public SySal.Imaging.Grain3D[] MakeGrainsFromClusters(SySal.Imaging.Cluster3D[][] cls, SySal.BasicTypes.Vector[] positions)
{
this.DemagCoefficients = new double[0];
this.MatchDX = new double[0];
this.MatchDY = new double[0];
System.Collections.ArrayList adx = new System.Collections.ArrayList();
System.Collections.ArrayList ady = new System.Collections.ArrayList();
int i;
int halfw = (int)(C.ImageWidth / 2);
int halfh = (int)(C.ImageHeight / 2);
ChainCluster[][] planes = new ChainCluster[positions.Length][];
System.Collections.ArrayList demags = new System.Collections.ArrayList();
int plane;
double c2x, c2y;
double px0 = positions[0].X;
double py0 = positions[0].Y;
double pz0 = positions[0].Z;
for (plane = 0; plane < planes.Length; plane++)
{
if (Progress != null)
{
Progress((double)plane / (double)planes.Length * 0.5);
}
if (ShouldStop != null && ShouldStop())
{
return(null);
}
planes[plane] = new ChainCluster[cls[plane].Length];
SySal.Imaging.Cluster3D [] cplanes = cls[plane];
double px = positions[plane].X;
double py = positions[plane].Y;
double pz = positions[plane].Z;
double pxd = px - px0;
double pyd = py - py0;
double pzd = pz - pz0;
double dmz = OptimizeDemagCoefficient ? 1 : Math.Pow(1.0 + C.DMagDZ, pzd);
for (i = 0; i < planes[plane].Length; i++)
{
ChainCluster cc = new ChainCluster();
cc.Cluster = cplanes[i].Cluster;
cc.Id = i;
cc.Plane = plane;
cc.Z = pz;
cc.Cluster.X = (cc.Cluster.X - halfw) * C.Pixel2Micron.X * dmz; // +px;
cc.Cluster.Y = (cc.Cluster.Y - halfh) * C.Pixel2Micron.Y * dmz; // +py;
c2y = cc.Cluster.X * cc.Cluster.X * C.XYCurvature * cc.Cluster.Y;
c2x = cc.Cluster.Y * cc.Cluster.Y * C.XYCurvature * cc.Cluster.X;
cc.Cluster.X += c2x;
cc.Cluster.Y += c2y;
cc.Z += C.ZCurvature * (cc.Cluster.X * cc.Cluster.X + cc.Cluster.Y * cc.Cluster.Y);
cc.Cluster.X += pxd;
cc.Cluster.Y += pyd;
planes[plane][i] = cc;
}
}
if (Progress != null)
{
Progress(0.5);
}
for (i = 0; i < planes.Length - 1; i++)
{
if (Progress != null)
{
Progress(0.5 + 0.5 * (double)i / (double)(planes.Length - 1));
}
if (ShouldStop != null && ShouldStop())
{
return(null);
}
SySal.Tracking.MIPEmulsionTrackInfo[] t1 = new SySal.Tracking.MIPEmulsionTrackInfo[planes[i].Length];
SySal.Tracking.MIPEmulsionTrackInfo[] t2 = new SySal.Tracking.MIPEmulsionTrackInfo[planes[i + 1].Length];
int j;
for (j = 0; j < t1.Length; j++)
{
ChainCluster cc = planes[i][j];
SySal.Tracking.MIPEmulsionTrackInfo info = new SySal.Tracking.MIPEmulsionTrackInfo();
info.Count = (ushort)cc.Cluster.Area;
info.AreaSum = (uint)j;
info.Intercept.X = cc.Cluster.X;
info.Intercept.Y = cc.Cluster.Y;
info.Intercept.Z = 0.0;
info.Slope.X = info.Slope.Y = info.Slope.Z = 0.0;
t1[j] = info;
}
for (j = 0; j < t2.Length; j++)
{
ChainCluster cc = planes[i + 1][j];
SySal.Tracking.MIPEmulsionTrackInfo info = new SySal.Tracking.MIPEmulsionTrackInfo();
info.Count = (ushort)cc.Cluster.Area;
info.AreaSum = (ushort)j;// cls.Id;
info.Intercept.X = cc.Cluster.X + 2.0 * (C.ClusterMatchMaxOffset + C.ClusterMatchPositionTolerance);
info.Intercept.Y = cc.Cluster.Y + 2.0 * (C.ClusterMatchMaxOffset + C.ClusterMatchPositionTolerance);
info.Intercept.Z = 0.0;
info.Slope.X = info.Slope.Y = info.Slope.Z = 0.0;
