/// <summary>
/// Define SimulationInput to describe homogeneous and two layer tissue
/// </summary>
/// <returns></returns>
private void GenerateReferenceDatabase()
{
var simulationOptions = new SimulationOptions(
0,
RandomNumberGeneratorType.MersenneTwister,
AbsorptionWeightingType.Discrete,
PhaseFunctionType.HenyeyGreenstein,
new List <DatabaseType>()
{
DatabaseType.pMCDiffuseReflectance
},
false, // track statistics
0.0, // RR threshold -> 0 = no RR performed
0);
var sourceInput = new DirectionalPointSourceInput(
new Position(0.0, 0.0, 0.0),
new Direction(0.0, 0.0, 1.0),
1);
var detectorInputs = new List <IDetectorInput>()
{
new ROfRhoDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 101)
},
new ROfRhoAndTimeDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 101), Time = new DoubleRange(0.0, 1.0, 101)
}
};
_referenceInputTwoLayerTissue = new SimulationInput(
100,
"",
simulationOptions,
sourceInput,
new MultiLayerTissueInput(
new ITissueRegion[]
{
new LayerRegion(
new DoubleRange(double.NegativeInfinity, 0.0),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0)),
new LayerRegion(
new DoubleRange(0.0, _layerThickness),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerRegion(
new DoubleRange(_layerThickness, 20.0),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerRegion(
new DoubleRange(20.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
detectorInputs);
_factor = 1.0 - Optics.Specular(
_referenceInputTwoLayerTissue.TissueInput.Regions[0].RegionOP.N,
_referenceInputTwoLayerTissue.TissueInput.Regions[1].RegionOP.N);
_referenceOutputTwoLayerTissue = new MonteCarloSimulation(_referenceInputTwoLayerTissue).Run();
_databaseTwoLayerTissue = pMCDatabase.FromFile("DiffuseReflectanceDatabase", "CollisionInfoDatabase");
}
/// <summary>
/// Creates an instance of PhotonDatabasePostProcessor for pMC database processing
/// </summary>
/// <param name="virtualBoundaryType">virtual boundary type</param>
/// <param name="detectorInputs">List of IDetectorInputs designating binning</param>
/// <param name="database">pMCDatabase</param>
/// <param name="databaseInput">Database information needed for post-processing</param>
public PhotonDatabasePostProcessor(
VirtualBoundaryType virtualBoundaryType,
IList <IDetectorInput> detectorInputs,
pMCDatabase database,
SimulationInput databaseInput)
: this(virtualBoundaryType, detectorInputs, databaseInput)
{
_pMCDatabase = database;
_ispMCPostProcessor = true;
}
public void execute_Monte_Carlo()
{
// delete previously generated files
clear_folders_and_files();
var simulationOptions = new SimulationOptions(
0,
RandomNumberGeneratorType.MersenneTwister,
AbsorptionWeightingType.Continuous,
PhaseFunctionType.HenyeyGreenstein,
new List <DatabaseType>()
{
DatabaseType.pMCDiffuseReflectance
},
false, // track statistics
0.0, // RR threshold -> 0 = no RR performed
0);
var sourceInput = new DirectionalPointSourceInput(
new Position(0.0, 0.0, 0.0),
new Direction(0.0, 0.0, 1.0),
1);
var detectorInputs = new List <IDetectorInput>()
{
new ROfRhoDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 101)
},
new ROfRhoAndTimeDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 101), Time = new DoubleRange(0.0, 1.0, 101)
},
new ROfFxDetectorInput()
{
Fx = new DoubleRange(0.0, 0.5, 11)
},
new ROfFxAndTimeDetectorInput()
{
Fx = new DoubleRange(0.0, 0.5, 11), Time = new DoubleRange(0.0, 1.0, 101)
}
};
_referenceInputOneLayerTissue = new SimulationInput(
100,
"", // can't create folder in isolated storage
simulationOptions,
sourceInput,
new MultiLayerTissueInput(
new ITissueRegion[]
{
new LayerTissueRegion(
new DoubleRange(double.NegativeInfinity, 0.0),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0)),
new LayerTissueRegion(
new DoubleRange(0.0, 20.0),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(20.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
detectorInputs);
_factor = 1.0 - Optics.Specular(
_referenceInputOneLayerTissue.TissueInput.Regions[0].RegionOP.N,
_referenceInputOneLayerTissue.TissueInput.Regions[1].RegionOP.N);
_referenceOutputOneLayerTissue = new MonteCarloSimulation(_referenceInputOneLayerTissue).Run();
_databaseOneLayerTissue = pMCDatabase.FromFile("DiffuseReflectanceDatabase", "CollisionInfoDatabase");
}
public void execute_Monte_Carlo()
{
// instantiate common classes
var simulationOptions = new SimulationOptions(
0,
RandomNumberGeneratorType.MersenneTwister,
AbsorptionWeightingType.Discrete,
PhaseFunctionType.HenyeyGreenstein,
new List <DatabaseType>()
{
DatabaseType.pMCDiffuseReflectance
}, // write database for pMC tests
false, // track statistics
0.0, // RR threshold -> 0 = no RR performed
