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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import numpy as np
import pytest
from mne.datasets import testing
from mne.datasets.testing import data_path
from mne.io import BaseRaw, read_raw_fif, read_raw_nirx
from mne.preprocessing.nirs import beer_lambert_law, optical_density
from mne.utils import _validate_type
testing_path = data_path(download=False)
fname_nirx_15_0 = testing_path / "NIRx" / "nirscout" / "nirx_15_0_recording"
fname_nirx_15_2 = testing_path / "NIRx" / "nirscout" / "nirx_15_2_recording"
fname_nirx_15_2_short = (
testing_path / "NIRx" / "nirscout" / "nirx_15_2_recording_w_short"
)
@testing.requires_testing_data
@pytest.mark.parametrize(
"fname", ([fname_nirx_15_2_short, fname_nirx_15_2, fname_nirx_15_0])
)
@pytest.mark.parametrize("fmt", ("nirx", "fif"))
def test_beer_lambert(fname, fmt, tmp_path):
"""Test converting NIRX files."""
assert fmt in ("nirx", "fif")
raw = read_raw_nirx(fname)
if fmt == "fif":
raw.save(tmp_path / "test_raw.fif")
raw = read_raw_fif(tmp_path / "test_raw.fif")
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
assert "hbo" not in raw
raw = beer_lambert_law(raw)
_validate_type(raw, BaseRaw, "raw")
assert "fnirs_cw_amplitude" not in raw
assert "fnirs_od" not in raw
assert "hbo" in raw
assert "hbr" in raw
@testing.requires_testing_data
def test_beer_lambert_unordered_errors():
"""NIRS data requires specific ordering and naming of channels."""
raw = read_raw_nirx(fname_nirx_15_0)
raw_od = optical_density(raw)
raw_od.pick([0, 1, 2])
with pytest.raises(ValueError, match="ordered"):
beer_lambert_law(raw_od)
# Test that an error is thrown if channel naming frequency doesn't match
# what is stored in loc[9], which should hold the light frequency too.
raw_od = optical_density(raw)
ch_name = raw.ch_names[0]
assert ch_name == "S1_D1 760"
idx = raw_od.ch_names.index(ch_name)
assert idx == 0
raw_od.info["chs"][idx]["loc"][9] = 770
raw_od.rename_channels({ch_name: ch_name.replace("760", "770")})
assert raw_od.ch_names[0] == "S1_D1 770"
with pytest.raises(ValueError, match="Exactly two frequencies"):
beer_lambert_law(raw_od)
@testing.requires_testing_data
def test_beer_lambert_v_matlab():
"""Compare MNE results to MATLAB toolbox."""
pymatreader = pytest.importorskip("pymatreader")
raw = read_raw_nirx(fname_nirx_15_0)
raw = optical_density(raw)
raw = beer_lambert_law(raw, ppf=(0.121, 0.121))
raw._data *= 1e6 # Scale to uM for comparison to MATLAB
matlab_fname = (
testing_path / "NIRx" / "nirscout" / "validation" / "nirx_15_0_recording_bl.mat"
)
matlab_data = pymatreader.read_mat(matlab_fname)
for idx in range(raw.get_data().shape[0]):
mean_error = np.mean(matlab_data["data"][:, idx] - raw._data[idx])
assert mean_error < 0.1
matlab_name = (
"S"
+ str(int(matlab_data["sources"][idx]))
+ "_D"
+ str(int(matlab_data["detectors"][idx]))
+ " "
+ matlab_data["type"][idx]
)
assert raw.info["ch_names"][idx] == matlab_name
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