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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 Accompanying code examples of the book "Introduction to Artificial Neural Networks and Deep Learning
Step1:  Chunking an Image Dataset for Minibatch Training using NumPy NPZ Archives
This notebook provides an example for how to organize a large dataset of images into chunks for quick access during minibatch learning. This approach uses NumPy .npz archive files and only requires having NumPy as a dependency so that this approach should be compatible with different Python-based machine learning and deep learning libraries and packages for further image (pre)processing and augmentation. 
While this approach performs reasonably well (sufficiently well for my applications), you may also be interested in TensorFlow's "Reading Data" guide to work with TfRecords and file queues.
0. The Dataset
Let's pretend we have a directory of images containing two subdirectories with images for training, validation, and testing. The following function will create such a dataset of images in PNG format locally for demonstration purposes.
Step2:  Note that the names of the subdirectories correspond directly to the class label of the images that are stored under it.
To make sure that the images look okay, the snippet below plots an example image from the subdirectory mnist_train/9/
Step3:  Note
Step4:  The .npz files we created are stored under a new directory, mnist_npz
Step5:  To check that the archiving worked correctly, we will now load one of those .npz archives. Note that we can now access each archive just like a python dictionary. Here the 'data' key contains the image data and the 'labels' key stores an array containing the corresponding class labels
Step6:  2. Loading Minibatches
The following cell implements a class for iterating over the MNIST images, based on the .npz archives, conveniently. 
Via the normalize parameter we additionally scale the image pixels to [0, 1] range, which typically helps with gradient-based optimization in practice.
The key functions (here
Step7:  The following for loop will iterate over the 45,000 training examples in our MNIST training set, yielding 50 images and labels at a time (note that we previously set aside 5000 training example as our validation datast).
Step8:  As we can see from the benchmark above, an iteration over one training epoch (45k images) is relatively fast.
Similarly, we could iterate over validation and test data via 
batch_loader.load_validation_epoch
batch_loader.load_test_epoch
3. Training a Model using TensorFlow's feed_dict
The following code demonstrate how we can feed our minibatches into a TensorFlow graph using a TensorFlow session's feed_dict.
Multilayer Perceptron Graph
Step9:  Training the Neural Network with Minibatches
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Python Code:
%load_ext watermark
%watermark -a 'Sebastian Raschka' -v -p tensorflow,numpy
Explanation: Accompanying code examples of the book "Introduction to Artificial Neural Networks and Deep Learning: A Practical Guide with Applications in Python" by Sebastian Raschka. All code examples are released under the MIT license. If you find this content useful, please consider supporting the work by buying a copy of the book.
Other code examples and content are available on GitHub. The PDF and ebook versions of the book are available through Leanpub.
End of explanation
# Note that executing the following code 
# cell will download the MNIST dataset
# and save all the 60,000 images as separate JPEG
# files. This might take a few minutes depending
# on your machine.
import numpy as np
from helper import mnist_export_to_jpg
np.random.seed(123)
mnist_export_to_jpg(path='./')
import os
for i in ('train', 'valid', 'test'):
    print('mnist_%s subdirectories' % i, os.listdir('mnist_%s' % i))
Explanation: Chunking an Image Dataset for Minibatch Training using NumPy NPZ Archives
This notebook provides an example for how to organize a large dataset of images into chunks for quick access during minibatch learning. This approach uses NumPy .npz archive files and only requires having NumPy as a dependency so that this approach should be compatible with different Python-based machine learning and deep learning libraries and packages for further image (pre)processing and augmentation. 
While this approach performs reasonably well (sufficiently well for my applications), you may also be interested in TensorFlow's "Reading Data" guide to work with TfRecords and file queues.
0. The Dataset
Let's pretend we have a directory of images containing two subdirectories with images for training, validation, and testing. The following function will create such a dataset of images in PNG format locally for demonstration purposes.
End of explanation
%matplotlib inline
import matplotlib.image as mpimg
import matplotlib.pyplot as plt
import os
some_img = os.path.join('./mnist_train/9/', os.listdir('./mnist_train/9/')[0])
img = mpimg.imread(some_img)
print(img.shape)
plt.imshow(img, cmap='binary');
Explanation: Note that the names of the subdirectories correspond directly to the class label of the images that are stored under it.
To make sure that the images look okay, the snippet below plots an example image from the subdirectory mnist_train/9/:
End of explanation
import numpy as np
import glob
def images_to_pickles(data_stempath='./mnist_', which_set='train', 
                      archive_size=5000, width=28, height=28, channels=1,
                      shuffle=False, seed=None):
    
