montage.py

# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#          Denis Engemann <denis.engemann@gmail.com>
#          Martin Luessi <mluessi@nmr.mgh.harvard.edu>
#          Eric Larson <larson.eric.d@gmail.com>
#          Marijn van Vliet <w.m.vanvliet@gmail.com>
#          Jona Sassenhagen <jona.sassenhagen@gmail.com>
#          Teon Brooks <teon.brooks@gmail.com>
#          Christian Brodbeck <christianbrodbeck@nyu.edu>
#          Stefan Appelhoff <stefan.appelhoff@mailbox.org>
#          Joan Massich <mailsik@gmail.com>
#
# License: Simplified BSD

from collections import OrderedDict
from dataclasses import dataclass
from copy import deepcopy
import os.path as op
import re

import numpy as np

from ..defaults import HEAD_SIZE_DEFAULT
from .._freesurfer import get_mni_fiducials
from ..viz import plot_montage
from ..transforms import (
    apply_trans,
    get_ras_to_neuromag_trans,
    _sph_to_cart,
    _topo_to_sph,
    _frame_to_str,
    Transform,
    _verbose_frames,
    _fit_matched_points,
    _quat_to_affine,
    _ensure_trans,
)
from ..io._digitization import (
    _count_points_by_type,
    _ensure_fiducials_head,
    _get_dig_eeg,
    _make_dig_points,
    write_dig,
    _read_dig_fif,
    _format_dig_points,
    _get_fid_coords,
    _coord_frame_const,
    _get_data_as_dict_from_dig,
)
from ..io.meas_info import create_info
from ..io.open import fiff_open
from ..io.pick import pick_types, _picks_to_idx, channel_type
from ..io.constants import FIFF, CHANNEL_LOC_ALIASES
from ..utils import (
    warn,
    copy_function_doc_to_method_doc,
    _pl,
    verbose,
    _check_option,
    _validate_type,
    _check_fname,
    _on_missing,
    fill_doc,
    _docdict,
)

from ._dig_montage_utils import _read_dig_montage_egi
from ._dig_montage_utils import _parse_brainvision_dig_montage


@dataclass
class _BuiltinStandardMontage:
    name: str
    description: str


_BUILTIN_STANDARD_MONTAGES = [
    _BuiltinStandardMontage(
        name="standard_1005",
        description="Electrodes are named and positioned according to the "
        "international 10-05 system (343+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="standard_1020",
        description="Electrodes are named and positioned according to the "
        "international 10-20 system (94+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="standard_alphabetic",
        description="Electrodes are named with LETTER-NUMBER combinations "
        "(A1, B2, F4, …) (65+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="standard_postfixed",
        description="Electrodes are named according to the international "
        "10-20 system using postfixes for intermediate positions "
        "(100+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="standard_prefixed",
        description="Electrodes are named according to the international "
        "10-20 system using prefixes for intermediate positions "
        "(74+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="standard_primed",
        description="Electrodes are named according to the international "
        "10-20 system using prime marks (' and '') for "
        "intermediate positions (100+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="biosemi16",
        description="BioSemi cap with 16 electrodes (16+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="biosemi32",
        description="BioSemi cap with 32 electrodes (32+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="biosemi64",
        description="BioSemi cap with 64 electrodes (64+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="biosemi128",
        description="BioSemi cap with 128 electrodes (128+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="biosemi160",
        description="BioSemi cap with 160 electrodes (160+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="biosemi256",
        description="BioSemi cap with 256 electrodes (256+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="easycap-M1",
        description="EasyCap with 10-05 electrode names (74 locations)",
    ),
    _BuiltinStandardMontage(
        name="easycap-M10",
        description="EasyCap with numbered electrodes (61 locations)",
    ),
    _BuiltinStandardMontage(
        name="easycap-M43",
        description="EasyCap with numbered electrodes (64 locations)",
    ),
    _BuiltinStandardMontage(
        name="EGI_256",
        description="Geodesic Sensor Net (256 locations)",
    ),
    _BuiltinStandardMontage(
        name="GSN-HydroCel-32",
        description="HydroCel Geodesic Sensor Net and Cz (33+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="GSN-HydroCel-64_1.0",
        description="HydroCel Geodesic Sensor Net (64+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="GSN-HydroCel-65_1.0",
        description="HydroCel Geodesic Sensor Net and Cz (65+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="GSN-HydroCel-128",
        description="HydroCel Geodesic Sensor Net (128+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="GSN-HydroCel-129",
        description="HydroCel Geodesic Sensor Net and Cz (129+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="GSN-HydroCel-256",
        description="HydroCel Geodesic Sensor Net (256+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="GSN-HydroCel-257",
        description="HydroCel Geodesic Sensor Net and Cz (257+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="mgh60",
        description="The (older) 60-channel cap used at MGH (60+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="mgh70",
        description="The (newer) 70-channel BrainVision cap used at MGH "
        "(70+3 locations)",
    ),
    _BuiltinStandardMontage(
        name="artinis-octamon",
        description="Artinis OctaMon fNIRS (8 sources, 2 detectors)",
    ),
    _BuiltinStandardMontage(
        name="artinis-brite23",
        description="Artinis Brite23 fNIRS (11 sources, 7 detectors)",
    ),
    _BuiltinStandardMontage(
        name="brainproducts-RNP-BA-128",
        description="Brain Products with 10-10 electrode names (128 channels)",
    ),
]


def _check_get_coord_frame(dig):
    dig_coord_frames = sorted(set(d["coord_frame"] for d in dig))
    if len(dig_coord_frames) != 1:
        raise RuntimeError(
            "Only a single coordinate frame in dig is supported, got "
            f"{dig_coord_frames}"
        )
    return _frame_to_str[dig_coord_frames.pop()] if dig_coord_frames else None


def get_builtin_montages(*, descriptions=False):
    """Get a list of all standard montages shipping with MNE-Python.

    The names of the montages can be passed to :func:`make_standard_montage`.

    Parameters
    ----------
    descriptions : bool
        Whether to return not only the montage names, but also their
        corresponding descriptions. If ``True``, a list of tuples is returned,
        where the first tuple element is the montage name and the second is
        the montage description. If ``False`` (default), only the names are
        returned.

        .. versionadded:: 1.1

    Returns
    -------
    montages : list of str | list of tuple
        If ``descriptions=False``, the names of all builtin montages that can
        be used by :func:`make_standard_montage`.

        If ``descriptions=True``, a list of tuples ``(name, description)``.
    """
    if descriptions:
        return [(m.name, m.description) for m in _BUILTIN_STANDARD_MONTAGES]
    else:
        return [m.name for m in _BUILTIN_STANDARD_MONTAGES]


def make_dig_montage(
    ch_pos=None,
    nasion=None,
    lpa=None,
    rpa=None,
    hsp=None,
    hpi=None,
    coord_frame="unknown",
):
    r"""Make montage from arrays.

