static void Main(string[] args)
{
var coefficients = new Coefficients.Coefficients(Directory.GetCurrentDirectory());
var absorption = coefficients.ObtainAbsorptionCoefficients(660);
var scatteringCoefficients = Coefficients.Coefficients.ObtainScatteringCoefficients(660);
var data400 = Scatter.Scatterlight(450, 0.1, 0.3, 0.05, 0.05, 1, 3, 0.150, 0.9, Directory.GetCurrentDirectory());
var data660 = Scatter.Scatterlight(660, 0.1, 0.3, 0.05, 0.05, 1, 3, 0.150, 0.9, Directory.GetCurrentDirectory());
var data900 = Scatter.Scatterlight(900, 0.1, 0.3, 0.05, 0.05, 1, 3, 0.150, 0.9, Directory.GetCurrentDirectory());
var datas = new List <ScatterData>
{
data400,
data660,
data900
};
var wavelengths = new List <int> {
450, 660, 900
};
CalculateRatio(datas, wavelengths);
}
private static double CalculateRatio(List <ScatterData> datas, List <int> waveLengths)
{
var coefficients = new Coefficients.Coefficients(Directory.GetCurrentDirectory());
var R11 = datas[0].DetectedPhotons1 / datas[0].DetectedPhotons2;
var R22 = datas[1].DetectedPhotons1 / datas[1].DetectedPhotons2;
var R33 = datas[2].DetectedPhotons1 / datas[2].DetectedPhotons2;
var R12 = R11 / R22;
var R13 = R11 / R33;
var alpha12 = Math.Log(R12);
var alpha13 = Math.Log(R13);
var alpha1 = coefficients.ObtainAbsorptionCoefficients((uint)waveLengths[0]);
var alpha2 = coefficients.ObtainAbsorptionCoefficients((uint)waveLengths[1]);
var alpha3 = coefficients.ObtainAbsorptionCoefficients((uint)waveLengths[2]);
var alphaD1 = alpha1.AbsorptionBlood;
var alphaD2 = alpha2.AbsorptionBlood;
var alphaD3 = alpha3.AbsorptionBlood;
var alphaO1 = alpha1.AbsorptionOxygenatedBlood;
var alphaO2 = alpha2.AbsorptionOxygenatedBlood;
var alphaO3 = alpha3.AbsorptionOxygenatedBlood;
var topLine = alpha12 * (alphaD3 + alphaD1) - alpha13 * (alphaD1 + alphaD2);
var bottomLine = alpha13 * (alpha1.AbsorptionOxygenatedBlood - alpha2.AbsorptionOxygenatedBlood +
alpha1.AbsorptionBlood - alpha2.AbsorptionBlood) -
alpha12 * (alpha1.AbsorptionOxygenatedBlood + alpha3.AbsorptionOxygenatedBlood -
alpha1.AbsorptionBlood - alpha3.AbsorptionBlood);
var ratio = Math.Sqrt(Math.Pow(topLine / bottomLine, 2));
return(ratio);
}
/// <summary>
/// Calculates scattering through tissue for a specific wavelength
/// </summary>
/// <param name="wavelength">wavelength (nanometers)</param>
/// <param name="distanceToDetector1">Distance to first detector (in cm)</param>
/// <param name="distanceToDetector2">Distance to second detector (in cm) Det2 > Det 1</param>
/// <param name="width">Half width of both the light source and the detectors (cm)</param>
/// <param name="dSkin">Thickness of the skin (cm)</param>
/// <param name="dMuscle">Thickness of the msucle (cm)</param>
/// <param name="dBone">Thickness of the bone. Photons that go trought the bone are dropped</param>
/// <param name="concentrationBlood">Concentration of hemoglobin ~150g/liter</param>
/// <param name="ratioOxygen">Ration of oxygenated to deoxyganted hemoglobin (between 0 and 1)</param>
public static ScatterData Scatterlight(uint wavelength, double distanceToDetector1, double distanceToDetector2,
double width, double dSkin, double dMuscle, double dBone, double concentrationBlood, double ratioOxygen, string resourceBasePath)
{
/*
* We place the two detectors as a ring around the light source
* and bound the model volume by 5*distanceToDetector2
*
* For absorption, each photon is given a starting weight, which is reduced by absorption
*/
double xBound, yBound, zBound;
