Module xelo2.bids.physio
Expand source code
import gzip
from json import dump
from logging import getLogger
from bidso.utils import replace_extension
from .utils import make_bids_name
from .io.dataglove import parse_dataglove_log
from .io.pulse_and_resp_scanner import parse_scanner_physio
from .io.flip import parse_flip_physio
lg = getLogger(__name__)
def convert_physio(rec, dest_path, name):
"""Convert physiological signal to BIDS format.
Parameters
----------
rec : instance of Recording
recording of type 'physio' (like dataglove or heart rate)
dest_path : path
full path to modality folder
name : dict
dictionary with parts to make bids name
Notes
-----
StartTime in the .json file gives the offset from the start of the recording.
If the tsv contains a "time" column, the "time" info is already aligned
with the recording (so you don't need to add StartTime).
"""
for file in rec.list_files():
if file.format == 'dataglove':
name['recording'] = 'recording-dataglove'
tsv, hdr = parse_dataglove_log(file.path)
elif file.format == 'scanphyslog':
name['recording'] = 'recording-resp'
tsv, hdr = parse_scanner_physio(file.path)
elif file.format == 'flip':
name['recording'] = 'recording-flip'
tsv, hdr = parse_flip_physio(file.path)
else:
lg.info(f'There is no function to convert "{file.format}" physio')
return
hdr['StartTime'] = rec.offset
for time_col in ('time', 'time [s]'):
if time_col in tsv.columns:
tsv[time_col] += rec.offset
if name['recording'] is None:
lg.warning('No file associated with physio recording')
return
physio_tsv = dest_path / f'{make_bids_name(name, "physio")}'
_write_physio(tsv, physio_tsv)
physio_json = replace_extension(physio_tsv, '.json')
with physio_json.open('w') as f:
dump(hdr, f, indent=2)
def _write_physio(physio, physio_tsv):
content = physio.to_csv(sep='\t', index=False, header=False, float_format='%.6f')
with gzip.open(physio_tsv, 'wb') as f:
f.write(content.encode())Functions
def convert_physio(rec, dest_path, name)-
Convert physiological signal to BIDS format.
Parameters
rec:instanceofRecording- recording of type 'physio' (like dataglove or heart rate)
dest_path:path- full path to modality folder
name:dict- dictionary with parts to make bids name
Notes
StartTime in the .json file gives the offset from the start of the recording. If the tsv contains a "time" column, the "time" info is already aligned with the recording (so you don't need to add StartTime).
Expand source code
def convert_physio(rec, dest_path, name): """Convert physiological signal to BIDS format. Parameters ---------- rec : instance of Recording recording of type 'physio' (like dataglove or heart rate) dest_path : path full path to modality folder name : dict dictionary with parts to make bids name Notes ----- StartTime in the .json file gives the offset from the start of the recording. If the tsv contains a "time" column, the "time" info is already aligned with the recording (so you don't need to add StartTime). """ for file in rec.list_files(): if file.format == 'dataglove': name['recording'] = 'recording-dataglove' tsv, hdr = parse_dataglove_log(file.path) elif file.format == 'scanphyslog': name['recording'] = 'recording-resp' tsv, hdr = parse_scanner_physio(file.path) elif file.format == 'flip': name['recording'] = 'recording-flip' tsv, hdr = parse_flip_physio(file.path) else: lg.info(f'There is no function to convert "{file.format}" physio') return hdr['StartTime'] = rec.offset for time_col in ('time', 'time [s]'): if time_col in tsv.columns: tsv[time_col] += rec.offset if name['recording'] is None: lg.warning('No file associated with physio recording') return physio_tsv = dest_path / f'{make_bids_name(name, "physio")}' _write_physio(tsv, physio_tsv) physio_json = replace_extension(physio_tsv, '.json') with physio_json.open('w') as f: dump(hdr, f, indent=2)