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 ResNet(stack_fn,
preact,
use_bias,
model_name='resnet',
include_top=True,
input_tensor=None,
input_shape=None,
pooling=None,
classes=1000,
**kwargs):
"""Instantiates the ResNet, ResNetV2, and ResNeXt architecture.
Optionally loads weights pre-trained on ImageNet.
Note that the data format convention used by the model is
the one specified in your Keras config at `~/.keras/keras.json`.
# Arguments
stack_fn: a function that returns output tensor for the
stacked residual blocks.
preact: whether to use pre-activation or not
(True for ResNetV2, False for ResNet and ResNeXt).
use_bias: whether to use biases for convolutional layers or not
(True for ResNet and ResNetV2, False for ResNeXt).
model_name: string, model name.
include_top: whether to include the fully-connected
layer at the top of the network.
input_tensor: optional Keras tensor
(i.e. output of `layers.Input()`)
to use as image input for the model.
input_shape: optional shape tuple, only to be specified
if `include_top` is False (otherwise the input shape
has to be `(224, 224, 3)` (with `channels_last` data format)
or `(3, 224, 224)` (with `channels_first` data format).
It should have exactly 3 inputs channels.
pooling: optional pooling mode for feature extraction
when `include_top` is `False`.
- `None` means that the output of the model will be
the 4D tensor output of the
last convolutional layer.
- `avg` means that global average pooling
will be applied to the output of the
last convolutional layer, and thus
the output of the model will be a 2D tensor.
- `max` means that global max pooling will
be applied.
classes: optional number of classes to classify images
into, only to be specified if `include_top` is True, and
if no `weights` argument is specified.
# Returns
A Keras model instance.
# Raises
ValueError: in case of invalid argument for `weights`,
or invalid input shape.
"""
if input_tensor is None:
img_input = layers.Input(shape=input_shape)
else:
if not backend.is_keras_tensor(input_tensor):
img_input = layers.Input(tensor=input_tensor, shape=input_shape)
else:
img_input = input_tensor
bn_axis = 3 if backend.image_data_format() == 'channels_last' else 1
x = layers.ZeroPadding3D(padding=3, name='conv1_pad')(img_input)
x = layers.Conv3D(64, 7, strides=2, use_bias=use_bias, name='conv1_conv')(x)
if preact is False:
x = layers.BatchNormalization(axis=bn_axis, epsilon=1.001e-5,
name='conv1_bn')(x)
x = layers.Activation('relu', name='conv1_relu')(x)
x = layers.ZeroPadding3D(padding=1, name='pool1_pad')(x)
x = layers.MaxPooling3D(3, strides=2, name='pool1_pool')(x)
x = stack_fn(x)
if preact is True:
x = layers.BatchNormalization(axis=bn_axis, epsilon=1.001e-5,
name='post_bn')(x)
x = layers.Activation('relu', name='post_relu')(x)
if include_top:
x = layers.GlobalAveragePooling3D(name='avg_pool')(x)
x = layers.Dense(classes, activation='softmax', name='probs')(x)
else:
if pooling == 'avg':
x = layers.GlobalAveragePooling3D(name='avg_pool')(x)
elif pooling == 'max':
x = layers.GlobalMaxPooling3D(name='max_pool')(x)
# Ensure that the model takes into account
# any potential predecessors of `input_tensor`.
if input_tensor is not None:
inputs = keras_utils.get_source_inputs(input_tensor)
else:
