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Feature-Extraction/dist/client/mne/channels/channels.py

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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from __future__ import annotations # only needed for Python ≤ 3.9
import os.path as op
import string
import sys
from collections import OrderedDict
from copy import deepcopy
from dataclasses import dataclass
from functools import partial
from pathlib import Path
import numpy as np
from scipy.io import loadmat
from scipy.sparse import csr_array, lil_array
from scipy.spatial import Delaunay
from scipy.stats import zscore
from .._fiff.constants import FIFF
from .._fiff.meas_info import ( # noqa F401
Info,
MontageMixin,
_merge_info,
_rename_comps,
_unit2human, # TODO: pybv relies on this, should be made public
create_info,
)
from .._fiff.pick import (
_check_excludes_includes,
_pick_data_channels,
_picks_by_type,
_picks_to_idx,
_second_rules,
channel_indices_by_type,
channel_type,
pick_channels,
pick_info,
pick_types,
)
from .._fiff.proj import setup_proj
from .._fiff.reference import add_reference_channels, set_eeg_reference
from .._fiff.tag import _rename_list
from ..bem import _check_origin
from ..defaults import HEAD_SIZE_DEFAULT, _handle_default
from ..utils import (
_check_dict_keys,
_check_fname,
_check_option,
_check_preload,
_get_stim_channel,
_on_missing,
_validate_type,
fill_doc,
legacy,
logger,
verbose,
warn,
)
def _get_meg_system(info):
"""Educated guess for the helmet type based on channels."""
have_helmet = True
for ch in info["chs"]:
if ch["kind"] == FIFF.FIFFV_MEG_CH:
# Only take first 16 bits, as higher bits store CTF grad comp order
coil_type = ch["coil_type"] & 0xFFFF
nmag = np.sum([c["kind"] == FIFF.FIFFV_MEG_CH for c in info["chs"]])
if coil_type == FIFF.FIFFV_COIL_NM_122:
system = "122m"
break
elif coil_type // 1000 == 3: # All Vectorview coils are 30xx
system = "306m"
break
elif (
coil_type == FIFF.FIFFV_COIL_MAGNES_MAG
or coil_type == FIFF.FIFFV_COIL_MAGNES_GRAD
):
system = "Magnes_3600wh" if nmag > 150 else "Magnes_2500wh"
break
elif coil_type == FIFF.FIFFV_COIL_CTF_GRAD:
system = "CTF_275"
break
elif coil_type == FIFF.FIFFV_COIL_KIT_GRAD:
system = "KIT"
# Our helmet does not match very well, so let's just create it
have_helmet = False
break
elif coil_type == FIFF.FIFFV_COIL_BABY_GRAD:
system = "BabySQUID"
break
elif coil_type == FIFF.FIFFV_COIL_ARTEMIS123_GRAD:
system = "ARTEMIS123"
have_helmet = False
break
elif coil_type == FIFF.FIFFV_COIL_KERNEL_OPM_MAG_GEN1:
system = "Kernel_Flux"
have_helmet = True
break
else:
system = "unknown"
have_helmet = False
return system, have_helmet
@verbose
def equalize_channels(instances, copy=True, verbose=None):
"""Equalize channel picks and ordering across multiple MNE-Python objects.
First, all channels that are not common to each object are dropped. Then,
using the first object in the list as a template, the channels of each
object are re-ordered to match the template. The end result is that all
given objects define the same channels, in the same order.
Parameters
----------
instances : list
A list of MNE-Python objects to equalize the channels for. Objects can
be of type Raw, Epochs, Evoked, AverageTFR, Forward, Covariance,
CrossSpectralDensity or Info.
copy : bool
When dropping and/or re-ordering channels, an object will be copied
when this parameter is set to ``True``. When set to ``False`` (the
default) the dropping and re-ordering of channels happens in-place.
.. versionadded:: 0.20.0
%(verbose)s
Returns
-------
equalized_instances : list
A list of MNE-Python objects that have the same channels defined in the
same order.
Notes
-----
This function operates inplace.
"""
from ..cov import Covariance
from ..epochs import BaseEpochs
from ..evoked import Evoked
from ..forward import Forward
from ..io import BaseRaw
from ..time_frequency import BaseTFR, CrossSpectralDensity
# Instances need to have a `ch_names` attribute and a `pick_channels`
# method that supports `ordered=True`.
allowed_types = (
BaseRaw,
BaseEpochs,
Evoked,
BaseTFR,
Forward,
Covariance,
CrossSpectralDensity,
Info,
)
allowed_types_str = (
"Raw, Epochs, Evoked, TFR, Forward, Covariance, CrossSpectralDensity or Info"
)
for inst in instances:
_validate_type(
inst, allowed_types, "Instances to be modified", allowed_types_str
)
chan_template = instances[0].ch_names
logger.info("Identifying common channels ...")
channels = [set(inst.ch_names) for inst in instances]
common_channels = set(chan_template).intersection(*channels)
all_channels = set(chan_template).union(*channels)
dropped = list(set(all_channels - common_channels))
# Preserve the order of chan_template
order = np.argsort([chan_template.index(ch) for ch in common_channels])
common_channels = np.array(list(common_channels))[order].tolist()
# Update all instances to match the common_channels list
reordered = False
equalized_instances = []
for inst in instances:
# Only perform picking when needed
if inst.ch_names != common_channels:
if isinstance(inst, Info):
sel = pick_channels(
inst.ch_names, common_channels, exclude=[], ordered=True
)
inst = pick_info(inst, sel, copy=copy, verbose=False)
else:
if copy:
inst = inst.copy()
# TODO change to .pick() once CSD, Cov, and Fwd have `.pick()` methods
inst.pick_channels(common_channels, ordered=True)
if len(inst.ch_names) == len(common_channels):
reordered = True
equalized_instances.append(inst)
if dropped:
logger.info(f"Dropped the following channels:\n{dropped}")
elif reordered:
logger.info("Channels have been re-ordered.")
return equalized_instances
def unify_bad_channels(insts):
"""Unify bad channels across a list of instances.
All instances must be of the same type and have matching channel names and channel
order. The ``.info["bads"]`` of each instance will be set to the union of
``.info["bads"]`` across all instances.
Parameters
----------
insts : list
List of instances (:class:`~mne.io.Raw`, :class:`~mne.Epochs`,
:class:`~mne.Evoked`, :class:`~mne.time_frequency.Spectrum`,
:class:`~mne.time_frequency.EpochsSpectrum`) across which to unify bad channels.
Returns
-------
insts : list
List of instances with bad channels unified across instances.
See Also
--------
mne.channels.equalize_channels
mne.channels.rename_channels
mne.channels.combine_channels
Notes
-----
This function modifies the instances in-place.
.. versionadded:: 1.6
"""
from ..epochs import Epochs
from ..evoked import Evoked
from ..io import BaseRaw
from ..time_frequency.spectrum import BaseSpectrum
# ensure input is list-like
_validate_type(insts, (list, tuple), "insts")
# ensure non-empty
if len(insts) == 0:
raise ValueError("insts must not be empty")
# ensure all insts are MNE objects, and all the same type
inst_type = type(insts[0])
valid_types = (BaseRaw, Epochs, Evoked, BaseSpectrum)
for inst in insts:
_validate_type(inst, valid_types, "each object in insts")
if type(inst) is not inst_type:
raise ValueError("All insts must be the same type")
# ensure all insts have the same channels and channel order
ch_names = insts[0].ch_names
for inst in insts[1:]:
dif = set(inst.ch_names) ^ set(ch_names)
if len(dif):
raise ValueError(
"Channels do not match across the objects in insts. Consider calling "
"equalize_channels before calling this function."
)
elif inst.ch_names != ch_names:
raise ValueError(
"Channel names are sorted differently across instances. Please use "
"mne.channels.equalize_channels."
