public void Update(Tissue t)
{
var _context = new ApplicationDbContext();
_context.Entry(t).State = EntityState.Modified;
_context.SaveChanges();
}
public override void SetupSimulation()
{
logFrequency = 1;
nbCellTypes = 3;
nbOfSimulationSteps = 10;
//*
popSize = 148;
popMaxSize = 343;
Tissue t1 = new Tissue(25, 125, new Cylinder34(new Vector(.5f, .5f, .5f)));
Tissue t2 = new Tissue(98, popMaxSize, new Cylinder34(new Vector(.5f, 1f, .5f)));
Tissue t3 = new Tissue(25, 125, new Cylinder34(new Vector(.5f, .5f, .5f)));
List <Tissue> tissueList = new List <Tissue>()
{
t1, t2, t3
};
cellPopulation = new CellPopulation(popSize, popMaxSize, tissueList, true);
//Helper.SetNCubedInN(125);
//t1.PositionCells(false);
//Helper.SetNCubedInN(popMaxSize);
//t2.PositionCells(false, new Vector(0, t1.reference.y + t1.mesh.innerRadius.y + t2.mesh.innerRadius.y, 0));
Helper.SetNCubedInN(popMaxSize);
t2.PositionCells(false);
Helper.SetNCubedInN(125);
t1.PositionCells(false, new Vector(0, t2.reference.y - 4 * t2.mesh.innerRadius.y - t1.mesh.innerRadius.y, 0));
Helper.SetNCubedInN(125);
t3.PositionCells(false, new Vector(0, t2.reference.y + t3.mesh.innerRadius.y, 0));
//*/
nbCellTypes = tissueList.Count;
}
public void Insert(Tissue t)
{
var _context = new DataContext();
_context.Tissues.Add(t);
_context.SaveChanges();
}
public void Delete(Tissue t)
{
var _context = new ApplicationDbContext();
_context.Tissues.Remove(t);
_context.SaveChanges();
}
public AStar(VG.Map.Tissue t)
{
this.map = t;
nodeGrid = new AStarNode[200][];
openSet = new bool[200][];
closedSet= new bool[200][];
cacheable = new bool[200][];
for (int i = 0; i < 200; i++)
{
nodeGrid[i] = new AStarNode[200];
openSet[i] = new bool[200];
closedSet[i] = new bool[200];
cacheable[i] = new bool[200];
}
// prepare cacheable set
EntityCollection aznCol = map.get_EntitiesByType(EntityEnum.AZN);
for (int i = 0; i < aznCol.Count; i++)
cacheable[aznCol[i].X][aznCol[i].Y] = true;
EntityCollection hpCol = map.get_EntitiesByType(EntityEnum.HoshimiPoint);
for (int i = 0; i < hpCol.Count; i++)
cacheable[hpCol[i].X][hpCol[i].Y] = true;
//cache PierreIP
cacheable[Global.MYAI.PierreTeamInjectionPoint.X][Global.MYAI.PierreTeamInjectionPoint.Y] = true;
cache = new System.Collections.Hashtable( (hpCol.Count * hpCol.Count) + (aznCol.Count * aznCol.Count) );
aznCol = null; // garbage-collected
hpCol = null;
}
public void Delete(Tissue t)
{
var _context = new DataContext();
_context.Tissues.Remove(t);
_context.SaveChanges();
}
public void validate_spectral_generation_of_OpticalProperties_with_tissue()
{
var scatterer = new IntralipidScatterer(0.01);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.01);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.99);
var _twoLayerSDAForwardSolver = new TwoLayerSDAForwardSolver();
var _oneLayerPointSourceForwardSolver = new PointSourceSDAForwardSolver();
var n = 1.4;
var wvs = new DoubleRange(650, 1000, 36).AsEnumerable().ToArray();
var rho = 10;
var tissue = new Tissue(
new IChromophoreAbsorber[] { fatAbsorber, waterAbsorber },
scatterer,
"test_tissue",
n);
var ops = wvs.Select(wv => tissue.GetOpticalProperties(wv)).ToArray();
var fs = new PointSourceSDAForwardSolver();
var reflectanceVsWavelength = fs.ROfRho(ops, rho);
Assert.NotNull(reflectanceVsWavelength);
Assert.AreEqual(reflectanceVsWavelength.Length, wvs.Length);
// check that change in scattering changes the reflectance
Assert.IsTrue(reflectanceVsWavelength[0] != reflectanceVsWavelength[1]);
// check that change in absorption changes the reflectance
Assert.IsTrue(reflectanceVsWavelength[1] != reflectanceVsWavelength[2]);
}
public void validate_ROfFxAndFt_With_Wavelength()
{
// used values for tissue=liver
var scatterer = new PowerLawScatterer(0.84, 0.55);
var hbAbsorber = new ChromophoreAbsorber(ChromophoreType.Hb, 66);
var hbo2Absorber = new ChromophoreAbsorber(ChromophoreType.HbO2, 124);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.02);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.87);
var n = 1.4;
var wvs = new double[] { 650, 700 };
var fxs = new double[] { 0.0, 0.5 };
var fts = new double[] { 0.0, 0.50 };
var tissue = new Tissue(
new IChromophoreAbsorber[] { hbAbsorber, hbo2Absorber, fatAbsorber, waterAbsorber },
scatterer,
"test_tissue",
n);
var ops = wvs.Select(wv => tissue.GetOpticalProperties(wv)).ToArray();
var fs = new DistributedPointSourceSDAForwardSolver();
var rVsWavelength = fs.ROfFxAndFt(ops, fxs, fts);
// return from ROfFxAndFt is new double[ops.Length * fxs.Length * fts.Length];
// order is: (ops0,fxs0,fts0), (ops0,fxs0,ts1)...(ops0,fxs0,ftsnt-1)
// (ops0,fxs1,fts0), (ops0,fxs1,ts1)...(ops0,fxs1,ftsnt-1)
// ...
// (ops0,fxsnf-1,fts0),.................(ops0,fxsnf-1,ftsnt-1)
// ... repeat above with ops1...
// [0] -> ops0=650, fx0=0.0, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[0].Real - 1.890007) < 0.000001); // API match
Assert.IsTrue(Math.Abs(rVsWavelength[0].Imaginary - 0.0) < 0.000001); // API match
// [1] -> ops0=650, fx0=0.0, fts1=0.5
Assert.IsTrue(Math.Abs(rVsWavelength[1].Real - 1.888160) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[1].Imaginary + 0.045122) < 0.000001);
// [2] -> ops0=650, fx1=0.5, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[2].Real - 0.562537) < 0.000001); // API match
Assert.IsTrue(Math.Abs(rVsWavelength[2].Imaginary - 0.0) < 0.000001); // API match
// [3] -> ops0=650, fx1=0.5, fts1=0.5
Assert.IsTrue(Math.Abs(rVsWavelength[3].Real - 0.562543) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[3].Imaginary + 0.000799) < 0.000001);
// [4] -> ops1=700, fx0=0.0, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[4].Real - 2.118427) < 0.000001); // API match
Assert.IsTrue(Math.Abs(rVsWavelength[4].Imaginary - 0.0) < 0.000001); // API match
// [5] -> ops1=700, fx0=0.0, fts1=0.5
Assert.IsTrue(Math.Abs(rVsWavelength[5].Real - 2.113377) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[5].Imaginary + 0.071758) < 0.000001);
// [6] -> ops1=700, fx1=0.5, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[6].Real - 0.543539) < 0.000001); // API match
Assert.IsTrue(Math.Abs(rVsWavelength[6].Imaginary - 0.0) < 0.000001); // API match
// [7] -> ops1=700, fx1=0.5, fts1=0.5
Assert.IsTrue(Math.Abs(rVsWavelength[7].Real - 0.543546) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[7].Imaginary + 0.000651) < 0.000001);
}
public void validate_ROfRhoAndFt_With_Wavelength()
{
// used values for tissue=liver
var scatterer = new PowerLawScatterer(0.84, 0.55);
var hbAbsorber = new ChromophoreAbsorber(ChromophoreType.Hb, 66);
var hbo2Absorber = new ChromophoreAbsorber(ChromophoreType.HbO2, 124);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.02);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.87);
var n = 1.4;
var wvs = new double[] { 650, 700 };
var rhos = new double[] { 0.5, 1.625 };
var fts = new double[] { 0.0, 0.50 };
var tissue = new Tissue(
new IChromophoreAbsorber[] { hbAbsorber, hbo2Absorber, fatAbsorber, waterAbsorber },
scatterer,
"test_tissue",
n);
var ops = wvs.Select(wv => tissue.GetOpticalProperties(wv)).ToArray();
var fs = new PointSourceSDAForwardSolver();
var rVsWavelength = fs.ROfRhoAndFt(ops, rhos, fts);
// return from ROfRhoAndFt is new double[ops.Length * rhos.Length * fts.Length];
// order is: (ops0,rhos0,fts0), (ops0,rhos0,fts1)...(ops0,rhos0,ftsnt-1)
// (ops0,rhos1,fts0), (ops0,rhos1,fts1)...(ops0,rhos1,ftsnt-1)
// ...
