def filter(raw: mne.io.BaseRaw, subject: str, session: Optional[str],
run: Optional[str], l_freq: Optional[float],
h_freq: Optional[float],
l_trans_bandwidth: Optional[Union[float, Literal['auto']]],
h_trans_bandwidth: Optional[Union[float, Literal['auto']]]) -> None:
"""Filter data channels (MEG and EEG)."""
data_type = 'empty-room' if subject == 'emptyroom' else 'experimental'
if l_freq is not None and h_freq is None:
msg = (f'High-pass filtering {data_type} data; lower bound: '
f'{l_freq} Hz')
elif l_freq is None and h_freq is not None:
msg = (f'Low-pass filtering {data_type} data; upper bound: '
f'{h_freq} Hz')
elif l_freq is not None and h_freq is not None:
msg = (f'Band-pass filtering {data_type} data; range: '
f'{l_freq} – {h_freq} Hz')
else:
msg = (f'Not applying frequency filtering to {data_type} data.')
logger.info(**gen_log_kwargs(
message=msg, subject=subject, session=session, run=run))
if l_freq is None and h_freq is None:
return
raw.filter(l_freq=l_freq,
h_freq=h_freq,
l_trans_bandwidth=l_trans_bandwidth,
h_trans_bandwidth=h_trans_bandwidth,
filter_length='auto',
phase='zero',
fir_window='hamming',
fir_design='firwin')
def resample(raw: mne.io.BaseRaw, subject: str, session: Optional[str],
run: Optional[str], sfreq: Optional[float]) -> None:
if not sfreq:
return
data_type = 'empty-room' if subject == 'emptyroom' else 'experimental'
msg = f'Resampling {data_type} data to {sfreq:.1f} Hz'
logger.info(**gen_log_kwargs(
message=msg,
subject=subject,
session=session,
run=run,
))
raw.resample(sfreq, npad='auto')
def make_ecg_epochs(*,
cfg,
raw: mne.io.BaseRaw,
subject: str,
session: str,
run: Optional[str] = None) -> Optional[mne.BaseEpochs]:
# ECG either needs an ecg channel, or avg of the mags (i.e. MEG data)
if ('ecg' in raw.get_channel_types() or 'meg' in cfg.ch_types
or 'mag' in cfg.ch_types):
msg = 'Creating ECG epochs …'
logger.info(**gen_log_kwargs(
message=msg, subject=subject, session=session, run=run))
ecg_epochs = create_ecg_epochs(raw,
baseline=(None, -0.2),
tmin=-0.5,
tmax=0.5)
if len(ecg_epochs) == 0:
msg = ('No ECG events could be found. Not running ECG artifact '
'detection.')
logger.info(**gen_log_kwargs(
message=msg, subject=subject, session=session, run=run))
ecg_epochs = None
else:
msg = ('No ECG or magnetometer channels are present. Cannot '
'automate artifact detection for ECG')
logger.info(**gen_log_kwargs(
message=msg, subject=subject, session=session, run=run))
ecg_epochs = None
return ecg_epochs
def filter_for_ica(*,
cfg,
raw: mne.io.BaseRaw,
subject: str,
session: str,
run: Optional[str] = None) -> None:
"""Apply a high-pass filter if needed."""
if cfg.ica_l_freq is None:
msg = (f'Not applying high-pass filter (data is already filtered, '
f'cutoff: {raw.info["highpass"]} Hz).')
logger.info(**gen_log_kwargs(
message=msg, subject=subject, session=session, run=run))
else:
msg = f'Applying high-pass filter with {cfg.ica_l_freq} Hz cutoff …'
logger.info(**gen_log_kwargs(
message=msg, subject=subject, session=session, run=run))
raw.filter(l_freq=cfg.ica_l_freq, h_freq=None)
def _channel_text_scrub(raw: mne.io.BaseRaw):
"""
Clean and formats the channel text inside a MNE-Raw data structure.
Parameters
----------
raw : MNE-raw data structure
"""
def _reformatchanlabel(label): # noqa
"""Process a single channel label.
To make sure it is:
- upper case
- removed unnecessary strings (POL, eeg, -ref)
- removed empty spaces
"""
# hard coded replacement rules
# label = str(label).replace("POL ", "").upper()
label = str(label).replace("POL", "").upper()
label = label.replace("EEG", "").replace("-REF", "") # .replace("!","1")
# replace "Grid" with 'G' label
label = label.replace("GRID", "G")
# for BIDS format, you cannot have blank channel name
if label == "":
label = "N/A"
return label
# apply channel scrubbing
raw = raw.rename_channels(lambda x: x.upper())
# encapsulated into a try statement in case there are blank channel names
# after scrubbing these characters
try:
raw = raw.rename_channels(
lambda x: x.strip(".")
) # remove dots from channel names
raw = raw.rename_channels(
lambda x: x.strip("-")
) # remove dashes from channel names
except ValueError as e:
logger.error(f"Ran into an issue when debugging: {raw.info}")
logger.exception(e)
raw = raw.rename_channels(lambda x: x.replace(" ", ""))
raw = raw.rename_channels(
lambda x: x.replace("’", "'")
) # remove dashes from channel names
raw = raw.rename_channels(
lambda x: x.replace("`", "'")
) # remove dashes from channel names
raw = raw.rename_channels(lambda x: _reformatchanlabel(x))
return raw
def __init__(self, fpath=None, raw: mne.io.BaseRaw = None, type: str = "fif"):
# if raw != None and fpath == None:
# raise RuntimeError("Pass in a file path to save data!")
#
# if fpath != None and raw == None:
# raise RuntimeError("Pass in a MNE Raw object to save!")
if fpath != None and raw != None:
if not os.path.exists(os.path.dirname(fpath)):
fdir = os.path.dirname(fpath)
raise RuntimeError(
"Filepath you passed to save data does not exist. Please "
f"first create the corresponding directory: {fdir}"
)
if type == "fif":
self.saveas_fif(fpath, raw.get_data(return_times=False), raw.info)
def channel_text_scrub(cls, raw: mne.io.BaseRaw):
"""
Cleans and formats the channel text inside a MNE-Raw data structure.
TODO: ACCOUNT FOR - BEING IN BIPOLAR MONTAGE CHANNEL LABELS.
Parameters
----------
raw : MNE-raw data structure
Returns
-------
"""
def _reformatchanlabel(label):
"""
Helper function to process a single channel label to make sure it is:
- upper case
- removed unnecessary strings (POL, eeg, -ref)
- removed empty spaces
:param label: (str) a contact label that may have extra chars, or be improperly cased
:return: label (str) the reformatted string that is uppercase and w/o spaces
"""
# hard coded replacement rules
# label = str(label).replace("POL ", "").upper()
label = str(label).replace("POL", "").upper()
label = label.replace("EEG", "").replace("-REF", "")
# replace "Grid" with 'G' label
label = label.replace("GRID", "G")
# for BIDS format, you cannot have blank channel name
if label == "":
label = "N/A"
return label
# apply channel scrubbing
raw.rename_channels(lambda x: x.upper())
raw.rename_channels(
lambda x: x.strip(".")) # remove dots from channel names
raw.rename_channels(
lambda x: x.strip("-")) # remove dashes from channel names
raw.rename_channels(lambda x: x.replace(" ", ""))
raw.rename_channels(
lambda x: x.replace("’", "'")) # remove dashes from channel names
raw.rename_channels(
lambda x: x.replace("`", "'")) # remove dashes from channel names
raw.rename_channels(lambda x: _reformatchanlabel(x))
return raw