def __init__(self):
self.tree_id = None
self.score = None
self.tree_type = None
self.root = None
self.depth = 0
self.size = 0
self.program = []
self.func_nodes = []
self.term_nodes = []
self.input_nodes = []
self.parser = TreeParser()
def setUp(self):
self.config = {
"max_population": 10,
"tree_generation": {
"tree_type": "SYMBOLIC_REGRESSION",
"method": "RAMPED_HALF_AND_HALF_METHOD",
"initial_max_depth": 3
},
"function_nodes": [
{"type": "FUNCTION", "arity": 2, "name": "ADD"},
{"type": "FUNCTION", "arity": 2, "name": "SUB"},
{"type": "FUNCTION", "arity": 2, "name": "MUL"},
{"type": "FUNCTION", "arity": 2, "name": "DIV"},
{"type": "FUNCTION", "arity": 1, "name": "COS"},
{"type": "FUNCTION", "arity": 1, "name": "SIN"}
],
"terminal_nodes": [
{"type": "CONSTANT", "value": 1.0},
{"type": "INPUT", "name": "x"},
{"type": "INPUT", "name": "y"},
{
"type": "RANDOM_CONSTANT",
"data_range": {
"upper_bound": 10.0,
"lower_bound": -10.0,
"decimal_places": 1
}
}
],
"input_variables": [
{"name": "x"},
{"name": "y"}
]
}
self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION")
self.generator = TreeGenerator(self.config)
self.parser = TreeParser()
def setUp(self):
self.config = {
"max_population": 10,
"tree_generation": {
"method": "FULL_METHOD",
"initial_max_depth": 4
},
"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}
],
"terminal_nodes": [
{"type": "CONSTANT", "value": 1.0},
{"type": "INPUT", "name": "x"},
{"type": "INPUT", "name": "y"},
{"type": "INPUT", "name": "z"}
],
"input_variables": [
{"name": "x"},
{"name": "y"},
{"name": "z"}
]
}
self.t_parser = TreeParser()
self.tree = Tree()
node_x = Node(NodeType.INPUT, name="x")
node_y = Node(NodeType.INPUT, name="y")
node_z = Node(NodeType.INPUT, name="z")
self.tree.input_nodes.append(node_x)
self.tree.input_nodes.append(node_y)
self.tree.input_nodes.append(node_z)
def setUp(self):
self.config = {
"tree_generation": {
"method": "GROW_METHOD",
"initial_max_depth": 4
},
"mutation": {
"methods": [
"POINT_MUTATION", "HOIST_MUTATION", "SUBTREE_MUTATION",
"SHRINK_MUTATION", "EXPAND_MUTATION"
],
"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": "INPUT",
"name": "x"
}],
"input_variables": [{
"type": "INPUT",
"name": "x"
}]
}
self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION")
self.generator = TreeGenerator(self.config)
self.parser = TreeParser()
self.mutation = TreeMutation(self.config)
# create nodes
left_node = Node(NodeType.CONSTANT, value=1.0)
right_node = Node(NodeType.INPUT, name="x")
cos_func = Node(NodeType.FUNCTION,
name="COS",
arity=1,
branches=[left_node])
sin_func = Node(NodeType.FUNCTION,
name="SIN",
arity=1,
branches=[right_node])
add_func = Node(NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[cos_func, sin_func])
# create tree
self.tree = Tree()
self.tree.root = add_func
self.tree.update_program()
self.tree.update_func_nodes()
self.tree.update_term_nodes()
class Tree(object):
def __init__(self):
self.tree_id = None
self.score = None
self.tree_type = None
self.root = None
self.depth = 0
self.size = 0
self.program = []
self.func_nodes = []
self.term_nodes = []
self.input_nodes = []
self.parser = TreeParser()
def valid(self, config_input_nodes):
# convert config input nodes from dict to list of Nodes
check_list = []
for node in config_input_nodes:
check_list.append(node["name"])
# convert tree input nodes
tree_input_nodes = []
for node in self.input_nodes:
tree_input_nodes.append(node.name)
result = set(check_list) - set(tree_input_nodes)
