enas_elm.py

'''
Created on April , 2021
@author:
'''

## Import libraries in python
import argparse
import time
import json
import logging
import sys
import os
import math
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import random
import importlib
from scipy.stats import randint, expon, uniform
import glob
import tensorflow as tf
import sklearn as sk
from sklearn import svm
from sklearn.utils import shuffle
from sklearn import metrics
from sklearn import preprocessing
from sklearn import pipeline
from sklearn.metrics import mean_squared_error
from math import sqrt


from utils.elm_network import network_fit

from utils.hpelm import ELM, HPELM
from utils.elm_task import SimpleNeuroEvolutionTask
from utils.ea_multi import GeneticAlgorithm


# random seed predictable
jobs = 1



current_dir = os.path.dirname(os.path.abspath(__file__))
data_filedir = os.path.join(current_dir, 'N-CMAPSS')
data_filepath = os.path.join(current_dir, 'N-CMAPSS', 'N-CMAPSS_DS02-006.h5')
sample_dir_path = os.path.join(data_filedir, 'Samples_whole')

model_temp_path = os.path.join(current_dir, 'Models', 'elm_rep.h5')
tf_temp_path = os.path.join(current_dir, 'TF_Model_tf')

pic_dir = os.path.join(current_dir, 'Figures')


# Log file path of EA in csv
# directory_path = current_dir + '/EA_log'
directory_path = os.path.join(current_dir, 'EA_log')

if not os.path.exists(pic_dir):
    os.makedirs(pic_dir)

if not os.path.exists(directory_path):
    os.makedirs(directory_path)    

'''
load array from npz files
'''
def load_part_array (sample_dir_path, unit_num, win_len, stride, part_num):
    filename =  'Unit%s_win%s_str%s_part%s.npz' %(str(int(unit_num)), win_len, stride, part_num)
    filepath =  os.path.join(sample_dir_path, filename)
    loaded = np.load(filepath)
    return loaded['sample'], loaded['label']

def load_part_array_merge (sample_dir_path, unit_num, win_len, win_stride, partition):
    sample_array_lst = []
    label_array_lst = []
    print ("Unit: ", unit_num)
    for part in range(partition):
      print ("Part.", part+1)
      sample_array, label_array = load_part_array (sample_dir_path, unit_num, win_len, win_stride, part+1)
      sample_array_lst.append(sample_array)
      label_array_lst.append(label_array)
    sample_array = np.dstack(sample_array_lst)
    label_array = np.concatenate(label_array_lst)
    sample_array = sample_array.transpose(2, 0, 1)
    print ("sample_array.shape", sample_array.shape)
    print ("label_array.shape", label_array.shape)
    return sample_array, label_array


def load_array (sample_dir_path, unit_num, win_len, stride, sampling):
    filename =  'Unit%s_win%s_str%s_smp%s.npz' %(str(int(unit_num)), win_len, stride, sampling)
    filepath =  os.path.join(sample_dir_path, filename)
    loaded = np.load(filepath)

    return loaded['sample'].transpose(2, 0, 1), loaded['label']


def shuffle_array(sample_array, label_array):
    ind_list = list(range(len(sample_array)))
    print("ind_list befor: ", ind_list[:10])
    print("ind_list befor: ", ind_list[-10:])
    ind_list = shuffle(ind_list)
    print("ind_list after: ", ind_list[:10])
    print("ind_list after: ", ind_list[-10:])
    print("Shuffeling in progress")
    shuffle_sample = sample_array[ind_list, :, :]
    shuffle_label = label_array[ind_list,]
    return shuffle_sample, shuffle_label

def figsave(history, h1,h2,h3,h4, bs, lr, sub):
    fig_acc = plt.figure(figsize=(15, 8))
    plt.plot(history.history['loss'])
    plt.plot(history.history['val_loss'])
    plt.title('Training', fontsize=24)
    plt.ylabel('loss', fontdict={'fontsize': 18})
    plt.xlabel('epoch', fontdict={'fontsize': 18})
    plt.legend(['Training loss', 'Validation loss'], loc='upper left', fontsize=18)
    plt.show()
    print ("saving file:training loss figure")
    fig_acc.savefig(pic_dir + "/elm_enas_training_h1%s_h2%s_h3%s_h4%s_bs%s_sub%s_lr%s.png" %(int(h1), int(h2), int(h3), int(h4), int(bs), int(sub), str(lr)))
    return


