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
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
|
# Author: Daniel G Wakeman <dwakeman@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import os.path as op
from copy import deepcopy
from functools import partial
import pytest
import numpy as np
from scipy.io import savemat
from numpy.testing import assert_array_equal, assert_equal
from mne.channels import (rename_channels, read_ch_connectivity,
find_ch_connectivity, make_1020_channel_selections)
from mne.channels.channels import (_ch_neighbor_connectivity,
_compute_ch_connectivity)
from mne.io import (read_info, read_raw_fif, read_raw_ctf, read_raw_bti,
read_raw_eeglab)
from mne.io.constants import FIFF
from mne.utils import _TempDir, run_tests_if_main
from mne import pick_types, pick_channels
from mne.datasets import testing
base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
raw_fname = op.join(base_dir, 'test_raw.fif')
def test_reorder_channels():
"""Test reordering of channels."""
raw = read_raw_fif(raw_fname, preload=True).crop(0, 0.1)
raw_new = raw.copy().reorder_channels(raw.ch_names[::-1])
assert_array_equal(raw[:][0], raw_new[:][0][::-1])
raw_new.reorder_channels(raw_new.ch_names[::-1][1:-1])
raw.drop_channels(raw.ch_names[:1] + raw.ch_names[-1:])
assert_array_equal(raw[:][0], raw_new[:][0])
with pytest.raises(ValueError, match='repeated'):
raw.reorder_channels(raw.ch_names[:1] + raw.ch_names[:1])
def test_rename_channels():
"""Test rename channels."""
info = read_info(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
pytest.raises(ValueError, rename_channels, info, mapping)
# Test improper mapping configuration
mapping = {'MEG 2641': 1.0}
pytest.raises(TypeError, rename_channels, info, mapping)
# Test non-unique mapping configuration
mapping = {'MEG 2641': 'MEG 2642'}
pytest.raises(ValueError, rename_channels, info, mapping)
# Test bad input
pytest.raises(ValueError, rename_channels, info, 1.)
pytest.raises(ValueError, rename_channels, info, 1.)
# Test name too long (channel names must be less than 15 characters)
A16 = 'A' * 16
mapping = {'MEG 2641': A16}
pytest.raises(ValueError, rename_channels, info, mapping)
# Test successful changes
# Test ch_name and ch_names are changed
info2 = deepcopy(info) # for consistency at the start of each test
info2['bads'] = ['EEG 060', 'EOG 061']
mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
rename_channels(info2, mapping)
assert info2['chs'][374]['ch_name'] == 'EEG060'
assert info2['ch_names'][374] == 'EEG060'
assert info2['chs'][375]['ch_name'] == 'EOG061'
assert info2['ch_names'][375] == 'EOG061'
assert_array_equal(['EEG060', 'EOG061'], info2['bads'])
info2 = deepcopy(info)
rename_channels(info2, lambda x: x.replace(' ', ''))
assert info2['chs'][373]['ch_name'] == 'EEG059'
info2 = deepcopy(info)
info2['bads'] = ['EEG 060', 'EEG 060']
rename_channels(info2, mapping)
assert_array_equal(['EEG060', 'EEG060'], info2['bads'])
def test_set_channel_types():
"""Test set_channel_types."""
raw = read_raw_fif(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
pytest.raises(ValueError, raw.set_channel_types, mapping)
# Test change to illegal channel type
mapping = {'EOG 061': 'xxx'}
pytest.raises(ValueError, raw.set_channel_types, mapping)
# Test changing type if in proj (avg eeg ref here)
mapping = {'EEG 058': 'ecog', 'EEG 059': 'ecg', 'EEG 060': 'eog',
'EOG 061': 'seeg', 'MEG 2441': 'eeg', 'MEG 2443': 'eeg',
