class TreeCrossoverTests(unittest.TestCase): def setUp(self): self.config = { "tree_generation": { "initial_max_depth": 4 }, "crossover": { "method": "POINT_CROSSOVER", "probability": 1.0 }, "function_nodes": [{ "type": "FUNCTION", "name": "ADD", "arity": 2 }, { "type": "FUNCTION", "name": "SUB", "arity": 2 }, { "type": "FUNCTION", "name": "MUL", "arity": 2 }, { "type": "FUNCTION", "name": "DIV", "arity": 2 }, { "type": "FUNCTION", "name": "COS", "arity": 1 }, { "type": "FUNCTION", "name": "SIN", "arity": 1 }, { "type": "FUNCTION", "name": "RAD", "arity": 1 }], "terminal_nodes": [{ "type": "CONSTANT", "value": 1.0 }, { "type": "CONSTANT", "value": 2.0 }, { "type": "CONSTANT", "value": 2.0 }, { "type": "CONSTANT", "value": 3.0 }, { "type": "CONSTANT", "value": 4.0 }, { "type": "CONSTANT", "value": 5.0 }, { "type": "CONSTANT", "value": 6.0 }, { "type": "CONSTANT", "value": 7.0 }, { "type": "CONSTANT", "value": 8.0 }, { "type": "CONSTANT", "value": 9.0 }, { "type": "CONSTANT", "value": 10.0 }], "input_variables": [{ "type": "INPUT", "name": "x" }] } self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION") self.generator = TreeGenerator(self.config) self.crossover = TreeCrossover(self.config) self.parser = TreeParser() # create nodes left_node_1 = Node(NodeType.INPUT, name="x") right_node_1 = Node(NodeType.CONSTANT, value=2.0) node = Node(NodeType.CONSTANT, value=2.0) left_node_2 = Node(NodeType.CONSTANT, value=3.0) right_node_2 = Node(NodeType.CONSTANT, value=4.0) cos_func_1 = Node(NodeType.FUNCTION, name="ADD", arity=2, branches=[left_node_1, right_node_1]) sin_func_1 = Node(NodeType.FUNCTION, name="SIN", arity=1, branches=[node]) cos_func_2 = Node(NodeType.FUNCTION, name="COS", arity=1, branches=[left_node_2]) sin_func_2 = Node(NodeType.FUNCTION, name="SIN", arity=1, branches=[right_node_2]) add_func = Node(NodeType.FUNCTION, name="ADD", arity=2, branches=[cos_func_1, sin_func_1]) sub_func = Node(NodeType.FUNCTION, name="SUB", arity=2, branches=[sin_func_2, cos_func_2]) # create tree_1 self.tree_1 = Tree() self.tree_1.root = add_func self.tree_1.update() print self.tree_1 # create tree_2 self.tree_2 = Tree() self.tree_2.root = sub_func self.tree_2.update() def tearDown(self): del self.config del self.generator del self.parser def build_tree_str(self, tree): tree_str = "" for node in tree.program: if hasattr(node, "name") and node.name is not None: tree_str += "node:{0} addr:{1}\n".format(node.name, id(node)) else: tree_str += "node:{0} addr:{1}\n".format(node.value, id(node)) return tree_str def tree_equals(self, tree_1_str, tree_2_str): if tree_1_str == tree_2_str: return True else: return False def test_point_crossover(self): # record before crossover tree_1_before = self.build_tree_str(self.tree_1) tree_2_before = self.build_tree_str(self.tree_2) # point crossover self.crossover.point_crossover(self.tree_1, self.tree_2) # record after crossover tree_1_after = self.build_tree_str(self.tree_1) tree_2_after = self.build_tree_str(self.tree_2) print("Before Crossover") print("\nTree 1") print(tree_1_before) print("\nTree 2") print(tree_2_before) print("\nAfter Crossover") print("\nTree 1") print(tree_1_after) print("\nTree 2") print(tree_2_after) # asserts self.assertTrue(self.tree_equals(tree_1_before, tree_1_before)) self.assertTrue(self.tree_equals(tree_2_before, tree_2_before)) self.assertTrue(self.tree_equals(tree_1_after, tree_1_after)) self.assertTrue(self.tree_equals(tree_2_after, tree_2_after)) self.assertFalse(self.tree_equals(tree_1_before, tree_1_after)) self.assertFalse(self.tree_equals(tree_2_before, tree_2_after)) def test_common_region_point_crossover(self): # record before crossover tree_1_before = self.build_tree_str(self.tree_1) tree_2_before = self.build_tree_str(self.tree_2) # point crossover self.crossover.common_region_point_crossover(self.tree_1, self.tree_2) # record after crossover tree_1_after = self.build_tree_str(self.tree_1) tree_2_after = self.build_tree_str(self.tree_2) print("Before Crossover") print("\nTree 1") print(tree_1_before) print("\nTree 2") print(tree_2_before) print("\nAfter