/// <summary>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
//Source starts at the origin
Position finalPosition = SourceDefaults.DefaultPosition.Clone();
// sample angular distribution
Direction finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
_polarAngleEmissionRange,
_azimuthalAngleEmissionRange,
Rng);
//Find the relevent polar and azimuthal pair for the direction
_rotationalAnglesOfPrincipalSourceAxis = SourceToolbox.GetPolarAzimuthalPairFromDirection(_direction);
//Rotation and translation
SourceToolbox.UpdateDirectionPositionAfterGivenFlags(
ref finalPosition,
ref finalDirection,
_rotationalAnglesOfPrincipalSourceAxis,
_pointLocation,
_rotationAndTranslationFlags);
var photon = new Photon(finalPosition, finalDirection, 1.0, tissue, _initialTissueRegionIndex, Rng);
return(photon);
}
/// <summary>
/// Returns direction for a given position
/// </summary>
/// <param name="position">position</param>
/// <returns>new direction</returns>
protected override Direction GetFinalDirection(Position position)
{
return(SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
_polarAngleEmissionRange,
_azimuthalAngleEmissionRange,
Rng));
}
/// <summary>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
// sample angular distribution
Direction finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(_polarAngleRangeToDefineSphericalSurface, _azimuthalAngleRangeToDefineSphericalSurface, Rng);
//Source starts from anywhere in the sphere
Position finalPosition = GetFinalPositionFromProfileType(finalDirection, _radius, Rng);
//Lambertian distribution (uniform hemispherical distribution)
PolarAzimuthalAngles polarAzimuthalPair = SourceToolbox.GetPolarAzimuthalPairForGivenAngleRangeRandom(
SourceDefaults.DefaultHalfPolarAngleRange.Clone(),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng);
//Avoid updating the finalDirection during following rotation
Position dummyPosition = finalPosition;
//Rotate polar azimutahl angle by polarAzimuthalPair vector
SourceToolbox.UpdateDirectionPositionAfterRotatingByGivenAnglePair(polarAzimuthalPair, ref finalDirection, ref dummyPosition);
//Find the relevent polar and azimuthal pair for the direction
PolarAzimuthalAngles _rotationalAnglesOfPrincipalSourceAxis = SourceToolbox.GetPolarAzimuthalPairFromDirection(_newDirectionOfPrincipalSourceAxis);
//Translation and source rotation
SourceToolbox.UpdateDirectionPositionAfterGivenFlags(
ref finalPosition,
ref finalDirection,
_rotationalAnglesOfPrincipalSourceAxis,
_translationFromOrigin,
_rotationAndTranslationFlags);
var photon = new Photon(finalPosition, finalDirection, 1.0, tissue, _initialTissueRegionIndex, Rng);
return(photon);
}
/// <summary>
/// Returns Lambertian direction - all fluorescence emission is Lambertian
/// </summary>
/// <returns>new direction</returns>
private static Direction GetFinalDirection(Random rng)
{
//Lambertian distribution
return(SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
SourceDefaults.DefaultFullPolarAngleRange.Clone(),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
rng));
}
public void validate_static_method_getdirectionforgivenpolarazimuthalanglerangerandom()
{
Random rng = new MathNet.Numerics.Random.MersenneTwister(0);
var dir = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(_polRange, _aziRange, rng);
Assert.Less(Math.Abs(dir.Ux - _tp[34]), ACCEPTABLE_PRECISION);
Assert.Less(Math.Abs(dir.Uy - _tp[35]), ACCEPTABLE_PRECISION);
Assert.Less(Math.Abs(dir.Uz - _tp[36]), ACCEPTABLE_PRECISION);
}
/// <summary>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
double curved = 2 * Math.PI * _fiberRadius * _fiberHeightZ * _curvedSurfaceEfficiency;
double bottom = Math.PI * _fiberRadius * _fiberRadius * _bottomSurfaceEfficiency;
Direction finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
SourceDefaults.DefaultHalfPolarAngleRange.Clone(),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng);
Position finalPosition = SourceDefaults.DefaultPosition.Clone();
if (_fiberRadius > 0.0)
{
if (Rng.NextDouble() > bottom / (curved + bottom)) //Consider
{ /* Curved surface */
// To utilize the final direction given above, we can assume a tube
// parallel to the y-axis. We can rotate it about the x-axis by pi/2
// to compute the new direction.
