Package org.graphstream.ui.layout.springbox

Class BarnesHutLayout

java.lang.Object
org.graphstream.stream.SourceBase
org.graphstream.ui.layout.springbox.BarnesHutLayout
All Implemented Interfaces:
AttributeSink, ElementSink, Pipe, Sink, Source, Layout, org.miv.pherd.ParticleBoxListener
Direct Known Subclasses:
LinLog, SpringBox
public abstract class BarnesHutLayout
extends SourceBase
implements Layout, org.miv.pherd.ParticleBoxListener
Base implementation of a Barnes-Hut space decomposition and particle interaction algorithm to be used for force-based layout algorithms.

This base class creates the space decomposition method and manages the main loop of the simulation. The simulation is made of NodeParticle and EdgeSpring elements that are created and linked for you in response to graph events received via the Sink interface. However you have to provide an implementation of the abstract NodeParticle class (by overriding the abstract method newNodeParticle(String)).

As almost all the repulsion/attraction forces computation is done in the NodeParticle class, this is the most important one.

This algorithm can be configured using several attributes put on the graph :

  • layout.force : a floating point number (default 0.5f), that allows to define the importance of movement of each node at each computation step. The larger the value the quicker nodes move to their position of lowest energy. However too high values can generate non stable layouts and oscillations.
  • layout.quality : an integer between 0 and 4. With value 0 the layout is faster but it also can be farther from equilibrium. With value 4 the algorithm tries to be as close as possible from equilibrium (the n-tree and Barnes-Hut algorithms are disabled), but the computation can take a lot of time (the algorithm becomes O(n^2)). TODO change this into layout.barneshut or something similar.
You can also put the following attributes on nodes :
  • layout.weight : The force of repulsion of a node. The larger the value, the more the node repulses its neighbors.
And on edges :
  • layout.weight : the multiplier for the desired edge length. By default the algorithm tries to make each edge of length one. This is the position of lowest energy for a spring. This coefficient allows to modify this target spring length. Value larger than one will make the edge longer. Values between 0 and 1 will make the edge smaller.
  • layout.stabilization-limit : the stabilization of a layout is a number between 0 and 1. 1 means fully stable, but this value is rare. Therefore one can consider the layout stable at a lower value. The default is 0.9. You can fix it with this attribute.

  • Constructor Details

    • BarnesHutLayout

      public BarnesHutLayout()
      New 2D Barnes-Hut simulation.

    • BarnesHutLayout

      public BarnesHutLayout​(boolean is3D)
      New Barnes-Hut simulation.
      Parameters:
      is3D - If true the simulation dimensions count is 3 else 2.

    • BarnesHutLayout

      public BarnesHutLayout​(boolean is3D, Random randomNumberGenerator)
      New Barnes-Hut simulation.
      Parameters:
      is3D - If true the simulation dimensions count is 3 else 2.
      randomNumberGenerator - The random number generator to use.

  • Method Details

    • getLowPoint

      public Point3 getLowPoint()
      Description copied from interface: Layout
      Smallest point in space of the layout bounding box.
      Specified by:
      getLowPoint in interface Layout

    • getHiPoint

      public Point3 getHiPoint()
      Description copied from interface: Layout
      Largest point in space of the layout bounding box.
      Specified by:
      getHiPoint in interface Layout

    • randomXInsideBounds

      public double randomXInsideBounds()

    • randomYInsideBounds

      public double randomYInsideBounds()

    • randomZInsideBounds

      public double randomZInsideBounds()

    • getCenterPoint

      public Point3 getCenterPoint()

    • getGravityFactor

      public double getGravityFactor()
      A gravity factor that attracts all nodes to the center of the layout to avoid flying components. If set to zero, the gravity computation is disabled.
      Returns:
      The gravity factor, usually between 0 and 1.

    • setGravityFactor

      public void setGravityFactor​(double value)
      Set the gravity factor that attracts all nodes to the center of the layout to avoid flying components. If set to zero, the gravity computation is disabled.
      Parameters:
      value - The new gravity factor, usually between 0 and 1.

    • getSpatialIndex

      public org.miv.pherd.ParticleBox getSpatialIndex()
      The spatial index as a n-tree.
      Returns:
      The n-tree.

