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
|
# -*- coding: utf-8 -*-
import os
from os import path as op
import shutil
import glob
import pytest
from numpy.testing import assert_equal, assert_allclose
import matplotlib
from mne import concatenate_raws, read_bem_surfaces
from mne.commands import (mne_browse_raw, mne_bti2fiff, mne_clean_eog_ecg,
mne_compute_proj_ecg, mne_compute_proj_eog,
mne_coreg, mne_kit2fiff,
mne_make_scalp_surfaces, mne_maxfilter,
mne_report, mne_surf2bem, mne_watershed_bem,
mne_compare_fiff, mne_flash_bem, mne_show_fiff,
mne_show_info)
from mne.datasets import testing, sample
from mne.io import read_raw_fif
from mne.utils import (run_tests_if_main, _TempDir, requires_mne,
requires_mayavi, requires_tvtk, requires_freesurfer,
traits_test, ArgvSetter)
matplotlib.use('Agg')
base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
raw_fname = op.join(base_dir, 'test_raw.fif')
subjects_dir = op.join(testing.data_path(download=False), 'subjects')
def check_usage(module, force_help=False):
"""Ensure we print usage."""
args = ('--help',) if force_help else ()
with ArgvSetter(args) as out:
try:
module.run()
except SystemExit:
pass
assert 'Usage: ' in out.stdout.getvalue()
@pytest.mark.slowtest
def test_browse_raw():
"""Test mne browse_raw."""
check_usage(mne_browse_raw)
with ArgvSetter(('--raw', raw_fname)):
with pytest.warns(None): # mpl show warning sometimes
mne_browse_raw.run()
def test_bti2fiff():
"""Test mne bti2fiff."""
check_usage(mne_bti2fiff)
def test_compare_fiff():
"""Test mne compare_fiff."""
check_usage(mne_compare_fiff)
def test_show_fiff():
"""Test mne compare_fiff."""
check_usage(mne_show_fiff)
with ArgvSetter((raw_fname,)):
mne_show_fiff.run()
with ArgvSetter((raw_fname, '--tag=102')):
mne_show_fiff.run()
@requires_mne
def test_clean_eog_ecg():
"""Test mne clean_eog_ecg."""
check_usage(mne_clean_eog_ecg)
tempdir = _TempDir()
raw = concatenate_raws([read_raw_fif(f)
for f in [raw_fname, raw_fname, raw_fname]])
raw.info['bads'] = ['MEG 2443']
use_fname = op.join(tempdir, op.basename(raw_fname))
raw.save(use_fname)
with ArgvSetter(('-i', use_fname, '--quiet')):
mne_clean_eog_ecg.run()
fnames = glob.glob(op.join(tempdir, '*proj.fif'))
assert len(fnames) == 2 # two projs
fnames = glob.glob(op.join(tempdir, '*-eve.fif'))
assert len(fnames) == 3 # raw plus two projs
@pytest.mark.slowtest
def test_compute_proj_ecg_eog():
"""Test mne compute_proj_ecg/eog."""
for fun in (mne_compute_proj_ecg, mne_compute_proj_eog):
check_usage(fun)
tempdir = _TempDir()
use_fname = op.join(tempdir, op.basename(raw_fname))
bad_fname = op.join(tempdir, 'bads.txt')
with open(bad_fname, 'w') as fid:
fid.write('MEG 2443\n')
shutil.copyfile(raw_fname, use_fname)
with ArgvSetter(('-i', use_fname, '--bad=' + bad_fname,
'--rej-eeg', '150')):
with pytest.warns(None): # samples, sometimes
fun.run()
fnames = glob.glob(op.join(tempdir, '*proj.fif'))
assert len(fnames) == 1
fnames = glob.glob(op.join(tempdir, '*-eve.fif'))
assert len(fnames) == 1
def test_coreg():
"""Test mne coreg."""
assert hasattr(mne_coreg, 'run')
def test_kit2fiff():
"""Test mne kit2fiff."""
