def genetic(param_grid_dic, fun):
#%%
from importlib import reload
import genetic as g
reload(g)
gene_names = list(param_grid_dic.keys())
genes_grid = param_grid_dic
gene_result = g.genetic_algorithm(fun,
genes_grid,
init_pop=None,
pop_size=30,
n_gen=10,
mutation_prob=0.1,
normalize=g.normalizer(2.0, 0.01),
seed=1336)
#%% 0.7407
gene_result = g.genetic_algorithm(
fun,
gene_names,
genes_grid,
init_pop=None,
pop_size=30,
n_gen=10,
mutation_prob=0.2,
#normalize = g.normalizer( 1.0, 0.3),
seed=1337)
#%%
return gene_result
def genetic(param_grid_dic, fun, seed=1336):
#%%
from importlib import reload
import genetic as G
reload(G)
genes_grid = param_grid_dic
best_val, best_idxs, fun_eval = G.genetic_algorithm(fun,
genes_grid,
init_pop=None,
pop_size=10,
n_gen=30,
mutation_prob=0.1,
normalize=g.normalizer(
2.0, 0.01),
seed=seed)
# First set of experiments
#best_val, best_idxs, fun_eval = G.genetic_algorithm( fun, genes_grid,
# init_pop = None, pop_size = 30, n_gen=10,
# mutation_prob=0.1,
# normalize = g.normalizer( 2.0, 0.01),
# seed=seed )
print(best_val, fun_eval.eval_cnt())
#%%
return fun_eval
def genetic_with_local_search(random_constructor, edgelist):
population = genetic_algorithm(edgelist, random_constructor, 5, 1.2, 10)
neighborhood_factory = NeighborhoodFactory(edgelist, 'Reversal')
best = None
for p in population:
new = local_search(p, best_improvement, neighborhood_factory)
if best == None or new < best:
best = new
print('New best is {}'.format(best.obj))
return best
import random
import numpy
import Problem, genetic
from utils import *
# generate TSP problem
size = 5
loc = list(range(size))
start = random.randint(0, size - 1)
map = init_matrix(numpy.random.random((size, 2)))
print("size=%s" % (size))
# genetic algorithm
ga_result = genetic.genetic_algorithm(loc, map, 2000, 10)
print("Genetic algorithm's optional result is %s and the order is %s" %
(ga_result[0], ga_result[1]))
from hillclimb import hillclimb
from simulated_annealing import simulated_annealing
from genetic import genetic_algorithm
print("Daftar algoritma yang akan digunakan:\n" + \
"1. Hill Climbing\n" + \
"2. Simulated Annealing\n" + \
"3. Genetic Algorithm\n")
input_algorithm = int(input("Pilih Algoritma yang diinginkan: "))
while input_algorithm < 0 and input_algorithm > 3:
print("Algoritma tidak ada dalam pilihan.")
input_algorithm = input("Pilih Algoritma yang diinginkan: ")
input_file = input("Masukkan nama file input: ")
if input_algorithm == 1:
hillclimb(input_file)
elif input_algorithm == 2:
simulated_annealing(input_file)
elif input_algorithm == 3:
init_pop = input(
"Masukkan jumlah Initial Population. Harus power of 2 (4096): ")
epoch_length = input("Masukkan jumlah Epoch Length (1000): ")
if init_pop == "" and epoch_length == "":
genetic_algorithm(input_file)
else:
if init_pop == "": genetic_algorithm(input_file, int(epoch_length))
elif epoch_length == "": genetic_algorithm(input_file, int(init_pop))
else: genetic_algorithm(input_file, int(init_pop), int(epoch_length))
def train( iterations, sample_size, reduce, positive_train, negative_train, test_data, test_label):
f1_original_clr = []
f1_original = []
f1_dca = []
f1_clr = []
f1_ilr = []
roc_original_clr = []
roc_original = []
roc_dca = []
roc_clr = []
roc_ilr = []
for _ in range( iterations ):
# Select a smaller size
#Select a random set from the train data
train_sample_data, train_sample_label = split_train_test( positive_train, negative_train, sample_size )
f1_original_data, roc_original_data = train_svm(train_sample_data, train_sample_label, test_data,
test_label)
f1_original.append( f1_original_data )
roc_original.append( roc_original_data )
train_sample_data[train_sample_data == 0] = 0.1e-32
test_data[test_data == 0] = 0.1e-32
clr_original_train = clr(train_sample_data)
clr_original_test = clr(test_data)
scaler = StandardScaler()
clr_original_train = np.nan_to_num(scaler.fit_transform(clr_original_train))
clr_original_test = np.nan_to_num(scaler.fit_transform(clr_original_test))
