def run_evol_alg(self,
ea_pars={},
of="mlu",
parallel=None,
max_cpus=1,
save_file=None):
## parallel & max_cpus - being ignored for now !!!!
## save_file as well
self.of = of
popsize = ea_pars.get("pop_size", 100)
maxevals = ea_pars.get("max_evaluations", 10000)
localrate = ea_pars.get("local_opt_rate", 0.2)
numgen = int(maxevals / popsize) + 1
indsize = len(self.ord_users) * len(self.ord_services)
if self.opt_rout_weig:
indsize += self.composite.network.number_edges()
#lower_limits = [0]*(len(self.ord_users)*len(self.ord_services))
upper_limits = []
for u in range(len(self.ord_users)):
for k in range(len(self.ord_services)):
upper_limits.append(self.number_servers[k] - 1)
if self.opt_rout_weig:
#lower_limits.extend ( [0]*self.composite.network.number_edges() )
upper_limits.extend([self.maxw] *
self.composite.network.number_edges())
creator.create("FitnessMin", base.Fitness, weights=(-1.0, ))
creator.create("Individual", list, fitness=creator.FitnessMin)
toolbox = base.Toolbox()
toolbox.register("individual", tools.initIterate, creator.Individual,
self.generate_solution_random)
toolbox.register("population", tools.initRepeat, list,
toolbox.individual)
toolbox.register("evaluate", self.evaluate_serv_assig)
# toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mate", tools.cxUniform, indpb=0.05)
toolbox.register("mutate",
self.single_inteligent_mut,
localrate=localrate,
maxtries=50)
# toolbox.register("mutate", tools.mutUniformInt, low = 1, up = upper_limits, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
pop = toolbox.population(n=popsize)
hof = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", numpy.mean)
stats.register("std", numpy.std)
stats.register("min", numpy.min)
stats.register("max", numpy.max)
pop, log = algorithms.eaSimple(pop,
toolbox,
cxpb=0.5,
mutpb=1.0,
ngen=numgen,
stats=stats,
halloffame=hof,
verbose=True)
#print(pop)
#print(log)
best_sol = hof[0]
res = {}
res["popsize"] = popsize
res["evals"] = maxevals
if self.opt_rout_weig:
size_assig = len(self.ord_users) * len(self.ord_services)
assig = self.decode_serv_assig(best_sol[:size_assig])
w = self.decode_weights(best_sol[size_assig:])
res["of_value"] = self.composite.of_normalized_penalty(
assig, True, self.mincost, sp_weights=w)
of = self.composite.of_normalized_penalty(assig,
False,
self.mincost,
sp_weights=w,
return_dic=True)
res["of_fh"] = of["fh"]
res["of_e2e"] = of["e2e"]
res["of_cost"] = of["cost"]
res["of_cong"] = of["cong"]
else:
assig = self.decode_serv_assig(best_sol)
res["of_value"] = self.composite.of_normalized_penalty(
assig, True, self.mincost)
of = self.composite.of_normalized_penalty(assig,
False,
self.mincost,
return_dic=True)
res["of_fh"] = of["fh"]
res["of_e2e"] = of["e2e"]
res["of_cost"] = of["cost"]
if not self.composite.congestion_cost: ## reporting congestion even if not used in the optimization
dem = self.composite.generate_e2e_demands(assig.dic_assig)
l = Loads(self.composite.network)
l.add_loads_from_paths(self.composite.del_paths, dem)
if self.composite.cong_of == "mlu": cong = l.mlu()[0]
elif self.composite.cong_of == "alu": cong = l.alu()
elif self.composite.cong_of == "fortz":
co = CongestionOptimization(self.composite.network, dem)
phiu = co.phi_uncap()
cong = l.fortz_of(phiu) - 1.0
print("Congestion (not optimized):", cong)
res["of_cong"] = cong
else:
res["of_cong"] = of["cong"]
print("Objective function value: ", res["of_value"])
# NEED TO CHECK HOW TO SAVE Logbook to file
# if (save_file is not None):
# f = open(save_file, "w")
# f.write(log)
# f.close()
return assig, res
def main(difficulty,
p_cross,
p_mutate,
p_flip,
bias,
n_pop,
n_gen,
load_dir=None,
start_game=False):
# combined resolution of all monitors
# screen_res = 3*1920, 1080
screen_res = 2560, 1440
# location of the retry button
retry_pos = screen_res[0] / 2 + 200, screen_res[1] / 2 + 240
# somewhere else inside the game window
click_pos = screen_res[0] / 2 + 280, screen_res[1] / 2 + 240
# delay added between actions
click_delay = 0.01
# path to where the game stores high scores and death logs
root = Path(
'/home/j/.wine/drive_c/users/j/Local Settings/Application Data/')
root = os.path.join(root,
'Chicken_Wings_2020_test_ver_{}'.format(difficulty))
hiscores = os.path.join(root, 'hiscores.txt')
deathlog = os.path.join(root, 'deathlog.txt')
# path to where results will be stored
results_dir = 'results'
bot_hiscores = os.path.join(results_dir, 'bot_hiscores.txt')
bot_deathlog = os.path.join(results_dir, 'bot_deathlog.txt')
# define fitness
creator.create('Fitness', base.Fitness, weights=(1., 1.))
creator.create('Individual', list, fitness=creator.Fitness)
# register an individual and a population
t = base.Toolbox()
t.register('individual', tools.initRepeat, creator.Individual, 0, n=0)
t.register('population', tools.initRepeat, list, t.individual, n=n_pop)
# register evolutionary operators
t.register("mate", cxOnePointBiased, bias=bias)
t.register("mutate",
mutUniformIntBiased,
low=-1,
up=1,
indpb=p_flip,
bias=bias)
t.register("select", tools.selTournament, tournsize=3)
t.register(
"evaluate",
partial(evaluate,
click_delay=click_delay,
click_pos=click_pos,
retry_pos=retry_pos,
hiscores=hiscores,
deathlog=deathlog,
bot_hiscores=bot_hiscores,
bot_deathlog=bot_deathlog))
# create folder to save results
if not os.path.isdir(results_dir):
os.mkdir(results_dir)
open(bot_hiscores, 'w').close()
open(bot_deathlog, 'w').close()
res = Results(results_dir)
# initialise the algorithm
if load_dir:
history = load_all(load_dir, creator.Individual)
res.gen, init_pop = history[-1]
for gen, pop in history:
print_stats(pop, gen)
else:
init_pop = t.population()
# start the game
if start_game:
exe_path = Path('/home/j/chicken_wings/{}.exe'.format(difficulty))
game = Thread(target=wine, args=(exe_path, ), daemon=True)
game.start()
time.sleep(10)
# begin training
ea = algorithms.eaMuPlusLambda
ea(init_pop, t, n_gen, n_gen, p_cross, p_mutate, n_gen, None, res, False)
def defensegan_ga(fgsm_image, params, netG, z_array):
initial_population = torch.tensor(np.asarray(z_array), device=device)
initial_population = initial_population.view(params['r'],
params['nz']).numpy()
def evalFunc(individual):
individual = torch.from_numpy(individual).view(1, params['nz'], 1, 1)
fitness = np.linalg.norm(
netG(individual).view(28, 28).detach().numpy() -
fgsm_image.view(28, 28).detach().numpy(),
ord=2)**2,
return fitness
def initIndividual(icls, content):
return icls(content)
def initPopulation(pcls, ind_init):
return pcls(ind_init(c) for c in initial_population)
creator.create("FitnessMin", base.Fitness, weights=(-1.0, ))
creator.create("Individual", np.ndarray,
fitness=creator.FitnessMin) # minimizing the fitness value
toolbox = base.Toolbox()
CXPB, MUTPB = 0.95, 0.05
toolbox.register("attr_float", random.random)
toolbox.register("individual", initIndividual, creator.Individual)
toolbox.register("population", initPopulation, list, toolbox.individual)
toolbox.register("evaluate", evalFunc)
toolbox.register("mate", tools.cxUniform, indpb=0.1)
toolbox.register("mutate", tools.mutGaussian, mu=0, sigma=0.1, indpb=0.1)
toolbox.register("select", tools.selRoulette)
random.seed(777)
# pop = toolbox.population(n=POPULATION)
pop = toolbox.population()
# print("Start of evolution")
# Evaluate the entire population
# print(fitnesses) -> [(84,), (105,), (96,), (104,), (94,), ... ] 이런식으로 저장됨.
fitnesses = list(map(toolbox.evaluate, pop))
minfit = 1000000.0
elit = None
for ind, fit in zip(pop, fitnesses):
if fit[0] < minfit:
minfit = fit[0]
elit = ind
ind.fitness.values = fit
# Extracting all the fitnesses of
fits = [ind.fitness.values[0] for ind in pop]
# Select the next generation individuals
# len(pop) -> 50, len(pop[0]) -> 5
offspring = toolbox.select(pop, len(pop) - 1)
# Clone the selected individuals
offspring = [elit] + list(map(toolbox.clone, offspring))
# Apply crossover and mutation on the offspring
'''
they modify those individuals within the toolbox container
and we do not need to reassign their results.
'''
# TODO: gaussian mutation maybe better..
# want to customize mutation method... there is no proper mutation operator in deap.tools...
for child1, child2 in zip(offspring[::2], offspring[1::2]):
if random.random() < MUTPB:
size = min(len(child1), len(child2))
for i in range(5):
cxpoint = random.randint(2, size - 1)
mtpoint = cxpoint - 1
# cxpoint -1 위치 : mutate
beta = random.random()
child1[mtpoint] = child1[mtpoint] - beta * (child1[mtpoint] -
child2[mtpoint])
child2[mtpoint] = child1[mtpoint] + beta * (child1[mtpoint] -
child2[mtpoint])
# crossover : one point crossover (temporary crossover algorithm)
# child1[cxpoint:], child2[cxpoint:] = child2[cxpoint:], child1[cxpoint:]
del child1.fitness.values
del child2.fitness.values
for child1, child2 in zip(offspring[::2], offspring[1::2]):
if random.random() < CXPB:
toolbox.mate(child1, child2)
toolbox.mate(child1, child2)
toolbox.mate(child1, child2)
toolbox.mate(child1, child2)
del child1.fitness.values
del child2.fitness.values
for mutant in offspring:
if random.random() < MUTPB:
toolbox.mutate(mutant)
del mutant.fitness.values
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# The population is entirely replaced by the offspring
pop[:] = offspring
# Gather all the fitnesses in one list and print the stats
fits = [ind.fitness.values[0] for ind in pop]
length = len(pop)
mean = sum(fits) / length
sum2 = sum(x * x for x in fits)
std = abs(sum2 / length - mean**2)**0.5
# print("mean:{}, std:{}\n".format(mean, std))
return [z for z in pop]
def generaGenetico():
creator.create("FitnessMin", base.Fitness, weights=(-1,)) #Es -1 porque queremos minimizar.
creator.create("Individuo", list, fitness=creator.FitnessMin) #Hacemos que la fitness sea el FitnessMin
toolbox1 = base.Toolbox()
toolbox1.register("attr_int", random.randint, 0, NUMERO_COLORES-1) #Este atributo es cada casilla del cromosoma, queremos que sea un INT entre [0, Colores-1]
toolbox1.register("individuo", tools.initRepeat, creator.Individuo,
toolbox1.attr_int, n=LONGITUD_CROMOSOMA)
mejorSolucionEncontrada=None
temperatura= LONGITUD_CROMOSOMA*250 + NUMERO_COLORES #Le asignamos un poco más del fitness máximo
#El usuario ha pedidio iteraciones de SA
if ITERACIONES_SA>0:
poblacion_sa=list()
for i in range(0,POBLACION_INICIAL):
mejorSolucionEncontrada, temperatura, estado= simulatedAnnelingGeneraPoblacion(mejorSolucionEncontrada,temperatura)
poblacion_sa.append(estado)
for i in range(0, ITERACIONES_SA-1):
mejorSolucionEncontrada, temperatura, poblacion_sa= ejecutaSimulatedAnneling(poblacion_sa,mejorSolucionEncontrada,temperatura)
#EL usuario ha pedido iteraciones de AG
if ITERACIONES_AG>0:
toolbox1.register('población', tools.initRepeat,
container=list, func=toolbox1.individuo, n=POBLACION_INICIAL)
toolbox1.register('evaluate', evaluacion1)
toolbox1.register('mate', tools.cxOnePoint)
toolbox1.register('mutate', tools.mutUniformInt,low=0, up=NUMERO_COLORES-1, indpb=PROB_GENMUT) #La mutación hace que cambia un el valor del individuo entre 0 y nº colores -1.
