/
_3d.py
3425 lines (3065 loc) · 138 KB
/
_3d.py
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# -*- coding: utf-8 -*-
"""Functions to make 3D plots with M/EEG data."""
# 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>
# Mainak Jas <mainak@neuro.hut.fi>
# Mark Wronkiewicz <wronk.mark@gmail.com>
#
# License: Simplified BSD
from itertools import cycle
import os.path as op
import warnings
from collections.abc import Iterable
from functools import partial
from dataclasses import dataclass
from typing import Optional
import numpy as np
from ._dipole import (_check_concat_dipoles, _plot_dipole_mri_outlines,
_plot_dipole_3d)
from ..defaults import DEFAULTS
from ..fixes import _crop_colorbar, _get_img_fdata
from .._freesurfer import (_read_mri_info, _check_mri, _get_head_surface,
_get_skull_surface)
from ..io import _loc_to_coil_trans
from ..io.pick import (pick_types, channel_type, pick_info,
_FNIRS_CH_TYPES_SPLIT, _MEG_CH_TYPES_SPLIT)
from ..io.constants import FIFF
from ..io.meas_info import read_fiducials, create_info
from ..source_space import (_ensure_src, _create_surf_spacing, _check_spacing,
SourceSpaces, read_freesurfer_lut)
from ..surface import (get_meg_helmet_surf, _read_mri_surface, _DistanceQuery,
_project_onto_surface, _reorder_ccw, _CheckInside)
from ..transforms import (apply_trans, rot_to_quat, combine_transforms,
_get_trans, _ensure_trans, Transform, rotation,
read_ras_mni_t, _print_coord_trans, _find_trans,
transform_surface_to, _frame_to_str,
_get_transforms_to_coord_frame)
from ..utils import (get_subjects_dir, logger, _check_subject, verbose, warn,
has_nibabel, check_version, fill_doc, _pl, get_config,
_ensure_int, _validate_type, _check_option, _to_rgb)
from ._3d_overlay import _LayeredMesh
from .utils import (mne_analyze_colormap, _get_color_list,
plt_show, tight_layout, figure_nobar, _check_time_unit)
from ..bem import ConductorModel, _bem_find_surface, _ensure_bem_surfaces
verbose_dec = verbose
FIDUCIAL_ORDER = (FIFF.FIFFV_POINT_LPA, FIFF.FIFFV_POINT_NASION,
FIFF.FIFFV_POINT_RPA)
# XXX: to unify with digitization
def _fiducial_coords(points, coord_frame=None):
"""Generate 3x3 array of fiducial coordinates."""
points = points or [] # None -> list
if coord_frame is not None:
points = [p for p in points if p['coord_frame'] == coord_frame]
points_ = {p['ident']: p for p in points if
p['kind'] == FIFF.FIFFV_POINT_CARDINAL}
if points_:
return np.array([points_[i]['r'] for i in FIDUCIAL_ORDER])
else:
# XXX eventually this should probably live in montage.py
if coord_frame is None or coord_frame == FIFF.FIFFV_COORD_HEAD:
# Try converting CTF HPI coils to fiducials
out = np.empty((3, 3))
out.fill(np.nan)
for p in points:
if p['kind'] == FIFF.FIFFV_POINT_HPI:
if np.isclose(p['r'][1:], 0, atol=1e-6).all():
out[0 if p['r'][0] < 0 else 2] = p['r']
elif np.isclose(p['r'][::2], 0, atol=1e-6).all():
out[1] = p['r']
if np.isfinite(out).all():
return out
return np.array([])
@fill_doc
def plot_head_positions(pos, mode='traces', cmap='viridis', direction='z',
show=True, destination=None, info=None, color='k',
axes=None):
"""Plot head positions.
Parameters
----------
pos : ndarray, shape (n_pos, 10) | list of ndarray
The head position data. Can also be a list to treat as a
concatenation of runs.
mode : str
Can be 'traces' (default) to show position and quaternion traces,
or 'field' to show the position as a vector field over time.
cmap : colormap
Colormap to use for the trace plot, default is "viridis".
direction : str
Can be any combination of "x", "y", or "z" (default: "z") to show
directional axes in "field" mode.
show : bool
Show figure if True. Defaults to True.
destination : str | array-like, shape (3,) | None
The destination location for the head, assumed to be in head
coordinates. See :func:`mne.preprocessing.maxwell_filter` for
details.
.. versionadded:: 0.16
%(info)s If provided, will be used to show the destination position when
``destination is None``, and for showing the MEG sensors.
.. versionadded:: 0.16
color : color object
The color to use for lines in ``mode == 'traces'`` and quiver
arrows in ``mode == 'field'``.
.. versionadded:: 0.16
axes : array-like, shape (3, 2)
The matplotlib axes to use. Only used for ``mode == 'traces'``.
.. versionadded:: 0.16
Returns
-------
fig : instance of matplotlib.figure.Figure
The figure.
