public void verify_that_GetFinalPositionAndWeight_samples_from_CDFOfRhoAndZ_correctly()
{
var countArray = new int[_aOfRhoAndZDetector.Rho.Count - 1,
_aOfRhoAndZDetector.Z.Count - 1];
ITissueInput tissueInput = new SingleInfiniteCylinderTissueInput();
ITissue tissue = tissueInput.CreateTissue(AbsorptionWeightingType.Discrete,
PhaseFunctionType.HenyeyGreenstein, 0);
tissue.Regions[1] = _rhozLoaderCDF.FluorescentTissueRegion;
for (int i = 0; i < 100; i++)
{
var photon = _fluorEmissionAOfRhoAndZSourceCDF.GetNextPhoton(tissue);
// verify that photons start within range of midpoints of voxels in bounding cylinder
var rho = Math.Sqrt(photon.DP.Position.X * photon.DP.Position.X +
photon.DP.Position.Y * photon.DP.Position.Y);
Assert.IsTrue(rho <= 3.5);
Assert.IsTrue((photon.DP.Position.Z >= 0.5) && (photon.DP.Position.Z <= 1.5));
Assert.IsTrue(Math.Abs(photon.DP.Weight - 1.0) < 1e-6);
int irho = (int)(Math.Floor(rho));
int iz = (int)(Math.Floor(photon.DP.Position.Z));
countArray[irho, iz] += 1;
}
// check that countArray is > 1 in region of AOfRhoAndZ
Assert.AreEqual(countArray[0, 0], 2);
Assert.AreEqual(countArray[0, 1], 4);
Assert.AreEqual(countArray[1, 0], 11);
Assert.AreEqual(countArray[1, 1], 7);
Assert.AreEqual(countArray[2, 0], 12);
Assert.AreEqual(countArray[2, 1], 19);
Assert.AreEqual(countArray[3, 0], 22);
Assert.AreEqual(countArray[3, 1], 23);
}
public void Initialize(ITissue tissue, Random rng)
{
// intialize any necessary class fields here
_tissue = tissue;
_rng = rng;
//_ops = _tissue.Regions.Select(r => r.RegionOP).ToArray();
// assign any user-defined outputs (except arrays...we'll make those on-demand)
TallyCount = 0;
NumSubregions = _tissue.Regions.Count;
// if the data arrays are null, create them (only create second moment if TallySecondMoment is true)
Mean = Mean ?? new double[X.Count - 1, Y.Count - 1, MTBins.Count - 1];
SecondMoment = SecondMoment ?? (TallySecondMoment ? new double[X.Count - 1, Y.Count - 1, MTBins.Count - 1] : null);
TotalMTOfZ = TotalMTOfZ ?? new double[X.Count - 1, Y.Count - 1, Z.Count - 1];
DynamicMTOfZ = DynamicMTOfZ ?? new double[X.Count - 1, Y.Count - 1, Z.Count - 1];
TotalMTOfZSecondMoment = TotalMTOfZSecondMoment ?? new double[X.Count - 1, Y.Count - 1, Z.Count - 1];
DynamicMTOfZSecondMoment = DynamicMTOfZSecondMoment ?? new double[X.Count - 1, Y.Count - 1, Z.Count - 1];
// Fractional MT has FractionalMTBins.Count numnber of bins PLUS 2, one for =1, an d one for =0
FractionalMT = FractionalMT ?? new double[X.Count - 1, Y.Count - 1, MTBins.Count - 1, FractionalMTBins.Count + 1];
SubregionCollisions = new double[NumSubregions, 2]; // 2nd index: 0=static, 1=dynamic
// intialize any other necessary class fields here
_bloodVolumeFraction = BloodVolumeFraction;
}
public void verify_that_GetFinalPositionAndWeight_samples_from_UnifOfRhoAndZ_sampling_correctly()
{
ITissueInput tissueInput = new SingleInfiniteCylinderTissueInput();
ITissue tissue = tissueInput.CreateTissue(AbsorptionWeightingType.Discrete,
PhaseFunctionType.HenyeyGreenstein, 0);
tissue.Regions[1] = _xyzLoaderUnif.FluorescentTissueRegion;
for (int i = 0; i < 100; i++)
{
var photon = _fluorEmissionAOfRhoAndZSourceUnif.GetNextPhoton(tissue);
// verify that photons start within range of midpoints of voxels in infinite cylinder
Assert.IsTrue(photon.DP.Position.X <= 3.5);
Assert.AreEqual(photon.DP.Position.Y, 0);
Assert.IsTrue((photon.DP.Position.Z >= 0.5) && (photon.DP.Position.Z <= 1.5));