if len(list(result)) == 0:
return True
else:
return False
def get_linked_node(self, target_node):
try:
index = self.program.index(target_node) + 1
for node in self.program[index:]:
if node.has_value_node(target_node) is not False:
return node
except ValueError:
return None
def replace_node(self, target_node, replace_with, override_update=False):
linked_node = self.get_linked_node(target_node)
branch_index = linked_node.has_value_node(target_node)
linked_node.branches[branch_index] = replace_with
if override_update is False:
self.update()
def equals(self, tree):
if len(self.program) != len(tree.program):
return False
index = 0
for node in self.program:
equals = node.equals(tree.program[index])
if equals is False:
return False
index += 1
return True
def update_program(self):
del self.program[:]
self.program = self.parser.post_order_traverse(self.root)
def update_func_nodes(self):
del self.func_nodes[:]
for node in self.program:
if node.is_function():
if node is not self.root:
self.func_nodes.append(node)
def update_term_nodes(self):
del self.term_nodes[:]
for node in self.program:
if node.is_terminal():
self.term_nodes.append(node)
def update_input_nodes(self):
del self.input_nodes[:]
for node in self.program:
if node.is_input():
self.input_nodes.append(node)
def update_tree_info(self):
self.size = len(self.program)
self.branches = len(self.term_nodes) + len(self.input_nodes)
def update(self):
self.program = self.parser.parse_tree(self, self.root)
def __str__(self):
if self.tree_type == "CLASSIFICATION_TREE":
return self.parser.parse_classification_tree(self.root)
else:
return self.parser.parse_equation(self.root)
def to_dict(self):
self_dict = {
"id": id(self),
"score": self.score,
"size": self.size,
"depth": self.depth,
"func_nodes_len": len(self.func_nodes),
"term_nodes_len": len(self.term_nodes),
"input_nodes_len": len(self.input_nodes),
"func_nodes": [str(node) for node in self.func_nodes],
"term_nodes": [str(node) for node in self.term_nodes],
"input_nodes": [str(node) for node in self.input_nodes],
"program": str(self)
}
return self_dict
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 setUp(self):
self.config = {
"max_population":
10,
"tree_generation": {
"tree_type": "SYMBOLIC_REGRESSION",
"method": "RAMPED_HALF_AND_HALF_METHOD",
"initial_max_depth": 3
},
"function_nodes": [{
"type": "FUNCTION",
"arity": 2,
"name": "ADD"
}, {
"type": "FUNCTION",
"arity": 2,
"name": "SUB"
}, {
"type": "FUNCTION",
"arity": 2,
"name": "MUL"
}, {
"type": "FUNCTION",
"arity": 2,
"name": "DIV"
}, {
"type": "FUNCTION",
"arity": 1,
"name": "COS"
}, {
"type": "FUNCTION",
"arity": 1,
"name": "SIN"
}],
"terminal_nodes": [{
"type": "CONSTANT",
"value": 1.0
}, {
"type": "INPUT",
"name": "x"
}, {
"type": "INPUT",
"name": "y"
}, {
"type": "RANDOM_CONSTANT",
"data_range": {
"upper_bound": 10.0,
"lower_bound": -10.0,
"decimal_places": 1
}
}],
"input_variables": [{
"name": "x"
}, {
"name": "y"
}]
}
self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION")
self.generator = TreeGenerator(self.config)
self.parser = TreeParser()
class TreeGeneratorTests(unittest.TestCase):
def setUp(self):
self.config = {
"max_population":
10,
"tree_generation": {
"tree_type": "SYMBOLIC_REGRESSION",
"method": "RAMPED_HALF_AND_HALF_METHOD",
"initial_max_depth": 3
},
"function_nodes": [{
"type": "FUNCTION",
"arity": 2,
"name": "ADD"
}, {
"type": "FUNCTION",
"arity": 2,
"name": "SUB"
}, {
"type": "FUNCTION",
"arity": 2,
"name": "MUL"
}, {
"type": "FUNCTION",