"""
from ..chpi import head_pos_to_trans_rot_t
from ..preprocessing.maxwell import _check_destination
import matplotlib.pyplot as plt
_check_option('mode', mode, ['traces', 'field'])
dest_info = dict(dev_head_t=None) if info is None else info
destination = _check_destination(destination, dest_info, head_frame=True)
if destination is not None:
destination = _ensure_trans(destination, 'head', 'meg') # probably inv
destination = destination['trans'][:3].copy()
destination[:, 3] *= 1000
if not isinstance(pos, (list, tuple)):
pos = [pos]
for ii, p in enumerate(pos):
p = np.array(p, float)
if p.ndim != 2 or p.shape[1] != 10:
raise ValueError('pos (or each entry in pos if a list) must be '
'dimension (N, 10), got %s' % (p.shape,))
if ii > 0: # concatenation
p[:, 0] += pos[ii - 1][-1, 0] - p[0, 0]
pos[ii] = p
borders = np.cumsum([len(pp) for pp in pos])
pos = np.concatenate(pos, axis=0)
trans, rot, t = head_pos_to_trans_rot_t(pos) # also ensures pos is okay
# trans, rot, and t are for dev_head_t, but what we really want
# is head_dev_t (i.e., where the head origin is in device coords)
use_trans = np.einsum('ijk,ik->ij', rot[:, :3, :3].transpose([0, 2, 1]),
-trans) * 1000
use_rot = rot.transpose([0, 2, 1])
use_quats = -pos[:, 1:4] # inverse (like doing rot.T)
surf = rrs = lims = None
if info is not None:
meg_picks = pick_types(info, meg=True, ref_meg=False, exclude=())
if len(meg_picks) > 0:
rrs = 1000 * np.array([info['chs'][pick]['loc'][:3]
for pick in meg_picks], float)
if mode == 'traces':
lims = np.array((rrs.min(0), rrs.max(0))).T
else: # mode == 'field'
surf = get_meg_helmet_surf(info)
transform_surface_to(surf, 'meg', info['dev_head_t'],
copy=False)
surf['rr'] *= 1000.
helmet_color = DEFAULTS['coreg']['helmet_color']
if mode == 'traces':
if axes is None:
axes = plt.subplots(3, 2, sharex=True)[1]
else:
axes = np.array(axes)
if axes.shape != (3, 2):
raise ValueError('axes must have shape (3, 2), got %s'
% (axes.shape,))
fig = axes[0, 0].figure
labels = ['xyz', ('$q_1$', '$q_2$', '$q_3$')]
for ii, (quat, coord) in enumerate(zip(use_quats.T, use_trans.T)):
axes[ii, 0].plot(t, coord, color, lw=1., zorder=3)
axes[ii, 0].set(ylabel=labels[0][ii], xlim=t[[0, -1]])
axes[ii, 1].plot(t, quat, color, lw=1., zorder=3)
axes[ii, 1].set(ylabel=labels[1][ii], xlim=t[[0, -1]])
for b in borders[:-1]:
for jj in range(2):
axes[ii, jj].axvline(t[b], color='r')
for ii, title in enumerate(('Position (mm)', 'Rotation (quat)')):
axes[0, ii].set(title=title)
axes[-1, ii].set(xlabel='Time (s)')
if rrs is not None:
pos_bads = np.any([(use_trans[:, ii] <= lims[ii, 0]) |
(use_trans[:, ii] >= lims[ii, 1])
for ii in range(3)], axis=0)
for ii in range(3):
oidx = list(range(ii)) + list(range(ii + 1, 3))
# knowing it will generally be spherical, we can approximate
# how far away we are along the axis line by taking the
# point to the left and right with the smallest distance
from scipy.spatial.distance import cdist
dists = cdist(rrs[:, oidx], use_trans[:, oidx])
left = rrs[:, [ii]] < use_trans[:, ii]
left_dists_all = dists.copy()
left_dists_all[~left] = np.inf
# Don't show negative Z direction
if ii != 2 and np.isfinite(left_dists_all).any():
idx = np.argmin(left_dists_all, axis=0)
left_dists = rrs[idx, ii]
bads = ~np.isfinite(
left_dists_all[idx, np.arange(len(idx))]) | pos_bads
left_dists[bads] = np.nan
axes[ii, 0].plot(t, left_dists, color=helmet_color,
ls='-', lw=0.5, zorder=2)
else:
axes[ii, 0].axhline(lims[ii][0], color=helmet_color,
ls='-', lw=0.5, zorder=2)
right_dists_all = dists
right_dists_all[left] = np.inf
if np.isfinite(right_dists_all).any():
idx = np.argmin(right_dists_all, axis=0)
right_dists = rrs[idx, ii]
bads = ~np.isfinite(
right_dists_all[idx, np.arange(len(idx))]) | pos_bads
right_dists[bads] = np.nan
axes[ii, 0].plot(t, right_dists, color=helmet_color,
ls='-', lw=0.5, zorder=2)
else:
axes[ii, 0].axhline(lims[ii][1], color=helmet_color,
ls='-', lw=0.5, zorder=2)
for ii in range(3):
axes[ii, 1].set(ylim=[-1, 1])
if destination is not None:
vals = np.array([destination[:, 3],
rot_to_quat(destination[:, :3])]).T.ravel()
for ax, val in zip(fig.axes, vals):
ax.axhline(val, color='r', ls=':', zorder=2, lw=1.)