xBound = yBound = 5.0 * distanceToDetector2;
zBound = dSkin + dMuscle + dBone;
var coefficients = new Coefficients.Coefficients(resourceBasePath);
var scatteringCoefficients = Coefficients.Coefficients.ObtainScatteringCoefficients(wavelength);
var absorptionCoefficients = coefficients.ObtainAbsorptionCoefficients(wavelength);
var absorptionCoefficient = Coefficients.Coefficients.CalculateAbsorptionCoefficient(absorptionCoefficients.AbsorptionBlood,
absorptionCoefficients.AbsorptionOxygenatedBlood, concentrationBlood, ratioOxygen);
// Assume the ares of the light emitter is 0.1 cm^2 and that contact with the skin is not perfect
var numPhotons = 5000000; //5e6
var randomInstance = RandomDistribution.Instance;
var xPos = randomInstance.UniformDistribution(-width, width, numPhotons);
var yPos = randomInstance.UniformDistribution(-width, width, numPhotons);
var zPos = randomInstance.UniformDistribution(0, 1 / scatteringCoefficients.MuSkin, numPhotons);
var distance = new List <double>(numPhotons);
for (int i = 0; i < numPhotons; i++)
{
distance.Add(0);
}
var amplitude = new List <double>(numPhotons);
for (int i = 0; i < numPhotons; i++)
{
amplitude.Add(100);
}
var keepScattering = true;
var idsInModel = new List <int>();
for (int i = 0; i < numPhotons; i++)
{
idsInModel.Add(i);
}
double detectedPhotons1 = 0, detectedPhotons2 = 0;
bool firstD1 = true, firstD2 = true;
List <double> lengthsToD1 = new List <double>();
List <double> lengthsToD2 = new List <double>();
while (keepScattering)
{
// Remove all photons outside the model boundaries from the calculation
//var size = xPos.Count;
//var tempX = new List<double>(size);
//var tempY = new List<double>(size);
//var tempZ = new List<double>(size);
//var tempDistance = new List<double>(size);
//foreach (var index in idsInModel)
//{
// tempX.Add(xPos[index]);
// tempY.Add(yPos[index]);
// tempZ.Add(zPos[index]);
// tempDistance.Add(distance[index]);
//}
//xPos = new List<double>(tempX);
//yPos = new List<double>(tempY);
//zPos = new List<double>(tempZ);
//distance = new List<double>(tempDistance);
var tempList = new List <double>(xPos);
xPos = FilterOnIndexes(xPos, idsInModel);
yPos = FilterOnIndexes(yPos, idsInModel);
zPos = FilterOnIndexes(zPos, idsInModel);
distance = FilterOnIndexes(distance, idsInModel);
//xPos = xPos.Where(item => idsInModel.Contains(xPos.IndexOf(item))).ToList();
//yPos = yPos.Where(item => idsInModel.Contains(yPos.IndexOf(item))).ToList();
//zPos = zPos.Where(item => idsInModel.Contains(zPos.IndexOf(item))).ToList();
//distance = distance.Where(item => distance.Contains(distance.IndexOf(item))).ToList();
//Determine which photons are in which tissue and their indexes
amplitude = FilterOnIndexes(amplitude, idsInModel);
//amplitude = amplitude.Where(item => idsInModel.Contains(amplitude.IndexOf(item))).ToList();
//var idxSkin = idsInModel.Where(index => zPos[index] <= dSkin).ToList(); //TODO veranderd dit zodat het niet meer gebruik maakt van idsInModel maar gewoon de index returnt van het item in de lijst waar de waarde voor geldt
var idxSkin = new List <int>();
for (int i = 0; i < zPos.Count; i++)
{
if (zPos[i] <= dSkin)
{
idxSkin.Add(i);
}
}
var numInSkin = idxSkin.Count;
//var idxmuscle = idsInModel.Where(index => zPos[index] <= dMuscle && zPos[index] > dSkin).ToList();
var idxMuscle = new List <int>();
for (int i = 0; i < zPos.Count; i++)
{
if (zPos[i] <= dMuscle && zPos[i] > dSkin)
{
idxMuscle.Add(i);
}
}
var numInMuscle = idxMuscle.Count;