toolbox1.register('select', tools.selTournament, tournsize=3)
salon_fama1 = tools.HallOfFame(1)
random.seed(12345)
if ITERACIONES_SA>0:
poblacion_inicial=poblacion_sa
else:
poblacion_inicial=toolbox1.población()
población, registro = algorithms.eaSimple(poblacion_inicial,
toolbox1,
cxpb=PROB_CRUCE, # Probabilidad de que dos individuos contiguos se crucen
mutpb=PROB_MUTACION, # Probabilidad de que un individuo mute
ngen=ITERACIONES_AG, # Número de generaciones
halloffame=salon_fama1)
#Elegimos el ganador
if ITERACIONES_AG>0:
ganador= salon_fama1[0]
if ITERACIONES_SA>0 and evaluacion1(ganador)[0] > evaluacion1(mejorSolucionEncontrada)[0]:
ganador=mejorSolucionEncontrada
else:
ganador=mejorSolucionEncontrada
print("LONGITUD DEL CROMOSOMA = "+str(LONGITUD_CROMOSOMA))
print("NÚMERO DE COLORES = "+str(NUMERO_COLORES))
print("POBLACIÓN INCIAL = "+str(POBLACION_INICIAL))
print("PROBABILIDAD DE CRUCE = "+str(PROB_CRUCE))
print("PROBABILIDAD DE MUTACION = "+str(PROB_MUTACION))
print("La solución se representará como una lista donde la posición indica el vértice y el valor en la lista indicará un tipo de color")
print('La mejor solución encontrada ha sido:')
print(ganador)
print('Individuo con fitness: '+str(evaluacion1(ganador)[0]))
return ganador
def run():
for i in range(number_of_runs):
###################################################################
#EVOLUTIONARY ALGORITHM
###################################################################
#TYPE
#Create minimizing fitness class w/ single objective:
creator.create('FitnessMin', base.Fitness, weights=(-1.0, ))
#Create individual class:
creator.create('Individual', list, fitness=creator.FitnessMin)
#TOOLBOX
toolbox = base.Toolbox()
#Register function to create a number in the interval [1-100?]:
#toolbox.register('init_params', )
#Register function to use initRepeat to fill individual w/ n calls to rand_num:
toolbox.register('individual',
tools.initRepeat,
creator.Individual,
np.random.random,
n=number_of_params)
#Register function to use initRepeat to fill population with individuals:
toolbox.register('population', tools.initRepeat, list,
toolbox.individual)
#GENETIC OPERATORS:
# Register evaluate fxn = evaluation function, individual to evaluate given later
toolbox.register('evaluate', scorefxn_helper)
# Register mate fxn = two points crossover function
toolbox.register('mate', tools.cxTwoPoint)
# Register mutate by swapping two points of the individual:
toolbox.register('mutate',
tools.mutPolynomialBounded,
eta=0.1,
low=0.0,
up=1.0,
indpb=0.2)
# Register select = size of tournament set to 3
toolbox.register('select', tools.selTournament, tournsize=3)
#EVOLUTION!
pop = toolbox.population(n=number_of_individuals)
hof = tools.HallOfFame(1)
stats = tools.Statistics(key=lambda ind: [ind.fitness.values, ind])
stats.register('all', np.copy)
# using built in eaSimple algo
pop, logbook = algorithms.eaSimple(pop,
toolbox,
cxpb=crossover_rate,
mutpb=mutation_rate,
ngen=number_of_generations,
stats=stats,
halloffame=hof,
verbose=False)
# print(f'Run number completed: {i}')
###################################################################
#MAKE LISTS
###################################################################
# Find best scores and individuals in population
arr_best_score = []
arr_best_ind = []
for a in range(len(logbook)):
scores = []
for b in range(len(logbook[a]['all'])):
scores.append(logbook[a]['all'][b][0][0])
#print(a, np.nanmin(scores), np.nanargmin(scores))
arr_best_score.append(np.nanmin(scores))
#logbook is of type 'deap.creator.Individual' and must be loaded later
#don't want to have to load it to view data everytime, thus numpy
ind_np = np.asarray(logbook[a]['all'][np.nanargmin(scores)][1])
ind_np_conv = convert_individual(ind_np, arr_conversion_matrix,
number_of_params)
arr_best_ind.append(ind_np_conv)
#arr_best_ind.append(np.asarray(logbook[a]['all'][np.nanargmin(scores)][1]))
# print('Best individual is:\n %s\nwith fitness: %s' %(arr_best_ind[-1],arr_best_score[-1]))
###################################################################
#PICKLE
###################################################################
arr_to_pickle = [arr_best_score, arr_best_ind]
def get_filename(val):
filename_base = dir_to_use + '/' + stripped_name + '_'
if val < 10:
toret = '000' + str(val)
elif 10 <= val < 100:
toret = '00' + str(val)
elif 100 <= val < 1000:
toret = '0' + str(val)
else:
toret = str(val)
return filename_base + toret + '.pickled'
counter = 0
filename = get_filename(counter)
while os.path.isfile(filename) == True:
counter += 1
filename = get_filename(counter)
pickle.dump(arr_to_pickle, open(filename, 'wb'))
lower_w = -1
sigma = 1
tau = 1 / np.sqrt(n_weights)
mut_prob = 0.1
mate_prob = 0.8
average_pops = []
std_pops = []
best_per_gen = []
player_means = []
best_overall = 0
noimprove = 0
log = tools.Logbook()
tlbx = base.Toolbox()
env.state_to_log()
###############################################################################
################################ Functions ####################################
###############################################################################
# Register and create deap functions and classes
def register_deap_functions():
creator.create("FitnessMax", base.Fitness, weights=(1.0, ))
creator.create("Individual",
np.ndarray,
fitness=creator.FitnessMax,
lifepoints=1)
def cmaes(dim, f, y_target=0.0):
'''Return x for which f(x) is minimal. Stop early when y-target is reached.'''
if dim < 2 or 10000 < dim:
print("nparams value is invalid, must be in [2, 10000]")
return None
population_size = max(
math.ceil(4 + 3 * math.log(dim) + 0.5),
dim // 2) # dim/2 is result of experiments by Maarten on dim > 100
population_size *= 2
ngen = 600 # 25 + int(0.2*dim) # result of experiments by Maarten
print("dimension of problem space ", dim)
print("population size ", population_size)
print("generations ", ngen)
#random.seed(42)
#np.random.seed(42)
creator.create("FitnessMin", base.Fitness, weights=(-1.0, ))
creator.create("Individual", list, fitness=creator.FitnessMin)
nhops = 10
for hop in range(nhops):
centroid = [random.randint(-3, 3) for i in range(dim)]
strategy = cma.Strategy(centroid=centroid,
sigma=0.5,
lambda_=population_size)
toolbox = base.Toolbox()
toolbox.register("generate", strategy.generate, creator.Individual)
toolbox.register("update", strategy.update)
evaluation_count, best_x, best_y = 0, [1] * dim, None
try:
for gen in range(ngen):
population = toolbox.generate()
if False:
for i in range(len(population)):
for j in range(dim):
population[i][j] = round(
population[i][j] * 1000) / 1000
for x in population:
y = f(x)
x.fitness.values = (y, )
evaluation_count += 1
if best_y is None or best_y > y:
best_x, best_y = copy.deepcopy(x), copy.deepcopy(y)
if False:
x_str = ", ".join([
f"{xi:.6f}"
if xi != round(xi) else f"{int(round(xi))}"
for xi in best_x
])
print(f" gen {gen}, f({x_str}) = {best_y:.6f}")
if best_y <= y_target:
break
toolbox.update(population)
x_str = ", ".join([
f"{xi:.12f}" if xi != round(xi) else f"{int(round(xi))}"
for xi in best_x
])
print(
f"evaluations {evaluation_count} evaluations f({x_str}) = {best_y:.12f}"
)
except:
pass
return best_x, best_y
def driver(NGEN=NGEN, CXPB=CXPB, MUTPB=MUTPB, POP_SIZE=POP_SIZE):
# Initialize our fitness function
creator.create("FitnessMax", base.Fitness, weights=(1.0, ))
# Set our individual class to be composed of resort maps
creator.create("Individual", Resort_Map, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
# Register a function to make random maps for population generation
toolbox.register("individual", gen_algoth.rand_map)
# Register the population
toolbox.register("population",
tools.initRepeat,
list,
toolbox.individual,
n=POP_SIZE)
toolbox.register("mate", gen_algoth.cross)
toolbox.register("mutate", gen_algoth.mutate)
toolbox.register("select", tools.selTournament, tournsize=5)
toolbox.register("evaluate", gen_algoth.call_fitness)
pop = toolbox.population()
invalid = [ind for ind in pop if ind.fitness == None]
fitnesses = list(toolbox.map(toolbox.evaluate, invalid))
for ind, fit in zip(invalid, fitnesses):
ind.fitness = fit
total_fitness = 0
progression_avg = []
progression_max = []
for g in range(NGEN):
sys.stdout.write("\rRunning generation " + str(g) +
" Average Fitness: {}".format(total_fitness /
POP_SIZE) +
"\033[K")
selected = toolbox.select(pop, POP_SIZE)
total_fitness = 0
# Clone selected
offspring = list(map(toolbox.clone, selected))
for child1, child2 in zip(offspring[::2], offspring[1::2]):
if random.random() < CXPB:
toolbox.mate(child1, child2)
child1.fitness = None
child2.fitness = None
for mutant in offspring:
if random.random() < MUTPB:
toolbox.mutate(mutant)
mutant.fitness = None
invalid = [ind for ind in offspring if ind.fitness == None]
fitnesses = list(toolbox.map(toolbox.evaluate, invalid))
for ind, fit in zip(invalid, fitnesses):
ind.fitness = fit
# Replace the population with the offspring
pop[:] = offspring
fitness_list = [ind.fitness for ind in pop]
total_fitness = sum(fitness_list)
max_fitness = max(fitness_list)
progression_avg.append(total_fitness / POP_SIZE)
progression_max.append(max_fitness)
print("")
fittest = pop[0]
fit = fittest.fitness
for ind in pop[1:]:
if ind.fitness > fit:
fit = ind.fitness
fittest = ind
return (ind, fit, progression_avg, progression_max)
def optimization(p_data, p_model, p_type, p_params, p_iter):
"""
optimization with genetic algorithms
Parameters
----------
p_data: pd.DataFrame
p_model: str
p_params: dict
Returns
----------
References
----------
https://deap.readthedocs.io
"""
# Delete, if exists, genetic algorithm functional classes
try:
del creator.FitnessMax_en
del creator.Individual_en
except AttributeError:
pass
# Initialize genetic algorithm object
creator.create("FitnessMax_en", base.Fitness, weights=(1.0, ))
creator.create("Individual_en", list, fitness=creator.FitnessMax_en)
toolbox_en = base.Toolbox()
# Define how each gene will be generated (e.g. criterion is a random choice from the criterion list).
toolbox_en.register("attr_ratio", random.choice, p_params['ratio'])
toolbox_en.register("attr_c", random.choice, p_params['c'])
# This is the order in which genes will be combined to create a chromosome
toolbox_en.register("Individual_en",
tools.initCycle,
creator.Individual_en,
(toolbox_en.attr_ratio, toolbox_en.attr_c),
n=1)
# Population definition
toolbox_en.register("population", tools.initRepeat, list,
toolbox_en.Individual_en)
# -------------------------------------------------------------------------------- Mutation function -- #
def mutate_en(individual):
# select which parameter to mutate
gene = random.randint(0, len(p_params) - 1)
if gene == 0:
individual[0] = random.choice(p_params['ratio'])
elif gene == 1:
individual[1] = random.choice(p_params['c'])
return individual,
# ------------------------------------------------------------------------------ Evaluation function -- #
def evaluate_en(eva_individual):
# output of genetic algorithm
chromosome = {'ratio': eva_individual[0], 'c': eva_individual[1]}
# evaluation with fitness metric for classification model
if p_type == 'classification':
# model results
model = logistic_reg(p_data=p_data,
p_params=chromosome,
p_model=p_model,
p_iter=p_iter)
# fitness measure
model_fit = model['metrics']['auc']
# always return a tupple
return model_fit,
# evaluation with fitness metric for regression model
elif p_type == 'regression':
# model results
model = ols_reg(p_data=p_data,
p_params=chromosome,
p_model=p_model,
p_iter=p_iter)
# Fitness measure
model_fit = model['metrics']['r2']
# always return a tupple
return model_fit,
# error in type of model
else:
return 'error: invalid type of model'
toolbox_en.register("mate", tools.cxOnePoint)
toolbox_en.register("mutate", mutate_en)
toolbox_en.register("select", tools.selTournament, tournsize=10)
toolbox_en.register("evaluate", evaluate_en)
population_size = 50
crossover_probability = 0.8
mutation_probability = 0.1
number_of_generations = 4
en_pop = toolbox_en.population(n=population_size)
en_hof = tools.HallOfFame(10)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", np.mean)
stats.register("std", np.std)
stats.register("min", np.min)
stats.register("max", np.max)
# Genetic Algorithm Implementation
en_pop, en_log = algorithms.eaSimple(population=en_pop,
toolbox=toolbox_en,
stats=stats,
cxpb=crossover_probability,
mutpb=mutation_probability,
ngen=number_of_generations,
halloffame=en_hof,
verbose=True)
# transform the deap objects into list so it can be serialized and stored with pickle
en_pop = [list(pop) for pop in list(en_pop)]
en_log = [list(log) for log in list(en_log)]
en_hof = [list(hof) for hof in list(en_hof)]
return {'population': en_pop, 'logs': en_log, 'hof': en_hof}
def generate(x,
y,
points_classes,
mode='fast',
verbose=False,
return_fitness_solution=False,
return_evolution_data=False,
NGEN=20,
TAM_POPULATION=10,
mating_prob=0.5,
mating_mutation_prob=0.7,
mutation_prob=0.1,
tournsize=3):
""" Convert oRGB color into sRGB color.
Parameterss
-----------
x : float list
list of x components.
y : float list
list of y components.
mode : string
Avaible values: 'fast', 'custom' and 'optimized'.
Default value is 'fast'.
verbose: bool
Flag for displaying log messages. Default value is False.
return_fitness_solution: bool
If true, the function will also return the fitness value of the solution.
Default value is False.
return_evolution_data: bool
Default value is False.
If true, the function will also return a list with best fitness value for every generation.
Default value is False.
NGEN: int
Number of generations in the genetic algorithm.
Default value for 'fast' mode is 20 and for 'optimized' is 300.
TAM_POPULATION: int.
Size of the genetic algorithm population.
Default value for 'fast' and 'optimized' modes is 10.
mating_prob: float
Probability of mating in crossover function. Value between 1 and 0.
Default value for 'fast' and 'optimized' modes is 0.5
mating_mutation_prob: float
Probability of mutation during crossover function. Value between 1 and 0.
Default value for 'fast' and 'optimized' modes is 0.7
mutation_prob: float
Probability of mutation in mutation function. Value between 1 and 0.