else: # mode == 'field':
from matplotlib.colors import Normalize
from mpl_toolkits.mplot3d.art3d import Line3DCollection
from mpl_toolkits.mplot3d import Axes3D # noqa: F401, analysis:ignore
fig, ax = plt.subplots(1, subplot_kw=dict(projection='3d'))
# First plot the trajectory as a colormap:
# http://matplotlib.org/examples/pylab_examples/multicolored_line.html
pts = use_trans[:, np.newaxis]
segments = np.concatenate([pts[:-1], pts[1:]], axis=1)
norm = Normalize(t[0], t[-2])
lc = Line3DCollection(segments, cmap=cmap, norm=norm)
lc.set_array(t[:-1])
ax.add_collection(lc)
# now plot the head directions as a quiver
dir_idx = dict(x=0, y=1, z=2)
kwargs = dict(pivot='tail')
for d, length in zip(direction, [5., 2.5, 1.]):
use_dir = use_rot[:, :, dir_idx[d]]
# draws stems, then heads
array = np.concatenate((t, np.repeat(t, 2)))
ax.quiver(use_trans[:, 0], use_trans[:, 1], use_trans[:, 2],
use_dir[:, 0], use_dir[:, 1], use_dir[:, 2], norm=norm,
cmap=cmap, array=array, length=length, **kwargs)
if destination is not None:
ax.quiver(destination[0, 3],
destination[1, 3],
destination[2, 3],
destination[dir_idx[d], 0],
destination[dir_idx[d], 1],
destination[dir_idx[d], 2], color=color,
length=length, **kwargs)
mins = use_trans.min(0)
maxs = use_trans.max(0)
if surf is not None:
ax.plot_trisurf(*surf['rr'].T, triangles=surf['tris'],
color=helmet_color, alpha=0.1, shade=False)
ax.scatter(*rrs.T, s=1, color=helmet_color)
mins = np.minimum(mins, rrs.min(0))
maxs = np.maximum(maxs, rrs.max(0))
scale = (maxs - mins).max() / 2.
xlim, ylim, zlim = (maxs + mins)[:, np.newaxis] / 2. + [-scale, scale]
ax.set(xlabel='x', ylabel='y', zlabel='z',
xlim=xlim, ylim=ylim, zlim=zlim)
_set_aspect_equal(ax)
ax.view_init(30, 45)
tight_layout(fig=fig)
plt_show(show)
return fig
def _set_aspect_equal(ax):
# XXX recent MPL throws an error for 3D axis aspect setting, not much
# we can do about it at this point
try:
ax.set_aspect('equal')
except NotImplementedError:
pass
@verbose
def plot_evoked_field(evoked, surf_maps, time=None, time_label='t = %0.0f ms',
n_jobs=None, fig=None, vmax=None, n_contours=21,
*, interaction='terrain', verbose=None):
"""Plot MEG/EEG fields on head surface and helmet in 3D.
Parameters
----------
evoked : instance of mne.Evoked
The evoked object.
surf_maps : list
The surface mapping information obtained with make_field_map.
time : float | None
The time point at which the field map shall be displayed. If None,
the average peak latency (across sensor types) is used.
time_label : str | None
How to print info about the time instant visualized.
%(n_jobs)s
fig : instance of Figure3D | None
If None (default), a new figure will be created, otherwise it will
plot into the given figure.
.. versionadded:: 0.20
vmax : float | None
Maximum intensity. Can be None to use the max(abs(data)).
.. versionadded:: 0.21
n_contours : int
The number of contours.
.. versionadded:: 0.21
%(interaction_scene)s
Defaults to ``'terrain'``.
.. versionadded:: 1.1
%(verbose)s
Returns
-------
fig : instance of Figure3D
The figure.
"""
# Update the backend
from .backends.renderer import _get_renderer
types = [t for t in ['eeg', 'grad', 'mag'] if t in evoked]
_validate_type(vmax, (None, 'numeric'), 'vmax')
n_contours = _ensure_int(n_contours, 'n_contours')
_check_option('interaction', interaction, ['trackball', 'terrain'])
time_idx = None
if time is None:
time = np.mean([evoked.get_peak(ch_type=t)[1] for t in types])
del types
if not evoked.times[0] <= time <= evoked.times[-1]:
raise ValueError('`time` (%0.3f) must be inside `evoked.times`' % time)
time_idx = np.argmin(np.abs(evoked.times - time))
# Plot them
alphas = [1.0, 0.5]
colors = [(0.6, 0.6, 0.6), (1.0, 1.0, 1.0)]
colormap = mne_analyze_colormap(format='vtk')
colormap_lines = np.concatenate([np.tile([0., 0., 255., 255.], (127, 1)),
np.tile([0., 0., 0., 255.], (2, 1)),
np.tile([255., 0., 0., 255.], (127, 1))])
renderer = _get_renderer(fig, bgcolor=(0.0, 0.0, 0.0), size=(600, 600))
renderer.set_interaction(interaction)
for ii, this_map in enumerate(surf_maps):
surf = this_map['surf']
map_data = this_map['data']
map_type = this_map['kind']
map_ch_names = this_map['ch_names']
if map_type == 'eeg':
pick = pick_types(evoked.info, meg=False, eeg=True)
else:
pick = pick_types(evoked.info, meg=True, eeg=False, ref_meg=False)
ch_names = [evoked.ch_names[k] for k in pick]
set_ch_names = set(ch_names)
set_map_ch_names = set(map_ch_names)
if set_ch_names != set_map_ch_names:
message = ['Channels in map and data do not match.']
