def _write_dig_bids(bids_path, raw, overwrite=False, verbose=True):
"""Write BIDS formatted DigMontage from Raw instance.
Handles coordinatesystem.json and electrodes.tsv writing
from DigMontage.
Parameters
----------
bids_path : BIDSPath
Path in the BIDS dataset to save the ``electrodes.tsv``
and ``coordsystem.json`` file for. ``datatype``
attribute must be ``eeg``, or ``ieeg``. For ``meg``
data, ``electrodes.tsv`` are not saved.
raw : instance of Raw
The data as MNE-Python Raw object.
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
# 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)
# create electrodes/coordsystem files using a subset of entities
# that are specified for these files in the specification
coord_file_entities = {
'root': bids_path.root,
'datatype': bids_path.datatype,
'subject': bids_path.subject,
'session': bids_path.session,
'acquisition': bids_path.acquisition,
'space': bids_path.space
}
datatype = bids_path.datatype
electrodes_path = BIDSPath(**coord_file_entities, suffix='electrodes',
extension='.tsv')
coordsystem_path = BIDSPath(**coord_file_entities, suffix='coordsystem',
extension='.json')
if verbose:
print("Writing electrodes file to... ", electrodes_path)
print("Writing coordsytem file to... ", coordsystem_path)
if datatype == "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_path.update(space=coord_frame)
electrodes_path.update(space=coord_frame)
coord_frame = 'Other'
# Now write the data to the elec coords and the coordsystem
_electrodes_tsv(raw, electrodes_path,
datatype, overwrite, verbose)
_coordsystem_json(raw=raw, unit=unit, hpi_coord_system='n/a',
sensor_coord_system=coord_frame,
fname=coordsystem_path, datatype=datatype,
overwrite=overwrite, verbose=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_path))
elif datatype == '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_path, datatype,
overwrite, verbose)
_coordsystem_json(raw=raw, unit='m', hpi_coord_system='n/a',
sensor_coord_system='CapTrak',
fname=coordsystem_path, datatype=datatype,
overwrite=overwrite, verbose=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'.")
def _write_dig_bids(bids_path,
raw,
montage=None,
acpc_aligned=False,
overwrite=False):
"""Write BIDS formatted DigMontage from Raw instance.
Handles coordinatesystem.json and electrodes.tsv writing
from DigMontage.
Parameters
----------
bids_path : mne_bids.BIDSPath
Path in the BIDS dataset to save the ``electrodes.tsv``
and ``coordsystem.json`` file for. ``datatype``
attribute must be ``eeg``, or ``ieeg``. For ``meg``
data, ``electrodes.tsv`` are not saved.
raw : mne.io.Raw
The data as MNE-Python Raw object.
montage : mne.channels.DigMontage | None
The montage to use rather than the one in ``raw`` if it
must be transformed from the "head" coordinate frame.
acpc_aligned : bool
Whether "mri" space is aligned to ACPC.
overwrite : bool
Whether to overwrite the existing file.
Defaults to False.
"""
# write electrodes data for iEEG and EEG
unit = "m" # defaults to meters
if montage is None:
montage = raw.get_montage()
else:
# prevent transformation back to "head", only should be used
# in this specific circumstance
if bids_path.datatype == 'ieeg':
montage.remove_fiducials()
raw.set_montage(montage)
# get coordinate frame from digMontage
digpoint = montage.dig[0]
if any(digpoint['coord_frame'] != _digpoint['coord_frame']
for _digpoint in montage.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 bids_path.datatype == 'ieeg' and mne_coord_frame == 'mri':
if acpc_aligned:
coord_frame = 'ACPC'
else:
raise RuntimeError(
'`acpc_aligned` is False, if your T1 is not aligned '
'to ACPC and the coordinates are in fact in ACPC '
'space there will be no way to relate the coordinates '
'to the T1. If the T1 is ACPC-aligned, use '
'`acpc_aligned=True`')
# create electrodes/coordsystem files using a subset of entities
# that are specified for these files in the specification
coord_file_entities = {
'root': bids_path.root,
'datatype': bids_path.datatype,
'subject': bids_path.subject,
'session': bids_path.session,
'acquisition': bids_path.acquisition,
'space': bids_path.space
}
datatype = bids_path.datatype
electrodes_path = BIDSPath(**coord_file_entities,
suffix='electrodes',
extension='.tsv')
coordsystem_path = BIDSPath(**coord_file_entities,
suffix='coordsystem',
extension='.json')
logger.info(f'Writing electrodes file to... {electrodes_path}')
logger.info(f'Writing coordsytem file to... {coordsystem_path}')
if datatype == 'ieeg':
if coord_frame is not None:
# XXX: To improve when mne-python allows coord_frame='unknown'
# coordinate frame is either
coordsystem_path.update(space=coord_frame)
electrodes_path.update(space=coord_frame)
# Now write the data to the elec coords and the coordsystem
_write_electrodes_tsv(raw, electrodes_path, datatype, overwrite)
_write_coordsystem_json(raw=raw,
unit=unit,
hpi_coord_system='n/a',
sensor_coord_system=(coord_frame,
mne_coord_frame),
fname=coordsystem_path,
datatype=datatype,
overwrite=overwrite)
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_path))
elif datatype == '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
_write_electrodes_tsv(raw, electrodes_path, datatype, overwrite)
_write_coordsystem_json(raw=raw,
unit='m',
hpi_coord_system='n/a',
sensor_coord_system='CapTrak',
fname=coordsystem_path,
datatype=datatype,
overwrite=overwrite)
else:
warn("Skipping EEG electrodes.tsv... "
"Setting montage not possible if anatomical "
"landmarks (NAS, LPA, RPA) are missing, "
"and coord_frame is not 'head'.")