)
# collect bads as dict keys so that insertion order is preserved, then cast to list
all_bads = dict()
for inst in insts:
all_bads.update(dict.fromkeys(inst.info["bads"]))
all_bads = list(all_bads)
# update bads on all instances
for inst in insts:
inst.info["bads"] = all_bads
return insts
class ReferenceMixin(MontageMixin):
"""Mixin class for Raw, Evoked, Epochs."""
@verbose
def set_eeg_reference(
self,
ref_channels="average",
projection=False,
ch_type="auto",
forward=None,
*,
joint=False,
verbose=None,
):
"""Specify which reference to use for EEG data.
Use this function to explicitly specify the desired reference for EEG.
This can be either an existing electrode or a new virtual channel.
This function will re-reference the data according to the desired
reference.
Parameters
----------
%(ref_channels_set_eeg_reference)s
%(projection_set_eeg_reference)s
%(ch_type_set_eeg_reference)s
%(forward_set_eeg_reference)s
%(joint_set_eeg_reference)s
%(verbose)s
Returns
-------
inst : instance of Raw | Epochs | Evoked
Data with EEG channels re-referenced. If ``ref_channels='average'``
and ``projection=True`` a projection will be added instead of
directly re-referencing the data.
%(set_eeg_reference_see_also_notes)s
"""
return set_eeg_reference(
self,
ref_channels=ref_channels,
copy=False,
projection=projection,
ch_type=ch_type,
forward=forward,
joint=joint,
)[0]
class UpdateChannelsMixin:
"""Mixin class for Raw, Evoked, Epochs, Spectrum, AverageTFR."""
@verbose
@legacy(alt="inst.pick(...)")
def pick_types(
self,
meg=False,
eeg=False,
stim=False,
eog=False,
ecg=False,
emg=False,
ref_meg="auto",
*,
misc=False,
resp=False,
chpi=False,
exci=False,
ias=False,
syst=False,
seeg=False,
dipole=False,
gof=False,
bio=False,
ecog=False,
fnirs=False,
csd=False,
dbs=False,
temperature=False,
gsr=False,
eyetrack=False,
include=(),
exclude="bads",
selection=None,
verbose=None,
):
"""Pick some channels by type and names.
Parameters
----------
%(pick_types_params)s
%(verbose)s
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
pick_channels
Notes
-----
.. versionadded:: 0.9.0
"""
idx = pick_types(
self.info,
meg=meg,
eeg=eeg,
stim=stim,
eog=eog,
ecg=ecg,
emg=emg,
ref_meg=ref_meg,
misc=misc,
resp=resp,
chpi=chpi,
exci=exci,
ias=ias,
syst=syst,
seeg=seeg,
dipole=dipole,
gof=gof,
bio=bio,
ecog=ecog,
fnirs=fnirs,
csd=csd,
dbs=dbs,
temperature=temperature,
gsr=gsr,
eyetrack=eyetrack,
include=include,
exclude=exclude,
selection=selection,
)
self._pick_drop_channels(idx)
# remove dropped channel types from reject and flat
if getattr(self, "reject", None) is not None:
# use list(self.reject) to avoid RuntimeError for changing dictionary size
# during iteration
for ch_type in list(self.reject):
if ch_type not in self:
del self.reject[ch_type]
if getattr(self, "flat", None) is not None:
for ch_type in list(self.flat):
if ch_type not in self:
del self.flat[ch_type]
return self
@verbose
@legacy(alt="inst.pick(...)")
def pick_channels(self, ch_names, ordered=True, *, verbose=None):
"""Pick some channels.
Parameters
----------
ch_names : list
The list of channels to select.
%(ordered)s
%(verbose)s
.. versionadded:: 1.1
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
drop_channels
pick_types
reorder_channels
Notes
-----
The channel names given are assumed to be a set, i.e. the order
does not matter. The original order of the channels is preserved.
You can use ``reorder_channels`` to set channel order if necessary.
.. versionadded:: 0.9.0
"""
picks = pick_channels(self.info["ch_names"], ch_names, ordered=ordered)
return self._pick_drop_channels(picks)
@verbose
def pick(self, picks, exclude=(), *, verbose=None):
"""Pick a subset of channels.
Parameters
----------
%(picks_all)s
exclude : list | str
Set of channels to exclude, only used when picking based on
types (e.g., exclude="bads" when picks="meg").
%(verbose)s
.. versionadded:: 0.24.0
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
"""
picks = _picks_to_idx(self.info, picks, "all", exclude, allow_empty=False)
self._pick_drop_channels(picks)
# remove dropped channel types from reject and flat
if getattr(self, "reject", None) is not None:
# use list(self.reject) to avoid RuntimeError for changing dictionary size
# during iteration
for ch_type in list(self.reject):
if ch_type not in self:
del self.reject[ch_type]
if getattr(self, "flat", None) is not None:
for ch_type in list(self.flat):
if ch_type not in self:
del self.flat[ch_type]
return self
def reorder_channels(self, ch_names):
"""Reorder channels.
Parameters
----------
ch_names : list
The desired channel order.
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
drop_channels
pick_types
pick_channels
Notes
-----
Channel names must be unique. Channels that are not in ``ch_names``
are dropped.
.. versionadded:: 0.16.0
"""
_check_excludes_includes(ch_names)
idx = list()
for ch_name in ch_names:
ii = self.ch_names.index(ch_name)
if ii in idx:
raise ValueError(f"Channel name repeated: {ch_name}")
idx.append(ii)
return self._pick_drop_channels(idx)
@fill_doc
def drop_channels(self, ch_names, on_missing="raise"):
"""Drop channel(s).
Parameters
----------
ch_names : iterable or str
Iterable (e.g. list) of channel name(s) or channel name to remove.
%(on_missing_ch_names)s
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
reorder_channels
pick_channels
pick_types
Notes
-----
.. versionadded:: 0.9.0
"""
if isinstance(ch_names, str):
ch_names = [ch_names]
try:
all_str = all([isinstance(ch, str) for ch in ch_names])
except TypeError:
raise ValueError(
f"'ch_names' must be iterable, got type {type(ch_names)} ({ch_names})."
)
if not all_str:
raise ValueError(
"Each element in 'ch_names' must be str, got "
f"{[type(ch) for ch in ch_names]}."
)
missing = [ch for ch in ch_names if ch not in self.ch_names]
if len(missing) > 0:
msg = "Channel(s) {0} not found, nothing dropped."
_on_missing(on_missing, msg.format(", ".join(missing)))
bad_idx = [self.ch_names.index(ch) for ch in ch_names if ch in self.ch_names]
idx = np.setdiff1d(np.arange(len(self.ch_names)), bad_idx)
if len(idx) == 0:
raise ValueError("All channels would be dropped.")
return self._pick_drop_channels(idx)
@verbose
def _pick_drop_channels(self, idx, *, verbose=None):
# avoid circular imports
from ..io import BaseRaw
msg = "adding, dropping, or reordering channels"
if isinstance(self, BaseRaw):
if self._projector is not None:
_check_preload(self, f"{msg} after calling .apply_proj()")
else:
_check_preload(self, msg)
if getattr(self, "picks", None) is not None:
self.picks = self.picks[idx]
if getattr(self, "_read_picks", None) is not None:
self._read_picks = [r[idx] for r in self._read_picks]
if hasattr(self, "_cals"):
self._cals = self._cals[idx]
pick_info(self.info, idx, copy=False)
for key in ("_comp", "_projector"):
mat = getattr(self, key, None)
if mat is not None:
setattr(self, key, mat[idx][:, idx])
if hasattr(self, "_dims"): # Spectrum and "new-style" TFRs
axis = self._dims.index("channel")
else: # All others (Evoked, Epochs, Raw) have chs axis=-2
axis = -2
if hasattr(self, "_data"): # skip non-preloaded Raw
self._data = self._data.take(idx, axis=axis)
else:
assert isinstance(self, BaseRaw) and not self.preload
if isinstance(self, BaseRaw):
self.annotations._prune_ch_names(self.info, on_missing="ignore")
self._orig_units = {
k: v for k, v in self._orig_units.items() if k in self.ch_names
}
self._pick_projs()
return self
def _pick_projs(self):
"""Keep only projectors which apply to at least 1 data channel."""
drop_idx = []
for idx, proj in enumerate(self.info["projs"]):
if not set(self.info["ch_names"]) & set(proj["data"]["col_names"]):
drop_idx.append(idx)
for idx in drop_idx:
logger.info(f"Removing projector {self.info['projs'][idx]}")
if drop_idx and hasattr(self, "del_proj"):
self.del_proj(drop_idx)
return self
def add_channels(self, add_list, force_update_info=False):
"""Append new channels to the instance.
