def evalFunc_Availability(individual, Original, constraints=[]):
userSize = Original.shape[0]
permissionSize = Original.shape[1]
accs = statistics.Accs(individual[0], Original)
if (constraints and
not feasible(individual, userSize, permissionSize, constraints)):
worstCase_accs = Original.sum()
fitness = worstCase_accs
else:
fitness = accs
return fitness,
def printStatistics(population, OriginalFile, topk=1):
Original = numpy.matrix(parser.read(OriginalFile))
#top_inds = population
top_inds = tools.selNSGA2(population, k=topk)
i = 0
for top_ind in top_inds:
conf = statistics.Conf(top_ind[0], Original)
accs = statistics.Accs(top_ind[0], Original)
roleCnt = statistics.RoleCnt(top_ind[0])
urCnt = statistics.URCnt(top_ind[0])
rpCnt = statistics.RPCnt(top_ind[0])
print("\nTOP INDIVIDUAL: " + str(i))
print("conf: " + str(conf))
print("accs: " + str(accs))
print("roleCnt: " + str(roleCnt))
print("urCnt: " + str(urCnt))
print("rpCnt: " + str(rpCnt))
i += 1
def evalFunc_AvgRoleConfViolations_Availability(individual,
Original,
constraints=[]):
numberOfRoles = len(individual[0])
userSize = Original.shape[0]
permissionSize = Original.shape[1]
accs = statistics.Accs(individual[0], Original)
if (constraints and
not feasible(individual, userSize, permissionSize, constraints)):
worstCase_fitness = 3
fitness = worstCase_fitness
else:
sumOfRoleConfViolations = 0
for r in range(0, numberOfRoles):
role_array = decoder.resolveGeneIntoBoolArray(
individual[0][r], userSize, permissionSize)
role_conf, role_accs = matrixOps.compareMatrices(
role_array, Original)
sumOfRoleConfViolations += role_conf
avgRoleConfViolation = sumOfRoleConfViolations / numberOfRoles
worstCase_avgRoleConfViolation = Original.size - Original.sum()
bestCase_avgRoleConfViolation = 0
range_avgRoleConfViolation = worstCase_avgRoleConfViolation - bestCase_avgRoleConfViolation + 1
avgRoleConfViolation_normalized = (avgRoleConfViolation -
bestCase_avgRoleConfViolation +
1) / range_avgRoleConfViolation
worstCase_accs = Original.sum(
) # All permissions are assigned directly to user
bestCase_accs = 0 # No direct assignements required
range_accs = worstCase_accs - bestCase_accs + 1
accs_normalized = (accs - bestCase_accs + 1) / range_accs
fitness = avgRoleConfViolation_normalized + accs_normalized
return fitness,
def evolution_multi(Original,
evalFunc,
populationSize,
CXPB,
addRolePB,
removeRolePB,
removeUserPB,
removePermissionPB,
addUserPB,
addPermissionPB,
NGEN,
freq,
numberTopRoleModels,
optimization,
fortin=False,
untilSolutionFound=False,
pickleFile="",
checkpoint=False,
prevFiles="",
userAttributeValues=[],
constraints=[],
printPopulations=False,
pop_directory="",
fixedRoleCnt=0):
# Validations
if (len(evalFunc) < 2):
raise ValueError("Less than 2 objectives not possible")
if (len(evalFunc) > 3):
raise ValueError("More than 3 objectives not supported")
if (not (populationSize % 4 == 0)):
raise ValueError("Population size has to be a multiple of 4")
logger.debug("Prepare evolutionary algorithm...")
time = []
results = defaultdict(list)
genStart = 0
population = []
# Create Logbook
logbook = tools.Logbook()
# Register Optimization
weights = ()
for obj in evalFunc:
if (obj == "FBasic" or obj == "FEdge"):
weights += (1.0, )
else:
weights += (-1.0, )
creator.create("FitnessMinMax", base.Fitness, weights=weights)
creator.create("Individual", list, fitness=creator.FitnessMinMax)
# Get Checkpoint
'''if (checkpoint and len(prevFiles)!=0):
prevFile = prevFiles[0]
if (os.path.isfile(prevFile)):
print("Read checkpoint...")
