cedalion.nirs.common

Shared NIRS utilities: extinction coefficients and channel-distance helpers.

Functions

channel_distances(amplitudes, geo3d)

Calculate distances between channels.

get_extinction_coefficients(spectrum, ...)

Provide a matrix of extinction coefficients from tabulated data.

split_long_short_channels(ts, geo3d[, ...])

Split a time series into two based on channel distances.
cedalion.nirs.common.get_extinction_coefficients(spectrum: str, wavelengths: ArrayLike)[source]

Provide a matrix of extinction coefficients from tabulated data.

Parameters:

  • spectrum –

    The type of spectrum to use. Currently supported options are:

    • "prahl": Molar extinction coefficients compiled by S. A. Prahl (Prahl [Pra98]) from data by W. B. Gratzer (Med. Res. Council Labs, London) and N. Kollias (Harvard Medical School). Tabulated values originally distributed with Homer2/3. Units in the source file are cm⁻¹/(mol/L); cedalion converts to mm⁻¹/M on load.

  • wavelengths – An array-like object containing the wavelengths at which to calculate the extinction coefficients.

Returns:

A matrix of extinction coefficients with dimensions "chromo"

(chromophore, e.g. HbO/HbR) and "wavelength" (e.g. 750, 850, …) in units of mm⁻¹/M.

Return type:

xr.DataArray

Note

To convert this data to absorbance A, multiply by the molar concentration and the pathlength. For example, if x is the number of grams per liter and a 1 cm cuvette is being used, then the absorbance is given by

  1. [(1/cm)/(moles/liter)] (x) [g/liter] (1) [cm]

A = —————————————————

66,500 [g/mole]

using 66,500 as the gram molecular weight of hemoglobin. To convert this data to absorption coefficient in (cm⁻1), multiply by the molar concentration and 2.303, µa = (2.303) e (x g/liter)/(66,500 g Hb/mole) where x is the number of grams per liter. A typical value of x for whole blood is x=150 g Hb/liter.

cedalion.nirs.common.channel_distances(amplitudes: cdt.NDTimeSeries, geo3d: cdt.LabeledPoints)[source]

Calculate distances between channels.

Parameters:

  • amplitudes – A DataArray representing the amplitudes with dimensions (channel, *).

  • geo3d (xr.DataArray) – A DataArray containing the 3D coordinates of the channels with dimensions (channel, pos).

Returns:

A DataArray containing the calculated distances between

source and detector channels. The resulting DataArray has the dimension ‘channel’.

Return type:

dists (xr.DataArray)

cedalion.nirs.common.split_long_short_channels(
ts: cdt.NDTimeSeries,
geo3d: cdt.LabeledPoints,
distance_threshold: cdt.QLength = <Quantity(1.5,
'centimeter')>,
)[source]

Split a time series into two based on channel distances.

Parameters:

  • ts (cdt.NDTimeSeries) – Time series to split.

  • geo3d (cdt.LabeledPoints) – 3D coordinates of the optodes.

  • distance_threshold (Quantity) – Distance threshold for splitting the channels.

Returns:

time series with channel distances >= distance_threshold ts_short : time series with channel distances < distance_threshold

Return type:

ts_long