mainGPU_v2.py

from __future__ import print_function
import os,time,cv2, sys, math
import tensorflow as tf
import tensorflow.contrib.slim as slim
import numpy as np
import time, datetime
import argparse
import random
import os, sys
import subprocess
os.environ['TF_CPP_MIN_LOG_LEVEL']='2'
from tensorflow.python.client import device_lib

import pywt
import helpers
import utils_ as utils
from utils_ import get_model
from pywt import wavedec2
import matplotlib.pyplot as plt


#from custom_model import build_encoder_decoder_skip
config = tf.ConfigProto(log_device_placement=False)


def str2bool(v):
    if v.lower() in ('yes', 'true', 't', 'y', '1'):
        return True
    elif v.lower() in ('no', 'false', 'f', 'n', '0'):
        return False
    else:
        raise argparse.ArgumentTypeError('Boolean value expected.')
config.gpu_options.allow_growth = True
parser = argparse.ArgumentParser()
parser.add_argument('--num_epochs', type=int, default=100, help='Number of epochs to train for')
parser.add_argument('--save', type=int, default=4, help='Interval for saving weights')
parser.add_argument('--gpu', type=str, default='0', help='Choose GPU device to be used')
parser.add_argument('--mode', type=str, default="train", help='Select "train", "test", or "predict" mode. \
    Note that for prediction mode you have to specify an image to run the model on.')
parser.add_argument('--checkpoint', type=str, default="checkpoint", help='Checkpoint folder.')
parser.add_argument('--class_balancing', type=str2bool, default=False, help='Whether to use median frequency class weights to balance the classes in the loss')
parser.add_argument('--image', type=str, default=None, help='The image you want to predict on. Only valid in "predict" mode.')
parser.add_argument('--continue_training', type=str2bool, default=False, help='Whether to continue training from a checkpoint')
parser.add_argument('--dataset', type=str, default='lashan', help='Dataset you are using.')
parser.add_argument('--load_data', type=str2bool, default=True, help='Dataset loading type.')
parser.add_argument('--act', type=str2bool, default=True, help='True if sigmoid or false for softmax')
parser.add_argument('--crop_height', type=int, default=224, help='Height of cropped input image to network')
parser.add_argument('--crop_width', type=int, default=224, help='Width of cropped input image to network')
parser.add_argument('--batch_size', type=int, default=8, help='Number of images in each batch')
parser.add_argument('--num_val_images', type=int, default=200, help='The number of images to used for validations')
parser.add_argument('--h_flip', type=str2bool, default=True, help='Whether to randomly flip the image horizontally for data augmentation')
parser.add_argument('--v_flip', type=str2bool, default=True, help='Whether to randomly flip the image vertically for data augmentation')
parser.add_argument('--brightness', type=float, default=None, help='Whether to randomly change the image brightness for data augmentation. Specifies the max bightness change.')
parser.add_argument('--rotation', type=float, default=None, help='Whether to randomly rotate the image for data augmentation. Specifies the max rotation angle.')
parser.add_argument('--model', type=str, default="dunet", help='The model you are using. Currently supports:\
    encoder-decoder, deepUNet,attentionNet, deep, UNet')
args = parser.parse_args()
gpu = str(args.gpu)
os.environ['CUDA_VISIBLE_DEVICES']=  gpu
#os.environ["CUDA_VISIBLE_DEVICES"] = '0'
# Get a list of the training, validation, and testing file paths

def load_divided(dataset_dir):
    train_input_names=[]
    train_output_names=[]
    val_input_names=[]
    val_output_names=[]
    test_input_names=[]
    test_output_names=[]
    cwd = os.getcwd()

    for file in os.listdir(dataset_dir + "/train"):
        train_input_names.append(cwd + "/" + dataset_dir + "/train/" + file)
    for file in os.listdir(dataset_dir + "/train_labels"):
        train_output_names.append(cwd + "/" + dataset_dir + "/train_labels/" + file)
    for file in os.listdir(dataset_dir + "/val"):
        val_input_names.append(cwd + "/" + dataset_dir + "/val/" + file)
    for file in os.listdir(dataset_dir + "/val_labels"):
        val_output_names.append(cwd + "/" + dataset_dir + "/val_labels/" + file)
    if args.mode =='test':
        for file in os.listdir(dataset_dir + "/test"):
            test_input_names.append(cwd + "/" + dataset_dir + "/test/" + file)
        for file in os.listdir(dataset_dir + "/test_labels"):
            test_output_names.append(cwd + "/" + dataset_dir + "/test_labels/" + file)
    return train_input_names, train_output_names, val_input_names, val_output_names, test_input_names, test_output_names

