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main_just_src.py
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import array
import random
import time
import numpy
from math import sqrt
import cluster
from deap import algorithms
from deap import base
from deap import benchmarks
from deap.benchmarks.tools import diversity, convergence
from deap import creator
from deap import tools
import os
from population import *
from network import Neterr
from chromosome import Chromosome, crossover
import traceback
n_hidden = 100
indim = 32
outdim = 5
network_obj_src = Neterr(indim, outdim, n_hidden, change_to_target=0, rng=random)
network_obj_tar = Neterr(indim, outdim, n_hidden, change_to_target=2, rng=random)
creator.create("FitnessMin", base.Fitness, weights=(-1.0, -1.0))
creator.create("Individual", Chromosome, fitness=creator.FitnessMin)
print("here network object created")
toolbox = base.Toolbox()
def minimize_src(individual):
outputarr = network_obj_src.feedforward_ne(individual, final_activation=network.softmax)
neg_log_likelihood_val = give_neg_log_likelihood(outputarr, network_obj_src.resty)
mean_square_error_val = give_mse(outputarr, network_obj_src.resty)
# anyways not using these as you can see in 'creator.create("FitnessMin", base.Fitness, weights=(-1.0, -1.0, 0.0, 0.0))'
# return neg_log_likelihood_val, mean_square_error_val, false_positve_rat, false_negative_rat
return neg_log_likelihood_val, mean_square_error_val
def mycross(ind1, ind2, gen_no):
child1 = crossover(ind1, ind2, gen_no, inputdim=indim, outputdim=outdim)
child2 = crossover(ind1, ind2, gen_no, inputdim=indim, outputdim=outdim)
return child1, child2
def mymutate(ind1):
new_ind = ind1.do_mutation(rate_conn_weight= 0.2, rate_conn_itself= 0.1, rate_node= 0.05, weight_factor = 1,inputdim = indim, outputdim = outdim, max_hidden_unit= n_hidden, rng = random)
return new_ind
def initIndividual(ind_class, inputdim, outputdim):
ind = ind_class(inputdim, outputdim)
return ind
old_chromosome = None
toolbox.register("individual", initIndividual, creator.Individual, indim, outdim)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("mate", mycross)
toolbox.register("mutate", mymutate)
toolbox.register("select", tools.selNSGA2)
bp_rate = 0.1
def main(seed=None, play=0, NGEN=40, MU=4 * 10):
# random.seed(seed)
# MU has to be a multiple of 4. period.
CXPB = 0.9
stats = tools.Statistics(lambda ind: ind.fitness.values[1])
# stats.register("avg", numpy.mean, axis=0)
# stats.register("std", numpy.std, axis=0)
stats.register("min", numpy.min, axis=0)
stats.register("max", numpy.max, axis=0)
logbook = tools.Logbook()
logbook.header = "gen", "evals", "std", "min", "avg", "max"
toolbox.register("evaluate", minimize_src)
time1 = time.time()
pop_src = toolbox.population(n=MU)
time2 = time.time()
print("After population initialisation", time2 - time1)
print(type(pop_src))
# print("population initialized")
# network_obj = Neterr(indim, outdim, n_hidden, np.random)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in pop_src if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
time3 = time.time()
print("After feedforward", time3 - time2)
# This is just to assign the crowding distance to the individuals
# no actual selection is done
pop_src = toolbox.select(pop_src, len(pop_src))
# print( "first population selected, still outside main loop")
# print(pop)
record = stats.compile(pop_src)
logbook.record(gen=0, evals=len(invalid_ind), **record)
print(logbook.stream)
maxi = 0
stri = ''
flag = 0
# Begin the generational process
# print(pop.__dir__())
time4 = time.time()
for gen in range(1, NGEN):
# Vary the population
if gen == 1:
time6 = time.time()
if gen == NGEN - 1:
time7 = time.time()
print()
print("here in gen no.", gen)
offspring = tools.selTournamentDCD(pop_src, len(pop_src))
offspring = [toolbox.clone(ind) for ind in offspring]
if play:
if play == 1:
pgen = NGEN * 0.1
elif play == 2:
pgen = NGEN * 0.9
if gen == int(pgen):
print("gen:", gen, "doing clustering")
to_bp_lis = cluster.give_cluster_head(offspring, int(MU * bp_rate))
