cedalion.nirs package

Submodules

cedalion.nirs.common module

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

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/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

cedalion.nirs.cw module

Functionality for continous wave NIRS.

cedalion.nirs.cw.int2od(amplitudes: cdt.NDTimeSeries, return_baseline: bool = False)[source]

Calculate optical density from intensity amplitude data.

Computes the log-ratio of intensity relative to its temporal mean, implementing the first step of the modified Beer-Lambert law (Delpy et al. [DCvdZ+88], Villringer and Chance [VC97]).

Parameters:

amplitudes (xr.DataArray, (time, channel, *)) – amplitude data.
return_baseline (bool, optional) – If True, also return the baseline data used for OD conversion (useful to get back to intensity). Defaults to False.

Returns:

(xr.DataArray, (time, channel,*): The optical density data. baseline: (xr.DataArray, (channel, *)): The intensity baseline data

(average time series) used for conversion to OD.

Return type:

od

cedalion.nirs.cw.od2int(od: cdt.NDTimeSeries, baseline: cdt.NDTimeSeries)[source]

Recover intensity amplitude data from optical density data.

Parameters:

od (xr.DataArray, (time, channel, *)) – The optical density data.
baseline (xr.DataArray, (channel, *)) – The intensity baseline data (average time series) that was used for conversion to DO.

Returns:

The amplitude data.

Return type:

amplitudes (xr.DataArray, (time, channel, *))

cedalion.nirs.cw.od2conc( od: cdt.NDTimeSeries, geo3d: cdt.LabeledPoints, dpf: DataArray, spectrum: str = 'prahl', )[source]

Calculate concentration changes from optical density data.

Applies the modified Beer-Lambert law (Delpy et al. [DCvdZ+88], Villringer and Chance [VC97]) to convert optical density changes to haemoglobin concentration changes (HbO, HbR).

Parameters:

od (xr.DataArray, (channel, wavelength, *)) – The optical density data array
geo3d (xr.DataArray) – The 3D coordinates of the optodes.
dpf (xr.DataArray, (wavelength, *)) – The differential pathlength factor data
spectrum (str, optional) – The type of spectrum to use for calculating extinction coefficients. Defaults to “prahl”.

Returns:

A data array containing concentration changes by channel.

Return type:

conc (xr.DataArray, (channel, *))

cedalion.nirs.cw.conc2od( conc: cdt.NDTimeSeries, geo3d: cdt.LabeledPoints, dpf: DataArray, spectrum: str = 'prahl', )[source]

Calculate optical density data from concentration changes.

Parameters:

conc (xr.DataArray, (channel, *)) – The concentration changes by channel.
geo3d (xr.DataArray) – The 3D coordinates of the optodes.
dpf (xr.DataArray, (wavelength, *)) – The differential pathlength factor data.
spectrum (str, optional) – The type of spectrum to use for calculating extinction coefficients. Defaults to “prahl”.

Returns:

A data array containing: optical density data.

Return type:

od (xr.DataArray, (channel, wavelength, *))

cedalion.nirs.cw.beer_lambert( amplitudes: cdt.NDTimeSeries, geo3d: cdt.LabeledPoints, dpf: DataArray, spectrum: str = 'prahl', )[source]

Calculate concentration changes from amplitude via the modified Beer-Lambert law.

Convenience wrapper combining int2od() and od2conc(). Implements the modified Beer-Lambert law (Delpy et al. [DCvdZ+88], Villringer and Chance [VC97]).

Parameters:

amplitudes (xr.DataArray, (channel, wavelength, *)) – The input data array containing the raw intensities.
geo3d (xr.DataArray) – The 3D coordinates of the optodes.
dpf (xr.DataArray, (wavelength,*)) – The differential pathlength factors
spectrum (str, optional) – The type of spectrum to use for calculating extinction coefficients. Defaults to “prahl”.

Returns:

A data array containing: concentration changes according to the modified Beer-Lambert law.

Return type:

conc (xr.DataArray, (channel, *))

cedalion.nirs.fd module

Functionality for frequency-domain NIRS.

cedalion.nirs.td module

Functionality for time-domain NIRS.

Module contents

Functionality to process NIRS data.