inputs = img_input
# Create model.
model = models.Model(inputs, x, name=model_name)
return model
def VGG16(sideLength):
'''
VGG16 3D CNN Implementation
'''
#try decreasing strides
#compare with and without batch norm
input = keras.Input(shape=(sideLength, sideLength, sideLength, 1))
x = layers.ZeroPadding3D(padding=(1,1,1))(input)
x = layers.Conv3D(64, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(64, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.MaxPooling3D((2,2,2), strides=(2,2,2))(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(128, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(128, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.MaxPooling3D((2,2,2), strides=(2,2,2))(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(256, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(256, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(256, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.MaxPooling3D((2,2,2), strides=(2,2,2))(x)
'''
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(512, 3, 1, activation='relu')(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(512, 3, 1, activation='relu')(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(512, 3, 1, activation='relu')(x)
x = layers.MaxPooling3D((2,2,2), strides=(2,2,2))(x)
'''
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(512, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(512, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.ZeroPadding3D((1,1,1))(x)
x = layers.Conv3D(512, 3, 1)(x)
x = layers.BatchNormalization()(x)
x = layers.Activation('relu')(x)
x = layers.MaxPooling3D((2,2,2), strides=(2,2,2))(x)
x = layers.Flatten()(x)
x = layers.Dense(4096, activation='relu')(x)
x = layers.Dropout(0.5)(x)
x = layers.Dense(4096, activation='relu')(x)
x = layers.Dropout(0.5)(x)
output = layers.Dense(1, activation='sigmoid')(x)
model = keras.Model(input, output, name='VGG16')
return model
def f(x):
y = layers.Conv3D(filters, (1, 1),
strides=stride,
use_bias=False,
name="res{}{}_branch2a".format(
stage_char, block_char),
**parameters)(x)
y = BatchNormalizationFreeze(axis=axis,
epsilon=1e-5,
freeze=freeze_bn,
name="bn{}{}_branch2a".format(
stage_char, block_char))(y)
y = layers.Activation("relu",
name="res{}{}_branch2a_relu".format(
stage_char, block_char))(y)
y = layers.ZeroPadding3D(padding=1,
name="padding{}{}_branch2b".format(
stage_char, block_char))(y)
y = layers.Conv3D(filters,
kernel_size,
use_bias=False,
name="res{}{}_branch2b".format(
stage_char, block_char),
**parameters)(y)
y = BatchNormalizationFreeze(axis=axis,
epsilon=1e-5,
freeze=freeze_bn,
name="bn{}{}_branch2b".format(
stage_char, block_char))(y)
y = layers.Activation("relu",
name="res{}{}_branch2b_relu".format(
stage_char, block_char))(y)
y = layers.Conv3D(filters * 4, (1, 1),
use_bias=False,
name="res{}{}_branch2c".format(
stage_char, block_char),
**parameters)(y)
y = BatchNormalizationFreeze(axis=axis,
epsilon=1e-5,
freeze=freeze_bn,
name="bn{}{}_branch2c".format(
stage_char, block_char))(y)
if block == 0:
shortcut = layers.Conv3D(filters * 4, (1, 1),
strides=stride,
use_bias=False,
name="res{}{}_branch1".format(
stage_char, block_char),
**parameters)(x)
shortcut = BatchNormalizationFreeze(axis=axis,
epsilon=1e-5,
freeze=freeze_bn,
name="bn{}{}_branch1".format(
stage_char,
block_char))(shortcut)
else:
shortcut = x
y = layers.Add(name="res{}{}".format(stage_char, block_char))(
[y, shortcut])
y = layers.Activation("relu",
name="res{}{}_relu".format(
stage_char, block_char))(y)
return y
def Vox_discriminator(input_shape, n_filters=64, kernel_size=4, norm="batch"):
"""Instantiate Discriminator.
Adapted from https://arxiv.org/abs/2003.13653
Parameters
----------
input_shape: list or tuple of four ints, the shape of the input data. Omit
the batch dimension, and include the number of channels.
n_filters: int, number of filters. default is set 64.
kernal_size: int, size of the kernal of conv layers. Default kernal size
is set to be 4.
norm: str, to set batch or instance norm.
Returns
----------
Model object.