cp = pickle.load(open(prevFile, "rb"))
population = cp["population"]
genStart = int(cp["generation"])
Original = cp["Original"]
results=cp["results"]
time=cp["time"]
prevFiles=cp["prevFiles"]
prevFiles.append(prevFile)
logbook=cp["logbook"]
random.setstate(cp["rndstate"])
print("DONE.\n")
else:
print("Checkpoint file does not exit")
else:
print("Use checkpoint: False")
checkpoint = False'''
userSize = int(Original.shape[0])
permissionSize = int(Original.shape[1])
# Toolbox
toolbox = base.Toolbox()
# Chromosome generator
toolbox.register("chromosome",
init.generateChromosome,
userSize,
userSize,
permissionSize,
optimization=optimization,
fixedRoleCnt=fixedRoleCnt)
# Structure initializers
toolbox.register("individual", tools.initRepeat, creator.Individual,
toolbox.chromosome, 1)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
# Genetic Operators
toolbox.register("evaluate",
evals.evalFunc_Multi,
Original=Original,
evalFunc=evalFunc,
userAttributeValues=userAttributeValues,
constraints=constraints)
toolbox.register("mate", operators.mateFunc, optimization=optimization)
toolbox.register("mutate",
operators.mutFunc,
addRolePB=addRolePB,
removeRolePB=removeRolePB,
removeUserPB=removeUserPB,
removePermissionPB=removePermissionPB,
addUserPB=addUserPB,
addPermissionPB=addPermissionPB,
userSize=userSize,
permissionSize=permissionSize,
optimization=[optimization, optimization])
if (fortin):
toolbox.register("preselect", fortin2013.selTournamentFitnessDCD)
toolbox.register("select", fortin2013.selNSGA2)
else:
toolbox.register("preselect", tools.selTournamentDCD)
toolbox.register("select", tools.selNSGA2)
# Register statistics
statsConf = tools.Statistics(
key=lambda ind: statistics.Conf(ind[0], Original))
statsAccs = tools.Statistics(
key=lambda ind: statistics.Accs(ind[0], Original))
statsRoleCnt = tools.Statistics(key=lambda ind: statistics.RoleCnt(ind[0]))
statsURCnt = tools.Statistics(key=lambda ind: statistics.URCnt(ind[0]))
statsRPCnt = tools.Statistics(key=lambda ind: statistics.RPCnt(ind[0]))
statsInterp = tools.Statistics(
key=lambda ind: statistics.Interp(ind[0], userAttributeValues))
mstats = None
if (len(evalFunc) >= 2):
statsFitness1 = tools.Statistics(key=lambda ind: ind.fitness.values[0])
statsFitness2 = tools.Statistics(key=lambda ind: ind.fitness.values[1])
mstats = tools.MultiStatistics(fitnessObj1=statsFitness1,
fitnessObj2=statsFitness2,
Conf=statsConf,
Accs=statsAccs,
RoleCnt=statsRoleCnt,
URCnt=statsURCnt,
RPCnt=statsRPCnt,
Interp=statsInterp)
if (len(evalFunc) == 3):
statsFitness3 = tools.Statistics(key=lambda ind: ind.fitness.values[2])
mstats = tools.MultiStatistics(fitnessObj1=statsFitness1,
fitnessObj2=statsFitness2,
fitnessObj3=statsFitness3,
Conf=statsConf,
Accs=statsAccs,
RoleCnt=statsRoleCnt,
URCnt=statsURCnt,
RPCnt=statsRPCnt,
Interp=statsInterp)
mstats.register("avg", numpy.mean)
mstats.register("std", numpy.std)
mstats.register("min", numpy.min)
mstats.register("max", numpy.max)
logbook.header = "gen", "evals"
for o in range(1, len(evalFunc) + 1):
logbook.chapters["fitnessObj" +
str(o)].header = "min", "avg", "max", "std"
logbook.chapters["Conf"].header = "min", "avg", "max", "std"
logbook.chapters["Accs"].header = "min", "avg", "max", "std"
logbook.chapters["RoleCnt"].header = "min", "avg", "max", "std"
logbook.chapters["URCnt"].header = "min", "avg", "max", "std"
