def screen_observer(population, num_generations, num_evaluations, args):
import numpy
population = list(population)
population.sort(reverse=True)
worst_fit = population[-1].fitness
best_fit = population[0].fitness
med_fit = numpy.median([p.fitness for p in population])
avg_fit = numpy.mean([p.fitness for p in population])
std_fit = numpy.std([p.fitness for p in population], ddof=1)
if(num_generations % 50 != 0):
return
print('Generation Evaluation Worst Best Median Average Std Dev ')
print('---------- ---------- ---------- ---------- ---------- ---------- ----------')
print('{0:10} {1:10} {2:10} {3:10} {4:10} {5:10} {6:10}\n'.format(num_generations, num_evaluations, worst_fit, best_fit, med_fit, avg_fit, std_fit))
print('Current Population: (id,fitness,todo,2 bit solution)')
print('----------------------------------------------------------------------------')
for i, c in enumerate(population):
#f = CGPPhenotype(enc, c.candidate)
#exp = f([Symbol('x'), RealNumber(1.0)])
pass
for i, c in enumerate(population):
#f = CGPPhenotype(enc, c.candidate)
#exp = f([Symbol('x'), RealNumber(1.0)])
phe = SMCGPPhenotype(enc, c.candidate)
#print i, c.fitness, phe.todo_list, phe
print i, c.fitness, [p.__name__ for p in phe.todo_list], phe.get_modified()
def test_overwrite(self):
gen1 = [input_gene(), input_gene(), mod_gene(mod.overwrite,[2,1],[1,1,2]), func_gene(3,[1,1]), func_gene(4,[2,1]), output_gene(1)]
func = SMCGPPhenotype(self.enc, list(gen1))
modified = func.get_modified()
assert len(modified.candidate) == len(func.candidate)
assert func.candidate[3] == modified.candidate[3]
assert func.candidate[4] == modified.candidate[4]
def fitness(candidates, args):
sel_cases, sel_targets = select_test_cases(all_cases, all_targets, 100)
fitness = []
for cand in candidates:
fit = 0
func = SMCGPPhenotype(enc, cand)
iii=0
for cases, targets in zip(sel_cases, sel_targets):
iii += 1
func = func.get_modified()
if not func.is_valid():
break
case_fit = 0
for case, target in zip(cases, targets):
solution = func(case)[0]
if solution == target:
#print solution, target, case
case_fit += 1
fit += case_fit
if case_fit != len(cases):
break
#print "cases", iii
fitness.append(fit)
return fitness
def test_dup(self):
gen1 = [input_gene(), input_gene(), mod_gene(mod.duplicate,[2,1],[1,2,1]), func_gene(3,[1,1]), func_gene(4,[2,1]), output_gene(1)]
func = SMCGPPhenotype(self.enc, list(gen1))
modified = func.get_modified()
assert len(modified.candidate) == len(func.candidate) + 2
assert func.candidate[3:4] == modified.candidate[3:4]
assert func.candidate[3:4] == modified.candidate[5:6]
def test_scale_connections(self):
gen1 = [input_gene(), input_gene(), mod_gene(mod.scale_connections,[2,1],[1,2,3]), func_gene(3,[1,1]), func_gene(4,[2,1]), output_gene(1)]
func = SMCGPPhenotype(self.enc, list(gen1))
modified = func.get_modified()
assert len(modified.candidate) == len(func.candidate)
assert func.candidate[3].inputs[0] * 3 == modified.candidate[3].inputs[0]
assert func.candidate[3].inputs[1] * 3 == modified.candidate[3].inputs[1]
def test_change_functions(self):
gen1 = [input_gene(), input_gene(),func_gene(3,[1,1]),func_gene(4,[1,1]),
mod_gene(mod.change_connection,[2,1],[2,0,2]),
mod_gene(mod.change_function,[2,1],[2,3,0]),