def load_nondivided(dataset_dir):
    train_input_names=[]
    train_output_names=[]
    val_input_names=[]
    val_output_names=[]
    test_input_names=[]
    test_output_names=[]

    all_files = []
    cwd = os.getcwd()
    for file in os.listdir(dataset_dir + "/sat"):
        all_files.append(file)

    selected_val = random.sample(all_files, len(all_files)//18)
    train_input_names= [ cwd + "/" + dataset_dir + "/sat/" + name for name in all_files if name not in selected_val]
    train_output_names= [ cwd + "/" + dataset_dir + "/gt/" + name for name in all_files if name not in selected_val]
    val_input_names= [ cwd + "/" + dataset_dir + "/sat/" + name for name in selected_val]
    val_output_names= [ cwd + "/" + dataset_dir + "/gt/" + name for name in selected_val]
    print('Training data length : {} and validation data length: {}'.format(len(train_input_names), len(val_input_names)))
    return train_input_names,train_output_names, val_input_names, val_output_names, test_input_names, test_output_names


def prepare_data(dataset_dir=args.dataset, type=args.load_data):
    if type:
        train_input_names, train_output_names, val_input_names, val_output_names, test_input_names, test_output_names = load_divided(dataset_dir)
    else:
        train_input_names, train_output_names, val_input_names, val_output_names, test_input_names, test_output_names = load_nondivided(dataset_dir)

    print('Training data length : {} and validation data length: {}'.format(len(train_input_names), len(val_input_names)))
    train_input_names.sort(),train_output_names.sort(), val_input_names.sort(), val_output_names.sort(), test_input_names.sort(), test_output_names.sort()
    return train_input_names,train_output_names, val_input_names, val_output_names, test_input_names, test_output_names

def check_available_gpus():
    local_devices = device_lib.list_local_devices()
    gpu_names = [x.name for x in local_devices if x.device_type == 'GPU']
    gpu_num = len(gpu_names)

    print('{0} GPUs are detected : {1}'.format(gpu_num, gpu_names))

    return gpu_names

def get_names(gpus):
    n_gpus = len(gpus)
    if n_gpus == 1:
        return gpus[0],gpus[0], gpus[0], gpus[0]
    if n_gpus == 2:
        return gpus[0],gpus[0], gpus[1], gpus[1]
    if n_gpus == 3:
        return gpus[0], gpus[1], gpus[2], gpus[0]
    if n_gpus == 4:
        return gpus[0], gpus[1], gpus[2], gpus[3]

def load_image(path):
    #print(path)
    image = cv2.cvtColor(cv2.imread(path,-1), cv2.COLOR_BGR2RGB)
    h, w = args.crop_height, args.crop_width
    image = cv2.resize(image,(h, w))

    return image

def load_image_gray(path):
    img = cv2.imread(path, -1)

    image = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
    image = cv2.resize(image,(256, 256))
    return image

def data_augmentation(input_image, output_image):
    # Data augmentation
    #print (input_image.shape, output_image.shape)
    dice = random.random()
    crop_width, crop_height = args.crop_width, args.crop_height
    if dice >= 0.15:
        crop_height, crop_width = input_image.shape[1], input_image.shape[0]
    input_image, output_image = utils.random_crop(input_image, output_image, args.crop_height, args.crop_width)

    if args.h_flip and random.randint(0,1):
        input_image = cv2.flip(input_image, 1)
        output_image = cv2.flip(output_image, 1)
    if args.v_flip and random.randint(0,1):
        input_image = cv2.flip(input_image, 0)
        output_image = cv2.flip(output_image, 0)
    if args.brightness:
        factor = random.uniform(-1*args.brightness, args.brightness)
        table = np.array([((i / 255.0) ** factor) * 255 for i in np.arange(0, 256)]).astype(np.uint8)
        input_image = cv2.LUT(input_image, table)
    if args.rotation:
        angle = random.uniform(-1*args.rotation, args.rotation)
    if args.rotation:
        M = cv2.getRotationMatrix2D((input_image.shape[1]//2, input_image.shape[0]//2), angle, 1.0)
        input_image = cv2.warpAffine(input_image, M, (input_image.shape[1], input_image.shape[0]), flags=cv2.INTER_NEAREST)
        output_image = cv2.warpAffine(output_image, M, (output_image.shape[1], output_image.shape[0]), flags=cv2.INTER_NEAREST)

    return input_image, output_image

def download_checkpoints(model_name):
    subprocess.check_output(["python", "get_pretrained_checkpoints.py", "--model=" + model_name])

