def test_doesnt_change_elc_montages(tmp_path):
montage_orig = read_montage('standard_1005')
save_montage(montage_orig, tmp_path)
saved_path = op.join(tmp_path, 'standard_1005.elc')
montage_saved = read_montage(saved_path)
assert montage_orig.ch_names == montage_saved.ch_names
assert np.allclose(montage_orig.pos, montage_saved.pos)
assert np.allclose(montage_orig.lpa, montage_saved.lpa)
assert np.allclose(montage_orig.rpa, montage_saved.rpa)
assert np.allclose(montage_orig.nasion, montage_saved.nasion)
assert montage_orig.kind == montage_saved.kind
def creat_mne_raw_object(fname, read_events=True):
"""
Creates a mne raw instance from csv file
Arguments
fname: file path
read_events: boolean indicating whether we want to read events file
"""
data = pd.read_csv(fname)
# get chanel names
ch_names = list(data.columns[1:])
# read EEG standard montage from mne
montage = read_montage('standard_1005', ch_names)
ch_type = ['eeg'] * len(ch_names)
data = 1e-6 * np.array(data[ch_names]).T
if read_events:
ev_fname = fname.replace('_data', '_events')
events = pd.read_csv(ev_fname)
events_names = events.columns[1:] #ignore id column
events_data = np.array(events[events_names]).T
# define channel type, the first is EEG, the last 6 are stimulations
ch_type.extend(['stim'] * 6)
ch_names.extend(events_names)
# concatenate event file and data
data = np.concatenate((data, events_data))
# create and populate MNE info structure
info = create_info(ch_names,
sfreq=500.0,
ch_types=ch_type,
montage=montage)
info['filename'] = fname
# create raw object
raw = RawArray(data, info, verbose=False)
return raw
def _get_single_subject_data(self, subject):
"""return data for a single subject"""
fname = '%s/s%02d.mat' % (self.base_folder, subject)
data = loadmat(fname,
squeeze_me=True,
struct_as_record=False,
verify_compressed_data_integrity=False)['eeg']
eeg_ch_names = [
'Fp1', 'AF7', 'AF3', 'F1', 'F3', 'F5', 'F7', 'FT7', 'FC5', 'FC3',
'FC1', 'C1', 'C3', 'C5', 'T7', 'TP7', 'CP5', 'CP3', 'CP1', 'P1',
'P3', 'P5', 'P7', 'P9', 'PO7', 'PO3', 'O1', 'Iz', 'Oz', 'POz',
'Pz', 'CPz', 'FPz', 'FP2', 'AF8', 'AF4', 'AFz', 'Fz', 'F2', 'F4',
'F6', 'F8', 'FT8', 'FC6', 'FC4', 'FC2', 'FCz', 'Cz', 'C2', 'C4',
'C6', 'T8', 'TP8', 'CP6', 'CP4', 'CP2', 'P2', 'P4', 'P6', 'P8',
'P10', 'PO8', 'PO4', 'O2'
]
emg_ch_names = ['EMG1', 'EMG2', 'EMG3', 'EMG4']
ch_names = eeg_ch_names + emg_ch_names + ['Stim']
ch_types = ['eeg'] * 64 + ['misc'] * 4 + ['stim']
montage = read_montage('standard_1005')
eeg_data_l = np.vstack([data.imagery_left * 1e-6, data.imagery_event])
eeg_data_r = np.vstack(
[data.imagery_right * 1e-6, data.imagery_event * 2])
eeg_data = np.hstack([eeg_data_l, eeg_data_r])
info = create_info(ch_names=ch_names,
ch_types=ch_types,
sfreq=data.srate,
montage=montage)
raw = RawArray(data=eeg_data, info=info, verbose=False)
return [raw]
def plotRawEEG(self,
event_code1=769,
event_code2=770,
filename="",
bad_ch=[]):
tmin, tmax = -1., 4.
event_id = dict(class1=event_code1, class2=event_code2)
# load file
raw_fnames = [filename]
raw_files = [
read_raw_edf(f, preload=True, stim_channel='auto')
for f in raw_fnames
]
raw = concatenate_raws(raw_files)
montage = channels.read_montage('standard_1020')
raw.set_montage(montage)
raw.info['bads'] = bad_ch
events = find_events(raw, shortest_event=0)
# Apply band-pass filter
raw.filter(1., 45., fir_design='firwin', skip_by_annotation='edge')
# plot channels
raw.plot(block=True,
lowpass=40,
title="EEG Traces : Click on channels to exclude them!")
