def get_model(x):
x = layers.Conv3D(64, (3, 3, 3),
strides=(1, 1, 1),
padding='same',
activation='relu')(x)
x = layers.MaxPool3D((2, 2, 1), strides=(2, 2, 1), padding='same')(x)
# x = layers.SpatialDropout3D(0.35)(x)
x = layers.Conv3D(128, (3, 3, 3),
strides=(1, 1, 1),
padding='same',
activation='relu')(x)
x = layers.MaxPool3D((2, 2, 2), strides=(2, 2, 2), padding='same')(x)
# x = layers.SpatialDropout3D(0.35)(x)
x = layers.Conv3D(128, (3, 3, 3),
strides=(1, 1, 1),
padding='same',
activation='relu')(x)
x = layers.MaxPool3D((2, 2, 2), strides=(2, 2, 2), padding='same')(x)
# x = layers.SpatialDropout3D(0.35)(x)
x = layers.Conv3D(256, (3, 3, 3),
strides=(1, 1, 1),
padding='same',
activation='relu')(x)
x = layers.MaxPool3D((2, 2, 2), strides=(2, 2, 2))(x)
# x = layers.SpatialDropout3D(0.35)(x)
# x = layers.Conv3D(256, (3, 3, 3), strides=(1, 1, 1), padding='same',
# activation='relu')(x)
# x = layers.SpatialDropout3D(0.5)(x)
# x = layers.MaxPool3D((2, 2, 2), strides=(2, 2, 2), padding='same')(x)
x = layers.Flatten()(x)
return x
def get_model(width=128, height=128, depth=64):
"""build a 3D convolutional neural network model"""
inputs = keras.Input((width, height, depth, 1))
x = layers.Conv3D(filters=64, kernel_size=3, activation="relu")(inputs)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.Conv3D(filters=64, kernel_size=3, activation="relu")(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.Conv3D(filters=128, kernel_size=3, activation="relu")(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.Conv3D(filters=256, kernel_size=3, activation="relu")(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.GlobalAveragePooling3D()(x)
x = layers.Dense(units=512, activation="relu")(x)
x = layers.Dropout(0.3)(x)
outputs = layers.Dense(units=1, activation="sigmoid")(x)
# Define the model.
model = keras.Model(inputs, outputs, name="3dcnn")
return model
def get_model(width=32, height=32, depth=20):
"""Build a 3D convolutional neural network model."""
inputs = keras.Input((width, height, depth, 1))
x = layers.Conv3D(filters=32, kernel_size=3, activation="relu")(inputs)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.Conv3D(filters=32, kernel_size=4, activation="relu")(x)
x = layers.MaxPool3D(pool_size=(1, 1, 2))(x)
x = layers.BatchNormalization()(x)
x = layers.Conv3D(filters=32, kernel_size=3, activation="relu")(x)
x = layers.MaxPool3D(pool_size=(2, 2, 1))(x)
x = layers.BatchNormalization()(x)
x = layers.GlobalMaxPool3D()(x)
x = layers.Dense(units=64, activation="relu")(x)
x = layers.Dropout(0.3)(x)
x = layers.Dense(units=128, activation="relu")(x)
x = layers.Dropout(0.3)(x)
outputs = layers.Dense(units=1, activation='sigmoid')(x)
# Define the model.
model = keras.Model(inputs, outputs, name="3dcnn")
return model
def build_network(input_shapes, output_size, training, name = 'TreatmentRecommder'):
'''
build the network for covid-19 prediction of how long a patient can be cured
'''
dtype = tf.float32
#treatment information
treatment_info = KL.Input(shape = input_shapes[0], dtype = dtype, name='treatment_info')
#imaing information: CNN features from CT images
image_info = KL.Input(shape = input_shapes[1]+[1], dtype = dtype, name='image_info')
base_filters = 16
x11 = KL.Conv3D(base_filters, (3, 3, 3), activation='relu', padding='same', name = 'x11')(image_info)
x12 = KL.Conv3D(base_filters, (3, 3, 3), activation='relu', padding='same', name = 'x12')(x11)
x13 = KL.Conv3D(base_filters, (3, 3, 3), activation='relu', padding='same', name = 'x13')(x12)
d1 = KL.MaxPool3D()(x13)
x21 = KL.Conv3D(base_filters*2, (3, 3, 3), activation='relu', padding='same', name = 'x21')(d1)
x22 = KL.Conv3D(base_filters*2, (3, 3, 3), activation='relu', padding='same', name = 'x22')(x21)
d2 = KL.MaxPool3D()(x22)
x31 = KL.Conv3D(base_filters*4, (3, 3, 3), activation='relu', padding='same', name = 'x31')(d2)
x32 = KL.Conv3D(base_filters*4, (3, 3, 3), activation='relu', padding='same', name = 'x32')(x31)
d3 = KL.MaxPool3D()(x32)
x41 = KL.Conv3D(base_filters*8, (3, 3, 3), activation='relu', padding='same', name = 'x41')(d3)