"""
inputs = layers.Input(input_shape, name="input_image")
targets = layers.Input(input_shape, name="target_image")
Nfilter_start = n_filters
depth = 3
def encoder_step(inputs, n_filters, kernel_size, norm="instance"):
x = layers.Conv3D(
n_filters,
kernel_size,
strides=2,
kernel_initializer="he_normal",
padding="same",
)(inputs)
if norm == "instance":
x = InstanceNormalization()(x)
if norm == "batch":
x = layers.BatchNormalization()(x)
x = layers.LeakyReLU()(x)
x = layers.Dropout(0.2)(x)
return x
x = layers.Concatenate()([inputs, targets])
for d in range(depth):
if d == 0:
x = encoder_step(
x, Nfilter_start * np.power(2, d), kernel_size, norm="None"
)
else:
x = encoder_step(x, Nfilter_start * np.power(2, d), kernel_size, norm=norm)
x = layers.ZeroPadding3D()(x)
x = layers.Conv3D(
Nfilter_start * (2**depth),
kernel_size,
strides=1,
padding="valid",
kernel_initializer="he_normal",
)(x)
if norm == "instance":
x = InstanceNormalization()(x)
if norm == "batch":
x = layers.BatchNormalization()(x)
x = layers.LeakyReLU()(x)
x = layers.ZeroPadding3D()(x)
last = layers.Conv3D(
1,
kernel_size,
strides=1,
padding="valid",
kernel_initializer="he_normal",
name="output_discriminator",
)(x)
return Model(inputs=[targets, inputs], outputs=last, name="Discriminator")
def make_base_cnn_3d(image_shape=(20, 100, 100), name='base_cnn', nlayers=18):
"""Make a CNN network for a single image.
Args:
image_shape: tuple of ints
Shape of input images in pixels
name: string
Name for model
nlayers: int
Number of layers in the model: 18 or 34
Returns:
Keras model
"""
if nlayers not in [8, 18, 34]:
raise ValueError('nlayers must be 8, 18 or 34.')
img_input = layers.Input(shape=image_shape + (1, )) # Channels last.
x = layers.ZeroPadding3D(padding=(1, 3, 3), name='conv1_pad')(img_input)
x = layers.Conv3D(64, (3, 7, 7),
strides=(2, 2, 2),
padding='valid',
kernel_initializer='he_normal',
name='conv1')(x)
x = layers.BatchNormalization(name='bn_conv1')(x)
x = layers.Activation('relu')(x)
x = layers.ZeroPadding3D(padding=(1, 1, 1), name='pool1_pad')(x)
x = layers.MaxPooling3D((3, 3, 3), strides=(2, 2, 2))(x)
if nlayers == 8:
x = layers.ZeroPadding3D(padding=(1, 3, 3), name='conv2_pad')(x)
x = layers.Conv3D(64, (3, 7, 7),
strides=(2, 2, 2),
padding='valid',
kernel_initializer='he_normal',
name='conv2')(x)
x = conv_block_3d(x, (3, 3, 3), [64, 64],
stage=2,
block='a',
strides=(2, 2, 2))
x = identity_block_3d(x, (3, 3, 3), [64, 64], stage=2, block='b')
x = conv_block_3d(x, (3, 3, 3), [128, 128],
stage=3,
block='a',
strides=(2, 1, 1))
x = identity_block_3d(x, (3, 3, 3), [128, 128], stage=3, block='b')
x = conv_block_3d(x, (3, 3, 3), [128, 128],
stage=4,
block='a',
strides=(1, 1, 1))
x = identity_block_3d(x, (3, 3, 3), [128, 128], stage=4, block='b')
if nlayers == 18:
x = conv_block_3d(x, (3, 3, 3), [64, 64],
stage=2,
block='a',
strides=(2, 1, 1))
x = identity_block_3d(x, (3, 3, 3), [64, 64], stage=2, block='b')
x = conv_block_3d(x, (3, 3, 3), [128, 128],
stage=3,
block='a',
strides=(2, 2, 2))
x = identity_block_3d(x, (3, 3, 3), [128, 128], stage=3, block='b')
x = conv_block_3d(x, (3, 3, 3), [256, 256],
stage=4,
block='a',
