def test_average_to_channel_groups():
sample_folder = mne.datasets.sample.data_path()
sample_fname = os.path.join(sample_folder, 'MEG', 'sample',
'sample_audvis_raw.fif')
raw = mne.io.read_raw_fif(sample_fname, preload=True)
info = raw.info
data = raw._data
ch_names = info['ch_names'][:20]
meg_channel_groups = get_default_channel_groups(info, 'meg')
eeg_channel_groups = get_default_channel_groups(info, 'eeg')
# find out to which channel group each of the channels belongs to
results = []
for ch_name in ch_names:
for ch_group_name, ch_group in meg_channel_groups.items():
if ch_name in ch_group:
results.append((ch_name, ch_group_name))
labels, averaged_data = average_to_channel_groups(
raw._data[:, 0:100], info, ch_names, {
'meg': meg_channel_groups,
'eeg': eeg_channel_groups
})
# check that the localization of data is same before and after averaging
assert (set([result[1] for result in results
]) == set([label[1] for label in labels]))
def _create_averages(mne_evoked, channel_groups):
mne_evoked = mne_evoked.copy().drop_channels(mne_evoked.info['bads'])
data_labels, averaged_data = average_to_channel_groups(
mne_evoked.data, mne_evoked.info, mne_evoked.info['ch_names'],
channel_groups)
return data_labels, averaged_data
def save_tfr_channel_averages(experiment, tfr_name, blmode, blstart, blend,
tmin, tmax, fmin, fmax):
"""
"""
column_names = []
row_descs = []
csv_data = []
channel_groups = experiment.channel_groups
# accumulate csv contents
for subject in experiment.subjects.values():
tfr = subject.tfr.get(tfr_name)
if not tfr:
continue
ch_names = tfr.ch_names
info = tfr.info
for key, mne_tfr in tfr.content.items():
# crop and correct to baseline
mne_tfr = mne_tfr.copy().crop(tmin=tmin,
tmax=tmax,
fmin=fmin,
fmax=fmax)
times = mne_tfr.times
column_names = format_floats(times)
freqs = format_floats(mne_tfr.freqs)
data = mne.baseline.rescale(mne_tfr.data,
times,
baseline=(blstart, blend),
mode=blmode)
data_labels, averaged_data = average_to_channel_groups(
data, info, ch_names, channel_groups)
if not data_labels:
raise Exception('No channel groups matching the data found')
for ix in range(averaged_data.shape[0]):
for iy in range(averaged_data.shape[1]):
ch_type, area = data_labels[ix]
csv_data.append(averaged_data[ix, iy].tolist())
row_desc = (subject.name, key, ch_type, area, freqs[iy])
row_descs.append(row_desc)
folder = filemanager.create_timestamped_folder(experiment)
fname = tfr_name + '_all_subjects_channel_averages_tfr.csv'
path = os.path.join(folder, fname)
filemanager.save_csv(path, csv_data, column_names, row_descs)
logging.getLogger('ui_logger').info('Saved the csv file to ' + path)
def plot_tfr_averages(experiment, subject, tfr_name, tfr_condition, blmode,
blstart, blend, tmin, tmax, fmin, fmax):
meggie_tfr = subject.tfr[tfr_name]
if blmode:
bline = (blstart, blend)
mode = blmode
else:
bline = None
mode = None
tfr = meggie_tfr.content.get(tfr_condition)
logging.getLogger('ui_logger').info("Plotting TFR channel averages...")