    if not os.path.exists('%snpz' % data_stempath):
        os.mkdir('%snpz' % data_stempath)
        
    img_paths = [p for p in glob.iglob('%s%s/**/*.jpg' % 
                                   (data_stempath, which_set), recursive=True)]
    if shuffle:
        rgen = np.random.RandomState(seed)
        paths = rgen.shuffle(img_paths)
    
    idx, file_idx = 0, 1
    data = np.zeros((archive_size, height, width, channels), dtype=np.uint8)
    labels = np.zeros(archive_size, dtype=np.uint8)
    for path in img_paths:
        if idx >= archive_size - 1:
            idx = 0
            savepath = os.path.join('%snpz' % data_stempath, '%s_%d.npz' % 
                                    (which_set, file_idx))
            file_idx += 1
            np.savez(savepath, data=data, labels=labels)
        label = int(os.path.basename(os.path.dirname(path)))
        image = mpimg.imread(path)
        
        if len(image.shape) == 2:
            data[idx] = image[:, :, np.newaxis]
        labels[idx] = label
        idx += 1
images_to_pickles(which_set='train', shuffle=True, seed=1)
images_to_pickles(which_set='valid', shuffle=True, seed=1)
images_to_pickles(which_set='test', shuffle=True, seed=1)
Explanation: Note: The JPEG format introduces a few artifacts that we can see in the image above. In this case, we use JPEG instead of PNG. Here, JPEG is used for demonstration purposes since that's still format many image datasets are stored in.
1. Chunking Images into NumPy NPZ Archive Files
The following wrapper function creates .npz archive files training, testing, and validation. It will group images together into integer arrays that are then saved as .npz archive files. The number of rows (images) in each .npz archive will be equal to the archive_size argument.
End of explanation
os.listdir('mnist_npz')
Explanation: The .npz files we created are stored under a new directory, mnist_npz:
End of explanation
data = np.load('mnist_npz/test_1.npz')
print(data['data'].shape)
print(data['labels'].shape)
plt.imshow(data['data'][0][:, :, -1], cmap='binary');
print('Class label:', data['labels'][0])
Explanation: To check that the archiving worked correctly, we will now load one of those .npz archives. Note that we can now access each archive just like a python dictionary. Here the 'data' key contains the image data and the 'labels' key stores an array containing the corresponding class labels:
End of explanation
class BatchLoader():
    def __init__(self, minibatches_path, 
                 normalize=True):
        
        self.normalize = normalize
        self.train_batchpaths = [os.path.join(minibatches_path, f)
                                 for f in os.listdir(minibatches_path)
                                 if 'train' in f]
        self.valid_batchpaths = [os.path.join(minibatches_path, f)
                                 for f in os.listdir(minibatches_path)
                                 if 'valid' in f]
        self.test_batchpaths = [os.path.join(minibatches_path, f)
                                 for f in os.listdir(minibatches_path)
                                 if 'train' in f]
        self.num_train = 45000
        self.num_valid = 5000
        self.num_test = 10000
        self.n_classes = 10
    def load_train_epoch(self, batch_size=50, onehot=False,
                         shuffle_within=False, shuffle_paths=False,
                         seed=None):
        for batch_x, batch_y in self._load_epoch(which='train',
                                                 batch_size=batch_size,
                                                 onehot=onehot,
                                                 shuffle_within=shuffle_within,
                                                 shuffle_paths=shuffle_paths,
                                                 seed=seed):
            yield batch_x, batch_y
    def load_test_epoch(self, batch_size=50, onehot=False,
                        shuffle_within=False, shuffle_paths=False, 
                        seed=None):
        for batch_x, batch_y in self._load_epoch(which='test',
                                                 batch_size=batch_size,
                                                 onehot=onehot,
                                                 shuffle_within=shuffle_within,
                                                 shuffle_paths=shuffle_paths,
                                                 seed=seed):
            yield batch_x, batch_y
            