def _get_single_subject_data(self, subject):
"""return data for a single subject"""
sessions = []
if self.imagined:
sessions.append('imagination')
if self.executed:
sessions.append('execution')
out = {}
for session in sessions:
paths = self.data_path(subject, session=session)
eog = ['eog-l', 'eog-m', 'eog-r']
montage = read_montage('standard_1005')
data = {}
for ii, path in enumerate(paths):
raw = read_raw_edf(path,
montage=montage,
eog=eog,
misc=range(64, 96),
preload=True,
verbose='ERROR')
# there is nan in the data
raw._data[np.isnan(raw._data)] = 0
data['run_%d' % ii] = raw
out[session] = data
return out
def test_montage():
"""Test making montages"""
# no pep8
input_str = ["""FidNz 0.00000 10.56381 -2.05108
FidT9 -7.82694 0.45386 -3.76056
FidT10 7.82694 0.45386 -3.76056""",
"""// MatLab Sphere coordinates [degrees] Cartesian coordinates
// Label Theta Phi Radius X Y Z off sphere surface
E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011
E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000
E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000""",
"""# ASA electrode file
ReferenceLabel avg
UnitPosition mm
NumberPositions= 68
Positions
-86.0761 -19.9897 -47.9860
85.7939 -20.0093 -48.0310
0.0083 86.8110 -39.9830
Labels
LPA
RPA
Nz
""",
"""Site Theta Phi
Fp1 -92 -72
Fp2 92 72
F3 -60 -51
""",
"""346
EEG F3 -62.027 -50.053 85
EEG Fz 45.608 90 85
EEG F4 62.01 50.103 85
"""]
kinds = ['test.sfp', 'test.csd', 'test.elc', 'test.txt', 'test.elp']
for kind, text in zip(kinds, input_str):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
assert_equal(len(montage.ch_names), 3)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (3, 3))
assert_equal(montage.kind, kind[:-4])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2, montage.pos, 4)
# test with last
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
apply_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
pos3 = np.array([c['eeg_loc'][:, 0] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
def _get_single_subject_data(self, subject):
"""return data for a single subject"""
data_path = '/Users/emmanuelkalunga/Documents/School/EEG_covariance_classification/data/dataset-ssvep-exoskeleton/'
path_subject = data_path + 'subject{0:0>2}/'.format(subject)
raw_files = []
sample_rate = 256
ch_names = [
'Oz', 'O1', 'O2', 'PO3', 'POz', 'PO7', 'PO8', 'PO4', 'Stim'
]
ch_types = ['eeg'] * 8 + ['stim']
montage = read_montage('standard_1005')
info = create_info(ch_names=ch_names,
ch_types=ch_types,
sfreq=256.,
montage=montage)
for fn in os.listdir(path_subject):
if fn.endswith('.pz'):
with gzip.open(path_subject + fn, 'rb') as f:
o = pickle.load(f, encoding='latin1')
raw_signal = o['raw_signal']
event_pos = o['event_pos'].reshape((o['event_pos'].shape[0]))
event_type = o['event_type'].reshape(
(o['event_type'].shape[0]))
data = pd.DataFrame(raw_signal)
data['Stim'] = 0
data.loc[event_pos[np.where(event_type >= 33024)],
'Stim'] = event_type[np.where(event_type >= 33024)]
raw_files.append(
RawArray(data=data.values.T, info=info, verbose=False))
return raw_files
def _convert_run(run, ch_names=None, ch_types=None, verbose=None):
"""Convert one run to raw."""
# parse eeg data
event_id = {}
n_chan = run.X.shape[1]
montage = read_montage('standard_1005')
eeg_data = 1e-6 * run.X
sfreq = run.fs
if not ch_names:
ch_names = ['EEG%d' % ch for ch in range(1, n_chan + 1)]
montage = None # no montage
if not ch_types:
ch_types = ['eeg'] * n_chan
trigger = np.zeros((len(eeg_data), 1))
# some runs does not contains trials i.e baseline runs
if len(run.trial) > 0:
trigger[run.trial - 1, 0] = run.y
eeg_data = np.c_[eeg_data, trigger]
ch_names = ch_names + ['stim']
ch_types = ch_types + ['stim']
event_id = {ev: (ii + 1) for ii, ev in enumerate(run.classes)}
info = create_info(ch_names=ch_names,
ch_types=ch_types,
sfreq=sfreq,
montage=montage)
raw = RawArray(data=eeg_data.T, info=info, verbose=verbose)
return raw, event_id
def _get_single_subject_data(self, subject):
"""return data for a single subject"""
fname = self.data_path(subject)
data = loadmat(fname, squeeze_me=True, struct_as_record=False,
verify_compressed_data_integrity=False)['eeg']
eeg_ch_names = ['Fp1', 'AF7', 'AF3', 'F1', 'F3', 'F5', 'F7', 'FT7',
'FC5', 'FC3', 'FC1', 'C1', 'C3', 'C5', 'T7', 'TP7',
'CP5', 'CP3', 'CP1', 'P1', 'P3', 'P5', 'P7', 'P9',
'PO7', 'PO3', 'O1', 'Iz', 'Oz', 'POz', 'Pz', 'CPz',
'FPz', 'FP2', 'AF8', 'AF4', 'AFz', 'Fz', 'F2', 'F4',
'F6', 'F8', 'FT8', 'FC6', 'FC4', 'FC2', 'FCz', 'Cz',
'C2', 'C4', 'C6', 'T8', 'TP8', 'CP6', 'CP4', 'CP2',
'P2', 'P4', 'P6', 'P8', 'P10', 'PO8', 'PO4', 'O2']
emg_ch_names = ['EMG1', 'EMG2', 'EMG3', 'EMG4']
ch_names = eeg_ch_names + emg_ch_names + ['Stim']
ch_types = ['eeg'] * 64 + ['emg'] * 4 + ['stim']
montage = read_montage('standard_1005')
eeg_data_l = np.vstack([data.imagery_left * 1e-6, data.imagery_event])
eeg_data_r = np.vstack([data.imagery_right * 1e-6,
data.imagery_event * 2])
# trials are already non continuous. edge artifact can appears but
# are likely to be present during rest / inter-trial activity
eeg_data = np.hstack([eeg_data_l, eeg_data_r])
info = create_info(ch_names=ch_names, ch_types=ch_types,
sfreq=data.srate, montage=montage)
raw = RawArray(data=eeg_data, info=info, verbose=False)
return {'session_0': {'run_0': raw}}