logbook.chapters["RPCnt"].header = "min", "avg", "max", "std"
logbook.chapters["Interp"].header = "min", "avg", "max", "std"
# Creating the population
if (not population):
logger.info("Generate new population of " + str(populationSize) +
" individuals")
population = toolbox.population(n=populationSize)
solutionFound = [None, None, None]
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if (fit[0] == 0):
solutionFound[0] = 0
if (fit[1] == 0):
solutionFound[1] = 0
if (max(fit) == 0):
solutionFound[2] = 0
# Save population in JSON file
if (printPopulations):
pop_subdirectory = pop_directory + "\\Generation_" + str(genStart)
#if not os.path.exists(pop_subdirectory):
# os.makedirs(pop_subdirectory)
utils.saveDiversity(genStart, population,
pop_subdirectory + "_diversity.json")
utils.savePopulation(genStart, population,
pop_subdirectory + "_population.pkl")
#visual.showBestResult(population, genStart, Original, pop_subdirectory+"\\Individual", "Individual", "Individual from Generation "+str(genStart), False, False, True, False)
# Log statistics for first generation
if ((len(logbook) == 0)
or (logbook.pop(len(logbook) - 1)["gen"] != genStart)):
record = mstats.compile(population)
logbook.record(gen=genStart, evals=len(invalid_ind), **record)
printText = "Generation " + str(genStart) + ":\t" + str(
logbook.stream) + "\n"
for o in range(1, len(evalFunc) + 1):
printText += "\n" + str(
logbook.chapters["fitnessObj" + str(o)].stream)
printText += str(logbook.chapters["Conf"].stream)+"\n"\
+str(logbook.chapters["Accs"].stream)+"\n"+\
str(logbook.chapters["RoleCnt"].stream)+"\n"\
+str(logbook.chapters["URCnt"].stream)+"\n"\
+str(logbook.chapters["RPCnt"].stream)+"\n"\
+str(logbook.chapters["Interp"].stream)
logger.info(printText)
# Begin the evolution
logger.info("Start evolution...")
start = datetime.datetime.now()
logger.info("Start time: " + str(start))
#hof = tools.HallOfFame(maxsize=1)
# This is just to assign the crowding distance to the individuals
# no actual selection is done
population = toolbox.select(population, len(population))
generation = genStart + 1
stop = False
logger.info("Start evolution with Generation " + str(genStart))
while ((not stop) and (generation <= genStart + NGEN)):
# Vary the population
offspring = toolbox.preselect(population, len(population))
offspring = [toolbox.clone(ind) for ind in offspring]
for ind1, ind2 in zip(offspring[::2], offspring[1::2]):
if random.random() <= CXPB:
toolbox.mate(ind1, ind2)
toolbox.mutate(ind1)
toolbox.mutate(ind2)
del ind1.fitness.values, ind2.fitness.values
#offspring = algorithms.varOr(population, toolbox, 100, cxpb=CXPB, mutpb=MUTPB)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if (not solutionFound[0] and fit[0] == 0):
solutionFound[0] = generation
if (not solutionFound[1] and fit[1] == 0):
solutionFound[1] = generation
if (not solutionFound[2] and max(fit) == 0):
solutionFound[2] = generation
#if (fit[0] == 0):
# stop = True
# Select the next generation population
population = toolbox.select(population + offspring, len(population))
# Add Fitness values to results
if generation % freq == 0:
for ind in population:
results[generation].append(ind.fitness.values)
# Log statistics for generation
record = mstats.compile(population)
logbook.record(gen=generation, evals=len(invalid_ind), **record)
printText = "Generation " + str(generation) + ":\t" + str(