// verify sampling is proceeding in coded sequence
// detector center=(0,0,1) radius=4, rho=[0 4] 4 bins, z=[0 2] 2 bins
var ir = DetectorBinning.WhichBin(DetectorBinning.GetRho(
photon.DP.Position.X, photon.DP.Position.Y),
_rhozLoaderUnif.Rho.Count - 1, _rhozLoaderUnif.Rho.Delta, _rhozLoaderUnif.Rho.Start);
var iz = DetectorBinning.WhichBin(photon.DP.Position.Z, _rhozLoaderUnif.Z.Count - 1, _rhozLoaderUnif.Z.Delta, _rhozLoaderUnif.Z.Start);
var rhozNorm = (_rhozLoaderUnif.Rho.Start + (ir + 0.5) * _rhozLoaderUnif.Rho.Delta) * 2.0 * Math.PI * _rhozLoaderUnif.Rho.Delta * _rhozLoaderUnif.Z.Delta;
// verify weight at location is equal to AOfRhoAndZ note: setup with single y bin
// expected: Map [ 1 1 1 1; 1 1 1 1] row major
// expected: A [ 1 3 5 7; 2 4 6 8] row major
Assert.IsTrue(Math.Abs(photon.DP.Weight -
_rhozLoaderUnif.AOfRhoAndZ[ir, iz] * rhozNorm) < 1e-6);
}
}
/*/// <summary>
* /// Surface molecular pattern of the cell. An array of bits each of which represents a nucleotide.
* /// </summary>
* public MolecularPattern Pattern
* {
* get { return pattern; }
* }*/
#endregion
#region Public Methods
/*public Cell(CellType type, ITissue parent, MolecularPattern initialPattern)
* {
* Type = type;
* Parent = parent;
* pattern = initialPattern;
* maturationLevel = CellMaturationLevel.Immature;
* Start();
* }*/
public Cell(CellType type, ITissue parent)
{
Type = type;
Parent = parent;
maturationLevel = CellMaturationLevel.Immature;
Start();
}
public void verify_that_GetFinalPositionAndWeight_samples_from_UnifOfXAndYAndZ_sampling_correctly()
{
ITissueInput tissueInput = new SingleInfiniteCylinderTissueInput();
ITissue tissue = tissueInput.CreateTissue(AbsorptionWeightingType.Discrete,
PhaseFunctionType.HenyeyGreenstein, 0);
tissue.Regions[3] = _xyzLoaderUnif.FluorescentTissueRegion;
var xyzNorm = _xyzLoaderUnif.X.Delta * _xyzLoaderUnif.Y.Delta * _xyzLoaderUnif.Z.Delta;
int ix, iz;
for (int i = 0; i < 100; i++)
{
var photon = _fluorEmissionAOfXAndYAndZSourceUnif.GetNextPhoton(tissue);
// verify that photons start within range of midpoints of voxels in infinite cylinder
Assert.IsTrue((photon.DP.Position.X >= -0.5) && (photon.DP.Position.X <= 0.5));
Assert.AreEqual(photon.DP.Position.Y, 0);
Assert.IsTrue((photon.DP.Position.Z >= 0.5) && (photon.DP.Position.Z <= 1.5));
// verify sampling is proceeding in coded sequence
// detector x=[-2 2] 4 bins, y=[-10 10] 1 bin, z=[0 3] 3 bins
ix = (int)(photon.DP.Position.X + 0.5) + 1;
iz = (int)(Math.Floor(photon.DP.Position.Z));
// verify weight at location is equal to AOfXAndYAndZ note: setup with single y bin
// expected: Map [ 0 1 1 0; 0 1 1 0; 0 0 0 0] row major
// expected: A [ 1 4 7 10; 2 5 8 11; 3 6 9 12] row major
Assert.IsTrue(Math.Abs(photon.DP.Weight -
_xyzLoaderUnif.AOfXAndYAndZ[ix, 0, iz] * xyzNorm) < 1e-6);
}
}
public static UnmanagedTissue ToUnmanagedTissue(this ITissue tissptr)
{
UnmanagedTissue unmanagedTissue = new UnmanagedTissue();
// comment to rework later
//unmanagedTissue.num_layers = tissptr.num_layers;
////unmanagedTissue.z_focus = tissptr.z_focus;
////unmanagedTissue.NA = tissptr.NA;
//unmanagedTissue.cylinder_radius = tissptr.cylinder_radius;
//unmanagedTissue.cylinder_height = tissptr.cylinder_height;
//unmanagedTissue.zup = tissptr.zup;
//unmanagedTissue.zlow = tissptr.zlow;
//unmanagedTissue.do_ellip_layer = tissptr.do_ellip_layer;
