def _down_block(tensor,
num_filters,
kernel_size=3,
padding='same',
strides=2,
shortcut=True,
activation='lrelu',
dropout_rate=None,
dropout_wrn=False,
down_sampling='strided_conv',
initializer='orthogonal',
batchnorm=True,
name=''):
tensor = Conv3D(kernel_size=1, filters=num_filters)(tensor)
tensor = _resnet_block(tensor,
num_filters,
kernel_size,
shortcut=shortcut,
padding=padding,
activation=activation,
initializer='orthogonal',
dropout_rate=dropout_rate,
dropout_wrn=dropout_wrn,
batchnorm=batchnorm,
name=name)
skip_tensor = tensor
# down-sampling
if down_sampling == 'strided_conv':
tensor = Conv3D(filters=num_filters,
kernel_size=kernel_size * 2 - 1,
strides=strides,
padding=padding,
kernel_initializer=initializer)(tensor)
elif down_sampling == 'maxpool':
tensor = Conv3D(filters=num_filters,
kernel_size=kernel_size,
padding=padding,
kernel_initializer=initializer)(tensor)
tensor = MaxPool3D(strides)(tensor)
elif down_sampling == 'avgpool':
tensor = Conv3D(filters=num_filters,
kernel_size=kernel_size,
padding=padding,
kernel_initializer=initializer)(tensor)
tensor = AvgPool2D(strides)(tensor)
else:
raise ValueError(
'down_sampling should be one of [ \'strided_conv\', \'maxpool\' ]')
return tensor, skip_tensor
def cnn_model_3d_mdn(self,
voxel_dim,
deviation_channels,
num_of_mixtures=5):
"""Build the 3D Model with a Mixture Density Network output the gives parameters of a Gaussian Mixture Model as output, to be used if the system is expected to be collinear (Multi-Stage Assembly Systems) i.e. a single input can have multiple outputs
Functions for predicting and sampling from a MDN.py need to used when deploying a MDN based model
refer https://publications.aston.ac.uk/id/eprint/373/1/NCRG_94_004.pdf for more details on the working of a MDN model
refer https://arxiv.org/pdf/1709.02249.pdf to understand how a MDN model can be leveraged to estimate the epistemic and aleatoric unceratninty present in manufacturing sytems based on the data collected
:param voxel_dim: The voxel dimension of the input, reuired to build input to the 3D CNN model
:type voxel_dim: int (required)
:param voxel_channels: The number of voxel channels in the input structure, required to build input to the 3D CNN model
:type voxel_channels: int (required)
:param number_of_mixtures: The number of mixtures in the Gaussian Mixture Model output, defaults to 5, can be increased if higher collinearity is expected
:type number_of_mixtures: int
"""
assert self.model_type == "regression", "Mixture Density Network Should be a Regression Model"
from tensorflow.keras.layers import Conv3D, MaxPool3D, Flatten, Dense
from tensorflow.keras.models import Sequential
import mdn
model = Sequential()
model.add(
Conv3D(32,
kernel_size=(5, 5, 5),
strides=(2, 2, 2),
activation='relu',
input_shape=(voxel_dim, voxel_dim, voxel_dim,
deviation_channels)))
model.add(
Conv3D(32,
kernel_size=(4, 4, 4),
strides=(2, 2, 2),
activation='relu'))
model.add(
Conv3D(32,
kernel_size=(3, 3, 3),
strides=(1, 1, 1),
activation='relu'))
model.add(MaxPool3D(pool_size=(2, 2, 2)))
model.add(Flatten())
model.add(
Dense(128,
kernel_regularizer=regularizers.l2(0.02),
activation='relu'))
#model.add(Dropout(0.3))
model.add(Dense(self.output_dimension, activation=final_layer_avt))
model.add(mdn.MDN(self.output_dimension, num_of_mixtures))
model.compile(loss=mdn.get_mixture_loss_func(self.output_dimension,
num_of_mixtures),
optimizer='adam')
print("3D CNN Mixture Density Network model successfully compiled")
return model
def Fast_body(x, layers, block):
fast_inplanes = 8
lateral = []
x = Conv_BN_ReLU(8, kernel_size=(5, 7, 7), strides=(1, 2, 2))(x)
x = MaxPool3D(pool_size=(1, 3, 3), strides=(1, 2, 2), padding='same')(x)
lateral_p1 = Conv3D(8 * 2,
kernel_size=(5, 1, 1),
strides=(8, 1, 1),
padding='same',
use_bias=False)(x)
lateral.append(lateral_p1)
x, fast_inplanes = make_layer_fast(x,
block,
8,
layers[0],
head_conv=3,
fast_inplanes=fast_inplanes)
lateral_res2 = Conv3D(32 * 2,
kernel_size=(5, 1, 1),
strides=(8, 1, 1),
padding='same',
use_bias=False)(x)
lateral.append(lateral_res2)
x, fast_inplanes = make_layer_fast(x,
block,
16,
layers[1],
stride=2,
head_conv=3,
fast_inplanes=fast_inplanes)
lateral_res3 = Conv3D(64 * 2,
kernel_size=(5, 1, 1),
strides=(8, 1, 1),
padding='same',
use_bias=False)(x)
lateral.append(lateral_res3)
x, fast_inplanes = make_layer_fast(x,
block,
32,
layers[2],
stride=2,
head_conv=3,
fast_inplanes=fast_inplanes)
lateral_res4 = Conv3D(128 * 2,
kernel_size=(5, 1, 1),
strides=(8, 1, 1),
padding='same',
use_bias=False)(x)
lateral.append(lateral_res4)
x, fast_inplanes = make_layer_fast(x,
block,
64,
layers[3],
stride=2,
head_conv=3,
fast_inplanes=fast_inplanes)
x = GlobalAveragePooling3D()(x)
return x, lateral
def cnn_model_3d_aleatoric(self, voxel_dim, deviation_channels):
"""Build the 3D Model with a heteroeskedastic aleatoric loss, this enables different standard deviation of each predicted value, to be used when the expected sensor noise is heteroskedastic
:param voxel_dim: The voxel dimension of the input, required to build input to the 3D CNN model
:type voxel_dim: int (required)
:param voxel_channels: The number of voxel channels in the input structure, required to build input to the 3D CNN model
:type voxel_channels: int (required)
"""
if (self.model_type == "regression"):
final_layer_avt = 'linear'
if (self.model_type == "classification"):
final_layer_avt = 'softmax'
