def doMutation(self, chromosomeBeforeM, generationAfterM, flagMutation, fitnessList, i):
Pm = self.Pm
dice = []
length = len(chromosomeBeforeM.genes)
chromosome = Chromosome([], length)
geneFlag = []
for j in range(length):
dice.append(float('%.2f' % random.uniform(0.0, 1.0)))
if dice[j] > Pm:
chromosome.genes.append(chromosomeBeforeM.genes[j])
geneFlag.append(0)
if dice[j] <= Pm:
chromosome.genes.append(
float('%.2f' % random.uniform(0.0, 1.0)))
geneFlag.append(1)
check = sum(geneFlag)
if check == 0:
flagMutation[i] = 0
chromosome.fitness = fitnessList[i]
else:
flagMutation[i] = 1
#---clustering----
clustering = Clustering(chromosomeBeforeM, self.data, self.kmax)
chromosome = clustering.calcChildFit(
chromosome)
#------------------
generationAfterM.chromosomes.append(chromosome)
return generationAfterM
def _initial_population(self):
for i in range(self._m):
random_gene = self._random_gene_generator(self._n)
chromosome = Chromosome(random_gene, 0)
chromosome.fitness = self._evaluator(chromosome)
self._evaluation_counter += 1
self._population.append(chromosome)
def random():
c = Chromosome(self._data.dimension)
# Avoid duplicates
while c in self._population:
c = Chromosome(self._data.dimension)
c.dist = self._data.tour_dist(c.tour)
return c
def download_chromosome(self, name):
chromosome = Chromosome(name, self.assembly)
path = chromosome.path()
directory = os.path.dirname(chromosome.path())
if not os.path.isdir(directory):
os.makedirs(directory)
self.log('Created directory {}'.format(directory), True)
uri = URI + chromosome.filename()
self.log('Downloading from {} to {}'.format(uri, path), True)
r = requests.get(uri, stream=True)
# TODO can we do this in fewer than 3 passes?
with open(path, 'wb') as fd:
for chunk in r.iter_content(chunk_size=1024):
fd.write(chunk)
with open(path, 'r') as f:
header = f.readline()
content = f.read().replace('\n', '')
with open(path, 'w') as f:
f.write(header)
f.write(content)
f.write('\n')
self.log('...Complete', True)
def download_chromosome(self, name):
chromosome = Chromosome(name, self.assembly)
path = chromosome.path()
directory = os.path.dirname(chromosome.path())
if not os.path.isdir(directory):
os.makedirs(directory)
self.log('Created directory {}'.format(directory), True)
uri = URI + chromosome.filename()
self.log(
'Downloading from {} to {}'.format(uri, path), True)
r = requests.get(uri, stream=True)
