def events_save_events(self,evt=None,condition=None,postfix="evt",
picks=None,reject=None,proj=False,
save_condition={"events":True,"epochs":True,"evoked":True}):
from jumeg.jumeg_4raw_data_plot import jumeg_4raw_data_plot as jplt
jplt.verbose = self.verbose
ep,bc = self.events_apply_epochs_and_baseline(self.raw,evt=evt,reject=reject,proj=proj,picks=picks)
postfix += '_' + condition
if bc:
postfix += '_bc'
#--- save events to txt file
if save_condition["events"]:
fname = jumeg_base.get_fif_name(raw=self.raw,postfix=postfix,extention=".eve",update_raw_fname=False)
mne.event.write_events( fname,evt['events'] )
print" ---> done jumeg epocher save events as => EVENTS :" +fname
#--- save epoch data
if save_condition["epochs"]:
fname = jumeg_base.get_fif_name(raw=self.raw,postfix=postfix,extention="-epo.fif",update_raw_fname=False)
ep.save( fname )
print" ---> done jumeg epocher save events as => EPOCHS :" +fname
#--- save averaged data
if save_condition["evoked"]:
fname = jumeg_base.get_fif_name(raw=self.raw,postfix=postfix,extention="-ave.fif",update_raw_fname=False)
mne.write_evokeds( fname,ep.average() )
print" ---> done jumeg epocher save events as => EVOKED (averaged) :" +fname
fname = jumeg_base.get_fif_name(raw=self.raw,postfix=postfix,extention="-ave",update_raw_fname=False)
#--- plot evoked
fname = jplt.plot_evoked(ep,fname=fname,condition=condition,show_plot=False,save_plot=True,plot_dir='plots')
print" ---> done jumeg epocher plot evoked (averaged) :" +fname
def test_evoked_standard_error():
"""Test calculation and read/write of standard error
"""
raw, events, picks = _get_data()
tempdir = _TempDir()
epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
baseline=(None, 0))
evoked = [epochs.average(), epochs.standard_error()]
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), evoked)
evoked2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), [0, 1])
evoked3 = [read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 'Unknown'),
read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 'Unknown',
kind='standard_error')]
for evoked_new in [evoked2, evoked3]:
assert_true(evoked_new[0]._aspect_kind ==
FIFF.FIFFV_ASPECT_AVERAGE)
assert_true(evoked_new[0].kind == 'average')
assert_true(evoked_new[1]._aspect_kind ==
FIFF.FIFFV_ASPECT_STD_ERR)
assert_true(evoked_new[1].kind == 'standard_error')
for ave, ave2 in zip(evoked, evoked_new):
assert_array_almost_equal(ave.data, ave2.data)
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
def analyze_rest(subject, args, hcp_params, run_index=0, calc_rest_from_raw=False, calc_rest_from_epochs=True):
flags = {}
if not op.isfile(meg.RAW):
raw = read_raw_data(run_index, hcp_params, 1, 60)
raw.save(meg.RAW)
else:
raw = mne.io.read_raw_fif(meg.RAW)
meg.COR = op.join(op.join(HCP_DIR, 'hcp-meg', subject, '{}-head_mri-trans.fif'.format(subject)))
epo_fname = meg.EPO.format(cond='all')
evo_fname = meg.EVO.format(cond='all')
if not op.isfile(epo_fname) or not op.isfile(evo_fname):
epochs = hcp.read_epochs(run_index=run_index, **hcp_params)
evoked = epochs.average()
epochs.save(epo_fname)
mne.write_evokeds(evo_fname, evoked)
else:
epochs = mne.read_epochs(epo_fname)
meg.calc_fwd_inv_wrapper(subject, args)
args.snr = 1.0 # use smaller SNR for raw data
# args.overwrite_labels_data = True
# args.n_jobs = 1
if calc_rest_from_raw:
meg.calc_labels_avg_for_rest_wrapper(args, raw)
elif calc_rest_from_epochs:
args.single_trial_stc = True
flags, stcs_conds, stcs_num = meg.calc_stc_per_condition_wrapper(
subject, None, args.inverse_method, args, flags, None, epochs)
flags = meg.calc_labels_avg_per_condition_wrapper(
subject, None, args.atlas, args.inverse_method, stcs_conds, args, flags, stcs_num, raw, epochs)
print('sdf')
def split_baseline(fif_fnames, clips_length=6, shift=6, overwrite=False):
output_fol = op.join(utils.get_parent_fol(fif_fnames[0]), 'new_baselines')
if not overwrite and op.isdir(output_fol) and len(
glob.glob(op.join(output_fol, '*.fif'))) > 0:
return glob.glob(op.join(output_fol, '*.fif'))
utils.make_dir(output_fol)
data = []
for fif_fname in fif_fnames:
clip = mne.read_evokeds(fif_fname)[0]
freq = clip.info['sfreq']
step = int(freq * clips_length)
start_t, end_t = 0, len(clip.times)
while start_t + clips_length * freq < end_t:
new_clip = mne.EvokedArray(clip.data[:, start_t:start_t + step],
clip.info,
comment='baseline')
data.append(new_clip.data[0, :10])
mne.write_evokeds(
op.join(
output_fol, '{}_{}.fif'.format(utils.namebase(fif_fname),
int(start_t / freq))),
new_clip)
start_t += int(freq * shift)
data = np.array(data)
return glob.glob(op.join(output_fol, '*.fif'))
def test_evoked_standard_error():
"""Test calculation and read/write of standard error
"""
epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
baseline=(None, 0))
evoked = [epochs.average(), epochs.standard_error()]
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), evoked)
evoked2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), [0, 1])
evoked3 = [read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 'Unknown'),
read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 'Unknown',
kind='standard_error')]
for evoked_new in [evoked2, evoked3]:
assert_true(evoked_new[0]._aspect_kind ==
FIFF.FIFFV_ASPECT_AVERAGE)
assert_true(evoked_new[0].kind == 'average')
assert_true(evoked_new[1]._aspect_kind ==
FIFF.FIFFV_ASPECT_STD_ERR)
assert_true(evoked_new[1].kind == 'standard_error')
for ave, ave2 in zip(evoked, evoked_new):
assert_array_almost_equal(ave.data, ave2.data)
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
def test_evoked_resample():
"""Test for resampling of evoked data
"""
tempdir = _TempDir()
# upsample, write it out, read it in
ave = read_evokeds(fname, 0)
sfreq_normal = ave.info['sfreq']
ave.resample(2 * sfreq_normal)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave_up = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
# compare it to the original
ave_normal = read_evokeds(fname, 0)
# and compare the original to the downsampled upsampled version
ave_new = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
ave_new.resample(sfreq_normal)
assert_array_almost_equal(ave_normal.data, ave_new.data, 2)
assert_array_almost_equal(ave_normal.times, ave_new.times)
assert_equal(ave_normal.nave, ave_new.nave)
assert_equal(ave_normal._aspect_kind, ave_new._aspect_kind)
assert_equal(ave_normal.kind, ave_new.kind)
assert_equal(ave_normal.last, ave_new.last)
assert_equal(ave_normal.first, ave_new.first)
# for the above to work, the upsampling just about had to, but
# we'll add a couple extra checks anyway
assert_true(len(ave_up.times) == 2 * len(ave_normal.times))
assert_true(ave_up.data.shape[1] == 2 * ave_normal.data.shape[1])
def analyze_task(subject, args, hcp_params):
flags = {}
events = dict(face=1, tools=2)
baseline = (-0.5, 0)
all_events = collect_events(hcp_params)
files_exist = all([
op.isfile(meg.get_cond_fname(meg.EPO, event))
and op.isfile(meg.get_cond_fname(meg.EVO, event))
for event in events.keys()
])
if not files_exist:
epochs_hcp, evokeds_from_epochs_hcp = using_preprocessed_epochs(
all_events, events, baseline, hcp_params)
for event in events.keys():
epochs_hcp[event].save(meg.get_cond_fname(meg.EPO, event))
mne.write_evokeds(meg.get_cond_fname(meg.EVO, event),
evokeds_from_epochs_hcp[event])
flags = meg.calc_fwd_inv_wrapper(subject, args, events, flags)
flags, stcs_conds, _ = meg.calc_stc_per_condition_wrapper(
subject, events, args.inverse_method, args, flags)
flags = meg.calc_labels_avg_per_condition_wrapper(subject, events,
args.atlas,
args.inverse_method,
stcs_conds, args, flags)
def test_evoked_resample():
"""Test for resampling of evoked data"""
tempdir = _TempDir()
# upsample, write it out, read it in
ave = read_evokeds(fname, 0)
sfreq_normal = ave.info['sfreq']
ave.resample(2 * sfreq_normal, npad=100)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave_up = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
# compare it to the original
ave_normal = read_evokeds(fname, 0)
# and compare the original to the downsampled upsampled version
ave_new = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
ave_new.resample(sfreq_normal, npad=100)
assert_array_almost_equal(ave_normal.data, ave_new.data, 2)
assert_array_almost_equal(ave_normal.times, ave_new.times)
assert_equal(ave_normal.nave, ave_new.nave)
assert_equal(ave_normal._aspect_kind, ave_new._aspect_kind)
assert_equal(ave_normal.kind, ave_new.kind)
assert_equal(ave_normal.last, ave_new.last)
assert_equal(ave_normal.first, ave_new.first)
# for the above to work, the upsampling just about had to, but
# we'll add a couple extra checks anyway
assert_true(len(ave_up.times) == 2 * len(ave_normal.times))
assert_true(ave_up.data.shape[1] == 2 * ave_normal.data.shape[1])
def run_evoked(subject, session=None):
bids_path = BIDSPath(subject=subject,
session=session,
task=config.get_task(),
acquisition=config.acq,
run=None,
recording=config.rec,
space=config.space,
extension='.fif',
datatype=config.get_datatype(),
root=config.deriv_root)
processing = None
if config.use_ica or config.use_ssp:
processing = 'clean'
fname_in = bids_path.copy().update(processing=processing, suffix='epo',
check=False)
fname_out = bids_path.copy().update(suffix='ave', check=False)
msg = f'Input: {fname_in}, Output: {fname_out}'
logger.info(gen_log_message(message=msg, step=6, subject=subject,
session=session))
epochs = mne.read_epochs(fname_in, preload=True)
msg = 'Creating evoked data based on experimental conditions …'
logger.info(gen_log_message(message=msg, step=6, subject=subject,
session=session))
all_evoked = dict()
if isinstance(config.conditions, dict):
for new_cond_name, orig_cond_name in config.conditions.items():
evoked = epochs[orig_cond_name].average()
evoked.comment = evoked.comment.replace(orig_cond_name,
new_cond_name)
all_evoked[new_cond_name] = evoked
else:
for condition in config.conditions:
evoked = epochs[condition].average()
all_evoked[condition] = evoked
if config.contrasts:
msg = 'Contrasting evoked responses …'
logger.info(gen_log_message(message=msg, step=6, subject=subject,
session=session))
for contrast in config.contrasts:
cond_1, cond_2 = contrast
evoked_diff = mne.combine_evoked([all_evoked[cond_1],
all_evoked[cond_2]],
weights=[1, -1])
all_evoked[contrast] = evoked_diff
evokeds = list(all_evoked.values())
mne.write_evokeds(fname_out, evokeds)
if config.interactive:
for evoked in evokeds:
evoked.plot()
def plot_average_sensors(subject, windows, condition, modality, bad_channels):
import mne
import matplotlib.pyplot as plt
if modality == 'meeg':
return
evokes = []
info = None
title = '{}-{}-{}-windows'.format(subject, modality, condition)
root_dir = op.join(EEG_DIR if modality == 'eeg' else MEG_DIR, subject)
figures_fol = utils.make_dir(
op.join(MMVT_DIR, subject, 'epilepsy-figures', 'average-sensors'))
fig_fname = op.join(figures_fol, '{}.jpg'.format(title))
meg_evoked_fname = op.join(root_dir, '{}.fif'.format(title))
for window_fname in windows:
evoked = mne.read_evokeds(window_fname)[0]
evoked = evoked.pick_types(meg=modality == 'meg',
eeg=modality == 'eeg',
exclude=bad_channels)
if info is None:
info = evoked.info
evokes.append(evoked.data)
evokes = np.array(evokes).mean(0)
evoked_object = mne.EvokedArray(evokes, info, comment=title)
fig = evoked_object.plot(window_title=title,
spatial_colors=True,
show=False)
fig.tight_layout()
plt.savefig(fig_fname, dpi=300)
plt.close()
mne.write_evokeds(meg_evoked_fname, evoked_object)
def _calc_evoked(params):
subject, events_id, epochs = params
evoked = {}
for cond_name in events_id.keys():
evoked[cond_name] = epochs[cond_name].average()
evo = op.join(LOCAL_ROOT_DIR, 'evo', '{}_ecr_{}-ave.fif'.format(subject, cond_name))
mne.write_evokeds(evo, evoked[cond_name])
return evoked
def save_content(self):
"""Saves the mne.Evoked to a fif file in the evoked directory.