# Get the names of the classes so we can record the evaluation results
class_names_list, label_values = helpers.get_label_info(os.path.join(args.dataset, "class_dict.csv"))
class_names_string = ""
for class_name in class_names_list:
    if not class_name == class_names_list[-1]:
        class_names_string = class_names_string + class_name + ", "
    else:
        class_names_string = class_names_string + class_name
print('LABEL VALUES: ',label_values)
print(class_names_string)
num_classes = len(label_values)
gpus = check_available_gpus()
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
sess=tf.Session(config=config)
model = args.model

# Get the selected model.
# Some of they require pre-trained ResNet
print("Preparing the model ...", model)

input = tf.placeholder(tf.float32,shape=[None, None, None, 3], name='inputs')
output = tf.placeholder(tf.float32,shape=[None, None, None, num_classes], name='output')

keep_prob = tf.placeholder(tf.float32)
input_A = tf.split(input, int(len(gpus)))
output_A = tf.split(output, int(len(gpus)))

# Load the data
print("Loading the data ...")
train_input_names,train_output_names, val_input_names, val_output_names, test_input_names, test_output_names = prepare_data()

if model == 'sunet':
    aux_output = tf.placeholder(tf.float32, shape=[None, None, None, num_classes], name='aux')


network = None
init_fn = None
if model != 'ssunet':
    network = get_model(model, input, num_classes, keep_prob, args.gpu)
else:
    network, _ = get_model(model, input, num_classes, keep_prob, args.gpu)
act = args.act
# Compute your softmax cross entropy loss
loss = None
loss_l = []
#sigs = ['unet', 'Unet', 'UNet', 'deepunet', 'deepUnet', 'dlink', 'fusion', 'dunet', 'newunet', 'deep', 'dil']
if args.class_balancing:
    print("Computing class weights for", args.dataset, "...")
    class_weights = utils.compute_class_weights(labels_dir=args.dataset + "/train_labels", label_values=label_values)
    if act:
        for gpu_id in range(len(gpus)):
            with tf.device(tf.DeviceSpec(device_type='GPU', device_index=gpu_id)):
                with tf.variable_scope(tf.get_variable_scope(), reuse=(gpu_id > 0)):
                    network = get_model(model, input_A[gpu_id], num_classes, keep_prob, args.gpu)
                    unweighted_loss = (tf.nn.sigmoid_cross_entropy_with_logits(logits=network, labels=output_A[gpu_id]))
                    loss_l.append((unweighted_loss * class_weights))
    else:
        unweighted_loss = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(logits=network, labels=output))
        loss = tf.reduce_mean(unweighted_loss * class_weights)
else:
    if act:
        for gpu_id in range(len(gpus)):
            with tf.device(tf.DeviceSpec(device_type='GPU', device_index=gpu_id)):
                with tf.variable_scope(tf.get_variable_scope(), reuse=(gpu_id > 0)):
                    network = get_model(model, input_A[gpu_id], num_classes, keep_prob, args.gpu)
                    #network = tf.sigmoid(network)
                    #_loss = utils.dice_loss(network, output_A[gpu_id])
                    _loss = (tf.nn.sigmoid_cross_entropy_with_logits(logits=network, labels=output_A[gpu_id]))
                    loss_l.append(_loss)
        #loss = tf.reduce_mean(tf.nn.sigmoid_cross_entropy_with_logits(logits=network, labels=output))
    else:
        loss = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(logits=network, labels=output))
    #network = tf.nn.sigmoid(network)
    #loss = tf.losses.mean_squared_error(predictions=network, labels=output)
#loss = tf.reduce_mean(loss_l)
loss = tf.reduce_mean(tf.concat(loss_l, axis=0))
opt = tf.train.AdamOptimizer(learning_rate=0.0001).minimize(loss, var_list=[var for var in tf.trainable_variables()],colocate_gradients_with_ops=True)
saver=tf.train.Saver(max_to_keep=1000)
sess.run(tf.global_variables_initializer())

utils.count_params()

