def discriminator(model, input_image, reuse=False, initial_size=(4, 4), max_size=None, name=None, depth=1, transition=False, alpha_transition=0, **kwargs):
import tensorflow as tf
"""
"""
with tf.variable_scope(name) as scope:
convs = []
if reuse:
scope.reuse_variables()
# fromRGB
convs += [leaky_relu(DnConv(input_image, output_dim=model.get_filter_num(depth), kernel_size=(1,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_y_rgb_conv_{}'.format(input_image.shape[1]), dim=model.dim))]
for i in range(depth):
# Convolutional blocks. TODO: Replace with block module.
convs += [leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(depth - i), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_n_conv_1_{}'.format(convs[-1].shape[1]), dim=model.dim))]
convs += [leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(depth - 1 - i), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_n_conv_2_{}'.format(convs[-1].shape[1]), dim=model.dim))]
# Calculate Next Downsample Ratio
# Whoever can calculate this in a less dumb way than this gets a Fields Medal.
if max_size is None:
downsample_ratio = (2,) * model.dim
else:
reference_shape = []
current_shape = input_image.shape
for idx, cshape in enumerate(current_shape):
reference_shape += [current_shape[idx] // initial_size[idx]]
downsample_ratio = []
for size_idx, size in enumerate(max_size):
if size // initial_size[size_idx] > min(reference_shape):
downsample_ratio += [1]
else:
downsample_ratio += [2]
downsample_ratio = tuple(downsample_ratio)
convs[-1] = DnAveragePooling(convs[-1], downsample_ratio, dim=model.dim)
if i == 0 and transition:
transition_conv = DnAveragePooling(input_image, downsample_ratio, dim=model.dim)
transition_conv = leaky_relu(DnConv(transition_conv, output_dim=model.get_filter_num(depth - 1), kernel_size=(1,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_y_rgb_conv_{}'.format(transition_conv.shape[1]), dim=model.dim))
convs[-1] = alpha_transition * convs[-1] + (1 - alpha_transition) * transition_conv
convs += [minibatch_state_concat(convs[-1])]
convs[-1] = leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(0), kernel_size=(3,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_n_conv_1_{}'.format(convs[-1].shape[1]), dim=model.dim))
output = tf.reshape(convs[-1], [tf.shape(convs[-1])[0], np.prod(initial_size) * model.get_filter_num(0)])
# Currently erroring
# discriminate_output = dense(output, output_size=1, name='discriminator_n_fully')
discriminate_output = tf.layers.dense(output, 1, name='discriminator_n_1_fully')
return tf.nn.sigmoid(discriminate_output), discriminate_output
def discriminator(model, input_image, reuse=False, name=None, depth=1, transition=False, **kwargs):
"""
"""
with tf.variable_scope(name) as scope:
if reuse:
scope.reuse_variables()
if transition:
transition_conv = DnAveragePooling(input_image, (2,) * model.dim, dim=model.dim)
transition_conv = leaky_relu(DnConv(transition_conv, output_dim=model.get_filter_num(depth - 1), kernel_size=(1,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_y_rgb_conv_{}'.format(transition_conv.shape[1]), dim=model.dim))
convs = []
# fromRGB
convs += [leaky_relu(DnConv(input_image, output_dim=model.get_filter_num(depth), kernel_size=(1,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_y_rgb_conv_{}'.format(input_image.shape[1]), dim=model.dim))]
for i in range(depth):
convs += [leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(depth - i), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_n_conv_1_{}'.format(convs[-1].shape[1]), dim=model.dim))]
convs += [leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(depth - 1 - i), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_n_conv_2_{}'.format(convs[-1].shape[1]), dim=model.dim))]
convs[-1] = DnAveragePooling(convs[-1], dim=model.dim)
convs += [minibatch_state_concat(convs[-1])]
convs[-1] = leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(0), kernel_size=(3,) * model.dim, stride_size=(1,) * model.dim, name='discriminator_n_conv_1_{}'.format(convs[-1].shape[1]), dim=model.dim))
#for D -- what's going on with the channel number here?
