public void validate_FluenceOfRhoAndZAndTime_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testfluenceofrhoandzandtime";
IDetectorInput detectorInput = new FluenceOfRhoAndZAndTimeDetectorInput()
{
Rho = new DoubleRange(0, 10, 3),
Z = new DoubleRange(0, 10, 3),
Time = new DoubleRange(0, 1, 4),
TallySecondMoment = true,
Name = detectorName,
};
var detector = (FluenceOfRhoAndZAndTimeDetector)detectorInput.CreateDetector();
detector.Mean = new double[, , ] {
{ { 1, 2, 3 }, { 4, 5, 6 } }, { { 7, 8, 9 }, { 10, 11, 12 } }
};
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (FluenceOfRhoAndZAndTimeDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean[0, 0, 0], 1);
Assert.AreEqual(dcloned.Mean[0, 0, 1], 2);
Assert.AreEqual(dcloned.Mean[0, 0, 2], 3);
Assert.AreEqual(dcloned.Mean[0, 1, 0], 4);
Assert.AreEqual(dcloned.Mean[0, 1, 1], 5);
Assert.AreEqual(dcloned.Mean[0, 1, 2], 6);
Assert.AreEqual(dcloned.Mean[1, 0, 0], 7);
Assert.AreEqual(dcloned.Mean[1, 0, 1], 8);
Assert.AreEqual(dcloned.Mean[1, 0, 2], 9);
Assert.AreEqual(dcloned.Mean[1, 1, 0], 10);
Assert.AreEqual(dcloned.Mean[1, 1, 1], 11);
Assert.AreEqual(dcloned.Mean[1, 1, 2], 12);
}
/// <summary>
/// constructor that load excitation simulation AOfRhoAndZ
/// </summary>
public AOfRhoAndZLoader(string inputFolder, string infile, int fluorescentTissueRegionIndex)
{
if (infile != "")
{
var inputPath = "";
if (inputFolder == "")
{
inputPath = infile;
}
else
{
inputPath = inputFolder + @"/" + infile;
}
var aOfRhoAndZDetector = (AOfRhoAndZDetector) DetectorIO.ReadDetectorFromFile(
"AOfRhoAndZ", inputFolder);
// use DoubleRange X,Y,Z to match detector dimensions
Rho = ((AOfRhoAndZDetector) aOfRhoAndZDetector).Rho;
Z = ((AOfRhoAndZDetector) aOfRhoAndZDetector).Z;
AOfRhoAndZ = ((AOfRhoAndZDetector) aOfRhoAndZDetector).Mean;
var exciteInfile = SimulationInput.FromFile(inputPath);
FluorescentTissueRegion = exciteInfile.TissueInput.Regions[fluorescentTissueRegionIndex];
// separate setup of arrays so can unit test method
InitializeFluorescentRegionArrays();
SetupRegionIndices();
}
else
{
throw new ArgumentException("infile string is empty");
}
}
public void validate_pMCROfRhoDetector_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testpmcrofrho";
IDetectorInput detectorInput = new pMCROfRhoDetectorInput()
{
Rho = new DoubleRange(0, 10, 4),
PerturbedOps = new List <OpticalProperties>()
{
new OpticalProperties()
},
PerturbedRegionsIndices = new List <int>()
{
1
},
TallySecondMoment = true, // tally SecondMoment
Name = detectorName,
};
var detector = (pMCROfRhoDetector)detectorInput.CreateDetector();
detector.Mean = new double[] { 100, 200, 300 };
detector.SecondMoment = new double[] { 50, 150, 250 };
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (pMCROfRhoDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
// ckh: not sure how I would read in 2nd moment data in detector + "_2"
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean[0], 100);
Assert.AreEqual(dcloned.Mean[1], 200);
Assert.AreEqual(dcloned.Mean[2], 300);
}