SourceToolbox.UpdateDirectionAfterRotatingAroundXAxis(-0.5 * Math.PI, finalDirection);
//Sample tube perimeter first to compute x and y coordinates
finalPosition = SourceToolbox.GetPositionAtCirclePerimeter(finalPosition,
_fiberRadius,
Rng);
//Sample tube height to compute z coordinate
finalPosition.Z = _fiberHeightZ * (Rng.NextDouble() - 0.5);
}
else
{ /* Bottom Surface */
//Shift finalPosition by _fiberHeightZ / 2
finalPosition = new Position(0.0, 0.0, _fiberHeightZ * 0.5);
//Sample the bottom face to find x, y coordinates of the emission
finalPosition = SourceToolbox.GetPositionInACircleRandomFlat(finalPosition,
0.0,
_fiberRadius,
Rng);
}
}
//Find the relevent polar and azimuthal pair for the direction
PolarAzimuthalAngles _rotationalAnglesOfPrincipalSourceAxis = SourceToolbox.GetPolarAzimuthalPairFromDirection(_newDirectionOfPrincipalSourceAxis);
//Translation and source rotation
SourceToolbox.UpdateDirectionPositionAfterGivenFlags(
ref finalPosition,
ref finalDirection,
_rotationalAnglesOfPrincipalSourceAxis,
_translationFromOrigin,
_rotationAndTranslationFlags);
var photon = new Photon(finalPosition, finalDirection, 1.0, tissue, _initialTissueRegionIndex, Rng);
return photon;
}
/// <summary>
/// Returns direction for a given position
/// </summary>
/// <param name="position">position</param>
/// <returns>new direction</returns>
protected override Direction GetFinalDirection(Position position)
{
var azimuthalAngleEmissionRange = SourceDefaults.DefaultAzimuthalAngleRange.Clone();
var polarAngleEmissionRange = SourceDefaults.DefaultFullPolarAngleRange.Clone();
//Sample angular distribution
Direction finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(polarAngleEmissionRange, azimuthalAngleEmissionRange, Rng);
return(finalDirection);
}
/// <summary>
/// Returns direction for a given position
/// </summary>
/// <param name="position">position</param>
/// <returns>new direction</returns>
protected override Direction GetFinalDirection(Position position)
{
if (_lineLength == 0.0)
{
return(SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
new DoubleRange(0.0, Math.Abs(_thetaConvOrDiv)),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng));
}
// sign is negative for diverging and positive positive for converging
var polarAngle = SourceToolbox.UpdatePolarAngleForDirectionalSources(
0.5 * _lineLength,
position.X,
_thetaConvOrDiv);
return(SourceToolbox.GetDirectionForGiven2DPositionAndGivenPolarAngle(polarAngle, position));
}
/// <summary>
/// Returns direction for a given position
/// </summary>
/// <param name="position">position</param>
/// <returns>new direction</returns>
protected override Direction GetFinalDirection(Position position)
{
if ((_rectLengthX == 0.0) && (_rectWidthY == 0.0))
{
return(SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
new DoubleRange(0.0, Math.Abs(_thetaConvOrDiv)),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng));
}
else
{
// sign is negative for diverging and positive positive for converging
var polarAngle = SourceToolbox.UpdatePolarAngleForDirectionalSources(
_rectLengthX,
Math.Sqrt(position.X * position.X + position.Y * position.Y),
_thetaConvOrDiv);
return(SourceToolbox.GetDirectionForGiven2DPositionAndGivenPolarAngle(polarAngle, position));
}
}
/// <summary>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
//sample angular distribution
Direction finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
SourceDefaults.DefaultHalfPolarAngleRange.Clone(),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng);
//Translate the photon to _tubeRadius length below the origin. Ring lies on yz plane.
Position finalPosition = new Position(0.0, 0.0, _tubeRadius);
//Sample a ring that emits photons outside.