x42 = KL.Conv3D(base_filters*8, (3, 3, 3), activation='relu', padding='same', name = 'x42')(x41)
d4 = KL.MaxPool3D()(x42)
x51 = KL.Conv3D(base_filters*16, (3, 3, 3), activation='relu', padding='same', name = 'x51')(d4)
x52 = KL.Conv3D(base_filters*16, (3, 3, 3), activation='relu', padding='same', name = 'x52')(x51)
d5 = KL.MaxPool3D()(x52)
cnn_GAP = KL.GlobalAveragePooling3D(name='CNN_GAP')(d5)
cnn_cof = KL.Dense(1, activation='relu', name='cnn_cof')(cnn_GAP)
#patient information
patient_info = KL.Input(shape = input_shapes[2], dtype = dtype, name='patient_info')
pcnn_info = KL.Concatenate()([patient_info, cnn_cof])
#cured probability distruibution subnetwork
w_pcnn_info = SA_Module(pcnn_info, training)
fc1 = KL.Dense(256, activation='relu', name='fc1')(KL.Concatenate()([w_pcnn_info, cnn_GAP, treatment_info]))
fc2 = KL.Dense(512, activation='relu', name='fc2')(fc1)
fc3 = KL.Dense(512, activation='relu', name='fc3')(fc2)
fc_cls = KL.Dense(256, activation='relu', name='fc_cls')(fc3)
fc_cls = KL.Dropout(0.4)(fc_cls, training = training)
severity_cls_preds = KL.Dense(output_size[0],activation='softmax', name='severity_cls_preds')(fc_cls)
fc_reg = KL.Dense(256, activation='relu', name='fc_reg')(fc3)
fc_reg = KL.Dropout(0.4)(fc_reg, training = training)
risk_reg_preds = KL.Dense(output_size[1],activation='softmax', name='risk_reg_preds')(fc_reg)
model = KM.Model([treatment_info,image_info,patient_info], [severity_cls_preds, risk_reg_preds], name=name)
return model
def build_model(input_shape, target_size, dropout=0):
"""Construct the CosmoFlow 3D CNN model"""
conv_args = dict(kernel_size=2, padding='valid')
model = tf.keras.models.Sequential([
layers.Conv3D(16, input_shape=input_shape, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
layers.Conv3D(16, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
layers.Conv3D(16, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
layers.Conv3D(16, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
layers.Conv3D(16, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
layers.Flatten(),
layers.Dropout(dropout),
layers.Dense(128),
layers.LeakyReLU(),
layers.Dropout(dropout),
layers.Dense(64),
layers.LeakyReLU(),
layers.Dropout(dropout),
layers.Dense(target_size, activation='tanh'),
layers.Lambda(scale_1p2)
])
return model
def create_model(height=240, width=320):
# shape of input: 1 block has 10 frames x height x width x 3 channels (RGB)
input = tf.keras.Input((10, height, width, 3))
# 1st Conv3D block includes Conv3D with 8 filters, MaxPool3D and BatchNormalization
x = layers.Conv3D(filters=8, kernel_size=(3, 3, 3),
activation='relu')(input)
x = layers.MaxPool3D(pool_size=(2, 2, 2))(x)
x = layers.BatchNormalization()(x)
# 2nd Conv3D block includes Conv3D with 16 filters, MaxPool3D and BatchNormalization
x = layers.Conv3D(filters=16, kernel_size=(3, 3, 3), activation='relu')(x)
x = layers.MaxPool3D(pool_size=(2, 2, 2))(x)
x = layers.BatchNormalization()(x)
# 3rd Conv3D block includes Conv3D with 32 filters, MaxPool3D and BatchNormalization
x = layers.Conv3D(filters=32, kernel_size=(3, 3, 3),
activation='relu')(input)
x = layers.MaxPool3D(pool_size=(1, 2, 2))(x)
x = layers.BatchNormalization()(x)
# Fully-connected block includes GlobalAveragePooling3D, Fully-Connected layer with 512 units and DropOut for Regularization
x = layers.GlobalAveragePooling3D()(x)
x = layers.Dense(units=512, activation='relu')(x)
x = layers.DropOut(0.7)(x)
# output shape (1,) produces value between [0, 1]
output = layers.Dense(units=1, activation='sigmoid')(x)
model = tf.keras.Model(input, output, name='3DCNN')
return model
def setup_model(self):
nl = self.hparams['num_latent_layers']
autoencoder_layers = [
tfl.Conv3D(64, (2, 2, 2), padding="same", name='conv_4_conv'),
tfl.Activation(tf.nn.relu, name='conv_4_activation'),
tfl.MaxPool3D((2, 2, 2), name='conv_4_maxpool'),
tfl.Conv3D(128, (2, 2, 2), padding="same", name='conv_3_conv'),
tfl.Activation(tf.nn.relu, name='conv_3_activation'),
tfl.MaxPool3D((2, 2, 2), name='conv_3_maxpool'),