//unmanagedTissue.ellip_x = tissptr.ellip_x;
//unmanagedTissue.ellip_y = tissptr.ellip_y;
//unmanagedTissue.ellip_z = tissptr.ellip_z;
//unmanagedTissue.ellip_rad_x = tissptr.ellip_rad_x;
//unmanagedTissue.ellip_rad_y = tissptr.ellip_rad_y;
//unmanagedTissue.ellip_rad_z = tissptr.ellip_rad_z;
//unmanagedTissue.layer_z_min = tissptr.layer_z_min;
//UnmanagedIO.Assign1DPointer(ref Tissue.Regions, ref unmanagedTissue.layerprops);
return(unmanagedTissue);
}
/// <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>
/// Surface molecular pattern of the cell. An array of bits each of which represents a nucleotide.
/// </summary>
public MolecularPattern Pattern
{
get { return pattern; }
}*/
#endregion
#region Public Methods
/*public Cell(CellType type, ITissue parent, MolecularPattern initialPattern)
{
Type = type;
Parent = parent;
pattern = initialPattern;
maturationLevel = CellMaturationLevel.Immature;
Start();
}*/
public Cell(CellType type, ITissue parent)
{
Type = type;
Parent = parent;
maturationLevel = CellMaturationLevel.Immature;
Start();
}
/// <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>
/// Class that keeps a photon's data as it moves through the tissue
/// </summary>
/// <param name="p">Position</param>
/// <param name="d">Direction</param>
/// <param name="tissue">Tissue></param>
/// <param name="currentTissueRegionIndex">integer index within ITissue definition indicating photon's current position</param>
/// <param name="generator">Random Number Generator</param>
public Photon(
Position p,
Direction d,
ITissue tissue,
int currentTissueRegionIndex,
Random generator)
{
DP = new PhotonDataPoint(
p,
d,
1.0, // weight
0.0, // total time
PhotonStateType.Alive);
//PreviousDP = null;
History = new PhotonHistory(tissue.Regions.Count);
History.AddDPToHistory(DP); // add initial datapoint
S = 0.0;
SLeft = 0.0;
CurrentRegionIndex = currentTissueRegionIndex;
// flag to determin whether passing through specular or not
// the following assumes tissues considered are slabs, only ones we have coded to date
// todo: make more general to handle other types of tissues
_firstTimeEnteringDomain = true;
if (CurrentRegionIndex >= 1) // photon does not go through specular
{
_firstTimeEnteringDomain = false;
}
CurrentTrackIndex = 0;
_tissue = tissue;
SetAbsorbAction(_tissue.AbsorptionWeightingType);
SetScatterAction(_tissue.PhaseFunctionType);
_rng = generator;
_russianRouletteWeightThreshold = _tissue.RussianRouletteWeightThreshold;
}
public DendriticCell(ITissue parent, ProcessSpampHandler spampProcessor,
ProcessSdampHandler sdampProcessor, ProcessAntigenHandler <T> antigenProcessor)
: base(CellType.APC, parent)
{
OnProcessSpamp = spampProcessor;
OnProcessSdamp = sdampProcessor;
OnProcessAntigen = antigenProcessor;
}
/// <summary>
/// controller for history type detectors
/// </summary>
/// <param name="detectors">IEnumerable of IHistoryDetector</param>
/// <param name="tissue">ITissue</param>
public HistoryDetectorController(IEnumerable <IHistoryDetector> detectors, ITissue tissue)
{
//_detectors = (from d in detectors
// where d is IHistoryDetector
// select d).ToList();
_detectors = detectors.ToList();
_tissue = tissue;
}
/// <summary>
/// generic volume virtual boundary, used to capture all internal volume detectors e.g. FluenceOfRhoAndZ
/// </summary>
/// <param name="tissue">ITissue</param>
/// <param name="detectorController">IDetectorController</param>
