def breed_loop(N, data, gdata, save_interval):
ffts = []
min_errs = []
for n in range(N):
# print("Generation:", n)
errors, goal = gen.fit_all(data, gdata)
new_data = np.zeros(np.shape(data))
for i in range(len(data)//2):
if goal:
print("Goal!")
r = np.arange(len(errors))
i1, i2 = np.random.choice(r, 2, p=errors)
cross1, cross2 = gen.crossover(data[i1], data[i2])
cross1, cross2 = gen.mutate(cross1, get_temp(n+1)), gen.mutate(cross2, get_temp(n+1))
# cross1, cross2 = gen.mutate(cross1, .5), gen.mutate(cross2, .5)
new_data[i], new_data[i+(len(data)//2)] = cross1, cross2
if n % save_interval == 0 and i == 0:
play_fft(cross1)
data = new_data
if n % 25 == 0:
print(f'min error {np.amin(errors)}')
min_errs.append(np.amin(errors))
return ffts, min_errs
def main():
pop_size = 1000
max_runs = 50
mutate_ratio = 0.2
# Which data set to use.
mode = 1
random.seed()
pop = []
# Create a random population of trees.
for i in range(pop_size):
pop.append(ExprTree(mode))
print "Population created."
for tree in pop:
print tree
for i in range(max_runs):
print "Beginning crossover " + str(i) + ":"
# Crossover and mutate population.
genetic.mutate(pop, mutate_ratio, mode)
pop = genetic.crossover(pop, mode)
print "Crossover " + str(i) + " complete."
def spawn_child(self, nb=1, train=False):
if len(self.nn_bots) > 0:
for i in range(nb):
nb1 = random.randint(0, len(self.nn_bots) - 1)
nb2 = random.randint(0, len(self.nn_bots) - 1)
parent1 = self.nn_bots[nb1] # parent 1
parent2 = self.nn_bots[nb2] # parent 2
# create a child by breeding to random bots
child_weights = croisement(parent1.model.weights,
parent2.model.weights, 1)[0]
mutate(child_weights, 1, 1)
if self.current_nb_step % 2 == 0:
x, y = self.g_free_xy(parent1.x, parent1.y, 4)
else:
x, y = self.g_free_xy(parent2.x, parent2.y, 4)
child = NN_bot(self.map, x, y, self, train=train)
child.model.weights = child_weights
self.map.board[x, y, 0] = 1
self.bots.append(child)
self.nn_bots.append(child)
else:
self.load_bots(nb, train)
def test_mutation(function1, function2):
"""Test mutation function"""
population = [
[1523, 42, 0, 1, 1, 2045, 537, 1, 1, 2, 2, 0, 0],
[1971, 117, 0, 1, 0, 1140, 1737, 1, 1, 2, 2, 0, 0],
[882, 101, 1, 0, 0, 986, 644, 0, 1, 1, 5, 0, 0],
[1529, 70, 1, 1, 1, 1462, 1834, 0, 0, 1, 1, 1, 0],
]
expected_result = [
[1523, 42, 0, 1, 1, 2045, 537, 1, 1, 2, 2, 0, 0],
[1971, 117, 0, 1, 0, 1140, 1737, 1, 1, 2, 2, 0, 0],
[882, 101, 1, 0, 0, 986, 644, 0, 1, 1, 5, 0, 0],
[1529, 70, 1, 1, 1, 1462, 1834, 0, 0, 1, 1, 1, 0]
]
result = genetic.mutate(population)
assert(result == expected_result)
def main():
map_size = 100
p_type = 10 # dont get when we will use it
max_route_length = 150
population_size = 30
number_of_each_new_generation = 10
number_of_couples = int(
(population_size - number_of_each_new_generation) / 2)
probability = 0.05
the_map = initialize(p_type, map_size)
population = create_starting_population(max_route_length, population_size,
the_map)
last_distance = 1000000000
for i in range(0, 100):
scores = score_population(population, the_map)
new_population = []
best = population[np.argmin(scores)]
number_of_moves = len(best)
distance = fitness(best, the_map)
if distance != last_distance:
print(
'Iteration %i: Best so far is %i steps for a distance of %f' %
(i, number_of_moves, distance))
plot_best(the_map, best, i)
for j in range(0, number_of_couples):
new_route1, new_route2 = crossover(
population[pick_breeder(scores)],
population[pick_breeder(scores)])
