def myDenseNetv2Dropout(input_shape, dropout_rate=0.3):
"""
"""
bn_axis = -1 if K.image_data_format() == 'channels_last' else 1
input_tensor = Input(shape=input_shape) #48, 240, 360, 1
x = Conv3D(16, (3, 3, 3),
strides=(1, 2, 2),
use_bias=False,
padding='same',
name='block0_conv1')(input_tensor) #[48, 120, 180]
x = BatchNormalization(axis=bn_axis, epsilon=1.001e-5,
name='block0_bn1')(x)
x = Activation('relu', name='block0_relu1')(x)
x = Conv3D(16, (3, 3, 3),
strides=(1, 1, 1),
use_bias=False,
padding='same',
name='block0_conv2')(x) #[48, 120, 180]
x = _denseBlock(x, [16, 16], 'block_11') #[48, 120, 180]
x = _transit_block(x, 16, 'block13') #[48, 120, 180]
x = SpatialDropout3D(dropout_rate)(x)
x = MaxPooling3D((2, 2, 2), strides=(2, 2, 2),
padding='same')(x) #[24, 60, 90]
x = _denseBlock(x, [24, 24, 24], 'block_21') #[24, 60, 90]
x = _transit_block(x, 24, 'block23') #[24, 60, 90]
x = SpatialDropout3D(dropout_rate)(x)
x = MaxPooling3D((2, 2, 2), strides=(2, 2, 2),
padding='same')(x) #[12, 30, 45]
x = _denseBlock(x, [32, 32, 32, 32], 'block_31') #[12, 30, 45]
x = SpatialDropout3D(dropout_rate)(x)
x = MaxPooling3D((2, 2, 2), strides=(2, 2, 2),
padding='same')(x) #[6, 15, 23]
x = BatchNormalization(axis=bn_axis,
epsilon=1.001e-5,
name='block_final_bn')(x)
x = Activation('relu', name='block_final_relu')(x)
##############above are bae####################
x = _denseBlock(x, [32, 32], 'EGFR_block_11')
x = MaxPooling3D((1, 2, 2), strides=(1, 2, 2),
padding='same')(x) #[6, 8, 12, 64]
x = SpatialDropout3D(dropout_rate)(x)
x = _transit_block(x, 64, 'EGFR_block_12') #[6, 8, 12, 64]
x = GlobalAveragePooling3D()(x)
x = Dense(1, activation='sigmoid', name='EGFR_global_pred')(x)
# create model
model = Model(input_tensor, x, name='myDense')
plot_model(model, 'myDenseNetv2.png', show_shapes=True)
return model
def __init__(self, modelnet, args):
# TODO: Define a suitable model, and either `.compile` it, or prepare
# optimizer and loss manually.
inp = Input(shape=(modelnet.H, modelnet.W, modelnet.D, modelnet.C))
hidden = Conv3D(24, (3,3,3), activation=None, padding='same')(inp)
hidden = SpatialDropout3D(0.4)(hidden)
hidden = BatchNormalization()(hidden)
hidden = Activation(tf.nn.relu)(hidden)
hidden = Conv3D(24, (3,3,3), activation=None, padding='same')(hidden)
hidden = SpatialDropout3D(0.4)(hidden)
hidden = BatchNormalization()(hidden)
hidden = Activation(tf.nn.relu)(hidden)
hidden = MaxPooling3D((2,2,2))(hidden)
hidden = Conv3D(48, (3,3,3), activation=None)(hidden)
hidden = BatchNormalization()(hidden)
hidden = Activation(tf.nn.relu)(hidden)
hidden = Conv3D(48, (3,3,3), activation=None)(hidden)
hidden = BatchNormalization()(hidden)
hidden = Activation(tf.nn.relu)(hidden)
hidden = MaxPooling3D((2,2,2))(hidden)
hidden = Conv3D(96, (3,3,3), activation=None)(hidden)
hidden = BatchNormalization()(hidden)
hidden = Activation(tf.nn.relu)(hidden)
hidden = Conv3D(96, (3,3,3), activation=None)(hidden)
hidden = BatchNormalization()(hidden)
hidden = Activation(tf.nn.relu)(hidden)
hidden = MaxPooling3D((2,2,2))(hidden)
hidden = GlobalAveragePooling3D()(hidden)
output = Dense(len(modelnet.LABELS), activation=tf.nn.softmax)(hidden)
self.model = tf.keras.Model(inputs=inp, outputs=output)
self.model.compile(
optimizer=tf.optimizers.Adam(),
loss=tf.losses.SparseCategoricalCrossentropy(),
metrics=[tf.metrics.SparseCategoricalAccuracy(name="accuracy")]
)
self.tb_callback=tf.keras.callbacks.TensorBoard(args.logdir, update_freq=1000, profile_batch=1)
self.tb_callback.on_train_end = lambda *_: None
def up_stage(inputs,
skip,
filters,
kernel_size=3,
activation="relu",
padding="SAME"):
up = UpSampling3D()(inputs)
up = Conv3D(filters, 2, activation=activation, padding=padding)(up)
up = GroupNormalization()(up)
merge = concatenate([skip, up])
merge = GroupNormalization()(merge)
convu = Conv3D(filters,
kernel_size,
activation=activation,
padding=padding)(merge)
convu = GroupNormalization()(convu)
convu = Conv3D(filters,
kernel_size,
activation=activation,
padding=padding)(convu)
convu = GroupNormalization()(convu)
convu = SpatialDropout3D(0.5)(convu, training=True)
return convu
def create_context_module(input_layer, n_level_filters, dropout_rate=0.3, data_format="channels_last"):
layer1 = ReflectionPadding3D()(input_layer)
convolution1 = create_convolution_block(input_layer=layer1, n_filters=n_level_filters)
dropout = SpatialDropout3D(rate=dropout_rate, data_format=data_format)(convolution1)
layer2 = ReflectionPadding3D()(dropout)
convolution2 = create_convolution_block(input_layer=layer2, n_filters=n_level_filters)
return convolution2
def _conv_block(x, filters):
bn_scale = PARAMS['bn_scale']
activation = PARAMS['activation']
kernel_initializer = PARAMS['kernel_initializer']
weight_decay = PARAMS['weight_decay']
bottleneck = PARAMS['bottleneck']
dropout_rate = PARAMS['dropout_rate']
x = BatchNormalization(scale=bn_scale, axis=-1)(x)
x = activation()(x)
x = Conv3D(filters * bottleneck,
kernel_size=(1, 1, 1),
padding='same',
use_bias=False,
kernel_initializer=kernel_initializer,
kernel_regularizer=l2_penalty(weight_decay))(x)
if dropout_rate is not None:
x = SpatialDropout3D(dropout_rate)(x)
