private static ValidationResult ValidateTissueInput(ITissueInput tissueInput)
{
// for all types of tissues, check that OPs are non-negative (g could be neg)
if (tissueInput.Regions.Any(r => r.RegionOP.Mua < 0.0) ||
tissueInput.Regions.Any(r => r.RegionOP.Musp < 0.0) ||
tissueInput.Regions.Any(r => r.RegionOP.N < 0.0))
{
return(new ValidationResult(
false,
"Tissue optical properties mua, mus', n need to be non-negative",
"Please check optical properties"));
}
if (tissueInput is MultiLayerTissueInput)
{
return(MultiLayerTissueInputValidation.ValidateInput(tissueInput));
}
if (tissueInput is SingleEllipsoidTissueInput)
{
return(SingleEllipsoidTissueInputValidation.ValidateInput(tissueInput));
}
if (tissueInput is SingleVoxelTissueInput)
{
return(SingleVoxelTissueInputValidation.ValidateInput(tissueInput));
}
if (tissueInput is BoundingCylinderTissueInput)
{
return(BoundingCylinderTissueInputValidation.ValidateInput(tissueInput));
}
return(new ValidationResult(
true,
"Tissue input must be valid",
"Validation skipped for tissue input " + tissueInput + ". No matching validation rules were found."));
}
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>
///
/// </summary>
/// <param name="input"></param>
public FemMultiRegionTissueViewModel(ITissueInput input)
{
_input = input;
switch (input.TissueType)
{
case "MultiEllipsoid":
var multiEllipsoidTissueInput = ((MultiEllipsoidTissueInput)_input);
_tissueRegionsVM = new ObservableCollection <object>(
multiEllipsoidTissueInput.LayerRegions.Select((r, i) => (object)new LayerRegionViewModel(
(LayerTissueRegion)r,
"Layer " + i + (r.IsAir() ? " (Air)" : " (Tissue)"))));
_inclusionRegionsVM = new ObservableCollection <object>(
multiEllipsoidTissueInput.EllipsoidRegions.Select((r, i) => (object)new EllipsoidRegionViewModel(
(EllipsoidTissueRegion)r,
"Inclusion " + i + (r.IsAir() ? " (Air)" : " (Tissue)"))));
break;
default:
throw new ArgumentOutOfRangeException();
}
_currentTissueRegionIndex = 0;
_currentInclusionRegionIndex = 0;
}
public MultiRegionTissueViewModel(ITissueInput input)
{
_input = input;
switch (input.TissueType)
{
case "MultiLayer":
var multiLayerTissueInput = ((MultiLayerTissueInput)_input);
_regionsVM = new ObservableCollection <object>(
multiLayerTissueInput.Regions.Select((r, i) => (object)new LayerRegionViewModel(
(LayerTissueRegion)r,
"Layer " + i)));
break;
case "SingleEllipsoid":
var singleEllipsoidTissueInput = ((SingleEllipsoidTissueInput)_input);
_regionsVM = new ObservableCollection <object>(
singleEllipsoidTissueInput.LayerRegions
.Select((r, i) => (object)new LayerRegionViewModel(
(LayerTissueRegion)r,
"Layer " + i))
.Concat(new EllipsoidRegionViewModel((EllipsoidTissueRegion)singleEllipsoidTissueInput.EllipsoidRegion,
"Ellipsoid Region")));
break;
default:
throw new ArgumentOutOfRangeException();
}
_currentRegionIndex = 0;
}
/// <summary>
///
/// </summary>
/// <param name="tissueInput"></param>
private void UpdateTissueInputVM(ITissueInput tissueInput)
{
switch (tissueInput.TissueType)
{
case "MultiEllipsoid":
TissueInputVM = new FemMultiRegionTissueViewModel(tissueInput);
break;
default:
throw new ArgumentOutOfRangeException();
}
}
// todo: revisit to make signatures here and in Tissue/TissueInput class signatures strongly typed
/// <summary>
/// Method to return ITissue given inputs
/// </summary>
/// <param name="ti">ITissueInput</param>
/// <param name="awt">AbsorptionWeightingType enum</param>
/// <param name="pft">PhaseFunctionType enum</param>
/// <param name="russianRouletteWeightThreshold">Russian Roulette weight threshold</param>
/// <returns>ITissue</returns>
public static ITissue GetTissue(ITissueInput ti, AbsorptionWeightingType awt, PhaseFunctionType pft, double russianRouletteWeightThreshold)
{
ITissue t = ti.CreateTissue(awt, pft, russianRouletteWeightThreshold);
if (t == null)
{
throw new ArgumentException(
"Problem generating ITissue instance. Check that TissueInput, ti, has a matching ITissue definition.");
}
return(t);
}
/// <summary>
/// Method to validate that the tissue layers are contiguous and don't overlap
/// </summary>
/// <param name="input">tissue input in SimulationInput</param>
/// <returns></returns>
public static ValidationResult ValidateInput(ITissueInput input)
{
var layers = input.Regions.Select(region => (LayerTissueRegion)region).ToArray();
// other stuff could go here...
