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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 numpy as np
from ...io import BaseRaw
from ...io.constants import FIFF
from ...utils import _validate_type, warn, verbose
from ..nirs import _validate_nirs_info
@verbose
def optical_density(raw, *, verbose=None):
r"""Convert NIRS raw data to optical density.
Parameters
----------
raw : instance of Raw
The raw data.
%(verbose)s
Returns
-------
raw : instance of Raw
The modified raw instance.
"""
raw = raw.copy().load_data()
_validate_type(raw, BaseRaw, 'raw')
picks = _validate_nirs_info(raw.info, fnirs='cw_amplitude')
# The devices measure light intensity. Negative light intensities should
# not occur. If they do it is likely due to hardware or movement issues.
# Set all negative values to abs(x), this also has the benefit of ensuring
# that the means are all greater than zero for the division below.
if np.any(raw._data[picks] <= 0):
warn("Negative intensities encountered. Setting to abs(x)")
min_ = np.inf
for pi in picks:
np.abs(raw._data[pi], out=raw._data[pi])
min_ = min(min_, raw._data[pi].min() or min_)
# avoid == 0
for pi in picks:
np.maximum(raw._data[pi], min_, out=raw._data[pi])
for pi in picks:
data_mean = np.mean(raw._data[pi])
raw._data[pi] /= data_mean
np.log(raw._data[pi], out=raw._data[pi])
raw._data[pi] *= -1
raw.info['chs'][pi]['coil_type'] = FIFF.FIFFV_COIL_FNIRS_OD
return raw
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