def _get_single_subject_data(self, subject):
"""return data for a single subject"""
fname = '%s/subject %02d/with occular artifact/cnt.mat' % (self.base_folder, subject)
fname_mrk = '%s/subject %02d/with occular artifact/mrk.mat' % (self.base_folder, subject)
raws = []
data = loadmat(fname, squeeze_me=True, struct_as_record=False)['cnt']
mrk = loadmat(fname_mrk, squeeze_me=True, struct_as_record=False)['mrk']
montage = read_montage('standard_1005')
if self.motor:
runs = [0, 2, 4]
else:
runs = [1, 3, 5]
for ii in runs:
eeg = data[ii].x.T * 1e-6
trig = np.zeros((1, eeg.shape[1]))
idx = (mrk[ii].time - 1) // 5
trig[0, idx] = mrk[ii].event.desc // 16
eeg = np.vstack([eeg, trig])
ch_names = list(data[ii].clab) + ['Stim']
ch_types = ['eeg'] * 30 + ['eog'] * 2 + ['stim']
info = create_info(ch_names=ch_names, ch_types=ch_types,
sfreq=200., montage=montage)
raw = RawArray(data=eeg, info=info, verbose=False)
raws.append(raw)
return raws
def creat_mne_raw_object(fname, read_events = True):
print ("loading data from %s" %fname)
data = pd.read_csv(fname)
ch_names = list(data.columns[1:])
montage = read_montage('standard_1005', ch_names)
ch_type = ['eeg']*len(ch_names)
data = 1e-6*np.array(data[ch_names]).T
if read_events:
ev_fname = fname.replace('_data', '_events')
print (ev_fname)
events = pd.read_csv(ev_fname)
events_names = events.columns[1:]
events_data = np.array(events[events_names]).T
ch_type.extend(['stim']*6)
ch_names.extend(events_names)
data = np.concatenate((data, events_data))
info = create_info(ch_names, sfreq=500.0, ch_types=ch_type, montage=montage)
info['filename'] = fname
raw = RawArray(data, info, verbose=True)
return raw
def _convert_run_bbci(run, ch_types, verbose=None):
"""Convert one run to raw."""
# parse eeg data
montage = read_montage('standard_1005')
eeg_data = 1e-6 * run.X
sfreq = run.fs
ch_names = list(run.channels)
trigger = np.zeros((len(eeg_data), 1))
trigger[run.trial - 1, 0] = run.y
event_id = {ev: (ii + 1) for ii, ev in enumerate(run.classes)}
flash = np.zeros((len(eeg_data), 1))
flash[run.trial - 1, 0] = run.y_stim + 2
ev_fl = {'Stim%d' % (stim): (stim + 2) for stim in np.unique(run.y_stim)}
event_id.update(ev_fl)
eeg_data = np.c_[eeg_data, trigger, flash]
ch_names = ch_names + ['Target', 'Flash']
ch_types = ch_types + ['stim'] * 2
info = create_info(ch_names=ch_names,
ch_types=ch_types,
sfreq=sfreq,
montage=montage)
raw = RawArray(data=eeg_data.T, info=info, verbose=verbose)
return raw, event_id
def creat_mne_raw_object(fname):
"""Create a mne raw instance from csv file"""
# Read EEG file
data = pd.read_csv(fname)
# get chanel names
ch_names = list(data.columns[1:])
# read EEG standard montage from mne
montage = read_montage('standard_1005', ch_names)
# events file
ev_fname = fname.replace('_data', '_events')
# read event file
events = pd.read_csv(ev_fname)
events_names = events.columns[1:]
events_data = np.array(events[events_names]).T
# concatenate event file and data
data = np.concatenate((1e-6 * np.array(data[ch_names]).T, events_data))
# define channel type, the first is EEG, the last 6 are stimulations
ch_type = ['eeg'] * len(ch_names) + ['stim'] * 6
# create and populate MNE info structure
ch_names.extend(events_names)
info = create_info(ch_names,
sfreq=500.0,
ch_types=ch_type,
montage=montage)
info['filename'] = fname
# create raw object
raw = RawArray(data, info, verbose=False)
return raw
def _infer_eeg_placement_scheme(raw):
"""Based on the channel names, try to infer an EEG placement scheme.
Parameters
----------
raw : instance of Raw
The data as MNE-Python Raw object.
Returns
-------
placement_scheme : str
Description of the EEG placement scheme. Will be "n/a" for unsuccessful
extraction.
"""
placement_scheme = 'n/a'
# Check if the raw data contains eeg data at all
if 'eeg' not in raw:
return placement_scheme
# How many of the channels in raw are based on the extended 10/20 system
raw.load_data()
sel = pick_types(raw.info, meg=False, eeg=True)
ch_names = [raw.ch_names[i] for i in sel]
channel_names = [ch.lower() for ch in ch_names]
montage1005 = read_montage(kind='standard_1005')
montage1005_names = [ch.lower() for ch in montage1005.ch_names]
if set(channel_names).issubset(set(montage1005_names)):
placement_scheme = 'based on the extended 10/20 system'
return placement_scheme
def creat_mne_raw_object(fname,read_events):
# Read EEG file
data = pd.read_csv(fname)
# get chanel names
ch_names = list(data.columns[1:])
# read EEG standard montage from mne
montage = read_montage('standard_1005',ch_names)
ch_type = ['eeg']*len(ch_names)
data = 1e-6*np.array(data[ch_names]).T
if read_events:
# events file
ev_fname = fname.replace('_data','_events')
# read event file
events = pd.read_csv(ev_fname)
events_names = events.columns[1:]
events_data = np.array(events[events_names]).T
# define channel type, the first is EEG, the last 6 are stimulations
ch_type.extend(['stim']*6)
ch_names.extend(events_names)
# concatenate event file and data
data = np.concatenate((data,events_data))
# create and populate MNE info structure
info = create_info(ch_names,sfreq=500.0, ch_types=ch_type, montage=montage)
info['filename'] = fname
# create raw object
raw = RawArray(data,info,verbose=False)
return raw
def _convert_run_epfl(run, verbose=None):
"""Convert one run to raw."""
