def solve(self):
"""
This method solves the problem using NTGA algorithm
"""
generation_limit = int(config.get('run_config', 'generation_limit'))
self.generate_initial_population()
new_population = []
print("Generation limit:", str(generation_limit))
for i in range(generation_limit):
print("generation: ", i)
self.population = self.evaluate(self.population)
self.non_dominated_set.adds(self.population)
while len(new_population) < self.population_size:
parents = self.selection()
children = mutation(crossover(parents))
for child in children:
count = 0
while (child in new_population) or children[0] == children[1]:
count += 1
mutate(child)
if count > 100:
break
new_population += children
self.population = new_population
new_population = []
return self.non_dominated_set
def get_good_solution(task,
crossover_rate=CROSSOVER_RATE,
mutation_rate=MUTATION_RATE,
tournament_size=TOURNAMENT_SIZE,
population_size=POPULATION_SIZE):
best_individuals_values = np.empty(MAX_ITERATIONS)
population = init_population(task, population_size)
outer_iterator = 0
best_individual = 0
best_individual_value = 0
global_best_individual = 0
global_best_individual_value = 0
print('Initial value of the knapsack =',
population.individuals[0].evaluate())
while outer_iterator < MAX_ITERATIONS:
inner_iterator = 0
new_population = Population()
while inner_iterator < population_size:
parent1 = tournament(population, tournament_size)
parent2 = tournament(population, tournament_size)
child = crossover(parent1, parent2, crossover_rate)
mutate(child, mutation_rate)
new_population.add_individual(child)
inner_iterator += 1
best_individual = population.best_individual()
best_individual_value = best_individual.evaluate()
if best_individual_value >= global_best_individual_value:
global_best_individual = best_individual
global_best_individual_value = best_individual_value
new_population.set_first_individual(global_best_individual)
population = new_population
best_individuals_values[outer_iterator] = global_best_individual_value
outer_iterator += 1
return global_best_individual, best_individuals_values
def main(pop_size, mutation_rate, nr_generations):
growth = []
# 1. Create the population
population = initial_population(pop_size)
for j in range(nr_generations):
# population = nextgeneration(population, mutation_rate)
listscores = []
genfitness = 0
# 2. Determine fitness
# check for the entire population the fitness
for index, data in enumerate(population):
fitness = fitnesscheck(data)
listscores.append([index, fitness])
genfitness += fitness
print("De "+ str(j) + "e generatie heeft een gemiddelde score van ", genfitness/pop_size)
# Make N new individuals for the next generation
newpopulation = []
for i in range(pop_size):
# 3. Select the mating pool
# Kiest twee parents tournament style
win1, win2 = pickparents(pop_size, listscores)
# 4. Breed
# Crossbreed een nieuw child
newpopulation.append(cross(population[win1], population[win2]))
# 5. Mutate
mutation_decision = random.randint(0, 100)
if mutation_decision > 90:
mutate(newpopulation[i])
population = newpopulation
growth.append(genfitness/pop_size)
print(growth)
plt.plot(growth)
plt.show()
with open("endresult.txt", "w") as txt_file:
for data in population:
for line in data:
txt_file.write(" ".join(str(line)) + "\n")
def GA(M, N, MaxGen, Pc, Pm, Er, bb, method):
population = innit.initialize(M, N)
fitness = []
for i in range(M):
fitness.append(bb.fitnes(population.genes[i]))
population['fitness'] = fitness
newpop = np.array(population.drop(['fitness'], axis=1))
print("generation #{0}".format(1))
fitnesses = [0]
for i in range(1, MaxGen):
print("generation #{0}".format(i + 1))
for j in range(0, M, 2):
p1, p2 = sel.selection(population)
chilld1, chilld2 = cs.cross(p1, p2, Pc, method)
child1 = mt.mutate(chilld1, Pm)
child2 = mt.mutate(chilld2, Pm)
newpop[j] = child1
newpop[j + 1] = child2
newpopulation = pd.DataFrame(newpop, columns=['genes'])
fitness1 = []
for i in range(M):
fitness1.append(bb.fitnes(newpopulation.genes[i]))
newpopulation['fitness'] = fitness1
newpopulation = el.ellist(newpopulation, Er)
population = newpopulation.copy()
newpopulation.sort_values(['fitness'], inplace=True, ascending=False)
newpopulation = newpopulation.reset_index(drop=True)
maxx = max(newpopulation.fitness)
#print(maxx)
#print(maxx,newpopulation.genes[newpopulation.fitness == maxx].iloc[0])
fitnesses.append(maxx)
return fitnesses
def operate(gen_in, mu_in, lamb_da_in, boundary_in, gen, maxgen):
crosser = np.random.randint(0, 7)
lambda_gen = crossover(crosser,
gen_in,
mu_in,
lamb_da_in,
objective_function,
BLX_alpha=0.5,
SPX_epsilon=1,
SBX_n=2,
UNDX_sigma_xi=0.8,
UNDX_sigma_eta=0.707,
DE_K=0.5,
DE_F=0.3)
mutant = np.random.randint(0, 7)
lambda_gen = mutate(mutant,
lambda_gen,
boundary_in,
gen,
objective_function,
normal_sigma=0.5,
uniform_pm=0.1,
boundary_pm=0.1,
maxgen=maxgen,
b=5,
cauchy_sigma=0.5,
delta_max=20,
n=2,
DE_K=0.5,
DE_F=0.3)
fixme = np.random.randint(0, 2)
return fix(fixme, lambda_gen, boundary_in)
def genetic_algorithm(tournament_size=TOURNAMENT_SIZE,
crossover_rate=CROSSOVER_RATE,
mutation_rate=MUTATION_RATE,
population_size=POPULATION_SIZE):
task = read(input_file=OUTPUT_FILE)
population = init_population(NUMBER_OF_ITEMS, population_size)
best_ind = []
i = 0
new_pop_val = []
while i < ITERATIONS:
# print(i)
j = 0
new_pop_arr = []
while j < population_size:
parent1 = population.tournament(tournament_size, task)
parent2 = population.tournament(tournament_size, task)
child = crossover(parent1, parent2, crossover_rate)
mutated_child = mutate(child, mutation_rate)
new_pop_arr.append(mutated_child)
j += 1
population = Population(new_pop_arr)
i += 1
best_from_pop = population.tournament(population_size, task)
best_evaluated = best_from_pop.best_individual(task)
new_pop_val.append(best_evaluated)
return new_pop_val
def next_generation(previous_generation):
next_generation = []
if (previous_generation == None):
for _ in range(constant.mew):
individual = Individual()
#individual.set_fitness(classification_rate(individual.features)
#print(str(individual.features)+" fitness: "+str(individual.fitness))
next_generation.append(individual)
return next_generation
#individuls retained from previous population
individuals_to_retain = best_individuals(previous_generation,
constant.retain_previous)
for individual in individuals_to_retain:
#print("retained"+str(individual.features)+" fitness: "+str(individual.fitness))
next_generation.append(individual)
#crossover population
#mating_pool=[]
#for _ in range(constant.mating_pool_size):
#to_mate=select_individual(previous_generation)
#mating_pool.append(to_mate)
for _ in range(constant.mew - constant.retain_previous):
male = select_individual(previous_generation)
#print("male selected for mating"+str(male.features)+" fitness: "+str(male.fitness))
female = select_individual(previous_generation)
#print("female selected for mating"+str(female.features)+" fitness: "+str(female.fitness))
child = crossover(male, female)
#print("after crossover"+str(child.features)+" fitness: "+str(child.fitness))
mutated_child = mutate(child)
#print("after mutation"+str(mutated_child.features)+" fitness: "+str(mutated_child.fitness))
next_generation.append(mutated_child)
return next_generation
def main(popsize,gens):
growth = []
# Opent random start population
alldata = genrandomstart(popsize)
for j in range(gens):
listscores = []
genfitness = 0
# check for the entire population the fitness
for index, data in enumerate(alldata):
fitness = fitnesscheck(data)
listscores.append([index, fitness])
genfitness += fitness
print("De "+ str(j) + "e generatie heeft een gemiddelde score van ", genfitness/popsize)
# Make N new individuals for the next generation
newpopulation = []
for i in range(int(popsize/2)):
# Kiest twee parents tournament style
win1, win2 = pickparents(popsize, listscores)
# Crossbreed een nieuw child
child1,child2 = cross(alldata[win1], alldata[win2])
newpopulation.append(child1)
newpopulation.append(child2)
print("nieuwe ronde, nieuwe kansen")
for j in range(2):
print(j)
mutation_decision = random.randint(0, 100)
if mutation_decision > 90:
mutate(newpopulation[2*i+j])
alldata = newpopulation
growth.append(genfitness/popsize)
print(growth)
plt.plot(growth)
plt.show()
with open("endresult.txt", "w") as txt_file:
for data in alldata:
for line in data:
txt_file.write(" ".join(str(line)) + "\n")
def breed(inputfile, outputdir):
ip = open(inputfile)
breedParams = ip.read()
ip.close()
breedParams = breedParams.split("\n")