x = BatchNormalization(scale=bn_scale, axis=-1)(x)
x = activation()(x)
x = Conv3D(filters,
kernel_size=(3, 3, 3),
padding='same',
use_bias=True,
kernel_initializer=kernel_initializer,
kernel_regularizer=l2_penalty(weight_decay))(x)
return x
def get_small_3d_unet(input_shape):
img_input = Input(input_shape)
conv1 = conv_block_simple_3D(img_input, 32, "conv1_1")
conv1 = conv_block_simple_3D(conv1, 32, "conv1_2")
pool1 = MaxPooling3D((2, 2, 2),
strides=(2, 2, 2),
padding="same",
name="pool1",
data_format='channels_first')(conv1)
conv2 = conv_block_simple_3D(pool1, 64, "conv2_1")
conv2 = conv_block_simple_3D(conv2, 64, "conv2_2")
conv2 = conv_block_simple_3D(conv2, 64, "conv2_3")
up3 = concatenate(
[UpSampling3D(data_format='channels_first')(conv2), conv1], axis=1)
conv3 = conv_block_simple_3D(up3, 32, "conv3_1")
conv3 = conv_block_simple_3D(conv3, 32, "conv3_2")
conv3 = SpatialDropout3D(rate=0.2, data_format='channels_first')(conv3)
prediction = Conv3D(1, (1, 1, 1),
activation="sigmoid",
name="prediction",
data_format='channels_first')(conv3)
model = Model(img_input, prediction)
return model
def get_model(input_shape):
return Sequential([
InputLayer(input_shape=input_shape),
Conv3D(16, (4, 3, 3),
activation='relu',
bias_regularizer=l2(0.0001),
kernel_regularizer=l2(0.0001),
name="conv3d_0"),
SpatialDropout3D(0.4),
MaxPooling3D(),
Conv3D(32, (3, 3, 3),
activation='relu',
bias_regularizer=l2(0.0001),
kernel_regularizer=l2(0.0001),
name="conv3d_1"),
SpatialDropout3D(0.4),
MaxPooling3D(),
Conv3D(64, (1, 3, 3),
activation='relu',
bias_regularizer=l2(0.0001),
kernel_regularizer=l2(0.0001),
name="conv3d_2"),
SpatialDropout3D(0.35),
MaxPooling3D(),
Flatten(),
Dense(256,
activation='relu',
bias_regularizer=l2(0.0001),
kernel_regularizer=l2(0.0001),
name="dense_0"),
Dropout(0.5),
Dense(128,
activation='relu',
bias_regularizer=l2(0.0001),
kernel_regularizer=l2(0.0001),
name="dense_1"),
Dropout(0.25),
Dense(2,
activation='softmax',
bias_regularizer=l2(0.0001),
kernel_regularizer=l2(0.0001),
name="softmax")
])
def get_simple_3d_unet(input_shape):
img_input = Input(input_shape)
conv1 = conv_block_simple_3D(img_input, 32, "conv1_1")
conv1 = conv_block_simple_3D(conv1, 32, "conv1_2")
pool1 = MaxPooling3D((2, 2, 2),
strides=(2, 2, 2),
padding="same",
name="pool1",
data_format='channels_first')(conv1)
conv2 = conv_block_simple_3D(pool1, 64, "conv2_1")
conv2 = conv_block_simple_3D(conv2, 64, "conv2_2")
pool2 = MaxPooling3D((2, 2, 2),
strides=(2, 2, 2),
padding="same",
name="pool2",
data_format='channels_first')(conv2)
conv3 = conv_block_simple_3D(pool2, 128, "conv3_1")
conv3 = conv_block_simple_3D(conv3, 128, "conv3_2")
pool3 = MaxPooling3D((2, 2, 2),
strides=(2, 2, 2),
padding="same",
name="pool3",
data_format='channels_first')(conv3)
conv4 = conv_block_simple_3D(pool3, 256, "conv4_1")
conv4 = conv_block_simple_3D(conv4, 256, "conv4_2")
conv4 = conv_block_simple_3D(conv4, 256, "conv4_3")
up5 = concatenate(
[UpSampling3D(data_format='channels_first')(conv4), conv3], axis=1)
conv5 = conv_block_simple_3D(up5, 128, "conv5_1")
conv5 = conv_block_simple_3D(conv5, 128, "conv5_2")
up6 = concatenate(
[UpSampling3D(data_format='channels_first')(conv5), conv2], axis=1)
conv6 = conv_block_simple_3D(up6, 64, "conv6_1")
conv6 = conv_block_simple_3D(conv6, 64, "conv6_2")
up7 = concatenate(
[UpSampling3D(data_format='channels_first')(conv6), conv1], axis=1)
conv7 = conv_block_simple_3D(up7, 32, "conv7_1")
conv7 = conv_block_simple_3D(conv7, 32, "conv7_2")
conv7 = SpatialDropout3D(rate=0.2, data_format='channels_first')(conv7)
prediction = Conv3D(1, (1, 1, 1),
activation="sigmoid",
name="prediction",
data_format='channels_first')(conv7)
model = Model(img_input, prediction)
return model
def dropout_vnet(input_shape=(280, 280, 280, 1),
kernel_size=3,
activation="relu",
padding="SAME",
**kwargs):
inputs = Input(input_shape)
conv1, pool1 = down_stage(inputs,
16,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv2, pool2 = down_stage(pool1,
32,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv3, pool3 = down_stage(pool2,
64,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv4, _ = down_stage(pool3,
128,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv4 = SpatialDropout3D(0.5)(conv4, training=True)
conv5 = up_stage(conv4,
conv3,
64,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv6 = up_stage(conv5,
conv2,
32,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv7 = up_stage(conv6,
conv1,
16,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv8 = end_stage(conv7,
kernel_size=kernel_size,
activation=activation,
padding=padding)
return Model(inputs=inputs, outputs=conv8)
def create_context_module(input_layer,
n_level_filters,
dropout_rate=0.3,
data_format="channels_first"):
convolution1 = create_convolution_block(input_layer=input_layer,
n_filters=n_level_filters)
dropout = SpatialDropout3D(rate=dropout_rate,
data_format=data_format)(convolution1)
convolution2 = create_convolution_block(input_layer=dropout,
n_filters=n_level_filters)
return convolution2
def up_stage(inputs,
skip,
filters,
kernel_size=3,
activation="relu",
padding="SAME"):
"""decoding block of the VNet model.