Parameters
----------
add_list : list
A list of objects to append to self. Must contain all the same
type as the current object.
force_update_info : bool
If True, force the info for objects to be appended to match the
values in ``self``. This should generally only be used when adding
stim channels for which important metadata won't be overwritten.
.. versionadded:: 0.12
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
drop_channels
Notes
-----
If ``self`` is a Raw instance that has been preloaded into a
:obj:`numpy.memmap` instance, the memmap will be resized.
"""
# avoid circular imports
from ..epochs import BaseEpochs
from ..io import BaseRaw
from ..time_frequency import EpochsTFR
_validate_type(add_list, (list, tuple), "Input")
# Object-specific checks
for inst in add_list + [self]:
_check_preload(inst, "adding channels")
if isinstance(self, BaseRaw):
con_axis = 0
comp_class = BaseRaw
elif isinstance(self, BaseEpochs):
con_axis = 1
comp_class = BaseEpochs
elif isinstance(self, EpochsTFR):
con_axis = 1
comp_class = EpochsTFR
else:
con_axis = 0
comp_class = type(self)
for inst in add_list:
_validate_type(inst, comp_class, "All input")
data = [inst._data for inst in [self] + add_list]
# Make sure that all dimensions other than channel axis are the same
compare_axes = [i for i in range(data[0].ndim) if i != con_axis]
shapes = np.array([dat.shape for dat in data])[:, compare_axes]
for shape in shapes:
if not ((shapes[0] - shape) == 0).all():
raise ValueError(
"All data dimensions except channels must match, got "
f"{shapes[0]} != {shape}"
)
del shapes
# Create final data / info objects
infos = [self.info] + [inst.info for inst in add_list]
new_info = _merge_info(infos, force_update_to_first=force_update_info)
# Now update the attributes
if (
isinstance(self._data, np.memmap)
and con_axis == 0
and sys.platform != "darwin"
): # resizing not available--no mremap
# Use a resize and fill in other ones
out_shape = (sum(d.shape[0] for d in data),) + data[0].shape[1:]
n_bytes = np.prod(out_shape) * self._data.dtype.itemsize
self._data.flush()
self._data.base.resize(n_bytes)
self._data = np.memmap(
self._data.filename, mode="r+", dtype=self._data.dtype, shape=out_shape
)
assert self._data.shape == out_shape
assert self._data.nbytes == n_bytes
offset = len(data[0])
for d in data[1:]:
this_len = len(d)
self._data[offset : offset + this_len] = d
offset += this_len
else:
self._data = np.concatenate(data, axis=con_axis)
self.info = new_info
if isinstance(self, BaseRaw):
self._cals = np.concatenate(
[getattr(inst, "_cals") for inst in [self] + add_list]
)
# We should never use these since data are preloaded, let's just
# set it to something large and likely to break (2 ** 31 - 1)
extra_idx = [2147483647] * sum(info["nchan"] for info in infos[1:])
assert all(len(r) == infos[0]["nchan"] for r in self._read_picks)
self._read_picks = [
np.concatenate([r, extra_idx]) for r in self._read_picks
]
assert all(len(r) == self.info["nchan"] for r in self._read_picks)
for other in add_list:
self._orig_units.update(other._orig_units)
elif isinstance(self, BaseEpochs):
self.picks = np.arange(self._data.shape[1])
if hasattr(self, "_projector"):
activate = False if self._do_delayed_proj else self.proj
self._projector, self.info = setup_proj(
self.info, False, activate=activate
)
return self
@fill_doc
def add_reference_channels(self, ref_channels):
"""Add reference channels to data that consists of all zeros.
Adds reference channels to data that were not included during
recording. This is useful when you need to re-reference your data
to different channels. These added channels will consist of all zeros.
Parameters
----------
%(ref_channels)s
Returns
-------
inst : instance of Raw | Epochs | Evoked
The modified instance.
"""
return add_reference_channels(self, ref_channels, copy=False)
class InterpolationMixin:
"""Mixin class for Raw, Evoked, Epochs."""
@verbose
def interpolate_bads(
self,
reset_bads=True,
mode="accurate",
origin="auto",
method=None,
exclude=(),
verbose=None,
):
"""Interpolate bad MEG and EEG channels.
Operates in place.
Parameters
----------
reset_bads : bool
If True, remove the bads from info.
mode : str
Either ``'accurate'`` or ``'fast'``, determines the quality of the
Legendre polynomial expansion used for interpolation of channels
using the minimum-norm method.
origin : array-like, shape (3,) | str
Origin of the sphere in the head coordinate frame and in meters.
Can be ``'auto'`` (default), which means a head-digitization-based
origin fit.
.. versionadded:: 0.17
method : dict | str | None
Method to use for each channel type.
- ``"meg"`` channels support ``"MNE"`` (default) and ``"nan"``
- ``"eeg"`` channels support ``"spline"`` (default), ``"MNE"`` and ``"nan"``
- ``"fnirs"`` channels support ``"nearest"`` (default) and ``"nan"``
- ``"ecog"`` channels support ``"spline"`` (default) and ``"nan"``
- ``"seeg"`` channels support ``"spline"`` (default) and ``"nan"``
None is an alias for::
method=dict(meg="MNE", eeg="spline", fnirs="nearest")
If a :class:`str` is provided, the method will be applied to all channel
types supported and available in the instance. The method ``"nan"`` will
replace the channel data with ``np.nan``.
.. warning::
Be careful when using ``method="nan"``; the default value
``reset_bads=True`` may not be what you want.
.. versionadded:: 0.21
exclude : list | tuple
The channels to exclude from interpolation. If excluded a bad
channel will stay in bads.
%(verbose)s
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
Notes
-----
The ``"MNE"`` method uses minimum-norm projection to a sphere and back.
.. versionadded:: 0.9.0
"""
from .interpolation import (
_interpolate_bads_ecog,
_interpolate_bads_eeg,
_interpolate_bads_meeg,
_interpolate_bads_nan,
_interpolate_bads_nirs,
_interpolate_bads_seeg,
)
_check_preload(self, "interpolation")
_validate_type(method, (dict, str, None), "method")
method = _handle_default("interpolation_method", method)
ch_types = self.get_channel_types(unique=True)
# figure out if we have "mag" for "meg", "hbo" for "fnirs", ... to filter the
# "method" dictionary and keep only keys that correspond to existing channels.
for ch_type in ("meg", "fnirs"):
for sub_ch_type in _second_rules[ch_type][1].values():
if sub_ch_type in ch_types:
ch_types.remove(sub_ch_type)
if ch_type not in ch_types:
ch_types.append(ch_type)
keys2delete = set(method) - set(ch_types)
for key in keys2delete:
del method[key]
valids = {
"eeg": ("spline", "MNE", "nan"),
"meg": ("MNE", "nan"),
"fnirs": ("nearest", "nan"),
"ecog": ("spline", "nan"),
"seeg": ("spline", "nan"),
}
for key in method:
_check_option("method[key]", key, tuple(valids))
_check_option(f"method['{key}']", method[key], valids[key])
logger.info("Setting channel interpolation method to %s.", method)
idx = _picks_to_idx(self.info, list(method), exclude=(), allow_empty=True)
if idx.size == 0 or len(pick_info(self.info, idx)["bads"]) == 0:
warn("No bad channels to interpolate. Doing nothing...")
