def test_add_individual(self): mlc_repo = self.__get_new_repo() # mlc repository is empty self.assertEqual(mlc_repo.count_individual(), 0) # add the first individual indiv_id, exists = mlc_repo.add_individual( Individual("(root (+ 1 1))")) self.assertEqual(indiv_id, 1) self.assertFalse(exists) self.assertEqual(mlc_repo.count_individual(), 1) # trying to add an Individual with the same value indiv_id, exists = mlc_repo.add_individual( Individual("(root (+ 1 1))")) self.assertEqual(indiv_id, 1) self.assertTrue(exists) self.assertEqual(mlc_repo.count_individual(), 1) # adds another individual indiv_id, exists = mlc_repo.add_individual( Individual("(root (+ 2 2))")) self.assertEqual(indiv_id, 2) self.assertFalse(exists) self.assertEqual(mlc_repo.count_individual(), 2)
def create(self, gen_size): ramp = np.array(self._config.get_list('GP', 'ramp'), dtype='float') center = (np.max(ramp) + np.amin(ramp)) / 2 sigma = self._config.getint('GP', 'gaussigma') distrib = self.__create_gaussian_distribution(ramp, center, sigma, gen_size) # Append a zero to the begginning of the array distrib = np.concatenate((np.array([0.]), distrib)) lg.logger_.debug('[MIXED_RAMP_GAUSS] Distribution generated: ' + np.array_str(distrib)) i = 0 j = 0 while j < len(distrib) - 1: # Change th maxdepth propery while we generate the first generation Individual.set_maxdepthfirst(ramp[j]) aux = distrib[j] + round((distrib[j + 1] - distrib[j]) / 2) # Numpy ranges doesn't include the last element as in python. # Increment the max value by 1 to correct this effect indiv_indexes_1 = np.arange(1, aux + 1, dtype=int) indiv_indexes_2 = np.arange(1, distrib[j + 1] + 1, dtype=int) i = self._fill_creation(indiv_indexes_1, i, 1) i = self._fill_creation(indiv_indexes_2, i, 3) j += 1
def test_reload_individuals_from_file(self): with saved(Config.get_instance()) as config: config.set("BEHAVIOUR", "save", "true") config.set("BEHAVIOUR", "savedir", "test.db") config.set("POPULATION", "sensor_spec", "false") config.set("POPULATION", "sensors", "0") config.set("OPTIMIZATION", "simplify", "false") mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [2, 1, 2] mlc_repo.add_population(p) # check status self.assertEqual(mlc_repo.count_individual(), 2) self.assertEqual(mlc_repo.count_population(), 1) # reload mlc_repository using another instance mlc_repo = self.__get_new_repo() self.assertEqual(mlc_repo.count_individual(), 2) self.assertEqual(mlc_repo.count_population(), 1)
def test_remove_population_to_from_bad_values(self): mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) mlc_repo.add_individual(Individual("(root (+ 3 3))")) mlc_repo.add_individual(Individual("(root (+ 4 4))")) mlc_repo.add_individual(Individual("(root (+ 5 5))")) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 1, 1] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [2, 2, 2] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [3, 3, 3] mlc_repo.add_population(p) self.assertEqual(mlc_repo.count_population(), 3) # Remove all generations (1 to 3) mlc_repo.remove_population_to(10) self.assertEqual(mlc_repo.count_population(), 0)
def test_parameter_controls_mutate_hoist(self): # save and restore original configuration with saved(Config.get_instance()): Config.get_instance().set("POPULATION", "controls", "5") individual = Individual( '(root (/ (exp (/ 8.2118 S0)) (* (* S0 (* 1.6755 -0.0699)) (log (exp -3.2288)))) (* (+ (sin -9.8591) (exp S0)) -9.4159) 0.0290 (* (log (* (+ -5.0573 -6.2191) S0)) (/ (cos (log S0)) (cos (tanh 2.2886)))) (log -8.6795))' ) new_ind = individual.mutate(Individual.MutationType.HOIST) self.assertEqual( new_ind.get_value(), "(root (log (exp -3.2288)) (* (+ (sin -9.8591) (exp S0)) -9.4159) 0.0290 (* (log (* (+ -5.0573 -6.2191) S0)) (/ (cos (log S0)) (cos (tanh 2.2886)))) (log -8.6795))" ) new_ind = individual.mutate(Individual.MutationType.HOIST) self.assertEqual( new_ind.get_value(), "(root (/ (exp (/ 8.2118 S0)) (* (* S0 (* 1.6755 -0.0699)) (log (exp -3.2288)))) (exp S0) 0.0290 (* (log (* (+ -5.0573 -6.2191) S0)) (/ (cos (log S0)) (cos (tanh 2.2886)))) (log -8.6795))" ) new_ind = individual.mutate(Individual.MutationType.HOIST) self.assertEqual( new_ind.get_value(), "(root (* S0 (* 1.6755 -0.0699)) (* (+ (sin -9.8591) (exp S0)) -9.4159) 0.0290 (* (log (* (+ -5.0573 -6.2191) S0)) (/ (cos (log S0)) (cos (tanh 2.2886)))) (log -8.6795))" )
