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added Prahl1998 reference and copyright note
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avolu committed Apr 19, 2024
1 parent c11265a commit 32e0a8d
Showing 1 changed file with 15 additions and 2 deletions.
17 changes: 15 additions & 2 deletions src/cedalion/nirs.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ def get_extinction_coefficients(spectrum: str, wavelengths: ArrayLike):
Args:
spectrum (str): The type of spectrum to use. Currently supported options are:
- "prahl": Extinction coefficients based on the Prahl absorption spectrum.
- "prahl": Extinction coefficients based on the Prahl absorption spectrum (Prahl1998).
wavelengths (ArrayLike): An array-like object containing the wavelengths at which
to calculate the extinction coefficients.
Expand All @@ -25,7 +25,20 @@ def get_extinction_coefficients(spectrum: str, wavelengths: ArrayLike):
with units of "mm^-1 / M".
References:
(:cite:t:`Prahl1998`)
(Prahl 1998) - taken from Homer2/3, Copyright 2004 - 2006 - The General Hospital Corporation and President and Fellows of Harvard University.
"These values for the molar extinction coefficient e in [cm-1/(moles/liter)]
were compiled by Scott Prahl (prahl@ece.ogi.edu) using data from
W. B. Gratzer, Med. Res. Council Labs, Holly Hill, London
N. Kollias, Wellman Laboratories, Harvard Medical School, Boston
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
(e) [(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."
"""
if spectrum == "prahl":
with resources.open_text(
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