// (ops0,rhosnr-1,fts0),.................(ops0,rhosnr-1,ftsnt-1)
// ... repeat above with ops1...
// [0] -> ops0=650, rho0=0.5, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[0].Real - 0.037575) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[0].Imaginary - 0.0) < 0.000001);
// [1] -> ops0=650, rho0=0.5, fts1=0.5
Assert.IsTrue(Math.Abs(rVsWavelength[1].Real - 0.037511) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[1].Imaginary + 0.001200) < 0.000001);
// [2] -> ops0=650, rho1=1.635, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[2].Real - 0.009306) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[2].Imaginary - 0.0) < 0.000001);
// [3] -> ops0=650, rho1=1.635, fts1=0.5
Assert.IsTrue(Math.Abs(rVsWavelength[3].Real - 0.009255) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[3].Imaginary + 0.000674) < 0.000001);
// [4] -> ops1=700, rho0=0.5, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[4].Real - 0.036425) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[4].Imaginary - 0.0) < 0.000001);
// [5] -> ops1=700, rho0=0.5, fts1=0.5
Assert.IsTrue(Math.Abs(rVsWavelength[5].Real - 0.036310) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[5].Imaginary + 0.001446) < 0.000001);
// [6] -> ops1=700, rho1=1.635, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[6].Real - 0.010657) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[6].Imaginary - 0.0) < 0.000001);
// [7] -> ops1=700, rho1=1.635, fts1=0.5
Assert.IsTrue(Math.Abs(rVsWavelength[7].Real - 0.010558) < 0.000001);
Assert.IsTrue(Math.Abs(rVsWavelength[7].Imaginary + 0.000929) < 0.000001);
}
public void validate_ROfFxAndTime_With_Wavelength()
{
// used values for tissue=liver
var scatterer = new PowerLawScatterer(0.84, 0.55);
var hbAbsorber = new ChromophoreAbsorber(ChromophoreType.Hb, 66);
var hbo2Absorber = new ChromophoreAbsorber(ChromophoreType.HbO2, 124);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.02);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.87);
var n = 1.4;
var wvs = new double[] { 650, 700 };
var fxs = new double[] { 0.0, 0.5 };
var times = new double[] { 0.05, 0.10 };
var tissue = new Tissue(
new IChromophoreAbsorber[] { hbAbsorber, hbo2Absorber, fatAbsorber, waterAbsorber },
scatterer,
"test_tissue",
n);
var ops = wvs.Select(wv => tissue.GetOpticalProperties(wv)).ToArray();
var rVsWavelength = ComputationFactory.ComputeReflectance(
new DistributedPointSourceSDAForwardSolver(),
SolutionDomainType.ROfFxAndTime,
ForwardAnalysisType.R,
new object[]
{
ops,
fxs,
times
});
// return from ROfFxAndTime is new double[ops.Length * fxs.Length * ts.Length];
// order is: (ops0,fxs0,ts0), (ops0,fxs0,ts1)...(ops0,fxs0,tsnt-1)
// (ops0,fxs1,ts0), (ops0,fxs1,ts1)...(ops0,fxs1,tsnt-1)
// ...
// (ops0,fxsnf-1,ts0),................(ops0,fxsnf-1,tsnt-1)
// ... repeat above with ops1...
// [0] -> ops0=650, fx0=0.0, ts0=0.05
Assert.IsTrue(Math.Abs(rVsWavelength[0] - 1.558702) < 0.000001);
// [1] -> ops0=650, fx0=0.0, ts1=0.10
Assert.IsTrue(Math.Abs(rVsWavelength[1] - 0.391871) < 0.000001);
// [2] -> ops0=650, fx1=0.5, ts0=0.05
Assert.IsTrue(Math.Abs(rVsWavelength[2] - 5.023055e-12) < 0.000001e-12);
// [3] -> ops0=650, fx1=0.5, ts1=0.10
Assert.IsTrue(Math.Abs(rVsWavelength[3] - 1.032586e-13) < 0.000001e-13);
// [4] -> ops1=700, fx0=0.0, ts0=0.05
Assert.IsTrue(Math.Abs(rVsWavelength[4] - 2.218329) < 0.000001);
// [5] -> ops1=700, fx1=0.5, ts1=0.10
Assert.IsTrue(Math.Abs(rVsWavelength[5] - 0.797200) < 0.000001);
// [6] -> ops1=700, fx0=0.0, ts0=0.05
Assert.IsTrue(Math.Abs(rVsWavelength[6] - 1.347053e-12) < 0.000001e-12);
// [7] -> ops1=700, fx1=0.5, ts1=0.10
Assert.IsTrue(Math.Abs(rVsWavelength[7] - 2.052883e-13) < 0.000001e-13);
}
public void validate_ROfRhoAndTime_With_Wavelength()
{
// used values for tissue=liver
var scatterer = new PowerLawScatterer(0.84, 0.55);
var hbAbsorber = new ChromophoreAbsorber(ChromophoreType.Hb, 66);
var hbo2Absorber = new ChromophoreAbsorber(ChromophoreType.HbO2, 124);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.02);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.87);
var n = 1.4;
var wvs = new double[] { 650, 700 };
var rhos = new double[] { 0.5, 1.625 };
var times = new double[] { 0.05, 0.10 };
var tissue = new Tissue(
new IChromophoreAbsorber[] { hbAbsorber, hbo2Absorber, fatAbsorber, waterAbsorber },
scatterer,
"test_tissue",
n);
var ops = wvs.Select(wv => tissue.GetOpticalProperties(wv)).ToArray();
var rVsWavelength = ComputationFactory.ComputeReflectance(
new PointSourceSDAForwardSolver(),
SolutionDomainType.ROfRhoAndTime,
ForwardAnalysisType.R,
new object[]
{
ops,
rhos,
times
});
// return from ROfRhoAndTime is new double[ops.Length * rhos.Length * ts.Length];
// order is: (ops0,rhos0,ts0), (ops0,rhos0,ts1)...(ops0,rhos0,tsnt-1)
// (ops0,rhos1,ts0), (ops0,rhos1,ts1)...(ops0,rhos1,tsnt-1)
// ...
// (ops0,rhosnr-1,ts0),.................(ops0,rhosnr-1,tsnt-1)
// ... repeat above with ops1...