output = tf.reshape(convs[-1], [tf.shape(convs[-1])[0], 4 * 4 * model.get_filter_num(0)])
# Currently erroring
# discriminate_output = dense(output, output_size=1, name='discriminator_n_fully')
discriminate_output = tf.layers.dense(output, model.get_filter_num(0), name='discriminator_n_1_fully')
discriminate_output = tf.layers.dense(discriminate_output, 1, name='discriminator_n_2_fully')
return tf.nn.sigmoid(discriminate_output), discriminate_output
def unet(model, input_tensor, backend='tensorflow'):
from keras.layers.merge import concatenate
left_outputs = []
for level in range(model.depth):
filter_num = int(model.max_filter / (2 ** (model.depth - level)) / model.downsize_filters_factor)
if level == 0:
left_outputs += [DnConv(input_tensor, filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_downsampling_conv_{}_1'.format(level), backend=backend)]
left_outputs[level] = DnConv(left_outputs[level], 2 * filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_downsampling_conv_{}_2'.format(level), backend=backend)
else:
left_outputs += [DnMaxPooling(left_outputs[level - 1], pool_size=model.pool_size, dim=model.dim, backend=backend)]
left_outputs[level] = DnConv(left_outputs[level], filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_downsampling_conv_{}_1'.format(level), backend=backend)
left_outputs[level] = DnConv(left_outputs[level], 2 * filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_downsampling_conv_{}_2'.format(level), backend=backend)
if model.dropout is not None and model.dropout != 0:
left_outputs[level] = DnDropout(model.dropout)(left_outputs[level])
if model.batch_norm:
left_outputs[level] = DnBatchNormalization(left_outputs[level])
right_outputs = [left_outputs[model.depth - 1]]
for level in range(model.depth):
filter_num = int(model.max_filter / (2 ** (level)) / model.downsize_filters_factor)
if level > 0:
right_outputs += [DnUpsampling(right_outputs[level - 1], pool_size=model.pool_size, dim=model.dim, backend=backend)]
right_outputs[level] = concatenate([right_outputs[level], left_outputs[model.depth - level - 1]], axis=model.dim + 1)
right_outputs[level] = DnConv(right_outputs[level], filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_upsampling_conv_{}_1'.format(level), backend=backend)
right_outputs[level] = DnConv(right_outputs[level], int(filter_num / 2), model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_upsampling_conv_{}_2'.format(level), backend=backend)
else:
continue
if model.dropout is not None and model.dropout != 0:
right_outputs[level] = DnDropout(model.dropout)(right_outputs[level])
if model.batch_norm:
right_outputs[level] = DnBatchNormalization()(right_outputs[level])
output_layer = DnConv(right_outputs[level], 1, (1, ) * model.dim, stride_size=(1,) * model.dim, dim=model.dim, name='end_conv', backend=backend)
# TODO: Brainstorm better way to specify outputs
if model.input_tensor is not None:
return output_layer
return model.model
def build_model(self):
self.output_layer = DnConv(self.inputs,
1,
self.kernel_size,
stride_size=(1, ) * self.dim,
dim=self.dim,
name='minimal_conv',
backend='keras')
if self.input_tensor is None:
super(MinimalKerasCNN, self).build()
return self.model
else:
return self.output_layer
def build_model(self):
output_layer = DnConv(self.inputs,
1,
self.kernel_size,
stride_size=(1, ) * self.dim,
dim=self.dim,
name='minimal_conv',
backend='keras')
# TODO: Brainstorm better way to specify outputs
if self.input_tensor is not None:
return output_layer
if self.output_type == 'regression':
self.model = Model(inputs=self.inputs, outputs=output_layer)
self.model.compile(optimizer=Nadam(lr=self.initial_learning_rate),
loss='mean_squared_error',
metrics=['mean_squared_error'])
if self.output_type == 'binary_label':
act = Activation('sigmoid')(output_layer)
self.model = Model(inputs=self.inputs, outputs=act)
self.model.compile(optimizer=Nadam(lr=self.initial_learning_rate),
loss=dice_coef_loss,
metrics=[dice_coef])
if self.output_type == 'categorical_label':
act = Activation('softmax')(output_layer)
self.model = Model(inputs=self.inputs, outputs=act)
self.model.compile(optimizer=Nadam(lr=self.initial_learning_rate),
loss='categorical_crossentropy',
metrics=['categorical_accuracy'])
super(MinimalKerasCNN, self).build()
return self.model
def generator(model, latent_var, depth=1, initial_size=4, reuse=False, transition=False, alpha_transition=0, name=None):
"""
"""
with tf.variable_scope(name) as scope:
convs = []
if reuse:
scope.reuse_variables()
convs += [tf.reshape(latent_var, [tf.shape(latent_var)[0]] + [1] * model.dim + [model.latent_size])]
