cnn.py

import time
import math
import random
import cv2
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import tensorflow as tf
import dataset
from sklearn.metrics import confusion_matrix
from datetime import timedelta
import tensorflow as tf

# Convolutional Layer 1.
filter_size1 = 5          # Convolution filters are 5 x 5 pixels.
num_filters1 = 16         # There are 16 of these filters.

# Convolutional Layer 2.
filter_size2 = 5          # Convolution filters are 5 x 5 pixels.
num_filters2 = 36         # There are 36 of these filters.

# Fully-connected layer.
fc_size = 128             # Number of neurons in fully-connected layer.

# Number of color channels for the images: 1 channel for gray-scale.
num_channels = 1

# image dimensions (only squares for now)
img_size = 28

# class info
classes = ['0', '1', '2']
num_classes = len(classes)

# Size of image when flattened to a single dimension
img_size_flat = img_size * img_size

# Tuple with height and width of images used to reshape arrays.
img_shape = (img_size, img_size)

# batch size
batch_size = 64

# validation split
validation_size = .16

# how long to wait after validation loss stops improving before terminating training
early_stopping = None  # use None if you don't want to implement early stoping

train_path = 'data/train/'
test_path = 'data/test/'
checkpoint_dir = "ckpts/"

data = dataset.read_train_sets(train_path, img_size, classes, validation_size=validation_size)
test_images, test_ids = dataset.read_test_set(test_path, img_size)

print("Size of:")
print("- Training-set:\t\t{}".format(len(data.train.labels)))
print("- Test-set:\t\t{}".format(len(test_images)))
print("- Validation-set:\t{}".format(len(data.valid.labels)))


def plot_images(images, cls_true, cls_pred=None):
    if len(images) == 0:
        print("no images to show")
        return
    else:
        random_indices = random.sample(range(len(images)), min(len(images), 9))

    images, cls_true = zip(*[(images[i], cls_true[i]) for i in random_indices])

    # Create figure with 3x3 sub-plots.
    fig, axes = plt.subplots(3, 3)
    fig.subplots_adjust(hspace=0.3, wspace=0.3)

    for i, ax in enumerate(axes.flat):
        # Plot image.
        ax.imshow(images[i].reshape(img_size, img_size))

        # Show true and predicted classes.
        if cls_pred is None:
            xlabel = "True: {0}".format(cls_true[i])
        else:
            xlabel = "True: {0}, Pred: {1}".format(cls_true[i], cls_pred[i])

        # Show the classes as the label on the x-axis.
        ax.set_xlabel(xlabel)

        # Remove ticks from the plot.
        ax.set_xticks([])
        ax.set_yticks([])

    # Ensure the plot is shown correctly with multiple plots
    # in a single Notebook cell.
    plt.show()

# Get some random images and their labels from the train set.
images, cls_true  = data.train.images, data.train.cls

# Plot the images and labels using our helper-function above.
# plot_images(images=images, cls_true=cls_true)


def  new_weights(shape):
    return tf.Variable(tf.truncated_normal(shape, stddev=0.05))

def new_biases(length):
    return tf.Variable(tf.constant(0.05, shape=[length]))

def new_conv_layer(input,              # The previous layer.
                   num_input_channels, # Num. channels in prev. layer.
                   filter_size,        # Width and height of each filter.
                   num_filters,        # Number of filters.
                   use_pooling=True):  # Use 2x2 max-pooling.