# If a pre-trained ResNet is required, load the weights.
# This must be done AFTER the variables are initialized with sess.run(tf.global_variables_initializer())
if init_fn is not None:
    init_fn(sess)

# Load a previous checkpoint if desired
check = args.checkpoint
if not os.path.isdir(check):
    os.makedirs(check)
#model_checkpoint_name = "/media/cesar/My Passport/models" + args.model + "_" + args.dataset + ".ckpt"
model_checkpoint_name = check+"/latest_model_" + args.model + "_" + args.dataset + ".ckpt"

if args.continue_training or not args.mode == "train":
    print('Loaded latest model checkpoint')
    saver.restore(sess, model_checkpoint_name)

avg_scores_per_epoch = []



if args.mode == "train":

    print("\n***** Begin training *****")
    print("Dataset -->", args.dataset)
    print("Model -->", args.model)
    print("Crop Height -->", args.crop_height)
    print("Crop Width -->", args.crop_width)
    print("Num Epochs -->", args.num_epochs)
    print("Batch Size -->", args.batch_size)
    print("Num Classes -->", num_classes)

    print("Data Augmentation:")
    print("\tVertical Flip -->", args.v_flip)
    print("\tHorizontal Flip -->", args.h_flip)
    print("\tBrightness Alteration -->", args.brightness)
    print("\tRotation -->", args.rotation)
    print("")

    avg_loss_per_epoch = []

    # Which validation images do we want
    val_indices = []
    num_vals = min(args.num_val_images, len(val_input_names))

    # Set random seed to make sure models are validated on the same validation images.
    # So you can compare the results of different models more intuitively.
    random.seed(16)
    val_indices=random.sample(range(0,len(val_input_names)),num_vals)

    # Do the training here
    for epoch in range(0, args.num_epochs):

        current_losses = []

        cnt=0

        # Equivalent to shuffling
        id_list = np.random.permutation(len(train_input_names))

        num_iters = int(np.floor(len(id_list) / args.batch_size))
        st = time.time()
        epoch_st=time.time()
        for i in range(num_iters):
            # st=time.time()

            input_image_batch = []
            output_image_batch = []
            #wave1 = []
            #wave2 = []
            #wave3 = []
            #wave4 = []

            # Collect a batch of images
            for j in range(args.batch_size):
                index = i*args.batch_size + j
                id = id_list[index]
                input_image = load_image(train_input_names[id])[:args.crop_height, :args.crop_width]
                #input_image[:, :, 0] -= 103.939
                #input_image[:, :, 1] -= 116.779
                #input_image[:, :, 2] -= 123.68

                output_image = load_image(train_output_names[id])[:args.crop_height, :args.crop_width]
                #input_img = np.float32(input_image)
                #input_image_gray = load_image_gray(train_input_names[id])[:args.crop_height, :args.crop_width]

                with tf.device('/cpu:0'):

                    input_image, output_image = data_augmentation(input_image, output_image)
                    # Prep the data. Make sure the labels are in one-hot format
                    input_image = np.float32(input_image) / 255.0
                    #output_image = np.reshape(output_image, (3, 224, 224))
                    output_image = np.float32(helpers.one_hot_it(label=output_image, label_values=label_values))


                input_image_batch.append(np.expand_dims(input_image, axis=0))
                output_image_batch.append(np.expand_dims(output_image, axis=0))

            # ***** THIS CAUSES A MEMORY LEAK AS NEW TENSORS KEEP GETTING CREATED *****
            # input_image = tf.image.crop_to_bounding_box(input_image, offset_height=0, offset_width=0,
            #                                               target_height=args.crop_height, target_width=args.crop_width).eval(session=sess)
            # output_image = tf.image.crop_to_bounding_box(output_image, offset_height=0, offset_width=0,
            #                                               target_height=args.crop_height, target_width=args.crop_width).eval(session=sess)
            # ***** THIS CAUSES A MEMORY LEAK AS NEW TENSORS KEEP GETTING CREATED *****