return self
for ch_type in method.copy():
idx = _picks_to_idx(self.info, ch_type, exclude=(), allow_empty=True)
if len(pick_info(self.info, idx)["bads"]) == 0:
method.pop(ch_type)
logger.info("Interpolating bad channels.")
needs_origin = [key != "seeg" and val != "nan" for key, val in method.items()]
if any(needs_origin):
origin = _check_origin(origin, self.info)
for ch_type, interp in method.items():
if interp == "nan":
_interpolate_bads_nan(self, ch_type, exclude=exclude)
if method.get("eeg", "") == "spline":
_interpolate_bads_eeg(self, origin=origin, exclude=exclude)
meg_mne = method.get("meg", "") == "MNE"
eeg_mne = method.get("eeg", "") == "MNE"
if meg_mne or eeg_mne:
_interpolate_bads_meeg(
self,
mode=mode,
meg=meg_mne,
eeg=eeg_mne,
origin=origin,
exclude=exclude,
method=method,
)
if method.get("fnirs", "") == "nearest":
_interpolate_bads_nirs(self, exclude=exclude)
if method.get("ecog", "") == "spline":
_interpolate_bads_ecog(self, origin=origin, exclude=exclude)
if method.get("seeg", "") == "spline":
_interpolate_bads_seeg(self, exclude=exclude)
if reset_bads is True:
if "nan" in method.values():
warn(
"interpolate_bads was called with method='nan' and "
"reset_bads=True. Consider setting reset_bads=False so that the "
"nan-containing channels can be easily excluded from later "
"computations."
)
self.info["bads"] = [ch for ch in self.info["bads"] if ch in exclude]
return self
@verbose
def rename_channels(info, mapping, allow_duplicates=False, *, verbose=None):
"""Rename channels.
Parameters
----------
%(info_not_none)s Note: modified in place.
%(mapping_rename_channels_duplicates)s
%(verbose)s
"""
_validate_type(info, Info, "info")
info._check_consistency()
bads = list(info["bads"]) # make our own local copies
ch_names = list(info["ch_names"])
# first check and assemble clean mappings of index and name
if isinstance(mapping, dict):
_check_dict_keys(
mapping,
ch_names,
key_description="channel name(s)",
valid_key_source="info",
)
new_names = [
(ch_names.index(ch_name), new_name) for ch_name, new_name in mapping.items()
]
elif callable(mapping):
new_names = [(ci, mapping(ch_name)) for ci, ch_name in enumerate(ch_names)]
else:
raise ValueError(f"mapping must be callable or dict, not {type(mapping)}")
# check we got all strings out of the mapping
for new_name in new_names:
_validate_type(new_name[1], "str", "New channel mappings")
# do the remapping locally
for c_ind, new_name in new_names:
for bi, bad in enumerate(bads):
if bad == ch_names[c_ind]:
bads[bi] = new_name
ch_names[c_ind] = new_name
# check that all the channel names are unique
if len(ch_names) != len(np.unique(ch_names)) and not allow_duplicates:
raise ValueError("New channel names are not unique, renaming failed")
# do the remapping in info
info["bads"] = []
ch_names_mapping = dict()
for ch, ch_name in zip(info["chs"], ch_names):
ch_names_mapping[ch["ch_name"]] = ch_name
ch["ch_name"] = ch_name
# .get b/c fwd info omits it
_rename_comps(info.get("comps", []), ch_names_mapping)
if "projs" in info: # fwd might omit it
for proj in info["projs"]:
proj["data"]["col_names"][:] = _rename_list(
proj["data"]["col_names"], ch_names_mapping
)
info._update_redundant()
info["bads"] = bads
info._check_consistency()
def _recursive_flatten(cell, dtype):
"""Unpack mat files in Python."""
if len(cell) > 0:
while not isinstance(cell[0], dtype):
cell = [c for d in cell for c in d]
return cell
@dataclass
class _BuiltinChannelAdjacency:
name: str
description: str
fname: str
source_url: str | None
_ft_neighbor_url_t = string.Template(
"https://github.com/fieldtrip/fieldtrip/raw/master/template/neighbours/$fname"
)
_BUILTIN_CHANNEL_ADJACENCIES = [
_BuiltinChannelAdjacency(
name="biosemi16",
description="Biosemi 16-electrode cap",
fname="biosemi16_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="biosemi16_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="biosemi32",
description="Biosemi 32-electrode cap",
fname="biosemi32_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="biosemi32_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="biosemi64",
description="Biosemi 64-electrode cap",
fname="biosemi64_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="biosemi64_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="bti148",
description="BTI 148-channel system",
fname="bti148_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="bti148_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="bti248",
description="BTI 248-channel system",
fname="bti248_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="bti248_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="bti248grad",
description="BTI 248 gradiometer system",
fname="bti248grad_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="bti248grad_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="ctf64",
description="CTF 64 axial gradiometer",
fname="ctf64_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="ctf64_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="ctf151",
description="CTF 151 axial gradiometer",
fname="ctf151_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="ctf151_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="ctf275",
description="CTF 275 axial gradiometer",
fname="ctf275_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="ctf275_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="easycap32ch-avg",
description="",
fname="easycap32ch-avg_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="easycap32ch-avg_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="easycap64ch-avg",
description="",
fname="easycap64ch-avg_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="easycap64ch-avg_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="easycap128ch-avg",
description="",
fname="easycap128ch-avg_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="easycap128ch-avg_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="easycapM1",
description="Easycap M1",
fname="easycapM1_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="easycapM1_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="easycapM11",
description="Easycap M11",
fname="easycapM11_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="easycapM11_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="easycapM14",
description="Easycap M14",
fname="easycapM14_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="easycapM14_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="easycapM15",
description="Easycap M15",
fname="easycapM15_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="easycapM15_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="KIT-157",
description="",
fname="KIT-157_neighb.mat",
source_url=None,
),
_BuiltinChannelAdjacency(
name="KIT-208",
description="",
fname="KIT-208_neighb.mat",
source_url=None,
),
_BuiltinChannelAdjacency(
name="KIT-NYU-2019",
description="",
fname="KIT-NYU-2019_neighb.mat",
source_url=None,
),
_BuiltinChannelAdjacency(
name="KIT-UMD-1",
description="",
fname="KIT-UMD-1_neighb.mat",
source_url=None,
),
_BuiltinChannelAdjacency(
name="KIT-UMD-2",
description="",
fname="KIT-UMD-2_neighb.mat",
source_url=None,
),
_BuiltinChannelAdjacency(
name="KIT-UMD-3",
description="",
fname="KIT-UMD-3_neighb.mat",
source_url=None,
),
_BuiltinChannelAdjacency(
name="KIT-UMD-4",
description="",
fname="KIT-UMD-4_neighb.mat",
source_url=None,
),
_BuiltinChannelAdjacency(
name="neuromag306mag",
description="Neuromag306, only magnetometers",
fname="neuromag306mag_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="neuromag306mag_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="neuromag306planar",
description="Neuromag306, only planar gradiometers",
fname="neuromag306planar_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="neuromag306planar_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="neuromag122cmb",
description="Neuromag122, only combined planar gradiometers",
fname="neuromag122cmb_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="neuromag122cmb_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="neuromag306cmb",
description="Neuromag306, only combined planar gradiometers",
fname="neuromag306cmb_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="neuromag306cmb_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="ecog256",
description="ECOG 256channels, average referenced",
fname="ecog256_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="ecog256_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="ecog256bipolar",
description="ECOG 256channels, bipolar referenced",
fname="ecog256bipolar_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="ecog256bipolar_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="eeg1010_neighb",
description="",
fname="eeg1010_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="eeg1010_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="elec1005",
description="Standard 10-05 system",
fname="elec1005_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="elec1005_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="elec1010",
description="Standard 10-10 system",
fname="elec1010_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="elec1010_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="elec1020",
description="Standard 10-20 system",
fname="elec1020_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="elec1020_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="itab28",
description="ITAB 28-channel system",
fname="itab28_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="itab28_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="itab153",
description="ITAB 153-channel system",
fname="itab153_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="itab153_neighb.mat"),
),
_BuiltinChannelAdjacency(
name="language29ch-avg",
description="MPI for Psycholinguistic: Averaged 29-channel cap",
fname="language29ch-avg_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="language29ch-avg_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="mpi_59_channels",
description="MPI for Psycholinguistic: 59-channel cap",
fname="mpi_59_channels_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="mpi_59_channels_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="yokogawa160",
description="",
fname="yokogawa160_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="yokogawa160_neighb.mat"), # noqa: E501
),
_BuiltinChannelAdjacency(
name="yokogawa440",
description="",
fname="yokogawa440_neighb.mat",
source_url=_ft_neighbor_url_t.substitute(fname="yokogawa440_neighb.mat"), # noqa: E501
),
]
@fill_doc
def get_builtin_ch_adjacencies(*, descriptions=False):
"""Get a list of all FieldTrip neighbor definitions shipping with MNE.