diff = set_map_ch_names - set_ch_names
if len(diff):
message += ['%s not in data file. ' % list(diff)]
diff = set_ch_names - set_map_ch_names
if len(diff):
message += ['%s not in map file.' % list(diff)]
raise RuntimeError(' '.join(message))
data = np.dot(map_data, evoked.data[pick, time_idx])
# Make a solid surface
if vmax is None:
vmax = np.max(np.abs(data))
vmax = float(vmax)
alpha = alphas[ii]
mesh = _LayeredMesh(
renderer=renderer,
vertices=surf['rr'],
triangles=surf['tris'],
normals=surf['nn'],
)
mesh.map()
color = _to_rgb(colors[ii], alpha=True)
cmap = np.array([(0, 0, 0, 0,), color])
ctable = np.round(cmap * 255).astype(np.uint8)
mesh.add_overlay(
scalars=np.ones(len(data)),
colormap=ctable,
rng=[0, 1],
opacity=alpha,
name='surf',
)
# Now show our field pattern
mesh.add_overlay(
scalars=data,
colormap=colormap,
rng=[-vmax, vmax],
opacity=1.,
name='field',
)
# And the field lines on top
if n_contours > 0:
renderer.contour(surface=surf, scalars=data, contours=n_contours,
vmin=-vmax, vmax=vmax, opacity=alpha,
colormap=colormap_lines)
if time_label is not None:
if '%' in time_label:
time_label %= (1e3 * evoked.times[time_idx])
renderer.text2d(x_window=0.01, y_window=0.01, text=time_label)
renderer.set_camera(azimuth=10, elevation=60)
renderer.show()
return renderer.scene()
@verbose
def plot_alignment(info=None, trans=None, subject=None, subjects_dir=None,
surfaces='auto', coord_frame='auto',
meg=None, eeg='original', fwd=None,
dig=False, ecog=True, src=None, mri_fiducials=False,
bem=None, seeg=True, fnirs=True, show_axes=False, dbs=True,
fig=None, interaction='terrain', verbose=None):
"""Plot head, sensor, and source space alignment in 3D.
Parameters
----------
%(info)s If None (default), no sensor information will be shown.
%(trans)s
%(subject)s Can be omitted if ``src`` is provided.
%(subjects_dir)s
surfaces : str | list | dict
Surfaces to plot. Supported values:
* scalp: one of 'head', 'outer_skin' (alias for 'head'),
'head-dense', or 'seghead' (alias for 'head-dense')
* skull: 'outer_skull', 'inner_skull', 'brain' (alias for
'inner_skull')
* brain: one of 'pial', 'white', 'inflated', or 'brain'
(alias for 'pial').
Can be dict to specify alpha values for each surface. Use None
to specify default value. Specified values must be between 0 and 1.
for example::
surfaces=dict(brain=0.4, outer_skull=0.6, head=None)
Defaults to 'auto', which will look for a head surface and plot
it if found.
.. note:: For single layer BEMs it is recommended to use ``'brain'``.
coord_frame : 'auto' | 'head' | 'meg' | 'mri'
The coordinate frame to use. If ``'auto'`` (default), chooses ``'mri'``
if ``trans`` was passed, and ``'head'`` otherwise.
.. versionchanged:: 1.0
Defaults to ``'auto'``.
%(meg)s
%(eeg)s
%(fwd)s
dig : bool | 'fiducials'
If True, plot the digitization points; 'fiducials' to plot fiducial
points only.
%(ecog)s
src : instance of SourceSpaces | None
If not None, also plot the source space points.
mri_fiducials : bool | str
Plot MRI fiducials (default False). If ``True``, look for a file with
the canonical name (``bem/{subject}-fiducials.fif``). If ``str``,
it can be ``'estimated'`` to use :func:`mne.coreg.get_mni_fiducials`,
otherwise it should provide the full path to the fiducials file.
.. versionadded:: 0.22
Support for ``'estimated'``.
bem : list of dict | instance of ConductorModel | None
Can be either the BEM surfaces (list of dict), a BEM solution or a
sphere model. If None, we first try loading
``'$SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-$SOURCE.fif'``, and then look
for ``'$SUBJECT*$SOURCE.fif'`` in the same directory. For
``'outer_skin'``, the subjects bem and bem/flash folders are searched.
