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Merge branch 'master' into 42a-inaccurate-fdpm-amplitude-and-phase-de…
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…rivative-values-with-respect-to-mu_a-and-mu_s
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@hayakawa16
hayakawa16 committed Feb 29, 2024
2 parents 92cd391 + a73fab5 commit 49af8cc
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7 changes: 7 additions & 0 deletions matlab/post_processing/loadMCResults.m
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Expand Up @@ -22,6 +22,13 @@
SurfaceFiber.SecondMoment = SurfaceFiber_txt.SecondMoment;
SurfaceFiber.Stdev = sqrt((SurfaceFiber.SecondMoment - (SurfaceFiber.Mean .* SurfaceFiber.Mean)) / (json.N));
results{di}.SurfaceFiber = SurfaceFiber;
case 'SlantedRecessedFiber'
SlantedRecessedFiber.Name = detector.Name;
SlantedRecessedFiber_txt = readAndParseJson([datadir slash detector.Name '.txt']);
SlantedRecessedFiber.Mean = SlantedRecessedFiber_txt.Mean;
SlantedRecessedFiber.SecondMoment = SlantedRecessedFiber_txt.SecondMoment;
SlantedRecessedFiber.Stdev = sqrt((SlantedRecessedFiber.SecondMoment - (SlantedRecessedFiber.Mean .* SlantedRecessedFiber.Mean)) / (json.N));
results{di}.SlantedRecessedFiber = SlantedRecessedFiber;
case 'RDiffuse'
RDiffuse.Name = detector.Name;
RDiffuse_txt = readAndParseJson([datadir slash detector.Name '.txt']);
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11 changes: 10 additions & 1 deletion matlab/post_processing/load_results_script.m
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Expand Up @@ -15,6 +15,7 @@
outdir = '.';

show.SurfaceFiber = 1;
show.SlantedRecessedFiber = 1;
show.RDiffuse = 1;
show.ROfRho = 1;
show.ROfRhoRecessed = 1;
Expand Down Expand Up @@ -94,7 +95,15 @@
num2str(results{di}.SurfaceFiber.Mean - 3 * results{di}.SurfaceFiber.Stdev) ' - ' ...
num2str(results{di}.SurfaceFiber.Mean + 3 * results{di}.SurfaceFiber.Stdev)]);
end


if isfield(results{di}, 'SlantedRecessedFiber') && show.SlantedRecessedFiber
disp(['Total reflectance captured by SlantedRecessedFiber detector: ' num2str(results{di}.SlantedRecessedFiber.Mean)]);
disp(['Standard Deviation captured by SlantedRecessedFiber detector: ' num2str(results{di}.SlantedRecessedFiber.Stdev)]);
disp(['+/- 3sigma by SlantedRecessedFiber detector: ' ...
num2str(results{di}.SlantedRecessedFiber.Mean - 3 * results{di}.SlantedRecessedFiber.Stdev) ' - ' ...
num2str(results{di}.SlantedRecessedFiber.Mean + 3 * results{di}.SlantedRecessedFiber.Stdev)]);
end

if isfield(results{di}, 'RDiffuse') && show.RDiffuse
disp(['Total reflectance captured by RDiffuse detector: ' num2str(results{di}.RDiffuse.Mean)]);
end
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3 changes: 3 additions & 0 deletions ...turesValidation/TissueInputs/MultiConcentricInfiniteCylinderTissueInputValidationTests.cs
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Expand Up @@ -56,6 +56,7 @@ public void validate_underlying_multilayer_tissue_definition()
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}

/// <summary>
/// Test to check that infinite cylinders have non-zero axis definitions.
/// </summary>
Expand Down Expand Up @@ -231,6 +232,7 @@ public void validate_infinite_cylinders_are_within_tissue_layer()
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}

/// <summary>
/// Test to check that infinite cylinders refractive index matches refractive index of surrounding layer
/// </summary>
Expand Down Expand Up @@ -276,6 +278,7 @@ public void validate_infinite_cylinders_refractive_index_matches_that_of_surroun
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}