// [0] -> ops0=650, rho0=0.5, ts0=0.05
Assert.IsTrue(Math.Abs(rVsWavelength[0] - 0.044606) < 0.000001); // API match
// [1] -> ops0=650, rho0=0.5, ts1=0.10
Assert.IsTrue(Math.Abs(rVsWavelength[1] - 0.005555) < 0.000001);
// [2] -> ops0=650, rho1=1.635, ts0=0.05
Assert.IsTrue(Math.Abs(rVsWavelength[2] - 0.036900) < 0.000001); // API match
// [3] -> ops0=650, rho1=1.635, ts1=0.10
Assert.IsTrue(Math.Abs(rVsWavelength[3] - 0.005053) < 0.000001);
// [4] -> ops1=700, rho0=0.5, ts0=0.05
Assert.IsTrue(Math.Abs(rVsWavelength[4] - 0.057894) < 0.000001); // API match
// [5] -> ops1=700, rho0=0.5, ts1=0.10
Assert.IsTrue(Math.Abs(rVsWavelength[5] - 0.010309) < 0.000001);
// [6] -> ops1=700, rho1=1.635, ts0=0.05
Assert.IsTrue(Math.Abs(rVsWavelength[6] - 0.048493) < 0.000001); // API match
// [7] -> ops1=700, rho1=1.635, ts1=0.10
Assert.IsTrue(Math.Abs(rVsWavelength[7] - 0.009434) < 0.000001);
}
public static bool isPointOK(Tissue tissue, int X, int Y)
{
if (!tissue.IsInMap(X, Y))
{
return(false);
}
return(tissue[X, Y].AreaType == AreaEnum.HighDensity |
tissue[X, Y].AreaType == AreaEnum.MediumDensity |
tissue[X, Y].AreaType == AreaEnum.LowDensity);
}
public IActionResult Add(Tissue tissue)
{
var result = _tissueService.Add(tissue);
if (result.Success)
{
return(Ok(result));
}
return(BadRequest(result));
}
public IResult <Tissue> Add(Tissue tissue)
{
var result = BusinessRules <Tissue> .Checker(DuplicateNameChecker(tissue.Name));
if (result != null)
{
foreach (var error in result)
{
return(new FailResult <Tissue>(error.Message));
}
}
_tissueDal.Add(tissue);
return(new SuccessResult <Tissue>(Messages.success, tissue));
}
public static Point getValidPoint(Tissue tissue, Point p)
{
if (isPointOK(tissue, p.X, p.Y))
{
return(p);
}
int dist = 1;
while (true)
{
//up
for (int iX = -dist; iX < dist + 1; iX++)
{
if (isPointOK(tissue, p.X + iX, p.Y + dist))
{
return(new Point(p.X + iX, p.Y + dist));
}
}
//down
for (int iX = -dist; iX < dist + 1; iX++)
{
if (isPointOK(tissue, p.X + iX, p.Y - dist))
{
return(new Point(p.X + iX, p.Y - dist));
}
}
//left
for (int iY = -dist; iY < dist + 1; iY++)
{
if (isPointOK(tissue, p.X - dist, p.Y + iY))
{
return(new Point(p.X - dist, p.Y + iY));
}
}
//right
for (int iY = -dist; iY < dist + 1; iY++)
{
if (isPointOK(tissue, p.X + dist, p.Y + iY))
{
return(new Point(p.X + dist, p.Y + iY));
}
}
dist++;
}
}
public ActionResult CreateNewTissue(Tissue tissue)
{
ViewBag.Error = "";
try
{
if (ModelState.IsValid)
{
repoTissue.Insert(tissue.Name);
return(RedirectToAction("TissuesManagement"));
}
}
catch
{
ViewBag.Error = "Die Gewebeart ist schon vorhanden!";
}
return(View(tissue));
}
public override void SetupSimulation()
{
logFrequency = 1;
logVTK = true;
nbOfSimulationSteps = 1000;
popSize = 1;
popMaxSize = 128;
Tissue t1 = new Tissue(1, popMaxSize);
List <Tissue> tissueList = new List <Tissue>()
{
t1
};
nbCellTypes = tissueList.Count;
cellPopulation = new CellPopulation(popSize, popMaxSize, tissueList);
Helper.SetNCubedInN(popMaxSize);
cellPopulation.PositionCells(false);
}
public AStar(VG.Map.Tissue t)
{
this.map = t;
nodeGrid = new AStarNode[200][];
openSet = new bool[200][];
closedSet = new bool[200][];
cacheable = new bool[200][];
for (int i = 0; i < 200; i++)
{
nodeGrid[i] = new AStarNode[200];
openSet[i] = new bool[200];
closedSet[i] = new bool[200];
cacheable[i] = new bool[200];
}
// prepare cacheable set
EntityCollection aznCol = map.get_EntitiesByType(EntityEnum.AZN);
for (int i = 0; i < aznCol.Count; i++)
{
cacheable[aznCol[i].X][aznCol[i].Y] = true;
}
EntityCollection hpCol = map.get_EntitiesByType(EntityEnum.HoshimiPoint);
for (int i = 0; i < hpCol.Count; i++)
{
cacheable[hpCol[i].X][hpCol[i].Y] = true;
}
//cache PierreIP
cacheable[Global.MYAI.PierreTeamInjectionPoint.X][Global.MYAI.PierreTeamInjectionPoint.Y] = true;
cache = new System.Collections.Hashtable((hpCol.Count * hpCol.Count) + (aznCol.Count * aznCol.Count));
aznCol = null; // garbage-collected
hpCol = null;
}
public override void SetupSimulation()
{
nbOfSimulationSteps = 1000;
logFrequency = 1;
logVTK = false;
popSize = 4;
popMaxSize = 8;
Icosahedron42 mesh = new Icosahedron42();
Tissue t1 = new Tissue(4, popMaxSize, mesh);
List <Tissue> tissueList = new List <Tissue>()
{
t1
};
nbCellTypes = tissueList.Count;
cellPopulation = new CellPopulation(popSize, popMaxSize, tissueList, 1);
Helper.SetNCubedInN(popMaxSize);
cellPopulation.PositionCells(false);
}
public override void SetupSimulation()
{
nbOfSimulationSteps = 2000;
logFrequency = 10;
//logVTK = true;
popSize = 8;
popMaxSize = 64;
Cylinder34 mesh = new Cylinder34(new Vector(.5f, 1f, .5f), false);
Tissue t1 = new Tissue(8, popMaxSize, mesh);
List <Tissue> tissueList = new List <Tissue>()
{
t1
};
nbCellTypes = tissueList.Count;
cellPopulation = new CellPopulation(popSize, popMaxSize, tissueList, 2);
Helper.SetNCubedInN(popMaxSize);
cellPopulation.PositionCells(false);
}
/// <summary>
/// Serialize to a JSON object
/// </summary>
public new void SerializeJson(Utf8JsonWriter writer, JsonSerializerOptions options, bool includeStartObject = true)
{
if (includeStartObject)
{
writer.WriteStartObject();
}
((Fhir.R4.Models.BackboneElement) this).SerializeJson(writer, options, false);
if (Tissue != null)
{
writer.WritePropertyName("tissue");
Tissue.SerializeJson(writer, options);
}
if (Value != null)
{
writer.WritePropertyName("value");
Value.SerializeJson(writer, options);
}
if (!string.IsNullOrEmpty(SupportingInformation))
{
writer.WriteString("supportingInformation", (string)SupportingInformation !);
}
if (_SupportingInformation != null)
{
writer.WritePropertyName("_supportingInformation");
_SupportingInformation.SerializeJson(writer, options);
}
if (includeStartObject)
{
writer.WriteEndObject();
}
}
public override void SetupSimulation()
{
nbCellTypes = 1;
nbOfSimulationSteps = 1000;
popSize = 25;
popMaxSize = 125;
//Cylinder34 mesh = new Cylinder34();
//HexagonalCylinder42 mesh = new HexagonalCylinder42(1f);
//Console.WriteLine(mesh.innerRadius);
Tissue t1 = new Tissue(25, popMaxSize, new Cylinder34(new Vector(.5f, .5f, .5f)));
List <Tissue> tissueList = new List <Tissue>()
{
t1
};
nbCellTypes = tissueList.Count;
cellPopulation = new CellPopulation(popSize, popMaxSize, tissueList);
Helper.SetNCubedInN(popMaxSize);
cellPopulation.PositionCells(false);
}
public override IDeepCopyable CopyTo(IDeepCopyable other)
{
var dest = other as WithdrawalPeriodComponent;
if (dest == null)
{
throw new ArgumentException("Can only copy to an object of the same type", "other");
}
base.CopyTo(dest);
if (Tissue != null)
{
dest.Tissue = (Hl7.Fhir.Model.CodeableConcept)Tissue.DeepCopy();
}
if (Value != null)
{
dest.Value = (Hl7.Fhir.Model.Quantity)Value.DeepCopy();
}
if (SupportingInformationElement != null)
{
dest.SupportingInformationElement = (Hl7.Fhir.Model.FhirString)SupportingInformationElement.DeepCopy();
}
return(dest);
}
public InitDataContext()
{
var _context = new DataContext();
if (_context.Stains.Count() == 0)
{
var stains = new List <Stain>
{
new Stain {
Name = "HE"
},
new Stain {
Name = "Periodic Acid Schiff (PAS)"
},
new Stain {
Name = "Giemsa"
},
new Stain {
Name = "Iron (Prussian Blue)"
},
new Stain {
Name = "HC"
},
new Stain {
Name = "Alcian Blue"
},
new Stain {
Name = "Alcian Blue+PAS"
},
new Stain {
Name = "Gomori Trichrome blue"
},
new Stain {
Name = "Gomori Trichrome green"
},
new Stain {
Name = "EvG"
},
new Stain {
Name = "AFB"
},
new Stain {
Name = "GMS"
},
new Stain {
Name = "Gram"
},
new Stain {
Name = "Toluidine Blue"
},
new Stain {
Name = "Acid fast"
},
new Stain {
Name = "Congo red for amyloid"
},
new Stain {
Name = "Jones methenamine silver for basement membrane and mesangium"
},
new Stain {
Name = "Sudan black for lipids & lipochrome pigments"
},
new Stain {
Name = "Verhoeff's method for elastin"
},
new Stain {
Name = "Warthin-Starry method for bacteria"
},
new Stain {
Name = "Weigert’s iron hematoxylin"
},
new Stain {
Name = "Electron micrograph (EM)"
},
new Stain {
Name = "Methenamine Silver"
},
new Stain {
Name = "Jones’ Basement Membrane"
},
new Stain {
Name = "DMABR"
}
};
stains.ForEach(s => _context.Stains.Add(s));
_context.SaveChanges();
