text: # Copyright 2016 Google Inc. 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.
  # ==============================================================================
  """A library to train Inception using multiple GPU's with synchronous updates.
  """
  from __future__ import absolute_import
  from __future__ import division
  from __future__ import print_function
  
  import copy
  from datetime import datetime
  import os.path
  import re
  import time
  
  import numpy as np
  import tensorflow as tf
  
  from NerveSegmentation import image_processing
  from NerveSegmentation import inception_model as inception
  from NerveSegmentation.slim import slim
  
  FLAGS = tf.app.flags.FLAGS
  
  tf.app.flags.DEFINE_string('train_dir', '/tmp/imagenet_train',
                             """Directory where to write event logs """
                             """and checkpoint.""")
  tf.app.flags.DEFINE_integer('max_steps', 10000000,
                              """Number of batches to run.""")
  tf.app.flags.DEFINE_string('subset', 'train',
                             """Either 'train' or 'test'.""")
  
  # Flags governing the hardware employed for running TensorFlow.
  tf.app.flags.DEFINE_integer('num_gpus', 1,
                              """How many GPUs to use.""")
  tf.app.flags.DEFINE_boolean('log_device_placement', False,
                              """Whether to log device placement.""")
  
  # Flags governing the type of training.
  tf.app.flags.DEFINE_boolean('fine_tune', False,
                              """If set, randomly initialize the final layer """
                              """of weights in order to train the network on a """
                              """new task.""")
  tf.app.flags.DEFINE_string('pretrained_model_checkpoint_path', '',
                             """If specified, restore this pretrained model """
                             """before beginning any training.""")
  
  # **IMPORTANT**
  # Please note that this learning rate schedule is heavily dependent on the
  # hardware architecture, batch size and any changes to the model architecture
  # specification. Selecting a finely tuned learning rate schedule is an
  # empirical process that requires some experimentation. Please see README.md
  # more guidance and discussion.
  #
  # With 8 Tesla K40's and a batch size = 256, the following setup achieves
  # precision@1 = 73.5% after 100 hours and 100K steps (20 epochs).
  # Learning rate decay factor selected from http://arxiv.org/abs/1404.5997.
  tf.app.flags.DEFINE_float('initial_learning_rate', 0.001,
                            """Initial learning rate.""")
  tf.app.flags.DEFINE_float('num_epochs_per_decay', 30.0,
                            """Epochs after which learning rate decays.""")
  tf.app.flags.DEFINE_float('learning_rate_decay_factor', 0.0000001,
                            """Learning rate decay factor.""")
  
  
  def _tower_loss(images, labels, num_classes, scope):
      """Calculate the total loss on a single tower running the ImageNet model.
  
      We perform 'batch splitting'. This means that we cut up a batch across
      multiple GPU's. For instance, if the batch size = 32 and num_gpus = 2,
      then each tower will operate on an batch of 16 images.
  
      Args:
        images: Images. 4D tensor of size [batch_size, FLAGS.image_size,
                                           FLAGS.image_size, 3].
        labels: 1-D integer Tensor of [batch_size].
        num_classes: number of classes
        scope: unique prefix string identifying the ImageNet tower, e.g.
          'tower_0'.
  
      Returns:
         Tensor of shape [] containing the total loss for a batch of data
      """
      # When fine-tuning a model, we do not restore the logits but instead we
      # randomly initialize the logits. The number of classes in the output of the
      # logit is the number of classes in specified Dataset.
      restore_logits = not FLAGS.fine_tune
  
      # Build inference Graph.
      logits = inception.inference(images, num_classes, for_training=True,
                                   restore_logits=restore_logits,
                                   scope=scope)
  
      # Build the portion of the Graph calculating the losses. Note that we will
      # assemble the total_loss using a custom function below.
      split_batch_size = images.get_shape().as_list()[0]
      inception.loss(logits, labels, batch_size=split_batch_size)
  
      # Assemble all of the losses for the current tower only.
      losses = tf.get_collection(slim.losses.LOSSES_COLLECTION, scope)
  
      # Calculate the total loss for the current tower.
      regularization_losses = tf.get_collection(tf.GraphKeys.REGULARIZATION_LOSSES)
      total_loss = tf.add_n(losses + regularization_losses, name='total_loss')
  
      # Compute the moving average of all individual losses and the total loss.
      loss_averages = tf.train.ExponentialMovingAverage(0.9, name='avg')
      loss_averages_op = loss_averages.apply(losses + [total_loss])
  
      # Attach a scalar summmary to all individual losses and the total loss; do the
      # same for the averaged version of the losses.
      for l in losses + [total_loss]:
          # Remove 'tower_[0-9]/' from the name in case this is a multi-GPU training
          # session. This helps the clarity of presentation on TensorBoard.
          loss_name = re.sub('%s_[0-9]*/' % inception.TOWER_NAME, '', l.op.name)
          # Name each loss as '(raw)' and name the moving average version of the loss
          # as the original loss name.
          tf.scalar_summary(loss_name + ' (raw)', l)
          tf.scalar_summary(loss_name, loss_averages.average(l))
  
      with tf.control_dependencies([loss_averages_op]):
          total_loss = tf.identity(total_loss)
      return total_loss
  
  
  def _average_gradients(tower_grads):
      """Calculate the average gradient for each shared variable across all towers.
  
