def assess_bads(raw_fname, is_eroom=False):
'''Code sampled from MNE python website
https://mne.tools/dev/auto_tutorials/preprocessing/\
plot_60_maxwell_filtering_sss.html'''
from mne.preprocessing import find_bad_channels_maxwell
raw = mne.io.read_raw_fif(raw_fname)
if raw.times[-1] > 60.0:
raw.crop(tmax=60)
raw.info['bads'] = []
raw_check = raw.copy()
if is_eroom == False:
auto_noisy_chs, auto_flat_chs, auto_scores = find_bad_channels_maxwell(
raw_check,
cross_talk=None,
calibration=None,
return_scores=True,
verbose=True)
else:
auto_noisy_chs, auto_flat_chs, auto_scores = find_bad_channels_maxwell(
raw_check,
cross_talk=None,
calibration=None,
return_scores=True,
verbose=True,
coord_frame="meg")
return {'noisy': auto_noisy_chs, 'flat': auto_flat_chs}
def find_bad_channels_maxwell_util(raw_):
""" Inplace update of bad channels.
Find noisy and flat channels according to the Maxwell filter.
"""
raw_.info['bads'] = []
raw_check = raw_.copy()
auto_noisy_chs, auto_flat_chs, auto_scores = find_bad_channels_maxwell(
raw_check,
# cross_talk=crosstalk_file,
calibration=fine_cal_file,
return_scores=True,
verbose=True,
coord_frame="meg")
print("auto_noisy_chs", auto_noisy_chs)
print("auto_flat_chs", auto_flat_chs)
bads = raw_.info['bads'] + auto_noisy_chs + auto_flat_chs
raw_.info['bads'] = bads
raw_.auto_scores = auto_scores
def find_bad_channels(raw, subject, session, task, run):
if (config.find_flat_channels_meg and not config.find_noisy_channels_meg):
msg = 'Finding flat channels.'
elif (config.find_noisy_channels_meg
and not config.find_flat_channels_meg):
msg = 'Finding noisy channels using Maxwell filtering.'
else:
msg = ('Finding flat channels, and noisy channels using '
'Maxwell filtering.')
logger.info(
gen_log_message(message=msg, step=1, subject=subject, session=session))
bids_path = BIDSPath(subject=subject,
session=session,
task=task,
run=run,
acquisition=config.acq,
processing=config.proc,
recording=config.rec,
space=config.space,
suffix=config.get_datatype(),
datatype=config.get_datatype(),
root=config.deriv_root)
auto_noisy_chs, auto_flat_chs, auto_scores = find_bad_channels_maxwell(
raw=raw,
calibration=get_mf_cal_fname(subject, session),
cross_talk=get_mf_ctc_fname(subject, session),
return_scores=True)
preexisting_bads = raw.info['bads'].copy()
bads = preexisting_bads.copy()
if config.find_flat_channels_meg:
msg = f'Found {len(auto_flat_chs)} flat channels.'
logger.info(
gen_log_message(message=msg,
step=1,
subject=subject,
session=session))
bads.extend(auto_flat_chs)
if config.find_noisy_channels_meg:
msg = f'Found {len(auto_noisy_chs)} noisy channels.'
logger.info(
gen_log_message(message=msg,
step=1,
subject=subject,
session=session))
bads.extend(auto_noisy_chs)
bads = sorted(set(bads))
raw.info['bads'] = bads
msg = f'Marked {len(raw.info["bads"])} channels as bad.'
logger.info(
gen_log_message(message=msg, step=1, subject=subject, session=session))
if config.find_noisy_channels_meg:
auto_scores_fname = bids_path.copy().update(suffix='scores',
extension='.json',
check=False)
with open(auto_scores_fname, 'w') as f:
json_tricks.dump(auto_scores,
fp=f,
allow_nan=True,
sort_keys=False)
if config.interactive:
import matplotlib.pyplot as plt
config.plot_auto_scores(auto_scores)
plt.show()
