public void setup()
{
var name = Assembly.GetExecutingAssembly().FullName;
var assemblyName = new AssemblyName(name).Name;
// AOfXAndYAndZ in resource is defined by:
// single layer tissue with embedded infinite cylinder center=(0,0,1) radius=1
// detector x=[-2 2] 4 bins, y=[-10 10] 1 bin, z=[0 3] 3 bins
_aOfXAndYAndZDetector = (dynamic)DetectorIO.ReadDetectorFromFileInResources(
"AOfXAndYAndZ", "Resources/sourcetest/", assemblyName);
// overwrite statistical data in Mean with deterministic values to test
int count = 1;
for (int i = 0; i < _aOfXAndYAndZDetector.X.Count - 1; i++)
{
for (int j = 0; j < _aOfXAndYAndZDetector.Y.Count - 1; j++)
{
for (int k = 0; k < _aOfXAndYAndZDetector.Z.Count - 1; k++)
{
_aOfXAndYAndZDetector.Mean[i, j, k] = count; // make all nonzero and unique
++count;
}
}
}
DetectorIO.WriteDetectorToFile(_aOfXAndYAndZDetector, "sourcetest");
FileIO.CopyFileFromResources(
"Resources/sourcetest/inputAOfXAndYAndZ.txt", "sourcetest/inputAOfXAndYAndZ.txt", assemblyName);
// following setup is used to test FluorescenceEmissionSource CDF sampling method
_fluorEmissionAOfXAndYAndZSourceCDF = new FluorescenceEmissionAOfXAndYAndZSource(
"sourcetest", "inputAOfXAndYAndZ.txt", 3, SourcePositionSamplingType.CDF);
// empty infileFolder will initialize AOfXAndYAndZLoader with no AOfXAndYAndZ read
_fluorEmissionAOfXAndYAndZSourceCDF.Loader = new AOfXAndYAndZLoader(
"sourcetest", "inputAOfXAndYAndZ.txt", 3);
_xyzLoaderCDF = _fluorEmissionAOfXAndYAndZSourceCDF.Loader;
_xyzLoaderCDF.InitializeFluorescentRegionArrays();
// following setup is used to test FluorescenceEmissionSource Unif sampling method
_fluorEmissionAOfXAndYAndZSourceUnif = new FluorescenceEmissionAOfXAndYAndZSource(
"sourcetest", "inputAOfXAndYAndZ.txt", 3, SourcePositionSamplingType.Uniform);
// empty infileFolder will initialize AOfXAndYAndZLoader with no AOfXAndYAndZ read
_fluorEmissionAOfXAndYAndZSourceUnif.Loader = new AOfXAndYAndZLoader(
"sourcetest", "inputAOfXAndYAndZ.txt", 3);
_xyzLoaderUnif = _fluorEmissionAOfXAndYAndZSourceCDF.Loader;
_xyzLoaderCDF.InitializeFluorescentRegionArrays();
// AOfRhoAndZ in resource is defined by:
// single layer tissue with embedded infinite cylinder center=(0,0,1) radius=4
// detector rho=[0 4] 4 bins, z=[0 2] 2 bins
_aOfRhoAndZDetector = (dynamic)DetectorIO.ReadDetectorFromFileInResources(
"AOfRhoAndZ", "Resources/sourcetest/", assemblyName);
// overwrite statistical data in Mean with deterministic values to test
count = 1;
for (int i = 0; i < _aOfRhoAndZDetector.Rho.Count - 1; i++)
{
for (int k = 0; k < _aOfRhoAndZDetector.Z.Count - 1; k++)
{
_aOfRhoAndZDetector.Mean[i, k] = count; // make all nonzero and unique
++count;
}
}
DetectorIO.WriteDetectorToFile(_aOfRhoAndZDetector, "sourcetest");
FileIO.CopyFileFromResources(
"Resources/sourcetest/inputAOfRhoAndZ.txt", "sourcetest/inputAOfRhoAndZ.txt", assemblyName);
// following setup is used to test FluorescenceEmissionSource CDF sampling method
_fluorEmissionAOfRhoAndZSourceCDF = new FluorescenceEmissionAOfRhoAndZSource(
