def copyfile_kit(src, dest, subject_id, session_id,
task, run, _init_kwargs):
"""Copy and rename KIT files to a new location.
Parameters
----------
src : str
Path to the source raw .con or .sqd folder.
dest : str
Path to the destination of the new bids folder.
subject_id : str | None
The subject ID. Corresponds to "sub".
session_id : str | None
The session identifier. Corresponds to "ses".
task : str | None
The task identifier. Corresponds to "task".
run : int | None
The run number. Corresponds to "run".
_init_kwargs : dict
Extract information of marker and headpoints
"""
# create parent directories in case it does not exist yet
_mkdir_p(op.dirname(dest))
# KIT data requires the marker file to be copied over too
sh.copyfile(src, dest)
data_path = op.split(dest)[0]
datatype = 'meg'
if 'mrk' in _init_kwargs:
hpi = _init_kwargs['mrk']
acq_map = dict()
if isinstance(hpi, list):
if _get_mrk_meas_date(hpi[0]) > _get_mrk_meas_date(hpi[1]):
raise ValueError('Markers provided in incorrect order.')
_, marker_ext = _parse_ext(hpi[0])
acq_map = dict(zip(['pre', 'post'], hpi))
else:
_, marker_ext = _parse_ext(hpi)
acq_map[None] = hpi
for key, value in acq_map.items():
marker_path = BIDSPath(
subject=subject_id, session=session_id, task=task, run=run,
acquisition=key, suffix='markers', extension=marker_ext,
datatype=datatype)
sh.copyfile(value, op.join(data_path, marker_path.basename))
for acq in ['elp', 'hsp']:
if acq in _init_kwargs:
position_file = _init_kwargs[acq]
task, run, acq = None, None, acq.upper()
position_ext = '.pos'
position_path = BIDSPath(
subject=subject_id, session=session_id, task=task, run=run,
acquisition=acq, suffix='headshape', extension=position_ext,
datatype=datatype)
sh.copyfile(position_file,
op.join(data_path, position_path.basename))
def _get_sidecar_json_update_file(_get_bids_test_dir):
"""Return path to a sidecar JSON updating file."""
bids_root = _get_bids_test_dir
sample_scripts = op.join(bids_root, 'sourcedata')
sidecar_fpath = op.join(sample_scripts, 'sidecarjson_update.json')
_mkdir_p(sample_scripts)
update_json = {
'InstitutionName': 'mne-bids',
'InstitutionAddress': 'Internet',
'MEGChannelCount': 300,
'MEGREFChannelCount': 6,
'SEEGChannelCount': 0,
}
_write_json(sidecar_fpath, update_json, overwrite=True)
return sidecar_fpath
