def network(input, is_training, num_outputs_embedding, actual_network, filters=64, levels=7, activation='relu', normalize=False, data_format='channels_first', padding='same'):
if activation == 'selu':
activation = tf.nn.selu
kernel_initializer = selu_initializer
elif activation == 'relu':
activation = tf.nn.relu
kernel_initializer = he_initializer
elif activation == 'tanh':
activation = tf.nn.tanh
kernel_initializer = selu_initializer
padding = padding
embedding_axis = 1 if data_format == 'channels_first' else 4
if normalize:
embeddings_activation = lambda x, name: tf.nn.l2_normalize(x, dim=embedding_axis, name=name, epsilon=1e-4)
else:
if activation == tf.nn.selu:
embeddings_activation = tf.nn.selu
else:
embeddings_activation = None
embeddings_normalization = lambda x, name: tf.nn.l2_normalize(x, dim=embedding_axis, name=name, epsilon=1e-4)
with tf.variable_scope('unet_0'):
unet = actual_network(num_filters_base=filters, kernel=[3, 3, 3], num_levels=levels, data_format=data_format, kernel_initializer=kernel_initializer, activation=activation, is_training=is_training, name='unet', padding=padding)
unet_out = unet(input, is_training)
embeddings = conv3d(unet_out, kernel_size=[1, 1, 1], name='embeddings', filters=num_outputs_embedding, kernel_initializer=kernel_initializer, activation=embeddings_activation, data_format=data_format, is_training=is_training, padding=padding)
with tf.variable_scope('unet_1'):
normalized_embeddings = embeddings_normalization(embeddings, 'embeddings_normalized')
input_concat = concat_channels([input, normalized_embeddings], name='input_concat', data_format=data_format)
unet = actual_network(num_filters_base=filters, kernel=[3, 3, 3], num_levels=levels, data_format=data_format, kernel_initializer=kernel_initializer, activation=activation, is_training=is_training, name='unet', padding=padding)
unet_out = unet(input_concat, is_training)
embeddings_2 = conv3d(unet_out, kernel_size=[1, 1, 1], name='embeddings', filters=num_outputs_embedding, kernel_initializer=kernel_initializer, activation=embeddings_activation, data_format=data_format, is_training=is_training, padding=padding)
return embeddings, embeddings_2
def network_unet(input,
num_heatmaps,
is_training,
data_format='channels_first'):
num_filters_base = 64
activation = tf.nn.relu
node = conv3d(input,
filters=num_filters_base,
kernel_size=[3, 3, 3],
name='conv0',
activation=activation,
data_format=data_format,
is_training=is_training)
scnet_local = UnetClassic3D(num_filters_base=num_filters_base,
num_levels=5,
double_filters_per_level=False,
normalization=None,
activation=activation,
data_format=data_format)
unet_out = scnet_local(node, is_training)
heatmaps = conv3d(
unet_out,
filters=num_heatmaps,
kernel_size=[3, 3, 3],
name='heatmaps',
kernel_initializer=tf.truncated_normal_initializer(stddev=0.0001),
activation=None,
data_format=data_format,
is_training=is_training)
return heatmaps, heatmaps, heatmaps
def conv(self, node, current_level, postfix, is_training):
return conv3d(node,
self.num_filters(current_level), [3, 3, 3],
name='conv' + postfix,
activation=self.activation,
normalization=self.normalization,
is_training=is_training,
data_format=self.data_format,
padding=self.padding)
def conv(self, node, current_level, postfix, is_training):
return conv3d(node,
self.num_filters(current_level),
self.kernel_size,
name='conv' + postfix,
activation=self.activation,
normalization=None,
is_training=is_training,
data_format=self.data_format,
kernel_initializer=self.kernel_initializer,
padding=self.padding)
def network_u(input,
is_training,
num_labels,
data_format='channels_first',
activation='relu',
padding='same',
actual_network=None,
*args,
**kwargs):
"""
The U-Net
:param input: Input tensor.
:param num_labels: Number of outputs.
:param is_training: True, if training network.
:param data_format: 'channels_first' or 'channels_last'
:param actual_network: The actual u-net instance used as the local appearance network.
:param padding: Padding parameter passed to the convolution operations.
:param activation: The activation function. 'relu' or 'selu'
:param args: Not used.