    Parameters
    ----------
    ch_pos : dict | None
        Dictionary of channel positions. Keys are channel names and values
        are 3D coordinates - array of shape (3,) - in native digitizer space
        in m.
    nasion : None | array, shape (3,)
        The position of the nasion fiducial point.
        This point is assumed to be in the native digitizer space in m.
    lpa : None | array, shape (3,)
        The position of the left periauricular fiducial point.
        This point is assumed to be in the native digitizer space in m.
    rpa : None | array, shape (3,)
        The position of the right periauricular fiducial point.
        This point is assumed to be in the native digitizer space in m.
    hsp : None | array, shape (n_points, 3)
        This corresponds to an array of positions of the headshape points in
        3d. These points are assumed to be in the native digitizer space in m.
    hpi : None | array, shape (n_hpi, 3)
        This corresponds to an array of HPI points in the native digitizer
        space. They only necessary if computation of a ``compute_dev_head_t``
        is True.
    coord_frame : str
        The coordinate frame of the points. Usually this is ``'unknown'``
        for native digitizer space.
        Other valid values are: ``'head'``, ``'meg'``, ``'mri'``,
        ``'mri_voxel'``, ``'mni_tal'``, ``'ras'``, ``'fs_tal'``,
        ``'ctf_head'``, and ``'ctf_meg'``.

        .. note::
            For custom montages without fiducials, this parameter must be set
            to ``'head'``.

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    DigMontage
    read_dig_captrak
    read_dig_egi
    read_dig_fif
    read_dig_localite
    read_dig_polhemus_isotrak
    """
    _validate_type(ch_pos, (dict, None), "ch_pos")
    if ch_pos is None:
        ch_names = None
    else:
        ch_names = list(ch_pos)
    dig = _make_dig_points(
        nasion=nasion,
        lpa=lpa,
        rpa=rpa,
        hpi=hpi,
        extra_points=hsp,
        dig_ch_pos=ch_pos,
        coord_frame=coord_frame,
    )

    return DigMontage(dig=dig, ch_names=ch_names)


class DigMontage:
    """Montage for digitized electrode and headshape position data.

    .. warning:: Montages are typically created using one of the helper
                 functions in the ``See Also`` section below instead of
                 instantiating this class directly.

    Parameters
    ----------
    dig : list of dict
        The object containing all the dig points.
    ch_names : list of str
        The names of the EEG channels.

    See Also
    --------
    read_dig_captrak
    read_dig_dat
    read_dig_egi
    read_dig_fif
    read_dig_hpts
    read_dig_localite
    read_dig_polhemus_isotrak
    make_dig_montage

    Notes
    -----
    .. versionadded:: 0.9.0
    """

    def __init__(self, *, dig=None, ch_names=None):
        dig = list() if dig is None else dig
        _validate_type(item=dig, types=list, item_name="dig")
        ch_names = list() if ch_names is None else ch_names
        n_eeg = sum([1 for d in dig if d["kind"] == FIFF.FIFFV_POINT_EEG])
        if n_eeg != len(ch_names):
            raise ValueError(
                "The number of EEG channels (%d) does not match the number"
                " of channel names provided (%d)" % (n_eeg, len(ch_names))
            )

        self.dig = dig
        self.ch_names = ch_names

    def __repr__(self):
        """Return string representation."""
        n_points = _count_points_by_type(self.dig)
        return (
            "<DigMontage | {extra:d} extras (headshape), {hpi:d} HPIs,"
            " {fid:d} fiducials, {eeg:d} channels>"
        ).format(**n_points)

    @copy_function_doc_to_method_doc(plot_montage)
    def plot(
        self,
        scale_factor=20,
        show_names=True,
        kind="topomap",
        show=True,
        sphere=None,
        *,
        axes=None,
        verbose=None,
    ):
        return plot_montage(
            self,
            scale_factor=scale_factor,
            show_names=show_names,
            kind=kind,
            show=show,
            sphere=sphere,
            axes=axes,
        )

    @fill_doc
    def rename_channels(self, mapping, allow_duplicates=False):
        """Rename the channels.

        Parameters
        ----------
        %(mapping_rename_channels_duplicates)s

        Returns
        -------
        inst : instance of DigMontage
            The instance. Operates in-place.
        """
        from .channels import rename_channels

        temp_info = create_info(list(self._get_ch_pos()), 1000.0, "eeg")
        rename_channels(temp_info, mapping, allow_duplicates)
        self.ch_names = temp_info["ch_names"]

    @verbose
    def save(self, fname, *, overwrite=False, verbose=None):
        """Save digitization points to FIF.

        Parameters
        ----------
        fname : path-like
            The filename to use. Should end in .fif or .fif.gz.
        %(overwrite)s
        %(verbose)s
        """
        coord_frame = _check_get_coord_frame(self.dig)
        write_dig(fname, self.dig, coord_frame, overwrite=overwrite)

    def __iadd__(self, other):
        """Add two DigMontages in place.

        Notes
        -----
        Two DigMontages can only be added if there are no duplicated ch_names
        and if fiducials are present they should share the same coordinate
        system and location values.
        """

        def is_fid_defined(fid):
            return not (fid.nasion is None and fid.lpa is None and fid.rpa is None)

        # Check for none duplicated ch_names
        ch_names_intersection = set(self.ch_names).intersection(other.ch_names)
        if ch_names_intersection:
            raise RuntimeError(
                (
                    "Cannot add two DigMontage objects if they contain duplicated"
                    " channel names. Duplicated channel(s) found: {}."
                ).format(", ".join(["%r" % v for v in sorted(ch_names_intersection)]))
            )

        # Check for unique matching fiducials
        self_fid, self_coord = _get_fid_coords(self.dig)
        other_fid, other_coord = _get_fid_coords(other.dig)

        if is_fid_defined(self_fid) and is_fid_defined(other_fid):
            if self_coord != other_coord:
                raise RuntimeError(
                    "Cannot add two DigMontage objects if "
                    "fiducial locations are not in the same "
                    "coordinate system."
                )

            for kk in self_fid:
                if not np.array_equal(self_fid[kk], other_fid[kk]):
                    raise RuntimeError(
                        "Cannot add two DigMontage objects if "
                        "fiducial locations do not match "
                        "(%s)" % kk
                    )

            # keep self
            self.dig = _format_dig_points(
                self.dig
                + [d for d in other.dig if d["kind"] != FIFF.FIFFV_POINT_CARDINAL]
            )
        else:
            self.dig = _format_dig_points(self.dig + other.dig)

        self.ch_names += other.ch_names
        return self

    def copy(self):
        """Copy the DigMontage object.

        Returns
        -------
        dig : instance of DigMontage
            The copied DigMontage instance.
        """
        return deepcopy(self)

    def __add__(self, other):
        """Add two DigMontages."""
        out = self.copy()
        out += other
        return out

    def __eq__(self, other):
        """Compare different DigMontage objects for equality.

        Returns
        -------
        Boolean output from comparison of .dig
        """
        return self.dig == other.dig and self.ch_names == other.ch_names

    def _get_ch_pos(self):
        pos = [d["r"] for d in _get_dig_eeg(self.dig)]
        assert len(self.ch_names) == len(pos)
        return OrderedDict(zip(self.ch_names, pos))

    def _get_dig_names(self):
        NAMED_KIND = (FIFF.FIFFV_POINT_EEG,)
        is_eeg = np.array([d["kind"] in NAMED_KIND for d in self.dig])
        assert len(self.ch_names) == is_eeg.sum()
        dig_names = [None] * len(self.dig)
        for ch_name_idx, dig_idx in enumerate(np.where(is_eeg)[0]):
            dig_names[dig_idx] = self.ch_names[ch_name_idx]

        return dig_names

    def get_positions(self):
        """Get all channel and fiducial positions.