"arity": 2,
"name": "DIV"
}, {
"type": "FUNCTION",
"arity": 1,
"name": "COS"
}, {
"type": "FUNCTION",
"arity": 1,
"name": "SIN"
}],
"terminal_nodes": [{
"type": "CONSTANT",
"value": 1.0
}, {
"type": "INPUT",
"name": "x"
}, {
"type": "INPUT",
"name": "y"
}, {
"type": "RANDOM_CONSTANT",
"data_range": {
"upper_bound": 10.0,
"lower_bound": -10.0,
"decimal_places": 1
}
}],
"input_variables": [{
"name": "x"
}, {
"name": "y"
}]
}
self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION")
self.generator = TreeGenerator(self.config)
self.parser = TreeParser()
def tearDown(self):
del self.config
del self.generator
del self.parser
def test_generate_func_node(self):
# SYMBOLIC REGRESSION TREES
for i in range(100):
node = self.generator.generate_func_node()
self.assertEquals(node.node_type, NodeType.FUNCTION)
# CLASSIFICATION TREES
self.config["tree_generation"]["tree_type"] = "CLASSIFICATION_TREE"
self.config["function_nodes"] = [{
"type": "CLASS_FUNCTION",
"name": "GREATER_THAN",
"arity": 2,
"data_range": {
"lower_bound": 0.0,
"upper_bound": 10.0,
"decimal_places": 1
}
}]
self.config["class_attributes"] = [
"attrubte_1", "attrubte_2", "attrubte_3"
]
generator = TreeGenerator(self.config)
for i in range(100):
node = generator.generate_func_node()
class_attribute = node.class_attribute
self.assertEquals(node.node_type, NodeType.CLASS_FUNCTION)
self.assertTrue(class_attribute in self.config["class_attributes"])
def test_resolve_random_constant(self):
upper_bound = 10.0
lower_bound = -10.0
decimal_places = 0
for i in range(100):
n_details = {
"type": "RANDOM_CONSTANT",
"data_range": {
"lower_bound": lower_bound,
"upper_bound": upper_bound,
"decimal_places": decimal_places
}
}
new_n_details = self.generator.resolve_random_constant(n_details)
node_type = new_n_details["type"]
node_value = new_n_details["value"]
self.assertEquals(node_type, "CONSTANT")
self.assertTrue(upper_bound >= node_value)
self.assertTrue(lower_bound <= node_value)
self.assertEquals(node_value, int(node_value))
upper_bound = 100.0
lower_bound = -100.0
decimal_places = 1
for i in range(100):
n_details = {
"type": "RANDOM_CONSTANT",
"data_range": {
"lower_bound": lower_bound,
"upper_bound": upper_bound,
"decimal_places": decimal_places
}
}
new_n_details = self.generator.resolve_random_constant(n_details)
node_type = new_n_details["type"]
node_value = new_n_details["value"]
self.assertEquals(node_type, "CONSTANT")
self.assertTrue(upper_bound >= node_value)
self.assertTrue(lower_bound <= node_value)
node_value = decimal.Decimal(str(node_value))
node_decimal_places = abs(node_value.as_tuple().exponent)
self.assertEquals(decimal_places, node_decimal_places)
def test_generate_term_node(self):
for i in range(100):
node = self.generator.generate_term_node()
self.assertTrue(node.node_type == NodeType.CONSTANT
or NodeType.INPUT)
def test_full_method(self):
tests = 1
for i in xrange(tests):
tree = self.generator.full_method()
# asserts
init_max = self.config["tree_generation"]["initial_max_depth"]
self.assertEquals(tree.depth, init_max)
self.assertTrue(tree.size > init_max)
def test_grow_method(self):
tests = 1000
for i in xrange(tests):
tree = self.generator.grow_method()
# asserts
init_max = self.config["tree_generation"]["initial_max_depth"]
self.assertEquals(tree.depth, init_max)
self.assertTrue(tree.size > init_max)
def test_generate_tree_from_dict(self):
population = self.generator.init()
tree = population.individuals[0]
tree_dict = self.parser.tree_to_dict(tree, tree.root)