var organs = new List <Organ> {
new Organ {
Name = "Organ"
},
new Organ {
Name = "Liver"
},
new Organ {
Name = "Kidney"
},
new Organ {
Name = "Lung"
},
new Organ {
Name = "Spleen"
},
new Organ {
Name = "Heart"
},
new Organ {
Name = "Skin"
},
new Organ {
Name = "Intestine"
},
new Organ {
Name = "Submucosa"
},
new Organ {
Name = "Stomach"
},
new Organ {
Name = "Urinary bladder"
},
new Organ {
Name = "Gallbladder"
},
new Organ {
Name = "Blood vessel"
},
new Organ {
Name = "Muscles"
},
new Organ {
Name = "Thyroid"
},
new Organ {
Name = "Skeleton"
},
new Organ {
Name = "Breast"
},
new Organ {
Name = "V****a"
},
new Organ {
Name = "Uterus"
},
new Organ {
Name = "Ovar"
},
new Organ {
Name = "Cervix"
},
new Organ {
Name = "Prostate"
}
};
organs.ForEach(o => _context.Organs.Add(o));
_context.SaveChanges();
var reglament = new Reglament
{
Titel = "Default ",
AcceptanceValue = 70,
Edges = 200,
Scaling = 1.0,
SharpnessThresholdValue = 0.3,
TileSize = 512,
Status = true,
};
_context.Reglaments.Add(reglament);
_context.SaveChanges();
var tissue = new Tissue {
Name = "Tissue"
};
_context.Tissues.Add(tissue);
_context.SaveChanges();
}
}
public List <parentMetabolite> ListOfMetabolites; //metabolite object, level (apriori normalized or non-normalized)
public sampleForTissueAndCharge(List <string> _metabolitebVals, List <msMetabolite> _lom)
{
Id = _metabolitebVals.ElementAt(publicVariables.indexToStartFrom - 3);
Tissue = _metabolitebVals.ElementAt(publicVariables.indexToStartFrom - 2);
Charge = _metabolitebVals.ElementAt(publicVariables.indexToStartFrom - 1);
Phenotype = (clinicalData.List_clinicalData.Any(x => x.Id == Id)) ? clinicalData.List_clinicalData.First(x => x.Id == Id).Phenotype : "U";
ListOfNumClinicalData = new List <sampleClinicalData>();
// add sample weight values
if (clinicalData.List_clinicalData.First(x => x.Id == Id).SampleWeight_covariates.Count != 0)
{
ListOfNumClinicalData.Add(new sampleClinicalData()
{
name = "sampleweight",
n_value = ((publicVariables.prefixValues.mixed == publicVariables.prefix || publicVariables.prefixValues.gcms == publicVariables.prefix)
? clinicalData.List_clinicalData.First(x => x.Id == Id).SampleWeight_covariates.Where(x => x.tissue.ToLower() == Tissue.ToLower()).Average(x => x.weight.Imputed)
: clinicalData.List_clinicalData.First(x => x.Id == Id).SampleWeight_covariates
.First(x => x.tissue.ToLower() == Tissue.ToLower() && x.charge.ToLower() == Charge.ToLower()).weight.Imputed),
typeOf = sampleClinicalData.type.numeric
});
}
// add numerical clinical data
foreach (KeyValuePair <string, imputedValues> kvp_nv in clinicalData.List_clinicalData.First(x => x.Id == Id).Numerical_covariates)
{
ListOfNumClinicalData.Add(new sampleClinicalData()
{
name = kvp_nv.Key,
n_value = kvp_nv.Value.Imputed,
typeOf = sampleClinicalData.type.numeric
});
}
// add categorical clinical data
foreach (KeyValuePair <string, string> kvp_cv in clinicalData.List_clinicalData.First(x => x.Id == Id).Categorical_covariates)
{
ListOfNumClinicalData.Add(new sampleClinicalData()
{
name = kvp_cv.Key,
c_value = kvp_cv.Value,
typeOf = sampleClinicalData.type.categorical
});
}
// add metabolite levels values
ListOfMetabolites = new List <parentMetabolite>();
foreach (msMetabolite _m in _lom)
{
if (string.IsNullOrEmpty(_metabolitebVals.ElementAt(_m.In_Index)) || string.IsNullOrWhiteSpace(_metabolitebVals.ElementAt(_m.In_Index)))
{
ListOfMetabolites.Add(new parentMetabolite()
{
mtbltDetails = _m,
mtbltVals = new imputedValues()
{
Imputed = -1,
Non_imputed = -1
}
});
}
else
{
ListOfMetabolites.Add(new parentMetabolite()
{
mtbltDetails = _m,
mtbltVals = new imputedValues()
{
Imputed = Convert.ToDouble(_metabolitebVals.ElementAt(_m.In_Index)),
Non_imputed = Convert.ToDouble(_metabolitebVals.ElementAt(_m.In_Index))
}
});
}
}
}
public IResult <Tissue> Update(Tissue tissue)
{
return(new SuccessResult <Tissue>(Messages.success, tissue));
}
public static Point getValidPoint(Tissue tissue, Point p)
{
if (isPointOK(tissue, p.X, p.Y))
return p;
int dist = 1;
while (true)
{
//up
for (int iX = -dist; iX < dist + 1; iX++)
if (isPointOK(tissue, p.X + iX, p.Y + dist))
return new Point(p.X + iX, p.Y + dist);
//down
for (int iX = -dist; iX < dist + 1; iX++)
if (isPointOK(tissue, p.X + iX, p.Y - dist))
return new Point(p.X + iX, p.Y - dist);
//left
for (int iY = -dist; iY < dist + 1; iY++)
if (isPointOK(tissue, p.X - dist, p.Y + iY))
return new Point(p.X - dist, p.Y + iY);
//right
for (int iY = -dist; iY < dist + 1; iY++)
if (isPointOK(tissue, p.X + dist, p.Y + iY))
return new Point(p.X + dist, p.Y + iY);
dist++;
}
}
private double[,] CalculateRates(Tissue tissue, List<Point> missionTravelPoints, List<Point> neurocontrollers, Point pierreIP)
{
//StreamWriter weightsWrite = new StreamWriter("c:\\weights.txt");
//StreamWriter ratesWrite = new StreamWriter("c:\\rates.txt");
neurocontrollers.Add(pierreIP);
double[,] rates = new double[tissue.Height, tissue.Width];
for (int i = 0; i < tissue.Height; ++i)
{
for (int j = 0; j < tissue.Width; ++j)
{
Entity entity = tissue.getElement(i, j);
Double dist = this.GetDistance(pierreIP, new Point(i,j));
if (pierreIP.X == i && pierreIP.Y == j)
{
rates[i, j] = 0;//weightsWrite.Write("P|");ratesWrite.Write("P|");
continue;
}
if (null == entity)
{
rates[i, j] += EmptyPointWeight;
}
if (this.NeuroControllerInRange(new Point(i, j), neurocontrollers, 14))
{
rates[i, j] += NeuroControllerInRangeWeight;
}
if (null != entity && EntityEnum.AZN == entity.EntityType)
{
rates[i, j] += AZNPointsWeight;
}
if (null != entity && EntityEnum.HoshimiPoint == entity.EntityType)
{
rates[i, j] += HoshimiPointsWeight;
}
if (missionTravelPoints.Contains(new Point(i, j)))
{
rates[i, j] += ObjectivesPointsWeight;
}
if (neurocontrollers.Contains(new Point(i, j)))
{
rates[i, j] += NeuroControllerWeight;
}
//weightsWrite.Write("("+i+","+j+")" + rates[i, j].ToString() + "|");
rates[i, j] = rates[i, j] / dist;
//ratesWrite.Write("("+i+","+j+")"+rates[i, j].ToString() + "|");
}
//weightsWrite.WriteLine("");
//ratesWrite.WriteLine("");
}
//weightsWrite.Close();
//ratesWrite.Close();
return rates;
}
public Point GetInjectionPoint(Tissue tissue, List<Point> missionTravelPoints, List<Point> hoshimiPoints, List<Point> aznPoints, List<Point> neurocontrollers, Point pierreIP)
{
// Usar técnica de agrupamentos de SInt para agrupar hoshimi e azn points mais próximos?
Point bestPoint = new Point(100, 100);
double bestRate = -1;
double[,] rates = CalculateRates(tissue, missionTravelPoints, neurocontrollers, pierreIP);
for (int i = 0; i < tissue.Height; ++i)
{
for (int j = 0; j < tissue.Width; ++j)
{
if (rates[i, j] > bestRate && AreaEnum.Bone != tissue[i,j].AreaType)
{
bestRate = rates[i, j];
bestPoint = new Point(i, j);
}
}
}
return bestPoint;
}
public static bool isPointOK(Tissue tissue, int X, int Y)
{
if (!tissue.IsInMap(X, Y)) return false;
return tissue[X, Y].AreaType == AreaEnum.HighDensity |
tissue[X, Y].AreaType == AreaEnum.MediumDensity |
tissue[X, Y].AreaType == AreaEnum.LowDensity;
}
public void validate_ROfFxAndFt_With_Wavelength()
{
// used values for tissue=liver
var scatterer = new PowerLawScatterer(0.84, 0.55);
var hbAbsorber = new ChromophoreAbsorber(ChromophoreType.Hb, 66);
var hbo2Absorber = new ChromophoreAbsorber(ChromophoreType.HbO2, 124);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.02);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.87);
var n = 1.4;
var wvs = new double[] { 650, 700 };
var fxs = new double[] { 0.0, 0.5 };
var fts = new double[] { 0.0, 0.50 };
var tissue = new Tissue(
new IChromophoreAbsorber[] { hbAbsorber, hbo2Absorber, fatAbsorber, waterAbsorber },
scatterer,
"test_tissue",
n);
var ops = wvs.Select(wv => tissue.GetOpticalProperties(wv)).ToArray();
var rVsWavelength = ComputationFactory.ComputeReflectance(
new DistributedPointSourceSDAForwardSolver(),
SolutionDomainType.ROfFxAndFt,
ForwardAnalysisType.R,
new object[]
{
ops,
fxs,
fts
});
// return from ROfFxAndFt is new double[ops.Length * fxs.Length * fts.Length];
// order is: (ops0,fxs0,fts0)real, (ops0,fxs0,ts1)real...(ops0,fxs0,ftsnt-1)real
// (ops0,fxs1,fts0)real, (ops0,fxs1,ts1)real...(ops0,fxs1,ftsnt-1)real
// ...