    • getLastStepTime

      public long getLastStepTime()
      Description copied from interface: Layout
      Time in nanoseconds used by the last call to step().
      Specified by:
      getLastStepTime in interface Layout

    • getLayoutAlgorithmName

      public abstract String getLayoutAlgorithmName()
      Description copied from interface: Layout
      Name of the layout algorithm.
      Specified by:
      getLayoutAlgorithmName in interface Layout

    • getNodeMovedCount

      public int getNodeMovedCount()
      Description copied from interface: Layout
      How many nodes moved during the last step?. When this method returns zero, the layout stabilized.
      Specified by:
      getNodeMovedCount in interface Layout

    • getStabilization

      public double getStabilization()
      Description copied from interface: Layout
      Estimate of how close to stabilization the layout algorithm is.
      Specified by:
      getStabilization in interface Layout
      Returns:
      a value between 0 and 1. 1 means fully stabilized.

    • getStabilizationLimit

      public double getStabilizationLimit()
      Description copied from interface: Layout
      Above which value a correct stabilization is achieved?
      Specified by:
      getStabilizationLimit in interface Layout
      Returns:
      The stabilization limit.

    • getSteps

      public int getSteps()
      Description copied from interface: Layout
      Number of calls made to step() so far.
      Specified by:
      getSteps in interface Layout

    • getQuality

      public double getQuality()
      Description copied from interface: Layout
      The current layout algorithm quality. A number between 0 and 1 with 1 the highest (but probably slowest) quality.
      Specified by:
      getQuality in interface Layout
      Returns:
      A number between 0 and 1.

    • is3D

      public boolean is3D()

    • getForce

      public double getForce()
      Description copied from interface: Layout
      The current layout force.
      Specified by:
      getForce in interface Layout
      Returns:
      A real number.

    • getRandom

      public Random getRandom()

    • getEnergies

      public Energies getEnergies()

    • getBarnesHutTheta

      public double getBarnesHutTheta()
      The Barnes-Hut theta value used to know if we use a pole or not.
      Returns:
      The theta value (between 0 and 1).

    • getViewZone

      public double getViewZone()

    • setSendNodeInfos

      public void setSendNodeInfos​(boolean on)
      Description copied from interface: Layout
      If true, node informations messages are sent for every node. This is mainly for debugging and slows down the process a lot. The contents of the node information is specific to the algorithm, and sent via a specific "layout.info" attribute.
      Specified by:
      setSendNodeInfos in interface Layout
      Parameters:
      on - If true, send node informations to a "layout.info" attribute.

    • setBarnesHutTheta

      public void setBarnesHutTheta​(double theta)
      Change the barnes-hut theta parameter allowing to know if we use a pole or not.
      Parameters:
      theta - The new value for theta (between 0 and 1).

    • setForce

      public void setForce​(double value)
      Description copied from interface: Layout
      The general "speed" of the algorithm. For some algorithm this will have no effect. For most "dynamic" algorithms, this change the way iterations toward stabilization are done.
      Specified by:
      setForce in interface Layout
      Parameters:
      value - A number in [0..1].

    • setStabilizationLimit

      public void setStabilizationLimit​(double value)
      Description copied from interface: Layout
      Change the stabilization limit for this layout algorithm.

      The stabilization is a number between 0 and 1 that indicates how close to stabilization (no nodes need to move) the layout is. The value 1 means the layout is fully stabilized. Naturally this is often only an indication only, for some algorithms, it is difficult to determine if the layout is correct or acceptable enough. You can get the actual stabilization limit using Layout.getStabilizationLimit(). You can get the actual stabilization using Layout.getStabilization().

      Be careful, most layout classes do not use the stabilization limit, this number is mostly used the process that control the layout, like the LayoutRunner for example. The stabilization limit is only an indication with a default set for each layout algorithm. However this default can be changed using this method, or by storing on the graph an attribute "layout.stabilization-limit" (or "layout.stabilisation-limit").

      The convention is that the value 0 means that the process controlling the layout will not stop the layout (will therefore not consider the stabilization limit). In other words the layout will compute endlessly.

      Specified by:
      setStabilizationLimit in interface Layout
      Parameters:
      value - The new stabilization limit, 0 means no need to stabilize. Else a value larger than zero or equal to 1 is accepted.

    • setQuality

      public void setQuality​(double qualityLevel)
      Description copied from interface: Layout
      Set the overall quality level, a number between 0 and 1 with 1 the highest quality available, but often with a slower computation.
      Specified by:
      setQuality in interface Layout
      Parameters:
      qualityLevel - The quality level, a number between 0 and 1.