SourceToolbox.UpdateDirectionPositionAfterRotatingAroundXAxis(
2.0 * Math.PI * Rng.NextDouble(),
ref finalDirection,
ref finalPosition);
//Ring lies on xy plane. z= 0;
SourceToolbox.UpdateDirectionPositionAfterRotatingAroundYAxis(
0.5 * Math.PI,
ref finalDirection,
ref finalPosition);
//Sample tube height
finalPosition.Z = _tubeHeightZ * (2.0 * Rng.NextDouble() - 1.0);
//Find the relevent polar and azimuthal pair for the direction
PolarAzimuthalAngles _rotationalAnglesOfPrincipalSourceAxis = SourceToolbox.GetPolarAzimuthalPairFromDirection(_newDirectionOfPrincipalSourceAxis);
//Translation and source rotation
SourceToolbox.UpdateDirectionPositionAfterGivenFlags(
ref finalPosition,
ref finalDirection,
_rotationalAnglesOfPrincipalSourceAxis,
_translationFromOrigin,
_rotationAndTranslationFlags);
var photon = new Photon(finalPosition, finalDirection, tissue, _initialTissueRegionIndex, Rng);
return(photon);
}
/// <summary>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
//sample angular distribution
Direction finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
SourceDefaults.DefaultHalfPolarAngleRange.Clone(),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng);
Position finalPosition = SourceDefaults.DefaultPosition.Clone();
if (_tubeRadius > 0.0)
{
// To utilize the final direction given above, we can assume a tube
// parallel to the y-axis. We can rotate it about the x-axis by pi/2
// to compute the new direction.
SourceToolbox.UpdateDirectionAfterRotatingAroundXAxis(0.5 * Math.PI, finalDirection);
//Sample tube perimeter first to compute x and y coordinates
finalPosition = SourceToolbox.GetPositionAtCirclePerimeter(finalPosition,
_tubeRadius,
Rng);
//Sample tube height to compute z coordinate
finalPosition.Z = _tubeHeightZ * (Rng.NextDouble() - 0.5);
}
//Find the relevent polar and azimuthal pair for the direction
PolarAzimuthalAngles _rotationalAnglesOfPrincipalSourceAxis = SourceToolbox.GetPolarAzimuthalPairFromDirection(_newDirectionOfPrincipalSourceAxis);
//Translation and source rotation
SourceToolbox.UpdateDirectionPositionAfterGivenFlags(
ref finalPosition,
ref finalDirection,
_rotationalAnglesOfPrincipalSourceAxis,
_translationFromOrigin,
_rotationAndTranslationFlags);
var photon = new Photon(finalPosition, finalDirection, 1.0, tissue, _initialTissueRegionIndex, Rng);
return(photon);
}
/// <summary>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
//Sample emitting side
String cSide = SelectEmittingSurface(
_cubeLengthX,
_cubeWidthY,
_cubeHeightZ,
Rng);
//sample angular distribution
Direction finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
_polarAngleEmissionRange,
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng);
Position tempPosition = null;
Position finalPosition = null;
switch (cSide)
{
case "xpos":
tempPosition = GetFinalPosition(_beamDiameterFWHM, _cubeHeightZ, _cubeWidthY, Rng);
finalPosition.X = 0.5 * _cubeLengthX;
finalPosition.Y = tempPosition.Y;
finalPosition.Z = tempPosition.X;
finalDirection = SourceToolbox.UpdateDirectionAfterRotatingAroundXAxis(0.5 * Math.PI, finalDirection);
break;
case "xneg":
tempPosition = GetFinalPosition(_beamDiameterFWHM, _cubeHeightZ, _cubeWidthY, Rng);
finalPosition.X = -0.5 * _cubeLengthX;
finalPosition.Y = tempPosition.Y;
finalPosition.Z = tempPosition.X;
finalDirection = SourceToolbox.UpdateDirectionAfterRotatingAroundXAxis(-0.5 * Math.PI, finalDirection);
break;
case "ypos":
tempPosition = GetFinalPosition(_beamDiameterFWHM, _cubeLengthX, _cubeHeightZ, Rng);
finalPosition.X = tempPosition.X;
finalPosition.Y = 0.5 * _cubeWidthY;
finalPosition.Z = tempPosition.Y;
finalDirection = SourceToolbox.UpdateDirectionAfterRotatingAroundYAxis(0.5 * Math.PI, finalDirection);
break;
case "yneg":