# parse eeg data
event_id = {}
montage = read_montage('standard_1005')
eeg_data = 1e-6 * run.eeg
sfreq = run.header.SampleRate
ch_names = list(run.header.Label[:-1])
ch_types = ['eeg'] * len(ch_names)
trigger = np.zeros((len(eeg_data), 1))
for ii, typ in enumerate(run.header.EVENT.TYP):
if typ in [6, 9]: # Error
trigger[run.header.EVENT.POS[ii] - 1, 0] = 2
elif typ in [5, 10]: # correct
trigger[run.header.EVENT.POS[ii] - 1, 0] = 1
eeg_data = np.c_[eeg_data, trigger]
ch_names = ch_names + ['stim']
ch_types = ch_types + ['stim']
event_id = {'correct': 1, 'error': 2}
info = create_info(ch_names=ch_names,
ch_types=ch_types,
sfreq=sfreq,
montage=montage)
raw = RawArray(data=eeg_data.T, info=info, verbose=verbose)
return raw, event_id
def load_muse_csv_as_raw(filename, sfreq=256., ch_ind=[0, 1, 2, 3],
stim_ind=5, replace_ch_names=None, verbose=1):
"""Load CSV files into a Raw object.
Args:
filename (str or list): path or paths to CSV files to load
Keyword Args:
subject_nb (int or str): subject number. If 'all', load all
subjects.
session_nb (int or str): session number. If 'all', load all
sessions.
sfreq (float): EEG sampling frequency
ch_ind (list): indices of the EEG channels to keep
stim_ind (int): index of the stim channel
replace_ch_names (dict or None): dictionary containing a mapping to
rename channels. Useful when an external electrode was used.
Returns:
(mne.io.array.array.RawArray): loaded EEG
"""
n_channel = len(ch_ind)
raw = []
for fname in filename:
# read the file
data = pd.read_csv(fname, index_col=0)
# name of each channels
ch_names = list(data.columns)[0:n_channel] + ['Stim']
if replace_ch_names is not None:
ch_names = [c if c not in replace_ch_names.keys()
else replace_ch_names[c] for c in ch_names]
# type of each channels
ch_types = ['eeg'] * n_channel + ['stim']
montage = read_montage('standard_1005')
# get data and exclude Aux channel
data = data.values[:, ch_ind + [stim_ind]].T
# convert in Volts (from uVolts)
data[:-1] *= 1e-6
# create MNE object
info = create_info(ch_names=ch_names, ch_types=ch_types,
sfreq=sfreq, montage=montage, verbose=verbose)
raw.append(RawArray(data=data, info=info, verbose=verbose))
# concatenate all raw objects
if len(raw) > 0:
raws = concatenate_raws(raw, verbose=verbose)
else:
print('No files for subject with filename ' + str(filename))
raws = raw
return raws
def test_overwrite(tmp_path):
saved_path = op.join(tmp_path, 'GSN-HydroCel-128.elc')
Path(saved_path).touch()
montage_orig = read_montage('GSN-HydroCel-128')
save_montage(montage_orig, tmp_path, overwrite=True)
montage_saved = read_montage(saved_path)
scale = 1000 # in when loading elc mne-python converts to meters
# Channels names should be good up to fiducials
assert montage_orig.ch_names[3:] == montage_saved.ch_names[3:]
assert np.allclose(montage_orig.pos, montage_saved.pos * scale)
assert np.allclose(montage_orig.lpa, montage_saved.lpa * scale)
assert np.allclose(montage_orig.rpa, montage_saved.rpa * scale)
assert np.allclose(montage_orig.nasion, montage_saved.nasion * scale)
assert montage_orig.kind == montage_saved.kind
def _set_raw_montage(raw):
"""Set montage for the raw object."""
montage = read_montage('standard_1005')
raw.rename_channels(lambda x: str(x.strip('.')).upper() if str(x.strip(
'.')).upper() in montage.ch_names else str(x.strip('.')))
raw.rename_channels(dict(Cpz='CPz', Poz='POz', Fcz='FCz', Afz='AFz'))
raw.set_channel_types({'Fp1': 'eog'}) # artificially make an EOG channel
raw.set_montage(montage)
def test_read_locs():
"""Test reading EEGLAB locs."""
pos = read_montage(locs_montage_fname).pos
expected = [[0., 9.99779165e-01, -2.10157875e-02],
[3.08738197e-01, 7.27341573e-01, -6.12907052e-01],
[-5.67059636e-01, 6.77066318e-01, 4.69067752e-01],
[0., 7.14575231e-01, 6.99558616e-01]]
assert_allclose(pos[:4], expected, atol=1e-7)
def validate_ch_names(list_of_ch_names, kind='standard_1005'):
montage = read_montage(kind)
upper_list_of_ch_names = [ch.upper() for ch in list_of_ch_names]
upper_montage_ch_names = [ch.upper() for ch in montage.ch_names]
if DEBUG or seems_to_come_from_neuromag(list_of_ch_names):
bool_indices = [True for ch in upper_list_of_ch_names]
else:
bool_indices = [ch in upper_montage_ch_names for ch in upper_list_of_ch_names]
return bool_indices
def test_plot_montage():
"""Test plotting montages
"""
m = read_montage('easycap-M1')
m.plot()
m.plot(show_names=True)
d = read_dig_montage(hsp, hpi, elp, point_names)
d.plot()
d.plot(show_names=True)
def _set_raw_montage(raw):
"""Set montage for the raw object."""