"sourcetest", "inputAOfRhoAndZ.txt", 3, SourcePositionSamplingType.CDF);
// empty infileFolder will initialize AOfRhoAndZLoader with no AOfRhoAndZ read
_fluorEmissionAOfRhoAndZSourceCDF.Loader = new AOfRhoAndZLoader(
"sourcetest", "inputAOfRhoAndZ.txt", 3);
_rhozLoaderCDF = _fluorEmissionAOfRhoAndZSourceCDF.Loader;
_rhozLoaderCDF.InitializeFluorescentRegionArrays();
// following setup is used to test FluorescenceEmissionSource Unif sampling method
_fluorEmissionAOfRhoAndZSourceUnif = new FluorescenceEmissionAOfRhoAndZSource(
"sourcetest", "inputAOfRhoAndZ.txt", 3, SourcePositionSamplingType.Uniform);
// empty infileFolder will initialize AOfRhoAndZLoader with no AOfRhoAndZ read
_fluorEmissionAOfRhoAndZSourceUnif.Loader = new AOfRhoAndZLoader(
"sourcetest", "inputAOfRhoAndZ.txt", 3);
_rhozLoaderUnif = _fluorEmissionAOfRhoAndZSourceCDF.Loader;
_rhozLoaderCDF.InitializeFluorescentRegionArrays();
}
public void setup()
{
// set up MC simulation that generated the absorbed energy detector results in embedded resources
//var input = new SimulationInput(
//100,
//"test",
//new SimulationOptions(
// 0, // random number generator seed, -1=random seed, 0=fixed seed
// RandomNumberGeneratorType.MersenneTwister,
// AbsorptionWeightingType.Discrete,
// PhaseFunctionType.HenyeyGreenstein,
// new List<DatabaseType>() { }, // databases to be written
// false, // track statistics
// 0.0, // RR threshold -> no RR performed
// 0),
// new DirectionalPointSourceInput(
// new Position(0.0, 0.0, 0.0),
// new Direction(0.0, 0.0, 1.0),
// 0), // 0=start in air, 1=start in tissue
// new SingleInfiniteCylinderTissueInput(
// new InfiniteCylinderTissueRegion(
// new Position(0, 0, 1),
// 1.0,
// new OpticalProperties(0.05, 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, 100.0),
// 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 AOfXAndYAndZDetectorInput(){
// X =new DoubleRange(-2, 2, 5),
// Y =new DoubleRange(-10, 10, 2),
// Z =new DoubleRange(0, 3, 4)}
// }
//);
//var output = new MonteCarloSimulation(input).Run(); //NOTE: this puts output in Vts.MCCL/bin/Debug
var name = Assembly.GetExecutingAssembly().FullName;
var assemblyName = new AssemblyName(name).Name;
_aOfXAndYAndZDetector = (dynamic)DetectorIO.ReadDetectorFromFileInResources(
"AOfXAndYAndZ", "Resources/sourcetest/", assemblyName);
// overwrite statistical data in Mean with deterministic values to test
int count = 1;
for (int i = 0; i < _aOfXAndYAndZDetector.X.Count - 1; i++)
{
for (int j = 0; j < _aOfXAndYAndZDetector.Y.Count - 1; j++)
{
for (int k = 0; k < _aOfXAndYAndZDetector.Z.Count - 1; k++)
{
_aOfXAndYAndZDetector.Mean[i, j, k] = count; // make all nonzero and unique
++count;
}
}
}
DetectorIO.WriteDetectorToFile(_aOfXAndYAndZDetector, "sourcetest");
FileIO.CopyFileFromResources(
"Resources/sourcetest/input.txt", "sourcetest/input.txt", assemblyName);
// following setup is used to test FluorescenceEmissionSource
_fluorescenceEmissionAOfXAndYAndZSource = new FluorescenceEmissionAOfXAndYAndZSource(
