Thesis-NoiseDetection-CNN/train_model.py

import numpy as np
import pandas as pd
import sys, os, argparse
import json

import cv2

from sklearn.utils import shuffle

from keras.preprocessing.image import ImageDataGenerator
from keras.models import Sequential
from keras.layers import Conv2D, MaxPooling2D, AveragePooling2D
from keras.layers import Activation, Dropout, Flatten, Dense, BatchNormalization
from keras import backend as K
import tensorflow as tf

from keras.utils import plot_model

from modules.utils import config as cfg
from sklearn.metrics import roc_auc_score, accuracy_score, precision_score, recall_score, f1_score

img_width, img_height = 200, 200
batch_size = 32

def auc(y_true, y_pred):
    auc = tf.metrics.auc(y_true, y_pred)[1]
    K.get_session().run(tf.local_variables_initializer())
    #K.get_session().run(tf.local_variables_initializer())
    return auc

def generate_model(_input_shape):

    model = Sequential()

    model.add(Conv2D(60, (2, 2), input_shape=_input_shape))
    model.add(Activation('relu'))
    model.add(MaxPooling2D(pool_size=(2, 2)))

    model.add(Conv2D(40, (2, 2)))
    model.add(Activation('relu'))
    model.add(MaxPooling2D(pool_size=(2, 2)))

    model.add(Conv2D(20, (2, 2)))
    model.add(Activation('relu'))
    model.add(MaxPooling2D(pool_size=(2, 2)))

    model.add(Flatten())

    model.add(Dense(140))
    model.add(Activation('relu'))
    model.add(BatchNormalization())
    model.add(Dropout(0.4))

    model.add(Dense(120))
    model.add(Activation('relu'))
    model.add(BatchNormalization())
    model.add(Dropout(0.4))

    model.add(Dense(80))
    model.add(Activation('relu'))
    model.add(BatchNormalization())
    model.add(Dropout(0.4))

    model.add(Dense(40))
    model.add(Activation('relu'))
    model.add(BatchNormalization())
    model.add(Dropout(0.4))

    model.add(Dense(20))
    model.add(Activation('relu'))
    model.add(BatchNormalization())
    model.add(Dropout(0.4))

    model.add(Dense(1))
    model.add(Activation('sigmoid'))

    model.compile(loss='binary_crossentropy',
                  optimizer='rmsprop',
                  metrics=['accuracy', auc])

    return model


def main():

    parser = argparse.ArgumentParser(description="Train Keras model and save it into .json file")

    parser.add_argument('--data', type=str, help='dataset filename prefix (without .train and .test)', required=True)
    parser.add_argument('--output', type=str, help='output file name desired for model (without .json extension)', required=True)
    parser.add_argument('--batch_size', type=int, help='batch size used as model input', default=cfg.keras_batch)
    parser.add_argument('--epochs', type=int, help='number of epochs used for training model', default=cfg.keras_epochs)
    parser.add_argument('--val_size', type=int, help='percent of validation data during training process', default=cfg.val_dataset_size)
    parser.add_argument('--n_channels', type=int, help='number of canals for 3D', default=1)

    args = parser.parse_args()

    p_data_file  = args.data
    p_output     = args.output
    p_batch_size = args.batch_size
    p_epochs     = args.epochs
    p_val_size   = args.val_size
    p_n_channels = args.n_channels

    # specify the number of dimensions
    if K.image_data_format() == 'channels_first':
        input_shape = (p_n_channels, img_width, img_height)
    else:
        input_shape = (img_width, img_height, p_n_channels)
        
    ########################
    # 1. Get and prepare data
    ########################
    print("Preparing data...")
    dataset_train = pd.read_csv(p_data_file + '.train', header=None, sep=";")
    dataset_test = pd.read_csv(p_data_file + '.test', header=None, sep=";")

    print("Train set size : ", len(dataset_train))
    print("Test set size : ", len(dataset_test))

    # default first shuffle of data
    dataset_train = shuffle(dataset_train)
    dataset_test = shuffle(dataset_test)

    print("Reading all images data...")