            # memory()

            if args.batch_size == 1:
                input_image_batch = input_image_batch[0]
                output_image_batch = output_image_batch[0]
            else:
                input_image_batch = np.squeeze(np.stack(input_image_batch, axis=1))
                output_image_batch = np.squeeze(np.stack(output_image_batch, axis=1))

            # Do the training
            _,current=sess.run([opt,loss],feed_dict={input:input_image_batch,output:output_image_batch, keep_prob:0.5})#, wavelet1:wave1, wavelet2:wave2, wavelet3: wave3, wavelet4: wave4, keep_prob:0.25 })
            current_losses.append(current)
            cnt = cnt + args.batch_size
            if cnt % 20 == 0:
                string_print = "Epoch = %d Count = %d Current_Loss = %.4f Time = %.2f"%(epoch,cnt,current,time.time()-st)
                utils.LOG(string_print)
                st = time.time()

        mean_loss = np.mean(current_losses)
        avg_loss_per_epoch.append(mean_loss)

        # Create directories if needed
        if not os.path.isdir("%s/%04d"%(check,epoch)):
            os.makedirs("%s/%04d"%(check,epoch))

        saver.save(sess,model_checkpoint_name)

        if val_indices != 0 and epoch % 50 == 0:
            saver.save(sess,"%s/%04d/model.ckpt"%(check,epoch))


        target=open("%s/%04d/val_scores.csv"%(check,epoch),'w')
        target.write("val_name, avg_accuracy, precision, recall, f1 score, mean iou \n")
        target.write(class_names_string)

        scores_list = []
        class_scores_list = []
        precision_list = []
        recall_list = []
        f1_list = []
        iou_list = []


        # Do the validation on a small set of validation images
        for ind in val_indices:
            input_image = np.float32(load_image(val_input_names[ind])[:args.crop_height, :args.crop_width])
            #input_image[:, :, 0] -= 103.939
            #input_image[:, :, 1] -= 116.779
            #input_image[:, :, 2] -= 123.68

            input_image = np.expand_dims(input_image, axis=0)/255.0
            gt = load_image(val_output_names[ind])[:args.crop_height, :args.crop_width]
            gt = helpers.reverse_one_hot(helpers.one_hot_it(gt, label_values))
            #img_ar = np.array(gt)
            file_name = utils.filepath_to_name(val_input_names[ind])
            input_l = []
        for _ in range(len(gpus)):
            input_l.append(input_image)
            input_l = np.squeeze(np.stack(input_l, axis=1))
        if len(gpus) == 1:
            input_l = np.expand_dims(input_l, axis=0)
        if model != 'ssunet':
            output_image = sess.run(network,feed_dict={input:input_l, keep_prob:1.0})#, wavelet1:wav1, wavelet2:wav2, wavelet3: wav3, wavelet4: wav4, keep_prob:1.0})
        else:
            output_image, aux_out = sess.run(network,feed_dict={input:input_image, keep_prob:1.0})#, wavelet1:wav1, wavelet2:wav2, wavelet3: wav3, wavelet4: wav4, keep_prob:1.0})
            output_image = np.array(aux_out[0,:,:,:])
            output_image = helpers.reverse_one_hot(output_image)
            out_vis_image = helpers.colour_code_segmentation(output_image, label_values)
            cv2.imwrite("%s/%04d/%s_aux_pred.png"%(check,epoch, file_name),cv2.cvtColor(np.uint8(out_vis_image), cv2.COLOR_RGB2BGR))


            output_image = np.array(output_image[0,:,:,:])
            output_image = helpers.reverse_one_hot(output_image)
            out_vis_image = helpers.colour_code_segmentation(output_image, label_values)

            accuracy, class_accuracies, prec, rec, f1, iou = utils.evaluate_segmentation(pred=output_image, label=gt, num_classes=num_classes)

            target.write("\n %s, %f, %f, %f, %f, %f \n"%(file_name, accuracy, prec, rec, f1, iou))
            for item in class_accuracies:
                target.write(", %f"%(item))
            target.write("\n")

            scores_list.append(accuracy)
            class_scores_list.append(class_accuracies)
            precision_list.append(prec)
            recall_list.append(rec)
            f1_list.append(f1)
            iou_list.append(iou)

            gt = helpers.colour_code_segmentation(gt, label_values)

