public void Test_deserialize_spectral_data()
{
var postData = "{\"spectralPlotType\":\"musp\",\"plotName\":\"μs'\",\"tissueType\":\"Skin\",\"absorberConcentration\":[{\"label\":\"Hb\",\"value\":28.4,\"units\":\"μM\"},{\"label\":\"HbO2\",\"value\":22.4,\"units\":\"μM\"},{\"label\":\"H2O\",\"value\":0.7,\"units\":\"vol. frac.\"},{\"label\":\"Fat\",\"value\":0,\"units\":\"vol. frac.\"},{\"label\":\"Melanin\",\"value\":0.0051,\"units\":\"vol. frac.\"}],\"bloodConcentration\":{\"totalHb\":50.8,\"bloodVolume\":0.021844,\"stO2\":0.4409448818897638},\"scatteringType\":\"PowerLaw\",\"powerLawScatterer\":{\"a\":1.2,\"b\":1.42},\"intralipidScatterer\":{\"volumeFraction\":0.01},\"mieScatterer\":{\"particleRadius\":0.5,\"ParticleRefractiveIndexMismatch\":1.4,\"MediumRefractiveIndexMismatch\":1,\"volumeFraction\":0.01},\"xAxis\":{\"start\":650,\"stop\":1000,\"count\":36}}";
var xAxis = new DoubleRange(650, 1000, 36);
var powerLawScatterer = new PowerLawScatterer(1.2, 1.42);
var intralipidScatterer = new IntralipidScatterer(0.01);
var mieScatterer = new MieScatterer(0.5, 1.4, 1, 0.01);
var absorberConcentrations = new[] { new LabelValuePair()
{
Label = "Hb", Value = 28.4
} };
var spectralPlotParameters = JsonConvert.DeserializeObject <SpectralPlotParameters>(postData);
Assert.AreEqual(xAxis.Start, spectralPlotParameters.XAxis.Start);
Assert.AreEqual(xAxis.Stop, spectralPlotParameters.XAxis.Stop);
Assert.AreEqual(xAxis.Count, spectralPlotParameters.XAxis.Count);
Assert.AreEqual(xAxis.Delta, spectralPlotParameters.XAxis.Delta);
Assert.IsNull(spectralPlotParameters.YAxis);
Assert.AreEqual(SpectralPlotType.Musp, spectralPlotParameters.SpectralPlotType);
Assert.AreEqual("μs'", spectralPlotParameters.PlotName);
Assert.IsNull(spectralPlotParameters.Tissue);
Assert.IsNull(spectralPlotParameters.Wavelengths);
Assert.AreEqual("Skin", spectralPlotParameters.TissueType);
Assert.AreEqual(ScatteringType.PowerLaw, spectralPlotParameters.ScatteringType);
Assert.AreEqual(absorberConcentrations[0].Label, spectralPlotParameters.AbsorberConcentration[0].Label);
Assert.AreEqual(absorberConcentrations[0].Value, spectralPlotParameters.AbsorberConcentration[0].Value);
Assert.AreEqual(powerLawScatterer.A, spectralPlotParameters.PowerLawScatterer.A);
Assert.AreEqual(intralipidScatterer.VolumeFraction, spectralPlotParameters.IntralipidScatterer.VolumeFraction);
Assert.AreEqual(mieScatterer.ParticleRadius, spectralPlotParameters.MieScatterer.ParticleRadius);
}
public void validate_spectral_generation_of_OpticalProperties_with_scatterers_and_absorbers()
{
var scatterer = new IntralipidScatterer(0.01);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.01);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.99);
var wvs = new DoubleRange(650, 1000, 36).AsEnumerable().ToArray();
var n = 1.4;
var rho = 10;
var ops = wvs.Select(wv =>
{
var mua = fatAbsorber.GetMua(wv) + waterAbsorber.GetMua(wv);
var musp = scatterer.GetMusp(wv);
var g = scatterer.GetG(wv);
return(new OpticalProperties(mua, musp, g, n));
}).ToArray();
var fs = new PointSourceSDAForwardSolver();
var reflectanceVsWavelength = fs.ROfRho(ops, rho);
Assert.NotNull(reflectanceVsWavelength);
Assert.AreEqual(reflectanceVsWavelength.Length, wvs.Length);
// check that change in scattering changes the reflectance
Assert.IsTrue(reflectanceVsWavelength[0] != reflectanceVsWavelength[1]);