"""
try:
mne.write_evokeds(self._path, list(self.content.values()))
except Exception as exc:
raise Exception("Writing evokeds failed. Please check that the "
"entire experiment folder has write permissions.")
def average_evokeds(session):
# Container for all conditions:
all_evokeds = defaultdict(list)
for subject in config.get_subjects():
fname_in = BIDSPath(subject=subject,
session=session,
task=config.get_task(),
acquisition=config.acq,
run=None,
recording=config.rec,
space=config.space,
suffix='ave',
extension='.fif',
datatype=config.get_datatype(),
root=config.deriv_root,
check=False)
msg = f'Input: {fname_in}'
logger.info(
gen_log_message(message=msg,
step=9,
subject=subject,
session=session))
evokeds = mne.read_evokeds(fname_in)
for idx, evoked in enumerate(evokeds):
all_evokeds[idx].append(evoked) # Insert into the container
for idx, evokeds in all_evokeds.items():
all_evokeds[idx] = mne.grand_average(
evokeds, interpolate_bads=config.interpolate_bads_grand_average
) # Combine subjects
subject = 'average'
fname_out = BIDSPath(subject=subject,
session=session,
task=config.get_task(),
acquisition=config.acq,
run=None,
processing=config.proc,
recording=config.rec,
space=config.space,
suffix='ave',
extension='.fif',
datatype=config.get_datatype(),
root=config.deriv_root,
check=False)
if not fname_out.fpath.parent.exists():
os.makedirs(fname_out.fpath.parent)
msg = f'Saving grand-averaged evoked sensor data: {fname_out}'
logger.info(
gen_log_message(message=msg, step=9, subject=subject, session=session))
mne.write_evokeds(fname_out, list(all_evokeds.values()))
return list(all_evokeds.values())
def run_evoked(subject, session=None):
bids_path = BIDSPath(subject=subject,
session=session,
task=config.get_task(),
acquisition=config.acq,
run=None,
recording=config.rec,
space=config.space,
extension='.fif',
datatype=config.get_datatype(),
root=config.deriv_root)
processing = None
if config.use_ica or config.use_ssp:
processing = 'clean'
fname_in = bids_path.copy().update(processing=processing,
suffix='epo',
check=False)
fname_out = bids_path.copy().update(suffix='ave', check=False)
msg = f'Input: {fname_in}, Output: {fname_out}'
logger.info(
gen_log_message(message=msg, step=6, subject=subject, session=session))
epochs = mne.read_epochs(fname_in, preload=True)
msg = 'Creating evoked data based on experimental conditions …'
logger.info(
gen_log_message(message=msg, step=6, subject=subject, session=session))
evokeds = []
for condition in config.conditions:
evoked = epochs[condition].average()
evokeds.append(evoked)
if config.contrasts:
msg = 'Contrasting evoked responses …'
logger.info(
gen_log_message(message=msg,
step=6,
subject=subject,
session=session))
for contrast in config.contrasts:
cond_1, cond_2 = contrast
evoked_1 = epochs[cond_1].average()
evoked_2 = epochs[cond_2].average()
evoked_diff = mne.combine_evoked([evoked_1, evoked_2],
weights=[1, -1])
evokeds.append(evoked_diff)
mne.write_evokeds(fname_out, evokeds)
if config.interactive:
for evoked in evokeds:
evoked.plot()
def compute_epochs_cov_evokeds(subject):
"""Epoch, compute noise covariance and average.
params:
subject : str
the subject id to be loaded
"""
raw = Raw(save_folder + "%s_filtered_ica_mc_raw_tsss.fif" % subject,
preload=True)
# Select events to extract epochs from.
event_id = {'ent_left': 1,
'ent_right': 2,
'ctl_left': 4,
'ctl_right': 8}
# Setup for reading the raw data
events = mne.find_events(raw, min_duration=0.01)
picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=False, eog=False,
include=include, exclude='bads')
# Read epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), reject=reject,
preload=True)
epochs.save(epochs_folder + "%s_filtered_ica_mc_tsss-epo.fif" % subject)
# Plot epochs.
# epochs.plot(trellis=False)
# Look at channels that caused dropped events, showing that the subject's
# blinks were likely to blame for most epochs being dropped
epochs.drop_bad_epochs()
fig = epochs.plot_drop_log(subject=subject, show=False)
fig.savefig(epochs_folder + "pics/%s_drop_log.png" % subject)
# Make noise cov
cov = compute_covariance(epochs, tmin=None, tmax=0, method="auto")
mne.write_cov(epochs_folder + "%s-cov.fif" % subject, cov)
# Average epochs and get evoked data corresponding to the left stimulation
###########################################################################
# Save evoked responses for different conditions to disk
# average epochs and get Evoked datasets
evokeds = [epochs[cond].average() for cond in ['ent_left', 'ent_right',
'ctl_left', 'ctl_right']]
evokeds = [epochs[cond].average() for cond in epochs.event_id.keys()]
# save evoked data to disk
mne.write_evokeds(epochs_folder +
'%s_filtered_ica_mc_raw_tsss-ave.fif' % subject, evokeds)
plt.close("all")
def calc_evoked(indices, epochs_fname, overwrite_epochs=False, overwrite_evoked=False):
epochs = mne.read_epochs(epochs_fname, preload=False)
print(epochs.events.shape)
for event_name, event_indices in indices.items():
evoked_event_fname = meg.get_cond_fname(meg.EVO, event_name)
epochs_event_fname = meg.get_cond_fname(meg.EPO, event_name)
if not op.isfile(epochs_event_fname) or overwrite_epochs:
print('Saving {} epochs to {}, events num: {}'.format(event_name, epochs_event_fname, len(event_indices)))
event_epochs = epochs[event_indices]
event_epochs.save(epochs_event_fname)
if not op.isfile(evoked_event_fname) or overwrite_evoked:
print('Saving {} evoked to {}'.format(event_name, evoked_event_fname))
mne.write_evokeds(evoked_event_fname, event_epochs.average())
def calc_evoked(indices, epochs_fname, overwrite_epochs=False, overwrite_evoked=False):
epochs = mne.read_epochs(epochs_fname, preload=False)
print(epochs.events.shape)
for event_name, event_indices in indices.items():
evoked_event_fname = meg.get_cond_fname(meg.EVO, event_name)
epochs_event_fname = meg.get_cond_fname(meg.EPO, event_name)
if not op.isfile(epochs_event_fname) or overwrite_epochs:
print('Saving {} epochs to {}, events num: {}'.format(event_name, epochs_event_fname, len(event_indices)))
event_epochs = epochs[event_indices]
event_epochs.save(epochs_event_fname)
if not op.isfile(evoked_event_fname) or overwrite_evoked:
print('Saving {} evoked to {}'.format(event_name, evoked_event_fname))
mne.write_evokeds(evoked_event_fname, event_epochs.average())
def test_shift_time_evoked():
"""Test for shifting of time scale."""
