def _update_qc_reviewers(entries):
"""
Support function for update_checklist(). Updates QC info on the dashboard.
"""
try:
user = dashboard.get_default_user()
except:
raise MetadataException(
"Can't update dashboard QC information without "
"a default dashboard user defined. Please add "
"'DEFAULT_DASH_USER' to your config file.")
for subject in entries:
timepoint = dashboard.get_subject(subject)
if not timepoint or not timepoint.sessions:
raise MetadataException("{} not found in the in the dashboard "
"database.".format(subject))
comment = entries[subject]
if not comment:
# User was just registering a new QC entry. As long as the
# session exists in the database there is no work to do.
continue
for num in timepoint.sessions:
session = timepoint.sessions[num]
if session.is_qcd():
# Dont risk writing over QC-ers from the dashboard.
continue
session.sign_off(user.id)
def _fetch_blacklist(
scan=None,
subject=None,
bids_ses=None,
study=None,
config=None,
use_bids=False,
):
"""
Helper function for 'read_blacklist()'. Gets the blacklist contents from
the dashboard's database
"""
if not (scan or subject or study or config):
raise MetadataException(
"Can't retrieve dashboard blacklist info "
"without either 1) a scan name 2) a subject "
"ID 3) a study ID or 4) a datman config "
"object"
)
if scan:
if use_bids:
db_scan = dashboard.get_bids_scan(scan)
else:
db_scan = dashboard.get_scan(scan)
if db_scan and db_scan.blacklisted():
try:
return db_scan.get_comment()
except Exception:
return db_scan.get_comment()
return
if subject:
if use_bids or bids_ses:
if not bids_ses:
bids_ses = "01"
db_subject = dashboard.get_bids_subject(subject, bids_ses, study)
else:
db_subject = dashboard.get_subject(subject)
blacklist = db_subject.get_blacklist_entries()
else:
if config:
study = config.study_name
db_study = dashboard.get_project(study)
blacklist = db_study.get_blacklisted_scans()
entries = {}
for entry in blacklist:
if use_bids:
if not entry.scan.bids_name:
# Ignore scans without a bids name if bids was requested
continue
scan_name = entry.scan.bids_name
else:
scan_name = str(entry.scan) + "_" + entry.scan.description
entries[scan_name] = entry.comment
return entries
def _fetch_blacklist(scan=None, subject=None, study=None, config=None):
"""
Helper function for 'read_blacklist()'. Gets the blacklist contents from
the dashboard's database
"""
if not (scan or subject or study or config):
raise MetadataException(
"Can't retrieve dashboard blacklist info "
"without either 1) a scan name 2) a subject ID 3) a study ID or "
"4) a datman config object")
if scan:
db_scan = dashboard.get_scan(scan)
if db_scan and db_scan.blacklisted():
try:
return db_scan.get_comment().encode('utf-8')
except:
return db_scan.get_comment()
return
if subject:
db_subject = dashboard.get_subject(subject)
blacklist = db_subject.get_blacklist_entries()
else:
if config:
study = config.study_name
db_study = dashboard.get_project(study)
blacklist = db_study.get_blacklisted_scans()
entries = {}
for entry in blacklist:
scan_name = str(entry.scan) + "_" + entry.scan.description
try:
scan_name = scan_name.encode('utf-8')
comment = entry.comment.encode('utf-8')
except:
comment = entry.comment
entries[scan_name] = comment
return entries
def process_subject(subject, cfg, be, bids_dir, rewrite):
"""
Convert subject in DATMAN folder to BIDS-style
"""
ident = scanid.parse(subject)
subscan = scan.Scan(subject, cfg)
bids_sub = ident.get_bids_name()
bids_ses = ident.timepoint
exp_path = make_bids_template(bids_dir, "sub-" + bids_sub,
"ses-" + bids_ses)
dm_to_bids = []
if dashboard.dash_found:
db_subject = dashboard.get_subject(subject)
db_subject.add_bids(bids_sub, bids_ses)
# Construct initial BIDS transformation info
scan_list = list(sort_by_series(subscan.niftis))
for i, series in enumerate(scan_list):
# Construct bids name
logger.info("Processing {}".format(series))
bids_dict = get_tag_bids_spec(cfg, series.tag, series.site)
if not bids_dict:
continue
bids_dict.update({"sub": bids_sub, "ses": bids_ses})
# Deal with reference scans
if bids_dict.get('is_ref', False):
target_dict = get_tag_bids_spec(cfg, scan_list[i + 1].tag,
series.site)
bids_dict.update({'task': target_dict['task']})
bids_prefix = be.construct_bids_name(bids_dict)
class_path = os.path.join(exp_path, bids_dict["class"])
# Make dm2bids transformation file, update source if applicable
bidsfiles = BIDSFile(bids_sub, bids_ses, series, class_path,
bids_prefix, bids_dict).update_source(cfg, be)
if bidsfiles is None:
logger.error("Cannot find derivative of {}".format(series))
logger.warning("Skipping!")
continue
if isinstance(bidsfiles, list):
dm_to_bids.extend(bidsfiles)
else:
dm_to_bids.append(bidsfiles)
# Apply prioritization calls
dm_to_bids = prioritize_scans(dm_to_bids)
# Prepare fieldmap information (requires knowledge about all scans)
dm_to_bids = prepare_fieldmaps(dm_to_bids)
# Transfer files over
for k in dm_to_bids:
if os.path.exists(k.dest_nii) and not rewrite:
logger.info("Output file {} already exists!".format(k.dest_nii))
continue
k.transfer_files()
if dashboard.dash_found:
db_series = dashboard.get_scan(k.series.path)
db_series.add_bids(str(k))
return