public void validate_pMCROfRhoAndTimeDetector_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testpmcrofrhoandtime";
IDetectorInput detectorInput = new pMCROfRhoAndTimeDetectorInput()
{
Rho = new DoubleRange(0, 10, 3),
Time = new DoubleRange(0, 1, 4),
PerturbedOps = new List <OpticalProperties>()
{
new OpticalProperties()
},
PerturbedRegionsIndices = new List <int>()
{
1
},
TallySecondMoment = true, // tally SecondMoment
Name = detectorName,
};
var detector = (pMCROfRhoAndTimeDetector)detectorInput.CreateDetector();
detector.Mean = new double[, ] {
{ 1, 2, 3 }, { 4, 5, 6 }
};
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (pMCROfRhoAndTimeDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean[0, 0], 1);
Assert.AreEqual(dcloned.Mean[0, 1], 2);
Assert.AreEqual(dcloned.Mean[0, 2], 3);
Assert.AreEqual(dcloned.Mean[1, 0], 4);
Assert.AreEqual(dcloned.Mean[1, 1], 5);
Assert.AreEqual(dcloned.Mean[1, 2], 6);
}
public void validate_AOfRhoAndZDetector_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testaofrhoandz";
IDetectorInput detectorInput = new AOfRhoAndZDetectorInput()
{
Rho = new DoubleRange(0, 10, 3),
Z = new DoubleRange(0, 1, 4),
TallySecondMoment = false,
Name = detectorName,
};
var detector = (AOfRhoAndZDetector)detectorInput.CreateDetector();
detector.Mean = new double[, ] {
{ 1, 2, 3 }, { 4, 5, 6 }
};
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (AOfRhoAndZDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean[0, 0], 1);
Assert.AreEqual(dcloned.Mean[0, 1], 2);
Assert.AreEqual(dcloned.Mean[0, 2], 3);
Assert.AreEqual(dcloned.Mean[1, 0], 4);
Assert.AreEqual(dcloned.Mean[1, 1], 5);
Assert.AreEqual(dcloned.Mean[1, 2], 6);
}
public void validate_TDiffuseDetector_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testtdiffuse";
IDetectorInput detectorInput = new TDiffuseDetectorInput()
{
TallySecondMoment = false, Name = detectorName
};
var detector = (TDiffuseDetector)detectorInput.CreateDetector();
detector.Mean = 100;
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (TDiffuseDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean, 100);
}
/// <summary>
/// constructor that load excitation simulation AOfXAndYAndZ
/// </summary>
public AOfXAndYAndZLoader(string inputFolder, string infile, int fluorescentTissueRegionIndex)
{
if (infile != "")
{
var inputPath = "";
if (inputFolder == "")
{
inputPath = infile;
}
else
{
inputPath = inputFolder + @"/" + infile;
}
var aOfXAndYAndZDetector = (AOfXAndYAndZDetector)DetectorIO.ReadDetectorFromFile(
"AOfXAndYAndZ", inputFolder);
// use DoubleRange X,Y,Z to match detector dimensions
X = ((AOfXAndYAndZDetector)aOfXAndYAndZDetector).X;
Y = ((AOfXAndYAndZDetector)aOfXAndYAndZDetector).Y;
Z = ((AOfXAndYAndZDetector)aOfXAndYAndZDetector).Z;
AOfXAndYAndZ = ((AOfXAndYAndZDetector)aOfXAndYAndZDetector).Mean;
var exciteInfile = SimulationInput.FromFile(inputPath);
FluorescentTissueRegion = exciteInfile.TissueInput.Regions[fluorescentTissueRegionIndex];
BoundedTissueRegion = null;
// check if tissue bounded CH: can this be made more generic?
