/// <summary>
/// Constructor to create the chromophore spectrum
/// </summary>
/// <param name="wavelengths">A list of wavelengths</param>
/// <param name="spectrum">A list of spectral values</param>
/// <param name="name">The name of the chromophore absorber</param>
/// <param name="coeffType">The chromophore coefficient type</param>
/// <param name="absUnits">The absorption coefficient units</param>
/// <param name="molarUnit">The molar units</param>
/// <param name="wavelengthUnit">The wavelength units</param>
public ChromophoreSpectrum(List <double> wavelengths, List <double> spectrum, string name, ChromophoreCoefficientType coeffType, AbsorptionCoefficientUnit absUnits, MolarUnit molarUnit, WavelengthUnit wavelengthUnit)
{
ChromophoreCoefficientType = coeffType;
AbsorptionCoefficientUnit = absUnits;
WavelengthUnit = wavelengthUnit;
MolarUnit = molarUnit;
Name = name;
Spectrum = spectrum;
Wavelengths = wavelengths;
}
private ChromophoreSpectrum CreateChromophoreSpectrum()
{
string name = "Melanin";
AbsorptionCoefficientUnit muaUnit = AbsorptionCoefficientUnit.InverseMillimeters;
MolarUnit molarUnit = MolarUnit.None;
ChromophoreCoefficientType coeffType = ChromophoreCoefficientType.FractionalAbsorptionCoefficient;
// populate list of wavelengths
List <double> wavelengths = new List <double>();
wavelengths.Add(0.0);
wavelengths.Add(1.0);
wavelengths.Add(2.0);
// populate list of values
List <double> values = new List <double>();
values.Add(0.1);
values.Add(1.1);
values.Add(2.1);
return(new ChromophoreSpectrum(wavelengths, values, name, coeffType, muaUnit, molarUnit, WavelengthUnit.Nanometers));
}
private ChromophoreSpectrumDictionary CreateDictionary()
{
string name = "Melanin";
AbsorptionCoefficientUnit muaUnit = AbsorptionCoefficientUnit.InverseMillimeters;
MolarUnit molarUnit = MolarUnit.MicroMolar;
ChromophoreCoefficientType coeffType = ChromophoreCoefficientType.FractionalAbsorptionCoefficient;
// populate list of wavelengths
List <double> wavelengths = new List <double>();
wavelengths.Add(0.0);
wavelengths.Add(1.0);
wavelengths.Add(2.0);
// populate list of values
List <double> values = new List <double>();
values.Add(0.1);
values.Add(1.1);
values.Add(2.1);
ChromophoreSpectrum chromophoreSpectrum = new ChromophoreSpectrum(wavelengths, values, name, coeffType, muaUnit, molarUnit, WavelengthUnit.Nanometers);
var testDictionary = new ChromophoreSpectrumDictionary();
testDictionary.Add(chromophoreSpectrum.Name, chromophoreSpectrum);
name = "HbO2";
muaUnit = AbsorptionCoefficientUnit.InverseMillimeters;
molarUnit = MolarUnit.MicroMolar;
coeffType = ChromophoreCoefficientType.MolarAbsorptionCoefficient;
chromophoreSpectrum = new ChromophoreSpectrum(wavelengths, values, name, coeffType, muaUnit, molarUnit, WavelengthUnit.Nanometers);
testDictionary.Add(chromophoreSpectrum.Name, chromophoreSpectrum);
return(testDictionary);
}
/// <summary>
/// Method to convert coefficient values
/// </summary>
/// <param name="CoefficientValue">The coefficient value to convert</param>
/// <param name="Unit">An enum representing the units of the value to convert</param>
/// <param name="MolarUnit">An enum to represent a molar based coefficient</param>
/// <returns>The converted value as a double</returns>
public static double ConvertCoefficient(this double CoefficientValue, AbsorptionCoefficientUnit Unit, MolarUnit MolarUnit)
{
double coeff;
switch (Unit)
{
case AbsorptionCoefficientUnit.InverseMillimeters:
default:
coeff = CoefficientValue;
break;
case AbsorptionCoefficientUnit.InverseMeters:
coeff = CoefficientValue / 1000; //10^3
break;
case AbsorptionCoefficientUnit.InverseCentimeters:
coeff = CoefficientValue / 10;
break;
case AbsorptionCoefficientUnit.InverseMicrometers:
coeff = CoefficientValue * 1000; //10^3
break;
}
//molar coefficient applied
switch (MolarUnit)
{
case MolarUnit.MicroMolar:
default:
return(coeff);
case MolarUnit.MilliMolar:
return(coeff / 1000); //10^3
case MolarUnit.Molar:
return(coeff / 1000000); //10^6
case MolarUnit.NanoMolar:
return(coeff * 1000);
}
}
/// <summary>
/// Passes the molar unit enum and the absorption coefficient unit enum and returns it as a string
/// </summary>
/// <param name="molarUnit">The molar unit enum</param>
/// <param name="absorptionCoefficientUnit">an absorption coefficient enum</param>
/// <returns>A string representing the molar units</returns>
public static string getSpectralUnit(MolarUnit molarUnit, AbsorptionCoefficientUnit absorptionCoefficientUnit)
{
string mU;
string aCU;
string sU;
switch (molarUnit)
{
case MolarUnit.None:
mU = "";
break;
case MolarUnit.Molar:
mU = "M";
break;
case MolarUnit.MilliMolar:
mU = "mM";
break;
case MolarUnit.MicroMolar:
mU = "uM";
break;
case MolarUnit.NanoMolar:
mU = "nM";
break;
default:
throw new Exception("Unknown molar unit");
}
switch (absorptionCoefficientUnit)
{
case AbsorptionCoefficientUnit.InverseCentimeters:
aCU = "cm";
break;
case AbsorptionCoefficientUnit.InverseMeters:
aCU = "m";
break;
case AbsorptionCoefficientUnit.InverseMicrometers:
aCU = "um";
break;
case AbsorptionCoefficientUnit.InverseMillimeters:
aCU = "mm";
break;
default:
throw new Exception("Unknown absorption coefficient unit");
}
if (molarUnit == MolarUnit.None)
{
sU = "1/" + aCU;
}
else
{
sU = "1/(" + aCU + "*" + mU + ")";
}
return(sU);
}
/// <summary>
/// Constructor to create the chromophore spectrum starting with empty lists
/// </summary>
/// <param name="name">The name of the chromophore absorber</param>
/// <param name="coeffType">The chromophore coefficient type</param>
/// <param name="absUnits">The absorption coefficient units</param>
/// <param name="molarUnit">The molar units</param>
/// <param name="wavelengthUnit">The wavelength units</param>
public ChromophoreSpectrum(string name, ChromophoreCoefficientType coeffType, AbsorptionCoefficientUnit absUnits, MolarUnit molarUnit, WavelengthUnit wavelengthUnit)
: this(new List <double>(), new List <double>(), name, coeffType, absUnits, molarUnit, wavelengthUnit)
{
}