Parameters
----------
inputs: tf.layer for encoding stage.
filters: list or tuple of four ints, the shape of the input data. Omit
the batch dimension, and include the number of channels.
kernal_size: int, size of the kernal of conv layers. Default kernal size
is set to be 3.
activation: str or optimizer object, the non-linearity to use. All
tf.activations are allowed to use
Returns
----------
decoded module.
"""
up = UpSampling3D()(inputs)
up = Conv3D(filters, 2, activation=activation, padding=padding)(up)
up = GroupNormalization()(up)
merge = concatenate([skip, up])
merge = GroupNormalization()(merge)
convu = Conv3D(filters,
kernel_size,
activation=activation,
padding=padding)(merge)
convu = GroupNormalization()(convu)
convu = Conv3D(filters,
kernel_size,
activation=activation,
padding=padding)(convu)
convu = GroupNormalization()(convu)
convu = SpatialDropout3D(0.5)(convu, training=True)
return convu
def _get_dropout_layer(self, layer_idx):
if layer_idx in self.dropout_contraction_levels:
dropout_level = self.dropout_levels[
self.dropout_contraction_levels.index(layer_idx)]
if self.spatial_dropout:
if self.image_shape is None or len(self.image_shape) < 3:
return SpatialDropout2D(
dropout_level,
name="{}_l{}_dropout".format(self.name, layer_idx)
if self.name else None)
else:
return SpatialDropout3D(
dropout_level,
name="{}_l{}_dropout".format(self.name, layer_idx)
if self.name else None)
else:
return Dropout(
dropout_level,
name="{}_l{}_dropout".format(self.name, layer_idx)
if self.name else None)
else:
return None
def residual_block_3d(input, number_of_filters):
block = convB_3d_layer(input, number_of_filters)
block = SpatialDropout3D(rate=0.3, data_format=data_format)(block)
block = convB_3d_layer(block, number_of_filters)
return (block)
def __init__(self,
input_shape=(4, 160, 192, 128),
output_channels=3,
l2_reg_weight=1e-5,
weight_L2=0.1,
weight_KL=0.1,
dice_e=1e-8,
test_mode=True,
n_gpu=1,
GL_weight=1,
VL_weight=0.1,
**kwargs):
super().__init__(**kwargs)
self.c, self.H, self.W, self.D = input_shape
self.n = self.c * self.H * self.W * self.D
assert len(input_shape) == 4, "Input shape must be a 4-tuple"
if test_mode is not True:
assert (self.c %
4) == 0, "The no. of channels must be divisible by 4"
assert (self.H % 16) == 0 and (self.W % 16) == 0 and (
self.D %
16) == 0, "All the input dimensions must be divisible by 16"
self.l2_regularizer = l2(
l2_reg_weight) if l2_reg_weight is not None else None
self.input_shape_p = input_shape
self.output_channels = output_channels
self.l2_reg_weight = l2_reg_weight
self.weight_L2 = weight_L2
self.weight_KL = weight_KL
self.dice_e = dice_e
self.GL_weight = GL_weight
self.VL_weight = VL_weight
self.LossVAE = LossVAE(weight_L2, weight_KL, self.n)
## The Initial Block
self.Input_x1 = Conv3D(filters=32,
kernel_size=(3, 3, 3),
strides=1,
padding='same',
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Input_x1')
## Dropout (0.2)
self.spatial_dropout = SpatialDropout3D(0.2,
data_format='channels_first')
## Green Block x1 (output filters = 32)
self.x1 = green_block(32, regularizer=self.l2_regularizer, name='x1')
self.Enc_DownSample_32 = Conv3D(filters=32,
kernel_size=(3, 3, 3),
strides=2,
padding='same',
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Enc_DownSample_32')
## Green Block x2 (output filters = 64)
self.Enc_64_1 = green_block(64,
regularizer=self.l2_regularizer,
name='Enc_64_1')
self.x2 = green_block(64, regularizer=self.l2_regularizer, name='x2')
self.Enc_DownSample_64 = Conv3D(filters=64,
kernel_size=(3, 3, 3),
strides=2,
padding='same',
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Enc_DownSample_64')
## Green Blocks x2 (output filters = 128)
self.Enc_128_1 = green_block(128,
regularizer=self.l2_regularizer,
name='Enc_128_1')
self.x3 = green_block(128, regularizer=self.l2_regularizer, name='x3')
self.Enc_DownSample_128 = Conv3D(
filters=128,
kernel_size=(3, 3, 3),
strides=2,
padding='same',
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Enc_DownSample_128')
## Green Blocks x4 (output filters = 256)
self.Enc_256_1 = green_block(256,
regularizer=self.l2_regularizer,
name='Enc_256_1')
self.Enc_256_2 = green_block(256,
regularizer=self.l2_regularizer,
name='Enc_256_2')
self.Enc_256_3 = green_block(256,
regularizer=self.l2_regularizer,
name='Enc_256_3')
self.x4 = green_block(256, regularizer=self.l2_regularizer, name='x4')
# -------------------------------------------------------------------------
# Decoder
# -------------------------------------------------------------------------
## GT (Groud Truth) Part
# -------------------------------------------------------------------------
### Green Block x1 (output filters=128)
self.Dec_GT_ReduceDepth_128 = Conv3D(
filters=128,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_GT_ReduceDepth_128')
self.Dec_GT_UpSample_128 = UpSampling3D(size=2,
data_format='channels_first',
name='Dec_GT_UpSample_128')
self.Input_Dec_GT_128 = Add(name='Input_Dec_GT_128')
self.Dec_GT_128 = green_block(128,
regularizer=self.l2_regularizer,
name='Dec_GT_128')
### Green Block x1 (output filters=64)
self.Dec_GT_ReduceDepth_64 = Conv3D(
filters=64,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_GT_ReduceDepth_64')
self.Dec_GT_UpSample_64 = UpSampling3D(size=2,