tree_generated = self.generator.generate_tree_from_dict(tree_dict)
program_str = ""
for i in tree.program:
if i.name is not None:
program_str += i.name
else:
program_str += str(i.value)
generated_str = ""
for i in tree_generated.program:
if i.name is not None:
generated_str += i.name
else:
generated_str += str(i.value)
self.assertEquals(program_str, generated_str)
def test_init(self):
population = self.generator.init()
self.assertEquals(len(population.individuals), 10)
class TreeGeneratorTests(unittest.TestCase):
def setUp(self):
self.config = {
"max_population": 10,
"tree_generation": {
"tree_type": "SYMBOLIC_REGRESSION",
"method": "RAMPED_HALF_AND_HALF_METHOD",
"initial_max_depth": 3
},
"function_nodes": [
{"type": "FUNCTION", "arity": 2, "name": "ADD"},
{"type": "FUNCTION", "arity": 2, "name": "SUB"},
{"type": "FUNCTION", "arity": 2, "name": "MUL"},
{"type": "FUNCTION", "arity": 2, "name": "DIV"},
{"type": "FUNCTION", "arity": 1, "name": "COS"},
{"type": "FUNCTION", "arity": 1, "name": "SIN"}
],
"terminal_nodes": [
{"type": "CONSTANT", "value": 1.0},
{"type": "INPUT", "name": "x"},
{"type": "INPUT", "name": "y"},
{
"type": "RANDOM_CONSTANT",
"data_range": {
"upper_bound": 10.0,
"lower_bound": -10.0,
"decimal_places": 1
}
}
],
"input_variables": [
{"name": "x"},
{"name": "y"}
]
}
self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION")
self.generator = TreeGenerator(self.config)
self.parser = TreeParser()
def tearDown(self):
del self.config
del self.generator
del self.parser
def test_generate_func_node(self):
# SYMBOLIC REGRESSION TREES
for i in range(100):
node = self.generator.generate_func_node()
self.assertEquals(node.node_type, NodeType.FUNCTION)
# CLASSIFICATION TREES
self.config["tree_generation"]["tree_type"] = "CLASSIFICATION_TREE"
self.config["function_nodes"] = [
{
"type": "CLASS_FUNCTION",
"name": "GREATER_THAN",
"arity": 2,
"data_range": {
"lower_bound": 0.0,
"upper_bound": 10.0,
"decimal_places": 1
}
}
]
self.config["class_attributes"] = [
"attrubte_1",
"attrubte_2",
"attrubte_3"
]
generator = TreeGenerator(self.config)
for i in range(100):
node = generator.generate_func_node()
class_attribute = node.class_attribute
self.assertEquals(node.node_type, NodeType.CLASS_FUNCTION)
self.assertTrue(class_attribute in self.config["class_attributes"])
def test_resolve_random_constant(self):
upper_bound = 10.0
lower_bound = -10.0
decimal_places = 0
for i in range(100):
n_details = {
"type": "RANDOM_CONSTANT",
"data_range": {
"lower_bound": lower_bound,
"upper_bound": upper_bound,
"decimal_places": decimal_places
}
}
new_n_details = self.generator.resolve_random_constant(n_details)
node_type = new_n_details["type"]
node_value = new_n_details["value"]
self.assertEquals(node_type, "CONSTANT")
self.assertTrue(upper_bound >= node_value)
self.assertTrue(lower_bound <= node_value)
self.assertEquals(node_value, int(node_value))
upper_bound = 100.0
lower_bound = -100.0
decimal_places = 1
for i in range(100):
n_details = {
"type": "RANDOM_CONSTANT",
"data_range": {
"lower_bound": lower_bound,
"upper_bound": upper_bound,
"decimal_places": decimal_places
}
}
new_n_details = self.generator.resolve_random_constant(n_details)
node_type = new_n_details["type"]
node_value = new_n_details["value"]
self.assertEquals(node_type, "CONSTANT")
self.assertTrue(upper_bound >= node_value)
self.assertTrue(lower_bound <= node_value)
node_value = decimal.Decimal(str(node_value))