/// <param name="name">string name</param>
public GenericVolumeVirtualBoundary(ITissue tissue, IDetectorController detectorController, string name)
{
VirtualBoundaryType = VirtualBoundaryType.GenericVolumeBoundary;
PhotonStateType = PhotonStateType.PseudoGenericVolumeVirtualBoundary;
_detectorController = detectorController;
Name = name;
}
/// <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>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
//Source starts from anywhere in the tissue region of fluorescence
Position finalPosition = GetFinalPosition(Rng);
Direction finalDirection = GetFinalDirection(Rng);
var photon = new Photon(finalPosition, finalDirection, tissue, _initialTissueRegionIndex, Rng);
return(photon);
}
public void Initialize(ITissue tissue, Random rng)
{
// assign any user-defined outputs (except arrays...we'll make those on-demand)
TallyCount = 0;
// if the data arrays are null, create them (only create second moment if TallySecondMoment is true)
Mean = Mean ?? new double[Rho.Count - 1];
SecondMoment = SecondMoment ?? (TallySecondMoment ? new double[Rho.Count - 1] : null);
// intialize any other necessary class fields here
}
// 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>
/// Implements Get next photon
/// </summary>
/// <param name="tissue">tissue</param>
/// <returns>photon</returns>
public Photon GetNextPhoton(ITissue tissue)
{
//Source starts from anywhere in the tissue region of fluorescence
Position finalPosition = GetFinalPositionAndWeight(Rng, out _weight);
//Starting weight based on sampling method
//Lambertian direction
Direction finalDirection = GetFinalDirection(Rng);
var photon = new Photon(finalPosition, finalDirection, _weight, tissue, _initialTissueRegionIndex, Rng);
return(photon);
}
/// <summary>
/// Static method to instantiate correct CollisionInfoDatabaseWriter given a
/// virtual boundary DatabaseType, path to where to output database and database filename.
/// </summary>
/// <param name="databaseType">database type enum</param>
/// <param name="tissue">ITissue to know how many regions</param>
/// <param name="filePath">path string of database output</param>
/// <param name="outputName">filename string of database file</param>
/// <returns>a CollisionInfoDatabaseWriter</returns>
public static CollisionInfoDatabaseWriter GetCollisionInfoDatabaseWriter(
DatabaseType databaseType, ITissue tissue, string filePath, string outputName)
{
switch (databaseType)
{
default:
case DatabaseType.pMCDiffuseReflectance:
return(new CollisionInfoDatabaseWriter(VirtualBoundaryType.pMCDiffuseReflectance,
Path.Combine(filePath, outputName, "CollisionInfoDatabase"),
tissue.Regions.Count()));
}
}
public void Initialize(ITissue tissue, Random rng)
{
_tissue = tissue;
// assign any user-defined outputs (except arrays...we'll make those on-demand)
TallyCount = 0;
NumSubregions = _tissue.Regions.Count;
// if the data arrays are null, create them (only create second moment if TallySecondMoment is true)
Mean = Mean ?? new double[Rho.Count - 1, NumSubregions, Time.Count - 1];
SecondMoment = SecondMoment ?? (TallySecondMoment ? new double[Rho.Count - 1, NumSubregions, Time.Count - 1] : null);
FractionalTime = FractionalTime ?? new double[Rho.Count - 1, NumSubregions];
}
/// <summary>
/// Method to instantiate a single IDetectorInput. This method is called by
/// the method below that instantiates a list of detectors.