    # Shape of the filter-weights for the convolution.
    # This format is determined by the TensorFlow API.
    shape = [filter_size, filter_size, num_input_channels, num_filters]

    # Create new weights aka. filters with the given shape.
    weights = new_weights(shape=shape)

    # Create new biases, one for each filter.
    biases = new_biases(length=num_filters)

    # Create the TensorFlow operation for convolution.
    # Note the strides are set to 1 in all dimensions.
    # The first and last stride must always be 1,
    # because the first is for the image-number and
    # the last is for the input-channel.
    # But e.g. strides=[1, 2, 2, 1] would mean that the filter
    # is moved 2 pixels across the x- and y-axis of the image.
    # The padding is set to 'SAME' which means the input image
    # is padded with zeroes so the size of the output is the same.
    layer = tf.nn.conv2d(input=input,
                         filter=weights,
                         strides=[1, 1, 1, 1],
                         padding='SAME')

    # Add the biases to the results of the convolution.
    # A bias-value is added to each filter-channel.
    layer += biases

    # Use pooling to down-sample the image resolution?
    if use_pooling:
        # This is 2x2 max-pooling, which means that we
        # consider 2x2 windows and select the largest value
        # in each window. Then we move 2 pixels to the next window.
        layer = tf.nn.max_pool(value=layer,
                               ksize=[1, 2, 2, 1],
                               strides=[1, 2, 2, 1],
                               padding='SAME')

    # Rectified Linear Unit (ReLU).
    # It calculates max(x, 0) for each input pixel x.
    # This adds some non-linearity to the formula and allows us
    # to learn more complicated functions.
    layer = tf.nn.relu(layer)

    # Note that ReLU is normally executed before the pooling,
    # but since relu(max_pool(x)) == max_pool(relu(x)) we can
    # save 75% of the relu-operations by max-pooling first.

    # We return both the resulting layer and the filter-weights
    # because we will plot the weights later.
    return layer, weights


def flatten_layer(layer):
    # Get the shape of the input layer.
    layer_shape = layer.get_shape()

    # The shape of the input layer is assumed to be:
    # layer_shape == [num_images, img_height, img_width, num_channels]

    # The number of features is: img_height * img_width * num_channels
    # We can use a function from TensorFlow to calculate this.
    num_features = layer_shape[1:4].num_elements()

    # Reshape the layer to [num_images, num_features].
    # Note that we just set the size of the second dimension
    # to num_features and the size of the first dimension to -1
    # which means the size in that dimension is calculated
    # so the total size of the tensor is unchanged from the reshaping.
    layer_flat = tf.reshape(layer, [-1, num_features])

    # The shape of the flattened layer is now:
    # [num_images, img_height * img_width * num_channels]

    # Return both the flattened layer and the number of features.
    return layer_flat, num_features

def new_fc_layer(input,          # The previous layer.
                 num_inputs,     # Num. inputs from prev. layer.
                 num_outputs,    # Num. outputs.
                 use_relu=True): # Use Rectified Linear Unit (ReLU)?

    # Create new weights and biases.
    weights = new_weights(shape=[num_inputs, num_outputs])
    biases = new_biases(length=num_outputs)

    # Calculate the layer as the matrix multiplication of
    # the input and weights, and then add the bias-values.
    layer = tf.matmul(input, weights) + biases

    # Use ReLU?
    if use_relu:
        layer = tf.nn.relu(layer)

    return layer

x = tf.placeholder(tf.float32, shape=[None, img_size_flat], name='x')
x_image = tf.reshape(x, [-1, img_size, img_size, num_channels])

y_true = tf.placeholder(tf.float32, shape=[None, num_classes], name='y_true')
y_true_cls = tf.argmax(y_true, axis=1)


layer_conv1, weights_conv1 = \
    new_conv_layer(input=x_image,
                   num_input_channels=num_channels,
                   filter_size=filter_size1,
                   num_filters=num_filters1,
                   use_pooling=True)

layer_conv2, weights_conv2 = \
    new_conv_layer(input=layer_conv1,
                   num_input_channels=num_filters1,
                   filter_size=filter_size2,
                   num_filters=num_filters2,

                   use_pooling=True)
layer_flat, num_features = flatten_layer(layer_conv2)
layer_fc1 = new_fc_layer(input=layer_flat,
                         num_inputs=num_features,
                         num_outputs=fc_size,
                         use_relu=True)

layer_fc2 = new_fc_layer(input=layer_fc1,
                         num_inputs=fc_size,
                         num_outputs=num_classes,
                         use_relu=False)