data_format='channels_first',
name='Dec_GT_UpSample_64')
self.Input_Dec_GT_64 = Add(name='Input_Dec_GT_64')
self.Dec_GT_64 = green_block(64,
regularizer=self.l2_regularizer,
name='Dec_GT_64')
### Green Block x1 (output filters=32)
self.Dec_GT_ReduceDepth_32 = Conv3D(
filters=32,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_GT_ReduceDepth_32')
self.Dec_GT_UpSample_32 = UpSampling3D(size=2,
data_format='channels_first',
name='Dec_GT_UpSample_32')
self.Input_Dec_GT_32 = Add(name='Input_Dec_GT_32')
self.Dec_GT_32 = green_block(32,
regularizer=self.l2_regularizer,
name='Dec_GT_32')
### Blue Block x1 (output filters=32)
self.Input_Dec_GT_Output = Conv3D(
filters=32,
kernel_size=(3, 3, 3),
strides=1,
padding='same',
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Input_Dec_GT_Output')
### Output Block
self.Dec_GT_Output = Conv3D(filters=self.output_channels,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
activation='sigmoid',
name='Dec_GT_Output')
## VAE (Variational Auto Encoder) Part
# -------------------------------------------------------------------------
### VD Block (Reducing dimensionality of the data)
self.Dec_VAE_VD_GN = GroupNormalization(groups=8,
axis=1,
name='Dec_VAE_VD_GN')
self.Dec_VAE_VD_relu = Activation('relu', name='Dec_VAE_VD_relu')
self.Dec_VAE_VD_Conv3D = Conv3D(filters=16,
kernel_size=(3, 3, 3),
strides=2,
padding='same',
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_VAE_VD_Conv3D')
# Not mentioned in the paper, but the author used a Flattening layer here.
self.Dec_VAE_VD_Flatten = Flatten(name='Dec_VAE_VD_Flatten')
self.Dec_VAE_VD_Dense = Dense(256, name='Dec_VAE_VD_Dense')
### VDraw Block (Sampling)
self.Dec_VAE_VDraw_Mean = Dense(128, name='Dec_VAE_VDraw_Mean')
self.Dec_VAE_VDraw_Var = Dense(128, name='Dec_VAE_VDraw_Var')
# self.Dec_VAE_VDraw_Sampling = Lambda(sampling, name='Dec_VAE_VDraw_Sampling')
self.Dec_VAE_VDraw_Sampling = sampling()
### VU Block (Upsizing back to a depth of 256)
c1 = 1
self.VU_Dense1 = Dense(
(c1) * (self.H // 16) * (self.W // 16) * (self.D // 16))
self.VU_relu = Activation('relu')
self.VU_reshape = Reshape(
((c1), (self.H // 16), (self.W // 16), (self.D // 16)))
self.Dec_VAE_ReduceDepth_256 = Conv3D(
filters=256,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_VAE_ReduceDepth_256')
self.Dec_VAE_UpSample_256 = UpSampling3D(size=2,
data_format='channels_first',
name='Dec_VAE_UpSample_256')
### Green Block x1 (output filters=128)
self.Dec_VAE_ReduceDepth_128 = Conv3D(
filters=128,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_VAE_ReduceDepth_128')
self.Dec_VAE_UpSample_128 = UpSampling3D(size=2,
data_format='channels_first',
name='Dec_VAE_UpSample_128')
self.Dec_VAE_128 = green_block(128,
regularizer=self.l2_regularizer,
name='Dec_VAE_128')
### Green Block x1 (output filters=64)
self.Dec_VAE_ReduceDepth_64 = Conv3D(
filters=64,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_VAE_ReduceDepth_64')
self.Dec_VAE_UpSample_64 = UpSampling3D(size=2,
data_format='channels_first',
name='Dec_VAE_UpSample_64')
self.Dec_VAE_64 = green_block(64,
regularizer=self.l2_regularizer,
name='Dec_VAE_64')
### Green Block x1 (output filters=32)
self.Dec_VAE_ReduceDepth_32 = Conv3D(
filters=32,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_VAE_ReduceDepth_32')
self.Dec_VAE_UpSample_32 = UpSampling3D(size=2,
data_format='channels_first',
name='Dec_VAE_UpSample_32')
self.Dec_VAE_32 = green_block(32,
regularizer=self.l2_regularizer,
name='Dec_VAE_32')
### Blue Block x1 (output filters=32)
self.Input_Dec_VAE_Output = Conv3D(
filters=32,
kernel_size=(3, 3, 3),
strides=1,
padding='same',
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Input_Dec_VAE_Output')
### Output Block
self.Dec_VAE_Output = Conv3D(filters=self.c,
kernel_size=(1, 1, 1),
strides=1,
kernel_regularizer=self.l2_regularizer,
data_format='channels_first',
name='Dec_VAE_Output')
def SE_U_Net_3D(image_shape,
activation='elu',
feature_maps=[32, 64, 128, 256],
depth=3,
drop_values=[0.1, 0.1, 0.1, 0.1],
spatial_dropout=False,
batch_norm=False,
k_init='he_normal',
loss_type="bce",
optimizer="sgd",
lr=0.001,
n_classes=1):
"""Create 3D U-Net with squeeze-excite blocks.
Reference `Squeeze and Excitation Networks <https://arxiv.org/abs/1709.01507>`_.
Parameters
----------
image_shape : 3D tuple
Dimensions of the input image.
activation : str, optional
Keras available activation type.
feature_maps : array of ints, optional
Feature maps to use on each level. Must have the same length as the
``depth+1``.
depth : int, optional
Depth of the network.
drop_values : float, optional
Dropout value to be fixed.
spatial_dropout : bool, optional
Use spatial dropout instead of the `normal` dropout.
batch_norm : bool, optional
Make batch normalization.
k_init : string, optional
Kernel initialization for convolutional layers.
loss_type : str, optional
Loss type to use, three type available: ``bce`` (Binary Cross Entropy)
, ``w_bce`` (Weighted BCE, based on weigth maps) and ``w_bce_dice``
(Weighted loss: ``weight1*BCE + weight2*Dice``).
optimizer : str, optional
Optimizer used to minimize the loss function. Posible options: ``sgd``
or ``adam``.
lr : float, optional
Learning rate value.
n_classes: int, optional
Number of classes.