/// <summary>
/// Test to check two layer tissue with one layer enclosing concentric infinite cylinders works
/// </summary>
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207 changes: 207 additions & 0 deletions ...DataStructuresValidation/TissueInputs/SingleInfiniteCylinderTissueInputValidationTests.cs
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@@ -0,0 +1,207 @@
using System.Collections.Generic;
using NUnit.Framework;
using Vts.Common;
using Vts.MonteCarlo;
using Vts.MonteCarlo.Detectors;
using Vts.MonteCarlo.Sources;
using Vts.MonteCarlo.Tissues;

namespace Vts.Test.MonteCarlo.DataStructuresValidation.TissueInputs
{
[TestFixture]
public class SingleInfiniteCylinderTissueInputValidationTests
{
/// <summary>
/// Test to check that underlying MultiLayerTissue is good
/// </summary>
[Test]
public void validate_underlying_multilayer_tissue_definition()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleInfiniteCylinderTissueInput(
new InfiniteCylinderTissueRegion(
new Position(0, 0, 10),
2.0,
new OpticalProperties()),
// define layer tissues that are incorrect
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(100.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List<IDetectorInput>()
{
new FluenceOfXAndYAndZDetectorInput()
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}

/// <summary>
/// Test to check that infinite cylinders have non-zero axis definitions.
/// </summary>
[Test]
public void validate_infinite_cylinder_has_nonzero_radii()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleInfiniteCylinderTissueInput(
// set one infinite cylinder radius to 0.0
new InfiniteCylinderTissueRegion(
new Position(0, 0, 1),
0.0, // radius=0
new OpticalProperties()),
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))
}
),
new List<IDetectorInput>()
{
new FluenceOfXAndYAndZDetectorInput()
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}

/// <summary>
/// Test to check that at least one tissue layer is defined
/// </summary>
[Test]
public void validate_at_least_one_tissue_layer_defined()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleInfiniteCylinderTissueInput(
new InfiniteCylinderTissueRegion(
new Position(0, 0, 1),
2.0,
new OpticalProperties()),
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, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List<IDetectorInput>()
{
new FluenceOfXAndYAndZDetectorInput()
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}

/// <summary>
/// Test to check that infinite cylinder is entirely contained within tissue layer
/// </summary>
[Test]
public void validate_infinite_cylinders_are_within_tissue_layer()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleInfiniteCylinderTissueInput(
// set infinite cylinder radius to go beyond layer
new InfiniteCylinderTissueRegion(
new Position(0, 0, 1),
15.0,
new OpticalProperties()),
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))
}
),
new List<IDetectorInput>()
{
new FluenceOfXAndYAndZDetectorInput()
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}

/// <summary>
/// Test to check two layer tissue with one layer enclosing concentric infinite cylinders works
/// </summary>
[Test]
public void validate_infinite_cylinder_within_one_layer_of_multilayer_works()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleInfiniteCylinderTissueInput(
new InfiniteCylinderTissueRegion(
new Position(0, 0, 5),
2.0,
new OpticalProperties(1.0, 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, 10.0),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(10.0, 20.0),
new OpticalProperties(0.1, 1.5, 0.8, 1.3)),
new LayerTissueRegion(
new DoubleRange(20.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List<IDetectorInput>()
{
new FluenceOfXAndYAndZDetectorInput()
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsTrue(result.IsValid);
}
}
}
76 changes: 53 additions & 23 deletions src/Vts.Test/MonteCarlo/Tissues/InfiniteCylinderTissueRegionTests.cs
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Expand Up @@ -37,32 +37,34 @@ public void Validate_infiniteCylinder_properties()
Assert.AreEqual(0.8, _infiniteCylinderTissueRegion.RegionOP.G);
Assert.AreEqual(1.4, _infiniteCylinderTissueRegion.RegionOP.N);
}