# TODO: refactor the padding on this step. Or replace with a dense layer?
convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(0), kernel_size=(4,) * model.dim, stride_size=(1,) * model.dim, padding='Other', name='generator_n_conv_1_{}'.format(convs[-1].shape[1]), dim=model.dim)), model.dim)
convs += [tf.reshape(convs[-1], [tf.shape(latent_var)[0]] + [initial_size] * model.dim + [model.get_filter_num(0)])]
convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(0), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, name='generator_n_conv_2_{}'.format(convs[-1].shape[1]), dim=model.dim)), dim=model.dim)
for i in range(depth):
if i == depth - 1 and transition:
#To RGB
transition_conv = DnConv(convs[-1], output_dim=model.channels, kernel_size=(1,) * model.dim, stride_size=(1,) * model.dim, name='generator_y_rgb_conv_{}'.format(convs[-1].shape[1]), dim=model.dim)
transition_conv = DnUpsampling(transition_conv, (2,) * model.dim, dim=model.dim)
convs += [DnUpsampling(convs[-1], (2,) * model.dim, dim=model.dim)]
convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(i + 1), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, name='generator_n_conv_1_{}'.format(convs[-1].shape[1]), dim=model.dim)), dim=model.dim)
convs += [DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(i + 1), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, name='generator_n_conv_2_{}'.format(convs[-1].shape[1]), dim=model.dim)), dim=model.dim)]
#To RGB
convs += [DnConv(convs[-1], output_dim=model.channels, kernel_size=(1,) * model.dim, stride_size=(1,) * model.dim, name='generator_y_rgb_conv_{}'.format(convs[-1].shape[1]), dim=model.dim)]
if transition:
convs[-1] = (1 - alpha_transition) * transition_conv + alpha_transition * convs[-1]
return convs[-1]
def generator(model, latent_var, depth=1, initial_size=(4, 4), max_size=None, reuse=False, transition=False, alpha_transition=0, name=None):
"""Summary
Parameters
----------
model : TYPE
Description
latent_var : TYPE
Description
depth : int, optional
Description
initial_size : tuple, optional
Description
max_size : None, optional
Description
reuse : bool, optional
Description
transition : bool, optional
Description
alpha_transition : int, optional
Description
name : None, optional
Description
Returns
-------
TYPE
Description
"""
import tensorflow as tf
with tf.variable_scope(name) as scope:
convs = []
if reuse:
scope.reuse_variables()
convs += [tf.reshape(latent_var, [tf.shape(latent_var)[0]] + [1] * model.dim + [model.latent_size])]
# TODO: refactor the padding on this step. Or replace with a dense layer?
with tf.variable_scope('generator_n_conv_1_{}'.format(convs[-1].shape[1])):
convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(0), kernel_size=initial_size, stride_size=(1,) * model.dim, padding='Other', dim=model.dim)), model.dim)
convs += [tf.reshape(convs[-1], [tf.shape(latent_var)[0]] + list(initial_size) + [model.get_filter_num(0)])]
with tf.variable_scope('generator_n_conv_2_{}'.format(convs[-1].shape[1])):
convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(0), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, dim=model.dim)), dim=model.dim)
for i in range(depth):
# Calculate Next Upsample Ratio
if max_size is None:
upsample_ratio = (2,) * model.dim
else:
upsample_ratio = []
for size_idx, size in enumerate(max_size):
if size >= convs[-1].shape[size_idx + 1] * 2:
upsample_ratio += [2]
else:
upsample_ratio += [1]
upsample_ratio = tuple(upsample_ratio)