strides=(2, 2, 2))
x = identity_block_3d(x, (3, 3, 3), [256, 256], stage=4, block='b')
x = conv_block_3d(x, (3, 3, 3), [512, 512],
stage=5,
block='a',
strides=(1, 1, 1))
x = identity_block_3d(x, (3, 3, 3), [512, 512], stage=5, block='b')
if nlayers == 34:
x = conv_block_3d(x, (3, 3, 3), [64, 64],
stage=2,
block='a',
strides=(2, 1, 1))
x = identity_block_3d(x, (3, 3, 3), [64, 64], stage=2, block='b')
x = identity_block_3d(x, (3, 3, 3), [64, 64], stage=2, block='c')
x = conv_block_3d(x, (3, 3, 3), [128, 128],
stage=3,
block='a',
strides=(2, 2, 2))
x = identity_block_3d(x, (3, 3, 3), [128, 128], stage=3, block='b')
x = identity_block_3d(x, (3, 3, 3), [128, 128], stage=3, block='c')
x = identity_block_3d(x, (3, 3, 3), [128, 128], stage=3, block='d')
x = conv_block_3d(x, (3, 3, 3), [256, 256],
stage=4,
block='a',
strides=(2, 2, 2))
x = identity_block_3d(x, (3, 3, 3), [256, 256], stage=4, block='b')
x = identity_block_3d(x, (3, 3, 3), [256, 256], stage=4, block='c')
x = identity_block_3d(x, (3, 3, 3), [256, 256], stage=4, block='d')
x = identity_block_3d(x, (3, 3, 3), [256, 256], stage=4, block='e')
x = identity_block_3d(x, (3, 3, 3), [256, 256], stage=4, block='f')
x = conv_block_3d(x, (3, 3, 3), [512, 512],
stage=5,
block='a',
strides=(1, 1, 1))
x = identity_block_3d(x, (3, 3, 3), [512, 512], stage=5, block='b')
x = identity_block_3d(x, (3, 3, 3), [512, 512], stage=5, block='c')
return Model(img_input, x, name=name)
def resnet50_3d(inputs,
filter_ratio=1,
n=2,
include_fc_layer=False,
logits=True,
kernal1=(1, 1, 1),
kernal3=(1, 3, 3),
kernal7=(1, 7, 7),
num_layers=None):
"""
:param inputs: Keras Input object with desire shape
:type inputs:
:param filter_ratio:
:type filter_ratio:
:param n: # of categories
:type n: integer
:param include_fc_layer:
:type include_fc_layer:
:return:
:rtype:
"""
# --- Define kwargs dictionary
kwargs1 = {
'kernel_size': kernal1,
'padding': 'valid',
}
kwargs3 = {
'kernel_size': kernal3,
'padding': 'same',
}
kwargs7 = {
'kernel_size': kernal7,
'padding': 'valid',
}
# --- Define block components
conv1 = lambda x, filters, strides: layers.Conv3D(
filters=filters, strides=strides, **kwargs1)(x)
conv3 = lambda x, filters, strides: layers.Conv3D(
filters=filters, strides=strides, **kwargs3)(x)
relu = lambda x: layers.LeakyReLU()(x)
conv7 = lambda x, filters, strides: layers.Conv3D(
filters=filters, strides=strides, **kwargs7)(x)
max_pool = lambda x, pool_size, strides: layers.MaxPooling3D(
pool_size=pool_size, strides=strides, padding='valid')(x)
norm = lambda x: layers.BatchNormalization()(x)
add = lambda x, y: layers.Add()([x, y])
zeropad = lambda x, padding: layers.ZeroPadding3D(padding=padding)(x)
# --- Residual blocks
# conv blocks
conv_1 = lambda filters, x, strides: relu(
norm(conv1(x, filters, strides=strides)))
conv_2 = lambda filters, x: relu(norm(conv3(x, filters, strides=1)))
conv_3 = lambda filters, x: norm(conv1(x, filters, strides=1))
conv_sc = lambda filters, x, strides: norm(
conv1(x, filters, strides=strides))
conv_block = lambda filters1, filters2, x, strides: relu(
add(conv_sc(filters2, x, strides),
conv_3(filters2, conv_2(filters1, conv_1(filters1, x, strides)))))