# TODO can we do this in fewer than 3 passes?
with open(path, 'wb') as fd:
for chunk in r.iter_content(chunk_size=1024):
fd.write(chunk)
with open(path, 'r') as f:
header = f.readline()
content = f.read().replace('\n', '')
with open(path, 'w') as f:
f.write(header)
f.write(content)
f.write('\n')
self.log('...Complete', True)
def multi_points_crossover(parent1, parent2, parameters={'prob': 0.4, 'points_count': 'middle'}):
"""
:param parameters: dictionary of parameters that key = parameter name and value = parameter value
:param parent1: First parent chromosome, Gene, np.array with len [n^2,1]
:param parent2: Second parent chromosome, Gene, np.array with len [n^2,1]
:return: return two chromosome for each children, Chromosome
"""
if str(parameters['points_count']) == 'middle':
return default_cross_over(parent1, parent2)
if parameters['points_count'] > len(parent1.genotype) or parameters['points_count'] <= 0:
warnings.warn('points must be between 1 and size of genotype. parents will be returned', stacklevel=3)
return parent1, parent2
crossover_points = np.sort(
np.random.choice(np.arange(len(parent1.genotype)), replace=False, size=parameters['points_count']))
crossover_points = np.append(crossover_points, len(parent1.genotype))
# print('cross over points', crossover_points)
first_idx = 0
gen1, gen2 = np.zeros(len(parent1.genotype)), np.zeros(len(parent1.genotype))
for last_idx in crossover_points:
if np.random.random() <= parameters['prob']:
gen2[first_idx: last_idx] = parent2.genotype[first_idx: last_idx]
gen1[first_idx: last_idx] = parent1.genotype[first_idx: last_idx]
# print('same')
else:
gen1[first_idx: last_idx] = parent2.genotype[first_idx: last_idx]
gen2[first_idx: last_idx] = parent1.genotype[first_idx: last_idx]
# print('not same')
# print(gen1)
# print(gen2)
first_idx = last_idx
chromosome1, chromosome2 = Chromosome(gen1, 0), Chromosome(gen2, 0)
return chromosome1, chromosome2
def insert_transposition(chromosome: c.Chromosome) -> c.Chromosome:
"""
:param chromosome:
:return:
"""
inserted_gene_index, source_gene_genotype, inserted_gene_genotype = \
random_select_transposition(chromosome)
segment_length = rd.randint(1, Parameter.IS_elements_length)
pre_index = rd.randint(0, Parameter.gene_length - segment_length)
post_index = pre_index + segment_length
insert_index = rd.randint(0, Parameter.IS_elements_length - 1)
modified_length = post_index - pre_index + insert_index
if modified_length <= Parameter.head_length:
inserted_gene_genotype = \
inserted_gene_genotype[0: insert_index] + source_gene_genotype[pre_index: post_index] + \
inserted_gene_genotype[modified_length:]
else:
over_length = modified_length - Parameter.head_length
inserted_gene_genotype = \
inserted_gene_genotype[0: insert_index] + source_gene_genotype[pre_index: post_index - over_length] + \
inserted_gene_genotype[Parameter.head_length:]
chromosome.genes[inserted_gene_index].genotype = inserted_gene_genotype
chromosome.update()
return chromosome
def test_crossover_at_given_index_longer_chromosomes(
self, first_chromosome_seed: str, second_chromosome_seed: str,
crossover_index: int, first_chromosome_crossed_seed: str,
second_chromosome_crossed_seed: str):
first_chromosome = Chromosome(first_chromosome_seed)
second_chromosome = Chromosome(second_chromosome_seed)
first_chromosome_crossed = CrossedChromosomes(first_chromosome,
second_chromosome,
crossover_index).first()
second_chromosome_crossed = CrossedChromosomes(
first_chromosome, second_chromosome, crossover_index).second()
self.assertEqual(
first_chromosome_crossed,
Chromosome(first_chromosome_crossed_seed),
f"crossed: {first_chromosome_crossed.to_string()}, seed: {first_chromosome_crossed_seed}"
)
self.assertEqual(
second_chromosome_crossed,
Chromosome(second_chromosome_crossed_seed),
f"crossed: {second_chromosome_crossed.to_string()}, seed: {second_chromosome_crossed_seed}"
)
def test_mutate(self, chromosome_seed: str, mutated_seed: str,
injected_random_number: "List"):
chromosome = Chromosome(chromosome_seed)
chromosome_mutated = chromosome.mutate(injected_random_number)
self.assertEqual(chromosome_mutated, Chromosome(mutated_seed))
def start(self, gen_max, pop_size):
"""
:param gen_max: maximum number of generations
:param pop_size: initial population size
:return: best solution found
"""
self.population = []
self.population_size = 0
# self.results = []
self.best = None
gen = 1 # from first generation
self.generate_population(pop_size) # generate initial population
self.population_size = pop_size
if not quite:
pretty_print('Initital:')
self.print_chromosomes(self.population)
while gen <= gen_max:
gen += 1
# p = 1
new_population = list()
for p in range(self.population_size):
parents = random.sample(range(self.population_size), 2)
newbie = self.crossover(self.population[parents[0]],
self.population[parents[1]])
