Fix bug in transformer model: Changed the examples to specify the output size (#155)

* Changed the examples to specify the output size instead of the downsample_factor.

This is required by PR #57

* Address flake8 errors.

* Update readme and parameter descriptions.

transformer/README.md

@@ -28,13 +28,8 @@ transformer(U, theta, downsample_factor=1)
     theta: float   
         The output of the
         localisation network should be [num_batch, 6].
-    downsample_factor : float
-        A value of 1 will keep the original size of the image
-        Values larger than 1 will downsample the image. 
-        Values below 1 will upsample the image
-        example image: height = 100, width = 200
-        downsample_factor = 2
-        output image will then be 50, 100
+    out_size: tuple of two ints
+        The size of the output of the network
         
     
 #### Notes

transformer/cluttered_mnist.py

@@ -11,13 +11,11 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-# ==============================================================================
+# =============================================================================
 import tensorflow as tf
 from spatial_transformer import transformer
-from scipy import ndimage
 import numpy as np
-import matplotlib.pyplot as plt
-from tf_utils import conv2d, linear, weight_variable, bias_variable, dense_to_one_hot
+from tf_utils import weight_variable, bias_variable, dense_to_one_hot
 
 # %% Load data
 mnist_cluttered = np.load('./data/mnist_sequence1_sample_5distortions5x5.npz')
@@ -37,7 +35,7 @@ Y_test = dense_to_one_hot(y_test, n_classes=10)
 # %% Graph representation of our network
 
 # %% Placeholders for 40x40 resolution
-x = tf.placeholder(tf.float32, [None, 1600]) 
+x = tf.placeholder(tf.float32, [None, 1600])
 y = tf.placeholder(tf.float32, [None, 10])
 
 # %% Since x is currently [batch, height*width], we need to reshape to a
@@ -48,13 +46,15 @@ y = tf.placeholder(tf.float32, [None, 10])
 # dimension should not change size.
 x_tensor = tf.reshape(x, [-1, 40, 40, 1])
 
-# %% We'll setup the two-layer localisation network to figure out the parameters for an affine transformation of the input
+# %% We'll setup the two-layer localisation network to figure out the
+# %% parameters for an affine transformation of the input
 # %% Create variables for fully connected layer
 W_fc_loc1 = weight_variable([1600, 20])
 b_fc_loc1 = bias_variable([20])
 
 W_fc_loc2 = weight_variable([20, 6])
-initial = np.array([[1.,0, 0],[0,1.,0]]) # Use identity transformation as starting point
+# Use identity transformation as starting point
+initial = np.array([[1., 0, 0], [0, 1., 0]])
 initial = initial.astype('float32')
 initial = initial.flatten()
 b_fc_loc2 = tf.Variable(initial_value=initial, name='b_fc_loc2')
@@ -67,8 +67,10 @@ h_fc_loc1_drop = tf.nn.dropout(h_fc_loc1, keep_prob)
 # %% Second layer
 h_fc_loc2 = tf.nn.tanh(tf.matmul(h_fc_loc1_drop, W_fc_loc2) + b_fc_loc2)
 
-# %% We'll create a spatial transformer module to identify discriminative patches
-h_trans = transformer(x_tensor, h_fc_loc2, downsample_factor=1)
+# %% We'll create a spatial transformer module to identify discriminative
+# %% patches
+out_size = (40, 40)
+h_trans = transformer(x_tensor, h_fc_loc2, out_size)
 
 # %% We'll setup the first convolutional layer
 # Weight matrix is [height x width x input_channels x output_channels]
@@ -140,33 +142,32 @@ iter_per_epoch = 100
 n_epochs = 500
 train_size = 10000
 
-indices = np.linspace(0,10000 - 1,iter_per_epoch)
+indices = np.linspace(0, 10000 - 1, iter_per_epoch)
 indices = indices.astype('int')
 
 for epoch_i in range(n_epochs):
     for iter_i in range(iter_per_epoch - 1):
-    	batch_xs = X_train[indices[iter_i]:indices[iter_i+1]]
+        batch_xs = X_train[indices[iter_i]:indices[iter_i+1]]
         batch_ys = Y_train[indices[iter_i]:indices[iter_i+1]]
 