def score_calculator(y_predicted, y_actual):
    # Score metric
    h_array = y_predicted - y_actual
    s_array = np.zeros(len(h_array))
    for j, h_j in enumerate(h_array):
        if h_j < 0:
            s_array[j] = math.exp(-(h_j / 13)) - 1

        else:
            s_array[j] = math.exp(h_j / 10) - 1
    score = np.sum(s_array)
    return score


def release_list(a):
   del a[:]
   del a


def recursive_clean(directory_path):
    """clean the whole content of :directory_path:"""
    if os.path.isdir(directory_path) and os.path.exists(directory_path):
        files = glob.glob(directory_path + '*')
        for file_ in files:
            if os.path.isdir(file_):
                recursive_clean(file_ + '/')
            else:
                os.remove(file_)

units_index_train = [2.0, 5.0, 10.0, 16.0, 18.0, 20.0]
units_index_test = [11.0, 14.0, 15.0]



def main():
    # current_dir = os.path.dirname(os.path.abspath(__file__))
    parser = argparse.ArgumentParser(description='RPs creator')
    parser.add_argument('-w', type=int, default=50, help='sequence length', required=True)
    parser.add_argument('-s', type=int, default=1, help='stride of filter')
    parser.add_argument('-constant', type=float, default=1e-4, help='constant for #neurons penalty')
    parser.add_argument('-bs', type=int, default=1000, help='batch size')
    parser.add_argument('-ep', type=int, default=30, help='max epoch')
    parser.add_argument('-pt', type=int, default=20, help='patience')
    parser.add_argument('-vs', type=float, default=0.1, help='validation split')
    parser.add_argument('-lr', type=float, default=0.001, help='learning rate')
    parser.add_argument('-sub', type=int, default=1, help='subsampling stride')

    parser.add_argument('-t', type=int, required=True, help='trial')
    parser.add_argument('--sampling', type=int, default=1, help='sampling rate')

    parser.add_argument('--pop', type=int, default=50, required=False, help='population size of EA')
    parser.add_argument('--gen', type=int, default=50, required=False, help='generations of evolution')
    parser.add_argument('--device', type=str, default="GPU", help='Use "basic" if GPU with cuda is not available')
    parser.add_argument('--obj', type=str, default="moo", help='Use "soo" for single objective and "moo" for multiobjective')

    args = parser.parse_args()

    win_len = args.w
    win_stride = args.s
    partition = 3
    lr = args.lr
    cs = args.constant
    bs = args.bs
    ep = args.ep
    pt = args.pt
    vs = args.vs
    sub = args.sub
    sampling = args.sampling

    device = args.device
    obj = args.obj

    trial = args.t
    seed = trial
    random.seed(seed)
    np.random.seed(seed)

    train_units_samples_lst =[]
    train_units_labels_lst = []

    for index in units_index_train:
        print("Load data index: ", index)
        sample_array, label_array = load_array (sample_dir_path, index, win_len, win_stride, sampling)
        #sample_array, label_array = shuffle_array(sample_array, label_array)
        print("sample_array.shape", sample_array.shape)
        print("label_array.shape", label_array.shape)
        sample_array = sample_array[::sub]
        label_array = label_array[::sub]

        sample_array = sample_array.astype(np.float32)
        label_array = label_array.astype(np.float32)

        print("sub sample_array.shape", sample_array.shape)
        print("sub label_array.shape", label_array.shape)
        train_units_samples_lst.append(sample_array)
        train_units_labels_lst.append(label_array)

    sample_array = np.concatenate(train_units_samples_lst)
    label_array = np.concatenate(train_units_labels_lst)
    print ("samples are aggregated")

    release_list(train_units_samples_lst)
    release_list(train_units_labels_lst)
    train_units_samples_lst =[]
    train_units_labels_lst = []
    print("Memory released")

    sample_array, label_array = shuffle_array(sample_array, label_array)
    print("samples are shuffled")
    print("sample_array.shape", sample_array.shape)
    print("label_array.shape", label_array.shape)

    sample_array = sample_array.reshape(sample_array.shape[0], sample_array.shape[2])
    print("sample_array_reshape.shape", sample_array.shape)
    print("label_array_reshape.shape", label_array.shape)
    feat_len = sample_array.shape[1]
    num_samples = sample_array.shape[0]
    print ("feat_len", feat_len)

    train_sample_array = sample_array[:int(num_samples*(1-vs))]
    train_label_array = label_array[:int(num_samples*(1-vs))]
    val_sample_array = sample_array[int(num_samples*(1-vs))+1:]
    val_label_array = label_array[int(num_samples*(1-vs))+1:]

    print ("train_sample_array.shape", train_sample_array.shape)
    print ("train_label_array.shape", train_label_array.shape)
    print ("val_sample_array.shape", val_sample_array.shape)
    print ("val_label_array.shape", val_label_array.shape)

    sample_array = []
    label_array = []

