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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import numpy as np
import pytest as pytest
from numpy.testing import assert_allclose
from mne.datasets import testing
from mne.datasets.testing import data_path
from mne.io import BaseRaw, read_raw_nirx
from mne.preprocessing.nirs import optical_density
from mne.utils import _validate_type
fname_nirx = (
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]), 0.0)
assert_allclose(od.get_data([5])[0, :2], [0.69, -0.4], atol=test_tol)
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