Default value for 'fast' and 'optimized' modes is 0.1
tournsize: int
Size of the tournament in selection function.
Default value for 'fast' and 'optimized' modes is 3
Returns
-------
list : [c0, c1, c2, ..., ck-1]
List of size K (the number of point classes) with the generated colors in RGB space.
Each color is a three element list with values inside interval [0-1]
Notes
-----
There are three modes for using this function:
- 'fast': option by default. Uses default values for algorithm params.
- 'optimized': same as 'fast', but with more generations. This option is
indicated for cases with K >= 20. Notice that it will increase executing time.
- 'custom': it will take params indicated in the call of the function.
Fast mode is indicated for 20 diferent classes or below. It will provide best solution generated in 2.5s or at least 20 generations.
In case there is a need for using diferent params, custom mode allows customization of all parameters.
If only more executions are needed, optimized mode uses 300 generations, but that will also increase notably execution time.
"""
classes = list(OrderedDict.fromkeys(points_classes))
points_classes = numpy.array([classes.index(i) for i in points_classes])
points = numpy.array(list(zip(x, y)))
counter_classes = Counter(points_classes)
# Number of points and number of classses
N = points.shape[0]
K = len(classes)
if K == 1:
return randcolor_RGB()
distances = _distances
objective = _objective_norm
if N > 100:
distances = _distances_centroid
objective = _objective_cent
NGEN, TAM_POPULATION, mating_prob, mating_mutation_prob, mutation_prob, tournsize, use_time = _values_params(
mode, NGEN, TAM_POPULATION, mating_prob, mating_mutation_prob,
mutation_prob, tournsize)
# Configuration for optimization - maximization
creator.create('FitnessMax', base.Fitness, weights=(1.0, ))
# Individual definition
creator.create('Individual', list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register('color', randcolor_oRGB)
toolbox.register('individual',
tools.initRepeat,
creator.Individual,
toolbox.color,
n=K)
toolbox.register('Population', tools.initRepeat, list, toolbox.individual)
# Geometric distances
geom_distances = distances(N, K, points, points_classes)
# Toolbox configuration
toolbox.register('evaluate', objective, geom_distances, points_classes,
counter_classes)
toolbox.register('select', tools.selTournament, tournsize=tournsize)
toolbox.register('mate', tools.cxOnePoint)
toolbox.register('mutate', _mutation, indpb=mutation_prob)
# Initial population
population = toolbox.Population(TAM_POPULATION)
MIN_GEN = NGEN
gen = 0
# Genetic Algorithm
maxims = []
best_indivs = []
start_time = time()
while (use_time and (time() - start_time < 2.5 or gen < MIN_GEN)) or (
not use_time and gen < MIN_GEN):
offspring = algorithms.varAnd(population,
toolbox,
cxpb=mating_prob,
mutpb=mating_mutation_prob)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
top = tools.selBest(population, k=1)
top_fitness = objective(geom_distances, points_classes,
counter_classes, top[0])
if verbose:
print("Generation:", gen, "Best fitness:", top_fitness)
maxims.append(top_fitness)
best_indivs.append(top[0])
gen += 1
max_fitness = max(maxims)
winner = best_indivs[maxims.index(max_fitness)]
winner_RGB = [
list(oRGB_to_RGB(color[0], color[1], color[2])) for color in winner
]
array_colores = [winner_RGB[points_classes[i]] for i in range(0, N)]
evolution_data = [list(range(0, gen)), maxims]
if return_fitness_solution or return_evolution_data:
res = list()
res.append(array_colores)
if return_fitness_solution:
res.append(max_fitness)
if return_evolution_data:
res.append(evolution_data)
return res
return array_colores
def final_result_table(self):
# problem constants:
HARD_CONSTRAINT_PENALTY = 10 # the penalty factor for a hard-constraint violation
# Genetic Algorithm constants:
POPULATION_SIZE = 300
P_CROSSOVER = 0.9 # probability for crossover
P_MUTATION = 0.1 # probability for mutating an individual
MAX_GENERATIONS = 300
HALL_OF_FAME_SIZE = 30
# set the random seed:
RANDOM_SEED = 42
random.seed(RANDOM_SEED)
toolbox = base.Toolbox()
# create the nurse scheduling problem instance to be used:
nsp = staffSchedulingProblem(HARD_CONSTRAINT_PENALTY,
fileNAME=self.original_file)
# define a single objective, maximizing fitness strategy:
creator.create("FitnessMin", base.Fitness, weights=(-1.0, ))
# create the Individual class based on list:
creator.create("Individual", list, fitness=creator.FitnessMin)
# create an operator that randomly returns 0 or 1:
toolbox.register("Integers", random.randint, 0, 4)
# create the individual operator to fill up an Individual instance:
toolbox.register("individualCreator", tools.initRepeat,
creator.Individual, toolbox.Integers, len(nsp))
# create the population operator to generate a list of individuals:
toolbox.register("populationCreator", tools.initRepeat, list,
toolbox.individualCreator)
# fitness calculation
def getCost(individual):
return nsp.getCost(individual), # return a tuple
toolbox.register("evaluate", getCost)
# genetic operators:
toolbox.register("select", tools.selTournament, tournsize=2)
toolbox.register("mate", tools.cxTwoPoint)
# toolbox.register("mutate", tools.mutFlipBit, indpb=1.0/len(nsp))
toolbox.register("mutate",
tools.mutShuffleIndexes,
indpb=1.0 / len(nsp))
toolbox.register("mutate",
tools.mutUniformInt,
low=0,
up=4,
indpb=1.0 / len(nsp))
# create initial population (generation 0):
population = toolbox.populationCreator(n=POPULATION_SIZE)
# prepare the statistics object:
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("min", numpy.min)
stats.register("avg", numpy.mean)
# define the hall-of-fame object:
hof = tools.HallOfFame(HALL_OF_FAME_SIZE)
# perform the Genetic Algorithm flow with hof feature added:
population, logbook = eaSimpleWithElitism(population,
toolbox,
cxpb=P_CROSSOVER,
mutpb=P_MUTATION,
ngen=MAX_GENERATIONS,
stats=stats,
halloffame=hof,
verbose=True)
# print best solution found:
best = hof.items[0]
print("-- Best Individual = ", best)
print("-- Best Fitness = ", best.fitness.values[0])
print()
print("-- Schedule = ")
table_html_str = nsp.printScheduleInfo(best)
# # extract statistics:
# minFitnessValues, meanFitnessValues = logbook.select("min", "avg")
# # plot statistics:
# sns.set_style("whitegrid")
# plt.plot(minFitnessValues, color='red')
# plt.plot(meanFitnessValues, color='green')
# plt.xlabel('Generation')
# plt.ylabel('Min / Average Fitness')
# plt.title('Min and Average fitness over Generations')
# plt.show()
return table_html_str
def ga(self,
pop_count,
generations_number,
cx_prob,
mut_prob,
mut_change_exam_prob,
evaluate_func,
available_timeslots,
exams,
timeslot_to_day,
timeslot_to_dayslot,
print_best,
select_method=None,
meals1_indexes=None,
meals2_indexes=None,
meals3_indexes=None,
meals4_indexes=None,
meals5_indexes=None,
meals=None):
creator.create("FitnessMax", base.Fitness, weights=(1.0, ))
# base.Fitness is a type of deap.
logging.info('creator.FitnessMax: {}'.format(creator.FitnessMax))
creator.create("Individual", list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register("random_timeslot", random.randint, 0,
max(meals1_indexes))
toolbox.register("random_timeslot2", random.randint,
max(meals1_indexes) + 1, max(meals2_indexes))
toolbox.register("random_timeslot3", random.randint,
max(meals2_indexes) + 1, max(meals3_indexes))
toolbox.register("random_timeslot4", random.randint,
max(meals3_indexes) + 1, max(meals4_indexes))
toolbox.register("random_timeslot5", random.randint,
max(meals4_indexes) + 1, max(meals5_indexes))
# truyền biến vào hàm random_timeslot trong random_timeslot gọi hàm random.randint(), 2 biến 0 và (available_timeslots-1)
# hàm này dùng để xác định khoảng giá trị để random
toolbox.register("individual",
tools.initCycle,
creator.Individual, [
toolbox.random_timeslot,
toolbox.random_timeslot2,
toolbox.random_timeslot3,
toolbox.random_timeslot4,
toolbox.random_timeslot5,
],
n=10)
a = toolbox.individual()
# Tạo hàm individual, trong đó gọi hàm random_timeslot rồi lưu vào creator.individual, chạy hàm n lần
toolbox.register("population", tools.initRepeat, list,
toolbox.individual)
# lưu kết qquả của hàm individual ở trên vào trong population của toolbox.
# mate/crossover function: ghép đôi và tiến hoá
toolbox.register("mate", tools.cxOnePoint)
# tạo ra tuple của 2 thằng ngẫu nhiên. sử dụng random int của python
logging.info('available_timeslots: {}'.format(available_timeslots))
logging.info('mut_change_exam_prob: {}'.format(mut_change_exam_prob))
# toolbox.register("mutate", tools.mutUniformInt, low=0, up= 1, indpb=mut_change_exam_prob)
toolbox.register("mutate",
tools.mutUniformInt,
low=0,
up=1,
indpb=mut_change_exam_prob)
# toolbox.register("mutate", tools.mutShuffleIndexes, indpb=mut_change_exam_prob)
toolbox.register("evaluate", evaluate_func)
# gọi hàm evaluate_func
if select_method:
select_func, select_kwargs = select_method
else:
select_func, select_kwargs = tools.selTournament, {'tournsize': 3}
toolbox.register("select", select_func, **select_kwargs)
pop = toolbox.population(n=pop_count)
# chọn ngẫu nhiên 100 cá thể
# tập hợp mẫu tạo ra để chọn các cá thể, trong naỳ có 50 phần tử, mỗi phần tử có len=14.
best_ever = pop[0]
# Calculate fitness for first generation, chọn ra 100 cá thể, lấy cá thể tốt nhất
list_pop = []
list_best_ever = []
for ind in pop:
ind.fitness.values = toolbox.evaluate(ind)
list_pop.append((ind, ind.fitness.values))
if ind.fitness.values > best_ever.fitness.values:
best_ever = toolbox.clone(ind)
list_pop.sort(key=lambda x: x[1], reverse=True)
for i in range(50):
list_best_ever.append(list_pop[i][0])
# Lai ghép 50 thế hệ
logging.info("Algorithm start")
for gen in range(generations_number):
# while best_ever.fitness.values[0] < 0.02:
offspring = toolbox.select(list_best_ever, len(list_best_ever))
# Clone the selected individuals
# (nhân bản, set offspring = với pop, lấy 100 phần tử từ pop
offspring = list(map(toolbox.clone, offspring))
# Apply crossover on the offspring
for child1, child2 in zip(offspring[::2], offspring[1::2]):
# offspring[::2] : lấy ra các phần tử ở vị trí chẵn 0, 2, 4, 6,...
# offspring[1::2]: lấy ra các phần tử ở vj trí lẻ 1, 3, 5, 7,...
a = random.random()
if a < cx_prob: # cx_prob = 0.2
toolbox.mate(child1, child2)
# del dùng để xoá phần tử trong list
del child1.fitness.values
del child2.fitness.values
# Apply mutation on the offspring
for mutant in offspring:
self.check_ind(mutant)
if random.random(
) < mut_prob: # mut_prob = 0.1 cái này dùng để giới hạn lại số lần đột biến
logging.info('mutant: {}'.format(mutant))
# toolbox.mutate(mutant)
self.Mutate_new(mutant,
low=0,
up=1,
indpb=mut_change_exam_prob,
meals1_indexes=max(meals1_indexes),
meals2_indexes=max(meals2_indexes),
meals3_indexes=max(meals3_indexes),
meals4_indexes=max(meals4_indexes),
meals5_indexes=max(meals5_indexes))
print('mutant: {}'.format(mutant))
print(
'toolbox.mutate(mutant): ',
self.Mutate_new(mutant,
low=0,
up=1,
indpb=mut_change_exam_prob,
meals1_indexes=max(meals1_indexes),
meals2_indexes=max(meals2_indexes),
meals3_indexes=max(meals3_indexes),
meals4_indexes=max(meals4_indexes),
meals5_indexes=max(meals5_indexes)))
up = available_timeslots - 1
indpb = mut_change_exam_prob
del mutant.fitness.values
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
# tìm những cá thể không có fitness, là những cá thể đã biến đổi trước đó (lai hoặc đột biến)
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
print('fitnesses 2: ', list(fitnesses))
# tính fitness cho các cá thể đó lưu lại thành 1 danh sách
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# gán tương ứng các giá trị fitness đã được tính thành chỉ
# số fitness của cá thể tìm ra trong invalid_ind
# The population is entirely replaced by the offspring
pop[:] = offspring
current_best = tools.selBest(pop, k=1)[0]
if current_best.fitness.values > best_ever.fitness.values:
best_ever = toolbox.clone(ind)
logging.info("Algorithm end")
# Printing result
def print_individual(ind):
logging.info("Printing individual")
logging.info("Raw:{}".format(ind))
logging.info("Fitness:{}".format(ind.fitness.values))
logging.info(toolbox.evaluate(ind, inverse=False))
logging.info('meals: {}'.format(meals))
type_food = ''
for index in ind:
if meals[index].is_breakfast == 1:
type_food = 'Sáng: '
if meals[index].is_brunch == 1:
type_food = 'Xế: '
if meals[index].is_soup == 1:
type_food = 'Canh : '
if meals[index].is_main_lunch == 1:
type_food = 'Mặn: '
if meals[index].is_lunch == 1:
type_food = 'Tráng miệng: '
print('Stt: {} Món ăn: {} {}'.format(
index, type_food, meals[index].name))
if print_best:
print_individual(best_ever)
detail = self.create({
'date_start':
date.today() + timedelta(days=-date.today().weekday()),
'date_end':
date.today() + timedelta(days=-date.today().weekday() + 4),
})
menu_line_env = self.env['menu.automatic.weekly.line']
menu_food_line = self.env['meal.food.line']
list_meals = []
for i in range(5):
line_weekly = menu_line_env.create({
'menu_automatic_weekly_id':
detail.id,
'day_in_week':
i + 2,
'breakfast1':
meals[best_ever[0 + i * 10]].id,
'breakfast2':
meals[best_ever[5 + i * 10]].id,
'main_lunch':
meals[best_ever[3 + i * 10]].id,
'soup1':
meals[best_ever[2 + i * 10]].id,
'soup2':
meals[best_ever[7 + i * 10]].id,
'lunch':
meals[best_ever[4 + i * 10]].id,
'tea1':
meals[best_ever[1 + i * 10]].id,
'tea2':
meals[best_ever[6 + i * 10]].id,
})
list_meals.append(meals[best_ever[0 + i * 10]])
list_meals.append(meals[best_ever[5 + i * 10]])
list_meals.append(meals[best_ever[3 + i * 10]])
list_meals.append(meals[best_ever[2 + i * 10]])
list_meals.append(meals[best_ever[7 + i * 10]])
list_meals.append(meals[best_ever[4 + i * 10]])
list_meals.append(meals[best_ever[1 + i * 10]])
list_meals.append(meals[best_ever[6 + i * 10]])
for line in list_meals:
for nutrition in line.line_ids:
temp = menu_food_line.create({
'nutrition_id':
nutrition.nutrition_id.id,
'quantity':
nutrition.quantity,
'protein_a':
nutrition.protein_a,
'protein_v':
nutrition.protein_v,
'lipit_a':
nutrition.lipit_a,
'lipit_v':
nutrition.lipit_v,
'gluco':
nutrition.gluco,
'calo':
nutrition.calo,
'menu_automatic_id':
detail.id
})
return best_ever.fitness.values[0]
def main(problem: Problem = None, seed=None):
config = problem.config
random.seed(seed)