         if iter_i % 10 == 0:
             loss = sess.run(cross_entropy,
-                   feed_dict={
-                       x: batch_xs,
-                       y: batch_ys,
-                       keep_prob: 1.0
-                   })
+                            feed_dict={
+                                x: batch_xs,
+                                y: batch_ys,
+                                keep_prob: 1.0
+                            })
             print('Iteration: ' + str(iter_i) + ' Loss: ' + str(loss))
 
         sess.run(optimizer, feed_dict={
             x: batch_xs, y: batch_ys, keep_prob: 0.8})
-        
-        
-    print('Accuracy: ' + str(sess.run(accuracy,
-                   feed_dict={
-                       x: X_valid,
-                       y: Y_valid,
-                       keep_prob: 1.0
-                   })))
-    #theta = sess.run(h_fc_loc2, feed_dict={
+
+    print('Accuracy (%d): ' % epoch_i + str(sess.run(accuracy,
+                                                     feed_dict={
+                                                         x: X_valid,
+                                                         y: Y_valid,
+                                                         keep_prob: 1.0
+                                                     })))
+    # theta = sess.run(h_fc_loc2, feed_dict={
     #        x: batch_xs, keep_prob: 1.0})
-    #print(theta[0])
+    # print(theta[0])

transformer/example.py

@@ -17,42 +17,45 @@ from spatial_transformer import transformer
 from scipy import ndimage
 import numpy as np
 import matplotlib.pyplot as plt
-from tf_utils import conv2d, linear, weight_variable, bias_variable
 
 # %% Create a batch of three images (1600 x 1200)
-# %% Image retrieved from https://raw.githubusercontent.com/skaae/transformer_network/master/cat.jpg
+# %% Image retrieved from:
+# %% https://raw.githubusercontent.com/skaae/transformer_network/master/cat.jpg
 im = ndimage.imread('cat.jpg')
 im = im / 255.
 im = im.reshape(1, 1200, 1600, 3)
 im = im.astype('float32')
 
+# %% Let the output size of the transformer be half the image size.
+out_size = (600, 800)
+
 # %% Simulate batch
 batch = np.append(im, im, axis=0)
 batch = np.append(batch, im, axis=0)
 num_batch = 3
 
 x = tf.placeholder(tf.float32, [None, 1200, 1600, 3])
-x = tf.cast(batch,'float32')
+x = tf.cast(batch, 'float32')
 
 # %% Create localisation network and convolutional layer
 with tf.variable_scope('spatial_transformer_0'):
 
     # %% Create a fully-connected layer with 6 output nodes
-    n_fc = 6 
+    n_fc = 6
     W_fc1 = tf.Variable(tf.zeros([1200 * 1600 * 3, n_fc]), name='W_fc1')
 
     # %% Zoom into the image
-    initial = np.array([[0.5,0, 0],[0,0.5,0]]) 
+    initial = np.array([[0.5, 0, 0], [0, 0.5, 0]])
     initial = initial.astype('float32')
     initial = initial.flatten()
 
     b_fc1 = tf.Variable(initial_value=initial, name='b_fc1')
-    h_fc1 = tf.matmul(tf.zeros([num_batch ,1200 * 1600 * 3]), W_fc1) + b_fc1
-    h_trans = transformer(x, h_fc1, downsample_factor=2)
+    h_fc1 = tf.matmul(tf.zeros([num_batch, 1200 * 1600 * 3]), W_fc1) + b_fc1
+    h_trans = transformer(x, h_fc1, out_size)
 
 # %% Run session
 sess = tf.Session()
 sess.run(tf.initialize_all_variables())
 y = sess.run(h_trans, feed_dict={x: batch})
 
-# plt.imshow(y[0])
+# plt.imshow(y[0])

transformer/spatial_transformer.py

@@ -14,22 +14,23 @@
 # ==============================================================================
 import tensorflow as tf
 
+
 def transformer(U, theta, out_size, name='SpatialTransformer', **kwargs):
     """Spatial Transformer Layer
-    
+
     Implements a spatial transformer layer as described in [1]_.
     Based on [2]_ and edited by David Dao for Tensorflow.
-    
+
     Parameters
     ----------
-    U : float 
+    U : float
         The output of a convolutional net should have the
-        shape [num_batch, height, width, num_channels]. 
-    theta: float   
+        shape [num_batch, height, width, num_channels].
+    theta: float
         The output of the
         localisation network should be [num_batch, 6].
-    out_size: tuple of two floats
-        The size of the output of the network
+    out_size: tuple of two ints
+        The size of the output of the network (height, width)
 