// (ops0,fxsnf-1,fts0)real,.................(ops0,fxsnf-1,ftsnt-1)real
// ... repeat above with imag, then with ops1...
// [0] -> ops0=650, fx0=0.0, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[0] - 1.890007) < 0.000001); // API match
// [1] -> ops0=650, fx0=0.0, fts1=0.5 real
Assert.IsTrue(Math.Abs(rVsWavelength[1] - 1.888160) < 0.000001);
// [2] -> ops0=650, fx1=0.5, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[2] - 0.562537) < 0.000001); // API match
// [3] -> ops0=650, fx1=0.5, fts1=0.5 real
Assert.IsTrue(Math.Abs(rVsWavelength[3] - 0.562543) < 0.000001);
// [4] -> ops1=700, fx0=0.0, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[4] - 2.118427) < 0.000001); // API match
// [5] -> ops1=700, fx0=0.0, fts1=0.5 real
Assert.IsTrue(Math.Abs(rVsWavelength[5] - 2.113377) < 0.000001);
// [6] -> ops1=700, fx1=0.5, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[6] - 0.543539) < 0.000001); // API match
// [7] -> ops1=700, fx1=0.5, fts1=0.5 real
Assert.IsTrue(Math.Abs(rVsWavelength[7] - 0.543546) < 0.000001);
// [8] -> ops0=650, fx0=0.0, fts0=0.0 imag
Assert.IsTrue(Math.Abs(rVsWavelength[8] - 0.0) < 0.000001); // API match
// [9] -> ops0=650, fx0=0.0, fts1=0.5 imag
Assert.IsTrue(Math.Abs(rVsWavelength[9] + 0.045122) < 0.000001);
// [10] -> ops0=650, fx1=0.5, fts0=0.0 imag
Assert.IsTrue(Math.Abs(rVsWavelength[10] - 0.0) < 0.000001); // API match
// [11] -> ops0=650, fx1=0.5, fts1=0.5 imag
Assert.IsTrue(Math.Abs(rVsWavelength[11] + 0.000799) < 0.000001);
// [12] -> ops1=700, fx0=0.0, fts0=0.0 imag
Assert.IsTrue(Math.Abs(rVsWavelength[12] - 0.0) < 0.000001); // API match
// [13] -> ops1=700, fx0=0.0, fts1=0.5 imag
Assert.IsTrue(Math.Abs(rVsWavelength[13] + 0.071758) < 0.000001);
// [14] -> ops1=700, fx1=0.5, fts0=0.0 imag
Assert.IsTrue(Math.Abs(rVsWavelength[14] - 0.0) < 0.000001); // API match
// [15] -> ops1=700, fx1=0.5, fts1=0.5 imag
Assert.IsTrue(Math.Abs(rVsWavelength[15] + 0.000651) < 0.000001);
}
public ActionResult Index(HttpPostedFileBase file, WSI wsi, Stain stain, Organ organ, Tissue tissue)
{
//TODO
//Today only one value possible
//var tissue = _repoTissues.GetTissueByName("Tissue");
ISharpnessManager manager = new SharpnessManager();
//
var root = @"C:\Users\AnnaToshiba2\Desktop\WSI\Sharpness_WebApp_Uploads\";
var fileName = "";
wsi.WSIId = Guid.NewGuid();
string outputDir = Path.Combine(Path.GetDirectoryName(root), User.Identity.GetUserId(), "WSI " + wsi.WSIId + @"\");
if (!Directory.Exists(outputDir))
{
Directory.CreateDirectory(outputDir);
}
if (file.ContentLength > 0)
{
fileName = Path.GetFileName(file.FileName);
var path = Path.Combine(outputDir, fileName);
file.SaveAs(path);
wsi.Path = path;
wsi.UserId = User.Identity.GetUserId();
_repoWSIs.Insert(wsi);
}
var reportLink = User.Identity.GetUserId() + "/" + "WSI " + wsi.WSIId + "/" + fileName + " ";
var evaluationLink = root + reportLink.Replace("/", @"\");
Process first = new Process();
first.StartInfo.FileName = @"C:\Users\AnnaToshiba2\Documents\GitHub\sharpness\sharpness console App\SharpnessExplorationCurrent\SharpnessExplorationCurrent\bin\x64\Release\SharpnessExplorationCurrent.exe";
first.StartInfo.Arguments = String.Format(@"""{0}""", wsi.Path);
first.Start();
first.WaitForExit();
var report = new Report();
report.ReglamentId = _repoReglaments.GetReglamentByTitel("Default").ReglamentId;
report.Comment = "some words";
report.OrganName = organ.Name;
report.TissueName = tissue.Name;
report.WSIId = wsi.WSIId;
report.StainName = stain.Name;
report.SharpnessMapPath = outputDir + Path.GetFileNameWithoutExtension(fileName) + ".png";
report.SharpnessMapPathDebug = outputDir + Path.GetFileNameWithoutExtension(fileName) + "Debug.png";
var semaphoreValues = manager.GetSemaphoreValues(report.SharpnessMapPath);
var channelsValues = manager.GetChannelsValues(report.SharpnessMapPathDebug);
report.Semaphore_Red = semaphoreValues[0];
report.Semaphore_Green = semaphoreValues[1];
report.Semaphore_Yellow = semaphoreValues[2];
report.Red_Channel = channelsValues[0];
report.Blue_Channel = channelsValues[1];
if (semaphoreValues[1] > 70)
{
report.Evaluation = true;
}
else
{
report.Evaluation = false;
}
report.ReportLink = reportLink;
report.UserId = User.Identity.GetUserId();
_repoReports.Insert(report);
return(RedirectToAction("Report", new { ReportId = report.ReportId }));
}
public void validate_ROfRhoAndFt_With_Wavelength()
{
// used values for tissue=liver
var scatterer = new PowerLawScatterer(0.84, 0.55);
var hbAbsorber = new ChromophoreAbsorber(ChromophoreType.Hb, 66);
var hbo2Absorber = new ChromophoreAbsorber(ChromophoreType.HbO2, 124);
var fatAbsorber = new ChromophoreAbsorber(ChromophoreType.Fat, 0.02);
var waterAbsorber = new ChromophoreAbsorber(ChromophoreType.H2O, 0.87);
var n = 1.4;
var wvs = new double[] { 650, 700 };
var rhos = new double[] { 0.5, 1.625 };
var fts = new double[] { 0.0, 0.50 };
var tissue = new Tissue(
new IChromophoreAbsorber[] { hbAbsorber, hbo2Absorber, fatAbsorber, waterAbsorber },
scatterer,
"test_tissue",
n);
var ops = wvs.Select(wv => tissue.GetOpticalProperties(wv)).ToArray();
var rVsWavelength = ComputationFactory.ComputeReflectance(
new PointSourceSDAForwardSolver(),
SolutionDomainType.ROfRhoAndFt,
ForwardAnalysisType.R,
new object[]
{
ops,
rhos,
fts
});
// return from ROfRhoAndFt is new double[ops.Length * rhos.Length * fts.Length];
// order is: (ops0,rhos0,fts0)real, (ops0,rhos0,fts1)real...(ops0,rhos0,ftsnt-1)real
// (ops0,rhos1,fts0)real, (ops0,rhos1,fts1)real...(ops0,rhos1,ftsnt-1)real
// ...
// (ops0,rhosnr-1,fts0)real,.................(ops0,rhosnr-1,ftsnt-1)real
// ... repeat above with imag, then next ops1...