new_population.extend([new_route1, new_route2])
# mutate the current members of new_population
for j in range(0, len(new_population)):
new_population[j] = mutate(new_population[j], probability, the_map)
new_population.append(population[np.argmin(scores)])
while len(new_population) < population_size:
new_population.append(create_new_member(max_route_length, the_map))
population = new_population[::] # copy a values
def mitose(self):
if self.g_cd_repro() == 0:
self.incr_cd_repro(20)
self.incr_energy(-5) # loose of energy to make the child
# energy that will be transfered to the child
energy_to_child = 5
x = -1
y = -1
# TODO: faire une fonction pour rendre ca plus propre
if self.y - 2 > 0:
if self.map.cellLibre(self.x, self.y-1) == 0:
x = self.x
y = self.y - 1
elif self.y + 2 < self.map.height - 1:
if self.map.cellLibre(self.x, self.y+1) == 0:
x = self.x
y = self.y + 1
elif self.x - 2 > 0:
if self.map.cellLibre(self.x-1, self.y) == 0:
x = self.x - 1
y = self.y
elif self.x + 2 < self.map.height - 1:
if self.map.cellLibre(self.x+1, self.y) == 0:
x = self.x + 1
y = self.y
else:
# no place to put the child
self.incr_energy(energy_to_child)
self.incr_energy(-1)
if x == -1:
pass
else:
new_model = genetic.mutate(self.model.weights, 1, 1)
new_bot = NN_bot(self.map, x, y, self.sim, new_model)
new_bot.s_energy(energy_to_child)
self.sim.add_bots([new_bot])
ff = ff_init # ff used in the loop set to ff_init
ff_av = ff_av_init
ff_av_points, ff_max_points, ff_total_points, iteration_points = [], [], [], []
# MAIN LOOP
while ff_av < 1: # repeat until all individuals have fitness = 1
ff.sort(key=lambda tup: tup[0]) # sort ff by first digit in each tuple
selected = selections.select_rank(ff)
new_x = genetic.mate(x, selected, crossover_prob)
genetic.save_elite(x, new_x)
x = new_x
mutated = genetic.mutate(x, mutation_prob)
if mutated:
mutation_count += 1
ff = genetic.ff(x)
ff_av = genetic.ff_av(ff)
ff_max = genetic.ff_max(ff)
iterations += 1
ff_av_points.append(ff_av)
ff_max_points.append(ff_max)
ff_total_points.append(genetic.ff_total(ff))
iteration_points.append(iterations)
max_crossover = population_init / 2 * iterations
# popcpy = g.mutate(pop)
# print(popcpy)
# popcpy = g.mutate(pop)
# print(popcpy)
# popcpy = g.mutate(pop)
# print(popcpy)
# print(type(popcpy))
generations = 0
# print(pop[1])
while generations <= 100:
generations += 1
pop = g.mutate(pop)
newpop = [0 for _ in range(100)]
newpop[0] = pop[g.getBest(pop, fn.rast, -5.12, 5.12, 17)]
for i in range(1, len(newpop)):
newpop[i] = g.select(pop, fn.rast, -5.12, 5.12, 17)
pop = newpop
for i in range(100):
print(fn.rast(fn.decode(pop[i], -5.12, 5.12, 17)), end=" ")
print("\n")
def combo_scaling(iterations: int, plot: bool, show_matrix: bool,
population_size: int, mutation_probability: float,
initial_matrix: str, smoothness: float, eval_type: str,
breed: bool, breed_disable: int, save: bool,
shape_covariance: bool, normalize_by_cross_section: bool,
normalize_by_bins: bool, pseudoinverse: bool,
normalization_penalty: bool, custom_covariance: str) -> None:
if initial_matrix == 'ones':
original_matrix = np.ones((24, 24))
else:
with open(initial_matrix, 'rb') as f:
original_matrix = pickle.load(f).reshape((24, 24))
for i in range(24):
for j in range(i + 1, 24):
original_matrix[j][i] = 0
original_matrix = original_matrix.reshape(24 * 24)
experiments = [('minerva_neutrino', 156), ('minerva_antyneutrino', 60),
('T2K_neutrino', 58), ('T2K_antyneutrino', 58)]
experimental_data = []
