Virtual Photonics Technology Initiative

Conventional Monte Carlo

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Contents

Monte Carlo 1.0

Download:

To download the Monte Carlo 1.0 command-line application visit our CodePlex site.

Application Instructions

Additional Documentation

For a description of the command-line parameters and sample command-line inputs visit our documentation on CodePlex.

Simulation Input:

  1. Number of photons
  2. OutputName: name of folder to place results
  3. Simulation Options: Seed (-1=random, >=0 reproducible simulation)
  4. Simulation Options: Absorption Weighting Type (Analog, Discrete Absorption Weighting, Continuous Absorption Weighting)
  5. Simulation Options: Phase Function Type (Henyey-Greenstein, Bidirectional)
  6. Simulation Options: Track statistics (number of photons out top, bottom, killed and how killed)
  7. Simulation Options: Indicator to Write Histories to Binary File
  8. Simulation Options: Russian Roulette weight threshold, threshold > 0.0 (typical value 0.0001) game of chance with probability 0.1 played when photon weight below threshold, threshold=0.0 then no RR performed
  9. Source definition
  10. Tissue definition
  11. Detectors to be tallied

Simulation Output:

  1. Detector tallies written to binary files named [].
  2. Second moment tallies written to binary files named []_2.

Sources:

For descriptions of all sources click here.

directional point source
  • DirectionalPointSource (Position pointLocation, Direction direction, int initialTissueRegionIndex). This describes a directional point source with a specified orientation e.g.
  1. normal to tissue surface, starting inside tissue: Position=(0,0,0), Direction=(0,0,1), initialTissueRegionIndex=1.This photon does not go through Fresnel at the tissue surface.
  2. If Position=(0,0,0) and initialTissueRegionIndex=0, then the photon goes through Fresnel at the tissue surface. This means that some photons, depending on their direction, will be reflected at the tissue surface.

Tissues:

Tissues are comprised of Tissue Regions. Example input files are bundled with the MC1.0 download or can be downloaded from the VTS GUI using the Monte Carlo Solver Panel and clicking "Download Prototype Input Files".

  • MultiLayerTissue (IList<LayerRegion>).

MultiLayerTissue is comprised of LayerRegions, for example a homogeneous slab of thickness T would have 3 LayerRegions: 1) air above (layer [start, stop]=[-inf, 0]) , 2) tissue (layer [start, stop]=[0, T]), 3) air below (layer [start, stop]=[T, inf]). The layers should be specified in order from top to bottom and be contiguous, i.e. each layer stop location should agree with the next layer's start location.

  • SingleEllipsoidTissue (IList<LayerRegion> concat EllipsiodRegion)

SingleEllipsoidTissue is comprised of LayerRegions concatentated with an EllipsoidRegion. It is assumed that the ellipsoid is contained entirely within a layer region (the ellipsoid cannot span more than 1 layer region). It is also assumed that the refractive index of the ellipsoid is equal to that of the layer is within. Refractive index mismatch between ellipsoid and surrounding tissue layer is planned for a future release of the software.

Tissue Regions:

  • LayerRegion (DoubleRange zRange, OpticalProperties ops). This defines a layer infinite in extent along x,y-axes
  • EllipsoidRegion (Position center, double radiusX, double radiusY, double radiusZ, OpticalProperties ops).
  • CylinderRegion (Position center, double radius, double height, OpticalProperties ops).
  • VoxelRegion (DoubleRange x, DoubleRange y, DoubleRange z, OpticalProperties ops).

Detectors:

  • Absorbed Energy
  1. A(ρ,z) [AOfRhoAndZ]: captures deposited energy within volumes designated by cylindrical coordinates [rho,z: mm]. This has been implemented for analog, DAW absorption weighting and unit tested.
  • Fluence
  1. Fluence(ρ,z) [FluenceOfRhoAndZ]: captures fluence within volumes designed by cylindrical coordinates [rho,z: mm]. This has been implemented for analog, DAW absorption weighting and unit tested.
  • Reflectance
  1. Rd [RDiffuse]: captures total diffusely reflected photons (photons that have entered the tissue). This has been implemented for analog, DAW, CAW absorption weighting and unit tested
  2. R(angle) [ROfAngle]: captures reflected photons as a function of polar angle [theta: radians]. This has been implemented for analog, DAW, CAW absorption weighting and unit tested
  3. R(ρ,angle) [ROfRhoAndAngle]: captures reflected photons as a function of circular ring detectors on the surface of the tissue [rho: mm] and polar angle [theta: radians]. This has been implemented for analog, DAW, CAW absorption weighting and unit tested.
  4. R(ρ,ω) [RofRhoAndOmega]: captures reflected photons as a function of circular ring detectors on the surface of the tissue [rho: mm] and temporal frequency [omega: GHz]. This has been implemented for analog, DAW, CAW absorption weighting and unit tested.
  5. R(ρ,t) [ROfRhoAndTime]: captures reflected photons as a function of circular ring detectors on the surface of the tissue [rho: mm] and time [time: ns]. This has been implemented for analog, DAW, CAW absorption weighting and unit tested.
  6. R(ρ) [ROfRho]: captures reflected photons as a function of circular ring detectors on the surface of the tissue [rho: mm]. This has been implemented for analog, DAW, CAW absorption weighting and unit tested.
  7. R(x,y) [ROfXAndY]: captures reflected photons as a function of Cartesian detectors on the surface of the tissue [x,y: mm]. This has been implemented for analog, DAW, CAW absorption weighting and unit tested.
  • Transmittance
  1. Td [TDiffuse]: captures total diffusely transmitted photons. This has been implemented using analog, DAW, CAW absorption weighting and unit tested.
  2. T(angle) [TOfAngle]: captures transmitted photons as a function of polar angle [theta: radians]. This has been implemented for analog, DAW, CAW absorption weighting and unit tested.
  3. T(ρ,angle) [TOfRhoAndAngle]: captures transmitted photons as a function of circular ring detectors on the surface of the tissue [rho: mm] and polar angle [theta: radians]. This has been implemented for analog, DAW, CAW absorption weighting and unit tested.
  4. T(ρ) [TOfRho]: captures transmitted photons as a functino of polar angle [rho: radians]. This has been implementd for analog, DAW, CAW absorption weighting and unit tested.
  • Radiance
  1. Radiance(ρ,z,θ) [RadianceOfRhoAndZAndAngle]: captures radiance within volumes designated by cylindrical coordinates [rho,z: mm] and polar angle [theta: radians]. This has been implemented for analog, DAW absorption weighting and unit tested.
  2. Radiance(x,y,z,θ,φ) [RadianceOfXAndYAndZAndThetaAndPhi]: captures radiance within volumes designated by Cartesian coordinates [x,y,z: mm], polar angles [theta: radians], and azimuthal angles [phi: radians]. This has been implemented for analog, DAW absorption weighting and unit tested.
  • Momentum Transfer
  1. MomentumTransfer(ρ,z) [MomentumTransferOfRhoAndZ]


Command Line Application:

  • Command line application that allows the user to run a Monte Carlo

simulation given a SimulationInput xml file. Use "mc help" for options.

  • User can specify several MC simulations that execute in parallel

with varying optical properties.

Post Processing:

  • Command line post-processor that can read PhotonTerminationDatabase and

generate specified detector tally results. Use "mc_post help" for options.

Perturbation Monte Carlo (pMC):

  • Perturbation Monte Carlo (pMC) capabilities available that will provide

detector tally results for perturbed optical properties (mua and mus).

  1. R(rho)[pMCROfRho] DAW unit tested
  2. R(rho,t) [pMCROfRhoAndTime] DAW unit tested
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