def get_task():
if not task:
tasks = get_entity_vals(bids_root, entity_key='task')
if not tasks:
return None
else:
return tasks[0]
else:
return task
def get_runs():
runs_ = copy.deepcopy(runs) # Avoid clash with global variable.
if runs_ == 'all':
runs_ = get_entity_vals(bids_root, entity_key='run')
if not runs_:
return [None]
else:
return runs_
def get_sessions():
sessions_ = copy.deepcopy(sessions) # Avoid clash with global variable.
if sessions_ == 'all':
sessions_ = get_entity_vals(bids_root, entity_key='session')
if not sessions_:
return [None]
else:
return sessions_
def get_subjects():
if subjects_list == 'all':
s = get_entity_vals(bids_root, entity_key='subject')
else:
s = subjects_list
subjects = set(s) - set(exclude_subjects)
# Drop empty-room subject.
subjects = subjects - set(['emptyroom'])
return list(subjects)
def get_sessions():
sessions_ = copy.deepcopy(sessions) # Avoid clash with global variable.
env = os.environ
if env.get('MNE_BIDS_STUDY_SESSION'):
sessions_ = env['MNE_BIDS_STUDY_SESSION']
elif sessions_ == 'all':
sessions_ = get_entity_vals(bids_root, entity_key='session')
if not sessions_:
return [None]
else:
return sessions_
def get_runs():
runs_ = copy.deepcopy(runs) # Avoid clash with global variable.
valid_runs = get_entity_vals(bids_root, entity_key='run')
env = os.environ
if env.get('MNE_BIDS_STUDY_RUN'):
env_run = env['MNE_BIDS_STUDY_RUN']
raise ValueError(f'Invalid run. It can be {valid_runs} but '
f'got {env_run}')
runs_ = [env_run]
elif runs_ == 'all':
runs_ = valid_runs
if not runs_:
return [None]
else:
return runs_
def get_task() -> Optional[str]:
global task
env = os.environ
valid_tasks = get_entity_vals(bids_root, entity_key='task')
if env.get('MNE_BIDS_STUDY_TASK'):
task = env['MNE_BIDS_STUDY_TASK']
if task not in valid_tasks:
raise ValueError(f'Invalid task. It can be: '
f'{", ".join(valid_tasks)} but got: {task}')
if not task:
if not valid_tasks:
return None
else:
return valid_tasks[0]
else:
return task
def get_subjects() -> List[str]:
global subjects
env = os.environ
valid_subjects = get_entity_vals(bids_root, entity_key='subject')
if env.get('MNE_BIDS_STUDY_SUBJECT'):
env_subject = env['MNE_BIDS_STUDY_SUBJECT']
if env_subject not in valid_subjects:
raise ValueError(
f'Invalid subject. It can be {valid_subjects} but '
f'got {env_subject}')
s = [env_subject]
elif subjects == 'all':
s = valid_subjects
else:
s = subjects
subjects = set(s) - set(exclude_subjects)
# Drop empty-room subject.
subjects = subjects - set(['emptyroom'])
return sorted(subjects)
def make_report(root, session=None, verbose=True):
"""Create a methods paragraph string from BIDS dataset.
Summarizes the REQUIRED components in the BIDS specification
and also some RECOMMENDED components. Currently, the methods
paragraph summarize the:
- dataset_description.json file
- (optional) participants.tsv file
- (optional) datatype-agnostic files for (M/I)EEG data,
which reads files from the ``*_scans.tsv`` file.
Parameters
----------
root : str | pathlib.Path
The path of the root of the BIDS compatible folder.
session : str | None
The (optional) session for a item. Corresponds to "ses".
verbose : bool | None
Set verbose output to true or false.
Returns
-------
paragraph : str
The paragraph wrapped with 80 characters per line
describing the summary of the subjects.