# This is hardcoded. Put it in a config file later.
INITIALSETSZ = 10000
MATINGPOOLSZ = 10
#matingpool = []
#offsprings = []
MUTATIONRATE = 0.10
mutationpool = []
#for param in breedParams:
while len(breedParams) > 0:
param = random.choice(breedParams)
if not param:
break
breedParams.remove(param)
op = ' '.join(param.split())
op = outputdir + op + '.txt'
op = open(op, 'a')
seedgraphs = initialization.getSeedGraphs(INITIALSETSZ, param)
for i in range(int(len(seedgraphs) * MUTATIONRATE)):
mutationpool.append(random.choice(seedgraphs))
mutation.mutate(param, mutationpool)
del mutationpool[:]
matingpool = selection.selectGraphs(MATINGPOOLSZ, seedgraphs, param, op)
del seedgraphs[:]
maxiter = 10
for iter in range(maxiter):
offsprings = crossover.produceOffsprings(param, matingpool)
del matingpool[:]
for i in range(int(len(offsprings) * MUTATIONRATE)):
mutationpool.append(random.choice(offsprings))
mutation.mutate(param, mutationpool)
del mutationpool[:]
matingpool = selection.selectGraphs(MATINGPOOLSZ, offsprings, param, op)
del offsprings[:]
avlen = 0
for m in matingpool:
avlen += len(m)
avlen /= len(matingpool)
op.write('\n\n')
op.write('*****************')
op.close()
return
def mutate_pop(individual, mutpb, primitive_set, terminal_set):
offspring = []
# Replace
if random.random() < mutpb:
offspring.append((mutate(mutate_replace, primitive_set, terminal_set,
deepcopy(individual[0])), None))
# Insert
if random.random() < mutpb:
offspring.append((mutate(mutate_insert,
primitive_set,
terminal_set,
deepcopy(individual[0]),
use_input_ids=True), None))
# Shrink
if random.random() < mutpb:
offspring.append((mutate(mutate_shrink, primitive_set, terminal_set,
deepcopy(individual[0])), None))
return offspring
def genetic_algorithm(task,
crossover_rate=CROSSOVER_RATE,
mutation_rate=MUTATION_RATE,
tournament_size=TOURNAMENT_SIZE,
population_size=POPULATION_SIZE):
best_individuals_values = np.empty(MAX_ITERATIONS)
start_time = time.time()
population = init_population(task, population_size)
outer_iterator = 0
best_individual = 0
best_individual_value = 0
global_best_individual = 0
global_best_individual_value = 0
while outer_iterator < MAX_ITERATIONS:
inner_iterator = 0
new_population = Population()
while inner_iterator < population_size:
parent1 = tournament(population, tournament_size)
parent2 = tournament(population, tournament_size)
child = crossover(parent1, parent2, crossover_rate)
mutate(child, mutation_rate)
new_population.add_individual(child)
inner_iterator += 1
best_individual = population.best_individual()
best_individual_value = best_individual.evaluate()
if best_individual_value >= global_best_individual_value:
global_best_individual = best_individual
global_best_individual_value = best_individual_value
new_population.set_first_individual(global_best_individual)
population = new_population
best_individuals_values[outer_iterator] = global_best_individual_value
outer_iterator += 1
print("--- Genetic algorithm\'s execution time = %s seconds ---" %
(time.time() - start_time))
print('Genetic algorithm\'s final result =', global_best_individual_value)
def operate(gen_in, mu_in, lamb_da_in, boundary_in, gen, maxgen):
lambda_gen = crossover_UNDX(gen_in, mu_in, lamb_da_in)
mutant = np.random.randint(0, 6)
lambda_gen = mutate(mutant,
lambda_gen,
boundary_in,
gen,
normal_sigma=0.5,
uniform_pm=0.1,
boundary_pm=0.1,
maxgen=maxgen,
b=5,
cauchy_sigma=0.5,
delta_max=20,
n=2)
return reflect_fix(lambda_gen, boundary_in)
def multi_recombine(population, data1, data2, prob, mutations, cross):
'''
recombine 2 distinct sound samples through random crossover points
and mutate
parameters:
data1: 1D numpy array of first sound sample
data2: 1D numpy array of second sound sample
population: desired population size to be created
cross: desired number of crossover points
mutate: percent chance of each of the desired mutations occurs
mutations: number of mutations to perform
cross: number of crossover points
return:
a list of size population containing 1D numpy arrays
of the recombined sound samples
'''
#resize the smaller sound data to match the larger sound data
if (len(data1) != len(data2)):
if (len(data1) < len(data2)):
smaller = data1
larger = data2
else:
smaller = data2
larger = data1
multiple = int(len(larger) / len(smaller))
init = smaller
if (multiple >= 2):
for i in range(multiple - 1):
init = np.concatenate((init, smaller))
diff = len(larger) - multiple * len(smaller)
init = np.concatenate((init, smaller[0:diff]))
data1 = init
data2 = larger
dft1 = fft(data1)
dft2 = fft(data2)
if (len(dft1) % 2 == 1):
chop = int(len(dft1) / 2) + 1
next_chop = chop
else:
chop = int(len(dft1) / 2)
next_chop = chop + 1
#focusing on keeping the left portion of f1
f1 = dft1[1:chop]
f1_conj = np.flip(dft1[next_chop:len(dft1)])
f2 = dft2[1:chop]
f2_conj = np.flip(dft2[next_chop:len(dft2)])
resulting_list = []
for i in range(int(population / 2)):
max_range = range(int(len(f1) / 50), int(3 * len(f1) / 4))
crossover_points = random.sample(max_range, cross)
crossover_points.sort()
# the first slice in the sequence is always from f1, while
# the last slice is from f2 if the cross is odd otherwise it's f1
result1_seq = [f1[0:crossover_points[0]]]
result1_conj_seq = [f1_conj[0:crossover_points[0]]]
for i in range(cross - 1):
# if i even add from f2
if (i % 2 == 0):
result1_seq.append(f2[crossover_points[i]:crossover_points[i +
1]])
result1_conj_seq.append(
f2_conj[crossover_points[i]:crossover_points[i + 1]])
else:
result1_seq.append(f1[crossover_points[i]:crossover_points[i +
1]])
result1_conj_seq.append(
f1_conj[crossover_points[i]:crossover_points[i + 1]])
if (cross % 2 == 1):
result1_seq.append(f2[crossover_points[cross - 1]:len(f1)])
result1_conj_seq.append(f2_conj[crossover_points[cross -
1]:len(f1)])
else:
result1_seq.append(f1[crossover_points[cross - 1]:len(f1)])
result1_conj_seq.append(f1_conj[crossover_points[cross -
1]:len(f1)])
result2_seq = [f2[0:crossover_points[0]]]
result2_conj_seq = [f2_conj[0:crossover_points[0]]]
for i in range(cross - 1):
# if i even add from f1
if (i % 2 == 0):
result2_seq.append(f1[crossover_points[i]:crossover_points[i +
1]])
result2_conj_seq.append(
f1_conj[crossover_points[i]:crossover_points[i + 1]])
else:
result2_seq.append(f2[crossover_points[i]:crossover_points[i +
1]])
result2_conj_seq.append(
f2_conj[crossover_points[i]:crossover_points[i + 1]])
if (cross % 2 == 1):
result2_seq.append(f1[crossover_points[cross - 1]:len(f1)])
result2_conj_seq.append(f1_conj[crossover_points[cross -
1]:len(f1)])
else:
result2_seq.append(f2[crossover_points[cross - 1]:len(f1)])
result2_conj_seq.append(f2_conj[crossover_points[cross -
1]:len(f1)])
result1 = np.concatenate(result1_seq)