The names of the these neighbor definitions can be passed to
:func:`read_ch_adjacency`.
Parameters
----------
descriptions : bool
Whether to return not only the neighbor definition names, but also
their corresponding descriptions. If ``True``, a list of tuples is
returned, where the first tuple element is the neighbor definition name
and the second is the description. If ``False`` (default), only the
names are returned.
Returns
-------
neighbor_name : list of str | list of tuple
If ``descriptions=False``, the names of all builtin FieldTrip neighbor
definitions that can be loaded directly via :func:`read_ch_adjacency`.
If ``descriptions=True``, a list of tuples ``(name, description)``.
Notes
-----
.. versionadded:: 1.1
"""
if descriptions:
return sorted(
[(m.name, m.description) for m in _BUILTIN_CHANNEL_ADJACENCIES],
key=lambda x: x[0].casefold(), # only sort based on name
)
else:
return sorted([m.name for m in _BUILTIN_CHANNEL_ADJACENCIES], key=str.casefold)
@fill_doc
def read_ch_adjacency(fname, picks=None):
"""Read a channel adjacency ("neighbors") file that ships with MNE.
More information on these neighbor definitions can be found on the related
`FieldTrip documentation pages
<http://www.fieldtriptoolbox.org/template/neighbours/>`__.
Parameters
----------
fname : path-like | str
The path to the file to load, or the name of a channel adjacency
matrix that ships with MNE-Python.
.. note::
You can retrieve the names of all
built-in channel adjacencies via
:func:`mne.channels.get_builtin_ch_adjacencies`.
%(picks_all_notypes)s
Returns
-------
ch_adjacency : scipy.sparse.csr_array, shape (n_channels, n_channels)
The adjacency matrix.
ch_names : list
The list of channel names present in adjacency matrix.
See Also
--------
get_builtin_ch_adjacencies
mne.viz.plot_ch_adjacency
find_ch_adjacency
mne.stats.combine_adjacency
Notes
-----
If the neighbor definition you need is not shipped by MNE-Python,
you may use :func:`find_ch_adjacency` to compute the
adjacency matrix based on your 2D sensor locations.
Note that depending on your use case, you may need to additionally use
:func:`mne.stats.combine_adjacency` to prepare a final "adjacency"
to pass to the eventual function.
"""
if op.isabs(fname):
fname = str(
_check_fname(
fname=fname,
overwrite="read",
must_exist=True,
)
)
else: # built-in FieldTrip neighbors
ch_adj_name = fname
del fname
if ch_adj_name.endswith("_neighb.mat"): # backward-compat
ch_adj_name = ch_adj_name.replace("_neighb.mat", "")
if ch_adj_name not in get_builtin_ch_adjacencies():
raise ValueError(
f"No built-in channel adjacency matrix found with name: "
f"{ch_adj_name}. Valid names are: "
f'{", ".join(get_builtin_ch_adjacencies())}'
)
ch_adj = [a for a in _BUILTIN_CHANNEL_ADJACENCIES if a.name == ch_adj_name][0]
fname = ch_adj.fname
templates_dir = Path(__file__).resolve().parent / "data" / "neighbors"
fname = str(
_check_fname( # only needed to convert to a string
fname=templates_dir / fname,
overwrite="read",
must_exist=True,
)
)
nb = loadmat(fname)["neighbours"]
ch_names = _recursive_flatten(nb["label"], str)
temp_info = create_info(ch_names, 1.0)
picks = _picks_to_idx(temp_info, picks, none="all")
neighbors = [_recursive_flatten(c, str) for c in nb["neighblabel"].flatten()]
assert len(ch_names) == len(neighbors)
adjacency = _ch_neighbor_adjacency(ch_names, neighbors)
# picking before constructing matrix is buggy
adjacency = adjacency[picks][:, picks]
ch_names = [ch_names[p] for p in picks]
return adjacency, ch_names
def _ch_neighbor_adjacency(ch_names, neighbors):
"""Compute sensor adjacency matrix.
Parameters
----------
ch_names : list of str
The channel names.
neighbors : list of list
A list of list of channel names. The neighbors to
which the channels in ch_names are connected with.
Must be of the same length as ch_names.
Returns
-------
ch_adjacency : scipy.sparse.spmatrix
The adjacency matrix.
"""
if len(ch_names) != len(neighbors):
raise ValueError("`ch_names` and `neighbors` must have the same length")
set_neighbors = {c for d in neighbors for c in d}
rest = set_neighbors - set(ch_names)
if len(rest) > 0:
raise ValueError(
"Some of your neighbors are not present in the list of channel names"
)
for neigh in neighbors:
if not isinstance(neigh, list) and not all(isinstance(c, str) for c in neigh):
raise ValueError("`neighbors` must be a list of lists of str")
ch_adjacency = np.eye(len(ch_names), dtype=bool)
for ii, neigbs in enumerate(neighbors):
ch_adjacency[ii, [ch_names.index(i) for i in neigbs]] = True
ch_adjacency = csr_array(ch_adjacency)
return ch_adjacency
@fill_doc
def find_ch_adjacency(info, ch_type):
"""Find the adjacency matrix for the given channels.
This function tries to infer the appropriate adjacency matrix template
for the given channels. If a template is not found, the adjacency matrix
is computed using Delaunay triangulation based on 2D sensor locations.
Parameters
----------
%(info_not_none)s
ch_type : str | None
The channel type for computing the adjacency matrix. Currently
supports ``'mag'``, ``'grad'``, ``'eeg'`` and ``None``.
If ``None``, the info must contain only one channel type.
Returns
-------
ch_adjacency : scipy.sparse.csr_array, shape (n_channels, n_channels)
The adjacency matrix.
ch_names : list
The list of channel names present in adjacency matrix.
See Also
--------
mne.viz.plot_ch_adjacency
mne.stats.combine_adjacency
get_builtin_ch_adjacencies
read_ch_adjacency
Notes
-----
.. versionadded:: 0.15
Automatic detection of an appropriate adjacency matrix template only
works for MEG data at the moment. This means that the adjacency matrix
is always computed for EEG data and never loaded from a template file. If
you want to load a template for a given montage use
:func:`read_ch_adjacency` directly.
.. warning::
If Delaunay triangulation is used to calculate the adjacency matrix it
may yield partially unexpected results (e.g., include unwanted edges
between non-adjacent sensors). Therefore, it is recommended to check
(and, if necessary, manually modify) the result by inspecting it
via :func:`mne.viz.plot_ch_adjacency`.
Note that depending on your use case, you may need to additionally use
:func:`mne.stats.combine_adjacency` to prepare a final "adjacency"
to pass to the eventual function.
"""
from ..io.kit.constants import KIT_NEIGHBORS
if ch_type is None:
picks = channel_indices_by_type(info)
if sum([len(p) != 0 for p in picks.values()]) != 1:
raise ValueError(
"info must contain only one channel type if ch_type is None."