Defaults to None.
%(seeg)s
%(fnirs)s
.. versionadded:: 0.20
show_axes : bool
If True (default False), coordinate frame axis indicators will be
shown:
* head in pink.
* MRI in gray (if ``trans is not None``).
* MEG in blue (if MEG sensors are present).
.. versionadded:: 0.16
%(dbs)s
fig : Figure3D | None
PyVista scene in which to plot the alignment.
If ``None``, creates a new 600x600 pixel figure with black background.
.. versionadded:: 0.16
%(interaction_scene)s
.. versionadded:: 0.16
.. versionchanged:: 1.0
Defaults to ``'terrain'``.
%(verbose)s
Returns
-------
fig : instance of Figure3D
The figure.
See Also
--------
mne.viz.plot_bem
Notes
-----
This function serves the purpose of checking the validity of the many
different steps of source reconstruction:
- Transform matrix (keywords ``trans``, ``meg`` and ``mri_fiducials``),
- BEM surfaces (keywords ``bem`` and ``surfaces``),
- sphere conductor model (keywords ``bem`` and ``surfaces``) and
- source space (keywords ``surfaces`` and ``src``).
.. versionadded:: 0.15
"""
# Update the backend
from .backends.renderer import _get_renderer
meg, eeg, fnirs, warn_meg = _handle_sensor_types(meg, eeg, fnirs)
_check_option('interaction', interaction, ['trackball', 'terrain'])
info = create_info(1, 1000., 'misc') if info is None else info
_validate_type(info, "info")
# Handle surfaces:
if surfaces == 'auto' and trans is None:
surfaces = list() # if no `trans` can't plot mri surfaces
if isinstance(surfaces, str):
surfaces = [surfaces]
if isinstance(surfaces, dict):
user_alpha = surfaces.copy()
for key, val in user_alpha.items():
_validate_type(key, "str", f"surfaces key {repr(key)}")
_validate_type(val, (None, "numeric"), f"surfaces[{repr(key)}]")
if val is not None:
user_alpha[key] = float(val)
if not 0 <= user_alpha[key] <= 1:
raise ValueError(
f'surfaces[{repr(key)}] ({val}) must be'
' between 0 and 1'
)
else:
user_alpha = {}
surfaces = list(surfaces)
for si, s in enumerate(surfaces):
_validate_type(s, "str", f"surfaces[{si}]")
bem = _ensure_bem_surfaces(bem, extra_allow=(ConductorModel, None))
assert isinstance(bem, ConductorModel) or bem is None
_check_option('coord_frame', coord_frame, ['head', 'meg', 'mri', 'auto'])
if coord_frame == 'auto':
coord_frame = 'head' if trans is None else 'mri'
if src is not None:
src = _ensure_src(src)
src_subject = src._subject
subject = src_subject if subject is None else subject
if src_subject is not None and subject != src_subject:
raise ValueError(f'subject ("{subject}") did not match the '
f'subject name in src ("{src_subject}")')
# configure transforms
if trans == 'auto':
subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
trans = _find_trans(subject, subjects_dir)
picks = pick_types(info, meg=('sensors' in meg), ref_meg=('ref' in meg),
eeg=(len(eeg) > 0), ecog=ecog, seeg=seeg, dbs=dbs,
fnirs=(len(fnirs) > 0))
if trans is None:
# Some stuff is natively in head coords, others in MRI coords
msg = ('A head<->mri transformation matrix (trans) is required '
f'to plot %s in {coord_frame} coordinates, '
'`trans=None` is not allowed')
if fwd is not None:
fwd_frame = _frame_to_str[fwd['coord_frame']]
if fwd_frame != coord_frame:
raise ValueError(
msg % f'a {fwd_frame}-coordinate forward solution')
if src is not None:
src_frame = _frame_to_str[src[0]['coord_frame']]
if src_frame != coord_frame:
raise ValueError(
msg % f'a {src_frame}-coordinate source space')
if mri_fiducials is not False and coord_frame != 'mri':
raise ValueError(msg % 'mri fiducials')
# only enforce needing `trans` if there are channels in "head"/"device"
if picks.size and coord_frame == 'mri':
raise ValueError(msg % 'sensors')
# if only plotting sphere model no trans needed
if bem is not None:
if not bem['is_sphere']:
if coord_frame != 'mri':
raise ValueError(msg % 'a BEM')
elif surfaces not in (['brain'], []): # can only plot these
raise ValueError(msg % (', '.join(surfaces) + ' surfaces'))
elif len(surfaces) > 0 and coord_frame != 'mri':
raise ValueError(msg % (', '.join(surfaces) + ' surfaces'))
trans = Transform('head', 'mri') # not used so just use identity
# get transforms
head_mri_t = _get_trans(trans, 'head', 'mri')[0]
to_cf_t = _get_transforms_to_coord_frame(
info, head_mri_t, coord_frame=coord_frame)
# Surfaces:
# both the head and helmet will be in MRI coordinates after this
surfs = dict()
# Brain surface:
brain = sorted(
set(surfaces) & set(['brain', 'pial', 'white', 'inflated']))
if len(brain) > 1:
raise ValueError(
f'Only one brain surface can be plotted, got {brain}.')