    ## Parameters for the GA
    pop_size = args.pop
    n_generations = args.gen
    cx_prob = 0.5  # 0.25
    mut_prob = 0.5  # 0.7
    cx_op = "one_point"
    mut_op = "uniform"
    sel_op = "best"
    other_args = {
        'mut_gene_probability': 0.3  # 0.1
    }



    start = time.time()

    # log_file_path = log_path + 'log_%s_%s_pop-%s_gen-%s_%s.csv' % (
    # subdata_mode_list[subdata_mode], fitness_mode_list[fitness_mode], pop_size, n_generations, trial)
    # log_col = ['idx', 'stop_epoch', 'window_length', 'n_filters', 'kernel_size', 'n_conv_layer', 'LSTM1_units',
    #            'LSTM2_units', 'n_window',
    #            'val_rmse', 'val_score', 'rmse_combined', 'score_combined',
    #            'AIC', 'train_loss', 'mle_term', 'params_term', 'geno_list']
    # log_df = pd.DataFrame(columns=log_col, index=None)
    # log_df.to_csv(log_file_path, index=False)
    # print(log_df)


    # Save log file of EA in csv
    recursive_clean(directory_path)
    if not os.path.exists(directory_path):
        os.makedirs(directory_path)

    mutate_log_path = os.path.join(directory_path, 'mute_log_t-%s_%s_%s.csv' % (trial, pop_size, n_generations))  
    mutate_log_col = ['idx', 'params_1', 'params_2', 'params_3', 'params_4', 'fitness', 'penalty', 'val_rmse', 'gen']
    mutate_log_df = pd.DataFrame(columns=mutate_log_col, index=None)
    mutate_log_df.to_csv(mutate_log_path, index=False)

    # prft_path = os.path.join(directory_path, 'prft_out_%s_%s.csv' % (pop_size, n_generations))


    def log_function(population, gen, cs, mutate_log_path = mutate_log_path):
        for i in range(len(population)):
            indiv = population[i]
            lin_check = indiv[3]
            if  indiv == []:
                "non_mutated empty"
                pass
            else:
                # print ("i: ", i)
                indiv.append(indiv.fitness.values[0])

                # append penalty
                if lin_check == 1:
                    lin_nrn = 20
                else:
                    lin_nrn = 0


                num_nrn = indiv[1]*10 + indiv[2]*10 + lin_nrn
                penalty = num_nrn * cs
                val_rmse = indiv.fitness.values[0] - penalty

                indiv.append(penalty)
                indiv.append(val_rmse)

                # append val_rmse
                indiv.append(gen)

        temp_df = pd.DataFrame(np.array(population), index=None)
        temp_df.to_csv(mutate_log_path, mode='a', header=None)
        print("population saved")
        return

    start = time.time()

    # Assign & run EA
    task = SimpleNeuroEvolutionTask(
        train_sample_array = train_sample_array,
        train_label_array = train_label_array,
        val_sample_array = val_sample_array,
        val_label_array = val_label_array,
        constant = cs,
        batch=bs,
        model_path = model_temp_path,
        device = device,
        obj = obj
    )

    # aic = task.evaluate(individual_seed)

    ga = GeneticAlgorithm(
        task=task,
        population_size=pop_size,
        n_generations=n_generations,
        cx_probability=cx_prob,
        mut_probability=mut_prob,
        crossover_operator=cx_op,
        mutation_operator=mut_op,
        selection_operator=sel_op,
        jobs=jobs,
        log_function=log_function,
        cs = cs,
        **other_args
    )

    pop, log, hof, prtf = ga.run()

    print("Best individual:")
    print(hof[0])
    print(prtf)

    # Save to the txt file
    # hof_filepath = tmp_path + "hof/best_params_fn-%s_ps-%s_ng-%s.txt" % (csv_filename, pop_size, n_generations)
    # with open(hof_filepath, 'w') as f:
    #     f.write(json.dumps(hof[0]))

    print("Best individual is saved")
    end = time.time()
    print("EA time: ", end - start)
    print ("####################  EA COMPLETE / HOF TEST   ##############################")