def myloss(y_true, y_pred):
prediction = y_pred[:, 0:self.output_dimension]
log_variance = y_pred[:,
self.output_dimension:self.output_dimension +
1]
loss = tf.reduce_mean(0.5 * tf.exp(-1 * log_variance) *
tf.square(tf.abs(y_true - prediction)) +
0.5 * log_variance)
return loss
from tensorflow.keras.layers import Conv3D, MaxPool3D, Flatten, Dense
from tensorflow.keras.models import Sequential
model = Sequential()
model.add(
Conv3D(32,
kernel_size=(5, 5, 5),
strides=(2, 2, 2),
activation='relu',
input_shape=(voxel_dim, voxel_dim, voxel_dim,
deviation_channels)))
model.add(
Conv3D(32,
kernel_size=(4, 4, 4),
strides=(2, 2, 2),
activation='relu'))
model.add(
Conv3D(32,
kernel_size=(3, 3, 3),
strides=(1, 1, 1),
activation='relu'))
model.add(MaxPool3D(pool_size=(2, 2, 2)))
model.add(Flatten())
model.add(
Dense(128,
kernel_regularizer=regularizers.l2(0.02),
activation='relu'))
#model.add(Dropout(0.3))
model.add(Dense(self.output_dimension, activation=final_layer_avt))
model.compile(loss=myloss, optimizer='adam', metrics=['mae'])
print("3D CNN model Aleatoric successfully compiled")
return model
def AutoEncoderModel():
# encoder
X_input = Input((16, 128, 128, 3))
X = Conv3D(32, 3, padding='same')(X_input)
X = BatchNormalization()(X)
X = LeakyReLU()(X)
X = MaxPool3D(pool_size=(2, 2, 2), strides=(2, 2, 2), padding='valid')(X)
# current shape is 8x64x64x32
X = Conv3D(48, 3, padding='same')(X)
X = BatchNormalization()(X)
X = LeakyReLU()(X)
X = MaxPool3D(pool_size=(2, 2, 2), strides=(2, 2, 2), padding='valid')(X)
# current shape is 4x32x32x48
X = Conv3D(64, 3, padding='same')(X)
X = BatchNormalization()(X)
X = LeakyReLU()(X)
X = MaxPool3D(pool_size=(2, 2, 2), strides=(2, 2, 2), padding='valid')(X)
# current shape is 2x16x16x64
X = Conv3D(64, 3, padding='same')(X)
X = BatchNormalization()(X)
X = LeakyReLU()(X)
X = MaxPool3D(pool_size=(2, 2, 2), strides=(1, 1, 1), padding='same')(X)
# current shape is 2x16x16x64
# decoder
X = Conv3DTranspose(48, 2, strides=(2, 2, 2), padding='valid')(X)
X = BatchNormalization()(X)
X = LeakyReLU()(X)
# current shape is 4x32x32x48
X = Conv3DTranspose(32, 2, strides=(2, 2, 2), padding='valid')(X)
X = BatchNormalization()(X)
X = LeakyReLU()(X)
# current shape is 8x64x64x32
X = Conv3DTranspose(32, 2, strides=(2, 2, 2), padding='valid')(X)
X = BatchNormalization()(X)
X = LeakyReLU()(X)
# current shape is 16x128x128x32
X = Conv3D(3, 3, strides=(1, 1, 1), padding='same')(X)
X = Activation('sigmoid')(X)
# current shape is 16x128x128x3
model = Model(inputs=X_input, outputs=X, name='AutoEncoderModel')
return model
def video_tower(
shape=(5, 100, 100, 3), drop_ratio=0.5, kreg=1e-4, weights=None):
inputs = Input(shape=shape, name='v_in') # Input
x = Conv3D(96, (5, 7, 7),
padding='same',
activation='relu',
kernel_regularizer=l2(kreg),
data_format='channels_last',
name='s_av_v_conv1')(inputs) # conv1
x = MaxPool3D((1, 3, 3), padding='same', name='s_av_v_pool1')(x) # pool1
x = Conv3D(256, (1, 5, 5),
padding='same',
activation='relu',
kernel_regularizer=l2(kreg),
data_format='channels_last',
name='s_av_v_conv2')(x) # conv2
x = MaxPool3D((1, 3, 3), padding='same', name='s_av_v_pool2')(x) # pool2
x = Conv3D(256, (1, 3, 3),
padding='same',
activation='relu',
kernel_regularizer=l2(kreg),
data_format='channels_last',
name='s_av_v_conv3')(x) # conv3
x = Conv3D(256, (1, 3, 3),
padding='same',
activation='relu',
kernel_regularizer=l2(kreg),
data_format='channels_last',
name='s_av_v_conv4')(x) # conv4
x = Conv3D(256, (1, 3, 3),
padding='same',
activation='relu',
kernel_regularizer=l2(kreg),
data_format='channels_last',
name='s_av_v_conv5')(x) # conv5
x = MaxPool3D((1, 3, 3), padding='same', name='s_av_v_pool5')(x) # pool5
x = Conv3D(512, (1, 6, 6),
padding='same',
activation='relu',
kernel_regularizer=l2(kreg),
data_format='channels_last',
name='s_av_v_conv6')(x) # conv6
x = Flatten()(x)
return inputs, x
def build_sequence_model(input_shape_dict):
video_input_shape = [None] + input_shape_dict['video']
audio_input_shape = [None] + input_shape_dict['audio']
weight_decay = 0.005
# Video 3D Conv layers
video_input = Input(video_input_shape)
x = video_input
x = TimeDistributed(
Conv3D(8, (3, 3, 3),
strides=(1, 1, 1),
padding='same',
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay)))(x)
x = TimeDistributed(MaxPool3D((2, 2, 2), strides=(2, 2, 2),
padding='same'))(x)
video_output = TimeDistributed(Flatten())(x)
print(x.shape, video_output.shape)
# Audio 2D Conv layers
audio_input = Input(audio_input_shape)
x = Reshape(audio_input_shape + [1]) # add channel dim
x = TimeDistributed(
Conv2D(4, (3, 3),
strides=(1, 1),
padding='same',
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay)))(x)
x = TimeDistributed(MaxPool2D((2, 2), strides=(2, 2), padding='same'))(x)
audio_output = TimeDistributed(Flatten())(x)
# LSTM layers
x = concatenate([video_output, audio_output])
print(x.shape)
x = LSTM(16,
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay))(x)
print(x.shape)
# Fully-connected layers
x = Dense(16,
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay))(x)
# x = Dropout(0.2)(x)
fc_output = Dense(1,
activation='sigmoid',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay))(x)
model = Model(inputs=[video_input, audio_input], outputs=fc_output)
return model
def local_network_function(input_img):
# encoder
conv1 = Conv3D(256, (2, 2, 2), activation="relu",
padding="same")(input_img)