# identity blocks
identity_1 = lambda filters, x: relu(norm(conv1(x, filters, strides=1)))
identity_2 = lambda filters, x: relu(norm(conv3(x, filters, strides=1)))
identity_3 = lambda filters, x: norm(conv1(x, filters, strides=1))
identity_block = lambda filters1, filters2, x: relu(
add(
identity_3(filters2, identity_2(filters1, identity_1(filters1, x))
), x))
# --- ResNet-50 backbone
# stage 1 c2 1/4
res1 = max_pool(zeropad(
relu(
norm(
conv7(zeropad(inputs, (0, 3, 3)),
int(64 * filter_ratio),
strides=(1, 2, 2)))), (0, 1, 1)), (1, 3, 3),
strides=(1, 2, 2))
# stage 2 c2 1/4
res2 = layers.Lambda(lambda x: x, name='c2-output')(identity_block(
int(64 * filter_ratio), int(256 * filter_ratio),
identity_block(
int(64 * filter_ratio), int(256 * filter_ratio),
conv_block(int(64 * filter_ratio),
int(256 * filter_ratio),
res1,
strides=1))))
# stage 3 c3 1/8
res3 = layers.Lambda(lambda x: x, name='c3-output')(identity_block(
int(128 * filter_ratio), int(512 * filter_ratio),
identity_block(
int(128 * filter_ratio), int(512 * filter_ratio),
identity_block(
int(128 * filter_ratio), int(512 * filter_ratio),
conv_block(int(128 * filter_ratio),
int(512 * filter_ratio),
res2,
strides=(1, 2, 2))))))
# stage 4 c4 1/16
res4 = layers.Lambda(lambda x: x, name='c4-output')(identity_block(
int(256 * filter_ratio), int(1024 * filter_ratio),
identity_block(
int(256 * filter_ratio), int(1024 * filter_ratio),
identity_block(
int(256 * filter_ratio), int(1024 * filter_ratio),
identity_block(
int(256 * filter_ratio), int(1024 * filter_ratio),
identity_block(
int(256 * filter_ratio), int(1024 * filter_ratio),
conv_block(int(256 * filter_ratio),
int(1024 * filter_ratio),
res3,
strides=(1, 2, 2))))))))
# stage 5 c5 1/32
res5 = layers.Lambda(lambda x: x, name='c5-output')(identity_block(
int(512 * filter_ratio), int(2048 * filter_ratio),
identity_block(
int(512 * filter_ratio), int(2048 * filter_ratio),
conv_block(int(512 * filter_ratio),
int(2048 * filter_ratio),
res4,
strides=(1, 2, 2)))))
if num_layers:
avg_pool = layers.GlobalAveragePooling3D()(
[res1, res2, res3, res4, res5][num_layers - 1])
else:
avg_pool = layers.GlobalAveragePooling3D()(res5)
flatten = layers.Flatten()(avg_pool)
if logits:
logits = layers.Dense(n)(flatten)
else:
logits = layers.Dense(n, activation='softmax')
if include_fc_layer:
model = Model(inputs=inputs, outputs=logits)
else:
model = Model(inputs=inputs, outputs=res5)
return model
def retinanet_resnet(inputs, K, A):
"""Retinanet with resnet backbone. Classification and regression networks share weights across feature pyramid
layers"""
# --- Define kwargs dictionary
kwargs1 = {
'kernel_size': (1, 1, 1),
'padding': 'valid',
}
kwargs3 = {
'kernel_size': (1, 3, 3),
'padding': 'same',
}
kwargs7 = {
'kernel_size': (1, 7, 7),
'padding': 'valid',
}
# --- Define block components
conv1 = lambda x, filters, strides: layers.Conv3D(
filters=filters, strides=strides, **kwargs1)(x)
conv3 = lambda x, filters, strides: layers.Conv3D(
filters=filters, strides=strides, **kwargs3)(x)
relu = lambda x: layers.LeakyReLU()(x)
conv7 = lambda x, filters, strides: layers.Conv3D(