    • clear

      public void clear()
      Description copied from interface: Layout
      Clears the whole nodes and edges structures
      Specified by:
      clear in interface Layout

    • compute

      public void compute()
      Description copied from interface: Layout
      Method to call repeatedly to compute the layout.

      This method implements the layout algorithm proper. It must be called in a loop, until the layout stabilizes. You can know if the layout is stable by using the Layout.getNodeMovedCount() method that returns the number of node that have moved during the last call to step().

      The listener is called by this method, therefore each call to step() will also trigger layout events, allowing to reproduce the layout process graphically for example. You can insert the listener only when the layout stabilized, and then call step() anew if you do not want to observe the layout process.

      Specified by:
      compute in interface Layout

    • shake

      public void shake()
      Description copied from interface: Layout
      Add a random vector whose length is 10% of the size of the graph to all node positions.
      Specified by:
      shake in interface Layout

    • moveNode

      public void moveNode​(String id, double x, double y, double z)
      Description copied from interface: Layout
      Move a node by force to a new location. It is preferable to first freeze the node before moving it by force, and then un-freeze it.
      Specified by:
      moveNode in interface Layout
      Parameters:
      id - The node identifier.
      x - The node new X.
      y - The node new Y.
      z - The node new Z.

    • freezeNode

      public void freezeNode​(String id, boolean on)
      Description copied from interface: Layout
      Freeze or un-freeze a node. The freezed node position will not be changed by the algorithm until un-freezed.
      Specified by:
      freezeNode in interface Layout
      Parameters:
      id - The node identifier.
      on - If true the node is frozen.

    • particleAdded

      public void particleAdded​(Object id, double x, double y, double z, Object mark)

    • particleAdded

      public void particleAdded​(Object id, double x, double y, double z)
      Specified by:
      particleAdded in interface org.miv.pherd.ParticleBoxListener

    • particleMarked

      public void particleMarked​(Object id, Object mark)

    • particleMoved

      public void particleMoved​(Object id, double x, double y, double z)
      Specified by:
      particleMoved in interface org.miv.pherd.ParticleBoxListener

    • particleRemoved

      public void particleRemoved​(Object id)
      Specified by:
      particleRemoved in interface org.miv.pherd.ParticleBoxListener

    • stepFinished

      public void stepFinished​(int time)
      Specified by:
      stepFinished in interface org.miv.pherd.ParticleBoxListener

    • particleAttributeChanged

      public void particleAttributeChanged​(Object id, String attribute, Object newValue, boolean removed)
      Specified by:
      particleAttributeChanged in interface org.miv.pherd.ParticleBoxListener

    • edgeAdded

      public void edgeAdded​(String graphId, long time, String edgeId, String fromNodeId, String toNodeId, boolean directed)
      Description copied from interface: ElementSink
      An edge was inserted in graph.
      Specified by:
      edgeAdded in interface ElementSink
      Parameters:
      graphId - Identifier of the graph where the edge was added.
      edgeId - Identifier of the added edge.
      fromNodeId - Identifier of the first node of the edge.
      toNodeId - Identifier of the second node of the edge.
      directed - If true, the edge is directed.

    • nodeAdded

      public void nodeAdded​(String graphId, long time, String nodeId)
      Description copied from interface: ElementSink
      A node was inserted in the given graph.
      Specified by:
      nodeAdded in interface ElementSink
      Parameters:
      graphId - Identifier of the graph where the node was added.
      nodeId - Identifier of the added node.

    • edgeRemoved

      public void edgeRemoved​(String graphId, long time, String edgeId)
      Description copied from interface: ElementSink
      An edge of graph was removed.The nodes the edge connects may already have been removed from the graph.
      Specified by:
      edgeRemoved in interface ElementSink
      Parameters:
      graphId - The graph where the edge will be removed.
      edgeId - The edge that will be removed.

    • nodeRemoved

      public void nodeRemoved​(String graphId, long time, String nodeId)
      Description copied from interface: ElementSink
      A node was removed from the graph.
      Specified by:
      nodeRemoved in interface ElementSink
      Parameters:
      graphId - Identifier of the graph where the node will be removed.
      nodeId - Identifier of the removed node.

    • graphCleared

      public void graphCleared​(String graphId, long time)
      Description copied from interface: ElementSink
      The whole graph was cleared. All the nodes, edges and attributes of the graph are removed.
      Specified by:
      graphCleared in interface ElementSink
      Parameters:
      graphId - The graph cleared.