pool1 = MaxPool3D(pool_size=(2, 2, 2))(conv1)
conv2 = Conv3D(128, (2, 2, 2), activation="relu",
padding="same")(pool1)
pool2 = MaxPool3D(pool_size=(2, 2, 2))(conv2)
dens1 = Dense(64, activation="relu")(pool2)
dens2 = Dense(32, activation="relu")(dens1)
dens3 = Dense(64, activation="relu")(dens2)
dens4 = Dense(64, activation="relu")(dens3)
dens5 = Dense(64, activation="relu")(dens4)
dens6 = Dense(64, activation="relu")(dens5)
dense_out = Dense(1, activation=None)(dens6)
return dense_out
def cnn_model_3d(self, voxel_dim, deviation_channels):
"""Build the 3D Model using the specified loss function, the inputs are parsed from the assemblyconfig_<case_study_name>.py file
:param voxel_dim: The voxel dimension of the input, required to build input to the 3D CNN model
:type voxel_dim: int (required)
:param voxel_channels: The number of voxel channels in the input structure, required to build input to the 3D CNN model
:type voxel_channels: int (required)
"""
from tensorflow.keras.layers import Conv3D, MaxPool3D, Flatten, Dense, Dropout
from tensorflow.keras.models import Sequential
from tensorflow.keras import regularizers
if (self.output_type == "regression"):
final_layer_avt = 'linear'
if (self.output_type == "classification"):
final_layer_avt = 'softmax'
model = Sequential()
model.add(
Conv3D(32,
kernel_size=(5, 5, 5),
strides=(2, 2, 2),
activation='relu',
input_shape=(voxel_dim, voxel_dim, voxel_dim,
deviation_channels)))
model.add(
Conv3D(32,
kernel_size=(4, 4, 4),
strides=(2, 2, 2),
activation='relu'))
model.add(
Conv3D(32,
kernel_size=(3, 3, 3),
strides=(1, 1, 1),
activation='relu'))
model.add(MaxPool3D(pool_size=(2, 2, 2)))
model.add(Flatten())
model.add(
Dense(64,
kernel_regularizer=regularizers.l2(self.regularizer_coeff),
activation='relu'))
#model.add(Dropout(0.2))
model.add(
Dense(64,
kernel_regularizer=regularizers.l2(self.regularizer_coeff),
activation='relu'))
model.add(Dense(self.output_dimension, activation=final_layer_avt))
model.compile(loss=self.loss_function,
optimizer=self.optimizer,
metrics=['mae'])
print("3D CNN model successfully compiled")
return model
def create_unet(nx, ny, nz):
inputs = Input((nx, ny, nz, 1))
conv1 = Conv3D(32, (3, 3, 3), activation='relu', padding='same')(inputs)
conv1 = Conv3D(32, (3, 3, 3), activation='relu', padding='same')(conv1)
pool1 = MaxPool3D(pool_size=(2, 2, 2))(conv1)
conv2 = Conv3D(64, (3, 3, 3), activation='relu', padding='same')(pool1)
conv2 = Conv3D(64, (3, 3, 3), activation='relu', padding='same')(conv2)
pool2 = MaxPool3D(pool_size=(2, 2, 2))(conv2)
conv3 = Conv3D(128, (3, 3, 3), activation='relu', padding='same')(pool2)
conv3 = Conv3D(128, (3, 3, 3), activation='relu', padding='same')(conv3)
pool3 = MaxPool3D(pool_size=(2, 2, 2))(conv3)
conv4 = Conv3D(256, (3, 3, 3), activation='relu', padding='same')(pool3)
conv4 = Conv3D(256, (3, 3, 3), activation='relu', padding='same')(conv4)
up5 = UpSampling3D(size=(2, 2, 2))(conv4)
merge5 = concatenate([up5, conv3])
conv5 = Conv3D(128, (3, 3, 3), activation='relu', padding='same')(merge5)
conv5 = Conv3D(128, (3, 3, 3), activation='relu', padding='same')(conv5)
up6 = UpSampling3D(size=(2, 2, 2))(conv5)
merge6 = concatenate([up6, conv2])
conv6 = Conv3D(64, (3, 3, 3), activation='relu', padding='same')(merge6)
conv6 = Conv3D(64, (3, 3, 3), activation='relu', padding='same')(conv6)
up7 = UpSampling3D(size=(2, 2, 2))(conv6)
merge7 = concatenate([up7, conv1])
conv7 = Conv3D(32, (3, 3, 3), activation='relu', padding='same')(merge7)
conv7 = Conv3D(32, (3, 3, 3), activation='relu', padding='same')(conv7)
conv8 = Conv3D(1, (1, 1, 1), activation='sigmoid')(conv7)
model = Model(inputs=inputs, outputs=conv8)
model.compile(optimizer=Adam(lr=1.0E-5), loss=overlap_loss)
return model
def __init__(self):
super().__init__()
leaky_relu = LeakyReLU(alpha=0.01)
l2_regularizer = l2(0.001)
self.add(Conv3D(16, [3, 3, 1], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(Conv3D(16, [1, 1, 4], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(BatchNormalization())
self.add(MaxPool3D([1, 1, 2]))
self.add(Conv3D(32, [3, 3, 1], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(Conv3D(32, [1, 1, 4], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(BatchNormalization())
self.add(MaxPool3D([1, 1, 2]))
self.add(Conv3D(64, [3, 3, 1], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(Conv3D(64, [1, 1, 4], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(BatchNormalization())
self.add(MaxPool3D([1, 1, 2]))
self.add(Conv3D(128, [4, 4, 1], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(Conv3D(128, [1, 1, 4], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(BatchNormalization())
self.add(MaxPool3D([1, 1, 2]))
self.add(Conv3D(128, [1, 1, 4], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(BatchNormalization())
self.add(MaxPool3D([1, 1, 2]))
self.add(Conv3D(128, [1, 1, 4], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(BatchNormalization())
self.add(MaxPool3D([1, 1, 2]))
self.add(Conv3D(32, [1, 1, 9], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(Conv3D(16, [1, 1, 1], activation=leaky_relu, kernel_regularizer=l2_regularizer))
self.add(Conv3D(1, [1, 1, 1], activation=sigmoid))
self.add(Reshape([1]))
def build_classification_network(batch_size: int, nb_points: int,
subdivisions: Tuple[int, int,
int], variance: float):
"""
Build a classification network, using modified 3D Fisher Vectors as point cloud featurizer at the input.