f1_original_data_clr, roc_original_data_clr = train_svm( clr_original_train, train_sample_label, clr_original_test, test_label )
f1_original_clr.append ( f1_original_data_clr )
roc_original_clr.append( roc_original_data_clr )
matrices = genetic_algorithm( train_sample_data, reduce )
roc_dca_iterations = []
for br_matrix in matrices:
#br_matrix = matrices[0]
reduced_data = np.matmul(br_matrix, train_sample_data.transpose()).transpose()
reduced_test = np.matmul(br_matrix, test_data.transpose()).transpose()
f1_dca_data, roc_dca_data = train_svm( reduced_data, train_sample_label, reduced_test, test_label )
#f1_dca.append( f1_dca_data )
roc_dca_iterations.append( roc_dca_data )
#print ("DCA max", max(roc_dca_iterations) )
roc_dca.append( max(roc_dca_iterations) )
#print ( " PCA CLR train shape ", train_sample_data.shape )
# Do ILR and CLR transformation
# Set zeros to small values
train_sample_data[train_sample_data == 0] = 0.1e-32
test_data[test_data == 0] = 0.1e-32
clr_data_train = clr(train_sample_data)
clr_test = clr(test_data)
ilr_data_train = ilr( train_sample_data )
ilr_test = ilr( test_data )
np.savetxt("ilr_data.csv", ilr_data_train, delimiter=",")
# Do PCA to reduce dimensions
pca_clr = PCA(n_components = reduce)
pca_ilr = PCA(n_components = reduce)
#print ( "reduce ", reduce )
fit_train_clr = np.ascontiguousarray( pca_clr.fit_transform(clr_data_train) )
fit_test_clr = np.ascontiguousarray( pca_clr.transform(clr_test) )
fit_train_ilr = np.ascontiguousarray( pca_ilr.fit_transform(ilr_data_train) )
fit_test_ilr = np.ascontiguousarray( pca_ilr.transform(ilr_test) )
np.savetxt("ilr_data_pca.csv", fit_train_ilr, delimiter=",")
pca_clr_reduced_train = np.nan_to_num( fit_train_clr )
pca_ilr_reduced_train = np.nan_to_num( fit_train_ilr )
fit_test_clr = np.nan_to_num( fit_test_clr )
fit_test_ilr = np.nan_to_num( fit_test_ilr )
f1_pca_clr_data, roc_pca_clr_data = train_svm( pca_clr_reduced_train, train_sample_label, fit_test_clr, test_label )
f1_pca_ilr_data, roc_pca_ilr_data = train_svm( pca_ilr_reduced_train, train_sample_label, fit_test_ilr, test_label )
f1_clr.append( f1_pca_clr_data )
roc_clr.append( roc_pca_clr_data )
f1_ilr.append( f1_pca_ilr_data )
roc_ilr.append( roc_pca_ilr_data )
#print ( roc_original, roc_dca, roc_clr, roc_ilr)
return ( sum ( roc_original ) / iterations ) , ( sum ( roc_original_clr ) / iterations ), ( sum( roc_dca ) / iterations ) , ( sum( roc_clr ) / iterations ) , ( sum( roc_ilr ) / iterations )
m = re.search(pattern, "".join(f.readlines()))
name = m.group(1)
size = int(m.group(2))
numbers = [int(x) for x in "".join(m.group(3).split()).split(",")]
distances = []
position = 0
for i in range(size):
row = []
for j in range(i):
row.append(distances[j][i])
row.append(0)
row += numbers[position:position + size - i - 1]
position += size - i - 1
distances.append(row)
return distances
if __name__ == "__main__":
filename = sys.argv[2]
distances = generate_distance_matrix(filename)
algorithm = sys.argv[1]
if algorithm == 'genetic':
genetic.distances = distances
solution, length = genetic.genetic_algorithm()
elif algorithm == 'annealing':
annealing.distances = distances
solution, length = annealing.annealing_algorithm()
print(solution)
print(length)
#print(newp_cisat)
#scene.simul.trace(newp_cisat)
#raw_input("hit enter:")
"""
basepath = shortest.shortest_two(state)
tot, newp = pathcost(basepath, scene.simul.drone, state)
#scene.simul.trace(newp)
print("total cost of base path 2:", tot)
"""
print("Computing genetic algorithm path")
start = time.time()
best_path, max_list, avg_list = genetic.genetic_algorithm(
state,
genetic.A_star_dist,
genetic.fitness_d_water,
pop_size=10000,
num_generation=300,
lamda=10000,
mutation_prob=0.5)
end = time.time() - start
print("best answer: ", best_path)
print("max list: ", max_list)
print("avg list: ", avg_list)
tot2, newp2 = pathcost(best_path, scene.simul.drone, state)
tofile = [end, tot2, newp2]
pickle.dump(tofile, open(str(randseed) + "-gapath.pickle", "wb"))
print("Total cost of GA path:", tot2)
print("Elapsed Time: ", end)
if tot2 < tot:
print("Woohoo! Genetic path cost shorter!")