        Returns
        -------
        positions : dict
            A dictionary of the positions for channels (``ch_pos``),
            coordinate frame (``coord_frame``), nasion (``nasion``),
            left preauricular point (``lpa``),
            right preauricular point (``rpa``),
            Head Shape Polhemus (``hsp``), and
            Head Position Indicator(``hpi``).
            E.g.::

                {
                    'ch_pos': {'EEG061': [0, 0, 0]},
                    'nasion': [0, 0, 1],
                    'coord_frame': 'mni_tal',
                    'lpa': [0, 1, 0],
                    'rpa': [1, 0, 0],
                    'hsp': None,
                    'hpi': None
                }
        """
        # get channel positions as dict
        ch_pos = self._get_ch_pos()

        # get coordframe and fiducial coordinates
        montage_bunch = _get_data_as_dict_from_dig(self.dig)
        coord_frame = _frame_to_str.get(montage_bunch.coord_frame)

        # return dictionary
        positions = dict(
            ch_pos=ch_pos,
            coord_frame=coord_frame,
            nasion=montage_bunch.nasion,
            lpa=montage_bunch.lpa,
            rpa=montage_bunch.rpa,
            hsp=montage_bunch.hsp,
            hpi=montage_bunch.hpi,
        )
        return positions

    @verbose
    def apply_trans(self, trans, verbose=None):
        """Apply a transformation matrix to the montage.

        Parameters
        ----------
        trans : instance of mne.transforms.Transform
            The transformation matrix to be applied.
        %(verbose)s
        """
        _validate_type(trans, Transform, "trans")
        coord_frame = self.get_positions()["coord_frame"]
        trans = _ensure_trans(trans, fro=coord_frame, to=trans["to"])
        for d in self.dig:
            d["r"] = apply_trans(trans, d["r"])
            d["coord_frame"] = trans["to"]

    @verbose
    def add_estimated_fiducials(self, subject, subjects_dir=None, verbose=None):
        """Estimate fiducials based on FreeSurfer ``fsaverage`` subject.

        This takes a montage with the ``mri`` coordinate frame,
        corresponding to the FreeSurfer RAS (xyz in the volume) T1w
        image of the specific subject. It will call
        :func:`mne.coreg.get_mni_fiducials` to estimate LPA, RPA and
        Nasion fiducial points.

        Parameters
        ----------
        %(subject)s
        %(subjects_dir)s
        %(verbose)s

        Returns
        -------
        inst : instance of DigMontage
            The instance, modified in-place.

        See Also
        --------
        :ref:`tut-source-alignment`

        Notes
        -----
        Since MNE uses the FIF data structure, it relies on the ``head``
        coordinate frame. Any coordinate frame can be transformed
        to ``head`` if the fiducials (i.e. LPA, RPA and Nasion) are
        defined. One can use this function to estimate those fiducials
        and then use ``mne.channels.compute_native_head_t(montage)``
        to get the head <-> MRI transform.
        """
        # get coordframe and fiducial coordinates
        montage_bunch = _get_data_as_dict_from_dig(self.dig)

        # get the coordinate frame and check that it's MRI
        if montage_bunch.coord_frame != FIFF.FIFFV_COORD_MRI:
            raise RuntimeError(
                f'Montage should be in the "mri" coordinate frame '
                f"to use `add_estimated_fiducials`. The current coordinate "
                f"frame is {montage_bunch.coord_frame}"
            )

        # estimate LPA, nasion, RPA from FreeSurfer fsaverage
        fids_mri = list(get_mni_fiducials(subject, subjects_dir))

        # add those digpoints to front of montage
        self.dig = fids_mri + self.dig
        return self

    @verbose
    def add_mni_fiducials(self, subjects_dir=None, verbose=None):
        """Add fiducials to a montage in MNI space.

        Parameters
        ----------
        %(subjects_dir)s
        %(verbose)s

        Returns
        -------
        inst : instance of DigMontage
            The instance, modified in-place.

        Notes
        -----
        ``fsaverage`` is in MNI space and so its fiducials can be
        added to a montage in "mni_tal". MNI is an ACPC-aligned
        coordinate system (the posterior commissure is the origin)
        so since BIDS requires channel locations for ECoG, sEEG and
        DBS to be in ACPC space, this function can be used to allow
        those coordinate to be transformed to "head" space (origin
        between LPA and RPA).
        """
        montage_bunch = _get_data_as_dict_from_dig(self.dig)

        # get the coordinate frame and check that it's MNI TAL
        if montage_bunch.coord_frame != FIFF.FIFFV_MNE_COORD_MNI_TAL:
            raise RuntimeError(
                f'Montage should be in the "mni_tal" coordinate frame '
                f"to use `add_estimated_fiducials`. The current coordinate "
                f"frame is {montage_bunch.coord_frame}"
            )

        fids_mni = get_mni_fiducials("fsaverage", subjects_dir)
        for fid in fids_mni:
            # "mri" and "mni_tal" are equivalent for fsaverage
            assert fid["coord_frame"] == FIFF.FIFFV_COORD_MRI
            fid["coord_frame"] = FIFF.FIFFV_MNE_COORD_MNI_TAL
        self.dig = fids_mni + self.dig
        return self

    @verbose
    def remove_fiducials(self, verbose=None):
        """Remove the fiducial points from a montage.

        Parameters
        ----------
        %(verbose)s

        Returns
        -------
        inst : instance of DigMontage
            The instance, modified in-place.

        Notes
        -----
        MNE will transform a montage to the internal "head" coordinate
        frame if the fiducials are present. Under most circumstances, this
        is ideal as it standardizes the coordinate frame for things like
        plotting. However, in some circumstances, such as saving a ``raw``
        with intracranial data to BIDS format, the coordinate frame
        should not be changed by removing fiducials.
        """
        for d in self.dig.copy():
            if d["kind"] == FIFF.FIFFV_POINT_CARDINAL:
                self.dig.remove(d)
        return self


VALID_SCALES = dict(mm=1e-3, cm=1e-2, m=1)


def _check_unit_and_get_scaling(unit):
    _check_option("unit", unit, sorted(VALID_SCALES.keys()))
    return VALID_SCALES[unit]


def transform_to_head(montage):
    """Transform a DigMontage object into head coordinate.

    Parameters
    ----------
    montage : instance of DigMontage
        The montage.

    Returns
    -------
    montage : instance of DigMontage
        The montage after transforming the points to head
        coordinate system.

    Notes
    -----
    This function requires that the LPA, RPA and Nasion fiducial
    points are available. If they are not, they will be added based by
    projecting the fiducials onto a sphere with radius equal to the average
    distance of each point to the origin (in the given coordinate frame).

    This function assumes that all fiducial points are in the same coordinate
    frame (e.g. 'unknown') and it will convert all the point in this coordinate
    system to Neuromag head coordinate system.