logbook.stream) + "\t"
for o in range(1, len(evalFunc) + 1):
printText += str(
logbook.chapters["fitnessObj" + str(o)].stream) + "\t"
printText += str(logbook.chapters["Conf"].stream)+"\t"\
+str(logbook.chapters["Accs"].stream)+"\t"\
+str(logbook.chapters["RoleCnt"].stream)+"\t"\
+str(logbook.chapters["URCnt"].stream)+"\t"\
+str(logbook.chapters["RPCnt"].stream)+"\t"\
+str(logbook.chapters["Interp"].stream)
logger.info(printText)
if generation % int((genStart + NGEN) / 10) == 0:
if (printPopulations):
pop_subdirectory = pop_directory + "\\Generation_" + str(
generation)
#if not os.path.exists(pop_subdirectory):
# os.makedirs(pop_subdirectory)
utils.saveDiversity(generation, population,
pop_subdirectory + "_diversity.json")
utils.savePopulation(generation, population,
pop_subdirectory + "_population.pkl")
#visual.showBestResult(offspring, genStart, Original, pop_subdirectory+"\\Individual", "Individual", "Individual from Generation "+str(generation), False, False, True, False)
generation += 1
utils.printDiversity(pop_directory, int((genStart + NGEN) / 10))
utils.savePopulation(generation, population,
pop_subdirectory + "_population.pkl")
end = datetime.datetime.now()
timediff = end - start
time.append(timediff.total_seconds())
generation -= 1
# Print final population
#visual.printpopulation(population)
logger.info("==> Generation " + str(generation))
logger.info("DONE.\n")
# Set Checkpoint
fileExt = "_M"
for obj in evalFunc:
fileExt += "_" + obj[:5]
fileExt += "_" + str(len(population)) + "_" + str(generation)
'''if (checkpoint):
fileExt = "_cont_" + str(len(population)) + "_" + str(generation) + "_" + str(CXPB) + "_" + str(MUTPB_All)
pickleFile = "Checkpoint"+fileExt+".pkl"
print("Save checkpoint into "+str(pickleFile))
cp = dict(population=population,
generation=generation,
rndstate=random.getstate(),
Original=Original,
results=results,
time=time,
populationSize=populationSize,
CXPB=CXPB,
prevFiles=prevFiles,
MUTPB_All=MUTPB_All,
addRolePB=addRolePB,
removeRolePB=removeRolePB,
removeUserPB=removeUserPB,
removePermissionPB=removePermissionPB,
addUserPB=addUserPB,
addPermissionPB=addPermissionPB,
logbook=logbook)
pickle.dump(cp, open(pickleFile, "wb"), 2)
print("DONE.\n")'''
top = toolbox.select(population, k=numberTopRoleModels)
return population, results, generation, time, prevFiles, top, logbook, fileExt, solutionFound
def evolution(Original,
evalFunc,
populationSize,
tournsize,
CXPB,
MUTPB_All,
addRolePB,
removeRolePB,
removeUserPB,
removePermissionPB,
addUserPB,
addPermissionPB,
NGEN,
freq,
numberTopRoleModels,
optimization,
untilSolutionFound=False,
eval_weights=[],
pickleFile="",
checkpoint=False,
prevFiles="",
userAttributeValues=[],
constraints=[],
printPopulations=False,
pop_directory="",
fixedRoleCnt=0):
logger.info("Prepare evolutionary algorithm...")
time = []
results = defaultdict(list)
genStart = 0
population = []
# Create Logbook
logbook = tools.Logbook()
# Register Optimization
if (evalFunc == "FBasic" or evalFunc == "FEdge"):
creator.create("FitnessMinMax", base.Fitness,
weights=(1.0, )) # MAXIMIZATION
else:
creator.create("FitnessMinMax", base.Fitness,
weights=(-1.0, )) # MINIMIZATION
creator.create("Individual", list, fitness=creator.FitnessMinMax)
# Get Checkpoint
'''if (checkpoint and len(prevFiles)!=0):
prevFile = prevFiles[0]
if (os.path.isfile(prevFile)):
print("Read checkpoint...")