def test_update_individual_cost_in_generation(self): mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) # add first population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 2, 1] p._costs = [4, 5, 6] p._ev_time = [5, 6, 7] mlc_repo.add_population(p) # add second population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [2, 1, 2] p._costs = [8, 9, 10] p._ev_time = [11, 12, 13] mlc_repo.add_population(p) # update cost for individual 1 mlc_repo.update_individual_cost(1, 45, 46, generation=1) # check cost update in the first population p = mlc_repo.get_population(1) self.assertEqual(p._individuals, [1, 2, 1]) self.assertEqual(p._costs, [45, 5, 45]) self.assertEqual(p._ev_time, [46, 6, 46]) # check cost update in the second population p = mlc_repo.get_population(2) self.assertEqual(p._individuals, [2, 1, 2]) self.assertEqual(p._costs, [8, 9, 10]) self.assertEqual(p._ev_time, [11, 12, 13])
def test_get_individual_data(self): mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) mlc_repo.add_individual(Individual("(root (+ 3 3))")) mlc_repo.add_individual(Individual("(root (+ 4 4))")) # first population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 2, 1] p._costs = [4, 5, 6] p._ev_time = [5, 6, 7] mlc_repo.add_population(p) # second population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [3, 4, 2] p._costs = [7, 4, 9] p._ev_time = [8, 5, 10] mlc_repo.add_population(p) # check idividuals data loaded from the mlc_repo self.assertEqual(mlc_repo.count_population(), 2) # Individual 1 have two appearances in the first generation data = mlc_repo.get_individual_data(1) self.assertEqual(data.get_value(), "(root (+ 1 1))") self.assertEqual(data.get_appearances(), 2) self.assertEqual(data.get_cost_history(), {1: [(4.0, 5), (6.0, 7)]}) # Individual 2 have two appearances data = mlc_repo.get_individual_data(2) self.assertEqual(data.get_value(), "(root (+ 2 2))") self.assertEqual(data.get_appearances(), 2) self.assertEqual(data.get_cost_history(), { 1: [(5.0, 6)], 2: [(9.0, 10)] }) # Individual 3 have one appearances data = mlc_repo.get_individual_data(3) self.assertEqual(data.get_value(), "(root (+ 3 3))") self.assertEqual(data.get_appearances(), 1) self.assertEqual(data.get_cost_history(), {2: [(7.0, 8)]}) # Individual 4 have one appearances data = mlc_repo.get_individual_data(4) self.assertEqual(data.get_value(), "(root (+ 4 4))") self.assertEqual(data.get_appearances(), 1) self.assertEqual(data.get_cost_history(), {2: [(4.0, 5)]}) # get individual data from invalid individual try: data = mlc_repo.get_individual_data(100) self.assertTrue(False) except KeyError, ex: self.assertTrue(True)
def test_add_population(self): mlc_repo = self.__get_new_repo() mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) mlc_repo.add_individual(Individual("(root (+ 3 3))")) self.assertEqual(mlc_repo.count_individual(), 3) p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 2, 3] p._costs = [4, 5, 6] p._ev_time = [7, 8, 9] p._gen_method = [10, 11, 12] # add population to the mlc_repository self.assertEqual(mlc_repo.count_population(), 0) mlc_repo.add_population(p) self.assertEqual(mlc_repo.count_population(), 1) # obtain population p_from_repo = mlc_repo.get_population(1) # check population content self.assertEqual(p_from_repo._individuals, p._individuals) self.assertEqual(p_from_repo._costs, p._costs) self.assertEqual(p_from_repo._ev_time, p._ev_time) self.assertEqual(p_from_repo._gen_method, p._gen_method)