Returns
-------
model : Keras model
Model containing the U-Net.
Calling this function with its default parameters returns the following
network:
.. image:: img/unet_3d.png
:width: 100%
:align: center
Image created with `PlotNeuralNet <https://github.com/HarisIqbal88/PlotNeuralNet>`_.
"""
if len(feature_maps) != depth + 1:
raise ValueError("feature_maps dimension must be equal depth+1")
if len(drop_values) != depth + 1:
raise ValueError("'drop_values' dimension must be equal depth+1")
#dinamic_dim = (None,)*(len(image_shape)-1) + (image_shape[-1],)
#inputs = Input(dinamic_dim)
x = Input(image_shape)
inputs = x
if loss_type == "w_bce":
weights = Input(image_shape)
# List used to access layers easily to make the skip connections of the U-Net
l = []
# ENCODER
for i in range(depth):
x = Conv3D(feature_maps[i], (3, 3, 3),
activation=None,
kernel_initializer=k_init,
padding='same')(x)
x = BatchNormalization()(x) if batch_norm else x
x = Activation(activation)(x)
x = squeeze_excite_block(x)
if spatial_dropout and drop_values[i] > 0:
x = SpatialDropout3D(drop_values[i])(x)
elif drop_values[i] > 0 and not spatial_dropout:
x = Dropout(drop_values[i])(x)
x = Conv3D(feature_maps[i], (3, 3, 3),
activation=None,
kernel_initializer=k_init,
padding='same')(x)
x = BatchNormalization()(x) if batch_norm else x
x = Activation(activation)(x)
x = squeeze_excite_block(x)
l.append(x)
x = MaxPooling3D((2, 2, 2))(x)
# BOTTLENECK
x = Conv3D(feature_maps[depth], (3, 3, 3),
activation=None,
kernel_initializer=k_init,
padding='same')(x)
x = BatchNormalization()(x) if batch_norm else x
x = Activation(activation)(x)
if spatial_dropout and drop_values[depth] > 0:
x = SpatialDropout3D(drop_values[depth])(x)
elif drop_values[depth] > 0 and not spatial_dropout:
x = Dropout(drop_values[depth])(x)
x = Conv3D(feature_maps[depth], (3, 3, 3),
activation=None,
kernel_initializer=k_init,
padding='same')(x)
x = BatchNormalization()(x) if batch_norm else x
x = Activation(activation)(x)
# DECODER
for i in range(depth - 1, -1, -1):
x = Conv3DTranspose(feature_maps[i], (2, 2, 2),
strides=(2, 2, 2),
padding='same')(x)
x = concatenate([x, l[i]])
x = Conv3D(feature_maps[i], (3, 3, 3),
activation=None,
kernel_initializer=k_init,
padding='same')(x)
x = BatchNormalization()(x) if batch_norm else x
x = Activation(activation)(x)
x = squeeze_excite_block(x)
if spatial_dropout and drop_values[i] > 0:
x = SpatialDropout3D(drop_values[i])(x)
elif drop_values[i] > 0 and not spatial_dropout:
x = Dropout(drop_values[i])(x)
x = Conv3D(feature_maps[i], (3, 3, 3),
activation=None,
kernel_initializer=k_init,
padding='same')(x)
x = BatchNormalization()(x) if batch_norm else x
x = Activation(activation)(x)
x = squeeze_excite_block(x)
outputs = Conv3D(n_classes, (1, 1, 1), activation='sigmoid')(x)
# Loss type
if loss_type == "w_bce":
model = Model(inputs=[inputs, weights], outputs=[outputs])
else:
model = Model(inputs=[inputs], outputs=[outputs])
# Select the optimizer
if optimizer == "sgd":
opt = tf.keras.optimizers.SGD(lr=lr,
momentum=0.99,
decay=0.0,
nesterov=False)
elif optimizer == "adam":
opt = tf.keras.optimizers.Adam(lr=lr,
beta_1=0.9,
beta_2=0.999,
epsilon=None,
decay=0.0,
amsgrad=False)
else:
raise ValueError("Error: optimizer value must be 'sgd' or 'adam'")
# Compile the model
if loss_type == "bce":
if n_classes > 1:
model.compile(optimizer=opt,
loss='categorical_crossentropy',
metrics=[jaccard_index_softmax])
else:
model.compile(optimizer=opt,
loss='binary_crossentropy',
metrics=[jaccard_index])
elif loss_type == "w_bce":
model.compile(optimizer=opt,
loss=binary_crossentropy_weighted(weights),
metrics=[jaccard_index])
elif loss_type == "w_bce_dice":
model.compile(optimizer=opt,
loss=weighted_bce_dice_loss(w_dice=0.66, w_bce=0.33),
metrics=[jaccard_index])
else:
raise ValueError("'loss_type' must be 'bce', 'w_bce' or 'w_bce_dice'")
return model
def create_model_3D(self, input_shape, n_labels=2):
# Input layer
inputs = Input(input_shape)
# Cache contracting normalized conv layers
# for later copy & concatenate links
contracting_convs = {c: [] for c in self.feature_maps.keys()}
all_middle_chains = []
all_chains = []
for stride, feature_map in self.feature_maps.items():
# Start the CNN Model chain with adding the inputs as first tensor
cnn_chain = inputs
# Contracting layers
for i in range(0, len(feature_map)):
neurons = feature_map[i]
cnn_chain = conv_layer_3D(cnn_chain, neurons,
self.conv_layer_activation,
self.inst_norm,
self.inst_norm_params)
cnn_chain = conv_layer_3D(cnn_chain, neurons,
self.conv_layer_activation,
self.inst_norm,
self.inst_norm_params)
cnn_chain = SpatialDropout3D(self.dropout)(cnn_chain)
contracting_convs[stride].append(cnn_chain)
cnn_chain = MaxPooling3D(pool_size=(stride, stride,
stride))(cnn_chain)
# Middle Layer
neurons = feature_map[-1]
cnn_chain = conv_layer_3D(cnn_chain, neurons,
self.conv_layer_activation,
self.inst_norm, self.inst_norm_params)