tempPosition = GetFinalPosition(_beamDiameterFWHM, _cubeLengthX, _cubeHeightZ, Rng);
finalPosition.X = tempPosition.X;
finalPosition.Y = -0.5 * _cubeWidthY;
finalPosition.Z = tempPosition.Y;
finalDirection = SourceToolbox.UpdateDirectionAfterRotatingAroundYAxis(-0.5 * Math.PI, finalDirection);
break;
case "zpos":
tempPosition = GetFinalPosition(_beamDiameterFWHM, _cubeLengthX, _cubeWidthY, Rng);
finalPosition.X = tempPosition.X;
finalPosition.Y = tempPosition.Y;
finalPosition.Z = 0.5 * _cubeHeightZ;
break;
case "zneg":
tempPosition = GetFinalPosition(_beamDiameterFWHM, _cubeLengthX, _cubeWidthY, Rng);
finalPosition.X = tempPosition.X;
finalPosition.Y = tempPosition.Y;
finalPosition.Z = -0.5 * _cubeHeightZ;
//reverse signs
finalDirection.Uz = -finalDirection.Uz;
break;
}
//Find the relevent polar and azimuthal pair for the direction
PolarAzimuthalAngles _rotationalAnglesOfPrincipalSourceAxis = SourceToolbox.GetPolarAzimuthalPairFromDirection(_newDirectionOfPrincipalSourceAxis);
//Translation and source rotation
SourceToolbox.UpdateDirectionPositionAfterGivenFlags(
ref finalPosition,
ref finalDirection,
_rotationalAnglesOfPrincipalSourceAxis,
_translationFromOrigin,
_rotationAndTranslationFlags);
var photon = new Photon(finalPosition, finalDirection, tissue, _initialTissueRegionIndex, Rng);
return(photon);
}
/// <summary>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
double curved = 2 * Math.PI * _fiberRadius * _fiberHeightZ * _curvedSurfaceEfficiency;
double bottom = Math.PI * _fiberRadius * _fiberRadius * _bottomSurfaceEfficiency;
Direction finalDirection;
Position finalPosition;
if (_fiberRadius > 0.0)
{
if (Rng.NextDouble() > bottom / (curved + bottom))
{
//sample angular distribution
finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
SourceDefaults.DefaultHalfPolarAngleRange.Clone(),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng);
//Translate the photon to _tubeRadius length below the origin. Ring lies on yz plane.
finalPosition = new Position(0.0, 0.0, _fiberRadius);
//Sample a ring that emits photons outside.
SourceToolbox.UpdateDirectionPositionAfterRotatingAroundXAxis(
2.0 * Math.PI * Rng.NextDouble(),
ref finalDirection,
ref finalPosition);
//Ring lies on xy plane. z= 0;
SourceToolbox.UpdateDirectionPositionAfterRotatingAroundYAxis(
0.5 * Math.PI,
ref finalDirection,
ref finalPosition);
//Sample tube height
finalPosition.Z = _fiberHeightZ * (2.0 * Rng.NextDouble() - 1.0);
}
else
{
finalPosition = SourceToolbox.GetPositionInACircleRandomFlat(
SourceDefaults.DefaultPosition.Clone(),
0.0,
_fiberRadius,
Rng);
finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
SourceDefaults.DefaultHalfPolarAngleRange.Clone(),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng);
}
}
else
{
finalPosition = SourceToolbox.GetPositionInALineRandomFlat(
SourceDefaults.DefaultPosition.Clone(),
_fiberHeightZ,
Rng);
finalDirection = SourceToolbox.GetDirectionForGivenPolarAzimuthalAngleRangeRandom(
SourceDefaults.DefaultFullPolarAngleRange.Clone(),
SourceDefaults.DefaultAzimuthalAngleRange.Clone(),
Rng);
//Rotate 90degrees around y axis
SourceToolbox.UpdateDirectionPositionAfterRotatingAroundYAxis(
0.5 * Math.PI,
ref finalDirection,
ref finalPosition);
}
//Find the relevent polar and azimuthal pair for the direction
PolarAzimuthalAngles _rotationalAnglesOfPrincipalSourceAxis = SourceToolbox.GetPolarAzimuthalPairFromDirection(_newDirectionOfPrincipalSourceAxis);
//Translation and source rotation
SourceToolbox.UpdateDirectionPositionAfterGivenFlags(
ref finalPosition,
ref finalDirection,
_rotationalAnglesOfPrincipalSourceAxis,
_translationFromOrigin,
_rotationAndTranslationFlags);
var photon = new Photon(finalPosition, finalDirection, tissue, _initialTissueRegionIndex, Rng);
return(photon);
}