def test_get_individuals(self): mlc_repo = self.__get_new_repo() mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) # get individuals individual = mlc_repo.get_individual(1) self.assertEqual(individual.get_value(), "(root (+ 1 1))") individual = mlc_repo.get_individual(2) self.assertEqual(individual.get_value(), "(root (+ 2 2))") # get individual data data = mlc_repo.get_individual_data(1) self.assertEqual(data.get_appearances(), 0) self.assertEqual(data.get_value(), "(root (+ 1 1))") self.assertEqual(data.get_cost_history(), {}) data = mlc_repo.get_individual_data(2) self.assertEqual(data.get_appearances(), 0) self.assertEqual(data.get_value(), "(root (+ 2 2))") self.assertEqual(data.get_cost_history(), {}) # invalid id try: individual = mlc_repo.get_individual(3) self.assertTrue(False) except KeyError: self.assertTrue(True)
def test_add_one_individual_incomplete_population(self): base_creator = MixedRampedGauss() creator = IndividualSelection({Individual("1+1"): [0]}, base_creator) self.__fill_and_assert(fill_creator=creator, expected_pop_indexes=[1], expected_individuals={1: Individual("1+1")})
def test_remove_population_to(self): mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) mlc_repo.add_individual(Individual("(root (+ 3 3))")) mlc_repo.add_individual(Individual("(root (+ 4 4))")) mlc_repo.add_individual(Individual("(root (+ 5 5))")) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 1, 1] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [2, 2, 2] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [3, 3, 3] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [4, 4, 4] mlc_repo.add_population(p) self.assertEqual(mlc_repo.count_population(), 4) # remove generations 1 to 2 mlc_repo.remove_population_to(2) self.assertEqual(mlc_repo.count_population(), 2) p = mlc_repo.get_population(1) self.assertEqual(p._individuals, [3, 3, 3]) p = mlc_repo.get_population(2) self.assertEqual(p._individuals, [4, 4, 4]) # New generation must be number 3 p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [5, 5, 5] mlc_repo.add_population(p) self.assertEqual(mlc_repo.count_population(), 3) p = mlc_repo.get_population(1) self.assertEqual(p._individuals, [3, 3, 3]) p = mlc_repo.get_population(2) self.assertEqual(p._individuals, [4, 4, 4]) p = mlc_repo.get_population(3) self.assertEqual(p._individuals, [5, 5, 5])
def test_cut_generation(self): """ Cut a generation using remove_population_from/remove_population_last :return: """ mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) mlc_repo.add_individual(Individual("(root (+ 3 3))")) mlc_repo.add_individual(Individual("(root (+ 4 4))")) mlc_repo.add_individual(Individual("(root (+ 5 5))")) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 1, 1] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [2, 2, 2] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [3, 3, 3] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [4, 4, 4] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [5, 5, 5] mlc_repo.add_population(p) self.assertEqual(mlc_repo.count_population(), 5) # Cut population 4 mlc_repo.remove_population_from(4 + 1) mlc_repo.remove_population_to(4 - 1) # remove unused individuals mlc_repo.remove_unused_individuals() self.assertEqual(mlc_repo.count_population(), 1) self.assertEqual(mlc_repo.count_individual(), 1) p = mlc_repo.get_population(1) self.assertEqual(p._individuals, [4, 4, 4]) individual = mlc_repo.get_individual(4) self.assertEqual(individual.get_value(), "(root (+ 4 4))")
def test_remove_population_to_clear_generations(self): mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) mlc_repo.add_individual(Individual("(root (+ 3 3))")) mlc_repo.add_individual(Individual("(root (+ 4 4))")) mlc_repo.add_individual(Individual("(root (+ 5 5))")) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 1, 1] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [2, 2, 2] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [3, 3, 3] mlc_repo.add_population(p) self.assertEqual(mlc_repo.count_population(), 3) # Remove all generations (1 to 3) mlc_repo.remove_population_to(3) self.assertEqual(mlc_repo.count_population(), 0) # Insert populations again p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [3, 3, 3] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [4, 4, 4] mlc_repo.add_population(p) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [5, 5, 5] mlc_repo.add_population(p) self.assertEqual(mlc_repo.count_population(), 3) p = mlc_repo.get_population(1) self.assertEqual(p._individuals, [3, 3, 3]) p = mlc_repo.get_population(2) self.assertEqual(p._individuals, [4, 4, 4]) p = mlc_repo.get_population(3) self.assertEqual(p._individuals, [5, 5, 5])
