/// <summary>
/// Draws a BSpline curve from parent branch to new branch
/// </summary>
/// <param name="canvas"></param>
/// <param name="allBranches"></param>
public void DrawOriginCurve(Canvas canvas, List <BioBranch> allBranches)
{
OriginCurve = new Path();
System.Windows.Point outNode = allBranches[ParentBranchIndex].Twigs[ParentTwigIndex].HistoryNodeOUT;
System.Windows.Point inNode = this.Twigs[0].HistoryNodeIN;
int offset = (int)((inNode.X - outNode.X) / 2);
// Add a random factor to separate lines.
int randomY = Friends.GetRandomInt(0, 32);
System.Windows.Point P1 = new System.Windows.Point(outNode.X, outNode.Y + randomY);
System.Windows.Point P2 = new System.Windows.Point(outNode.X + offset, outNode.Y + randomY);
System.Windows.Point P3 = new System.Windows.Point(inNode.X - offset, inNode.Y + randomY);
System.Windows.Point P4 = new System.Windows.Point(inNode.X, inNode.Y + randomY);
OriginCurve.Data = Friends.MakeBezierGeometry(P1, P2, P3, P4);
OriginCurve.Stroke = Brushes.LightGray;
OriginCurve.StrokeThickness = 0.6;
//Canvas.SetLeft(OriginCurve, 0);
//Canvas.SetTop(OriginCurve, 0);
Canvas.SetZIndex(OriginCurve, -1);
canvas.Children.Add(OriginCurve);
}
/// <summary>
/// Single point crossover
/// </summary>
/// <param name="probability"></param>
public void CrossoverPop(double probability)
{
if (probability > 0)
{
int size = chromosomes[0].GetGenes().Length;
for (int i = 0; i < chromosomes.Length; i += 2)
{
if (Friends.GetRandomDouble() < probability)
{
int splice = Friends.GetRandomInt(0, size);
double[] limbo1 = new double[size];
double[] limbo2 = new double[size];
chromosomes[i].GetGenes().CopyTo(limbo1, 0);
chromosomes[i + 1].GetGenes().CopyTo(limbo2, 0);
for (int s = splice; s < size; s++)
{
limbo1[s] = chromosomes[i + 1].GetGenes()[s];
limbo2[s] = chromosomes[i].GetGenes()[s];
}
chromosomes[i].SetGenes(limbo1);
chromosomes[i + 1].SetGenes(limbo2);
}
}
}
}
/// <summary>
/// Calculate cluster centroids using k-means++
/// </summary>
/// <param name="numClusters"></param>
/// <returns></returns>
public double[][] calcClusterCentroidsInit(int numClusters)
{
int numGenes = chromosomes[0].GetGenes().Length;
//Initialise array
double[][] centroidVectorsInit = new double[numClusters][];
List <int> centroidChromoIndexes = new List <int>();
// 1. Choose random initial centroid
int rndCentroidChromo = Friends.GetRandomInt(0, chromosomes.Length);
centroidChromoIndexes.Add(rndCentroidChromo);
while (centroidChromoIndexes.Count < numClusters)
{
// 2. Calculate distance from each chromo to the nearest centroid that has already been chosen
//the distance to the nearest centroid for each chromosome
List <double> chromoDistances = new List <double>();
for (int i = 0; i < chromosomes.Length; i++)
{
//distances from one chromo to all of the already chosen centroids
List <double> distances = new List <double>();
for (int j = 0; j < centroidChromoIndexes.Count; j++)
{
int centroidIndex = centroidChromoIndexes[j];
distances.Add(Friends.calcDistance(chromosomes[i].GetGenes(), chromosomes[centroidIndex].GetGenes()));
}
chromoDistances.Add(distances.Min()); //if the chromosome compares to itself and is chosen as a centroid, the distance will be zero (fine as we choose the largest distance for all chromosomes afterwards)
}
//3. Choose next centroid furthest away from the already selected ones
int indexOfMaxDist = chromoDistances.IndexOf(chromoDistances.Max());
centroidChromoIndexes.Add(indexOfMaxDist);
}
//Update array
for (int i = 0; i < numClusters; i++)
{
centroidVectorsInit[i] = new double[numGenes];
for (int j = 0; j < numGenes; j++)
{
centroidVectorsInit[i][j] = chromosomes[centroidChromoIndexes[i]].GetGenes()[j];
}
}
return(centroidVectorsInit);
}
/// <summary>
/// Draws a BSpline curve from parent branch to new branch
/// </summary>
/// <param name="canvas"></param>
/// <param name="allBranches"></param>
public void DrawOriginCurve(Canvas canvas, List <BioBranch> allBranches)
{
OriginCurve = new Path();
System.Windows.Point outNode = allBranches[ParentBranchIndex].Twigs[ParentTwigIndex].HistoryNodeOUT;
System.Windows.Point inNode = this.Twigs[0].HistoryNodeIN;
int offset = (int)((inNode.X - outNode.X) / 2);
// Add a random factor to separate lines.
int randomY = Friends.GetRandomInt(0, 32);
System.Windows.Point P1 = new System.Windows.Point(outNode.X, outNode.Y + randomY);
System.Windows.Point P2 = new System.Windows.Point(outNode.X + offset, outNode.Y + randomY);
System.Windows.Point P3 = new System.Windows.Point(inNode.X - offset, inNode.Y + randomY);
System.Windows.Point P4 = new System.Windows.Point(inNode.X, inNode.Y + randomY);
OriginCurve.Data = Friends.MakeBezierGeometry(P1, P2, P3, P4);
OriginCurve.Stroke = Brushes.White;
OriginCurve.StrokeThickness = 0.6;
//Canvas.SetLeft(OriginCurve, 0);
//Canvas.SetTop(OriginCurve, 0);
Canvas.SetZIndex(OriginCurve, -1);
canvas.Children.Add(OriginCurve);
//Add outline circle
double s = 6;
System.Windows.Shapes.Ellipse nodule = new System.Windows.Shapes.Ellipse();
nodule.Height = s;
nodule.Width = s;
nodule.Fill = Brushes.White;
System.Windows.Shapes.Ellipse nodule2 = new System.Windows.Shapes.Ellipse();
nodule2.Height = s;
nodule2.Width = s;
nodule2.Fill = Brushes.White;
Canvas.SetLeft(nodule, P1.X - s / 2);
Canvas.SetTop(nodule, P1.Y - s / 2);
canvas.Children.Add(nodule);
Canvas.SetLeft(nodule2, P4.X - s / 2);
Canvas.SetTop(nodule2, P4.Y - s / 2);
canvas.Children.Add(nodule2);
}