tempdir = _TempDir()
# Shift backward
ave = read_evokeds(fname, 0).shift_time(-0.1, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
# Shift forward twice the amount
ave_bshift = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
ave_bshift.shift_time(0.2, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave_bshift)
# Shift backward again
ave_fshift = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
ave_fshift.shift_time(-0.1, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave_fshift)
ave_normal = read_evokeds(fname, 0)
ave_relative = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
assert_allclose(ave_normal.data, ave_relative.data, atol=1e-16, rtol=1e-3)
assert_array_almost_equal(ave_normal.times, ave_relative.times, 10)
assert_equal(ave_normal.last, ave_relative.last)
assert_equal(ave_normal.first, ave_relative.first)
# Absolute time shift
ave = read_evokeds(fname, 0)
ave.shift_time(-0.3, relative=False)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave_absolute = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
assert_allclose(ave_normal.data, ave_absolute.data, atol=1e-16, rtol=1e-3)
assert_equal(ave_absolute.first, int(-0.3 * ave.info['sfreq']))
def meg_calc_evokeds():
subj_files = glob.glob(out_dir + '*epochs*.fif')
subj_files.sort()
for n, fiff_file in enumerate(subj_files):
subj_id = os.path.split(fiff_file)[1][:5]
fname = out_dir + subj_id + 'cond-ave.fif'
epo = mne.read_epochs(fiff_file)
ev = [epo[x].average() for x in ['hap', 'sad', 'neu', 'rest']]
new = ev[0].copy()
new.comment = 'cond_av'
new.data = np.mean([ev[0].data, ev[1].data, ev[2].data], axis=0)
ev.append(new)
mne.write_evokeds(fname, ev)
def run_evoked(subject, autoreject=True):
if autoreject:
epo_fname = op.join(meg_dir, subject,
f'{subject}_audvis-filt-sss-ar-epo.fif')
else:
epo_fname = op.join(meg_dir, subject,
f'{subject}_audvis-filt-sss-ar-epo.fif')
evoked_fname = op.join(meg_dir, subject,
f'{subject}_audvis-filt-sss-ave.fif')
epochs = mne.read_epochs(epo_fname, preload=True)
# define evokeds
evoked_al = epochs['Auditory/Left'].average()
evoked_ar = epochs['Auditory/Right'].average()
evoked_vl = epochs['Visual/Left'].average()
evoked_vr = epochs['Visual/Right'].average()
# define contrasts
contrast_aud = mne.combine_evoked([evoked_al, -evoked_ar], 'equal')
contrast_vis = mne.combine_evoked([evoked_vl, -evoked_vr], 'equal')
# let's make trial-count-normalized ones for group statistics
epochs_eq = epochs.copy().equalize_event_counts(
['Auditory/Left', 'Auditory/Right', 'Visual/Left', 'Visual/Right'])[0]
evoked_al_eq = epochs_eq['Auditory/Left'].average()
evoked_ar_eq = epochs_eq['Auditory/Right'].average()
evoked_vl_eq = epochs_eq['Visual/Left'].average()
evoked_vr_eq = epochs_eq['Visual/Right'].average()
assert evoked_al_eq.nave == evoked_ar_eq.nave == evoked_vl_eq.nave
assert evoked_al_eq.nave == evoked_vr_eq.nave
# simplify comment
evoked_al.comment = 'aud_left'
evoked_ar.comment = 'aud_right'
evoked_vl.comment = 'vis_left'
evoked_vr.comment = 'vis_right'
contrast_aud.comment = 'aud_left_minus_right'
contrast_vis.comment = 'vis_left_minus_right'
evoked_al_eq.comment = 'aud_left_eq'
evoked_ar_eq.comment = 'aud_right_eq'
evoked_vl_eq.comment = 'vis_left_eq'
evoked_vr_eq.comment = 'vis_right_eq'
mne.write_evokeds(evoked_fname, [
evoked_al, evoked_ar, evoked_vl, evoked_vr, contrast_aud, contrast_vis,
evoked_al_eq, evoked_ar_eq, evoked_vl_eq, evoked_vr_eq
])
print(f'Created Evoked for {subject}')
def combine_evokes(subject, cond, sessions, filter_raw_data,
raw_data_filter_freqs):
freqs_str = '-{}-{}'.format(
raw_data_filter_freqs[0],
raw_data_filter_freqs[1]) if filter_raw_data else ''
combined_evoked_fname = op.join(MEG_DIR, subject,
'{}{}-ave.fif'.format(cond, freqs_str))
if not op.isfile(combined_evoked_fname):
all_evokes = []
for session in sessions:
evo_fname = op.join(
MEG_DIR, subject,
'{}-session{}{}-ave.fif'.format(cond, session, freqs_str))
evoked = mne.read_evokeds(evo_fname)[0]
evoked.apply_baseline()
all_evokes.append(evoked)
combined_evoked = mne.combine_evoked(all_evokes, 'nave')
combined_evoked.comment = cond
mne.write_evokeds(combined_evoked_fname, combined_evoked)
def container_results(evoked, evoked_ave, donor, out_file, verbose):
new_evoked = donor.copy()
new_evoked.info = evoked.info
new_evoked.nave = 98 #all
new_evoked.kind = "average"
new_evoked.times = evoked.times
new_evoked.first = 0
new_evoked.last = evoked.times.shape[0] - 1
ev_data = np.asarray(evoked_ave)
ev_data = ev_data[:, np.newaxis]
if verbose:
print('ev_data shape', ev_data.shape)
#mean across runs
ev_data = ev_data.mean(axis=0).mean(axis=0)
if verbose:
print('shape', ev_data.shape)
new_evoked.data = ev_data
if verbose:
print(out_file)
mne.write_evokeds(out_file, new_evoked)
def test_io_evoked():
"""Test IO for evoked data (fif + gz) with integer and str args"""
tempdir = _TempDir()
ave = read_evokeds(fname, 0)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))[0]
# This not being assert_array_equal due to windows rounding
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
assert_true(repr(ave))
# test compressed i/o
ave2 = read_evokeds(fname_gz, 0)
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
condition = 'Left Auditory'
assert_raises(ValueError, read_evokeds, fname, condition, kind='stderr')
assert_raises(ValueError,
read_evokeds,
fname,
condition,
kind='standard_error')
ave3 = read_evokeds(fname, condition)
assert_array_almost_equal(ave.data, ave3.data, 19)
# test read_evokeds and write_evokeds
aves1 = read_evokeds(fname)[1::2]
aves2 = read_evokeds(fname, [1, 3])
aves3 = read_evokeds(fname, ['Right Auditory', 'Right visual'])
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), aves1)
aves4 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))
for aves in [aves2, aves3, aves4]:
for [av1, av2] in zip(aves1, aves):
assert_array_almost_equal(av1.data, av2.data)
assert_array_almost_equal(av1.times, av2.times)
assert_equal(av1.nave, av2.nave)
assert_equal(av1.kind, av2.kind)
assert_equal(av1._aspect_kind, av2._aspect_kind)
assert_equal(av1.last, av2.last)
assert_equal(av1.first, av2.first)
assert_equal(av1.comment, av2.comment)
# test warnings on bad filenames
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
fname2 = op.join(tempdir, 'test-bad-name.fif')
write_evokeds(fname2, ave)
read_evokeds(fname2)
assert_naming(w, 'test_evoked.py', 2)
# constructor
assert_raises(TypeError, Evoked, fname)
def test_io_evoked():
"""Test IO for evoked data (fif + gz) with integer and str args
"""
tempdir = _TempDir()
ave = read_evokeds(fname, 0)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))[0]
# This not being assert_array_equal due to windows rounding
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
assert_true(repr(ave))
# test compressed i/o
ave2 = read_evokeds(fname_gz, 0)
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
condition = 'Left Auditory'
assert_raises(ValueError, read_evokeds, fname, condition, kind='stderr')
assert_raises(ValueError, read_evokeds, fname, condition,
kind='standard_error')
ave3 = read_evokeds(fname, condition)
assert_array_almost_equal(ave.data, ave3.data, 19)
# test read_evokeds and write_evokeds
aves1 = read_evokeds(fname)[1::2]
aves2 = read_evokeds(fname, [1, 3])
aves3 = read_evokeds(fname, ['Right Auditory', 'Right visual'])
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), aves1)
aves4 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))
for aves in [aves2, aves3, aves4]:
for [av1, av2] in zip(aves1, aves):
assert_array_almost_equal(av1.data, av2.data)
assert_array_almost_equal(av1.times, av2.times)
assert_equal(av1.nave, av2.nave)
assert_equal(av1.kind, av2.kind)
assert_equal(av1._aspect_kind, av2._aspect_kind)
assert_equal(av1.last, av2.last)
assert_equal(av1.first, av2.first)
assert_equal(av1.comment, av2.comment)
# test warnings on bad filenames
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
fname2 = op.join(tempdir, 'test-bad-name.fif')
write_evokeds(fname2, ave)
read_evokeds(fname2)
assert_naming(w, 'test_evoked.py', 2)
# constructor
assert_raises(TypeError, Evoked, fname)
def test_evoked_resample(tmp_path):
"""Test resampling evoked data."""
tempdir = str(tmp_path)
# upsample, write it out, read it in
ave = read_evokeds(fname, 0)
orig_lp = ave.info['lowpass']
sfreq_normal = ave.info['sfreq']
ave.resample(2 * sfreq_normal, npad=100)
assert ave.info['lowpass'] == orig_lp
fname_temp = op.join(tempdir, 'evoked-ave.fif')
write_evokeds(fname_temp, ave)
ave_up = read_evokeds(fname_temp, 0)
# compare it to the original
ave_normal = read_evokeds(fname, 0)
# and compare the original to the downsampled upsampled version
ave_new = read_evokeds(fname_temp, 0)
ave_new.resample(sfreq_normal, npad=100)
assert ave.info['lowpass'] == orig_lp
assert_array_almost_equal(ave_normal.data, ave_new.data, 2)
assert_array_almost_equal(ave_normal.times, ave_new.times)
assert_equal(ave_normal.nave, ave_new.nave)
assert_equal(ave_normal._aspect_kind, ave_new._aspect_kind)
assert_equal(ave_normal.kind, ave_new.kind)
assert_equal(ave_normal.last, ave_new.last)
assert_equal(ave_normal.first, ave_new.first)
# for the above to work, the upsampling just about had to, but
# we'll add a couple extra checks anyway
assert (len(ave_up.times) == 2 * len(ave_normal.times))
assert (ave_up.data.shape[1] == 2 * ave_normal.data.shape[1])
ave_new.resample(50)
assert ave_new.info['sfreq'] == 50.
assert ave_new.info['lowpass'] == 25.
def plot_erp(file_path_erp):
data_dict = dict()
count = 0
erp_files = _get_file_list(file_path_erp, 'sub', '-ave.fif')
for sub_id in erp_files.keys():
file_name = erp_files[sub_id]
evoked_list = mne.read_evokeds(file_name)
for event in evoked_list:
comment = event.comment
data = event.data
norm_data = normalize(
data, axis=1) # better normalize here for a prettier plot
if comment not in data_dict.keys():
data_dict[comment] = norm_data
else:
data_dict[comment] = data_dict[comment] + norm_data
count += 1
for comment in data_dict.keys():
data_dict[comment] = data_dict[comment] / (10000 * count)
# FAKE ONE
sub_id = list(erp_files.keys())[0]
file_name = erp_files[sub_id]
evoked_list = mne.read_evokeds(file_name)
for event in evoked_list:
comment = event.comment
event.data = data_dict[comment]
event.plot_joint(
title=comment) # maybe you don't want to plot right away
# save the faked one
file_name = file_path_erp + 'faked_summary-ave.fif'
mne.write_evokeds(file_name, evoked_list)
msg = '====finish faked_summary erp'
print(msg)
def test_shift_time_evoked():
""" Test for shifting of time scale
"""
tempdir = _TempDir()
# Shift backward
ave = read_evokeds(fname, 0)
ave.shift_time(-0.1, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
# Shift forward twice the amount
ave_bshift = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
ave_bshift.shift_time(0.2, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave_bshift)
# Shift backward again
ave_fshift = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
ave_fshift.shift_time(-0.1, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave_fshift)
ave_normal = read_evokeds(fname, 0)
ave_relative = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
assert_true(np.allclose(ave_normal.data, ave_relative.data,
atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave_normal.times, ave_relative.times, 10)
assert_equal(ave_normal.last, ave_relative.last)
assert_equal(ave_normal.first, ave_relative.first)
# Absolute time shift
ave = read_evokeds(fname, 0)
ave.shift_time(-0.3, relative=False)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave_absolute = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
assert_true(np.allclose(ave_normal.data, ave_absolute.data,
atol=1e-16, rtol=1e-3))
assert_equal(ave_absolute.first, int(-0.3 * ave.info['sfreq']))
def save_average(self):
if self.is_mmn():
deviant = self.epochs["Deviant"].average()
dfile = self.average_output_path("deviant")
logging.info(f"Saved evoked averages of deviant events to {dfile}")
mne.write_evokeds(dfile, deviant)
standard = self.epochs["Standard"].average()
sfile = self.average_output_path("standard")
mne.write_evokeds(sfile, standard)
logging.info(
f"Saved evoked averages of standard events to {sfile}")
average = self.epochs.average()
afile = self.average_output_path("all")
mne.write_evokeds(afile, average)
logging.info(f"Saved evoked averages to {afile}")
def test_dipole_fitting():
"""Test dipole fitting."""