def global_plus_local(f):
""" This function runs the whole approach global + local search """
iterations_genetic = 1 # iterations genetic algorithm
knowledge = 0.8 # level of knowledge
list_best_individuals = list(
) # to store the best individual of each genetic algorithm run
list_best_fitness = list(
) # to store the best fitness of the best individual of each run
list_generations = list() # to store the generations
list_drones_climbing = list()
list_evolution_max = list()
type_global = "Genetic"
type_local = "Hill Climbing"
f.write(type_global)
f.write("\n")
scenarios.generate_victim_positions_traces()
scenarios.partial_knowledge_generation(knowledge)
for i in range(0, iterations_genetic):
individual, fitness, generation, evol_max = genetic.genetic_algorithm(
"global_plus_local", i, knowledge)
list_best_individuals.append(individual)
list_best_fitness.append(fitness)
list_generations.append(generation)
list_evolution_max.append(evol_max)
length = len(list_best_fitness)
mean = sum(list_best_fitness) / length
sum2 = sum(x * x for x in list_best_fitness)
std = abs(sum2 / length - mean**2)**0.5
f.write("Results \n")
f.write("Max, Min, Mean, Std \n")
f.write(
str(max(list_best_fitness)) + "," + str(min(list_best_fitness)) + "," +
str(mean) + "," + str(std))
f.write("\n")
global_max = max(list_best_fitness)
index = miscelleneous.find_max(list_best_fitness)
plots.print_drones_data(list_best_individuals[index], f)
# LOCAL
f.write(type_local)
f.write("\n")
#list_dr = quality.init_modified(list_best_individuals[index], global_variables.num_drones) # To simulate different number of drones for the initial deployment and for the adaptation to the real conditions
#list_drones_climbing, records = local.hill_climbing(list_dr, list_best_individuals[index].fitness.values)
list_drones_climbing, records = local.hill_climbing(
list_best_individuals[index],
list_best_individuals[index].fitness.values)
f.write("Results \n")
f.write(str(quality.evaluate(list_drones_climbing)))
plots.print_drones_data(list_drones_climbing, f)
plots.positions(list_best_individuals[index], list_drones_climbing,
type_global, type_local)
plots.evolution_local(records, type_local)
plots.evolution_global(list_evolution_max[index], type_global)
print("######### FIRST DEPLOYMENT STATISTICS ################")
print(" Min %s" % min(list_best_fitness))
print(" Max %s" % max(list_best_fitness))
print(" Avg %s" % mean)
print(" Std %s" % std)
def only_global(f, type_algorithm, knowledge, fil, argument):
#iterations_genetic = 120
#iterations_genetic = 30 # how many times we run the algorithm
iterations_genetic = 30
iterations_pso = 1
list_best_individuals = list() # list of best individuals
list_best_fitness = list() # list of best fitnesses
list_generations = list() # list of generations
list_evolution_max = list()
list_covergence = list()
list_best_individuals_f1 = list() # list of best individuals
list_best_fitness_f1 = list() # list of best fitnesses
list_generations_f1 = list() # list of generations
list_evolution_max_f1 = list()
list_id_f1 = list()
list_covergence_f1 = list()
list_best_individuals_f2 = list() # list of best individuals
list_best_fitness_f2 = list() # list of best fitnesses
list_generations_f2 = list() # list of generations
list_evolution_max_f2 = list()
list_id_f2 = list()
list_covergence_f2 = list()
list_best_individuals_f3 = list() # list of best individuals
list_best_fitness_f3 = list() # list of best fitnesses
list_generations_f3 = list() # list of generations
list_evolution_max_f3 = list()
list_id_f3 = list()
list_covergence_f3 = list()
list_best_individuals_f4 = list() # list of best individuals
list_best_fitness_f4 = list() # list of best fitnesses
list_generations_f4 = list() # list of generations
list_evolution_max_f4 = list()
list_id_f4 = list()
list_covergence_f4 = list()
results_f1 = list()
results_f2 = list()
results_f3 = list()
results_f4 = list()
res = list()
# scenario generation
## basically, the victims are splitted into quadrants (4 :1.up-right,2.left-down,3.up-left,4.down-right)
## given the preferred number of ground nodes to display, the quadrants will appear
scenarios.generate_victim_positions_traces()
scenarios.partial_knowledge_generation(knowledge)
if type_algorithm == "genetic":
for i in range(0, iterations_genetic):
#
individual, fitness, generation, evol_max, convergence = genetic.genetic_algorithm(
"genetic", i, knowledge)
list_best_individuals.append(individual)