            im = cv2.imread(val_input_names[ind], -1)
            file_name = os.path.basename(val_input_names[ind])
            file_name = os.path.splitext(file_name)[0]
            cv2.imwrite("%s/%04d/%s_pred.png"%(check,epoch, file_name),cv2.cvtColor(np.uint8(out_vis_image), cv2.COLOR_RGB2BGR))
            cv2.imwrite("%s/%04d/%s_gt.png"%(check,epoch, file_name),cv2.cvtColor(np.uint8(gt), cv2.COLOR_RGB2BGR))
            cv2.imwrite("%s/%04d/%s_img.png"%(check,epoch, file_name),im)


        avg_score = np.mean(scores_list)
        class_avg_scores = np.mean(class_scores_list, axis=0)
        avg_scores_per_epoch.append(avg_score)
        avg_precision = np.mean(precision_list)
        avg_recall = np.mean(recall_list)
        avg_f1 = np.mean(f1_list)
        avg_iou = np.mean(iou_list)


        target.write("\n\n")
        target.write("%s, %s, %s, %s, %s"%('avg_score', 'avg_precision', 'avg_recall', 'avg_f1', 'avg_iou'))
        target.write("%f, %f, %f, %f, %f"%(avg_score, avg_precision, avg_recall, avg_f1, avg_iou))
        target.write("\n\n")
        for index, item in enumerate(class_avg_scores):
            target.write("%s = %f" % (class_names_list[index], item))
            target.write("\n")
        #target.write("\n")
        #target.write(" %04d = %f"% (epoch, avg_score))
        #target.write(" %04d:"% (epoch))
        #target.write("Validation precision = ", avg_precision)
        #target.write("Validation recall = ", avg_recall)
        #target.write("Validation F1 score = ", avg_f1)
        #target.write("Validation IoU score = ", avg_iou)

        target.close()

        print("\nAverage validation accuracy for epoch # %04d = %f"% (epoch, avg_score))
        print("Model name %s"%args.model)
        print("Average per class validation accuracies for epoch # %04d:"% (epoch))
        for index, item in enumerate(class_avg_scores):
            print("%s = %f" % (class_names_list[index], item))
        print("Validation precision = ", avg_precision)
        print("Validation recall = ", avg_recall)
        print("Validation F1 score = ", avg_f1)
        print("Validation IoU score = ", avg_iou)

        epoch_time=time.time()-epoch_st
        remain_time=epoch_time*(args.num_epochs-1-epoch)
        m, s = divmod(remain_time, 60)
        h, m = divmod(m, 60)
        if s!=0:
            train_time="Remaining training time = %d hours %d minutes %d seconds\n"%(h,m,s)
        else:
            train_time="Remaining training time : Training completed.\n"
        utils.LOG(train_time)
        scores_list = []

    fig = plt.figure(figsize=(11,8))
    ax1 = fig.add_subplot(111)


    ax1.plot(range(args.num_epochs), avg_scores_per_epoch)
    ax1.set_title("Average validation accuracy vs epochs")
    ax1.set_xlabel("Epoch")
    ax1.set_ylabel("Avg. val. accuracy")


    plt.savefig('accuracy_vs_epochs.png')

    plt.clf()

    ax1 = fig.add_subplot(111)


    ax1.plot(range(args.num_epochs), avg_loss_per_epoch)
    ax1.set_title("Average loss vs epochs")
    ax1.set_xlabel("Epoch")
    ax1.set_ylabel("Current loss")

    plt.savefig('loss_vs_epochs.png')

elif args.mode == "test":
    print("\n***** Begin testing *****")
    print("Dataset -->", args.dataset)
    print("Model -->", args.model)
    print("Crop Height -->", args.crop_height)
    print("Crop Width -->", args.crop_width)
    print("Num Classes -->", num_classes)
    print("")

    # Create directories if needed
    if not os.path.isdir("%s"%("Val")):
            os.makedirs("%s"%("Val"))

    target=open("%s/val_scores.csv"%("Val"),'w')
    target.write("val_name, avg_accuracy, precision, recall, f1 score, mean iou %s\n" % (class_names_string))
    scores_list = []
    class_scores_list = []
    precision_list = []
    recall_list = []
    f1_list = []
    iou_list = []
    run_times_list = []

