def perform_reference(self):
"""Estimate the true signal mean and interpolate bad channels.
This function implements the functionality of the `performReference` function
as part of the PREP pipeline on mne raw object.
Notes
-----
This function calls robust_reference first
Currently this function only implements the functionality of default
settings, i.e., doRobustPost
"""
# Phase 1: Estimate the true signal mean with robust referencing
self.robust_reference()
if self.noisy_channels["bad_all"]:
self.raw.info["bads"] = self.noisy_channels["bad_all"]
self.raw.interpolate_bads()
self.reference_signal = (np.nanmean(
self.raw.get_data(picks=self.reference_channels), axis=0) * 1e6)
rereferenced_index = [
self.ch_names_eeg.index(ch) for ch in self.rereferenced_channels
]
self.EEG = self.remove_reference(self.EEG, self.reference_signal,
rereferenced_index)
# Phase 2: Find the bad channels and interpolate
self.raw._data = self.EEG * 1e-6
noisy_detector = NoisyChannels(self.raw)
noisy_detector.find_all_bads(ransac=self.ransac)
# Record Noisy channels and EEG before interpolation
self.bad_before_interpolation = noisy_detector.get_bads(verbose=True)
self.EEG_before_interpolation = self.EEG.copy()
bad_channels = _union(self.bad_before_interpolation,
self.unusable_channels)
self.raw.info["bads"] = bad_channels
self.raw.interpolate_bads()
reference_correct = (np.nanmean(
self.raw.get_data(picks=self.reference_channels), axis=0) * 1e6)
self.EEG = self.raw.get_data() * 1e6
self.EEG = self.remove_reference(self.EEG, reference_correct,
rereferenced_index)
# reference signal after interpolation
self.reference_signal_new = self.reference_signal + reference_correct
# MNE Raw object after interpolation
self.raw._data = self.EEG * 1e-6
# Still noisy channels after interpolation
self.interpolated_channels = bad_channels
noisy_detector = NoisyChannels(self.raw)
noisy_detector.find_all_bads(ransac=self.ransac)
self.still_noisy_channels = noisy_detector.get_bads()
self.raw.info["bads"] = self.still_noisy_channels
return self
def robust_reference(self):
"""Detect bad channels and estimate the robust reference signal.
This function implements the functionality of the `robustReference` function
as part of the PREP pipeline on mne raw object.
Parameters
----------
ransac : boolean
Whether or not to use ransac
Returns
-------
noisy_channels: dictionary
A dictionary of names of noisy channels detected from all methods
after referencing
reference_signal: 1D Array
Estimation of the 'true' signal mean
"""
raw = self.raw.copy()
raw._data = removeTrend(raw.get_data(), sample_rate=self.sfreq)
# Determine unusable channels and remove them from the reference channels
noisy_detector = NoisyChannels(raw,
do_detrend=False,
random_state=self.random_state)
noisy_detector.find_all_bads(ransac=self.ransac)
self.noisy_channels_original = {
"bad_by_nan": noisy_detector.bad_by_nan,
"bad_by_flat": noisy_detector.bad_by_flat,
"bad_by_deviation": noisy_detector.bad_by_deviation,
"bad_by_hf_noise": noisy_detector.bad_by_hf_noise,
"bad_by_correlation": noisy_detector.bad_by_correlation,
"bad_by_ransac": noisy_detector.bad_by_ransac,
"bad_all": noisy_detector.get_bads(),
}
self.noisy_channels = self.noisy_channels_original.copy()
logger.info("Bad channels: {}".format(self.noisy_channels))
self.unusable_channels = _union(noisy_detector.bad_by_nan,
noisy_detector.bad_by_flat)
# According to the Matlab Implementation (see robustReference.m)
# self.unusable_channels = _union(self.unusable_channels,
# noisy_detector.bad_by_SNR)
# but maybe this makes no difference...
self.reference_channels = _set_diff(self.reference_channels,
self.unusable_channels)
# Get initial estimate of the reference by the specified method
signal = raw.get_data() * 1e6
self.reference_signal = (
np.nanmedian(raw.get_data(picks=self.reference_channels), axis=0) *
1e6)
reference_index = [
self.ch_names_eeg.index(ch) for ch in self.reference_channels
]
signal_tmp = self.remove_reference(signal, self.reference_signal,
reference_index)
# Remove reference from signal, iteratively interpolating bad channels
raw_tmp = raw.copy()
iterations = 0
noisy_channels_old = []
max_iteration_num = 4
while True:
raw_tmp._data = signal_tmp * 1e-6
noisy_detector = NoisyChannels(raw_tmp,
do_detrend=False,
random_state=self.random_state)
