1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
|
# -*- coding: utf-8 -*-
"""Test the compute_current_source_density function.
For each supported file format, implement a test.
"""
# Authors: Alex Rockhill <aprockhill@mailbox.org>
#
# License: BSD-3-Clause
import os
import os.path as op
from shutil import copyfile
import numpy as np
from numpy.testing import assert_allclose
import pytest
import mne
from mne.preprocessing.ieeg import project_sensors_onto_brain
from mne.datasets import testing
from mne.transforms import _get_trans
data_path = testing.data_path(download=False)
subjects_dir = op.join(data_path, 'subjects')
fname_trans = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc-trans.fif')
fname_raw = op.join(data_path, 'MEG', 'sample', 'sample_audvis_trunc_raw.fif')
@testing.requires_testing_data
def test_project_sensors_onto_brain(tmp_path):
"""Test projecting sensors onto the brain surface."""
tempdir = str(tmp_path)
raw = mne.io.read_raw_fif(fname_raw)
trans = _get_trans(fname_trans)[0]
# test informative error for no surface first
with pytest.raises(RuntimeError, match='requires generating a BEM'):
project_sensors_onto_brain(raw.info, trans, 'sample',
subjects_dir=tempdir)
brain_surf_fname = op.join(tempdir, 'sample', 'bem', 'brain.surf')
if not op.isdir(op.dirname(brain_surf_fname)):
os.makedirs(op.dirname(brain_surf_fname))
if not op.isfile(brain_surf_fname):
copyfile(op.join(subjects_dir, 'sample', 'bem', 'inner_skull.surf'),
brain_surf_fname)
# now make realistic ECoG grid
raw.pick_types(meg=False, eeg=True)
raw.load_data()
raw.set_eeg_reference([])
raw.set_channel_types({ch: 'ecog' for ch in raw.ch_names})
pos = np.zeros((49, 3))
pos[:, :2] = np.array(
np.meshgrid(np.linspace(0, 0.02, 7),
np.linspace(0, 0.02, 7))).reshape(2, -1).T
pos[:, 2] = 0.12
raw.drop_channels(raw.ch_names[49:])
raw.set_montage(mne.channels.make_dig_montage(
ch_pos=dict(zip(raw.ch_names[:49], pos)), coord_frame='head'))
raw.info = project_sensors_onto_brain(
raw.info, trans, 'sample', subjects_dir=tempdir)
# plot to check, should be projected down onto inner skull
# brain = mne.viz.Brain('sample', subjects_dir=subjects_dir, alpha=0.5,
# surf='white')
# brain.add_sensors(raw.info, trans=trans)
test_locs = [[0.00149, -0.001588, 0.133029],
[0.004302, 0.001959, 0.133922],
[0.008602, 0.00116, 0.133723]]
for ch, test_loc in zip(raw.info['chs'][:3], test_locs):
assert_allclose(ch['loc'][:3], test_loc, rtol=0.01)
|