tfl.Conv3D(256, (2, 2, 2), padding="same", name='conv_2_conv'),
tfl.Activation(tf.nn.relu, name='conv_2_activation'),
tfl.MaxPool3D((2, 2, 2), name='conv_2_maxpool'),
tfl.Conv3D(512, (2, 2, 2), padding="same", name='conv_1_conv'),
tfl.Activation(tf.nn.relu, name='conv_1_activation'),
tfl.MaxPool3D((2, 2, 2), name='conv_1_maxpool'),
tfl.Flatten(name='flatten'),
tfl.Dense(nl, activation='relu', name='latent'),
tfl.Dense(32768, activation='relu', name='expand'),
tfl.Reshape((4, 4, 4, 512), name='reshape'),
tfl.Conv3DTranspose(256, (
2,
2,
2,
),
strides=2,
name='deconv_1_deconv'),
tfl.Activation(tf.nn.relu, name='deconv_1_activation'),
tfl.Conv3DTranspose(128, (
2,
2,
2,
),
strides=2,
name='deconv_2_deconv'),
tfl.Activation(tf.nn.relu, name='deconv_2_activation'),
tfl.Conv3DTranspose(64, (
2,
2,
2,
),
strides=2,
name='deconv_3_deconv'),
tfl.Activation(tf.nn.relu, name='deconv_3_activation'),
tfl.Conv3DTranspose(1, (
2,
2,
2,
),
strides=2,
name='deconv_4_deconv'),
# tfl.Activation(tf.nn.relu, name='deconv_4_activation'),
# tfl.Conv3DTranspose(1, (2,2,2,), strides=1, name='deconv_5_deconv', padding="same"),
]
for l in autoencoder_layers:
self._add_layer(l)
def cnn3d(stand_alone=True):
inputs = layers.Input(shape=settings.TENSOR_SHAPE, name='rgb')
# 3D Convolutional Layers
x = layers.Conv3D(filters=64,
kernel_size=3,
strides=2,
padding='same',
activation="relu",
kernel_regularizer=regularizers.l2(l2=1e-4),
bias_regularizer=regularizers.l2(l2=1e-4))(inputs)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.Conv3D(filters=128,
kernel_size=3,
padding='same',
strides=1,
activation="relu",
kernel_regularizer=regularizers.l2(1e-4),
bias_regularizer=regularizers.l2(l2=1e-4))(x)
x = layers.MaxPool3D(pool_size=2, padding='same')(x)
x = layers.Conv3D(filters=256,
kernel_size=3,
strides=1,
padding='same',
activation="relu",
kernel_regularizer=regularizers.l2(1e-4),
bias_regularizer=regularizers.l2(l2=1e-4))(x)
x = layers.MaxPool3D(pool_size=2, padding='same')(x)
x = layers.Conv3D(filters=256,
kernel_size=3,
strides=1,
padding='same',
activation="relu",
kernel_regularizer=regularizers.l2(1e-4),
bias_regularizer=regularizers.l2(l2=1e-4))(x)
x = layers.MaxPool3D(pool_size=2, padding='same')(x)
x = layers.Flatten()(x)
if stand_alone:
x = layers.Dense(units=512, activation="relu")(x)
x = layers.Dropout(0.5)(x)
outputs = layers.Dense(units=settings.NUM_CLASSES,
activation="softmax")(x)
else:
x = layers.Dense(units=2048, activation="relu")(x)
x = layers.Dropout(0.4)(x)
outputs = layers.Dense(units=1024, activation="relu")(x)
# Define the model.
model = Model(inputs, outputs, name="3dcnn")
return model
def setup_model(self):
nl = self.params['num_latent_layers']
autoencoder_layers = [
tfl.Conv3D(64, (2,2,2), padding="same", name='conv_4_conv'),
tfl.Activation(tf.nn.relu, name='conv_4_activation'),
tfl.MaxPool3D((2,2,2), name='conv_4_maxpool'),
tfl.Conv3D(128, (2,2,2), padding="same", name='conv_3_conv'),
tfl.Activation(tf.nn.relu, name='conv_3_activation'),
tfl.MaxPool3D((2,2,2), name='conv_3_maxpool'),
tfl.Conv3D(256, (2,2,2), padding="same", name='conv_2_conv'),
tfl.Activation(tf.nn.relu, name='conv_2_activation'),
tfl.MaxPool3D((2,2,2), name='conv_2_maxpool'),
tfl.Conv3D(512, (2,2,2), padding="same", name='conv_1_conv'),
tfl.Activation(tf.nn.relu, name='conv_1_activation'),
tfl.MaxPool3D((2,2,2), name='conv_1_maxpool'),
tfl.Flatten( name='flatten'),
tfl.Dense(nl, activation='relu', name='latent'),
tfl.Dense(32768, activation='relu', name='expand'),
tfl.Reshape((4,4,4,512), name='reshape'),
tfl.Conv3DTranspose(256, (2,2,2,), strides=2, name='deconv_1_deconv'),
tfl.Activation(tf.nn.relu, name='deconv_1_activation'),
tfl.Conv3DTranspose(128, (2,2,2,), strides=2, name='deconv_2_deconv'),
tfl.Activation(tf.nn.relu, name='deconv_2_activation'),
tfl.Conv3DTranspose(64, (2,2,2,), strides=2, name='deconv_3_deconv'),
tfl.Activation(tf.nn.relu, name='deconv_3_activation'),
tfl.Conv3DTranspose(1, (2,2,2,), strides=2, name='deconv_4_deconv'),
# tfl.Activation(tf.nn.relu, name='deconv_4_activation'),
# tfl.Conv3DTranspose(1, (2,2,2,), strides=1, name='deconv_5_deconv', padding="same"),
]