montage = read_montage('standard_1005')
raw.rename_channels(lambda x: str(x.strip('.')).upper()
if str(x.strip('.')).upper() in
montage.ch_names else str(x.strip('.')))
raw.rename_channels(dict(Cpz='CPz', Poz='POz', Fcz='FCz', Afz='AFz'))
raw.set_channel_types({'Fp1': 'eog'}) # artificially make an EOG channel
raw.set_montage(montage)
def test_plot_montage():
"""Test plotting montages
"""
m = read_montage('easycap-M1')
m.plot()
m.plot(show_names=True)
d = read_dig_montage(hsp, hpi, elp, point_names)
d.plot()
d.plot(show_names=True)
def _load_data_003_2015(subject,
path=None,
force_update=False,
update_path=None,
base_url=BNCI_URL,
verbose=None):
"""Load data for 003-2015 dataset."""
if (subject < 1) or (subject > 10):
raise ValueError("Subject must be between 1 and 12. Got %d." % subject)
url = '{u}003-2015/s{s:d}.mat'.format(u=base_url, s=subject)
filename = data_path(url, path, force_update, update_path)[0]
raws = list()
event_id = {'Target': 2, 'Non-Target': 1}
from scipy.io import loadmat
data = loadmat(filename, struct_as_record=False, squeeze_me=True)
data = data['s%d' % subject]
sfreq = 256.
ch_names = [
'Fz', 'Cz', 'P3', 'Pz', 'P4', 'PO7', 'Oz', 'PO8', 'Target', 'Flash'
]
ch_types = ['eeg'] * 8 + ['stim'] * 2
montage = read_montage('standard_1005')
info = create_info(ch_names=ch_names,
ch_types=ch_types,
sfreq=sfreq,
montage=montage)
for run in [data.train, data.test]:
# flash events on the channel 9
flashs = run[9:10]
ix_flash = flashs[0] > 0
flashs[0, ix_flash] += 2 # add 2 to avoid overlapp on event id
flash_code = np.unique(flashs[0, ix_flash])
if len(flash_code) == 36:
# char mode
evd = {'Char%d' % ii: (ii + 2) for ii in range(1, 37)}
else:
# row / column mode
evd = {'Col%d' % ii: (ii + 2) for ii in range(1, 7)}
evd.update({'Row%d' % ii: (ii + 8) for ii in range(1, 7)})
# target events are on channel 10
targets = np.zeros_like(flashs)
targets[0, ix_flash] = run[10, ix_flash] + 1
eeg_data = np.r_[run[1:-2] * 1e-6, targets, flashs]
raw = RawArray(data=eeg_data, info=info, verbose=verbose)
raws.append(raw)
event_id.update(evd)
return raws, event_id
def validate_ch_names(list_of_ch_names, kind='standard_1005'):
montage = read_montage(kind)
upper_list_of_ch_names = [ch.upper() for ch in list_of_ch_names]
upper_montage_ch_names = [ch.upper() for ch in montage.ch_names]
if DEBUG or seems_to_come_from_neuromag(list_of_ch_names):
bool_indices = [True for ch in upper_list_of_ch_names]
else:
bool_indices = [ch in upper_montage_ch_names for ch in upper_list_of_ch_names]
return bool_indices
def view_montage(self):
montage = read_montage(self.montages.selectedItems()[0].data(0))
fig = montage.plot(show_names=True, show=False)
win = fig.canvas.manager.window
win.setWindowModality(Qt.WindowModal)
win.setWindowTitle("Montage")
win.findChild(QStatusBar).hide()
win.findChild(QToolBar).hide()
fig.show()
def test_standard_superset():
"""Test some properties that should hold for superset montages."""
with pytest.deprecated_call():
o_1005 = read_montage('standard_1005') # old montages
o_1020 = read_montage('standard_1020')
# new montages, tweaked to end up at the same size as the others
m_1005 = make_standard_montage('standard_1005', 0.0970)
m_1020 = make_standard_montage('standard_1020', 0.0991)
assert len(set(m_1005.ch_names) - set(m_1020.ch_names)) > 0
# XXX weird that this is not a proper superset...
assert set(m_1020.ch_names) - set(m_1005.ch_names) == {'O10', 'O9'}
c_1005 = m_1005._get_ch_pos()
for key, value in m_1020._get_ch_pos().items():
want = o_1020.pos[o_1020.ch_names.index(key)]
assert_allclose(value, want, err_msg=key, atol=1e-4)
if key not in ('O10', 'O9'):
assert_allclose(o_1005.pos[o_1005.ch_names.index(key)], want,
err_msg=key, atol=1e-4)
assert_allclose(c_1005[key], value, atol=1e-4, err_msg=key)
def bci_to_raw(self, data):
eeg_data = data[self.eeg_info[0], :]
ch_types = ['eeg'] * 16
montage = read_montage('standard_1020')
info = create_info(ch_names=self.eeg_info[2],
sfreq=self.eeg_info[1],
ch_types=ch_types,
montage=montage)
raw = RawArray(eeg_data, info)
return raw
def test_plot_defect_montage():
"""Test plotting defect montages (i.e. with duplicate labels)."""
# montage name and number of unique labels
montages = [('standard_1005', 342), ('standard_postfixed', 85),
('standard_primed', 85), ('standard_1020', 93)]
for name, n in montages:
m = read_montage(name)
fig = m.plot()
collection = fig.axes[0].collections[0]
assert collection._edgecolors.shape[0] == n
assert collection._facecolors.shape[0] == n
assert collection._offsets.shape[0] == n
def test_plot_defect_montage():
"""Test plotting defect montages (i.e. with duplicate labels)."""