data = tfr.data
ch_names = meggie_tfr.ch_names
channel_groups = experiment.channel_groups
data_labels, averaged_data = average_to_channel_groups(
data, meggie_tfr.info, ch_names, channel_groups)
if not data_labels:
raise Exception('No channel groups matching the data found')
sfreq = meggie_tfr.info['sfreq']
times = meggie_tfr.times
freqs = meggie_tfr.freqs
for idx in range(len(data_labels)):
data = averaged_data[idx]
labels = data_labels[idx]
info = mne.create_info(ch_names=['grand_average'],
sfreq=sfreq,
ch_types='mag')
tfr = mne.time_frequency.tfr.AverageTFR(info, data[np.newaxis, :],
times, freqs, 1)
title = 'TFR_{0}_{1}'.format(labels[1], labels[0])
# prevent interaction as no topography is involved now
def onselect(*args, **kwargs):
pass
tfr._onselect = onselect
fig = tfr.plot(baseline=bline,
mode=mode,
title=title,
fmin=fmin,
fmax=fmax,
tmin=tmin,
tmax=tmax)
fig.canvas.set_window_title(title)
def plot_spectrum_averages(experiment, name, log_transformed=True):
"""
"""
subject = experiment.active_subject
subject_name = subject.name
spectrum = subject.spectrum.get(name)
data = spectrum.content
freqs = spectrum.freqs
ch_names = spectrum.ch_names
channel_groups = experiment.channel_groups
info = subject.get_raw().info
colors = color_cycle(len(data))
logging.getLogger('ui_logger').info('Plotting spectrum channel averages..')
averages = {}
for idx, (key, psd) in enumerate(data.items()):
data_labels, averaged_data = average_to_channel_groups(
psd, info, ch_names, channel_groups)
if not data_labels:
raise Exception('No channel groups matching the data found.')
averages[key] = data_labels, averaged_data
shape = averaged_data.shape
for ii in range(shape[0]):
fig, ax = plt.subplots()
for color_idx, key in enumerate(averages.keys()):
ax.set_xlabel('Frequency (Hz)')
ax.set_ylabel('Power ({})'.format(
get_power_unit(averages[key][0][ii][0], log_transformed)))
if log_transformed:
curve = 10 * np.log10(averages[key][1][ii])
else:
curve = averages[key][1][ii]
ax.plot(freqs, curve, color=colors[color_idx], label=key)
ax.legend()
ch_type, ch_group = averages[key][0][ii]
title = 'spectrum_{0}_{1}_{2}'.format(name, ch_type, ch_group)
fig.canvas.set_window_title(title)
fig.suptitle(title)
plt.show()
def plot_spectrum_averages(subject,
channel_groups,
name,
log_transformed=True):
""" Plots spectrum averages.
"""
subject_name = subject.name
spectrum = subject.spectrum.get(name)
data = spectrum.content
freqs = spectrum.freqs
ch_names = spectrum.ch_names
info = spectrum.info
colors = color_cycle(len(data))
conditions = spectrum.content.keys()
averages = {}
for key, psd in sorted(data.items()):
data_labels, averaged_data = average_to_channel_groups(
psd, info, ch_names, channel_groups)
for label_idx, label in enumerate(data_labels):
if not label in averages:
averages[label] = []
averages[label].append((key, averaged_data[label_idx]))
ch_types = sorted(set([label[0] for label in averages.keys()]))
for ch_type in ch_types:
ch_groups = sorted(
[label[1] for label in averages.keys() if label[0] == ch_type])
def plot_fun(ax_idx, ax):
ch_group = ch_groups[ax_idx]
ax.set_title(ch_group)
ax.set_xlabel('Frequency (Hz)')
ax.set_ylabel('Power ({})'.format(
get_power_unit(ch_type, log_transformed)))
for color_idx, (key, curve) in enumerate(averages[(ch_type,
ch_group)]):
if log_transformed:
curve = 10 * np.log10(curve)
ax.plot(freqs, curve, color=colors[color_idx])
title = ' '.join([name, ch_type])
legend = list(zip(conditions, colors))
create_channel_average_plot(len(ch_groups), plot_fun, title, legend)
plt.show()
def create_averages(experiment, mne_evoked):
"""
"""
channel_groups = experiment.channel_groups
mne_evoked = mne_evoked.copy().drop_channels(mne_evoked.info['bads'])
data_labels, averaged_data = average_to_channel_groups(
mne_evoked.data, mne_evoked.info, mne_evoked.info['ch_names'],
channel_groups)
return data_labels, averaged_data
def plot_tse_averages(subject, tfr_name, blmode, blstart, blend, tmin, tmax,
fmin, fmax, channel_groups):
""" Plots tse averages.