t2[j] = info;
}
try
{
SySal.Processing.QuickMapping.Configuration qmc = (SySal.Processing.QuickMapping.Configuration)QM.Config;
qmc.FullStatistics = false;
qmc.UseAbsoluteReference = true;
qmc.PosTol = C.ClusterMatchPositionTolerance * 0.5;
qmc.SlopeTol = 1.0;
QM.Config = qmc;
int bkg = QM.Match(t1, t2, 0.0, C.ClusterMatchPositionTolerance * 0.25, C.ClusterMatchPositionTolerance * 0.25).Length;
for (j = 0; j < t2.Length; j++)
{
ChainCluster cc = planes[i + 1][j];
t2[j].Intercept.X = cc.Cluster.X;
t2[j].Intercept.Y = cc.Cluster.Y;
}
qmc.PosTol = C.ClusterMatchMaxOffset * 0.5;
QM.Config = qmc;
SySal.Scanning.PostProcessing.PatternMatching.TrackPair[] tp = QM.Match(t1, t2, 0.0, C.ClusterMatchMaxOffset * 0.25, C.ClusterMatchMaxOffset * 0.25);
double deltax = 0.0, deltay = 0.0, demagx = 0.0, demagy = 0.0;
double dummy = 0.0;
double q = (1.0 - (double)bkg / (double)tp.Length) * 0.25;
double[,] deltas = new double[tp.Length, 4];
for (j = 0; j < tp.Length; j++)
{
deltas[j, 0] = tp[j].Second.Info.Intercept.X;
deltas[j, 1] = tp[j].Second.Info.Intercept.Y;
deltas[j, 2] = tp[j].First.Info.Intercept.X - tp[j].Second.Info.Intercept.X;
deltas[j, 3] = tp[j].First.Info.Intercept.Y - tp[j].Second.Info.Intercept.Y;
}
int[] ids = NumericalTools.Fitting.PeakDataSel(deltas, new double[] { Math.Abs(halfw * C.Pixel2Micron.X) * 0.25, Math.Abs(halfh * C.Pixel2Micron.Y) * 0.25, C.ClusterMatchPositionTolerance * 0.5, C.ClusterMatchPositionTolerance * 0.5 }, -1.0, q);
double[] ws = new double[ids.Length];
double[] dws = new double[ids.Length];
for (j = 0; j < ids.Length; j++)
{
ws[j] = deltas[ids[j], 0];
dws[j] = deltas[ids[j], 2];
}
NumericalTools.ComputationResult resx = NumericalTools.Fitting.LinearFitSE(ws, dws, ref demagx, ref deltax, ref dummy, ref dummy, ref dummy, ref dummy, ref dummy);
for (j = 0; j < ids.Length; j++)
{
ws[j] = deltas[ids[j], 1];
dws[j] = deltas[ids[j], 3];
}
double dmagdeltaz = positions[i + 1].Z - positions[i].Z;
NumericalTools.ComputationResult resy = NumericalTools.Fitting.LinearFitSE(ws, dws, ref demagy, ref deltay, ref dummy, ref dummy, ref dummy, ref dummy, ref dummy);
if (resx == NumericalTools.ComputationResult.OK && resy == NumericalTools.ComputationResult.OK)
{
demags.Add(Math.Log(1.0 + demagx) / dmagdeltaz);
demags.Add(Math.Log(1.0 + demagy) / dmagdeltaz);
}
for (j = 0; j < t2.Length; j++)
{
ChainCluster cc = planes[i + 1][j];
t2[j].Intercept.X += deltax;
t2[j].Intercept.Y += deltay;
cc.Cluster.X += deltax;
cc.Cluster.Y += deltay;
}
qmc.PosTol = C.ClusterMatchPositionTolerance * 0.5;
QM.Config = qmc;
tp = QM.Match(t1, t2, 0.0, C.ClusterMatchPositionTolerance * 0.25, C.ClusterMatchPositionTolerance * 0.25);
foreach (SySal.Scanning.PostProcessing.PatternMatching.TrackPair tp1 in tp)
{
if (planes[i][tp1.First.Info.AreaSum].Next == null && planes[i + 1][tp1.Second.Info.AreaSum].PreviousSize == 0 &&
(planes[i][tp1.First.Info.AreaSum].Cluster.Area < planes[i + 1][tp1.Second.Info.AreaSum].Cluster.Area &&
planes[i][tp1.First.Info.AreaSum].Cluster.Area < planes[i][tp1.First.Info.AreaSum].PreviousSize) == false)
{
planes[i][tp1.First.Info.AreaSum].Next = planes[i + 1][tp1.Second.Info.AreaSum];