"""
points = Input(batch_shape=(batch_size, nb_points, 3), name="points")
fv = Modified3DFisherVectors(subdivisions, variance, flatten=False)(points)
fv = Reshape((-1, ) + subdivisions, name="reshape_3dmFV")(fv)
x = Permute((2, 3, 4, 1), name="permute_3dmFV")(fv)
# convolve
x = inception_block(x, nb_filters=64, name="block1")
x = inception_block(x, nb_filters=128, name="block2")
x = inception_block(x, nb_filters=256, name="block3")
x = MaxPool3D(name="block3_maxpool")(x)
x = inception_block(x, nb_filters=256, name="block4")
x = inception_block(x, nb_filters=512, name="block5")
x = MaxPool3D(name="block5_maxpool")(x)
x = Flatten(name="flatten")(x)
x = Dense(1024, name="fc1", activation="linear", use_bias=False)(x)
x = BatchNormalization(name="fc1_bn", fused=True)(x)
x = Activation("relu", name="fc1_relu")(x)
x = Dropout(0.3, name="dp1")(x)
x = Dense(256, name="fc2", activation="linear", use_bias=False)(x)
x = BatchNormalization(name="fc2_bn", fused=True)(x)
x = Activation("relu", name="fc2_relu")(x)
x = Dropout(0.3, name="dp2")(x)
x = Dense(128, name="fc3", activation="linear", use_bias=False)(x)
x = BatchNormalization(name="fc3_bn", fused=True)(x)
x = Activation("relu", name="fc3_relu")(x)
x = Dropout(0.3, name="dp3")(x)
x = Dense(40, name="output", activation="softmax")(x)
return tf.keras.models.Model(points, x)
def get_model(width=128, height=128, depth=64):
inputs = Input((width, height, depth, 1))
layer = Conv3D(filters=64, kernel_size=3, activation="relu")(inputs)
layer = MaxPool3D(pool_size=2)(layer)
layer = BatchNormalization()(layer)
layer = Conv3D(filters=64, kernel_size=3, activation="relu")(layer)
layer = MaxPool3D(pool_size=2)(layer)
layer = BatchNormalization()(layer)
layer = Conv3D(filters=128, kernel_size=3, activation="relu")(layer)
layer = MaxPool3D(pool_size=2)(layer)
layer = BatchNormalization()(layer)
layer = Conv3D(filters=256, kernel_size=3, activation="relu")(layer)
layer = MaxPool3D(pool_size=2)(layer)
layer = BatchNormalization()(layer)
layer = GlobalAveragePooling3D()(layer)
layer = Dense(units=512, activation="relu")(layer)
layer = Dropout(0.3)(layer)
outputs = Dense(units=1, activation="sigmoid")(layer)
# Define the model.
model = Model(inputs, outputs, name="3Dcnn")
initial_learning_rate = 0.0001
lr_schedule = ExponentialDecay(initial_learning_rate,
decay_steps=100000,
decay_rate=0.96,
staircase=True)
model.compile(
loss="binary_crossentropy",
optimizer=Adam(learning_rate=lr_schedule),
metrics=["acc"],
)
return model
def static_video(shape=(5, 100, 100, 3), weights=None):
"""
A static video model based on the description of arXiv:1906.10555v1 video tower, i.e., variation of VGGM.
shape = (window size, height, width, chans)
"""
inputs = Input(shape=shape, name='v_in') # Input
x = Conv3D(96, (5, 7, 7), padding='same', activation='relu',
data_format='channels_last', name='s_v_conv1')(inputs) # conv1
x = MaxPool3D((1, 3, 3), padding='same', name='s_v_pool1')(x) # pool1
x = Conv3D(256, (1, 5, 5), padding='same', activation='relu',
data_format='channels_last', name='s_v_conv2')(x) # conv2
x = MaxPool3D((1, 3, 3), padding='same', name='s_v_pool2')(x) # pool2
x = Conv3D(256, (1, 3, 3), padding='same', activation='relu',
data_format='channels_last', name='s_v_conv3')(x) # conv3
x = Conv3D(256, (1, 3, 3), padding='same', activation='relu',
data_format='channels_last', name='s_v_conv4')(x) # conv4
x = Conv3D(256, (1, 3, 3), padding='same', activation='relu',
data_format='channels_last', name='s_v_conv5')(x) # conv5
x = MaxPool3D((1, 3, 3), padding='same', name='s_v_pool5')(x) # pool5
x = Conv3D(512, (1, 6, 6), padding='same', activation='relu',
data_format='channels_last', name='s_v_conv6')(x) # conv6
x = Flatten()(x)
x = Dense(256, activation='relu', name='s_v_fc7')(x) # fc7
outputs = Dense(2, activation='softmax', name='main_out')(x) # fc7
model = Model(inputs=inputs, outputs=outputs)
if weights is not None:
model.load_weights(weights, by_name=True)
return model
def build(self, input_shape):
if len(input_shape) == 2:
self.conv_1 = Dense(100, activation='relu', input_shape=input_shape)
self.max_pool_1 = Dropout(0.2)
self.conv_2 = Dense(50, activation='relu')
self.max_pool_2 = Dropout(0.2)
elif len(input_shape) == 3:
self.conv_1 = Conv1D(20, kernel_size=5, activation='relu', input_shape=input_shape)
self.max_pool_1 = MaxPool1D()
self.conv_2 = Conv1D(50, kernel_size=5, activation='relu')
self.max_pool_2 = MaxPool1D()
elif len(input_shape) == 4:
self.conv_1 = Conv2D(20, kernel_size=5, activation='relu', input_shape=input_shape)
self.max_pool_1 = MaxPool2D()
self.conv_2 = Conv2D(50, kernel_size=5, activation='relu')
self.max_pool_2 = MaxPool2D()
elif len(input_shape) == 5:
self.conv_1 = Conv3D(20, kernel_size=5, activation='relu', input_shape=input_shape)
self.max_pool_1 = MaxPool3D()
self.conv_2 = Conv3D(50, kernel_size=5, activation='relu')
self.max_pool_2 = MaxPool3D()
else:
raise DimensionError("Input shape not covered by this model")
def conv3d(
inputs: Tensor,
filters: int,