# montage name and number of unique labels
montages = [('standard_1005', 342), ('standard_postfixed', 85),
('standard_primed', 85), ('standard_1020', 93)]
for name, n in montages:
m = read_montage(name)
fig = m.plot()
collection = fig.axes[0].collections[0]
assert collection._edgecolors.shape[0] == n
assert collection._facecolors.shape[0] == n
assert collection._offsets.shape[0] == n
def creat_mne_raw_object(fname, idx_subject, read_events='HO'):
"""Create a mne raw instance from csv file."""
# Read EEG file
# data = pd.read_csv(fname)
data = np.loadtxt(fname, delimiter=',')
data = data.T[2:, :]
# get chanel names
# ch_names = list(data.columns[1:])
ch_names = CH_NAMES
# read EEG standard montage from mne
montage = read_montage('standard_1005', ch_names)
ch_type = ['eeg'] * len(ch_names)
data = 1e-6 * np.array(data[:])
if read_events:
# events file
ev_fname = fname.replace('_data', '_events')
# read event file
events = pd.read_csv(ev_fname)
events_names = ['Nothing', 'Positive', 'Negative']
# events_data = np.array(events[events_names]).T
events_data = get_horizo_velocity() if read_events == 'HO' else \
get_vertic_velocity() if read_events == 'VE' else None
events_data = events_data.T[idx_subject, :]
events = np.zeros([3, events_data.shape[0]])
events[0, events_data == 0] = 1
events[1, events_data > 0] = 1
events[2, events_data < 0] = 1
# define channel type, the first is EEG, the last 6 are stimulations
ch_type.extend(['stim'] * 3)
# ch_names.extend(events_names)
ch_names = ch_names + events_names
# concatenate event file and data
data = np.concatenate((data, events))
# create and populate MNE info structure
info = create_info(ch_names,
sfreq=128.0,
ch_types=ch_type,
montage=montage)
info['experimento'] = fname
# create raw object
raw = RawArray(data, info, verbose=False)
return raw
def ch_names_to_2d_pos(list_of_ch_names, kind='standard_1005', azimuthal=True):
montage = read_montage(kind)
if DEBUG or seems_to_come_from_neuromag(list_of_ch_names):
return random.normal(size=(len(list_of_ch_names), 2))
upper_list_of_ch_names = [ch.upper() for ch in list_of_ch_names]
upper_montage_ch_names = [ch.upper() for ch in montage.ch_names]
indices = [upper_montage_ch_names.index(ch) if ch in upper_montage_ch_names else 0 for ch in upper_list_of_ch_names]
if len(list(indices)) < len(list_of_ch_names):
raise IndexError('Channels {} not found'.format(
set(upper_list_of_ch_names).difference(set(array(upper_montage_ch_names)[indices]))
))
pos = montage.pos[indices, :2] if not azimuthal else azimuthal_equidistant_projection(montage.pos[indices, :3])
return array(pos)
def ch_names_to_2d_pos(list_of_ch_names, kind='standard_1005', azimuthal=True):
montage = read_montage(kind)
if DEBUG or seems_to_come_from_neuromag(list_of_ch_names):
return random.normal(size=(len(list_of_ch_names), 2))
upper_list_of_ch_names = [ch.upper() for ch in list_of_ch_names]
upper_montage_ch_names = [ch.upper() for ch in montage.ch_names]
indices = [upper_montage_ch_names.index(ch) if ch in upper_montage_ch_names else 0 for ch in upper_list_of_ch_names]
if len(list(indices)) < len(list_of_ch_names):
raise IndexError('Channels {} not found'.format(
set(upper_list_of_ch_names).difference(set(array(upper_montage_ch_names)[indices]))
))
pos = montage.pos[indices, :2] if not azimuthal else azimuthal_equidistant_projection(montage.pos[indices, :3])
return array(pos)
def load_csv_as_raw(filename, sfreq, ch_ind, stim_ind, replace_ch_names):
"""Load CSV files into a Raw object.
Args:
filename (str or list): path or paths to CSV files to load
Keyword Args:
sfreq (float): EEG sampling frequency
ch_ind (list): indices of the EEG channels to keep
stim_ind (int): index of the stim channel
replace_ch_names (dict or None): dictionary containing a mapping to
rename channels.
Returns:
(mne.io.array.array.RawArray): loaded EEG
"""
n_channel = len(ch_ind)
raw = []
print(filename)
for fname in filename:
# read the file
data = pd.read_csv(fname, index_col=0)
# name of each channels
ch_names = list(data.columns)[0:n_channel] + ['Stim']
if replace_ch_names is not None:
ch_names = [
c if c not in replace_ch_names.keys() else replace_ch_names[c]
for c in ch_names
]
# type of each channels
ch_types = ['eeg'] * n_channel + ['stim']
montage = read_montage('standard_1005')
# get data and exclude Aux channel
data = data.values[:, ch_ind + [stim_ind]].T
# create MNE object
info = create_info(ch_names=ch_names,
ch_types=ch_types,
sfreq=sfreq,
montage=montage)
raw.append(RawArray(data=data, info=info))
# concatenate all raw objects
raws = concatenate_raws(raw)
return raws
def test_gen_raw_ch():
"""Test that _generate_raw responds to channel settings."""