if self.params['is_u_connected'] and self.params['use_final_unet_layer']:
extra_unet_layers = [
tfl.Conv3D(2, (1,1,1,), use_bias=False, name='unet_combine'),
# tfl.Activation(tf.nn.relu, name='unet_final_activation'),
]
if self.params['final_activation'] == 'sigmoid':
extra_unet_layers.append(tfl.Activation(tf.math.sigmoid, name='unet_final_activation'))
if self.params['final_activation'] == 'relu':
extra_unet_layers.append(tfl.Activation(tf.nn.relu, name='unet_final_activation'))
autoencoder_layers = autoencoder_layers + extra_unet_layers
for l in autoencoder_layers:
self._add_layer(l)
def make_encoder(inp_shape, batch_size, params):
"""Encoder of the autoencoder"""
inputs = inputs = {
'conditioned_occ': tf.keras.Input(batch_size=batch_size,
shape=inp_shape),
'known_occ': tf.keras.Input(batch_size=batch_size, shape=inp_shape),
'known_free': tf.keras.Input(batch_size=batch_size, shape=inp_shape),
}
# Autoencoder
x = tfl.concatenate([inputs['known_occ'], inputs['known_free']], axis=4)
for n_filter in [64, 128, 256, 512]:
x = tfl.Conv3D(n_filter, (
2,
2,
2,
), use_bias=True, padding="same")(x)
x = tfl.Activation(tf.nn.relu)(x)
x = tfl.MaxPool3D((2, 2, 2))(x)
x = tfl.Flatten()(x)
x = tfl.Dense(params['num_latent_layers'], activation='relu')(x)
x = tfl.Dense(32768, activation='relu')(x)
x = tfl.Reshape((4, 4, 4, 512))(x)
auto_encoder_features = x
return tf.keras.Model(inputs=inputs, outputs=auto_encoder_features)
def build_model(columns, rows, depth, output_units, kernel_size):
# Based on: https://keras.io/examples/vision/3D_image_classification/
pool_size = 2
# Handle small dimensions
if (columns <= 2 or rows <= 2):
pool_size = 1
kernel_size = 1
# Handle odd dimension lengths
if ((columns % 2 != 0) or (rows % 2 != 0)):
kernel_size = 1
inputs = keras.Input((depth, columns, rows, 1))
x = layers.Conv3D(filters=64, kernel_size=kernel_size,
activation="relu")(inputs)
x = layers.MaxPool3D(pool_size=pool_size)(x)
x = layers.BatchNormalization()(x)
x = layers.GlobalAveragePooling3D()(x)
x = layers.Dense(units=512, activation="relu")(x)
x = layers.Dropout(0.3)(x)
outputs = layers.Dense(units=output_units, activation="sigmoid")(x)
model = keras.Model(inputs, outputs, name="3DCNN")
return model
def __init__(self, kernel: tuple, stride=2, padding=0, scope='MPOOL'):
super(MaxPool, self).__init__(scope)
dim = len(kernel)
is_global = True if kernel[-1] < 0 else False
if is_global:
assert padding == 0
if dim == 1:
if is_global:
self.pool = _MP(1)
else:
self.pool = layers.MaxPool1D(kernel, stride)
pad_fn = layers.ZeroPadding1D
elif dim == 2:
if is_global:
self.pool = _MP(2)
else:
self.pool = layers.MaxPool2D(kernel, stride)
pad_fn = layers.ZeroPadding2D
elif dim == 3:
if is_global:
self.pool = _MP(3)
else:
self.pool = layers.MaxPool3D(kernel, stride)
pad_fn = layers.ZeroPadding3D
else:
raise Exception('NEBULAE ERROR ⨷ %d-d pooling is not supported.' % dim)
if isinstance(padding, int):
padding = dim * [[padding, padding]]
elif isinstance(padding, (list, tuple)):
padding = [(padding[2*d], padding[2*d+1]) for d in range(dim-1, -1, -1)]
self.pad = pad_fn(padding)
def __init__(self,
n_layer,
root_filters,
kernal_size=3,
pool_size=2,
use_bn=True,
use_res=True,
padding='SAME'):
super().__init__()
self.dw_layers = dict()
self.max_pools = dict()
for layer in range(n_layer):
filters = 2**layer * root_filters
dict_key = str(n_layer - layer - 1)
dw = _DownSampling(filters, kernal_size, 'dw_%d' % layer, use_bn,
use_res)
self.dw_layers[dict_key] = dw
pool = layers.MaxPool3D(pool_size, padding=padding)
self.max_pools[dict_key] = pool
self.flat = layers.Flatten()
self.f1 = layers.Dense(2048, use_bias=True, name='f1')
self.f2 = layers.Dense(512, use_bias=True, name='f2')
self.f3 = layers.Dense(64, use_bias=True, name='f3')
self.f_out = layers.Dense(1, use_bias=False, name='f_out')
def build_down_sampling_block(
self, filters: int, kernel_size: int, padding: str,
strides: int) -> Union[tf.keras.Model, tfkl.Layer]:
"""
Build a block for down-sampling.
