Thesis-NoiseDetection-CNN/train_model.py

# main imports
import numpy as np
import pandas as pd
import sys, os, argparse
import json

# model imports
import cnn_models as models
import tensorflow as tf
import keras
from keras import backend as K
from keras.callbacks import ModelCheckpoint
from sklearn.metrics import roc_auc_score, accuracy_score, precision_score, recall_score, f1_score
from keras.utils import to_categorical

# image processing imports
import cv2
from sklearn.utils import shuffle
from sklearn.model_selection import train_test_split

# config imports
sys.path.insert(0, '') # trick to enable import of main folder module

import custom_config as cfg


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 .val)', required=True)
    parser.add_argument('--output', type=str, help='output file name desired for model (without .json extension)', required=True)
    parser.add_argument('--tl', type=int, help='use or not of transfer learning (`VGG network`)', default=0, choices=[0, 1])
    parser.add_argument('--batch_size', type=int, help='batch size used as model input', default=64)
    parser.add_argument('--epochs', type=int, help='number of epochs used for training model', default=30)
    parser.add_argument('--chanels', type=int, help="given number of chanels if necessary", default=0)
    parser.add_argument('--size', type=str, help="Size of input images", default="100, 100")
    parser.add_argument('--val_size', type=float, help='percent of validation data during training process', default=0.3)


    args = parser.parse_args()

    p_data_file   = args.data
    p_output      = args.output
    p_tl          = args.tl
    p_batch_size  = args.batch_size
    p_epochs      = args.epochs
    p_chanels     = args.chanels
    p_size        = args.size.split(',')
    p_val_size    = args.val_size

    #p_val_size    = args.val_size
    initial_epoch = 0

    ########################
    # 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...")

    # getting number of chanel
    if p_chanels == 0:
        n_chanels = len(dataset_train[1][1].split('::'))
    else:
        n_chanels = p_chanels

    print("Number of chanels : ", n_chanels)
    img_width, img_height = [ int(s) for s in p_size ]

    # specify the number of dimensions
    if K.image_data_format() == 'chanels_first':
        if n_chanels > 1:
            input_shape = (1, n_chanels, img_width, img_height)
        else:
            input_shape = (n_chanels, img_width, img_height)

    else:
        if n_chanels > 1:
            input_shape = (1, img_width, img_height, n_chanels)
        else:
            input_shape = (img_width, img_height, n_chanels)

    # getting weighted class over the whole dataset
    noisy_df_train = dataset_train[dataset_train.iloc[:, 0] == 1]
    not_noisy_df_train = dataset_train[dataset_train.iloc[:, 0] == 0]
    nb_noisy_train = len(noisy_df_train.index)
    nb_not_noisy_train = len(not_noisy_df_train.index)

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

    noisy_samples = nb_noisy_test + nb_noisy_train
    not_noisy_samples = nb_not_noisy_test + nb_not_noisy_train

    total_samples = noisy_samples + not_noisy_samples

    print('noisy', noisy_samples)
    print('not_noisy', not_noisy_samples)
    print('total', total_samples)

    class_weight = {
        0: (noisy_samples / float(total_samples)),
        1: (not_noisy_samples / float(total_samples)),
    }



    final_df_train = dataset_train
    final_df_test = dataset_test

    # check if specific number of chanels is used
    if p_chanels == 0:
        # `::` is the separator used for getting each img path
        if n_chanels > 1:
            final_df_train[1] = final_df_train[1].apply(lambda x: [cv2.imread(path, cv2.IMREAD_GRAYSCALE) for path in x.split('::')])
            final_df_test[1] = final_df_test[1].apply(lambda x: [cv2.imread(path, cv2.IMREAD_GRAYSCALE) for path in x.split('::')])
        else:
            final_df_train[1] = final_df_train[1].apply(lambda x: cv2.imread(x, cv2.IMREAD_GRAYSCALE))
            final_df_test[1] = final_df_test[1].apply(lambda x: cv2.imread(x, cv2.IMREAD_GRAYSCALE))
    else:
        final_df_train[1] = final_df_train[1].apply(lambda x: cv2.imread(x))
        final_df_test[1] = final_df_test[1].apply(lambda x: cv2.imread(x))

    # reshape array data
    final_df_train[1] = final_df_train[1].apply(lambda x: np.array(x).reshape(input_shape))
    final_df_test[1] = final_df_test[1].apply(lambda x: np.array(x).reshape(input_shape))

