public void setup_simulation_input_components()
{
// delete previously generated files
clear_folders_and_files();
_detectorInputs = new List <IDetectorInput>()
{
new ROfRhoAndTimeDetectorInput()
{
Rho = new DoubleRange(0.0, 10.0, 101),
Time = new DoubleRange(0.0, 1, 101)
}
};
_sourceInput = new DirectionalPointSourceInput(
new Position(0.0, 0.0, 0.0),
new Direction(0.0, 0.0, 1.0),
1);
_tissueInput = new MultiLayerTissueInput(
new ITissueRegion[]
{
new LayerTissueRegion(
new DoubleRange(double.NegativeInfinity, 0.0),
new OpticalProperties(0.0, 1e-10, 0.0, 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, 0.0, 1.0))
}
);
}
/// <summary>
/// Monte Carlo simulation input data
/// </summary>
/// <param name="numberOfPhotons">long number indicating number of photons launched from source</param>
/// <param name="outputName">string indicating output name</param>
/// <param name="simulationOptions">options to execute simulation</param>
/// <param name="sourceInput">ISourceInput specifying source of light</param>
/// <param name="tissueInput">ITissueInput specifying tissue definition</param>
/// <param name="detectorInputs">IDetectorInput specifying which detectors to tally</param>
public SimulationInput(
long numberOfPhotons,
string outputName,
SimulationOptions simulationOptions,
ISourceInput sourceInput,
ITissueInput tissueInput,
IList <IDetectorInput> detectorInputs)
{
N = numberOfPhotons;
OutputName = outputName;
Options = simulationOptions;
SourceInput = sourceInput;
TissueInput = tissueInput;
DetectorInputs = detectorInputs ?? new List <IDetectorInput>();
}
private static ValidationResult ValidateSourceInput(ISourceInput sourceInput, ITissueInput tissueInput)
{
if ((sourceInput.InitialTissueRegionIndex < 0) ||
(sourceInput.InitialTissueRegionIndex > tissueInput.Regions.Length - 1))
{
return(new ValidationResult(
false,
"Source input not valid given tissue definition",
"Alter sourceInput.InitialTissueRegionIndex to be consistent with tissue definition"));
}
else
{
return(new ValidationResult(
true,
"Starting photons in region " + sourceInput.InitialTissueRegionIndex));
}
}
/// <summary>
/// Monte Carlo simulation input data
/// </summary>
/// <param name="numberOfPhotons">long number indicating number of photons launched from source</param>
/// <param name="outputName">string indicating output name</param>
/// <param name="simulationOptions">options to execute simulation</param>
/// <param name="sourceInput">ISourceInput specifying source of light</param>
/// <param name="tissueInput">ITissueInput specifying tissue definition</param>
/// <param name="detectorInputs">IDetectorInput specifying which detectors to tally</param>
public SimulationInput(
long numberOfPhotons,
string outputName,
SimulationOptions simulationOptions,
ISourceInput sourceInput,
ITissueInput tissueInput,
IList <IDetectorInput> detectorInputs)
{
N = numberOfPhotons;
OutputName = outputName;
Options = simulationOptions;
SourceInput = sourceInput;
TissueInput = tissueInput;
DetectorInputs = detectorInputs;
// check if detectorInputs list is null and if so make empty
if (DetectorInputs == null)
{
DetectorInputs = new List <IDetectorInput>()
{
};
}
}
public void execute_Monte_Carlo()
{
// instantiate common classes
_simulationOptions = new SimulationOptions(
0,
RandomNumberGeneratorType.MersenneTwister,
AbsorptionWeightingType.Discrete,
PhaseFunctionType.HenyeyGreenstein,
new List <DatabaseType>(),
false, // track statistics
0.0, // RR threshold -> 0 = no RR performed
0);
_source = new DirectionalPointSourceInput(
new Position(0.0, 0.0, 0.0),
new Direction(0.0, 0.0, 1.0),
1);
_tissue =
new MultiLayerWithSurfaceFiberTissueInput(
new SurfaceFiberTissueRegion(
new Position(0, 0, 0),
_detectorRadius, // needs to match SurfaceFiberDetectorInput
new OpticalProperties(0.01, 1.0, 0.8, 1.4)
),
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, 100.0),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(100.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
);
// tissue specification to verify MultiLayerWithSurfaceFiberTissue
// increases reflectance. If use this tissue need to change FinalTissueRegion
// for ALL detectors to 0
//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, 100.0),
// new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
// new LayerTissueRegion(
// new DoubleRange(100.0, double.PositiveInfinity),
// new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
// }
//);
_detectorOpen = new List <IDetectorInput>
{
new SurfaceFiberDetectorInput()
{
Center = new Position(0, 0, 0),
Radius = _detectorRadius,
TallySecondMoment = true,
N = 1.4,
NA = 1.4,
FinalTissueRegionIndex = 3
},
new ROfRhoDetectorInput() // 1mm wide ring to match fiber and 2 because beyond goes into 2nd
{
Rho = new DoubleRange(0.0, 2 * _detectorRadius, 3),
// since tissue w fiber specified -> photon will be in 3 upon exit
FinalTissueRegionIndex = 3,
NA = 1.4,
TallySecondMoment = true
},
};
_detectorNA = new List <IDetectorInput>
{
new SurfaceFiberDetectorInput()
{
Center = new Position(0, 0, 0),
Radius = _detectorRadius,
TallySecondMoment = true,
N = 1.4,
FinalTissueRegionIndex = 3,
NA = 0.39
},
new ROfRhoDetectorInput() // ring to match fiber detector
{
Rho = new DoubleRange(0.0, 2 * _detectorRadius, 3),
// since tissue w fiber specified -> photon will be in 3 upon exit
FinalTissueRegionIndex = 3,
NA = 0.39,
TallySecondMoment = true
},
};
_detectorNAOffCenter = new List <IDetectorInput>
{
new SurfaceFiberDetectorInput()
{
Center = new Position(_detectorRadius, 0, 0), // diam = [0, 2*radius]
Radius = _detectorRadius,
TallySecondMoment = true,
N = 1.4,
FinalTissueRegionIndex = 3,
NA = 1.4
},
new ROfRhoDetectorInput() // ring to match fiber detector
{
// place 1st rho bin center at _detectorRadius with width = 2*radius
Rho = new DoubleRange(_detectorRadius / 2, 2 * _detectorRadius + _detectorRadius / 2, 3),
// since tissue w fiber specified -> photon will be in 3 upon exit
FinalTissueRegionIndex = 3,
NA = 1.4,
TallySecondMoment = true
},
};
var _inputOpen = new SimulationInput(
100,
"",
_simulationOptions,
_source,
_tissue,
_detectorOpen);
_outputOpen = new MonteCarloSimulation(_inputOpen).Run();
var _inputNA = new SimulationInput(
100,
"",
_simulationOptions,
_source,
_tissue,
_detectorNA);
_outputNA = new MonteCarloSimulation(_inputNA).Run();
var _inputNAOffCenter = new SimulationInput(
100,
"",
_simulationOptions,
_source,
_tissue,
_detectorNAOffCenter);
_outputNAOffCenter = new MonteCarloSimulation(_inputNAOffCenter).Run();
}
/// <summary>
/// Method to instantiate the correct source given ISourceInput
/// </summary>
/// <param name="input">ISourceInput</param>
/// <param name="tissue">ITissue</param>
/// <param name="rng">random number generator instance</param>
/// <returns>ISource</returns>
public static ISource GetSource(ISourceInput input, Random rng)
{
var source = input.CreateSource(rng);
return(source);
}
