def run_report_sensor(*,
cfg: SimpleNamespace,
subject: str,
session: Optional[str] = None,
report: mne.Report) -> mne.Report:
import matplotlib.pyplot as plt
msg = 'Generating sensor-space analysis report …'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
if report is None:
report = _gen_empty_report(cfg=cfg, subject=subject, session=session)
bids_path = BIDSPath(subject=subject,
session=session,
task=cfg.task,
acquisition=cfg.acq,
run=None,
recording=cfg.rec,
space=cfg.space,
extension='.fif',
datatype=cfg.datatype,
root=cfg.deriv_root,
check=False)
fname_epo_clean = bids_path.copy().update(processing='clean', suffix='epo')
fname_ave = bids_path.copy().update(suffix='ave')
fname_decoding = bids_path.copy().update(processing=None,
suffix='decoding',
extension='.mat')
fname_tfr_pow = bids_path.copy().update(suffix='power+condition+tfr',
extension='.h5')
###########################################################################
#
# Visualize evoked responses.
#
if cfg.conditions is None:
conditions = []
elif isinstance(cfg.conditions, dict):
conditions = list(cfg.conditions.keys())
else:
conditions = cfg.conditions.copy()
conditions.extend(cfg.contrasts)
if conditions:
evokeds = mne.read_evokeds(fname_ave)
else:
evokeds = []
if evokeds:
msg = (f'Adding {len(conditions)} evoked signals and contrasts to the '
f'report.')
else:
msg = 'No evoked conditions or contrasts found.'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
for condition, evoked in zip(conditions, evokeds):
if cfg.analyze_channels:
evoked.pick(cfg.analyze_channels)
if condition in cfg.conditions:
title = f'Condition: {condition}'
tags = ('evoked', condition.lower().replace(' ', '-'))
else: # It's a contrast of two conditions.
title = f'Contrast: {condition[0]} – {condition[1]}'
tags = ('evoked', 'contrast',
f"{condition[0].lower().replace(' ', '-')}-"
f"{condition[1].lower().replace(' ', '-')}")
report.add_evokeds(evokeds=evoked, titles=title, tags=tags)
###########################################################################
#
# Visualize decoding results.
#
if cfg.decode:
msg = 'Adding time-by-time decoding results to the report.'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
epochs = mne.read_epochs(fname_epo_clean)
for contrast in cfg.contrasts:
cond_1, cond_2 = contrast
a_vs_b = f'{cond_1}+{cond_2}'.replace(op.sep, '')
processing = f'{a_vs_b}+{cfg.decoding_metric}'
processing = processing.replace('_', '-').replace('-', '')
fname_decoding_ = (fname_decoding.copy().update(
processing=processing))
decoding_data = loadmat(fname_decoding_)
del fname_decoding_, processing, a_vs_b
fig = plot_decoding_scores(
times=epochs.times,
cross_val_scores=decoding_data['scores'],
metric=cfg.decoding_metric)
title = f'Time-by-time Decoding: {cond_1} ./. {cond_2}'
caption = (f'{len(epochs[cond_1])} × {cond_1} ./. '
f'{len(epochs[cond_2])} × {cond_2}')
tags = ('epochs', 'contrast',
f"{contrast[0].lower().replace(' ', '-')}-"
f"{contrast[1].lower().replace(' ', '-')}")
report.add_figure(fig=fig, title=title, caption=caption, tags=tags)
plt.close(fig)
del decoding_data, cond_1, cond_2, title, caption
del epochs
###########################################################################
#
# Visualize TFR as topography.
#
if cfg.time_frequency_conditions is None:
conditions = []
elif isinstance(cfg.time_frequency_conditions, dict):
conditions = list(cfg.time_frequency_conditions.keys())
else:
conditions = cfg.time_frequency_conditions.copy()
if conditions:
msg = 'Adding TFR analysis results to the report.'
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
for condition in conditions:
cond = config.sanitize_cond_name(condition)
fname_tfr_pow_cond = str(fname_tfr_pow.copy()).replace(
"+condition+", f"+{cond}+")
power = mne.time_frequency.read_tfrs(fname_tfr_pow_cond)
fig = power[0].plot_topo(show=False,
fig_facecolor='w',
font_color='k',
border='k')
report.add_figure(fig=fig,
title=f'TFR: {condition}',
caption=f'TFR Power: {condition}',
tags=('time-frequency',
condition.lower().replace(' ', '-')))
plt.close(fig)
return report