// [0] -> ops0=650, rho0=0.5, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[0] - 0.037575) < 0.000001);
// [1] -> ops0=650, rho0=0.5, fts1=0.5 real
Assert.IsTrue(Math.Abs(rVsWavelength[1] - 0.037511) < 0.000001);
// [2] -> ops0=650, rho1=1.635, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[2] - 0.009306) < 0.000001);
// [3] -> ops0=650, rho1=1.635, fts1=0.5 real
Assert.IsTrue(Math.Abs(rVsWavelength[3] - 0.009255) < 0.000001);
// [4] -> ops1=700, rho0=0.5, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[4] - 0.036425) < 0.000001);
// [5] -> ops1=700, rho0=0.5, fts1=0.5 real
Assert.IsTrue(Math.Abs(rVsWavelength[5] - 0.036310) < 0.000001);
// [6] -> ops1=700, rho1=1.635, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[6] - 0.010657) < 0.000001);
// [7] -> ops1=700, rho1=1.635, fts1=0.5 real
Assert.IsTrue(Math.Abs(rVsWavelength[7] - 0.010558) < 0.000001);
// [8] -> ops0=650, rho0=0.5, fts0=0.0 imag
Assert.IsTrue(Math.Abs(rVsWavelength[8] - 0.0) < 0.000001);
// [9] -> ops0=650, rho0=0.5, fts1=0.5 imag
Assert.IsTrue(Math.Abs(rVsWavelength[9] + 0.001200) < 0.000001);
// [10] -> ops0=650, rho1=1.635, fts0=0.0 imag
Assert.IsTrue(Math.Abs(rVsWavelength[10] - 0.0) < 0.000001);
// [11] -> ops1=650, rho1=1.635, fts1=0.5 imag
Assert.IsTrue(Math.Abs(rVsWavelength[11] + 0.000674) < 0.000001);
// [12] -> ops1=700, rho0=0.5, fts0=0.0
Assert.IsTrue(Math.Abs(rVsWavelength[12] - 0.0) < 0.000001);
// [13] -> ops1=700, rho0=0.5, fts1=0.5 imag
Assert.IsTrue(Math.Abs(rVsWavelength[13] + 0.001446) < 0.000001);
// [14] -> ops1=700, rho1=1.635, fts0=0.0 real
Assert.IsTrue(Math.Abs(rVsWavelength[14] - 0.0) < 0.000001);
// [15] -> ops1=700, rho1=1.635, fts1=0.5 imag
Assert.IsTrue(Math.Abs(rVsWavelength[15] + 0.000929) < 0.000001);
}
public AStarSpecial(Tissue t)
: base(t)
{
}
public void MyAI_WhatToDoNextEvent()
{
numHunters = 0;
numScanners = 0;
numContainers = 0;
numDefender = 0;
numNeedle = 0;
numNavExpBot = 0;
numNavColBot = 0;
numUNavExpBot = 0;
numUNavColBot = 0;
numBlocker = 0;
numGuard = 0;
#region handle objectives
if (first1)
{
int jmlCol = 0;
int jmlExp = 0;
foreach (BaseObjective bo in Mission.Objectives)
{
if (bo.Status == ObjectiveStatus.ToBeDone)
{
if (bo is UniqueNavigationObjective)
{
UniqueNavigationObjective unav = (UniqueNavigationObjective)bo;
if (unav.NanoBotType == NanoBotType.NanoExplorer)
{
if (unav.NavPoints.Count > 20)
{
continue;
}
Global.NBUNAVEXPTOBUILD++;
listUNavExpObj.Add(new UniqueNavigationStruct(unav));
}
else if (unav.NanoBotType == NanoBotType.Unknown)
{
bool needStock = false;
foreach (NavPoint np in unav.NavPoints)
{
if (np.Stock > 0)
{
needStock = true;
break;
}
}
if (!needStock)
{
if (unav.NavPoints.Count > 20)
{
continue;
}
Global.NBUNAVEXPTOBUILD++;
listUNavExpObj.Add(new UniqueNavigationStruct(unav));
}
else
{
if (unav.NavPoints.Count > 13)
{
continue;
}
Global.NBUNAVCOLTOBUILD++;
listUNavColObj.Add(new UniqueNavigationStruct(unav));
}
}
else
{
if (unav.NavPoints.Count > 13)
{
continue;
}
Global.NBUNAVCOLTOBUILD++;
listUNavColObj.Add(new UniqueNavigationStruct(unav));
}
}
else if (bo is NavigationObjective)
{
NavigationObjective n = (NavigationObjective)bo;
if (n.NanoBotType == NanoBotType.NanoExplorer)
{
if (n.NavPoints.Count > 20)
{
continue;
}
jmlExp += n.NavPoints.Count;
listNavExpObj.Add(new NavigationStruct(n));
}
else if (n.NanoBotType == NanoBotType.Unknown)
{
bool needStock = false;
foreach (NavPoint np in n.NavPoints)
{
if (np.Stock > 0)
{
needStock = true;
break;
}
}
if (!needStock)
{
if (n.NavPoints.Count > 20)
{
continue;
}
jmlExp += n.NavPoints.Count;
listNavExpObj.Add(new NavigationStruct(n));
}
else
{
if (n.NavPoints.Count > 13)
{
continue;
}
jmlCol += n.NavPoints.Count;
listNavColObj.Add(new NavigationStruct(n));
}
}
else
{
if (n.NavPoints.Count > 13)
{
continue;
}
jmlCol += n.NavPoints.Count;
listNavColObj.Add(new NavigationStruct(n));
}
}
}
}
if (jmlExp > 0)
{
Global.NBNAVEXPTOBUILD = (jmlExp / 3);
if ((jmlExp % 3) > 0)
{
Global.NBNAVEXPTOBUILD++;
}
if (Global.NBNAVEXPTOBUILD > 5)
{
Global.NBNAVEXPTOBUILD = 5;
}
}
if (jmlCol > 0)
{
Global.NBNAVCOLTOBUILD = (jmlCol / 2);
if ((jmlCol % 2) > 0)
{
Global.NBNAVCOLTOBUILD++;
}
if (Global.NBNAVCOLTOBUILD > 5)
{
Global.NBNAVCOLTOBUILD = 7;
}
}
first1 = false;
}
#endregion
#region construct bots
foreach (NanoBot bot in this.NanoBots)
{
if (bot is HunterBot)
{
numHunters++;
((HunterBot)bot).DoNext(this);
}
else if (bot is DefenderBot)
{
numDefender++;
((DefenderBot)bot).DoNext(this);
}
else if (bot is ScannerBot)
{
numScanners++;
((ScannerBot)bot).DoNext(this);
}
else if (bot is ContainerBot)
{
numContainers++;
((ContainerBot)bot).DoNext(this);
}
else if (bot is GuardBot)
{
numGuard++;
((GuardBot)bot).DoNext(this);
}
else if (bot is NeedleBot)
{
numNeedle++;
((NeedleBot)bot).DoNext(this);
}
else if (bot is UniqueNavigationExplorerBot)
{
numUNavExpBot++;
((UniqueNavigationExplorerBot)bot).DoNext(this);
}
else if (bot is UniqueNavigationCollectorBot)
{
numUNavColBot++;
((UniqueNavigationCollectorBot)bot).DoNext(this);
}
else if (bot is NavigationExplorerBot)
{
numNavExpBot++;
((NavigationExplorerBot)bot).DoNext(this);
}
else if (bot is NavigationCollectorBot)
{
numNavColBot++;
((NavigationCollectorBot)bot).DoNext(this);
}
else if (bot is BlockerBot)
{
numBlocker++;
}
}
Point prevDest = this.AI.PointInfo;
bool stop = false;
if (firstInjected2)
{
bool taken = false;
foreach (NanoBotInfo bot in OtherNanoBotsInfo)
{
if ((bot.Location == AI.Location) && ((bot.NanoBotType == NanoBotType.NanoNeedle) || (bot.NanoBotType == NanoBotType.NanoBlocker)))
{
taken = true;
break;
}
}
if (!taken)
{
AI.Build(typeof(NeedleBot), "Needle");
//firstNeedleBuilt = true;
}
firstInjected2 = false;
}
if (numHunters < Global.NBHUNTERBOTTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(HunterBot), "Hunter");
//return;
}
if (numDefender < Global.NBDEFENDERTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(DefenderBot), "Defender");
//return;
}
if (numScanners < Global.NBSCANNERTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(ScannerBot), "Scanner");
//return;
}
if (numGuard < Global.NBGUARDTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(GuardBot), "Guard");
//return;
}
if (numContainers < Global.NBCONTAINERTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(ContainerBot), "Containr");
//return;
}
if (numUNavExpBot < Global.NBUNAVEXPTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(UniqueNavigationExplorerBot), "UNavExplr");
foreach (UniqueNavigationStruct o in MyAI.listUNavExpObj)
{
o.isAssigned = false;
}
foreach (NanoBot bot in NanoBots)
{
if (bot is UniqueNavigationExplorerBot)
{
((UniqueNavigationExplorerBot)bot).dapet = false;
}
}
//return;
}
if (numUNavColBot < Global.NBUNAVCOLTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(UniqueNavigationCollectorBot), "UNavColtr");