planes[i + 1][tp1.Second.Info.AreaSum].PreviousSize = planes[i][tp1.First.Info.AreaSum].Cluster.Area;
adx.Add(tp1.First.Info.Intercept.X - tp1.Second.Info.Intercept.X);
ady.Add(tp1.First.Info.Intercept.Y - tp1.Second.Info.Intercept.Y);
}
}
}
catch (Exception) { }
}
System.Collections.ArrayList achains = new System.Collections.ArrayList();
System.Collections.ArrayList grains = new System.Collections.ArrayList();
foreach (ChainCluster[] cplane in planes)
{
foreach (ChainCluster cc in cplane)
{
if (cc.Next != null)
{
cc.Next.Id = -1;
}
if (cc.Id >= 0)
{
achains.Add(cc);
}
}
}
foreach (ChainCluster cc in achains)
{
int totalc = 1;
ChainCluster cc1 = cc.Next;
while (cc1 != null)
{
cc1 = cc1.Next;
totalc++;
}
SySal.Imaging.Cluster3D[] cl3d = new SySal.Imaging.Cluster3D[totalc];
totalc = 0;
cc1 = cc;
uint gvolume = 0;
while (cc1 != null)
{
double dmz = OptimizeDemagCoefficient ? 1 : Math.Pow(1.0 + C.DMagDZ, positions[cc1.Plane].Z - positions[0].Z);
cl3d[totalc].Cluster = cc1.Cluster;
cl3d[totalc].Cluster.X = cl3d[totalc].Cluster.X / dmz + positions[0].X;
cl3d[totalc].Cluster.Y = cl3d[totalc].Cluster.Y / dmz + positions[0].Y;
cl3d[totalc].Layer = (uint)cc1.Plane;
cl3d[totalc].Z = cc1.Z;
gvolume += cc1.Cluster.Area;
cc1 = cc1.Next;
totalc++;
}
if (gvolume < C.MinGrainVolume)
{
continue;
}
grains.Add(SySal.Imaging.Grain3D.FromClusterCenters(cl3d));
}
this.DemagCoefficients = (double[])demags.ToArray(typeof(double));
this.MatchDX = (double[])adx.ToArray(typeof(double));
this.MatchDY = (double[])ady.ToArray(typeof(double));
if (Progress != null)
{
Progress(1.0);
}
return((SySal.Imaging.Grain3D[])grains.ToArray(typeof(SySal.Imaging.Grain3D)));
}
private static NumericalTools.ComputationResult IteratedAffineFocusing(double[] DX, double[] DY, double[] X, double[] Y, double[] SX, double[] SY, double postol, ref double[] alignpars)
{
int iteration, i, j;
double xtol = postol;
double ytol = postol;
NumericalTools.ComputationResult res = NumericalTools.ComputationResult.SingularityEncountered;
for (iteration = 0; iteration < 3; iteration++)
{
double[] mDX;
double[] mDY;
double[] mSX;
double[] mSY;
double[] mX;
double[] mY;
if (iteration == 0)
{
mDX = DX;
mDY = DY;
mSX = SX;
mSY = SY;
mX = X;
mY = Y;
}
else
{
double dx, dx2sum, dy, dy2sum;
dx2sum = dy2sum = 0.0;
bool[] take = new bool[DX.Length];
for (i = j = 0; i < take.Length; i++)
{
if (Math.Abs(dx = (DX[i] - alignpars[0] * X[i] - alignpars[1] * Y[i] - alignpars[4] - alignpars[6] * SX[i])) < xtol &&
Math.Abs(dy = (DY[i] - alignpars[2] * X[i] - alignpars[3] * Y[i] - alignpars[5] - alignpars[6] * SY[i])) < ytol)
{
dx2sum += dx * dx;
dy2sum += dy * dy;
take[i] = true;
j++;
}
}
if (j < 2)
{
return(NumericalTools.ComputationResult.SingularityEncountered);
}
xtol = 2.0 * Math.Sqrt(dx2sum / (j - 1));
ytol = 2.0 * Math.Sqrt(dy2sum / (j - 1));
mDX = new double[j];
mDY = new double[j];
mSX = new double[j];
mSY = new double[j];
mX = new double[j];
mY = new double[j];
for (i = j = 0; i < take.Length; i++)
{
if (take[i])
{
mDX[j] = DX[i];
mDY[j] = DY[i];
mSX[j] = SX[i];
mSY[j] = SY[i];
mX[j] = X[i];
mY[j] = Y[i];
j++;
}
}
}
res = NumericalTools.Fitting.Affine_Focusing(mDX, mDY, mX, mY, mSX, mSY, ref alignpars);
}
return(res);
}