assert (to_bp_lis[0] in offspring)
print("doing bp")
[item.modify_thru_backprop(indim, outdim, network_obj_src.rest_setx, network_obj_src.rest_sety,
epochs=10, learning_rate=0.1, n_par=10) for item in to_bp_lis]
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if gen == 1:
time8 = time.time()
if gen == NGEN - 1:
time9 = time.time()
dum_ctr = 0
for ind1, ind2 in zip(offspring[::2], offspring[1::2]):
flag = 0
if random.random() <= CXPB:
ind1, ind2 = toolbox.mate(ind1, ind2, gen)
ind1 = creator.Individual(indim, outdim, ind1 )
ind2 = creator.Individual( indim, outdim, ind2 )
flag = 1
maxi = max(maxi, ind1.node_ctr, ind2.node_ctr)
toolbox.mutate(ind1)
toolbox.mutate(ind2)
offspring[dum_ctr] = ind1
offspring[dum_ctr+1] = ind2
del offspring[dum_ctr].fitness.values, offspring[dum_ctr+1].fitness.values
dum_ctr+=2
if gen == 1:
print("1st gen after newpool",time.time() - time8)
if gen == NGEN-1:
print("last gen after newpool", time.time() - time9)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Select the next generation population
pop_src = toolbox.select(pop_src + offspring, MU)
record = stats.compile(pop_src)
logbook.record(gen=gen, evals=len(invalid_ind), **record)
anost = logbook.stream
liso = [item.rstrip() for item in anost.split("\t")]
mse = float(liso[3])
print(anost)
stri += anost + '\n'
print("generation done")
# file_ob.write(str(logbook.stream))
# print(len(pop))
# file_ob.close()
time5 = time.time()
print("Overall time", time5 - time4)
# print(stri)
print(' ------------------------------------src done------------------------------------------- ')
return pop_src, logbook
def note_this_string(new_st, stringh):
"""flag_ob = open("flag.txt","r+")
ctr = None
st = flag_ob.read()
flag = int(st.rstrip())
while flag ==1:
flag_ob.seek(0)
st = flag_ob.read()
flag = int(st.rstrip())
time.sleep(3)
if flag == 0:
flag = 1
flag_ob.seek(0)
flag_ob.write("1\n")
flag_ob.close()
'/home/robita/forgit/neuro-evolution/05/state/tf/indep_pima/input/model.ckpt.meta'
"""
name = "./ctr_folder/ctr" + stringh + ".txt"
if not os.path.isfile(name):
new_f = open(name, "w+")
new_f.write("0\n")
new_f.close()
ctr_ob = open(name, "r+")
strin = ctr_ob.read().rstrip()
assert (strin is not '')
ctr = int(strin)
ctr_ob.seek(0)
ctr_ob.write(str(ctr + 1) + "\n")
ctr_ob.close()
"""
flag_ob = open("flag.txt","w")
flag_ob.write("0\n")
flag_ob.close()
"""
new_file_ob = open("log_folder/log" + stringh + ".txt", "a+")
new_file_ob.write(str(ctr) + " " + new_st + "\n")
new_file_ob.close()
return ctr
def test_it_with_bp(play=1, NGEN=100, MU=4 * 25, play_with_whole_pareto=0):
pop, stats = main(play=play, NGEN=NGEN, MU=MU)
stringh = "_with_bp_main2_just_src" + str(play) + "_" + str(NGEN)
fronts = tools.sortNondominated(pop, len(pop))
if play_with_whole_pareto or len(fronts[0]) < 30:
pareto_front = fronts[0]
else:
pareto_front = random.sample(fronts[0], 30)
print("Pareto Front: ")
for i in range(len(pareto_front)):
print(pareto_front[i].fitness.values)
print("\ntest: test on one with min validation error",
network_obj_tar.test_err(min(pop, key=lambda x: x.fitness.values[1])))
tup = network_obj_tar.test_on_pareto_patch_correctone(pareto_front)
print("\n test: avg on sampled pareto set", tup)
st = str(network_obj_tar.test_err(min(pop, key=lambda x: x.fitness.values[1]))) + " " + str(tup)
print(note_this_string(st, stringh))
if __name__ == "__main__":
logf = open("log_error_just_src.txt", "a")
try:
test_it_with_bp(play=1, NGEN=100, MU=4 * 25, play_with_whole_pareto=1)
except Exception as e:
print("Error! Error! Error!")
logf.write('\n\n')
localtime = time.localtime(time.time())
logf.write(str(localtime)+'\n')
traceback.print_exc(file=logf)
logf.write('\n\n')
finally:
logf.close()
# file_ob.write( "test on one with min validation error " + str(neter.test_err(min(pop, key=lambda x: x.fitness.values[1]))))
# print(stats)
'''
import matplotlib.pyplot as plt
import numpy
front = numpy.array([ind.fitness.values for ind in pop])
plt.scatter(front[:,0], front[:,1], c="b")
plt.axis("tight")
plt.show()
'''