# DEAP framework setup
# We define a bi-objective fitness function.
# 1. Maximize the sparseness minus an amount due to the distance between members
# 2. Minimize the distance to the decision boundary
creator.create("FitnessMulti", base.Fitness, weights=config.fitness_weights)
creator.create("Individual", problem.deap_individual_class(), fitness=creator.FitnessMulti)
toolbox = base.Toolbox()
problem.toolbox = toolbox
# We need to define the individual, the evaluation function (OOBs), mutation
# toolbox.register("individual", tools.initIterate, creator.Individual)
toolbox.register("individual", problem.deap_generate_individual)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", problem.deap_evaluate_individual)
toolbox.register("mutate", problem.deap_mutate_individual)
toolbox.register("select", tools.selNSGA2)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("min", numpy.min, axis=0)
stats.register("max", numpy.max, axis=0)
stats.register("avg", numpy.mean, axis=0)
stats.register("std", numpy.std, axis=0)
logbook = tools.Logbook()
logbook.header = "gen", "evals", "min", "max", "avg", "std"
# Generate initial population.
log.info("### Initializing population....")
pop = toolbox.population(n=config.POPSIZE)
# Evaluate the initial population.
# Note: the fitness functions are all invalid before the first iteration since they have not been evaluated.
invalid_ind = [ind for ind in pop if not ind.fitness.valid]
problem.pre_evaluate_members(invalid_ind)
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
problem.archive.process_population(pop)
# This is just to assign the crowding distance to the individuals (no actual selection is done).
pop = toolbox.select(pop, len(pop))
record = stats.compile(pop)
logbook.record(gen=0, evals=len(invalid_ind), **record)
print(logbook.stream)
# Initialize the archive.
problem.on_iteration(0, pop, logbook)
# Begin the generational process
for gen in range(1, config.NUM_GENERATIONS):
# invalid_ind = [ind for ind in pop]
# fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
# for ind, fit in zip(invalid_ind, fitnesses):
# ind.fitness.values = fit
# Vary the population
offspring = tools.selTournamentDCD(pop, len(pop))
offspring = [ind.clone() for ind in offspring]
problem.reseed(pop, offspring)
for ind1, ind2 in zip(offspring[::2], offspring[1::2]):
toolbox.mutate(ind1)
toolbox.mutate(ind2)
del ind1.fitness.values, ind2.fitness.values
# Evaluate the individuals with an invalid fitness
to_eval = offspring + pop
invalid_ind = [ind for ind in to_eval]
problem.pre_evaluate_members(invalid_ind)
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
problem.archive.process_population(offspring + pop)
# Select the next generation population
pop = toolbox.select(pop + offspring, config.POPSIZE)
record = stats.compile(pop)
logbook.record(gen=gen, evals=len(invalid_ind), **record)
print(logbook.stream)
problem.on_iteration(gen, pop, logbook)
return pop, logbook
def run_mo(self, ea_pars={}, display=True):
popsize = ea_pars.get("pop_size", 100)
maxevals = ea_pars.get("max_evaluations", 10000)
# mutprob = ea_pars.get("mut_rate", 0.05)
localrate = ea_pars.get("local_opt_rate", 0.2)
algorithm = ea_pars.get("algorithm", "eaMuPlusLambda")
numgen = int(maxevals / popsize) + 1
indsize = len(self.ord_users) * len(self.ord_services)
if self.opt_rout_weig:
indsize += self.composite.network.number_edges()
#lower_limits = [0]*(len(self.ord_users)*len(self.ord_services))
upper_limits = []
for u in range(len(self.ord_users)):
for k in range(len(self.ord_services)):
upper_limits.append(self.number_servers[k] - 1)
if self.opt_rout_weig:
#lower_limits.extend ( [0]*self.composite.network.number_edges() )
upper_limits.extend([self.maxw] *
self.composite.network.number_edges())
if self.composite.congestion_cost:
creator.create("FitnessMin",
base.Fitness,
weights=(-1.0, -1.0, -1.0))
else:
creator.create("FitnessMin", base.Fitness, weights=(-1.0, -1.0))
creator.create("Individual", list, fitness=creator.FitnessMin)
toolbox = base.Toolbox()
toolbox.register("individual", tools.initIterate, creator.Individual,
self.generate_solution_random)
toolbox.register("population", tools.initRepeat, list,
toolbox.individual)
toolbox.register("evaluate", self.evaluate_serv_mo)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate",
self.single_inteligent_mut,
localrate=localrate,
maxtries=50)
# toolbox.register("mutate", tools.mutUniformInt, low = 1, up = upper_limits, indpb=mutprob)
toolbox.register("select", tools.selNSGA2)
if algorithm == "spea":
toolbox.register("select", tools.selSPEA2)
pop = toolbox.population(n=popsize)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", numpy.mean, axis=0)
# stats.register("std", numpy.std, axis = 0)
stats.register("min", numpy.min, axis=0)
# stats.register("max", numpy.max, axis = 0)
if algorithm == "eaMuPlusLambda" or algorithm == "spea":
pop = toolbox.select(pop, len(pop))
hof = tools.ParetoFront()
algorithms.eaMuPlusLambda(pop,
toolbox,
mu=popsize,
lambda_=popsize,
cxpb=0.5,
mutpb=0.5,
stats=stats,
ngen=numgen,
halloffame=hof,
verbose=display)
front = numpy.array([ind.fitness.values for ind in hof])
elif algorithm == "nsga":
invalid_ind = [ind for ind in pop if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
pop = toolbox.select(pop, len(pop))
logbook = tools.Logbook()
logbook.header = "gen", "evals", "avg", "min"
record = stats.compile(pop)
logbook.record(gen=0, evals=len(invalid_ind), **record)
print(logbook.stream)
for gen in range(1, numgen):
offspring = tools.selTournamentDCD(pop, len(pop))
offspring = [toolbox.clone(ind) for ind in offspring]
for ind1, ind2 in zip(offspring[::2], offspring[1::2]):
if random.random() <= 0.9:
toolbox.mate(ind1, ind2)
toolbox.mutate(ind1)
toolbox.mutate(ind2)
del ind1.fitness.values, ind2.fitness.values
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
pop = toolbox.select(pop + offspring, len(pop))
record = stats.compile(pop)
logbook.record(gen=gen, evals=len(invalid_ind), **record)
print(logbook.stream)
front = numpy.array([ind.fitness.values for ind in pop])
print(front)
return pop, stats, front
def SPEA2():
creator.create("FitnessMax", base.Fitness, weights=(
-1.0,
-1.0,
))
creator.create("Individual", list,
fitness=creator.FitnessMax) #@UndefinedVariable
toolbox = base.Toolbox()
toolbox.register("attr_float", my_rand)
toolbox.register("individual",
tools.initRepeat,
creator.Individual,
toolbox.attr_float,
n=20) #@UndefinedVariable
toolbox.register("evaluate", benchmarks.zdt1)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("mate",
tools.cxSimulatedBinaryBounded,
eta=0.5,
low=U,
up=V)
toolbox.register("mutate",
tools.mutPolynomialBounded,
eta=0.5,
low=U,
up=V,
indpb=1)
toolbox.register("select", tools.selSPEA2)
#toolbox.register("select", tools.selNSGA2)
#binary tournament selection
toolbox.register("selectTournament", tools.selTournament, tournsize=2)
# Step 1 Initialization
pop = toolbox.population(n=N)
archive = []
curr_gen = 1
while True:
# Step 2 Fitness assignement
for ind in pop:
ind.fitness.values = toolbox.evaluate(ind)
for ind in archive:
ind.fitness.values = toolbox.evaluate(ind)
# Step 3 Environmental selection
archive = toolbox.select(pop + archive, k=Nbar)
# Step 4 Termination
if curr_gen >= GEN:
final_set = archive
break
# Step 5 Mating Selection
mating_pool = toolbox.selectTournament(archive, k=N)
offspring_pool = map(toolbox.clone, mating_pool)
# Step 6 Variation
# crossover 100% and mutation 6%
for child1, child2 in zip(offspring_pool[::2], offspring_pool[1::2]):
toolbox.mate(child1, child2)
for mutant in offspring_pool:
if random.random() < 0.06:
toolbox.mutate(mutant)
pop = offspring_pool
print "gen", curr_gen
curr_gen += 1
# x, y = [], []
# for ind in pop:
# x.append(ind.fitness.values[0])
# y.append(ind.fitness.values[1])
# pylab.scatter(x,y)
# pylab.show()
x, y = [], []
for ind in final_set:
x.append(ind.fitness.values[0])
y.append(ind.fitness.values[1])
return x, y
#
# Evaluation parameters
#
NUM_JOINTS = num_joints
NDIM = 3
AMP, FRQ, PHS = 0, 1, 2
TOURN_SIZE = 3
#
# Register individual creator
# - amplitude : [0.1 1.5]
# - frequency : [0.1 3.0]
# - phase : [0.0 2*pi]
#
tb = base.Toolbox()
BOUND_LO = [0.1] + [0.1] + [0.0]
BOUND_HI = [1.5] + [3.0] + [math.pi * 2]
#
# Create individual object (array of floating point values)
#
def uniform(lo, hi):
"""Return a list of uniform values given the lists of hi and lo bounds."""
return [random.uniform(a, b) for a, b in zip(lo, hi)]
tb.register("attr_uniform", uniform, BOUND_LO, BOUND_HI)
tb.register("individual", tools.initIterate, creator.Individual,
tb.attr_uniform)
#
def init_individual(index, columns, initializer=None):
"""
Initializes the networks belonging to each individual as a pandas DataFrame. This is what
the similarities are calculated against.
Parameters:
:param index: the index names that you want
:param columns: the column names you want
:param initializer: determines if individuals are random or
initialized; if True, initialized from the initializer input,
else random
:Returns: pandas DataFrame
"""
ind = pd.DataFrame(0,index=index, columns=columns)
if initializer is not None:
# sets up the DataFrame with the initializer data
ind.loc[:, 2:] = initializer.loc[:,1:]
ind.loc[:, 'in'] = initializer.loc[:, 'in']
# sets the age
for i in index:
if ind.loc[i,'in'] != 0:
ind.loc[i,'age'] = 1
else:
ind.loc[i,'age'] = 0
# randomly flips a company in or out of the system
if random.random() < 0.05:
if ind.loc[i,'in'] == 0:
ind.loc[i,'in'] = 1
ind.loc[i,'age'] = 1
for j in index:
if i == j:
ind.loc[i,j] = 0
else:
if random.random() < 0.2:
ind.loc[i,j] = 1
ind.loc[j,i] = 1
else:
ind.loc[i,:] = 0
ind.loc[:,i] = 0
# randomly flips correlations
if ind.loc[i,'in'] == 1:
for j in index:
if random.random() < 0.05 and i != j:
ind.loc[i,j] = abs(ind.loc[i,j] - 1)
ind.loc[j,i] = ind.at[i,j]
else:
for i in index:
# randomly places companies in or out of the network
if random.random() < 0.2:
ind.loc[i,'in'] = 1
ind.loc[i,'age'] = 1
# randomly assigns correlations for companies in the network
if ind.loc[i,'in'] == 1:
for j in index:
if i == j:
ind.loc[i,j] = 0
else:
if random.random() < 0.2
ind.loc[i,j] = 1
ind.loc[j,i] = ind.at[i,j]
ind.fillna(0)
return ind
class Individual(object):
"""
Creates the individual class.
init parameters:
:param index: the index names that you want
:param columns: the column names you want
:param initializer: determines if individuals are random or
initialized; if True, initialized from the initializer input,
else random
Attributes:
:attr network: adjacency network
:attr age: age of each individual
:Returns: list of n-sized chunks
"""
def __init__(self, index, columns, initializer=None):
self.network = init_individual(index,columns,initializer)
self.age = 1
# structuring initializers
# FitnessMax => weights fitness by whoever is highest
creator.create("FitnessMax", base.Fitness, weights=(1.0,))
## WITHOUT INITIALIZATION ##
creator.create("Individual", Individual, fitness=creator.FitnessMax)
## WITH INITIALIZATION ##
# creator.create("Individual", Individual, fitness=creator.FitnessMax, comparisons[0])
toolbox = base.Toolbox()2
# creates the population
toolbox.register("individual", creator.Individual, stocks, full_cols, comparisons[0])
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
def eval_fitness(individual, comparison):
"""
Evaluates the fitness of each individual, in terms of similarity.