Crossover") print("\nTree 1") print(tree_1_after) print("\nTree 2") print(tree_2_after) def test_crossover(self): # record before crossover tree_1_before = self.build_tree_str(self.tree_1) tree_2_before = self.build_tree_str(self.tree_2) # point crossover self.crossover.crossover(self.tree_1, self.tree_2) # record after crossover tree_1_after = self.build_tree_str(self.tree_1) tree_2_after = self.build_tree_str(self.tree_2) print("Before Crossover") print("\nTree 1!") print(tree_1_before) print("\nTree 2!") print(tree_2_before) print("\nAfter Crossover") print("\nTree 1!") print(tree_1_after) print("\nTree 2!") print(tree_2_after) # asserts self.assertTrue(self.tree_equals(tree_1_before, tree_1_before)) self.assertTrue(self.tree_equals(tree_2_before, tree_2_before)) self.assertTrue(self.tree_equals(tree_1_after, tree_1_after)) self.assertTrue(self.tree_equals(tree_2_after, tree_2_after)) self.assertFalse(self.tree_equals(tree_1_before, tree_1_after)) self.assertFalse(self.tree_equals(tree_2_before, tree_2_after))
class TreeCrossoverTests(unittest.TestCase): def setUp(self): self.config = { "tree_generation": { "initial_max_depth": 4 }, "crossover": { "method": "POINT_CROSSOVER", "probability": 1.0 }, "function_nodes": [ {"type": "FUNCTION", "name": "ADD", "arity": 2}, {"type": "FUNCTION", "name": "SUB", "arity": 2}, {"type": "FUNCTION", "name": "MUL", "arity": 2}, {"type": "FUNCTION", "name": "DIV", "arity": 2}, {"type": "FUNCTION", "name": "COS", "arity": 1}, {"type": "FUNCTION", "name": "SIN", "arity": 1}, {"type": "FUNCTION", "name": "RAD", "arity": 1} ], "terminal_nodes": [ {"type": "CONSTANT", "value": 1.0}, {"type": "CONSTANT", "value": 2.0}, {"type": "CONSTANT", "value": 2.0}, {"type": "CONSTANT", "value": 3.0}, {"type": "CONSTANT", "value": 4.0}, {"type": "CONSTANT", "value": 5.0}, {"type": "CONSTANT", "value": 6.0}, {"type": "CONSTANT", "value": 7.0}, {"type": "CONSTANT", "value": 8.0}, {"type": "CONSTANT", "value": 9.0}, {"type": "CONSTANT", "value": 10.0} ], "input_variables": [ {"type": "INPUT", "name": "x"} ] } self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION") self.generator = TreeGenerator(self.config) self.crossover = TreeCrossover(self.config) self.parser = TreeParser() # create nodes left_node_1 = Node(NodeType.INPUT, name="x") right_node_1 = Node(NodeType.CONSTANT, value=2.0) node = Node(NodeType.CONSTANT, value=2.0) left_node_2 = Node(NodeType.CONSTANT, value=3.0) right_node_2 = Node(NodeType.CONSTANT, value=4.0) cos_func_1 = Node( NodeType.FUNCTION, name="ADD", arity=2, branches=[left_node_1, right_node_1] ) sin_func_1 = Node( NodeType.FUNCTION, name="SIN", arity=1, branches=[node] ) cos_func_2 = Node( NodeType.FUNCTION, name="COS", arity=1, branches=[left_node_2] ) sin_func_2 = Node( NodeType.FUNCTION, name="SIN", arity=1, branches=[right_node_2] ) add_func = Node( NodeType.FUNCTION, name="ADD", arity=2, branches=[cos_func_1, sin_func_1] ) sub_func = Node( NodeType.FUNCTION, name="SUB", arity=2, branches=[sin_func_2, cos_func_2] ) # create tree_1 self.tree_1 = Tree() self.tree_1.root = add_func self.tree_1.update() print self.tree_1 # create tree_2 self.tree_2 = Tree() self.tree_2.root = sub_func self.tree_2.update() def tearDown(self): del self.config del self.generator del self.parser def build_tree_str(self, tree): tree_str = "" for node in tree.program: if hasattr(node, "name") and node.name is not None: tree_str += "node:{0} addr:{1}\n".format(node.name, id(node)) else: tree_str += "node:{0} addr:{1}\n".format(node.value, id(node)) return tree_str def tree_equals(self, tree_1_str, tree_2_str): if tree_1_str == tree_2_str: return True else: return False def test_point_crossover(self): # record before crossover tree_1_before = self.build_tree_str(self.tree_1) tree_2_before = self.build_tree_str(self.tree_2) # point crossover self.crossover.point_crossover(self.tree_1, self.tree_2) # record after crossover tree_1_after = self.build_tree_str(self.tree_1) tree_2_after = self.build_tree_str(self.tree_2) print("Before Crossover") print("\nTree 1") print(tree_1_before) print("\nTree 