Examples of ca.nengo.model.Origin

ca.nengo.model.Origin

An source of information in a circuit model. Origins arise from Ensembles, ExternalInputs, and individual Neurons (although the latter Origins are mainly used internally within Ensembles, ie an Ensemble typically combines Neuron Origins into Ensemble Origins).

An Origin object will often correspond loosely to the anatomical origin of a neural projection in the brain. However, there is not a strict correspondance. In particular, an Origin object may relate specifically to a particular decoding of activity in an Ensemble. For example, suppose a bundle of axons bifurcates and terminates in two places. This would be modelled with two Origin objects if the postsynaptic Ensembles received different functions of the variables represented by the presynaptic Ensemble. So, an Origin is best thought about as a source of information in a certain form, rather than an anatomical source of axons.
@author Bryan Tripp


  /*
   * Test method for 'ca.bpt.cn.model.impl.NetworkImpl.getProjections()'
   */
  public void testGetProjections() throws StructuralException {
    Origin o1 = new ProjectionImplTest.MockOrigin("o1", 1);
    Origin o2 = new ProjectionImplTest.MockOrigin("o2", 1);
    Termination t1 = new ProjectionImplTest.MockTermination("t1", 1);
    Termination t2 = new ProjectionImplTest.MockTermination("t2", 1);
    Termination t3 = new ProjectionImplTest.MockTermination("t3", 2);


    myNetwork.addProjection(o1, t1);

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     * @throws StructuralException if named Origin does not exist
     * @see ca.nengo.model.ExpandableNode#removeTermination(java.lang.String)
     */
    public synchronized Origin removeOrigin(String name) throws StructuralException {
        if (myOrigins.containsKey(name)) {
            Origin result = myOrigins.remove(name);


            fireVisibleChangeEvent();
            return result;
        }
        throw new StructuralException("Origin " + name + " does not exist");

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 * @author Bryan Tripp
 */
public class AbstractEnsembleTest extends TestCase {


  public void testFindCommon1DOrigins() {
    Origin one = new BasicOrigin(null, "2D", 2, Units.UNK);
    Origin two = new BasicOrigin(null, "unique", 1, Units.UNK);
    Origin three = new BasicOrigin(null, "shared1", 1, Units.UNK);
    Origin four = new BasicOrigin(null, "shared2", 1, Units.UNK);
    
    List<Origin> shared = new ArrayList<Origin>(3);
    shared.add(one);
    shared.add(three);
    shared.add(four);
    
    List<Origin> notshared = new ArrayList<Origin>(4);
    notshared.add(one);
    notshared.add(three);
    notshared.add(four);
    notshared.add(two);
    
    Node[] nodes = new Node[3];
    nodes[0] = new AbstractNode("a", shared, new ArrayList<Termination>(1)) {
      private static final long serialVersionUID = 1L;


      @Override
      public void run(float startTime, float endTime)
          throws SimulationException {}


      @Override
      public void reset(boolean randomize) {}


      public Node[] getChildren() {
        return new Node[0];
      }


      public String toScript(HashMap<String, Object> scriptData) throws ScriptGenException {
        return "";
      }};    
    nodes[1] = new AbstractNode("b", shared, new ArrayList<Termination>(1)) {
      private static final long serialVersionUID = 1L;


      @Override
      public void run(float startTime, float endTime)
          throws SimulationException {}


      @Override
      public void reset(boolean randomize) {}


      public Node[] getChildren() {
        return new Node[0];
      }


      public String toScript(HashMap<String, Object> scriptData) throws ScriptGenException {
        return "";
      }};    
    nodes[2] = new AbstractNode("c", notshared, new ArrayList<Termination>(1)) {
      private static final long serialVersionUID = 1L;


      @Override
      public void run(float startTime, float endTime)
          throws SimulationException {}


      @Override
      public void reset(boolean randomize) {}


      public Node[] getChildren() {
        return new Node[0];
      }


      public String toScript(HashMap<String, Object> scriptData) throws ScriptGenException {
        return "";
      }};
    
    List<String> origins = AbstractEnsemble.findCommon1DOrigins(nodes);
    assertEquals(2, origins.size());
    assertTrue(origins.contains(three.getName()));
    assertTrue(origins.contains(four.getName()));
  }

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        result.myNodes[i] = (NEFEnsembleImpl) result.getNode(myNodes[i].getName());
      }
      
      // Clone array origins and ensemble terminations
      for (Origin exposedOrigin : getOrigins()) {
        Origin clonedOrigin = ((OriginWrapper) exposedOrigin).getBaseOrigin().clone(result);
        result.exposeOrigin(clonedOrigin, exposedOrigin.getName());
      }
      for (Termination exposedTermination : getTerminations()) {
        Termination clonedTermination = ((TerminationWrapper) exposedTermination).getBaseTermination().clone(result);
        result.exposeTermination(clonedTermination, exposedTermination.getName());