# Write the bad channels to disk.
bads_tsv_fname = bids_path.copy().update(suffix='bads',
extension='.tsv',
check=False)
bads_for_tsv = []
reasons = []
if config.find_flat_channels_meg:
bads_for_tsv.extend(auto_flat_chs)
reasons.extend(['auto-flat'] * len(auto_flat_chs))
preexisting_bads = set(preexisting_bads) - set(auto_flat_chs)
if config.find_noisy_channels_meg:
bads_for_tsv.extend(auto_noisy_chs)
reasons.extend(['auto-noisy'] * len(auto_noisy_chs))
preexisting_bads = set(preexisting_bads) - set(auto_noisy_chs)
preexisting_bads = list(preexisting_bads)
if preexisting_bads:
bads_for_tsv.extend(preexisting_bads)
reasons.extend(['pre-existing (before mne-study-template was run)'] *
len(preexisting_bads))
tsv_data = pd.DataFrame(dict(name=bads_for_tsv, reason=reasons))
tsv_data = tsv_data.sort_values(by='name')
tsv_data.to_csv(bads_tsv_fname, sep='\t', index=False)
raw_LD.info['bads'] = []
# For closer equivalence with MaxFilter, it's recommended to low-pass
# filter your data prior to running this function
raw_check_f = raw_fruit.copy().pick_types(exclude=()).load_data().filter(
None, 48)
raw_check_o = raw_odour.copy().pick_types(exclude=()).load_data().filter(
None, 48)
raw_check_m = raw_milk.copy().pick_types(exclude=()).load_data().filter(
None, 48)
raw_check_l = raw_LD.copy().pick_types(exclude=()).load_data().filter(
None, 48)
# Find MEG bad channels using Maxwell filtering
auto_noisy_chs_f, auto_flat_chs_f = find_bad_channels_maxwell(
raw_check_f,
cross_talk=cross_talk,
calibration=calibration,
verbose=True)
auto_noisy_chs_o, auto_flat_chs_o = find_bad_channels_maxwell(
raw_check_o,
cross_talk=cross_talk,
calibration=calibration,
verbose=True)
auto_noisy_chs_m, auto_flat_chs_m = find_bad_channels_maxwell(
raw_check_m,
cross_talk=cross_talk,
calibration=calibration,
verbose=True)
auto_noisy_chs_l, auto_flat_chs_l = find_bad_channels_maxwell(
raw_check_l,
cross_talk=cross_talk,
def find_bad_channels(raw, subject, session, task, run):
if (config.find_flat_channels_meg and not config.find_noisy_channels_meg):
msg = 'Finding flat channels.'
elif (config.find_noisy_channels_meg
and not config.find_flat_channels_meg):
msg = 'Finding noisy channels using Maxwell filtering.'
else:
msg = ('Finding flat channels, and noisy channels using '
'Maxwell filtering.')
logger.info(
gen_log_message(message=msg, step=1, subject=subject, session=session))
raw_lp_filtered_for_maxwell = (raw.copy().filter(l_freq=None, h_freq=40))
auto_noisy_chs, auto_flat_chs = find_bad_channels_maxwell(
raw=raw_lp_filtered_for_maxwell,
calibration=config.mf_cal_fname,
cross_talk=config.mf_ctc_fname)
del raw_lp_filtered_for_maxwell
preexisting_bads = raw.info['bads'].copy()
bads = preexisting_bads.copy()
if config.find_flat_channels_meg:
msg = f'Found {len(auto_flat_chs)} flat channels.'
logger.info(
gen_log_message(message=msg,
step=1,
subject=subject,
session=session))
bads.extend(auto_flat_chs)
if config.find_noisy_channels_meg:
msg = f'Found {len(auto_noisy_chs)} noisy channels.'
logger.info(
gen_log_message(message=msg,
step=1,
subject=subject,
session=session))
bads.extend(auto_noisy_chs)
bads = sorted(set(bads))
raw.info['bads'] = bads
msg = f'Marked {len(raw.info["bads"])} channels as bad.'
logger.info(
gen_log_message(message=msg, step=1, subject=subject, session=session))
# Write the bad channels to disk.
deriv_path = config.get_subject_deriv_path(subject=subject,
session=session,
kind=config.get_kind())
bids_basename = make_bids_basename(subject=subject,
session=session,
task=config.get_task(),
acquisition=config.acq,
run=run,
processing=config.proc,
recording=config.rec,
space=config.space)
bads_tsv_fname = op.join(deriv_path, f'{bids_basename}_bad_channels.tsv')
bads_for_tsv = []
reasons = []
if config.find_flat_channels_meg:
bads_for_tsv.extend(auto_flat_chs)
reasons.extend(['auto-flat'] * len(auto_flat_chs))
preexisting_bads = set(preexisting_bads) - set(auto_flat_chs)
if config.find_noisy_channels_meg:
bads_for_tsv.extend(auto_noisy_chs)
reasons.extend(['auto-noisy'] * len(auto_noisy_chs))
preexisting_bads = set(preexisting_bads) - set(auto_noisy_chs)
preexisting_bads = list(preexisting_bads)
if preexisting_bads:
bads_for_tsv.extend(preexisting_bads)
reasons.extend(['pre-existing (before mne-study-template was run)'] *
len(preexisting_bads))
tsv_data = pd.DataFrame(dict(name=bads_for_tsv, reason=reasons))
tsv_data = tsv_data.sort_values(by='name')
tsv_data.to_csv(bads_tsv_fname, sep='\t', index=False)
# Before we perform SSS we'll look for bad channels — ``MEG 2443`` is quite
# noisy.
#
# .. warning::
#
# It is critical to mark bad channels in ``raw.info['bads']`` *before*
# calling :func:`~mne.preprocessing.maxwell_filter` in order to prevent
# bad channel noise from spreading.
#
# Let's see if we can automatically detect it.
raw.info['bads'] = []
raw_check = raw.copy()
auto_noisy_chs, auto_flat_chs, auto_scores = find_bad_channels_maxwell(
raw_check,
cross_talk=crosstalk_file,
calibration=fine_cal_file,
return_scores=True,
verbose=True)
print(auto_noisy_chs) # we should find them!
