def SessionEndEP(session: BidsSession):
"""
1. Checks the series in the prepared folder
2. Extract KSS/VAS data from kss_dict to tsv file
3. Parces in-scan nBack and KSS/VAS log files
"""
# path contain destination folder, where
# all data files are placed
# session.getPath generates bids path based on
# subject and session id, eg. sub-001/ses-HCL
# if parameter empty==True, and no session,
# the generated path will still contain 'ses-'
# empty must be True in preparation plugin
path = os.path.join(preparefolder,
session.getPath(True))
out_path = os.path.join(path,
"MRI")
# checking if session contains correct series
if not dry_run:
checkSeries(out_path,
session.subject, session.session,
False)
############################################
# Retrieving in-scan task and KSS/VAS data #
############################################
if session.session == "ses-STROOP":
return 0
# where tsv files are
inp_dir = os.path.join(session.in_path, "inp")
# where tsv files should be
aux_dir = os.path.join(path, "auxiliary")
if not os.path.isdir(inp_dir):
raise NotADirectoryError(inp_dir)
# do not copy if we are in dry mode
if not dry_run:
os.makedirs(aux_dir, exist_ok=True)
# just copy file, in real life application
# you may parce files
for file in ("FCsepNBack.tsv", "VAS.tsv"):
file = os.path.join(inp_dir, file)
if not os.path.isfile(file):
raise FileNotFoundError(file)
shutil.copy2(file, aux_dir)
# copiyng correspondent json files
for file in ("FCsepNBack.json", "VAS.json"):
file = os.path.join(plugin_root, file)
if not os.path.isfile(file):
raise FileNotFoundError(file)
shutil.copy2(file, aux_dir)
def SessionEP(scan: BidsSession) -> int:
"""
Session files modifications
1. Stores the list of sequences in the session
2. Checks if session contains correct sequences
2. Checks if session HCL and LCL contains task and
KSS/VAS files
"""
######################################
# Initialisation of sesion variables #
######################################
# retrieving sequences and puttintg them into list
global seq_list
global seq_index
path = os.path.join(scan.in_path, "MRI")
seq_list = sorted(os.listdir(path))
# removing leading sequence number from name
seq_list = [s.split("-", 1)[1] for s in seq_list]
seq_index = -1
#################################
# Checking sequences in session #
#################################
checkSeries(path, scan.subject, scan.session, False)
#############################################
# Checking for existance of auxiliary files #
#############################################
# BidsSession.in_path contains current session folder path
aux_input = os.path.join(scan.in_path, "auxiliary")
if scan.session in ("ses-LCL", "ses-HCL"):
if not os.path.isdir(aux_input):
logger.error(
"Session {}/{} do not contain auxiliary folder".format(
scan.subject, scan.session))
return -1
for old, new in (("FCsepNBack.tsv", "task-rest_events.tsv"),
("FCsepNBack.json", "task-rest_events.json"),
("VAS.tsv", "task-rest_beh.tsv"),
("VAS.json", "task-rest_beh.json")):
source = "{}/{}".format(aux_input, old)
if not os.path.isfile(source):
logger.error("{}/{}: File {} not found".format(
scan.subject, scan.session, source))
def SessionEP(scan):
"""
Session files modification
1. Stores the list of sequences in session
2. Checks the sequences
3. Copies HCL and LCL task and KSS/VAS files
to bidsified dataset
"""
######################################
# Initialisation of sesion variables #
######################################
# retrieving list of sequences and puttintg them into list
global seq_list
global seq_index
path = os.path.join(scan.in_path, "MRI")
seq_list = sorted(os.listdir(path))
seq_list = [s.split("-", 1)[1] for s in seq_list]
seq_index = -1
#################################
# Checking sequences in session #
#################################
checkSeries(path, scan.subject, scan.session, False)
#############################################
# Checking for existance of auxiliary files #
#############################################
# all the copy instructions must be protected by
# if not dry_run
aux_input = os.path.join(scan.in_path, "auxiliary")
if scan.session in ("ses-LCL", "ses-HCL"):
if not os.path.isdir(aux_input):
logger.error("Session {}/{} do not contain auxiliary folder"
.format(scan.subject, scan.session))
raise FileNotFoundError("folder {} not found"
.format(aux_input))
beh = os.path.join(scan.in_path, "beh")
if not dry_run:
os.makedirs(beh, exist_ok=True)
for old, new in (("FCsepNBack.tsv", "task-rest_events.tsv"),
("FCsepNBack.json", "task-rest_events.json"),
("VAS.tsv", "task-rest_beh.tsv"),
("VAS.json", "task-rest_beh.json")):
source = "{}/{}".format(aux_input, old)
dest = "{}/{}_{}_{}".format(beh, scan.subject, scan.session, new)
if not os.path.isfile(source):
if dry_run:
logger.error("{}/{}: File {} not found"
.format(scan.subject, scan.session, source))
else:
logger.critical("{}/{}: File {} not found"
.format(scan.subject,
scan.session,
source))
raise FileNotFoundError(source)
if os.path.isfile(dest):
logger.warning("{}/{}: File {} already exists"
.format(scan.subject, scan.session, dest))
if not dry_run:
shutil.copy2(source, dest)