    • stepBegins

      public void stepBegins​(String graphId, long time, double step)
      Description copied from interface: ElementSink

      Since dynamic graphs are based on discrete event modifications, the notion of step is defined to simulate elapsed time between events. So a step is a event that occurs in the graph, it does not modify it but it gives a kind of timestamp that allow the tracking of the progress of the graph over the time.

      This kind of event is useful for dynamic algorithms that listen to the dynamic graph and need to measure the time in the graph's evolution.

      Specified by:
      stepBegins in interface ElementSink
      Parameters:
      graphId - Identifier of the graph where the step starts.
      time - A numerical value that may give a timestamp to track the evolution of the graph over the time.

    • graphAttributeAdded

      public void graphAttributeAdded​(String graphId, long time, String attribute, Object value)
      Description copied from interface: AttributeSink
      A graph attribute was added.
      Specified by:
      graphAttributeAdded in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the attribute changed.
      attribute - The attribute name.
      value - The attribute new value.

    • graphAttributeChanged

      public void graphAttributeChanged​(String graphId, long time, String attribute, Object oldValue, Object newValue)
      Description copied from interface: AttributeSink
      A graph attribute was changed.
      Specified by:
      graphAttributeChanged in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the attribute changed.
      attribute - The attribute name.
      oldValue - The attribute old value.
      newValue - The attribute new value.

    • graphAttributeRemoved

      public void graphAttributeRemoved​(String graphId, long time, String attribute)
      Description copied from interface: AttributeSink
      A graph attribute was removed.
      Specified by:
      graphAttributeRemoved in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the attribute was removed.
      attribute - The removed attribute name.

    • nodeAttributeAdded

      public void nodeAttributeAdded​(String graphId, long time, String nodeId, String attribute, Object value)
      Description copied from interface: AttributeSink
      A node attribute was added.
      Specified by:
      nodeAttributeAdded in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the change occurred.
      nodeId - Identifier of the node whose attribute changed.
      attribute - The attribute name.
      value - The attribute new value.

    • nodeAttributeChanged

      public void nodeAttributeChanged​(String graphId, long time, String nodeId, String attribute, Object oldValue, Object newValue)
      Description copied from interface: AttributeSink
      A node attribute was changed.
      Specified by:
      nodeAttributeChanged in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the change occurred.
      nodeId - Identifier of the node whose attribute changed.
      attribute - The attribute name.
      oldValue - The attribute old value.
      newValue - The attribute new value.

    • nodeAttributeRemoved

      public void nodeAttributeRemoved​(String graphId, long time, String nodeId, String attribute)
      Description copied from interface: AttributeSink
      A node attribute was removed.
      Specified by:
      nodeAttributeRemoved in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the attribute was removed.
      nodeId - Identifier of the node whose attribute was removed.
      attribute - The removed attribute name.

    • edgeAttributeAdded

      public void edgeAttributeAdded​(String graphId, long time, String edgeId, String attribute, Object value)
      Description copied from interface: AttributeSink
      A edge attribute was added.
      Specified by:
      edgeAttributeAdded in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the change occurred.
      edgeId - Identifier of the edge whose attribute changed.
      attribute - The attribute name.
      value - The attribute new value.

    • edgeAttributeChanged

      public void edgeAttributeChanged​(String graphId, long time, String edgeId, String attribute, Object oldValue, Object newValue)
      Description copied from interface: AttributeSink
      A edge attribute was changed.
      Specified by:
      edgeAttributeChanged in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the change occurred.
      edgeId - Identifier of the edge whose attribute changed.
      attribute - The attribute name.
      oldValue - The attribute old value.
      newValue - The attribute new value.

    • edgeAttributeRemoved

      public void edgeAttributeRemoved​(String graphId, long time, String edgeId, String attribute)
      Description copied from interface: AttributeSink
      A edge attribute was removed.
      Specified by:
      edgeAttributeRemoved in interface AttributeSink
      Parameters:
      graphId - Identifier of the graph where the attribute was removed.
      edgeId - Identifier of the edge whose attribute was removed.
      attribute - The removed attribute name.

    • newNodeParticle

      public abstract NodeParticle newNodeParticle​(String id)
      Factory method to create node particles.
      Parameters:
      id - The identifier of the new node/particle.
      Returns:
      The new node/particle.