"""
meggie_tfr = subject.tfr.get(tfr_name)
tses = _compute_tse(meggie_tfr, fmin, fmax)
ch_names = meggie_tfr.ch_names
info = meggie_tfr.info
colors = color_cycle(len(tses))
conditions = meggie_tfr.content.keys()
averages = {}
for key, tse in sorted(tses.items()):
data_labels, averaged_data = average_to_channel_groups(
tse, info, ch_names, channel_groups)
times, averaged_data = _crop_and_correct_to_baseline(
averaged_data, blmode, blstart, blend, tmin, tmax,
meggie_tfr.times)
for label_idx, label in enumerate(data_labels):
if not label in averages:
averages[label] = []
averages[label].append((key, times, averaged_data[label_idx]))
ch_types = sorted(set([label[0] for label in averages.keys()]))
for ch_type in ch_types:
ch_groups = sorted(
[label[1] for label in averages.keys() if label[0] == ch_type])
def plot_fun(ax_idx, ax):
ch_group = ch_groups[ax_idx]
ax.set_title(ch_group)
ax.set_xlabel('Time (s)')
ax.set_ylabel('Power ({})'.format(get_power_unit(ch_type, False)))
for color_idx, (key, times,
curve) in enumerate(averages[(ch_type, ch_group)]):
ax.plot(times, curve, color=colors[color_idx], label=key)
ax.axhline(0, color='black')
ax.axvline(0, color='black')
title = ' '.join([tfr_name, ch_type])
legend = list(zip(conditions, colors))
create_channel_average_plot(len(ch_groups), plot_fun, title, legend)
plt.show()
def plot_tse_averages(experiment, subject, tfr_name, blmode, blstart, blend,
tmin, tmax, fmin, fmax):
"""
"""
meggie_tfr = subject.tfr.get(tfr_name)
times, tses = _compute_tse(meggie_tfr, fmin, fmax, tmin, tmax, blmode,
blstart, blend)
ch_names = meggie_tfr.ch_names
info = meggie_tfr.info
colors = color_cycle(len(tses))
channel_groups = experiment.channel_groups
logging.getLogger('ui_logger').info('Plotting TSE channel averages..')
averages = {}
for idx, (key, tse) in enumerate(tses.items()):
data_labels, averaged_data = average_to_channel_groups(
tse, info, ch_names, channel_groups)
if not data_labels:
raise Exception('No channel groups matching the data found.')
averages[key] = data_labels, averaged_data
shape = averaged_data.shape
for ii in range(shape[0]):
fig, ax = plt.subplots()
for color_idx, key in enumerate(averages.keys()):
ax.set_xlabel('Time (s)')
ax.set_ylabel('Power ({})'.format(
get_power_unit(averages[key][0][ii][0], False)))
ax.plot(times,
averages[key][1][ii],
color=colors[color_idx],
label=key)
ax.axhline(0)
ax.legend()
ch_type, ch_group = averages[key][0][ii]
title = 'TSE_{0}_{1}_{2}'.format(tfr_name, ch_type, ch_group)
fig.canvas.set_window_title(title)
fig.suptitle(title)
plt.show()
def save_channel_averages(experiment, selected_name, log_transformed=False):
column_names = []
row_descs = []
csv_data = []
channel_groups = experiment.channel_groups
# accumulate csv contents
for subject in experiment.subjects.values():
spectrum = subject.spectrum.get(selected_name)
if not spectrum:
continue
ch_names = spectrum.ch_names
freqs = spectrum.freqs
info = subject.get_raw().info
for key, psd in spectrum.content.items():
data_labels, averaged_data = average_to_channel_groups(
psd, info, ch_names, channel_groups)
if not data_labels:
raise Exception('No channel groups matching the data found.')