print(auto_flat_chs) # none for this dataset
###############################################################################
#
# .. note:: `~mne.preprocessing.find_bad_channels_maxwell` needs to operate on
# a signal without line noise or cHPI signals. By default, it simply
# applies a low-pass filter with a cutoff frequency of 40 Hz to the
# data, which should remove these artifacts. You may also specify a
# different cutoff by passing the ``h_freq`` keyword argument. If you
# set ``h_freq=None``, no filtering will be applied. This can be
# useful if your data has already been preconditioned, for example
# using :func:`mne.chpi.filter_chpi`,
def maxwellfilter(
raw,
crosstalk_file,
fine_cal_file,
subject,
headpos_file=None,
compute_motion_params=True,
figdir="/tmp/",
outdir="/tmp/",
filtering=False,
filter_args=None,
):
"""
:param raw: Raw data to apply SSS on
:param crosstalk_file: crosstalk compensation file from the Elekta system to
reduce interference between gradiometers and magnetometers
:param fine_cal_file: site-specific sensor orientation and calibration
:param subject: str, subject identifier, takes the form '001'
:param headpos_file: str, path; If existing, read in head positions from a file
:param compute_motion_params: Boolean, whether to perform motion correction
:param figdir: str, path to directory to save figures in
:param outdir: str, path to save bids compliant sss-corrected data in
(derivatives directory)
:param filtering: if True, a filter function is ran on the data after SSS.
By default, it is a 40Hz low-pass filter.
:param filter_args: dict; if filtering is True, initializes a filter with the
arguments provided
:return:
"""
from mne.preprocessing import find_bad_channels_maxwell
if not compute_motion_params:
if not headpos_file or not os.path.exists(headpos_file):
logging.info(
f"Could not find or read head position files under the supplied"
f"path: {headpos_file}. Recalculating from scratch.")
head_pos = motion_estimation(subject, raw, figdir)
else:
logging.info(
f"Reading in head positions for subject sub-{subject} "
f"from {headpos_file}.")
head_pos = mne.chpi.read_head_pos(headpos_file)
else:
logging.info(f"Starting motion estimation for subject sub-{subject}.")
head_pos = motion_estimation(subject, raw, figdir)
raw.info["bads"] = []
raw_check = raw.copy()
preconditioned = False # TODO handle this here atm. Needs to become global.
if preconditioned:
# preconditioned is a global variable that is set to True if some form
# of filtering (CHPI and line noise removal or general filtering) has
# been applied.
# the data has been filtered, and we can pass h_freq=None
logging.info("Performing bad channel detection without filtering")
auto_noisy_chs, auto_flat_chs, auto_scores = find_bad_channels_maxwell(
raw_check,
cross_talk=crosstalk_file,
calibration=fine_cal_file,
return_scores=True,
verbose=True,
h_freq=None,
)
else:
# the data still contains line noise (50Hz) and CHPI coils. It will
# filter the data before extracting bad channels
auto_noisy_chs, auto_flat_chs, auto_scores = find_bad_channels_maxwell(
raw_check,
cross_talk=crosstalk_file,
calibration=fine_cal_file,
return_scores=True,
verbose=True,
)
logging.info(f"Found the following noisy channels: {auto_noisy_chs} \n "
f"and the following flat channels: {auto_flat_chs} \n"
f"for subject sub-{subject}")
bads = raw.info["bads"] + auto_noisy_chs + auto_flat_chs
raw.info["bads"] = bads
# free up space
del raw_check
# plot as a sanity check
for ch_type in ["grad", "mag"]:
plot_noisy_channel_detection(auto_scores,
ch_type=ch_type,
subject=subject,
outpath=figdir)
logging.info(f"Signal Space Separation with movement compensation "
f"starting for subject sub-{subject}")
raw_sss = mne.preprocessing.maxwell_filter(
raw,
cross_talk=crosstalk_file,
calibration=fine_cal_file,
head_pos=head_pos,
verbose=True,
)
if filtering:
logging.info(
f"Filtering raw SSS data for subject {subject}. The following "
f"additional parameters were passed: {filter_args}")
raw_sss_filtered = raw_sss.copy()
raw_sss_filtered = _filter_data(raw_sss_filtered, **filter_args)
# TODO: Downsample
plot_psd(raw_sss_filtered, subject, figdir, filtering)
# TODO: save file
return raw_sss_filtered
plot_psd(raw_sss, subject, figdir, filtering)
return raw_sss