node_decimal_places = abs(node_value.as_tuple().exponent)
self.assertEquals(decimal_places, node_decimal_places)
def test_generate_term_node(self):
for i in range(100):
node = self.generator.generate_term_node()
self.assertTrue(
node.node_type == NodeType.CONSTANT or NodeType.INPUT
)
def test_full_method(self):
tests = 1
for i in xrange(tests):
tree = self.generator.full_method()
# asserts
init_max = self.config["tree_generation"]["initial_max_depth"]
self.assertEquals(tree.depth, init_max)
self.assertTrue(tree.size > init_max)
def test_grow_method(self):
tests = 1000
for i in xrange(tests):
tree = self.generator.grow_method()
# asserts
init_max = self.config["tree_generation"]["initial_max_depth"]
self.assertEquals(tree.depth, init_max)
self.assertTrue(tree.size > init_max)
def test_generate_tree_from_dict(self):
population = self.generator.init()
tree = population.individuals[0]
tree_dict = self.parser.tree_to_dict(tree, tree.root)
tree_generated = self.generator.generate_tree_from_dict(tree_dict)
program_str = ""
for i in tree.program:
if i.name is not None:
program_str += i.name
else:
program_str += str(i.value)
generated_str = ""
for i in tree_generated.program:
if i.name is not None:
generated_str += i.name
else:
generated_str += str(i.value)
self.assertEquals(program_str, generated_str)
def test_init(self):
population = self.generator.init()
self.assertEquals(len(population.individuals), 10)
def test_evaluate(self):
random.seed(10)
# solution = {
# "results":
# [
# {"score": 15726642.002161335},
# {"score": 359.25843589015597},
# {"score": 92155571.22132382},
# {"score": 26186.46142920347},
# {"score": 15649304.847552022},
# {"score": 188.86069156360125},
# {"score": 23439.33097274221},
# ]
# }
# setup
config = {
"max_population" : 10,
"max_generation" : 5,
"tree_generation" : {
"method" : "GROW_METHOD",
"initial_max_depth" : 3
},
"evaluator": {
"use_cache" : True
},
"selection" : {
"method" : "TOURNAMENT_SELECTION",
"tournament_size": 5
},
"crossover" : {
"method" : "POINT_CROSSOVER",
"probability" : 0.8
},
"mutation" : {
"methods": [
"POINT_MUTATION",
"HOIST_MUTATION",
"SUBTREE_MUTATION",
"SHRINK_MUTATION",
"EXPAND_MUTATION"
],
"probability" : 0.9
},
"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}
],
"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}
],
"data_file" : "tests/data/sine.dat",
"input_variables" : [{"type": "INPUT", "name": "x"}],
"response_variables" : [{"name": "y"}]
}
parser = TreeParser()
population = TreeGenerator(config).init()
# create a dictionary of trees
data = {"config": config, "individuals": []}
for individual in population.individuals:
tree_json = parser.tree_to_dict(individual, individual.root)
data["individuals"].append(tree_json)
# make sure population size is equals to number of trees
population_size = len(population.individuals)
individuals = len(data["individuals"])
self.assertEquals(population_size, individuals)
# evaluating individuals
data = json.dumps(data)
host = "localhost"
port = 8080
req_type = "POST"
path = "evaluate"
response = self.transmit(host, port, req_type, path, data)
response = json.loads(response)
print response
def __init__(self, config):
self.config = config
self.gen_config = config["tree_generation"]
self.max_depth = self.gen_config.get("initial_max_depth", 0)
self.parser = TreeParser()
class TreeTests(unittest.TestCase):
def setUp(self):
self.config = {
"max_population": 10,
"tree_generation": {
"method": "FULL_METHOD",
"initial_max_depth": 4
},
