Spatial Transformer model

Shorten STN summary in README

relinked to data files

adding license header, editing AUTHORS file

adding tensorflow version

AUTHORS

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 # The email address is not required for organizations.
 
 Google Inc.
+David Dao <daviddao@broad.mit.edu>

transformer/README.md

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+# Spatial Transformer Network
+
+The Spatial Transformer Network [1] allows the spatial manipulation of data within the network.
+
+<div align="center">
+  <img width="600px" src="http://i.imgur.com/ExGDVul.png"><br><br>
+</div>
+
+### API 
+
+A Spatial Transformer Network implemented in Tensorflow 0.7 and based on [2].
+
+#### How to use
+
+<div align="center">
+  <img src="http://i.imgur.com/gfqLV3f.png"><br><br>
+</div>
+
+```python
+transformer(U, theta, downsample_factor=1)
+```
+
+#### Parameters
+
+    U : float 
+        The output of a convolutional net should have the
+        shape [num_batch, height, width, num_channels]. 
+    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
+        
+
+#### Notes
+To initialize the network to the identity transform init ``theta`` to :
+
+```python
+identity = np.array([[1., 0., 0.],
+                    [0., 1., 0.]]) 
+identity = identity.flatten()
+theta = tf.Variable(initial_value=identity)
+```        
+
+#### Experiments
+
+<div align="center">
+  <img width="600px" src="http://i.imgur.com/HtCBYk2.png"><br><br>
+</div>
+
+We used cluttered MNIST. Left column are the input images, right are the attended parts of the image by an STN.
+
+All experiments were run in Tensorflow 0.7.
+
+### References
+
+[1] Jaderberg, Max, et al. "Spatial Transformer Networks." arXiv preprint arXiv:1506.02025 (2015)
+
+[2] https://github.com/skaae/transformer_network/blob/master/transformerlayer.py

transformer/cluttered_mnist.py

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+# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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
+
+# %% Load data
+mnist_cluttered = np.load('./data/mnist_sequence1_sample_5distortions5x5.npz')
+
+X_train = mnist_cluttered['X_train']
+y_train = mnist_cluttered['y_train']
+X_valid = mnist_cluttered['X_valid']
+y_valid = mnist_cluttered['y_valid']
+X_test = mnist_cluttered['X_test']
+y_test = mnist_cluttered['y_test']
+
+# % turn from dense to one hot representation
+Y_train = dense_to_one_hot(y_train, n_classes=10)
+Y_valid = dense_to_one_hot(y_valid, n_classes=10)
+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]) 
+y = tf.placeholder(tf.float32, [None, 10])
+
+# %% Since x is currently [batch, height*width], we need to reshape to a
+# 4-D tensor to use it in a convolutional graph.  If one component of
+# `shape` is the special value -1, the size of that dimension is
+# computed so that the total size remains constant.  Since we haven't
+# defined the batch dimension's shape yet, we use -1 to denote this
+# 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
+# %% 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
+initial = initial.astype('float32')
+initial = initial.flatten()
+b_fc_loc2 = tf.Variable(initial_value=initial, name='b_fc_loc2')
+
+# %% Define the two layer localisation network
+h_fc_loc1 = tf.nn.tanh(tf.matmul(x, W_fc_loc1) + b_fc_loc1)
+# %% We can add dropout for regularizing and to reduce overfitting like so:
+keep_prob = tf.placeholder(tf.float32)
+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 setup the first convolutional layer
+# Weight matrix is [height x width x input_channels x output_channels]
+filter_size = 3
+n_filters_1 = 16
+W_conv1 = weight_variable([filter_size, filter_size, 1, n_filters_1])
+
+# %% Bias is [output_channels]
+b_conv1 = bias_variable([n_filters_1])
+
+# %% Now we can build a graph which does the first layer of convolution:
+# we define our stride as batch x height x width x channels
+# instead of pooling, we use strides of 2 and more layers
+# with smaller filters.
+
+h_conv1 = tf.nn.relu(
+    tf.nn.conv2d(input=h_trans,
+                 filter=W_conv1,
+                 strides=[1, 2, 2, 1],
+                 padding='SAME') +
+    b_conv1)
+
+# %% And just like the first layer, add additional layers to create
+# a deep net
+n_filters_2 = 16
+W_conv2 = weight_variable([filter_size, filter_size, n_filters_1, n_filters_2])
+b_conv2 = bias_variable([n_filters_2])
+h_conv2 = tf.nn.relu(
+    tf.nn.conv2d(input=h_conv1,
+                 filter=W_conv2,
+                 strides=[1, 2, 2, 1],
+                 padding='SAME') +
+    b_conv2)
+
+# %% We'll now reshape so we can connect to a fully-connected layer:
+h_conv2_flat = tf.reshape(h_conv2, [-1, 10 * 10 * n_filters_2])
+
+# %% Create a fully-connected layer:
+n_fc = 1024
+W_fc1 = weight_variable([10 * 10 * n_filters_2, n_fc])
+b_fc1 = bias_variable([n_fc])
+h_fc1 = tf.nn.relu(tf.matmul(h_conv2_flat, W_fc1) + b_fc1)
+
+h_fc1_drop = tf.nn.dropout(h_fc1, keep_prob)
+
+# %% And finally our softmax layer:
+W_fc2 = weight_variable([n_fc, 10])
+b_fc2 = bias_variable([10])
+y_pred = tf.nn.softmax(tf.matmul(h_fc1_drop, W_fc2) + b_fc2)
+
+# %% Define loss/eval/training functions
+cross_entropy = -tf.reduce_sum(y * tf.log(y_pred))
+opt = tf.train.AdamOptimizer()
+optimizer = opt.minimize(cross_entropy)
+grads = opt.compute_gradients(cross_entropy, [b_fc_loc2])
+
+# %% Monitor accuracy
+correct_prediction = tf.equal(tf.argmax(y_pred, 1), tf.argmax(y, 1))
+accuracy = tf.reduce_mean(tf.cast(correct_prediction, 'float'))
+
+# %% We now create a new session to actually perform the initialization the
+# variables:
+sess = tf.Session()
+sess.run(tf.initialize_all_variables())
+
+
+# %% We'll now train in minibatches and report accuracy, loss:
+iter_per_epoch = 100
+n_epochs = 500
+train_size = 10000
+
+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_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
+                   })
+            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={
+    #        x: batch_xs, keep_prob: 1.0})
+    #print(theta[0])

transformer/data/README.md

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+### How to get the data
+
+#### Cluttered MNIST
+
+The cluttered MNIST dataset can be found here [1] or can be generated via [2].
+
+Settings used for `cluttered_mnist.py` :
+
+```python
+
+ORG_SHP = [28, 28]
+OUT_SHP = [40, 40]
+NUM_DISTORTIONS = 8
+dist_size = (5, 5) 
+
+```
+
+[1] https://github.com/daviddao/spatial-transformer-tensorflow
+
+[2] https://github.com/skaae/recurrent-spatial-transformer-code/blob/master/MNIST_SEQUENCE/create_mnist_sequence.py

transformer/example.py

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+# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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
+
+# %% Create a batch of three images (1600 x 1200)
+# %% 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')
+
+# %% 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')
+
+# %% 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 
+    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 = 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)
+
+# %% Run session
+sess = tf.Session()
+sess.run(tf.initialize_all_variables())
+y = sess.run(h_trans, feed_dict={x: batch})
+
+# plt.imshow(y[0])