result1_conj = np.concatenate(result1_conj_seq)
result2 = np.concatenate(result2_seq)
result2_conj = np.concatenate(result2_conj_seq)
mutation.mutate(result1, result1_conj, prob, mutations)
mutation.mutate(result2, result2_conj, prob, mutations)
assert (len(result1) == len(result1_conj))
assert (len(result2) == len(result2_conj))
assert (len(result1) == len(result2))
assert (len(result1) == len(f1))
if (len(dft1) % 2 == 1):
beg = np.array([dft1[0]])
final1 = np.concatenate((beg, result1, np.flip(result1_conj)))
conv1 = np.real(ifft(final1))
loudest1 = np.amax(np.absolute(conv1))
resulting_list.append(np.float32(conv1 / loudest1))
final2 = np.concatenate((beg, result2, np.flip(result2_conj)))
conv2 = np.real(ifft(final2))
loudest2 = np.amax(np.absolute(conv2))
resulting_list.append(np.float32(conv2 / loudest2))
else:
beg = np.array([dft1[0]])
mid = np.array([dft1[chop]])
final1 = np.concatenate((beg, result1, mid, np.flip(result1_conj)))
conv1 = np.real(ifft(final1))
loudest1 = np.amax(np.absolute(conv1))
resulting_list.append(np.float32(conv1 / loudest1))
final2 = np.concatenate((beg, result2, mid, np.flip(result2_conj)))
conv2 = np.real(ifft(final2))
loudest2 = np.amax(np.absolute(conv2))
resulting_list.append(np.float32(conv2 / loudest2))
return resulting_list
def single_recombine(population, data1, data2, prob, mutations):
'''
recombine 2 distinct sound samples through 1 random crossover point
and mutate
parameters:
sampling_freq: Sampling frequency of both sound samples
data1: 1D numpy array of first sound sample
data2: 1D numpy array of second sound sample
population: desired population size to be created
cross: desired number of crossover points
mutate: percent chance of each of the desired mutations occurs
mutations: number of mutations to perform
return:
a list of size population containing 1D numpy arrays
of the recombined sound samples
'''
#resize the smaller sound data to match the larger sound data
if (len(data1) != len(data2)):
if (len(data1) < len(data2)):
smaller = data1
larger = data2
else:
smaller = data2
larger = data1
multiple = int(len(larger) / len(smaller))
init = smaller
if (multiple >= 2):
for i in range(multiple - 1):
init = np.concatenate((init, smaller))
diff = len(larger) - multiple * len(smaller)
init = np.concatenate((init, smaller[0:diff]))
data1 = init
data2 = larger
dft1 = fft(data1)
dft2 = fft(data2)
if (len(dft1) % 2 == 1):
chop = int(len(dft1) / 2) + 1
next_chop = chop
else:
chop = int(len(dft1) / 2)
next_chop = chop + 1
#focusing on keeping the left portion of f1
f1 = dft1[1:chop]
f1_conj = np.flip(dft1[next_chop:len(dft1)])
f2 = dft2[1:chop]
f2_conj = np.flip(dft2[next_chop:len(dft2)])
resulting_list = []
for i in range(int(population / 2)):
crossover_point = random.randint(int(len(f1) / 50),
int(3 * len(f1) / 4))
result1 = np.concatenate(
(f1[0:crossover_point], f2[crossover_point:len(f2)]))
result1_conj = np.concatenate(
(f1_conj[0:crossover_point], f2_conj[crossover_point:len(f2)]))
result2 = np.concatenate(
(f2[0:crossover_point], f1[crossover_point:len(f1)]))
result2_conj = np.concatenate(
(f2_conj[0:crossover_point], f1_conj[crossover_point:len(f1)]))
mutation.mutate(result1, result1_conj, prob, mutations)
mutation.mutate(result2, result2_conj, prob, mutations)
if (len(dft1) % 2 == 1):
beg = np.array([dft1[0]])
final1 = np.concatenate((beg, result1, np.flip(result1_conj)))
conv1 = np.real(ifft(final1))
loudest1 = np.amax(np.absolute(conv1))
resulting_list.append(np.float32(conv1 / loudest1))
final2 = np.concatenate((beg, result2, np.flip(result2_conj)))
conv2 = np.real(ifft(final2))
loudest2 = np.amax(np.absolute(conv2))
resulting_list.append(np.float32(conv2 / loudest2))
else:
beg = np.array([dft1[0]])
mid = np.array([dft1[chop]])
final1 = np.concatenate((beg, result1, mid, np.flip(result1_conj)))
conv1 = np.real(ifft(final1))
loudest1 = np.amax(np.absolute(conv1))
resulting_list.append(np.float32(conv1 / loudest1))
final2 = np.concatenate((beg, result2, mid, np.flip(result2_conj)))
conv2 = np.real(ifft(final2))
loudest2 = np.amax(np.absolute(conv2))
resulting_list.append(np.float32(conv2 / loudest2))
return resulting_list
def vrp_ga(m=0.2, gen=500, N=100, best_N=5, setup=1, plot_folder="plots/"):
"""
Complete function, optimizing the vehicle routing problem using genetic
algorithms and a custom crossover/mutation part.
Args
m mutation probability
gen number of generation (iterations)
N population size (must be divisable by 4)
best_N plotting the N best individuals each generation
setup number of setup (currently 1 and 2)
plot_folder path to save plots
"""
if N % 4 != 0:
raise ValueError(
"[!] 'N' (population size) has to be dividedable by 4!")
history = np.zeros((gen, best_N))
# create one test member, to load task
# cap = capacity of trucks in list
# demands = demands of cities
# dist = distance matrix
# tc = transportation costs of trucks
_, cap, demands, dist, tc = complete_init(task_nr=setup)
##### initialization
# create a list for our population with N elements, with multiple
# possible setups as numpy arrays
# [instead of doing a list of 2d arrays, we do one 3d array, where the
# first dimension stands for the members]
# population has 3 dimensions: members x trucks x cities
population = np.zeros((N, len(cap), len(demands)))
# fill the population array
for i in range(N):
population[i] = complete_init(task_nr=setup)[0]
for gen_idx in tqdm(range(gen)):
##### fitness
permutations = np.array(
[permute_way(member, dist, demands, cap) for member in population])
fitness_scores = np.array([
fitness_function(dist, permutation, member, tc)
for permutation, member in zip(permutations, population)
])
history[gen_idx] = sorted(fitness_scores)[-best_N:]
##### selection
selected_indx = roulette_wheel_selection(fitness_scores, int(N / 2))
selected_members = population[selected_indx]
np.random.shuffle(selected_members)
##### crossover
children = vrp_crossover(selected_members, cap, demands)
##### mutation
for i, child in enumerate(children):
if random.uniform(0, 1) < m:
children[i] = mutate(child, cap)
##### replacement
population = replacement(population,
children,
mode="delete-all",
n=len(children),
based_on_fitness=True,
fitness_old=fitness_scores)
##### plotting
plt.figure()
plt.plot(history)
plt.xlabel("Generations")
plt.savefig(plot_folder + "history" +
strftime("%Y-%m-%d %H:%M:%S", gmtime()) + ".png")
plt.show()
def run_iteration(dataset, features, feature_cdds, population, population_size,
elitism, evaluation_threshold, bacc_weight, uniqueness,
best_classifiers, crossover_probability,
mutation_probability, tournament_size, print_results):
"""
Runs a single genetic algorithm iteration.