# Detrend applied at the beginning of the function.
noisy_detector.find_all_bads(ransac=self.ransac)
self.noisy_channels["bad_by_nan"] = _union(
self.noisy_channels["bad_by_nan"], noisy_detector.bad_by_nan)
self.noisy_channels["bad_by_flat"] = _union(
self.noisy_channels["bad_by_flat"], noisy_detector.bad_by_flat)
self.noisy_channels["bad_by_deviation"] = _union(
self.noisy_channels["bad_by_deviation"],
noisy_detector.bad_by_deviation)
self.noisy_channels["bad_by_hf_noise"] = _union(
self.noisy_channels["bad_by_hf_noise"],
noisy_detector.bad_by_hf_noise)
self.noisy_channels["bad_by_correlation"] = _union(
self.noisy_channels["bad_by_correlation"],
noisy_detector.bad_by_correlation,
)
self.noisy_channels["bad_by_ransac"] = _union(
self.noisy_channels["bad_by_ransac"],
noisy_detector.bad_by_ransac)
self.noisy_channels["bad_all"] = _union(
self.noisy_channels["bad_all"], noisy_detector.get_bads())
logger.info("Bad channels: {}".format(self.noisy_channels))
if (iterations > 1 and (not self.noisy_channels["bad_all"] or set(
self.noisy_channels["bad_all"]) == set(noisy_channels_old))
or iterations > max_iteration_num):
break
noisy_channels_old = self.noisy_channels["bad_all"].copy()
if raw_tmp.info["nchan"] - len(self.noisy_channels["bad_all"]) < 2:
raise ValueError(
"RobustReference:TooManyBad "
"Could not perform a robust reference -- not enough good channels"
)
if self.noisy_channels["bad_all"]:
raw_tmp._data = signal * 1e-6
raw_tmp.info["bads"] = self.noisy_channels["bad_all"]
raw_tmp.interpolate_bads()
signal_tmp = raw_tmp.get_data() * 1e6
else:
signal_tmp = signal
self.reference_signal = (np.nanmean(
raw_tmp.get_data(picks=self.reference_channels), axis=0) * 1e6)
signal_tmp = self.remove_reference(signal, self.reference_signal,
reference_index)
iterations = iterations + 1
logger.info("Iterations: {}".format(iterations))
logger.info("Robust reference done")
return self.noisy_channels, self.reference_signal
def robust_reference(self, max_iterations=4):
"""Detect bad channels and estimate the robust reference signal.
This function implements the functionality of the `robustReference` function
as part of the PREP pipeline on mne raw object.
Parameters
----------
max_iterations : int, optional
The maximum number of iterations of noisy channel removal to perform
during robust referencing. Defaults to ``4``.
Returns
-------
noisy_channels: dict
A dictionary of names of noisy channels detected from all methods
after referencing.
reference_signal: np.ndarray, shape(n, )
Estimation of the 'true' signal mean
"""
raw = self.raw.copy()
raw._data = removeTrend(raw.get_data(),
self.sfreq,
matlab_strict=self.matlab_strict)
# Determine unusable channels and remove them from the reference channels
noisy_detector = NoisyChannels(
raw,
do_detrend=False,
random_state=self.random_state,
matlab_strict=self.matlab_strict,
)
noisy_detector.find_all_bads(**self.ransac_settings)
self.noisy_channels_original = noisy_detector.get_bads(as_dict=True)
self._extra_info["initial_bad"] = noisy_detector._extra_info
logger.info("Bad channels: {}".format(self.noisy_channels_original))
# Determine channels to use/exclude from initial reference estimation
self.unusable_channels = _union(
noisy_detector.bad_by_nan + noisy_detector.bad_by_flat,
noisy_detector.bad_by_SNR,
)
reference_channels = _set_diff(self.reference_channels,
self.unusable_channels)
# Initialize channels to permanently flag as bad during referencing
noisy = {
"bad_by_nan": noisy_detector.bad_by_nan,
"bad_by_flat": noisy_detector.bad_by_flat,
"bad_by_deviation": [],
"bad_by_hf_noise": [],
"bad_by_correlation": [],
"bad_by_SNR": [],
"bad_by_dropout": [],
"bad_by_ransac": [],
"bad_all": [],
}
# Get initial estimate of the reference by the specified method
signal = raw.get_data()
self.reference_signal = np.nanmedian(
raw.get_data(picks=reference_channels), axis=0)
reference_index = [
self.ch_names_eeg.index(ch) for ch in reference_channels
]
signal_tmp = self.remove_reference(signal, self.reference_signal,
reference_index)
# Remove reference from signal, iteratively interpolating bad channels
raw_tmp = raw.copy()
iterations = 0
previous_bads = set()
while True:
raw_tmp._data = signal_tmp
noisy_detector = NoisyChannels(
raw_tmp,
do_detrend=False,
random_state=self.random_state,
matlab_strict=self.matlab_strict,
)
