ca.nengo.model.neuron.impl
Class PyramidalNetwork

java.lang.Object
  ca.nengo.model.impl.NetworkImpl
      ca.nengo.model.neuron.impl.PyramidalNetwork

All Implemented Interfaces:

Network, Node, Probeable, Resettable, SimulationMode.ModeConfigurable, TaskSpawner, VisiblyMutable, VisiblyMutable.Listener, java.io.Serializable, java.lang.Cloneable

public class PyramidalNetwork
extends NetworkImpl

Non Linear Network This network is a model of Pyramidal Cells found in the central nervous system These cells contain an active dendritic tree with functional computation occuring within the dendrites themselves. The implementation chosen involves creating a network of Ensembles(dendrites and cell bodies) such that one ensemble of "dendrites" projects to a specific termination in the "soma" ensemble with weights chosen in such a way that only one node of the soma is given an input from a specific dendritic branch.

See Also:

Serialized Form

Nested Class Summary

static class

PyramidalNetwork.PoiraziDendriteFactory Creates neurons which are meant to model the dendrites of pyramidal cells Code is a modified version of NodeFactory written by Bryann Tripp

Nested classes/interfaces inherited from class ca.nengo.model.impl.NetworkImpl

NetworkImpl.OriginWrapper, NetworkImpl.TerminationWrapper

Nested classes/interfaces inherited from interface ca.nengo.util.VisiblyMutable

VisiblyMutable.Event, VisiblyMutable.Listener, VisiblyMutable.NameChangeEvent, VisiblyMutable.NodeRemovedEvent

Field Summary

Fields inherited from class ca.nengo.model.impl.NetworkImpl

DEFAULT_NAME, myNumGPU, myNumJavaThreads, myUseGPU

Constructor Summary

PyramidalNetwork()
Default constructor

PyramidalNetwork(java.lang.String name)
Gives a default of 1 dimension

PyramidalNetwork(java.lang.String name, int dim)
Gives a default number of 20 neurons and 100 dendrites per neuron

PyramidalNetwork(java.lang.String name, int dim, int size)
Gives a default subunit size of 100

PyramidalNetwork(java.lang.String name, int dim, int size, IndicatorPDF dendriteRange)

PyramidalNetwork(java.lang.String name, int dim, int size, IndicatorPDF dendriteRange, java.lang.String f)

PyramidalNetwork(java.lang.String name, int dim, int size, IndicatorPDF dendriteRange, java.lang.String f, boolean oneDim)

PyramidalNetwork(java.lang.String name, int dim, int size, IndicatorPDF dendriteRange, java.lang.String f, boolean oneDim, boolean LIFDendrites, boolean spikingLIFDendrites)

Method Summary

void	addDecodedTermination(java.lang.String name, float[][] transform, float tauPSC, boolean modulatory) Adds a standard decoded termination to the network
void	addOneDimTermination(java.lang.String name, int dimension) Default one dimension termination with no transform Sets a default transform of 1
void	addOneDimTermination(java.lang.String name, int dimension, float transform) Adds a one dimension termination to the network This allows the user to specify which dimension the input value should be stored in as opposed to sending in a weight matrix to do so A multiplier transform is also expected
void	createFunctionOriginDendrites() Creates an origin at the dendrite level with a user specified function The value calculated at the dendrites is then transferred to the soma ensemble
NEFEnsemble	getDendrites(int index) Mainly used for testing purposes when trying to find proper scale values
java.lang.String	getName()
Origin	getOrigin()
float	getRange(int index) For testing
float[]	getScales(int index) Gets the scale values for a particular dendritic ensemble
NEFEnsemble	getSoma()
void	makeNetwork() Creates nodes and calls methods to make all origins, terminations, and projections

Methods inherited from class ca.nengo.model.impl.NetworkImpl

addChangeListener, addNode, addProjection, addTasks, changed, clone, countNeurons, exposeOrigin, exposeState, exposeTermination, fixMode, getDocumentation, getExposedOriginName, getExposedTerminationName, getHistory, getMetaData, getMode, getNeuronCount, getNode, getNodeCount, getNodeOrigins, getNodes, getNodeTerminations, getOrigin, getOrigins, getProjections, getSimulator, getStepSize, getTasks, getTermination, getTerminations, getUseGPU, hideOrigin, hideState, hideTermination, killNeurons, killNeurons, listStates, removeChangeListener, removeNode, removeProjection, reset, run, run, setDocumentation, setMetaData, setMode, setMyMode, setName, setSimulator, setStepSize, setTasks, setTime, setUseGPU

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PyramidalNetwork

public PyramidalNetwork(java.lang.String name,
                        int dim,
                        int size,
                        IndicatorPDF dendriteRange,
                        java.lang.String f,
                        boolean oneDim,
                        boolean LIFDendrites,
                        boolean spikingLIFDendrites)
                 throws StructuralException

Parameters:

name - Name of the network

dim - Dimensions of the network

size - Number of pyramidal neurons in the network

dendriteRange - Range of dendrites per neuron

f - function to be calculated at the dendrites

oneDim - whether or not terminations to the network are unidimensional or multidimensional

LIFDendrites - Use LIF dendrites?

spikingLIFDendrites - Use spiking LIF dendrites?