def test_crossover_same_level_4(self): individual_1 = Individual("(root S0)", Config.get_instance()) individual_2 = Individual("(root S0)", Config.get_instance()) try: new_ind_1, new_ind_2, _ = individual_1.crossover(individual_2) self.assertFalse(True, "crossover with individual type 4 should fail") except OperationOverIndividualFail, ex: self.assertTrue(True)
def test_generate_from_value(self): individual = Individual( "(root (exp (tanh (- (tanh -8.049) (* 9.15 -6.848)))))") self.assertEquals( individual.get_value(), "(root (exp (tanh (- (tanh -8.049) (* 9.15 -6.848)))))") self.assertEquals(individual.get_formal(), "exp(tanh((tanh((-8.049)) - (9.15 .* (-6.848)))))") self.assertEquals(individual.get_complexity(), 20)
def test_compare_random_individuals(self): individual_1 = Individual.generate(individual_type=3, config=Config.get_instance()) RandomManager.clear_random_values() RandomManager.load_random_values(self._random_file) individual_2 = Individual.generate(individual_type=3, config=Config.get_instance()) self.assertTrue(individual_1.compare(individual_2))
def create(self, gen_size): MLCRepository.get_instance().add_individual( Individual("(root 1)")) MLCRepository.get_instance().add_individual( Individual("(root 2)")) MLCRepository.get_instance().add_individual( Individual("(root 3)")) MLCRepository.get_instance().add_individual( Individual("(root 4)")) MLCRepository.get_instance().add_individual( Individual("(root 5)"))
def test_remove_from_population(self): mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) mlc_repo.add_individual(Individual("(root (+ 3 3))")) mlc_repo.add_individual(Individual("(root (+ 4 4))")) # add first population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 2, 1] mlc_repo.add_population(p) # add second population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 2, 3] mlc_repo.add_population(p) # add third population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [1, 2, 4] mlc_repo.add_population(p) # remove last population mlc_repo.remove_population_from(2) # last generation must be removed self.assertEqual(mlc_repo.count_population(), 1) # first generation exists p = mlc_repo.get_population(1) self.assertEqual(p._individuals, [1, 2, 1]) # all individuals exists and the third individual do not appear in any generation self.assertEqual(mlc_repo.count_individual(), 4) # remove unused individuals deleted = mlc_repo.remove_unused_individuals() self.assertEqual(deleted, 2) self.assertEqual(mlc_repo.count_individual(), 2) individual = mlc_repo.get_individual(1) self.assertEqual(individual.get_value(), "(root (+ 1 1))") individual = mlc_repo.get_individual(2) self.assertEqual(individual.get_value(), "(root (+ 2 2))") try: individual = mlc_repo.get_individual(3) self.assertTrue(False) except KeyError: self.assertTrue(True)
def test_sensor_list(self): # save and restore original configuration with saved(Config.get_instance()): Config.get_instance().set("POPULATION", "sensor_list", "6,15,2,8,4,10") Config.get_instance().set("POPULATION", "sensors", "6") Config.get_instance().set("POPULATION", "sensor_spec", "true") Config.get_instance().set("POPULATION", "sensor_prob", "1.0") # test generate and mutate using sensor list individual = Individual.generate(individual_type=3, config=Config.get_instance()) self.assertEqual( individual.get_value(), '(root (sin (/ (+ (exp S6) (cos S10)) (/ (log S10) (log S4)))))' ) individual = Individual.generate(individual_type=3, config=Config.get_instance()) self.assertEqual( individual.get_value(), '(root (exp (* (- (tanh S6) (tanh S10)) (- (/ S6 S6) (/ S6 S4)))))' ) new_ind = self._individual_l2.mutate( Individual.MutationType.REMOVE_SUBTREE_AND_REPLACE) self.assertEqual( individual.get_value(), '(root (exp (* (- (tanh S6) (tanh S10)) (- (/ S6 S6) (/ S6 S4)))))' ) new_ind = self._individual_l2.mutate( Individual.MutationType.REMOVE_SUBTREE_AND_REPLACE) self.assertEqual( individual.get_value(), '(root (exp (* (- (tanh S6) (tanh S10)) (- (/ S6 S6) (/ S6 S4)))))' ) new_ind = self._individual_l2.mutate( Individual.MutationType.SHRINK) self.assertEqual( individual.get_value(), '(root (exp (* (- (tanh S6) (tanh S10)) (- (/ S6 S6) (/ S6 S4)))))' ) new_ind = self._individual_l2.mutate( Individual.MutationType.SHRINK) self.assertEqual( individual.get_value(), '(root (exp (* (- (tanh S6) (tanh S10)) (- (/ S6 S6) (/ S6 S4)))))' )
