public void run() {
PhysicalCylinder cyl = (PhysicalCylinder) cellElement.getPhysical();
// Juste temporary for getting a picture :
// if(cyl.getMassLocation()[2]<-100){
// return;
// }
double lengthBefore = cyl.getLength();
// not to thin?
if (cyl.getDiameter() < minimalBranchDiameter) {
if (cyl.lengthToProximalBranchingPoint()
> 7 + 10 * ECM.getRandomDouble()) { // so we don't end with short segments
return;
}
}
// can't leave
if (cantLeave != null) {
double currentCantLeaveConcntration = cyl.getExtracellularConcentration(cantLeave);
if (currentCantLeaveConcntration > maxConcentration) {
maxConcentration = currentCantLeaveConcntration;
}
if (currentCantLeaveConcntration < 0.95 * maxConcentration) {
cyl.setColor(Color.black);
return;
}
}
// find the gradients
double[] totalGradient = {0.0, 0.0, 0.0};
for (String s : attractants) {
double[] normalizedGrad = normalize(cyl.getExtracellularGradient(s));
totalGradient = add(totalGradient, normalizedGrad);
}
for (String s : repellents) {
double[] normalizedAntiGrad = scalarMult(-1.0, normalize(cyl.getExtracellularGradient(s)));
totalGradient = add(totalGradient, normalizedAntiGrad);
}
// if no gradient : go straight
if (attractants.isEmpty() && repellents.isEmpty()) {
totalGradient = movementDirection;
}
double[] newStepDirection =
add(
movementDirection,
scalarMult(directionWeight, totalGradient),
randomNoise(randomness, 3));
cyl.movePointMass(speed, newStepDirection);
movementDirection = normalize(add(scalarMult(5, movementDirection), newStepDirection));
// decrease diameter setDiameter
double lengthAfter = cyl.getLength();
double deltaL = lengthAfter - lengthBefore;
if (deltaL < 0) deltaL = 0;
cyl.setDiameter(cyl.getDiameter() * (1 - deltaL * linearDiameterDecrease));
}
public void setCellElement(CellElement cellElement) {
this.cellElement = cellElement;
this.movementDirection = cellElement.getPhysical().getXAxis();
}