#return xdawn.V
return csp.filters_[:nfilters]
for event_type in event_types:
events_behavior_type = fix_triggers(events_meg, events_behavior,
event_type='trigg' + event_type)
# Epoch raw data
epochs_list = list()
for run in range(1, n_runs):
fname_raw = op.join(path_data, subject, 'run%02i.fif' % run)
raw = Raw(fname_raw, preload=True)
raw.filter(.75, h_freq=30.0)
sel = events_behavior_type['meg_file'] == run
time_sample = events_behavior_type['meg_event_tsample'][sel]
trigger_value = events_behavior_type['meg_event_value'][sel]
events_meg = np.vstack((time_sample.astype(int),
np.zeros_like(time_sample, int),
trigger_value.astype(int))).T
event_id = {'ttl_%i' % ii: ii for ii in np.unique(events_meg[:, 2])}
epochs = Epochs(raw, events_meg, event_id=event_id,
tmin=-1.0, tmax=.500, preload=True)
# epochs.resample(128) # XXX BUG MNE when concatenate afterwards
epochs_list.append(epochs)
epochs = concatenate_epochs(epochs_list)
epochs.resample(128)
# Save data
fname = op.join(path_data, subject, 'epochs_%s.fif' % event_type)
epochs.save(fname)
fname = op.join(path_data, subject, 'behavior_%s.pkl' % event_type)
with open(fname, 'wb') as f:
pickle.dump(events_behavior_type, f)
######################################################################
# Decoding
# set up a classifier based on a regularized Logistic Regression
clf = LogisticRegression(C=1)
# force the classifer to output a probabilistic prediction
clf = force_predict(clf, axis=1)
# insert a z-score normalization step before the classification
clf = make_pipeline(StandardScaler(), clf)
# initialize the GAT object
gat = GeneralizationAcrossTime(clf=clf, scorer=scorer_auc, n_jobs=-1,
cv=10)
# select the trials where a target is presented
for contrast in ['HL', 'EU', 'PR']:
epochs_ = concatenate_epochs((epochs[contrast[0]],
epochs[contrast[1]]))
y = np.hstack((np.zeros(len(epochs[contrast[0]])),
np.ones(len(epochs[contrast[1]]))))
gat.fit(epochs_, y=y)
fname = op.join(data_path, 's%i_%s_fit.pkl' % (subject, contrast))
with open(fname, 'wb') as f:
pickle.dump(gat, f)
# TODO: should save y_pred separately
# predict + score
scores = gat.score(epochs_, y=y)
fname = op.join(data_path,
's%i_%s_scores.npy' % (subject, contrast))
np.save(fname, np.array(scores))
all_scores[contrast].append(np.array(scores))
# plot
0,
proj=False,
picks=picks,
baseline=None,
preload=True,
add_eeg_ref=False,
verbose=False)
# Workaround to be able to concatenate epochs with MNE
epochs_rest.times = epochs.times
y.extend([-1] * len(epochs_rest))
epochs_tot.append(epochs_rest)
# Concatenate all epochs
epochs = concatenate_epochs(epochs_tot)
# get data
X = epochs.get_data()
y = np.array(y)
# train CSP
csp = CSP(n_components=nfilters, reg='lws')
csp.fit(X, y)
################ Create Training Features #################################
# apply csp filters and rectify signal
feat = np.dot(csp.filters_[0:nfilters], raw._data[picks])**2
# smoothing by convolution with a rectangle window
feattr = np.array(
y.extend([1]*len(epochs))