amp = 100e-9
tempdir = _TempDir()
rng = np.random.RandomState(0)
fname_dtemp = op.join(tempdir, 'test.dip')
fname_sim = op.join(tempdir, 'test-ave.fif')
fwd = convert_forward_solution(read_forward_solution(fname_fwd),
surf_ori=False,
force_fixed=True,
use_cps=True)
evoked = read_evokeds(fname_evo)[0]
cov = read_cov(fname_cov)
n_per_hemi = 5
vertices = [
np.sort(rng.permutation(s['vertno'])[:n_per_hemi]) for s in fwd['src']
]
nv = sum(len(v) for v in vertices)
stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
evoked = simulate_evoked(fwd,
stc,
evoked.info,
cov,
nave=evoked.nave,
random_state=rng)
# For speed, let's use a subset of channels (strange but works)
picks = np.sort(
np.concatenate([
pick_types(evoked.info, meg=True, eeg=False)[::2],
pick_types(evoked.info, meg=False, eeg=True)[::2]
]))
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
write_evokeds(fname_sim, evoked)
# Run MNE-C version
run_subprocess([
'mne_dipole_fit',
'--meas',
fname_sim,
'--meg',
'--eeg',
'--noise',
fname_cov,
'--dip',
fname_dtemp,
'--mri',
fname_fwd,
'--reg',
'0',
'--tmin',
'0',
])
dip_c = read_dipole(fname_dtemp)
# Run mne-python version
sphere = make_sphere_model(head_radius=0.1)
with pytest.warns(RuntimeWarning, match='projection'):
dip, residuals = fit_dipole(evoked, cov, sphere, fname_fwd)
# Sanity check: do our residuals have less power than orig data?
data_rms = np.sqrt(np.sum(evoked.data**2, axis=0))
resi_rms = np.sqrt(np.sum(residuals**2, axis=0))
assert (data_rms > resi_rms * 0.95).all(), \
'%s (factor: %s)' % ((data_rms / resi_rms).min(), 0.95)
# Compare to original points
transform_surface_to(fwd['src'][0], 'head', fwd['mri_head_t'])
transform_surface_to(fwd['src'][1], 'head', fwd['mri_head_t'])
assert_equal(fwd['src'][0]['coord_frame'], FIFF.FIFFV_COORD_HEAD)
src_rr = np.concatenate([s['rr'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
src_nn = np.concatenate([s['nn'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
# MNE-C skips the last "time" point :(
out = dip.crop(dip_c.times[0], dip_c.times[-1])
assert (dip is out)
src_rr, src_nn = src_rr[:-1], src_nn[:-1]
# check that we did about as well
corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
for d in (dip_c, dip):
new = d.pos
diffs = new - src_rr
corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
gc_dists += [
180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori, axis=1)))
]
amp_errs += [np.sqrt(np.mean((amp - d.amplitude)**2))]
gofs += [np.mean(d.gof)]
if os.getenv('TRAVIS', 'false').lower() == 'true' and \
'OPENBLAS_NUM_THREADS' in os.environ:
# XXX possibly some OpenBLAS numerical differences make
# things slightly worse for us
factor = 0.7
else:
factor = 0.8
assert dists[0] / factor >= dists[1], 'dists: %s' % dists
assert corrs[0] * factor <= corrs[1], 'corrs: %s' % corrs
assert gc_dists[0] / factor >= gc_dists[1] * 0.8, \
'gc-dists (ori): %s' % gc_dists
assert amp_errs[0] / factor >= amp_errs[1],\
'amplitude errors: %s' % amp_errs
# This one is weird because our cov/sim/picking is weird
assert gofs[0] * factor <= gofs[1] * 2, 'gof: %s' % gofs
vis_r = epochs["visual", "right"].average()
all_evokeds = [aud_l, aud_r, vis_l, vis_r]
print(all_evokeds)
###############################################################################
# This can be simplified with a Python list comprehension:
all_evokeds = [epochs[cond].average() for cond in sorted(event_id.keys())]
print(all_evokeds)
# Then, we construct and plot an unweighted average of left vs. right trials
# this way, too:
mne.combine_evoked(all_evokeds, weights=(0.25, -0.25, 0.25, -0.25)).plot_joint()
###############################################################################
# Often, it makes sense to store Evoked objects in a dictionary or a list -
# either different conditions, or different subjects.
# If they are stored in a list, they can be easily averaged, for example,
# for a grand average across subjects (or conditions).
grand_average = mne.grand_average(all_evokeds)
mne.write_evokeds("/tmp/tmp-ave.fif", all_evokeds)
# If Evokeds objects are stored in a dictionary, they can be retrieved by name.
all_evokeds = dict((cond, epochs[cond].average()) for cond in event_id)
print(all_evokeds["left/auditory"])
# Besides for explicit access, this can be used for example to set titles.
for cond in all_evokeds:
all_evokeds[cond].plot_joint(title=cond)
def test_dipole_fitting():
"""Test dipole fitting."""
amp = 10e-9
tempdir = _TempDir()
rng = np.random.RandomState(0)
fname_dtemp = op.join(tempdir, 'test.dip')
fname_sim = op.join(tempdir, 'test-ave.fif')
fwd = convert_forward_solution(read_forward_solution(fname_fwd),
surf_ori=False, force_fixed=True)
evoked = read_evokeds(fname_evo)[0]
cov = read_cov(fname_cov)
n_per_hemi = 5
vertices = [np.sort(rng.permutation(s['vertno'])[:n_per_hemi])
for s in fwd['src']]
nv = sum(len(v) for v in vertices)
stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
evoked = simulate_evoked(fwd, stc, evoked.info, cov, snr=20,
random_state=rng)
# For speed, let's use a subset of channels (strange but works)
picks = np.sort(np.concatenate([
pick_types(evoked.info, meg=True, eeg=False)[::2],
pick_types(evoked.info, meg=False, eeg=True)[::2]]))
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
write_evokeds(fname_sim, evoked)
# Run MNE-C version
run_subprocess([
'mne_dipole_fit', '--meas', fname_sim, '--meg', '--eeg',
'--noise', fname_cov, '--dip', fname_dtemp,
'--mri', fname_fwd, '--reg', '0', '--tmin', '0',
])
dip_c = read_dipole(fname_dtemp)
# Run mne-python version
sphere = make_sphere_model(head_radius=0.1)
dip, residuals = fit_dipole(evoked, fname_cov, sphere, fname_fwd)
# Sanity check: do our residuals have less power than orig data?
data_rms = np.sqrt(np.sum(evoked.data ** 2, axis=0))
resi_rms = np.sqrt(np.sum(residuals ** 2, axis=0))
factor = 1.
# XXX weird, inexplicable differenc for 3.5 build we'll assume is due to
# Anaconda bug for now...
if os.getenv('TRAVIS', 'false') == 'true' and \
sys.version[:3] in ('3.5', '2.7'):
factor = 0.8
assert_true((data_rms > factor * resi_rms).all(),
msg='%s (factor: %s)' % ((data_rms / resi_rms).min(), factor))
# Compare to original points
transform_surface_to(fwd['src'][0], 'head', fwd['mri_head_t'])
transform_surface_to(fwd['src'][1], 'head', fwd['mri_head_t'])
src_rr = np.concatenate([s['rr'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
src_nn = np.concatenate([s['nn'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
# MNE-C skips the last "time" point :(
dip.crop(dip_c.times[0], dip_c.times[-1])
src_rr, src_nn = src_rr[:-1], src_nn[:-1]
# check that we did at least as well
corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
for d in (dip_c, dip):
new = d.pos
diffs = new - src_rr
corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
gc_dists += [180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori,
axis=1)))]
amp_errs += [np.sqrt(np.mean((amp - d.amplitude) ** 2))]
gofs += [np.mean(d.gof)]
assert_true(dists[0] >= dists[1] * factor, 'dists: %s' % dists)
assert_true(corrs[0] <= corrs[1] / factor, 'corrs: %s' % corrs)
assert_true(gc_dists[0] >= gc_dists[1] * factor,
'gc-dists (ori): %s' % gc_dists)
assert_true(amp_errs[0] >= amp_errs[1] * factor,
'amplitude errors: %s' % amp_errs)
assert_true(gofs[0] <= gofs[1] / factor, 'gof: %s' % gofs)
all_evokeds = [aud_l, aud_r, vis_l, vis_r]
print(all_evokeds)
###############################################################################
# This can be simplified with a Python list comprehension:
all_evokeds = [epochs[cond].average() for cond in sorted(event_id.keys())]
print(all_evokeds)
# Then, we construct and plot an unweighted average of left vs. right trials
# this way, too:
mne.combine_evoked(all_evokeds,
weights=(0.25, -0.25, 0.25, -0.25)).plot_joint()
