/// <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");
}
}
/// <summary>
/// method to read the simulation input from a specified or default file
/// </summary>
public static SimulationInput ReadSimulationInputFromFile(string inputFile)
{
try
{
if (string.IsNullOrEmpty(inputFile))
{
logger.Info(" *** No input file specified ***\n\nDefine an input file using mc.exe infile=infile_name.txt");
return(null);
}
//get the full path for the input file
var fullFilePath = Path.GetFullPath(inputFile);
string extension = Path.GetExtension(inputFile);
if (File.Exists(fullFilePath))
{
return(SimulationInput.FromFile(fullFilePath));
}
if (File.Exists(fullFilePath + ".txt"))
{
return(SimulationInput.FromFile(fullFilePath + ".txt"));
}
//throw a file not found exception
throw new FileNotFoundException("\nThe following input file could not be found: " + fullFilePath + " - type mc help=infile for correct syntax");
}
catch (Exception e)
{
Console.WriteLine(e.Message);
//Console.WriteLine(VtsJsonSerializer.TraceWriter.GetTraceMessages());
return(null);
}
}
public void validate_deserialized_class_is_correct_when_using_FileIO()
{
new SimulationInput {
N = 10
}.ToFile("test.txt");
var iCloned = SimulationInput.FromFile("test.txt");
Assert.AreEqual(iCloned.N, 10);
}
/// <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_deserialization_of_infile_for_Mus_and_Musp_inconsistent_specification()
{
var name = Assembly.GetExecutingAssembly().FullName;
var assemblyName = new AssemblyName(name).Name;
FileIO.CopyFileFromEmbeddedResources(
assemblyName + ".Resources.infile_unit_test_one_layer_ROfRho_Musp_and_Mus_inconsistent.txt",
"infile_unit_test_one_layer_ROfRho_Musp_and_Mus_inconsistent.txt", name);
string[] arguments = new string[]
{ "infile=infile_unit_test_one_layer_ROfRho_Musp_and_Mus_inconsistent.txt" };
Program.Main(arguments);
Assert.IsTrue(Directory.Exists("unit_test_one_layer_ROfRho_Musp_and_Mus_inconsistent"));
var writtenInfile = SimulationInput.FromFile(
"unit_test_one_layer_ROfRho_Musp_and_Mus_inconsistent/unit_test_one_layer_ROfRho_Musp_and_Mus_inconsistent.txt");
// infile specifies Mus=5.0 and Musp=1.2 with g=0.8
// when there is inconsistency in Mus and Musp specification, code modifies Mus to conform to Musp
// the following test verifies that Mus was modified accordingly
Assert.Less(Math.Abs(writtenInfile.TissueInput.Regions[1].RegionOP.Mus - 6.0), 1e-6);
}
// need to work on following
/// <summary>
/// Runs the Monte Carlo Post-processor
/// </summary>
public static void RunPostProcessor(PostProcessorInput input, string outputFolderPath)
{
// locate root folder for output, creating it if necessary
var path = string.IsNullOrEmpty(outputFolderPath)
? Path.GetFullPath(Directory.GetCurrentDirectory())
: Path.GetFullPath(outputFolderPath);
if (!Directory.Exists(path))
{
Directory.CreateDirectory(path);
}
// locate destination folder for output, creating it if necessary
var resultsFolder = Path.Combine(path, input.OutputName);
if (!Directory.Exists(resultsFolder))
{
Directory.CreateDirectory(resultsFolder);
}
SimulationOutput postProcessedOutput = null;
var databaseGenerationInputFile = SimulationInput.FromFile(Path.Combine(input.InputFolder, input.DatabaseSimulationInputFilename + ".txt"));
// check for pMC tallies first because could have ReflectanceTallies mixed in and want to load CollisionInfo
// Why not mirror the "on-the-fly" code, and allow for all kinds of detector inputs simultaneously? (dc 12/21/2011)
if (input.DetectorInputs.Where(di => di.TallyDetails.IspMCReflectanceTally).Any())
{
IList <IDetectorInput> pMCDetectorInputs;
pMCDetectorInputs = input.DetectorInputs;
var postProcessor = new PhotonDatabasePostProcessor(
VirtualBoundaryType.pMCDiffuseReflectance,
pMCDetectorInputs,
PhotonDatabaseFactory.GetpMCDatabase( // database filenames are assumed to be convention
VirtualBoundaryType.pMCDiffuseReflectance,
input.InputFolder),
databaseGenerationInputFile
);
postProcessedOutput = postProcessor.Run();
}
else if (input.DetectorInputs.Where(di => di.TallyDetails.IsReflectanceTally).Any())
{
var postProcessor = new PhotonDatabasePostProcessor(
VirtualBoundaryType.DiffuseReflectance,
input.DetectorInputs,
PhotonDatabaseFactory.GetPhotonDatabase( //database filenames are assumed to be convention
VirtualBoundaryType.DiffuseReflectance,
input.InputFolder),
databaseGenerationInputFile
);
postProcessedOutput = postProcessor.Run();
}
else if (input.DetectorInputs.Where(di => di.TallyDetails.IsTransmittanceTally).Any())
{
var postProcessor = new PhotonDatabasePostProcessor(
VirtualBoundaryType.DiffuseTransmittance,
input.DetectorInputs,
PhotonDatabaseFactory.GetPhotonDatabase( //database filenames are assumed to be convention
VirtualBoundaryType.DiffuseTransmittance,
input.InputFolder),
databaseGenerationInputFile
);
postProcessedOutput = postProcessor.Run();
}
else if (input.DetectorInputs.Where(di => di.TallyDetails.IsSpecularReflectanceTally).Any())
{
var postProcessor = new PhotonDatabasePostProcessor(
VirtualBoundaryType.SpecularReflectance,
input.DetectorInputs,
PhotonDatabaseFactory.GetPhotonDatabase( //database filenames are assumed to be convention
VirtualBoundaryType.SpecularReflectance,
input.InputFolder),
databaseGenerationInputFile
);
postProcessedOutput = postProcessor.Run();
}
var folderPath = input.OutputName;
if (!Directory.Exists(folderPath))
{
Directory.CreateDirectory(folderPath);
}
// save input file to output folder with results
input.ToFile(Path.Combine(resultsFolder, input.OutputName + ".txt"));
// save database generation input file to output folder
databaseGenerationInputFile.ToFile(Path.Combine(resultsFolder, input.OutputName + "_database_infile.txt"));
if (postProcessedOutput != null)
{
foreach (var result in postProcessedOutput.ResultsDictionary.Values)
{
// save all detector data to the specified folder
DetectorIO.WriteDetectorToFile(result, folderPath);
}
}
}