# Upsampling, with conversion to RGB if necessary.
if i == depth - 1 and transition:
transition_conv = DnConv(convs[-1], output_dim=model.channels, kernel_size=(1,) * model.dim, stride_size=(1,) * model.dim, dim=model.dim, name='generator_y_rgb_conv_{}'.format(convs[-1].shape[1]))
transition_conv = DnUpsampling(transition_conv, upsample_ratio, dim=model.dim)
convs += [DnUpsampling(convs[-1], upsample_ratio, dim=model.dim)]
# Convolutional blocks. TODO: Replace with block module.
with tf.variable_scope('generator_n_conv_1_{}'.format(convs[-1].shape[1])):
convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(i + 1), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, dim=model.dim)), dim=model.dim)
with tf.variable_scope('generator_n_conv_2_{}'.format(convs[-1].shape[1])):
convs += [DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(i + 1), kernel_size=(5,) * model.dim, stride_size=(1,) * model.dim, dim=model.dim)), dim=model.dim)]
# Conversion to RGB
convs += [DnConv(convs[-1], output_dim=model.channels, kernel_size=(1,) * model.dim, stride_size=(1,) * model.dim, name='generator_y_rgb_conv_{}'.format(convs[-1].shape[1]), dim=model.dim)]
if transition:
convs[-1] = (1 - alpha_transition) * transition_conv + alpha_transition * convs[-1]
return convs[-1]
def build_model(self):
""" A basic implementation of the U-Net proposed in https://arxiv.org/abs/1505.04597
TODO: specify optimizer
Returns
-------
Keras model or tensor
If input_tensor is provided, this will return a tensor. Otherwise,
this will return a Keras model.
"""
left_outputs = []
for level in range(self.depth):
filter_num = int(self.max_filter / (2**(self.depth - level)) /
self.downsize_filters_factor)
if level == 0:
left_outputs += [
DnConv(self.inputs,
filter_num,
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_{}'.format(level, 0),
backend='keras')
]
if self.dropout is not None and self.dropout != 0:
left_outputs[level] = Dropout(self.dropout)(
left_outputs[level])
if self.batch_norm:
left_outputs[level] = BatchNormalization()(
left_outputs[level])
for block_num in range(1, self.num_blocks):
left_outputs[level] = DnConv(
left_outputs[level],
filter_num *
(self.block_filter_growth_ratio**block_num),
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_{}'.format(
level, block_num),
backend='keras')
if self.dropout is not None and self.dropout != 0:
left_outputs[level] = Dropout(self.dropout)(
left_outputs[level])
if self.batch_norm:
left_outputs[level] = BatchNormalization()(
left_outputs[level])
else:
left_outputs += [
DnMaxPooling(left_outputs[level - 1],
pool_size=self.pool_size,
dim=self.dim,
backend='keras',
padding=self.pooling_padding)
]
for block_num in range(self.num_blocks):
left_outputs[level] = DnConv(
left_outputs[level],
filter_num *
(self.block_filter_growth_ratio**block_num),
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_{}'.format(
level, block_num),
backend='keras')
if self.dropout is not None and self.dropout != 0:
left_outputs[level] = Dropout(self.dropout)(
left_outputs[level])
if self.batch_norm:
left_outputs[level] = BatchNormalization()(
left_outputs[level])
right_outputs = [left_outputs[self.depth - 1]]
for level in range(self.depth):
filter_num = int(self.max_filter / (2**(level)) /
self.downsize_filters_factor)
if level > 0:
right_outputs += [
DnUpsampling(right_outputs[level - 1],
pool_size=self.pool_size,
dim=self.dim,
backend='keras')
]
if right_outputs[level].shape[1:-1] == left_outputs[
self.depth - level - 1].shape[1:-1]:
right_outputs[level] = concatenate([
right_outputs[level],
left_outputs[self.depth - level - 1]
],
axis=self.dim + 1)
else:
# Very complex code to facilitate dimension errors arising from odd-numbered patches.
# Is essentially same-padding, may have performance impacts on networks.
# Very tentative.
input_tensor = right_outputs[level]
concatenate_tensor = left_outputs[self.depth - level - 1]
padding = []
for dim in range(self.dim):
padding += [
int(concatenate_tensor.shape[dim + 1]) -
int(input_tensor.shape[dim + 1])
]
if len(padding) < self.dim:
padding += [1] * self.dim - len(self.padding)
lambda_dict = {
0: Lambda(lambda x: x[:, 0:padding[0], :, :, :]),
1: Lambda(lambda x: x[:, :, 0:padding[1], :, :]),
2: Lambda(lambda x: x[:, :, :, 0:padding[2], :])
}
for dim in range(self.dim):
tensor_slice = [slice(None)] + [
slice(padding[dim])
if i_dim == dim else slice(None)
for i_dim in range(self.dim)
] + [slice(None)]