This block changes the tensor shape (width, height, depth),
but it does not changes the number of channels.
:param filters: number of channels for output, arg for conv3d
:param kernel_size: arg for pool3d or conv3d
:param padding: arg for pool3d or conv3d
:param strides: arg for pool3d or conv3d
:return: a block consists of one or multiple layers
"""
if self._pooling:
return tfkl.MaxPool3D(pool_size=kernel_size,
strides=strides,
padding=padding)
else:
return layer.Conv3dBlock(
filters=filters,
kernel_size=kernel_size,
strides=strides,
padding=padding,
)
def vgg_3d_v1(input_shape=(38, 38, 6, 1), n_filters=32, kernel_size=(3, 3, 3)):
# No normalization, padding first to 40x40x8, same padding, max pooling
model = Sequential()
model.add(layers.ZeroPadding3D(padding=(1, 1, 1),
input_shape=input_shape)) # 40x40x8
model.add(
layers.Conv3D(filters=n_filters,
kernel_size=kernel_size,
padding='same',
activation='relu'))
model.add(
layers.Conv3D(filters=n_filters,
kernel_size=kernel_size,
padding='same',
activation='relu'))
model.add(layers.MaxPool3D(pool_size=(2, 2, 2))) # 20x20x4
model.add(
layers.Conv3D(filters=2 * n_filters,
kernel_size=kernel_size,
padding='same',
activation='relu'))
model.add(
layers.Conv3D(filters=2 * n_filters,
kernel_size=kernel_size,
padding='same',
activation='relu'))
model.add(
layers.Conv3D(filters=2 * n_filters,
kernel_size=kernel_size,
padding='same',
activation='relu'))
model.add(layers.MaxPool3D(pool_size=(2, 2, 2))) # 10x10x2
model.add(layers.Flatten())
model.add(layers.Dense(units=4 * n_filters, activation='relu'))
model.add(layers.Dropout(0.5))
model.add(layers.Dense(units=4 * n_filters, activation='relu'))
model.add(layers.Dropout(0.5))
model.add(layers.Dense(units=1, activation='sigmoid'))
return model
def make_encoder(inp_shape, params):
"""Basic VAE encoder"""
n_features = params['num_latent_layers']
return tf.keras.Sequential([
tfl.InputLayer(input_shape=inp_shape),
tfl.Conv3D(64, (2, 2, 2), padding="same"),
tfl.Activation(tf.nn.relu),
tfl.MaxPool3D((2, 2, 2)),
tfl.Conv3D(128, (2, 2, 2), padding="same"),
tfl.Activation(tf.nn.relu),
tfl.MaxPool3D((2, 2, 2)),
tfl.Conv3D(256, (2, 2, 2), padding="same"),
tfl.Activation(tf.nn.relu),
tfl.MaxPool3D((2, 2, 2)),
tfl.Conv3D(512, (2, 2, 2), padding="same"),
tfl.Activation(tf.nn.relu),
tfl.MaxPool3D((2, 2, 2)),
tfl.Flatten(),
tfl.Dense(n_features * 2)
])
def get_model(input_shape=(None, None, None, 1)):
inputs = layers.Input(shape=input_shape)
x = layers.Conv3D(filters=96, kernel_size=1, activation="relu")(inputs)
x = layers.MaxPool3D(strides=2)(x)
x = layers.BatchNormalization()(x)
x = fire_block(x, 128)
x = fire_block(x, 128)
x = fire_block(x, 256)
x = layers.MaxPool3D(strides=2)(x)
x = fire_block(x, 256)
x = fire_block(x, 384)
x = fire_block(x, 384)
x = fire_block(x, 512)
x = layers.MaxPool3D(strides=2)(x)
x = fire_block(x, 512)
x = layers.Conv3D(filters=1, kernel_size=1, activation="relu")(x)
x = layers.BatchNormalization()(x)
x = layers.GlobalAveragePooling3D()(x)
x = layers.Softmax()(x)
return tf.keras.Model(inputs=inputs, outputs=x, name="SqueezeNet")
def create_model():
inputs = tf.keras.Input(shape=(image_size, image_size, 3, 1))
prev_inputs = tf.keras.Input(shape=(image_size//2, image_size//2, 3, 6))
# Layer 1:
x11 = layers.Conv3D(3,(9,9,3),strides=(2,2,1), padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(inputs)
x11 = nonlinearity(x11)
x12 = layers.Conv3D(3,(6,6,3),strides=(2,2,1), padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(inputs)
x12 = nonlinearity(x12)
x13 = layers.Conv3D(3,(3,3,3),strides=1, padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(inputs)
x13 = layers.MaxPool3D(pool_size=(2,2,1))(x13)
x13 = nonlinearity(x13)
x1 = layers.Concatenate(axis=4)([x11,x12,x13])
# x1 = (batch, x//2, y//2, 3, 9) # layer 1 output
# Layer 2:
x21 = layers.Conv3D(6,(7,7,3),strides=1, padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(x1)
x21 = nonlinearity(x21)
x22 = layers.Conv3D(6,(7,7,3),strides=1, dilation_rate = (2,2,2), padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(x1)
rnn_input = nonlinearity(x22)
x23 = layers.Conv3D(6,(3,3,3),strides=1, padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(x1)
x23 = nonlinearity(x23)
x2 = layers.Concatenate(axis=4)([x21,x23,prev_inputs])
# x2 = (batch, x//2, y//2, z//2, 18) # layer 2 output
# rnn_input = (batch, x//2, y//2, z//2, 6)
# RNN layer
rnn_out = layers.Conv3D(6,(7,7,3),strides=1, dilation_rate = (3,3,3), padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(rnn_input)
# rnn_out = (batch, x//2, y//2, z//2, 6)
#Layer 3:
x3 = layers.Conv3D(1, (5,5,3), strides=1, padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(x2)
main_out = layers.Conv3DTranspose(1,(3,3,3),strides=(2,2,1), padding='SAME', kernel_initializer=tf.random_normal_initializer(0,0.02))(x3)