    .. versionchanged:: 1.2
       Fiducial points will be added automatically if the montage does not
       have them.
    """
    # Get fiducial points and their coord_frame
    native_head_t = compute_native_head_t(montage)
    montage = montage.copy()  # to avoid inplace modification
    if native_head_t["from"] != FIFF.FIFFV_COORD_HEAD:
        for d in montage.dig:
            if d["coord_frame"] == native_head_t["from"]:
                d["r"] = apply_trans(native_head_t, d["r"])
                d["coord_frame"] = FIFF.FIFFV_COORD_HEAD
    _ensure_fiducials_head(montage.dig)
    return montage


def read_dig_dat(fname):
    r"""Read electrode positions from a ``*.dat`` file.

    .. Warning::
        This function was implemented based on ``*.dat`` files available from
        `Compumedics <https://compumedicsneuroscan.com>`__ and might not work
        as expected with novel files. If it does not read your files correctly
        please contact the MNE-Python developers.

    Parameters
    ----------
    fname : path-like
        File from which to read electrode locations.

    Returns
    -------
    montage : DigMontage
        The montage.

    See Also
    --------
    read_dig_captrak
    read_dig_dat
    read_dig_egi
    read_dig_fif
    read_dig_hpts
    read_dig_localite
    read_dig_polhemus_isotrak
    make_dig_montage

    Notes
    -----
    ``*.dat`` files are plain text files and can be inspected and amended with
    a plain text editor.
    """
    from ._standard_montage_utils import _check_dupes_odict

    fname = _check_fname(fname, overwrite="read", must_exist=True)

    with open(fname, "r") as fid:
        lines = fid.readlines()

    ch_names, poss = list(), list()
    nasion = lpa = rpa = None
    for i, line in enumerate(lines):
        items = line.split()
        if not items:
            continue
        elif len(items) != 5:
            raise ValueError(
                "Error reading %s, line %s has unexpected number of entries:\n"
                "%s" % (fname, i, line.rstrip())
            )
        num = items[1]
        if num == "67":
            continue  # centroid
        pos = np.array([float(item) for item in items[2:]])
        if num == "78":
            nasion = pos
        elif num == "76":
            lpa = pos
        elif num == "82":
            rpa = pos
        else:
            ch_names.append(items[0])
            poss.append(pos)
    electrodes = _check_dupes_odict(ch_names, poss)
    return make_dig_montage(electrodes, nasion, lpa, rpa)


def read_dig_fif(fname):
    r"""Read digitized points from a .fif file.

    Note that electrode names are not present in the .fif file so
    they are here defined with the convention from VectorView
    systems (EEG001, EEG002, etc.)

    Parameters
    ----------
    fname : path-like
        FIF file from which to read digitization locations.

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    DigMontage
    read_dig_dat
    read_dig_egi
    read_dig_captrak
    read_dig_polhemus_isotrak
    read_dig_hpts
    read_dig_localite
    make_dig_montage
    """
    _check_fname(fname, overwrite="read", must_exist=True)
    # Load the dig data
    f, tree = fiff_open(fname)[:2]
    with f as fid:
        dig = _read_dig_fif(fid, tree)

    ch_names = []
    for d in dig:
        if d["kind"] == FIFF.FIFFV_POINT_EEG:
            ch_names.append("EEG%03d" % d["ident"])

    montage = DigMontage(dig=dig, ch_names=ch_names)
    return montage


def read_dig_hpts(fname, unit="mm"):
    """Read historical ``.hpts`` MNE-C files.

    Parameters
    ----------
    fname : path-like
        The filepath of .hpts file.
    unit : ``'m'`` | ``'cm'`` | ``'mm'``
        Unit of the positions. Defaults to ``'mm'``.

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    DigMontage
    read_dig_captrak
    read_dig_dat
    read_dig_egi
    read_dig_fif
    read_dig_localite
    read_dig_polhemus_isotrak
    make_dig_montage

    Notes
    -----
    The hpts format digitzer data file may contain comment lines starting
    with the pound sign (#) and data lines of the form::

         <*category*> <*identifier*> <*x/mm*> <*y/mm*> <*z/mm*>

    where:

    ``<*category*>``
        defines the type of points. Allowed categories are: ``hpi``,
        ``cardinal`` (fiducial), ``eeg``, and ``extra`` corresponding to
        head-position indicator coil locations, cardinal landmarks, EEG
        electrode locations, and additional head surface points,
        respectively.

    ``<*identifier*>``
        identifies the point. The identifiers are usually sequential
        numbers. For cardinal landmarks, 1 = left auricular point,
        2 = nasion, and 3 = right auricular point. For EEG electrodes,
        identifier = 0 signifies the reference electrode.

    ``<*x/mm*> , <*y/mm*> , <*z/mm*>``
        Location of the point, usually in the head coordinate system
        in millimeters. If your points are in [m] then unit parameter can
        be changed.

    For example::

        cardinal    2    -5.6729  -12.3873  -30.3671
        cardinal    1    -37.6782  -10.4957   91.5228
        cardinal    3    -131.3127    9.3976  -22.2363
        hpi    1    -30.4493  -11.8450   83.3601
        hpi    2    -122.5353    9.2232  -28.6828
        hpi    3    -6.8518  -47.0697  -37.0829
        hpi    4    7.3744  -50.6297  -12.1376
        hpi    5    -33.4264  -43.7352  -57.7756
        eeg    FP1  3.8676  -77.0439  -13.0212
        eeg    FP2  -31.9297  -70.6852  -57.4881
        eeg    F7  -6.1042  -68.2969   45.4939
        ...
    """
    from ._standard_montage_utils import _str_names, _str

    fname = _check_fname(fname, overwrite="read", must_exist=True)
    _scale = _check_unit_and_get_scaling(unit)

    out = np.genfromtxt(fname, comments="#", dtype=(_str, _str, "f8", "f8", "f8"))
    kind, label = _str_names(out["f0"]), _str_names(out["f1"])
    kind = [k.lower() for k in kind]
    xyz = np.array([out["f%d" % ii] for ii in range(2, 5)]).T
    xyz *= _scale
    del _scale
    fid_idx_to_label = {"1": "lpa", "2": "nasion", "3": "rpa"}
    fid = {
        fid_idx_to_label[label[ii]]: this_xyz
        for ii, this_xyz in enumerate(xyz)
        if kind[ii] == "cardinal"
    }
    ch_pos = {
        label[ii]: this_xyz for ii, this_xyz in enumerate(xyz) if kind[ii] == "eeg"
    }
    hpi = np.array([this_xyz for ii, this_xyz in enumerate(xyz) if kind[ii] == "hpi"])
    hpi.shape = (-1, 3)  # in case it's empty
    hsp = np.array([this_xyz for ii, this_xyz in enumerate(xyz) if kind[ii] == "extra"])
    hsp.shape = (-1, 3)  # in case it's empty
    return make_dig_montage(ch_pos=ch_pos, **fid, hpi=hpi, hsp=hsp)


def read_dig_egi(fname):
    """Read electrode locations from EGI system.

