Examples of ca.nengo.model.Network

ca.nengo.model.Network

A neural circuit, consisting of Nodes such as Ensembles and ExternalInputs. A Network is the usual object of a simulation. If you are new to this code, what you probably want to do is create some Neurons, group them into Ensembles, connect the Ensembles in a Network, and run the Network in a Simulator.

Note: Multiple steps are needed to add a Projection between Ensembles. First, an Origin must be created on the presynaptic Ensemble, and a Termination with the same dimensionality must be created on the post-synaptic Ensemble. Then the Origin and Termination can be connected with the method addProjection(Origin, Termination). We don't do this in one step (ie automatically create the necessary Origin and Termination as needed) because there are various ways of doing so, and in fact some types of Origins and Terminations can only be created in the course of constructing the Ensemble. Creation of an Origin or Termination can also be a complex process. Rather than try to abstract these varied procedures into something that can be driven from the Network level, we just assume here that the necessary Origins and Terminations exist, and provide a method for connecting them.
@author Bryan Tripp

                Ensemble ensemble = (Ensemble)node;
                UIEnsemble ensembleUI = new UIEnsemble(ensemble);
                addUINode(ensembleUI,false,false);
                
              } else if (node instanceof Network) {
                Network network = (Network)node;
                UINetwork networkUI = new UINetwork(network);
                addUINode(networkUI, false, false);
              } else {
                UserMessages.showError("Unsupported node type " + node.getClass().getSimpleName()
                    + " in EnsembleViewer");

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    }
  }


  protected String getExposedName() {
    if (getNodeParent() != null && getNodeParent().getNetworkParent() != null) {
      Network network = getNodeParent().getNetworkParent().getModel();
      if (network != null) {
        String exposedName = getExposedName(network);
        if (exposedName != null) {
          return exposedName;
        }

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  /**
   * UnExposes this origin/termination outside the Network
   */
  protected void unExpose() {
    UINetwork networkUI = getNodeParent().getNetworkParent();
    Network network = networkUI.getModel();
    if (network != null) {
      unExpose(network);
      showPopupMessage(getName() + " is UN-exposed on Network: " + network.getName());
    } else {
      UserMessages.showWarning("Cannot expose because no external network is available");
    }
  }

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        setName(term.getName());
    }


    @Override
    protected void destroyTerminationModel() {
        Network network = ((UINetwork) getParent()).getModel();
        network.hideTermination(getModel().getName());
        showPopupMessage("termination removed from network");
    }

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    try {
      if (nodeAttachedTo.getParentViewer() instanceof EnsembleViewer) {
        EnsembleViewer ensembleViewer = (EnsembleViewer) nodeAttachedTo.getParentViewer();


        UIEnsemble ensemble = ensembleViewer.getViewerParent();
        Network network = ensemble.getNetworkParent().getModel();


        probe = network.getSimulator().addProbe(ensemble.getName(),
            (Probeable) node,
            state,
            true);


      } else if (nodeAttachedTo.getNetworkParent() != null) {

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  /*
   * Test method for 'ca.nengo.sim.impl.WriteToDiskSimulatorListener'
   */
  public void testBasicWriting() throws StructuralException, SimulationException {
    Network network = new NetworkImpl();
    NEFEnsembleFactory factory = new NEFEnsembleFactoryImpl();
    NEFEnsemble ensemble = factory.make("Ensemble",100,2);
    File file = new File("testWTDSL.csv");
    
    network.addNode(ensemble);
    
    Probe probe = network.getSimulator().addProbe("Ensemble", "X", true);
    WriteToDiskSimulatorListener listener = new WriteToDiskSimulatorListener(file,probe,0.005f);
    
    network.getSimulator().addSimulatorListener(listener);
    network.getSimulator().run(0.0f, 1.0f, 0.001f);
    
    assertTrue(file.exists());
    assertTrue(file.length() > 0);
    assertTrue(file.delete());
  }

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  /*
   * Test method for 'ca.nengo.sim.impl.WriteToDiskSimulatorListener'
   */
  public void testInterval() throws StructuralException, SimulationException, FileNotFoundException {
    Network network = new NetworkImpl();
    NEFEnsembleFactory factory = new NEFEnsembleFactoryImpl();
    NEFEnsemble ensemble = factory.make("Ensemble",100,2);
    File file = new File("testWTDSL.csv");
    
    network.addNode(ensemble);
    
    float interval = 0.005f;
    float simLength = 1.0f;
    int numIntervals = (int)(simLength / interval);
    Probe probe = network.getSimulator().addProbe("Ensemble", "X", true);
    WriteToDiskSimulatorListener listener = new WriteToDiskSimulatorListener(file,probe,interval);
        
    network.getSimulator().addSimulatorListener(listener);
    network.getSimulator().run(0.0f, simLength, 0.001f);
    
        Scanner fileReader = new Scanner(file);
        int lineCount = 0;
      
        while (fileReader.hasNextLine()) {
          fileReader.nextLine();
          lineCount++;
        }
        
        assertEquals(numIntervals,lineCount);
        fileReader.close();
        network.getSimulator().removeSimulatorListener(listener);
        
        // Also tests multiple runs
        interval = 0.0f;
    numIntervals = 1000;
    listener = new WriteToDiskSimulatorListener(file,probe,interval);
    
    network.getSimulator().addSimulatorListener(listener);
    network.getSimulator().run(0.0f, simLength, 0.001f);
    
        fileReader = new Scanner(file);
        lineCount = 0;
      
        while (fileReader.hasNextLine()) {

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    @SuppressWarnings("unchecked")
  protected void post(Node node)
  {
        if (node instanceof Network && inTemplateNetwork <= 0)
        {
            Network net = (Network)node;
            parentNetwork.pop();