filters=filters, strides=strides, **kwargs7)(x)
max_pool = lambda x, pool_size, strides: layers.MaxPooling3D(
pool_size=pool_size, strides=strides, padding='valid')(x)
norm = lambda x: layers.BatchNormalization()(x)
add = lambda x, y: layers.Add()([x, y])
zeropad = lambda x, padding: layers.ZeroPadding3D(padding=padding)(x)
upsamp2x = lambda x: layers.UpSampling3D(size=(1, 2, 2))(x)
# --- Define stride-1, stride-2 blocks
# conv1 = lambda filters, x : relu(conv(x, filters, strides=1))
# conv2 = lambda filters, x : relu(conv(x, filters, strides=(2, 2)))
# --- Residual blocks
# conv blocks
conv_1 = lambda filters, x, strides: relu(
norm(conv1(x, filters, strides=strides)))
conv_2 = lambda filters, x: relu(norm(conv3(x, filters, strides=1)))
conv_3 = lambda filters, x: norm(conv1(x, filters, strides=1))
conv_sc = lambda filters, x, strides: norm(
conv1(x, filters, strides=strides))
conv_block = lambda filters1, filters2, x, strides: relu(
add(conv_3(filters2, conv_2(filters1, conv_1(filters1, x, strides))),
conv_sc(filters2, x, strides)))
# identity blocks
identity_1 = lambda filters, x: relu(norm(conv1(x, filters, strides=1)))
identity_2 = lambda filters, x: relu(norm(conv3(x, filters, strides=1)))
identity_3 = lambda filters, x: norm(conv1(x, filters, strides=1))
identity_block = lambda filters1, filters2, x: relu(
add(
identity_3(filters2, identity_2(filters1, identity_1(filters1, x))
), x))
# --- feature pyramid blocks
fp_block = lambda x, y: add(upsamp2x(x), conv1(y, 256, strides=1))
# --- classification head
class_subnet = classification_head(K, A)
# --- regression head
box_subnet = regression_head(A)
# --- ResNet-50 backbone
# stage 1 c2 1/4
res1 = max_pool(zeropad(
relu(
norm(
conv7(zeropad(inputs['dat'], (0, 3, 3)), 64,
strides=(1, 2, 2)))), (0, 1, 1)), (1, 3, 3),
strides=(1, 2, 2))
# stage 2 c2 1/4
res2 = identity_block(
64, 256, identity_block(64, 256, conv_block(64, 256, res1, strides=1)))
# stage 3 c3 1/8
res3 = identity_block(
128, 512,
identity_block(
128, 512,
identity_block(128, 512,
conv_block(128, 512, res2, strides=(1, 2, 2)))))
# stage 4 c4 1/16
res4 = identity_block(
256, 1024,
identity_block(
256, 1024,
identity_block(
256, 1024,
identity_block(
256, 1024,
identity_block(
256, 1024,
conv_block(256, 1024, res3, strides=(1, 2, 2)))))))
# stage 5 c5 1/32
res5 = identity_block(
512, 2048,
identity_block(512, 2048, conv_block(512,
2048,
res4,
strides=(1, 2, 2))))
# --- Feature Pyramid Network architecture
# p5 1/32
fp5 = conv1(res5, 256, strides=1)
# p4 1/16
fp4 = fp_block(fp5, res4)
p4 = conv3(fp4, 256, strides=1)
# p3 1/8
fp3 = fp_block(fp4, res3)
p3 = conv3(fp3, 256, strides=1)
# p6 1/4
# p6 = conv3(fp5, 256, strides=(2, 2))
# p7 1/2
# p7 = conv3(relu(p6), 256, strides=(2, 2))
feature_pyramid = [p3, p4, fp5]
# lambda layer that allows multiple outputs from a shared model to have specific names
# layers.Lambda(lambda x:x, name=name)()
# --- Class subnet
class_outputs = [class_subnet(features) for features in feature_pyramid]
# --- Box subnet
box_outputs = [box_subnet(features) for features in feature_pyramid]
# --- put class and box outputs in dictionary
logits = {