foreach (UniqueNavigationStruct o in MyAI.listUNavColObj)
{
o.isAssigned = false;
}
foreach (NanoBot bot in NanoBots)
{
if (bot is UniqueNavigationCollectorBot)
{
((UniqueNavigationCollectorBot)bot).dapet = false;
}
}
//return;
}
if (numNavExpBot < Global.NBNAVEXPTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(NavigationExplorerBot), "NavExplr");
// reset semua Navigasi
foreach (NavNode node in NavigationExplorerBot.allNodes)
{
node.Bot = null;
node.Done = false;
}
//foreach (NavigationStruct ns in MyAI.listNavExpObj)
//{
// if ((ns.isActive) && (ns.NavigationObj.Status == ObjectiveStatus.ToBeDone))
// {
// ns.isActive = false;
// }
//}
//return;
}
if (numNavColBot < Global.NBNAVCOLTOBUILD)
{
AI.StopMoving();
stop = true;
AI.Build(typeof(NavigationCollectorBot), "NavColtr");
// reset semua Navigasi
foreach (NavNode node in NavigationCollectorBot.allNodes)
{
node.Bot = null;
node.Done = false;
}
//foreach (NavigationStruct ns in MyAI.listNavColObj)
//{
// if ((ns.isActive) && (ns.NavigationObj.Status == ObjectiveStatus.ToBeDone))
// {
// ns.isActive = false;
// }
//}
//return;
}
if ((numBlocker < Global.NBBLOCKERTOBUILD) &&
(((!firstInjected) &&
(AI.Location != InjectionPointWanted) && (!skipped)))) //||
// (((this.CurrentTurn % 500) == 0) &&
// (this.NanoBots.Count < Utils.NbrMaxBots))
// ))
{
//bool isOnHP = false;
//foreach (Entity e in Tissue.GetEntitiesByType(EntityEnum.HoshimiPoint))
//{
// if ((e.X == AI.Location.X) && (e.Y == AI.Location.Y))
// {
// isOnHP = true;
// break;
// }
//}
//if (!isOnHP)
//{
bool isOnHP = false;
foreach (Entity e in Tissue.GetEntitiesByType(EntityEnum.HoshimiPoint))
{
if (AI.Location.X == e.X && AI.Location.Y == e.Y)
{
isOnHP = true;
break;
}
}
if (!isOnHP)
{
skipped = true;
AI.StopMoving();
stop = true;
AI.Build(typeof(BlockerBot), "Blockr");
}
//}
//return;
}
//if ((this.CurrentTurn >= 500) && (!Global.AllHPBuilt) && (NanoBots.Count < Utils.NbrMaxBots))
//{
// AI.StopMoving();
// stop = true;
// AI.Build(typeof(DummyCrapBot), "DummySht");
// //return;
//}
if (stop)
{
this.AI.MoveTo(Global.PF.FindWay(AI.Location, prevDest).Points);
}
// Filter Nanobots
ArrayList hunters = new ArrayList(Global.NBHUNTERBOTTOBUILD);
ArrayList defenders = new ArrayList(Global.NBDEFENDERTOBUILD);
ArrayList containers = new ArrayList(Global.NBCONTAINERTOBUILD);
ArrayList blockers = new ArrayList(Global.NBBLOCKERTOBUILD);
ArrayList scanners = new ArrayList(Global.NBSCANNERTOBUILD);
ArrayList unavcol = new ArrayList(Global.NBUNAVCOLTOBUILD);
ArrayList unavexp = new ArrayList(Global.NBUNAVEXPTOBUILD);
ArrayList navcol = new ArrayList(Global.NBNAVCOLTOBUILD);
ArrayList navexp = new ArrayList(Global.NBNAVEXPTOBUILD);
ArrayList guards = new ArrayList(Global.NBGUARDTOBUILD);
foreach (NanoBot bot in NanoBots)
{
if (bot is HunterBot)
{
hunters.Add((HunterBot)bot);
}
else if (bot is DefenderBot)
{
defenders.Add((DefenderBot)bot);
}
else if (bot is ContainerBot)
{
containers.Add((ContainerBot)bot);
}
else if (bot is BlockerBot)
{
blockers.Add((BlockerBot)bot);
}
else if ((bot is ScannerBot) || (bot is DummyCrapBot))
{
scanners.Add((ScannerBot)bot);
}
else if (bot is UniqueNavigationCollectorBot)
{
unavcol.Add((UniqueNavigationCollectorBot)bot);
}
else if (bot is UniqueNavigationExplorerBot)
{
unavexp.Add((UniqueNavigationExplorerBot)bot);
}
else if (bot is NavigationCollectorBot)
{
navcol.Add((NavigationCollectorBot)bot);
}
else if (bot is NavigationExplorerBot)
{
navexp.Add((NavigationExplorerBot)bot);
}
else if (bot is GuardBot)
{
guards.Add((GuardBot)bot);
}
}
#endregion
// update NeedleGrid Status
foreach (Entity e in this.Tissue.GetEntitiesByType(EntityEnum.HoshimiPoint))
{
foreach (NanoBotInfo bot in OtherNanoBotsInfo)
{
if ((bot.Location.X == e.X) &&
(bot.Location.Y == e.Y) &&
(bot.NanoBotType == NanoBotType.NanoNeedle) &&
(Global.NeedleGrid[e.X][e.Y] == null)
)
{
Global.NeedleGrid[e.X][e.Y] = new NeedleInfo();
Global.NeedleGrid[e.X][e.Y].Skipped = true;
}
}
// cek apakah ada NeedleBot yang dihancurkan WhiteCell
if ((Global.NeedleGrid[e.X][e.Y] != null) && (!Global.NeedleGrid[e.X][e.Y].Skipped))
{
// cek semua NeedleBot yang ada
bool found = false;
foreach (NanoBot bot in NanoBots)
{
if (bot is NeedleBot)
{
if ((bot.Location.X == e.X) && (bot.Location.Y == e.Y))
{
found = true;
break;
}
}
}
if (!found)
{
Global.NeedleGrid[e.X][e.Y] = null;
}
}
}
// cek apakah semua HP sudah penuh
if (!Global.AllHPBuilt)
{
bool adaYangKosong = false;
foreach (Entity e in Tissue.GetEntitiesByType(EntityEnum.HoshimiPoint))
{
Point pt = new Point(e.X, e.Y);
if (Global.NeedleGrid[pt.X][pt.Y] == null)
{
adaYangKosong = true;
break;
}
}
if (!adaYangKosong)
{
Global.AllHPBuilt = true;
}
}
#region AI logic
foreach (NanoBot bot in NanoBots)
{
if ((bot is DefenderBot) && (bot.State == NanoBotState.Defending))
{
this.AI.StopMoving(); // AI stop while Defender defends
return;
}
}
// cek tujuan, apakah sudah dibuat Needle oleh lawan
if (AI.State == NanoBotState.Moving)
{
if (Global.NeedleGrid[AI.PointInfo.X][AI.PointInfo.Y] != null)
{
AI.StopMoving();
return;
}
if (this.CurrentTurn % 10 == 0)
{
Point nearHP = Global.FindClosest(EntityEnum.HoshimiPoint, this.AI.Location, this.AI.NanoBotType);
if ((this.AI.PointInfo != nearHP) &&
(Global.GetPathLength(this.AI.Location, nearHP) < Global.GetPathLength(this.AI.Location, this.AI.PointInfo)))
{
this.AI.StopMoving();
this.AI.MoveTo(Global.PF.FindWay(this.AI.Location, nearHP).Points);
return;
}
}
}
if (this.AI.State == NanoBotState.WaitingOrders)
{
Random r = new Random();
Point dest = Point.Empty;
Point tempatBlocker = Point.Empty;
if ((Global.AllHPBuilt) && (NanoBots.Count < Utils.NbrMaxBots))
{
// penuhi batas maksimum bot
if (Global.NeedleGrid[AI.Location.X][AI.Location.Y] == null)
{
this.AI.Build(typeof(DummyNeedle), "Dummy");
Global.NeedleGrid[AI.Location.X][AI.Location.Y] = new NeedleInfo();
return;
}
else
{
dest = new Point(this.AI.Location.X + r.Next(-5, 5), this.AI.Location.Y + r.Next(-5, 5));
this.AI.MoveTo(Global.PF.FindWay(AI.Location, dest).Points);
return;
}
}
if (firstInjected)
{
dest = this.InjectionPointWanted;
firstInjected = false;
return;
}
else
{
if (!Global.AllHPBuilt)
{
dest = Global.FindClosest(EntityEnum.HoshimiPoint, this.AI.Location, NanoBotType.NanoAI);
}
else
{
dest = new Point(this.AI.Location.X + r.Next(-5, 5), this.AI.Location.Y + r.Next(-5, 5));
return;
}
}
if (dest == Point.Empty) // semua HP sudah diisi
{
Global.AllHPBuilt = true;
}
if ((AI.Location.X == tempatBlocker.X && AI.Location.Y == tempatBlocker.Y) && (firstInjected))
{
firstInjected = false;
AI.Build(typeof(BlockerBot));
return;
}
if (this.AI.Location != dest)
{
this.AI.MoveTo(Global.PF.FindWay(this.AI.Location, dest).Points);
return;
}
else
{