    def load_validation_epoch(self, batch_size=50, onehot=False,
                         shuffle_within=False, shuffle_paths=False, 
                         seed=None):
        for batch_x, batch_y in self._load_epoch(which='valid',
                                                 batch_size=batch_size,
                                                 onehot=onehot,
                                                 shuffle_within=shuffle_within,
                                                 shuffle_paths=shuffle_paths,
                                                 seed=seed):
            yield batch_x, batch_y
    def _load_epoch(self, which='train', batch_size=50, onehot=False,
                    shuffle_within=True, shuffle_paths=True, seed=None):
        if which == 'train':
            paths = self.train_batchpaths
        elif which == 'valid':
            paths = self.valid_batchpaths
        elif which == 'test':
            paths = self.test_batchpaths
        else:
            raise ValueError('`which` must be "train" or "test". Got %s.' %
                             which)
            
        rgen = np.random.RandomState(seed)
        if shuffle_paths:
            paths = rgen.shuffle(paths)
        for batch in paths:
            dct = np.load(batch)
            if onehot:
                labels = (np.arange(self.n_classes) == 
                          dct['labels'][:, None]).astype(np.uint8)
            else:
                labels = dct['labels']
            if self.normalize:
                # normalize to [0, 1] range
                data = dct['data'].astype(np.float32) / 255.
            else:
                data = dct['data']
            arrays = [data, labels]
            del dct
            indices = np.arange(arrays[0].shape[0])
            if shuffle_within:
                rgen.shuffle(indices)
            for start_idx in range(0, indices.shape[0] - batch_size + 1,
                                   batch_size):
                index_slice = indices[start_idx:start_idx + batch_size]
                yield (ary[index_slice] for ary in arrays)
Explanation: 2. Loading Minibatches
The following cell implements a class for iterating over the MNIST images, based on the .npz archives, conveniently. 
Via the normalize parameter we additionally scale the image pixels to [0, 1] range, which typically helps with gradient-based optimization in practice.
The key functions (here: generators) are
load_train_epoch
load_valid_epoch
load_test_epoch
These let us iterate over small chunks (determined via minibatch_size). Each of these functions will load the images from a particular .npz archive into memory (here: 5000 images) and yield minibatches of smaller or equal size (for example, 50 images at a time). Via the two shuffle parameters, we can further control if the images within each .npz archive should be shuffled, and if the order the .npz files are loaded should shuffled after each epoch. By setting onehot=True, the labels are converted into a onehot representation for convenience.
End of explanation
batch_loader = BatchLoader(minibatches_path='./mnist_npz/', 
                           normalize=True)
for batch_x, batch_y in batch_loader.load_train_epoch(batch_size=50, onehot=True):
    print(batch_x.shape)
    print(batch_y.shape)
    break
cnt = 0
for batch_x, batch_y in batch_loader.load_train_epoch(batch_size=50, onehot=True):
    cnt += batch_x.shape[0]
    
print('One training epoch contains %d images' % cnt)
def one_epoch():
    for batch_x, batch_y in batch_loader.load_train_epoch(batch_size=50, onehot=True):
        pass
    
% timeit one_epoch()
Explanation: The following for loop will iterate over the 45,000 training examples in our MNIST training set, yielding 50 images and labels at a time (note that we previously set aside 5000 training example as our validation datast).
End of explanation
import tensorflow as tf
##########################
### SETTINGS
##########################
# Hyperparameters
learning_rate = 0.1
training_epochs = 15
batch_size = 100
# Architecture
n_hidden_1 = 128
n_hidden_2 = 256
height, width = 28, 28
n_classes = 10
##########################
### GRAPH DEFINITION
##########################
g = tf.Graph()
with g.as_default():
    