cnn_chain = conv_layer_3D(cnn_chain, neurons,
self.conv_layer_activation,
self.inst_norm, self.inst_norm_params)
all_middle_chains.append(cnn_chain)
cnn_chain1 = concatenate(all_middle_chains)
cnn_chain1 = LayerNormalization(**self.layer_norm_params)(cnn_chain1)
for stride, feature_map in self.feature_maps.items():
# Start the CNN Model chain with adding the inputs as first tensor
cnn_chain = cnn_chain1
# Expanding Layers
for i in reversed(range(0, len(feature_map))):
neurons = feature_map[i]
cnn_chain = Conv3DTranspose(neurons, (stride, stride, stride),
strides=(stride, stride, stride),
padding='same')(cnn_chain)
cnn_chain = SpatialDropout3D(self.dropout)(cnn_chain)
cnn_chain = concatenate(
[cnn_chain, contracting_convs[stride][i]], axis=-1)
cnn_chain = conv_layer_3D(cnn_chain, neurons,
self.conv_layer_activation,
self.inst_norm,
self.inst_norm_params)
cnn_chain = conv_layer_3D(cnn_chain, neurons,
self.conv_layer_activation,
self.inst_norm,
self.inst_norm_params)
all_chains.append(cnn_chain)
# Output Layer
conv_out = Conv3D(n_labels, (1, 1, 1),
activation=self.activation)(concatenate(all_chains,
axis=-1))
# Create Model with associated input and output layers
model = Model(inputs=[inputs], outputs=[conv_out])
# Return model
return model
def create_model(conv_1,conv_2,conv_3,conv_4,conv_5,activation,initializer,conv_dropout,cnv_drp_rate,
filt_size,pool_size,l2_penalty,ff1,ff2,ff3,ff4,batch_norm,mom,ffdrop,drp_rate,
padding):
"""creates convolutional neural network with tensorflow keras layers in 3 distinct blocks"""
model=Sequential()
model.add(Conv3D(conv_1,filt_size,input_shape=(125,145,125,1),activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='conv_1',padding=padding))
model.add(Conv3D(conv_2,filt_size,activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='conv_2',padding=padding))
if conv_dropout == True:
model.add(SpatialDropout3D(cnv_drp_rate,name='spatial_dropout_1'))
model.add(MaxPooling3D(pool_size,name='max_pool_1'))
model.add(Conv3D(conv_3,filt_size,activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='conv_3',padding=padding))
model.add(Conv3D(conv_4,filt_size,activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='conv_4',padding=padding))
if conv_dropout == True:
model.add(SpatialDropout3D(cnv_drp_rate,name='spatial_dropout_2'))
model.add(MaxPooling3D(pool_size,name='max_pool_2'))
model.add(Conv3D(conv_5,filt_size,activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='conv_5',padding=padding))
if conv_dropout == True:
model.add(SpatialDropout3D(cnv_drp_rate,name='spatial_dropout_3'))
model.add(MaxPooling3D(pool_size,name='max_pool_3'))
model.add(Flatten(name='flatten'))
model.add(Dense(ff1,activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='dense_1'))
if batch_norm==True:
model.add(BatchNormalization(momentum=mom,name='batch_norm_1'))
if ffdrop==True:
model.add(Dropout(drp_rate,name='dense_dropout_1'))
model.add(Dense(ff2,activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='dense_2'))
if batch_norm==True:
model.add(BatchNormalization(momentum=mom,name='batch_norm_2'))
if ffdrop==True:
model.add(Dropout(drp_rate,name='dense_dropout_2'))
model.add(Dense(ff3,activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='dense_3'))
if batch_norm==True:
model.add(BatchNormalization(momentum=mom,name='batch_norm_3'))
if ffdrop==True:
model.add(Dropout(drp_rate,name='dense_dropout_3'))
model.add(Dense(ff4,activation=activation,
kernel_initializer=initializer,kernel_regularizer=l2(l2_penalty),
name='dense_4'))
model.add(Dense(1,activation='sigmoid',name='prediction'))
return(model)
def build_model(input_shape=(4, 160, 192, 128), output_channels=3, weight_L2=0.1, weight_KL=0.1, dice_e=1e-8):
"""
build_model(input_shape=(4, 160, 192, 128), output_channels=3, weight_L2=0.1, weight_KL=0.1)
-------------------------------------------
Creates the model used in the BRATS2018 winning solution
by Myronenko A. (https://arxiv.org/pdf/1810.11654.pdf)
Parameters
----------
`input_shape`: A 4-tuple, optional.
Shape of the input image. Must be a 4D image of shape (c, H, W, D),
where, each of H, W and D are divisible by 2^4, and c is divisible by 4.
Defaults to the crop size used in the paper, i.e., (4, 160, 192, 128).
`output_channels`: An integer, optional.
The no. of channels in the output. Defaults to 3 (BraTS 2018 format).
`weight_L2`: A real number, optional
The weight to be given to the L2 loss term in the loss function. Adjust to get best
results for your task. Defaults to 0.1.
`weight_KL`: A real number, optional
The weight to be given to the KL loss term in the loss function. Adjust to get best
results for your task. Defaults to 0.1.
`dice_e`: Float, optional
A small epsilon term to add in the denominator of dice loss to avoid dividing by
zero and possible gradient explosion. This argument will be passed to loss_gt function.
Returns
-------
`model`: A keras.models.Model instance
The created model.