def test_reload_individuals_in_memory_loss_data(self): mlc_repo = self.__get_new_repo() # add individuals mlc_repo.add_individual(Individual("(root (+ 1 1))")) mlc_repo.add_individual(Individual("(root (+ 2 2))")) # add population p = Population(3, 0, Config.get_instance(), mlc_repo) p._individuals = [2, 1, 2] # reload mlc_repository using another instance mlc_repo = self.__get_new_repo() self.assertEqual(mlc_repo.count_individual(), 0) self.assertEqual(mlc_repo.count_population(), 0)
def test_crossover_same_level_0(self): individual_1 = Individual("(root (cos 5.046))", Config.get_instance()) individual_2 = Individual("(root (cos 5.046))", Config.get_instance()) new_ind_1, new_ind_2, _ = individual_1.crossover(individual_2) self._assert_individual(new_ind_1, complexity=4, value="(root (cos 5.046))", formal="cos(5.046)") self._assert_individual(new_ind_2, complexity=4, value="(root (cos 5.046))", formal="cos(5.046)")
def _fill_creation(self, individuals, index, type): while index < len(individuals): indiv = Individual.generate(individual_type=type, config=Config.get_instance()) response = MLCRepository.get_instance().add_individual(indiv) if not response[1]: # The individual didn't exist indiv_number = individuals[index] lg.logger_.info('[FILL_CREATION] Generating individual N#' + str(indiv_number)) lg.logger_.debug('[FILL_CREATION] Individual N#' + str(indiv_number) + ' - Value: ' + indiv.get_value()) # Call the preevaluation function if it exists and if it is configured if self._config.getboolean('EVALUATOR', 'preevaluation'): callback = PreevaluationManager.get_callback().preev if callback is not None: if not callback(indiv): lg.logger_.info( '[FILL_CREATION] Preevaluation failed' '. Individual value: ' + indiv.get_value()) continue self._individuals.append((index, response[0])) index += 1 else: lg.logger_.debug('[FILL_CREATION] Replica created.') return index
def test_generate_individuals_types(self): individual = Individual.generate(individual_type=0, config=Config.get_instance()) self._assert_individual( individual, complexity=120, value= "(root (sin (+ (/ (cos -3.0973) (exp (log (* (* -1.3423 (tanh (log -3.5094))) (+ (/ (/ (* -9.1213 (cos (exp 3.6199))) (cos (* S0 (cos (- 5.0161 (sin 4.2656)))))) S0) (- (cos (* (+ (sin -9.8591) (exp S0)) -9.4159)) (log (* (- (tanh -8.5969) S0) (/ (exp (/ 8.2118 S0)) (* (* S0 (* 1.6755 -0.0699)) (log (exp -3.2288)))))))))))) S0)))", formal= "sin(((my_div(cos((-3.0973)),exp(my_log((((-1.3423) .* tanh(my_log((-3.5094)))) .* ((my_div((my_div(((-9.1213) .* cos(exp(3.6199))),cos((S0 .* cos((5.0161 - sin(4.2656))))))),S0)) + (cos(((sin((-9.8591)) + exp(S0)) .* (-9.4159))) - my_log(((tanh((-8.5969)) - S0) .* (my_div(exp((my_div(8.2118,S0))),((S0 .* (1.6755 .* (-0.0699))) .* my_log(exp((-3.2288))))))))))))))) + S0))" ) individual = Individual.generate(individual_type=1, config=Config.get_instance()) self._assert_individual( individual, complexity=24, value= "(root (- (sin (* (log -3.7260) (+ -5.0573 -6.2191))) (* 7.3027 (/ (cos S0) (* 4.7410 6.7097)))))", formal= "(sin((my_log((-3.7260)) .* ((-5.0573) + (-6.2191)))) - (7.3027 .* (my_div(cos(S0),(4.7410 .* 6.7097)))))" ) individual = Individual.generate(individual_type=2, config=Config.get_instance()) self._assert_individual( individual, complexity=15, value="(root (tanh (cos (+ (+ 5.4434 -3.1258) (+ S0 5.1136)))))", formal="tanh(cos(((5.4434 + (-3.1258)) + (S0 + 5.1136))))") individual = Individual.generate(individual_type=3, config=Config.get_instance()) self._assert_individual( individual, complexity=18, value="(root (log (sin (+ (log -6.2620) (* 8.3709 -6.7676)))))", formal="my_log(sin((my_log((-6.2620)) + (8.3709 .* (-6.7676)))))") individual = Individual.generate(individual_type=4, config=Config.get_instance()) self._assert_individual(individual, complexity=1, value="(root -0.6212)", formal="(-0.6212)")
