/// <summary>
/// Method to validate that the geometry of tissue layers and bounding cylinder agree with capabilities
/// of code.
/// </summary>
/// <param name="layers">list of LayerTissueRegion</param>
/// <param name="boundingCylinder">CylinderTissueRegion</param>
/// <returns>ValidationResult</returns>
private static ValidationResult ValidateGeometry(IList <LayerTissueRegion> layers,
CaplessCylinderTissueRegion boundingCylinder)
{
// check that layer definition is valid
var tempResult = MultiLayerTissueInputValidation.ValidateLayers(layers);
if (!tempResult.IsValid)
{
return(tempResult);
}
// test for air layers and eliminate from list
var tissueLayers = layers.Where(layer => !layer.IsAir());
var layersHeight = tissueLayers.Sum(layer => layer.ZRange.Delta);
if (boundingCylinder.Height != layersHeight)
{
tempResult = new ValidationResult(
false,
"BoundingCylinderTissueInput: bounding cylinder must have same height as tissue",
"BoundingCylinderTissueInput: make sure cylinder Height = depth of tissue");
}
if (!tempResult.IsValid)
{
return(tempResult);
}
// check that there is at least one layer of tissue
if (!tissueLayers.Any())
{
tempResult = new ValidationResult(
false,
"BoundingCylinderTissueInput: tissue layer is assumed to be at least a single layer with air layer above and below",
"BoundingCylinderTissueInput: redefine tissue definition to contain at least a single layer of tissue");
}
if (!tempResult.IsValid)
{
return(tempResult);
}
return(new ValidationResult(
true,
"BoundingCylinderTissueInput: geometry and refractive index settings validated"));
}
/// <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");
}
}
/// <summary>
/// Method to verify refractive index of tissue layer and bounding cylinder match.
/// Code does not yet include reflecting/refracting off bounding cylinder surface.
/// </summary>
/// <param name="layers">list of LayerTissueRegion</param>
/// <param name="boundingCylinder">CylinderTissueRegion></param>
/// <returns>ValidationResult</returns>
private static ValidationResult ValidateRefractiveIndexMatch(
IList <LayerTissueRegion> layers, CaplessCylinderTissueRegion boundingCylinder)
{
// for all tissue layers
for (int i = 1; i < layers.Count - 2; i++)
{
if (layers[i].RegionOP.N != boundingCylinder.RegionOP.N)
{
return(new ValidationResult(
false,
"BoundingCylinderTissueInput: refractive index of tissue layer must match that of bounding cylinder",
"Change N of bounding cylinder to match tissue layer N"));
}
}
return(new ValidationResult(
true,
"BoundingCylinderTissueInput: refractive index of tissue and bounding cylinder match"));
}