Parameters:
:param individual: the individual to be evaluated
:param comparison: the reference that similarity will be
calculated against
:Returns: float with similarity measure in range [0,1]
"""
adjacency = individual.network.loc[:,['in']+stocks]
for i in individual.network.index:
individual.network.loc[i,'age'] += 1
return jaccard(adjacency,comparison),
def mut_individual(individual, pexist):
"""
Mutates the individual network
init parameters:
:param individual: individual to be mutated
:param pexist: the probability of adding/removing a company from
the network
the pseudo-code goes as follows:
for each stock, with probability pexist switch in/out
if now out, reset every thing to 0
if now in, randomly initialize adjacencies and set age=1
choose a 10 adjacency terms from stocks that are in, and
changing them
reset the ages
:Returns: new individual network with age reset
"""
network = individual.network
for i in network.index.values:
age = network.loc[i,'age']
if random.random() < AGEDEP(age, pexist):
if network.loc[i,'in'] == 1:
network.loc[i, :] = 0
network.loc[:, i] = 0
if network.loc[i,'in'] == 0:
network.loc[i,'in'] = 1
network.loc[i,'age'] = 1
for j in network.columns.values[2:]:
if random.random() < 0.1 and i != j:
network.loc[i,j] = 1
network.loc[j,i] = network.at[i,j]
relevant = network.loc[network['in']==1]
for _ in range(10):
i = random.choice(relevant.index.values)
j = random.choice(relevant.columns.values[2:])
network.loc[i,j] = abs(network.at[i,j]-1)
network.loc[j,i] = network.at[i,j]
if network.loc[i][1:].sum() == 0:
network.loc[i,'in'] = 0
network.loc[i,'age'] = 0
individual.network = network
individual.age = 1
return individual,
def cross_over(ind1, ind2):
"""
Crossing-over with 2 individuals
init parameters:
:param ind1: individual 1
:param ind2: individual 2
the pseudo-code goes as follows:
randomly choose a crossing-over point
swap elements [0:cx,0:cx] from the 2 individuals
reset the ages
:Returns: new individual network with age reset
"""
network1 = ind1.network
network2 = ind2.network
size = min(len(network1.index), len(network2.index))
cx = random.randint(1, size - 1)
temp = network1.copy()
temp.iloc[:cx,:cx] = network2.iloc[:cx,:cx]
network2.iloc[:cx,:cx] = network1.iloc[:cx,:cx]
network1 = temp
ind1.network = network1
ind2.network = network2
ind1.age = 1
ind2.age = 1
return ind1, ind2
# set the DEAP equations
toolbox.register("evaluate", eval_fitness)
toolbox.register("mutate", mut_individual, pexist=0.3)
toolbox.register("select", tools.selBest)
toolbox.register("select2", tools.selTournament, tournsize=4)
toolbox.register("mate", cross_over)
def main():
"""
Genetic algorithm
the pseudo-code goes as follows:
initialize the population and parameters
initialize the statistics desired
GA_algorithm:
calculate fitnesses and print statistics
for NGEN generations:
create the offspring
re-evaluate fitnesses and select population
update ages of inidividuals
print statistics
return to max-fitnesses and oldest individuals at the end
:Returns: new individual network with age reset
"""
NGEN = len(comparisons)
MU = 50
CXPB = 0.5
MUTPB = 0.5
pop = toolbox.population(n=MU)
# hof = tools.HallOfFame(15)
hof=None
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", np.mean)
# stats.register("std", np.std)
stats.register("min", np.min)
stats.register("max", np.max)
def GA_algorithm(population, toolbox, cxpb, mutpb, ngen, stats=None,
halloffame=None, verbose=__debug__):
# original algorithm
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
fitnesses = toolbox.map(toolbox.evaluate, population, [comparisons[0]]*len(population))
for ind, fit in zip(population, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
logbook.record(gen=0, nevals=len(population), **record)
if verbose:
print(logbook.stream)
for g in range(1,NGEN):
# Vary the pool of individuals
offspring = algorithms.varAnd(population, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
fitnesses = toolbox.map(toolbox.evaluate, population+offspring, [comparisons[g]]*len(population+offspring))
for ind, fit in zip(population+offspring, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(offspring)
population[:10] = toolbox.select(population+offspring, 10)
population[10:] = toolbox.select2(population+offspring, 40)
for ind in population:
ind.age += 1
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
logbook.record(gen=g, nevals=len(population+offspring), **record)
if verbose:
print(logbook.stream)
ages = [ind.age for ind in population]
max_age = max(ages)
oldest_pop = [i.network for i in population if i.age == max_age]
oldest_pop[0].to_csv('oldest_GA_init.csv')
max_fit = max(fitnesses)
max_pop = [i.network for i in population if i.fitness.values == max_fit]
max_pop[0].to_csv('max_pop_GA_init.csv')
return population, logbook
GA_algorithm(pop, toolbox, cxpb=CXPB, mutpb=MUTPB, ngen=NGEN, stats=stats,
halloffame=hof)
return pop, stats, hof
if __name__ == "__main__":
main()
def _fit(self, X, y):
X, y = check_X_y(X, y, "csr")
# Initialization
cv = check_cv(self.cv, y, classifier=is_classifier(self.estimator))
scorer = check_scoring(self.estimator, scoring=self.scoring)
n_features = X.shape[1]
if self.max_features is not None:
if not isinstance(self.max_features, numbers.Integral):
raise TypeError(
"'max_features' should be an integer between 1 and {} features."
" Got {!r} instead.".format(n_features, self.max_features))
elif self.max_features < 1 or self.max_features > n_features:
raise ValueError(
"'max_features' should be between 1 and {} features."
" Got {} instead.".format(n_features, self.max_features))
max_features = self.max_features
else:
max_features = n_features
if not isinstance(self.n_gen_no_change,
(numbers.Integral, np.integer, type(None))):
raise ValueError(
"'n_gen_no_change' should either be None or an integer."
" {} was passed.".format(self.n_gen_no_change))
estimator = clone(self.estimator)
# Genetic Algorithm
toolbox = base.Toolbox()
toolbox.register("individual",
_createIndividual,
creator.Individual,
n=n_features,
max_features=max_features)
toolbox.register("population", tools.initRepeat, list,
toolbox.individual)
toolbox.register("evaluate",
_evalFunction,
estimator=estimator,
X=X,
y=y,
cv=cv,
scorer=scorer,
fit_params=self.fit_params,
max_features=max_features,
caching=self.caching,
scores_cache=self.scores_cache)
toolbox.register("mate",
tools.cxUniform,
indpb=self.crossover_independent_proba)
toolbox.register("mutate",
tools.mutFlipBit,
indpb=self.mutation_independent_proba)
toolbox.register("select",
tools.selTournament,
tournsize=self.tournament_size)
if self.n_jobs == 0:
raise ValueError("n_jobs == 0 has no meaning.")
elif self.n_jobs > 1:
pool = multiprocessing.Pool(processes=self.n_jobs)
toolbox.register("map", pool.map)
elif self.n_jobs < 0:
pool = multiprocessing.Pool(
processes=max(cpu_count() + 1 + self.n_jobs, 1))
toolbox.register("map", pool.map)
pop = toolbox.population(n=self.n_population)
hof = tools.HallOfFame(1, similar=np.array_equal)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", np.mean, axis=0)
stats.register("std", np.std, axis=0)
stats.register("min", np.min, axis=0)
stats.register("max", np.max, axis=0)
if self.verbose > 0:
print("Selecting features with genetic algorithm.")
_, log = _eaFunction(pop,
toolbox,
cxpb=self.crossover_proba,
mutpb=self.mutation_proba,
ngen=self.n_generations,
ngen_no_change=self.n_gen_no_change,
stats=stats,
halloffame=hof,
verbose=self.verbose)
if self.n_jobs != 1:
pool.close()
pool.join()
# Set final attributes
support_ = np.array(hof, dtype=np.bool)[0]
self.estimator_ = clone(self.estimator)
self.estimator_.fit(X[:, support_], y)
self.generation_scores_ = np.array(
[score for score, _ in log.select("max")])
self.n_features_ = support_.sum()
self.support_ = support_
return self
def run_ga_optimization(self, optimization_setting: OptimizationSetting, population_size=100, ngen_size=30, output=True):
""""""
# Get optimization setting and target
settings = optimization_setting.generate_setting_ga()
target_name = optimization_setting.target_name
if not settings:
self.output("优化参数组合为空，请检查")
return
if not target_name:
self.output("优化目标未设置，请检查")
return
# Define parameter generation function
def generate_parameter():
""""""
return random.choice(settings)
def mutate_individual(individual, indpb):
""""""
size = len(individual)
paramlist = generate_parameter()
for i in range(size):
if random.random() < indpb:
individual[i] = paramlist[i]
return individual,
# Create ga object function
global ga_target_name
global ga_strategy_class
global ga_setting
global ga_vt_symbol
global ga_interval
global ga_start
global ga_rate
global ga_slippage
global ga_size
global ga_pricetick
global ga_capital
global ga_end
global ga_mode
global ga_inverse
ga_target_name = target_name
ga_strategy_class = self.strategy_class
ga_setting = settings[0]
ga_vt_symbol = self.vt_symbol
ga_interval = self.interval
ga_start = self.start
ga_rate = self.rate
ga_slippage = self.slippage
ga_size = self.size
ga_pricetick = self.pricetick
ga_capital = self.capital
ga_end = self.end
ga_mode = self.mode
ga_inverse = self.inverse
# Set up genetic algorithem
toolbox = base.Toolbox()
toolbox.register("individual", tools.initIterate, creator.Individual, generate_parameter)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", mutate_individual, indpb=1)
toolbox.register("evaluate", ga_optimize)
toolbox.register("select", tools.selNSGA2)
total_size = len(settings)
pop_size = population_size # number of individuals in each generation
lambda_ = pop_size # number of children to produce at each generation
mu = int(pop_size * 0.8) # number of individuals to select for the next generation
cxpb = 0.95 # probability that an offspring is produced by crossover
mutpb = 1 - cxpb # probability that an offspring is produced by mutation
ngen = ngen_size # number of generation
pop = toolbox.population(pop_size)
hof = tools.ParetoFront() # end result of pareto front
stats = tools.Statistics(lambda ind: ind.fitness.values)
np.set_printoptions(suppress=True)
stats.register("mean", np.mean, axis=0)
stats.register("std", np.std, axis=0)
stats.register("min", np.min, axis=0)
stats.register("max", np.max, axis=0)
# Multiprocessing is not supported yet.
# pool = multiprocessing.Pool(multiprocessing.cpu_count())
# toolbox.register("map", pool.map)
# Run ga optimization
self.output(f"参数优化空间：{total_size}")
self.output(f"每代族群总数：{pop_size}")
self.output(f"优良筛选个数：{mu}")
self.output(f"迭代次数：{ngen}")
self.output(f"交叉概率：{cxpb:.0%}")
self.output(f"突变概率：{mutpb:.0%}")
start = time()
algorithms.eaMuPlusLambda(
pop,
toolbox,
mu,
lambda_,
cxpb,
mutpb,
ngen,
stats,
halloffame=hof
)
end = time()
cost = int((end - start))
self.output(f"遗传算法优化完成，耗时{cost}秒")
# Return result list
results = []
for parameter_values in hof:
setting = dict(parameter_values)
target_value = ga_optimize(parameter_values)[0]
results.append((setting, target_value, {}))
return results
def parameter_tuning(X_train,
feat_vec,
seizure_times,
f_s,
window_length,
window_overlap,
num_channels=145):
#creating types
creator.create("FitnessMax", base.Fitness, weights=(1.0, ))
creator.create("Individual", list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
#defining genes
#ranges are given by Gardner paper
t_per_min = 10 * f_s
t_per_max = 200 * f_s
MIN = np.tile([0.02, 0.25, 0.3, 0, 10, t_per_min], num_channels)
MAX = np.tile([.2, 10, 1, 1, 100, t_per_max], num_channels)
toolbox.register("attr_v", random.uniform, MIN[0], MAX[0])
toolbox.register("attr_g", random.uniform, MIN[1], MAX[1])
toolbox.register("attr_p", random.uniform, MIN[2], MAX[2])
toolbox.register("attr_w", random.uniform, MIN[3], MAX[3])
toolbox.register("attr_N", random.uniform, MIN[4], MAX[4])
toolbox.register("attr_T", random.uniform, MIN[5], MAX[5])
#defining an individual as a group of the four genes
toolbox.register("individual", tools.initCycle, creator.Individual,
(toolbox.attr_v, toolbox.attr_g, toolbox.attr_p,
toolbox.attr_w, toolbox.attr_N, toolbox.attr_T),
num_channels)
#defining the population as a list of individuals
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.decorate("population", within_constraints(MIN, MAX))
# register the fitness function
toolbox.register(
"evaluate",
lambda x: fitness_fn(x, X_train, feat_vec, seizure_times, f_s,
window_length, window_overlap, num_channels))
# register the crossover operator
# other options are: cxOnePoint, cxUniform (requires an indpb input, probably can just use CXPB)
# there are others, more particular than these options
toolbox.register("mate", tools.cxTwoPoint)
toolbox.decorate("mate", within_constraints(MIN, MAX))
# register a mutation operator with a probability to mutate of 0.05
# can change: mu, sigma, and indpb
# there are others, more particular than this
toolbox.register("mutate", tools.mutGaussian, mu=1, sigma=10, indpb=0.03)
toolbox.decorate("mutate", within_constraints(MIN, MAX))
