skinoptics.absorption_coefficient module¶
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- skinoptics.absorption_coefficient.Cmass_from_Cmolar(Cmolar, molar_mass)¶
Calculate the mass concentration from the molar concentration and the molar mass.
\(C_{mass} = M \mbox{ } C_{molar}\)
- Parameters:
Cmolar (float or np.ndarray) – molar concentration [M]
molar_mass (float) – molar mass [g mol^-1]
- Returns:
Cmass (float or np.ndarray) – mass concentration [g L^-1]
- skinoptics.absorption_coefficient.Cmolar_from_Cmass(Cmass, molar_mass)¶
Calculate the molar concentration from the mass concentration and the molar mass.
\(C_{molar} = \frac{C_{mass}}{M}\)
- Parameters:
Cmass (float or np.ndarray) – mass concentration [g L^-1]
molar_mass (float) – molar mass [g mol^-1]
- Returns:
Cmolar (float or np.ndarray) – molar concentration [M]
- skinoptics.absorption_coefficient.ext_eum_Sarna(lambda0)¶
- The extinction coefficient of EUMELANIN in phosphate buffer as a function of wavelength.Linear interpolation of data from Sarna & Swartz 2006 [SS06] (see their Fig. 16.3-a)graphically deduced by Jacques and publicly available atwavelength range: [210 nm, 820 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
ext (float or np.ndarray) – extinction coefficient [cm^-1 mL mg^-1]
- skinoptics.absorption_coefficient.ext_from_Abs_and_Cmass(Abs, Cmass, pathlength)¶
- Calculate the extinction coefficient from the absorbance, the mass concentrationand the pathlength.
\(\varepsilon_{mass}(\lambda) = \frac{Abs(\lambda)}{L \mbox{ } C_{mass}}\)
- Parameters:
Abs (float or np.ndarray) – absorbance [-]
Cmass (float) – mass concentration [g L^-1]
pathlength (float) – pathlength [cm]
- Returns:
ext (float or np.ndarray) – extinction coefficient [cm^-1 mL mg^-1]
- skinoptics.absorption_coefficient.ext_from_molarext(molarext, molar_mass)¶
- Calculate the extinction coefficient from the molar extinction coefficientand the molar mass.
\(\varepsilon_{mass}(\lambda) = \frac{\varepsilon_{molar}(\lambda)}{M}\)
- Parameters:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
molar_mass (float) – molar mass [g mol^-1]
- Returns:
ext (float or np.ndarray) – extinction coefficient [cm^-1 mL mg^-1]
- skinoptics.absorption_coefficient.ext_from_mua_and_Cmass(mua, Cmass)¶
- Calculate the extinction coefficient from the absorption coefficientand the mass concentration.For details please check Jacques 2013 [J13].
\(\varepsilon_{mass}(\lambda) = \frac{1}{\mbox{ln}(10)}\frac{\mu_a(\lambda)}{C_{mass}}\)
- Parameters:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
Cmass (float) – mass concentration [g L^-1]
- Returns:
ext (float or np.ndarray) – extinction coefficient [cm^-1 mL mg^-1]
- skinoptics.absorption_coefficient.ext_phe_Sarna(lambda0)¶
- The extinction coefficient of PHEOMELANIN in phosphate buffer as a function of wavelength.Linear interpolation of data from Sarna & Swartz 2006 [SS06] (see their Fig. 16.3-a)graphically deduced by Jacques and publicly available atwavelength range: [210 nm, 820 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
ext (float or np.ndarray) – extinction coefficient [cm^-1 mL mg^-1]
- skinoptics.absorption_coefficient.k_from_mua(mua, lambda0)¶
- Calculate the imaginary part of the complex refractive index from the absorption coefficientand the wavelength.For details please check Hecht 2002 [H02], Jacques 2013 [J13] and Griffiths 2017 [G17].