y_pred = tf.nn.softmax(layer_fc2)
y_pred_cls = tf.argmax(y_pred, axis=1)
cross_entropy = tf.nn.softmax_cross_entropy_with_logits(logits=layer_fc2,
                                                        labels=y_true)
cost = tf.reduce_mean(cross_entropy)

optimizer = tf.train.AdamOptimizer(learning_rate=1e-4).minimize(cost)
correct_prediction = tf.equal(y_pred_cls, y_true_cls)
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))

session = tf.Session()
session.run(tf.global_variables_initializer())
train_batch_size = 64

# Counter for total number of iterations performed so far.
# total_iterations = 0


def print_progress(epoch, feed_dict_train, feed_dict_validate, val_loss):
    # Calculate the accuracy on the training-set.
    acc = session.run(accuracy, feed_dict=feed_dict_train)
    val_acc = session.run(accuracy, feed_dict=feed_dict_validate)
    msg = "Epoch {0} --- Training Accuracy: {1:>6.1%}, Validation Accuracy: {2:>6.1%}, Validation Loss: {3:.3f}"
    print(msg.format(epoch + 1, acc, val_acc, val_loss))



# ======================================================================================================
def optimize(epoch):
    # Ensure we update the global variable rather than a local copy.
    # global total_iterations

    # Start-time used for printing time-usage below.
    start_time = time.time()

    best_val_loss = float("inf")
    patience = 0

    num_iteration = int(epoch*data.train.num_examples/batch_size)
    for i in range(num_iteration):
        # Get a batch of training examples.
        # x_batch now holds a batch of images and
        # y_true_batch are the true labels for those images.
        x_batch, y_true_batch, _, cls_batch = data.train.next_batch(train_batch_size)
        x_valid_batch, y_valid_batch, _, valid_cls_batch = data.valid.next_batch(train_batch_size)

        # Convert shape from [num examples, rows, columns, depth]
        # to [num examples, flattened image shape]

        x_batch = x_batch.reshape(train_batch_size, img_size_flat)
        x_valid_batch = x_valid_batch.reshape(train_batch_size, img_size_flat)


        # Put the batch into a dict with the proper names
        # for placeholder variables in the TensorFlow graph.
        feed_dict_train = {x: x_batch,
                           y_true: y_true_batch}

        feed_dict_validate = {x: x_valid_batch,
                              y_true: y_valid_batch}



        # Run the optimizer using this batch of training data.
        # TensorFlow assigns the variables in feed_dict_train
        # to the placeholder variables and then runs the optimizer.
        session.run(optimizer, feed_dict=feed_dict_train)

        # Print status at end of each epoch (defined as full pass through training dataset).
        if i % int(data.train.num_examples / batch_size) == 0:
            val_loss = session.run(cost, feed_dict=feed_dict_validate)
            epoch = int(i / int(data.train.num_examples / batch_size))

            print_progress(epoch, feed_dict_train, feed_dict_validate, val_loss)

            if early_stopping:
                if val_loss < best_val_loss:
                    best_val_loss = val_loss
                    patience = 0
                else:
                    patience += 1

                if patience == early_stopping:
                    break

    # Ending time.
    end_time = time.time()

    # Difference between start and end-times.
    time_dif = end_time - start_time

    # Print the time-usage.
    print("Time elapsed: " + str(timedelta(seconds=int(round(time_dif)))))


# ======================================================================================================

optimize(epoch=10)

def plot_example_errors(cls_pred, correct):
    # This function is called from print_test_accuracy() below.

    # cls_pred is an array of the predicted class-number for
    # all images in the test-set.

    # correct is a boolean array whether the predicted class
    # is equal to the true class for each image in the test-set.

