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
"""
from mne_bids.utils import make_bids_basename
# KIT data requires the marker file to be copied over too
sh.copyfile(src, dest)
data_path = op.split(dest)[0]
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_fname = make_bids_basename(subject=subject_id,
session=session_id,
task=task,
run=run,
acquisition=key,
suffix='markers%s' % marker_ext,
prefix=data_path)
sh.copyfile(value, marker_fname)
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_fname = make_bids_basename(subject=subject_id,
session=session_id,
task=task,
run=run,
acquisition=acq,
suffix='headshape%s' %
position_ext,
prefix=data_path)
sh.copyfile(position_file, position_fname)
def test_make_filenames():
"""Test that we create filenames according to the BIDS spec."""
# All keys work
prefix_data = dict(subject='one', session='two', task='three',
acquisition='four', run='five', processing='six',
recording='seven', suffix='suffix.csv')
assert make_bids_basename(**prefix_data) == 'sub-one_ses-two_task-three_acq-four_run-five_proc-six_recording-seven_suffix.csv' # noqa
# subsets of keys works
assert make_bids_basename(subject='one', task='three') == 'sub-one_task-three' # noqa
assert make_bids_basename(subject='one', task='three', suffix='hi.csv') == 'sub-one_task-three_hi.csv' # noqa
with pytest.raises(ValueError):
make_bids_basename(subject='one-two', suffix='there.csv')
def _write_dig_bids(electrodes_fname,
coordsystem_fname,
data_path,
raw,
kind,
overwrite=False,
verbose=True):
"""Write BIDS formatted DigMontage from Raw instance.
Handles coordinatesystem.json and electrodes.tsv writing
from DigMontage.
Parameters
----------
electrodes_fname : str
Filename to save the electrodes.tsv to.
coordsystem_fname : str
Filename to save the coordsystem.json to.
data_path : str | pathlib.Path
Path to the data directory
raw : instance of Raw
The data as MNE-Python Raw object.
kind : str
Type of the data as in ALLOWED_KINDS.
overwrite : bool
Whether to overwrite the existing file.
Defaults to False.
verbose : bool
Set verbose output to true or false.
"""
# write electrodes data for iEEG and EEG
unit = "m" # defaults to meters
params = _parse_bids_filename(electrodes_fname, verbose)
subject_id = params['sub']
session_id = params['ses']
acquisition = params['acq']
# get coordinate frame from digMontage
digpoint = raw.info['dig'][0]
if any(digpoint['coord_frame'] != _digpoint['coord_frame']
for _digpoint in raw.info['dig']):
warn("Not all digpoints have the same coordinate frame. "
"Skipping electrodes.tsv writing...")
return
# get the accepted mne-python coordinate frames
coord_frame_int = int(digpoint['coord_frame'])
mne_coord_frame = MNE_FRAME_TO_STR.get(coord_frame_int, None)
coord_frame = MNE_TO_BIDS_FRAMES.get(mne_coord_frame, None)
if verbose:
print("Writing electrodes file to... ", electrodes_fname)
print("Writing coordsytem file to... ", coordsystem_fname)
if kind == "ieeg":
if coord_frame is not None:
# XXX: To improve when mne-python allows coord_frame='unknown'
if coord_frame not in BIDS_IEEG_COORDINATE_FRAMES:
coordsystem_fname = make_bids_basename(
subject=subject_id,
session=session_id,
acquisition=acquisition,
space=coord_frame,
suffix='coordsystem.json',
prefix=data_path)
electrodes_fname = make_bids_basename(subject=subject_id,
session=session_id,
acquisition=acquisition,
space=coord_frame,
suffix='electrodes.tsv',
prefix=data_path)
coord_frame = 'Other'
# Now write the data to the elec coords and the coordsystem
_electrodes_tsv(raw, electrodes_fname, kind, overwrite, verbose)
_coordsystem_json(raw, unit, 'n/a', coord_frame, coordsystem_fname,
kind, overwrite, verbose)
else:
# default coordinate frame to mri if not available
warn("Coordinate frame of iEEG coords missing/unknown "
"for {}. Skipping reading "
"in of montage...".format(electrodes_fname))
elif kind == 'eeg':
# We only write EEG electrodes.tsv and coordsystem.json
# if we have LPA, RPA, and NAS available to rescale to a known
# coordinate system frame
coords = _extract_landmarks(raw.info['dig'])
landmarks = set(['RPA', 'NAS', 'LPA']) == set(list(coords.keys()))
# XXX: to be improved to allow rescaling if landmarks are present
# mne-python automatically converts unknown coord frame to head
if coord_frame_int == FIFF.FIFFV_COORD_HEAD and landmarks:
# Now write the data
_electrodes_tsv(raw, electrodes_fname, kind, overwrite, verbose)
_coordsystem_json(raw, 'm', 'RAS', 'CapTrak', coordsystem_fname,
kind, overwrite, verbose)
else:
warn("Skipping EEG electrodes.tsv... "
"Setting montage not possible if anatomical "
"landmarks (NAS, LPA, RPA) are missing, "
"and coord_frame is not 'head'.")