# TODO check child?
# newbie.mutate()
fit = self.fitness(newbie)
# self.results.append((newbie, fit))
new_population.append(newbie)
if self.best is None or self.best[1] > fit:
self.best = (newbie, fit)
if not quite:
pretty_print('%dth generation (after crossover): ' % gen)
self.print_chromosomes(new_population)
self.selection(self.population, new_population)
if not quite:
pretty_print('After selection (after crossover): ')
self.print_chromosomes(self.population)
mutants = []
for chrom in self.population:
new_v = []
new_v.extend(chrom.get())
new_chrom = Chromosome(new_v)
new_chrom.mutate()
fit = self.fitness(new_chrom)
mutants.append(new_chrom)
if self.best is None or self.best[1] > fit:
self.best = (chrom, fit)
if not quite:
pretty_print('%dth generation (after mutations): ' % gen)
self.print_chromosomes(mutants)
self.selection(self.population, mutants)
if not quite:
pretty_print('After selection (after mutations): ')
self.print_chromosomes(self.population)
return self.best
def gene_transposition(chromosome: c.Chromosome) -> c.Chromosome:
pre_gene_index = rd.randint(0, Parameter.num_of_genes - 1)
post_gene_index = rd.randint(0, Parameter.num_of_genes - 1)
chromosome.genes[pre_gene_index], chromosome.genes[post_gene_index]\
= chromosome.genes[post_gene_index], chromosome.genes[pre_gene_index]
chromosome.update()
return chromosome
def nwox_crossover(parent1, parent2, parameters=None):
"""
Non-Wrapping Order Crossover (NWOX) - (Cicirello 2006)
:param parent1: First parent chromosome, Gene, np.array with len [n^2,1]
:param parent2: Second parent chromosome, Gene, np.array with len [n^2,1]
:return: return two chromosome for each children, Chromosome
"""
crossover_points = np.sort(np.random.choice(np.arange(len(parent1.genotype)), replace=False, size=2))
gen1, gen2 = np.copy(parent1.genotype), np.copy(parent2.genotype)
# First, all those bits are left as hole which are presenting within the cut-points in other parent
gen1 = np.setdiff1d(gen1, parent2.genotype[crossover_points[0]: crossover_points[1] + 1], assume_unique=True)
gen2 = np.setdiff1d(gen2, parent1.genotype[crossover_points[0]: crossover_points[1] + 1], assume_unique=True)
gen1 = np.concatenate((gen1[:crossover_points[0]],
parent2.genotype[crossover_points[0]: crossover_points[1] + 1],
gen1[crossover_points[0]:]))
gen2 = np.concatenate((gen2[:crossover_points[0]],
parent1.genotype[crossover_points[0]: crossover_points[1] + 1],
gen2[crossover_points[0]:]))
chromosome1, chromosome2 = Chromosome(gen1, 0), Chromosome(gen2, 0)
return chromosome1, chromosome2
def order_one_crossover(parent1, parent2, parameters=None):
"""
:param parent1: First parent chromosome, Gene, np.array with shape = (1,len(parent))
:param parent2: Second parent chromosome, Gene, np.array with shape = (1,len(parent))
:return
"""
parent1 = parent1.genotype()
parent2 = parent2.genotype()
n = len(parent1.genotype)
start_substr = random.randint(0, n - 2)
end_substr = random.randint(start_substr + 1, n)
child1 = parent1.copy()
child2 = parent2.copy()
j = end_substr
i = end_substr
while j != start_substr:
if not parent1[i] in child2[start_substr:end_substr]:
child2[j] = parent1[i]
j = (j + 1) % n
i = (i + 1) % n
j = end_substr
i = end_substr
while j != start_substr:
if not parent2[i] in child1[start_substr:end_substr]:
child1[j] = parent2[i]
j = (j + 1) % n
i = (i + 1) % n
return Chromosome(child1, 0), Chromosome(child2, 0)
def time_to_procreate():
selected_index = []
for i in range(0, len(population)):
random_number = uniform(0, 1.0)
if random_number < crossover_rate:
selected_index.append(i)
for in_list_index, first_parent_index in enumerate(selected_index):
second_parent_index = 0
if in_list_index == len(selected_index) - 1:
second_parent_index = selected_index[0]
else:
second_parent_index = selected_index[in_list_index + 1]
first_parent = population[first_parent_index]
second_parent = population[second_parent_index]
random_point_genes = 2
first_parent_genes = first_parent.give_group_of_gens(
random_point_genes)
second_parent_genes = second_parent.data
second_parent_genes.pop(random_point_genes)
second_parent_genes.insert(random_point_genes, first_parent_genes)
son = Chromosome(second_parent_genes, fitness_function_procedure)
# Checamos si el hijo supera al padre en fitness
son.calculate_value()
if son.result > first_parent.result:
population.pop(first_parent_index)
population.insert(first_parent_index, son)
def elite_evaluation(new_population, old_population, problem):
# Verify if crossover returned better individuals
new_population.sort(
key=lambda x: Chromosome.compute_makespan(x, problem))
old_population.sort(
key=lambda x: Chromosome.compute_makespan(x, problem))
min_value_op = Chromosome.compute_makespan(new_population[0], problem)
min_value_np = Chromosome.compute_makespan(old_population[0], problem)
if min_value_np < min_value_op:
return new_population
else:
elite_population = []
# elite selection
define_10 = int(len(old_population) * 0.1)
best_10 = old_population[0:define_10]
# This takes only 90% of the best
best_90_sel = new_population[:-define_10]
elite_population.extend(best_10)
elite_population.extend(best_90_sel)
assert len(elite_population) == len(new_population)
return elite_population
def initialisation(self):
for _ in range(0, self.__param['popSize']):
c = Chromosome(self.__problParam)
path = c.repres
shuffle(path)
c.repres = path
self.__population.append(c)
def _mate_one(pair):
mother, father = pair
n = len(mother)
inv1 = inversion(list(mother.genes))
inv2 = inversion(list(father.genes))
line = randint(0, n - 1)
new_inv1 = inv1[0:line] + inv2[line:n]
new_inv2 = inv2[0:line] + inv1[line:n]
# line1 = randint(0, n - 1)
# line2 = randint(0, n - 1)
#
# if line1 > line2:
# line1, line2 = line2, line1
#
# new_inv1 = inv2[0:line1] + inv1[line1:line2] + inv2[line2:n]
# new_inv2 = inv1[0:line1] + inv2[line1:line2] + inv1[line2:n]
child1 = permutation(new_inv1)
child2 = permutation(new_inv2)
child1_chrome = Chromosome(child1)
child2_chrome = Chromosome(child2)
return child1_chrome, child2_chrome
def doCrossover(self, generation, i, index):
chromo = generation.chromosomes
length = chromo[0].length
cut = random.randint(1, length - 1)
parent1 = chromo[index[i]]
parent2 = chromo[index[i + 1]]
genesChild1 = parent1.genes[0:cut] + parent2.genes[cut:length]
genesChild2 = parent1.genes[cut:length] + parent2.genes[0:cut]
child1 = Chromosome(genesChild1, len(genesChild1))
child2 = Chromosome(genesChild2, len(genesChild2))
# ----clustering----
clustering = Clustering(generation, self.data, self.kmax)
child1 = clustering.calcChildFit(child1)