)
ch_type = channel_type(info, 0)
else:
_check_option("ch_type", ch_type, ["mag", "grad", "eeg"])
(
has_vv_mag,
has_vv_grad,
is_old_vv,
has_4D_mag,
ctf_other_types,
has_CTF_grad,
n_kit_grads,
has_any_meg,
has_eeg_coils,
has_eeg_coils_and_meg,
has_eeg_coils_only,
has_neuromag_122_grad,
has_csd_coils,
) = _get_ch_info(info)
conn_name = None
if has_vv_mag and ch_type == "mag":
conn_name = "neuromag306mag"
elif has_vv_grad and ch_type == "grad":
conn_name = "neuromag306planar"
elif has_4D_mag:
if "MEG 248" in info["ch_names"]:
idx = info["ch_names"].index("MEG 248")
grad = info["chs"][idx]["coil_type"] == FIFF.FIFFV_COIL_MAGNES_GRAD
mag = info["chs"][idx]["coil_type"] == FIFF.FIFFV_COIL_MAGNES_MAG
if ch_type == "grad" and grad:
conn_name = "bti248grad"
elif ch_type == "mag" and mag:
conn_name = "bti248"
elif "MEG 148" in info["ch_names"] and ch_type == "mag":
idx = info["ch_names"].index("MEG 148")
if info["chs"][idx]["coil_type"] == FIFF.FIFFV_COIL_MAGNES_MAG:
conn_name = "bti148"
elif has_CTF_grad and ch_type == "mag":
if info["nchan"] < 100:
conn_name = "ctf64"
elif info["nchan"] > 200:
conn_name = "ctf275"
else:
conn_name = "ctf151"
elif n_kit_grads > 0:
conn_name = KIT_NEIGHBORS.get(info["kit_system_id"])
if conn_name is not None:
logger.info(f"Reading adjacency matrix for {conn_name}.")
adjacency, ch_names = read_ch_adjacency(conn_name)
if conn_name.startswith("neuromag") and info["ch_names"][0].startswith("MEG "):
ch_names = [ch_name.replace("MEG", "MEG ") for ch_name in ch_names]
return adjacency, ch_names
logger.info(
"Could not find a adjacency matrix for the data. "
"Computing adjacency based on Delaunay triangulations."
)
return _compute_ch_adjacency(info, ch_type)
@fill_doc
def _compute_ch_adjacency(info, ch_type):
"""Compute channel adjacency matrix using Delaunay triangulations.
Parameters
----------
%(info_not_none)s
ch_type : str
The channel type for computing the adjacency matrix. Currently
supports ``'mag'``, ``'grad'`` and ``'eeg'``.
Returns
-------
ch_adjacency : scipy.sparse.csr_array, shape (n_channels, n_channels)
The adjacency matrix.
ch_names : list
The list of channel names present in adjacency matrix.
"""
from ..channels.layout import _find_topomap_coords, _pair_grad_sensors
from ..source_estimate import spatial_tris_adjacency
combine_grads = ch_type == "grad" and any(
[
coil_type in [ch["coil_type"] for ch in info["chs"]]
for coil_type in [FIFF.FIFFV_COIL_VV_PLANAR_T1, FIFF.FIFFV_COIL_NM_122]
]
)
picks = dict(_picks_by_type(info, exclude=[]))[ch_type]
ch_names = [info["ch_names"][pick] for pick in picks]
if combine_grads:
pairs = _pair_grad_sensors(info, topomap_coords=False, exclude=[])
if len(pairs) != len(picks):
raise RuntimeError(
"Cannot find a pair for some of the "
"gradiometers. Cannot compute adjacency "
"matrix."
)
# only for one of the pair
xy = _find_topomap_coords(info, picks[::2], sphere=HEAD_SIZE_DEFAULT)
else:
xy = _find_topomap_coords(info, picks, sphere=HEAD_SIZE_DEFAULT)
tri = Delaunay(xy)
neighbors = spatial_tris_adjacency(tri.simplices)
if combine_grads:
ch_adjacency = np.eye(len(picks), dtype=bool)
for idx, neigbs in zip(neighbors.row, neighbors.col):
for ii in range(2): # make sure each pair is included
for jj in range(2):
ch_adjacency[idx * 2 + ii, neigbs * 2 + jj] = True
ch_adjacency[idx * 2 + ii, idx * 2 + jj] = True # pair
ch_adjacency = csr_array(ch_adjacency)
else:
ch_adjacency = lil_array(neighbors)
ch_adjacency.setdiag(np.repeat(1, ch_adjacency.shape[0]))
ch_adjacency = ch_adjacency.tocsr()
return ch_adjacency, ch_names
@fill_doc
def fix_mag_coil_types(info, use_cal=False):
"""Fix magnetometer coil types.
Parameters
----------
%(info_not_none)s Corrections are done in-place.
use_cal : bool
If True, further refine the check for old coil types by checking
``info['chs'][ii]['cal']``.
Notes
-----
This function changes magnetometer coil types 3022 (T1: SQ20483N) and
3023 (T2: SQ20483-A) to 3024 (T3: SQ20950N) in the channel definition
records in the info structure.
Neuromag Vectorview systems can contain magnetometers with two
different coil sizes (3022 and 3023 vs. 3024). The systems
incorporating coils of type 3024 were introduced last and are used at
the majority of MEG sites. At some sites with 3024 magnetometers,
the data files have still defined the magnetometers to be of type
3022 to ensure compatibility with older versions of Neuromag software.
In the MNE software as well as in the present version of Neuromag
software coil type 3024 is fully supported. Therefore, it is now safe
to upgrade the data files to use the true coil type.
.. note:: The effect of the difference between the coil sizes on the
current estimates computed by the MNE software is very small.
Therefore the use of ``fix_mag_coil_types`` is not mandatory.
"""
old_mag_inds = _get_T1T2_mag_inds(info, use_cal)
for ii in old_mag_inds:
info["chs"][ii]["coil_type"] = FIFF.FIFFV_COIL_VV_MAG_T3
logger.info(
"%d of %d magnetometer types replaced with T3."
% (len(old_mag_inds), len(pick_types(info, meg="mag", exclude=[])))
)
info._check_consistency()
def _get_T1T2_mag_inds(info, use_cal=False):
"""Find T1/T2 magnetometer coil types."""
picks = pick_types(info, meg="mag", exclude=[])
old_mag_inds = []
# From email exchanges, systems with the larger T2 coil only use the cal
# value of 2.09e-11. Newer T3 magnetometers use 4.13e-11 or 1.33e-10
# (Triux). So we can use a simple check for > 3e-11.
for ii in picks:
ch = info["chs"][ii]
if ch["coil_type"] in (FIFF.FIFFV_COIL_VV_MAG_T1, FIFF.FIFFV_COIL_VV_MAG_T2):
if use_cal:
if ch["cal"] > 3e-11:
old_mag_inds.append(ii)
else:
old_mag_inds.append(ii)
return old_mag_inds
def _get_ch_info(info):
"""Get channel info for inferring acquisition device."""
