/// <summary>
/// method to determine index of region photon is about to enter
/// </summary>
/// <param name="photon">photon info including position and direction</param>
/// <returns>region index</returns>
public int GetNeighborRegionIndex(Photon photon)
{
if (photon.DP.Direction.Uz == 0.0)
{
throw new Exception("GetNeighborRegionIndex called and Photon not on boundary");
}
if (photon.DP.Direction.Uz > 0.0) // move to layer below if pointed down
{
return(Math.Min(photon.CurrentRegionIndex + 1, Regions.Count - 1));
}
else // pointed up
{
if (photon.CurrentRegionIndex == 1) // check if at surface
{
if (_surfaceFiberRegion.ContainsPosition(photon.DP.Position))
{
return(Regions.Count - 1); // return index of surfaceFiberRegion
}
return(0); // return air
}
else
{
if (photon.CurrentRegionIndex == 3) // in surfaceFiberRegion
{
return(0);
}
}
return(photon.CurrentRegionIndex - 1); // must be layer above
}
}
public void InitializeFluorescentRegionArrays()
{
MapOfXAndYAndZ = new int[X.Count - 1, Y.Count - 1, Z.Count - 1];
PDFOfXAndYAndZ = new double[X.Count - 1, Y.Count - 1, Z.Count - 1];
CDFOfXAndYAndZ = new double[X.Count - 1, Y.Count - 1, Z.Count - 1];
// the following algorithm assumes that if the midpoint of the voxel is inside the
// fluorescent tissue region, then it is part of emission
TotalProb = 0.0;
for (int i = 0; i < X.Count - 1; i++)
{
double xMidpoint = X.Start + i * X.Delta + X.Delta / 2;
for (int j = 0; j < Y.Count - 1; j++)
{
var yMidpoint = Y.Start + j * Y.Delta + Y.Delta / 2;
for (int k = 0; k < Z.Count - 1; k++)
{
var zMidpoint = Z.Start + k * Z.Delta + Z.Delta / 2;
//xMidpoint = -1.85; // debug code
//yMidpoint = 4.65;
//zMidpoint = 0.85;
// first check if in tissue region
bool inFluorescentTissue = FluorescentTissueRegion.ContainsPosition(
new Position(xMidpoint, yMidpoint, zMidpoint));
// next check if not in bounding region if exists
if (BoundedTissueRegion != null)
{
inFluorescentTissue = BoundedTissueRegion.ContainsPosition(
new Position(xMidpoint, yMidpoint, zMidpoint));
}
// default values of numeric array elements are set to 0 so no else needed
if (inFluorescentTissue)
{
MapOfXAndYAndZ[i, j, k] = 1;
PDFOfXAndYAndZ[i, j, k] = AOfXAndYAndZ[i, j, k];
TotalProb += AOfXAndYAndZ[i, j, k];
CDFOfXAndYAndZ[i, j, k] += TotalProb;
}
}
}
}
// create pdf and cdf
for (int i = 0; i < X.Count - 1; i++)
{
for (int j = 0; j < Y.Count - 1; j++)
{
for (int k = 0; k < Z.Count - 1; k++)
{
if (MapOfXAndYAndZ[i, j, k] == 1)
{
PDFOfXAndYAndZ[i, j, k] /= TotalProb;
CDFOfXAndYAndZ[i, j, k] /= TotalProb;
}
}
}
}
}
public void InitializeFluorescentRegionArrays()
{
MapOfRhoAndZ = new int[Rho.Count - 1, Z.Count - 1];
PDFOfRhoAndZ = new double[Rho.Count - 1, Z.Count - 1];
CDFOfRhoAndZ = new double[Rho.Count - 1, Z.Count - 1];
// the following algorithm assumes that if the midpoint of the voxel is inside the
// fluorescent tissue region, then it is part of emission
TotalProb = 0.0;
for (int i = 0; i < Rho.Count - 1; i++)
{
// following code assumes tissue region is cylindrical in nature
// therefore, if (rho,z) in region, (x=rho,0,z) is in region
var xMidpoint = Rho.Start + i * Rho.Delta + Rho.Delta / 2;
var yMidpoint = 0.0;
for (int k = 0; k < Z.Count - 1; k++)
{
var zMidpoint = Z.Start + k * Z.Delta + Z.Delta / 2;
bool inFluorescentTissue = FluorescentTissueRegion.ContainsPosition(
new Position(xMidpoint, yMidpoint, zMidpoint));
// next check if not in bounding region if exists
if (BoundedTissueRegion != null)
{
inFluorescentTissue = BoundedTissueRegion.ContainsPosition(
new Position(xMidpoint, yMidpoint, zMidpoint));
}
// default values of numeric array elements are set to 0 so no else needed
if (inFluorescentTissue)
{
MapOfRhoAndZ[i, k] = 1;
PDFOfRhoAndZ[i, k] = AOfRhoAndZ[i, k];
TotalProb += AOfRhoAndZ[i, k];
CDFOfRhoAndZ[i, k] += TotalProb;
}
}
}
// create pdf and cdf
for (int i = 0; i < Rho.Count - 1; i++)
{
for (int k = 0; k < Z.Count - 1; k++)
{
if (MapOfRhoAndZ[i, k] == 1)
{
PDFOfRhoAndZ[i, k] /= TotalProb;
CDFOfRhoAndZ[i, k] /= TotalProb;
}
}
}
}
/// <summary>
/// diffuse reflectance VB
/// </summary>
/// <param name="tissue">ITissue</param>
/// <param name="detectorController">IDetectorController</param>
/// <param name="name">string name</param>
public BoundingCylinderVirtualBoundary(ITissue tissue, IDetectorController detectorController, string name)
{
_boundingTissueRegion = tissue.Regions[tissue.Regions.Count - 1]; // bounding region always last by convention
_center = _boundingTissueRegion.Center;
_radius = ((CaplessCylinderTissueRegion)_boundingTissueRegion).Radius;
WillHitBoundary = dp =>
dp.StateFlag.HasFlag(PhotonStateType.PseudoBoundingVolumeTissueBoundary) &&
_boundingTissueRegion.ContainsPosition(dp.Position);
VirtualBoundaryType = VirtualBoundaryType.BoundingCylinderVolume;
PhotonStateType = PhotonStateType.PseudoBoundingCylinderVolumeVirtualBoundary;
_detectorController = detectorController;
Name = name;
}
/// <summary>
/// method to get tissue region index of photon's current position
/// </summary>
/// <param name="position">photon Position</param>
/// <returns>integer tissue region index</returns>
public int GetRegionIndex(Position position)
{
// if it's in the inclusion, return "3", otherwise, call the layer method to determine
return(_inclusionRegion.ContainsPosition(position) ? _inclusionRegionIndex : base.GetRegionIndex(position));
}
/// <summary>
/// method to get tissue region index of photon's current position
/// </summary>
/// <param name="position">photon Position</param>
/// <returns>integer tissue region index</returns>
public override int GetRegionIndex(Position position)
{
// if it's in the bounding region, return "3", otherwise, call the layer method to determine
return(!_boundingRegion.ContainsPosition(position) ? _boundingRegionExteriorIndex : base.GetRegionIndex(position));
}