# Detrend applied at the beginning of the function.
# Detect all currently bad channels
noisy_detector.find_all_bads(**self.ransac_settings)
noisy_new = noisy_detector.get_bads(as_dict=True)
# Specify bad channel types to ignore when updating noisy channels
# NOTE: MATLAB PREP ignores dropout channels, possibly by mistake?
# see: https://github.com/VisLab/EEG-Clean-Tools/issues/28
ignore = ["bad_by_SNR", "bad_all"]
if self.matlab_strict:
ignore += ["bad_by_dropout"]
# Update set of all noisy channels detected so far with any new ones
bad_chans = set()
for bad_type in noisy_new.keys():
noisy[bad_type] = _union(noisy[bad_type], noisy_new[bad_type])
if bad_type not in ignore:
bad_chans.update(noisy[bad_type])
noisy["bad_all"] = list(bad_chans)
logger.info("Bad channels: {}".format(noisy))
if (iterations > 1 and
(len(bad_chans) == 0 or bad_chans == previous_bads)
or iterations > max_iterations):
logger.info("Robust reference done")
self.noisy_channels = noisy
break
previous_bads = bad_chans.copy()
if raw_tmp.info["nchan"] - len(bad_chans) < 2:
raise ValueError(
"RobustReference:TooManyBad "
"Could not perform a robust reference -- not enough good channels"
)
if len(bad_chans) > 0:
raw_tmp._data = signal.copy()
raw_tmp.info["bads"] = list(bad_chans)
if self.matlab_strict:
_eeglab_interpolate_bads(raw_tmp)
else:
raw_tmp.interpolate_bads()
self.reference_signal = np.nanmean(
raw_tmp.get_data(picks=reference_channels), axis=0)
signal_tmp = self.remove_reference(signal, self.reference_signal,
reference_index)
iterations = iterations + 1
logger.info("Iterations: {}".format(iterations))
return self.noisy_channels, self.reference_signal
def perform_reference(self, max_iterations=4):
"""Estimate the true signal mean and interpolate bad channels.
Parameters
----------
max_iterations : int, optional
The maximum number of iterations of noisy channel removal to perform
during robust referencing. Defaults to ``4``.
This function implements the functionality of the `performReference` function
as part of the PREP pipeline on mne raw object.
Notes
-----
This function calls ``robust_reference`` first.
Currently this function only implements the functionality of default
settings, i.e., ``doRobustPost``.
"""
# Phase 1: Estimate the true signal mean with robust referencing
self.robust_reference(max_iterations)
# If we interpolate the raw here we would be interpolating
# more than what we later actually account for (in interpolated channels).
dummy = self.raw.copy()
dummy.info["bads"] = self.noisy_channels["bad_all"]
if self.matlab_strict:
_eeglab_interpolate_bads(dummy)
else:
dummy.interpolate_bads()
self.reference_signal = np.nanmean(
dummy.get_data(picks=self.reference_channels), axis=0)
del dummy
rereferenced_index = [
self.ch_names_eeg.index(ch) for ch in self.rereferenced_channels
]
self.EEG = self.remove_reference(self.EEG, self.reference_signal,
rereferenced_index)
# Phase 2: Find the bad channels and interpolate
self.raw._data = self.EEG
noisy_detector = NoisyChannels(self.raw,
random_state=self.random_state,
matlab_strict=self.matlab_strict)
noisy_detector.find_all_bads(**self.ransac_settings)
# Record Noisy channels and EEG before interpolation
self.bad_before_interpolation = noisy_detector.get_bads(verbose=True)
self.EEG_before_interpolation = self.EEG.copy()
self.noisy_channels_before_interpolation = noisy_detector.get_bads(
as_dict=True)
self._extra_info["interpolated"] = noisy_detector._extra_info
bad_channels = _union(self.bad_before_interpolation,
self.unusable_channels)
self.raw.info["bads"] = bad_channels
if self.matlab_strict:
_eeglab_interpolate_bads(self.raw)
else:
self.raw.interpolate_bads()
reference_correct = np.nanmean(
self.raw.get_data(picks=self.reference_channels), axis=0)
self.EEG = self.raw.get_data()
self.EEG = self.remove_reference(self.EEG, reference_correct,
rereferenced_index)
# reference signal after interpolation
self.reference_signal_new = self.reference_signal + reference_correct
# MNE Raw object after interpolation
self.raw._data = self.EEG
# Still noisy channels after interpolation
self.interpolated_channels = bad_channels
noisy_detector = NoisyChannels(self.raw,
random_state=self.random_state,
matlab_strict=self.matlab_strict)
noisy_detector.find_all_bads(**self.ransac_settings)
self.still_noisy_channels = noisy_detector.get_bads()
self.raw.info["bads"] = self.still_noisy_channels
self.noisy_channels_after_interpolation = noisy_detector.get_bads(
as_dict=True)
self._extra_info["remaining_bad"] = noisy_detector._extra_info
return self
def perform_reference(self):
"""Estimate the true signal mean and interpolate bad channels.
