GTree and GTreeGP – the tree chromosomes

This is the rooted tree representation, this chromosome representation can carry any data-type.

Default Parameters

Initializator

Initializators.GTreeInitializatorInteger()

The Integer Initializator for GTree

Mutator

Mutators.GTreeMutatorIntegerRange()

The Integer Range mutator for GTree

Crossover

Crossovers.GTreeCrossoverSinglePointStrict()

The Strict Single Point crossover for GTree

New in version 0.6: The GTree module.

Classes

class GTree.GTree(root_node=None)

The GTree class - The tree chromosome representation

Inheritance diagram for GTree.GTree:

Parameters:root_node – the root node of the tree

clone()

Return a new instance of the genome

Return type:new GTree instance

copy(g)

Copy the contents to the destination g

Parameters:g – the GTree genome destination

crossover

This is the reproduction function slot, the crossover. You can change the default crossover method using:

genome.crossover.set(Crossovers.G1DListCrossoverUniform)

evaluate(**args)

Called to evaluate genome

Parameters:args – this parameters will be passes to the evaluator

evaluator

This is the evaluation function slot, you can add a function with the set method:

genome.evaluator.set(eval_func)

getAllNodes()

Return a new list with all nodes

Return type:the list with all nodes

getFitnessScore()

Get the Fitness Score of the genome

Return type:genome fitness score

getHeight()

Return the tree height

Return type:the tree height

getNodeDepth(node)

Returns the depth of a node

Return type:the depth of the node, the depth of root node is 0

getNodeHeight(node)

Returns the height of a node

Note

If the node has no childs, the height will be 0.

Return type:the height of the node

getNodesCount(start_node=None)

Return the number of the nodes on the tree starting at the start_node, if start_node is None, then the method will count all the tree nodes.

Return type:the number of nodes

getParam(key, nvl=None)

Gets an internal parameter

Example:

>>> genome.getParam("rangemax")
100

Note

All the individuals of the population shares this parameters and uses the same instance of this dict.

Parameters:

• key – the key of param
• nvl – if the key doesn’t exist, the nvl will be returned

getRandomNode(node_type=0)

Returns a random node from the Tree

Parameters:node_type – 0 = Any, 1 = Leaf, 2 = Branch Return type:random node

getRawScore()

Get the Raw Score of the genome

Return type:genome raw score

getRoot()

Return the tree root node

Return type:the tree root node

getTraversalString(start_node=None, spc=0)

Returns a tree-formated string of the tree. This method is used by the __repr__ method of the tree

Return type:a string representing the tree

initializator

This is the initialization function of the genome, you can change the default initializator using the function slot:

genome.initializator.set(Initializators.G1DListInitializatorAllele)

In this example, the initializator Initializators.G1DListInitializatorAllele() will be used to create the initial population.

initialize(**args)

Called to initialize genome

Parameters:args – this parameters will be passed to the initializator

mutate(**args)

Called to mutate the genome

Parameters:args – this parameters will be passed to the mutator Return type:the number of mutations returned by mutation operator

mutator

This is the mutator function slot, you can change the default mutator using the slot set function:

genome.mutator.set(Mutators.G1DListMutatorSwap)

processNodes(cloning=False)

Creates a cache on the tree, this method must be called every time you change the shape of the tree. It updates the internal nodes list and the internal nodes properties such as depth and height.

resetStats()

Clear score and fitness of genome

setParams(**args)

Set the internal params

Example:

>>> genome.setParams(rangemin=0, rangemax=100, gauss_mu=0, gauss_sigma=1)

Note

All the individuals of the population shares this parameters and uses the same instance of this dict.

Parameters:args – this params will saved in every chromosome for genetic op. use

setRoot(root)

Sets the root of the tree

Parameters:root – the tree root node

traversal(callback, start_node=None)

Traversal the tree, this method will call the user-defined callback function for each node on the tree

Parameters:

• callback – a function
• start_node – the start node to begin the traversal

class GTree.GTreeGP(root_node=None, cloning=False)

The GTreeGP Class - The Genetic Programming Tree representation

Inheritance diagram for GTree.GTreeGP:

Parameters:root_node – the Root node of the GP Tree

clone()

Return a new instance of the genome

Return type:the new GTreeGP instance

compare(other)

This method will compare the currently tree with another one

Parameters:other – the other GTreeGP to compare

copy(g)

Copy the contents to the destination g

Parameters:g – the GTreeGP genome destination

evaluate(**args)

Called to evaluate genome

Parameters:args – this parameters will be passes to the evaluator

getAllNodes()

Return a new list with all nodes

Return type:the list with all nodes

getCompiledCode()

Get the compiled code for the Tree expression After getting the compiled code object, you just need to evaluate it using the eval() native Python method.