    Parameters
    ----------
    fname : path-like
        EGI MFF XML coordinates file from which to read digitization locations.

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    DigMontage
    read_dig_captrak
    read_dig_dat
    read_dig_fif
    read_dig_hpts
    read_dig_localite
    read_dig_polhemus_isotrak
    make_dig_montage
    """
    _check_fname(fname, overwrite="read", must_exist=True)

    data = _read_dig_montage_egi(
        fname=fname, _scaling=1.0, _all_data_kwargs_are_none=True
    )
    return make_dig_montage(**data)


def read_dig_captrak(fname):
    """Read electrode locations from CapTrak Brain Products system.

    Parameters
    ----------
    fname : path-like
        BrainVision CapTrak coordinates file from which to read EEG electrode
        locations. This is typically in XML format with the .bvct extension.

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    DigMontage
    read_dig_dat
    read_dig_egi
    read_dig_fif
    read_dig_hpts
    read_dig_localite
    read_dig_polhemus_isotrak
    make_dig_montage
    """
    _check_fname(fname, overwrite="read", must_exist=True)
    data = _parse_brainvision_dig_montage(fname, scale=1e-3)

    return make_dig_montage(**data)


def read_dig_localite(fname, nasion=None, lpa=None, rpa=None):
    """Read Localite .csv file.

    Parameters
    ----------
    fname : path-like
        File name.
    nasion : str | None
        Name of nasion fiducial point.
    lpa : str | None
        Name of left preauricular fiducial point.
    rpa : str | None
        Name of right preauricular fiducial point.

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    DigMontage
    read_dig_captrak
    read_dig_dat
    read_dig_egi
    read_dig_fif
    read_dig_hpts
    read_dig_polhemus_isotrak
    make_dig_montage
    """
    ch_pos = {}
    with open(fname) as f:
        f.readline()  # skip first row
        for row in f:
            _, name, x, y, z = row.split(",")
            ch_pos[name] = np.array((float(x), float(y), float(z))) / 1000

    if nasion is not None:
        nasion = ch_pos.pop(nasion)
    if lpa is not None:
        lpa = ch_pos.pop(lpa)
    if rpa is not None:
        rpa = ch_pos.pop(rpa)

    return make_dig_montage(ch_pos, nasion, lpa, rpa)


def _get_montage_in_head(montage):
    coords = set([d["coord_frame"] for d in montage.dig])
    montage = montage.copy()
    if len(coords) == 1 and coords.pop() == FIFF.FIFFV_COORD_HEAD:
        _ensure_fiducials_head(montage.dig)
        return montage
    else:
        return transform_to_head(montage)


def _set_montage_fnirs(info, montage):
    """Set the montage for fNIRS data.

    This needs to be different to electrodes as each channel has three
    coordinates that need to be set. For each channel there is a source optode
    location, a detector optode location, and a channel midpoint that must be
    stored. This function modifies info['chs'][#]['loc'] and info['dig'] in
    place.
    """
    from ..preprocessing.nirs import _validate_nirs_info

    # Validate that the fNIRS info is correctly formatted
    picks = _validate_nirs_info(info)

    # Modify info['chs'][#]['loc'] in place
    num_ficiduals = len(montage.dig) - len(montage.ch_names)
    for ch_idx in picks:
        ch = info["chs"][ch_idx]["ch_name"]
        source, detector = ch.split(" ")[0].split("_")
        source_pos = montage.dig[montage.ch_names.index(source) + num_ficiduals]["r"]
        detector_pos = montage.dig[montage.ch_names.index(detector) + num_ficiduals][
            "r"
        ]

        info["chs"][ch_idx]["loc"][3:6] = source_pos
        info["chs"][ch_idx]["loc"][6:9] = detector_pos
        midpoint = (source_pos + detector_pos) / 2
        info["chs"][ch_idx]["loc"][:3] = midpoint
        info["chs"][ch_idx]["coord_frame"] = FIFF.FIFFV_COORD_HEAD

    # Modify info['dig'] in place
    with info._unlock():
        info["dig"] = montage.dig


@fill_doc
def _set_montage(info, montage, match_case=True, match_alias=False, on_missing="raise"):
    """Apply montage to data.

    With a DigMontage, this function will replace the digitizer info with
    the values specified for the particular montage.

    Usually, a montage is expected to contain the positions of all EEG
    electrodes and a warning is raised when this is not the case.

    Parameters
    ----------
    %(info_not_none)s
    %(montage)s
    %(match_case)s
    %(match_alias)s
    %(on_missing_montage)s

    Notes
    -----
    This function will change the info variable in place.
    """
    _validate_type(montage, (DigMontage, None, str), "montage")
    if montage is None:
        # Next line modifies info['dig'] in place
        with info._unlock():
            info["dig"] = None
        for ch in info["chs"]:
            # Next line modifies info['chs'][#]['loc'] in place
            ch["loc"] = np.full(12, np.nan)
        return
    if isinstance(montage, str):  # load builtin montage
        _check_option(
            parameter="montage",
            value=montage,
            allowed_values=[m.name for m in _BUILTIN_STANDARD_MONTAGES],
        )
        montage = make_standard_montage(montage)

    mnt_head = _get_montage_in_head(montage)
    del montage

    def _backcompat_value(pos, ref_pos):
        if any(np.isnan(pos)):
            return np.full(6, np.nan)
        else:
            return np.concatenate((pos, ref_pos))

    # get the channels in the montage in head
    ch_pos = mnt_head._get_ch_pos()

    # only get the eeg, seeg, dbs, ecog channels
    picks = pick_types(
        info, meg=False, eeg=True, seeg=True, dbs=True, ecog=True, exclude=()
    )
    non_picks = np.setdiff1d(np.arange(info["nchan"]), picks)

    # get the reference position from the loc[3:6]
    chs = [info["chs"][ii] for ii in picks]
    non_names = [info["chs"][ii]["ch_name"] for ii in non_picks]
    del picks
    ref_pos = np.array([ch["loc"][3:6] for ch in chs])

    # keep reference location from EEG-like channels if they
    # already exist and are all the same.
    # Note: ref position is an empty list for fieldtrip data
    if len(ref_pos) and ref_pos[0].any() and (ref_pos[0] == ref_pos).all():
        eeg_ref_pos = ref_pos[0]
        # since we have an EEG reference position, we have
        # to add it into the info['dig'] as EEG000
        custom_eeg_ref_dig = True
    else:
        refs = set(ch_pos) & {"EEG000", "REF"}
        assert len(refs) <= 1
        eeg_ref_pos = np.zeros(3) if not refs else ch_pos.pop(refs.pop())
        custom_eeg_ref_dig = False
    del ref_pos