//var idxBone = idsInModel.Where(index => zPos[index] <= dBone && zPos[index] > dSkin + dMuscle).ToList();
var idxBone = new List <int>();
for (int i = 0; i < zPos.Count; i++)
{
if (zPos[i] <= dBone && zPos[i] > dSkin + dMuscle)
{
idxBone.Add(i);
}
}
var numInBone = idxBone.Count;
// Determine the distance each photon travels using the right scattering coefficient
// then use angles and that length to update photon positions
// Assume that the vast majority of blood is in the muscle not the skin or bone, hence the abs coefficient is 0
if (numInSkin > 0)
{
var data = Photons.Photons.UpdatePositions(xPos, yPos, zPos, distance, idxSkin, amplitude, numInSkin,
scatteringCoefficients.MuSkin, 0);
xPos = new List <double>(data.X);
yPos = new List <double>(data.Y);
zPos = new List <double>(data.Z);
amplitude = new List <double>(data.Amplitudes);
distance = new List <double>(data.TraveledDistances);
}
if (numInMuscle > 0)
{
var data = Photons.Photons.UpdatePositions(xPos, yPos, zPos, distance, idxMuscle, amplitude, numInMuscle,
scatteringCoefficients.MuMuscle, absorptionCoefficient);
xPos = new List <double>(data.X);
yPos = new List <double>(data.Y);
zPos = new List <double>(data.Z);
amplitude = new List <double>(data.Amplitudes);
distance = new List <double>(data.TraveledDistances);
}
// As with skin, we assume no blood in the bone(not true if you include marrow) ==> abs coef is 0
if (numInBone > 0)
{
var data = Photons.Photons.UpdatePositions(xPos, yPos, zPos, distance, idxBone, amplitude, numInBone,
scatteringCoefficients.MuBone, 0);
xPos = new List <double>(data.X);
yPos = new List <double>(data.Y);
zPos = new List <double>(data.Z);
amplitude = new List <double>(data.Amplitudes);
distance = new List <double>(data.TraveledDistances);
}
// Need to remove photons that are outside the calculation bounds and count up those that are detected
var indexes = Photons.Photons.FilterPhotons(xPos, yPos, zPos, xBound, zBound);
idsInModel = new List <int>(indexes);
numPhotons = idsInModel.Count;
// Calculate the intensity at each detector
var photons1 = Photons.Photons.DetectorPhotons(xPos, yPos, zPos, distance, amplitude,
distanceToDetector1, width);
var lengths1 = photons1.TraveledDistances;
detectedPhotons1 += photons1.TotalAmplitude;
var photons2 = Photons.Photons.DetectorPhotons(xPos, yPos, zPos, distance, amplitude,
distanceToDetector2, width);
var lengths2 = photons2.TraveledDistances;
detectedPhotons2 += photons2.TotalAmplitude;
if (firstD1)
{
lengthsToD1 = new List <double>(lengths1);
firstD1 = false;
}
else
{
lengthsToD1.AddRange(lengths1);
}
if (firstD2)
{
lengthsToD2 = new List <double>(lengths2);
firstD2 = false;
}
else
{
lengthsToD2.AddRange(lengths2);
}
// Check to see if we have sufficient signal-to-noise at both detectors
keepScattering = Photons.Photons.AreWeDone(detectedPhotons1, detectedPhotons2);
}
if (numPhotons < 100000)
{
// If we run out of photons before signal-to-noise is above threshold, inject some more
xPos.AddRange(randomInstance.UniformDistribution(-width, width, 5000000));
yPos.AddRange(randomInstance.UniformDistribution(-width, width, 5000000));
zPos.AddRange(randomInstance.UniformDistribution(0, 1 / scatteringCoefficients.MuSkin, 5000000));
for (int i = 0; i < 5000000; i++)
{
amplitude.Add(100);
}
idsInModel = Photons.Photons.FilterPhotons(xPos, yPos, zPos, xBound, zBound);
numPhotons = idsInModel.Count;
}
return(new ScatterData
{
DetectedPhotons1 = detectedPhotons1,
DetectedPhotons2 = detectedPhotons2,
LengthToD1 = lengthsToD1.Average(),
LengthToD2 = lengthsToD2.Average()
});
}