###############################################################################
# Often, it makes sense to store Evoked objects in a dictionary or a list -
# either different conditions, or different subjects.
# If they are stored in a list, they can be easily averaged, for example,
# for a grand average across subjects (or conditions).
grand_average = mne.grand_average(all_evokeds)
mne.write_evokeds('/tmp/tmp-ave.fif', all_evokeds)
# If Evokeds objects are stored in a dictionary, they can be retrieved by name.
all_evokeds = dict((cond, epochs[cond].average()) for cond in event_id)
print(all_evokeds['left/auditory'])
# Besides for explicit access, this can be used for example to set titles.
for cond in all_evokeds:
all_evokeds[cond].plot_joint(title=cond)
def test_dipole_fitting():
"""Test dipole fitting"""
amp = 10e-9
tempdir = _TempDir()
rng = np.random.RandomState(0)
fname_dtemp = op.join(tempdir, "test.dip")
fname_sim = op.join(tempdir, "test-ave.fif")
fwd = convert_forward_solution(read_forward_solution(fname_fwd), surf_ori=False, force_fixed=True)
evoked = read_evokeds(fname_evo)[0]
cov = read_cov(fname_cov)
n_per_hemi = 5
vertices = [np.sort(rng.permutation(s["vertno"])[:n_per_hemi]) for s in fwd["src"]]
nv = sum(len(v) for v in vertices)
stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
evoked = simulate_evoked(fwd, stc, evoked.info, cov, snr=20, random_state=rng)
# For speed, let's use a subset of channels (strange but works)
picks = np.sort(
np.concatenate(
[pick_types(evoked.info, meg=True, eeg=False)[::2], pick_types(evoked.info, meg=False, eeg=True)[::2]]
)
)
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
write_evokeds(fname_sim, evoked)
# Run MNE-C version
run_subprocess(
[
"mne_dipole_fit",
"--meas",
fname_sim,
"--meg",
"--eeg",
"--noise",
fname_cov,
"--dip",
fname_dtemp,
"--mri",
fname_fwd,
"--reg",
"0",
"--tmin",
"0",
]
)
dip_c = read_dipole(fname_dtemp)
# Run mne-python version
sphere = make_sphere_model(head_radius=0.1)
dip, residuals = fit_dipole(evoked, fname_cov, sphere, fname_fwd)
# Sanity check: do our residuals have less power than orig data?
data_rms = np.sqrt(np.sum(evoked.data ** 2, axis=0))
resi_rms = np.sqrt(np.sum(residuals ** 2, axis=0))
factor = 1.0
# XXX weird, inexplicable differenc for 3.5 build we'll assume is due to
# Anaconda bug for now...
if os.getenv("TRAVIS", "false") == "true" and sys.version[:3] in ("3.5", "2.7"):
factor = 0.8
assert_true((data_rms > factor * resi_rms).all(), msg="%s (factor: %s)" % ((data_rms / resi_rms).min(), factor))
# Compare to original points
transform_surface_to(fwd["src"][0], "head", fwd["mri_head_t"])
transform_surface_to(fwd["src"][1], "head", fwd["mri_head_t"])
src_rr = np.concatenate([s["rr"][v] for s, v in zip(fwd["src"], vertices)], axis=0)
src_nn = np.concatenate([s["nn"][v] for s, v in zip(fwd["src"], vertices)], axis=0)
# MNE-C skips the last "time" point :(
dip.crop(dip_c.times[0], dip_c.times[-1])
src_rr, src_nn = src_rr[:-1], src_nn[:-1]
# check that we did at least as well
corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
for d in (dip_c, dip):
new = d.pos
diffs = new - src_rr
corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
gc_dists += [180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori, axis=1)))]
amp_errs += [np.sqrt(np.mean((amp - d.amplitude) ** 2))]
gofs += [np.mean(d.gof)]
assert_true(dists[0] >= dists[1] * factor, "dists: %s" % dists)
assert_true(corrs[0] <= corrs[1] / factor, "corrs: %s" % corrs)
assert_true(gc_dists[0] >= gc_dists[1] * factor, "gc-dists (ori): %s" % gc_dists)
assert_true(amp_errs[0] >= amp_errs[1] * factor, "amplitude errors: %s" % amp_errs)
assert_true(gofs[0] <= gofs[1] / factor, "gof: %s" % gofs)
def test_io_evoked():
"""Test IO for evoked data (fif + gz) with integer and str args."""
tempdir = _TempDir()
ave = read_evokeds(fname, 0)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))[0]
# This not being assert_array_equal due to windows rounding
assert (np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
assert (repr(ave))
# test compressed i/o
ave2 = read_evokeds(fname_gz, 0)
assert (np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
condition = 'Left Auditory'
pytest.raises(ValueError, read_evokeds, fname, condition, kind='stderr')
pytest.raises(ValueError, read_evokeds, fname, condition,
kind='standard_error')
ave3 = read_evokeds(fname, condition)
assert_array_almost_equal(ave.data, ave3.data, 19)
# test read_evokeds and write_evokeds
aves1 = read_evokeds(fname)[1::2]
aves2 = read_evokeds(fname, [1, 3])
aves3 = read_evokeds(fname, ['Right Auditory', 'Right visual'])
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), aves1)
aves4 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))
for aves in [aves2, aves3, aves4]:
for [av1, av2] in zip(aves1, aves):
assert_array_almost_equal(av1.data, av2.data)
assert_array_almost_equal(av1.times, av2.times)
assert_equal(av1.nave, av2.nave)
assert_equal(av1.kind, av2.kind)
assert_equal(av1._aspect_kind, av2._aspect_kind)
assert_equal(av1.last, av2.last)
assert_equal(av1.first, av2.first)
assert_equal(av1.comment, av2.comment)
# test warnings on bad filenames
fname2 = op.join(tempdir, 'test-bad-name.fif')
with pytest.warns(RuntimeWarning, match='-ave.fif'):
write_evokeds(fname2, ave)
with pytest.warns(RuntimeWarning, match='-ave.fif'):
read_evokeds(fname2)
# constructor
pytest.raises(TypeError, Evoked, fname)
# MaxShield
fname_ms = op.join(tempdir, 'test-ave.fif')
assert (ave.info['maxshield'] is False)
ave.info['maxshield'] = True
ave.save(fname_ms)
pytest.raises(ValueError, read_evokeds, fname_ms)
with pytest.warns(RuntimeWarning, match='Elekta'):
aves = read_evokeds(fname_ms, allow_maxshield=True)
assert all(ave.info['maxshield'] is True for ave in aves)
aves = read_evokeds(fname_ms, allow_maxshield='yes')
assert (all(ave.info['maxshield'] is True for ave in aves))
def test_io_evoked(tmpdir):
"""Test IO for evoked data (fif + gz) with integer and str args."""
ave = read_evokeds(fname, 0)
ave_double = ave.copy()
ave_double.comment = ave.comment + ' doubled nave'
ave_double.nave = ave.nave * 2
write_evokeds(tmpdir.join('evoked-ave.fif'), [ave, ave_double])
ave2, ave_double = read_evokeds(op.join(tmpdir, 'evoked-ave.fif'))
assert ave2.nave * 2 == ave_double.nave
# This not being assert_array_equal due to windows rounding
assert (np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
assert (repr(ave))
# test compressed i/o
ave2 = read_evokeds(fname_gz, 0)
assert (np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
condition = 'Left Auditory'
pytest.raises(ValueError, read_evokeds, fname, condition, kind='stderr')
pytest.raises(ValueError,
read_evokeds,
fname,
condition,
kind='standard_error')
ave3 = read_evokeds(fname, condition)
assert_array_almost_equal(ave.data, ave3.data, 19)
# test read_evokeds and write_evokeds
aves1 = read_evokeds(fname)[1::2]
aves2 = read_evokeds(fname, [1, 3])
aves3 = read_evokeds(fname, ['Right Auditory', 'Right visual'])
write_evokeds(tmpdir.join('evoked-ave.fif'), aves1)
aves4 = read_evokeds(tmpdir.join('evoked-ave.fif'))
for aves in [aves2, aves3, aves4]:
for [av1, av2] in zip(aves1, aves):
assert_array_almost_equal(av1.data, av2.data)
assert_array_almost_equal(av1.times, av2.times)
assert_equal(av1.nave, av2.nave)
assert_equal(av1.kind, av2.kind)
assert_equal(av1._aspect_kind, av2._aspect_kind)
assert_equal(av1.last, av2.last)
assert_equal(av1.first, av2.first)
assert_equal(av1.comment, av2.comment)
# test saving and reading complex numbers in evokeds
ave_complex = ave.copy()
ave_complex._data = 1j * ave_complex.data
fname_temp = str(tmpdir.join('complex-ave.fif'))
ave_complex.save(fname_temp)
ave_complex = read_evokeds(fname_temp)[0]
assert_allclose(ave.data, ave_complex.data.imag)
# test warnings on bad filenames
fname2 = tmpdir.join('test-bad-name.fif')
with pytest.warns(RuntimeWarning, match='-ave.fif'):
write_evokeds(fname2, ave)
with pytest.warns(RuntimeWarning, match='-ave.fif'):
read_evokeds(fname2)
# test writing when order of bads doesn't match
fname3 = tmpdir.join('test-bad-order-ave.fif')
condition = 'Left Auditory'
ave4 = read_evokeds(fname, condition)
ave4.info['bads'] = ave4.ch_names[:3]
ave5 = ave4.copy()
ave5.info['bads'] = ave4.info['bads'][::-1]
write_evokeds(fname3, [ave4, ave5])
# constructor
pytest.raises(TypeError, Evoked, fname)
# MaxShield
fname_ms = tmpdir.join('test-ave.fif')
assert (ave.info['maxshield'] is False)
ave.info['maxshield'] = True
ave.save(fname_ms)
pytest.raises(ValueError, read_evokeds, fname_ms)
with pytest.warns(RuntimeWarning, match='Elekta'):
aves = read_evokeds(fname_ms, allow_maxshield=True)
assert all(ave.info['maxshield'] is True for ave in aves)
aves = read_evokeds(fname_ms, allow_maxshield='yes')
assert (all(ave.info['maxshield'] is True for ave in aves))
old_data = epochs_tmp.get_data()
data = np.empty_like(old_data)
for ii, e in enumerate(old_data):
data[ii] = np.dot(projector, e)
# got the threshold from Brainstorm (http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawAvg, 2000 fT)
epochs_clean = mne.epochs.EpochsArray(data, info, epochs_tmp.events, reject=dict(mag=2e-12), event_id=epochs_tmp.event_id, tmin=np.min(epochs_tmp.times))
# and check how different the averages get
evokeds_clean = [epochs_clean[name].average() for name in conds[:3]]
title = 'Averaged data after EOG and bad trials removal'
mne.viz.plot_topo(evokeds_clean, color=colors, title=title)
# save evoked responses for all 5 conditions
print 'Saving evoked data...'
evokeds_clean = [epochs_clean[name].average() for name in conds]
mne.write_evokeds(evoked_dir + subj + '_stop_BP1-35_DS120-ave.fif', evokeds_clean)
# output number of averages
for ev in evokeds_clean:
print ev.comment, ': %d averages'%ev.nave
# For the data tracker
print '=== Add to data tracker ==='
print 'Y\t%s\t%d\t%d\t%d'%(comps2use,evokeds_clean[1].nave,evokeds_clean[4].nave,evokeds_clean[0].nave)
print '==============='
# now that we know which epochs to drop, copy the log to the actual epochs structure and drop them
bad_epochs = [i for i,j in enumerate(epochs_clean.drop_log) if len(j)>0]
epochs.drop_epochs(bad_epochs)
# save epochs with (optional) EOG projection
print 'Saving epochs with optional SSP operators...'