cp = pickle.load(open(prevFile, "rb"))
population = cp["population"]
genStart = int(cp["generation"])
Original = cp["Original"]
results=cp["results"]
time=cp["time"]
prevFiles=cp["prevFiles"]
prevFiles.append(prevFile)
logbook=cp["logbook"]
random.setstate(cp["rndstate"])
print("DONE.\n")
else:
raise ValueError("Checkpoint file does not exit")
else:
print("Use checkpoint: False")
checkpoint = False'''
userSize = int(Original.shape[0])
permissionSize = int(Original.shape[1])
# Toolbox
toolbox = base.Toolbox()
# Register Chromosome Generator
toolbox.register("chromosome",
init.generateChromosome,
maxRoles=userSize,
userSize=userSize,
permissionSize=permissionSize,
optimization=optimization,
fixedRoleCnt=fixedRoleCnt)
# Register Individual and Population Initializers
toolbox.register("individual", tools.initRepeat, creator.Individual,
toolbox.chromosome, 1)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
# Register Evaluation Function
if (evalFunc == "FBasic"):
toolbox.register("evaluate",
evals.evalFunc_FBasic,
Original=Original,
weights=eval_weights,
constraints=constraints)
elif (evalFunc == "FEdge"):
toolbox.register("evaluate",
evals.evalFunc_FEdge,
Original=Original,
weights=eval_weights,
constraints=constraints)
elif (evalFunc == "FBasicMin"):
toolbox.register("evaluate",
evals.evalFunc_FBasicMin,
Original=Original,
weights=eval_weights,
constraints=constraints)
elif (evalFunc == "FEdgeMin"):
toolbox.register("evaluate",
evals.evalFunc_FEdgeMin,
Original=Original,
weights=eval_weights,
constraints=constraints)
elif (evalFunc == "FBasicMin_INT"):
toolbox.register("evaluate",
evals.evalFunc_FBasicMin_INT,
Original=Original,
weights=eval_weights,
userAttributeValues=userAttributeValues,
constraints=constraints)
elif (evalFunc == "FEdgeMin_INT"):
toolbox.register("evaluate",
evals.evalFunc_FEdgeMin_INT,
Original=Original,
weights=eval_weights,
userAttributeValues=userAttributeValues,
constraints=constraints)
elif (evalFunc == "WSC"):
toolbox.register("evaluate",
evals.evalFunc_WSC,
Original=Original,
weights=eval_weights,
constraints=constraints)
elif (evalFunc == "WSC_Star"):
toolbox.register("evaluate",
evals.evalFunc_WSC_Star,
Original=Original,
weights=eval_weights,
constraints=constraints)
elif (evalFunc == "WSC_Star_RoleDis"):
toolbox.register("evaluate",
evals.evalFunc_WSC_Star_RoleDis,
Original=Original,
weights=eval_weights,
constraints=constraints)
elif (evalFunc == "Violations"):
toolbox.register("evaluate",
evals.evalFunc_Violations,
Original=Original,
constraints=constraints)
elif (evalFunc == "AvgRoleConf_A"):
toolbox.register("evaluate",
evals.evalFunc_AvgRoleConfViolations_Availability,
Original=Original,
constraints=constraints)
elif (evalFunc == "Confidentiality"):
toolbox.register("evaluate",
evals.evalFunc_Confidentiality,
Original=Original,
constraints=constraints)
elif (evalFunc == "Availability"):
toolbox.register("evaluate",
evals.evalFunc_Availability,
Original=Original,
constraints=constraints)
elif (evalFunc == "RoleCnt"):
toolbox.register("evaluate",
evals.evalFunc_RoleCnt,
Original=Original,
constraints=constraints)
elif (evalFunc == "URCnt"):
toolbox.register("evaluate",
evals.evalFunc_URCnt,
Original=Original,
constraints=constraints)
elif (evalFunc == "RPCnt"):
toolbox.register("evaluate",
evals.evalFunc_RPCnt,
Original=Original,
constraints=constraints)
elif (evalFunc == "AvgRoleConf"):
toolbox.register("evaluate",
evals.evalFunc_AvgRoleConfViolations,
Original=Original,
constraints=constraints)
elif (evalFunc == "Interpretability"):
toolbox.register("evaluate",
evals.evalFunc_Interpretability,
