def load_candidates_from_bids(self):
"""
Loads the list of candidates from the BIDS study. List of
participants and their information will be stored in participants_info.
:return: list of dictionaries with participant information from BIDS
:rtype: list
"""
if self.verbose:
print('Grepping candidates from the BIDS layout...')
# grep the participant.tsv file and parse it
participants_info = None
for file in self.bids_layout.get(suffix='participants',
return_type='filename'):
# note file[0] returns the path to participants.tsv
if 'participants.tsv' in file:
participants_info = utilities.read_tsv_file(file)
else:
continue
self.candidates_list_validation(participants_info)
if self.verbose:
print('\t=> List of participants found:')
for participant in participants_info:
print('\t\t' + participant['participant_id'])
print('\n')
return participants_info
def __init__(self, scans_tsv_file, acquisition_file, verbose):
"""
Constructor method for the ScansTSV class
:param scans_tsv_file : path to the BIDS sub-XXX_scans.tsv file
:type scans_tsv_file : str
:param acquisition_file: path to the acquisition file (.nii, .set, .edf...)
:type acquisition_file: str
"""
self.verbose = verbose
# store files' paths
self.scans_tsv_file = scans_tsv_file
self.acquisition_file = acquisition_file
# read the TSV file and store the header names and data
self.tsv_entries = utilities.read_tsv_file(self.scans_tsv_file)
self.tsv_headers = self.tsv_entries[0]
# get the acquisition information for the acquisition file
self.acquisition_data = self.find_acquisition_data()
def fetch_and_insert_event_file(self,
physiological_file_id,
derivatives=None):
"""
Gather raw channel file information to insert into
physiological_task_event. Once all the information has been gathered,
it will call Physiological.insert_event_file that will perform the
insertion into physiological_task_event, linking it to the
PhysiologicalFileID already registered.
:param physiological_file_id: PhysiologicalFileID of the associated
physiological file already inserted into
the physiological_file table
:type physiological_file_id: int
:param derivatives: dictionary with derivative folder information if
the event file to insert is a derivative file.
Set by default to None when inserting raw file.
:type derivatives: dict
:return: channel file path in the /DATA_DIR/bids_import directory
:rtype: str
"""
# load the Physiological object that will be used to insert the
# physiological data into the database
physiological = Physiological(self.db, self.verbose)
# check if inserting derivatives to use the derivative_pattern to
# grep for the eeg file
derivative_pattern = None
derivative_path = None
if derivatives:
derivative_pattern = derivatives['derivative_name'] + "/sub-"
derivative_path = self.get_derivatives_path(derivatives)
event_file = BidsReader.grep_file(
files_list=self.events_files,
match_pattern='events.tsv',
derivative_pattern=derivative_pattern)
if not event_file:
message = "WARNING: no events file associated with " \
"physiological file ID " + str(physiological_file_id)
print(message)
return None
else:
result = physiological.grep_event_from_physiological_file_id(
physiological_file_id)
event_path = result[0]['FilePath'] if result else None
event_data = utilities.read_tsv_file(event_file)
if not result:
# copy the event file to the LORIS BIDS import directory
event_path = self.copy_file_to_loris_bids_dir(
event_file, derivative_path)
# get the blake2b hash of the task events file
blake2 = blake2b(event_file.encode('utf-8')).hexdigest()
# insert event data in the database
physiological.insert_event_file(event_data, event_path,
physiological_file_id, blake2)
return event_path