Parameters
----------
dataset : Pandas DataFrame
data set
features : list
list of features
feature_cdds : list
list of feature cdds dicts
population : list
list of classifiers (Classifier objects)
population_size : int
population size
elitism : bool
if True the best found solutions are added to the population in each selection operation
evaluation_threshold : float
classifier evaluation threshold
bacc_weight : float
weight of balanced accuracy in the multi-objective score
uniqueness : bool
if True only unique inputs in a classifier are counted, otherwise the input cdd score is multiplied by
the number of input
best_classifiers : BestSolutions object
includes best solutions
crossover_probability : float
crossover probability
mutation_probability : float
mutation probability
tournament_size : float
tournament size
print_results : bool
if True more information is shown, otherwise not all results are printed
Returns
-------
best_classifiers : BestSolutions object
includes all best classifiers
"""
# SELECTION
selected_parents = []
temp_population = []
if elitism is True:
temp_population = population.copy()
classifier_id = random.randrange(0, len(best_classifiers.solutions))
temp_population.append(best_classifiers.solutions[classifier_id])
for i in range(0, int(population_size / 2)): # iterate through population
# select two parents
if elitism is True:
first_parent_id, second_parent_id = selection.select(
temp_population, tournament_size)
# add new parents to selected parents
selected_parents.append(
temp_population[first_parent_id].__copy__())
selected_parents.append(
temp_population[second_parent_id].__copy__())
else:
first_parent_id, second_parent_id = selection.select(
population, tournament_size)
# add new parents to selected parents
selected_parents.append(population[first_parent_id].__copy__())
selected_parents.append(population[second_parent_id].__copy__())
population.clear() # empty population
# CROSSOVER
for i in range(0, int(population_size /
2)): # iterate through selected parents
crossover_rand = random.random(
) # randomly choose probability for crossover
first_parent_id = random.randrange(
0, len(selected_parents)) # randomly choose first parent id
first_parent = selected_parents[first_parent_id].__copy__(
) # copy first parent
del selected_parents[
first_parent_id] # remove parent from available parents
second_parent_id = random.randrange(
0, len(selected_parents)) # randomly choose second parent id
second_parent = selected_parents[second_parent_id].__copy__(
) # copy first parent
del selected_parents[
second_parent_id] # remove parent from available parents
# if the crossover_rand is lower than or equal to probability - apply crossover
if crossover_rand <= crossover_probability:
# crossover
first_child, second_child = crossover.crossover_parents(
first_parent, second_parent)
population.append(
first_child.__copy__()) # add children to the new population
population.append(second_child.__copy__())
else:
population.append(first_parent.__copy__()
) # if crossover not allowed - copy parents
population.append(second_parent.__copy__())
# MUTATION
population = mutation.mutate(population, features, mutation_probability,
evaluation_threshold)
# UPDATE THETA AND REMOVE RULE DUPLICATES
for classifier in population:
classifier.update_theta()
classifier.remove_duplicates()
# EVALUATION OF THE POPULATION
avg_population_score, best_classifiers = \
eval.evaluate_individuals(population=population,
dataset=dataset,
bacc_weight=bacc_weight,
feature_cdds=feature_cdds,
uniqueness=uniqueness,
best_classifiers=best_classifiers)
if print_results:
print("average population score: ", avg_population_score)
return best_classifiers
# Storing the average values over every single iteration
average_vol = []
average_num = []
average_value = []
for i in range(NUM_OF_ITERATIONS):
# Generate the initial population
population = gen.generate_pop(box_params, NUM_OF_INDIVIDUALS, ROTATIONS)
gen = 0
average_fitness = []
while gen < NUM_OF_GENERATIONS:
population, fitness = ft.evaluate(population, truck_dimension, box_params, total_value)
population = ns.rank(population, fitness)
offsprings = re.crossover(deepcopy(population), PC, k=K)
offsprings = mt.mutate(offsprings, PM1, PM2, ROTATIONS)
population = ss.select(population, offsprings, truck_dimension, box_params, total_value,
NUM_OF_INDIVIDUALS)
average_fitness.append(calc_average_fitness(population))
gen += 1
results = []
# Storing the final Rank 1 solutions
for key, value in population.items():
if value['Rank'] == 1:
results.append(value['result'])
# Plot using plotly
color_index = vis.draw_solution(pieces=packages)
vis.draw(results, color_index)
def break_bit_list(bit_list):
length = int(len(bit_list) / 2)
NS = []
NL = []
for i in range(length):
NS.append(bit_list[i])
NL.append(bit_list[i + length])
result = (NS, NL)
return result
def __bitlist_to_int(bitlist):
return int("".join(str(i) for i in bitlist), 2)
pop = population.init(POPULATION_SIZE, CROMOSSOME_SIZE, 'BIN', BOUNDS)
evaluations = fit.evaluate(fitness, pop)
#print(evaluations)
#print(selection.select(evaluations))
#selection.select(evaluations)
for _ in range(MAX_GENERATIONS):
evaluations = fit.evaluate(fitness, pop)
pop = selection.select(2, 1, evaluations)
pop = crossover.single_point(pop, CROSSOVER_PROB)
pop = mutation.mutate(pop, MUTATION_PROB)
evaluations.sort(key=lambda tup: tup[1])
print(evaluations)
def main():
global NFE
NFE = 0
CostFunction = MinOne # Cost Function
n_var = 20 # Number of Decision Variables
VarSize = np.array([1, n_var]) # Decision Variables Matrix Size
# GA Parameters
MaxIt = 500 # Maximum Number of Iterations
nPop = 10 # Population Size
pc = 0.8 # crossover Percentage
nc = 2 * round(pc * nPop / 2) # Number of Offsprings (Parnets)
pm = 0.1 # Mutation Percentage
nm = round(pm * nPop) # Number of Mutants
mu = 0.1 # Mutation Rate
beta = 8
class EmptyIndividual():
pass
Best = [EmptyIndividual() for i in range(MaxIt)]
pop = np.array([EmptyIndividual() for i in range(nPop)])
for i in range(nPop):
# Initialize Position
pop[i].Position = np.array(
[random.randint(0, 1) for i in range(n_var)])
# Evaluation
pop[i].Cost = CostFunction(pop[i].Position)
# Sort Population
Costs = np.array([pop[i].Cost for i in range(nPop)])
SortOrder = np.argsort(Costs)
pop = pop[SortOrder]
# Array to Hold Best Cost Values
BestCost = np.zeros([MaxIt, 1])
# Store Cost
WorstCost = pop[-1].Cost
# Array to Hold Number of Function Evaluations
nfe = np.zeros([MaxIt, 1])
for it in range(MaxIt):
# Calculate Selection Probabilities
P = np.expm1(-beta * Costs / WorstCost)
P = P / sum(P)
# crossover
popc = np.array([[EmptyIndividual() for i in range(int(nc / 2))],
[EmptyIndividual()
for i in range(int(nc / 2))]]).transpose()
for k in range(int(nc / 2)):
i1 = roulette_wheel_selection(P)
i2 = roulette_wheel_selection(P)
# Select Parents
p1 = pop[i1]
p2 = pop[i2]
# Apply crossover
popc[k, 0].Position, popc[k, 1].Position = crossover(
p1.Position, p2.Position)
# Evaluate Offsprings
popc[k, 0].Cost = CostFunction(popc[k, 0].Position)
popc[k, 1].Cost = CostFunction(popc[k, 1].Position)
popc = np.array([popc[i] for i in range(len(popc))]).transpose()
popc = np.concatenate((popc[0], popc[1]), axis=0)
# Mutation
popm = np.array([EmptyIndividual() for i in range(nm)])
for k in range(nm):
# Select Parent
i = random.randint(0, nPop - 1)
p = pop[i]
# Apply Mutation
popm[k].Position = mutate(np.array(p.Position), mu)
# Evaluate Mutant
popm[k].Cost = CostFunction(popm[k].Position)
# Create Merged Population
pop = np.concatenate((pop, popc, popm), axis=0)
# Sort Population
Costs = np.array([pop[i].Cost for i in range(len(pop))])
SortOrder = np.argsort(Costs)
Costs = Costs[SortOrder]
pop = pop[SortOrder]
# Truncation
pop = pop[0:nPop]
Costs = Costs[0:nPop]
# Store Best Cost Ever Found
BestCost[it] = pop[0].Cost
Best[it] = pop[0]
# Store Worst Cost Ever Found
WorstCost = pop[-1].Cost
# Store NFE
nfe[it] = NFE
# Show Iteration Information
print('Iteration', it, ': NFE = ', nfe[it], ', Best Cost = ',
BestCost[it], 'Chromosome: ', pop[0].Position)
def run_tests(num_to_check=10, smaller_num_to_check = 10):
import taut
veering_isosigs = parse_data_file("Data/veering_census.txt")
print("testing is_taut")
for sig in random.sample(veering_isosigs, num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
assert taut.is_taut(tri, angle), sig
print("testing isosig round trip")
for sig in random.sample(veering_isosigs, num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
recovered_sig = taut.isosig_from_tri_angle(tri, angle)