chs = info["chs"]
# Only take first 16 bits, as higher bits store CTF comp order
coil_types = {ch["coil_type"] & 0xFFFF for ch in chs}
channel_types = {ch["kind"] for ch in chs}
has_vv_mag = any(
k in coil_types
for k in [
FIFF.FIFFV_COIL_VV_MAG_T1,
FIFF.FIFFV_COIL_VV_MAG_T2,
FIFF.FIFFV_COIL_VV_MAG_T3,
]
)
has_vv_grad = any(
k in coil_types
for k in [
FIFF.FIFFV_COIL_VV_PLANAR_T1,
FIFF.FIFFV_COIL_VV_PLANAR_T2,
FIFF.FIFFV_COIL_VV_PLANAR_T3,
]
)
has_neuromag_122_grad = any(k in coil_types for k in [FIFF.FIFFV_COIL_NM_122])
is_old_vv = " " in chs[0]["ch_name"]
has_4D_mag = FIFF.FIFFV_COIL_MAGNES_MAG in coil_types
ctf_other_types = (
FIFF.FIFFV_COIL_CTF_REF_MAG,
FIFF.FIFFV_COIL_CTF_REF_GRAD,
FIFF.FIFFV_COIL_CTF_OFFDIAG_REF_GRAD,
)
has_CTF_grad = FIFF.FIFFV_COIL_CTF_GRAD in coil_types or (
FIFF.FIFFV_MEG_CH in channel_types
and any(k in ctf_other_types for k in coil_types)
)
# hack due to MNE-C bug in IO of CTF
# only take first 16 bits, as higher bits store CTF comp order
n_kit_grads = sum(
ch["coil_type"] & 0xFFFF == FIFF.FIFFV_COIL_KIT_GRAD for ch in chs
)
has_any_meg = any([has_vv_mag, has_vv_grad, has_4D_mag, has_CTF_grad, n_kit_grads])
has_eeg_coils = (
FIFF.FIFFV_COIL_EEG in coil_types and FIFF.FIFFV_EEG_CH in channel_types
)
has_eeg_coils_and_meg = has_eeg_coils and has_any_meg
has_eeg_coils_only = has_eeg_coils and not has_any_meg
has_csd_coils = (
FIFF.FIFFV_COIL_EEG_CSD in coil_types and FIFF.FIFFV_EEG_CH in channel_types
)
return (
has_vv_mag,
has_vv_grad,
is_old_vv,
has_4D_mag,
ctf_other_types,
has_CTF_grad,
n_kit_grads,
has_any_meg,
has_eeg_coils,
has_eeg_coils_and_meg,
has_eeg_coils_only,
has_neuromag_122_grad,
has_csd_coils,
)
@fill_doc
def make_1020_channel_selections(info, midline="z", *, return_ch_names=False):
"""Map hemisphere names to corresponding EEG channel names or indices.
This function uses a simple heuristic to separate channel names into three
Region of Interest-based selections: ``Left``, ``Midline`` and ``Right``.
The heuristic is that any of the channel names ending
with odd numbers are filed under ``Left``; those ending with even numbers
are filed under ``Right``; and those ending with the character(s) specified
in ``midline`` are filed under ``Midline``. Other channels are ignored.
This is appropriate for 10/20, 10/10, 10/05, …, sensor arrangements, but
not for other naming conventions.
Parameters
----------
%(info_not_none)s If channel locations are present, the channel lists will
be sorted from posterior to anterior; otherwise, the order specified in
``info["ch_names"]`` will be kept.
midline : str
Names ending in any of these characters are stored under the
``Midline`` key. Defaults to ``'z'``. Capitalization is ignored.
return_ch_names : bool
Whether to return channel names instead of channel indices.
.. versionadded:: 1.4.0
Returns
-------
selections : dict
A dictionary mapping from region of interest name to a list of channel
indices (if ``return_ch_names=False``) or to a list of channel names
(if ``return_ch_names=True``).
"""
_validate_type(info, "info")
try:
from .layout import find_layout
layout = find_layout(info)
pos = layout.pos
ch_names = layout.names
except RuntimeError: # no channel positions found
ch_names = info["ch_names"]
pos = None
selections = dict(Left=[], Midline=[], Right=[])
for pick, channel in enumerate(ch_names):
last_char = channel[-1].lower() # in 10/20, last char codes hemisphere
if last_char in midline:
selection = "Midline"
elif last_char.isdigit():
selection = "Left" if int(last_char) % 2 else "Right"
else: # ignore the channel
continue
selections[selection].append(pick)
if pos is not None:
# sort channels from front to center
# (y-coordinate of the position info in the layout)
selections = {
selection: np.array(picks)[pos[picks, 1].argsort()]
for selection, picks in selections.items()
}
# convert channel indices to names if requested
if return_ch_names:
for selection, ch_indices in selections.items():
selections[selection] = [info.ch_names[idx] for idx in ch_indices]
return selections
@verbose
def combine_channels(
inst, groups, method="mean", keep_stim=False, drop_bad=False, verbose=None
):
"""Combine channels based on specified channel grouping.
Parameters
----------
inst : instance of Raw, Epochs, or Evoked
An MNE-Python object to combine the channels for. The object can be of
type Raw, Epochs, or Evoked.
groups : dict
Specifies which channels are aggregated into a single channel, with
aggregation method determined by the ``method`` parameter. One new
pseudo-channel is made per dict entry; the dict values must be lists of
picks (integer indices of ``ch_names``). For example::
groups=dict(Left=[1, 2, 3, 4], Right=[5, 6, 7, 8])
Note that within a dict entry all channels must have the same type.
method : str | callable
Which method to use to combine channels. If a :class:`str`, must be one
of 'mean', 'median', or 'std' (standard deviation). If callable, the
callable must accept one positional input (data of shape ``(n_channels,
n_times)``, or ``(n_epochs, n_channels, n_times)``) and return an
:class:`array <numpy.ndarray>` of shape ``(n_times,)``, or ``(n_epochs,
n_times)``. For example with an instance of Raw or Evoked::
method = lambda data: np.mean(data, axis=0)
Another example with an instance of Epochs::
method = lambda data: np.median(data, axis=1)
Defaults to ``'mean'``.
keep_stim : bool
If ``True``, include stimulus channels in the resulting object.
Defaults to ``False``.
drop_bad : bool
If ``True``, drop channels marked as bad before combining. Defaults to
``False``.
%(verbose)s
Returns
-------
combined_inst : instance of Raw, Epochs, or Evoked
An MNE-Python object of the same type as the input ``inst``, containing
one virtual channel for each group in ``groups`` (and, if ``keep_stim``
is ``True``, also containing stimulus channels).
"""
from ..epochs import BaseEpochs, EpochsArray
from ..evoked import Evoked, EvokedArray
from ..io import BaseRaw, RawArray
ch_axis = 1 if isinstance(inst, BaseEpochs) else 0
ch_idx = list(range(inst.info["nchan"]))
ch_names = inst.info["ch_names"]
ch_types = inst.get_channel_types()
kwargs = dict()
if isinstance(inst, BaseEpochs):
kwargs["copy"] = False
inst_data = inst.get_data(**kwargs)
groups = OrderedDict(deepcopy(groups))
# Convert string values of ``method`` into callables
# XXX Possibly de-duplicate with _make_combine_callable of mne/viz/utils.py
if isinstance(method, str):
method_dict = {
key: partial(getattr(np, key), axis=ch_axis)
for key in ("mean", "median", "std")
}
try:
method = method_dict[method]
except KeyError:
raise ValueError(
'"method" must be a callable, or one of "mean", '
f'"median", or "std"; got "{method}".'
)
# Instantiate channel info and data
new_ch_names, new_ch_types, new_data = [], [], []
if not isinstance(keep_stim, bool):
raise TypeError(f'"keep_stim" must be of type bool, not {type(keep_stim)}.')
if keep_stim:
stim_ch_idx = list(pick_types(inst.info, meg=False, stim=True))
if stim_ch_idx:
new_ch_names = [ch_names[idx] for idx in stim_ch_idx]
new_ch_types = [ch_types[idx] for idx in stim_ch_idx]
new_data = [np.take(inst_data, idx, axis=ch_axis) for idx in stim_ch_idx]
else:
warn("Could not find stimulus channels.")
# Get indices of bad channels
ch_idx_bad = []
if not isinstance(drop_bad, bool):
raise TypeError(f'"drop_bad" must be of type bool, not {type(drop_bad)}.')
if drop_bad and inst.info["bads"]:
ch_idx_bad = pick_channels(ch_names, inst.info["bads"])
# Check correctness of combinations
for this_group, this_picks in groups.items():
# Check if channel indices are out of bounds
if not all(idx in ch_idx for idx in this_picks):
raise ValueError("Some channel indices are out of bounds.")
