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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,22 @@ | ||
| using Vts.Common; | ||
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| namespace Vts.Scripting.Utilities; | ||
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| public static class PlottingExtensions | ||
| { | ||
| public static double[] GetMidpoints(this DoubleRange endpointRange) | ||
| { | ||
| var endpoints = endpointRange.AsEnumerable().ToArray(); | ||
| if (endpoints.Length < 2) | ||
| { | ||
| throw new ArgumentException("Endpoints must have at least two elements"); | ||
| } | ||
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| var midpoints = new double[endpoints.Length - 1]; | ||
| for (int i = 0; i < midpoints.Length; i++) | ||
| { | ||
| midpoints[i] = endpoints[i + 1] - endpoints[i]; | ||
| } | ||
| return endpoints; | ||
| } | ||
| } |
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src/Vts.Scripting.Utilities/Vts.Scripting.Utilities.csproj
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| <Project Sdk="Microsoft.NET.Sdk"> | ||
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| <PropertyGroup> | ||
| <TargetFramework>net7.0</TargetFramework> | ||
| <ImplicitUsings>enable</ImplicitUsings> | ||
| <Nullable>enable</Nullable> | ||
| </PropertyGroup> | ||
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| <ItemGroup> | ||
| <ProjectReference Include="..\Vts\Vts.csproj" /> | ||
| </ItemGroup> | ||
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| </Project> |
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| Original file line number | Diff line number | Diff line change |
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| using Vts.Common; | ||
| using Vts.MonteCarlo.Detectors; | ||
| using Vts.MonteCarlo.Sources; | ||
| using Vts.MonteCarlo.Tissues; | ||
| using Vts.MonteCarlo; | ||
| using Vts; | ||
| using Vts.Scripting.Utilities; | ||
| using Plotly.NET.CSharp; | ||
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| // Example 01: run a simple Monte Carlo simulation with 1000 photons | ||
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| // set number of photons | ||
| var numPhotons = 1000; | ||
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| // define a point source beam normally incident at the origin | ||
| var sourceInput = new DirectionalPointSourceInput | ||
| { | ||
| SourceType = "DirectionalPoint", | ||
| PointLocation = new(x: 0, y: 0, z: 0), | ||
| Direction = new(ux: 0, uy: 0, uz: 1), | ||
| InitialTissueRegionIndex = 0 | ||
| }; | ||
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| // define a semi-infinite slab tissue geometry with air-tissue boundary (a bottom air layer is necessary) | ||
| var tissueInput = new MultiLayerTissueInput | ||
| { | ||
| Regions = new ITissueRegion[] | ||
| { | ||
| new LayerTissueRegion( | ||
| zRange: new(double.NegativeInfinity, 0), // air "z" range | ||
| op: new(mua: 0.0, musp: 1E-10, g: 1.0, n: 1.0)), // air optical properties | ||
| new LayerTissueRegion( | ||
| zRange: new(0, 100), // tissue "z" range ("semi-infinite" slab, 100mm thick) | ||
| op: new(mua: 0.01, musp: 1.0, g: 0.9, n: 1.4)), // tissue optical properties | ||
| new LayerTissueRegion( | ||
| zRange: new(100, double.PositiveInfinity), // air "z" range | ||
| op: new(mua: 0.0, musp: 1E-10, g: 1.0, n: 1.0)) // air optical properties | ||
| } | ||
| }; | ||
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| // define a single R(rho) detector by the endpoints of rho bins | ||
| var detectorInput = new ROfRhoDetectorInput { Rho = new(0, 40, 201), TallySecondMoment = true }; | ||
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| // create a SimulationInput object to define the simulation | ||
| var simulationInput = new SimulationInput | ||
| { | ||
| N = numPhotons, | ||
| SourceInput = sourceInput, | ||
| TissueInput = tissueInput, | ||
| DetectorInputs = new IDetectorInput[] { detectorInput }, | ||
| Options = new SimulationOptions | ||
| { | ||
| Seed = 0, // -1 will generate a random seed | ||
| AbsorptionWeightingType = AbsorptionWeightingType.Discrete, | ||
| PhaseFunctionType = PhaseFunctionType.HenyeyGreenstein | ||
| } | ||
| }; | ||