0);
var source = new DirectionalPointSourceInput(
new Position(0.0, 0.0, 0.0),
new Direction(0.0, 0.0, 1.0),
0); // start in air
var tissue = new MultiLayerTissueInput(
new ITissueRegion[]
{
new LayerTissueRegion(
new DoubleRange(double.NegativeInfinity, 0.0),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0)),
new LayerTissueRegion(
new DoubleRange(0.0, 10.0), // make tissue layer thin so transmittance results improved
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(10.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
});
var detectorsNA0 = new List <IDetectorInput>
{
new RDiffuseDetectorInput()
{
FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfAngleDetectorInput()
{
Angle = new DoubleRange(Math.PI / 2, Math.PI, 2), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfRhoDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfRhoAndAngleDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Angle = new DoubleRange(Math.PI / 2, Math.PI, 2), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfRhoAndTimeDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Time = new DoubleRange(0.0, 1.0, 11), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfRhoAndOmegaDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Omega = new DoubleRange(0.05, 1.0, 20), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfXAndYDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfXAndYAndTimeDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), Time = new DoubleRange(0, 1, 11), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfXAndYAndMaxDepthDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), MaxDepth = new DoubleRange(0, 10.0, 11), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfFxDetectorInput()
{
Fx = new DoubleRange(0.0, 0.5, 51), FinalTissueRegionIndex = 0, NA = 0.0
},
new ROfFxAndTimeDetectorInput()
{
Fx = new DoubleRange(0.0, 0.5, 51), Time = new DoubleRange(0.0, 1.0, 11), FinalTissueRegionIndex = 0, NA = 0.0
},
new RSpecularDetectorInput()
{
FinalTissueRegionIndex = 0, NA = 0.0
},
new TDiffuseDetectorInput()
{
FinalTissueRegionIndex = 2, NA = 0.0
},
new TOfAngleDetectorInput()
{
Angle = new DoubleRange(0.0, Math.PI / 2, 2), FinalTissueRegionIndex = 2, NA = 0.0
},
new TOfRhoAndAngleDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Angle = new DoubleRange(0.0, Math.PI / 2, 2), FinalTissueRegionIndex = 2, NA = 0.0
},
new TOfRhoDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), FinalTissueRegionIndex = 2, NA = 0.0
},
new TOfXAndYDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), FinalTissueRegionIndex = 2, NA = 0.0
},
new RadianceOfRhoAtZDetectorInput()
{
ZDepth = _dosimetryDepth, Rho = new DoubleRange(0.0, 10.0, 11), FinalTissueRegionIndex = 1, NA = 0.0
},
new ReflectedMTOfRhoAndSubregionHistDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
FinalTissueRegionIndex = 0,
NA = 0.0
},
new ReflectedMTOfXAndYAndSubregionHistDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11),
Y = new DoubleRange(-10.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
FinalTissueRegionIndex = 0,
NA = 0.0
},
new TransmittedMTOfRhoAndSubregionHistDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
FinalTissueRegionIndex = 2,
NA = 0.0
},
new TransmittedMTOfXAndYAndSubregionHistDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11),
Y = new DoubleRange(-10.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
FinalTissueRegionIndex = 2,
NA = 0.0
},
};
var input = new SimulationInput(
100,
"",
simulationOptions,
source,
tissue,
detectorsNA0);
_outputNA0 = new MonteCarloSimulation(input).Run();
_inputForPMC = input; // set pMC input to one that specified database generation
_pMCDatabase = pMCDatabase.FromFile("DiffuseReflectanceDatabase", "CollisionInfoDatabase"); // grab database
var detectorsNA0p3 = new List <IDetectorInput>
{
new RDiffuseDetectorInput()
{
FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfAngleDetectorInput()
{
Angle = new DoubleRange(Math.PI / 2, Math.PI, 2), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfRhoDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfRhoAndAngleDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Angle = new DoubleRange(Math.PI / 2, Math.PI, 2), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfRhoAndTimeDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Time = new DoubleRange(0.0, 1.0, 11), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfRhoAndOmegaDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Omega = new DoubleRange(0.05, 1.0, 20), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfXAndYDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfXAndYAndTimeDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), Time = new DoubleRange(0, 1, 11), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfXAndYAndMaxDepthDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), MaxDepth = new DoubleRange(0, 10.0, 11), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfFxDetectorInput()