brain = brain[0] if brain else False
if brain is not False:
surfaces.pop(surfaces.index(brain))
if bem is not None and bem['is_sphere'] and brain == 'brain':
surfs['lh'] = _bem_find_surface(bem, 'brain')
else:
brain = 'pial' if brain == 'brain' else brain
subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
for hemi in ['lh', 'rh']:
brain_fname = op.join(subjects_dir, subject, 'surf',
f'{hemi}.{brain}')
if not op.isfile(brain_fname):
raise RuntimeError(
f'No brain surface found for subject {subject}, '
f'expected {brain_fname} to exist')
surfs[hemi] = _read_mri_surface(brain_fname)
# Head surface:
head_keys = ('auto', 'head', 'outer_skin', 'head-dense', 'seghead')
head = [s for s in surfaces if s in head_keys]
if len(head) > 1:
raise ValueError('Can only supply one head-like surface name, '
f'got {head}')
head = head[0] if head else False
if head is not False:
surfaces.pop(surfaces.index(head))
elif 'projected' in eeg:
raise ValueError('A head surface is required to project EEG, '
'"head", "outer_skin", "head-dense" or "seghead" '
'must be in surfaces or surfaces must be "auto"')
# Skull surface:
skulls = [s for s in surfaces if s in ('outer_skull', 'inner_skull')]
for skull_name in skulls:
surfaces.pop(surfaces.index(skull_name))
skull = _get_skull_surface(
skull_name.split('_')[0], subject, subjects_dir, bem=bem)
skull['name'] = skull_name # set name for alpha
surfs[skull_name] = skull
# we've looked through all of them, raise if some remain
if len(surfaces) > 0:
raise ValueError(f'Unknown surface type{_pl(surfaces)}: {surfaces}')
# set colors and alphas
defaults = DEFAULTS['coreg']
no_deep = not (dbs or seeg) or \
pick_types(info, dbs=True, seeg=True).size == 0
max_alpha = 1.0 if no_deep else 0.75
hemi_val = 0.5
if src is None or (brain and any(s['type'] == 'surf' for s in src)):
hemi_val = max_alpha
alpha_range = np.linspace(max_alpha / 2., 0, 5)[:len(skulls) + 1]
if src is None and brain is False and len(skulls) == 0 and not show_axes:
head_alpha = max_alpha
else:
head_alpha = alpha_range[0]
alphas = dict(lh=hemi_val, rh=hemi_val)
colors = dict(lh=(0.5,) * 3, rh=(0.5,) * 3)
for idx, name in enumerate(skulls):
alphas[name] = alpha_range[idx + 1]
colors[name] = (0.95 - idx * 0.2, 0.85, 0.95 - idx * 0.2)
if brain is not False and brain in user_alpha:
alphas['lh'] = alphas['rh'] = user_alpha.pop(brain)
# replace default alphas with specified user_alpha
for k, v in user_alpha.items():
if v is not None:
alphas[k] = v
if k in head_keys and v is not None:
head_alpha = v
fid_colors = tuple(
defaults[f'{key}_color'] for key in ('lpa', 'nasion', 'rpa'))
# initialize figure
renderer = _get_renderer(fig, name=f'Sensor alignment: {subject}',
bgcolor=(0.5, 0.5, 0.5), size=(800, 800))
renderer.set_interaction(interaction)
# plot head
_, _, head_surf = _plot_head_surface(
renderer, head, subject, subjects_dir, bem, coord_frame,
to_cf_t, alpha=head_alpha)
# plot helmet
if 'helmet' in meg and pick_types(info, meg=True).size > 0:
_, _, src_surf = _plot_helmet(
renderer, info, to_cf_t, head_mri_t, coord_frame)
# plot surfaces
if brain and 'lh' not in surfs: # one layer sphere
assert bem['coord_frame'] == FIFF.FIFFV_COORD_HEAD
center = bem['r0'].copy()
center = apply_trans(to_cf_t['head'], center)
renderer.sphere(center, scale=0.01, color=colors['lh'],
opacity=alphas['lh'])
if show_axes:
_plot_axes(renderer, info, to_cf_t, head_mri_t)
# plot points
_check_option('dig', dig, (True, False, 'fiducials'))
if dig:
if dig is True:
_plot_hpi_coils(renderer, info, to_cf_t)
_plot_head_shape_points(renderer, info, to_cf_t)
_plot_head_fiducials(renderer, info, to_cf_t, fid_colors)
if mri_fiducials:
_plot_mri_fiducials(renderer, mri_fiducials, subjects_dir, subject,
to_cf_t, fid_colors)
for key, surf in surfs.items():
# Surfs can sometimes be in head coords (e.g., if coming from sphere)
assert isinstance(surf, dict), f'{key}: {type(surf)}'
surf = transform_surface_to(
surf, coord_frame, [to_cf_t['mri'], to_cf_t['head']], copy=True)
renderer.surface(surface=surf, color=colors[key],
opacity=alphas[key],
backface_culling=(key != 'helmet'))
# plot sensors (NB snapshot_brain_montage relies on the last thing being
# plotted being the sensors, so we need to do this after the surfaces)
if picks.size > 0:
_plot_sensors(renderer, info, to_cf_t, picks, meg, eeg, fnirs,
warn_meg, head_surf, 'm')
if src is not None:
atlas_ids, colors = read_freesurfer_lut()
for ss in src:
src_rr = ss['rr'][ss['inuse'].astype(bool)]
src_nn = ss['nn'][ss['inuse'].astype(bool)]
# update coordinate frame
src_trans = to_cf_t[_frame_to_str[src[0]['coord_frame']]]
src_rr = apply_trans(src_trans, src_rr)
src_nn = apply_trans(src_trans, src_nn, move=False)
# volume sources
if ss['type'] == 'vol':
seg_name = ss.get('seg_name', None)
if seg_name is not None and seg_name in colors:
color = colors[seg_name][:3]
color = tuple(i / 256. for i in color)
else:
color = (1., 1., 0.)