downsizing: bool = True,
loop: int = 2) -> Tensor:
if downsizing:
inputs = MaxPool3D(pool_size=(2, 2, 2))(inputs)
x = inputs
for _ in range(loop):
x = Conv3D(filters, (3, 3, 3), strides=(1, 1, 1), use_bias=False, padding='same')(x)
x = InstanceNormalization()(x)
x = Activation('relu')(x)
return x
def Slow_body(x, lateral, layers, block):
slow_inplanes = 64 + 64//8*2
x = Conv_BN_ReLU(64, kernel_size=(1, 7, 7), strides=(1, 2, 2))(x)
x = MaxPool3D(pool_size=(1, 3, 3), strides=(1, 2, 2), padding='same')(x)
x = Concatenate()([x, lateral[0]])
x, slow_inplanes = make_layer_slow(x, block, 64, layers[0], head_conv=1, slow_inplanes=slow_inplanes)
x = Concatenate()([x, lateral[1]])
x, slow_inplanes = make_layer_slow(x, block, 128, layers[1], stride=2, head_conv=1, slow_inplanes=slow_inplanes)
x = Concatenate()([x, lateral[2]])
x, slow_inplanes = make_layer_slow(x, block, 256, layers[2], stride=2, head_conv=1, slow_inplanes=slow_inplanes)
x = Concatenate()([x, lateral[3]])
x, slow_inplanes = make_layer_slow(x, block, 512, layers[3], stride=2, head_conv=1, slow_inplanes=slow_inplanes)
x = GlobalAveragePooling3D()(x)
return x
def __init__(self, filters_list):
super(MixedBlock, self).__init__()
self.cbl_0 = CBL(filters_list[0], kernel=[1, 1, 1])
self.cbl_1_1 = CBL(filters_list[1], kernel=[1, 1, 1])
self.cbl_1_2 = CBL(filters_list[2], kernel=[3, 3, 3])
self.cbl_2_1 = CBL(filters_list[3], kernel=[1, 1, 1])
self.cbl_2_2 = CBL(filters_list[4], kernel=[3, 3, 3])
self.maxpool3d_3 = MaxPool3D(pool_size=[3, 3, 3],
strides=[1, 1, 1],
padding='same')
self.cbl_3 = CBL(filters_list[5], kernel=[1, 1, 1])
def build_model():
model = Sequential()
model.add(Conv(8, (3, 3, 3), input_shape=(91, 109, 91, 1)))
model.add(BatchNormalization())
model.add(Activation('relu'))
model.add(MaxPool3D(pool_size=(2, 2, 2)))
model.add(Dropout(0.25))
#model.add(Conv(32, (3,3,3)))
#model.add(MaxPool3D())
#model.add(Dropout(0.25))
model.add(Flatten())
#model.add(Dense(4096, activation='relu'))
#model.add(Dense(1024, activation='relu'))
model.add(Dense(1, activation='sigmoid'))
return model
def build_SimpleNet_noOutput(input_shape, output_shape, outputsize_firstLayer, outputsize_secondLayer, outputsize_dense):
input_layer = Input(shape=input_shape, dtype='float32')
conv_layer = Conv3D(outputsize_firstLayer, kernel_size=3, padding='same', activation='relu')(input_layer)
max_pool = MaxPool3D(pool_size=(1, 3, 3), strides=2)(conv_layer)
norm = BatchNormalization()(conv_layer)
# dropout = Dropout(0.5)(norm)
conv_layer = Conv3D(outputsize_secondLayer, kernel_size=3, padding='same', activation='relu')(dropout)
max_pool = MaxPool3D(pool_size= (1, 3, 3), strides=2)(conv_layer)
norm = BatchNormalization()(conv_layer)
# dropout_base = Dropout(0.5)(norm)
flatten = Flatten()(dropout_base)
# dense = Dense(outputsize_dense, activation='relu')(flatten)
output = Dense(output_shape, activation='softmax')(dense)
model = Model(inputs=[input_layer], outputs=[dense])
# model.compile(loss='sparse_categorical_crossentropy',
# optimizer='Adam', #(learning_rate=0.00005)',
# metrics=['accuracy'])
return model
def FCN(self, n=None):
"""
fully convolutional neural network (doesn't work as intended when scaling up input dimension')
"""
input_layer = (64, 64, n, 3)
kernel_conv1 = (5, 5, 3)
kernel_conv2 = (3, 3, 3)
kernel_conv3 = (6, 6, 1)
kernal_softmax = (1, 1, 4)
model = Sequential()
model.add(InputLayer(input_layer))
model.add(
Conv3D(kernel_size=kernel_conv1,
filters=16,
strides=(2, 2, 1),
padding="valid",
activation='relu'))
model.add(
Conv3D(kernel_size=kernel_conv2,
filters=24,
strides=(2, 2, 1),
padding="valid",
activation='relu'))
model.add(
Conv3D(kernel_size=kernel_conv2,
filters=32,
strides=(2, 2, 1),
padding='valid',
activation='relu'))
model.add(
Conv3D(kernel_size=kernel_conv3,
filters=12,
strides=(2, 2, 1),
padding='valid',
activation='relu'))
model.add(MaxPool3D((1, 1, 4), strides=(1, 1, 1)))
model.add(
Conv3D(kernel_size=(1, 1, 1),
filters=2,
strides=(1, 1, 1),
padding='valid',
activation='softmax'))
model.compile(optimizer='adam',
loss='categorical_crossentropy',
metrics=[categorical_crossentropy, categorical_accuracy])
model.summary()
return (model)
def cnn_model_3d_tl(self, voxel_dim, deviation_channels):
"""Build the 3D Model with GlobalMAxPooling3D instead of flatten, this enables input for different voxel dimensions, to be used when the model needs to be leveraged for transfer learning with different size input
:param voxel_dim: The voxel dimension of the input, required to build input to the 3D CNN model
:type voxel_dim: int (required)
:param voxel_channels: The number of voxel channels in the input structure, required to build input to the 3D CNN model
:type voxel_channels: int (required)
"""
from tensorflow.keras.layers import Conv3D, MaxPool3D, Flatten, Dense, Dropout, Input
from tensorflow.keras.models import Model
from tensorflow.keras import regularizers
inputs = Input(shape=(
None,
None,
None,
3,
))
cnn3d_1 = Conv3D(32,
kernel_size=(5, 5, 5),