"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}
],
"terminal_nodes": [
{"type": "CONSTANT", "value": 1.0},
{"type": "INPUT", "name": "x"},
{"type": "INPUT", "name": "y"},
{"type": "INPUT", "name": "z"}
],
"input_variables": [
{"name": "x"},
{"name": "y"},
{"name": "z"}
]
}
self.t_parser = TreeParser()
self.tree = Tree()
node_x = Node(NodeType.INPUT, name="x")
node_y = Node(NodeType.INPUT, name="y")
node_z = Node(NodeType.INPUT, name="z")
self.tree.input_nodes.append(node_x)
self.tree.input_nodes.append(node_y)
self.tree.input_nodes.append(node_z)
def test_valid(self):
# assert valid
res = self.tree.valid(self.config["input_variables"])
self.assertTrue(res)
# assert fail valid
self.tree.input_nodes.pop()
res = self.tree.valid(self.config["input_variables"])
self.assertFalse(res)
def test_get_linked_node(self):
# setup
del self.tree.input_nodes[:]
left_node = Node(NodeType.INPUT, name="x")
right_node = Node(NodeType.INPUT, name="y")
add_func = Node(
NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[left_node, right_node]
)
self.tree.root = add_func
self.tree.program = self.t_parser.post_order_traverse(self.tree.root)
# pass test
linked_node = self.tree.get_linked_node(left_node)
self.assertTrue(linked_node is add_func)
linked_node = self.tree.get_linked_node(right_node)
self.assertTrue(linked_node is add_func)
# fail test
random_node = Node(NodeType.INPUT, name="z")
linked_node = self.tree.get_linked_node(random_node)
self.assertFalse(linked_node is add_func)
def test_replace_node(self):
# setup
node_x = Node(NodeType.INPUT, name="x")
node_y = Node(NodeType.INPUT, name="y")
add_func = Node(
NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[node_x, node_y]
)
# build tree
tree = Tree()
tree.root = add_func
tree.update_program()
# replace input node
new_node = Node(NodeType.INPUT, name="z")
before_replace = list(tree.program)
tree.replace_node(node_x, new_node)
after_replace = list(tree.program)
# assert
self.assertTrue(before_replace == before_replace)
self.assertTrue(after_replace == after_replace)
self.assertFalse(before_replace == after_replace)
self.assertTrue(add_func.branches[0] is new_node)
def test_equal(self):
# create nodes
left_node_1 = Node(NodeType.CONSTANT, value=1.0)
right_node_1 = 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="COS",
arity=1,
branches=[left_node_1]
)
sin_func_1 = Node(
NodeType.FUNCTION,
name="SIN",
arity=1,
branches=[right_node_1]
)
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
tree_1 = Tree()
tree_1.root = add_func
tree_1.update()
# create tree_2
tree_2 = Tree()
tree_2.root = sub_func
tree_2.update()
self.assertTrue(tree_1.equals(tree_1))
self.assertFalse(tree_1.equals(tree_2))
self.assertTrue(tree_2.equals(tree_2))
self.assertFalse(tree_2.equals(tree_1))
def test_str(self):
# setup
del self.tree.input_nodes[:]
left_node = Node(NodeType.INPUT, name="x")
right_node = Node(NodeType.INPUT, name="y")
add_func = Node(
NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[left_node, right_node]
)
self.tree.root = add_func
self.tree.program = self.t_parser.post_order_traverse(self.tree.root)
# assert
self.assertEquals(str(self.tree), "(x ADD y)")
def setUp(self):
random.seed(10)
self.config = {
"max_population": 10,
"tree_generation": {
"method": "FULL_METHOD",
"initial_max_depth": 4
},
"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}
],
"terminal_nodes": [
{"type": "CONSTANT", "value": 1.0},
{"type": "INPUT", "name": "x"},
{"type": "INPUT", "name": "y"},