main_out = layers.MaxPool3D(pool_size=(1,1,3))(main_out)
main_out = tf.keras.activations.sigmoid(main_out)
# main_out = (batch, x, y, 1)
model = tf.keras.Model(inputs=[inputs,prev_inputs], outputs=[main_out, rnn_out])
return model
def get_model_8L_(width=128, height=128, depth=64):
"""Build a 3D convolutional neural network model."""
inputs = keras.Input((width, height, depth, 1))
x = layers.Conv3D(filters=64, kernel_size=3, activation="relu")(inputs)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization(center=True, scale=True)(x)
x = layers.Dropout(0.2)(x)
x = layers.Conv3D(filters=64, kernel_size=3, activation="relu")(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization(center=True, scale=True)(x)
x = layers.Dropout(0.5)(x)
### add 64N layer ##################################################
x = layers.Conv3D(filters=64, kernel_size=3, activation="relu")(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization(center=True, scale=True)(x)
x = layers.Dropout(0.3)(x)
x = layers.Conv3D(filters=128, kernel_size=3, activation="relu")(x)
x = layers.MaxPool3D(pool_size=1)(x)
x = layers.BatchNormalization(center=True, scale=True)(x)
x = layers.Dropout(0.3)(x)
x = layers.Conv3D(filters=256, kernel_size=3, activation="relu")(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.GlobalAveragePooling3D()(x)
x = layers.Dense(units=512, activation="relu")(x)
x = layers.Dropout(0.3)(x)
outputs = layers.Dense(units=1, activation="sigmoid")(x)
# outputs = layers.Dense(units=1, activation="tanh", )(x)
# outputs = layers.Dense(units=1, activation="relu", )(x)
model = keras.Model(inputs, outputs, name="3dcnn")
return model
def get_model(width=224, height=224, depth=32):
"""Build a 3D convolutional neural network model."""
inputs = keras.Input((width, height, depth, 1))
x = layers.Conv3D(filters=64,
kernel_size=3,
activation="relu",
padding='same')(inputs)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.Conv3D(filters=64,
kernel_size=3,
activation="relu",
padding='same')(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.Conv3D(filters=128,
kernel_size=3,
activation="relu",
padding='same')(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.Conv3D(filters=256,
kernel_size=3,
activation="relu",
padding='same')(x)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.GlobalAveragePooling3D()(x)
x = layers.Dense(units=512, activation="relu")(x)
x = layers.Dropout(0.3)(x)
outputs = layers.Dense(units=51, activation="softmax")(x)
model = keras.Model(inputs, outputs, name="3dcnn")
return model
def FirstConvolution(inputs):
x = layers.BatchNormalization()(inputs)
x = layers.Activation('relu')(x)
x = layers.Conv3D(filters=bn_size * growth_rate,
kernel_size=(3, 7, 7),
activation=None,
strides=2,
padding='same',
use_bias=False)(x)
x = layers.MaxPool3D(pool_size=(2, 2, 2), strides=1, padding='same')(x)
return x
def build_model(input_shape, target_size, dropout=0):
conv_args = dict(kernel_size=2, padding="valid")
model = tf.keras.models.Sequential([
layers.Conv3D(16, input_shape=input_shape, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
#
layers.Conv3D(16, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
#
layers.Conv3D(16, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
#
layers.Conv3D(16, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
#
layers.Conv3D(16, **conv_args),
layers.LeakyReLU(),
layers.MaxPool3D(pool_size=2),
#
layers.Flatten(),
layers.Dropout(dropout),
#
layers.Dense(128),
layers.LeakyReLU(),
layers.Dropout(dropout),
#
layers.Dense(64),
layers.LeakyReLU(),
layers.Dropout(dropout),
#
layers.Dense(target_size, activation="tanh"),
layers.Lambda(scale_1p2),
])
return model
def __init__(self, hparams: Dict, batch_size: int, scenario: Base3DScenario):
super().__init__(hparams, batch_size)
self.scenario = scenario
self.raster_debug_pubs = [
rospy.Publisher(f'classifier_raster_debug_{i}', OccupancyStamped, queue_size=10, latch=False) for i in
range(4)]
self.local_env_bbox_pub = rospy.Publisher('local_env_bbox', BoundingBox, queue_size=10, latch=True)
self.classifier_dataset_hparams = self.hparams['classifier_dataset_hparams']
self.dynamics_dataset_hparams = self.classifier_dataset_hparams['fwd_model_hparams']['dynamics_dataset_hparams']
self.true_state_keys = self.classifier_dataset_hparams['true_state_keys']
self.pred_state_keys = [add_predicted(k) for k in self.classifier_dataset_hparams['predicted_state_keys']]
self.pred_state_keys.append(add_predicted('stdev'))
self.local_env_h_rows = self.hparams['local_env_h_rows']
self.local_env_w_cols = self.hparams['local_env_w_cols']
self.local_env_c_channels = self.hparams['local_env_c_channels']
self.rope_image_k = self.hparams['rope_image_k']