    # This raises based on info being subset/superset of montage
    info_names = [ch["ch_name"] for ch in chs]
    dig_names = mnt_head._get_dig_names()
    ref_names = [None, "EEG000", "REF"]

    if match_case:
        info_names_use = info_names
        dig_names_use = dig_names
        non_names_use = non_names
    else:
        ch_pos_use = OrderedDict((name.lower(), pos) for name, pos in ch_pos.items())
        info_names_use = [name.lower() for name in info_names]
        dig_names_use = [
            name.lower() if name is not None else name for name in dig_names
        ]
        non_names_use = [name.lower() for name in non_names]
        ref_names = [name.lower() if name is not None else name for name in ref_names]
        n_dup = len(ch_pos) - len(ch_pos_use)
        if n_dup:
            raise ValueError(
                "Cannot use match_case=False as %s montage "
                "name(s) require case sensitivity" % n_dup
            )
        n_dup = len(info_names_use) - len(set(info_names_use))
        if n_dup:
            raise ValueError(
                "Cannot use match_case=False as %s channel "
                "name(s) require case sensitivity" % n_dup
            )
        ch_pos = ch_pos_use
        del ch_pos_use
    del dig_names

    # use lookup table to match unrecognized channel names to known aliases
    if match_alias:
        alias_dict = (
            match_alias if isinstance(match_alias, dict) else CHANNEL_LOC_ALIASES
        )
        if not match_case:
            alias_dict = {
                ch_name.lower(): ch_alias.lower()
                for ch_name, ch_alias in alias_dict.items()
            }

        # excluded ch_alias not in info, to prevent unnecessary mapping and
        # warning messages based on aliases.
        alias_dict = {ch_name: ch_alias for ch_name, ch_alias in alias_dict.items()}
        info_names_use = [
            alias_dict.get(ch_name, ch_name) for ch_name in info_names_use
        ]
        non_names_use = [alias_dict.get(ch_name, ch_name) for ch_name in non_names_use]

    # warn user if there is not a full overlap of montage with info_chs
    missing = np.where([use not in ch_pos for use in info_names_use])[0]
    if len(missing):  # DigMontage is subset of info
        missing_names = [info_names[ii] for ii in missing]
        pl = _pl(missing)
        are_is = "are" if pl else "is"
        missing_coord_msg = (
            f"DigMontage is only a subset of info. There {are_is} "
            f"{len(missing)} channel position{pl} not present in the "
            f"DigMontage. The channel{pl} missing from the montage {are_is}:"
            f"\n\n{missing_names}.\n\nConsider using inst.rename_channels to "
            "match the montage nomenclature, or inst.set_channel_types if "
            f"{'these' if pl else 'this'} {are_is} not {'' if pl else 'an '}"
            f"EEG channel{pl}, or use the on_missing parameter if the channel "
            f"position{pl} {are_is} allowed to be unknown in your analyses."
        )
        _on_missing(on_missing, missing_coord_msg)

        # set ch coordinates and names from digmontage or nan coords
        for ii in missing:
            ch_pos[info_names_use[ii]] = [np.nan] * 3
    del info_names

    assert len(non_names_use) == len(non_names)
    # There are no issues here with fNIRS being in non_names_use because
    # these names are like "D1_S1_760" and the ch_pos for a fNIRS montage
    # will have entries "D1" and "S1".
    extra = np.where([non in ch_pos for non in non_names_use])[0]
    if len(extra):
        types = "/".join(sorted(set(channel_type(info, non_picks[ii]) for ii in extra)))
        names = [non_names[ii] for ii in extra]
        warn(
            f"Not setting position{_pl(extra)} of {len(extra)} {types} "
            f"channel{_pl(extra)} found in montage:\n{names}\n"
            "Consider setting the channel types to be of "
            f'{_docdict["montage_types"]} '
            "using inst.set_channel_types before calling inst.set_montage, "
            "or omit these channels when creating your montage."
        )

    for ch, use in zip(chs, info_names_use):
        # Next line modifies info['chs'][#]['loc'] in place
        if use in ch_pos:
            ch["loc"][:6] = _backcompat_value(ch_pos[use], eeg_ref_pos)
        ch["coord_frame"] = FIFF.FIFFV_COORD_HEAD
    del ch_pos

    # XXX this is probably wrong as it uses the order from the montage
    # rather than the order of our info['ch_names'] ...
    digpoints = [
        mnt_head.dig[ii]
        for ii, name in enumerate(dig_names_use)
        if name in (info_names_use + ref_names)
    ]

    # get a copy of the old dig
    if info["dig"] is not None:
        old_dig = info["dig"].copy()
    else:
        old_dig = []

    # determine if needed to add an extra EEG REF DigPoint
    if custom_eeg_ref_dig:
        # ref_name = 'EEG000' if match_case else 'eeg000'
        ref_dig_dict = {
            "kind": FIFF.FIFFV_POINT_EEG,
            "r": eeg_ref_pos,
            "ident": 0,
            "coord_frame": info["dig"].pop()["coord_frame"],
        }
        ref_dig_point = _format_dig_points([ref_dig_dict])[0]
        # only append the reference dig point if it was already
        # in the old dig
        if ref_dig_point in old_dig:
            digpoints.append(ref_dig_point)
    # Next line modifies info['dig'] in place
    with info._unlock():
        info["dig"] = _format_dig_points(digpoints, enforce_order=True)
    del digpoints

    # TODO: Ideally we would have a check like this, but read_raw_bids for ECoG
    # allows for a montage to be set without any fiducials, then silently the
    # info['dig'] can end up in the MNI_TAL frame... only because in our
    # conversion code, UNKNOWN is treated differently from any other frame
    # (e.g., MNI_TAL). We should clean this up at some point...
    # missing_fids = sum(
    #     d['kind'] == FIFF.FIFFV_POINT_CARDINAL for d in info['dig'][:3]) != 3
    # if missing_fids:
    #     raise RuntimeError(
    #         'Could not find all three fiducials in the montage, this should '
    #         'not happen. Please contact MNE-Python developers.')

    # Handle fNIRS with source, detector and channel
    fnirs_picks = _picks_to_idx(info, "fnirs", allow_empty=True)
    if len(fnirs_picks) > 0:
        _set_montage_fnirs(info, mnt_head)


def _read_isotrak_elp_points(fname):
    """Read Polhemus Isotrak digitizer data from a ``.elp`` file.

    Parameters
    ----------
    fname : path-like
        The filepath of .elp Polhemus Isotrak file.

    Returns
    -------
    out : dict of arrays
        The dictionary containing locations for 'nasion', 'lpa', 'rpa'
        and 'points'.
    """
    value_pattern = r"\-?\d+\.?\d*e?\-?\d*"
    coord_pattern = r"({0})\s+({0})\s+({0})\s*$".format(value_pattern)

    with open(fname) as fid:
        file_str = fid.read()

    points_str = [
        m.groups() for m in re.finditer(coord_pattern, file_str, re.MULTILINE)
    ]
    points = np.array(points_str, dtype=float)

    return {
        "nasion": points[0],
        "lpa": points[1],
        "rpa": points[2],
        "points": points[3:],
    }


def _read_isotrak_hsp_points(fname):
    """Read Polhemus Isotrak digitizer data from a ``.hsp`` file.

    Parameters
    ----------
    fname : path-like
        The filepath of .hsp Polhemus Isotrak file.