:param kwargs: Passed to actual_network()
:return: prediction
"""
if activation == 'relu':
kernel_initializer = he_initializer
activation = tf.nn.relu
else:
kernel_initializer = selu_initializer
activation = tf.nn.selu
local_kernel_initializer = tf.initializers.truncated_normal(stddev=0.001)
local_activation = None
with tf.variable_scope('local'):
unet = actual_network(data_format=data_format,
kernel_initializer=kernel_initializer,
activation=activation,
padding=padding,
**kwargs)
prediction = unet(input, is_training=is_training)
prediction = conv3d(prediction,
num_labels, [3, 3, 3],
name='output',
padding=padding,
kernel_initializer=local_kernel_initializer,
activation=local_activation,
is_training=is_training,
data_format=data_format)
return prediction
def network_unet(input, num_labels, is_training, data_format='channels_first'):
kernel_initializer = he_initializer
activation = tf.nn.relu
local_kernel_initializer = he_initializer
local_activation = None
padding = 'reflect'
with tf.variable_scope('unet'):
unet = UnetClassicAvgLinear3d(64,
4,
data_format=data_format,
double_filters_per_level=True,
kernel_initializer=kernel_initializer,
activation=activation,
padding=padding)
prediction = unet(input, is_training=is_training)
prediction = conv3d(prediction,
num_labels, [1, 1, 1],
name='output',
padding=padding,
kernel_initializer=local_kernel_initializer,
activation=local_activation,
is_training=is_training)
return prediction, prediction, prediction
def network_scn(input,
num_heatmaps,
is_training,
data_format='channels_first'):
num_filters_base = 64
activation = lambda x, name: tf.nn.leaky_relu(x, name=name, alpha=0.1)
padding = 'reflect'
heatmap_layer_kernel_initializer = tf.truncated_normal_initializer(
stddev=0.001)
downsampling_factor = 8
node = conv3d(input,
filters=num_filters_base,
kernel_size=[3, 3, 3],
name='conv0',
activation=activation,
data_format=data_format,
is_training=is_training)
scnet_local = SCNetLocal(num_filters_base=num_filters_base,
num_levels=4,
double_filters_per_level=False,
normalization=None,
activation=activation,
data_format=data_format,
padding=padding)
unet_out = scnet_local(node, is_training)
local_heatmaps = conv3d(
unet_out,
filters=num_heatmaps,
kernel_size=[3, 3, 3],
name='local_heatmaps',
kernel_initializer=heatmap_layer_kernel_initializer,
activation=None,
data_format=data_format,
is_training=is_training)
downsampled = avg_pool3d(local_heatmaps, [downsampling_factor] * 3,
name='local_downsampled',
data_format=data_format)
conv = conv3d(downsampled,
filters=num_filters_base,
kernel_size=[7, 7, 7],
name='sconv0',
activation=activation,
data_format=data_format,
is_training=is_training,
padding=padding)
conv = conv3d(conv,
filters=num_filters_base,
kernel_size=[7, 7, 7],
name='sconv1',
activation=activation,
data_format=data_format,
is_training=is_training,
padding=padding)
conv = conv3d(conv,
filters=num_filters_base,
kernel_size=[7, 7, 7],
name='sconv2',
activation=activation,
data_format=data_format,
is_training=is_training,
padding=padding)
conv = conv3d(conv,
filters=num_heatmaps,
kernel_size=[7, 7, 7],
name='spatial_downsampled',
kernel_initializer=heatmap_layer_kernel_initializer,
activation=tf.nn.tanh,
data_format=data_format,
is_training=is_training,
padding=padding)
spatial_heatmaps = upsample3d_cubic(conv, [downsampling_factor] * 3,
name='spatial_heatmaps',
data_format=data_format,
padding='valid_cropped')
heatmaps = local_heatmaps * spatial_heatmaps
return heatmaps, local_heatmaps, spatial_heatmaps
def network_scn(input, num_labels, is_training, data_format='channels_first'):
downsampling_factor = 4
kernel_initializer = he_initializer
activation = tf.nn.relu
local_kernel_initializer = he_initializer
local_activation = tf.nn.tanh
spatial_kernel_initializer = he_initializer
spatial_activation = None
padding = 'reflect'
with tf.variable_scope('unet'):
unet = UnetClassicAvgLinear3d(64,
4,
data_format=data_format,
double_filters_per_level=True,
kernel_initializer=kernel_initializer,
activation=activation,
padding=padding)
local_prediction = unet(input, is_training=is_training)
local_prediction = conv3d(local_prediction,
num_labels, [1, 1, 1],
name='local_prediction',
padding=padding,
kernel_initializer=local_kernel_initializer,