"""
c, H, W, D = input_shape
assert len(input_shape) == 4, "Input shape must be a 4-tuple"
assert (c % 4) == 0, "The no. of channels must be divisible by 4"
assert (H % 16) == 0 and (W % 16) == 0 and (D % 16) == 0, \
"All the input dimensions must be divisible by 16"
# -------------------------------------------------------------------------
# Encoder
# -------------------------------------------------------------------------
## Input Layer
inp = Input(input_shape)
## The Initial Block
x = Conv3D(
filters=32,
kernel_size=(3, 3, 3),
strides=1,
padding='same',
data_format='channels_first',
name='Input_x1')(inp)
## Dropout (0.2)
x = SpatialDropout3D(0.2, data_format='channels_first')(x)
## Green Block x1 (output filters = 32)
x1 = green_block(x, 32, name='x1')
x = Conv3D(
filters=32,
kernel_size=(3, 3, 3),
strides=2,
padding='same',
data_format='channels_first',
name='Enc_DownSample_32')(x1)
## Green Block x2 (output filters = 64)
x = green_block(x, 64, name='Enc_64_1')
x2 = green_block(x, 64, name='x2')
x = Conv3D(
filters=64,
kernel_size=(3, 3, 3),
strides=2,
padding='same',
data_format='channels_first',
name='Enc_DownSample_64')(x2)
## Green Blocks x2 (output filters = 128)
x = green_block(x, 128, name='Enc_128_1')
x3 = green_block(x, 128, name='x3')
x = Conv3D(
filters=128,
kernel_size=(3, 3, 3),
strides=2,
padding='same',
data_format='channels_first',
name='Enc_DownSample_128')(x3)
## Green Blocks x4 (output filters = 256)
x = green_block(x, 256, name='Enc_256_1')
x = green_block(x, 256, name='Enc_256_2')
x = green_block(x, 256, name='Enc_256_3')
x4 = green_block(x, 256, name='x4')
# -------------------------------------------------------------------------
# Decoder
# -------------------------------------------------------------------------
## GT (Groud Truth) Part
# -------------------------------------------------------------------------
### Green Block x1 (output filters=128)
x = Conv3D(
filters=128,
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
name='Dec_GT_ReduceDepth_128')(x4)
x = UpSampling3D(
size=2,
data_format='channels_first',
name='Dec_GT_UpSample_128')(x)
x = Add(name='Input_Dec_GT_128')([x, x3])
x = green_block(x, 128, name='Dec_GT_128')
### Green Block x1 (output filters=64)
x = Conv3D(
filters=64,
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
name='Dec_GT_ReduceDepth_64')(x)
x = UpSampling3D(
size=2,
data_format='channels_first',
name='Dec_GT_UpSample_64')(x)
x = Add(name='Input_Dec_GT_64')([x, x2])
x = green_block(x, 64, name='Dec_GT_64')
### Green Block x1 (output filters=32)
x = Conv3D(
filters=32,
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
name='Dec_GT_ReduceDepth_32')(x)
x = UpSampling3D(
size=2,
data_format='channels_first',
name='Dec_GT_UpSample_32')(x)
x = Add(name='Input_Dec_GT_32')([x, x1])
x = green_block(x, 32, name='Dec_GT_32')
### Blue Block x1 (output filters=32)
x = Conv3D(
filters=32,
kernel_size=(3, 3, 3),
strides=1,
padding='same',
data_format='channels_first',
name='Input_Dec_GT_Output')(x)
### Output Block
out_GT = Conv3D(
filters=output_channels, # No. of tumor classes is 3
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
activation='sigmoid',
name='Dec_GT_Output')(x)
## VAE (Variational Auto Encoder) Part
# -------------------------------------------------------------------------
### VD Block (Reducing dimensionality of the data)
x = GroupNormalization(groups=8, axis=1, name='Dec_VAE_VD_GN')(x4)
x = Activation('relu', name='Dec_VAE_VD_relu')(x)
x = Conv3D(
filters=16,
kernel_size=(3, 3, 3),
strides=2,
padding='same',
data_format='channels_first',
name='Dec_VAE_VD_Conv3D')(x)
# Not mentioned in the paper, but the author used a Flattening layer here.
x = Flatten(name='Dec_VAE_VD_Flatten')(x)
x = Dense(256, name='Dec_VAE_VD_Dense')(x)
### VDraw Block (Sampling)
z_mean = Dense(128, name='Dec_VAE_VDraw_Mean')(x)
z_var = Dense(128, name='Dec_VAE_VDraw_Var')(x)
x = Lambda(sampling, name='Dec_VAE_VDraw_Sampling')([z_mean, z_var])
### VU Block (Upsizing back to a depth of 256)
x = Dense((c//4) * (H//16) * (W//16) * (D//16))(x)
x = Activation('relu')(x)
x = Reshape(((c//4), (H//16), (W//16), (D//16)))(x)
x = Conv3D(
filters=256,
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
name='Dec_VAE_ReduceDepth_256')(x)
x = UpSampling3D(
size=2,
data_format='channels_first',
name='Dec_VAE_UpSample_256')(x)
### Green Block x1 (output filters=128)
x = Conv3D(
filters=128,
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
name='Dec_VAE_ReduceDepth_128')(x)
x = UpSampling3D(
size=2,
data_format='channels_first',
name='Dec_VAE_UpSample_128')(x)
x = green_block(x, 128, name='Dec_VAE_128')
### Green Block x1 (output filters=64)
x = Conv3D(
filters=64,
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
name='Dec_VAE_ReduceDepth_64')(x)
x = UpSampling3D(
size=2,
data_format='channels_first',
name='Dec_VAE_UpSample_64')(x)
x = green_block(x, 64, name='Dec_VAE_64')
### Green Block x1 (output filters=32)
x = Conv3D(
filters=32,
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
name='Dec_VAE_ReduceDepth_32')(x)
x = UpSampling3D(
size=2,
data_format='channels_first',
name='Dec_VAE_UpSample_32')(x)
x = green_block(x, 32, name='Dec_VAE_32')
### Blue Block x1 (output filters=32)
x = Conv3D(
filters=32,
kernel_size=(3, 3, 3),
strides=1,
padding='same',
data_format='channels_first',
name='Input_Dec_VAE_Output')(x)
### Output Block
out_VAE = Conv3D(
filters=4,
kernel_size=(1, 1, 1),
strides=1,
data_format='channels_first',
name='Dec_VAE_Output')(x)
# Build and Compile the model
out = out_GT
model = Model(inp, outputs=[out, out_VAE]) # Create the model
model.compile(
Adam(lr=1e-4),
[loss_gt(dice_e), loss_VAE(input_shape, z_mean, z_var, weight_L2=weight_L2, weight_KL=weight_KL)],
metrics=[dice_coefficient]
)
return model