{
Fx = new DoubleRange(0.0, 0.5, 51), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfFxAndTimeDetectorInput()
{
Fx = new DoubleRange(0.0, 0.5, 5), Time = new DoubleRange(0.0, 1.0, 11), FinalTissueRegionIndex = 0, NA = 0.3
},
new RSpecularDetectorInput()
{
FinalTissueRegionIndex = 0, NA = 0.3
},
new TDiffuseDetectorInput()
{
FinalTissueRegionIndex = 2, NA = 0.3
},
new TOfAngleDetectorInput()
{
Angle = new DoubleRange(0.0, Math.PI / 2, 2), FinalTissueRegionIndex = 2, NA = 0.3
},
new TOfRhoAndAngleDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Angle = new DoubleRange(0.0, Math.PI / 2, 2), FinalTissueRegionIndex = 2, NA = 0.3
},
new TOfRhoDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), FinalTissueRegionIndex = 2, NA = 0.3
},
new TOfXAndYDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), FinalTissueRegionIndex = 2, NA = 0.3
},
new RadianceOfRhoAtZDetectorInput()
{
ZDepth = _dosimetryDepth, Rho = new DoubleRange(0.0, 10.0, 11), FinalTissueRegionIndex = 1, NA = 0.3
},
new ReflectedMTOfRhoAndSubregionHistDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
FinalTissueRegionIndex = 0,
NA = 0.3
},
new ReflectedMTOfXAndYAndSubregionHistDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11),
Y = new DoubleRange(-10.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
FinalTissueRegionIndex = 0,
NA = 0.3
},
new TransmittedMTOfRhoAndSubregionHistDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
FinalTissueRegionIndex = 2,
NA = 0.3
},
new TransmittedMTOfXAndYAndSubregionHistDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11),
Y = new DoubleRange(-10.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
FinalTissueRegionIndex = 2,
NA = 0.3
},
};
input = new SimulationInput(
100,
"",
simulationOptions,
source,
tissue,
detectorsNA0p3);
_outputNA0p3 = new MonteCarloSimulation(input).Run();
var detectorsNoNASpecified = new List <IDetectorInput>
{
new RDiffuseDetectorInput()
{
},
new ROfAngleDetectorInput()
{
Angle = new DoubleRange(Math.PI / 2, Math.PI, 2)
},
new ROfRhoDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11)
},
new ROfRhoAndAngleDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Angle = new DoubleRange(Math.PI / 2, Math.PI, 2)
},
new ROfRhoAndTimeDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Time = new DoubleRange(0.0, 1.0, 11)
},
new ROfRhoAndOmegaDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Omega = new DoubleRange(0.05, 1.0, 20)
},
new ROfXAndYDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11)
},
new ROfXAndYAndTimeDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), Time = new DoubleRange(0, 1, 11), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfXAndYAndMaxDepthDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11), MaxDepth = new DoubleRange(0, 10.0, 11), FinalTissueRegionIndex = 0, NA = 0.3
},
new ROfFxDetectorInput()
{
Fx = new DoubleRange(0.0, 0.5, 51)
},
new ROfFxAndTimeDetectorInput()
{
Fx = new DoubleRange(0.0, 0.5, 5), Time = new DoubleRange(0.0, 1.0, 11)
},
new RSpecularDetectorInput()
{
},
new TDiffuseDetectorInput()
{
},
new TOfAngleDetectorInput()
{
Angle = new DoubleRange(0.0, Math.PI / 2, 2)
},
new TOfRhoAndAngleDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11), Angle = new DoubleRange(0.0, Math.PI / 2, 2)
},
new TOfRhoDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11)
},
new TOfXAndYDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11), Y = new DoubleRange(-10.0, 10.0, 11)
},
new RadianceOfRhoAtZDetectorInput()
{
ZDepth = _dosimetryDepth, Rho = new DoubleRange(0.0, 10.0, 11)
},
new ReflectedMTOfRhoAndSubregionHistDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
},
new ReflectedMTOfXAndYAndSubregionHistDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11),
Y = new DoubleRange(-10.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
},
new TransmittedMTOfRhoAndSubregionHistDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
},
new TransmittedMTOfXAndYAndSubregionHistDetectorInput()
{
X = new DoubleRange(-10.0, 10.0, 11),
Y = new DoubleRange(-10.0, 10.0, 11),
MTBins = new DoubleRange(0.0, 500.0, 5),
FractionalMTBins = new DoubleRange(0.0, 1.0, 11),
},
};
input = new SimulationInput(
100,
"",
simulationOptions,
source,
tissue,
detectorsNoNASpecified);
_outputNoNASpecified = new MonteCarloSimulation(input).Run();
}
