def test_grow_tree2():
np.random.seed(45345)
pset = pg.PrimitiveSet()
pset.addFunction(op.add, 2)
pset.addFunction(op.sub, 2)
pset.addTerminal(1)
pset.addTerminal(2)
pset.addTerminal(3)
pset.addVariable("x")
init_max_depth = 3
max_depth = 6
tree = pg.grow_tree(pset, init_max_depth, max_depth)
assert np.array_equal(tree, np.array([1, 4, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]))
def test_grow_tree1():
np.random.seed(45345)
pset = pg.PrimitiveSet(typed=True)
pset.addFunction(op.add, 2, [int, int, int])
pset.addFunction(op.sub, 2, [int, int, int])
pset.addTerminal(1, [int])
pset.addTerminal(2, [int])
pset.addTerminal(3, [int])
pset.addVariable("x", [int])
init_max_depth = 3
max_depth = 6
tree = pg.grow_tree(pset, init_max_depth, max_depth)
assert np.array_equal(tree, np.array([1, 4, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]))
def test_grow_tree_ephemeral_typed1():
np.random.seed(45345)
pset = pg.PrimitiveSet(typed=True)
pset.addFunction(op.add, 2, [float, float, float])
pset.addFunction(op.sub, 2, [float, float, float])
pset.addTerminal(float_constants, types=[float], ephemeral=True)
init_max_depth = 5
max_depth = 6
tree = pg.grow_tree(pset, init_max_depth, max_depth)
tree_str = pg.interpreter(pset, tree)
assert np.array_equal(tree, np.array([ 1, 4, 2, 2, 1, 5, 6, 2, 7, 8, 1, 1, 9, 10, 11, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]))
assert tree_str == 'add(0.6948470578046806, sub(sub(add(0.23851088045334068, 0.7485138905722925), sub(0.9421360052961212, 0.5983584346144624)), add(add(0.6952518271609337, 0.41227782045980343), 0.13638623666489624)))'
assert pset.num_primitives == 11
assert pset.ephemeral_cache == {3}
assert pset.ephemeral_constants == {4: (0.6948470578046806, [float]), 5: (0.23851088045334068, [float]), 6: (0.7485138905722925, [float]), 7: (0.9421360052961212, [float]), 8: (0.5983584346144624, [float]), 9: (0.6952518271609337, [float]), 10: (0.41227782045980343, [float]), 11: (0.13638623666489624, [float])}
def test_grow_tree3():
np.random.seed(12345)
pset = pg.PrimitiveSet(typed=True)
pset.addFunction(op.add, 2, [int, int, int])
pset.addFunction(op.sub, 2, [float, int, int])
pset.addFunction(op.mul, 2, [int, float, float])
pset.addFunction(op.truediv, 2, [float, float, float])
pset.addTerminal(1, [int])
pset.addTerminal(2, [int])
pset.addTerminal(3, [int])
pset.addTerminal(4.0, [float])
pset.addTerminal(5.0, [float])
pset.addTerminal(6.0, [float])
pset.addVariable("x", [float])
pset.addVariable("y", [int])
init_max_depth = 2
max_depth = 2
tree = pg.grow_tree(pset, init_max_depth, max_depth)
assert np.array_equal(tree, np.array([3, 9, 9, 0]))
def subtree_mutation(parent, pset=None, **kargs):
'''
SubTree Mutation
Args:
parent (TreeIndividual): the individual to be mutated
pset (PrimitiveSet): the set primitives allowed to be used
Returns:
mutated individual
'''
def arraycopy(src, src_pos, dest, dest_pos, length):
dest[dest_pos:dest_pos + length] = src[src_pos:src_pos + length]
def get_primitive_type(primitive):
if primitive in pset.ephemeral_constants:
_, p_type = pset.ephemeral_constants[primitive]
elif primitive in pset.terminals:
_, p_type = pset.terminals[primitive]
elif primitive in pset.variables:
_, p_type = pset.variables[primitive]
elif primitive in pset.functions:
_, _, p_type = pset.functions[primitive]
else:
p_type = None
raise AttributeError(
'This is a typed primitive set so types are required!')
return p_type[0]
offspring = pg.TreeIndividual(
tree=np.zeros(parent.genotype.size, dtype=parent.genotype.dtype))
# define tree cut points for subtree replacement
start1 = np.random.randint(parent.nodes)
end1 = pg.transverse_tree(pset, parent.genotype, start1)
# if typed subtree must return the appropriate type
if pset.typed:
primitive = parent.genotype[start1]
parent_type = get_primitive_type(primitive)
else:
parent_type = None
# TODO: the default values to set the size of the generated tree must be revised
# and a proper mechanism to set these values on a per-problem case must be available
# if typed set, start2 must be of the same type as start1
try:
subtree = pg.grow_tree(pset,
parent.depth - 1,
parent.depth,
initial_type=parent_type)
except:
e = sys.exc_info()[0]
print('%s' % e)
print('parent.depth: %s' % parent.depth)
start2 = 0
end2 = pg.transverse_tree(pset, subtree, start2)
len1 = start1 + (end2 - start2) + (parent.nodes - end1)
# produce offpsring 1
arraycopy(parent.genotype, 0, offspring.genotype, 0, start1)
num_elements = (end2 - start2)
arraycopy(subtree, start2, offspring.genotype, start1, num_elements)
num_elements = (parent.nodes - end1)
arraycopy(parent.genotype, end1, offspring.genotype,
start1 + (end2 - start2), num_elements)
# update tree metrics
offspring.depth, offspring.nodes = pg.count_tree_internals(
pset, offspring.genotype)
if offspring.nodes <= parent.genotype.size:
return offspring
else:
return parent