Many changes

• Removing legacy code
• Port to the new ci
• Estimate the size of the tfrecords file that will be created
• bug-fixes
• Add a new architecture for patch-based CNN
• Refactored the scripts to use the new click tools
• Changed the compute_statistics script completely
• Removed the unused predict_generic script
• Removed the unused train script and renamed train_generic to train

Fixes #50 (closed) #52 (closed) #48 (closed)

bob/learn/tensorflow/network/SimpleCNN.py

 import tensorflow as tf
 
 
-def base_architecture(input_layer, mode, kernerl_size, data_format, **kwargs):
+def create_conv_layer(inputs, mode, data_format, endpoints, number, filters,
+                      kernel_size, pool_size, pool_strides,
+                      add_batch_norm=False):
+    bn_axis = 1 if data_format.lower() == 'channels_first' else 3
+    training = mode == tf.estimator.ModeKeys.TRAIN
+
+    if add_batch_norm:
+        activation = None
+    else:
+        activation = tf.nn.relu
+
+    name = 'conv{}'.format(number)
+    conv = tf.layers.conv2d(
+        inputs=inputs,
+        filters=filters,
+        kernel_size=kernel_size,
+        padding="same",
+        activation=activation,
+        data_format=data_format)
+    endpoints[name] = conv
+
+    if add_batch_norm:
+        name = 'bn{}'.format(number)
+        bn = tf.layers.batch_normalization(
+            conv, axis=bn_axis, training=training)
+        endpoints[name] = bn
+
+        name = 'activation{}'.format(number)
+        bn_act = tf.nn.relu(bn)
+        endpoints[name] = bn_act
+    else:
+        bn_act = conv
+
+    name = 'pool{}'.format(number)
+    pool = tf.layers.max_pooling2d(
+        inputs=bn_act, pool_size=pool_size, strides=pool_strides,
+        padding='same', data_format=data_format)
+    endpoints[name] = pool
+
+    return pool
+
+
+def base_architecture(input_layer, mode, kernerl_size, data_format,
+                      add_batch_norm=False, **kwargs):
+    training = mode == tf.estimator.ModeKeys.TRAIN
     # Keep track of all the endpoints
     endpoints = {}
 
@@ -9,38 +53,18 @@ def base_architecture(input_layer, mode, kernerl_size, data_format, **kwargs):
     # Computes 32 features using a kernerl_size filter with ReLU
     # activation.
     # Padding is added to preserve width and height.
-    conv1 = tf.layers.conv2d(
-        inputs=input_layer,
-        filters=32,
-        kernel_size=kernerl_size,
-        padding="same",
-        activation=tf.nn.relu,
-        data_format=data_format)
-    endpoints['conv1'] = conv1
-
-    # Pooling Layer #1
-    # First max pooling layer with a 2x2 filter and stride of 2
-    pool1 = tf.layers.max_pooling2d(
-        inputs=conv1, pool_size=[2, 2], strides=2, data_format=data_format)
-    endpoints['pool1'] = pool1
+    pool1 = create_conv_layer(
+        inputs=input_layer, mode=mode, data_format=data_format,
+        endpoints=endpoints, number=1, filters=32, kernel_size=kernerl_size,
+        pool_size=(2, 2), pool_strides=2, add_batch_norm=add_batch_norm)
 
     # Convolutional Layer #2
     # Computes 64 features using a kernerl_size filter.
     # Padding is added to preserve width and height.
-    conv2 = tf.layers.conv2d(
-        inputs=pool1,
-        filters=64,
-        kernel_size=kernerl_size,
-        padding="same",
-        activation=tf.nn.relu,
-        data_format=data_format)
-    endpoints['conv2'] = conv2
-
-    # Pooling Layer #2
-    # Second max pooling layer with a 2x2 filter and stride of 2
-    pool2 = tf.layers.max_pooling2d(
-        inputs=conv2, pool_size=[2, 2], strides=2, data_format=data_format)
-    endpoints['pool2'] = pool2
+    pool2 = create_conv_layer(
+        inputs=pool1, mode=mode, data_format=data_format,
+        endpoints=endpoints, number=2, filters=64, kernel_size=kernerl_size,
+        pool_size=(2, 2), pool_strides=2, add_batch_norm=add_batch_norm)
 
     # Flatten tensor into a batch of vectors
     # TODO: use tf.layers.flatten in tensorflow 1.4 and above
@@ -49,13 +73,30 @@ def base_architecture(input_layer, mode, kernerl_size, data_format, **kwargs):
 
     # Dense Layer
     # Densely connected layer with 1024 neurons
+    if add_batch_norm:
+        activation = None
+    else:
+        activation = tf.nn.relu
+
     dense = tf.layers.dense(
-        inputs=pool2_flat, units=1024, activation=tf.nn.relu)
+        inputs=pool2_flat, units=1024, activation=activation)
     endpoints['dense'] = dense
 
+    if add_batch_norm:
+        name = 'bn{}'.format(3)
+        bn = tf.layers.batch_normalization(
+            dense, axis=1, training=training)
+        endpoints[name] = bn
+
+        name = 'activation{}'.format(3)
+        bn_act = tf.nn.relu(bn)
+        endpoints[name] = bn_act
+    else:
+        bn_act = dense
+
     # Add dropout operation; 0.6 probability that element will be kept
     dropout = tf.layers.dropout(
-        inputs=dense, rate=0.4, training=mode == tf.estimator.ModeKeys.TRAIN)
+        inputs=bn_act, rate=0.4, training=mode == tf.estimator.ModeKeys.TRAIN)
     endpoints['dropout'] = dropout
 
     return dropout, endpoints
@@ -67,12 +108,14 @@ def architecture(input_layer,
                  n_classes=2,
                  data_format='channels_last',
                  reuse=False,
+                 add_batch_norm=False,
                  **kwargs):
 
     with tf.variable_scope('SimpleCNN', reuse=reuse):
 
-        dropout, endpoints = base_architecture(input_layer, mode, kernerl_size,
-                                               data_format)
+        dropout, endpoints = base_architecture(
+            input_layer, mode, kernerl_size, data_format,
+            add_batch_norm=add_batch_norm)
         # Logits layer
         # Input Tensor Shape: [batch_size, 1024]
         # Output Tensor Shape: [batch_size, n_classes]
@@ -94,6 +137,7 @@ def model_fn(features, labels, mode, params=None, config=None):
         'kernerl_size': params.get('kernerl_size', None),
         'n_classes': params.get('n_classes', None),
         'data_format': params.get('data_format', None),
+        'add_batch_norm': params.get('add_batch_norm', None)
     }
     arch_kwargs = {k: v for k, v in arch_kwargs.items() if v is not None}
 
@@ -118,10 +162,14 @@ def model_fn(features, labels, mode, params=None, config=None):
 
     # Configure the training op
     if mode == tf.estimator.ModeKeys.TRAIN:
+        global_step = tf.train.get_or_create_global_step()
         optimizer = tf.train.GradientDescentOptimizer(
             learning_rate=learning_rate)
-        train_op = optimizer.minimize(
-            loss=loss, global_step=tf.train.get_or_create_global_step())
+        # for batch normalization to be updated as well:
+        update_ops = tf.get_collection(tf.GraphKeys.UPDATE_OPS)
+        with tf.control_dependencies(update_ops):
+            train_op = optimizer.minimize(
+                loss=loss, global_step=global_step)
         # Log accuracy and loss
         with tf.name_scope('train_metrics'):
             tf.summary.scalar('accuracy', accuracy[1])