'MEG 2442': 'hbo'}
pytest.raises(RuntimeError, raw.set_channel_types, mapping)
# Test type change
raw2 = read_raw_fif(raw_fname)
raw2.info['bads'] = ['EEG 059', 'EEG 060', 'EOG 061']
pytest.raises(RuntimeError, raw2.set_channel_types, mapping) # has prj
raw2.add_proj([], remove_existing=True)
with pytest.warns(RuntimeWarning, match='The unit for channel'):
raw2.set_channel_types(mapping)
info = raw2.info
assert info['chs'][372]['ch_name'] == 'EEG 058'
assert info['chs'][372]['kind'] == FIFF.FIFFV_ECOG_CH
assert info['chs'][372]['unit'] == FIFF.FIFF_UNIT_V
assert info['chs'][372]['coil_type'] == FIFF.FIFFV_COIL_EEG
assert info['chs'][373]['ch_name'] == 'EEG 059'
assert info['chs'][373]['kind'] == FIFF.FIFFV_ECG_CH
assert info['chs'][373]['unit'] == FIFF.FIFF_UNIT_V
assert info['chs'][373]['coil_type'] == FIFF.FIFFV_COIL_NONE
assert info['chs'][374]['ch_name'] == 'EEG 060'
assert info['chs'][374]['kind'] == FIFF.FIFFV_EOG_CH
assert info['chs'][374]['unit'] == FIFF.FIFF_UNIT_V
assert info['chs'][374]['coil_type'] == FIFF.FIFFV_COIL_NONE
assert info['chs'][375]['ch_name'] == 'EOG 061'
assert info['chs'][375]['kind'] == FIFF.FIFFV_SEEG_CH
assert info['chs'][375]['unit'] == FIFF.FIFF_UNIT_V
assert info['chs'][375]['coil_type'] == FIFF.FIFFV_COIL_EEG
for idx in pick_channels(raw.ch_names, ['MEG 2441', 'MEG 2443']):
assert info['chs'][idx]['kind'] == FIFF.FIFFV_EEG_CH
assert info['chs'][idx]['unit'] == FIFF.FIFF_UNIT_V
assert info['chs'][idx]['coil_type'] == FIFF.FIFFV_COIL_EEG
idx = pick_channels(raw.ch_names, ['MEG 2442'])[0]
assert info['chs'][idx]['kind'] == FIFF.FIFFV_FNIRS_CH
assert info['chs'][idx]['unit'] == FIFF.FIFF_UNIT_MOL
assert info['chs'][idx]['coil_type'] == FIFF.FIFFV_COIL_FNIRS_HBO
# Test meaningful error when setting channel type with unknown unit
raw.info['chs'][0]['unit'] = 0.
ch_types = {raw.ch_names[0]: 'misc'}
pytest.raises(ValueError, raw.set_channel_types, ch_types)
def test_read_ch_connectivity():
"""Test reading channel connectivity templates."""
tempdir = _TempDir()
a = partial(np.array, dtype='<U7')
# no pep8
nbh = np.array([[(['MEG0111'], [[a(['MEG0131'])]]),
(['MEG0121'], [[a(['MEG0111'])],
[a(['MEG0131'])]]),
(['MEG0131'], [[a(['MEG0111'])],
[a(['MEG0121'])]])]],
dtype=[('label', 'O'), ('neighblabel', 'O')])
mat = dict(neighbours=nbh)
mat_fname = op.join(tempdir, 'test_mat.mat')
savemat(mat_fname, mat, oned_as='row')
ch_connectivity, ch_names = read_ch_connectivity(mat_fname)
x = ch_connectivity
assert_equal(x.shape[0], len(ch_names))
assert_equal(x.shape, (3, 3))
assert_equal(x[0, 1], False)
assert_equal(x[0, 2], True)
assert np.all(x.diagonal())
pytest.raises(ValueError, read_ch_connectivity, mat_fname, [0, 3])
ch_connectivity, ch_names = read_ch_connectivity(mat_fname, picks=[0, 2])
assert_equal(ch_connectivity.shape[0], 2)
assert_equal(len(ch_names), 2)
ch_names = ['EEG01', 'EEG02', 'EEG03']
neighbors = [['EEG02'], ['EEG04'], ['EEG02']]
pytest.raises(ValueError, _ch_neighbor_connectivity, ch_names, neighbors)
neighbors = [['EEG02'], ['EEG01', 'EEG03'], ['EEG 02']]
pytest.raises(ValueError, _ch_neighbor_connectivity, ch_names[:2],
neighbors)
neighbors = [['EEG02'], 'EEG01', ['EEG 02']]
pytest.raises(ValueError, _ch_neighbor_connectivity, ch_names, neighbors)
connectivity, ch_names = read_ch_connectivity('neuromag306mag')
assert_equal(connectivity.shape, (102, 102))
assert_equal(len(ch_names), 102)
pytest.raises(ValueError, read_ch_connectivity, 'bananas!')