# Causes JSON Serialization Error.
# tensor_slice = Lambda(lambda x, tensor_slice=tensor_slice: x[tensor_slice])(input_tensor)
tensor_slice = lambda_dict[dim](input_tensor)
input_tensor = concatenate(
[input_tensor, tensor_slice], axis=dim + 1)
right_outputs[level] = concatenate(
[input_tensor, concatenate_tensor], axis=self.dim + 1)
for block_num in range(self.num_blocks):
right_outputs[level] = DnConv(
right_outputs[level],
filter_num //
(self.block_filter_growth_ratio**block_num),
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='upsampling_conv_{}_{}'.format(level, block_num),
backend='keras')
if self.dropout is not None and self.dropout != 0:
right_outputs[level] = Dropout(self.dropout)(
right_outputs[level])
if self.batch_norm:
right_outputs[level] = BatchNormalization()(
right_outputs[level])
self.output_layer = DnConv(right_outputs[level],
self.output_channels, (1, ) * self.dim,
stride_size=(1, ) * self.dim,
dim=self.dim,
name='end_conv',
backend='keras')
super(UNet, self).build_model()
def build_model(self):
""" A basic implementation of the U-Net proposed in https://arxiv.org/abs/1505.04597
TODO: specify optimizer
Returns
-------
Keras model or tensor
If input_tensor is provided, this will return a tensor. Otherwise,
this will return a Keras model.
"""
left_outputs = []
for level in range(self.depth):
filter_num = int(self.max_filter / (2**(self.depth - level)) /
self.downsize_filters_factor)
if level == 0:
left_outputs += [
DnConv(self.inputs,
filter_num,
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_{}'.format(level, 0),
backend='keras')
]
for block_num in range(1, self.num_blocks):
left_outputs[level] = DnConv(
left_outputs[level],
filter_num *
(self.block_filter_growth_ratio**block_num),
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_{}'.format(
level, block_num),
backend='keras')
else:
left_outputs += [
DnMaxPooling(left_outputs[level - 1],
pool_size=self.pool_size,
dim=self.dim,
backend='keras')
]
for block_num in range(self.num_blocks):
left_outputs[level] = DnConv(
left_outputs[level],
filter_num *
(self.block_filter_growth_ratio**block_num),
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_{}'.format(
level, block_num),
backend='keras')
if self.dropout is not None and self.dropout != 0:
left_outputs[level] = Dropout(self.dropout)(
left_outputs[level])
if self.batch_norm:
left_outputs[level] = BatchNormalization()(left_outputs[level])
right_outputs = [left_outputs[self.depth - 1]]
for level in range(self.depth):
filter_num = int(self.max_filter / (2**(level)) /
self.downsize_filters_factor)
if level > 0:
right_outputs += [
DnUpsampling(right_outputs[level - 1],
pool_size=self.pool_size,
dim=self.dim,
backend='keras')
]
right_outputs[level] = concatenate([
right_outputs[level], left_outputs[self.depth - level - 1]
],
axis=self.dim + 1)
for block_num in range(self.num_blocks):
right_outputs[level] = DnConv(
right_outputs[level],
filter_num //
(self.block_filter_growth_ratio**block_num),
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='upsampling_conv_{}_{}'.format(level, block_num),
backend='keras')
else:
continue
if self.dropout is not None and self.dropout != 0:
right_outputs[level] = Dropout(self.dropout)(
right_outputs[level])
if self.batch_norm:
right_outputs[level] = BatchNormalization()(
right_outputs[level])
self.output_layer = DnConv(right_outputs[level],
self.output_channels, (1, ) * self.dim,
stride_size=(1, ) * self.dim,
dim=self.dim,
name='end_conv',
backend='keras')
super(UNet, self).build_model()
def build_model(self):
""" A basic implementation of the U-Net proposed in https://arxiv.org/abs/1505.04597
TODO: specify optimizer
Returns
-------
Keras model or tensor
If input_tensor is provided, this will return a tensor. Otherwise,
this will return a Keras model.