child2 = clustering.calcChildFit(child2)
# -------------------
listA = []
listA.append(parent1)
listA.append(parent2)
listA.append(child1)
listA.append(child2)
# sort parent and child by fitness / dec
listA = sorted(listA, reverse=True,
key=lambda elem: elem.fitness)
generation.chromosomes[index[i]] = listA[0]
generation.chromosomes[index[i + 1]] = listA[1]
return generation
def __init__(self, parent1_id, parent2_id, num_nodes, level=2, gene_type='MOTIF'):
Chromosome.__init__(parent1_id, parent2_id, gene_type)
if level < 2:
raise ValueError('Invalid level value')
self._size = num_nodes
self._level = level
self._genes = None
self._num_params = 0
def _generate_random_population(self):
self.chromosomes = []
for _ in range(POP_SIZE):
c = Chromosome(self.goal)
c.calculate_fitness(self.graph, self.removed_graph)
self.chromosomes.append(c)
# sort population
self.chromosomes = sorted(self.chromosomes, key=lambda x: x.fitness)
def crossover(first_parent, second_parent):
crossover_point = np.random.randint(1, 3)
first_parent = copy.deepcopy(first_parent.get_genes())
second_parent = copy.deepcopy(second_parent.get_genes())
first_child = Chromosome(first_parent[:crossover_point]+second_parent[crossover_point:])
second_child = Chromosome((second_parent[:crossover_point] + first_parent[crossover_point:]))
return [first_child, second_child]
def initialisation(self):
for _ in range(0, self.pop_size):
r = [i for i in range(1, self.max_value)]
shuffle(r)
r = [0] + r
r.append(0)
cr = Chromosome(self.min_value, self.max_value, self.dim)
cr.repres = r
self.population.append(cr)
def single_point_crossover(first_parent, second_parent, crossover_point):
first_parent = first_parent.get_genes()
second_parent = second_parent.get_genes()
first_child = Chromosome(first_parent[:crossover_point] +
second_parent[crossover_point:])
second_child = Chromosome(
(second_parent[:crossover_point] + first_parent[crossover_point:]))
return [first_child, second_child]
def position_based_crossover(parent1, parent2, parameters=None):
"""
:param parameters: dictionary of parameters that key = parameter name and value = parameter value
:param parent1: First parent chromosome, Gene, np.array with size [1,n]
:param parent2: Second parent chromosome, Gene, np.array with size [1,n]
:return: return two chromosome for each children, Chromosome
"""
def find_cycle(parent1, parent2, cycle, first):
ind = np.where(parent2 == cycle[-1])[0][0]
cycle.append(parent1[ind])
if parent1[ind] == first:
return cycle
return find_cycle(parent1, parent2, cycle, first)
par_size = len(parent1.genotype)
points = np.random.choice(par_size, 3, replace=False)
gen1, gen2 = np.zeros(par_size, dtype=np.int), np.zeros(par_size, dtype=np.int)
for i in range(len(points)):
gen1[points[i]], gen2[points[i]] = parent2.genotype[points[i]], parent1.genotype[points[i]]
cycle_index = []
for i in range(par_size):
if i not in points:
cycle = [parent2.genotype[i]]
cycle_index.append(find_cycle(parent1.genotype, parent2.genotype, cycle, parent2.genotype[i]))
else:
cycle_index.append([])
for i in range(par_size):
if i not in points:
cycle = cycle_index[i]
for j in range(1, len(cycle)):
if cycle[j] not in gen1:
gen1[i] = cycle[j]
break
cycle_index = []
for i in range(par_size):
if i not in points:
cycle = [parent1.genotype[i]]
