def write_bads(bads_path, bads):
with open(bads_path, "w") as f:
f.write("\t".join(bads))
def annotate_fif(raw_path, bads_path, annot_path, is_emptyroom):
bads = read_bads(bads_path) if bads_path.exists() else None
annotations = read_annotations(annot_path) if annot_path.exists() else None
bads, annotations = inspect_fif(raw_path, bads, annotations, is_emptyroom)
write_bads(bads_path, bads)
annotations.save(str(annot_path))
if __name__ == "__main__":
args = parse_args(description=__doc__, args=sys.argv[1:], emptyroom=True)
subj, task, run, ses = args.subject, args.task, args.run, args.session
# input
raw = bp.root.fpath(subject=subj, task=task, run=run, session=ses)
# output
bads = bp.bads.fpath(subject=subj, task=task, run=run, session=ses)
annot = bp.annot.fpath(subject=subj, task=task, run=run, session=ses)
bads.parent.mkdir(exist_ok=True)
annotate_fif(raw, bads, annot, subj == "emptyroom")
"""Add associated emptyroom paths to sidecar json files"""
import sys
import json
from metacog import bp
from metacog.paths import dirs
from metacog.dataset_specific_utils import parse_args
from metacog.utils import setup_logging
logger = setup_logging(__file__)
args = parse_args(__doc__, sys.argv[1:], emptyroom=False)
subj, task, run = args.subject, args.task, args.run
json_path = bp.root_json.fpath(subject=subj, task=task, run=run)
raw_bp = bp.root.update(subject=subj, task=task, run=run, session=None)
logger.info(f"Reading json from {json_path}")
with open(json_path, "r") as f:
json_dict = json.load(f)
bp.er = raw_bp.find_empty_room()
associated_er_path = bp.er.fpath.relative_to(dirs.bids_root)
logger.info(f"Setting AssociatedEmptyRoom to {associated_er_path}")
json_dict["AssociatedEmptyRoom"] = str(associated_er_path)
logger.info(f"Writing json back to {json_path}")
with open(json_path, "w") as f:
json.dump(json_dict, f, indent=4)
def process_fif(src, dest, is_mult_runs):
raw = concat_runs(src) if is_mult_runs else read_raw_fif(src, preload=True)
raw.apply_proj()
raw.filter(
l_freq=cfg.concat_config["filter_freqs"][0],
h_freq=cfg.concat_config["filter_freqs"][1],
pad=cfg.concat_config["pad"],
)
raw.resample(sfreq=cfg.concat_config["resamp_freq"])
raw.save(dest, overwrite=True)
if __name__ == "__main__":
args = parse_args(__doc__, args=sys.argv[1:], emptyroom=True)
subj, task, run, ses = args.subject, args.task, args.run, args.session
run = 1 if args.task == cfg.tasks[0] else None
# input
bp.maxfilt_subj = bp.maxfilt.update(subject=subj, task=task, session=ses)
# output
filt = bp.filt.fpath(subject=subj, task=task, session=ses)
if task == "questions":
maxfilt = [
bp.maxfilt_subj.fpath(run=int(r)) for r in cfg.subj_runs[subj]
]
else:
maxfilt = bp.maxfilt_subj.fpath(run=run)