    # Run testing on ALL test images
    for ind in range(len(val_input_names)):
        sys.stdout.write("\rRunning test image %d / %d"%(ind+1, len(val_input_names)))
        sys.stdout.flush()

        input_image = np.expand_dims(np.float32(load_image(val_input_names[ind])[:args.crop_height, :args.crop_width]),axis=0)/255.0
        gt = load_image(val_output_names[ind])[:args.crop_height, :args.crop_width]
        gt = helpers.reverse_one_hot(helpers.one_hot_it(gt, label_values))

        st = time.time()
        output_image = sess.run(network,feed_dict={input:input_image})

        run_times_list.append(time.time()-st)

        output_image = np.array(output_image[0,:,:,:])

        output_image = helpers.reverse_one_hot(output_image)
        #print(output_image)
        # exit(1)
        out_vis_image = helpers.colour_code_segmentation(output_image, label_values)

        #accuracy, class_accuracies, prec, rec, f1, iou = utils.evaluate_segmentation(pred=output_image, label=gt, num_classes=num_classes)

        file_name = utils.filepath_to_name(val_input_names[ind])
        #target.write("%s, %f, %f, %f, %f, %f"%(file_name, accuracy, prec, rec, f1, iou))
        #for item in class_accuracies:
            #target.write(", %f"%(item))
        #target.write("\n")

        #scores_list.append(accuracy)
        #class_scores_list.append(class_accuracies)
        #precision_list.append(prec)
        #recall_list.append(rec)
        #f1_list.append(f1)
        #iou_list.append(iou)

        gt = helpers.colour_code_segmentation(gt, label_values)
        im = cv2.imread(val_input_names[ind])
        cv2.imwrite("%s/%s_pred.png"%("Val", file_name),cv2.cvtColor(np.uint8(out_vis_image), cv2.COLOR_RGB2BGR))
        cv2.imwrite("%s/%s_img.png"%("Val", file_name),im)

        cv2.imwrite("%s/%s_gt.png"%("Val", file_name),cv2.cvtColor(np.uint8(gt), cv2.COLOR_RGB2BGR))


    #target.close()

    #avg_score = np.mean(scores_list)
    #class_avg_scores = np.mean(class_scores_list, axis=0)
    #avg_precision = np.mean(precision_list)
    #avg_recall = np.mean(recall_list)
    #avg_f1 = np.mean(f1_list)
    #avg_iou = np.mean(iou_list)
    #avg_time = np.mean(run_times_list)


    #target.write("%s, %f, %f, %f, %f, %f"%(file_name, accuracy, prec, rec, f1, iou))
    #target.close()

    #print("Average test accuracy = ", avg_score)
    #print("Average per class test accuracies = \n")
    #for index, item in enumerate(class_avg_scores):
        #print("%s = %f" % (class_names_list[index], item))
    #print("Average precision = ", avg_precision)
    #print("Average recall = ", avg_recall)
    #print("Average F1 score = ", avg_f1)
    #rint("Average mean IoU score = ", avg_iou)
    #print("Average run time = ", avg_time)


elif args.mode == "predict":

    if args.image is None:
        ValueError("You must pass an image path when using prediction mode.")

    print("\n***** Begin prediction *****")
    print("Dataset -->", args.dataset)
    print("Model -->", args.model)
    print("Crop Height -->", args.crop_height)
    print("Crop Width -->", args.crop_width)
    print("Num Classes -->", num_classes)
    print("Image -->", args.image)
    print("")
    for ind in range(len(test_input_names)):
        sys.stdout.write("\rRunning prediction image %d / %d"%(ind+1, len(test_input_names)))
        sys.stdout.flush()

        input_image = np.expand_dims(np.float32(load_image(test_input_names[ind])[:args.crop_height, :args.crop_width]),axis=0)/255.0

        st = time.time()
        output_image = sess.run(network,feed_dict={input:input_image})

        run_time = time.time()-st

        output_image = np.array(output_image[0,:,:,:])
        output_image = helpers.reverse_one_hot(output_image)
        out_vis_image = helpers.colour_code_segmentation(output_image, class_dict)
        file_name = utils.filepath_to_name(test_input_names[ind])
        cv2.imwrite("%s/%s_pred.png"%("Test", file_name),cv2.cvtColor(np.uint8(out_vis_image), cv2.COLOR_RGB2BGR))

else:
    ValueError("Invalid mode selected.")