2") print(tree_2_before) print("\nAfter Crossover") print("\nTree 1") print(tree_1_after) print("\nTree 2") print(tree_2_after) # asserts self.assertTrue(self.tree_equals(tree_1_before, tree_1_before)) self.assertTrue(self.tree_equals(tree_2_before, tree_2_before)) self.assertTrue(self.tree_equals(tree_1_after, tree_1_after)) self.assertTrue(self.tree_equals(tree_2_after, tree_2_after)) self.assertFalse(self.tree_equals(tree_1_before, tree_1_after)) self.assertFalse(self.tree_equals(tree_2_before, tree_2_after)) def test_common_region_point_crossover(self): # record before crossover tree_1_before = self.build_tree_str(self.tree_1) tree_2_before = self.build_tree_str(self.tree_2) # point crossover self.crossover.common_region_point_crossover(self.tree_1, self.tree_2) # record after crossover tree_1_after = self.build_tree_str(self.tree_1) tree_2_after = self.build_tree_str(self.tree_2) print("Before Crossover") print("\nTree 1") print(tree_1_before) print("\nTree 2") print(tree_2_before) print("\nAfter Crossover") print("\nTree 1") print(tree_1_after) print("\nTree 2") print(tree_2_after) def test_crossover(self): # record before crossover tree_1_before = self.build_tree_str(self.tree_1) tree_2_before = self.build_tree_str(self.tree_2) # point crossover self.crossover.crossover(self.tree_1, self.tree_2) # record after crossover tree_1_after = self.build_tree_str(self.tree_1) tree_2_after = self.build_tree_str(self.tree_2) print("Before Crossover") print("\nTree 1!") print(tree_1_before) print("\nTree 2!") print(tree_2_before) print("\nAfter Crossover") print("\nTree 1!") print(tree_1_after) print("\nTree 2!") print(tree_2_after) # asserts self.assertTrue(self.tree_equals(tree_1_before, tree_1_before)) self.assertTrue(self.tree_equals(tree_2_before, tree_2_before)) self.assertTrue(self.tree_equals(tree_1_after, tree_1_after)) self.assertTrue(self.tree_equals(tree_2_after, tree_2_after)) self.assertFalse(self.tree_equals(tree_1_before, tree_1_after)) self.assertFalse(self.tree_equals(tree_2_before, tree_2_after))
class JSONStoreTests(unittest.TestCase): def setUp(self): self.config = { "max_population": 10, "tree_generation": { "method": "FULL_METHOD", "initial_max_depth": 4 }, "evaluator": { "use_cache": True }, "selection": { "method": "TOURNAMENT_SELECTION", "tournament_size": 2 }, "crossover": { "method": "POINT_CROSSOVER", "probability": 0.6 }, "mutation": { "methods": ["POINT_MUTATION"], "probability": 0.8 }, "function_nodes": [{ "type": "FUNCTION", "name": "ADD", "arity": 2 }, { "type": "FUNCTION", "name": "SUB", "arity": 2 }], "terminal_nodes": [ { "type": "CONSTANT", "value": 1.0 }, ], "input_variables": [{ "type": "INPUT", "name": "x" }], "data_file": "tests/data/sine.dat", "response_variables": [{ "name": "y" }], "recorder": { "store_file": "json_store_test.json", "compress": True } } config.load_data(self.config) self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION") self.generator = TreeGenerator(self.config) self.json_store = JSONStore(self.config) self.json_store.setup_store() self.population = self.generator.init() results = [] cache = {} evaluate(self.population.individuals, self.functions, self.config, results, cache, self.json_store) self.population.sort_individuals() self.selection = Selection(self.config, recorder=self.json_store) self.crossover = TreeCrossover(self.config, recorder=self.json_store) self.mutation = TreeMutation(self.config, recorder=self.json_store) def tearDown(self): self.json_store.delete_store() del self.config del self.functions del self.generator del self.population del self.json_store def test_setup_store(self): # assert file_exists = os.path.exists(self.config["recorder"]["store_file"]) self.assertEquals(file_exists, True) def test_purge_store(self): # write something to store file self.json_store.store_file.write("Hello World\n") self.json_store.store_file.close() # purge store file self.json_store.purge_store() # assert store_file = open(self.config["recorder"]["store_file"], "r").read() self.assertEquals(len(store_file), 0) def test_delete_store(self): # delete store