cycle_index.append(find_cycle(parent2.genotype, parent1.genotype, cycle, parent1.genotype[i]))
else:
cycle_index.append([])
for i in range(par_size):
if i not in points:
cycle = cycle_index[i]
for j in range(1, len(cycle)):
if cycle[j] not in gen2:
gen2[i] = cycle[j]
break
chromosome1, chromosome2 = Chromosome(gen1, 0), Chromosome(gen2, 0)
return chromosome1, chromosome2
def test_optional_threshold(self, chromosome_seed: str, mutated_seed: str,
injected_random_number: "List",
threshold: float):
chromosome = Chromosome(chromosome_seed)
chromosome_mutated = chromosome.mutate(injected_random_number,
threshold=threshold)
self.assertEqual(chromosome_mutated, Chromosome(mutated_seed))
def Mutation(chrom, alphabet, mutation_amount):
for i in range(mutation_amount):
char_to_replace = random.choice(chrom.Get_Value())
new_char = random.choice(alphabet)
chrom = Chromosome(chrom.Get_Value().replace(char_to_replace, new_char,
1))
return chrom
def crossover(c1, c2):
'''Takes as input 2 chromosomes and returns a new chromosome which is a mix of the first 2'''
c_new = Chromosome(len(advertisements))
for i in range(len(advertisements)):
if i % 2 == 0:
c_new.array[i] = c1.array[i]
else:
c_new.array[i] = c2.array[i]
return c_new
def initialPopulation(self, variable_config):
pop = []
chrom = Chromosome(variable_config)
for i in range(variable_config.D * variable_config.Np):
pop.append(chrom.initialChromosome(variable_config))
pop = np.array(pop)
pop = pop.reshape(
(variable_config.Np, (variable_config.D * variable_config.n)))
return pop
def ga(pixel_arr, constraints, pop_size=100, g_max=40, p_c=0.6, p_m=0.4, verbose=True):
start_time = time.time()
num_rows, num_cols = pixel_arr.shape[0], pixel_arr.shape[1]
population = [Chromosome(pixel_arr) for i in range(pop_size)]
avg_fitness = sum(c.fitness for c in population)
best_ind = max(population, key=lambda c: c.fitness)
if verbose:
print("Generation 0:")
print("Best fitness:", best_ind.fitness, "Avg fitness:", avg_fitness)
print("Number of segmentations:", max(best_ind.segments))
print("Edge value:", best_ind.edge_value)
print("Connectivity:", best_ind.connectivity)
print("Deviation:", best_ind.deviation)
print(f"Initial generation time: {time.time() - start_time}\n", flush=True)
for g in range(1, g_max+1):
start_time = time.time()
offspring = []
for i in range(pop_size//2):
p1 = parent_selection(population)
p2 = parent_selection(population)
if random() < p_c:
cutoff = randint(0, len(p1.genotype)-1)
c1_geno = crossover(p1.genotype, p2.genotype, cutoff)
c2_geno = crossover(p2.genotype, p1.genotype, cutoff)
else:
c1_geno = p1.genotype
c2_geno = p2.genotype
if random() < p_m:
c1_geno = mutate(c1_geno, num_rows, num_cols, arr, constraints)
if random() < p_m:
c2_geno = mutate(c2_geno, num_rows, num_cols, arr, constraints)
c1 = Chromosome(pixel_arr, c1_geno)
c2 = Chromosome(pixel_arr, c2_geno)
offspring.append(c1)
offspring.append(c2)
population = elitist_replacement(population, offspring)
avg_fitness = sum(c.fitness for c in population)
best_ind = max(population, key=lambda c: c.fitness)
if verbose:
print(f"Generation {g}:")
print("Best fitness:", best_ind.fitness, "Avg fitness:", avg_fitness)
print("Number of segmentations:", max(best_ind.segments))
print("Edge value:", best_ind.edge_value)
print("Connectivity:", best_ind.connectivity)