{"type": "INPUT", "name": "z"}
],
"input_variables": [
{"name": "x"},
{"name": "y"},
{"name": "z"}
]
}
self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION")
self.generator = TreeGenerator(self.config)
self.parser = TreeParser()
# create nodes
left_node = Node(NodeType.CONSTANT, value=1.0)
right_node = Node(NodeType.CONSTANT, value=2.0)
cos_func = Node(
NodeType.FUNCTION,
name="COS",
arity=1,
branches=[left_node]
)
sin_func = Node(
NodeType.FUNCTION,
name="SIN",
arity=1,
branches=[right_node]
)
add_func = Node(
NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[cos_func, sin_func]
)
# create tree
self.tree = Tree()
self.tree.root = add_func
self.tree.update_program()
self.tree.update_func_nodes()
self.tree.update_term_nodes()
class TreeParserTests(unittest.TestCase):
def setUp(self):
random.seed(10)
self.config = {
"max_population": 10,
"tree_generation": {
"method": "FULL_METHOD",
"initial_max_depth": 4
},
"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}
],
"terminal_nodes": [
{"type": "CONSTANT", "value": 1.0},
{"type": "INPUT", "name": "x"},
{"type": "INPUT", "name": "y"},
{"type": "INPUT", "name": "z"}
],
"input_variables": [
{"name": "x"},
{"name": "y"},
{"name": "z"}
]
}
self.functions = GPFunctionRegistry("SYMBOLIC_REGRESSION")
self.generator = TreeGenerator(self.config)
self.parser = TreeParser()
# create nodes
left_node = Node(NodeType.CONSTANT, value=1.0)
right_node = Node(NodeType.CONSTANT, value=2.0)
cos_func = Node(
NodeType.FUNCTION,
name="COS",
arity=1,
branches=[left_node]
)
sin_func = Node(
NodeType.FUNCTION,
name="SIN",
arity=1,
branches=[right_node]
)
add_func = Node(
NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[cos_func, sin_func]
)
# create tree
self.tree = Tree()
self.tree.root = add_func
self.tree.update_program()
self.tree.update_func_nodes()
self.tree.update_term_nodes()
def tearDown(self):
del self.config
del self.generator
del self.parser
def test_parse_tree(self):
# self.parser.print_tree(tree.root)
program = self.parser.parse_tree(self.tree, self.tree.root)
for i in program:
if i.name is not None:
print i.name
else:
print i.value
self.assertEquals(self.tree.size, 5)
self.assertEquals(self.tree.depth, 2)
self.assertEquals(len(self.tree.func_nodes), 2)
self.assertEquals(len(self.tree.term_nodes), 2)
self.assertEquals(len(self.tree.input_nodes), 0)
def test_parse_equation(self):
# self.parser.print_tree(tree.root)
equation = self.parser.parse_equation(self.tree.root)
self.assertEquals(equation, "((COS(1.0)) ADD (SIN(2.0)))")
def test_tree_to_dict(self):
solution = {
'program': [
{'type': 'CONSTANT', 'value': 1.0},
{'arity': 1, 'type': 'FUNCTION', 'name': 'COS'},
{'type': 'CONSTANT', 'value': 2.0},
{'arity': 1, 'type': 'FUNCTION', 'name': 'SIN'},
{'arity': 2, 'type': 'FUNCTION', 'root': True, 'name': 'ADD'}
]
}
results = self.parser.tree_to_dict(self.tree, self.tree.root)
self.assertEquals(results["program"], solution["program"])
def setUp(self):
self.config = {
"max_population":
10,
"tree_generation": {
"method": "FULL_METHOD",
"initial_max_depth": 4
},
"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
}],
"terminal_nodes": [{
"type": "CONSTANT",
"value": 1.0
}, {
"type": "INPUT",
"name": "x"
}, {
"type": "INPUT",
"name": "y"
}, {
"type": "INPUT",
"name": "z"
}],
"input_variables": [{
"name": "x"
}, {
"name": "y"
}, {
"name": "z"
}]
}
self.t_parser = TreeParser()
self.tree = Tree()
node_x = Node(NodeType.INPUT, name="x")
node_y = Node(NodeType.INPUT, name="y")
