Example #1
0
 public X_Movement_Module getCopy() {
   X_Movement_Module r = new X_Movement_Module();
   r.attractants = (Vector<String>) this.attractants.clone();
   r.repellents = (Vector<String>) this.repellents.clone();
   r.randomness = this.randomness;
   r.movementDirection = this.movementDirection.clone();
   r.directionWeight = this.directionWeight;
   r.copiedWhenNeuriteBranches = this.copiedWhenNeuriteBranches;
   r.minimalBranchDiameter = this.minimalBranchDiameter;
   r.cantLeave = this.cantLeave;
   r.maxConcentration = this.maxConcentration;
   r.linearDiameterDecrease = this.linearDiameterDecrease;
   return r;
 }
Example #2
0
  public static void main(String[] args) {
    // 1) Prepare the environment :
    // 		get a reference to the extracelular matrix (ECM)
    ECM ecm = ECM.getInstance();
    // 		add additional PhysicalNodes (for diffusion)
    int nbOfAdditionalNodes = 100;
    for (int i = 0; i < nbOfAdditionalNodes; i++) {
      double[] coord = randomNoise(500, 3);
      ecm.getPhysicalNodeInstance(coord);
    }

    // 2) Create some artificial chemical gradients
    // 		horizontal gaussian (peak concentration, peak coordinate, variance)
    ecm.addArtificialGaussianConcentrationZ(new Substance("A", Color.red), 1, 300, 100);
    ecm.addArtificialGaussianConcentrationZ(new Substance("B", Color.blue), 1, 00, 100);
    ecm.addArtificialGaussianConcentrationZ(new Substance("C", Color.green), 1, -300, 100);
    //		horizontal linerar gradient
    ecm.addArtificialLinearConcentrationZ(new Substance("D", Color.cyan), 1, 300, -300);
    //		vertical gaussian
    ecm.addArtificialGaussianConcentrationX(new Substance("E", Color.red), 1, 0, 100);
    ecm.addArtificialGaussianConcentrationX(new Substance("F", Color.green), 1, 300, 100);

    // 3) Create a 4-uple Cell-SomaElement-PhysicalSphere-SpaceNode at the desired location
    double[] cellLocation = new double[] {0, 0, 0};
    Cell cell = CellFactory.getCellInstance(cellLocation);
    cell.setColorForAllPhysicalObjects(Param.RED);

    // 4) Extend an axon from the cell
    NeuriteElement neurite = cell.getSomaElement().extendNewNeurite(new double[] {0, 0, 1});
    neurite.getPhysical().setDiameter(1.0);
    neurite.getPhysicalCylinder().setDiameter(3);
    // 5) Put a movementReceptor
    X_Movement_Module r = new X_Movement_Module();
    r.linearDiameterDecrease = 0.01;
    r.addAttractant("A");

    neurite.addLocalBiologyModule(r);

    // 6) Simulate
    Scheduler.simulate();
  }