def _layer(inputs, mode, layer_num, filters, kernel_size, dilation_rate,
is_mc_b, is_mc_g, use_expectation):
"""Layer building block of MeshNet.
Performs 3D convolution, activation, batch normalization, and dropout on
`inputs` tensor.
Args:
inputs : float `Tensor`, input tensor.
mode : string, a TensorFlow mode key.
layer_num : int, value to append to each operator name. This should be
the layer number in the network.
filters : int, number of 3D convolution filters.
kernel_size : int or tuple, size of 3D convolution kernel.
dilation_rate : int or tuple, rate of dilution in 3D convolution.
dropout_rate : float, the dropout rate between 0 and 1.
Returns:
`Tensor` of same type as `inputs`.
"""
training = mode == tf.estimator.ModeKeys.TRAIN
with tf.variable_scope('layer_{}'.format(layer_num)):
conv = vwn_conv.conv3d(inputs,
filters=filters,
kernel_size=kernel_size,
padding='SAME',
dilation_rate=dilation_rate,
activation=None,
is_mc=is_mc_g)
conv = concrete_dropout(conv,
is_mc_b,
filters,
use_expectation=use_expectation)
return tf.nn.relu(conv)
def model_fn(features,
labels,
mode,
params,
config=None):
"""MeshNet model function.
Args:
features: 5D float `Tensor`, input tensor. This is the first item
returned from the `input_fn` passed to `train`, `evaluate`, and
`predict`. Use `NDHWC` format.
labels: 4D float `Tensor`, labels tensor. This is the second item
returned from the `input_fn` passed to `train`, `evaluate`, and
`predict`. Labels should not be one-hot encoded.
mode: Optional. Specifies if this training, evaluation or prediction.
params: `dict` of parameters.
- n_classes: (required) number of classes to classify.
- optimizer: instance of TensorFlow optimizer. Required if
training.
- n_filters: number of filters to use in each convolution. The
original implementation used 21 filters to classify brainmask
and 71 filters for the multi-class problem.
- dropout_rate: rate of dropout. For example, 0.1 would drop 10% of
input units.
config: configuration object.
Returns:
`tf.estimator.EstimatorSpec`
Raises:
`ValueError` if required parameters are not in `params`.
"""
volume = features
if isinstance(volume, dict):
volume = features['volume']
required_keys = {'n_classes'}
default_params = {'optimizer': None, 'n_filters': 96, 'keep_prob': 0.5}
check_required_params(params=params, required_keys=required_keys)
set_default_params(params=params, defaults=default_params)
check_optimizer_for_training(optimizer=params['optimizer'], mode=mode)
tf.logging.debug("Parameters for model:")
tf.logging.debug(params)
# Dilation rate by layer.
dilation_rates = (
(1, 1, 1),
(1, 1, 1),
(1, 1, 1),
(2, 2, 2),
(4, 4, 4),
(8, 8, 8),
(1, 1, 1))
is_mc_v = tf.constant(False,dtype=tf.bool)
is_mc_b = tf.constant(True,dtype=tf.bool)
outputs = volume
for ii, dilation_rate in enumerate(dilation_rates):
outputs = _layer(
outputs, mode=mode, layer_num=ii + 1, filters=params['n_filters'],
kernel_size=3, dilation_rate=dilation_rate,keep_prob=params['keep_prob'], is_mc_v=is_mc_v, is_mc_b=is_mc_b)
with tf.variable_scope('logits'):
logits = vwn_conv.conv3d(
inputs=outputs, filters=params['n_classes'], kernel_size=(1, 1, 1),
padding='SAME', activation=None, is_mc=is_mc_v)
predicted_classes = tf.argmax(logits, axis=-1)
if mode == tf.estimator.ModeKeys.PREDICT:
predictions = {
'class_ids': predicted_classes,
'probabilities': tf.nn.softmax(logits),
'logits': logits,
}
export_outputs = {
'outputs': tf.estimator.export.PredictOutput(predictions)}
return tf.estimator.EstimatorSpec(
mode=mode,
predictions=predictions,
export_outputs=export_outputs)
if params['prior_path'] != None:
prior_np = np.load(params['prior_path'])
with tf.variable_scope("prior"):
i=-1
for v in tf.get_collection('ms'):
i += 1
if params['prior_path'] == None:
tf.add_to_collection('ms_prior',tf.Variable(tf.constant(0, dtype = v.dtype, shape = v.shape),trainable = False))
else:
tf.add_to_collection('ms_prior',tf.Variable(tf.convert_to_tensor(prior_np[0][i], dtype = tf.float32),trainable = False))
ms = tf.get_collection('ms')
ms_prior = tf.get_collection('ms_prior')
i=-1
for v in tf.get_collection('ms'):
i += 1
if params['prior_path'] == None:
tf.add_to_collection('sigmas_prior',tf.Variable(tf.constant(1, dtype = v.dtype, shape = v.shape),trainable = False))
else:
tf.add_to_collection('sigmas_prior',tf.Variable(tf.convert_to_tensor(prior_np[1][i], dtype = tf.float32),trainable = False))
sigmas = tf.get_collection('sigmas')
sigmas_prior = tf.get_collection('sigmas_prior')
nll_loss = tf.reduce_mean(tf.nn.sparse_softmax_cross_entropy_with_logits(labels=labels, logits=logits))
tf.summary.scalar('nll_loss', nll_loss)
n_examples = tf.constant(params['n_examples'],dtype=ms[0].dtype)
tf.summary.scalar('n_examples', n_examples)
l2_loss = tf.add_n([tf.reduce_sum((tf.square(ms[i] - ms_prior[i])) / ((tf.square(sigmas_prior[i]) + 1e-8) * 2.0)) for i in range(len(ms))], name = 'l2_loss') / n_examples
tf.summary.scalar('l2_loss', l2_loss)
loss = nll_loss + l2_loss
assert mode == tf.estimator.ModeKeys.TRAIN
global_step = tf.train.get_global_step()
update_ops = tf.get_collection(tf.GraphKeys.UPDATE_OPS)
with tf.control_dependencies(update_ops):
train_op = params['optimizer'].minimize(loss, global_step=global_step)
return tf.estimator.EstimatorSpec(mode=mode, loss=loss, train_op=train_op)