node_z = Node(NodeType.INPUT, name="z")
self.tree.input_nodes.append(node_x)
self.tree.input_nodes.append(node_y)
self.tree.input_nodes.append(node_z)
class TreeTests(unittest.TestCase):
def setUp(self):
self.config = {
"max_population":
10,
"tree_generation": {
"method": "FULL_METHOD",
"initial_max_depth": 4
},
"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
}],
"terminal_nodes": [{
"type": "CONSTANT",
"value": 1.0
}, {
"type": "INPUT",
"name": "x"
}, {
"type": "INPUT",
"name": "y"
}, {
"type": "INPUT",
"name": "z"
}],
"input_variables": [{
"name": "x"
}, {
"name": "y"
}, {
"name": "z"
}]
}
self.t_parser = TreeParser()
self.tree = Tree()
node_x = Node(NodeType.INPUT, name="x")
node_y = Node(NodeType.INPUT, name="y")
node_z = Node(NodeType.INPUT, name="z")
self.tree.input_nodes.append(node_x)
self.tree.input_nodes.append(node_y)
self.tree.input_nodes.append(node_z)
def test_valid(self):
# assert valid
res = self.tree.valid(self.config["input_variables"])
self.assertTrue(res)
# assert fail valid
self.tree.input_nodes.pop()
res = self.tree.valid(self.config["input_variables"])
self.assertFalse(res)
def test_get_linked_node(self):
# setup
del self.tree.input_nodes[:]
left_node = Node(NodeType.INPUT, name="x")
right_node = Node(NodeType.INPUT, name="y")
add_func = Node(NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[left_node, right_node])
self.tree.root = add_func
self.tree.program = self.t_parser.post_order_traverse(self.tree.root)
# pass test
linked_node = self.tree.get_linked_node(left_node)
self.assertTrue(linked_node is add_func)
linked_node = self.tree.get_linked_node(right_node)
self.assertTrue(linked_node is add_func)
# fail test
random_node = Node(NodeType.INPUT, name="z")
linked_node = self.tree.get_linked_node(random_node)
self.assertFalse(linked_node is add_func)
def test_replace_node(self):
# setup
node_x = Node(NodeType.INPUT, name="x")
node_y = Node(NodeType.INPUT, name="y")
add_func = Node(NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[node_x, node_y])
# build tree
tree = Tree()
tree.root = add_func
tree.update_program()
# replace input node
new_node = Node(NodeType.INPUT, name="z")
before_replace = list(tree.program)
tree.replace_node(node_x, new_node)
after_replace = list(tree.program)
# assert
self.assertTrue(before_replace == before_replace)
self.assertTrue(after_replace == after_replace)
self.assertFalse(before_replace == after_replace)
self.assertTrue(add_func.branches[0] is new_node)
def test_equal(self):
# create nodes
left_node_1 = Node(NodeType.CONSTANT, value=1.0)
right_node_1 = 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="COS",
arity=1,
branches=[left_node_1])
sin_func_1 = Node(NodeType.FUNCTION,
name="SIN",
arity=1,
branches=[right_node_1])
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
tree_1 = Tree()
tree_1.root = add_func
tree_1.update()
# create tree_2
tree_2 = Tree()
tree_2.root = sub_func
tree_2.update()
self.assertTrue(tree_1.equals(tree_1))
self.assertFalse(tree_1.equals(tree_2))
self.assertTrue(tree_2.equals(tree_2))
self.assertFalse(tree_2.equals(tree_1))
def test_str(self):
# setup
del self.tree.input_nodes[:]
left_node = Node(NodeType.INPUT, name="x")
right_node = Node(NodeType.INPUT, name="y")
add_func = Node(NodeType.FUNCTION,
name="ADD",
arity=2,
branches=[left_node, right_node])
self.tree.root = add_func
self.tree.program = self.t_parser.post_order_traverse(self.tree.root)
# assert
self.assertEquals(str(self.tree), "(x ADD y)")