if num in {88, 89, 92, 100}:
continue
for run in runs:
raw = load_subject(num, run)
fix_channels(raw)
add_montage(raw)
raw.pick_channels(ch_names)
# Band-pass filter to capture the relevant signal (alpha, beta,
# and mu ranges). Butterworth filter is implied by method='iir'
# with iir_params=None or left out.
raw.filter(7.0, 30.0, method='iir', n_jobs=n_cores)
ica = ICA(n_components=0.95, random_state=random_state)
ica.fit(raw, decim=3)
ica.apply(raw)
events = find_events(raw, consecutive=False)
epochs = Epochs(raw,
events,
event_id,
tmin,
tmax,
baseline=baseline,
preload=True,
proj=False)
evoked_avg = [epochs[cond].average() for cond in ['left_fist',
'right_fist']]
filename = splitext(raw.info['filename'])[0]
epochs.save(filename + '-epo.fif')
write_evokeds(filename + '-ave.fif', evoked_avg)
if saveEpochs:
fname_epochs = fstem + '_' + condstem + '-epo.fif'
epochs.save(respath + fname_epochs)
# Now save overall onset N100
epochs = mne.Epochs(raw,
eves,
event_id=condlists,
tmin=-0.4,
proj=True,
tmax=1.0,
baseline=(-0.2, 0.0),
reject=dict(grad=5000e-13, mag=5e-12))
evokeds += [
epochs.average(),
]
if saveEpochs:
fname_epochs = fstem + '_onset-epo.fif'
epochs.save(respath + fname_epochs)
if saveAve:
avename = subj + ssstag + '_' + para + '_collapse-ave.fif'
mne.write_evokeds(respath + avename, evokeds)
if saveCov:
# Compute covatiance
cov = compute_covariance(epochs, tmin=-0.2, tmax=0.0)
covname = subj + ssstag + '_' + para + '_collapse-cov.fif'
cov.save(respath + covname)
else:
subj = 'ABUTRIKQ'
# open the matched BP1-35Hz file and borrow its event labels
epochs_fname = epochs_dir + subj + '_stop_parsed_matched_BP1-35_DS120-epo.fif.gz'
epochs35 = mne.read_epochs(epochs_fname, proj=True)
epochs_fname = epochs_dir + subj + '_stop_parsed_BP1-100_DS300-epo.fif.gz'
epochs = mne.read_epochs(epochs_fname, proj=True)
# we need to drop events that were not matched
if len(epochs35.events) < len(epochs.events):
drop_me = np.arange(len(epochs.events))
drop_me[drop_me < len(epochs35.events)] = 0
drop_me = np.nonzero(drop_me)[0]
epochs.drop_epochs(drop_me)
epochs.event_id = epochs35.event_id
epochs.events = epochs35.events
# open the cleaned epochs file and grab its SSP operators and clean log
epochs_fname = epochs_dir + subj + '_stop_parsed_matched_clean_BP1-35_DS120-epo.fif.gz'
epochs35 = mne.read_epochs(epochs_fname, proj=True)
bad_epochs = [i for i, j in enumerate(epochs35.drop_log) if len(j) > 0]
epochs.drop_epochs(bad_epochs)
epochs.info['projs'] = epochs35.info['projs']
# make averaged file and save final result
print 'Saving epochs and evoked data with optional SSP operators...'
evokeds = [epochs[name].average() for name in conds]
mne.write_evokeds(evoked_dir + subj + '_stop_parsed_matched_BP1-100_DS300-ave.fif', evokeds)
new_fname = epochs_dir + subj + '_stop_parsed_matched_clean_BP1-100_DS300-epo.fif.gz'
epochs.save(new_fname)
def test_io_evoked():
"""Test IO for evoked data (fif + gz) with integer and str args
"""
ave = read_evokeds(fname, 0)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))[0]
# This not being assert_array_equal due to windows rounding
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
# test compressed i/o
ave2 = read_evokeds(fname_gz, 0)
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
condition = 'Left Auditory'
assert_raises(ValueError, read_evokeds, fname, condition, kind='stderr')
assert_raises(ValueError, read_evokeds, fname, condition,
kind='standard_error')
ave3 = read_evokeds(fname, condition)
assert_array_almost_equal(ave.data, ave3.data, 19)
# test deprecation warning for read_evoked and write_evoked
# XXX should be deleted for 0.9 release
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
ave = read_evoked(fname, setno=0)
assert_true(w[0].category == DeprecationWarning)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
write_evoked(op.join(tempdir, 'evoked-ave.fif'), ave)
assert_true(w[0].category == DeprecationWarning)
# test read_evokeds and write_evokeds
types = ['Left Auditory', 'Right Auditory', 'Left visual', 'Right visual']
aves1 = read_evokeds(fname)
aves2 = read_evokeds(fname, [0, 1, 2, 3])
aves3 = read_evokeds(fname, types)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), aves1)
aves4 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))
for aves in [aves2, aves3, aves4]:
for [av1, av2] in zip(aves1, aves):
assert_array_almost_equal(av1.data, av2.data)
assert_array_almost_equal(av1.times, av2.times)
assert_equal(av1.nave, av2.nave)
assert_equal(av1.kind, av2.kind)
assert_equal(av1._aspect_kind, av2._aspect_kind)
assert_equal(av1.last, av2.last)
assert_equal(av1.first, av2.first)
assert_equal(av1.comment, av2.comment)
# test warnings on bad filenames
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
fname2 = op.join(tempdir, 'test-bad-name.fif')
write_evokeds(fname2, ave)
read_evokeds(fname2)
assert_true(len(w) == 2)
n_ok = len(eps_ok)
n_dropped = len(drop_log) - n_ok
print('%d epochs ok, %d epochs rejected' % (n_ok, n_dropped))
if n_ok == 0:
print('Skipping category')
continue
print('Computing weighted average...')
w_snr_ok = w_snr[eps_ok]
weigh_epochs(data_epochs, w_snr_ok)
evoked = data_epochs.average()
evoked.comment = cat['comment']
evokeds.append(evoked)
if args.plot_snr and eps_ok:
plt.figure()
plt.plot(eps_ok, w_snr_ok)
plt.title('Per-epoch SNR for category: ' + cat['comment'])
plt.xlabel('Epoch n (good epochs only)')
plt.ylabel('Epoch weight (unnormalized)')
figs = True
""" Write all resulting evoked objects to a fiff file. """
if evokeds:
fn = fnbase + '_chpi_weighted-ave.fif'
print('Saving', fn)
mne.write_evokeds(fn, evokeds)
if args.plot_snr and figs:
plt.show()
def save_epochs(p, subjects, in_names, in_numbers, analyses, out_names,
out_numbers, must_match, decim, run_indices):
"""Generate epochs from raw data based on events
Can only complete after preprocessing is complete.
Parameters
----------
p : instance of Parameters
Analysis parameters.
subjects : list of str
Subject names to analyze (e.g., ['Eric_SoP_001', ...]).
in_names : list of str
Names of input events.
in_numbers : list of list of int
Event numbers (in scored event files) associated with each name.
analyses : list of str
Lists of analyses of interest.
out_names : list of list of str
Event types to make out of old ones.
out_numbers : list of list of int
Event numbers to convert to (e.g., [[1, 1, 2, 3, 3], ...] would create
three event types, where the first two and last two event types from
the original list get collapsed over).
must_match : list of int
Indices from the original in_names that must match in event counts
before collapsing. Should eventually be expanded to allow for
ratio-based collapsing.
decim : int | list of int
Amount to decimate.
run_indices : array-like | None
Run indices to include.
"""
in_names = np.asanyarray(in_names)
old_dict = dict()
for n, e in zip(in_names, in_numbers):
old_dict[n] = e
# let's do some sanity checks
if len(in_names) != len(in_numbers):
raise RuntimeError('in_names (%d) must have same length as '
'in_numbers (%d)' %
(len(in_names), len(in_numbers)))
if np.any(np.array(in_numbers) <= 0):
raise ValueError('in_numbers must all be > 0')
if len(out_names) != len(out_numbers):
raise RuntimeError('out_names must have same length as out_numbers')
for name, num in zip(out_names, out_numbers):
num = np.array(num)
if len(name) != len(np.unique(num[num > 0])):
raise RuntimeError('each entry in out_names must have length '
'equal to the number of unique elements in the '
'corresponding entry in out_numbers:\n%s\n%s' %
(name, np.unique(num[num > 0])))
if len(num) != len(in_names):
raise RuntimeError('each entry in out_numbers must have the same '
'length as in_names')
if (np.array(num) == 0).any():
raise ValueError('no element of out_numbers can be zero')
ch_namess = list()
drop_logs = list()
sfreqs = set()
for si, subj in enumerate(subjects):
if p.disp_files:
print(' Loading raw files for subject %s.' % subj)
epochs_dir = op.join(p.work_dir, subj, p.epochs_dir)
if not op.isdir(epochs_dir):
os.mkdir(epochs_dir)
evoked_dir = op.join(p.work_dir, subj, p.inverse_dir)
if not op.isdir(evoked_dir):
os.mkdir(evoked_dir)
# read in raw files
raw_names = get_raw_fnames(p, subj, 'pca', False, False,
run_indices[si])
first_samps = []
last_samps = []
for raw_fname in raw_names:
raw = read_raw_fif(raw_fname, preload=False)
first_samps.append(raw._first_samps[0])
last_samps.append(raw._last_samps[-1])
raw = [read_raw_fif(fname, preload=False) for fname in raw_names]
_fix_raw_eog_cals(raw) # EOG epoch scales might be bad!