     References
     ----------
@@ -37,24 +38,25 @@ def transformer(U, theta, out_size, name='SpatialTransformer', **kwargs):
             Max Jaderberg, Karen Simonyan, Andrew Zisserman, Koray Kavukcuoglu
             Submitted on 5 Jun 2015
     .. [2]  https://github.com/skaae/transformer_network/blob/master/transformerlayer.py
-            
+
     Notes
     -----
     To initialize the network to the identity transform init
     ``theta`` to :
         identity = np.array([[1., 0., 0.],
-                             [0., 1., 0.]]) 
+                             [0., 1., 0.]])
         identity = identity.flatten()
         theta = tf.Variable(initial_value=identity)
-        
+
     """
-    
+
     def _repeat(x, n_repeats):
         with tf.variable_scope('_repeat'):
-            rep = tf.transpose(tf.expand_dims(tf.ones(shape=tf.pack([n_repeats,])),1),[1,0])
+            rep = tf.transpose(
+                tf.expand_dims(tf.ones(shape=tf.pack([n_repeats, ])), 1), [1, 0])
             rep = tf.cast(rep, 'int32')
-            x = tf.matmul(tf.reshape(x,(-1, 1)), rep)
-            return tf.reshape(x,[-1])
+            x = tf.matmul(tf.reshape(x, (-1, 1)), rep)
+            return tf.reshape(x, [-1])
 
     def _interpolate(im, x, y, out_size):
         with tf.variable_scope('_interpolate'):
@@ -69,13 +71,13 @@ def transformer(U, theta, out_size, name='SpatialTransformer', **kwargs):
             height_f = tf.cast(height, 'float32')
             width_f = tf.cast(width, 'float32')
             out_height = out_size[0]
-            out_width = out_size[1] 
+            out_width = out_size[1]
             zero = tf.zeros([], dtype='int32')
             max_y = tf.cast(tf.shape(im)[1] - 1, 'int32')
             max_x = tf.cast(tf.shape(im)[2] - 1, 'int32')
 
             # scale indices from [-1, 1] to [0, width/height]
-            x = (x + 1.0)*(width_f) / 2.0 
+            x = (x + 1.0)*(width_f) / 2.0
             y = (y + 1.0)*(height_f) / 2.0
 
             # do sampling
@@ -98,8 +100,9 @@ def transformer(U, theta, out_size, name='SpatialTransformer', **kwargs):
             idx_c = base_y0 + x1
             idx_d = base_y1 + x1
 
-            # use indices to lookup pixels in the flat image and restore channels dim
-            im_flat = tf.reshape(im,tf.pack([-1, channels]))
+            # use indices to lookup pixels in the flat image and restore
+            # channels dim
+            im_flat = tf.reshape(im, tf.pack([-1, channels]))
             im_flat = tf.cast(im_flat, 'float32')
             Ia = tf.gather(im_flat, idx_a)
             Ib = tf.gather(im_flat, idx_b)
@@ -111,13 +114,13 @@ def transformer(U, theta, out_size, name='SpatialTransformer', **kwargs):
             x1_f = tf.cast(x1, 'float32')
             y0_f = tf.cast(y0, 'float32')
             y1_f = tf.cast(y1, 'float32')
-            wa = tf.expand_dims(((x1_f-x) * (y1_f-y)),1)
-            wb = tf.expand_dims(((x1_f-x) * (y-y0_f)),1)
-            wc = tf.expand_dims(((x-x0_f) * (y1_f-y)),1)
-            wd = tf.expand_dims(((x-x0_f) * (y-y0_f)),1)
+            wa = tf.expand_dims(((x1_f-x) * (y1_f-y)), 1)
+            wb = tf.expand_dims(((x1_f-x) * (y-y0_f)), 1)
+            wc = tf.expand_dims(((x-x0_f) * (y1_f-y)), 1)
+            wd = tf.expand_dims(((x-x0_f) * (y-y0_f)), 1)
             output = tf.add_n([wa*Ia, wb*Ib, wc*Ic, wd*Id])
             return output
-    
+
     def _meshgrid(height, width):
         with tf.variable_scope('_meshgrid'):
             # This should be equivalent to:
@@ -126,12 +129,12 @@ def transformer(U, theta, out_size, name='SpatialTransformer', **kwargs):
             #  ones = np.ones(np.prod(x_t.shape))
             #  grid = np.vstack([x_t.flatten(), y_t.flatten(), ones])
             x_t = tf.matmul(tf.ones(shape=tf.pack([height, 1])),
-                        tf.transpose(tf.expand_dims(tf.linspace(-1.0, 1.0, width),1),[1,0])) 
-            y_t = tf.matmul(tf.expand_dims(tf.linspace(-1.0, 1.0, height),1),
-                        tf.ones(shape=tf.pack([1, width]))) 
+                            tf.transpose(tf.expand_dims(tf.linspace(-1.0, 1.0, width), 1), [1, 0]))
+            y_t = tf.matmul(tf.expand_dims(tf.linspace(-1.0, 1.0, height), 1),
+                            tf.ones(shape=tf.pack([1, width])))
 
