Examples of Energies

org.graphstream.ui.layout.springbox.Energies
Represent the history of energy values for a force-based layout algorithm.
The main intended usage is with the various force layout algorithms that use a an "energy" minimization process to compute a layout. This class allows to store the energy at a current step of layout computation and to remember a history of such steps.

At a current step of layout computation, one can accumulate energy in the current cell of the energies buffer using {@link #accumulateEnergy(double)}. When the step finishes, one calls {@link #storeEnergy()} to store this accumulated energy in a cell of the memory, push a new cell on the memory and therefore start a new step.

At any time you can get the last energy value computed with {@link #getEnergy()}. Be careful this is not the energy currently accumulated but the value of the last energy stored with {@link #storeEnergy()}. You can also get at any time the average energy in the memory with {@link #getAverageEnergy()}, as well as an estimate of the stabilization (how much the energies are varying) using {@link #getStabilization()}.

Examples of org.graphstream.ui.layout.springbox.Energies

  @Override
  protected void repulsionN2(Vector3 delta) {
    SpringBox box = (SpringBox) this.box;
    boolean is3D = box.is3D();
    ParticleBox nodes = box.getSpatialIndex();
    Energies energies = box.getEnergies();
    Iterator<Object> i = nodes.getParticleIdIterator();


    while (i.hasNext()) {
      SpringBoxNodeParticle node = (SpringBoxNodeParticle) nodes
          .getParticle(i.next());


      if (node != this) {
        delta.set(node.pos.x - pos.x, node.pos.y - pos.y,
            is3D ? node.pos.z - pos.z : 0);


        double len = delta.normalize();


        if(len > 0) {
          if (len < box.k)
            len = box.k; // XXX NEW To prevent infinite
                  // repulsion.
        
          double factor = len != 0 ? ((box.K2 / (len * len)) * node.weight)
            : 0.00001;


          energies.accumulateEnergy(factor); // TODO check this
          delta.scalarMult(-factor);
          disp.add(delta);
        }
      }
    }

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Examples of org.graphstream.ui.layout.springbox.Energies

  }


  protected void recurseRepulsion(Cell cell, Vector3 delta) {
    SpringBox box = (SpringBox) this.box;
    boolean is3D = box.is3D();
    Energies energies = box.getEnergies();


    if (intersection(cell)) {
      if (cell.isLeaf()) {
        Iterator<? extends Particle> i = cell.getParticles();


        while (i.hasNext()) {
          SpringBoxNodeParticle node = (SpringBoxNodeParticle) i.next();


          if (node != this) {
            delta.set(node.pos.x - pos.x, node.pos.y - pos.y, is3D ? node.pos.z
                - pos.z : 0);


            double len = delta.normalize();


            if (len > 0)// && len < ( box.k * box.viewZone ) )
            {
              if (len < box.k)
                len = box.k; // XXX NEW To prevent infinite
                        // repulsion.
              double factor = len != 0 ? ((box.K2 / (len * len)) * node
                  .weight) : 0.00001;
              energies.accumulateEnergy(factor); // TODO check
                                // this
              repE += factor;
              delta.scalarMult(-factor);
              disp.add(delta);
            }
          }
        }
      } else {
        int div = cell.getSpace().getDivisions();


        for (int i = 0; i < div; i++)
          recurseRepulsion(cell.getSub(i), delta);
      }
    } else {
      if (cell != this.cell) {
        GraphCellData bary = (GraphCellData) cell.getData();


        double dist = bary.distanceFrom(pos);
        double size = cell.getSpace().getSize();


        if ((!cell.isLeaf())
            && ((size / dist) > box.getBarnesHutTheta())) {
          int div = cell.getSpace().getDivisions();


          for (int i = 0; i < div; i++)
            recurseRepulsion(cell.getSub(i), delta);
        } else {
          if (bary.weight != 0) {
            delta.set(bary.center.x - pos.x, bary.center.y - pos.y,
                is3D ? bary.center.z - pos.z : 0);


            double len = delta.normalize();


            if (len > 0) {
              if (len < box.k)
                len = box.k; // XXX NEW To prevent infinite
                        // repulsion.
              double factor = len != 0 ? ((box.K2 / (len * len)) * (bary.weight))
                  : 0.00001f;
              energies.accumulateEnergy(factor);
              delta.scalarMult(-factor);
              repE += factor;


              disp.add(delta);
            }

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Examples of org.graphstream.ui.layout.springbox.Energies


  @Override
  protected void attraction(Vector3 delta) {
    SpringBox box = (SpringBox) this.box;
    boolean is3D = box.is3D();
    Energies energies = box.getEnergies();
    int neighbourCount = neighbours.size();


    for (EdgeSpring edge : neighbours) {
      if (!edge.ignored) {
        NodeParticle other = edge.getOpposite(this);
        Point3 opos = other.getPosition();


        delta.set(opos.x - pos.x, opos.y - pos.y, is3D ? opos.z - pos.z
            : 0);


        double len = delta.normalize();
        double k = box.k * edge.weight;
        double factor = box.K1 * (len - k);


