OrganismManager.py

"""
    Class       : Computer Architecture, FALL 2011, Olin College
    Project     : 
    Author      : Shane Moon, Paul Booth
    Date        : 11/10/2011
    File Name   : OrganismManager.py
    Description :
"""

import testOrgs
import random
import selector
import matplotlib.pyplot as pyplot
from copy import deepcopy
import os
import cProfile
import pstats
import matplotlib.pyplot as pyplot
from TreeOrganism import TreeOrganism

class OrganismManager:
    def __init__(self, organismType, population, survival, mutateNum, terminator, 
        resultMap, verilogWriteFileName = 'organism.v', 
        verilogModuleName = None, **kwargs):
        """
            organisms  : <List> of <Organism>s
            population : the maximum number of <Organism>s
            survival   : the number of <Organism>s that will survive
                         each generation
            mutateNum  : the number of <Organism>s that will be only mutated
                         The other organisms will be crossovered, not mutated
            threshold  : fitness at which the simulation stops
            resultMap  : <testOrgs.SimulationMap> of correct behavior
        """
        assert (survival > 0), "At least one Organism should survive."
        assert (population > 0), "At least one Organism should exist."
        assert (population >= survival + mutateNum), \
                                         "population should be greater than " \
                                         "survival and mutateNum."
        
        self.generationNumber = 0
        
        self.organismType = organismType
        
        self.organisms = []
        self.population = population
        self.survival = survival
        self.mutateNum = mutateNum
        self.terminator = terminator

        self.crossoverNum = population - (survival + mutateNum)
        
        self._resultMap = resultMap
        self._numberOfInputs = resultMap.getNumberOfInputs()
        self._numberOfOutputs = resultMap.getNumberOfOutputs()
        
        self._selectorPmf = None
        
        self.verilogWriteFileName = verilogWriteFileName
        
        if verilogModuleName is None:
            verilogModuleName = verilogWriteFileName.split('.')[0]
            
        self.verilogModuleName = verilogModuleName
        
        self.kwargs = kwargs

    def __str__(self):
        s = "Population : %i \n" % (self.population)
        s += '\n'.join(str(organism) for organism in self.organisms)
        return s

    def getNumberOfInputs(self):
        return self._numberOfInputs
    
    def getNumberOfOutputs(self):
        return self._numberOfOutputs

    def _updateSelectorPmf(self):
        
        self._selectorPmf = selector.MakeOrganismPmfFromOrganisms(self.organisms)

    def selectOrganism(self):
        """
            Return Type: <Organism>
            Selects one <Organism> from the list, with higher possibility
            of choosing the one with higher fitness.
        """
        
        return self._selectorPmf.Random()

    def generateParents(self):
        generatorPmf = self._selectorPmf.Copy()
        parent1 = generatorPmf.Random()
        generatorPmf.Remove(parent1)
        generatorPmf.Normalize()
        parent2 = generatorPmf.Random()
        return parent1,parent2

    def updateOrganisms(self,visualize=False):
        """
            Return Type: void
            1. Keep (self.survival) <Organism>s from the
               previous generation based on fitness
            2. Selects two <Organism>s from the list, crossover them and add
               a new <Organism>
            3. Repeat 2. (population - survival) times
            4. Sort the list by their fitness.
        """
        newGeneration = [];
        generatorPmf = self._selectorPmf.Copy()
        for i in range(self.survival):
            replicatedOrganism = generatorPmf.Random()
            generatorPmf.Remove(replicatedOrganism)
            generatorPmf.Normalize()
            newGeneration.append(replicatedOrganism)
        
        generatorPmf = self._selectorPmf
        for i in range(self.mutateNum):
            replicatedOrganism = deepcopy(generatorPmf.Random())
            replicatedOrganism.mutate()
            newGeneration.append(replicatedOrganism)

        for i in range(self.crossoverNum):
            p1,p2 = self.generateParents()
            # print parent1, "\nORGANISM crossing over with\n", parent2
            newOrganism = p1.crossover(p2)
            newGeneration.append(newOrganism)
        
        map( lambda organism : organism.evaluate(self._resultMap),
             newGeneration)
        
        self.organisms = newGeneration
        self._updateSelectorPmf()
        