Original=Original,
userAttributeValues=userAttributeValues,
constraints=constraints)
else:
raise ValueError('Evaluation function not known')
# Register Variation Operators
toolbox.register("mate", operators.mateFunc, optimization=optimization)
toolbox.register("mutate",
operators.mutFunc,
addRolePB=addRolePB,
removeRolePB=removeRolePB,
removeUserPB=removeUserPB,
removePermissionPB=removePermissionPB,
addUserPB=addUserPB,
addPermissionPB=addPermissionPB,
userSize=userSize,
permissionSize=permissionSize,
optimization=[optimization, optimization])
toolbox.register("select", tools.selTournament, tournsize=tournsize)
# Register Statistics
statsFitness = tools.Statistics(key=lambda ind: ind.fitness.values[0])
statsConf = tools.Statistics(
key=lambda ind: statistics.Conf(ind[0], Original))
statsAccs = tools.Statistics(
key=lambda ind: statistics.Accs(ind[0], Original))
statsRoleCnt = tools.Statistics(key=lambda ind: statistics.RoleCnt(ind[0]))
statsURCnt = tools.Statistics(key=lambda ind: statistics.URCnt(ind[0]))
statsRPCnt = tools.Statistics(key=lambda ind: statistics.RPCnt(ind[0]))
statsInterp = tools.Statistics(
key=lambda ind: statistics.Interp(ind[0], userAttributeValues))
mstats = tools.MultiStatistics(Fitness=statsFitness,
Conf=statsConf,
Accs=statsAccs,
RoleCnt=statsRoleCnt,
URCnt=statsURCnt,
RPCnt=statsRPCnt,
Interp=statsInterp)
mstats.register("avg", numpy.mean)
mstats.register("std", numpy.std)
mstats.register("min", numpy.min)
mstats.register("max", numpy.max)
logbook.header = "gen", "evals"
logbook.chapters["Fitness"].header = "min", "avg", "max", "std"
logbook.chapters["Conf"].header = "min", "avg", "max", "std"
logbook.chapters["Accs"].header = "min", "avg", "max", "std"
logbook.chapters["RoleCnt"].header = "min", "avg", "max", "std"
logbook.chapters["URCnt"].header = "min", "avg", "max", "std"
logbook.chapters["RPCnt"].header = "min", "avg", "max", "std"
logbook.chapters["Interp"].header = "min", "avg", "max", "std"
# Creating the population
if (not population):
logger.info("Generate new population of " + str(populationSize) +
" individuals")
population = toolbox.population(n=populationSize)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
if (evalFunc == "WSC_Star_RoleDis"):
fitnesses = [
toolbox.evaluate(population=population, individual=ind)
for ind in invalid_ind
]
else:
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Save population in JSON file
if (printPopulations):
pop_subdirectory = pop_directory + "\\Generation_" + str(genStart)
#if not os.path.exists(pop_subdirectory):
# os.makedirs(pop_subdirectory)
utils.saveDiversity(genStart, population,
pop_subdirectory + "_diversity.json")
utils.savePopulation(genStart, population,
pop_subdirectory + "_population.pkl")
#visual.showBestResult(population, genStart, Original, pop_subdirectory+"\\Individual", "Individual", "Individual from Generation "+str(genStart), False, False, True, False)
# Log statistics for first generation
if ((len(logbook) == 0)
or (logbook.pop(len(logbook) - 1)["gen"] != genStart)):
record = mstats.compile(population)
logbook.record(gen=genStart, evals=len(invalid_ind), **record)
logger.info("Generation " + str(genStart) + ":\t" +
str(logbook.stream) + "\n" +
str(logbook.chapters["Fitness"].stream) + "\n" +
str(logbook.chapters["Conf"].stream) + "\n" +
str(logbook.chapters["Accs"].stream) + "\n" +
str(logbook.chapters["RoleCnt"].stream) + "\n" +
str(logbook.chapters["URCnt"].stream) + "\n" +
str(logbook.chapters["RPCnt"].stream) + "\n" +
str(logbook.chapters["Interp"].stream))
# Begin the evolution
logger.info("Start evolution...")