def test_random_generate(self): individual = Individual.generate(individual_type=3, config=Config.get_instance()) self.assertEquals( individual.get_value(), "(root (sin (/ (+ (exp -2.6118) (cos S0)) (/ (log 5.9383) (log -4.5037)))))" ) self.assertEquals( individual.get_formal(), "sin((my_div((exp((-2.6118)) + cos(S0)),(my_div(my_log(5.9383),my_log((-4.5037)))))))" ) self.assertEquals(individual.get_complexity(), 28)
def setUp(self): set_logger("testing") # Load randoms from file random_file = './mlc/unit_matlab_randoms.txt' RandomManager.clear_random_values() RandomManager.load_random_values(random_file) config = Config.get_instance() config.read( os.path.join(mlc_config_path.get_test_path(), 'mlc/individual/configuration.ini')) self._individual_l0 = Individual("(root (cos 5.046))") self._individual_l1 = Individual( "(root (log (sin (exp (tanh 3.6284)))))") self._individual_l2 = Individual( "(root (cos (* (+ (* -1.912 -9.178) (cos S0)) 3.113)))") self._individual_l3 = Individual( "(root (log (/ (* (sin 4.37) (- -8.815 -3.902)) (log (+ 2.025 -8.685)))))" ) self._individual_l4 = Individual("(root S0)")
def __load_individuals(self): individuals = {} conn = self.__get_db_connection() cursor = conn.execute(stmt_get_all_individuals()) for row in cursor: new_individual = Individual(str(row[1]), SQLSaveFormal.from_sql(row[2]), row[3]) individuals[row[0]] = new_individual cursor.close() conn.commit() return individuals
def test_crossover_same_level_2(self): individual_1 = Individual( "(root (cos (* (+ (* -1.912 -9.178) (cos S0)) 3.113)))", Config.get_instance()) individual_2 = Individual( "(root (cos (* (+ (* -1.912 -9.178) (cos S0)) 3.113)))", Config.get_instance()) new_ind_1, new_ind_2, _ = individual_1.crossover(individual_2) self._assert_individual( new_ind_1, complexity=8, value="(root (cos (* (* -1.912 -9.178) 3.113)))", formal="cos((((-1.912) .* (-9.178)) .* 3.113))") self._assert_individual( new_ind_2, complexity=18, value= "(root (cos (* (+ (+ (* -1.912 -9.178) (cos S0)) (cos S0)) 3.113)))", formal= "cos((((((-1.912) .* (-9.178)) + cos(S0)) + cos(S0)) .* 3.113))")
def test_compare(self): individual_1 = Individual( "(root (exp (tanh (- (tanh -8.049) (* 9.15 -6.848)))))") individual_2 = Individual( "(root (exp (tanh (- (tanh -8.049) (* 9.15 -6.848)))))") self.assertTrue(individual_1.compare(individual_2)) individual_different = Individual( "(root (cos (+ (sin (log -0.7648)) (exp (tanh 3.6284)))))") self.assertFalse(individual_1.compare(individual_different))
def get_gen_creator(self): """ Return an IndividualSelection creator if the user added individuals manually. Return None if this was not the case """ if not self._individuals: logger.info("[FIRST_INDIV] No individual") return None gen_method = Config.get_instance().get('GP', 'generation_method') fill_creator = CreationFactory.make(gen_method) # Creat the dictionary of individuals indivs_dict = {} for index in xrange(len(self._individuals)): indiv = Individual(self._individuals[index]) indivs_dict[indiv] = [index] return IndividualSelection(indivs_dict, fill_creator)
def test_individual_value(parent, experiment_name, log_prefix, indiv_value, config): try: """ Evaluate an individual in order to check its correctness. Handle Exceptions """ LispTreeExpr.check_expression(indiv_value) individual = Individual.generate(config=config, rhs_value=indiv_value) callback = EvaluatorFactory.get_callback() return callback.cost(individual) except ExprException, err: # Print the error message returned in the exception, # removing the prefix ([EXPR_EXCEPTION]]) QMessageBox.critical(parent, "Invalid Individual", "Individual inserted is not well-formed. " "Error Msg: {0}" .format(err.message[err.message.find(']') + 2:])) logger.error("{0} Experiment {1} - " "Individual inserted is not well-formed. " "Error Msg: {2}" .format(log_prefix, experiment_name, err.message[err.message.find(']') + 2:]))