run=list(filter(lambda x: "run-" in x, labels))
if run:
runValue=run[0].split('-')[1]
entities['run']=runValue
except KeyError:
customLabels= None
entities['subject']=subject
if session_label != "nosession":
entities['session']=session_label
files = layout.get(return_type='file', **entities)
if files:
sourcefile = files[0]
entities = layout.parse_file_entities(sourcefile)
entities['extension'] = 'json'
files = layout.get(return_type='file', **entities)
if files:
sourcejson = files[0]
else:
sourcejson = None
else:
sourcefile = None
try:
destination = item["destination"]
except KeyError:
destination = []
logtext (LOGFILE, 'No Destination provided for copy')
class BidsDirectory(object):
"""BIDS directory querying, currently a wrapper for pybids.BIDSLayout
"""
def __init__(self, directory):
self.root = directory
def index(self, reindexing=False):
"""Map out BIDS structure in the directory
Will insert missing dataset_description.json for fmriprep
"""
self.layout = BIDSLayout(
self.root,
derivatives=True,
## variant was replaced by desc in the spec
## but some datasets have not been updated
## and we don't want to include e.g. ICASSO runs
ignore=[re.compile('_variant-')]
)
if self.has_pipeline_with_missing_description('fmriprep'):
assert not reindexing
self.insert_pipeline_description('fmriprep')
self.index(reindexing=True)
def has_pipeline_with_missing_description(self, pipeline_name):
pipeline_dir = os.path.join(self.root, 'derivatives', pipeline_name)
desc_file = os.path.join(pipeline_dir, 'dataset_description.json')
if os.path.isdir(pipeline_dir):
return not os.path.isfile(desc_file)
return False
def insert_pipeline_description(self, pipeline_name):
pipeline_dir = os.path.join(self.root, 'derivatives', pipeline_name)
desc_file = os.path.join(pipeline_dir, 'dataset_description.json')
desc = copy.deepcopy(self.layout.description)
desc["PipelineDescription"] = {"Name": pipeline_name}
with open(desc_file, 'w') as fh:
json.dump(desc, fh)
time.sleep(0.1)
def get_preprocessed_subjects_ids(self):
return self.layout.get(return_type='id', target='subject')
def get_tasks_for_subject(self, subject):
return self.layout.get(
subject=subject,
return_type='id',
target='task'
)
def get_sessions_for_task_and_subject(self, task, subject):
return self.layout.get(
subject=subject,
task=task,
return_type='id',
target='session'
)
def get_filepaths_bold_runs(self, subject, task, session):
return sorted(self.layout.get(
subject=subject,
task=task,
session=session,
suffix='preproc',
return_type='file'
))
def get_filepaths_event_runs(self, subject, task, session):
return sorted(self.layout.get(
subject=subject,
task=task,
session=session,
suffix='events',
return_type='file'
))
def get_metas_boldfiles(self, files):
"""Return metadata for raw files corresponding to the given files
Args:
files (list): List of filepaths for fmriprep preprocessed runs
Returns:
list: List of metadata dictionaries
"""
metas = []
keys = ('subject', 'task', 'session', 'run')
for derivfile in files:
entities = self.layout.parse_file_entities(derivfile)
query = {k:entities[k] for k in keys if k in entities}
query['suffix'] = 'bold' # get metadata from raw
metas.append(self.layout.get(**query)[0].metadata)
return metas
def subject_id_from_number(self, sub_num):
ids = self.layout.get(return_type='id', target='subject')
for nzeros in [0, 2]:
candidate = str(sub_num).zfill(nzeros)
if candidate in ids:
return candidate
def match_run_files(self, bold_files, evnt_files):
"""Ensure that bold and event files are matched by run
Args:
bold_files (list): List of bold files
evnt_files (list): List of events files
Returns:
(tuple): Tuple of modified (bold_files, evnt_files)
"""
get_ents = self.layout.parse_file_entities
runs_bold = [get_ents(f)['run'] for f in bold_files]
runs_evnt = [get_ents(f)['run'] for f in evnt_files]
runs_both = set(runs_bold).intersection(set(runs_evnt))
def in_both(fpath):
return get_ents(fpath)['run'] in runs_both
return (
list(filter(in_both, bold_files)),
list(filter(in_both, evnt_files))
)