    """ Creates a new instance of the training-validation task and computes the fitness of the current individual """

    l2_parms_lst = [1e-2, 1e-3, 1e-4, 1e-5, 1e-6]
    l2_parm = l2_parms_lst[hof[0][0] - 1]
    type_neuron_lst = ["tanh", "sigm", "lin"]

    lin_check = hof[0][3]
    num_neuron_lst = []
    for n in range(2):
        num_neuron_lst.append(hof[0][n + 1] * 10)
    if lin_check == 1:
        num_neuron_lst.append(20)
    else:
        num_neuron_lst.append(0)

    print("HoF l2_params: ", l2_parm)
    print("HoF lin_check: ", lin_check)
    print("HoF num_neuron_lst: ", num_neuron_lst)
    print("HoF type_neuron_lst: ", type_neuron_lst)

    feat_len = train_sample_array.shape[1]
    best_elm_class = network_fit(feat_len,
                          l2_parm, lin_check,
                          num_neuron_lst, type_neuron_lst, model_temp_path, device, bs)
    best_elm_net = best_elm_class.trained_model()

    # Train the best network
    sample_array = np.concatenate((train_sample_array, val_sample_array))
    label_array = np.concatenate((train_label_array, val_label_array))

    start = time.time()

    print ("sample_array.shape", sample_array.shape)
    print("label_array.shape", label_array.shape)
    best_elm_net.train(sample_array, label_array, "R")
    print("individual trained...evaluation in progress...")
    neurons_lst, norm_check = best_elm_net.summary()
    print("summary: ", neurons_lst, norm_check)

    end = time.time()


    output_lst = []
    truth_lst = []

    # Test
    for index in units_index_test:
        print ("test idx: ", index)
        sample_array, label_array = load_array(sample_dir_path, index, win_len, win_stride, sampling)
        # estimator = load_model(tf_temp_path, custom_objects={'rmse':rmse})
        print("sample_array.shape", sample_array.shape)
        print("label_array.shape", label_array.shape)
        sample_array = sample_array[::sub]
        label_array = label_array[::sub]
        print("sub sample_array.shape", sample_array.shape)
        print("sub label_array.shape", label_array.shape)
        sample_array = sample_array.reshape(sample_array.shape[0], sample_array.shape[2])
        print("sample_array_reshape.shape", sample_array.shape)
        print("label_array_reshape.shape", label_array.shape)

        sample_array = sample_array.astype(np.float32)
        label_array = label_array.astype(np.float32)

        # estimator = load_model(model_temp_path)

        y_pred_test = best_elm_net.predict(sample_array)
        output_lst.append(y_pred_test)
        truth_lst.append(label_array)

    print(output_lst[0].shape)
    print(truth_lst[0].shape)

    print(np.concatenate(output_lst).shape)
    print(np.concatenate(truth_lst).shape)

    output_array = np.concatenate(output_lst)[:, 0]
    trytg_array = np.concatenate(truth_lst)
    print(output_array.shape)
    print(trytg_array.shape)

    output_array = output_array.flatten()
    print(output_array.shape)
    print(trytg_array.shape)
    score = score_calculator(output_array, trytg_array)
    print("score: ", score)

    rms = sqrt(mean_squared_error(output_array, trytg_array))
    print(rms)
    rms = round(rms, 2)
    score = round(score, 2)


    for idx in range(len(units_index_test)):
        print(output_lst[idx])
        print(truth_lst[idx])
        fig_verify = plt.figure(figsize=(24, 10))
        plt.plot(output_lst[idx], color="green")
        plt.plot(truth_lst[idx], color="red", linewidth=2.0)
        plt.title('Unit%s inference' %str(int(units_index_test[idx])), fontsize=30)
        plt.yticks(fontsize=20)
        plt.xticks(fontsize=20)
        plt.ylabel('RUL', fontdict={'fontsize': 24})
        plt.xlabel('Timestamps', fontdict={'fontsize': 24})
        plt.legend(['Predicted', 'Truth'], loc='upper right', fontsize=28)
        plt.ylim([-20, 80])
        plt.show()
        fig_verify.savefig(pic_dir + "/best_elm_unit%s_test_pop%s_gen%s_rmse-%s_score-%s.png" %(str(int(units_index_test[idx])),
                                                                              str(args.pop), str(args.gen), str(rms), str(score)))

    print("BEST model training time: ", end - start)
    print("HOF phenotype: ", [l2_parms_lst[hof[0][0] - 1], hof[0][1] * 10, hof[0][2] * 10, hof[0][3]])
    print(" test RMSE: ", rms)
    print(" test Score: ", score)




if __name__ == '__main__':
    main()