# Can't check
check_usage(mne_kit2fiff, force_help=True)
@requires_tvtk
@testing.requires_testing_data
def test_make_scalp_surfaces():
"""Test mne make_scalp_surfaces."""
check_usage(mne_make_scalp_surfaces)
# Copy necessary files to avoid FreeSurfer call
tempdir = _TempDir()
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, 'sample', 'bem')
os.mkdir(subj_dir)
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
orig_fs = os.getenv('FREESURFER_HOME', None)
if orig_fs is not None:
del os.environ['FREESURFER_HOME']
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
os.environ['_MNE_TESTING_SCALP'] = 'true'
dense_fname = op.join(subj_dir, 'sample-head-dense.fif')
medium_fname = op.join(subj_dir, 'sample-head-medium.fif')
try:
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
pytest.raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['FREESURFER_HOME'] = tempdir # don't actually use it
mne_make_scalp_surfaces.run()
assert op.isfile(dense_fname)
assert op.isfile(medium_fname)
pytest.raises(IOError, mne_make_scalp_surfaces.run) # no overwrite
finally:
if orig_fs is not None:
os.environ['FREESURFER_HOME'] = orig_fs
else:
del os.environ['FREESURFER_HOME']
del os.environ['_MNE_TESTING_SCALP']
# actually check the outputs
head_py = read_bem_surfaces(dense_fname)
assert_equal(len(head_py), 1)
head_py = head_py[0]
head_c = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem',
'sample-head-dense.fif'))[0]
assert_allclose(head_py['rr'], head_c['rr'])
def test_maxfilter():
"""Test mne maxfilter."""
check_usage(mne_maxfilter)
with ArgvSetter(('-i', raw_fname, '--st', '--movecomp', '--linefreq', '60',
'--trans', raw_fname)) as out:
with pytest.warns(RuntimeWarning, match="Don't use"):
os.environ['_MNE_MAXFILTER_TEST'] = 'true'
try:
mne_maxfilter.run()
finally:
del os.environ['_MNE_MAXFILTER_TEST']
for check in ('maxfilter', '-trans', '-movecomp'):
assert check in out.stdout.getvalue(), check
@pytest.mark.slowtest
@requires_mayavi
@traits_test
@testing.requires_testing_data
def test_report():
"""Test mne report."""
check_usage(mne_report)
tempdir = _TempDir()
use_fname = op.join(tempdir, op.basename(raw_fname))
shutil.copyfile(raw_fname, use_fname)
with ArgvSetter(('-p', tempdir, '-i', use_fname, '-d', subjects_dir,
'-s', 'sample', '--no-browser', '-m', '30')):
with pytest.warns(None): # contour levels
mne_report.run()
fnames = glob.glob(op.join(tempdir, '*.html'))
assert len(fnames) == 1
def test_surf2bem():
"""Test mne surf2bem."""
check_usage(mne_surf2bem)
@pytest.mark.slowtest
@pytest.mark.ultraslowtest
@requires_freesurfer
@testing.requires_testing_data
def test_watershed_bem():
"""Test mne watershed bem."""
check_usage(mne_watershed_bem)
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
mridata_path_new = op.join(tempdir, 'sample', 'mri')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(mridata_path_new)
if op.exists(op.join(mridata_path, 'T1')):
shutil.copytree(op.join(mridata_path, 'T1'), op.join(mridata_path_new,
'T1'))
if op.exists(op.join(mridata_path, 'T1.mgz')):
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-o'),
disable_stdout=False, disable_stderr=False):
mne_watershed_bem.run()
@pytest.mark.slowtest
@pytest.mark.ultraslowtest
@requires_freesurfer
@sample.requires_sample_data
def test_flash_bem():
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Using the sample dataset
subjects_dir = op.join(sample.data_path(download=False), 'subjects')
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
mridata_path_new = op.join(tempdir, 'sample', 'mri')
os.makedirs(op.join(mridata_path_new, 'flash'))
os.makedirs(op.join(tempdir, 'sample', 'bem'))
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
shutil.copyfile(op.join(mridata_path, 'brain.mgz'),
op.join(mridata_path_new, 'brain.mgz'))
# Copy the available mri/flash/mef*.mgz files from the dataset
files = glob.glob(op.join(mridata_path, 'flash', 'mef*.mgz'))
for infile in files:
shutil.copyfile(infile, op.join(mridata_path_new, 'flash',
op.basename(infile)))
# Test mne flash_bem with --noconvert option
# (since there are no DICOM Flash images in dataset)
currdir = os.getcwd()
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
disable_stdout=False, disable_stderr=False):
mne_flash_bem.run()
os.chdir(currdir)
def test_show_info():
"""Test mne show_info."""
check_usage(mne_show_info)
with ArgvSetter((raw_fname,)):
mne_show_info.run()
run_tests_if_main()
|