      Note that this function provides a synchronization point across all towers.
  
      Args:
        tower_grads: List of lists of (gradient, variable) tuples. The outer list
          is over individual gradients. The inner list is over the gradient
          calculation for each tower.
      Returns:
         List of pairs of (gradient, variable) where the gradient has been averaged
         across all towers.
      """
      average_grads = []
      for grad_and_vars in zip(*tower_grads):
          # Note that each grad_and_vars looks like the following:
          #   ((grad0_gpu0, var0_gpu0), ... , (grad0_gpuN, var0_gpuN))
          grads = []
          for g, _ in grad_and_vars:
              # Add 0 dimension to the gradients to represent the tower.
              expanded_g = tf.expand_dims(g, 0)
  
              # Append on a 'tower' dimension which we will average over below.
              grads.append(expanded_g)
  
          # Average over the 'tower' dimension.
          grad = tf.concat(0, grads)
          grad = tf.reduce_mean(grad, 0)
  
          # Keep in mind that the Variables are redundant because they are shared
          # across towers. So .. we will just return the first tower's pointer to
          # the Variable.
          v = grad_and_vars[0][1]
          grad_and_var = (grad, v)
          average_grads.append(grad_and_var)
      return average_grads
  
  
  def train(dataset):
      """Train on dataset for a number of steps."""
      with tf.Graph().as_default(), tf.device('/cpu:0'):
          # Create a variable to count the number of train() calls. This equals the
          # number of batches processed * FLAGS.num_gpus.
          global_step = tf.get_variable(
              'global_step', [],
              initializer=tf.constant_initializer(0), trainable=False)
  
          # Calculate the learning rate schedule.
          num_batches_per_epoch = (dataset.num_examples_per_epoch() /
                                   FLAGS.batch_size)
          decay_steps = int(num_batches_per_epoch * FLAGS.num_epochs_per_decay)
  
          # Decay the learning rate exponentially based on the number of steps.
          lr = tf.train.exponential_decay(FLAGS.initial_learning_rate,
                                          global_step,
                                          decay_steps,
                                          FLAGS.learning_rate_decay_factor,
                                          staircase=True)
  
          # Create an optimizer that performs gradient descent.
          opt = tf.train.AdamOptimizer(lr)
  
          # Get images and labels for ImageNet and split the batch across GPUs.
          assert FLAGS.batch_size % FLAGS.num_gpus == 0, (
              'Batch size must be divisible by number of GPUs')
          split_batch_size = int(FLAGS.batch_size / FLAGS.num_gpus)
  
          # Override the number of preprocessing threads to account for the increased
          # number of GPU towers.
          num_preprocess_threads = FLAGS.num_preprocess_threads * FLAGS.num_gpus
          images, labels = image_processing.distorted_inputs(
              dataset,
              num_preprocess_threads=num_preprocess_threads)
  
          input_summaries = copy.copy(tf.get_collection(tf.GraphKeys.SUMMARIES))
  
          # Number of classes in the Dataset label set plus 1.
          # Label 0 is reserved for an (unused) background class.
          num_classes = dataset.num_classes() + 1
  
          # Split the batch of images and labels for towers.
          images_splits = tf.split(0, FLAGS.num_gpus, images)
          labels_splits = tf.split(0, FLAGS.num_gpus, labels)
  
          # Calculate the gradients for each model tower.
          tower_grads = []
          for i in xrange(FLAGS.num_gpus):
              with tf.device('/gpu:%d' % i):
                  with tf.name_scope('%s_%d' % (inception.TOWER_NAME, i)) as scope:
                      # Force all Variables to reside on the CPU.
                      with slim.arg_scope([slim.variables.variable], device='/cpu:0'):
                          # Calculate the loss for one tower of the ImageNet model. This
                          # function constructs the entire ImageNet model but shares the
                          # variables across all towers.
                          loss = _tower_loss(images_splits[i], labels_splits[i], num_classes,
                                             scope)
  