strides=(2, 2, 2),
activation='relu')(inputs)
cnn3d_2 = Conv3D(32,
kernel_size=(4, 4, 4),
strides=(2, 2, 2),
activation='relu')(cnn3d_1)
cnn3d_3 = Conv3D(32,
kernel_size=(3, 3, 3),
strides=(1, 1, 1),
activation='relu')(cnn3d_2)
max_pool3d = MaxPool3D(pool_size=(2, 2, 2))(cnn3d_3)
pooled_layer = GlobalMaxPooling3D()(max_pool3d)
dense_1 = Dense(128,
kernel_regularizer=regularizers.l2(
self.regularizer_coeff),
activation='relu')(pooled_layer)
predictions = Dense(self.output_dimension,
activation=final_layer_avt)(dense_1)
model = Model(inputs=inputs, outputs=predictions)
model.compile(loss=self.loss_function,
optimizer=self.optimizer,
metrics=['mae'])
return model
def build_model(input_shape_dict):
video_input_shape = input_shape_dict['video']
audio_input_shape = input_shape_dict['audio']
weight_decay = 0.005
# Video 3D Conv layers
video_input = Input(video_input_shape)
x = Conv3D(8, (3, 3, 3),
strides=(1, 1, 1),
padding='same',
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay))(video_input)
x = MaxPool3D((2, 2, 2), strides=(2, 2, 2), padding='same')(x)
video_output = Flatten()(x)
# Audio 2D Conv layers
audio_input = Input(audio_input_shape)
x = expand_dims(audio_input) # add channel dim
x = Conv2D(4, (3, 3),
strides=(1, 1),
padding='same',
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay))(x)
x = MaxPool2D((2, 2), strides=(2, 2), padding='same')(x)
audio_output = Flatten()(x)
# Fully-connected layers
fc_input = concatenate([video_output, audio_output])
x = Dense(16,
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay))(fc_input)
# x = Dropout(0.2)(x)
fc_output = Dense(1,
activation='sigmoid',
kernel_initializer='he_uniform',
kernel_regularizer=l2(weight_decay))(x)
model = Model(inputs=[video_input, audio_input], outputs=fc_output)
return model
def model(self, lr=0.1):
input_layer = (64, 64, 10, 3)
kernel_conv1 = (5, 5, 3)
kernel_conv2 = (3, 3, 3)
kernel_conv3 = (6, 6, 1)
kernal_softmax = (1, 1, 4)
model = Sequential()
model.add(InputLayer(input_layer))
model.add(
Conv3D(kernel_size=kernel_conv1,
filters=16,
strides=(2, 2, 1),
padding='valid',
activation='relu'))
model.add(
Conv3D(kernel_size=kernel_conv2,
filters=24,
strides=(2, 2, 1),
padding='valid',
activation='relu'))
model.add(
Conv3D(kernel_size=kernel_conv2,
filters=32,
strides=(2, 2, 1),
padding='valid',
activation='relu'))
model.add(
Conv3D(kernel_size=kernel_conv3,
filters=12,
strides=(2, 2, 1),
padding='valid',
activation='relu'))
model.add(MaxPool3D(kernal_softmax))
model.add(Flatten())
model.add(Dense(2, activation='softmax'))
opt = SGD(learning_rate=lr)
model.compile(optimizer=opt,
loss='categorical_crossentropy',
metrics=[categorical_crossentropy, categorical_accuracy])
return (model)
def down_sampling(Input,
target_size,
kernel_size=3,
padding="same",
activation="relu",
stride=1):
conv = Conv3D(target_size,
kernel_size,
padding=padding,
strides=stride,
activation=activation,
kernel_initializer='he_normal')(Input)
conv = Conv3D(target_size,
kernel_size,
padding=padding,
strides=stride,
activation=activation,
kernel_initializer='he_normal')(conv)
pool = MaxPool3D(pool_size=(2, 2, 2))(conv)
return conv, pool
def __init__(self, target_time_offsets):
# deltatime to try: -30 min, -1h, -1h30, -2h, -3h, -4h, -5h
super(cnn3d, self).__init__()
self.conv1 = Conv3D(filters=64,
kernel_size=(3, 3, 3),
padding='same',
activation='relu',
input_shape=(7, 64, 64, 5))
self.conv2 = Conv3D(filters=64,
kernel_size=(4, 4, 4),
padding='same',
activation='relu')
self.conv3 = Conv3D(filters=32,
kernel_size=(2, 2, 2),
padding='same',
activation='relu')
self.maxpool1 = MaxPool3D(pool_size=(2, 2, 2), padding='same')
self.flatten = Flatten()
self.d1 = Dense(264, activation='relu')
self.d2 = Dense(len(target_time_offsets), activation="linear")
def get_appearance_encoder(self):
app_shape = tuple([None] + list(self.appearance_shape)[2:])
inputs = Input(shape=app_shape, name='encoder_app_input')
x = inputs
x = TimeDistributed(
ImageNormalization2D(norm_method='whole_image',
name='imgnrm_ae'))(x)
for i in range(int(math.log(app_shape[1], 2))):
x = Conv3D(self.n_filters, (1, 3, 3),
strides=1,
padding='same',
use_bias=False,
name='conv3d_ae{}'.format(i))(x)
x = BatchNormalization(axis=-1, name='bn_ae{}'.format(i))(x)
x = Activation('relu', name='relu_ae{}'.format(i))(x)
x = MaxPool3D(pool_size=(1, 2, 2))(x)
x = Lambda(lambda t: tf.squeeze(t, axis=(2, 3)))(x)
x = Dense(self.encoder_dim, name='dense_aeout')(x)
x = BatchNormalization(axis=-1, name='bn_aeout')(x)
x = Activation('relu', name='appearance_embedding')(x)
return Model(inputs=inputs, outputs=x)
def bn_feature_net_3D(receptive_field=61,
n_frames=5,
input_shape=(5, 256, 256, 1),
n_features=3,
n_channels=1,
reg=1e-5,
n_conv_filters=64,
n_dense_filters=200,
VGG_mode=False,
init='he_normal',
norm_method='std',
location=False,
dilated=False,
padding=False,
padding_mode='reflect',
multires=False,
include_top=True,
temporal=None,
residual=False,
temporal_kernel_size=3):
"""Creates a 3D featurenet.