list_best_fitness.append(fitness)
list_generations.append(generation)
list_evolution_max.append(evol_max)
list_covergence.append(convergence)
#print convergence
print("list_covergence STEP ", list_covergence)
stat = miscelleneous.statistics(list_best_fitness)
stat_convergence = miscelleneous.statistics(list_covergence)
data_results = pd.DataFrame(
[stat], columns=["maximum", "minimum", "mean", "std", "index"])
data_convergence = pd.DataFrame(
[stat_convergence],
columns=["maximum", "minimum", "mean", "std", "index"])
data_results.to_csv(fil + "results.csv")
data_convergence.to_csv(fil + "convergence.csv")
f.write("The best solution of population 1\n")
plots.print_drones_data(list_best_individuals[stat["index"]],
list_evolution_max[stat["index"]], f)
if type_algorithm == "pso":
for i in range(0, iterations_pso):
individual, fitness, = pso.pso_algorithm()
list_best_individuals.append(individual)
list_best_fitness.append(fitness)
if type_algorithm == "multi_population":
for i in range(0, iterations_genetic):
## print the iterations
print("Iteration genetic : ", i)
if len(argument) > 1: ## input : initial positions
res = ga_multi_population.ga_multi_population(
argument, type_algorithm, i, knowledge)
else: ## classic search with no individuals to start with
res = ga_multi_population.ga_multi_population(
None, type_algorithm, i, knowledge)
## 4 * iterations_genetic number of ga_multi_population : each node in the queue (ring schema)
## has THE SAME : iterations_genetic (30) results
for i, r in enumerate(res):
if i == 0:
results_f1.append(r)
if i == 1:
results_f2.append(r)
if i == 2:
results_f3.append(r)
if i == 3:
results_f4.append(r)
if type_algorithm == "multi_population":
for r in results_f1:
list_best_fitness_f1.append(r.best_fitness)
list_best_individuals_f1.append(r.best)
list_evolution_max_f1.append(r.best_evolution)
list_id_f1.append(r.id)
list_covergence_f1.append(r.convergence_generation)
for r in results_f2:
list_best_fitness_f2.append(r.best_fitness)
list_best_individuals_f2.append(r.best)
list_evolution_max_f2.append(r.best_evolution)
list_id_f2.append(r.id)
list_covergence_f2.append(r.convergence_generation)
for r in results_f3:
list_best_fitness_f3.append(r.best_fitness)
list_best_individuals_f3.append(r.best)
list_evolution_max_f3.append(r.best_evolution)
list_id_f3.append(r.id)
list_covergence_f3.append(r.convergence_generation)
for r in results_f4:
list_best_fitness_f4.append(r.best_fitness)
list_best_individuals_f4.append(r.best)
list_evolution_max_f4.append(r.best_evolution)
list_id_f4.append(r.id)
list_covergence_f4.append(r.convergence_generation)
stat1 = miscelleneous.statistics(list_best_fitness_f1)
stat2 = miscelleneous.statistics(list_best_fitness_f2)
stat3 = miscelleneous.statistics(list_best_fitness_f3)
stat4 = miscelleneous.statistics(list_best_fitness_f4)
'''
x=0
for v in (list_covergence_f1,list_covergence_f2,list_covergence_f3,list_covergence_f4) :
print(x," : ",v)
x=x+1
'''
stat_convergence1 = miscelleneous.statistics(list_covergence_f1)
stat_convergence2 = miscelleneous.statistics(list_covergence_f2)
stat_convergence3 = miscelleneous.statistics(list_covergence_f3)
stat_convergence4 = miscelleneous.statistics(list_covergence_f4)
data_results = pd.DataFrame(
[stat1, stat2, stat3, stat4],
columns=["maximum", "minimum", "mean", "std", "index"])
data_results.to_csv(fil + "results.csv")
data_convergence = pd.DataFrame(
[
stat_convergence1, stat_convergence2, stat_convergence3,
stat_convergence4
],
columns=["maximum", "minimum", "mean", "std", "index"])
data_convergence.to_csv(fil + "convergence.csv")
f.write("The best solution of population 1\n")
plots.print_drones_data(list_best_individuals_f1[stat1["index"]],
list_evolution_max_f1[stat1["index"]], f)
f.write("The best solution of population 2\n")
plots.print_drones_data(list_best_individuals_f2[stat2["index"]],
list_evolution_max_f2[stat2["index"]], f)
f.write("The best solution of population 3\n")
plots.print_drones_data(list_best_individuals_f3[stat3["index"]],
list_evolution_max_f3[stat3["index"]], f)
f.write("The best solution of population 4\n")
plots.print_drones_data(list_best_individuals_f4[stat4["index"]],
list_evolution_max_f4[stat4["index"]], f)
if type_algorithm == "multi_objective":
pareto_global = tools.ParetoFront()
for i in range(0, iterations_genetic):
pareto = ga_multi_objective.genetic_algorithm(
"multi_objective", i, knowledge)
pareto_global.update(pareto)
plots.print_pareto(pareto_global, f)