assert sig == recovered_sig, sig
# we only test this round trip - the other round trip does not
# make sense because tri->isosig is many to one.
import transverse_taut
print("testing is_transverse_taut")
for sig in random.sample(veering_isosigs, num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
assert transverse_taut.is_transverse_taut(tri, angle), sig
non_transverse_taut_isosigs = parse_data_file("Data/veering_non_transverse_taut_examples.txt")
print("testing not is_transverse_taut")
for sig in non_transverse_taut_isosigs:
tri, angle = taut.isosig_to_tri_angle(sig)
assert not transverse_taut.is_transverse_taut(tri, angle), sig
import veering
print("testing is_veering")
for sig in random.sample(veering_isosigs, num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
assert veering.is_veering(tri, angle), sig
# tri, angle = taut.isosig_to_tri_angle("cPcbbbdxm_10")
# explore_mobius_surgery_graph(tri, angle, max_tetrahedra = 12)
# # tests to see that it makes only veering triangulations as it goes
import veering_dehn_surgery
print("testing veering_dehn_surgery")
for sig in random.sample(veering_isosigs, num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
for face_num in veering_dehn_surgery.get_mobius_strip_indices(tri):
(tri_s, angle_s, face_num_s) = veering_dehn_surgery.veering_mobius_dehn_surgery(tri, angle, face_num)
assert veering.is_veering(tri_s, angle_s), sig
import veering_fan_excision
print("testing veering_fan_excision")
m003, _ = taut.isosig_to_tri_angle('cPcbbbdxm_10')
m004, _ = taut.isosig_to_tri_angle('cPcbbbiht_12')
for sig in random.sample(veering_isosigs, num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
tet_types = veering.is_veering(tri, angle, return_type = "tet_types")
if tet_types.count("toggle") == 2:
excised_tri, _ = veering_fan_excision.excise_fans(tri, angle)
assert ( excised_tri.isIsomorphicTo(m003) != None or
excised_tri.isIsomorphicTo(m004) != None ), sig
import pachner
print("testing pachner with taut structure")
for sig in random.sample(veering_isosigs, num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
face_num = random.randrange(tri.countTriangles())
result = pachner.twoThreeMove(tri, face_num, angle = angle, return_edge = True)
if result != False:
tri2, angle2, edge_num = result
tri3, angle3 = pachner.threeTwoMove(tri2, edge_num, angle = angle2)
assert taut.isosig_from_tri_angle(tri, angle) == taut.isosig_from_tri_angle(tri3, angle3), sig
import branched_surface
import regina
print("testing branched_surface and pachner with branched surface")
for sig in random.sample(veering_isosigs, num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
tri_original = regina.Triangulation3(tri) #copy
branch = branched_surface.upper_branched_surface(tri, angle, return_lower = random.choice([True, False]))
### test branch isosig round trip
sig_with_branch = branched_surface.isosig_from_tri_angle_branch(tri, angle, branch)
tri2, angle2, branch2 = branched_surface.isosig_to_tri_angle_branch(sig_with_branch)
assert (branch == branch2) and (angle == angle2), sig
branch_original = branch[:] #copy
face_num = random.randrange(tri.countTriangles())
out = pachner.twoThreeMove(tri, face_num, branch = branch, return_edge = True)
if out != False:
tri, possible_branches, edge_num = out
tri, branch = pachner.threeTwoMove(tri, edge_num, branch = possible_branches[0])
all_isoms = tri.findAllIsomorphisms(tri_original)
all_branches = [branched_surface.apply_isom_to_branched_surface(branch, isom) for isom in all_isoms]
assert branch_original in all_branches, sig
import flow_cycles
import drill
print("testing taut and branched drill + semiflows on drillings")
for sig in random.sample(veering_isosigs, smaller_num_to_check):
tri, angle = taut.isosig_to_tri_angle(sig)
branch = branched_surface.upper_branched_surface(tri, angle) ### also checks for veering and transverse taut
found_loops = flow_cycles.find_flow_cycles(tri, branch)
for loop in random.sample(found_loops, min(len(found_loops), 5)): ## drill along at most 5 loops
tri, angle = taut.isosig_to_tri_angle(sig)
branch = branched_surface.upper_branched_surface(tri, angle)
tri_loop = flow_cycles.flow_cycle_to_triangle_loop(tri, branch, loop)
if tri_loop != False:
if not flow_cycles.tri_loop_is_boundary_parallel(tri_loop, tri):
drill.drill(tri, tri_loop, angle = angle, branch = branch, sig = sig)
assert branched_surface.has_non_sing_semiflow(tri, branch), sig
print("all basic tests passed")
try:
import snappy
import snappy_util
snappy_working = True
except:
print("failed to import from snappy?")
snappy_working = False
if snappy_working:
print("testing algebraic intersection")
census = snappy.OrientableCuspedCensus() # not a set or list, so can't use random.sample
for i in range(10):
M = random.choice(census)
n = M.num_cusps()
peripheral_curves = M.gluing_equations()[-2*n:]
for i in range(2*n):
for j in range(i, 2*n):
alg_int = snappy_util.algebraic_intersection(peripheral_curves[i], peripheral_curves[j])
if i % 2 == 0 and j == i + 1:
assert alg_int == 1, M.name()
else:
assert alg_int == 0, M.name()
if snappy_working:
import veering_drill_midsurface_bdy
print("testing veering drilling and filling")
for sig in random.sample(veering_isosigs[:3000], num_to_check):
T, per = veering_drill_midsurface_bdy.drill_midsurface_bdy(sig)
M = snappy.Manifold(T.snapPea())
M.set_peripheral_curves("shortest")
L = snappy_util.get_slopes_from_peripherals(M, per)
M.dehn_fill(L)
N = snappy.Manifold(sig.split("_")[0])
assert M.is_isometric_to(N), sig
if snappy_working:
print("all tests depending on snappy passed")
