public void validate_only_one_perturbed_region_index_specified()
{
var tissueInput = new MultiLayerTissueInput();
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
tissueInput,
new List <IDetectorInput>()
{
new dMCdROfRhodMuaDetectorInput()
{
Rho = new DoubleRange(0.0, 100.0),
// set perturbed ops to reference ops
PerturbedOps = new List <OpticalProperties>()
{
tissueInput.Regions[0].RegionOP,
tissueInput.Regions[1].RegionOP,
tissueInput.Regions[2].RegionOP
},
PerturbedRegionsIndices = new List <int>()
{
1, 2
}
}
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_ellipsoid_is_within_tissue_layer()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleEllipsoidTissueInput(
new EllipsoidTissueRegion(new Position(0, 0, 0), 1.0, 1.0, 1.0, new OpticalProperties()),
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, 20.0),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(20.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List <IDetectorInput>()
{
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_voxel_refractive_index_matches_that_of_surrounding_layer()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleVoxelTissueInput(
new VoxelTissueRegion(new DoubleRange(-5, 5),
new DoubleRange(-5, 5),
new DoubleRange(1, 2),
new OpticalProperties(0.01, 1.0, 0.9, 1.3)),
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, 20.0),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(20.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List <IDetectorInput>()
{
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_at_least_one_tissue_layer_defined()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleVoxelTissueInput(
new VoxelTissueRegion(),
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, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List <IDetectorInput>()
{
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_voxel_has_nonzero_dimensions()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleVoxelTissueInput(
// set ellipsoid axis to 0.0
new VoxelTissueRegion(new DoubleRange(0, 0),
new DoubleRange(-10, 10),
new DoubleRange(1, 5),
new OpticalProperties()),
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, 20.0),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(20.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List <IDetectorInput>()
{
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_voxel_is_within_tissue_layer()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new SingleVoxelTissueInput(
new VoxelTissueRegion(new DoubleRange(-5, 5),
new DoubleRange(-5, 5),
new DoubleRange(0, 10), // eheck that voxel not at surface
new OpticalProperties()),
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, 20.0),
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(20.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List <IDetectorInput>()
{
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
private void MC_LoadSimulationInput_Executed(object sender, ExecutedEventArgs e)
{
using (var stream = StreamFinder.GetLocalFilestreamFromOpenFileDialog("txt"))
{
if (stream != null)
{
var simulationInput = FileIO.ReadFromJsonStream <SimulationInput>(stream);
var validationResult = SimulationInputValidation.ValidateInput(simulationInput);
if (validationResult.IsValid)
{
_simulationInputVM.SimulationInput = simulationInput;
logger.Info(() => "Simulation input loaded.\r");
}
else
{
logger.Info(() => "Simulation input not loaded - JSON format not valid.\r");
}
}
else
{
logger.Info(() => "JSON File not loaded.\r");
}
}
}
public void validate_layers_have_ZRange_Count_set_to_2()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new MultiLayerTissueInput(
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, 10.0)
{
Count = 10
},
new OpticalProperties(0.01, 1.0, 0.8, 1.4)),
new LayerTissueRegion(
new DoubleRange(10.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
}
),
new List <IDetectorInput>()
{
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_top_and_bottom_layers_are_air()
{
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
new MultiLayerTissueInput(
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 List <IDetectorInput>()
{
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_null_detector_input_is_invalid_when_no_database_specified()
{
// generate input without any detector inputs and no database specified
var input = new SimulationInput() // default constructor has empty list of databases
{
DetectorInputs = new List <IDetectorInput> {
}
};
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_angled_source_and_cylindrical_detectors_are_not_defined_together()
{
// generate input with angled source and cylindrical detector
var input = new SimulationInput()
{
SourceInput = new DirectionalPointSourceInput(
new Position(0, 0, 0), new Direction(1.0 / Math.Sqrt(2), 0, 1.0 / Math.Sqrt(2)), 1),
DetectorInputs = new List <IDetectorInput> {
new ROfRhoDetectorInput()
}
};
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_null_detector_input_is_valid_when_database_specified()
{
// generate input without any detector inputs but with database specified
var input = new SimulationInput()
{
DetectorInputs = new List <IDetectorInput> {
}
};
input.Options.Databases = new List <DatabaseType> {
DatabaseType.DiffuseReflectance
};