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| // create the simulation | ||
| var simulation = new MonteCarloSimulation(simulationInput); | ||
|
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| // run the simulation | ||
| var simulationOutput = simulation.Run(); | ||
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| // plot the results | ||
| var detectorMidpoints = detectorInput.Rho.GetMidpoints(); | ||
| var logReflectance = simulationOutput.R_r.Select(r => Math.Log(r)).ToArray(); | ||
| Chart.Point<double, double, string>( | ||
| x: detectorMidpoints, | ||
| y: logReflectance | ||
| ).WithTraceInfo("log(R) vs rho [mm-2]", ShowLegend: true) | ||
| .WithXAxisStyle<double, double, string>(Title: Plotly.NET.Title.init("rho [mm]")) | ||
| .WithYAxisStyle<double, double, string>(Title: Plotly.NET.Title.init("log(R(rho)) [mm-2]")) | ||
| .Show(); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| using Vts.MonteCarlo.Detectors; | ||
| using Vts.MonteCarlo.Sources; | ||
| using Vts.MonteCarlo.Tissues; | ||
| using Vts.MonteCarlo; | ||
| using Vts; | ||
| using Vts.Scripting.Utilities; | ||
| using Plotly.NET.CSharp; | ||
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| // Example 10: run R(fx) detector results | ||
|
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| // set number of photons | ||
| var numPhotons = 1000; | ||
|
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| // define a point source beam normally incident at the origin | ||
| var sourceInput = new DirectionalPointSourceInput | ||
| { | ||
| SourceType = "DirectionalPoint", | ||
| PointLocation = new(x: 0, y: 0, z: 0), | ||
| Direction = new(ux: 0, uy: 0, uz: 1), | ||
| InitialTissueRegionIndex = 0 | ||
| }; | ||
|
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| // define a semi-infinite slab tissue geometry with air-tissue boundary (a bottom air layer is necessary) | ||
| var tissueInput = new MultiLayerTissueInput | ||
| { | ||
| Regions = new ITissueRegion[] | ||
| { | ||
| new LayerTissueRegion( | ||
| zRange: new(double.NegativeInfinity, 0), // air "z" range | ||
| op: new(mua: 0.0, musp: 1E-10, g: 1.0, n: 1.0)), // air optical properties | ||
| new LayerTissueRegion( | ||
| zRange: new(0, 100), // tissue "z" range ("semi-infinite" slab, 100mm thick) | ||
| op: new(mua: 0.01, musp: 1.0, g: 0.9, n: 1.4)), // tissue optical properties | ||
| new LayerTissueRegion( | ||
| zRange: new(100, double.PositiveInfinity), // air "z" range | ||
| op: new(mua: 0.0, musp: 1E-10, g: 1.0, n: 1.0)) // air optical properties | ||
| } | ||
| }; | ||
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| // define a single R(fx) detector at spatial frequencies fx | ||
| var detectorInput = new ROfFxDetectorInput { Fx = new(0, 1, 101), TallySecondMoment = true }; | ||
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| // create a SimulationInput object to define the simulation | ||
| var simulationInput = new SimulationInput | ||
| { | ||
| N = numPhotons, | ||
| SourceInput = sourceInput, | ||
| TissueInput = tissueInput, | ||
| DetectorInputs = new IDetectorInput[] { detectorInput }, | ||
| Options = new SimulationOptions | ||
| { | ||
| Seed = 0, // -1 will generate a random seed | ||
| AbsorptionWeightingType = AbsorptionWeightingType.Discrete, | ||
| PhaseFunctionType = PhaseFunctionType.HenyeyGreenstein | ||
| } | ||
| }; | ||
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| // create the simulation | ||
| var simulation = new MonteCarloSimulation(simulationInput); | ||
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| // run the simulation | ||
| var simulationOutput = simulation.Run(); | ||
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| // plot the results | ||
| var detectorMidpoints = detectorInput.Fx.GetMidpoints(); | ||
| var reflectance = simulationOutput.R_fx.Select(r => r.Magnitude).ToArray(); | ||
| Chart.Point<double, double, string>( | ||
| x: detectorMidpoints, | ||
| y: reflectance | ||
| ).WithTraceInfo("R vs fx [unitless]", ShowLegend: true) | ||
| .WithXAxisStyle<double, double, string>(Title: Plotly.NET.Title.init("fx [mm-1]")) | ||
| .WithYAxisStyle<double, double, string>(Title: Plotly.NET.Title.init("R(fx) [unitless]")) | ||
| .Show(); |
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