# operator for selecting individuals for breeding the next generation
# other options are: tournament: randonly picks tournsize out of population, chosses fittest, and has that be
# a parent. continues until number of parents is equal to size of population.
# there are others, more particular than this
toolbox.register("select", tools.selTournament, tournsize=3)
#toolbox.register("select", tools.selRoulette)
#create an initial population of size 20
pop = toolbox.population(n=20)
# CXPB is the probability with which two individuals are crossed
CXPB = 0.3
# MUTPB is the probability for mutating an individual
MUTPB = 0.5
# NGEN is the number of generations until final parameters are picked
NGEN = 40
print("Start of evolution")
# find the fitness of every individual in the population
fitnesses = list(map(toolbox.evaluate, pop))
#assigning each fitness to the individual it represents
for ind, fit in zip(pop, fitnesses):
ind.fitness.values = fit
#defining variables to keep track of best indivudals throughout species
best_species_genes = tools.selBest(pop, 1)[0]
best_species_value = best_species_genes.fitness.values
best_gen = 0
next_mean = 1
prev_mean = 0
#start evolution
for g in range(NGEN):
if abs(next_mean - prev_mean) > 0.005:
prev_mean = next_mean
# Select the next generation's parents
parents = toolbox.select(pop, len(pop))
# Clone the parents and call them offspring: crossover and mutation will be performed below
offspring = list(map(toolbox.clone, parents))
# Apply crossover to children in offspring with probability CXPB
for child1, child2 in zip(offspring[::2], offspring[1::2]):
# cross two individuals with probability CXPB
if random.random() < CXPB:
toolbox.mate(child1, child2)
del child1.fitness.values
del child2.fitness.values
# Apply mutation to children in offspring with probability MUTPB
for mutant in offspring:
if random.random() < MUTPB:
toolbox.mutate(mutant)
del mutant.fitness.values
# Find the fitnessess for all the children for whom fitness changed
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Offspring becomes the new population
pop[:] = offspring
#updating best species values
#if max(fitnesses):
if max(fitnesses) > best_species_value:
best_species_genes = tools.selBest(pop, 1)[0]
best_species_value = best_species_genes.fitness.values
best_gen = g
#best_next_obj = max(fitnesses)
fits = [ind.fitness.values[0] for ind in pop]
length = len(pop)
next_mean = sum(fits) / length
best_ind_finalgen = tools.selBest(pop, 1)[0]
print("Best individual in final population is %s with fitness value %s" %
(best_ind_finalgen, best_ind_finalgen.fitness.values))
print(
"Best individual in species is %s and occurred during generation %s with fitness %s"
% (best_species_genes, best_gen, best_species_value))
#will return v for all channels, g for all channels, p for all channels, weights for all channels, adapt_rate for all channels, and Tper for all channels
return best_species_genes[0::6], best_species_genes[
1::6], best_species_genes[2::6], best_species_genes[
3::6], best_species_genes[4::6], best_species_genes[5::6]
def SelectPictureGA(para_grid):
"""
利用GA进行素材调优
"""
# 初始化
creator.create("FitnessMax", base.Fitness, weights=(1.0,))
creator.create("Individual", list, fitness=creator.FitnessMax)
# 初始种群生成
toolbox = base.Toolbox()
toolbox.register("attr_float", select_parameter, para_grid)
toolbox.register("population", tools.initRepeat, list, toolbox.attr_float)
# 进化器生成
toolbox.register("evaluate", eva_max)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", mutCounter, para_grid=para_grid)
toolbox.register("select", tools.selTournament, tournsize=3)
# 生成器初始化参数
population = toolbox.population(n=40)
CXPB, MUTPB, NGEN = 0.5, 0.2, 50
# 此处添加模拟点击率函数
WriteRandom(population)
# 模拟点击率函数结束
# 选择初始化种群
fitnesses = map(toolbox.evaluate, population)
for ind, fit in zip(population, fitnesses):
ind.fitness.values = fit
for g in range(NGEN):
# Select the next generation individuals
offspring = toolbox.select(population, len(population))
# Clone the selected individuals
offspring = list(map(toolbox.clone, offspring))
# Apply crossover and mutation on the offspring
for child1, child2 in zip(offspring[::2], offspring[1::2]):
if random.random() < CXPB:
toolbox.mate(child1, child2)
del child1.fitness.values
del child2.fitness.values
for mutant in offspring:
if random.random() < MUTPB:
toolbox.mutate(mutant)
del mutant.fitness.values
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
# 此处添加模拟点击率函数
WriteRandom(invalid_ind)
# 模拟点击率函数结束
fitnesses = map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# The population is entirely replaced by the offspring
population[:] = offspring
return population
import random
from deap import base
from deap import creator
from deap import tools
# 这里这个base.Fitness是干嘛的？？？
creator.create("FitnessMax", base.Fitness, weights=(1.0, ))
# 这里的list，fitness是参数，干嘛的？？？
creator.create("Individual", list, fitness=creator.FitnessMax)
toolbox = base.Toolbox() # base是个很基本的类啊！！！看来很重要
# Attribute generator: define 'attr_bool' to be an attribute ('gene')
# which corresponds to integers sampled uniformly
# from the range [0,1] (i.e. 0 or 1 with equal
# probability)
toolbox.register("attr_bool", random.randint, 0, 1) # 包含了0,1的随机整数。不明白这里是干嘛的？？？
# Structure initializers: define 'individual' to be an individual
# consisting of 100 'attr_bool' elements ('genes')
toolbox.register(
"individual",
tools.initRepeat,
creator.Individual, # tools.initRepeat是干嘛的？？？
toolbox.attr_bool,
100)
# define the population to be a list of 'individual's
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
def es_toolbox(strategy_name,
i_shape,
evaluate,
model_type,
imutpb=None,
imutmu=None,
imutsigma=None):
"""Initializes and configures the DEAP toolbox for evolving the parameters of a model.
Args:
strategy_name (str): The strategy that is being used for evolution
i_shape (int or tuple): Size or shape of an individual in the population
evaluate (function): Function to evaluate an entire population
model_type (str): A string specifying whether we're optimizing on a neural network
or field programmable gate array
imutpb (float): Mutation probability for each individual's attribute
imutmu (float): Mean parameter for the Gaussian Distribution we're mutating an attribute from
imutsigma (float): Sigma parameter for the Gaussian Distribution we're mutating an attribute from
Returns:
toolbox (deap.base.Toolbox): Configured DEAP Toolbox for the algorithm.
"""
logger.log("Initializing toolbox...")
# Set seed
seed = int(time.time())
random.seed(seed)
logger.log('TOOLBOX.PY random seed is {}'.format(seed))
logger.start_timer()
# Initialize Toolbox
toolbox = base.Toolbox()
logger.stop_timer('TOOLBOX.PY Initializing toolbox')
logger.start_timer()
# Defining tools specific to model
size = np.prod(i_shape)
if model_type == "nn":
# ATTRIBUTE
toolbox.register("attribute", random.random)
logger.stop_timer('TOOLBOX.PY register("attribute")')
# INDIVIDUAL
logger.start_timer()
toolbox.register("individual",
getattr(tools, 'initRepeat'),
getattr(creator, 'Individual'),
getattr(toolbox, 'attribute'),
n=i_shape)
logger.stop_timer('TOOLBOX.PY register("individual")')
# MUTATION
logger.start_timer()
toolbox.register("mutate",
getattr(tools, 'mutGaussian'),
mu=imutmu,
sigma=imutsigma,
indpb=imutpb)
logger.stop_timer('TOOLBOX.PY register("mutate")')
# POPULATION
logger.start_timer()
def init_population(ind_class, n):
pop = np.random.uniform(low=-1, high=1, size=(n, size))
return [ind_class(ind) for ind in pop]
toolbox.register("population", init_population,
getattr(creator, 'Individual'))
logger.stop_timer('TOOLBOX.PY register("population")')
# MATING
logger.start_timer()
toolbox.register("mate", getattr(tools, 'cxTwoPoint'))
logger.stop_timer('TOOLBOX.PY register("mate")')
elif model_type == "fpga":
# ATTRIBUTE
logger.start_timer()
toolbox.register("attribute", np.random.choice, [False, True])
logger.stop_timer('TOOLBOX.PY register("attribute")')
# MUTATION
logger.start_timer()
def mutate_individual(ind, indpb):
idx = np.argwhere(
np.random.choice([False, True], size, p=[1 - indpb, indpb]))
ind[idx] = np.invert(ind[idx])
return ind
toolbox.register("mutate", mutate_individual, indpb=imutpb)
logger.stop_timer('TOOLBOX.PY register("mutate")')
# POPULATION
logger.start_timer()
def init_population(ind_class, n):
pop = np.random.choice([False, True], size=(n, size))
return [ind_class(ind) for ind in pop]
toolbox.register("population", init_population,
getattr(creator, 'Individual'))
logger.stop_timer('TOOLBOX.PY register("population")')
# MATING
logger.start_timer()
from varro.fpga.cross_over import cross_over
toolbox.register("mate", cross_over)
logger.stop_timer('TOOLBOX.PY register("mate")')
# SELECTION METHOD
logger.start_timer()
if strategy_name == 'nsr-es':
toolbox.register("select_elite", getattr(
tools, 'selSPEA2')) # Use Multi-objective selection method
toolbox.register("select", getattr(tools, 'selRandom'))
else:
toolbox.register("select_elite",
getattr(tools, 'selTournament'),
tournsize=3)
toolbox.register("select", getattr(tools, 'selRandom'))
logger.stop_timer('TOOLBOX.PY register("select")')
# EVALUATE
logger.start_timer()
toolbox.register("evaluate", evaluate)
logger.stop_timer('TOOLBOX.PY register("evaluate")')
return toolbox
def gaVRPTW(instName,
unitCost,
initCost,
waitCost,
delayCost,
indSize,
popSize,
cxPb,
mutPb,
NGen,
exportCSV=False,
customizeData=False):
if customizeData:
jsonDataDir = os.path.join(BASE_DIR, 'data', 'json_customize')
else:
jsonDataDir = os.path.join(BASE_DIR, 'data', 'json')
jsonFile = os.path.join(jsonDataDir, '%s.json' % instName)
with open(jsonFile) as f:
instance = load(f)
creator.create('FitnessMax', base.Fitness, weights=(1.0, ))
creator.create('Individual', list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
# Attribute generator
toolbox.register('indexes', random.sample, range(1, indSize + 1), indSize)
# Structure initializers
toolbox.register('individual', tools.initIterate, creator.Individual,
toolbox.indexes)
toolbox.register('population', tools.initRepeat, list, toolbox.individual)
# Operator registering
toolbox.register('evaluate',
evalVRPTW,
instance=instance,
unitCost=unitCost,
initCost=initCost,
waitCost=waitCost,
delayCost=delayCost)
toolbox.register('select', tools.selRoulette)
toolbox.register('mate', cxPartialyMatched)
toolbox.register('mutate', mutInverseIndexes)
pop = toolbox.population(n=popSize)
# Results holders for exporting results to CSV file
csvData = []
print('Start of evolution')
# Evaluate the entire population
fitnesses = list(map(toolbox.evaluate, pop))
for ind, fit in zip(pop, fitnesses):
ind.fitness.values = fit
print(' Evaluated %d individuals' % len(pop))
# Begin the evolution
for g in range(NGen):
print('-- Generation %d --' % g)
# Select the next generation individuals
offspring = toolbox.select(pop, len(pop))
# Clone the selected individuals
offspring = list(map(toolbox.clone, offspring))
# Apply crossover and mutation on the offspring
for child1, child2 in zip(offspring[::2], offspring[1::2]):
if random.random() < cxPb:
toolbox.mate(child1, child2)
del child1.fitness.values
del child2.fitness.values
for mutant in offspring:
if random.random() < mutPb:
toolbox.mutate(mutant)
del mutant.fitness.values
# Evaluate the individuals with an invalid fitness
invalidInd = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = map(toolbox.evaluate, invalidInd)
for ind, fit in zip(invalidInd, fitnesses):
ind.fitness.values = fit
print(' Evaluated %d individuals' % len(invalidInd))
# The population is entirely replaced by the offspring
pop[:] = offspring
# Gather all the fitnesses in one list and print the stats
fits = [ind.fitness.values[0] for ind in pop]
length = len(pop)
mean = sum(fits) / length
sum2 = sum(x * x for x in fits)
std = abs(sum2 / length - mean**2)**0.5
print(' Min %s' % min(fits))
print(' Max %s' % max(fits))
print('Avg %s' % mean)
print(' Std %s' % std)
# Write data to holders for exporting results to CSV file
if exportCSV:
csvRow = {
'generation': g,
'evaluated_individuals': len(invalidInd),
'min_fitness': min(fits),
'max_fitness': max(fits),
'avg_fitness': mean,
'std_fitness': std,
}
csvData.append(csvRow)
print('-- End of (successful) evolution --')
bestInd = tools.selBest(pop, 1)[0]
print('Best individual: %s' % bestInd)
print('Fitness: %s' % bestInd.fitness.values[0])
printRoute(ind2route(bestInd, instance))
print('Total cost: %s' % (1 / bestInd.fitness.values[0]))
if exportCSV:
csvFilename = '%s_uC%s_iC%s_wC%s_dC%s_iS%s_pS%s_cP%s_mP%s_nG%s.csv' % (
instName, unitCost, initCost, waitCost, delayCost, indSize,
popSize, cxPb, mutPb, NGen)
csvPathname = os.path.join(BASE_DIR, 'results', csvFilename)
print('Write to file: %s' % csvPathname)
makeDirsForFile(pathname=csvPathname)
if not exist(pathname=csvPathname, overwrite=True):
with open(csvPathname, 'w') as f:
fieldnames = [
'generation', 'evaluated_individuals', 'min_fitness',
'max_fitness', 'avg_fitness', 'std_fitness'
]
writer = DictWriter(f, fieldnames=fieldnames, dialect='excel')
writer.writeheader()
for csvRow in csvData:
writer.writerow(csvRow)
def run_ga(logger):
if logger is None:
raise Exception("Error: logger is None!")