-            x_t_flat = tf.reshape(x_t,(1, -1))
-            y_t_flat = tf.reshape(y_t,(1, -1))
+            x_t_flat = tf.reshape(x_t, (1, -1))
+            y_t_flat = tf.reshape(y_t, (1, -1))
 
             ones = tf.ones_like(x_t_flat)
             grid = tf.concat(0, [x_t_flat, y_t_flat, ones])
@@ -141,7 +144,7 @@ def transformer(U, theta, out_size, name='SpatialTransformer', **kwargs):
         with tf.variable_scope('_transform'):
             num_batch = tf.shape(input_dim)[0]
             height = tf.shape(input_dim)[1]
-            width = tf.shape(input_dim)[2]            
+            width = tf.shape(input_dim)[2]
             num_channels = tf.shape(input_dim)[3]
             theta = tf.reshape(theta, (-1, 2, 3))
             theta = tf.cast(theta, 'float32')
@@ -150,37 +153,39 @@ def transformer(U, theta, out_size, name='SpatialTransformer', **kwargs):
             height_f = tf.cast(height, 'float32')
             width_f = tf.cast(width, 'float32')
             out_height = out_size[0]
-            out_width = out_size[1] 
+            out_width = out_size[1]
             grid = _meshgrid(out_height, out_width)
-            grid = tf.expand_dims(grid,0)
-            grid = tf.reshape(grid,[-1])
-            grid = tf.tile(grid,tf.pack([num_batch]))
-            grid = tf.reshape(grid,tf.pack([num_batch, 3, -1])) 
-            
+            grid = tf.expand_dims(grid, 0)
+            grid = tf.reshape(grid, [-1])
+            grid = tf.tile(grid, tf.pack([num_batch]))
+            grid = tf.reshape(grid, tf.pack([num_batch, 3, -1]))
+
             # Transform A x (x_t, y_t, 1)^T -> (x_s, y_s)
             T_g = tf.batch_matmul(theta, grid)
-            x_s = tf.slice(T_g, [0,0,0], [-1,1,-1])
-            y_s = tf.slice(T_g, [0,1,0], [-1,1,-1])
-            x_s_flat = tf.reshape(x_s,[-1])
-            y_s_flat = tf.reshape(y_s,[-1])
+            x_s = tf.slice(T_g, [0, 0, 0], [-1, 1, -1])
+            y_s = tf.slice(T_g, [0, 1, 0], [-1, 1, -1])
+            x_s_flat = tf.reshape(x_s, [-1])
+            y_s_flat = tf.reshape(y_s, [-1])
 
             input_transformed = _interpolate(
-                  input_dim, x_s_flat, y_s_flat,
-                  out_size)
+                input_dim, x_s_flat, y_s_flat,
+                out_size)
 
-            output = tf.reshape(input_transformed, tf.pack([num_batch, out_height, out_width, num_channels]))
+            output = tf.reshape(
+                input_transformed, tf.pack([num_batch, out_height, out_width, num_channels]))
             return output
-    
+
     with tf.variable_scope(name):
         output = _transform(theta, U, out_size)
         return output
 
+
 def batch_transformer(U, thetas, out_size, name='BatchSpatialTransformer'):
     """Batch Spatial Transformer Layer
 
     Parameters
     ----------
-    
+
     U : float
         tensor of inputs [num_batch,height,width,num_channels]
     thetas : float
@@ -196,4 +201,3 @@ def batch_transformer(U, thetas, out_size, name='BatchSpatialTransformer'):
         indices = [[i]*num_transforms for i in xrange(num_batch)]
         input_repeated = tf.gather(U, tf.reshape(indices, [-1]))
         return transformer(input_repeated, thetas, out_size)
-