def test_mutate_for_100_percent_chance_for_add_connection_mutation(self):
# probability for each mutation
mutation_coefficients = dict(add_connection=1.0, split_connection=0.0, change_weight=0.0,
new_connection_abs_max_weight=5.0, max_weight_mutation=5.0)
weight = 0.0
genome = Genome([[1, 3, weight, True], [1, 4, weight, True], [2, 3, weight, True]], 2, 2)
genome.mutate(mutation_coefficients)
self.assertEqual([(1, 3), (1, 4), (2, 3), (2, 4)], genome.get_connections_ids())
def test_json_generation(self):
genome = Genome([[1, 3, 0, True], [1, 4, 0, True], [2, 3, 0, True], [2, 4, 0, True]], 2, 2)
genome_from_json = Genome.from_json(genome.to_json())
self.assertEqual(genome.get_connections(), genome_from_json.get_connections())
self.assertEqual(genome.input_size, genome_from_json.input_size)
self.assertEqual(genome.output_size, genome_from_json.output_size)
self.assertEqual(genome.input_node_ids, genome_from_json.input_node_ids)
self.assertEqual(genome.output_node_ids, genome_from_json.output_node_ids)
def test_mutate_for_100_percent_chance_for_weight_mutation(self):
# probability for each mutation
mutation_coefficients = dict(add_connection=0.0, split_connection=0.0, change_weight=1.0,
new_connection_abs_max_weight=5.0, max_weight_mutation=5.0)
weight = 0.0
genome = Genome([[1, 2, weight, True]], 1, 1)
genome.mutate(mutation_coefficients)
# add new connection/node mutation
(source_id, dest_id, new_weight, enable) = genome.get_connections()[0]
self.assertNotAlmostEqual(weight, new_weight)
def test_get_nodes(self):
genome = Genome([[1, 3, 0, True], [1, 4, 0, True], [2, 3, 0, True], [2, 4, 0, True]], 2, 1)
nodes = genome.get_nodes()
self.assertEqual(nodes[0].node_type, 'input')
self.assertEqual(nodes[0].node_id, 1)
self.assertEqual(nodes[1].node_type, 'input')
self.assertEqual(nodes[1].node_id, 2)
self.assertEqual(nodes[2].node_type, 'output')
self.assertEqual(nodes[2].node_id, 3)
self.assertEqual(nodes[3].node_type, 'hidden')
self.assertEqual(nodes[3].node_id, 4)
def test_reproduce_differently_fit_genomes(self):
genome1 = Genome([[1, 3, 0, True], [2, 4, 0, True]], 2, 2)
genome2 = Genome([[1, 4, 0, True], [2, 3, 0, True]], 2, 2)
genome1.fitness = 2.0
genome2.fitness = 1.0
child = Genome.reproduce(genome1, genome2)
self.assertEqual([(1, 3), (2, 4)], child.get_connections_ids())
genome1.fitness = 1.0
genome2.fitness = 2.0
child = Genome.reproduce(genome1, genome2)
self.assertEqual([(1, 4), (2, 3)], child.get_connections_ids())
def test_reproduce_equally_fit_genomes_with_overlapping_connections(self):
genome1 = Genome([[1, 3, 0, True], [2, 4, 0, True], [1, 4, 1, True]], 2, 2)
# genome2 becomes independent copy of genome 1 (same invocation numbers)
genome2 = Genome._reproduce_equal_genomes(genome1, genome1)
# add different connection
genome2._create_connection_genes([[2, 3, 0, True]])
# change genome 2 (1,4) conneciton weight
genome2.connection_genes[(1, 4)].weight = 5
genome1.fitness = 1.0
genome2.fitness = 1.0
child = Genome.reproduce(genome1, genome2)
self.assertEqual([(1, 3), (1, 4), (2, 3), (2, 4)], child.get_connections_ids())
overlapping_connection = child.connection_genes[(1, 4)]
weight = overlapping_connection.weight
self.assertTrue(weight == 1 or weight == 5)
def get_offsprings_from_group(self, group_key, group_offspring_amount,