        // delta.scalarMult( factor );
        delta.scalarMult(factor * (1f / (neighbourCount * 0.1f)));
        // ^^^ XXX NEW inertia based on the node degree. This is one
        // of the amelioration of the Spring-Box algorithm. Compare
        // it to the Force-Atlas algorithm that does this on
        // **repulsion**.


        disp.add(delta);
        attE += factor;
        energies.accumulateEnergy(factor);
      }
    }
  }

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Examples of org.graphstream.ui.layout.springbox.Energies

  @Override
  protected void repulsionN2(Vector3 delta) {
    LinLog box = (LinLog) this.box;
    boolean is3D = box.is3D();
    ParticleBox nodes = box.getSpatialIndex();
    Energies energies = box.getEnergies();
    Iterator<Object> i = nodes.getParticleIdIterator();
    int deg = neighbours.size();


    while (i.hasNext()) {
      LinLogNodeParticle node = (LinLogNodeParticle) nodes
          .getParticle(i.next());


      if (node != this) {
        delta.set(node.pos.x - pos.x, node.pos.y - pos.y,
            is3D ? node.pos.z - pos.z : 0);


//        double len = delta.normalize();
        double len = delta.length();


        if(len > 0) {
          double degFactor = box.edgeBased ? deg * node.neighbours.size() : 1;
          double factor = 1;
          double r = box.r;


          factor = -degFactor * (Math.pow(len, r-2)) * node.weight * weight * box.rFactor;


          if(factor < -box.maxR) { factor = -box.maxR; }
          
          energies.accumulateEnergy(factor); // TODO check this
          delta.scalarMult(factor);
          disp.add(delta);
          repE += factor;
        }
      }

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Examples of org.graphstream.ui.layout.springbox.Energies

  }


  protected void recurseRepulsion(Cell cell, Vector3 delta) {
    LinLog box = (LinLog) this.box;
    boolean is3D = box.is3D();
    Energies energies = box.getEnergies();
    int deg = neighbours.size();


    if (intersection(cell)) {
      if (cell.isLeaf()) {
        Iterator<? extends Particle> i = cell.getParticles();


        while (i.hasNext()) {
          LinLogNodeParticle node = (LinLogNodeParticle) i.next();


          if (node != this) {
            delta.set(node.pos.x - pos.x, node.pos.y - pos.y, is3D ? node.pos.z
                - pos.z : 0);


            //double len = delta.normalize();
            double len = delta.length();


            if (len > 0) {
              double degFactor = box.edgeBased ? deg * node.neighbours.size() : 1;
              double factor = 1;
              double r = box.r;
              
              factor = -degFactor * (Math.pow(len, r-2)) * node.weight * weight * box.rFactor;
              
              if(factor < -box.maxR) { factor = -box.maxR; }


              energies.accumulateEnergy(factor);  // TODO check this
              delta.scalarMult(factor);
              disp.add(delta);
              repE += factor;
            }
          }
        }
      } else {
        int div = cell.getSpace().getDivisions();


        for (int i = 0; i < div; i++)
          recurseRepulsion(cell.getSub(i), delta);
      }
    } else {
      if (cell != this.cell) {
        GraphCellData bary = (GraphCellData) cell.getData();
        double dist = bary.distanceFrom(pos);
        double size = cell.getSpace().getSize();


        if ((!cell.isLeaf())
            && ((size / dist) > box.getBarnesHutTheta())) {
          int div = cell.getSpace().getDivisions();


          for (int i = 0; i < div; i++)
            recurseRepulsion(cell.getSub(i), delta);
        } else {
          if (bary.weight != 0) {
            delta.set(bary.center.x - pos.x, bary.center.y - pos.y,
                is3D ? bary.center.z - pos.z : 0);


            //double len = delta.normalize();
            double len = delta.length();


            if (len > 0) {
              double degFactor = box.edgeBased ? deg * bary.degree : 1;
              double factor = 1;
              double r = box.r;
              
              factor = -degFactor * (Math.pow(len, r-2)) * bary.weight * weight * box.rFactor;


              if(factor < -box.maxR) { factor = -box.maxR; }
              
              energies.accumulateEnergy(factor);  // TODO check this
              delta.scalarMult(factor);
              disp.add(delta);
              repE += factor;
            }
          }

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Examples of org.graphstream.ui.layout.springbox.Energies


  @Override
  protected void attraction(Vector3 delta) {
    LinLog box = (LinLog) this.box;
    boolean is3D = box.is3D();
    Energies energies = box.getEnergies();


    for (EdgeSpring edge : neighbours) {
      if (!edge.ignored) {
        LinLogNodeParticle other = (LinLogNodeParticle) edge.getOpposite(this);


        delta.set(other.pos.x - pos.x, other.pos.y - pos.y, is3D ? other.pos.z - pos.z : 0);


//        double len = delta.normalize();
        double len = delta.length();


        if(len > 0) {
          double factor = 1;
          double a = box.a;


          factor = (Math.pow(len, a-2)) * edge.weight * box.aFactor;


          energies.accumulateEnergy(factor);
          delta.scalarMult(factor);
          disp.add(delta);
          attE += factor;
        }
      }

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