self.json_store.delete_store() # assert file_exists = os.path.exists(self.config["recorder"]["store_file"]) self.assertEquals(file_exists, False) def test_record_population(self): self.json_store.record_population(self.population) record = self.json_store.generation_record self.assertNotEquals(record, {}) self.assertEquals(record["population"]["generation"], 0) def test_record_selection(self): # record selection self.selection.select(self.population) # assert record = self.json_store.generation_record # import pprint # pprint.pprint(record) self.assertNotEquals(record, {}) self.assertEquals(record["selection"]["selected"], 10) def test_record_crossover(self): # record crossover tree_1 = self.population.individuals[0] tree_2 = self.population.individuals[1] self.crossover.crossover(tree_1, tree_2) # assert record = self.json_store.generation_record self.assertNotEquals(record, {}) def test_record_mutation(self): # record mutation tree = self.population.individuals[0] self.mutation.mutate(tree) # assert record = self.json_store.generation_record # pprint.pprint(record) self.assertNotEquals(record, {}) def test_record_evaulation(self): # record evaluation results = [] evaluate(self.population.individuals, self.functions, self.config, results, recorder=self.json_store) # assert record = self.json_store.generation_record # import pprint # pprint.pprint(record) self.assertEquals(record["evaluation"]["cache_size"], 10) self.assertEquals(record["evaluation"]["match_cached"], 0) def test_record_to_file(self): # write record to file and close self.json_store.record_population(self.population) self.json_store.record_to_file() self.json_store.store_file.close() # open up the file and restore json to dict store_file = open(self.config["recorder"]["store_file"], "r").read() data = json.loads(store_file) # assert tests self.assertNotEquals(data, {}) self.assertEquals(data["population"]["generation"], 0) def test_summarize_store(self): # write record to file and close self.json_store.setup_store() self.json_store.record_population(self.population) for i in range(5): tree_1 = self.population.individuals[0] tree_2 = self.population.individuals[1] self.crossover.crossover(tree_1, tree_2) for i in range(10): tree = self.population.individuals[0] self.mutation.mutate(tree) self.json_store.record_to_file() self.json_store.store_file.close() # summarize self.json_store.summarize_store() # assert store_file = open(self.config["recorder"]["store_file"], "r") line = json.loads(store_file.read()) store_file.close() self.assertIsNotNone(line) def test_finalize(self): # write record to file and close self.json_store.setup_store() self.json_store.record_population(self.population) self.json_store.record_to_file() self.json_store.store_file.close() # zip the store file self.json_store.finalize() # assert store_fp = self.config["recorder"]["store_file"] store_fp = list(os.path.splitext(store_fp)) # split ext store_fp[1] = ".zip" # change ext to zip store_fp = "".join(store_fp) file_exists = os.path.exists(store_fp) self.assertEquals(file_exists, True)
class JSONStoreTests(unittest.TestCase): def setUp(self): self.config = { "max_population" : 10, "tree_generation" : { "method" : "FULL_METHOD", "initial_max_depth" : 4 }, "evaluator" : { "use_cache": True }, "selection" : { "method" : "TOURNAMENT_SELECTION", "tournament_size": 2 }, "crossover" : { "method" : "POINT_CROSSOVER", "probability" : 0.6 }, "mutation" : { "methods": ["POINT_MUTATION"], "probability" : 0.8 }, "function_nodes" : [ {"type": "FUNCTION", "name": "ADD", "arity": 2}, {"type": "FUNCTION", "name": "SUB", "arity": 2} ], "terminal_nodes" : [ {"type": "CONSTANT", "value": 1.0}, ], "input_variables" : [ {"type": "INPUT", "name": "x"} ], "data_file" : "tests/data/sine.dat", "response_variables" : [{"name": "y"}], "recorder" : { "store_file": "json_store_test.json", "compress": True } } config.load_data(self.config) self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION") self.generator = TreeGenerator(self.config) self.json_store = JSONStore(self.config) self.json_store.setup_store() self.population = self.generator.init() results = [] cache = {} evaluate( self.population.individuals, self.functions, self.config, results, cache, self.json_store ) self.population.sort_individuals() self.selection = Selection(self.config, recorder=self.json_store) self.crossover = TreeCrossover(self.config, recorder=self.json_store) self.mutation = TreeMutation(self.config, recorder=self.json_store) def tearDown(self): self.json_store.delete_store() del self.config del self.functions del self.generator del self.population del self.json_store def test_setup_store(self): # assert file_exists = os.path.exists(self.config["recorder"]["store_file"]) self.assertEquals(file_exists, True) def test_purge_store(self): # write something to store file self.json_store.store_file.write("Hello World\n") self.json_store.store_file.close() # purge store file self.json_store.purge_store() # assert store_file = open(self.config["recorder"]["store_file"], "r").read() self.assertEquals(len(store_file), 0) def test_delete_store(self): # delete store self.json_store.delete_store() # assert file_exists = os.path.exists(self.config["recorder"]["store_file"]) self.assertEquals(file_exists, False) def test_record_population(self): self.json_store.record_population(self.population) record = self.json_store.generation_record self.assertNotEquals(record, {}) self.assertEquals(record["population"]["generation"], 0) def test_record_selection(self): # record selection self.selection.select(self.population) # assert record = self.json_store.generation_record # import pprint # pprint.pprint(record) self.assertNotEquals(record, {}) self.assertEquals(record["selection"]["selected"], 10) def test_record_crossover(self): # record crossover tree_1 = self.population.individuals[0] tree_2 = self.population.individuals[1] self.crossover.crossover(tree_1, tree_2) # assert record = self.json_store.generation_record self.assertNotEquals(record, {}) def test_record_mutation(self): # record mutation tree = self.population.individuals[0] self.mutation.mutate(tree) # assert record = self.json_store.generation_record # pprint.pprint(record) self.assertNotEquals(record, {}) def test_record_evaulation(self): # record evaluation results = [] evaluate( self.population.individuals, self.functions, self.config, results, recorder=self.json_store ) # assert record = self.json_store.generation_record # import pprint # pprint.pprint(record) self.assertEquals(record["evaluation"]["cache_size"], 10) self.assertEquals(record["evaluation"]["match_cached"], 0) def test_record_to_file(self): # write record to file and close self.json_store.record_population(self.population) self.json_store.record_to_file() self.json_store.store_file.close() # open up the file and restore json to dict store_file = open(self.config["recorder"]["store_file"], "r").read() data = json.loads(store_file) # assert tests self.assertNotEquals(data, {}) self.assertEquals(data["population"]["generation"], 0) def test_summarize_store(self): # write record to file and close self.json_store.setup_store() self.json_store.record_population(self.population) for i in range(5): tree_1 = self.population.individuals[0] tree_2 = self.population.individuals[1] self.crossover.crossover(tree_1, tree_2) for i in range(10): tree = self.population.individuals[0] self.mutation.mutate(tree) self.json_store.record_to_file() self.json_store.store_file.close() # summarize self.json_store.summarize_store() # assert store_file = open(self.config["recorder"]["store_file"], "r") line = json.loads(store_file.read()) store_file.close() self.assertIsNotNone(line) def test_finalize(self): # write record to file and close self.json_store.setup_store() self.json_store.record_population(self.population) self.json_store.record_to_file() self.json_store.store_file.close() # zip the store file self.json_store.finalize() # assert store_fp = self.config["recorder"]["store_file"] store_fp = list(os.path.splitext(store_fp)) # split ext store_fp[1] = ".zip" # change ext to zip store_fp = "".join(store_fp) file_exists = os.path.exists(store_fp) self.assertEquals(file_exists, True)