def randomize( self, nMax, np, cp, p = 0.500000 ): '''Randomizes this genome by creating a directed graph containing up to nMax nodes. Sets the number of node and connection parameters to np and cp, respectively. The optional connection probability, p, specifies the probability that a connection will be made from one node to another.''' count = 0 nodes = breve.objectList() m = None n = None connection = None keep = breve.hash() self.deleteRootNode() count = ( breve.randomExpression( ( nMax - 1 ) ) + 1 ) if ( count < 2 ): count = ( count + 1 ) nodes = breve.createInstances( breve.GADirectedGraphNodes, count ) nodes.setParameterLength( np ) nodes.randomizeParameters() for n in nodes: for m in nodes: if ( ( n != m ) and ( breve.randomExpression( 1.000000 ) < p ) ): connection = n.connect( m, [] ) connection.setParameterLength( cp ) connection.randomizeParameters() self.rootNode = self.pickRootNode( nodes ) if ( not self.rootNode ): self.rootNode = breve.createInstances( breve.GADirectedGraphNode, 1 ) self.rootNode.setParameterLength( np ) self.rootNode.randomizeParameters() for n in self.rootNode.getConnectedNodes(): keep[ n ] = 1 for n in nodes: if ( not keep[ n ] ): breve.deleteInstances( n ) self.addDependency( self.rootNode )
def __init__( self ): breve.Abstract.__init__( self ) self.blueChemicalMatrix = None self.chemicalConcentrationMatrix = breve.hash() self.chemicals = breve.objectList() self.diffusingChemicals = breve.objectList() self.exponentiallyDecayingChemicals = breve.objectList() self.greenChemicalMatrix = None self.gridPointer = None self.linearlyDecayingChemicals = breve.objectList() self.location = breve.vector() self.patchSize = breve.vector() self.patchVolume = 0 self.patches = breve.objectList() self.redChemicalMatrix = None self.tempMatrix = None self.xSize = 0 self.ySize = 0 self.zSize = 0
def randomize(self, nMax, np, cp, p=0.500000):
'''Randomizes this genome by creating a directed graph containing up to nMax nodes. Sets the number of node and connection parameters to np and cp, respectively. The optional connection probability, p, specifies the probability that a connection will be made from one node to another.'''
count = 0
nodes = breve.objectList()
m = None
n = None
connection = None
keep = breve.hash()
self._nodeParamCount = np
self._connParamCount = cp
self.deleteRootNode()
count = (breve.randomExpression((nMax - 1)) + 1)
if (count < 2):
count = (count + 1)
nodes = breve.createInstances(breve.GADirectedGraphNodes, count)
nodes.setParameterLength(np)
nodes.randomizeParameters()
for n in nodes:
for m in nodes:
if ((n != m) and (breve.randomExpression(1.000000) < p)):
connection = n.connect(m, [])
connection.setParameterLength(cp)
connection.randomizeParameters()
self.rootNode = self.pickRootNode(nodes)
if (not self.rootNode):
self.rootNode = breve.createInstances(breve.GADirectedGraphNode, 1)
self.rootNode.setParameterLength(np)
self.rootNode.randomizeParameters()
for n in self.rootNode.getConnectedNodes():
keep[n] = 1
for n in nodes:
if (not keep[n]):
breve.deleteInstances(n)
self.addDependency(self.rootNode)
def destroyConnectedObjects( self ): '''Initiates a recursive freeing of this object and all connected objects, both directly and indiretly connected.''' h = breve.hash() self.internalDestroyConnectedObjects( h )
def crossover( self, p1, p2 ): '''Sets this child's genome to be a genetic crossover of p1 and p2.''' positions = breve.hash() keep = breve.hash() childnodes = breve.objectList() nodes2 = breve.objectList() nodes1 = breve.objectList() source = None temp = None connection = None index = 0 n = 0 cross = 0 max = 0 first = 0 self.deleteRootNode() if breve.randomExpression( 1 ): temp = p1 p1 = p2 p2 = temp nodes1 = p1.getRoot().getConnectedNodes() nodes2 = p2.getRoot().getConnectedNodes() n = 0 while ( n < breve.length( nodes1 ) ): positions[ nodes1[ n ] ] = n n = ( n + 1 ) n = 0 while ( n < breve.length( nodes2 ) ): positions[ nodes2[ n ] ] = n n = ( n + 1 ) first = breve.randomExpression( 1 ) max = breve.length( nodes2 ) cross = breve.randomExpression( ( max - 1 ) ) if ( cross >= breve.length( nodes1 ) ): cross = breve.length( nodes1 ) if ( max < 2 ): childnodes.append( breve.createInstances( breve.GADirectedGraphNodes, 1 ) ) else: childnodes = breve.createInstances( breve.GADirectedGraphNodes, max ) n = 0 while ( n < max ): if ( n < cross ): source = nodes1[ n ] else: source = nodes2[ n ] childnodes[ n ].setParameters( source.getParameters() ) for connection in source.getConnections(): index = positions[ connection.getTarget() ] if ( index >= breve.length( childnodes ) ): index = breve.randomExpression( ( breve.length( childnodes ) - 1 ) ) childnodes[ n ].connect( childnodes[ index ], connection.getParameters() ) n = ( n + 1 ) self.rootNode = self.pickRootNode( childnodes ) if ( not self.rootNode ): self.rootNode = childnodes[ 0 ] keep[ self.rootNode ] = 1 for temp in self.rootNode.getConnectedNodes(): keep[ temp ] = 1 for temp in childnodes: if ( not keep[ temp ] ): print '''freeing ''', temp breve.deleteInstances( temp ) self.addDependency( self.rootNode )
def printConnectedObjects(self):
'''Initiates a recursive printing of all connected objects in the graph.'''
