ec.cgp.representation
Class VectorSpeciesCGP

java.lang.Object
  ec.Species
      ec.vector.VectorSpecies
          ec.cgp.representation.VectorSpeciesCGP

All Implemented Interfaces:

ec.Prototype, ec.Setup, java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

FloatVectorSpecies, IntegerVectorSpecies

public abstract class VectorSpeciesCGP
extends ec.vector.VectorSpecies

The CGPVectorSpecies handles much of the behavior and representation of Cartesian Genetic Programs. It is here that the phenotype/genotype mappings and various representational constraints are imposed.

Author:

David Oranchak, doranchak@gmail.com, http://oranchak.com

See Also:

Serialized Form

Field Summary

static int	GENE_ARGUMENT Gene position that represents a function argument
static int	GENE_FUNCTION Gene position that represents a function reference
static int	GENE_OUTPUT Gene position that represents an output node
int	maxArity Max arity of the function set
int	numFunctions Number of functions in the function set.
int	numInputs Number of input nodes.
int	numNodes Number of function call nodes comprising the CGP.
int	numOutputs Number of output nodes
static java.lang.String	P_FUNCTIONS
static java.lang.String	P_MAX_ARITY
static java.lang.String	P_NUM_FUNCTIONS
static java.lang.String	P_NUM_INPUTS
static java.lang.String	P_NUM_NODES
static java.lang.String	P_NUM_OUTPUTS
static java.lang.String	P_VECTORSPECIES configuration names used in the parameter files

Fields inherited from class ec.vector.VectorSpecies

C_ANY_POINT, C_ONE_POINT, C_TWO_POINT, chunksize, crossoverProbability, crossoverType, genomeSize, mutationProbability, P_CHUNKSIZE, P_CROSSOVERPROB, P_CROSSOVERTYPE, P_GENOMESIZE, P_MUTATIONPROB, V_ANY_POINT, V_ONE_POINT, V_TWO_POINT

Fields inherited from class ec.Species

f_prototype, i_prototype, P_FITNESS, P_INDIVIDUAL, P_PIPE, pipe_prototype

Constructor Summary

VectorSpeciesCGP()

Method Summary

int	computeMaxGene(int position, float[] genome) Computes max possible gene value for the given position.
int	computeMaxGene(int position, int[] genome) Computes max possible gene value for the given position.
ec.util.Parameter	defaultBase() Returns the default base for this prototype.
int	function(int position, float[] genome) Determine the function number from the given genome and position (int version).
int	function(int position, int[] genome) Determine the function number from the given genome and position (float version).
(package private) int	functionSub(int position) Computation shared by both function(position, genome) methods.
int	interpretFloat(int pos, float[] genome) Interprets float at position pos based on max possible int represented by that position.
int	nodeNumber(int position, float[] genome) Determine the node number from the given genome position.
int	nodeNumber(int position, int[] genome) Determine the node number from the given genome position.
int	numGenes() Computes the total number of gene values needed for all function and output nodes (a gene in this sense is a single element of the underlying genome vector)
int	phenotype(int position, float[] genome) From the given genome position, determine the phenotype (float version)
int	phenotype(int position, int[] genome) From the given genome position, determine the phenotype (int version)
static java.lang.String	phenotypeDescription(int phenotype) Get a simple description of the given phenotype
int	positionFromNodeNumber(int nodeNumber) Determine the start position of the given node number.
void	setup(ec.EvolutionState state, ec.util.Parameter base) The default version of setup(...) loads requested pipelines and calls setup(...) on them and normalizes their probabilities.
java.lang.String	toString()

Methods inherited from class ec.vector.VectorSpecies

newIndividual

Methods inherited from class ec.Species

clone, newIndividual, newIndividual

Methods inherited from class java.lang.Object

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

Field Detail

GENE_OUTPUT

public static final int GENE_OUTPUT

Gene position that represents an output node

See Also:

Constant Field Values

GENE_FUNCTION

public static final int GENE_FUNCTION

Gene position that represents a function reference

See Also:

Constant Field Values

GENE_ARGUMENT

public static final int GENE_ARGUMENT

Gene position that represents a function argument

See Also:

Constant Field Values

P_VECTORSPECIES

public static final java.lang.String P_VECTORSPECIES

configuration names used in the parameter files

See Also:

Constant Field Values

P_NUM_NODES

public static final java.lang.String P_NUM_NODES

See Also:

Constant Field Values

P_NUM_INPUTS

public static final java.lang.String P_NUM_INPUTS

See Also:

Constant Field Values

P_NUM_OUTPUTS

public static final java.lang.String P_NUM_OUTPUTS

See Also:

Constant Field Values

P_NUM_FUNCTIONS

public static final java.lang.String P_NUM_FUNCTIONS

See Also:

Constant Field Values

P_MAX_ARITY

public static final java.lang.String P_MAX_ARITY

See Also:

Constant Field Values

P_FUNCTIONS

public static final java.lang.String P_FUNCTIONS

See Also:

Constant Field Values

numNodes

public int numNodes

Number of function call nodes comprising the CGP. Does not include output nodes.

numInputs

public int numInputs

Number of input nodes. Includes any automatically-managed constants (see CGPProblem).

numOutputs

public int numOutputs

Number of output nodes

numFunctions

public int numFunctions

Number of functions in the function set.

maxArity

public int maxArity

Max arity of the function set

Constructor Detail

VectorSpeciesCGP

public VectorSpeciesCGP()

Method Detail

numGenes

public int numGenes()

Computes the total number of gene values needed for all function and output nodes (a gene in this sense is a single element of the underlying genome vector)

function

public int function(int position,
                    float[] genome)

Determine the function number from the given genome and position (int version).

function

public int function(int position,
                    int[] genome)

Determine the function number from the given genome and position (float version).

functionSub

int functionSub(int position)

Computation shared by both function(position, genome) methods. Returns function position that corresponds to the given position.

phenotype

public int phenotype(int position,
                     int[] genome)

From the given genome position, determine the phenotype (int version)

phenotype

public int phenotype(int position,
                     float[] genome)

From the given genome position, determine the phenotype (float version)

interpretFloat

public int interpretFloat(int pos,
                          float[] genome)

Interprets float at position pos based on max possible int represented by that position.

computeMaxGene

public int computeMaxGene(int position,
                          int[] genome)

Computes max possible gene value for the given position. Min gene value is assumed to always be zero. The max value depends on the phenotype of the given position.

computeMaxGene

public int computeMaxGene(int position,
                          float[] genome)

Computes max possible gene value for the given position. Min gene value is assumed to always be zero. The max value depends on the phenotype of the given position.

nodeNumber

public int nodeNumber(int position,
                      int[] genome)

Determine the node number from the given genome position. Function arguments refer to node numbers. Inputs are numbered from [0, numInputs - 1]. Function nodes are numbered from [numInputs, numInputs + numNodes - 1]. Output nodes are numbered from [numInputs + numNodes, numInputs + numNodes + numOuputs - 1].

nodeNumber

public int nodeNumber(int position,
                      float[] genome)

Determine the node number from the given genome position. Function arguments refer to node numbers. Inputs are numbered from [0, numInputs - 1]. Function nodes are numbered from [numInputs, numInputs + numNodes - 1]. Output nodes are numbered from [numInputs + numNodes, numInputs + numNodes + numOuputs - 1].

positionFromNodeNumber

public int positionFromNodeNumber(int nodeNumber)

Determine the start position of the given node number. WARNING: do not call this with a nodeNumber < numInputs, because the inputs are not represented in the genome.

defaultBase

public ec.util.Parameter defaultBase()

Description copied from interface: ec.Prototype

Returns the default base for this prototype. This should generally be implemented by building off of the static base() method on the DefaultsForm object for the prototype's package. This should be callable during setup(...).

Specified by:

defaultBase in interface ec.Prototype

Overrides:

defaultBase in class ec.vector.VectorSpecies

setup

public void setup(ec.EvolutionState state,
                  ec.util.Parameter base)

Description copied from class: ec.Species

The default version of setup(...) loads requested pipelines and calls setup(...) on them and normalizes their probabilities. If your individual prototype might need to know special things about the species (like parameters stored in it), then when you override this setup method, you'll need to set those parameters BEFORE you call super.setup(...), because the setup(...) code in Species sets up the prototype.

Specified by:

setup in interface ec.Prototype

Specified by:

setup in interface ec.Setup

Overrides:

setup in class ec.vector.VectorSpecies

See Also:

Prototype.setup(EvolutionState,Parameter)

phenotypeDescription

public static java.lang.String phenotypeDescription(int phenotype)

Get a simple description of the given phenotype

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object