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# -*- coding: utf-8 -*-
"""Dipole viz specific functions."""
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
import os.path as op
import numpy as np
from .utils import plt_show, _validate_if_list_of_axes
from .._freesurfer import _get_head_surface, _estimate_talxfm_rigid
from ..surface import read_surface
from ..transforms import apply_trans, invert_transform, _get_trans
from ..utils import _validate_type, _check_option, get_subjects_dir
def _check_concat_dipoles(dipole):
from ..dipole import Dipole, _concatenate_dipoles
if not isinstance(dipole, Dipole):
dipole = _concatenate_dipoles(dipole)
return dipole
def _plot_dipole_mri_outlines(dipoles, *, subject, trans, ax, subjects_dir,
color, scale, coord_frame, show, block,
head_source, title, surf, width):
from matplotlib.collections import LineCollection, PatchCollection
from matplotlib.patches import Circle
from scipy.spatial import ConvexHull
import matplotlib.pyplot as plt
extra = 'when mode is "outlines"'
trans = _get_trans(trans, fro='head', to='mri')[0]
_check_option('coord_frame', coord_frame, ['head', 'mri', 'mri_rotated'],
extra=extra)
_validate_type(surf, (str, None), 'surf')
_check_option('surf', surf, ('white', 'pial', None))
if ax is None:
_, ax = plt.subplots(
1, 3, figsize=(7, 2.5), squeeze=True, constrained_layout=True)
_validate_if_list_of_axes(ax, 3, name='ax')
dipoles = _check_concat_dipoles(dipoles)
color = 'r' if color is None else color
scale = 0.03 if scale is None else scale
width = 0.015 if width is None else width
fig = ax[0].figure
surfs = dict()
hemis = ('lh', 'rh')
if surf is not None:
for hemi in hemis:
surfs[hemi] = read_surface(
op.join(subjects_dir, subject, 'surf',
f'{hemi}.{surf}'), return_dict=True)[2]
surfs[hemi]['rr'] /= 1000.
subjects_dir = get_subjects_dir(subjects_dir)
surfs['head'] = _get_head_surface(head_source, subject, subjects_dir)
del head_source
mri_trans = head_trans = np.eye(4)
if coord_frame in ('mri', 'mri_rotated'):
head_trans = trans['trans']
if coord_frame == 'mri_rotated':
rot = _estimate_talxfm_rigid(subject, subjects_dir)
rot[:3, 3] = 0.
head_trans = rot @ head_trans
mri_trans = rot @ mri_trans
else:
assert coord_frame == 'head'
mri_trans = invert_transform(trans)['trans']
for s in surfs.values():
s['rr'] = 1000 * apply_trans(mri_trans, s['rr'])
del mri_trans
levels = dict()
if surf is not None:
use_rr = np.concatenate([surfs[key]['rr'] for key in hemis])
else:
use_rr = surfs['head']['rr']
views = [('Axial', 'XY'), ('Coronal', 'XZ'), ('Sagittal', 'YZ')]
# axial: 25% up the Z axis
axial = float(np.percentile(use_rr[:, 2], 20.))
coronal = float(np.percentile(use_rr[:, 1], 55.))
for key in hemis + ('head',):
levels[key] = dict(Axial=axial, Coronal=coronal)
if surf is not None:
levels['rh']['Sagittal'] = float(
np.percentile(surfs['rh']['rr'][:, 0], 50))
levels['head']['Sagittal'] = 0.
for ax_, (name, coords) in zip(ax, views):
idx = list(map(dict(X=0, Y=1, Z=2).get, coords))
miss = np.setdiff1d(np.arange(3), idx)[0]
pos = 1000 * apply_trans(head_trans, dipoles.pos)
ori = 1000 * apply_trans(head_trans, dipoles.ori, move=False)
lims = dict()
for ii, char in enumerate(coords):
lim = surfs['head']['rr'][:, idx[ii]]
lim = np.array([lim.min(), lim.max()])
lims[char] = lim
ax_.quiver(
pos[:, idx[0]], pos[:, idx[1]],
scale * ori[:, idx[0]], scale * ori[:, idx[1]],
color=color, pivot='middle', zorder=5,
scale_units='xy', angles='xy', scale=1.,
width=width, minshaft=0.5, headwidth=2.5, headlength=2.5,
headaxislength=2)
coll = PatchCollection(
[Circle((x, y), radius=scale * 1000 * width * 6)
for x, y in zip(pos[:, idx[0]], pos[:, idx[1]])],
linewidths=0., facecolors=color, zorder=6)
for key, surf in surfs.items():
try:
level = levels[key][name]
except KeyError:
continue
if key != 'head':
rrs = surf['rr'][:, idx]
tris = ConvexHull(rrs).simplices
segments = LineCollection(
rrs[:, [0, 1]][tris],
linewidths=1, linestyles='-', colors='k', zorder=3,
alpha=0.25)
ax_.add_collection(segments)
ax_.tricontour(
surf['rr'][:, idx[0]], surf['rr'][:, idx[1]],
surf['tris'], surf['rr'][:, miss],
levels=[level], colors='k', linewidths=1.0, linestyles=['-'],
zorder=4, alpha=0.5)
# TODO: this breaks the PatchCollection in MPL
# for coll in h.collections:
# coll.set_clip_on(False)
ax_.add_collection(coll)
ax_.set(
title=name, xlim=lims[coords[0]], ylim=lims[coords[1]],
xlabel=coords[0] + ' (mm)', ylabel=coords[1] + ' (mm)')
for spine in ax_.spines.values():
spine.set_visible(False)
ax_.grid(True, ls=':', zorder=2)
ax_.set_aspect('equal')
if title is not None:
fig.suptitle(title)
plt_show(show, block=block)
return fig
def _plot_dipole_3d(dipoles, *, coord_frame, color, fig, trans, scale, mode):
from .backends.renderer import _get_renderer
_check_option('coord_frame', coord_frame, ('head', 'mri'))
color = 'r' if color is None else color
scale = 0.005 if scale is None else scale
renderer = _get_renderer(fig=fig, size=(600, 600))
pos = dipoles.pos
ori = dipoles.ori
if coord_frame != 'head':
trans = _get_trans(trans, fro='head', to=coord_frame)[0]
pos = apply_trans(trans, pos)
ori = apply_trans(trans, ori)
renderer.sphere(center=pos, color=color, scale=scale)
if mode == 'arrow':
x, y, z = pos.T
u, v, w = ori.T
renderer.quiver3d(x, y, z, u, v, w, scale=3 * scale,
color=color, mode='arrow')
renderer.show()
fig = renderer.scene()
return fig
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