h = breve.hash()
self.printConnectedObjectsInternal(h)
def destroyConnectedObjects(self):
"""Initiates a recursive freeing of this object and all connected objects, both directly and indiretly connected."""
h = breve.hash()
self.destroyConnectedObjectsInternal(h)
def __init__(self):
breve.GeneticAlgorithm.__init__(self)
self.h = breve.hash()
SimsGA.init(self)
def printConnectedObjects( self ): '''Initiates a recursive printing of all connected objects in the graph.''' h = breve.hash() self.printConnectedObjects( h )
def crossover(self, p1, p2):
'''Sets this child's genome to be a genetic crossover of p1 and p2.'''
positions = breve.hash()
keep = breve.hash()
childnodes = breve.objectList()
nodes2 = breve.objectList()
nodes1 = breve.objectList()
source = None
temp = None
connection = None
index = 0
n = 0
cross = 0
max = 0
first = 0
self._connParamCount = p1['_connParamCount']
self._nodeParamCount = p1['_nodeParamCount']
self.deleteRootNode()
if breve.randomExpression(1):
temp = p1
p1 = p2
p2 = temp
nodes1 = p1.getRoot().getConnectedNodes()
nodes2 = p2.getRoot().getConnectedNodes()
n = 0
while (n < breve.length(nodes1)):
positions[nodes1[n]] = n
n = (n + 1)
n = 0
while (n < breve.length(nodes2)):
positions[nodes2[n]] = n
n = (n + 1)
first = breve.randomExpression(1)
max = breve.length(nodes2)
cross = breve.randomExpression((max - 1))
if (cross >= breve.length(nodes1)):
cross = breve.length(nodes1)
if (max < 2):
childnodes.append(
breve.createInstances(breve.GADirectedGraphNodes, 1))
else:
childnodes = breve.createInstances(breve.GADirectedGraphNodes, max)
n = 0
while (n < max):
if (n < cross):
source = nodes1[n]
else:
source = nodes2[n]
childnodes[n].setParameters(source.getParameters())
for connection in source.getConnections():
index = positions[connection.getTarget()]
if (index >= breve.length(childnodes)):
index = breve.randomExpression(
(breve.length(childnodes) - 1))
childnodes[n].connect(childnodes[index],
connection.getParameters())
n = (n + 1)
self.rootNode = self.pickRootNode(childnodes)
if (not self.rootNode):
self.rootNode = childnodes[0]
keep[self.rootNode] = 1
for temp in self.rootNode.getConnectedNodes():
keep[temp] = 1
for temp in childnodes:
if (not keep[temp]):
breve.deleteInstances(temp)
self.addDependency(self.rootNode)
def __init__( self ): breve.GeneticAlgorithmIndividual.__init__( self ) self.genome = None self.h = breve.hash() SimsGAIndividual.init( self )
def __init__( self ): breve.GeneticAlgorithm.__init__( self ) self.h = breve.hash() SimsGA.init( self )
def printConnectedObjects(self):
"""Initiates a recursive printing of all connected objects in the graph."""
h = breve.hash()
self.printConnectedObjectsInternal(h)
def getConnectedNodes(self):
"""Recursively generates a list of all nodes connected to this root node, both directly and indirectly."""
h = breve.hash()
return self.getConnectedNodesInternal(h, [])
def duplicate(self):
"""Duplicates the object, which triggers recursive duplication of all connected objects. To be used on root nodes only."""
h = breve.hash()
return self.duplicateInternal(h)
def getConnectedNodes( self ): '''Recursively generates a list of all nodes connected to this root node, both directly and indirectly.''' h = breve.hash() return self.internalGetConnectedNodes( h, [] )
def mutate( self ): '''Mutates the object, which triggers recursive mutation of all connected objects. To be used on root nodes only.''' h = breve.hash() return self.mutate( h )
def destroyConnectedObjects(self):
'''Initiates a recursive freeing of this object and all connected objects, both directly and indiretly connected.'''
h = breve.hash()
self.destroyConnectedObjectsInternal(h)
def getConnectedNodes(self):
'''Recursively generates a list of all nodes connected to this root node, both directly and indirectly.'''
h = breve.hash()
return self.getConnectedNodesInternal(h, [])
def mutate(self):
'''Mutates the object, which triggers recursive mutation of all connected objects. To be used on root nodes only.'''
h = breve.hash()
return self.mutateInternal(h)
def __init__(self):
breve.GeneticAlgorithmIndividual.__init__(self)
self.genome = None
self.h = breve.hash()
SimsGAIndividual.init(self)
def duplicate(self):
'''Duplicates the object, which triggers recursive duplication of all connected objects. To be used on root nodes only.'''
h = breve.hash()
return self.duplicate(h)