# epochs signal for 1.5 second after the movement, this correspond to the
# rest period.
epochs_rest = Epochs(raw, events, {'after' : 1}, 0.5, 2, proj=False,
picks=picks, baseline=None, preload=True,
add_eeg_ref=False, verbose=False)
# Workaround to be able to concatenate epochs with MNE
epochs_rest.times = epochs.times
y.extend([-1]*len(epochs_rest))
epochs_tot.append(epochs_rest)
# Concatenate all epochs
epochs = concatenate_epochs(epochs_tot)
# get data
X = epochs.get_data()
y = np.array(y)
# train CSP
csp = CSP(n_components=nfilters, reg='lws')
csp.fit(X,y)
################ Create Training Features #################################
# apply csp filters and rectify signal
feat = np.dot(csp.filters_[0:nfilters],raw._data[picks])**2
# smoothing by convolution with a rectangle window
feattr = np.array(Parallel(n_jobs=-1)(delayed(convolve)(feat[i],boxcar(nwin),'full') for i in range(nfilters)))
def run(subjectsNum, classifier, subFile):
print 'hi as we go'
subjects = range(1, subjectsNum)
ids_tot = []
pred_tot = []
true = np.empty((0, 6))
# design a butterworth bandpass filter
freqs = [7, 30]
b, a = butter(5, np.array(freqs) / 250.0, btype='bandpass')
# CSP parameters
# Number of spatial filter to use
nfilters = 4
# convolution
# window for smoothing features
nwin = 250
# training subsample
subsample = 10
# submission file
submission_file = subFile
cols = [
'HandStart', 'FirstDigitTouch', 'BothStartLoadPhase', 'LiftOff',
'Replace', 'BothReleased'
]
for subject in subjects:
epochs_tot = []
y = []
################ READ DATA ################################################
fnames = glob(
'/Users/camasa/Documents/University/Grad/DM_Pro/train1/subj%d_series*_data.csv'
% (subject))
# read and concatenate all the files
raw = concatenate_raws(
[creat_mne_raw_object(fname) for fname in fnames])
# pick eeg signal
picks = pick_types(raw.info, eeg=True)
# Filter data for alpha frequency and beta band
# Note that MNE implement a zero phase (filtfilt) filtering not compatible
# with the rule of future data.
# Here we use left filter compatible with this constraint.
# The function parallelized for speeding up the script
raw._data[picks] = np.array(
Parallel(n_jobs=-1)(delayed(lfilter)(b, a, raw._data[i])
for i in picks))
################ CSP Filters training #####################################
# get event posision corresponding to HandStart
events = find_events(raw, stim_channel='HandStart', verbose=False)
# epochs signal for 2 second after the event
epochs = Epochs(raw,
events, {'during': 1},
0,
2,
proj=False,
picks=picks,
baseline=None,
preload=True,
verbose=False)
epochs_tot.append(epochs)
y.extend([1] * len(epochs))
# epochs signal for 2 second before the event, this correspond to the
# rest period.
epochs_rest = Epochs(raw,
events, {'before': 1},
-2,
0,
proj=False,
picks=picks,
baseline=None,
preload=True,
verbose=False)
# Workaround to be able to concatenate epochs with MNE
epochs_rest.times = epochs.times
y.extend([-1] * len(epochs_rest))
epochs_tot.append(epochs_rest)
# Concatenate all epochs
epochs = concatenate_epochs(epochs_tot)
# get data
X = epochs.get_data()
y = np.array(y)
# train CSP
csp = CSP(n_components=nfilters, reg='ledoit_wolf')
csp.fit(X, y)
################ Create Training Features #################################
# apply csp filters and rectify signal
feat = np.dot(csp.filters_[0:nfilters], raw._data[picks])**2
# smoothing by convolution with a rectangle window
feattr = np.array(
Parallel(n_jobs=-1)(
delayed(convolve)(feat[i], boxcar(nwin), 'full')
for i in range(nfilters)))
feattr = np.log(feattr[:, 0:feat.shape[1]])
# training labels
# they are stored in the 6 last channels of the MNE raw object
labels = raw._data[32:]
################ Create test Features #####################################
# read test data
fnames = glob(
'/Users/camasa/Documents/University/Grad/DM_Pro/test1val/subj%d_series*_data.csv'
% (subject))
raw = concatenate_raws(
[creat_mne_raw_object(fname) for fname in fnames])
raw._data[picks] = np.array(
Parallel(n_jobs=-1)(delayed(lfilter)(b, a, raw._data[i])
for i in picks))
# read ids
ids = np.concatenate(
[np.array(pd.read_csv(fname)['id']) for fname in fnames])
ids_tot.append(ids)
# apply preprocessing on test data
feat = np.dot(csp.filters_[0:nfilters], raw._data[picks])**2
featte = np.array(
Parallel(n_jobs=-1)(