"""
left_outputs = []
for level in range(self.depth):
filter_num = int(self.max_filter / (2**(self.depth - level)) /
self.downsize_filters_factor)
if level == 0:
left_outputs += [
DnConv(self.inputs,
filter_num,
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_1'.format(level),
backend='keras')
]
left_outputs[level] = DnConv(
left_outputs[level],
2 * filter_num,
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_2'.format(level),
backend='keras')
else:
left_outputs += [
DnMaxPooling(left_outputs[level - 1],
pool_size=self.pool_size,
dim=self.dim,
backend='keras')
]
left_outputs[level] = DnConv(
left_outputs[level],
filter_num,
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_1'.format(level),
backend='keras')
left_outputs[level] = DnConv(
left_outputs[level],
2 * filter_num,
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='downsampling_conv_{}_2'.format(level),
backend='keras')
if self.dropout is not None and self.dropout != 0:
left_outputs[level] = Dropout(self.dropout)(
left_outputs[level])
if self.batch_norm:
left_outputs[level] = BatchNormalization()(left_outputs[level])
right_outputs = [left_outputs[self.depth - 1]]
for level in range(self.depth):
filter_num = int(self.max_filter / (2**(level)) /
self.downsize_filters_factor)
if level > 0:
right_outputs += [
DnUpsampling(right_outputs[level - 1],
pool_size=self.pool_size,
dim=self.dim,
backend='keras')
]
right_outputs[level] = concatenate([
right_outputs[level], left_outputs[self.depth - level - 1]
],
axis=self.dim + 1)
right_outputs[level] = DnConv(
right_outputs[level],
filter_num,
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='upsampling_conv_{}_1'.format(level),
backend='keras')
right_outputs[level] = DnConv(
right_outputs[level],
int(filter_num / 2),
kernel_size=self.kernel_size,
stride_size=(1, ) * self.dim,
activation=self.activation,
padding=self.padding,
dim=self.dim,
name='upsampling_conv_{}_2'.format(level),
backend='keras')
else:
continue
if self.dropout is not None and self.dropout != 0:
right_outputs[level] = Dropout(self.dropout)(
right_outputs[level])
if self.batch_norm:
right_outputs[level] = BatchNormalization()(
right_outputs[level])
self.output_layer = DnConv(right_outputs[level],
1, (1, ) * self.dim,
stride_size=(1, ) * self.dim,
dim=self.dim,
name='end_conv',
backend='keras')
# TODO: Brainstorm better way to specify outputs
if self.input_tensor is None:
if self.output_type == 'regression':
self.model = Model(inputs=self.inputs,
outputs=self.output_layer)
self.model.compile(
optimizer=Nadam(lr=self.initial_learning_rate),
loss='mean_squared_error',
metrics=['mean_squared_error'])
if self.output_type == 'dice':
act = Activation('sigmoid')(self.output_layer)
self.model = Model(inputs=self.inputs, outputs=act)
self.model.compile(
optimizer=Nadam(lr=self.initial_learning_rate),
loss=dice_coef_loss,
metrics=[dice_coef])
if self.output_type == 'binary_label':
act = Activation('sigmoid')(self.output_layer)
self.model = Model(inputs=self.inputs, outputs=act)
self.model.compile(
optimizer=Nadam(lr=self.initial_learning_rate),
loss='binary_crossentropy',
metrics=['binary_accuracy'])
if self.output_type == 'categorical_label':
act = Activation('softmax')(self.output_layer)
self.model = Model(inputs=self.inputs, outputs=act)
self.model.compile(
optimizer=Nadam(lr=self.initial_learning_rate),
loss='categorical_crossentropy',
metrics=['categorical_accuracy'])
super(UNet, self).build()
return self.model
else:
return
def unet(model, input_tensor, backend='tensorflow'):
left_outputs = []
for level in range(model.depth):
filter_num = int(model.max_filter / (2 ** (model.depth - level)) / model.downsize_filters_factor)
if level == 0:
left_outputs += [DnConv(input_tensor, filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_downsampling_conv_{}_1'.format(level), backend=backend)]
left_outputs[level] = DnConv(left_outputs[level], 2 * filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_downsampling_conv_{}_2'.format(level), backend=backend)