# In EGI 256, E31 sensor has no neighbour
a = partial(np.array)
nbh = np.array([[(['E31'], []),
(['E1'], [[a(['E2'])],
[a(['E3'])]]),
(['E2'], [[a(['E1'])],
[a(['E3'])]]),
(['E3'], [[a(['E1'])],
[a(['E2'])]])]],
dtype=[('label', 'O'), ('neighblabel', 'O')])
mat = dict(neighbours=nbh)
mat_fname = op.join(tempdir, 'test_isolated_mat.mat')
savemat(mat_fname, mat, oned_as='row')
ch_connectivity, ch_names = read_ch_connectivity(mat_fname)
x = ch_connectivity.todense()
assert_equal(x.shape[0], len(ch_names))
assert_equal(x.shape, (4, 4))
assert np.all(x.diagonal())
assert not np.any(x[0, 1:])
assert not np.any(x[1:, 0])
# Check for neighbours consistency. If a sensor is marked as a neighbour,
# then it should also have its neighbours defined.
a = partial(np.array)
nbh = np.array([[(['E31'], []),
(['E1'], [[a(['E8'])],
[a(['E3'])]]),
(['E2'], [[a(['E1'])],
[a(['E3'])]]),
(['E3'], [[a(['E1'])],
[a(['E2'])]])]],
dtype=[('label', 'O'), ('neighblabel', 'O')])
mat = dict(neighbours=nbh)
mat_fname = op.join(tempdir, 'test_error_mat.mat')
savemat(mat_fname, mat, oned_as='row')
pytest.raises(ValueError, read_ch_connectivity, mat_fname)
def test_get_set_sensor_positions():
"""Test get/set functions for sensor positions."""
raw1 = read_raw_fif(raw_fname)
picks = pick_types(raw1.info, meg=False, eeg=True)
pos = np.array([ch['loc'][:3] for ch in raw1.info['chs']])[picks]
raw_pos = raw1._get_channel_positions(picks=picks)
assert_array_equal(raw_pos, pos)
ch_name = raw1.info['ch_names'][13]
pytest.raises(ValueError, raw1._set_channel_positions, [1, 2], ['name'])
raw2 = read_raw_fif(raw_fname)
raw2.info['chs'][13]['loc'][:3] = np.array([1, 2, 3])
raw1._set_channel_positions([[1, 2, 3]], [ch_name])
assert_array_equal(raw1.info['chs'][13]['loc'],
raw2.info['chs'][13]['loc'])
@testing.requires_testing_data
def test_1020_selection():
"""Test making a 10/20 selection dict."""
base_dir = op.join(testing.data_path(download=False), 'EEGLAB')
raw_fname = op.join(base_dir, 'test_raw.set')
loc_fname = op.join(base_dir, 'test_chans.locs')
with pytest.warns(RuntimeWarning, match='Events .* dropped'):
raw = read_raw_eeglab(raw_fname, montage=loc_fname)
for input in ("a_string", 100, raw, [1, 2]):
pytest.raises(TypeError, make_1020_channel_selections, input)
sels = make_1020_channel_selections(raw.info)
# are all frontal channels placed before all occipital channels?
for name, picks in sels.items():
fs = min([ii for ii, pick in enumerate(picks)
if raw.ch_names[pick].startswith("F")])
ps = max([ii for ii, pick in enumerate(picks)
if raw.ch_names[pick].startswith("O")])
assert fs > ps
# are channels in the correct selection?
fz_c3_c4 = [raw.ch_names.index(ch) for ch in ("Fz", "C3", "C4")]
for channel, roi in zip(fz_c3_c4, ("Midline", "Left", "Right")):
assert channel in sels[roi]
@testing.requires_testing_data
def test_find_ch_connectivity():
"""Test computing the connectivity matrix."""
data_path = testing.data_path()
raw = read_raw_fif(raw_fname, preload=True)
sizes = {'mag': 828, 'grad': 1700, 'eeg': 386}
nchans = {'mag': 102, 'grad': 204, 'eeg': 60}
for ch_type in ['mag', 'grad', 'eeg']:
conn, ch_names = find_ch_connectivity(raw.info, ch_type)
# Silly test for checking the number of neighbors.
assert_equal(conn.getnnz(), sizes[ch_type])
assert_equal(len(ch_names), nchans[ch_type])
pytest.raises(ValueError, find_ch_connectivity, raw.info, None)
# Test computing the conn matrix with gradiometers.
conn, ch_names = _compute_ch_connectivity(raw.info, 'grad')
assert_equal(conn.getnnz(), 2680)
# Test ch_type=None.
raw.pick_types(meg='mag')
find_ch_connectivity(raw.info, None)
bti_fname = op.join(data_path, 'BTi', 'erm_HFH', 'c,rfDC')
bti_config_name = op.join(data_path, 'BTi', 'erm_HFH', 'config')
raw = read_raw_bti(bti_fname, bti_config_name, None)
_, ch_names = find_ch_connectivity(raw.info, 'mag')
assert 'A1' in ch_names
ctf_fname = op.join(data_path, 'CTF', 'testdata_ctf_short.ds')
raw = read_raw_ctf(ctf_fname)
_, ch_names = find_ch_connectivity(raw.info, 'mag')
assert 'MLC11' in ch_names
pytest.raises(ValueError, find_ch_connectivity, raw.info, 'eog')
run_tests_if_main()
|
