main2-iterative.py

import array
import random
import sys
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

n_hidden = 100
indim = 8
outdim = 2
network_obj = Neterr(indim, outdim, n_hidden, np.random)
creator.create("FitnessMin", base.Fitness, weights=(-1.0, -1.0, 0.0, 0.0))
creator.create("Individual", Chromosome, fitness=creator.FitnessMin)

toolbox = base.Toolbox()


def minimize(individual):
    outputarr = network_obj.feedforward_ne(individual)

    neg_log_likelihood_val = give_neg_log_likelihood(outputarr, network_obj.resty)
    mean_square_error_val = give_mse(outputarr, network_obj.resty)
    false_positve_rat = give_false_positive_ratio(outputarr, network_obj.resty)
    false_negative_rat = give_false_negative_ratio(outputarr, network_obj.resty)

    return neg_log_likelihood_val, mean_square_error_val, false_positve_rat, false_negative_rat


def mycross(ind1, ind2, gen_no):
    child1 = crossover(ind1, ind2, gen_no, inputdim=8, outputdim=2)
    child2 = crossover(ind1, ind2, gen_no, inputdim=8, outputdim=2)

    return child1, child2


def mymutate(ind1):
    new_ind = ind1.do_mutation(0.2, 0.1, 0.05, indim, outdim, n_hidden, numpy.random)
    return new_ind


def initIndividual(ind_class, inputdim, outputdim):
    ind = ind_class(inputdim, outputdim)
    return ind


toolbox.register("individual", initIndividual, creator.Individual, indim, outdim)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)

toolbox.register("evaluate", minimize)
toolbox.register("mate", mycross)
toolbox.register("mutate", mymutate)
toolbox.register("select", tools.selNSGA2)

bp_rate = 0.05


def main(seed=None, play = 0, NGEN = 40, MU = 4 * 10):
    random.seed(seed)


      # this 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"
    pop = toolbox.population(n=MU)
    #network_obj = Neterr(indim, outdim, n_hidden, np.random)
    # Evaluate the individuals with an invalid fitness
    invalid_ind = [ind for ind in pop if not ind.fitness.valid]
    fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
    for ind, fit in zip(invalid_ind, fitnesses):
        ind.fitness.values = fit

    # This is just to assign the crowding distance to the individuals
    # no actual selection is done
    pop = toolbox.select(pop, len(pop))
    # print(pop)
    record = stats.compile(pop)
    logbook.record(gen=0, evals=len(invalid_ind), **record)
    print(logbook.stream)
    maxi = 0
    stri = ''
    flag= 0
    # Begin the generational process
    # print(pop.__dir__())
    for gen in range(1, NGEN):

        # Vary the population
        offspring = tools.selTournamentDCD(pop, len(pop))
        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.rest_setx, network_obj.rest_sety, epochs=10, learning_rate=0.1, n_par=10) for item in to_bp_lis]

        for ind1, ind2 in zip(offspring[::2], offspring[1::2]):
            # print(ind1.fitness.values)
            """if not flag :
                ind1.modify_thru_backprop(indim, outdim, network_obj.rest_setx, network_obj.rest_sety, epochs=10, learning_rate=0.1, n_par=10)
                flag = 1
                print("just testing")
            """

            if random.random() <= CXPB:
                toolbox.mate(ind1, ind2, gen)
            maxi = max(maxi, ind1.node_ctr, ind2.node_ctr)
            toolbox.mutate(ind1)
            toolbox.mutate(ind2)
            del ind1.fitness.values, ind2.fitness.values

        # 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 = toolbox.select(pop + offspring, MU)

        record = stats.compile(pop)
        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])
        if (mse <= 115 ):
            print("already achieved a decent performance(validation), breaking at gen_no.", gen)
            break
        print(anost)
        stri += anost + '\n'
        # file_ob.write(str(logbook.stream))
        # print(len(pop))
        # file_ob.close()
    #print(stri)

    return pop, 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_without_bp():
    pop, stats = main()
    stringh = "_without_bp"
    fronts = tools.sortNondominated(pop, len(pop))
    if 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)

    neter = Neterr(indim, outdim, n_hidden, np.random)

    print("\ntest: test on one with min validation error", neter.test_err(min(pop, key=lambda x: x.fitness.values[1])))
    tup = neter.test_on_pareto_patch(pareto_front)

    print("\n test: avg on sampled pareto set", tup[0], "least found avg", tup[1])

    st = str(neter.test_err(min(pop, key=lambda x: x.fitness.values[1]))) + " " + str(tup[0]) + " " + str(tup[1])
    print(note_this_string(st, stringh))


def test_it_with_bp( arghv, play = 1,NGEN = 100, MU = 4*25):
    
    pop, stats = main( play = play, NGEN = NGEN, MU = MU)
    stringh = "_with_bp"+str(play)+"_"+ arghv
    fronts = tools.sortNondominated(pop, len(pop))
    if 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)

    neter = Neterr(indim, outdim, n_hidden, np.random)

    print("\ntest: test on one with min validation error", neter.test_err(min(pop, key=lambda x: x.fitness.values[1])))
    tup = neter.test_on_pareto_patch_correctone(pareto_front)

    print("\n test: avg on sampled pareto set", tup)

    st = str(neter.test_err(min(pop, key=lambda x: x.fitness.values[1]))) + " " + str(tup) 
    print(note_this_string(st, stringh))


if __name__ == "__main__":
    ngen = int(sys.argv[1])
    test_it_with_bp(arghv= sys.argv[1], play = 1, NGEN = ngen, MU = 4*25)

    # 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()'''