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# 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
import numpy as np
from mne.datasets.testing import data_path
from mne.io import read_raw_nirx, BaseRaw, read_raw_fif
from mne.preprocessing.nirs import optical_density, beer_lambert_law
from mne.utils import _validate_type, requires_version
from mne.datasets import testing
testing_path = data_path(download=False)
fname_nirx_15_0 = op.join(testing_path,
'NIRx', 'nirscout', 'nirx_15_0_recording')
fname_nirx_15_2 = op.join(testing_path,
'NIRx', 'nirscout', 'nirx_15_2_recording')
fname_nirx_15_2_short = op.join(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)
@requires_version('pymatreader')
@testing.requires_testing_data
def test_beer_lambert_v_matlab():
"""Compare MNE results to MATLAB toolbox."""
from pymatreader import read_mat
raw = read_raw_nirx(fname_nirx_15_0)
raw = optical_density(raw)
raw = beer_lambert_law(raw, ppf=0.121)
raw._data *= 1e6 # Scale to uM for comparison to MATLAB
matlab_fname = op.join(testing_path,
'NIRx', 'nirscout', 'validation',
'nirx_15_0_recording_bl.mat')
matlab_data = 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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