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TreeOrganism.py
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TreeOrganism.py
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"""
Class : Computer Architecture, FALL 2011, Olin College
Project :
Author : Shane Moon, Paul Booth
Date : 11/24/2011
File Name : TreeOrganism.py
Description :
"""
import random
import testOrgs
import Organism
import Tree
from Terminator import AbstractTerminator
import ete2a1 as ete2
class TreeOrganism(Organism.AbstractOrganism):
treeCrossOverProbability = .7
treeMutateProbability = .1
def __init__(self, verilogFilePath, numInputs, numOutputs,
randomInit=False, maxDepth=10, inputProbability = .5, moduleName='organism'):
# inputProbability should be reconsidered, and not just passed in
# We should develop a way to decide what this value should be
self.maxDepth = maxDepth
self.inputProbability = inputProbability
self.trees = []
#print moduleName,'here'
Organism.AbstractOrganism.__init__(self, verilogFilePath,
numInputs, numOutputs, randomInit=randomInit,
moduleName=moduleName)
def __str__(self):
return self.toEteTree().get_ascii(show_internal=True)
def visualize(self, filename):
Tree.eteVisualize(self.toEteTree(), filename)
def toEteTree(self):
"""
Return Type: <ete2.Tree>
"""
raw = ""
for i in range(len(self.trees)):
raw += "(%s)out%s," %(self.trees[i].root.__str__(), str(i))
return ete2.Tree("(%s)org;" %raw[0:-1], format = 1)
def randomInitialize(self):
"""
Return Type: void
"""
for i in range(self.numOutputs):
self.trees.append(
Tree.Tree(
self.numInputs, self.maxDepth,self.inputProbability)
)
def crossover(self, otherParent):
"""
Return Type: <TreeOrganism>
Crossovers self with another <TreeOrganism>, and returns a new
<TreeOrganism>.
"""
result = TreeOrganism(self.verilogFilePath, self.numInputs,
self.numOutputs, randomInit=False, maxDepth=self.maxDepth,
inputProbability=self.inputProbability, moduleName=self.moduleName)
for i in range(self.numOutputs):
selfTree = self.trees[i]
otherTree = otherParent.trees[i]
if (random.random() > TreeOrganism.treeCrossOverProbability):
#print "not crosovered"
if (random.random() < .5):
result.trees.append(selfTree)
else:
result.trees.append(otherTree)
else:
#print "crosovered"
if (random.random() < .5):
result.trees.append(selfTree.crossover(otherTree))
else:
result.trees.append(otherTree.crossover(selfTree))
return result
def mutate(self):
"""
Return Type: void
Mutates stuff
"""
for i in range(len(self.trees)):
if (random.random() < TreeOrganism.treeMutateProbability):
self.trees[i].mutate()
def toVerilog(self, filepath, moduleName):
"""
Writes Organism to a verilog file.
"""
moduleInputs = ['input%d'%i for i in xrange(self.numInputs)]
moduleInputsTxt = ','.join(moduleInputs)
moduleOutputsTxt = ','.join('output%d'%i for i in xrange(self.numOutputs))
moduleArgsTxt = '%s,%s'%(moduleOutputsTxt,moduleInputsTxt)
layerTxts = ['\toutput %s;'%moduleOutputsTxt,'\tinput %s;'%moduleInputsTxt]
for idx,tree in enumerate(self.trees):
# self.gate -> what type of gate it is
layerTxts.append(tree.toVerilog(idx)+'\n')
body = '\n'.join(layerTxts)
fin = open(filepath,'w')
fin.write(Organism.verilogFromTemplate(moduleName,moduleArgsTxt,body))
fin.close()
def fitnessFunction(self,inputs,actualOutputs,correctOutputs):
"""
Return Type: float
"""
# Needs to be implemented #
bonus = 0.0
numCorrectOutputs = 0
for i in xrange(self.numOutputs):
if all( correctOutputs[idx][i] == a[i] for idx,a in enumerate(actualOutputs) ):
numCorrectOutputs += 1
bonus += sum(
int(correctOutputs[idx][i] == a[i])
for idx,a in enumerate(actualOutputs) ) / float(len(actualOutputs))
self.numCorrectOutputs = numCorrectOutputs
return (bonus+numCorrectOutputs*2.0) - self.count()/1000. #**2 + 0.1 - self.count()/1000. #+ random.random()
def getTrees(self):
return self.trees
def replaceTree(self, tree, index):
self.trees[index] = tree
def count(self):
return sum(tree.count() for tree in self.trees)
class TreeOrganismTerminator(AbstractTerminator):
def __init__(self, maxNumberOfGates, maxNumberOfGenerations):
self.maxNumberOfGates = maxNumberOfGates
AbstractTerminator.__init__(self,maxNumberOfGenerations)
def isFinished(self,organism,generationNumber):
self.currentBestOrganism = organism
if generationNumber > self.maxNumberOfGenerations:
end = True
self.success = False
else:
if organism.numCorrectOutputs == organism.numOutputs and \
organism.count() < self.maxNumberOfGates:
end = True
self.success = True
else:
end = False
self.success = False
return end
if __name__ == '__main__':
#defaultResult = testOrgs.testOrganism('fourBoolCorrect.v', '', 4, 2, 'fourBool',clearFiles=True)
#simMap = testOrgs.SimulationMap(defaultResult)
#a = TreeOrganism('fourBool.v',4,2,randomInit=True,moduleName='fourBool')
#b = a.evaluate(simMap)
#print a
#print b
tree1 = TreeOrganism('tree.v',4,2,randomInit=True,maxDepth=3,moduleName='tree')
tree2 = TreeOrganism('tree.v',4,2,randomInit=True,maxDepth=3,moduleName='tree')
print "--------------------------------------"
print tree1
print "--------------------------------------"
print tree2
print "--------------------------------------"
print tree1.crossover(tree2)
print "--------------------------------------"
tree1.visualize('test.png')
#tree1.toVerilog('delme.v','delme')
#print 'toVerilog() method test successful (no errors)'