\(k(\lambda) = \frac{\mu_a(\lambda)}{4\pi}\lambda\)
- Parameters:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
k (float or np.ndarray) – imaginary part of the complex refractive index [-]
- skinoptics.absorption_coefficient.k_wat_Hale(lambda0)¶
- The imaginary part of the complex refractive index of WATER as a function of wavelength.Linear interpolation of data from Hale & Querry 1973 [HQ73] (see their Table I).wavelength range: [200 nm, 200 μm]temperature: 25 ºC
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
k (float or np.ndarray) – imaginary part of the complex refractive index [-]
- skinoptics.absorption_coefficient.k_wat_Segelstein(lambda0)¶
- The imaginary part of the complex refractive index of WATER as a function of wavelength.Linear interpolation of data from D. J. Segelstein’s M.S. Thesis 1981 [S81] collectedby S. Prahl and publicly available at <https://omlc.org/spectra/water/abs/index.html>.wavelength range: [10 nm, 10 m]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
k (float or np.ndarray) – imaginary part of the complex refractive index [-]
- skinoptics.absorption_coefficient.molarext_bil_Li(lambda0)¶
- The molar extinction coefficient of BILIRUBIN in chloroform as a function of wavelength.Linear interpolation of experimental data obtained with a Cary 3 by J. Li on 1997,scaled to match 55,000 cm^-1 M^-1 at 450.8 nm [AF90] and publicly available by S. PrahlThe data is also available at PhotochemCAD [TL23]wavelength range: [239.75 nm, 700 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
- skinoptics.absorption_coefficient.molarext_deo_Prahl(lambda0)¶
- The molar extinction coefficient for DEOXYHEMOGLOBIN in water as a function of wavelength.Linear interpolation of data from various sources compiled by S. Prahl and publiclyavailable at <https://omlc.org/spectra/hemoglobin/>.wavelength range: [250 nm, 1000 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
- skinoptics.absorption_coefficient.molarext_eum_Sarna(lambda0)¶
- The molar extinction coefficient of EUMELANIN in phosphate buffer as a function of wavelength.Linear interpolation of data from Sarna & Swartz 2006 [SS06] (see their Fig. 16.3-a)graphically deduced by Jacques and publicly available atwavelength range: [210 nm, 820 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
- skinoptics.absorption_coefficient.molarext_from_Abs_and_Cmolar(Abs, Cmolar, pathlength)¶
- Calculate the molar extinction coefficient from the absorbance, the molar concentrationand the pathlength.
\(\varepsilon_{molar}(\lambda) = \frac{Abs(\lambda)}{L \mbox{ } C_{molar}}\)
- Parameters:
Abs (float or np.ndarray) – absorbance [-]
Cmolar (float) – molar concentration [g L^-1]
pathlength (float) – pathlength [cm]
- Returns:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
- skinoptics.absorption_coefficient.molarext_from_ext(ext, molar_mass)¶
- Calculate the molar extinction coefficient from the extinction coefficientand the molar mass.
\(\varepsilon_{molar}(\lambda) = M \mbox{ } \varepsilon_{mass}(\lambda)\)
- Parameters:
ext (float or np.ndarray) – extinction coefficient [cm^-1 mL mg^-1]
molar_mass (float) – molar mass [g mol^-1]
- Returns:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
- skinoptics.absorption_coefficient.molarext_from_mua_Cmolar(mua, Cmolar)¶
- Calculate the molar extinction coefficient from the absorption coefficientand the molar concentration.For details please check Jacques 2013 [J13].