stats = tools.Statistics(lambda individual: individual.fitness.values)
stats.register("best", np.min, axis=0)
logbook = tools.Logbook()
logbook.header = 'ga', "best"
result = []
toolbox = base.Toolbox()
toolbox.register("individual", init_individual)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
# toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mate", Utils.get_instance().crossover_new_method)
toolbox.register("mutate", Utils.get_instance().mutate_new_method)
toolbox.register("select", tools.selTournament, tournsize=10)
toolbox.register("evaluate", Utils.get_instance().cal_fitness)
for time in range(Utils.get_instance().num_run):
pop = toolbox.population(Utils.get_instance().pop_size)
best_ind = toolbox.clone(pop[0])
prev = -1 # use for termination
count_term = 0 # use for termination
for _ in range(Utils.get_instance().num_generation):
offsprings = map(toolbox.clone, toolbox.select(pop, len(pop) - 1))
offsprings = algorithms.varAnd(offsprings, toolbox,
Utils.get_instance().cx_pb,
Utils.get_instance().mut_pb)
offsprings.append(best_ind)
min_value = float('inf')
invalid_individuals = []
fitness = toolbox.map(toolbox.evaluate, offsprings)
for ind, fit in zip(offsprings, fitness):
if fit == float('inf'):
print("!!!")
else:
invalid_individuals.append(ind)
fitness = toolbox.map(toolbox.evaluate, invalid_individuals)
for ind, fit in zip(invalid_individuals, fitness):
ind.fitness.values = [fit]
if min_value > fit:
min_value = fit
best_ind = toolbox.clone(ind)
b = round(min_value, 6)
if prev == b:
count_term += 1
else:
count_term = 0
pop[:] = invalid_individuals[:]
logger.info(f"{time} - {_} : {b}")
prev = b
if count_term == Utils.get_instance().terminate:
break
record = stats.compile(pop)
logbook.record(ga=time + 1, **record)
logger.info(logbook.stream)
result.append(min_value)
avg = np.mean(result)
std = np.std(result)
mi = np.min(result)
ma = np.max(result)
logger.info([mi, ma, avg, std])
def CMAES_MO(var,weights,funcs_l,sigma,verbose = True, MAXITER = 100, STAGNATION_ITER =10, lambda_=3, mu =5):
NRESTARTS = 10 # Initialization + 9 I-POP restarts
creator.create("MaFitness", base.Fitness, weights=weights)
creator.create("Individual", list, fitness=creator.MaFitness)
toolbox = base.Toolbox()
eval_funcs = lambda x: tuple([f(x) for f in funcs_l])
toolbox.register("evaluate", eval_funcs)
S.Swarm.controller.rez_params()
S.model = var
c = S.extract_genotype()
init_func = lambda c, sigma, size: np.random.normal(c, sigma, size)
toolbox.register("attr_float", init_func, c, sigma, len(var))
toolbox.register("individual", tools.initIterate, creator.Individual, toolbox.attr_float)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", eval_funcs)
halloffame = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: np.array([ind.fitness.values]))
stats.register("average", np.mean)
stats.register("std", np.std)
stats.register("min", np.min)
stats.register("max", np.max)
logbooks = list()
bestvalues = list()
medianvalues = list()
i = 0
t=0
while i < (NRESTARTS):
pop = toolbox.population(n=mu)
strategy = cma.StrategyMultiObjective(centroid=c, sigma=sigma, lambda_=lambda_,population=pop)
toolbox.register("generate", strategy.generate, creator.Individual)
toolbox.register("update", strategy.update)
logbooks.append(tools.Logbook())
logbooks[-1].header = "gen", "evals", "restart", "regime", "std", "min", "avg", "max"
conditions = {"MaxIter": False, "TolHistFun": False, "EqualFunVals": False,
"TolX": False, "TolUpSigma": False, "Stagnation": False,
"ConditionCov": False, "NoEffectAxis": False, "NoEffectCoor": False}
while not any(conditions.values()):
if(t%5 == 0):
S.Swarm.controller.visibility = True
else:
S.Swarm.controller.visibility = False
t = t + 1
# Generate a new population
population = pop + toolbox.generate()
# Evaluate the individuals
fitnesses = toolbox.map(toolbox.evaluate, population)
for ind, fit in zip(population, fitnesses):
ind.fitness.values = fit
halloffame.update(population)
record = stats.compile(population)
logbooks[-1].record(gen=t, restart = i, **record)
if verbose:
print(logbooks[-1].stream)
# Update the strategy with the evaluated individuals
toolbox.update(population)
# Log the best and median value of this population
bestvalues.append(population[-1].fitness.values)
medianvalues.append(population[int(round(len(population)/2.))].fitness.values)
if t >= MAXITER:
# The maximum number of iteration per CMA-ES ran
conditions["MaxIter"] = True
if len(bestvalues) > STAGNATION_ITER and len(medianvalues) > STAGNATION_ITER and \
np.median(bestvalues[-20:]) >= np.median(
bestvalues[-STAGNATION_ITER:-STAGNATION_ITER + 20]) and \
np.median(medianvalues[-20:]) >= np.median(
medianvalues[-STAGNATION_ITER:-STAGNATION_ITER + 20]):
# Stagnation occured
conditions["Stagnation"] = True
pop = [p.fitness.values for p in population[-1:-mu]]
stop_causes = [k for k, v in conditions.items() if v]
print( "Stopped because of condition%s %s" % ((":" if len(stop_causes) == 1 else "s:"), ",".join(stop_causes)))
i += 1
def __init__(
self,
problem: Problem,
mutation: Union[Mutation, DeapMutation] = None,
crossover: DeapCrossover = None,
selection: DeapSelection = None,
encoding: Optional[Union[str, Dict[str, Any]]] = None,
objectives: Optional[Union[str, List[str]]] = None,
objective_weights: Optional[List[float]] = None,
pop_size: int = None,
max_evals: int = None,
mut_rate: float = None,
crossover_rate: float = None,
deap_verbose: bool = None,
):
self._default_crossovers = {
TypeAttribute.LIST_BOOLEAN: DeapCrossover.CX_UNIFORM,
TypeAttribute.LIST_INTEGER: DeapCrossover.CX_ONE_POINT,
TypeAttribute.LIST_INTEGER_SPECIFIC_ARRITY: DeapCrossover.CX_ONE_POINT,
TypeAttribute.PERMUTATION: DeapCrossover.CX_UNIFORM_PARTIALY_MATCHED,
}
self._default_mutations = {
TypeAttribute.LIST_BOOLEAN: DeapMutation.MUT_FLIP_BIT,
TypeAttribute.LIST_INTEGER: DeapMutation.MUT_UNIFORM_INT,
TypeAttribute.LIST_INTEGER_SPECIFIC_ARRITY: DeapMutation.MUT_UNIFORM_INT,
TypeAttribute.PERMUTATION: DeapMutation.MUT_SHUFFLE_INDEXES,
}
self._default_selection = DeapSelection.SEL_TOURNAMENT
self.params_objective_function = ParamsObjectiveFunction(
objective_handling=ObjectiveHandling.MULTI_OBJ,
objectives=objectives,
weights=objective_weights,
sense_function=ModeOptim.MAXIMIZATION,
)
self.evaluate_sol, _ = build_evaluate_function_aggregated(
problem=problem, params_objective_function=self.params_objective_function
)
self.problem = problem
if pop_size is not None:
self._pop_size = pop_size
else:
self._pop_size = 100
if max_evals is not None:
self._max_evals = max_evals
else:
self._max_evals = 100 * self._pop_size
print(
"No value specified for max_evals. Using the default 10*pop_size - This should really be set carefully"
)
if mut_rate is not None:
self._mut_rate = mut_rate
else:
self._mut_rate = 0.1
if crossover_rate is not None:
self._crossover_rate = crossover_rate
else:
self._crossover_rate = 0.9
self.problem = problem
if deap_verbose is not None:
self._deap_verbose = deap_verbose
else:
self._deap_verbose = True
# set encoding
register_solution: EncodingRegister = problem.get_attribute_register()
self._encoding_name = None
self._encoding_variable_name = None
if encoding is not None and isinstance(encoding, str):
# check name specified is in problem register
print(encoding)
if encoding in register_solution.dict_attribute_to_type.keys():
self._encoding_name = encoding
self._encoding_variable_name = register_solution.dict_attribute_to_type[
self._encoding_name
]["name"]
self._encoding_type = register_solution.dict_attribute_to_type[
self._encoding_name
]["type"][0]
self.n = register_solution.dict_attribute_to_type[self._encoding_name][
"n"
]
if self._encoding_type == TypeAttribute.LIST_INTEGER:
self.arrity = register_solution.dict_attribute_to_type[
self._encoding_name
]["arrity"]
self.arrities = [self.arrity for i in range(self.n)]
else:
self.arrity = None
if self._encoding_type == TypeAttribute.LIST_INTEGER_SPECIFIC_ARRITY:
self.arrities = register_solution.dict_attribute_to_type[
self._encoding_name
]["arrities"]
# else:
# self.arrities = None
if encoding is not None and isinstance(encoding, Dict):
# check there is a type key and a n key
if (
"name" in encoding.keys()
and "type" in encoding.keys()
and "n" in encoding.keys()
):
self._encoding_name = "custom"
self._encoding_variable_name = encoding["name"]
self._encoding_type = encoding["type"][0]
self.n = encoding["n"]
if "arrity" in encoding.keys():
self.arrity = encoding["arrity"]
self.arrities = [self.arrity for i in range(self.n)]
if "arrities" in encoding.keys():
self.arrities = register_solution.dict_attribute_to_type[
self._encoding_name
]["arrities"]
else:
print(
"Erroneous encoding provided as input (encoding name not matching encoding of problem or custom "
"definition not respecting encoding dict entry format, trying to use default one instead"
)
if self._encoding_name is None:
if len(register_solution.dict_attribute_to_type.keys()) == 0:
raise Exception(
"An encoding of type TypeAttribute should be specified or at least 1 TypeAttribute "
"should be defined in the RegisterSolution of your Problem"
)
print(register_solution.dict_attribute_to_type)
print(register_solution.dict_attribute_to_type.keys())
self._encoding_name = list(register_solution.dict_attribute_to_type.keys())[
0
]
self._encoding_variable_name = register_solution.dict_attribute_to_type[
self._encoding_name
]["name"]
self._encoding_type = register_solution.dict_attribute_to_type[
self._encoding_name
]["type"][
0
] # TODO : while it's usually a list we could also have a unique value(not a list)
self.n = register_solution.dict_attribute_to_type[self._encoding_name]["n"]
if self._encoding_type == TypeAttribute.LIST_INTEGER:
self.arrity = register_solution.dict_attribute_to_type[
self._encoding_name
]["arrity"]
self.arrities = [self.arrity for i in range(self.n)]
else:
self.arrity = None
if self._encoding_type == TypeAttribute.LIST_INTEGER_SPECIFIC_ARRITY:
self.arrities = register_solution.dict_attribute_to_type[
self._encoding_name
]["arrities"]
# else:
# self.arrities = None
if self._encoding_type == TypeAttribute.LIST_BOOLEAN:
self.arrity = 2
self.arities = [2 for i in range(self.n)]
print(
"Encoding used by the GA: "
+ self._encoding_name
+ ": "
+ str(self._encoding_type)
+ " of length "
+ str(self.n)
)
self._objectives = objectives
print("_objectives: ", self._objectives)
self._objective_weights = objective_weights
if (
(self._objective_weights is None)
or self._objective_weights is not None
and (len(self._objective_weights) != len(self._objectives))
):
print(
"Objective weight issue: no weight given or size of weights and objectives lists mismatch. "
"Setting all weights to default 1 value."
