cedalion.nirs.cw

Functionality for continous wave NIRS.

Functions

`beer_lambert`(amplitudes, geo3d, dpf[, spectrum])	Calculate concentration changes from amplitude using the modified BL law.
`conc2od`(conc, geo3d, dpf[, spectrum])	Calculate optical density data from concentration changes.
`int2od`(amplitudes[, return_baseline])	Calculate optical density from intensity amplitude data.
`od2conc`(od, geo3d, dpf[, spectrum])	Calculate concentration changes from optical density data.
`od2int`(od, baseline)	Recover intensity amplitude data from optical density data.

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

Calculate optical density from intensity amplitude data.

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 DO.

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.

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 using the modified BL law.

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 mBLL.

Return type:

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