# surface and discrete sources
else:
color = (1., 1., 0.)
if len(src_rr) > 0:
renderer.quiver3d(
x=src_rr[:, 0], y=src_rr[:, 1], z=src_rr[:, 2],
u=src_nn[:, 0], v=src_nn[:, 1], w=src_nn[:, 2],
color=color, mode='cylinder', scale=3e-3,
opacity=0.75, glyph_height=0.25,
glyph_center=(0., 0., 0.), glyph_resolution=20,
backface_culling=True)
if fwd is not None:
_plot_forward(renderer, fwd,
to_cf_t[_frame_to_str[fwd['coord_frame']]])
renderer.set_camera(azimuth=90, elevation=90,
distance=0.6, focalpoint=(0., 0., 0.))
renderer.show()
return renderer.scene()
def _handle_sensor_types(meg, eeg, fnirs):
"""Handle plotting inputs for sensors types."""
if eeg is True:
eeg = ['original']
elif eeg is False:
eeg = list()
warn_meg = meg is not None # only warn if the value is explicit
if meg is True:
meg = ['helmet', 'sensors', 'ref']
elif meg is None:
meg = ['helmet', 'sensors']
elif meg is False:
meg = list()
if fnirs is True:
fnirs = ['pairs']
elif fnirs is False:
fnirs = list()
if isinstance(meg, str):
meg = [meg]
if isinstance(eeg, str):
eeg = [eeg]
if isinstance(fnirs, str):
fnirs = [fnirs]
for kind, var in zip(('eeg', 'meg', 'fnirs'), (eeg, meg, fnirs)):
if not isinstance(var, (list, tuple)) or \
not all(isinstance(x, str) for x in var):
raise TypeError(
f'{kind} must be list or tuple of str, got {type(kind)}')
for xi, x in enumerate(meg):
_check_option(f'meg[{xi}]', x, ('helmet', 'sensors', 'ref'))
for xi, x in enumerate(eeg):
_check_option(f'eeg[{xi}]', x, ('original', 'projected'))
for xi, x in enumerate(fnirs):
_check_option(f'fnirs[{xi}]', x, ('channels', 'pairs',
'sources', 'detectors'))
return meg, eeg, fnirs, warn_meg
@verbose
def _ch_pos_in_coord_frame(info, to_cf_t, warn_meg=True, verbose=None):
"""Transform positions from head/device/mri to a coordinate frame."""
from ..forward import _create_meg_coils
chs = dict(ch_pos=dict(), sources=dict(), detectors=dict())
unknown_chs = list() # prepare for chs with unknown coordinate frame
type_counts = dict()
for idx in range(info['nchan']):
ch_type = channel_type(info, idx)
if ch_type in type_counts:
type_counts[ch_type] += 1
else:
type_counts[ch_type] = 1
type_slices = dict(ch_pos=slice(0, 3))
if ch_type in _FNIRS_CH_TYPES_SPLIT:
# add sensors and detectors too for fNIRS
type_slices.update(sources=slice(3, 6), detectors=slice(6, 9))
for type_name, type_slice in type_slices.items():
if ch_type in _MEG_CH_TYPES_SPLIT + ('ref_meg',):
coil_trans = _loc_to_coil_trans(info['chs'][idx]['loc'])
# Here we prefer accurate geometry in case we need to
# ConvexHull the coil, we want true 3D geometry (and not, for
# example, a straight line / 1D geometry)
this_coil = [info['chs'][idx]]
try:
coil = _create_meg_coils(this_coil, acc='accurate')[0]
except RuntimeError: # we don't have an accurate one
coil = _create_meg_coils(this_coil, acc='normal')[0]
# store verts as ch_coord
ch_coord, triangles = _sensor_shape(coil)
ch_coord = apply_trans(coil_trans, ch_coord)
if len(ch_coord) == 0 and warn_meg:
warn(f'MEG sensor {info.ch_names[idx]} not found.')