                      # Reuse variables for the next tower.
                      tf.get_variable_scope().reuse_variables()
  
                      # Retain the summaries from the final tower.
                      summaries = tf.get_collection(tf.GraphKeys.SUMMARIES, scope)
  
                      # Retain the Batch Normalization updates operations only from the
                      # final tower. Ideally, we should grab the updates from all towers
                      # but these stats accumulate extremely fast so we can ignore the
                      # other stats from the other towers without significant detriment.
                      batchnorm_updates = tf.get_collection(slim.ops.UPDATE_OPS_COLLECTION,
                                                            scope)
  
                      # Calculate the gradients for the batch of data on this ImageNet
                      # tower.
                      grads = opt.compute_gradients(loss)
  
                      # Keep track of the gradients across all towers.
                      tower_grads.append(grads)
  
          # We must calculate the mean of each gradient. Note that this is the
          # synchronization point across all towers.
          grads = _average_gradients(tower_grads)
  
          # Add a summaries for the input processing and global_step.
          summaries.extend(input_summaries)
  
          # Add a summary to track the learning rate.
          summaries.append(tf.scalar_summary('learning_rate', lr))
  
          # Add histograms for gradients.
          for grad, var in grads:
              if grad is not None:
                  summaries.append(
                      tf.histogram_summary(var.op.name + '/gradients', grad))
  
          # Apply the gradients to adjust the shared variables.
          apply_gradient_op = opt.apply_gradients(grads, global_step=global_step)
  
          # Add histograms for trainable variables.
          for var in tf.trainable_variables():
              summaries.append(tf.histogram_summary(var.op.name, var))
  
          # Track the moving averages of all trainable variables.
          # Note that we maintain a "double-average" of the BatchNormalization
          # global statistics. This is more complicated then need be but we employ
          # this for backward-compatibility with our previous models.
          variable_averages = tf.train.ExponentialMovingAverage(
              inception.MOVING_AVERAGE_DECAY, global_step)
  
          # Another possiblility is to use tf.slim.get_variables().
          variables_to_average = (tf.trainable_variables() +
                                  tf.moving_average_variables())
          variables_averages_op = variable_averages.apply(variables_to_average)
  
          # Group all updates to into a single train op.
          batchnorm_updates_op = tf.group(*batchnorm_updates)
          train_op = tf.group(apply_gradient_op, variables_averages_op,
                              batchnorm_updates_op)
  
          # Create a saver.
          saver = tf.train.Saver(tf.all_variables())
  
          # Build the summary operation from the last tower summaries.
          summary_op = tf.merge_summary(summaries)
  
          # Build an initialization operation to run below.
          init = tf.initialize_all_variables()
  
          # Start running operations on the Graph. allow_soft_placement must be set to
          # True to build towers on GPU, as some of the ops do not have GPU
          # implementations.
          sess = tf.Session(config=tf.ConfigProto(
              allow_soft_placement=True,
              log_device_placement=FLAGS.log_device_placement))
          sess.run(init)
  
          if FLAGS.pretrained_model_checkpoint_path:
              assert tf.gfile.Exists(FLAGS.pretrained_model_checkpoint_path)
              variables_to_restore = tf.get_collection(
                  slim.variables.VARIABLES_TO_RESTORE)
              restorer = tf.train.Saver(variables_to_restore)
              restorer.restore(sess, FLAGS.pretrained_model_checkpoint_path)
              print('%s: Pre-trained model restored from %s' %
                    (datetime.now(), FLAGS.pretrained_model_checkpoint_path))
  
          # Start the queue runners.
          tf.train.start_queue_runners(sess=sess)
  
          summary_writer = tf.train.SummaryWriter(
              FLAGS.train_dir,
              graph_def=sess.graph.as_graph_def(add_shapes=True))
  
          for step in xrange(FLAGS.max_steps):
              start_time = time.time()
              _, loss_value = sess.run([train_op, loss])
              duration = time.time() - start_time
  
              assert not np.isnan(loss_value), 'Model diverged with loss = NaN'
  
              if step % 10 == 0:
                  examples_per_sec = FLAGS.batch_size / float(duration)
                  format_str = ('%s: step %d, loss = %.2f (%.1f examples/sec; %.3f '
                                'sec/batch)')
                  print(format_str % (datetime.now(), step, loss_value,
                                      examples_per_sec, duration))
  
              if step % 100 == 0:
                  summary_str = sess.run(summary_op)
                  summary_writer.add_summary(summary_str, step)
  
              # Save the model checkpoint periodically.
              if step % 5000 == 0 or (step + 1) == FLAGS.max_steps:
                  checkpoint_path = os.path.join(FLAGS.train_dir, 'model.ckpt')
                  saver.save(sess, checkpoint_path, global_step=step)
  