Return type:compiled python code

getFitnessScore()

Get the Fitness Score of the genome

Return type:genome fitness score

getHeight()

Return the tree height

Return type:the tree height

getNodeDepth(node)

Returns the depth of a node

Return type:the depth of the node, the depth of root node is 0

getNodeHeight(node)

Returns the height of a node

Note

If the node has no childs, the height will be 0.

Return type:the height of the node

getNodesCount(start_node=None)

Return the number of the nodes on the tree starting at the start_node, if start_node is None, then the method will count all the tree nodes.

Return type:the number of nodes

getParam(key, nvl=None)

Gets an internal parameter

Example:

>>> genome.getParam("rangemax")
100

Note

All the individuals of the population shares this parameters and uses the same instance of this dict.

Parameters:

• key – the key of param
• nvl – if the key doesn’t exist, the nvl will be returned

getPreOrderExpression(start_node=None)

Return the pre order expression string of the Tree, used to python eval.

Return type:the expression string

getRandomNode(node_type=0)

Returns a random node from the Tree

Parameters:node_type – 0 = Any, 1 = Leaf, 2 = Branch Return type:random node

getRawScore()

Get the Raw Score of the genome

Return type:genome raw score

getRoot()

Return the tree root node

Return type:the tree root node

getSExpression(start_node=None)

Returns a tree-formated string (s-expression) of the tree.

Return type:a S-Expression representing the tree

getTraversalString(start_node=None, spc=0)

Returns a tree-formated string of the tree. This method is used by the __repr__ method of the tree

Return type:a string representing the tree

initialize(**args)

Called to initialize genome

Parameters:args – this parameters will be passed to the initializator

mutate(**args)

Called to mutate the genome

Parameters:args – this parameters will be passed to the mutator Return type:the number of mutations returned by mutation operator

processNodes(cloning=False)

Creates a cache on the tree, this method must be called every time you change the shape of the tree. It updates the internal nodes list and the internal nodes properties such as depth and height.

resetStats()

Clear score and fitness of genome

setParams(**args)

Set the internal params

Example:

>>> genome.setParams(rangemin=0, rangemax=100, gauss_mu=0, gauss_sigma=1)

Note

All the individuals of the population shares this parameters and uses the same instance of this dict.

Parameters:args – this params will saved in every chromosome for genetic op. use

setRoot(root)

Sets the root of the tree

Parameters:root – the tree root node

traversal(callback, start_node=None)

Traversal the tree, this method will call the user-defined callback function for each node on the tree

Parameters:

• callback – a function
• start_node – the start node to begin the traversal

writeDotGraph(graph, startNode=0)

Write a graph to the pydot Graph instance

Parameters:

• graph – the pydot Graph instance
• startNode – used to plot more than one individual

writeDotImage(filename)

Writes a image representation of the individual

Parameters:filename – the output file image

writeDotRaw(filename)

Writes the raw dot file (text-file used by dot/neato) with the representation of the individual

Parameters:filename – the output file, ex: individual.dot

static writePopulationDot(ga_engine, filename, format='jpeg', start=0, end=0)

Writes to a graphical file using pydot, the population of trees

Example:

>>> GTreeGP.writePopulationDot(ga_engine, "pop.jpg", "jpeg", 0, 10)

This example will draw the first ten individuals of the population into the file called “pop.jpg”.

Parameters:

• ga_engine – the GA Engine
• filename – the filename, ie. population.jpg
• start – the start index of individuals
• end – the end index of individuals

static writePopulationDotRaw(ga_engine, filename, start=0, end=0)

Writes to a raw dot file using pydot, the population of trees

Example:

>>> GTreeGP.writePopulationDotRaw(ga_engine, "pop.dot", 0, 10)

This example will draw the first ten individuals of the population into the file called “pop.dot”.