delayed(convolve)(feat[i], boxcar(nwin), 'full')
for i in range(nfilters)))
featte = np.log(featte[:, 0:feat.shape[1]])
tru = raw._data[32:].T
# feattrNorm = normalize(feattr)
# featteNorm = normalize(featte)
#
# ctr, rtr = feattr.shape
# ctt, rtt = featte.shape
# print ctr, rtr
# print ctt, rtt
############## Train classifiers ########################################
if classifier == 'LR':
lr = LogisticRegression()
pred = np.empty((len(ids), 6))
for i in range(6):
print('LR Train subject %d, class %s' % (subject, cols[i]))
lr.fit(feattr[:, ::subsample].T, labels[i, ::subsample])
pred[:, i] = lr.predict_proba(featte.T)[:, 1]
# pred_tot.append(pred)
# true = np.r_[true,tru]
elif classifier == 'MLP':
mlp = MLPClassifier(solver='sgd',
learning_rate='adaptive',
hidden_layer_sizes=(1000, ),
learning_rate_init=0.0005,
max_iter=1000000,
shuffle=False)
pred = np.empty((len(ids), 6))
for i in range(6):
print('MLP Train subject %d, class %s' % (subject, cols[i]))
mlp.fit(feattr[:, ::subsample].T, labels[i, ::subsample])
pred[:, i] = mlp.predict_proba(featte.T)[:, 1]
# pred_tot.append(pred)
# true = np.r_[true,tru]
# elif classifier == 'SVC':
# svr = SVC()
# pred = np.empty((len(ids),6))
# for i in range(6):
# print('SVC Train subject %d, class %s' % (subject, cols[i]))
# svr.fit(feattr[:,::subsample].T,labels[i,::subsample])
# pred[:,i] = svr.predict(featte.T)[:,1]
elif classifier == 'RF':
rf = RandomForestClassifier(n_estimators=100,
max_features='auto',
n_jobs=-1)
pred = np.empty((len(ids), 6))
for i in range(6):
print('RF Train subject %d, class %s' % (subject, cols[i]))
rf.fit(feattr[:, ::subsample].T, labels[i, ::subsample])
pred[:, i] = rf.predict_proba(featte.T)[:, 1]
#score =
elif classifier == 'SVC':
svc = LinearSVC()
pred = np.empty((len(ids), 6))
for i in range(6):
print('RF Train subject %d, class %s' % (subject, cols[i]))
svc.fit(feattr[:, ::subsample].T, labels[i, ::subsample])
pred[:, i] = svc.predict(featte.T) #[:,1]
pred_tot.append(pred)
true = np.r_[true, tru]
data = np.concatenate(pred_tot)
# score = mlp.score(true,data)
# print score
# auc = roc_auc_score(true,data)
# print auc
# fpr = dict()
# tpr = dict()
# thresholds = dict()
# roc_auc = dict()
#
# for i in range(6):
# fpr, tpr, _ = roc_curve(true[:,i], data[:,i])
# roc_auc[i] = auc(fpr[i], tpr[i])
# for j in range(6):
# plt.figure()
# lw = i
# plt.plot(fpr[j], tpr[j], color='darkorange',
# lw=lw, label='ROC curve (area = %0.2f)' % roc_auc[j])
# plt.plot([0, 1], [0, 1], color='navy', lw=lw, linestyle='--')
# plt.xlim([0.0, 1.0])
# plt.ylim([0.0, 1.05])
# plt.xlabel('False Positive Rate')
# plt.ylabel('True Positive Rate')
# plt.title('Receiver operating characteristic example')
# plt.legend(loc="lower right")
# plt.savefig('/Users/camasa/Desktop/roc%d.eps' % (j),format='eps')
# plt.show()
# create pandas object for sbmission
submission = pd.DataFrame(index=np.concatenate(ids_tot),
columns=cols,
data=np.concatenate(pred_tot))
# write file
submission.to_csv(submission_file, index_label='id', float_format='%.5f')
trueLabels = pd.DataFrame(index=np.concatenate(ids_tot),
columns=cols,
data=true)
trueLabels.to_csv('TrueLabels.csv', index_label='id', float_format='%.5f')
def separateXY(epochs):
if isinstance(epochs, list):
epochs = concatenate_epochs(epochs)
labels = epochs.events[:, -1]
return (epochs.get_data() * 1000, labels)
def make_cue_epoch_tf(subject):
"""Create cue epochs during WM task """
fname_raw = op.join(path_data, subject)
# Read behavioral file
fname_bhv = list()
files = os.listdir(op.join(path_data, subject, 'behavdata'))
fname_bhv.extend(([
op.join(fname_raw + '/behavdata/') + f for f in files if 'WorkMem' in f
]))
for fname_behavior in fname_bhv:
events_behavior = get_events_from_mat(fname_behavior)
# Read raw MEG data and extract event triggers
runs = list()
files = os.listdir(fname_raw)
runs.extend(([op.join(fname_raw + '/') + f for f in files if '.ds' in f]))
events_meg = list()
for run_number, this_run in enumerate(runs):
fname_raw = op.join(path_data, subject, this_run)
print(fname_raw)
raw = read_raw_ctf(fname_raw, preload=True, system_clock='ignore')
channel_trigger = np.where(np.array(raw.ch_names) == 'USPT001')[0][0]
# replace 255 values with 0
trigger_baseline = np.where(raw._data[channel_trigger, :] == 255)[0]
raw._data[channel_trigger, trigger_baseline] = 0.