else:
ch_coord = info['chs'][idx]['loc'][type_slice]
ch_coord_frame = info['chs'][idx]['coord_frame']
if ch_coord_frame not in (FIFF.FIFFV_COORD_UNKNOWN,
FIFF.FIFFV_COORD_DEVICE,
FIFF.FIFFV_COORD_HEAD,
FIFF.FIFFV_COORD_MRI):
raise RuntimeError(
f'Channel {info.ch_names[idx]} has coordinate frame '
f'{ch_coord_frame}, must be "meg", "head" or "mri".')
# set unknown as head first
if ch_coord_frame == FIFF.FIFFV_COORD_UNKNOWN:
unknown_chs.append(info.ch_names[idx])
ch_coord_frame = FIFF.FIFFV_COORD_HEAD
ch_coord = apply_trans(
to_cf_t[_frame_to_str[ch_coord_frame]], ch_coord)
if ch_type in _MEG_CH_TYPES_SPLIT + ('ref_meg',):
chs[type_name][info.ch_names[idx]] = (ch_coord, triangles)
else:
chs[type_name][info.ch_names[idx]] = ch_coord
if unknown_chs:
warn(f'Got coordinate frame "unknown" for {unknown_chs}, assuming '
'"head" coordinates.')
logger.info('Channel types::\t' + ', '.join(
[f'{ch_type}: {count}' for ch_type, count in type_counts.items()]))
return chs['ch_pos'], chs['sources'], chs['detectors']
def _plot_head_surface(renderer, head, subject, subjects_dir, bem,
coord_frame, to_cf_t, alpha, color=None):
"""Render a head surface in a 3D scene."""
color = DEFAULTS['coreg']['head_color'] if color is None else color
actor = None
src_surf = dst_surf = None
if head is not False:
src_surf = _get_head_surface(head, subject, subjects_dir, bem=bem)
src_surf = transform_surface_to(
src_surf, coord_frame, [to_cf_t['mri'], to_cf_t['head']],
copy=True)
actor, dst_surf = renderer.surface(
surface=src_surf, color=color, opacity=alpha,
backface_culling=False)
return actor, dst_surf, src_surf
def _plot_helmet(renderer, info, to_cf_t, head_mri_t, coord_frame,
alpha=0.25, color=None):
color = DEFAULTS['coreg']['helmet_color'] if color is None else color
src_surf = get_meg_helmet_surf(info, head_mri_t)
assert src_surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
src_surf = transform_surface_to(
src_surf, coord_frame, [to_cf_t['mri'], to_cf_t['head']], copy=True)
actor, dst_surf = renderer.surface(
surface=src_surf, color=color, opacity=alpha,
backface_culling=False)
return actor, dst_surf, src_surf
def _plot_axes(renderer, info, to_cf_t, head_mri_t):
"""Render different axes a 3D scene."""
axes = [(to_cf_t['head'], (0.9, 0.3, 0.3))] # always show head
if not np.allclose(head_mri_t['trans'], np.eye(4)): # Show MRI
axes.append((to_cf_t['mri'], (0.6, 0.6, 0.6)))
if pick_types(info, meg=True).size > 0: # Show MEG
axes.append((to_cf_t['meg'], (0., 0.6, 0.6)))
actors = list()
for ax in axes:
x, y, z = np.tile(ax[0]['trans'][:3, 3], 3).reshape((3, 3)).T
u, v, w = ax[0]['trans'][:3, :3]
actor, _ = renderer.sphere(center=np.column_stack((x[0], y[0], z[0])),
color=ax[1], scale=3e-3)
actors.append(actor)
actor, _ = renderer.quiver3d(x=x, y=y, z=z, u=u, v=v, w=w,
mode='arrow', scale=2e-2, color=ax[1],
scale_mode='scalar', resolution=20,
scalars=[0.33, 0.66, 1.0])
actors.append(actor)
return actors
def _plot_head_fiducials(renderer, info, to_cf_t, fid_colors):
defaults = DEFAULTS['coreg']
car_loc = _fiducial_coords(info['dig'], FIFF.FIFFV_COORD_HEAD)
car_loc = apply_trans(to_cf_t['head'], car_loc)
if len(car_loc) == 0:
warn('Digitization points not found. Cannot plot digitization.')
actors = list()
for color, data in zip(fid_colors, car_loc):
actor, _ = renderer.sphere(center=data, color=color,
scale=defaults['dig_fid_scale'],
opacity=defaults['dig_fid_opacity'],
backface_culling=True)
actors.append(actor)
return actors
def _plot_mri_fiducials(renderer, mri_fiducials, subjects_dir, subject,
to_cf_t, fid_colors):
from ..coreg import get_mni_fiducials
defaults = DEFAULTS['coreg']