Throws:

StructuralException - if name isn't unique

PyramidalNetwork

public PyramidalNetwork(java.lang.String name,
                        int dim,
                        int size,
                        IndicatorPDF dendriteRange,
                        java.lang.String f,
                        boolean oneDim)
                 throws StructuralException

Parameters:

name - Name of the network

dim - Dimensions of the network

size - Number of pyramidal neurons in the network

dendriteRange - Range of dendrites per neuron

f - function to be calculated at the dendrites

oneDim - whether or not terminations to the network are unidimensional or multidimensional

Throws:

StructuralException - if name is taken

PyramidalNetwork

public PyramidalNetwork(java.lang.String name,
                        int dim,
                        int size,
                        IndicatorPDF dendriteRange,
                        java.lang.String f)
                 throws StructuralException

Parameters:

name - Name of the network

dim - Dimensions of the network

size - Number of pyramidal neurons in the network

dendriteRange - Range of dendrites per neuron

f - function to be calculated at the dendrites

Throws:

StructuralException - if name isn't unique

PyramidalNetwork

public PyramidalNetwork(java.lang.String name,
                        int dim,
                        int size,
                        IndicatorPDF dendriteRange)
                 throws StructuralException

Parameters:

name - Name of the network

dim - Dimensions of the network

size - Number of pyramidal neurons in the network

dendriteRange - Range of dendrites per neuron

Throws:

StructuralException - if name isn't unique

PyramidalNetwork

public PyramidalNetwork(java.lang.String name,
                        int dim,
                        int size)
                 throws StructuralException

Gives a default subunit size of 100

Parameters:

name - Name of the network

dim - Dimensions of the network

size - Number of pyramidal neurons in the network

Throws:

StructuralException - if name isn't unique

PyramidalNetwork

public PyramidalNetwork(java.lang.String name,
                        int dim)
                 throws StructuralException

Gives a default number of 20 neurons and 100 dendrites per neuron

Parameters:

name - Name of the network

dim - Dimensions of the network

Throws:

StructuralException - if name isn't unique

PyramidalNetwork

public PyramidalNetwork(java.lang.String name)
                 throws StructuralException

Gives a default of 1 dimension

Parameters:

name - Name of the network

Throws:

StructuralException - if name isn't unique

PyramidalNetwork

public PyramidalNetwork()
                 throws StructuralException

Default constructor

Throws:

StructuralException - if name isn't unique

Method Detail

makeNetwork

public void makeNetwork()
                 throws StructuralException

Creates nodes and calls methods to make all origins, terminations, and projections

Throws:

StructuralException - if name isn't unique

getDendrites

public NEFEnsemble getDendrites(int index)

Mainly used for testing purposes when trying to find proper scale values

Parameters:

index - index number of dendritic tree

Returns:

Dendritic ensemble at given index number

getName

public java.lang.String getName()

Specified by:

getName in interface Node

Overrides:

getName in class NetworkImpl

Returns:

Name of Node (must be unique in a Network)

See Also:

Node.getName()

createFunctionOriginDendrites

public void createFunctionOriginDendrites()
                                   throws StructuralException

Creates an origin at the dendrite level with a user specified function The value calculated at the dendrites is then transferred to the soma ensemble

Throws:

StructuralException - if decoded origin already exists

getRange

public float getRange(int index)

For testing

Parameters:

index - dendrite ensemble for which range is being returned

Returns:

the range of scale values for a particular dendrite ensemble

getScales

public float[] getScales(int index)

Gets the scale values for a particular dendritic ensemble

Parameters:

index - index number for dendritic ensemble

Returns:

returns the scale value for each node in the ensemble

getOrigin

public Origin getOrigin()
                 throws StructuralException

Returns:

Exposed network origin X (from the soma)

Throws:

StructuralException - if origin doesn't exist

addDecodedTermination

public void addDecodedTermination(java.lang.String name,
                                  float[][] transform,
                                  float tauPSC,
                                  boolean modulatory)
                           throws StructuralException

Adds a standard decoded termination to the network

Parameters:

name - Name of the termination

transform - Weight matrix for the termination

tauPSC - PSC time constant

modulatory - Modulatory?

Throws:

StructuralException - if termination already exists

addOneDimTermination

public void addOneDimTermination(java.lang.String name,
                                 int dimension,
                                 float transform)
                          throws StructuralException

Adds a one dimension termination to the network This allows the user to specify which dimension the input value should be stored in as opposed to sending in a weight matrix to do so A multiplier transform is also expected

Parameters:

name - Name of the termination

dimension - Dimension for input to be stored in

transform - Transform for input value

Throws:

StructuralException - if termination exists

addOneDimTermination

public void addOneDimTermination(java.lang.String name,
                                 int dimension)
                          throws StructuralException

Default one dimension termination with no transform Sets a default transform of 1

Parameters:

name - Name of the termination

dimension - Dimension input values are to be stored in

Throws:

StructuralException - if termination exists

getSoma

public NEFEnsemble getSoma()

Returns:

Soma ensemble