'cls-c3': layers.Lambda(lambda x: x, name='cls-c3')(class_outputs[0]),
'reg-c3': layers.Lambda(lambda x: x, name='reg-c3')(box_outputs[0]),
'cls-c4': layers.Lambda(lambda x: x, name='cls-c4')(class_outputs[1]),
'reg-c4': layers.Lambda(lambda x: x, name='reg-c4')(box_outputs[1]),
'cls-c5': layers.Lambda(lambda x: x, name='cls-c5')(class_outputs[2]),
'reg-c5': layers.Lambda(lambda x: x, name='reg-c5')(box_outputs[2])
}
model = Model(inputs=inputs, outputs=logits)
return model
def mj_genNetHeadChannel3Dself64Inflated(winlen=10):
the_input_shape = (winlen, 64, 64, 3)
headBranch = Sequential(name="headBranchSelf64")
headBranch.add(
layers.ZeroPadding3D(padding=(0, 1, 1),
input_shape=the_input_shape,
name="zp3d_1"))
headBranch.add(
layers.Conv3D(32, (3, 4, 4),
strides=(1, 2, 2),
padding='valid',
data_format='channels_last',
activation='linear',
name="hconv3d_1"))
headBranch.add(layers.LeakyReLU(alpha=0.2, name="lkrelu_1"))
headBranch.add(layers.ZeroPadding3D(padding=(0, 1, 1), name="zp3d_2"))
headBranch.add(
layers.Conv3D(64, (3, 4, 4),
strides=(1, 2, 2),
padding='valid',
data_format='channels_last',
activation='linear',
name="hconv3d_2"))
headBranch.add(
layers.BatchNormalization(momentum=0.99, epsilon=1e-05, name='bn_1'))
headBranch.add(layers.LeakyReLU(alpha=0.2, name="lkrelu_2"))
if winlen >= 10:
headBranch.add(layers.ZeroPadding3D(padding=(0, 1, 1), name="zp3d_3"))
headBranch.add(
layers.Conv3D(128, (3, 4, 4),
strides=(1, 2, 2),
padding='valid',
data_format='channels_last',
activation='linear',
name="hconv3d_3"))
headBranch.add(
layers.BatchNormalization(momentum=0.99,
epsilon=1e-05,
name='bn_2'))
headBranch.add(layers.LeakyReLU(alpha=0.2, name="lkrelu_3"))
headBranch.add(layers.ZeroPadding3D(padding=(0, 1, 1), name="zp3d_4"))
headBranch.add(
layers.Conv3D(256, (3, 4, 4),
strides=(1, 2, 2),
padding='valid',
data_format='channels_last',
activation='linear',
name="hconv3d_4"))
headBranch.add(
layers.BatchNormalization(momentum=0.99,
epsilon=1e-05,
name='bn_3'))
headBranch.add(layers.LeakyReLU(alpha=0.2, name="lkrelu_4"))
headBranch.add(
layers.Conv3D(256, (2, 4, 4),
strides=(1, 2, 2),
padding='valid',
data_format='channels_last',
activation='linear',
name="embedding"))
else:
headBranch.add(layers.ZeroPadding3D(padding=(0, 1, 1), name="zp3d_3"))
headBranch.add(
layers.Conv3D(128, (1, 4, 4),
strides=(1, 2, 2),
padding='valid',
data_format='channels_last',
activation='linear',
name="hconv3d_3"))
headBranch.add(
layers.BatchNormalization(momentum=0.99,
epsilon=1e-05,
name='bn_2'))
headBranch.add(layers.LeakyReLU(alpha=0.2, name="lkrelu_3"))
headBranch.add(layers.ZeroPadding3D(padding=(0, 1, 1), name="zp3d_4"))
headBranch.add(
layers.Conv3D(256, (1, 4, 4),
strides=(1, 2, 2),
padding='valid',
data_format='channels_last',
activation='linear',
name="hconv3d_4"))
headBranch.add(
layers.BatchNormalization(momentum=0.99,
epsilon=1e-05,
name='bn_3'))
headBranch.add(layers.LeakyReLU(alpha=0.2, name="lkrelu_4"))
headBranch.add(
layers.Conv3D(256, (1, 4, 4),
strides=(1, 2, 2),
padding='valid',
data_format='channels_last',
activation='linear',
name="embedding"))
return headBranch