raw = concatenate_raws(raw)
# read in events
events = _read_events(p, subj, run_indices[si], raw)
this_decim = _handle_decim(decim[si], raw.info['sfreq'])
new_sfreq = raw.info['sfreq'] / this_decim
if p.disp_files:
print(' Epoching data (decim=%s -> sfreq=%0.1f Hz).' %
(this_decim, new_sfreq))
if new_sfreq not in sfreqs:
if len(sfreqs) > 0:
warnings.warn('resulting new sampling frequency %s not equal '
'to previous values %s' % (new_sfreq, sfreqs))
sfreqs.add(new_sfreq)
epochs_fnames, evoked_fnames = get_epochs_evokeds_fnames(
p, subj, analyses)
mat_file, fif_file = epochs_fnames
if p.autoreject_thresholds:
assert len(p.autoreject_types) > 0
assert all(a in ('mag', 'grad', 'eeg', 'ecg', 'eog')
for a in p.autoreject_types)
from autoreject import get_rejection_threshold
print(' Computing autoreject thresholds', end='')
rtmin = p.reject_tmin if p.reject_tmin is not None else p.tmin
rtmax = p.reject_tmax if p.reject_tmax is not None else p.tmax
temp_epochs = Epochs(raw,
events,
event_id=None,
tmin=rtmin,
tmax=rtmax,
baseline=_get_baseline(p),
proj=True,
reject=None,
flat=None,
preload=True,
decim=this_decim,
reject_by_annotation=p.reject_epochs_by_annot)
kwargs = dict()
if 'verbose' in get_args(get_rejection_threshold):
kwargs['verbose'] = False
new_dict = get_rejection_threshold(temp_epochs, **kwargs)
use_reject = dict()
msgs = list()
for k in p.autoreject_types:
msgs.append('%s=%d %s' % (k, DEFAULTS['scalings'][k] *
new_dict[k], DEFAULTS['units'][k]))
use_reject[k] = new_dict[k]
print(': ' + ', '.join(msgs))
hdf5_file = fif_file.replace('-epo.fif', '-reject.h5')
assert hdf5_file.endswith('.h5')
write_hdf5(hdf5_file, use_reject, overwrite=True)
else:
use_reject = _handle_dict(p.reject, subj)
# create epochs
flat = _handle_dict(p.flat, subj)
use_reject, use_flat = _restrict_reject_flat(use_reject, flat, raw)
epochs = Epochs(raw,
events,
event_id=old_dict,
tmin=p.tmin,
tmax=p.tmax,
baseline=_get_baseline(p),
reject=use_reject,
flat=use_flat,
proj=p.epochs_proj,
preload=True,
decim=this_decim,
on_missing=p.on_missing,
reject_tmin=p.reject_tmin,
reject_tmax=p.reject_tmax,
reject_by_annotation=p.reject_epochs_by_annot)
del raw
if epochs.events.shape[0] < 1:
epochs.plot_drop_log()
raise ValueError('No valid epochs')
drop_logs.append(epochs.drop_log)
ch_namess.append(epochs.ch_names)
# only kept trials that were not dropped
sfreq = epochs.info['sfreq']
# now deal with conditions to save evoked
if p.disp_files:
print(' Matching trial counts and saving data to disk.')
for var, name in ((out_names, 'out_names'), (out_numbers,
'out_numbers'),
(must_match, 'must_match'), (evoked_fnames,
'evoked_fnames')):
if len(var) != len(analyses):
raise ValueError('len(%s) (%s) != len(analyses) (%s)' %
(name, len(var), len(analyses)))
for analysis, names, numbers, match, fn in zip(analyses, out_names,
out_numbers, must_match,
evoked_fnames):
# do matching
numbers = np.asanyarray(numbers)
nn = numbers[numbers >= 0]
new_numbers = []
for num in numbers:
if num > 0 and num not in new_numbers:
# Eventually we could relax this requirement, but not
# having it in place is likely to cause people pain...
if any(num < n for n in new_numbers):
raise RuntimeError('each list of new_numbers must be '
' monotonically increasing')
new_numbers.append(num)
new_numbers = np.array(new_numbers)
in_names_match = in_names[match]
# use some variables to allow safe name re-use
offset = max(epochs.events[:, 2].max(), new_numbers.max()) + 1
safety_str = '__mnefun_copy__'
assert len(new_numbers) == len(names) # checked above
if p.match_fun is None:
# first, equalize trial counts (this will make a copy)
e = epochs[list(in_names[numbers > 0])]
if len(in_names_match) > 1:
e.equalize_event_counts(in_names_match)
# second, collapse relevant types
for num, name in zip(new_numbers, names):
collapse = [
x for x in in_names[num == numbers] if x in e.event_id
]
combine_event_ids(e,
collapse,
{name + safety_str: num + offset},
copy=False)
for num, name in zip(new_numbers, names):
e.events[e.events[:, 2] == num + offset, 2] -= offset
e.event_id[name] = num
del e.event_id[name + safety_str]
else: # custom matching
e = p.match_fun(epochs.copy(), analysis, nn, in_names_match,
names)
# now make evoked for each out type
evokeds = list()
n_standard = 0
kinds = ['standard']
if p.every_other:
kinds += ['even', 'odd']
for kind in kinds:
for name in names:
this_e = e[name]
if kind == 'even':
this_e = this_e[::2]
elif kind == 'odd':
this_e = this_e[1::2]
else:
assert kind == 'standard'
if len(this_e) > 0:
ave = this_e.average(picks='all')
stde = this_e.standard_error(picks='all')
if kind != 'standard':
ave.comment += ' %s' % (kind, )
stde.comment += ' %s' % (kind, )
evokeds.append(ave)
evokeds.append(stde)
if kind == 'standard':
n_standard += 2
write_evokeds(fn, evokeds)
naves = [
str(n) for n in sorted(
set([evoked.nave for evoked in evokeds[:n_standard]]))
]
naves = ', '.join(naves)
if p.disp_files:
print(' Analysis "%s": %s epochs / condition' %
(analysis, naves))
if p.disp_files:
print(' Saving epochs to disk.')
if 'mat' in p.epochs_type:
spio.savemat(mat_file,
dict(epochs=epochs.get_data(),
events=epochs.events,
sfreq=sfreq,
drop_log=epochs.drop_log),
do_compression=True,
oned_as='column')
if 'fif' in p.epochs_type:
epochs.save(fif_file, **_get_epo_kwargs())
if p.plot_drop_logs:
for subj, drop_log in zip(subjects, drop_logs):
plot_drop_log(drop_log, threshold=p.drop_thresh, subject=subj)
subj, cnt, len(behavior), len(event_order)) # saving changes to Epoch epochs.event_id = new_event_ids epochs.events = new_events print 'Downsampling %s...' % subj epochs.resample(300) # let's save a version without dropping based on SSPs red_epochs = epochs.copy() no_interest = np.nonzero(red_epochs.events[:, 2] < 13)[0] red_epochs.drop_epochs(no_interest) print 'Saving epochs and evoked data...' evokeds = [red_epochs[name].average() for name in ['STI-correct', 'STI-incorrect']] mne.write_evokeds(dir_out + subj + '_stop_parsed_matched_BP1-100_DS300-ave.fif', evokeds) new_fname = dir_out + subj + '_stop_parsed_matched_BP1-100_DS300-epo.fif.gz' red_epochs.save(new_fname) # now we save a version after cleaning with SSPs # grab SSP vectors from previous cleanup sessions epochs_fname = clean_dir + subj + '_stop_parsed_matched_clean_BP1-35_DS120-epo.fif.gz' epochs35 = mne.read_epochs(epochs_fname, proj=True) bad_epochs = [i for i, j in enumerate(epochs35.drop_log) if len(j) > 0] epochs.drop_epochs(bad_epochs) epochs.info['projs'] = epochs35.info['projs'] # removing the epochs we don't want, need to do it again because indices # changed after removing bad epochs based on SSP no_interest = np.nonzero(epochs.events[:, 2] < 13)[0] epochs.drop_epochs(no_interest)
picks=picks,
baseline=(None, 0),
reject=dict(eeg=80e-6, eog=150e-6),
preload=True)
epochs.plot()
# Look at channels that caused dropped events, showing that the subject's
# blinks were likely to blame for most epochs being dropped
epochs.drop_bad_epochs()
epochs.plot_drop_log(subject='sample')
# Average epochs and get evoked data corresponding to the left stimulation
evoked = epochs['Left'].average()
evoked.save('sample_audvis_eeg-ave.fif') # save evoked data to disk
###############################################################################
# View evoked response
evoked.plot()
###############################################################################
# Save evoked responses for different conditions to disk
# average epochs and get Evoked datasets
evokeds = [epochs[cond].average() for cond in ['Left', 'Right']]
# save evoked data to disk
mne.write_evokeds('sample_auditory_and_visual_eeg-ave.fif', evokeds)
picks = mne.pick_types(raw.info, meg=False, eeg=True, stim=False, eog=True,
include=include, exclude='bads')
# Read epochs
epochs = mne.Epochs(raw, events, event_ids, tmin, tmax, picks=picks,
baseline=(None, 0), reject=dict(eeg=80e-6, eog=150e-6))
# Let's equalize the trial counts in each condition
epochs.equalize_event_counts(['AudL', 'AudR', 'VisL', 'VisR'], copy=False)
# Now let's combine some conditions
combine_event_ids(epochs, ['AudL', 'AudR'], {'Auditory': 12}, copy=False)
combine_event_ids(epochs, ['VisL', 'VisR'], {'Visual': 34}, copy=False)
# average epochs and get Evoked datasets
evokeds = [epochs[cond].average() for cond in ['Auditory', 'Visual']]
# save evoked data to disk
mne.write_evokeds('sample_auditory_and_visual_eeg-ave.fif', evokeds)
###############################################################################
# View evoked response
import matplotlib.pyplot as plt
plt.clf()
ax = plt.subplot(2, 1, 1)
evokeds[0].plot(axes=ax)
plt.title('EEG evoked potential, auditory trials')
plt.ylabel('Potential (uV)')
ax = plt.subplot(2, 1, 2)
evokeds[1].plot(axes=ax)
plt.title('EEG evoked potential, visual trials')
plt.ylabel('Potential (uV)')
plt.show()
def test_dipole_fitting():
"""Test dipole fitting"""
amp = 10e-9
tempdir = _TempDir()
rng = np.random.RandomState(0)
fname_dtemp = op.join(tempdir, 'test.dip')
fname_sim = op.join(tempdir, 'test-ave.fif')
fwd = convert_forward_solution(read_forward_solution(fname_fwd),
surf_ori=False, force_fixed=True)
evoked = read_evokeds(fname_evo)[0]
cov = read_cov(fname_cov)
n_per_hemi = 5
vertices = [np.sort(rng.permutation(s['vertno'])[:n_per_hemi])
for s in fwd['src']]
nv = sum(len(v) for v in vertices)
stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
with warnings.catch_warnings(record=True): # semi-def cov
evoked = generate_evoked(fwd, stc, evoked, cov, snr=20,
random_state=rng)
# For speed, let's use a subset of channels (strange but works)
picks = np.sort(np.concatenate([
pick_types(evoked.info, meg=True, eeg=False)[::2],
pick_types(evoked.info, meg=False, eeg=True)[::2]]))
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
write_evokeds(fname_sim, evoked)
# Run MNE-C version
run_subprocess([
'mne_dipole_fit', '--meas', fname_sim, '--meg', '--eeg',
'--noise', fname_cov, '--dip', fname_dtemp,
'--mri', fname_fwd, '--reg', '0', '--tmin', '0',
])
dip_c = read_dipole(fname_dtemp)
# Run mne-python version
sphere = make_sphere_model(head_radius=0.1)
dip, residuals = fit_dipole(evoked, fname_cov, sphere, fname_fwd)