Parameters:

• ga_engine – the GA Engine
• filename – the filename, ie. population.dot
• start – the start index of individuals
• end – the end index of individuals

class GTree.GTreeNode(data, parent=None)

The GTreeNode class - The node representation

Inheritance diagram for GTree.GTreeNode:

Parameters:

• data – the root node of the tree
• parent – the parent node, if root, this must be None

addChild(child)

Adds a child to the node

Parameters:child – the node to be added

clone()

Return a new instance of the genome

Return type:new GTree instance

copy(g)

Copy the contents to the destination g

Parameters:g – the GTreeNode genome destination

getChild(index)

Returns the index-child of the node

Return type:child node

getChilds()

Return the childs of the node

Warning

use .getChilds()[:] if you’ll change the list itself, like using childs.reverse(), otherwise the original genome child order will be changed.

Return type:a list of nodes

getData()

Return the data of the node

Return type:the data of the node

getParent()

Get the parent node of the node

Return type:the parent node

isLeaf()

Return True if the node is a leaf

Return type:True or False

newNode(data)

Created a new child node

Parameters:data – the data of the new created node

replaceChild(older, newer)

Replaces a child of the node

Parameters:

• older – the child to be replaces
• newer – the new child which replaces the older

setData(data)

Sets the data of the node

Parameters:data – the data of the node

setParent(parent)

Sets the parent of the node

Parameters:parent – the parent node

swapNodeData(node)

Swaps the node data with another node

Parameters:node – the node to do the data swap

class GTree.GTreeNodeGP(data, node_type=0, parent=None)

The GTreeNodeGP Class - The Genetic Programming Node representation

Inheritance diagram for GTree.GTreeNodeGP:

Parameters:

• data – the node data
• type – the node type
• parent – the node parent

addChild(child)

Adds a child to the node

Parameters:child – the node to be added

clone()

Return a new copy of the node

Return type:the new GTreeNodeGP instance

compare(other)

Compare this node with other

Parameters:other – the other GTreeNodeGP

copy(g)

Copy the contents to the destination g

Parameters:g – the GTreeNodeGP genome destination

getChild(index)

Returns the index-child of the node

Return type:child node

getChilds()

Return the childs of the node

Warning

use .getChilds()[:] if you’ll change the list itself, like using childs.reverse(), otherwise the original genome child order will be changed.

Return type:a list of nodes

getData()

Gets the node internal data

Return type:the internal data

getParent()

Get the parent node of the node

Return type:the parent node

getType()

Get the node type

Return type:the node type is type of Consts.nodeType

isLeaf()

Return True if the node is a leaf

Return type:True or False

newNode(data)

Creates a new node and adds this node as children of current node

Parameters:data – the internal node data

replaceChild(older, newer)

Replaces a child of the node

Parameters:

• older – the child to be replaces
• newer – the new child which replaces the older

setData(data)

Sets the node internal data

Parameters:data – the internal data

setParent(parent)

Sets the parent of the node

Parameters:parent – the parent node

setType(node_type)

Sets the node type

Parameters:node_type – the node type is type of Consts.nodeType

swapNodeData(node)

Swaps the node data and type with another node

Parameters:node – the node

GTree.buildGTreeFull(depth, value_callback, max_siblings, max_depth)

Random generates a Tree structure using the value_callback for data generation and the method “Full”

Parameters:

• depth – the initial depth, zero
• value_callback – the function which generates the random values for nodes
• max_siblings – the maximum number of sisters of a node
• max_depth – the maximum depth of the tree

Return type:

the root node of created tree

GTree.buildGTreeGPFull(ga_engine, depth, max_depth)

Creates a new random GTreeGP root node with subtrees using the “Full” method.

Parameters:

• ga_engine – the GA Core
• depth – the initial depth

Max_depth :

the maximum depth of the tree

Return type:

the root node

GTree.buildGTreeGPGrow(ga_engine, depth, max_depth)

Creates a new random GTreeGP root node with subtrees using the “Grow” method.

Parameters:

• ga_engine – the GA Core
• depth – the initial depth

Max_depth :

the maximum depth of the tree

Return type:

the root node

GTree.buildGTreeGrow(depth, value_callback, max_siblings, max_depth)

Random generates a Tree structure using the value_callback for data generation and the method “Grow”

Parameters:

• depth – the initial depth, zero
• value_callback – the function which generates the random values for nodes
• max_siblings – the maximum number of sisters of a node
• max_depth – the maximum depth of the tree

Return type:

the root node of created tree

GTree.checkTerminal(terminal)

Do some check on the terminal, to evaluate ephemeral constants

Parameters:terminal – the terminal string

GTree.gpdec(**kwds)

This is a decorator to use with genetic programming non-terminals

It currently accepts the attributes: shape, color and representation.