left_genomes):
group_to_reproduce = self.groups[group_key]
parents = group_to_reproduce.get_parents(self.r_factor)
offsprings = []
while (len(offsprings) != group_offspring_amount):
first_parent = random.choice(parents)
second_parent = random.choice(parents)
# Make a child
offspring = Genome.reproduce(first_parent, second_parent)
# Mutate it
offspring.mutate(self.mutation_coefficients)
# Now try to fit it into this group
if self._is_group_fitting_for_offspring(
group_to_reproduce.get_representative(), offspring):
offsprings.append(offspring)
else:
left_genomes.append(offspring)
return offsprings
def test_genome_creation_with_loop(self):
with self.assertRaises(Exception):
Genome([[1, 1, 0, True]], 1, 0)
def test_mutate_split_conneciton_to_genome_with_disabled_connection(self):
genome = Genome([[1, 2, 0, False]], 1, 1)
genome._mutate_split_connection()
self.assertEqual([(1, 2)], genome.get_connections_ids())
def test_mutate_change_weight_for_genome_with_disabled_connection(self):
weight = 0.0
genome = Genome([[1, 2, weight, False]], 1, 1)
genome._mutate_change_weight(1.0)
(source_id, dest_id, new_weight, enable) = genome.get_connections()[0]
self.assertAlmostEqual(weight, new_weight)
def test_connections_sorting_by_innovation_number(self):
genome = Genome([[1, 3, 0, True], [1, 4, 0, True], [2, 3, 0, True], [2, 4, 0, True]], 2, 1)
connections = sort_connections_by_innovation_number(genome.connection_genes)
self.assertLess(connections[0].innovation_number, connections[1].innovation_number)
self.assertLess(connections[1].innovation_number, connections[2].innovation_number)
self.assertLess(connections[2].innovation_number, connections[3].innovation_number)
def test_mutate_new_connection_to_not_full_genome(self):
full_genome = Genome([[1, 3, 0, True], [1, 4, 0, True], [2, 3, 0, True]], 2, 2)
full_genome._mutate_new_connection(1.0)
self.assertEqual([(1, 3), (1, 4), (2, 3), (2, 4)], full_genome.get_connections_ids())
def test_compatibility_distance(self):
genome = Genome([[1, 3, 0, True], [1, 4, 0, True], [2, 3, 0, True], [2, 4, 0, True]], 2, 2)
genome2 = Genome([[1, 4, 0, True], [1, 2, 0, True], [1, 3, 0, True]], 1, 3)
coefficients = dict(excess_factor=1.0, disjoint_factor=1.0, weight_difference_factor=1.0)
genome.compatibility_distance(genome2, coefficients)
def test_get_connections(self):
genome = Genome([[2, 3, 0, True], [1, 4, 0, True], [1, 3, 0, True], [2, 4, 0, True]], 2, 2)
connections = sorted(genome.get_connections())
self.assertEqual(connections, [(1, 3, 0, True), (1, 4, 0, True), (2, 3, 0, True), (2, 4, 0, True)])
def test_get_connections_ids(self):
genome = Genome([[1, 3, 0, True], [1, 4, 0, True], [2, 3, 0, True], [2, 4, 0, True]], 2, 2)
genome2 = Genome([[1, 4, 0, True], [1, 2, 0, True], [1, 3, 0, True]], 1, 3)
self.assertEqual(genome.get_connections_ids(), [(1, 3), (1, 4), (2, 3), (2, 4)])
self.assertEqual(genome2.get_connections_ids(), [(1, 2), (1, 3), (1, 4)])
def test_uniqueness_of_connections(self):
connections = [[1, 2, 0, True], [1, 2, 0, True]]
with self.assertRaises(Exception):
Genome(connections, 1, 1)
def test_genome_creation_with_empty_node(self):
with self.assertRaises(Exception):
Genome([[1, None, 0, True], [1, 4, 0, True], [2, 3, 0, True], [2, 4, 0, True]], 1, 2)