\(\varepsilon_{molar}(\lambda) = \frac{1}{\mbox{ln}(10)}\frac{\mu_a(\lambda)}{C_{molar}}\)
- Parameters:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
Cmolar (float) – molar concentration [M]
- Returns:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
- skinoptics.absorption_coefficient.molarext_oxy_Prahl(lambda0)¶
- The molar extinction coefficient of OXYHEMOGLOBIN in water as a function of wavelength.Linear interpolation of data from various sources compiled by S. Prahl and publiclyavailable at <https://omlc.org/spectra/hemoglobin/>.wavelength range: [250 nm, 1000 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
- skinoptics.absorption_coefficient.molarext_phe_Sarna(lambda0)¶
- The molar extinction coefficient of PHEOMELANIN in phosphate buffer as a function of wavelength.Linear interpolation of data from Sarna & Swartz 2006 [SS06] (see their Fig. 16.3-a)graphically deduced by Jacques and publicly available atwavelength range: [210 nm, 820 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
- skinoptics.absorption_coefficient.mua_DE_Salomatina(lambda0)¶
- The absoption coefficient of human DERMIS as a function of wavelength.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [370 nm, 1600 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_EP_Salomatina(lambda0)¶
- The absoption coefficient of human EPIDERMIS as a function of wavelength.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [370 nm, 1600 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_HY_Salomatina(lambda0)¶
- The absoption coefficient of human HYPODERMIS as a function of wavelength.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [374 nm, 1600 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_SCC_Salomatina(lambda0)¶
- The absoption coefficient of SQUAMOUS CELL CARCINOMA as a function of wavelength.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [370 nm, 1600 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_baseline(lambda0)¶
- The baseline absorption coefficient as a function of wavelength.Equation proposed by S. Jacques based on data for bloodless rat skin.For details please check <https://omlc.org/news/jan98/skinoptics.html>.
\(\mu_a^{bas}(\lambda) = 0.0244 + 8.53\mbox{ exp}(-(\lambda-154)/66.2)\)
wavelength range: [350 nm, 1100 nm]- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_baseline2(lambda0)¶
- The baseline absorption coefficient as a function of wavelength.Equation based on data for neonatal skin.For details please check <https://omlc.org/news/jan98/skinoptics.html>.
\(\mu_a^{bas}(\lambda) = 7.84 \times 10^7 \times \lambda^{-3.255}\)
wavelength range: [450 nm, 750 nm]- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_bil_Li(lambda0, Cmass_bil, molar_mass_bil=585)¶
- The absorption coefficient of BILIRUBIN in chloroform as a function of wavelength.Calculated from
skinoptics.absorption_coefficient.molarext_bil_Li()
for a specificbilirubin mass concentration.wavelength range: [239.75 nm, 700 nm]- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
Cmass_bil (float) – bilirubin mass concentration [g/L]
molarmass_bil (float) – molar mass of bilirubin [g/mol] (default to 585. [DJV11])
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_deo_Bosschaart(lambda0)¶
- The absorption coefficient of DEOXIGENIZED BLOOD (saturation = 0%) as a function of wavelength.Linear interpolation of data from Bosschaart et. al. 2014 [B*14].wavelength range: [251 nm, 1995 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_deo_Prahl(lambda0, Cmass_deo=150, molar_mass_deo=64500)¶
- The absorption coefficient of DEOXYHEMOGLOBIN in water as a function of wavelength.Calculated from
skinoptics.absorption_coefficient.molarext_deo_Prahl()
for a specificdeoxyhemoglobin mass concentration.wavelength range: [250 nm, 1000 nm]- Parameters:
lambda0 (float or np.ndarray.) – wavelength [nm]
Cmass_oxy (float) – deoxyhemoglobin mass concentration [g/L] (default to 150. [S*23])
molar_mass_deo (float) – molar mass of deoxyhemoglobin [g/mol] (default to 64500. [B90])
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_fat_vanVeen(lambda0)¶
- The absorption coefficient of (pig lard) FAT as a function of wavelength.Linear interpolation of data from van Veen et al. 2005 [v*05] collected and processedby S. Prahl and publicly available at <https://omlc.org/spectra/fat/>.wavelength range: [429 nm, 1098 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_from_ext_and_Cmass(ext, Cmass)¶
- Calculate the absorption coefficient from the extinction coefficient and the mass concentration.For details please check Jacques 2013 [J13].
\(\mu_a(\lambda) = \mbox{ln}(10) \mbox{ } C_{mass} \mbox{ } \varepsilon_{mass}(\lambda)\)
- Parameters:
ext (float or np.ndarray) – extinction coefficient [cm^-1 mL mg^-1]
Cmass (float) – mass concentration [g L^-1]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_from_k(k, lambda0)¶
- Calculate the absorption coefficient from the imaginary part of the complex refractive indexand the wavelength.For details please check Hecht 2002 [H02], Jacques 2013 [J13] and Griffiths 2017 [G17].