    tf.set_random_seed(123)
    # Input data
    tf_x = tf.placeholder(tf.float32, [None, height, width, 1], name='features')
    tf_x_flat = tf.reshape(tf_x, shape=[-1, height*width])
    tf_y = tf.placeholder(tf.int32, [None, n_classes], name='targets')
    # Model parameters
    weights = {
        'h1': tf.Variable(tf.truncated_normal([width*height, n_hidden_1], stddev=0.1)),
        'h2': tf.Variable(tf.truncated_normal([n_hidden_1, n_hidden_2], stddev=0.1)),
        'out': tf.Variable(tf.truncated_normal([n_hidden_2, n_classes], stddev=0.1))
    }
    biases = {
        'b1': tf.Variable(tf.zeros([n_hidden_1])),
        'b2': tf.Variable(tf.zeros([n_hidden_2])),
        'out': tf.Variable(tf.zeros([n_classes]))
    }
    # Multilayer perceptron
    layer_1 = tf.add(tf.matmul(tf_x_flat, weights['h1']), biases['b1'])
    layer_1 = tf.nn.relu(layer_1)
    layer_2 = tf.add(tf.matmul(layer_1, weights['h2']), biases['b2'])
    layer_2 = tf.nn.relu(layer_2)
    out_layer = tf.matmul(layer_2, weights['out']) + biases['out']
    # Loss and optimizer
    loss = tf.nn.softmax_cross_entropy_with_logits(logits=out_layer, labels=tf_y)
    cost = tf.reduce_mean(loss, name='cost')
    optimizer = tf.train.GradientDescentOptimizer(learning_rate=learning_rate)
    train = optimizer.minimize(cost, name='train')
    # Prediction
    correct_prediction = tf.equal(tf.argmax(tf_y, 1), tf.argmax(out_layer, 1))
    accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32), name='accuracy')
Explanation: As we can see from the benchmark above, an iteration over one training epoch (45k images) is relatively fast.
Similarly, we could iterate over validation and test data via 
batch_loader.load_validation_epoch
batch_loader.load_test_epoch
3. Training a Model using TensorFlow's feed_dict
The following code demonstrate how we can feed our minibatches into a TensorFlow graph using a TensorFlow session's feed_dict.
Multilayer Perceptron Graph
End of explanation
##########################
### TRAINING & EVALUATION
##########################
batch_loader = BatchLoader(minibatches_path='./mnist_npz/', 
                           normalize=True)
# preload small validation set
# by unpacking the generator
[valid_data] = batch_loader.load_validation_epoch(batch_size=5000, 
                                                   onehot=True)
valid_x, valid_y = valid_data[0], valid_data[1]
del valid_data
with tf.Session(graph=g) as sess:
    sess.run(tf.global_variables_initializer())
    for epoch in range(training_epochs):
        avg_cost = 0.
        n_batches = 0
        for batch_x, batch_y in batch_loader.load_train_epoch(batch_size=batch_size, 
                                                              onehot=True, 
                                                              seed=epoch):
            n_batches += 1
            _, c = sess.run(['train', 'cost:0'], feed_dict={'features:0': batch_x,
                                                            'targets:0': batch_y.astype(np.int)})
            avg_cost += c
        
        train_acc = sess.run('accuracy:0', feed_dict={'features:0': batch_x,
                                                      'targets:0': batch_y})
        
        valid_acc = sess.run('accuracy:0', feed_dict={'features:0': valid_x,
                                                      'targets:0': valid_y})  
        
        print("Epoch: %03d | AvgCost: %.3f" % (epoch + 1, avg_cost / n_batches), end="")
        print(" | MbTrain/Valid ACC: %.3f/%.3f" % (train_acc, valid_acc))
        
        
    # imagine test set is too large to fit into memory:
    test_acc, cnt = 0., 0
    for test_x, test_y in batch_loader.load_test_epoch(batch_size=100, 
                                                       onehot=True):   
        cnt += 1
        acc = sess.run(accuracy, feed_dict={'features:0': test_x,
                                            'targets:0': test_y})
        test_acc += acc
    print('Test ACC: %.3f' % (test_acc / cnt))
Explanation: Training the Neural Network with Minibatches
End of explanation
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