if (exciteInfile.TissueInput.TissueType == "BoundingCylinder")
{
var cylinderIndex = exciteInfile.TissueInput.Regions.Length - 1;
CaplessCylinderTissueRegion boundingCylinder =
(CaplessCylinderTissueRegion)exciteInfile.TissueInput.Regions[cylinderIndex];
BoundedTissueRegion = new CaplessCylinderTissueRegion(
boundingCylinder.Center,
boundingCylinder.Radius,
boundingCylinder.Height,
boundingCylinder.RegionOP);
}
// separate setup of arrays so can unit test method
InitializeFluorescentRegionArrays();
SetupRegionIndices();
}
else
{
throw new ArgumentException("infile string is empty");
}
}
public void validate_ROfRhoDetector_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testrofrho";
IDetectorInput detectorInput = new ROfRhoDetectorInput()
{
Rho = new DoubleRange(0, 10, 4), TallySecondMoment = false, Name = detectorName
};
var detector = (ROfRhoDetector)detectorInput.CreateDetector();
detector.Mean = new double[] { 100, 200, 300 };
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (ROfRhoDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean[0], 100);
Assert.AreEqual(dcloned.Mean[1], 200);
Assert.AreEqual(dcloned.Mean[2], 300);
}
public void validate_RDiffuseDetector_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testrdiffuse";
IDetectorInput detectorInput = new RDiffuseDetectorInput()
{
TallySecondMoment = true, Name = detectorName
};
var detector = (RDiffuseDetector)detectorInput.CreateDetector();
detector.Mean = 100;
detector.SecondMoment = 50;
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (RDiffuseDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean, 100);
Assert.AreEqual(dcloned.SecondMoment, 50); // 0D detectors 2nd moment written to .txt file
}
public void validate_output_folders_and_files_correct_when_using_geninfile_infile()
{
string[] arguments = new string[] { "infile=infile_PostProcessor_pMC_ROfRhoROfRhoAndTime.txt" };
Program.Main(arguments);
Assert.IsTrue(Directory.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime"));
// verify infile gets written to output folder
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/PostProcessor_pMC_ROfRhoROfRhoAndTime.txt"));
// verify detectors specified in MCPP infile get written
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRhoReference.txt"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRhoReference"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRhoReference_2"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRho_mus1p5.txt"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRho_mus1p5"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRho_mus1p5_2"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRho_mus0p5.txt"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRho_mus0p5"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRho_mus0p5_2"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRhoAndTime_mus1p5.txt"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRhoAndTime_mus1p5"));
Assert.IsFalse(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/pMCROfRhoAndTime_mus1p5_2"));
// added regular detectors into this infile in PPInputProvider -> verify they are there
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/ROfRho.txt"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/ROfRho"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/ROfRhoAndTime.txt"));
Assert.IsTrue(File.Exists("PostProcessor_pMC_ROfRhoROfRhoAndTime/ROfRhoAndTime"));
// check that can read detectors in
var readDetector = DetectorIO.ReadDetectorFromFile(
"pMCROfRhoReference", "PostProcessor_pMC_ROfRhoROfRhoAndTime");
Assert.IsInstanceOf <IDetector>(readDetector);
readDetector = DetectorIO.ReadDetectorFromFile(
"pMCROfRhoAndTime_mus1p5", "PostProcessor_pMC_ROfRhoROfRhoAndTime");
Assert.IsInstanceOf <IDetector>(readDetector);
readDetector = DetectorIO.ReadDetectorFromFile(
"ROfRho", "PostProcessor_pMC_ROfRhoROfRhoAndTime");
Assert.IsInstanceOf <IDetector>(readDetector);
readDetector = DetectorIO.ReadDetectorFromFile(
"ROfRhoAndTime", "PostProcessor_pMC_ROfRhoROfRhoAndTime");
Assert.IsInstanceOf <IDetector>(readDetector);
}
public void validate_ROfRhoAndOmegaDetector_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testrofrhoandomega";
IDetectorInput detectorInput = new ROfRhoAndOmegaDetectorInput()
{
Rho = new DoubleRange(0, 10, 3),
Omega = new DoubleRange(0, 1, 4),
TallySecondMoment = true, // tally Second Moment
Name = detectorName,
};
var detector = (ROfRhoAndOmegaDetector)detectorInput.CreateDetector();
detector.Mean = new Complex[, ]
{
{
1 + Complex.ImaginaryOne * 1, 2 + Complex.ImaginaryOne * 2, 3 + Complex.ImaginaryOne * 3,
4 + Complex.ImaginaryOne * 4
},
{
5 + Complex.ImaginaryOne * 5, 6 + Complex.ImaginaryOne * 6, 7 + Complex.ImaginaryOne * 7,
8 + Complex.ImaginaryOne * 8
}
};
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (ROfRhoAndOmegaDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean[0, 0], 1 + Complex.ImaginaryOne * 1);
Assert.AreEqual(dcloned.Mean[0, 1], 2 + Complex.ImaginaryOne * 2);
Assert.AreEqual(dcloned.Mean[0, 2], 3 + Complex.ImaginaryOne * 3);
Assert.AreEqual(dcloned.Mean[0, 3], 4 + Complex.ImaginaryOne * 4);