/// </summary>
/// <param name="detectorInput">IEnumerable of IDetectorInput</param>
/// <param name="tissue">ITissue</param>
/// <param name="rng">random number generator</param>
/// <returns>List of IDetector</returns>
public static IDetector GetDetector(IDetectorInput detectorInput, ITissue tissue, Random rng)
{
if (detectorInput == null)
{
return(null);
}
var detector = detectorInput.CreateDetector();
detector.Initialize(tissue, rng);
return(detector);
}
public HelperTCell(ITissue parent, int mpLen)
: base(CellType.Helper, parent)
{
Activators = new List<Address>();
// generate a random molecular pattern
// NOTE: pattern vectors should be normalized
var pat = new double[mpLen];
for (int i = 0; i < mpLen; i++)
{
pat[i] = RandGen.NextDouble();
}
Pattern = new MolecularPattern(pat);
}
// /// <summary>
// /// This static method instantiates a list of virtual boundaries
// /// and the appropriate detectors are deposited into it.
// /// </summary>
// /// <param name="detectors"></param>
// /// <returns></returns>
// public static IList<IVirtualBoundary> GetVirtualBoundaries(
// IList<IVirtualBoundaryInput> virtualBoundaryGroups, ITissue tissue, bool tallySecondMoment)
// {
// // this sql returns all VBs even when only RSpecularDetector in detectors
// //var virtualBoundaries =
// // from vb in EnumHelper.GetValues<VirtualBoundaryType>() // for each virtual boundary type
// // where detectors.Select(d => d.TallyType.AppliesToBoundary(vb)).First() // where any detectors apply
// // let vbDetectors = detectors.Where(d => d.TallyType.AppliesToBoundary(vb)).ToList() // gather the appropriate detectors
// // select GetVirtualBoundary(vb, tissue, vbDetectors); // and instantiate the vb with the appropriate detectors
// var virtualBoundaries = new List<IVirtualBoundary>();
// foreach (var vbg in virtualBoundaryGroups)
// {
// var detectors = DetectorFactory.GetDetectors(
// vbg.DetectorInputs, tissue, tallySecondMoment);
// var detectorController = DetectorControllerFactory.GetDetectorController(
// vbg.VirtualBoundaryType, detectors);
// if (detectors.Count > 0)
// {
// var vb = GetVirtualBoundary(vbg.VirtualBoundaryType, tissue, detectorController);
// if (vb != null)
// virtualBoundaries.Add(vb);
// }
// }
// return virtualBoundaries.ToList();
// }
/// <summary>
/// method that gets appropriate VB
/// </summary>
/// <param name="vbType">VirtualBoundaryType</param>
/// <param name="tissue">ITissue</param>
/// <param name="detectorController">IDetectorController</param>
/// <returns>IVirtualBoundary</returns>
public static IVirtualBoundary GetVirtualBoundary(
VirtualBoundaryType vbType, ITissue tissue, IDetectorController detectorController)
{
IVirtualBoundary vb = null;
// todo: predicate defines
switch (vbType)
{
case VirtualBoundaryType.DiffuseReflectance:
vb = new DiffuseReflectanceVirtualBoundary(
tissue, detectorController, VirtualBoundaryType.DiffuseReflectance.ToString());
break;
case VirtualBoundaryType.DiffuseTransmittance:
vb = new DiffuseTransmittanceVirtualBoundary(
tissue, detectorController, VirtualBoundaryType.DiffuseTransmittance.ToString());
break;
case VirtualBoundaryType.SpecularReflectance:
// reflecting off first layer without transporting in medium