# find triggers
events_meg_ = mne.find_events(raw)
# Add 48ms to the trigger events (according to delay with photodiod)
events_meg_ = np.array(events_meg_, float)
events_meg_[:, 0] += round(.048 * raw.info['sfreq'])
events_meg_ = np.array(events_meg_, int)
# to keep the run from which the event was found
events_meg_[:, 1] = run_number
events_meg.append(events_meg_)
# concatenate all meg events
events_meg = np.vstack(events_meg)
# add trigger index to meg_events
events_target = range(1, 126)
events_cue = range(126, 130)
events_probe = range(130, 141)
triggidx_array = []
for trigg in events_meg[:, 2]:
if trigg in events_target:
triggidx = 1
elif trigg in events_cue:
triggidx = 2
elif trigg in events_probe:
triggidx = 3
triggidx_array.append(triggidx)
events_meg = np.insert(events_meg, 3, triggidx_array, axis=1)
# Compare MEG and bhv triggers and save events_behavior for each event
event_type = 'Cue'
events_behavior_type = []
events_behavior_type = fix_triggers(events_meg,
events_behavior,
event_type='trigg' + event_type)
epochs_list = list()
# Read raw MEG, filter and epochs
for run_number, this_run in enumerate(runs):
fname_raw = op.join(path_data, subject, this_run)
print(fname_raw)
raw = read_raw_ctf(fname_raw, preload=True, system_clock='ignore')
events_meg_run = make_events_run(events_behavior_type, run_number)
event_id = {
'ttl_%i' % ii: ii
for ii in np.unique(events_meg_run[:, 2])
}
tmin = -.200
tmax = 1.500
epochs = Epochs(raw,
events_meg_run,
event_id=event_id,
tmin=tmin,
tmax=tmax,
preload=True,
baseline=None,
decim=10)
# Copy dev_head_t of the first run to others run
if run_number == 0:
dev_head_t = epochs.info['dev_head_t']
else:
epochs.info['dev_head_t'] = dev_head_t
# Apply baseline from beginning of epoch to t0
epochs.apply_baseline((-0.2, 0.))
epochs_list.append(epochs)
epochs = concatenate_epochs(epochs_list)
epochs.pick_types(meg=True, ref_meg=False)
events = events_behavior_type
events = complete_behavior(events)
return epochs, events
event_id=event_id_bsl,
tmin=-.200,
tmax=0.,
preload=True,
baseline=None,
decim=10)
# Apply baseline of Target
bsl_channels = pick_types(epochs.info, meg=True)
bsl_data = epochs_baseline.get_data()[:, bsl_channels, :]
bsl_data = np.mean(bsl_data, axis=2)
epochs._data[:, bsl_channels, :] -= bsl_data[:, :, np.newaxis]
else:
# Apply baseline from beginning of epoch to t0
epochs.apply_baseline((-0.2, 0.))
epochs_list.append(epochs)
epochs = concatenate_epochs(epochs_list)
# Save epochs and hdf5 behavior
suffix = '' if target_baseline else '_bsl'
session = '_2' if subject[-1:] == '2' else '_1'
fname = op.join(path_data, subject,
'behavior_%s%s.hdf5' % (event_type, session))
write_hdf5(fname, events_behavior_type, overwrite=True)
fname = op.join(path_data, subject,
'epochs_%s%s%s.fif' % (event_type, suffix, session))
epochs.save(fname)
# concatenate the two sessions when 2nd one is existing
subject = sys.argv[1]
suffix = '' if target_baseline else '_bsl'
for event_type in event_types:
subject_2 = subject + '_2'