// sebelum buat NeedleBot, cek apakah jumlah NanoBot sudah sampai batas max
if (NanoBots.Count >= Utils.NbrMaxBots)
{
bool destroyOne = false;
// cek apakah PierreAI dead -> bisa destroy hunters, scanners dan defenders
if (Global.isPierreAIDead)
{
if (hunters.Count > 0)
{
((HunterBot)hunters[0]).ForceAutoDestruction();
Global.NBHUNTERBOTTOBUILD -= 1;
destroyOne = true;
}
if ((!destroyOne) && (defenders.Count > 0))
{
((DefenderBot)defenders[0]).ForceAutoDestruction();
Global.NBDEFENDERTOBUILD -= 1;
destroyOne = true;
}
if ((!destroyOne) && (scanners.Count > 0))
{
((ScannerBot)scanners[0]).ForceAutoDestruction();
Global.NBSCANNERTOBUILD -= 1;
destroyOne = true;
}
}
if (!destroyOne)
{
bool selesai = true;
foreach (BaseObjective b in Mission.Objectives)
{
if ((b is NavigationObjective) && (b.Status == ObjectiveStatus.ToBeDone))
{
selesai = false;
break;
}
}
if (selesai) // jika semua NavigationObjective selesai -> bisa destroy NavigationBots
{
if (navexp.Count > 0)
{
((NavigationExplorerBot)navexp[0]).ForceAutoDestruction();
Global.NBNAVEXPTOBUILD -= 1;
destroyOne = true;
}
if ((!destroyOne) && (navcol.Count > 0))
{
((NavigationCollectorBot)navcol[0]).ForceAutoDestruction();
Global.NBNAVCOLTOBUILD -= 1;
destroyOne = true;
}
}
}
if (!destroyOne)
{
bool selesai = true;
foreach (BaseObjective b in Mission.Objectives)
{
if ((b is UniqueNavigationObjective) && (b.Status == ObjectiveStatus.ToBeDone))
{
selesai = false;
break;
}
}
if (selesai) // jika semua UniqueNavigationObjective selesai
{ // -> bisa destroy UniqueNavigationBots
if (navexp.Count > 0)
{
((UniqueNavigationExplorerBot)unavexp[0]).ForceAutoDestruction();
Global.NBUNAVEXPTOBUILD -= 1;
destroyOne = true;
}
if ((!destroyOne) && (navcol.Count > 0))
{
((UniqueNavigationCollectorBot)unavcol[0]).ForceAutoDestruction();
Global.NBUNAVCOLTOBUILD -= 1;
destroyOne = true;
}
}
}
// navigation dan defender udah abis -> blocker dan containers
if (!destroyOne)
{
if (blockers.Count > 0)
{
((BlockerBot)blockers[0]).ForceAutoDestruction();
Global.NBBLOCKERTOBUILD -= 1;
destroyOne = true;
}
if ((!destroyOne) && (guards.Count > 0))
{
((GuardBot)guards[0]).ForceAutoDestruction();
Global.NBGUARDTOBUILD -= 1;
destroyOne = true;
}
if ((!destroyOne) && (containers.Count > 4))
{
((ContainerBot)containers[0]).ForceAutoDestruction();
Global.NBCONTAINERTOBUILD -= 1;
destroyOne = true;
}
}
}
else
{
this.AI.Build(typeof(NeedleBot), "Needle");
Global.NbNeedle++;
Global.NeedleGrid[this.AI.Location.X][this.AI.Location.Y] = new NeedleInfo();
Global.NeedleGrid[this.AI.Location.X][this.AI.Location.Y].NeedleBuilt = true;
//Global.NeedleGrid[this.AI.Location.X][this.AI.Location.Y].NeedleTargetted = false;
if (nextGroup < arrGroup.Length)
{
arrGroup[nextGroup].NeedleLocation = this.AI.Location;
arrGroup[nextGroup].IsSet = true;
arrGroup[nextGroup].Done = false;
//Global.NeedleGrid[this.AI.Location.X][this.AI.Location.Y].NeedleTargetted = true;
nextGroup++;
}
else
{
//kalo semua udah di set, cari yang terdekat
int jmin = int.MaxValue;
Group sel = null;
foreach (NanoBot bot in NanoBots)
{
if (bot is ContainerBot)
{
ContainerBot b = (ContainerBot)bot;
if ((b.group.Done) && (b.Stock != 0) && (!b.group.IsSet))
{
//int jarak = MyAI.squareDist(this.AI.Location, b.Location);
int jarak = Global.GetPathLength(this.AI.Location, b.Location);
if (jarak < jmin)
{
jmin = jarak;
sel = b.group;
}
}
}
}
if (sel != null)
{
sel.NeedleLocation = this.AI.Location;
sel.IsSet = true;
sel.Done = false;
//Global.NeedleGrid[this.AI.Location.X][this.AI.Location.Y].NeedleTargetted = true;
}
else
{
// semua grup sudah diAssign, masukkan ke HPList
Global.HPList.Add(this.AI.Location);
}
}
return;
}
}
}
#endregion
}
public ActionResult Index(HttpPostedFileBase file, WSI wsi, Stain stain, Organ organ, Tissue tissue)
{
//TODO
var reglement = manager.GetReglement(stain.Name, organ.Name);
//var sharpnessEvaluationParameters = '+' + reglament.TileSize.ToString() + '+' + reglament.SharpnessThresholdValue+ '+' + reglament.Scaling.ToString()+ '+' + reglament.Edges.ToString();
//Directory for WSI Uploads on the Server
var root = @"C:\Users\AnnaToshiba2\Desktop\WSI\Sharpness_WebApp_Uploads\";
var fileName = "";
wsi.WSIId = Guid.NewGuid();
//Create a directory for a report and WSI
string outputDir = Path.Combine(Path.GetDirectoryName(root), User.Identity.GetUserName(), "WSI " + wsi.WSIId + @"\");
if (!Directory.Exists(outputDir))
{
Directory.CreateDirectory(outputDir);
}
if (file.ContentLength > 0)
{
fileName = Path.GetFileName(file.FileName);
var path = Path.Combine(outputDir, fileName);
file.SaveAs(path);
wsi.Path = path;
wsi.UserId = User.Identity.GetUserId();
repoWSIs.Insert(wsi);
}
//Generate a report link for the Viewer
var reportLink = User.Identity.GetUserName() + "/" + "WSI " + wsi.WSIId + "/" + fileName + " ";
var evaluationLink = root + reportLink.Replace("/", @"\");
//External sharpness console app
Process sharpnessConsoleApp = new Process();
//Path to the sharpness console app
sharpnessConsoleApp.StartInfo.FileName = @"C:\Users\AnnaToshiba2\Documents\GitHub\sharpness\sharpness console App\SharpnessExplorationCurrent\SharpnessExplorationCurrent\bin\x64\Release\SharpnessExplorationCurrent.exe";
//WSI Path + Reglemnets arguments
//structure -> wsi.path#(separator)#tileSize#threshold#scale#edges
sharpnessConsoleApp.StartInfo.Arguments = String.Format(@"""{0}""", wsi.Path + "#" + reglement.TileSize.ToString() + "#" + reglement.Scaling.ToString() + "#" + reglement.SharpnessThresholdValue.ToString() + "#" + reglement.Edges.ToString());
sharpnessConsoleApp.Start();
sharpnessConsoleApp.WaitForExit();
var report = new Report();
//TODO
//only one reglement is possible
report.ReglementId = reglement.ReglementId;
report.Comment = "Kommentar";
report.OrganName = organ.Name;
if (tissue != null)
{
report.TissueName = tissue.Name;
}
if (tissue == null)
{
report.TissueName = null;
}
report.WSIId = wsi.WSIId;
report.StainName = stain.Name;
report.SharpnessMapPath = outputDir + Path.GetFileNameWithoutExtension(fileName) + ".png";
report.SharpnessMapPathDebug = outputDir + Path.GetFileNameWithoutExtension(fileName) + "Debug.png";
var semaphoreValues = manager.GetSemaphoreValues(report.SharpnessMapPath);
var channelsValues = manager.GetChannelsValues(report.SharpnessMapPathDebug);
report.Semaphore_Red = semaphoreValues[0];
report.Semaphore_Green = semaphoreValues[1];
report.Semaphore_Yellow = semaphoreValues[2];
report.Red_Channel = channelsValues[0];
report.Blue_Channel = channelsValues[1];
if (semaphoreValues[1] > reglement.AcceptanceValue)
{
report.Evaluation = true;
}
else
{
report.Evaluation = false;
}
report.ReportLink = reportLink;
report.UserId = User.Identity.GetUserId();
repoReports.Insert(report);
return(RedirectToAction("Report", new { ReportId = report.ReportId }));
}