print("Deviation:", best_ind.deviation)
print(f"Time elapsed: {time.time() - start_time}\n", flush=True)
return best_ind
def test_exe(self):
p1 = Chromosome("111100111100120000000013")
p2 = Chromosome("000012131313111112001112")
crossover_point = 4
children = OnePoint().exe(p1, p2, crossover_point)
expected_1 = Chromosome("111112131313111112001112")
expected_2 = Chromosome("000000111100120000000013")
self.assertEqual(children[0].solution, expected_1.solution)
self.assertEqual(children[1].solution, expected_2.solution)
def tournament_pair(self):
mother = self.getByTournament()
father = self.getByTournament()
# create larger population
size = self.params["NumChromes"]
mothers = [Chromosome(str(mother)) for i in range(0, size/2)]
fathers = [Chromosome(str(father)) for i in range(0, size/2)]
return zip(mothers, fathers)
def testRecombinate():
first = Chromosome()
second = Chromosome()
print(first.dnArray)
print(second.dnArray)
print(first.arithmeticArray)
print(second.arithmeticArray)
first.recombinate(second)
print(first.dnArray)
print(second.dnArray)
print(first.arithmeticArray)
def populate(self, size, chromosome_blueprint):
self.size = size
self.gene_count = len(chromosome_blueprint)
for n in range(0, size):
c = Chromosome.construct(chromosome_blueprint)
self.chromosomes.append(c)
def crossover(parent1, parent2, p_crossover):
'''
Performs crossover with the parents to produce the offspring
:param parent1:
:param parent2:
:param p_crossover:
:param p_mutation:
:return: tuple (child1, child2)
'''
#par1_chromo = parent1['chromosome']
#par2_chromo = parent2['chromosome']
#child1_chromo = copy.deepcopy(par1_chromo)
#child2_chromo = copy.deepcopy(par2_chromo)
#gets the arrays with values to perform the exchange
p1_array = parent1['chromosome'].to_array()
p2_array = parent2['chromosome'].to_array()
#initially, children are copies of parents
c1_array = copy.copy(p1_array)
c2_array = copy.copy(p2_array)
assert len(c1_array) == len(c2_array)
length = len(c1_array)
if random.random() < p_crossover:
#select crossover point
xover_point = random.randint(1, length - 1)
#print type(par1_chromo._genes), type(child1_chromo._genes)
#performs one-point exchange around the xover point
c1_array[0: xover_point] = p1_array[0: xover_point]
c1_array[xover_point: length] = p2_array[xover_point: length]
c2_array[0: xover_point] = p2_array[0: xover_point]
c2_array[xover_point: length] = p1_array[xover_point: length]
#builds new chromosomes from the (possibly crossovered) arrays
child1_chromo = Chromosome.from_array(c1_array)
child2_chromo = Chromosome.from_array(c2_array)
return (
{'chromosome': child1_chromo, 'fitness': 0, 'reliability': 0},
{'chromosome': child2_chromo, 'fitness': 0, 'reliability': 0}
)
def get_missing_chromosomes(self):
missing_chromosomes = []
for name, length in Chromosome.sorted_chromosome_length_tuples(self.assembly):
chromosome = Chromosome(name, self.assembly)
filepath = chromosome.path()
if not os.path.isfile(filepath):
missing_chromosomes.append(name)
else:
expected_size = length + len(chromosome.header()) + 1
size = os.path.getsize(filepath)
if size != expected_size:
missing_chromosomes.append(name)
os.remove(filepath)
return missing_chromosomes
def multiply(self):
"""Generate offspring until we're back to the right population size.