vb = new SpecularReflectanceVirtualBoundary(
tissue, detectorController, VirtualBoundaryType.SpecularReflectance.ToString());
break;
case VirtualBoundaryType.SurfaceRadiance:
vb = new RadianceVirtualBoundary(
detectorController, VirtualBoundaryType.SurfaceRadiance.ToString());
break;
case VirtualBoundaryType.GenericVolumeBoundary:
vb = new GenericVolumeVirtualBoundary(
tissue, detectorController, VirtualBoundaryType.GenericVolumeBoundary.ToString());
break;
case VirtualBoundaryType.pMCDiffuseReflectance:
vb = new pMCDiffuseReflectanceVirtualBoundary(
tissue, detectorController, VirtualBoundaryType.DiffuseReflectance.ToString());
break;
case VirtualBoundaryType.BoundingCylinderVolume:
vb = new BoundingCylinderVirtualBoundary(
tissue, detectorController, VirtualBoundaryType.BoundingCylinderVolume.ToString());
break;
default:
throw new ArgumentOutOfRangeException("Virtual boundary type not recognized: " + vbType);
}
return(vb);
}
public void Initialize(ITissue tissue, Random rng)
{
// assign any user-defined outputs (except arrays...we'll make those on-demand)
TallyCount = 0;
// if the data arrays are null, create them (only create second moment if TallySecondMoment is true)
Mean = Mean ?? new double[X.Count - 1, Y.Count - 1, Z.Count - 1, Time.Count - 1];
SecondMoment = SecondMoment ?? (TallySecondMoment ? new double[X.Count - 1, Y.Count - 1, Z.Count - 1, Time.Count - 1] : null);
// intialize any other necessary class fields here
_absorptionWeightingMethod = AbsorptionWeightingMethods.GetVolumeAbsorptionWeightingMethod(tissue, this);
_tissue = tissue;
_ops = _tissue.Regions.Select(r => r.RegionOP).ToArray();
_tallyForOnePhoton = _tallyForOnePhoton ?? (TallySecondMoment ? new double[X.Count - 1, Y.Count - 1, Z.Count - 1, Time.Count - 1] : null);
}
public void Initialize(ITissue tissue, Random rng)
{
// assign any user-defined outputs (except arrays...we'll make those on-demand)
TallyCount = 0;
// if the data arrays are null, create them (only create second moment if TallySecondMoment is true)
Mean = Mean ?? new double[Rho.Count - 1, Time.Count - 1];
SecondMoment = SecondMoment ?? (TallySecondMoment ? new double[Rho.Count - 1, Time.Count - 1] : null);
// intialize any other necessary class fields here
_perturbedOps = PerturbedOps;
_referenceOps = tissue.Regions.Select(r => r.RegionOP).ToList();
_perturbedRegionsIndices = PerturbedRegionsIndices;
_absorbAction = AbsorptionWeightingMethods.GetpMCTerminationAbsorptionWeightingMethod(tissue, this);
}
public void Initialize(ITissue tissue, Random rng)
{
// assign any user-defined outputs (except arrays...we'll make those on-demand)
TallyCount = 0;
// if the data arrays are null, create them (only create second moment if TallySecondMoment is true)
Mean = new double();
if (TallySecondMoment)
{
SecondMoment = new double();
}
// initialize any other necessary class fields here
_tissue = tissue;
}
public HelperTCell(ITissue parent, int mpLen)
: base(CellType.Helper, parent)
{
Activators = new List <Address>();
// generate a random molecular pattern
// NOTE: pattern vectors should be normalized
var pat = new double[mpLen];
for (int i = 0; i < mpLen; i++)
{
pat[i] = RandGen.NextDouble();
}
Pattern = new MolecularPattern(pat);
}
/// <summary>
