/**
* Calculates the min and max boundaries of the structure after it has been transformed into its
* canonical orientation.
*/
private void calcBoundaries() {
minBoundary.x = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.y = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.z = Double.MAX_VALUE;
maxBoundary.z = Double.MIN_VALUE;
xzRadiusMax = Double.MIN_VALUE;
Point3d probe = new Point3d();
for (Point3d[] list : subunits.getTraces()) {
for (Point3d p : list) {
probe.set(p);
transformationMatrix.transform(probe);
minBoundary.x = Math.min(minBoundary.x, probe.x);
maxBoundary.x = Math.max(maxBoundary.x, probe.x);
minBoundary.y = Math.min(minBoundary.y, probe.y);
maxBoundary.y = Math.max(maxBoundary.y, probe.y);
minBoundary.z = Math.min(minBoundary.z, probe.z);
maxBoundary.z = Math.max(maxBoundary.z, probe.z);
xzRadiusMax = Math.max(xzRadiusMax, Math.sqrt(probe.x * probe.x + probe.z * probe.z));
}
}
// System.out.println("MinBoundary: " + minBoundary);
// System.out.println("MaxBoundary: " + maxBoundary);
// System.out.println("zxRadius: " + xzRadiusMax);
}
private double[] springPenalty(Vector3d xi, Vector3d xj, double dist) {
double[] F = new double[6];
// collision normal
Vector3d n = xi.minus(xj);
n = n.dot(1 / n.norm());
F[0] = -(k * (n.x()) * (-2 * proximity + dist));
F[1] = -(k * (n.y()) * (-2 * proximity + dist));
F[2] = -(k * (n.z()) * (-2 * proximity + dist));
F[3] = -F[0];
F[4] = -F[1];
F[5] = -F[2];
return F;
}