    # 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)

    print("----------------------------------------------------------")
    print("Validation split is now set at", p_val_size)
    print("----------------------------------------------------------")

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

    y_dataset_train = final_df_train.iloc[:,0]
    y_dataset_test = final_df_test.iloc[:,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
    #######################

    # create backup folder for current model
    model_backup_folder = os.path.join(cfg.backup_model_folder, p_output)
    if not os.path.exists(model_backup_folder):
        os.makedirs(model_backup_folder)

    # add of callback models
    filepath = os.path.join(cfg.backup_model_folder, p_output, p_output + "-{accuracy:02f}-{val_accuracy:02f}__{epoch:02d}.hdf5")
    checkpoint = ModelCheckpoint(filepath, monitor='val_accuracy', verbose=1, save_best_only=True, mode='max')
    callbacks_list = [checkpoint]

    
    # check if backup already exists
    weights_filepath = None
    backups = sorted(os.listdir(model_backup_folder))

    if len(backups) > 0:

        # retrieve last backup epoch of model 
        last_model_backup = None
        max_last_epoch = 0

        for backup in backups:

            last_epoch = int(backup.split('__')[1].replace('.h5', ''))

            if last_epoch > max_last_epoch and last_epoch < p_epochs:
                max_last_epoch = last_epoch
                last_model_backup = backup

        if last_model_backup is None:
            print("Epochs asked is already computer. Noee")
            sys.exit(1)

        initial_epoch = max_last_epoch
        print("-------------------------------------------------")
        print("Previous backup model found",  last_model_backup, "with already", initial_epoch, " epoch(s) done...")
        print("Resuming from epoch", str(initial_epoch + 1))
        print("-------------------------------------------------")

        # load weights
        weights_filepath = os.path.join(model_backup_folder, last_model_backup)

    print(n_chanels)
    model = models.get_model(n_chanels, input_shape, p_tl, weights_filepath)
    model.summary()

    # prepare train and validation dataset
    X_train, X_val, y_train, y_val = train_test_split(x_data_train, y_dataset_train, test_size=p_val_size, shuffle=False)

    y_train = to_categorical(y_train)
    y_val = to_categorical(y_val)
    y_test = to_categorical(y_dataset_test)

    print("Fitting model with custom class_weight", class_weight)
    model.fit(X_train, y_train, 
        validation_data=(X_val, y_val), 
        initial_epoch=initial_epoch, 
        epochs=p_epochs, 
        batch_size=p_batch_size, 
        callbacks=callbacks_list, 
        class_weight=class_weight)

    score = model.evaluate(X_val, y_val, batch_size=p_batch_size)

    print("Accuracy score on val dataset ", score)

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

    # save the model into HDF5 file
    model_output_path = os.path.join(cfg.output_models, p_output + '.h5')
    model.save(model_output_path)

    # Get results obtained from model
    y_train_prediction = model.predict(X_train)
    y_val_prediction = model.predict(X_val)
    y_test_prediction = model.predict(x_dataset_test)

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

    y_train_prediction = np.argmax(y_train_prediction, axis=1)
    y_val_prediction = np.argmax(y_val_prediction, axis=1)

    acc_train_score = accuracy_score(y_train, y_train_prediction)
    acc_val_score = accuracy_score(y_val, y_val_prediction)
    acc_test_score = accuracy_score(y_test, y_test_prediction)

    roc_train_score = roc_auc_score(y_train, y_train_prediction)
    roc_val_score = roc_auc_score(y_val, y_val_prediction)
    roc_test_score = roc_auc_score(y_test, y_val_prediction)

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

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

    # write header if necessary
    if not os.path.exists(perf_file_path):
        with open(perf_file_path, 'w') as f:
            f.write('name;train_acc;val_acc;test_acc;train_auc;val_auc;test_auc;\n')
            
    # add information into file
    with open(perf_file_path, 'a') as f:
        line = p_output + ';' + str(acc_train_score) + ';' + str(acc_val_score) + ';' \
                        + str(acc_test_score) + ';' + str(roc_train_score) + ';' \
                        + str(roc_val_score) + ';' + str(roc_test_score) + '\n'
        f.write(line)

    print("You can now run your model with your own `test` dataset")

if __name__== "__main__":
    main()