raw = _generate_raw(duration=1, n_chan=1)
assert_sequence_equal(raw.ch_names, ['0', 'STI 014'])
raw = _generate_raw(duration=1, n_chan=1, ch_names=['bob'])
assert_sequence_equal(raw.ch_names, ['bob', 'STI 014'])
raw = _generate_raw(duration=1, n_chan=1, ch_names='standard_1020')
montage = read_montage('standard_1020')
raw = raw.pick_types(eeg=True)
assert_true(np.all([ch in montage.ch_names for ch in raw.ch_names]))
def view_montage(self):
if self.montage_path == '':
kind = self.montages.selectedItems()[0].data(0)
montage = read_montage(kind)
else:
from ..utils.montage import xyz_to_montage
montage = xyz_to_montage(self.montage_path)
fig = montage.plot(show_names=True, show=False)
win = fig.canvas.manager.window
win.setWindowModality(Qt.WindowModal)
win.setWindowTitle("Montage")
win.findChild(QStatusBar).hide()
win.findChild(QToolBar).hide()
fig.show()
def add_montage(mne_raw, channels='data/misc/channel-names.txt'):
'''
Creates 'standard_1005' montage with corrected channel names and
adds it to MNE raw object.
Arguments:
mne_raw: MNE Raw object
Returns:
MNE Raw object (modified in place)
'''
ch_names = open(channels).read().splitlines()
montage = read_montage('standard_1005', ch_names=ch_names)
mne_raw.set_montage(montage)
def test_set_montage():
"""Test setting a montage."""
raw = read_raw_fif(fif_fname)
orig_pos = np.array([ch['loc'][:3] for ch in raw.info['chs']
if ch['ch_name'].startswith('EEG')])
raw.set_montage('mgh60') # test loading with string argument
new_pos = np.array([ch['loc'][:3] for ch in raw.info['chs']
if ch['ch_name'].startswith('EEG')])
assert ((orig_pos != new_pos).all())
r0 = _fit_sphere(new_pos)[1]
assert_allclose(r0, [0., -0.016, 0.], atol=1e-3)
# mgh70 has no 61/62/63/64 (these are EOG/ECG)
mon = read_montage('mgh70')
assert 'EEG061' not in mon.ch_names
assert 'EEG074' in mon.ch_names
def toMNE(X, y=None):
"""Tranform array into MNE for epoching."""
ch_names = getChannelNames()
montage = read_montage('standard_1005', ch_names)
ch_type = ['eeg']*len(ch_names)
data = X.T
if y is not None:
y = y.transpose()
ch_type.extend(['stim']*6)
event_names = getEventNames()
ch_names.extend(event_names)
# concatenate event file and data
data = np.concatenate((data, y))
info = create_info(ch_names, sfreq=500.0, ch_types=ch_type,
montage=montage)
raw = RawArray(data, info, verbose=False)
return raw
def test_plot_montage():
"""Test plotting montages."""
m = read_montage('easycap-M1')
m.plot()
plt.close('all')
m.plot(kind='3d')
plt.close('all')
m.plot(kind='3d', show_names=True)
plt.close('all')
m.plot(kind='topomap')
plt.close('all')
m.plot(kind='topomap', show_names=True)
plt.close('all')
d = read_dig_montage(hsp, hpi, elp, point_names)
assert '0 channels' in repr(d)
with pytest.raises(RuntimeError, match='No valid channel positions'):
d.plot()
d = read_dig_montage(fif=fif_fname)
assert '61 channels' in repr(d)
def convert_to_raw(file_series, file_events):
"""Create a mne raw instance from csv file"""
data = pd.read_csv(file_series)
channels = list(data.columns[1:])
m1 = read_montage('standard_1005',channels)
ch_type = ['eeg']*len(channels)
data = 1e-6*np.array(data[channels]).T
# read event file
events_data = pd.read_csv(file_events)
events_names = events_data.columns[1:]
events_data = np.array(events_data[events_names]).T
#print events_data
# define channel type, the first is EEG, the last 6 are stimulations
ch_type.extend(['stim']*6)
channels.extend(events_names)
# concatenate event file and data
data = np.concatenate((data,events_data))
info = create_info(channels, sfreq=500.0, ch_types=ch_type, montage=m1)
info['filename'] = file_series
raw = RawArray(data,info,verbose=False)
print raw
print raw[0:]
print raw[0][0]
print raw[0][1]
return raw
def test_plot_montage():
"""Test plotting montages."""
import matplotlib.pyplot as plt
m = read_montage('easycap-M1')
m.plot()
plt.close('all')
m.plot(kind='3d')
plt.close('all')
m.plot(kind='3d', show_names=True)
plt.close('all')
m.plot(kind='topomap')
plt.close('all')
m.plot(kind='topomap', show_names=True)
plt.close('all')
d = read_dig_montage(hsp, hpi, elp, point_names)
d.plot()
plt.close('all')
d.plot(kind='3d')
plt.close('all')
d.plot(kind='3d', show_names=True)
plt.close('all')
def create_mne_raw_object(fname, read_events=True):
"""Create a mne raw instance from csv file."""