    # Negate the boolean array.
    incorrect = (correct == False)

    # Get the images from the test-set that have been
    # incorrectly classified.
    images = data.train.images[incorrect]

    # Get the predicted classes for those images.
    cls_pred = cls_pred[incorrect]

    # Get the true classes for those images.
    cls_true = data.train.cls[incorrect]

    # Plot the first 9 images.
    plot_images(images=images[0:9],
                cls_true=cls_true[0:9],
                cls_pred=cls_pred[0:9])



def plot_confusion_matrix(cls_pred):
    # This is called from print_test_accuracy() below.

    # cls_pred is an array of the predicted class-number for
    # all images in the test-set.

    # Get the true classifications for the test-set.
    cls_true = data.train.cls

    # Get the confusion matrix using sklearn.
    cm = confusion_matrix(y_true=cls_true,
                          y_pred=cls_pred)

    # Print the confusion matrix as text.
    print(cm)

    # Plot the confusion matrix as an image.
    plt.matshow(cm)

    # Make various adjustments to the plot.
    plt.colorbar()
    tick_marks = np.arange(num_classes)
    plt.xticks(tick_marks, range(num_classes))
    plt.yticks(tick_marks, range(num_classes))
    plt.xlabel('Predicted')
    plt.ylabel('True')

    # Ensure the plot is shown correctly with multiple plots
    # in a single Notebook cell.
    plt.show()

# Split the test-set into smaller batches of this size.
test_batch_size = 256

# Counter for total number of iterations performed so far.
# total_iterations = 0


def print_validation_accuracy(show_example_errors=False,
                              show_confusion_matrix=False):
    # Number of images in the test-set.
    num_test = len(data.valid.images)

    # Allocate an array for the predicted classes which
    # will be calculated in batches and filled into this array.
    cls_pred = np.zeros(shape=num_test, dtype=np.int)

    # Now calculate the predicted classes for the batches.
    # We will just iterate through all the batches.
    # There might be a more clever and Pythonic way of doing this.

    # The starting index for the next batch is denoted i.
    i = 0

    while i < num_test:
        # The ending index for the next batch is denoted j.
        j = min(i + batch_size, num_test)

        # Get the images from the test-set between index i and j.
        images = data.valid.images[i:j, :].reshape(batch_size, img_size_flat)

        # Get the associated labels.
        labels = data.valid.labels[i:j, :]

        # Create a feed-dict with these images and labels.
        feed_dict = {x: images,
                     y_true: labels}

        # Calculate the predicted class using TensorFlow.
        cls_pred[i:j] = session.run(y_pred_cls, feed_dict=feed_dict)

        # Set the start-index for the next batch to the
        # end-index of the current batch.
        i = j

    cls_true = np.array(data.valid.cls)
    cls_pred = np.array([classes[x] for x in cls_pred])

    # Create a boolean array whether each image is correctly classified.
    correct = (cls_true == cls_pred)

    # Calculate the number of correctly classified images.
    # When summing a boolean array, False means 0 and True means 1.
    correct_sum = correct.sum()

    # Classification accuracy is the number of correctly classified
    # images divided by the total number of images in the test-set.
    acc = float(correct_sum) / num_test

    # Print the accuracy.
    msg = "Accuracy on Test-Set: {0:.1%} ({1} / {2})"
    print(msg.format(acc, correct_sum, num_test))

    # Plot some examples of mis-classifications, if desired.
    if show_example_errors:
        print("Example errors:")
        plot_example_errors(cls_pred=cls_pred, correct=correct)

    # Plot the confusion matrix, if desired.
    if show_confusion_matrix:
        print("Confusion Matrix:")
        plot_confusion_matrix(cls_pred=cls_pred)

print_validation_accuracy()



# with tf.Session() as sess:
#     writer = tf.summary.FileWriter('./data/sample', sess.graph)
#     tf.summary.scalar('Accuracy', accuracy)
#     tf.summary.scalar('Cost', cross_entropy)
#     tf.summary.histogram('Cost', cost)
#     summaries = tf.summary.merge_all()
#     sess.run(tf.global_variables_initializer())

# from tensorboard import main as tb
# tf.flags.FLAGS.logdir = "data/"
# tb.main()