"""
while len(self.chromosomes) < self.size:
x = random.choice(self.chromosomes)
y = random.choice(self.chromosomes)
chromosome = Chromosome.offspring(x, y, self.crossover_rate, self.mutation_rate)
self.chromosomes.append(chromosome)
def generate_new_population(M, seed=True):
chrs=[]
if seed:
# Seeding one chromosome with one
# minmin chromosome
for _ in itertools.repeat(None, P_SIZE-1):
chrs.append(Chromosome(M))
# Seed min-min
ch = Chromosome(M, tabu_list=None, empty=True)
mapping = minmin.run(M)
if DEBUG: print mapping, mapping.makespan()
for t in range(mapping._model.ntasks):
ch.map.assign(t, mapping.machine(t))
chrs.append(ch)
print "Seeded chromosome value:", ch.value()
else:
# No seeding happens here
for _ in itertools.repeat(None, P_SIZE):
chrs.append(Chromosome(M))
return chrs
def download_chromosomes(self):
to_download = self.get_missing_chromosomes()
self.log("Downloading {} chromosomes".format(len(to_download)))
for name in to_download:
chromosome = Chromosome(name, self.assembly)
self.log(chromosome.path())
path = chromosome.path()
directory = os.path.dirname(chromosome.path())
if not os.path.isdir(directory):
os.makedirs(directory)
self.log('created directory {}'.format(directory), True)
self.log('Downloading {} to {}'.format(self.uri + chromosome.filename(), path))
r = requests.get(self.uri + chromosome.filename(), stream=True)
with open(path, 'wb') as fd:
for chunk in r.iter_content(chunk_size=1024):
fd.write(chunk)
self.log('Complete')
run_build_test_suite(self.assembly)
def setUp(self):
self.chromosome_manager = ChromosomeManager(42)
self.chromosome = Chromosome(self.chromosome_manager)
class ChromosomeTestCase(unittest.TestCase):
chromosome = None
def setUp(self):
self.chromosome_manager = ChromosomeManager(42)
self.chromosome = Chromosome(self.chromosome_manager)
def test_str(self):
self.chromosome.binary_string = '010111000011101100101010011111010100'
self.assertEqual(str(self.chromosome), '010111000011101100101010011111010100')
def test_evaluation_with_correct_data(self):
self.chromosome.binary_string = '010111000011101100101010011111010100'
self.chromosome.evaluate(5)
self.assertEqual(self.chromosome.result, 5)
self.assertEqual(self.chromosome.score, 1e18)
def test_evaluation_with_incorrect_data(self):
self.chromosome.binary_string = '111111111111111111111111111111111111'
self.chromosome.evaluate(20)
self.assertEqual(self.chromosome.result, 0)
self.assertEqual(self.chromosome.score, 0.05)
def test_evaluation_with_correct_and_incorrect_data(self):
self.chromosome.binary_string = '011011100001101010110101100110111100'
self.chromosome.evaluate(10)
self.assertEqual(self.chromosome.result, 11)
self.assertEqual(self.chromosome.score, 1)
def test_evaluation_with_zero_division(self):
self.chromosome.binary_string = '001011111111111111111111110111110000'
self.chromosome.evaluate(5)
self.assertEqual(self.chromosome.result, 2)
self.assertEqual(self.chromosome.score, 1 / 3)
def test_fill_with_random_values(self):
self.chromosome.fill_with_random_values()
self.assertEqual(len(self.chromosome.binary_string), 36)
for char in self.chromosome.binary_string:
self.assertTrue(0 <= int(char) <= 1)
def test_mutate(self):
original_binary_string = '010111000011101100101010011111010100'
self.chromosome.binary_string = original_binary_string
mutated_chars = self.chromosome.mutate(0.1)
levenshtein_distance = self._get_levenshtein_distance(original_binary_string, self.chromosome.binary_string)
self.assertEqual(mutated_chars, levenshtein_distance)
def test_mutate_full(self):
original_binary_string = '010111000011101100101010011111010100'
reversed_string = '101000111100010011010101100000101011'
self.chromosome.binary_string = original_binary_string
mutated_chars = self.chromosome.mutate(1)
self.assertEqual(mutated_chars, 36)
self.assertEqual(self.chromosome.binary_string, reversed_string)
def _get_levenshtein_distance(self, string1, string2):
self.assertEqual(len(string1), len(string2))
length = len(string1)
different_chars_count = 0
for i in range(0, length):
if string1[i] != string2[i]:
different_chars_count += 1
return different_chars_count
def testComputeSum():
first = Chromosome()
print(toRealExpression(first.arithmeticArray))
first.computeSum()
def prepare_chromosomes(size):
Chromosome._possible_splits = Chromosome.generate_possible_splits(size)
CircularChromosome._possible_splits = CircularChromosome.generate_possible_splits(size)