# try:
# from hashlib import md5
# from os import remove
# import pyx
# from boundary_triangulation import draw_triangulation_boundary_from_veering_isosig
# pyx_working = True
# except:
# print("failed to import from pyx?")
# pyx_working = False
# ladders_style_sigs = {
# "cPcbbbiht_12": "f34c1fdf65db9d02994752814803ae01",
# "gLLAQbecdfffhhnkqnc_120012": "091c85b4f4877276bfd8a955b769b496",
# "kLALPPzkcbbegfhgijjhhrwaaxnxxn_1221100101": "a0f15a8454f715f492c74ce1073a13a4",
# }
# geometric_style_sigs = {
# "cPcbbbiht_12": "1e74d0b68160c4922e85a5adb20a0f1d",
# "gLLAQbecdfffhhnkqnc_120012": "856a1fce74eb64f519bcda083303bd8f",
# "kLALPPzkcbbegfhgijjhhrwaaxnxxn_1221100101": "33bd23b34c5d977a103fa50ffe63120a",
# }
# args = {
# "draw_boundary_triangulation":True,
# "draw_triangles_near_poles": False,
# "ct_depth":-1,
# "ct_epsilon":0.03,
# "global_drawing_scale": 4,
# "delta": 0.2,
# "ladder_width": 10.0,
# "ladder_height": 20.0,
# "draw_labels": True,
# }
# shapes_data = read_from_pickle("Data/veering_shapes_up_to_ten_tetrahedra.pkl")
# if pyx_working:
# for sig in ladders_style_sigs:
# print("testing boundary triangulation pictures, ladder style", sig)
# args["tet_shapes"] = shapes_data[sig]
# args["style"] = "ladders"
# file_name = draw_triangulation_boundary_from_veering_isosig(sig, args = args)
# f = open(file_name, "rb")
# file_hash = md5(f.read())
# assert file_hash.hexdigest() == ladders_style_sigs[sig]
# f.close()
# remove(file_name)
# if pyx_working:
# for sig in geometric_style_sigs:
# print("testing boundary triangulation pictures, ladder style", sig)
# args["tet_shapes"] = shapes_data[sig]
# args["style"] = "geometric"
# file_name = draw_triangulation_boundary_from_veering_isosig(sig, args = args)
# f = open(file_name, "rb")
# file_hash = md5(f.read())
# assert file_hash.hexdigest() == geometric_style_sigs[sig]
# f.close()
# remove(file_name)
# if pyx_working:
# print("all tests depending on pyx passed")
veering_polys = {
"cPcbbbiht_12": [-4, -1, 1, 4],
"eLMkbcddddedde_2100": [-2, -2, -2, -1, -1, -1, -1, 1, 1, 1, 1, 1, 1, 2, 2],
"gLLAQbecdfffhhnkqnc_120012": [-1, -1, -1, -1, 1, 1, 1, 1],
"gLLPQcdfefefuoaaauo_022110": [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1, 1, 1, 1],
}
# veering_polys = { ### old
# "cPcbbbiht_12": "a^3 - 4*a^2 + 4*a - 1",
# "eLMkbcddddedde_2100": "a^6*b - a^6 - 2*a^5*b - a^4*b^2 + a^5 + 2*a^4*b + a^3*b^2 - 2*a^3*b + a^3 + 2*a^2*b + a*b^2 - a^2 - 2*a*b - b^2 + b",
# "gLLAQbecdfffhhnkqnc_120012": "a^7 + a^6 + a^5 + a^4 - a^3 - a^2 - a - 1",
# "gLLPQcdfefefuoaaauo_022110": "a^12*b^3 - a^11*b^2 - a^10*b^3 - a^10*b^2 - a^7*b^3 - a^7*b^2 - a^6*b^3 + a^7*b + a^5*b^2 - a^6 - a^5*b - a^5 - a^2*b - a^2 - a*b + 1",
# }
taut_polys = {
"cPcbbbiht_12": [-3, 1, 1],
"eLMkbcddddedde_2100": [-1, -1, -1, 1, 1],
"iLLAwQcccedfghhhlnhcqeesr_12001122": [],
}
# taut_polys = { ### old
# "cPcbbbiht_12": "a^2 - 3*a + 1",
# "eLMkbcddddedde_2100": "a^2*b - a^2 - a*b - b^2 + b",
# "iLLAwQcccedfghhhlnhcqeesr_12001122": "0",
# }
torus_bundles = [
"cPcbbbiht_12",
"eLMkbcdddhhqqa_1220",
"gLMzQbcdefffhhqqqdl_122002",
]
measured = [
"gLLAQbecdfffhhnkqnc_120012",
"iLLALQcccedhgghhlnxkxrkaa_12001112",
"iLLAwQcccedfghhhlnhcqeesr_12001122",
]
empties = [
"fLAMcaccdeejsnaxk_20010",
"gLALQbcbeeffhhwsras_211220",
"hLALAkbcbeefgghhwsraqj_2112202",
]
try:
from sage.rings.integer_ring import ZZ
sage_working = True
except:
print("failed to import from sage?")
sage_working = False
if sage_working:
import taut_polytope
print("testing is_layered")
for sig in veering_isosigs[:17]:
assert taut_polytope.is_layered(sig), sig
for sig in veering_isosigs[17:21]:
assert not taut_polytope.is_layered(sig), sig
if sage_working:
import fibered
print("testing is_fibered")
mflds = parse_data_file("Data/mflds_which_fiber.txt")
mflds = [line.split("\t")[0:2] for line in mflds]
for (name, kind) in random.sample(mflds, num_to_check):
assert fibered.is_fibered(name) == (kind == "fibered"), name
if sage_working:
import veering_polynomial
import taut_polynomial
print("testing veering poly")
for sig in veering_polys:
p = veering_polynomial.veering_polynomial(sig)
assert check_polynomial_coefficients(p, veering_polys[sig]), sig
### Nov 2021: sage 9.4 changed how smith normal form works, which changed our polynomials
### to equivalent but not equal polynomials. To avoid this kind of change breaking things
### in the future, we changed to comparing the list of coefficients.
# assert p.__repr__() == veering_polys[sig]
print("testing taut poly")
for sig in taut_polys:
p = taut_polynomial.taut_polynomial_via_tree(sig)
assert check_polynomial_coefficients(p, taut_polys[sig]), sig
# assert p.__repr__() == taut_polys[sig]
print("testing divide")
for sig in random.sample(veering_isosigs[:3000], num_to_check):
p = veering_polynomial.veering_polynomial(sig)
q = taut_polynomial.taut_polynomial_via_tree(sig)
if q == 0:
assert p == 0, sig
else:
assert q.divides(p), sig
if sage_working:
print("testing alex")
for sig in random.sample(veering_isosigs[:3000], num_to_check):
snap_sig = sig.split("_")[0]
M = snappy.Manifold(snap_sig)
if M.homology().betti_number() == 1:
assert taut_polynomial.taut_polynomial_via_tree(sig, mode = "alexander") == M.alexander_polynomial(), sig
if sage_working:
# would be nice to automate this - need to fetch the angle
# structure say via z_charge.py...
print("testing is_torus_bundle")
for sig in torus_bundles:
assert taut_polytope.is_torus_bundle(sig), sig
if sage_working:
# ditto
print("testing is_layered")
for sig in torus_bundles:
assert taut_polytope.is_layered(sig), sig
print("testing measured")
for sig in measured:
assert taut_polytope.LMN_tri_angle(sig) == "M", sig
print("testing empty")
for sig in empties:
assert taut_polytope.LMN_tri_angle(sig) == "N", sig
if sage_working: # warning - this takes random amounts of time!
print("testing hom dim")