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsTrue(result.IsValid);
}
public void validate_detector_input_not_implemented_is_invalid()
{
// generate input with detector input not implemented yet
var input = new SimulationInput()
{
Options = new SimulationOptions()
{
AbsorptionWeightingType = AbsorptionWeightingType.Continuous
},
DetectorInputs = new List <IDetectorInput> {
new RadianceOfXAndYAndZAndThetaAndPhiDetectorInput()
}
};
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_voxel_tissue_and_ROfFx_detectors_are_not_defined_together()
{
// generate input embedded ellipsoid tissue and cylindrical detector
var input = new SimulationInput()
{
TissueInput = new SingleVoxelTissueInput()
{
VoxelRegion = new VoxelTissueRegion()
},
DetectorInputs = new List <IDetectorInput> {
new ROfFxDetectorInput()
}
};
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_ellipsoid_tissue_with_off_zaxis_center_and_cylindrical_detectors_are_not_defined_together()
{
// generate input embedded ellipsoid tissue and cylindrical detector
var input = new SimulationInput()
{
TissueInput = new SingleEllipsoidTissueInput()
{
EllipsoidRegion = new EllipsoidTissueRegion()
{
Center = new Position(1, 1, 0)
}
},
DetectorInputs = new List <IDetectorInput> {
new ROfRhoDetectorInput()
}
};
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_ellipsoid_tissue_without_cylindrical_symmetry_and_cylindrical_detectors_are_not_defined_together()
{
// generate input embedded ellipsoid tissue and cylindrical detector
var input = new SimulationInput()
{
TissueInput = new SingleEllipsoidTissueInput()
{
EllipsoidRegion = new EllipsoidTissueRegion()
{
Dx = 1.0, Dy = 2.0
}
},
DetectorInputs = new List <IDetectorInput> {
new ROfRhoDetectorInput()
}
};
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_code_checks_that_detector_defined_on_tissue_surface()
{
var tissueInput = new MultiLayerTissueInput();
var input = new SimulationInput(
10,
"",
new SimulationOptions(),
new DirectionalPointSourceInput(),
tissueInput,
new List <IDetectorInput>()
{
new SurfaceFiberDetectorInput()
{
Center = new Position(0, 0, 10)
}
}
);
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
public void validate_tissue_optical_properties_are_non_negative()
{
// generate input embedded ellipsoid tissue and cylindrical detector
var input = new SimulationInput()
{
TissueInput = new MultiLayerTissueInput(
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(-1.0, 1.0, 0.8, 1.4)), // make mua negative
new LayerTissueRegion(
new DoubleRange(100.0, double.PositiveInfinity),
new OpticalProperties(0.0, 1e-10, 1.0, 1.0))
})
};
var result = SimulationInputValidation.ValidateInput(input);
Assert.IsFalse(result.IsValid);
}
private void MC_ExecuteMonteCarloSolver_Executed(object sender, ExecutedEventArgs e)
{
if (!EnoughRoomInIsolatedStorage(50))
{
logger.Info(() => "\rSimulation not run. Please allocate more than 50MB of storage space.\r");
Commands.IsoStorage_IncreaseSpaceQuery.Execute();
return;
}
_newResultsAvailable = false;
var input = _simulationInputVM.SimulationInput;
var validationResult = SimulationInputValidation.ValidateInput(input);
if (!validationResult.IsValid)
{
logger.Info(() => "\rSimulation input not valid.\rRule: " + validationResult.ValidationRule +
(!string.IsNullOrEmpty(validationResult.Remarks) ? "\rDetails: " + validationResult.Remarks : "") + ".\r");
return;
}
_simulation = new MonteCarloSimulation(input);
_currentCancellationTokenSource = new CancellationTokenSource();
CancellationToken cancelToken = _currentCancellationTokenSource.Token;
TaskScheduler scheduler = TaskScheduler.FromCurrentSynchronizationContext();
var t = Task.Factory.StartNew(() => _simulation.Run(), TaskCreationOptions.LongRunning);
var c = t.ContinueWith((antecedent) =>
{
SolverDemoView.Current.Dispatcher.BeginInvoke(delegate()
{
_output = antecedent.Result;
_newResultsAvailable = _simulation.ResultsAvailable;
var rOfRhoDetectorInputs = _simulationInputVM.SimulationInput.DetectorInputs.
Where(di => di.Name == "ROfRho");
if (rOfRhoDetectorInputs.Any())
{
logger.Info(() => "Creating R(rho) plot...");
var detectorInput = (ROfRhoDetectorInput)rOfRhoDetectorInputs.First();
double[] independentValues = detectorInput.Rho.AsEnumerable().ToArray();
DoubleDataPoint[] points = null;
//var showPlusMinusStdev = true;
//if(showPlusMinusStdev && _output.R_r2 != null)
//{
// var stdev = Enumerable.Zip(_output.R_r, _output.R_r2, (r, r2) => Math.Sqrt((r2 - r * r) / nPhotons)).ToArray();
// var rMinusStdev = Enumerable.Zip(_output.R_r, stdev, (r,std) => r-std).ToArray();
// var rPlusStdev = Enumerable.Zip(_output.R_r, stdev, (r,std) => r+std).ToArray();
// points = Enumerable.Zip(
// independentValues.Concat(independentValues).Concat(independentValues),
// rMinusStdev.Concat(_output.R_r).Concat(rPlusStdev),
// (x, y) => new Point(x, y));
//}
//else
//{
points = Enumerable.Zip(
independentValues,
_output.R_r,
(x, y) => new DoubleDataPoint(x, y)).ToArray();
//}
PlotAxesLabels axesLabels = GetPlotLabels();
Commands.Plot_SetAxesLabels.Execute(axesLabels);
string plotLabel = GetPlotLabel();
Commands.Plot_PlotValues.Execute(new[] { new PlotData(points, plotLabel) });
logger.Info(() => "done.\r");
}
var fluenceDetectorInputs = _simulationInputVM.SimulationInput.DetectorInputs.