# TODO: add stdev to states keys?
self.state_keys = self.hparams['state_keys']
self.action_keys = self.hparams['action_keys']
self.conv_layers = []
self.pool_layers = []
for n_filters, kernel_size in self.hparams['conv_filters']:
conv = layers.Conv3D(n_filters,
kernel_size,
activation='relu',
kernel_regularizer=keras.regularizers.l2(self.hparams['kernel_reg']),
bias_regularizer=keras.regularizers.l2(self.hparams['bias_reg']))
pool = layers.MaxPool3D(self.hparams['pooling'])
self.conv_layers.append(conv)
self.pool_layers.append(pool)
if self.hparams['batch_norm']:
self.batch_norm = layers.BatchNormalization()
self.dense_layers = []
for hidden_size in self.hparams['fc_layer_sizes']:
dense = layers.Dense(hidden_size,
activation='relu',
kernel_regularizer=keras.regularizers.l2(self.hparams['kernel_reg']),
bias_regularizer=keras.regularizers.l2(self.hparams['bias_reg']))
self.dense_layers.append(dense)
# self.local_env_shape = (self.local_env_h_rows, self.local_env_w_cols, self.local_env_c_channels)
# self.encoder = tf.keras.applications.ResNet50(include_top=False, weights=None, input_shape=self.local_env_shape)
self.lstm = layers.LSTM(self.hparams['rnn_size'], unroll=True, return_sequences=True)
self.output_layer = layers.Dense(1, activation=None)
self.sigmoid = layers.Activation("sigmoid")
def __init__(self):
super(Sunset3DModel, self).__init__()
self.conv1 = layers.Conv3D(12, (3, 3, 3),
activation='relu',
padding='same')
self.conv2 = layers.Conv3D(24, (3, 3, 3),
activation='relu',
padding='same')
self.maxpooling = layers.MaxPool3D(pool_size=(2, 2, 2))
self.flatten = layers.Flatten()
self.dense1 = layers.Dense(1024, activation=tf.nn.relu)
self.dense2 = layers.Dense(1024, activation=tf.nn.relu)
self.dense3 = layers.Dense(4, activation=None)
def FirstConvolution(inputs):
x = layers.BatchNormalization()(inputs)
x = layers.Activation('relu')(x)
x = layers.Conv3D(filters=16,
kernel_size=(3, 7, 7),
activation=None,
strides=2,
padding='same',
use_bias=False)(x)
print('First 3D Conv:', x.shape)
x = layers.MaxPool3D(pool_size=(3, 3, 3),
strides=(1, 2, 2),
padding='same')(x)
return x
def create_model_fc(input, output):
print('Creating model...')
model = models.Sequential(
[
layers.Conv3D(filters=16,
kernel_size=3,
activation='relu',
input_shape=input),
layers.Dropout(rate=0.4),
layers.Conv3D(filters=16, kernel_size=3, activation='relu'),
layers.Dropout(rate=0.4),
layers.MaxPool3D(pool_size=2),
layers.Conv3D(filters=32, kernel_size=3, activation='relu'),
layers.Dropout(rate=0.4),
layers.Conv3D(filters=32, kernel_size=3, activation='relu'),
layers.Dropout(rate=0.4),
layers.MaxPool3D(pool_size=2),
layers.Conv3D(filters=64, kernel_size=3, activation='relu'),
layers.Dropout(rate=0.4),
layers.Conv3D(filters=64, kernel_size=3, activation='relu'),
layers.Dropout(rate=0.4),
layers.MaxPool3D(pool_size=2),
layers.Flatten(),
# layers.Dense(10, activation='relu'),
# layers.Dropout(0.2),
layers.Dense(output, activation='softmax')
],
name='VGG-6_3D')
model.compile(optimizer='adam',
loss='sparse_categorical_crossentropy',
metrics=['accuracy'])
print('Creation successful!')