# Check if heterogeneous sensor type combinations
this_ch_type = np.array(ch_types)[this_picks]
if len(set(this_ch_type)) > 1:
types = ", ".join(set(this_ch_type))
raise ValueError(
"Cannot combine sensors of different types; "
f'"{this_group}" contains types {types}.'
)
# Remove bad channels
these_bads = [idx for idx in this_picks if idx in ch_idx_bad]
this_picks = [idx for idx in this_picks if idx not in ch_idx_bad]
if these_bads:
logger.info(
f"Dropped the following channels in group {this_group}: {these_bads}"
)
# Check if combining less than 2 channel
if len(set(this_picks)) < 2:
warn(
f'Less than 2 channels in group "{this_group}" when '
f'combining by method "{method}".'
)
# If all good create more detailed dict without bad channels
groups[this_group] = dict(picks=this_picks, ch_type=this_ch_type[0])
# Combine channels and add them to the new instance
for this_group, this_group_dict in groups.items():
new_ch_names.append(this_group)
new_ch_types.append(this_group_dict["ch_type"])
this_picks = this_group_dict["picks"]
this_data = np.take(inst_data, this_picks, axis=ch_axis)
new_data.append(method(this_data))
new_data = np.swapaxes(new_data, 0, ch_axis)
info = create_info(
sfreq=inst.info["sfreq"], ch_names=new_ch_names, ch_types=new_ch_types
)
# create new instances and make sure to copy important attributes
if isinstance(inst, BaseRaw):
combined_inst = RawArray(new_data, info, first_samp=inst.first_samp)
elif isinstance(inst, BaseEpochs):
combined_inst = EpochsArray(
new_data,
info,
events=inst.events,
event_id=inst.event_id,
tmin=inst.times[0],
baseline=inst.baseline,
)
if inst.metadata is not None:
combined_inst.metadata = inst.metadata.copy()
elif isinstance(inst, Evoked):
combined_inst = EvokedArray(
new_data, info, tmin=inst.times[0], baseline=inst.baseline
)
return combined_inst
# NeuroMag channel groupings
_SELECTIONS = [
"Vertex",
"Left-temporal",
"Right-temporal",
"Left-parietal",
"Right-parietal",
"Left-occipital",
"Right-occipital",
"Left-frontal",
"Right-frontal",
]
_EEG_SELECTIONS = ["EEG 1-32", "EEG 33-64", "EEG 65-96", "EEG 97-128"]
def _divide_to_regions(info, add_stim=True):
"""Divide channels to regions by positions."""
picks = _pick_data_channels(info, exclude=[])
chs_in_lobe = len(picks) // 4
pos = np.array([ch["loc"][:3] for ch in info["chs"]])
x, y, z = pos.T
frontal = picks[np.argsort(y[picks])[-chs_in_lobe:]]
picks = np.setdiff1d(picks, frontal)
occipital = picks[np.argsort(y[picks])[:chs_in_lobe]]
picks = np.setdiff1d(picks, occipital)
temporal = picks[np.argsort(z[picks])[:chs_in_lobe]]
picks = np.setdiff1d(picks, temporal)
lt, rt = _divide_side(temporal, x)
lf, rf = _divide_side(frontal, x)
lo, ro = _divide_side(occipital, x)
lp, rp = _divide_side(picks, x) # Parietal lobe from the remaining picks.
# Because of the way the sides are divided, there may be outliers in the
# temporal lobes. Here we switch the sides for these outliers. For other
# lobes it is not a big problem because of the vicinity of the lobes.
with np.errstate(invalid="ignore"): # invalid division, greater compare
zs = np.abs(zscore(x[rt]))
outliers = np.array(rt)[np.where(zs > 2.0)[0]]
rt = list(np.setdiff1d(rt, outliers))
with np.errstate(invalid="ignore"): # invalid division, greater compare
zs = np.abs(zscore(x[lt]))
outliers = np.append(outliers, (np.array(lt)[np.where(zs > 2.0)[0]]))
lt = list(np.setdiff1d(lt, outliers))
l_mean = np.mean(x[lt])
r_mean = np.mean(x[rt])
for outlier in outliers:
if abs(l_mean - x[outlier]) < abs(r_mean - x[outlier]):
lt.append(outlier)
else:
rt.append(outlier)
if add_stim:
stim_ch = _get_stim_channel(None, info, raise_error=False)
if len(stim_ch) > 0:
for region in [lf, rf, lo, ro, lp, rp, lt, rt]:
region.append(info["ch_names"].index(stim_ch[0]))
return OrderedDict(
[
("Left-frontal", lf),
("Right-frontal", rf),
("Left-parietal", lp),
("Right-parietal", rp),
("Left-occipital", lo),
("Right-occipital", ro),
("Left-temporal", lt),
("Right-temporal", rt),
]
)
def _divide_side(lobe, x):
"""Make a separation between left and right lobe evenly."""
lobe = np.asarray(lobe)
median = np.median(x[lobe])
left = lobe[np.where(x[lobe] < median)[0]]
right = lobe[np.where(x[lobe] > median)[0]]
medians = np.where(x[lobe] == median)[0]
left = np.sort(np.concatenate([left, lobe[medians[1::2]]]))
right = np.sort(np.concatenate([right, lobe[medians[::2]]]))
return list(left), list(right)
@verbose
def read_vectorview_selection(name, fname=None, info=None, verbose=None):
"""Read Neuromag Vector View channel selection from a file.
Parameters
----------
name : str | list of str
Name of the selection. If a list, the selections are combined.
Supported selections are: ``'Vertex'``, ``'Left-temporal'``,
``'Right-temporal'``, ``'Left-parietal'``, ``'Right-parietal'``,
``'Left-occipital'``, ``'Right-occipital'``, ``'Left-frontal'`` and
``'Right-frontal'``. Selections can also be matched and combined by
spcecifying common substrings. For example, ``name='temporal`` will
produce a combination of ``'Left-temporal'`` and ``'Right-temporal'``.
fname : path-like
Filename of the selection file (if ``None``, built-in selections are
used).
%(info)s Used to determine which channel naming convention to use, e.g.
``'MEG 0111'`` (with space) for old Neuromag systems and ``'MEG0111'``
(without space) for new ones.
%(verbose)s
Returns
-------
sel : list of str
List with channel names in the selection.
"""
# convert name to list of string
if not isinstance(name, (list, tuple)):
name = [name]
if isinstance(info, Info):
picks = pick_types(info, meg=True, exclude=())
if len(picks) > 0 and " " not in info["ch_names"][picks[0]]:
spacing = "new"
else:
spacing = "old"
elif info is not None:
raise TypeError(f"info must be an instance of Info or None, not {type(info)}")
else: # info is None
spacing = "old"
# use built-in selections by default
if fname is None:
fname = op.join(op.dirname(__file__), "..", "data", "mne_analyze.sel")
fname = str(_check_fname(fname, must_exist=True, overwrite="read"))
# use this to make sure we find at least one match for each name
name_found = {n: False for n in name}
with open(fname) as fid:
sel = []
for line in fid:
line = line.strip()
# skip blank lines and comments
if len(line) == 0 or line[0] == "#":
continue
# get the name of the selection in the file
pos = line.find(":")
if pos < 0:
logger.info('":" delimiter not found in selections file, skipping line')
continue
sel_name_file = line[:pos]
# search for substring match with name provided
for n in name:
if sel_name_file.find(n) >= 0:
sel.extend(line[pos + 1 :].split("|"))
name_found[n] = True
break
# make sure we found at least one match for each name
for n, found in name_found.items():
if not found:
raise ValueError(f'No match for selection name "{n}" found')
# make the selection a sorted list with unique elements
sel = list(set(sel))
sel.sort()
if spacing == "new": # "new" or "old" by now, "old" is default
sel = [s.replace("MEG ", "MEG") for s in sel]
return sel
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