Where(di => di.Name == "FluenceOfRhoAndZ");
if (fluenceDetectorInputs.Any())
{
logger.Info(() => "Creating Fluence(rho,z) map...");
var detectorInput = (FluenceOfRhoAndZDetectorInput)fluenceDetectorInputs.First();
var rhosMC = detectorInput.Rho.AsEnumerable().ToArray();
var zsMC = detectorInput.Z.AsEnumerable().ToArray();
var rhos = Enumerable.Zip(rhosMC.Skip(1), rhosMC.Take(rhosMC.Length - 1), (first, second) => (first + second) / 2).ToArray();
var zs = Enumerable.Zip(zsMC.Skip(1), rhosMC.Take(zsMC.Length - 1), (first, second) => (first + second) / 2).ToArray();
var dRhos = Enumerable.Select(rhos, rho => 2 * Math.PI * Math.Abs(rho) * detectorInput.Rho.Delta).ToArray();
var dZs = Enumerable.Select(zs, z => detectorInput.Z.Delta).ToArray();
if (_mapArrayBuffer == null || _mapArrayBuffer.Length != _output.Flu_rz.Length * 2)
{
_mapArrayBuffer = new double[_output.Flu_rz.Length * 2];
}
// flip the array (since it goes over zs and then rhos, while map wants rhos and then zs
for (int zi = 0; zi < zs.Length; zi++)
{
for (int rhoi = 0; rhoi < rhos.Length; rhoi++)
{
_mapArrayBuffer[rhoi + rhos.Length + rhos.Length * 2 * zi] = _output.Flu_rz[rhoi, zi];
}
var localRhoiForReverse = 0;
for (int rhoi = rhos.Length - 1; rhoi >= 0; rhoi--, localRhoiForReverse++)
{
_mapArrayBuffer[localRhoiForReverse + rhos.Length * 2 * zi] = _output.Flu_rz[rhoi, zi];
}
}
var twoRhos = Enumerable.Concat(rhos.Reverse().Select(rho => - rho), rhos).ToArray();
var twoDRhos = Enumerable.Concat(dRhos.Reverse(), dRhos).ToArray();
var mapData = new MapData(_mapArrayBuffer, twoRhos, zs, twoDRhos, dZs);
Commands.Maps_PlotMap.Execute(mapData);
logger.Info(() => "done.\r");
}
// save results to isolated storage
logger.Info(() => "Saving simulation results to temporary directory...");
//var detectorFolder = Path.Combine(TEMP_RESULTS_FOLDER, input.OutputName);
//// create the root directory
//FileIO.CreateDirectory(TEMP_RESULTS_FOLDER);
// create the detector directory, removing stale files first if they exist
FileIO.CreateEmptyDirectory(TEMP_RESULTS_FOLDER);
// write detector to file
input.ToFile(Path.Combine(TEMP_RESULTS_FOLDER, "infile_" + input.OutputName + ".txt"));
foreach (var result in _output.ResultsDictionary.Values)
{
// save all detector data to the specified folder
DetectorIO.WriteDetectorToFile(result, TEMP_RESULTS_FOLDER);
}
var store = IsolatedStorageFile.GetUserStoreForApplication();
if (store.DirectoryExists(TEMP_RESULTS_FOLDER))
{
var currentAssembly = Assembly.GetExecutingAssembly();
// get all the files we want to zip up
var fileNames = store.GetFileNames(TEMP_RESULTS_FOLDER + @"\*");
// copy the MATLAB files to isolated storage and get their names so they can be included in the zip file
var matlabFiles = FileIO.CopyFolderFromEmbeddedResources("Matlab", TEMP_RESULTS_FOLDER, currentAssembly.FullName, false);
// then, zip all the files together and store *that* .zip to isolated storage as well (can't automatically copy to user folder due to security restrictions)
var allFiles = matlabFiles.Concat(fileNames).Distinct();
try
{
FileIO.ZipFiles(allFiles, TEMP_RESULTS_FOLDER, input.OutputName + ".zip");
}
catch (SecurityException)
{
logger.Error(() => "\rProblem saving results to file.\r");
}
}
logger.Info(() => "done.\r");
});
},
cancelToken,
TaskContinuationOptions.OnlyOnRanToCompletion,
scheduler);
}
public static ValidationResult ValidateSimulationInput(SimulationInput input)
{
return(SimulationInputValidation.ValidateInput(input));
}