    Returns
    -------
    out : dict of arrays
        The dictionary containing locations for 'nasion', 'lpa', 'rpa'
        and 'points'.
    """

    def get_hsp_fiducial(line):
        return np.fromstring(line.replace("%F", ""), dtype=float, sep="\t")

    with open(fname) as ff:
        for line in ff:
            if "position of fiducials" in line.lower():
                break

        nasion = get_hsp_fiducial(ff.readline())
        lpa = get_hsp_fiducial(ff.readline())
        rpa = get_hsp_fiducial(ff.readline())

        _ = ff.readline()
        line = ff.readline()
        if line:
            n_points, n_cols = np.fromstring(line, dtype=int, sep="\t")
            points = np.fromstring(
                string=ff.read(),
                dtype=float,
                sep="\t",
            ).reshape(-1, n_cols)
            assert points.shape[0] == n_points
        else:
            points = np.empty((0, 3))

    return {"nasion": nasion, "lpa": lpa, "rpa": rpa, "points": points}


def read_dig_polhemus_isotrak(fname, ch_names=None, unit="m"):
    """Read Polhemus digitizer data from a file.

    Parameters
    ----------
    fname : path-like
        The filepath of Polhemus ISOTrak formatted file.
        File extension is expected to be ``'.hsp'``, ``'.elp'`` or ``'.eeg'``.
    ch_names : None | list of str
        The names of the points. This will make the points
        considered as EEG channels. If None, channels will be assumed
        to be HPI if the extension is ``'.elp'``, and extra headshape
        points otherwise.
    unit : ``'m'`` | ``'cm'`` | ``'mm'``
        Unit of the digitizer file. Polhemus ISOTrak systems data is usually
        exported in meters. Defaults to ``'m'``.

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    DigMontage
    make_dig_montage
    read_polhemus_fastscan
    read_dig_captrak
    read_dig_dat
    read_dig_egi
    read_dig_fif
    read_dig_localite
    """
    VALID_FILE_EXT = (".hsp", ".elp", ".eeg")
    fname = str(_check_fname(fname, overwrite="read", must_exist=True))
    _scale = _check_unit_and_get_scaling(unit)

    _, ext = op.splitext(fname)
    _check_option("fname", ext, VALID_FILE_EXT)

    if ext == ".elp":
        data = _read_isotrak_elp_points(fname)
    else:
        # Default case we read points as hsp since is the most likely scenario
        data = _read_isotrak_hsp_points(fname)

    if _scale != 1:
        data = {key: val * _scale for key, val in data.items()}
    else:
        pass  # noqa

    if ch_names is None:
        keyword = "hpi" if ext == ".elp" else "hsp"
        data[keyword] = data.pop("points")

    else:
        points = data.pop("points")
        if points.shape[0] == len(ch_names):
            data["ch_pos"] = OrderedDict(zip(ch_names, points))
        else:
            raise ValueError(
                (
                    "Length of ``ch_names`` does not match the number of points"
                    " in {fname}. Expected ``ch_names`` length {n_points:d},"
                    " given {n_chnames:d}"
                ).format(fname=fname, n_points=points.shape[0], n_chnames=len(ch_names))
            )

    return make_dig_montage(**data)


def _is_polhemus_fastscan(fname):
    header = ""
    with open(fname, "r") as fid:
        for line in fid:
            if not line.startswith("%"):
                break
            header += line

    return "FastSCAN" in header


@verbose
def read_polhemus_fastscan(
    fname, unit="mm", on_header_missing="raise", *, verbose=None
):
    """Read Polhemus FastSCAN digitizer data from a ``.txt`` file.

    Parameters
    ----------
    fname : path-like
        The path of ``.txt`` Polhemus FastSCAN file.
    unit : ``'m'`` | ``'cm'`` | ``'mm'``
        Unit of the digitizer file. Polhemus FastSCAN systems data is usually
        exported in millimeters. Defaults to ``'mm'``.
    %(on_header_missing)s
    %(verbose)s

    Returns
    -------
    points : array, shape (n_points, 3)
        The digitization points in digitizer coordinates.

    See Also
    --------
    read_dig_polhemus_isotrak
    make_dig_montage
    """
    VALID_FILE_EXT = [".txt"]
    fname = str(_check_fname(fname, overwrite="read", must_exist=True))
    _scale = _check_unit_and_get_scaling(unit)

    _, ext = op.splitext(fname)
    _check_option("fname", ext, VALID_FILE_EXT)

    if not _is_polhemus_fastscan(fname):
        msg = "%s does not contain a valid Polhemus FastSCAN header" % fname
        _on_missing(on_header_missing, msg)

    points = _scale * np.loadtxt(fname, comments="%", ndmin=2)
    _check_dig_shape(points)
    return points


def _read_eeglab_locations(fname):
    ch_names = np.genfromtxt(fname, dtype=str, usecols=3).tolist()
    topo = np.loadtxt(fname, dtype=float, usecols=[1, 2])
    sph = _topo_to_sph(topo)
    pos = _sph_to_cart(sph)
    pos[:, [0, 1]] = pos[:, [1, 0]] * [-1, 1]

    return ch_names, pos


def read_custom_montage(fname, head_size=HEAD_SIZE_DEFAULT, coord_frame=None):
    """Read a montage from a file.

    Parameters
    ----------
    fname : path-like
        File extension is expected to be:
        ``'.loc'`` or ``'.locs'`` or ``'.eloc'`` (for EEGLAB files),
        ``'.sfp'`` (BESA/EGI files), ``'.csd'``,
        ``'.elc'``, ``'.txt'``, ``'.csd'``, ``'.elp'`` (BESA spherical),
        ``'.bvef'`` (BrainVision files),
        ``'.csv'``, ``'.tsv'``, ``'.xyz'`` (XYZ coordinates).
    head_size : float | None
        The size of the head (radius, in [m]). If ``None``, returns the values
        read from the montage file with no modification. Defaults to 0.095m.
    coord_frame : str | None
        The coordinate frame of the points. Usually this is ``"unknown"``
        for native digitizer space. Defaults to None, which is ``"unknown"``
        for most readers but ``"head"`` for EEGLAB.

        .. versionadded:: 0.20

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    make_dig_montage
    make_standard_montage

    Notes
    -----
    The function is a helper to read electrode positions you may have
    in various formats. Most of these format are weakly specified
    in terms of units, coordinate systems. It implies that setting
    a montage using a DigMontage produced by this function may
    be problematic. If you use a standard/template (eg. 10/20,
    10/10 or 10/05) we recommend you use :func:`make_standard_montage`.
    If you can have positions in memory you can also use
    :func:`make_dig_montage` that takes arrays as input.
    """
    from ._standard_montage_utils import (
        _read_theta_phi_in_degrees,
        _read_sfp,
        _read_csd,
        _read_elc,
        _read_elp_besa,
        _read_brainvision,
        _read_xyz,
    )