"""
# high level summary
subjects = get_entity_vals(root, entity_key='subject')
sessions = get_entity_vals(root, entity_key='session')
modalities = get_datatypes(root)
# only summarize allowed modalities (MEG/EEG/iEEG) data
# map them to a pretty looking string
datatype_map = {
'meg': 'MEG',
'eeg': 'EEG',
'ieeg': 'iEEG',
}
modalities = [
datatype_map[datatype] for datatype in modalities
if datatype in datatype_map.keys()
]
# REQUIRED: dataset_description.json summary
dataset_summary = _summarize_dataset(root)
# RECOMMENDED: participants summary
participant_summary = _summarize_participants_tsv(root)
# RECOMMENDED: scans summary
scans_summary = _summarize_scans(root, session=session, verbose=verbose)
# turn off 'recommended' report summary
# if files are not available to summarize
if not participant_summary:
participant_template = ''
else:
content = f'{FUNCTION_TEMPLATE}{PARTICIPANTS_TEMPLATE}'
participant_template = Template(content=content)
participant_template = participant_template.substitute(
**participant_summary)
if verbose:
print(f'The participant template found: {participant_template}')
dataset_summary['PARTICIPANTS_TEMPLATE'] = str(participant_template)
if not scans_summary:
datatype_agnostic_template = ''
else:
datatype_agnostic_template = DATATYPE_AGNOSTIC_TEMPLATE
dataset_summary.update({
'system': modalities,
'n_subjects': len(subjects),
'n_sessions': len(sessions),
'sessions': sessions,
})
# XXX: add channel summary for modalities (ieeg, meg, eeg)
# create the content and mne Template
# lower-case templates are "Recommended",
# while upper-case templates are "Required".
content = f'{FUNCTION_TEMPLATE}{BIDS_DATASET_TEMPLATE}' \
f'{datatype_agnostic_template}'
paragraph = Template(content=content)
paragraph = paragraph.substitute(**dataset_summary, **scans_summary)
# Clean paragraph
paragraph = paragraph.replace('\n', ' ')
paragraph = paragraph.replace(' ', ' ')
return '\n'.join(textwrap.wrap(paragraph, width=80))
def make_report(root, session=None, verbose=None):
"""Create a methods paragraph string from BIDS dataset.
Summarizes the REQUIRED components in the BIDS specification
and also some RECOMMENDED components. Currently, the methods
paragraph summarize the:
- dataset_description.json file
- (optional) participants.tsv file
- (optional) datatype-agnostic files for (M/I)EEG data,
which reads files from the ``*_scans.tsv`` file.
Parameters
----------
root : path-like
The path of the root of the BIDS compatible folder.
session : str | None
The (optional) session for a item. Corresponds to "ses".
%(verbose)s
Returns
-------
paragraph : str
The paragraph wrapped with 80 characters per line
describing the summary of the subjects.
"""
# high level summary
subjects = get_entity_vals(root, entity_key='subject')
sessions = get_entity_vals(root, entity_key='session')
modalities = get_datatypes(root)
# only summarize allowed modalities (MEG/EEG/iEEG) data
# map them to a pretty looking string
datatype_map = {
'meg': 'MEG',
'eeg': 'EEG',
'ieeg': 'iEEG',
}
modalities = [
datatype_map[datatype] for datatype in modalities
if datatype in datatype_map.keys()
]
# REQUIRED: dataset_description.json summary
dataset_summary = _summarize_dataset(root)
# RECOMMENDED: participants summary
participant_summary = _summarize_participants_tsv(root)
# RECOMMENDED: scans summary
scans_summary = _summarize_scans(root, session=session)
dataset_agnostic_summary = scans_summary.copy()
dataset_agnostic_summary['system'] = _pretty_str(modalities)
# turn off 'recommended' report summary
# if files are not available to summarize
if not participant_summary:
participants_info = ''
else:
particpants_info_template = jinja_env.get_template(
'participants.jinja')
participants_info = particpants_info_template.render(
**participant_summary)
logger.info(f'The participant template found: {participants_info}')
if not scans_summary:
datatype_agnostic_info = ''
else:
datatype_agnostic_template = jinja_env.get_template(
'datatype_agnostic.jinja')
datatype_agnostic_info = datatype_agnostic_template.render(
**dataset_agnostic_summary)
dataset_summary.update({
'n_subjects': len(subjects),
'participants_info': participants_info,
'n_sessions': len(sessions),
'sessions': _pretty_str(sessions),
})
# XXX: add channel summary for modalities (ieeg, meg, eeg)
# create the content and mne Template
# lower-case templates are "Recommended",
# while upper-case templates are "Required".
dataset_summary_template = jinja_env.get_template('dataset_summary.jinja')
dataset_summary_info = dataset_summary_template.render(**dataset_summary)
# Concatenate info and clean the paragraph
paragraph = f'{dataset_summary_info}\n{datatype_agnostic_info}'
paragraph = paragraph.replace('\n', ' ')
while ' ' in paragraph:
paragraph = paragraph.replace(' ', ' ')
return '\n'.join(textwrap.wrap(paragraph, width=80))