Assert.AreEqual(dcloned.Mean[1, 0], 5 + Complex.ImaginaryOne * 5);
Assert.AreEqual(dcloned.Mean[1, 1], 6 + Complex.ImaginaryOne * 6);
Assert.AreEqual(dcloned.Mean[1, 2], 7 + Complex.ImaginaryOne * 7);
Assert.AreEqual(dcloned.Mean[1, 3], 8 + Complex.ImaginaryOne * 8);
}
public void demonstrate_user_defined_detector_usage()
{
DetectorFactory.RegisterDetector(typeof(ROfXDetectorInput), typeof(ROfXDetector));
var detectorInput = new ROfXDetectorInput
{
TallyType = "ROfX",
Name = "My First R(x) Detector",
TallySecondMoment = true,
X = new DoubleRange(0, 10, 101),
};
var simInput = new SimulationInput
{
DetectorInputs = new[] { detectorInput },
N = 100,
};
var sim = simInput.CreateSimulation();
var results = sim.Run();
IDetector detector;
var detectorExists = results.ResultsDictionary.TryGetValue(detectorInput.Name, out detector);
Assert.IsTrue(detectorExists);
var firstValue = ((ROfXDetector)detector).Mean.FirstOrDefault();
Assert.IsTrue(firstValue != 0);
DetectorIO.WriteDetectorToFile(detector, "user_defined_detector");
var deserializedDetector = DetectorIO.ReadDetectorFromFile("user_defined_detector", "");
}
public void validate_ReflectedMTOfRhoAndSubregionHistDetector_deserialized_class_is_correct_when_using_WriteReadDetectorToFile()
{
string detectorName = "testreflectedmtofrhoandsubregionhist";
var tissue = new MultiLayerTissue(
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, 0.7, 1.33)),
new LayerTissueRegion(
new DoubleRange(100.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
);
IDetectorInput detectorInput = new ReflectedMTOfRhoAndSubregionHistDetectorInput()
{
Rho = new DoubleRange(0, 10, 3),
MTBins = new DoubleRange(0, 10, 3),
FractionalMTBins = new DoubleRange(0, 1, 2),
TallySecondMoment = true, // tally SecondMoment
Name = detectorName,
};
var detector = (ReflectedMTOfRhoAndSubregionHistDetector)detectorInput.CreateDetector();
// need to initialize detector so that NumSubregions gets set
detector.Initialize(tissue, null);
// Mean has dimensions [Rho.Count - 1, MTBins.Count - 1]
detector.Mean = new double[, ] {
{ 1, 2 }, { 3, 4 }
};
// FractionalMT has dimensions [Rho.Count - 1, MTBins.Count - 1, NumSubregions, FractionalMTBins.Count + 1]=[2,2,3,3]
detector.FractionalMT = new double[, , , ] {
{ { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 9 } }, { { 10, 11, 12 }, { 13, 14, 15 }, { 16, 17, 18 } } }, { { { 19, 20, 21 }, { 22, 23, 24 }, { 25, 26, 27 } }, { { 28, 29, 30 }, { 31, 32, 33 }, { 34, 35, 36 } } }
};
DetectorIO.WriteDetectorToFile(detector, "");
var dcloned = (ReflectedMTOfRhoAndSubregionHistDetector)DetectorIO.ReadDetectorFromFile(detectorName, "");
Assert.AreEqual(dcloned.Name, detectorName);
Assert.AreEqual(dcloned.Mean[0, 0], 1);
Assert.AreEqual(dcloned.Mean[0, 1], 2);
Assert.AreEqual(dcloned.Mean[1, 0], 3);
Assert.AreEqual(dcloned.Mean[1, 1], 4);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 0, 0], 1);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 0, 1], 2);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 0, 2], 3);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 1, 0], 4);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 1, 1], 5);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 1, 2], 6);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 2, 0], 7);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 2, 1], 8);
Assert.AreEqual(dcloned.FractionalMT[0, 0, 2, 2], 9);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 0, 0], 10);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 0, 1], 11);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 0, 2], 12);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 1, 0], 13);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 1, 1], 14);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 1, 2], 15);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 2, 0], 16);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 2, 1], 17);
Assert.AreEqual(dcloned.FractionalMT[0, 1, 2, 2], 18);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 0, 0], 19);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 0, 1], 20);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 0, 2], 21);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 1, 0], 22);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 1, 1], 23);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 1, 2], 24);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 2, 0], 25);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 2, 1], 26);
Assert.AreEqual(dcloned.FractionalMT[1, 0, 2, 2], 27);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 0, 0], 28);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 0, 1], 29);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 0, 2], 30);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 1, 0], 31);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 1, 1], 32);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 1, 2], 33);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 2, 0], 34);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 2, 1], 35);
Assert.AreEqual(dcloned.FractionalMT[1, 1, 2, 2], 36);
}