\(\mu_a(\lambda) = 4\pi \frac{k(\lambda)}{\lambda}\)
- Parameters:
k (float or np.ndarray) – imaginary part of the complex refractive index [-]
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_from_molarext_and_Cmolar(molarext, Cmolar)¶
- Calculate the absorption coefficient from the molar extinction coefficientand the molar concentration.For details please check Jacques 2013 [J13].
\(\mu_a(\lambda) = \mbox{ln}(10) \mbox{ } C_{molar} \mbox{ } \varepsilon_{molar}(\lambda)\)
- Parameters:
molarext (float or np.ndarray) – molar extinction coefficient [cm^-1 M^-1]
Cmolar (float) – molar concentration [M]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_iBCC_Salomatina(lambda0)¶
- The absoption coefficient of INFILTRATIVE BASAL CELL CARCINOMA as a function of wavelength.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [370 nm, 1600 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_mel_Jacques(lambda0)¶
- The absoption coefficient of a MELANOSOME as a function of wavelength.Equation proposed by S. Jacques based on data from various sources.For details please check <https://omlc.org/news/jan98/skinoptics.html>.
\(\mu_a^{mel} (\lambda) = 6.6 \times 10^{10} \times \lambda^{-3.33}\)
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_nBCC_Salomatina(lambda0)¶
- The absoption coefficient of NODULAR BASAL CELL CARCINOMA as a function of wavelength.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [370 nm, 1600 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_oxy_Bosschaart(lambda0)¶
- The absorption coefficient of OXYGENIZED BLOOD (saturation > 98%) as a function of wavelength.Linear interpolation of data from Bosschaart et. al. 2014 [B*14].wavelength range: [251 nm, 1995 nm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_oxy_Prahl(lambda0, Cmass_oxy=150, molar_mass_oxy=64500)¶
- The absorption coefficient of OXYHEMOGLOBIN in water as a function of wavelength.Calculated from
skinoptics.absorption_coefficient.molarext_oxy_Prahl()
for a specificoxyhemoglobin mass concentration.wavelength range: [250 nm, 1000 nm]- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
Cmass_oxy (float) – oxyhemoglobin mass concentration [g/L] (default to 150. [S*23])
molar_mass_oxy (float) – molar mass of oxyhemoglobin [g/mol] (default to 64500. [B90])
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_wat_Hale(lambda0)¶
- The absorption coefficient of WATER as a function of wavelength.Linear interpolation of data from Hale & Querry 1973 [HQ73] collected and processedby S. Prahl and publicly available at <https://omlc.org/spectra/water/abs/index.html>.
wavelength range: [200 nm, 200 μm]
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.mua_wat_Segelstein(lambda0)¶
- The absorption coefficient of WATER as a function of wavelength.Linear interpolation of data from D. J. Segelstein’s M.S. Thesis 1981 [S81],collected by S. Prahl and publicly available at <https://omlc.org/spectra/water/abs/index.html>.wavelength range: [10 nm, 10 m].
- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
mua (float or np.ndarray) – absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.std_mua_DE_Salomatina(lambda0)¶
- The standard deviation respective to
skinoptics.absorption_coefficient.mua_DE_Salomatina()
.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [370 nm, 1600 nm]- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
std_mua (float or np.ndarray) – standard deviation of the absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.std_mua_EP_Salomatina(lambda0)¶
- The standard deviation respective to
skinoptics.absorption_coefficient.mua_EP_Salomatina()
.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [370 nm, 1600 nm]- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
std_mua (float or np.ndarray) – standard deviation of the absorption coefficient [mm^-1]
- skinoptics.absorption_coefficient.std_mua_HY_Salomatina(lambda0)¶
- The standard deviation respective to
skinoptics.absorption_coefficient.mua_HY_Salomatina()
.Linear interpolation of experimental data from Salomatina et al. 2006 [S*06],publicly available at <https://sites.uml.edu/abl/optical-properties-2/>.wavelength range: [370 nm, 1600 nm]- Parameters:
lambda0 (float or np.ndarray) – wavelength [nm]
- Returns:
std_mua (float or np.ndarray) – standard deviation of the absorption coefficient [mm^-1]