    SUPPORTED_FILE_EXT = {
        "eeglab": (
            ".loc",
            ".locs",
            ".eloc",
        ),
        "hydrocel": (".sfp",),
        "matlab": (".csd",),
        "asa electrode": (".elc",),
        "generic (Theta-phi in degrees)": (".txt",),
        "standard BESA spherical": (".elp",),  # NB: not same as polhemus elp
        "brainvision": (".bvef",),
        "xyz": (".csv", ".tsv", ".xyz"),
    }

    fname = str(_check_fname(fname, overwrite="read", must_exist=True))
    _, ext = op.splitext(fname)
    _check_option("fname", ext, list(sum(SUPPORTED_FILE_EXT.values(), ())))

    if ext in SUPPORTED_FILE_EXT["eeglab"]:
        if head_size is None:
            raise ValueError("``head_size`` cannot be None for '{}'".format(ext))
        ch_names, pos = _read_eeglab_locations(fname)
        scale = head_size / np.median(np.linalg.norm(pos, axis=-1))
        pos *= scale

        montage = make_dig_montage(
            ch_pos=OrderedDict(zip(ch_names, pos)),
            coord_frame="head",
        )

    elif ext in SUPPORTED_FILE_EXT["hydrocel"]:
        montage = _read_sfp(fname, head_size=head_size)

    elif ext in SUPPORTED_FILE_EXT["matlab"]:
        montage = _read_csd(fname, head_size=head_size)

    elif ext in SUPPORTED_FILE_EXT["asa electrode"]:
        montage = _read_elc(fname, head_size=head_size)

    elif ext in SUPPORTED_FILE_EXT["generic (Theta-phi in degrees)"]:
        if head_size is None:
            raise ValueError("``head_size`` cannot be None for '{}'".format(ext))
        montage = _read_theta_phi_in_degrees(
            fname, head_size=head_size, fid_names=("Nz", "LPA", "RPA")
        )

    elif ext in SUPPORTED_FILE_EXT["standard BESA spherical"]:
        montage = _read_elp_besa(fname, head_size)

    elif ext in SUPPORTED_FILE_EXT["brainvision"]:
        montage = _read_brainvision(fname, head_size)

    elif ext in SUPPORTED_FILE_EXT["xyz"]:
        montage = _read_xyz(fname)

    if coord_frame is not None:
        coord_frame = _coord_frame_const(coord_frame)
        for d in montage.dig:
            d["coord_frame"] = coord_frame

    return montage


def compute_dev_head_t(montage):
    """Compute device to head transform from a DigMontage.

    Parameters
    ----------
    montage : DigMontage
        The `~mne.channels.DigMontage` must contain the fiducials in head
        coordinate system and hpi points in both head and
        meg device coordinate system.

    Returns
    -------
    dev_head_t : Transform
        A Device-to-Head transformation matrix.
    """
    _, coord_frame = _get_fid_coords(montage.dig)
    if coord_frame != FIFF.FIFFV_COORD_HEAD:
        raise ValueError(
            "montage should have been set to head coordinate "
            "system with transform_to_head function."
        )

    hpi_head = np.array(
        [
            d["r"]
            for d in montage.dig
            if (
                d["kind"] == FIFF.FIFFV_POINT_HPI
                and d["coord_frame"] == FIFF.FIFFV_COORD_HEAD
            )
        ],
        float,
    )
    hpi_dev = np.array(
        [
            d["r"]
            for d in montage.dig
            if (
                d["kind"] == FIFF.FIFFV_POINT_HPI
                and d["coord_frame"] == FIFF.FIFFV_COORD_DEVICE
            )
        ],
        float,
    )

    if not (len(hpi_head) == len(hpi_dev) and len(hpi_dev) > 0):
        raise ValueError(
            (
                "To compute Device-to-Head transformation, the same number of HPI"
                " points in device and head coordinates is required. (Got {dev}"
                " points in device and {head} points in head coordinate systems)"
            ).format(dev=len(hpi_dev), head=len(hpi_head))
        )

    trans = _quat_to_affine(_fit_matched_points(hpi_dev, hpi_head)[0])
    return Transform(fro="meg", to="head", trans=trans)


@verbose
def compute_native_head_t(montage, *, on_missing="warn", verbose=None):
    """Compute the native-to-head transformation for a montage.

    This uses the fiducials in the native space to transform to compute the
    transform to the head coordinate frame.

    Parameters
    ----------
    montage : instance of DigMontage
        The montage.
    %(on_missing_fiducials)s

        .. versionadded:: 1.2
    %(verbose)s

    Returns
    -------
    native_head_t : instance of Transform
        A native-to-head transformation matrix.
    """
    # Get fiducial points and their coord_frame
    fid_coords, coord_frame = _get_fid_coords(montage.dig, raise_error=False)
    if coord_frame is None:
        coord_frame = FIFF.FIFFV_COORD_UNKNOWN
    if coord_frame == FIFF.FIFFV_COORD_HEAD:
        native_head_t = np.eye(4)
    else:
        fid_keys = ("nasion", "lpa", "rpa")
        for key in fid_keys:
            this_coord = fid_coords[key]
            if this_coord is None or np.any(np.isnan(this_coord)):
                msg = (
                    f"Fiducial point {key} not found, assuming identity "
                    f"{_verbose_frames[coord_frame]} to head transformation"
                )
                _on_missing(on_missing, msg, error_klass=RuntimeError)
                native_head_t = np.eye(4)
                break
        else:
            native_head_t = get_ras_to_neuromag_trans(
                *[fid_coords[key] for key in fid_keys]
            )
    return Transform(coord_frame, "head", native_head_t)


def make_standard_montage(kind, head_size="auto"):
    """Read a generic (built-in) standard montage that ships with MNE-Python.

    Parameters
    ----------
    kind : str
        The name of the montage to use.

        .. note::
            You can retrieve the names of all
            built-in montages via :func:`mne.channels.get_builtin_montages`.
    head_size : float | None | str
        The head size (radius, in meters) to use for spherical montages.
        Can be None to not scale the read sizes. ``'auto'`` (default) will
        use 95mm for all montages except the ``'standard*'``, ``'mgh*'``, and
        ``'artinis*'``, which are already in fsaverage's MRI coordinates
        (same as MNI).

    Returns
    -------
    montage : instance of DigMontage
        The montage.

    See Also
    --------
    get_builtin_montages
    make_dig_montage
    read_custom_montage

    Notes
    -----
    Individualized (digitized) electrode positions should be read in using
    :func:`read_dig_captrak`, :func:`read_dig_dat`, :func:`read_dig_egi`,
    :func:`read_dig_fif`, :func:`read_dig_polhemus_isotrak`,
    :func:`read_dig_hpts`, or manually made with :func:`make_dig_montage`.

    .. versionadded:: 0.19.0
    """
    from ._standard_montage_utils import standard_montage_look_up_table

    _validate_type(kind, str, "kind")
    _check_option(
        parameter="kind",
        value=kind,
        allowed_values=[m.name for m in _BUILTIN_STANDARD_MONTAGES],
    )
    _validate_type(head_size, ("numeric", str, None), "head_size")
    if isinstance(head_size, str):
        _check_option("head_size", head_size, ("auto",), extra="when str")
        if kind.startswith(("standard", "mgh", "artinis")):
            head_size = None
        else:
            head_size = HEAD_SIZE_DEFAULT
    return standard_montage_look_up_table[kind](head_size=head_size)


def _check_dig_shape(pts):
    _validate_type(pts, np.ndarray, "points")
    if pts.ndim != 2 or pts.shape[-1] != 3:
        raise ValueError(f"Points must be of shape (n, 3) instead of {pts.shape}")