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Add Run label #32

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Add Run label #32

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10 changes: 10 additions & 0 deletions fnirsapp_qr.json
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,16 @@
"list": true,
"value-key": "[SessionLabel]"
},
{
"command-line-flag": "--run-label",
"description": "The label(s) of the run(s) that should be analyzed. The label corresponds to run-<session_label> from the BIDS spec (so it does not include \"run-\"). If this parameter is not provided all sessions should be analyzed. Multiple runs can be specified with a space separated list.",
"id": "run_label",
"name": "run-label",
"optional": true,
"type": "String",
"list": true,
"value-key": "[RunLabel]"
},
{
"command-line-flag": "--task-label",
"description": "The label(s) of the tasks(s) that should be analyzed. The label corresponds to task-<subject_label> from the BIDS spec. If this parameter is not provided all tasks should be analyzed. Multiple tasks can be specified with a space separated list.",
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83 changes: 60 additions & 23 deletions fnirsapp_qr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,14 @@ def fnirsapp_qr(command, env={}):
'all sessions should be analyzed. Multiple sessions '
'can be specified with a space separated list.',
nargs="+")
parser.add_argument('--run-label',
help='The label(s) of the run(s) that should be '
'analyzed. The label corresponds to '
'run-<run-label> from the BIDS spec (so it does '
'not include "run-"). If this parameter is not provided '
'all runs should be analyzed. Multiple runs '
'can be specified with a space separated list.',
nargs="+")
parser.add_argument('--sci-threshold', type=float, default=0.0,
help='Threshold below which a channel is marked as bad.')
parser.add_argument('--pp-threshold', type=float, default=0.0,
Expand Down Expand Up @@ -125,6 +133,19 @@ def create_report(app_name=None, pargs=None):
logger.info(f" Sessions: {sess}")


logger.info("Extracting run metadata.")
sess = []
if args.session_label:
logger.info(" Run data provided as input argument.")
runs = args.session_label
else:
logger.info(" Run data will be extracted from data.")
runs = get_entity_vals(args.input_datasets, 'run')
if len(runs) == 0:
runs = [None]
logger.info(f" Runs: {runs}")


logger.info("Extracting tasks metadata.")
tasks = []
if args.task_label:
Expand Down Expand Up @@ -294,29 +315,45 @@ def run_report(path, path_out):
for sub in subs:
for task in tasks:
for ses in sess:

logger.info(f"Processing: sub-{sub}/ses-{ses}/task-{task}")
exec_files[f"sub-{sub}_ses-{ses}_task-{task}"] = dict()

in_path = BIDSPath(subject=sub, task=task, session=ses,
root=f"{args.input_datasets}",
datatype="nirs", suffix="nirs",
extension=".snirf")

exec_files[f"sub-{sub}_ses-{ses}_task-{task}"]["FileName"] = str(in_path.fpath)
exec_files[f"sub-{sub}_ses-{ses}_task-{task}"]["FileHash"] = hashlib.md5(open(in_path.fpath, 'rb').read()).hexdigest()

out_path = BIDSPath(subject=sub, task=task, session=ses,
root=f"{args.output_location}",
datatype="nirs", suffix="qualityReport",
extension=".html", check=False)

if op.exists(in_path):
logger.info(f" Found file: {in_path}")
out_path.fpath.parent.mkdir(exist_ok=True, parents=True)
run_report(in_path, out_path)
else:
logger.info(f" No file exists: {in_path}")
for run in runs:
if len(runs) > 1 :
logger.info(f"Processing: sub-{sub}/ses-{ses}/run-{run}/task-{task}")
exec_files[f"sub-{sub}_ses-{ses}_task-{task}_run-{run}"] = dict()

in_path = BIDSPath(subject=sub, task=task, session=ses, run = rub,
root=f"{args.input_datasets}",
datatype="nirs", suffix="nirs",
extension=".snirf")
exec_files[f"sub-{sub}_ses-{ses}_task-{task}_run-{run}"]["FileName"] = str(in_path.fpath)
exec_files[f"sub-{sub}_ses-{ses}_task-{task}_run-{run}"]["FileHash"] = hashlib.md5(open(in_path.fpath, 'rb').read()).hexdigest()
out_path = BIDSPath(subject=sub, task=task, session=ses,run=run,
root=f"{args.output_location}",
datatype="nirs", suffix="qualityReport",
extension=".html", check=False)
else
logger.info(f"Processing: sub-{sub}/ses-{ses}/task-{task}")
exec_files[f"sub-{sub}_ses-{ses}_task-{task}"] = dict()

in_path = BIDSPath(subject=sub, task=task, session=ses,
root=f"{args.input_datasets}",
datatype="nirs", suffix="nirs",
extension=".snirf")

exec_files[f"sub-{sub}_ses-{ses}_task-{task}"]["FileName"] = str(in_path.fpath)
exec_files[f"sub-{sub}_ses-{ses}_task-{task}"]["FileHash"] = hashlib.md5(open(in_path.fpath, 'rb').read()).hexdigest()

out_path = BIDSPath(subject=sub, task=task, session=ses,
root=f"{args.output_location}",
datatype="nirs", suffix="qualityReport",
extension=".html", check=False)

if op.exists(in_path):
logger.info(f" Found file: {in_path}")
out_path.fpath.parent.mkdir(exist_ok=True, parents=True)
run_report(in_path, out_path)
else:
logger.info(f" No file exists: {in_path}")


exec_rep["Files"] = exec_files
exec_path = f"{args.input_datasets}/execution"
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