def create_unet_model3D(input_image_size,
n_labels=1,
layers=4,
lowest_resolution=16,
convolution_kernel_size=(5, 5, 5),
deconvolution_kernel_size=(5, 5, 5),
pool_size=(2, 2, 2),
strides=(1, 1, 1),
mode='classification',
output_activation='tanh',
activation='relu',
init_lr=0.0001,
dropout=0.2,
dropout_type='spatial',
batchnorm=False):
"""
Create a 3D Unet model
Example
-------
unet_model = create_unet_model3D( (128,128,128,1), 1, 4)
"""
layers = np.arange(layers)
number_of_classification_labels = n_labels
inputs = Input(shape=input_image_size)
## ENCODING PATH ##
encoding_convolution_layers = []
pool = None
conv_tot = 0
for i in range(len(layers)):
number_of_filters = lowest_resolution * 2**(layers[i])
conv_tot += 1
if i == 0:
conv = Conv3D(filters=number_of_filters,
kernel_size=convolution_kernel_size,
activation=activation,
padding='same',
name='conv3d_' + str(conv_tot))(inputs)
else:
conv = Conv3D(filters=number_of_filters,
kernel_size=convolution_kernel_size,
activation=activation,
padding='same',
name='conv3d_' + str(conv_tot))(pool)
if dropout is not None:
if dropout_type is 'spatial':
conv = SpatialDropout3D(dropout)(conv)
else:
conv = Dropout(dropout)(conv)
if batchnorm is True:
conv = BatchNormalization(axis=4)(conv)
conv_tot += 1
encoding_convolution_layers.append(
Conv3D(filters=number_of_filters,
kernel_size=convolution_kernel_size,
activation=activation,
padding='same',
name='conv3d_' + str(conv_tot))(conv))
if i < len(layers) - 1:
pool = MaxPooling3D(pool_size=pool_size, name='pool_' + str(i))(
encoding_convolution_layers[i])
## DECODING PATH ##
outputs = encoding_convolution_layers[len(layers) - 1]
conv_tot += 1
print(conv_tot)
for j in range(1, len(layers)):
if j < len(layers) - 1:
decon_kernel_size = deconvolution_kernel_size
else:
decon_kernel_size = deconvolution_kernel_size
number_of_filters = lowest_resolution * 2**(len(layers) - layers[j] -
1)
tmp_deconv = Conv3DTranspose(filters=number_of_filters,
kernel_size=decon_kernel_size,
padding='same',
name='trans_' + str(j))(outputs)
tmp_deconv = UpSampling3D(size=pool_size,
name='upsamp_' + str(j))(tmp_deconv)
outputs = Concatenate(axis=4, name='concat_' + str(j))(
[tmp_deconv, encoding_convolution_layers[len(layers) - j - 1]])
conv_tot += 1
outputs = Conv3D(filters=number_of_filters,
kernel_size=convolution_kernel_size,
activation=activation,
padding='same',
name='conv3d_' + str(conv_tot))(outputs)
if dropout is not None:
if dropout_type is 'spatial':
outputs = SpatialDropout3D(dropout)(outputs)
else:
outputs = Dropout(dropout)(outputs)
if batchnorm is True:
outputs = BatchNormalization(axis=4)(outputs)
conv_tot += 1
outputs = Conv3D(filters=number_of_filters,
kernel_size=convolution_kernel_size,
activation=activation,
padding='same',
name='conv3d_' + str(conv_tot))(outputs)
if dropout is not None:
if dropout_type is 'spatial':
outputs = SpatialDropout3D(dropout)(outputs)
else:
outputs = Dropout(dropout)(outputs)
if batchnorm is True:
outputs = BatchNormalization(axis=4)(outputs)
if mode == 'classification':
if number_of_classification_labels == 1:
outputs = Conv3D(filters=number_of_classification_labels,
kernel_size=(1, 1, 1),
activation='sigmoid')(outputs)
else:
outputs = Conv3D(filters=number_of_classification_labels,
kernel_size=(1, 1, 1),
activation='softmax')(outputs)
unet_model = Model(inputs=inputs, outputs=outputs)
if number_of_classification_labels == 1:
unet_model.compile(loss=jaccard_distance,
optimizer=opt.Adam(lr=init_lr),
metrics=[
'binary_accuracy', 'binary_crossentropy',
dice_coefficient_bin
])
else:
unet_model.compile(
loss='categorical_crossentropy',
optimizer=opt.Adam(lr=init_lr),
metrics=['categorical_accuracy', 'categorical_crossentropy'])
elif mode == 'regression':
conv_tot += 1
outputs = Conv3D(filters=1,
kernel_size=(1, 1, 1),
activation=output_activation,
name='conv3d_' + str(conv_tot))(outputs)
unet_model = Model(inputs=inputs, outputs=outputs)
unet_model.compile(loss='mse',
optimizer=opt.Adam(lr=init_lr),
metrics=[correlation, correlation_gm, mse_gm])
else:
raise ValueError(
'mode must be either `classification` or `regression`')
return unet_model
def vnet(n_classes=1,
input_shape=(128, 128, 128, 1),
kernel_size=3,
activation="relu",
padding="SAME",
**kwargs):
"""Instantiate a 3D VNet Architecture.
VNet model: a 3D deep neural network model adapted from
https://arxiv.org/pdf/1606.04797.pdf adatptations include groupnorm
and spatial dropout.
Parameters
----------
n_classes: int, number of classes to classify. For binary applications, use
a value of 1.
input_shape: list or tuple of four ints, the shape of the input data. Omit
the batch dimension, and include the number of channels.
kernal_size: int, size of the kernal of conv layers. Default kernal size
is set to be 3.
activation: str or optimizer object, the non-linearity to use. All
tf.activations are allowed to use
Returns
----------
Model object.
"""
inputs = Input(input_shape)
conv1, pool1 = down_stage(inputs,
16,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv2, pool2 = down_stage(pool1,
32,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv3, pool3 = down_stage(pool2,
64,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv4, _ = down_stage(pool3,
128,
kernel_size=kernel_size,
activation=activation,
padding=padding)
conv4 = SpatialDropout3D(0.5)(conv4, training=True)
conv5 = up_stage(
conv4,
conv3,
64,
kernel_size=kernel_size,
activation=activation,
padding=padding,
)
conv6 = up_stage(
conv5,
conv2,
32,
kernel_size=kernel_size,
activation=activation,
padding=padding,
)
conv7 = up_stage(
conv6,
conv1,
16,
kernel_size=kernel_size,
activation=activation,
padding=padding,
)
conv8 = end_stage(
conv7,
n_classes=n_classes,
kernel_size=kernel_size,
activation=activation,
padding=padding,
)
return Model(inputs=inputs, outputs=conv8)