/// <summary>
/// Validate method RayIntersectBoundary return correct result
/// Validate method ContainsPositions return correct Boolean. ContainsPosition is true if inside
/// or *on* boundary.
/// </summary>
[Test]
public void Verify_RayIntersectBoundary_method_returns_correct_result()
public void Verify_ContainsPosition_method_returns_correct_result()
{
var photon = new Photon
{
DP =
{
Position = new Position(0, 0, 3),
Direction = new Direction(1, 0, 0)
},
S = 2.0 // definitely intersect
};
var result = _infiniteCylinderTissueRegion.RayIntersectBoundary(photon, out var distanceToBoundary);
Assert.AreEqual(true, result);
Assert.AreEqual(1.0, distanceToBoundary);
photon.S = 0.5; // definitely don't intersect
result = _infiniteCylinderTissueRegion.RayIntersectBoundary(photon, out distanceToBoundary);
Assert.AreEqual(false, result);
Assert.AreEqual(double.PositiveInfinity, distanceToBoundary);
photon.S = 1.0; // ends right at boundary => both out and no intersection
result = _infiniteCylinderTissueRegion.RayIntersectBoundary(photon, out distanceToBoundary);
Assert.AreEqual(false, result);
Assert.AreEqual(double.PositiveInfinity, distanceToBoundary);
var result = _infiniteCylinderTissueRegion.ContainsPosition(new Position(0, 0, 3.0)); // inside
Assert.IsTrue(result);
result = _infiniteCylinderTissueRegion.ContainsPosition(new Position(0, 0, 2.0)); // on boundary
Assert.IsTrue(result);
}
/// <summary>
/// Validate method OnBoundary return correct Boolean.
/// </summary>
[Test]
public void Verify_OnBoundary_method_returns_correct_result()
{
// OnBoundary returns false if *exactly* on boundary
var result = _infiniteCylinderTissueRegion.OnBoundary(new Position(0, 0, 2.0));
Assert.IsFalse(result);
// but returns true if outside infinite cylinder which doesn't make sense but it is how code is written
// and all unit tests (linux included) are based on this wrong return
result = _infiniteCylinderTissueRegion.OnBoundary(new Position(0, 0, 0.5));
Assert.IsTrue(result);
result = _infiniteCylinderTissueRegion.OnBoundary(new Position(0, 0, 2.0));
Assert.IsFalse(result);
}

/// <summary>
Expand All @@ -83,11 +85,39 @@ public void Verify_SurfaceNormal_method_returns_correct_result()
const double x = 0.3; // pick any x value and determine z on cylinder
var z = Math.Sqrt(_infiniteCylinderTissueRegion.Radius * _infiniteCylinderTissueRegion.Radius - x * x);
const double y = 1.11; // pick any y value
result = _infiniteCylinderTissueRegion.SurfaceNormal(new Position(x, y, z));
result = _infiniteCylinderTissueRegion.SurfaceNormal(new Position(x, y, z));
Assert.IsTrue(Math.Abs(result.Ux - 0.145072) < 1e-6);
Assert.AreEqual(0, result.Uy); // surface normal on infinite cylinder should *always* have Uz=0
Assert.IsTrue(Math.Abs(result.Uz + 0.989421) < 1e-6);
}

/// <summary>
/// Validate method RayIntersectBoundary return correct result
/// </summary>
[Test]
public void Verify_RayIntersectBoundary_method_returns_correct_result()
{
var photon = new Photon
{
DP =
{
Position = new Position(0, 0, 3),
Direction = new Direction(1, 0, 0)
},
S = 2.0 // definitely intersect
};
var result = _infiniteCylinderTissueRegion.RayIntersectBoundary(photon, out var distanceToBoundary);
Assert.AreEqual(true, result);
Assert.AreEqual(1.0, distanceToBoundary);
photon.S = 0.5; // definitely don't intersect
result = _infiniteCylinderTissueRegion.RayIntersectBoundary(photon, out distanceToBoundary);
Assert.AreEqual(false, result);
Assert.AreEqual(double.PositiveInfinity, distanceToBoundary);
photon.S = 1.0; // ends right at boundary => both out and no intersection
result = _infiniteCylinderTissueRegion.RayIntersectBoundary(photon, out distanceToBoundary);
Assert.AreEqual(false, result);
Assert.AreEqual(double.PositiveInfinity, distanceToBoundary);
}

}
}
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