for experiment, bins in experiments:
data = utils.import_data_from_path(f"Data/{experiment}")
experiment_info = utils.load_experimental_data(experiment)
if "minerva" in experiment:
events = utils.events_to_cross_section(
data.events.reshape(
(24 * 24, -1)), data.nof_events, data.cross_section,
experiment_info[0].shape, *experiment_info[4:6])
if custom_covariance and experiment == 'minerva_neutrino':
with open(custom_covariance, 'rb') as f:
covariance_matrix = np.linalg.pinv(pickle.load(f))
if shape_covariance:
if experiment == 'minerva_neutrino':
import covariance_matrix
covariance = covariance_matrix.covariance
elif experiment == 'minerva_antyneutrino':
from minerva_antyneutrino import minerva_antyneutrino_covariance
covariance = minerva_antyneutrino_covariance
if custom_covariance and experiment == 'minerva_neutrino':
with open(custom_covariance, 'rb') as f:
covariance = pickle.load(f)
data = experiment_info[0].reshape(-1)
shape_matrix, _, _ = utils.shape_matrix_extraction(
data, covariance)
covariance_matrix = shape_matrix
if pseudoinverse:
covariance_matrix = np.linalg.pinv(covariance_matrix)
else:
covariance_matrix = np.linalg.inv(covariance_matrix)
experiment_info[2] = covariance_matrix
else:
events = data.events
experimental_data.append(
Experiment(experiment, events, experiment_info, bins))
combined_score = Combined_score(experimental_data, normalization_penalty)
# tmp_matrix = np.ones((24 * 24))
score = combined_score(original_matrix, normalize_by_bins,
normalize_by_cross_section)
print(f"Score without reweighting:\n{score}")
population = [original_matrix]
population += [
mutate(original_matrix, mutation_probability, smoothness)
for _ in range(1, population_size)
]
if eval_type == 'chi2_cov':
key = lambda m: np.sum(m[0][:, 0])
elif eval_type == 'chi2_std':
key = lambda m: np.sum(m[0][:, 1])
elif eval_type == 'chi2_both':
key = lambda m: np.sum(m[0])
smoothness = smoothness if 0 < smoothness < 1 else 0
start = time.time()
try:
for i_no in range(1, iterations + 1):
chi2 = [
combined_score(population[i], normalize_by_bins,
normalize_by_cross_section)
for i in range(population_size)
]
population_with_score = list(zip(chi2, population))
population_with_score.sort(key=key, reverse=False)
print(i_no, population_with_score[0][0][:, 0],
sum(population_with_score[0][0][:, 0]))
if breed_disable:
if i_no > breed_disable:
breed = False
if breed:
population = new_population(population_with_score,
mutation_probability, smoothness)
else:
population[0] = population_with_score[0][1]
for i in range(1, population_size):
population[i] = mutate(population_with_score[0][1],
mutation_probability, smoothness)
except KeyboardInterrupt:
print("Manually stopped computation")
elapsed = time.time() - start
minutes = elapsed / 60
seconds = int(elapsed) % 60
print(f"Calculated in: {int(minutes)}m{seconds}s")
if save:
save_chi2 = population_with_score[0][0]
config = {
'iterations': i_no,
'population_size': population_size,
'mutation_probability': mutation_probability,
'initial_matrix': initial_matrix,
'smoothness': smoothness if smoothness else 1,
'eval_type': eval_type,
'breed': breed,
'chi2_cov': save_chi2[:, 0],
'chi2_std': save_chi2[:, 1]
}
summed_chi2 = np.sum(save_chi2, axis=0)
name = f'scale_cov{summed_chi2[0]:.2f}_std{summed_chi2[1]:.2f}.pkl'
with open(os.path.join('Combined_scaling', name), 'wb') as file:
pickle.dump(population_with_score[0][1].reshape(24, 24), file)
pickle.dump(config, file)
print(f"Scaling matrix saved to {name}")