start = datetime.datetime.now()
logger.info("Start time: " + str(start))
#hof = tools.HallOfFame(maxsize=1)
generation = genStart + 1
stop = False
logger.info("Start evolution with Generation " + str(genStart))
while ((not stop) and (generation <= genStart + NGEN)):
population = toolbox.select(population, k=len(population))
offspring = algorithms.varAnd(population,
toolbox,
cxpb=CXPB,
mutpb=MUTPB_All)
# Evaluate individuals, which need a evaluation
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
if (evalFunc == "WSC_Star_RoleDis"):
fitnesses = [
toolbox.evaluate(population=offspring, individual=ind)
for ind in invalid_ind
]
else:
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Stop condition
if (untilSolutionFound):
array = decoder.resolveRoleModelChromosomeIntoBoolArray(
ind[0], Original.shape[0], Original.shape[1])
conf, accs = matrixOps.compareMatrices(array, Original)
stop = (conf + accs) == 0
# Add Fitness values to results
if generation % freq == 0:
for ind in offspring:
results[generation].append(ind.fitness.values)
# Log statistics for generation
'''record = stats.compile(offspring)
logbook.record(gen=generation, evals=len(invalids), **record)
logger.info("Generation "+str(generation)+":\t"+str(logbook.stream))'''
record = mstats.compile(offspring)
logbook.record(gen=generation, evals=len(invalid_ind), **record)
logger.info("Generation " + str(generation) + ":\t" +
str(logbook.stream) + "\t" +
str(logbook.chapters["Fitness"].stream) + "\t\t" +
str(logbook.chapters["Conf"].stream) + "\t\t" +
str(logbook.chapters["Accs"].stream) + "\t\t" +
str(logbook.chapters["RoleCnt"].stream) + "\t\t" +
str(logbook.chapters["URCnt"].stream) + "\t\t" +
str(logbook.chapters["RPCnt"].stream) + "\t\t" +
str(logbook.chapters["Interp"].stream))
if generation % int((genStart + NGEN) / 10) == 0:
if (printPopulations):
pop_subdirectory = pop_directory + "\\Generation_" + str(
generation)
#if not os.path.exists(pop_subdirectory):
# os.makedirs(pop_subdirectory)
utils.saveDiversity(generation, population,
pop_subdirectory + "_diversity.json")
#utils.savePopulation(generation,population,pop_subdirectory+"_population.pkl")
#visual.showBestResult(offspring, genStart, Original, pop_subdirectory+"\\Individual", "Individual", "Individual from Generation "+str(generation), False, False, True, False)
population = offspring
generation += 1
utils.printDiversity(pop_directory, int((genStart + NGEN) / 10))
utils.savePopulation(generation, population,
pop_subdirectory + "_population.pkl")
end = datetime.datetime.now()
timediff = end - start
time.append(timediff.total_seconds())
generation -= 1
# Print final population
#visual.printpopulation(population)
logger.info("==> Generation " + str(generation))
logger.info("DONE.\n")
# Set Checkpoint
fileExt = "_S_" + evalFunc + "_" + str(
len(population)) + "_" + str(generation)
'''
if (checkpoint):
fileExt = "_cont_" + str(len(population)) + "_" + str(generation) + "_" + str(CXPB) + "_" + str(MUTPB_All)
pickleFile = "Checkpoint"+fileExt+".pkl"
print("Save checkpoint into "+str(pickleFile))
cp = dict(population=population,
generation=generation,
rndstate=random.getstate(),
Original=Original,
results=results,
time=time,
populationSize=populationSize,
CXPB=CXPB,
prevFiles=prevFiles,
MUTPB_All=MUTPB_All,
addRolePB=addRolePB,
removeRolePB=removeRolePB,
removeUserPB=removeUserPB,
removePermissionPB=removePermissionPB,
addUserPB=addUserPB,
addPermissionPB=addPermissionPB,
logbook=logbook)
pickle.dump(cp, open(pickleFile, "wb"), 2)
print("DONE.\n")
'''
return population, results, generation, time, prevFiles, tools.selBest(
population, k=numberTopRoleModels), logbook, fileExt