activation=local_activation,
is_training=is_training)
with tf.variable_scope('spatial_configuration'):
local_prediction_pool = avg_pool3d(local_prediction,
[downsampling_factor] * 3,
name='local_prediction_pool')
scconv = conv3d(local_prediction_pool,
64, [5, 5, 5],
name='scconv0',
padding=padding,
kernel_initializer=kernel_initializer,
activation=activation,
is_training=is_training)
scconv = conv3d(scconv,
64, [5, 5, 5],
name='scconv1',
padding=padding,
kernel_initializer=kernel_initializer,
activation=activation,
is_training=is_training)
scconv = conv3d(scconv,
64, [5, 5, 5],
name='scconv2',
padding=padding,
kernel_initializer=kernel_initializer,
activation=activation,
is_training=is_training)
spatial_prediction_pool = conv3d(
scconv,
num_labels, [5, 5, 5],
name='spatial_prediction_pool',
padding=padding,
kernel_initializer=spatial_kernel_initializer,
activation=spatial_activation,
is_training=is_training)
spatial_prediction = upsample3d_linear(spatial_prediction_pool,
[downsampling_factor] * 3,
name='spatial_prediction',
padding='valid_cropped')
with tf.variable_scope('combination'):
prediction = local_prediction * spatial_prediction
return prediction, local_prediction, spatial_prediction
def spatial_configuration_net(input,
num_labels,
is_training,
data_format='channels_first',
actual_network=None,
padding=None,
spatial_downsample=8,
*args,
**kwargs):
"""
The spatial configuration net.
:param input: Input tensor.
:param num_labels: Number of outputs.
:param is_training: True, if training network.
:param data_format: 'channels_first' or 'channels_last'
:param actual_network: The actual u-net instance used as the local appearance network.
:param padding: Padding parameter passed to the convolution operations.
:param spatial_downsample: Downsamping factor for the spatial configuration stage.
:param args: Not used.
:param kwargs: Not used.
:return: heatmaps, local_heatmaps, spatial_heatmaps
"""
num_filters_base = 64
activation = lambda x, name: tf.nn.leaky_relu(x, name=name, alpha=0.1)
heatmap_layer_kernel_initializer = tf.truncated_normal_initializer(
stddev=0.001)
downsampling_factor = spatial_downsample
node = conv3d(input,
filters=num_filters_base,
kernel_size=[3, 3, 3],
name='conv0',
activation=activation,
data_format=data_format,
is_training=is_training)
scnet_local = actual_network(num_filters_base=num_filters_base,
num_levels=4,
double_filters_per_level=False,
normalization=None,
activation=activation,
data_format=data_format,
padding=padding)
unet_out = scnet_local(node, is_training)
local_heatmaps = conv3d(
unet_out,
filters=num_labels,
kernel_size=[3, 3, 3],
name='local_heatmaps',
kernel_initializer=heatmap_layer_kernel_initializer,
activation=None,
data_format=data_format,
is_training=is_training)
downsampled = avg_pool3d(local_heatmaps, [downsampling_factor] * 3,
name='local_downsampled',
data_format=data_format)
conv = conv3d(downsampled,
filters=num_filters_base,
kernel_size=[7, 7, 7],
name='sconv0',
activation=activation,
data_format=data_format,
is_training=is_training,
padding=padding)
conv = conv3d(conv,
filters=num_filters_base,
kernel_size=[7, 7, 7],
name='sconv1',
activation=activation,
data_format=data_format,
is_training=is_training,
padding=padding)
conv = conv3d(conv,
filters=num_filters_base,
kernel_size=[7, 7, 7],
name='sconv2',
activation=activation,
data_format=data_format,
is_training=is_training,
padding=padding)
conv = conv3d(conv,
filters=num_labels,
kernel_size=[7, 7, 7],
name='spatial_downsampled',
kernel_initializer=heatmap_layer_kernel_initializer,
activation=tf.nn.tanh,
data_format=data_format,
is_training=is_training,
padding=padding)
if data_format == 'channels_last':
# suppose that 'channels_last' means CPU
# resize_trilinear is much faster on CPU
spatial_heatmaps = resize_tricubic(conv,
factors=[downsampling_factor] * 3,
name='spatial_heatmaps',
data_format=data_format)
else:
# suppose that 'channels_first' means GPU
# upsample3d_linear is much faster on GPU
spatial_heatmaps = upsample3d_cubic(conv,
factors=[downsampling_factor] * 3,
name='spatial_heatmaps',
data_format=data_format,
padding='valid_cropped')
heatmaps = local_heatmaps * spatial_heatmaps
return heatmaps, local_heatmaps, spatial_heatmaps