# Read EEG file
data = pd.read_csv(fname)
print fname, data.shape
# get chanel names
ch_names = list(data.columns[1:])
print ch_names
# read EEG standard montage from mne
montage = read_montage("standard_1005", ch_names)
ch_type = ["eeg"] * len(ch_names)
data = 1e-6 * np.array(data[ch_names]).T
if read_events:
# events file
ev_fname = fname.replace("_data", "_events")
# read event file
events = pd.read_csv(ev_fname)
events_names = events.columns[1:]
events_data = np.array(events[events_names]).T
# define channel type, the first is EEG, the last 6 are stimulations
ch_type.extend(["stim"] * 6)
ch_names.extend(events_names)
# concatenate event file and data
data = np.concatenate((data, events_data))
# create and populate MNE info structure
info = create_info(ch_names, sfreq=500.0, ch_types=ch_type, montage=montage)
info["filename"] = fname
# create raw object
raw = RawArray(data, info, verbose=False)
return raw
def test_plot_montage():
"""Test plotting montages
"""
read_montage('easycap-M1').plot()
def importbdf(bdfname, nchans=34, refchans=['EXG1', 'EXG2'],
hptsname=None, mask=255, extrachans=[],
exclude=None, verbose=None):
"""Wrapper around mne-python to import BDF files
Parameters
----------
bdfname - Name of the biosemi .bdf filename with full path
nchans - Number of EEG channels (including references)
(Optional) By default, 34 (32 + 2 references)
refchans - list of strings with reference channel names
(Optional) By default ['EXG1','EXG2'].
Use None for average reference.
hptsname - Name of the electrode position file in .hpts format with path
(Optional) By default a 32 channel Biosemi layout is used. If
the nchans is >= 64 and < 96, a 64 channel Biosemi layout is
used. If nchans >= 96, a 96 channel biosemi layout is used.
Formats other than .hpts will also likely work, but behavior
may vary.
mask - Integer mask to use for trigger channel (Default is 255).
extrachans - Additional channels other than EEG and EXG that may be in the
bdf file. These will be marked as MISC in mne-python.
Specify as list of names.
excllude - List of channel names to exclude from importing
verbose - bool, str, int, or None (Optional)
The verbosity of messages to print. If a str, it can be either DEBUG,
INFO, WARNING, ERROR, or CRITICAL.
Returns
-------
raw - MNE raw data object of rereferences and preloaded data
eves - Event list (3 column array as required by mne.Epochs)
Requires
--------
mne-python module > release 0.7
"""
# Default HPTS file
if(hptsname is None):
anlffr_root = os.path.dirname(sys.modules['anlffr'].__file__)
if nchans >= 64 and nchans < 96:
logger.info('Number of channels is greater than 64.'
' Hence loading a 64 channel montage.')
hptspath = os.path.join(anlffr_root, 'helper/sysfiles/')
hptsname = 'biosemi64'
montage = read_montage(kind=hptsname, path=hptspath,
transform=True)
misc = ['EXG3', 'EXG4', 'EXG5', 'EXG6', 'EXG7', 'EXG8']
else:
if nchans >= 96:
logger.info('Number of channels is greater than 96.'
' Hence loading a 96 channel montage.')
hptspath = os.path.join(anlffr_root, 'helper/sysfiles/')
hptsname = 'biosemi96'
montage = read_montage(kind=hptsname, path=hptspath,
transform=True)
misc = ['EXG3', 'EXG4', 'EXG5', 'EXG6', 'EXG7', 'EXG8']
else:
if nchans == 2:
logger.info('Number of channels is 2.'
'Guessing ABR montage.')
montage = None
misc = []
else:
logger.info('Loading a default 32 channel montage.')
hptspath = os.path.join(anlffr_root, 'helper/sysfiles/')
hptsname = 'biosemi32'
montage = read_montage(kind=hptsname, path=hptspath,
transform=True)
misc = ['EXG3', 'EXG4', 'EXG5', 'EXG6', 'EXG7', 'EXG8']
misc += extrachans
raw = edf.read_raw_edf(bdfname, montage=montage, preload=True,
misc=misc, exclude=exclude, stim_channel='Status')
# Rereference
if refchans is not None:
sys.stdout.write('Re-referencing data to: ' + ' '.join(refchans))
(raw, ref_data) = set_eeg_reference(raw, refchans, copy=False)
raw.info['bads'] += refchans
else:
# Add average reference operator for possible use later
ave_ref_operator = make_eeg_average_ref_proj(raw.info, activate=False)
raw = raw.add_proj(ave_ref_operator)
eves = find_events(raw, shortest_event=1, mask=mask)
return (raw, eves)
def test_montage():
"""Test making montages"""
tempdir = _TempDir()
# no pep8
input_str = ["""FidNz 0.00000 10.56381 -2.05108
FidT9 -7.82694 0.45386 -3.76056
FidT10 7.82694 0.45386 -3.76056""",
"""// MatLab Sphere coordinates [degrees] Cartesian coordinates
// Label Theta Phi Radius X Y Z off sphere surface
E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011
E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000
E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000""", # noqa
"""# ASA electrode file
ReferenceLabel avg
UnitPosition mm
NumberPositions= 68
Positions
-86.0761 -19.9897 -47.9860
85.7939 -20.0093 -48.0310
0.0083 86.8110 -39.9830
Labels
LPA
RPA
Nz
""",
"""Site Theta Phi
Fp1 -92 -72
Fp2 92 72
F3 -60 -51
""",
"""346
EEG F3 -62.027 -50.053 85
EEG Fz 45.608 90 85
EEG F4 62.01 50.103 85
""",
"""
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
"""]
kinds = ['test.sfp', 'test.csd', 'test.elc', 'test.txt', 'test.elp',
'test.hpts']
for kind, text in zip(kinds, input_str):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
assert_equal(len(montage.ch_names), 3)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (3, 3))
assert_equal(montage.kind, op.splitext(kind)[0])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2, montage.pos, 4)
# test transform
input_str = """
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal nasion -91 0 -42
cardinal lpa 0 -91 -42
cardinal rpa 0 91 -42
"""
kind = 'test_fid.hpts'
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index('nasion')
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index('lpa')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index('rpa')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
apply_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
pos3 = np.array([c['eeg_loc'][:, 0] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])