This function implements the functionality of the `performReference` function
as part of the PREP pipeline on mne raw object.
Notes
-----
This function calls ``robust_reference`` first.
Currently this function only implements the functionality of default
settings, i.e., ``doRobustPost``.
"""
# Phase 1: Estimate the true signal mean with robust referencing
self.robust_reference()
# If we interpolate the raw here we would be interpolating
# more than what we later actually account for (in interpolated channels).
dummy = self.raw.copy()
dummy.info["bads"] = self.noisy_channels["bad_all"]
dummy.interpolate_bads()
self.reference_signal = (
np.nanmean(dummy.get_data(picks=self.reference_channels), axis=0) * 1e6
)
del dummy
rereferenced_index = [
self.ch_names_eeg.index(ch) for ch in self.rereferenced_channels
]
self.EEG = self.remove_reference(
self.EEG, self.reference_signal, rereferenced_index
)
# Phase 2: Find the bad channels and interpolate
self.raw._data = self.EEG * 1e-6
noisy_detector = NoisyChannels(self.raw, random_state=self.random_state)
noisy_detector.find_all_bads(ransac=self.ransac)
# Record Noisy channels and EEG before interpolation
self.bad_before_interpolation = noisy_detector.get_bads(verbose=True)
self.EEG_before_interpolation = self.EEG.copy()
self.noisy_channels_before_interpolation = {
"bad_by_nan": noisy_detector.bad_by_nan,
"bad_by_flat": noisy_detector.bad_by_flat,
"bad_by_deviation": noisy_detector.bad_by_deviation,
"bad_by_hf_noise": noisy_detector.bad_by_hf_noise,
"bad_by_correlation": noisy_detector.bad_by_correlation,
"bad_by_SNR": noisy_detector.bad_by_SNR,
"bad_by_dropout": noisy_detector.bad_by_dropout,
"bad_by_ransac": noisy_detector.bad_by_ransac,
"bad_all": noisy_detector.get_bads(),
}
bad_channels = _union(self.bad_before_interpolation, self.unusable_channels)
self.raw.info["bads"] = bad_channels
self.raw.interpolate_bads()
reference_correct = (
np.nanmean(self.raw.get_data(picks=self.reference_channels), axis=0) * 1e6
)
self.EEG = self.raw.get_data() * 1e6
self.EEG = self.remove_reference(
self.EEG, reference_correct, rereferenced_index
)
# reference signal after interpolation
self.reference_signal_new = self.reference_signal + reference_correct
# MNE Raw object after interpolation
self.raw._data = self.EEG * 1e-6
# Still noisy channels after interpolation
self.interpolated_channels = bad_channels
noisy_detector = NoisyChannels(self.raw, random_state=self.random_state)
noisy_detector.find_all_bads(ransac=self.ransac)
self.still_noisy_channels = noisy_detector.get_bads()
self.raw.info["bads"] = self.still_noisy_channels
self.noisy_channels_after_interpolation = {
"bad_by_nan": noisy_detector.bad_by_nan,
"bad_by_flat": noisy_detector.bad_by_flat,
"bad_by_deviation": noisy_detector.bad_by_deviation,
"bad_by_hf_noise": noisy_detector.bad_by_hf_noise,
"bad_by_correlation": noisy_detector.bad_by_correlation,
"bad_by_SNR": noisy_detector.bad_by_SNR,
"bad_by_dropout": noisy_detector.bad_by_dropout,
"bad_by_ransac": noisy_detector.bad_by_ransac,
"bad_all": noisy_detector.get_bads(),
}
return self