)
self._objective_weights = [1 for i in range(len(self._objectives))]
if selection is None:
self._selection_type = self._default_selection
else:
self._selection_type = selection
nobj = len(self._objectives)
ref_points = tools.uniform_reference_points(nobj=nobj)
# DEAP toolbox setup
self._toolbox = base.Toolbox()
# Define representation
creator.create("fitness", base.Fitness, weights=tuple(self._objective_weights))
creator.create(
"individual", list, fitness=creator.fitness
) # associate the fitness function to the individual type
# Create the individuals required by the encoding
if self._encoding_type == TypeAttribute.LIST_BOOLEAN:
self._toolbox.register(
"bit", random.randint, 0, 1
) # Each element of a solution is a bit (i.e. an int between 0 and 1 incl.)
self._toolbox.register(
"individual",
tools.initRepeat,
creator.individual,
self._toolbox.bit,
n=self.n,
) # An individual (aka solution) contains n bits
elif self._encoding_type == TypeAttribute.PERMUTATION:
self._toolbox.register(
"permutation_indices", random.sample, range(self.n), self.n
)
self._toolbox.register(
"individual",
tools.initIterate,
creator.individual,
self._toolbox.permutation_indices,
)
elif self._encoding_type == TypeAttribute.LIST_INTEGER:
self._toolbox.register("int_val", random.randint, 0, self.arrity - 1)
self._toolbox.register(
"individual",
tools.initRepeat,
creator.individual,
self._toolbox.int_val,
n=self.n,
)
elif self._encoding_type == TypeAttribute.LIST_INTEGER_SPECIFIC_ARRITY:
gen_idx = lambda: [
random.randint(0, arrity - 1) for arrity in self.arrities
]
self._toolbox.register(
"individual", tools.initIterate, creator.individual, gen_idx
)
self._toolbox.register(
"population",
tools.initRepeat,
list,
self._toolbox.individual,
n=self._pop_size,
) # A population is made of pop_size individuals
# Define objective function
self._toolbox.register(
"evaluate",
self.evaluate_problem,
)
# Define crossover
if crossover is None:
self._crossover = self._default_crossovers[self._encoding_type]
else:
self._crossover = crossover
# if self._encoding_type == TypeAttribute.LIST_BOOLEAN:
if self._crossover == DeapCrossover.CX_UNIFORM:
self._toolbox.register("mate", tools.cxUniform, indpb=self._crossover_rate)
elif self._crossover == DeapCrossover.CX_ONE_POINT:
self._toolbox.register("mate", tools.cxOnePoint)
elif self._crossover == DeapCrossover.CX_TWO_POINT:
self._toolbox.register("mate", tools.cxTwoPoint)
# elif self._encoding_type == TypeAttribute.PERMUTATION:
elif self._crossover == DeapCrossover.CX_UNIFORM_PARTIALY_MATCHED:
self._toolbox.register("mate", tools.cxUniformPartialyMatched, indpb=0.5)
elif self._crossover == DeapCrossover.CX_ORDERED:
self._toolbox.register("mate", tools.cxOrdered)
elif self._crossover == DeapCrossover.CX_PARTIALY_MATCHED:
self._toolbox.register("mate", tools.cxPartialyMatched)
else:
print("Crossover of specified type not handled!")
# Define mutation
if mutation is None:
self._mutation = self._default_mutations[self._encoding_type]
else:
self._mutation = mutation
if isinstance(self._mutation, Mutation):
self._toolbox.register(
"mutate",
generic_mutate_wrapper,
problem=self.problem,
encoding_name=self._encoding_variable_name,
indpb=self._mut_rate,
solution_fn=self.problem.get_solution_type(),
custom_mutation=mutation,
)
elif isinstance(self._mutation, DeapMutation):
if self._mutation == DeapMutation.MUT_FLIP_BIT:
self._toolbox.register(
"mutate", tools.mutFlipBit, indpb=self._mut_rate
) # Choice of mutation operator
elif self._mutation == DeapMutation.MUT_SHUFFLE_INDEXES:
self._toolbox.register(
"mutate", tools.mutShuffleIndexes, indpb=self._mut_rate
) # Choice of mutation operator
elif self._mutation == DeapMutation.MUT_UNIFORM_INT:
# self._toolbox.register("mutate", tools.mutUniformInt, low=0, up=self.arrity-1, indpb=self._mut_rate)
self._toolbox.register(
"mutate",
tools.mutUniformInt,
low=0,
up=self.arrities,
indpb=self._mut_rate,
)
# No choice of selection: In NSGA, only 1 selection: Non Dominated Sorted Selection
self._toolbox.register("select", tools.selNSGA3, ref_points=ref_points)
def NSGA(funcs_l, weights, var, sigma, MU=4, NGEN=50,wide_search=1.5):
IND_SIZE = len(var)
creator.create("MaFitness", base.Fitness, weights=weights)
creator.create("Individual", list, fitness=creator.MaFitness)
toolbox = base.Toolbox()
records = {}
eval_funcs = lambda x: tuple([f(x) for f in funcs_l])
toolbox.register("evaluate", eval_funcs)
S.model = var
c = S.extract_genotype()
print("c = ",c)
init_func = lambda c, sigma, size: np.random.normal(c, sigma, size)
bound_max = list(wide_search*c)
bound_min = list(-wide_search*c)
toolbox.register("attr_float", init_func, c, sigma, len(var))
toolbox.register("individual", tools.initIterate, creator.Individual, toolbox.attr_float)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
paretofront = tools.ParetoFront()
#toolbox.register("mutate", tools.mutGaussian, mu=c, sigma=sigma, indpb=1.0 / IND_SIZE)
toolbox.register("mutate", tools.mutPolynomialBounded, low=bound_min, up=bound_max, eta=20.0, indpb=1.0 / IND_SIZE)
toolbox.register("mate", tools.cxSimulatedBinaryBounded, low=bound_min, up=bound_min, eta=20.0)
toolbox.register("select", tools.selNSGA2)
CXPB = 0.6
L = []
turing_spot = tools.Statistics(lambda ind: ind.fitness.values[0])
rectanglitude = tools.Statistics(lambda ind: ind.fitness.values[1])
mstats = tools.MultiStatistics(Rectanglitude=rectanglitude ,Turing_Spot = turing_spot)
mstats.register("avg", np.mean, axis=0)
mstats.register("max", np.max, axis=0)
logbook = tools.Logbook()
pop = toolbox.population(n=MU)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in pop if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# This is just to assign the crowding distance to the individuals
# no actual selection is done
pop = toolbox.select(pop, len(pop))
record = mstats.compile(pop)
#print("Record =" ,record)
logbook.record( **record)
print(logbook.stream)
# Begin the generational process
for gen in range(1, NGEN):
# Vary the population
if(gen%5==0):
S.Swarm.controller.withVisiblite(True)
offspring = tools.selTournamentDCD(pop, len(pop))
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
# 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
# Select the next generation population
pop = toolbox.select(pop + offspring, MU)
record = mstats.compile(pop)
logbook.record(g=gen, **record)
records[gen] = record
print(logbook.stream)
return pop, paretofront,records
data = input_output.read_dataset_list(DATASET_FOLDER, files)
data_test = input_output.read_dataset_list(DATASET_FOLDER, [file_test])
X_train, y_train, X_test, y_test = input_output.balance_dataset(
data, data_columns=list(range(0, n_att)), label_column=75, test_size=0)
#_, _, X_test, y_test = input_output.balance_dataset(data_test, data_columns = list(range(0,n_att)), label_column = 76, test_size = 0.999)
X_test = data_test[data_test.columns[0:75]].values
y_test = data_test[data_test.columns[76]].values
# One hot vector
y_train = np.array([[x, int(not x)] for x in y_train])
y_test = np.array([[x, int(not x)] for x in y_test])
toolbox = base.Toolbox()
# Individual and population
toolbox.register("expr", gp.genHalfAndHalf, pset=pset, min_=1, max_=3)
toolbox.register("individual", tools.initIterate, creator.Individual,
toolbox.expr)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("compile", gp.compile, pset=pset)
# Evaluation method
toolbox.register("evaluate",
fitness.eval_tree,
clf=classifier,
X_train=X_train,
y_train=y_train,
X_test=X_test,
y_true=y_test,
def evolution(
env: Environment, number_of_rays: int, ray_distribution: str,
angle_lower_bound: int, angle_upper_bound: int,
length_lower_bound: int, length_upper_bound: int,
no_of_reflective_segments: int, distance_limit: int, length_limit: int,
population_size: int, number_of_generations: int, xover_prob: float,
mut_angle_prob: float, mut_length_prob: float,
shift_segment_prob: float, rotate_segment_prob: float,
resize_segment_prob: float, tilt_base_prob: float, base_length: int,
base_slope: int, base_angle_limit_min: int, base_angle_limit_max: int):
# Initiating evolutionary algorithm
creator.create("Fitness", base.Fitness, weights=(1.0, ))
base.Fitness.weights = (1.0, 10.0, 5.0, -1.0)
creator.create("Individual", Component, fitness=creator.Fitness)
toolbox = base.Toolbox()
toolbox.register("individual",
creator.Individual,
env=env,
number_of_rays=number_of_rays,
ray_distribution=ray_distribution,
angle_lower_bound=angle_lower_bound,
angle_upper_bound=angle_upper_bound,
length_lower_bound=length_lower_bound,
length_upper_bound=length_upper_bound,
no_of_reflective_segments=no_of_reflective_segments,
distance_limit=distance_limit,
length_limit=length_limit,
base_length=base_length,
base_slope=base_slope)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", evaluate)
if env.quality_criterion == "nsgaii":
toolbox.register("select", tools.selNSGA2)
else:
toolbox.register("select", tools.selTournament, tournsize=2)
# Initiating first population
pop = toolbox.population(n=population_size)
# Evaluating fitness
fitnesses = []
for item in pop:
fitnesses.append(evaluate(item, env))
for ind, fit in zip(pop, fitnesses):
ind.fitness = fit
if env.quality_criterion != "nsgaii":
if env.configuration == "two connected":
stats_line = f"generation, best fitness, average fitness, fitness array, left segment angle, " \
f"left segment length, right segment angle, right segment length \n"
else:
stats_line = f"generation, best fitness, average fitness, fitness array, reflective segments \n"
log_stats_init(f"stats", stats_line)
# Initiating elitism
if env.quality_criterion == "nsgaii":
pop = toolbox.select(pop, len(pop))
hof = tools.ParetoFront()
hof.update(pop)
else:
hof = HallOfFame(1)
hof.update(pop)
print("Start of evolution")
# Begin the evolution
for g in range(number_of_generations):
# A new generation
print(f"-- Generation {g} --")
# Select the next generation individuals
if env.quality_criterion == "nsgaii":
offspring = tools.selTournamentDCD(pop, len(pop))
offspring = [toolbox.clone(ind) for ind in offspring]
else:
offspring = toolbox.select(pop, len(pop))
offspring = list(map(toolbox.clone, offspring))
# Apply crossover and mutation on the offspring
for child1, child2 in zip(offspring[::2], offspring[1::2]):
# cross two individuals with probability xover_prob
if env.configuration == "multiple free":
if random.random() < xover_prob:
x_over_multiple_segments(child1, child2)
# fitness values of the children must be recalculated later
child1.fitness = None
child2.fitness = None
if env.configuration == "two connected":
if random.random() < xover_prob:
x_over_two_segments(child1, child2)
# fitness values of the children must be recalculated later
child1.fitness = None
child2.fitness = None
for mutant in offspring:
if env.configuration == "multiple free":
if random.random() < shift_segment_prob:
mutant.reflective_segments = shift_one_segment(
mutant.reflective_segments, "x")
mutant.fitness = None
if random.random() < shift_segment_prob:
mutant.reflective_segments = shift_one_segment(
mutant.reflective_segments, "y")
mutant.fitness = None
if random.random() < rotate_segment_prob:
mutant.reflective_segments = rotate_one_segment(
mutant.reflective_segments)
mutant.fitness = None
if random.random() < resize_segment_prob:
mutant.reflective_segments = resize_one_segment(
mutant.reflective_segments)
mutant.fitness = None
if random.random() < tilt_base_prob:
mutant.base_slope = tilt_base(mutant.base_slope,
base_angle_limit_min,
base_angle_limit_max)
mutant.calculate_base()
mutant.original_rays = mutant.sample_rays(
number_of_rays, ray_distribution)
mutant.fitness = None
if env.configuration == "two connected":
if random.random() < mut_angle_prob:
mutate_angle(mutant)
mutant.fitness = None
if random.random() < mut_length_prob:
mutate_length(mutant, length_upper_bound,
length_lower_bound)
mutant.fitness = None
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if ind.fitness is None]
fitnesses = []
for item in invalid_ind:
fitnesses.append(evaluate(item, env))
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness = fit
if env.quality_criterion == "nsgaii":
pop = toolbox.select(offspring + pop, population_size)
else:
pop[:] = offspring
hof.update(pop)
best_ind = hof[0]
fitnesses = []
for item in pop:
fitnesses.append(item.fitness)
print(fitnesses)
if env.configuration == "two connected" and env.quality_criterion != "nsgaii":
stats_line = f"{g+1}, {best_ind.fitness}, {sum(fitnesses) / population_size}, {best_ind.fitness_array}, " \
f"left angle: {180-best_ind.left_angle+best_ind.base_slope}, " \
f"left length: {best_ind.left_length_coef*best_ind.base_length}, " \
f"right angle: {best_ind.right_angle-best_ind.base_slope}, " \
f"right length: {best_ind.right_length_coef*best_ind.base_length} "
log_stats_append(f"stats", stats_line)
if env.configuration == "multiple free" and env.quality_criterion != "nsgaii":
stats_line = f"{g + 1}, {best_ind.fitness}, {sum(fitnesses) / population_size}, {best_ind.fitness_array}, "
for reflective_segment in best_ind.reflective_segments:
dimensions = f" start: {reflective_segment.p1}, end: {reflective_segment.p2}"
stats_line = stats_line + dimensions
log_stats_append(f"stats", stats_line)
print(f"Best individual has fitness: {best_ind.fitness}")
draw(best_ind, f"best{g}", env)
if env.quality_criterion == "nsgaii":
unique = choose_unique(hof, env.configuration)
stats_line = f"index, fitness array"
log_stats_init(f"stats", stats_line)
for index in range(len(unique)):
draw(unique[index], f"unique{index}", env)
if env.configuration == "two connected":
stats_line = f"{index}, {unique[index].fitness}," \
f"left angle: {180-unique[index].left_angle+unique[index].base_slope}, " \
f"left length: {unique[index].left_length_coef*unique[index].base_length}, " \
f"right angle: {unique[index].right_angle-unique[index].base_slope}, " \
f"right length: {unique[index].right_length_coef*unique[index].base_length} "
else:
stats_line = f"{index}, {unique[index].fitness}, {unique[index].base_slope}"
for reflective_segment in unique[index].reflective_segments:
dimensions = f" start: {reflective_segment.p1}, end: {reflective_segment.p2}"
stats_line = stats_line + dimensions
log_stats_append(f"stats", stats_line)
print("-- End of (successful) evolution --")
print("--")