if log_transformed:
csv_data.extend(10 * np.log10(averaged_data.tolist()))
else:
csv_data.extend(averaged_data.tolist())
column_names = format_floats(freqs)
for ch_type, area in data_labels:
row_desc = (subject.name, key, ch_type, area)
row_descs.append(row_desc)
folder = filemanager.create_timestamped_folder(experiment)
fname = selected_name + '_all_subjects_channel_averages_spectrum.csv'
path = os.path.join(folder, fname)
filemanager.save_csv(path, csv_data, column_names, row_descs)
logging.getLogger('ui_logger').info('Saved the csv file to ' + path)
def save_tse_channel_averages(experiment, tfr_name, blmode, blstart, blend,
tmin, tmax, fmin, fmax):
"""
"""
column_names = []
row_descs = []
csv_data = []
channel_groups = experiment.channel_groups
# accumulate csv contents
for subject in experiment.subjects.values():
tfr = subject.tfr.get(tfr_name)
if not tfr:
continue
times, tses = _compute_tse(tfr, fmin, fmax, tmin, tmax, blmode,
blstart, blend)
column_names = format_floats(times)
for key, tse in tses.items():
data_labels, averaged_data = average_to_channel_groups(
tse, tfr.info, tfr.ch_names, channel_groups)
if not data_labels:
raise Exception('No channel groups matching the data found.')
csv_data.extend(averaged_data.tolist())
for ch_type, area in data_labels:
row_desc = (subject.name, key, ch_type, area)
row_descs.append(row_desc)
folder = filemanager.create_timestamped_folder(experiment)
fname = tfr_name + '_all_subjects_channel_averages_tfr.csv'
path = os.path.join(folder, fname)
filemanager.save_csv(path, csv_data, column_names, row_descs)
logging.getLogger('ui_logger').info('Saved the csv file to ' + path)
def plot_tfr_averages(subject, tfr_name, tfr_condition, blmode, blstart, blend,
tmin, tmax, fmin, fmax, channel_groups):
""" Plots tfr averages.
"""
meggie_tfr = subject.tfr[tfr_name]
if blmode:
bline = (blstart, blend)
mode = blmode
else:
bline = None
mode = None
tfr = meggie_tfr.content.get(tfr_condition)
data = tfr.data
ch_names = meggie_tfr.ch_names
sfreq = meggie_tfr.info['sfreq']
times = meggie_tfr.times
freqs = meggie_tfr.freqs
# compared to spectrums, evoked and tse, tfr is plotted with only one condition.
# it makes the plotting a bit simpler. we will also misuse
# AverageTFR object to do the heavy work.
data_labels, averaged_data = average_to_channel_groups(
data, meggie_tfr.info, ch_names, channel_groups)
averages = {}
for label_idx, label in enumerate(data_labels):
averages[label] = averaged_data[label_idx]
ch_types = sorted(set([label[0] for label in data_labels]))
for ch_type in ch_types:
ch_groups = sorted(
[label[1] for label in data_labels if label[0] == ch_type])
def plot_fun(ax_idx, ax):
ch_group = ch_groups[ax_idx]
ax.set_title(ch_group)
info = mne.create_info(ch_names=['grand_average'],
sfreq=sfreq,
ch_types='mag')
tfr = mne.time_frequency.tfr.AverageTFR(
info, averages[(ch_type, ch_group)][np.newaxis, :], times,
freqs, 1)
# prevent interaction as no topography is involved now
def onselect(*args, **kwargs):
pass
tfr._onselect = onselect
tfr.plot(baseline=bline,
mode=mode,
title='',
fmin=fmin,
fmax=fmax,
tmin=tmin,
tmax=tmax,
axes=ax)
title = ' '.join([tfr_name, tfr_condition, ch_type])
create_channel_average_plot(len(ch_groups), plot_fun, title)