"sourcetest", "input.txt", 3);
// empty infileFolder will initialize AOfXAndYAndZLoader with no AOfXAndYAndZ read
_fluorescenceEmissionAOfXAndYAndZSource.Loader = new AOfXAndYAndZLoader(
"sourcetest", "input.txt", 3);
_loader = _fluorescenceEmissionAOfXAndYAndZSource.Loader;
_loader.InitializeFluorescentRegionArrays();
}
/// <summary>
/// InitializeVectorsAndInterpolators reads in reference database and initializes data
/// Note that the reference data is now in mm/ns so no conversion needed
/// </summary>
private void InitializeVectorsAndInterpolators()
{
// load R(rho,time) reference data
var rOfRhoAndTime = (dynamic)DetectorIO.ReadDetectorFromFileInResources("ROfRhoAndTime", "Modeling/Resources/" + folder, _assemblyName);
nrReference = rOfRhoAndTime.Rho.Count - 1;
drReference = rOfRhoAndTime.Rho.Delta;
ntReference = rOfRhoAndTime.Time.Count - 1;
dtReference = rOfRhoAndTime.Time.Delta;
// assume mus' used by Kienle
muspReference = 1.0;
RhoReference = new DoubleRange(drReference / 2, drReference * nrReference - drReference / 2, nrReference).AsEnumerable().ToArray();
TimeReference = new DoubleRange(dtReference / 2, dtReference * ntReference - dtReference / 2, ntReference).AsEnumerable().ToArray();
RReferenceOfRhoAndTime = new double[nrReference, ntReference];
for (int ir = 0; ir < nrReference; ir++)
{
double sum = 0.0;
for (int it = 0; it < ntReference; it++)
{
RReferenceOfRhoAndTime[ir, it] = rOfRhoAndTime.Mean[ir, it];
sum += rOfRhoAndTime.Mean[ir, it]; // debug line
}
}
// load R(fx,time) reference data
var rOfFxAndTime = (dynamic)DetectorIO.ReadDetectorFromFileInResources("ROfFxAndTime", "Modeling/Resources/" + folder, _assemblyName);
nfxReference = rOfFxAndTime.Fx.Count;
dfxReference = 1.0 / nfxReference;
FxReference = new DoubleRange(dfxReference / 2, dfxReference * nfxReference - dfxReference / 2, nfxReference).AsEnumerable().ToArray();
RReferenceOfFxAndTime = new double[nfxReference, ntReference];
for (int ifx = 0; ifx < nfxReference; ifx++)
{
for (int it = 0; it < ntReference; it++) // this only goes to 800 not 801 because ntReference determined from ROfRhoAndTime.txt
{
RReferenceOfFxAndTime[ifx, it] = rOfFxAndTime.Mean[ifx, it].Real;
}
}
////if (File.Exists("Resources/" + folder + @"R_fxt"))
//if (true)
//{
// RReferenceOfFxAndTime = (double[,])FileIO.ReadArrayFromBinaryInResources<double>("Modeling/Resources/" +
// folder + @"R_fxt", _assemblyName);
//}
//else
//{
// double[] RReferenceOfRhoAndTj = new double[nrReference];
// double[] RReferenceOfFxAndTj = new double[nfxReference];
// for (int j = 0; j < ntReference; j++)
// {
// for (int k = 0; k < nrReference; k++)
// {
// RReferenceOfRhoAndTj[k] = RReferenceOfRhoAndTime[k, j]; // get ROfRho at a particular Time Tj
// }
// for (int i = 0; i < nfxReference; i++)
// {
// RReferenceOfFxAndTime[i, j] = LinearDiscreteHankelTransform.GetHankelTransform(RhoReference,
// RReferenceOfRhoAndTj, drReference, dfxReference * i);
// }
// }
// FileIO.WriteArrayToBinary<double>(RReferenceOfFxAndTime, @"/R_fxt");
//}
}