Args:
receptive_field (int): the receptive field of the neural network.
n_frames (int): Number of frames.
input_shape (tuple): If no input tensor, create one with this shape.
n_features (int): Number of output features
n_channels (int): number of input channels
reg (int): regularization value
n_conv_filters (int): number of convolutional filters
n_dense_filters (int): number of dense filters
VGG_mode (bool): If ``multires``, uses ``VGG_mode``
for multiresolution
init (str): Method for initalizing weights.
norm_method (str): Normalization method to use with the
:mod:`deepcell.layers.normalization.ImageNormalization3D` layer.
location (bool): Whether to include a
:mod:`deepcell.layers.location.Location3D` layer.
dilated (bool): Whether to use dilated pooling.
padding (bool): Whether to use padding.
padding_mode (str): Type of padding, one of 'reflect' or 'zero'
multires (bool): Enables multi-resolution mode
include_top (bool): Whether to include the final layer of the model
temporal (str): Type of temporal operation
residual (bool): Whether to use temporal information as a residual
temporal_kernel_size (int): size of 2D kernel used in temporal convolutions
Returns:
tensorflow.keras.Model: 3D FeatureNet
"""
# Create layers list (x) to store all of the layers.
# We need to use the functional API to enable the multiresolution mode
x = []
win = (receptive_field - 1) // 2
win_z = (n_frames - 1) // 2
if dilated:
padding = True
if K.image_data_format() == 'channels_first':
channel_axis = 1
time_axis = 2
row_axis = 3
col_axis = 4
if not dilated:
input_shape = (n_channels, n_frames, receptive_field,
receptive_field)
else:
channel_axis = -1
time_axis = 1
row_axis = 2
col_axis = 3
if not dilated:
input_shape = (n_frames, receptive_field, receptive_field,
n_channels)
x.append(Input(shape=input_shape))
x.append(
ImageNormalization3D(norm_method=norm_method,
filter_size=receptive_field)(x[-1]))
if padding:
if padding_mode == 'reflect':
x.append(ReflectionPadding3D(padding=(win_z, win, win))(x[-1]))
elif padding_mode == 'zero':
x.append(ZeroPadding3D(padding=(win_z, win, win))(x[-1]))
if location:
x.append(Location3D()(x[-1]))
x.append(Concatenate(axis=channel_axis)([x[-2], x[-1]]))
layers_to_concat = []
rf_counter = receptive_field
block_counter = 0
d = 1
while rf_counter > 4:
filter_size = 3 if rf_counter % 2 == 0 else 4
x.append(
Conv3D(n_conv_filters, (1, filter_size, filter_size),
dilation_rate=(1, d, d),
kernel_initializer=init,
padding='valid',
kernel_regularizer=l2(reg))(x[-1]))
x.append(BatchNormalization(axis=channel_axis)(x[-1]))
x.append(Activation('relu')(x[-1]))
block_counter += 1
rf_counter -= filter_size - 1
if block_counter % 2 == 0:
if dilated:
x.append(
DilatedMaxPool3D(dilation_rate=(1, d, d),
pool_size=(1, 2, 2))(x[-1]))
d *= 2
else:
x.append(MaxPool3D(pool_size=(1, 2, 2))(x[-1]))
if VGG_mode:
n_conv_filters *= 2
rf_counter = rf_counter // 2
if multires:
layers_to_concat.append(len(x) - 1)
if multires:
c = []
for l in layers_to_concat:
output_shape = x[l].get_shape().as_list()
target_shape = x[-1].get_shape().as_list()
time_crop = (0, 0)
row_crop = int(output_shape[row_axis] - target_shape[row_axis])
if row_crop % 2 == 0:
row_crop = (row_crop // 2, row_crop // 2)
else:
row_crop = (row_crop // 2, row_crop // 2 + 1)
col_crop = int(output_shape[col_axis] - target_shape[col_axis])
if col_crop % 2 == 0:
col_crop = (col_crop // 2, col_crop // 2)
else:
col_crop = (col_crop // 2, col_crop // 2 + 1)
cropping = (time_crop, row_crop, col_crop)
c.append(Cropping3D(cropping=cropping)(x[l]))
x.append(Concatenate(axis=channel_axis)(c))
x.append(
Conv3D(n_dense_filters, (1, rf_counter, rf_counter),
dilation_rate=(1, d, d),
kernel_initializer=init,
padding='valid',
kernel_regularizer=l2(reg))(x[-1]))
x.append(BatchNormalization(axis=channel_axis)(x[-1]))
x.append(Activation('relu')(x[-1]))
x.append(
Conv3D(n_dense_filters, (n_frames, 1, 1),
dilation_rate=(1, d, d),
kernel_initializer=init,
padding='valid',
kernel_regularizer=l2(reg))(x[-1]))
x.append(BatchNormalization(axis=channel_axis)(x[-1]))
feature = Activation('relu')(x[-1])
def __merge_temporal_features(feature,
mode='conv',
residual=False,
n_filters=256,
n_frames=3,
padding=True,
temporal_kernel_size=3):
if mode is None:
return feature
mode = str(mode).lower()
if mode == 'conv':
x = Conv3D(n_filters,
(n_frames, temporal_kernel_size, temporal_kernel_size),
kernel_initializer=init,
padding='same',
activation='relu',
kernel_regularizer=l2(reg))(feature)
elif mode == 'lstm':
x = ConvLSTM2D(filters=n_filters,
kernel_size=temporal_kernel_size,
padding='same',
kernel_initializer=init,
activation='relu',
kernel_regularizer=l2(reg),
return_sequences=True)(feature)
elif mode == 'gru':
x = ConvGRU2D(filters=n_filters,
kernel_size=temporal_kernel_size,
padding='same',
kernel_initializer=init,
activation='relu',
kernel_regularizer=l2(reg),
return_sequences=True)(feature)
else:
raise ValueError(
'`temporal` must be one of "conv", "lstm", "gru" or None')
if residual is True:
temporal_feature = Add()([feature, x])
else:
temporal_feature = x
temporal_feature_normed = BatchNormalization(
axis=channel_axis)(temporal_feature)
return temporal_feature_normed
temporal_feature = __merge_temporal_features(
feature,
mode=temporal,
residual=residual,
n_filters=n_dense_filters,
n_frames=n_frames,
padding=padding,
temporal_kernel_size=temporal_kernel_size)
x.append(temporal_feature)
x.append(
TensorProduct(n_dense_filters,
kernel_initializer=init,
kernel_regularizer=l2(reg))(x[-1]))