            HashMap<String, Object> toScriptArgs = new HashMap<String, Object>();
            toScriptArgs.put("prefix", prefixes.get(node) + spaceDelimiter);
            toScriptArgs.put("isSubnet", !topLevel);
            toScriptArgs.put("netName", prefixes.get(node));
            toScriptArgs.put("spaceDelim", spaceDelimiter);
            
            try {
                String code = net.toPostScript(toScriptArgs);
                script.append(code);
            } catch(ScriptGenException e) {
                System.out.println(e.getMessage());
            }

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        Ensemble ensemble = (Ensemble)node;
        for (int i = 0; i < myNodeOrigins.length; i++)
          origins[i] = ensemble.getNodes()[i].getOrigin(myNodeOrigins[i].getName());
      }
      if (node instanceof Network) {
        Network network = (Network)node;
        for (int i = 0; i < myNodeOrigins.length; i++)
          origins[i] = network.getNodes()[i].getOrigin(myNodeOrigins[i].getName());
      }
      result.myNodeOrigins = origins;
      return result;
    } catch (StructuralException e) {
      throw new CloneNotSupportedException("Error cloning EnsembleOrigin: " + e.getMessage());

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//    error2 = getError(reference, negativeOptimal);
//    assertTrue(error2 > 1e-10 && error2 < 3.5e-4 && error2 < error);
//  }


  public void testAddBias2D() throws StructuralException, SimulationException {
    Network network = new NetworkImpl();
    FunctionInput input = new FunctionInput("input", new Function[]{new IdentityFunction(1, 0)}, Units.UNK);
    network.addNode(input);
    NEFEnsembleFactory ef = new NEFEnsembleFactoryImpl();
    int n = 300;
    NEFEnsemble pre = ef.make("pre", n, 2);
    pre.addDecodedTermination("input", MU.uniform(2, 1, 1), .005f, false);
    network.addNode(pre);
    network.addProjection(input.getOrigin(FunctionInput.ORIGIN_NAME), pre.getTermination("input"));
    NEFEnsemble post = ef.make("post", n, 2);
    network.addNode(post);
    post.addDecodedTermination("input", MU.I(2), .01f, false);
    Projection p = network.addProjection(pre.getOrigin(NEFEnsemble.X), post.getTermination("input"));


    DecodedOrigin o = (DecodedOrigin) pre.getOrigin(NEFEnsemble.X);
    DecodedTermination t = (DecodedTermination) post.getTermination("input");
    float[][] directWeights = MU.prod(post.getEncoders(), MU.prod(t.getTransform(), MU.transpose(o.getDecoders())));
    System.out.println("Direct weights: " + MU.min(directWeights) + " to " + MU.max(directWeights));


    Probe probe = network.getSimulator().addProbe(post.getName(), NEFEnsemble.X, true);
    network.setMode(SimulationMode.CONSTANT_RATE);
    network.run(-1.5f, 1);
    network.setMode(SimulationMode.DEFAULT);
    float[] reference = MU.transpose(DataUtils.filter(probe.getData(), .01f).getValues())[0];


    network.run(-1.5f, 1);
//    Plotter.plot(probe.getData(), "mixed weights");
    float[] mixed = MU.transpose(DataUtils.filter(probe.getData(), .01f).getValues())[0];
    getError(reference, mixed);


    p.addBias(300, .005f, .01f, true, false);
    BiasOrigin bo = (BiasOrigin) pre.getOrigin("post_input");
    BiasTermination bt = (BiasTermination) post.getTermination("input (bias)");
    assertTrue(MU.min(getNetWeights(directWeights, bo, bt)) > -1e-10);
    network.run(-1.5f, 1);
//    Plotter.plot(probe.getData(), "positive non-optimal");
//    float[] positiveNonOptimal = MU.transpose(DataUtils.filter(probe.getData(), .01f).getValues())[0];
//    float error = getError(reference, positiveNonOptimal);
//    assertTrue(error > 1e-10 && error < 5e-4);
    p.removeBias();


    p.addBias(300, .005f, .01f, true, true);
    bo = (BiasOrigin) pre.getOrigin("post_input");
    bt = (BiasTermination) post.getTermination("input (bias)");
    assertTrue(MU.min(getNetWeights(directWeights, bo, bt)) > -1e-10);
    network.run(-1.5f, 1);
//    Plotter.plot(probe.getData(), "positive optimal");
//    float[] positiveOptimal = MU.transpose(DataUtils.filter(probe.getData(), .01f).getValues())[0];
//    float error2 = getError(reference, positiveOptimal);
//    assertTrue(error2 > 1e-10 && error2 < 2.5e-4 && error2 < error);
    p.removeBias();

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Related Classes of ca.nengo.model.Network

ca.nengo.examples.IntegratorExample

ca.nengo.model.impl.EnsembleOrigin

ca.nengo.model.impl.EnsembleTermination

ca.nengo.model.impl.NetworkImpl

ca.nengo.model.impl.ProjectionImplTest

ca.nengo.model.nef.impl.NEFEnsembleImplTest

ca.nengo.model.neuron.impl.ALIFSpikeGeneratorTest

ca.nengo.model.neuron.impl.IzhikevichSpikeGeneratorTest

ca.nengo.model.neuron.impl.PoissonSpikeGeneratorTest

ca.nengo.plot.PlotterFunctional

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