mod_gene(mod.change_parameter,[2,1],[2,0,3]), output_gene(1)]
func = SMCGPPhenotype(self.enc, list(gen1))
modified = func.get_modified()
assert modified.candidate[2].function == modified.candidate[3].function
assert modified.candidate[2].inputs[0] == 3
assert modified.candidate[2].vars[0] == 3
assert len(modified.candidate) == len(func.candidate)
def test_del_add(self):
gen1 = [input_gene(), input_gene(), mod_gene(mod.add,[2,1],[3,3,0]), mod_gene(mod.delete,[2,1],[1,1,0]), func_gene(3,[1,2]), func_gene(4,[2,1]), output_gene(1)]
func = SMCGPPhenotype(self.enc, list(gen1))
modified = func.get_modified()
assert len(func.candidate) == 7
#print len(modified.candidate)
assert len(modified.candidate) == 9
deleted = gen1[4]
#print deleted
#print modified.candidate
assert deleted not in modified.candidate
assert func.candidate[:3] == modified.candidate[:3]
assert func.candidate[5:] == modified.candidate[7:]
def test_del(self):
gen1 = [input_gene(), input_gene(), mod_gene(mod.delete,[2,1],[1,2,0]), func_gene(3,[1,1]), func_gene(4,[2,1]),func_gene(4,[2,1]), output_gene(1)]
func = SMCGPPhenotype(self.enc, list(gen1))
modified = func.get_modified()
assert len(func.candidate) == 7
assert len(modified.candidate) == 5
assert func.candidate[:3] == modified.candidate[:3]
assert func.candidate[5:] == modified.candidate[3:]
mod2 = modified.get_modified()
print func.candidate
print modified.candidate
print mod2.candidate
assert len(mod2.candidate) == 3; #no more to delete
assert modified.candidate[:3] == mod2.candidate[:3]
def test_add(self):
gen1 = [input_gene(), input_gene(), mod_gene(mod.add,[2,1],[1,2,0]), func_gene(3,[1,1]), func_gene(4,[2,1]), output_gene(1)]
func = SMCGPPhenotype(self.enc, list(gen1))
modified = func.get_modified()
assert len(func.candidate) == 6
assert len(modified.candidate) == 8
assert func.candidate[:3] == modified.candidate[:3]
assert func.candidate[3:] == modified.candidate[5:]
#print "mod", modified.candidate
mod2 = modified.get_modified()
#print "mod2", mod2.candidate
#print "mod2",len(mod2.candidate)
assert len(mod2.candidate) == 10
assert modified.candidate[:3] == mod2.candidate[:3]
assert modified.candidate[3:] == mod2.candidate[5:]
def test_dup_scale(self):
gen1 = [input_gene(), input_gene(), mod_gene(mod.duplicate_and_scale,[2,1],[1,2,3]), func_gene(3,[1,1]), func_gene(4,[2,1]), output_gene(1)]
func = SMCGPPhenotype(self.enc, list(gen1))
modified = func.get_modified()
assert len(modified.candidate) == len(func.candidate) + 2
assert func.candidate[3:4] == modified.candidate[3:4]
assert func.candidate[3].function == modified.candidate[5].function
assert func.candidate[3].vars[0] == modified.candidate[5].vars[0]
assert func.candidate[3].vars[1] == modified.candidate[5].vars[1]
assert func.candidate[3].inputs[0] * 3 == modified.candidate[5].inputs[0]
assert func.candidate[3].inputs[1] * 3 == modified.candidate[5].inputs[1]
assert func.candidate[4].function == modified.candidate[6].function
assert func.candidate[4].vars[0] == modified.candidate[6].vars[0]
assert func.candidate[4].vars[1] == modified.candidate[6].vars[1]
assert func.candidate[4].inputs[0] * 3 == modified.candidate[6].inputs[0]
assert func.candidate[4].inputs[1] * 3 == modified.candidate[6].inputs[1]