x.append(BatchNormalization(axis=channel_axis)(x[-1]))
x.append(Activation('relu')(x[-1]))
x.append(
TensorProduct(n_features,
kernel_initializer=init,
kernel_regularizer=l2(reg))(x[-1]))
if not dilated:
x.append(Flatten()(x[-1]))
if include_top:
x.append(Softmax(axis=channel_axis, dtype=K.floatx())(x[-1]))
model = Model(inputs=x[0], outputs=x[-1])
return model
def d3UNet(img_depth, img_height, img_width, img_channels):
inputs = Input((img_depth, img_height, img_width, img_channels))
s = Lambda(lambda x: x / 255) (inputs)
c1 = Conv3D(filters=16, kernel_size=(3, 3, 3), activation='elu', kernel_initializer='he_normal',
padding='same', data_format = dataformat, name='Conv1_1') (s)
c1 = Dropout(0.2) (c1)
c1 = Conv3D(16, kernel_size=(3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv1_2') (c1)
p1 = MaxPool3D(pool_size=(2, 2, 2), name='Pool1') (c1)
#Conv2
c2 = Conv3D(32, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv2_1') (p1)
c2 = Dropout(0.1) (c2)
c2 = Conv3D(32, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv2_2') (c2)
p2 = MaxPool3D(pool_size=(2, 2, 2), name='Pool2') (c2)
# Conv3
c3 = Conv3D(64, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv3_1') (p2)
c3 = Dropout(0.3) (c3)
c3 = Conv3D(64, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv3_2') (c3)
p3 = MaxPool3D((2, 2, 2), name='Pool3') (c3)
# Conv4
c4 = Conv3D(128, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv4_1') (p3)
c4 = Dropout(0.3) (c4)
c4 = Conv3D(128, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv4_2') (c4)
p4 = MaxPool3D(pool_size=(2, 2, 2), name='Pool4') (c4)
# Conv5
c5 = Conv3D(256, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv5_1') (p4)
c5 = Dropout(0.4) (c5)
c5 = Conv3D(256, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv5_2') (c5)
# Up6
u6 = Conv3DTranspose(128, (2, 2, 2), strides=(2, 2, 2), padding='same', name='ConvT1', data_format=dataformat) (c5)
u6 = concatenate([u6, c4], axis=4)
c6 = Conv3D(128, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv6_1') (u6)
c6 = Dropout(0.3) (c6)
c6 = Conv3D(128, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv6_2') (c6)
# Up7
u7 = Conv3DTranspose(64, (2, 2, 2), strides=(2, 2, 2), padding='same', name='ConvT2', data_format=dataformat) (c6)
u7 = concatenate([u7, c3])
c7 = Conv3D(64, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv7_1') (u7)
c7 = Dropout(0.3) (c7)
c7 = Conv3D(64, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv7_2') (c7)
# Up8
u8 = Conv3DTranspose(32, (2, 2, 2), strides=(2, 2, 2), padding='same', name='ConvT3', data_format=dataformat) (c7)
u8 = concatenate([u8, c2])
c8 = Conv3D(32, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv8_1') (u8)
c8 = Dropout(0.2) (c8)
c8 = Conv3D(32, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv8_2') (c8)
# Up9
u9 = Conv3DTranspose(filters=16, kernel_size=(2, 2, 2), strides=(2, 2, 2), padding='same', name='ConvT4', data_format=dataformat) (c8)
u9 = concatenate([u9, c1], axis=4)
c9 = Conv3D(16, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv9_1') (u9)
c9 = Dropout(0.2) (c9)
c9 = Conv3D(16, (3, 3, 3), activation='elu', kernel_initializer='he_normal', padding='same',
data_format = dataformat, name = 'Conv9_2') (c9)
outputs = Conv3D(1, (1, 1, 1), activation='sigmoid', name='Output') (c9)
model = Model(inputs=[inputs], outputs=[outputs])
return model
def cnn3d(channels=3, pixels_x=96, pixels_y=96, output_size=7):
model = Sequential(name='conv3d')
model.add(
Input(shape=(None, pixels_x, pixels_y, channels), name='input_conv3d'))
model.add(
Conv3D(filters=16,
kernel_size=(3, 3, 3),
strides=(2, 2, 2),
padding='same',
kernel_initializer='glorot_normal',
name="Conv_1"))
model.add(TimeDistributed(BatchNormalization(), name="bn_1"))
model.add(TimeDistributed(LeakyReLU(alpha=0.3), name="lr_1"))
model.add(
Conv3D(filters=64,
kernel_size=(3, 3, 3),
strides=(2, 2, 2),
padding='same',
kernel_initializer='glorot_normal',
name="Conv_2"))
model.add(TimeDistributed(BatchNormalization(), name="bn_2"))
model.add(TimeDistributed(LeakyReLU(alpha=0.3), name="lr_2"))
model.add(
Conv3D(filters=128,
kernel_size=(3, 3, 3),
strides=(1, 1, 1),
padding='same',
kernel_initializer='glorot_normal',
name="Conv_3"))
model.add(TimeDistributed(BatchNormalization(), name="bn_3"))
model.add(MaxPool3D(pool_size=(2, 2, 2), padding='valid', name="mp_3"))
model.add(TimeDistributed(LeakyReLU(alpha=0.3), name="lr_3"))
model.add(
Conv3D(filters=256,
kernel_size=(3, 3, 3),
strides=(1, 2, 2),
padding='same',
kernel_initializer='glorot_normal',
name="Conv_4"))
model.add(TimeDistributed(BatchNormalization(), name="bn_4"))
model.add(TimeDistributed(LeakyReLU(alpha=0.3), name="lr_4"))
model.add(TimeDistributed(Dropout(0.25), name="dropout_4"))
model.add(
Conv3D(filters=512,
kernel_size=(3, 3, 3),
strides=(1, 1, 1),
padding='same',
kernel_initializer='glorot_normal',
name="Conv_5"))
model.add(TimeDistributed(BatchNormalization(), name="bn_5"))
model.add(TimeDistributed(LeakyReLU(alpha=0.3), name="lr_5"))
model.add(TimeDistributed(Dropout(0.3), name="dropout_5"))
model.add(GlobalAveragePooling3D())
model.add(BatchNormalization(name="bn_6"))
model.add(LeakyReLU(alpha=0.3, name="lr_6"))
model.add(Dropout(0.5, name="dropout_6"))
model.add(Dense(units=128, kernel_regularizer=regularizers.l2(0.005)))
model.add(BatchNormalization(name="bn_7"))
model.add(LeakyReLU(alpha=0.3, name="lr_7"))
model.add(Dropout(0.5, name="dropout_7"))
model.add(Dense(output_size, name="output"))
model.add(Softmax())
return model