for sig in random.sample(veering_isosigs[:3000], 3): # magic number
# dimension = zero if and only if nothing is carried.
assert (taut_polytope.taut_cone_homological_dim(sig) == 0) == (taut_polytope.LMN_tri_angle(sig) == "N"), sig
if sage_working:
boundary_cycles = {
("eLMkbcddddedde_2100",(2,5,5,1,3,4,7,1)): "((-7, -7, 0, 0, 4, -3, 7, 0), (7, 7, 0, 0, -4, 3, -7, 0))",
("iLLLQPcbeegefhhhhhhahahha_01110221",(0,1,0,0,0,1,0,0,0,0,0,0,1,0,1,0)): "((0, 0, -1, 1, 1, 0, 1, 1, -1, 0, 0, 0, 0, 1, 0, 1), (0, 0, 1, -1, -1, 0, -1, -1, 1, 0, 0, 0, 0, -1, 0, -1))",
("ivvPQQcfhghgfghfaaaaaaaaa_01122000",(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)): "((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2), (1, 1, 0, 2, -1, 0, -3, 1, 2, -1, -2, 0, 3, -2, -1, 0), (-2, 0, -3, 1, 2, -1, 0, 2, -1, 0, 3, 1, -2, 1, 0, -1), (0, -2, 1, -3, 0, -1, 2, 0, -1, 2, -1, 1, 0, 1, -2, 3))",
}
taut_polys_with_cycles = {
("eLMkbcddddedde_2100", ((7, 7, 0, 0, -4, 3, -7, 0),)): [-1, -1, -1, 1, 1],
("iLLLQPcbeegefhhhhhhahahha_01110221", ((0, 0, 1, -1, -1, 0, -1, -1, 1, 0, 0, 0, 0, -1, 0, -1),)): [1, 1, 2],
("ivvPQQcfhghgfghfaaaaaaaaa_01122000", ((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2), (1, 1, 0, 2, -1, 0, -3, 1, 2, -1, -2, 0, 3, -2, -1, 0))): [-4, -1, -1, 1, 1],
}
# taut_polys_with_cycles = {
# ("eLMkbcddddedde_2100", ((7, 7, 0, 0, -4, 3, -7, 0),)): "a^14 - a^8 - a^7 - a^6 + 1",
# ("iLLLQPcbeegefhhhhhhahahha_01110221", ((0, 0, 1, -1, -1, 0, -1, -1, 1, 0, 0, 0, 0, -1, 0, -1),)): "a^2 + 2*a + 1",
# ("ivvPQQcfhghgfghfaaaaaaaaa_01122000", ((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2), (1, 1, 0, 2, -1, 0, -3, 1, 2, -1, -2, 0, 3, -2, -1, 0))): "a*b^2 - a^2 - 4*a*b - b^2 + a",
# }
taut_polys_image = {
('eLMkbcddddedde_2100', ((7, 8, -1, 0, -4, 4, -8, 0),)):[-1, -1, -1, 1, 1],
('ivvPQQcfhghgfghfaaaaaaaaa_01122000', ((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2),)):[-2, -2, -1, -1, 1, 1],
('ivvPQQcfhghgfghfaaaaaaaaa_01122000', ((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2), (1, 1, 0, 2, -1, 0, -3, 1, 2, -1, -2, 0, 3, -2, -1, 0))):[-4, -1, -1, 1, 1]
}
# taut_polys_image = {
# ('eLMkbcddddedde_2100', ((7, 8, -1, 0, -4, 4, -8, 0),)):"a^16 - a^9 - a^8 - a^7 + 1",
# ('ivvPQQcfhghgfghfaaaaaaaaa_01122000', ((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2),)):"a*b^2*c - 2*a*b*c - b^2*c - a^2 - 2*a*b + a",
# ('ivvPQQcfhghgfghfaaaaaaaaa_01122000', ((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2), (1, 1, 0, 2, -1, 0, -3, 1, 2, -1, -2, 0, 3, -2, -1, 0))):"a*b^2 - a^2 - 4*a*b - b^2 + a"
# }
alex_polys_with_cycles = {
("eLMkbcddddedde_2100",((7, 7, 0, 0, -4, 3, -7, 0),)): [-2, -1, -1, -1, 1, 1, 1, 2],
("iLLLQPcbeegefhhhhhhahahha_01110221", ((0, 0, 1, -1, -1, 0, -1, -1, 1, 0, 0, 0, 0, -1, 0, -1),)): [-3, -1, 1, 3],
("ivvPQQcfhghgfghfaaaaaaaaa_01122000", ((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2), (1, 1, 0, 2, -1, 0, -3, 1, 2, -1, -2, 0, 3, -2, -1, 0))): [-1, -1, 1, 1],
}
# alex_polys_with_cycles = {
# ("eLMkbcddddedde_2100",((7, 7, 0, 0, -4, 3, -7, 0),)): "a^15 - a^14 + a^9 - 2*a^8 + 2*a^7 - a^6 + a - 1",
# ("iLLLQPcbeegefhhhhhhahahha_01110221", ((0, 0, 1, -1, -1, 0, -1, -1, 1, 0, 0, 0, 0, -1, 0, -1),)): "3*a^3 - a^2 + a - 3",
# ("ivvPQQcfhghgfghfaaaaaaaaa_01122000", ((1, 1, 2, 0, -1, 2, 1, -3, 0, -1, 0, -2, -1, 0, 3, -2), (1, 1, 0, 2, -1, 0, -3, 1, 2, -1, -2, 0, 3, -2, -1, 0))): "a*b^2 - a^2 - b^2 + a",
# }
if sage_working:
import taut_carried
print("testing boundary cycles")
for sig, surface in boundary_cycles:
surface_list = list(surface)
cycles = taut_carried.boundary_cycles_from_surface(sig, surface_list)
cycles = tuple(tuple(cycle) for cycle in cycles)
assert cycles.__repr__() == boundary_cycles[(sig, surface)], sig
if sage_working:
print("testing taut with cycles")
for sig, cycles in taut_polys_with_cycles:
cycles_in = [list(cycle) for cycle in cycles]
p = taut_polynomial.taut_polynomial_via_tree(sig, cycles_in)
assert check_polynomial_coefficients(p, taut_polys_with_cycles[(sig, cycles)]), sig
# assert p.__repr__() == taut_polys_with_cycles[(sig, cycles)]
if sage_working:
print("testing taut with images")
for sig, cycles in taut_polys_image:
cycles_in = [list(cycle) for cycle in cycles]
p = taut_polynomial.taut_polynomial_image(sig, cycles_in)
assert check_polynomial_coefficients(p, taut_polys_image[(sig, cycles)]), sig
# assert p.__repr__() == taut_polys_image[(sig, cycles)]
if sage_working:
print("testing alex with cycles")
for sig, cycles in alex_polys_with_cycles:
cycles_in = [list(cycle) for cycle in cycles]
p = taut_polynomial.taut_polynomial_via_tree(sig, cycles_in, mode = "alexander")
assert check_polynomial_coefficients(p, alex_polys_with_cycles[(sig, cycles)]), sig
# assert p.__repr__() == alex_polys_with_cycles[(sig, cycles)]
if sage_working:
import edge_orientability
import taut_euler_class
print("testing euler and edge orientability")
for sig in random.sample(veering_isosigs[:3000], 3):
# Theorem: If (tri, angle) is edge orientable then e = 0.
assert not ( edge_orientability.is_edge_orientable(sig) and
(taut_euler_class.order_of_euler_class_wrapper(sig) == 2) ), sig
if sage_working:
# Theorem: If (tri, angle) is edge orientable then taut poly = alex poly.
# taut_polynomial.taut_polynomial_via_tree(sig, mode = "alexander") ==
# taut_polynomial.taut_polynomial_via_tree(sig, mode = "taut")
pass
if sage_working:
print("testing exotics")
for sig in random.sample(veering_isosigs[:3000], 3):
tri, angle = taut.isosig_to_tri_angle(sig)
T = veering.veering_triangulation(tri, angle)
is_eo = T.is_edge_orientable()
for angle in T.exotic_angles():
assert taut_polytope.taut_cone_homological_dim(tri, angle) == 0, sig
assert is_eo == transverse_taut.is_transverse_taut(tri, angle), sig
### test for drill_midsurface_bdy: drill then fill, check you get the same manifold
if sage_working:
from sage.combinat.words.word_generators import words
from sage.modules.free_module_integer import IntegerLattice
from sage.modules.free_module import VectorSpace
from sage.matrix.constructor import Matrix
import z_charge
import z2_taut
import regina
ZZ2 = ZZ.quotient(ZZ(2))
sig_starts = ["b+-LR", "b++LR"]
print("testing lattice for punc torus bundle")
for i in range(3):
for sig_start in sig_starts:
sig = sig_start + str(words.RandomWord(8, 2, "LR")) # 8 is a magic number
M = snappy.Manifold(sig)
tri = regina.Triangulation3(M)
t, A = z_charge.sol_and_kernel(M)
B = z_charge.leading_trailing_deformations(M)
C = z2_taut.cohomology_loops(tri)
AA = IntegerLattice(A)
BB = IntegerLattice(B)
assert AA == BB.saturation(), sig
dim = 3*M.num_tetrahedra()
V = VectorSpace(ZZ2, dim)
AA = V.subspace(A)
BB = V.subspace(B)
CM = Matrix(ZZ2, C)
CC = CM.right_kernel()
assert AA.intersection(CC) == BB , sig
## so l-t defms are the part of the kernel that doesn't flip over
if sage_working:
print("testing charges for punc torus bundle")
for i in range(3):
for sig_start in sig_starts:
sig = sig_start + str(words.RandomWord(8, 2, "LR")) # 8 is a magic number
M = snappy.Manifold(sig)
assert z_charge.can_deal_with_reduced_angles(M), sig
if sage_working:
import carried_surface
import mutation
print("testing building carried surfaces and mutations")
sigs_weights = [
['iLLLPQccdgefhhghqrqqssvof_02221000', (0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0)],