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    public void setStates(float endTime) throws SimulationException {
        if (myLastPlasticityTime < endTime) {
            for (PlasticEnsembleTermination pet : myPlasticEnsembleTerminations.values()) {
                try {
                    Origin origin = this.getOrigin(pet.getOriginName());
                    pet.setOriginState(origin.getName(), origin.getValues(), endTime);
                    pet.setTerminationState(endTime);


                    if (pet instanceof ModulatedPlasticEnsembleTermination) {
                        DecodedTermination modTerm = (DecodedTermination)
                            this.getTermination(((ModulatedPlasticEnsembleTermination) pet).getModTermName());

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   */
    @Override
    public TimeSeries getHistory(String stateName) throws SimulationException {
    TimeSeries result = null;


    Origin origin = myDecodedOrigins.get(stateName);
    DecodedTermination t = myDecodedTerminations.get(stateName);


    if (origin != null) {
      if (t != null)
        ourLogger.warn("Warning, probe set on ensemble with matching origin/termination names (\"" + 
            stateName + "\"), probing origin by default");
      
        origin.setRequiredOnCPU(true);
      float[] vals = ((RealOutput) origin.getValues()).getValues();
      Units[] units = new Units[vals.length];
      for (int i = 0; i < vals.length; i++) {
        units[i] = origin.getValues().getUnits();
      }
      result = new TimeSeriesImpl(new float[]{myTime}, new float[][]{vals}, units);
    } else if (t != null) {
      result = t.getHistory(DecodedTermination.OUTPUT);
      } else if (t == null && stateName.endsWith(":STP")) {

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    return result;
  }


  public void stopProbing(String stateName){
    Origin origin = myDecodedOrigins.get(stateName);
    
    if (origin != null) {
        origin.setRequiredOnCPU(false);
    }
  }

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  /**
   * @see ca.nengo.model.Network#exposeOrigin(ca.nengo.model.Origin,
   *      java.lang.String)
   */
  public void exposeOrigin(Origin origin, String name) {
    Origin temp;


    temp = new OriginWrapper(this, origin, name);


    myExposedOrigins.put(name, temp );
    myExposedOriginNames.put(origin, name);

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    //TODO: this works with a single Projection impl & no params; should add Projection.copy(Origin, Termination, Network)?
    result.myProjectionMap = new HashMap<Termination, Projection>(10);
    for (Projection oldProjection : getProjections()) {
      try {
        Origin newOrigin = result.getNode(oldProjection.getOrigin().getNode().getName())
          .getOrigin(oldProjection.getOrigin().getName());
        Termination newTermination = result.getNode(oldProjection.getTermination().getNode().getName())
          .getTermination(oldProjection.getTermination().getName());
        Projection newProjection = new ProjectionImpl(newOrigin, newTermination, result);
        result.myProjectionMap.put(newTermination, newProjection);
      } catch (StructuralException e) {
        throw new CloneNotSupportedException("Problem copying Projectio: " + e.getMessage());
      }
    }


    result.myExposedOrigins = new HashMap<String, Origin>(10);
    result.myExposedOriginNames = new HashMap<Origin, String>(10);
    result.OrderedExposedOrigins = new LinkedList <Origin> ();
    for (Origin exposed : getOrigins()) {
      String name = exposed.getName();
      Origin wrapped = ((OriginWrapper) exposed).getWrappedOrigin();
      try {
        // Check to see if referenced node is the network itself. If it is, handle the origin differently.
        if (wrapped.getNode().getName() != myName ) {
          Origin toExpose = result.getNode(wrapped.getNode().getName()).getOrigin(wrapped.getName());
          result.exposeOrigin(toExpose, name);
        }
      } catch (StructuralException e) {
        throw new CloneNotSupportedException("Problem exposing Origin: " + e.getMessage());
      }

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Related Classes of ca.nengo.model.Origin

ca.nengo.math.impl.MultiLevelKLNetworkPartitioner

ca.nengo.model.impl.AbstractEnsemble

ca.nengo.model.impl.AbstractEnsembleTest

ca.nengo.model.impl.FunctionInputTest

ca.nengo.model.impl.NetworkArrayImpl

ca.nengo.model.impl.NetworkImpl

ca.nengo.model.impl.NetworkImplTest

ca.nengo.model.impl.ProjectionImpl

ca.nengo.model.nef.impl.DecodableEnsembleImpl

ca.nengo.model.plasticity.impl.PlasticEnsembleImpl

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