        if visualize:
            self.visualize()

    def populate(self,visualize=True):
        """
            Return Type: void
            Populates <Organism>s and store them in self.organisms
        """
        
        for i in range(self.population):
            randOrganism = self.getRandomOrganism()
            self.organisms.append(randOrganism)
        self._updateSelectorPmf()
        
        if visualize:
            self.visualize()

    def getRandomOrganism(self):
        randOrganism = self.organismType(
            self.verilogWriteFileName,
            self.getNumberOfInputs(),
            self.getNumberOfOutputs(),
            randomInit=True,
            moduleName=self.verilogModuleName,
            **self.kwargs
            )
        
        randOrganism.evaluate(self._resultMap)
        return randOrganism

    def execute(self,visualize=False, filename=""):
        """
            Return Type: void
            MainLoop
        """
        self.writeSimulation()
        self.populate(visualize)
        
        key = lambda org: org.getFitness()
        
        if visualize:
            pyplot.ion()
        
        while not self.terminator.isFinished(
            max(self.organisms,key=key),self.generationNumber
            ):
            self.generationNumber += 1
            self.updateOrganisms(visualize)
        
        bestOrganism = self.terminator.getBestOrganism()
        print "final fitness: ", bestOrganism.getFitness()
        bestOrganism.toVerilog('Winner.v', self.verilogModuleName)
        
        if visualize:
            pyplot.show()
            pyplot.ioff()

            if isinstance(bestOrganism,TreeOrganism):
                bestOrganism.visualize(filename)
        
        return (self.terminator.getSuccess(),self.generationNumber)
        #self.deleteSimulation()
    
    def writeSimulation(self):
        testOrgs.writeSimulation(
            os.path.join('TestCode','%s.v'%'organismTest'),
            self.verilogWriteFileName,
            self._numberOfInputs,
            self._numberOfOutputs,
            self.verilogModuleName
        )
        
    def deleteSimulation(self):
        try:
            os.remove(os.path.join('TestCode','%s.v'%'organismTest'))
            os.remove(os.path.join('TestCode','%s.v'%'organismTest'))
        except:
            print "Error clearing files!"
            print "Files are to be cleared, but the files probably don't exist."
    
    def visualize(self):
        selector.drawOrganismPmfAsCdf(
            self._selectorPmf, self.generationNumber,
            max(self.organisms,key=lambda org: org.getFitness()).getFitness()
        )

def main():
    
    import testOrgs
    from BooleanLogic import BooleanLogicOrganism
    from TreeOrganism import TreeOrganism, TreeOrganismTerminator
    
    defaultResult = testOrgs.testOrganism('fourBoolCorrect.v', '', 4, 4,'fourBool',clearFiles=True)
    #defaultResult = testOrgs.testOrganism('b4mux.v', '', 6, 1,'b4_1mux',clearFiles=True)
    #defaultResult = testOrgs.testOrganism('4bAdder.v', '', 8, 5,'fourBitAdder',clearFiles=True)
    simMap = testOrgs.SimulationMap(defaultResult)
    
    #manager = OrganismManager(BooleanLogicOrganism,
    #    10,2,16,simMap,verilogWriteFileName = 'fourBool.v',nLayers = 1)
    #manager = OrganismManager(TreeOrganism,
    #    15,3,1,simMap,verilogWriteFileName = 'b4mux_organism.v',
    #    maxDepth=10,inputProbability=.15)
    
    manager = OrganismManager(TreeOrganism,50,12,13,
        TreeOrganismTerminator(30,500),simMap,verilogWriteFileName='fourBool.v',
        maxDepth=3,inputProbability=.8)
    #manager = OrganismManager(TreeOrganism,
    #    100,10,25,simMap,verilogWriteFileName = 'fourBitAdder_organism.v',
    #    maxDepth=3,inputProbability=.2)
        
    success, numberOfGenerations = manager.execute(True)
    print success, numberOfGenerations

def profile():
    cProfile.run('main()', 'profileResults')
    p = pstats.Stats('profileResults')
    p.strip_dirs().sort_stats( 'cum').print_stats(15)

if __name__ == '__main__':
    main()
    #profile()