    # `:` is the separator used for getting each img path
    if p_n_channels > 1:
        dataset_train[1] = dataset_train[1].split(':').apply(lambda x: cv2.imread(x, cv2.IMREAD_GRAYSCALE).reshape(input_shape))
        dataset_test[1] = dataset_test[1].split(':').apply(lambda x: cv2.imread(x, cv2.IMREAD_GRAYSCALE).reshape(input_shape))
    else:
        dataset_train[1] = dataset_train[1].apply(lambda x: cv2.imread(x, cv2.IMREAD_GRAYSCALE).reshape(input_shape))
        dataset_test[1] = dataset_test[1].apply(lambda x: cv2.imread(x, cv2.IMREAD_GRAYSCALE).reshape(input_shape))

    # get dataset with equal number of classes occurences
    noisy_df_train = dataset_train[dataset_train.ix[:, 0] == 1]
    not_noisy_df_train = dataset_train[dataset_train.ix[:, 0] == 0]
    nb_noisy_train = len(noisy_df_train.index)

    noisy_df_test = dataset_test[dataset_test.ix[:, 0] == 1]
    not_noisy_df_test = dataset_test[dataset_test.ix[:, 0] == 0]
    nb_noisy_test = len(noisy_df_test.index)

    final_df_train = pd.concat([not_noisy_df_train[0:nb_noisy_train], noisy_df_train])
    final_df_test = pd.concat([not_noisy_df_test[0:nb_noisy_test], noisy_df_test])

    # shuffle data another time
    final_df_train = shuffle(final_df_train)
    final_df_test = shuffle(final_df_test)

    final_df_train_size = len(final_df_train.index)
    final_df_test_size = len(final_df_test.index)

    # use of the whole data set for training
    x_dataset_train = final_df_train.ix[:,1:]
    x_dataset_test = final_df_test.ix[:,1:]

    y_dataset_train = final_df_train.ix[:,0]
    y_dataset_test = final_df_test.ix[:,0]

    x_data_train = []
    for item in x_dataset_train.values:
        #print("Item is here", item)
        x_data_train.append(item[0])

    x_data_train = np.array(x_data_train)

    x_data_test = []
    for item in x_dataset_test.values:
        #print("Item is here", item)
        x_data_test.append(item[0])

    x_data_test = np.array(x_data_test)


    print("End of loading data..")

    print("Train set size (after balancing) : ", final_df_train_size)
    print("Test set size (after balancing) : ", final_df_test_size)

    #######################
    # 2. Getting model
    #######################

    model = generate_model(input_shape)
    model.summary()
 
    model.fit(x_data_train, y_dataset_train.values, validation_split=p_val_size, epochs=p_epochs, batch_size=p_batch_size)

    score = model.evaluate(x_data_test, y_dataset_test, batch_size=p_batch_size)

    if not os.path.exists(cfg.saved_models_folder):
        os.makedirs(cfg.saved_models_folder)

    # save the model into HDF5 file
    model_output_path = os.path.join(cfg.saved_models_folder, p_output + '.json')
    json_model_content = model.to_json()

    with open(model_output_path, 'w') as f:
        print("Model saved into ", model_output_path)
        json.dump(json_model_content, f, indent=4)

    model.save_weights(model_output_path.replace('.json', '.h5'))

    # Get results obtained from model
    y_train_prediction = model.predict(x_data_train)
    y_test_prediction = model.predict(x_data_test)

    y_train_prediction = [1 if x > 0.5 else 0 for x in y_train_prediction]
    y_test_prediction = [1 if x > 0.5 else 0 for x in y_test_prediction]

    acc_train_score = accuracy_score(y_dataset_train, y_train_prediction)
    acc_test_score = accuracy_score(y_dataset_test, y_test_prediction)

    f1_train_score = f1_score(y_dataset_train, y_train_prediction)
    f1_test_score = f1_score(y_dataset_test, y_test_prediction)

    recall_train_score = recall_score(y_dataset_train, y_train_prediction)
    recall_test_score = recall_score(y_dataset_test, y_test_prediction)

    pres_train_score = precision_score(y_dataset_train, y_train_prediction)
    pres_test_score = precision_score(y_dataset_test, y_test_prediction)

    roc_train_score = roc_auc_score(y_dataset_train, y_train_prediction)
    roc_test_score = roc_auc_score(y_dataset_test, y_test_prediction)

    # save model performance
    if not os.path.exists(cfg.models_information_folder):
        os.makedirs(cfg.models_information_folder)

    perf_file_path = os.path.join(cfg.models_information_folder, cfg.csv_model_comparisons_filename)

    with open(perf_file_path, 'a') as f:
        line = p_output + ';' + str(len(dataset_train)) + ';' + str(len(dataset_test)) + ';' \
                        + str(final_df_train_size) + ';' + str(final_df_test_size) + ';' \
                        + str(acc_train_score) + ';' + str(acc_test_score) + ';' \
                        + str(f1_train_score) + ';' + str(f1_test_score) + ';' \
                        + str(recall_train_score) + ';' + str(recall_test_score) + ';' \
                        + str(pres_train_score) + ';' + str(pres_test_score) + ';' \
                        + str(roc_train_score) + ';' + str(roc_test_score) + '\n'
        f.write(line)

if __name__== "__main__":
    main()