else:
left_outputs += [DnMaxPooling(left_outputs[level - 1], pool_size=model.pool_size, dim=model.dim, backend=backend)]
left_outputs[level] = DnConv(left_outputs[level], filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_downsampling_conv_{}_1'.format(level), backend=backend)
left_outputs[level] = DnConv(left_outputs[level], 2 * filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_downsampling_conv_{}_2'.format(level), backend=backend)
if model.dropout is not None and model.dropout != 0:
left_outputs[level] = DnDropout(model.dropout)(left_outputs[level])
if model.batch_norm:
left_outputs[level] = DnBatchNormalization(left_outputs[level])
right_outputs = [left_outputs[model.depth - 1]]
for level in range(model.depth):
filter_num = int(model.max_filter / (2 ** (level)) / model.downsize_filters_factor)
if level > 0:
right_outputs += [DnUpsampling(right_outputs[level - 1], pool_size=model.pool_size, dim=model.dim, backend=backend)]
right_outputs[level] = concatenate([right_outputs[level], left_outputs[model.depth - level - 1]], axis=model.dim + 1)
right_outputs[level] = DnConv(right_outputs[level], filter_num, model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_upsampling_conv_{}_1'.format(level), backend=backend)
right_outputs[level] = DnConv(right_outputs[level], int(filter_num / 2), model.kernel_size, stride_size=(1,) * model.dim, activation=model.activation, padding=model.padding, dim=model.dim, name='unet_upsampling_conv_{}_2'.format(level), backend=backend)
else:
continue
if model.dropout is not None and model.dropout != 0:
right_outputs[level] = DnDropout(model.dropout)(right_outputs[level])
if model.batch_norm:
right_outputs[level] = DnBatchNormalization()(right_outputs[level])
output_layer = DnConv(right_outputs[level], 1, (1, ) * model.dim, stride_size=(1,) * model.dim, dim=model.dim, name='end_conv', backend=backend)
# TODO: Brainstorm better way to specify outputs
if model.input_tensor is not None:
return output_layer
return model.model
# def progressive_generator(model, latent_var, progressive_depth=1, name=None, transition=False, alpha_transition=0.0):
# with tf.variable_scope(name) as scope:
# convs = []
# convs += [tf.reshape(latent_var, [model.training_batch_size, 1, 1, model.latent_size])]
# convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(1, depth), kernel_size=(4, 4), stride_size=(1,) * model.dim, padding='Other', name='generator_n_1_conv', dim=model.dim)))
# convs += [tf.reshape(convs[-1], [model.training_batch_size, 4, 4, model.get_filter_num(1, depth)])] # why necessary? --andrew
# convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(1, depth), stride_size=(1,) * model.dim, name='generator_n_2_conv', dim=model.dim)))
# for i in range(progressive_depth - 1):
# if i == progressive_depth - 2 and transition: # redundant conditions? --andrew
# #To RGB
# # Don't totally understand this yet, diagram out --andrew
# transition_conv = DnConv(convs[-1], output_dim=model.channels, kernel_size=(1, 1), stride_size=(1,) * model.dim, name='generator_y_rgb_conv_{}'.format(convs[-1].shape[1]), dim=model.dim)
# transition_conv = upscale(transition_conv, 2)
# convs += [upscale(convs[-1], 2)]
# convs[-1] = DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(i + 1, depth), stride_size=(1,) * model.dim, name='generator_n_conv_1_{}'.format(convs[-1].shape[1]), dim=model.dim)))
# convs += [DnPixelNorm(leaky_relu(DnConv(convs[-1], output_dim=model.get_filter_num(i + 1, depth), stride_size=(1,) * model.dim, name='generator_n_conv_2_{}'.format(convs[-1].shape[1]), dim=model.dim)))]
# #To RGB
# convs += [DnConv(convs[-1], output_dim=model.channels, kernel_size=(1, 1), stride_size=(1,) * model.dim, name='generator_y_rgb_conv_{}'.format(convs[-1].shape[1]), dim=model.dim)]
# if transition:
# convs[-1] = (1 - alpha_transition) * transition_conv + alpha_transition * convs[-1]
# return convs[-1]