var tempResult = ValidateLayers(layers);
if (tempResult.IsValid)
{
tempResult = ValidateTopAndBottomLayersAreAir(layers);
}
return(tempResult);
}
/// <summary>
/// General constructor for simulation inputs
/// </summary>
/// <param name="meshDataInput">Input data for spatial and angular mesh</param>
/// <param name="simulationOptionsInput">Mesh simulation options input</param>
/// <param name="extSourceInput">Specifying external source</param>
/// <param name="intSourceInput">Specifying internal source</param>
/// <param name="tissueInput">Specifying tissue definition</param>
public SimulationInput(
SquareMeshDataInput meshDataInput,
MeshSimulationOptions simulationOptionsInput,
IExtFemSourceInput extSourceInput,
IIntFemSourceInput intSourceInput,
ITissueInput tissueInput
)
{
MeshDataInput = meshDataInput;
SimulationOptionsInput = simulationOptionsInput;
ExtSourceInput = extSourceInput;
IntSourceInput = intSourceInput;
TissueInput = tissueInput;
}
/// <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>();
}
public MultiRegionTissueViewModel(ITissueInput input)
{
_currentRegionIndex = 0;
_input = input;
switch (input.TissueType)
{
case "MultiLayer":
var multiLayerTissueInput = (MultiLayerTissueInput)_input;
_regionsVM = new ObservableCollection <object>(
multiLayerTissueInput.Regions.Select((r, i) => (object)new LayerRegionViewModel(
(LayerTissueRegion)r,
StringLookup.GetLocalizedString("Label_Layer") + i)));
break;
case "SingleEllipsoid":
var singleEllipsoidTissueInput = (SingleEllipsoidTissueInput)_input;
_regionsVM = new ObservableCollection <object>(
singleEllipsoidTissueInput.LayerRegions
.Select((r, i) => (object)new LayerRegionViewModel(
(LayerTissueRegion)r,
StringLookup.GetLocalizedString("Label_Layer") + i))
.Concat(
new EllipsoidRegionViewModel(
(EllipsoidTissueRegion)singleEllipsoidTissueInput.EllipsoidRegion,
StringLookup.GetLocalizedString("Label_EllipsoidRegion"))));
break;
case "SingleVoxel":
var singleVoxelTissueInput = (SingleVoxelTissueInput)_input;
_regionsVM = new ObservableCollection <object>(
singleVoxelTissueInput.LayerRegions
.Select((r, i) => (object)new LayerRegionViewModel(
(LayerTissueRegion)r,
StringLookup.GetLocalizedString("Label_Layer") + i))
.Concat(
new VoxelRegionViewModel(
(VoxelTissueRegion)singleVoxelTissueInput.VoxelRegion,
StringLookup.GetLocalizedString("Label_VoxelRegion"))));
break;
default:
throw new InvalidEnumArgumentException(StringLookup.GetLocalizedString("Error_NoTissueTypeExists"));
}
}
/// <summary>
/// Main validation method for SingleVoxelTissueInput.
/// </summary>
/// <param name="input">tissue input defined in SimulationInput</param>
/// <returns>ValidationResult</returns>
public static ValidationResult ValidateInput(ITissueInput input)
{
var layers = ((SingleVoxelTissueInput)input).LayerRegions.Select(region => (LayerTissueRegion)region).ToArray();
var voxel = (VoxelTissueRegion)((SingleVoxelTissueInput)input).VoxelRegion;
ValidationResult tempResult;
tempResult = ValidateGeometry(layers, voxel);
if (!tempResult.IsValid)
{
return(tempResult);
}
tempResult = ValidateRefractiveIndexMatch(layers, voxel);
if (!tempResult.IsValid)
{
return(tempResult);
}
return(tempResult);
}
/// <summary>
/// Main validation method for BoundingCylinderTissueInput.
/// </summary>
/// <param name="input">tissue input defined in SimulationInput</param>
/// <returns>ValidationResult</returns>
public static ValidationResult ValidateInput(ITissueInput input)
{
var layers = ((BoundingCylinderTissueInput)input).LayerRegions.Select(region => (LayerTissueRegion)region).ToArray();
var boundingCylinder = (CaplessCylinderTissueRegion)((BoundingCylinderTissueInput)input).CylinderRegion;
ValidationResult tempResult;
tempResult = ValidateGeometry(layers, boundingCylinder);
if (!tempResult.IsValid)
{
return(tempResult);
}
tempResult = ValidateRefractiveIndexMatch(layers, boundingCylinder);
if (!tempResult.IsValid)
{
return(tempResult);
}
return(tempResult);
}
private static ValidationResult ValidateTissueInput(ITissueInput tissueInput)
{
if (tissueInput is MultiLayerTissueInput)
{
return(MultiLayerTissueInputValidation.ValidateInput(tissueInput));
}
if (tissueInput is SingleEllipsoidTissueInput)
{
return(SingleEllipsoidTissueInputValidation.ValidateInput(tissueInput));
}
if (tissueInput is SingleVoxelTissueInput)
{
return(SingleVoxelTissueInputValidation.ValidateInput(tissueInput));
}
return(new ValidationResult(
true,
"Tissue input must be valid",
"Validation skipped for tissue input " + tissueInput + ". No matching validation rules were found."));
}
/// <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>()
{
};
}
}
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));
}
}
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();
}