return model
def make_stack_net_v3(inp_shape, batch_size, params):
"""
Just an Autoencoder. Used to verify against v4
"""
filter_size = [2, 2, 2]
n_filters = [64, 128, 256, 512]
inputs = {
'conditioned_occ': tf.keras.Input(batch_size=batch_size,
shape=inp_shape),
'known_occ': tf.keras.Input(batch_size=batch_size, shape=inp_shape),
'known_free': tf.keras.Input(batch_size=batch_size, shape=inp_shape),
}
# Autoencoder
x = tfl.concatenate([inputs['known_occ'], inputs['known_free']], axis=4)
for n_filter in [64, 128, 256, 512]:
x = tfl.Conv3D(n_filter, (
2,
2,
2,
), use_bias=True, padding="same")(x)
x = tfl.Activation(tf.nn.relu)(x)
x = tfl.MaxPool3D((2, 2, 2))(x)
x = tfl.Flatten()(x)
x = tfl.Dense(params['num_latent_layers'], activation='relu')(x)
x = tfl.Dense(32768, activation='relu')(x)
x = tfl.Reshape((4, 4, 4, 512))(x)
for n_filter in [256, 128, 64, 12]:
x = tfl.Conv3DTranspose(n_filter, (
2,
2,
2,
),
use_bias=True,
strides=2)(x)
x = tfl.Activation(tf.nn.relu)(x)
x = tfl.Conv3D(1, (1, 1, 1), use_bias=True)(x)
x = tfl.Activation(tf.nn.sigmoid)(x)
output = {"predicted_occ": x, "predicted_free": 1 - x}
return tf.keras.Model(inputs=inputs, outputs=output)
def build_model(columns, rows, depth, output_units):
# Based on: https://keras.io/examples/vision/3D_image_classification/
inputs = keras.Input((depth, columns, rows, 1))
x = layers.Conv3D(filters=64,
kernel_size=settings.KERNEL_SIZE,
activation="relu")(inputs)
x = layers.MaxPool3D(pool_size=2)(x)
x = layers.BatchNormalization()(x)
x = layers.GlobalAveragePooling3D()(x)
x = layers.Dense(units=512, activation="relu")(x)
x = layers.Dropout(0.3)(x)
outputs = layers.Dense(units=output_units, activation="sigmoid")(x)
model = keras.Model(inputs, outputs, name="3DCNN")
return model
def __init__(self,
n_class,
n_layer,
root_filters,
kernal_size=3,
pool_size=2,
use_bn=False,
use_res=True,
padding='SAME',
concat_or_add='concat'):
super().__init__()
self.dw_layers = dict()
self.up_layers = dict()
self.max_pools = dict()
for layer in range(n_layer):
filters = 2**layer * root_filters
dict_key = str(n_layer - layer - 1)
dw = _DownSampling(filters, kernal_size, 'dw_%d' % layer, use_bn,
use_res)
self.dw_layers[dict_key] = dw
if layer < n_layer - 1:
pool = layers.MaxPool3D(pool_size, padding=padding)
self.max_pools[dict_key] = pool
for layer in range(n_layer - 2, -1, -1):
filters = 2**(layer + 1) * root_filters
dict_key = str(n_layer - layer - 1)
up = _UpSampling(filters, kernal_size, pool_size, concat_or_add)
self.up_layers[dict_key] = up
stddev = np.sqrt(2 / (kernal_size**2 * root_filters))
self.conv_out = layers.Conv3D(
n_class,
1,
padding=padding,
use_bias=False,
kernel_initializer=initializers.TruncatedNormal(stddev=stddev),
name='conv_out')
filter_size = [2,2,2]
n_filters = [64, 128, 256, 512]
inputs = {'conditioned_occ':tf.keras.Input(batch_size=batch_size, shape=inp_shape),
'known_occ':tf.keras.Input(batch_size=batch_size, shape=inp_shape),
'known_free':tf.keras.Input(batch_size=batch_size, shape=inp_shape),
}
# Autoencoder
x = tfl.concatenate([inputs['known_occ'], inputs['known_free']], axis=4)
for n_filter in [64, 128, 256, 512]:
x = tfl.Conv3D(n_filter, (2,2,2,), use_bias=True, padding="same")(x)
x = tfl.Activation(tf.nn.relu)(x)
x = tfl.MaxPool3D((2,2,2))(x)
x = tfl.Flatten()(x)
x = tfl.Dense(params['num_latent_layers'], activation='relu')(x)
x = tfl.Dense(32768, activation='relu')(x)
x = tfl.Reshape((4,4,4,512))(x)
for n_filter in [256, 128, 64, 12]:
x = tfl.Conv3DTranspose(n_filter, (2,2,2,), use_bias=True, strides=2)(x)
x = tfl.Activation(tf.nn.relu)(x)
x = tfl.Conv3D(1, (1,1,1), use_bias=True)(x)
x = tfl.Activation(tf.nn.sigmoid)(x)
output = {"predicted_occ":x, "predicted_free":1 - x}
return tf.keras.Model(inputs=inputs, outputs=output)