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
|
# Authors: Robert Luke <mail@robertluke.net>
# Eric Larson <larson.eric.d@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
import os.path as op
import pytest as pytest
import numpy as np
from numpy.testing import assert_allclose
from mne.datasets.testing import data_path
from mne.io import read_raw_nirx, BaseRaw
from mne.preprocessing.nirs import optical_density
from mne.utils import _validate_type
from mne.datasets import testing
fname_nirx = op.join(data_path(download=False),
'NIRx', 'nirscout', 'nirx_15_2_recording_w_short')
@testing.requires_testing_data
def test_optical_density():
"""Test return type for optical density."""
raw = read_raw_nirx(fname_nirx, preload=False)
assert 'fnirs_cw_amplitude' in raw
assert 'fnirs_od' not in raw
raw = optical_density(raw)
_validate_type(raw, BaseRaw, 'raw')
assert 'fnirs_cw_amplitude' not in raw
assert 'fnirs_od' in raw
with pytest.raises(RuntimeError, match='on continuous wave'):
optical_density(raw)
@testing.requires_testing_data
def test_optical_density_zeromean():
"""Test that optical density can process zero mean data."""
raw = read_raw_nirx(fname_nirx, preload=True)
raw._data[4] -= np.mean(raw._data[4])
raw._data[4, -1] = 0
with np.errstate(invalid='raise', divide='raise'):
with pytest.warns(RuntimeWarning, match='Negative'):
raw = optical_density(raw)
assert 'fnirs_od' in raw
@testing.requires_testing_data
def test_optical_density_manual():
"""Test optical density on known values."""
test_tol = 0.01
raw = read_raw_nirx(fname_nirx, preload=True)
# log(1) = 0
raw._data[4] = np.ones((145))
# log(0.5)/-1 = 0.69
# log(1.5)/-1 = -0.40
test_data = np.tile([0.5, 1.5], 73)[:145]
raw._data[5] = test_data
od = optical_density(raw)
assert_allclose(od.get_data([4]), 0.)
assert_allclose(od.get_data([5])[0, :2], [0.69, -0.4], atol=test_tol)
|