// check that change in absorption changes the reflectance
Assert.IsTrue(reflectanceVsWavelength[1] != reflectanceVsWavelength[2]);
}
public void validate_spectral_generation_of_OpticalProperties_with_tissue()
{
var scatterer = new IntralipidScatterer(0.01);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.01);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.99);
var _twoLayerSDAForwardSolver = new TwoLayerSDAForwardSolver();
var _oneLayerPointSourceForwardSolver = new PointSourceSDAForwardSolver();
var n = 1.4;
var wvs = new DoubleRange(650, 1000, 36).AsEnumerable().ToArray();
var rho = 10;
var tissue = new Tissue(
new IChromophoreAbsorber[] { fatAbsorber, waterAbsorber },
scatterer,
"test_tissue",
n);
var ops = wvs.Select(wv => tissue.GetOpticalProperties(wv)).ToArray();
var fs = new PointSourceSDAForwardSolver();
var reflectanceVsWavelength = fs.ROfRho(ops, rho);
Assert.NotNull(reflectanceVsWavelength);
Assert.AreEqual(reflectanceVsWavelength.Length, wvs.Length);
// check that change in scattering changes the reflectance
Assert.IsTrue(reflectanceVsWavelength[0] != reflectanceVsWavelength[1]);
// check that change in absorption changes the reflectance
Assert.IsTrue(reflectanceVsWavelength[1] != reflectanceVsWavelength[2]);
}
public override IScatterer ReadJson(JsonReader reader, Type objectType, IScatterer existingValue, bool hasExistingValue,
JsonSerializer serializer)
{
IScatterer scatterer;
double volumeFraction;
// Load the JSON for the scatterer into a JObject
var jsonObject = JObject.Load(reader);
var currentToken = reader.Path;
ScatteringType scatteringType;
switch (existingValue)
{
case PowerLawScatterer _:
scatteringType = ScatteringType.PowerLaw;
break;
case IntralipidScatterer _:
scatteringType = ScatteringType.Intralipid;
break;
case MieScatterer _:
scatteringType = ScatteringType.Mie;
break;
default:
var scattererEnum = currentToken.Replace("Scatterer", "");
Enum.TryParse <ScatteringType>(scattererEnum, true, out scatteringType);
break;
}
switch (scatteringType)
{
case ScatteringType.Intralipid:
if (jsonObject["volumeFraction"] != null)
{
volumeFraction = jsonObject["volumeFraction"].Value <double>();
scatterer = new IntralipidScatterer(volumeFraction);
}
else
{
scatterer = new IntralipidScatterer();
}
break;
case ScatteringType.Mie:
if (jsonObject["particleRadius"] != null && jsonObject["particleRefractiveIndex"] != null && jsonObject["mediumRefractiveIndex"] != null && jsonObject["volumeFraction"] != null)
{
var particleRadius = jsonObject["particleRadius"].Value <double>();
var particleRefractiveIndex = jsonObject["particleRefractiveIndex"].Value <double>();
var mediumRefractiveIndex = jsonObject["mediumRefractiveIndex"].Value <double>();
volumeFraction = jsonObject["volumeFraction"].Value <double>();
scatterer = new MieScatterer(particleRadius, particleRefractiveIndex, mediumRefractiveIndex, volumeFraction);
}
else
{
scatterer = new MieScatterer();
}
break;
case ScatteringType.PowerLaw:
if (jsonObject["a"] != null && jsonObject["b"] != null)
{
var a = jsonObject["a"].Value <double>();
var b = jsonObject["b"].Value <double>();
scatterer = new PowerLawScatterer(a, b);
}
else
{
scatterer = new PowerLawScatterer();
}
break;
default:
scatterer = new PowerLawScatterer();
break;
}
// Return the scatterer
return(scatterer);
}