/// diffuse transmittance VB
/// </summary>
/// <param name="tissue">ITissue</param>
/// <param name="detectorController">IDetectorController</param>
/// <param name="name">string name</param>
public DiffuseTransmittanceVirtualBoundary(ITissue tissue, IDetectorController detectorController, string name)
{
_zPlanePosition = ((LayerTissueRegion)tissue.Regions.Where(r => r is LayerTissueRegion).Last()).ZRange.Start;
WillHitBoundary = dp =>
dp.StateFlag.HasFlag(PhotonStateType.PseudoTransmittedTissueBoundary) &&
dp.Direction.Uz > 0 &&
Math.Abs(dp.Position.Z - _zPlanePosition) < 10E-16;
VirtualBoundaryType = VirtualBoundaryType.DiffuseTransmittance;
PhotonStateType = PhotonStateType.PseudoDiffuseTransmittanceVirtualBoundary;
_detectorController = detectorController;
Name = name;
}
public void Initialize(ITissue tissue, Random rng)
{
// intialize any necessary class fields here
_tissue = tissue;
_ops = _tissue.Regions.Select(r => r.RegionOP).ToArray();
// assign any user-defined outputs (except arrays...we'll make those on-demand)
TallyCount = 0;
NumSubregions = _tissue.Regions.Count;
// if the data arrays are null, create them (only create second moment if TallySecondMoment is true)
Mean = Mean ?? new double[Rho.Count - 1, MTBins.Count - 1];
SecondMoment = SecondMoment ?? (TallySecondMoment ? new double[Rho.Count - 1, MTBins.Count - 1] : null);
// Fractional MT has FractionalMTBins.Count numnber of bins PLUS 2, one for =1, an d one for =0
FractionalMT = FractionalMT ?? new double[Rho.Count - 1, MTBins.Count - 1, NumSubregions, FractionalMTBins.Count + 1];
}
/// <summary>
/// class for perturbation Monte Carlo (pMC) diffuse reflectance virtual boundary
/// </summary>
/// <param name="tissue">ITissue</param>
/// <param name="detectorController">IDetectorController</param>
/// <param name="name">string name</param>
public pMCDiffuseReflectanceVirtualBoundary(ITissue tissue, IDetectorController detectorController, string name)
{
_zPlanePosition = ((LayerTissueRegion)tissue.Regions[0]).ZRange.Stop;
WillHitBoundary = dp =>
dp.StateFlag.HasFlag(PhotonStateType.PseudoReflectedTissueBoundary) &&
dp.Direction.Uz < 0 &&
Math.Abs(dp.Position.Z - _zPlanePosition) < 10E-16;
VirtualBoundaryType = VirtualBoundaryType.pMCDiffuseReflectance;
PhotonStateType = PhotonStateType.PseudoDiffuseReflectanceVirtualBoundary;
_detectorController = detectorController;
Name = name;
}
/// <summary>
/// generic volume virtual boundary, used to capture all internal volume detectors
/// </summary>
/// <param name="tissue">ITissue</param>
/// <param name="detectorController">IDetectorController</param>
/// <param name="name">string name</param>
public GenericVolumeVirtualBoundary(ITissue tissue, IDetectorController detectorController, string name)
{
//_zPlanePosition = ((LayerTissueRegion)tissue.Regions[0]).ZRange.Stop;
//WillHitBoundary = dp =>
// dp.StateFlag.Has(PhotonStateType.Transmitted) &&
// dp.Direction.Uz < 0 &&
// Math.Abs(dp.Position.Z - _zPlanePosition) < 10E-16;
VirtualBoundaryType = VirtualBoundaryType.GenericVolumeBoundary;
PhotonStateType = PhotonStateType.PseudoGenericVolumeVirtualBoundary;
_detectorController = detectorController;
Name = name;
}
/// <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;
}