# Sanity check: do our residuals have less power than orig data?
data_rms = np.sqrt(np.sum(evoked.data ** 2, axis=0))
resi_rms = np.sqrt(np.sum(residuals ** 2, axis=0))
assert_true((data_rms > resi_rms).all())
# Compare to original points
transform_surface_to(fwd['src'][0], 'head', fwd['mri_head_t'])
transform_surface_to(fwd['src'][1], 'head', fwd['mri_head_t'])
src_rr = np.concatenate([s['rr'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
src_nn = np.concatenate([s['nn'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
# MNE-C skips the last "time" point :(
dip.crop(dip_c.times[0], dip_c.times[-1])
src_rr, src_nn = src_rr[:-1], src_nn[:-1]
# check that we did at least as well
corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
for d in (dip_c, dip):
new = d.pos
diffs = new - src_rr
corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
gc_dists += [180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori,
axis=1)))]
amp_errs += [np.sqrt(np.mean((amp - d.amplitude) ** 2))]
gofs += [np.mean(d.gof)]
assert_true(dists[0] >= dists[1], 'dists: %s' % dists)
assert_true(corrs[0] <= corrs[1], 'corrs: %s' % corrs)
assert_true(gc_dists[0] >= gc_dists[1], 'gc-dists (ori): %s' % gc_dists)
assert_true(amp_errs[0] >= amp_errs[1], 'amplitude errors: %s' % amp_errs)
print(' PSDs')
psds = np.abs(
np.fft.rfft(epochs.get_data()[:, picks], axis=-1, n=n_fft))
freqs = np.fft.rfftfreq(n_fft, 1. / epochs.info['sfreq'])
# psds, freqs = mne.time_frequency.psd_multitaper(
# epochs, fmin, fmax, picks=picks, n_jobs=12)
info = mne.pick_info(epochs.info, picks)
info['sfreq'] = 1. / np.diff(freqs[:2])[0]
psds = np.mean(psds, axis=0) # average of an average is okay here
evoked = mne.EvokedArray(psds,
info,
tmin=freqs[0],
nave=len(epochs),
comment=kind)
evokeds.append(evoked)
mne.write_evokeds(op.join(psd_dir, subject + '_psd-ave.fif'), evokeds)
flim = [1, 50]
fnames = sorted(glob.glob(op.join(psd_dir, 'f2f_*_OTP_psd-ave.fif')))
evokeds = list()
for kind in kinds:
evoked = [mne.read_evokeds(fname, kind) for fname in fnames]
use_names = set(evoked[0].ch_names)
for e in evoked[1:]:
use_names = use_names & set(e.ch_names)
use_names = list(use_names)
for e in evoked:
e.pick_channels(use_names)
evoked = mne.combine_evoked(evoked, 'nave')
evoked.crop(*flim)
evoked.comment = kind.capitalize()
def test_shift_time_evoked():
"""Test for shifting of time scale."""
tempdir = _TempDir()
# Shift backward
ave = read_evokeds(fname, 0).shift_time(-0.1, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
# Shift forward twice the amount
ave_bshift = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
ave_bshift.shift_time(0.2, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave_bshift)
# Shift backward again
ave_fshift = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
ave_fshift.shift_time(-0.1, relative=True)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave_fshift)
ave_normal = read_evokeds(fname, 0)
ave_relative = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
assert_allclose(ave_normal.data, ave_relative.data, atol=1e-16, rtol=1e-3)
assert_array_almost_equal(ave_normal.times, ave_relative.times, 8)
assert_equal(ave_normal.last, ave_relative.last)
assert_equal(ave_normal.first, ave_relative.first)
# Absolute time shift
ave = read_evokeds(fname, 0)
ave.shift_time(-0.3, relative=False)
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave_absolute = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
assert_allclose(ave_normal.data, ave_absolute.data, atol=1e-16, rtol=1e-3)
assert_equal(ave_absolute.first, int(-0.3 * ave.info['sfreq']))
# subsample shift
shift = 1e-6 # 1 µs, should be well below 1/sfreq
ave = read_evokeds(fname, 0)
times = ave.times
ave.shift_time(shift)
assert_allclose(times + shift, ave.times, atol=1e-16, rtol=1e-12)
# test handling of Evoked.first, Evoked.last
ave = read_evokeds(fname, 0)
first_last = np.array([ave.first, ave.last])
# should shift by 0 samples
ave.shift_time(1e-6)
assert_array_equal(first_last, np.array([ave.first, ave.last]))
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave_loaded = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
assert_array_almost_equal(ave.times, ave_loaded.times, 8)
# should shift by 57 samples
ave.shift_time(57. / ave.info['sfreq'])
assert_array_equal(first_last + 57, np.array([ave.first, ave.last]))
write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
ave_loaded = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
assert_array_almost_equal(ave.times, ave_loaded.times, 8)
all_evokeds = [aud_l, aud_r, vis_l, vis_r]
print(all_evokeds)
###############################################################################
# This can be simplified with a Python list comprehension:
all_evokeds = [epochs[cond].average() for cond in sorted(event_id.keys())]
print(all_evokeds)
# Then, we construct and plot an unweighted average of left vs. right trials
# this way, too:
mne.combine_evoked(
all_evokeds, weights=(0.25, -0.25, 0.25, -0.25)).plot_joint(**joint_kwargs)
###############################################################################
# Often, it makes sense to store Evoked objects in a dictionary or a list -
# either different conditions, or different subjects.
# If they are stored in a list, they can be easily averaged, for example,
# for a grand average across subjects (or conditions).
grand_average = mne.grand_average(all_evokeds)
mne.write_evokeds('/tmp/tmp-ave.fif', all_evokeds)
# If Evokeds objects are stored in a dictionary, they can be retrieved by name.
all_evokeds = dict((cond, epochs[cond].average()) for cond in event_id)
print(all_evokeds['left/auditory'])
# Besides for explicit access, this can be used for example to set titles.
for cond in all_evokeds:
all_evokeds[cond].plot_joint(title=cond, **joint_kwargs)
# Set up pick list: EEG + STI 014 - bad channels (modify to your needs)
include = [] # or stim channels ['STI 014']
# raw.info['bads'] += ['EEG 053'] # bads + 1 more
# pick EEG and MEG channels
picks = mne.pick_types(raw.info, meg=True, eeg=False, stim=False, eog=True,
include=include, exclude='bads')
# Read epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), reject=reject,
preload=True)
# Plot epochs.
epochs.plot(trellis=False, title='Auditory left/right')
# Look at channels that caused dropped events, showing that the subject's
# blinks were likely to blame for most epochs being dropped
epochs.drop_bad_epochs()
epochs.plot_drop_log(subject='sample')
# Average epochs and get evoked data corresponding to the left stimulation
###############################################################################
# Save evoked responses for different conditions to disk
# average epochs and get Evoked datasets
evokeds = [epochs[cond].average() for cond in ['ent_left', 'ent_right',
'ctl_left', 'ctl_right']]
# save evoked data to disk
mne.write_evokeds('0001_p_03_filter_ds_ica-mc_raw_tsss-ave.fif', evokeds)
def test_dipole_fitting():
"""Test dipole fitting."""
amp = 100e-9
tempdir = _TempDir()
rng = np.random.RandomState(0)
fname_dtemp = op.join(tempdir, 'test.dip')
fname_sim = op.join(tempdir, 'test-ave.fif')
fwd = convert_forward_solution(read_forward_solution(fname_fwd),
surf_ori=False, force_fixed=True,
use_cps=True)
evoked = read_evokeds(fname_evo)[0]
cov = read_cov(fname_cov)
n_per_hemi = 5
vertices = [np.sort(rng.permutation(s['vertno'])[:n_per_hemi])
for s in fwd['src']]
nv = sum(len(v) for v in vertices)
stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
evoked = simulate_evoked(fwd, stc, evoked.info, cov, nave=evoked.nave,
random_state=rng)
# For speed, let's use a subset of channels (strange but works)
picks = np.sort(np.concatenate([
pick_types(evoked.info, meg=True, eeg=False)[::2],
pick_types(evoked.info, meg=False, eeg=True)[::2]]))
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
write_evokeds(fname_sim, evoked)
# Run MNE-C version
run_subprocess([
'mne_dipole_fit', '--meas', fname_sim, '--meg', '--eeg',
'--noise', fname_cov, '--dip', fname_dtemp,
'--mri', fname_fwd, '--reg', '0', '--tmin', '0',
])
dip_c = read_dipole(fname_dtemp)
# Run mne-python version
sphere = make_sphere_model(head_radius=0.1)
with pytest.warns(RuntimeWarning, match='projection'):
dip, residual = fit_dipole(evoked, cov, sphere, fname_fwd)
assert isinstance(residual, Evoked)
# Sanity check: do our residuals have less power than orig data?
data_rms = np.sqrt(np.sum(evoked.data ** 2, axis=0))
resi_rms = np.sqrt(np.sum(residual.data ** 2, axis=0))
assert (data_rms > resi_rms * 0.95).all(), \
'%s (factor: %s)' % ((data_rms / resi_rms).min(), 0.95)
# Compare to original points
transform_surface_to(fwd['src'][0], 'head', fwd['mri_head_t'])
transform_surface_to(fwd['src'][1], 'head', fwd['mri_head_t'])
assert_equal(fwd['src'][0]['coord_frame'], FIFF.FIFFV_COORD_HEAD)
src_rr = np.concatenate([s['rr'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
src_nn = np.concatenate([s['nn'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
# MNE-C skips the last "time" point :(
out = dip.crop(dip_c.times[0], dip_c.times[-1])
assert (dip is out)
src_rr, src_nn = src_rr[:-1], src_nn[:-1]
# check that we did about as well
corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
for d in (dip_c, dip):
new = d.pos
diffs = new - src_rr
corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
gc_dists += [180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori,
axis=1)))]
amp_errs += [np.sqrt(np.mean((amp - d.amplitude) ** 2))]
gofs += [np.mean(d.gof)]
# XXX possibly some OpenBLAS numerical differences make
# things slightly worse for us
factor = 0.7
assert dists[0] / factor >= dists[1], 'dists: %s' % dists
assert corrs[0] * factor <= corrs[1], 'corrs: %s' % corrs
assert gc_dists[0] / factor >= gc_dists[1] * 0.8, \
'gc-dists (ori): %s' % gc_dists
assert amp_errs[0] / factor >= amp_errs[1],\
'amplitude errors: %s' % amp_errs
# This one is weird because our cov/sim/picking is weird
assert gofs[0] * factor <= gofs[1] * 2, 'gof: %s' % gofs