['jLLAvQQcedehihiihiinasmkutn_011220000', (2, 0, 1, 0, 0, 0, 1, 2, 0, 2, 0, 2, 1, 0, 0, 0, 1, 0)],
['jLLAvQQcedehihiihiinasmkutn_011220000', (0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0)],
['jLLLMPQcdgfhfhiiihshassspiq_122201101', (0, 0, 4, 0, 4, 1, 0, 2, 2, 0, 1, 0, 0, 4, 0, 4, 0, 0)]
]
strata = [
((1, 2), [2, 2]),
((2, 4), [5, 5, 1, 1]),
((0, 3), [2, 0, 0]),
((6, 1), [22])
]
orders_of_veering_symmetry_groups = [4, 2, 2, 2]
for i in range(len(sigs_weights)):
tri, angle = taut.isosig_to_tri_angle(sigs_weights[i][0])
weights = sigs_weights[i][1]
surface, edge_colours = carried_surface.build_surface(tri, angle, weights, return_edge_colours = True)
assert strata[i] == carried_surface.stratum_from_weights_surface(weights, surface)
veering_isoms = carried_surface.veering_symmetry_group(surface, edge_colours)
assert len(veering_isoms) == orders_of_veering_symmetry_groups[i]
isom = veering_isoms[1]
mutation.mutate(tri, angle, weights, isom, quiet = True)
if i == 0:
assert tri.isoSig() == 'ivLLQQccfhfeghghwadiwadrv'
#print('svof to wadrv passed')
elif i == 1:
assert tri.isoSig() == 'jvLLAQQdfghhfgiiijttmtltrcr'
#print('smkutn to tltrcr passed')
elif i == 2:
assert tri.isoSig() == 'jLLMvQQcedehhiiihiikiwnmtxk'
#print('smkutn to mtxk passed')
elif i == 3:
assert tri.isoSig() == 'jLLALMQcecdhggiiihqrwqwrafo'
#print('spiq to rafo passed')
if sage_working:
print("all tests depending on sage passed")
newGeneration=[]
for j in range(populationLimit):
fitnessVal = fitnessFunction.fitnessFunction(population[j],city)
if fitnessVal < bestVal:
bestVal = fitnessVal
bestAns = population[j]
for k in range(populationLimit):
for l in range((k+1), populationLimit):
# child = population[k]
child = crossover.crossover(population[k],population[l],city)
newGeneration.append(child)
for member in newGeneration:
member = mutation.mutate(member)
for m in range(populationLimit):
newGeneration.append(population[m])
population = top.top(populationLimit,newGeneration,city)
print bestAns
print bestVal
elapsed = time.clock()
def mutation_1(generation):
generation = mutation.mutate(generation)
return generation
def ga(chord_progression,
n=40,
num_iter=200,
prob_local=.5,
ngram_generate=None):
"""genetic algorithm
Args:
chord_progression ((int, int)[]): chord progression which is a list of (chord_root, duration)
n (int, optional): Defaults at 40. Population size.
num_iter (int, optional): Defaults at 200. Specifies number of iterations of GA before termination
prob_local (float, optional): Defaults at .5. Probability of mutations
ngram_generate (None, optional): Defaults at None. If True, use ngram to initialize population. Otherwise, randomly initialize.
Returns:
(int, (int, int)[]))[]: Chromosome list of final generation in the genetic algorithm
"""
d = sum([d for (_, d) in chord_progression]) # d is total duration of song
chromosome_list = initialize_chromosomes(
n, d, chord_progression,
ngram_generate=ngram_generate) # list of (fitness, genotype)
elitism_coef = 25 # how many elites to keep in each round
for i in range(0, num_iter):
new_chromosome_list = []
# Elitism?
# keep the highest fitness chromosome
chromosome_list.sort(key=lambda x: x[0]) # sort by increasing fitness
to_print = str(i) + ". " + str(chromosome_list[-1][0])
print to_print
for i, chrom in enumerate(reversed(chromosome_list)):
if i >= elitism_coef:
break
new_chromosome_list.append(chrom)
# new_chromosome_list.append(chromosome_list[-1])
# Crossover n times
for i in range(n - elitism_coef):
parent1 = tournament_selection(chromosome_list, 4, .9)
parent2 = tournament_selection(chromosome_list, 4, .9)
(child1_genotype, child2_genotype) = crossover(parent1, parent2, d)
# calculate fitness of both children, and add higher to chromosomes
fitness1 = calc_fitness(child1_genotype, chord_progression)
fitness2 = calc_fitness(child2_genotype, chord_progression)
if fitness1 > fitness2:
new_chromosome_list.append((fitness1, child1_genotype))
else:
new_chromosome_list.append((fitness2, child2_genotype))
# Mutate based on certain probabilities
# decide on hill-climbing (don't replace parent if it was not at
# least as fit!)
for i, chrom in enumerate(new_chromosome_list):
if i < elitism_coef: # maintain elitism
continue
old_genotype = chrom[1][:]
old_fitness = chrom[0]
new_genotype = mutate(chrom, d, prob_local=prob_local) # 1
new_fitness = calc_fitness(new_genotype, chord_progression)
if new_fitness >= old_fitness: # hill climbing implemented here
new_chromosome_list[i] = (new_fitness, new_genotype)
else:
new_chromosome_list[i] = (old_fitness, old_genotype)
chromosome_list = new_chromosome_list
chromosome_list.sort(reverse=True,
key=lambda x: x[0]) # sort by decreasing fitness
return chromosome_list
def ga(chord_progression, n=40, num_iter=200, prob_local=.5, ngram_generate=None):
"""genetic algorithm
Args:
chord_progression ((int, int)[]): chord progression which is a list of (chord_root, duration)
n (int, optional): Defaults at 40. Population size.
num_iter (int, optional): Defaults at 200. Specifies number of iterations of GA before termination
prob_local (float, optional): Defaults at .5. Probability of mutations
ngram_generate (None, optional): Defaults at None. If True, use ngram to initialize population. Otherwise, randomly initialize.
Returns:
(int, (int, int)[]))[]: Chromosome list of final generation in the genetic algorithm
"""
d = sum([d for (_, d) in chord_progression]) # d is total duration of song
chromosome_list = initialize_chromosomes(n, d, chord_progression, ngram_generate=ngram_generate) # list of (fitness, genotype)
elitism_coef = 25 # how many elites to keep in each round
for i in range(0, num_iter):
new_chromosome_list = []
# Elitism?
# keep the highest fitness chromosome
chromosome_list.sort(key=lambda x: x[0]) # sort by increasing fitness
to_print = str(i) + ". " + str(chromosome_list[-1][0])
print to_print
for i, chrom in enumerate(reversed(chromosome_list)):
if i >= elitism_coef:
break
new_chromosome_list.append(chrom)
# new_chromosome_list.append(chromosome_list[-1])
# Crossover n times
for i in range(n-elitism_coef):
parent1 = tournament_selection(chromosome_list, 4, .9)
parent2 = tournament_selection(chromosome_list, 4, .9)
(child1_genotype, child2_genotype) = crossover(parent1, parent2, d)
# calculate fitness of both children, and add higher to chromosomes
fitness1 = calc_fitness(child1_genotype, chord_progression)
fitness2 = calc_fitness(child2_genotype, chord_progression)
if fitness1 > fitness2:
new_chromosome_list.append((fitness1, child1_genotype))
else:
new_chromosome_list.append((fitness2, child2_genotype))
# Mutate based on certain probabilities
# decide on hill-climbing (don't replace parent if it was not at
# least as fit!)
for i, chrom in enumerate(new_chromosome_list):
if i < elitism_coef: # maintain elitism
continue
old_genotype = chrom[1][:]
old_fitness = chrom[0]
new_genotype = mutate(chrom, d, prob_local=prob_local) # 1
new_fitness = calc_fitness(new_genotype, chord_progression)
if new_fitness >= old_fitness: # hill climbing implemented here
new_chromosome_list[i] = (new_fitness, new_genotype)
else:
new_chromosome_list[i] = (old_fitness, old_genotype)
chromosome_list = new_chromosome_list
chromosome_list.sort(reverse=True, key=lambda x: x[0]) # sort by decreasing fitness
return chromosome_list