def make_symmetrical_block(feature_shape, params):
activation = get_activation(params["activation"])
bias_initializer = get_initializer(params["bias_initializer"])
kernel_initializer = get_initializer(params["kernel_initializer"])
input_ = Input(shape=feature_shape)
feature_size = reduce(mul, feature_shape)
layer = Reshape([
feature_size,
])(input_)
layer = Dense(
feature_size,
activation=activation,
use_bias=True,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(layer)
for _ in range(int(params.get("additional_dense_layer", False))):
layer = Dense(
feature_size,
activation=activation,
use_bias=True,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(layer)
return Model(inputs=input_, outputs=layer)
def make_one_level_model(feature_shape: Tuple, params: Dict):
activation = get_activation(params["activation"])
bias_initializer = get_initializer(params["bias_initializer"])
kernel_initializer = get_initializer(params["kernel_initializer"])
z_half_dim = feature_shape[0] // 2 + feature_shape[0] % 2
y_half_dim = feature_shape[1] // 2 + feature_shape[1] % 2
x_half_dim = feature_shape[2] // 2 + feature_shape[2] % 2
symmetrical_block_shape = (z_half_dim, y_half_dim, x_half_dim,
feature_shape[3])
block_dimension = reduce(mul, symmetrical_block_shape) * 8
inputs = [
Input(shape=[block_dimension]),
Input(shape=feature_shape),
]
prev_block, new_block = inputs
oct1, oct2, oct3, oct4, oct5, oct6, oct7, oct8 = get_octants(new_block)
sym_block = make_symmetrical_block(symmetrical_block_shape, params)
r1 = sym_block(oct1)
r2 = sym_block(oct2)
r3 = sym_block(oct3)
r4 = sym_block(oct4)
r5 = sym_block(oct5)
r6 = sym_block(oct6)
r7 = sym_block(oct7)
r8 = sym_block(oct8)
new_block = Concatenate(axis=1)([r1, r2, r3, r4, r5, r6, r7, r8])
dense_in = Dense(
block_dimension,
activation=None,
use_bias=False,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(new_block)
layer = Dense(
block_dimension,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(prev_block)
layer = Add()([dense_in, layer])
layer = activation(layer)
layer = Dense(
block_dimension,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(layer)
layer = Add()([layer, prev_block]) # residual connection
layer = activation(layer)
return Model(inputs=inputs, outputs=layer)
def make_symmetrical_end_block(feature_size, params):
activation = get_activation(params["activation"])
bias_initializer = get_initializer(params["bias_initializer"])
kernel_initializer = get_initializer(params["kernel_initializer"])
input_ = Input(shape=(feature_size, ))
layer = input_
for i in range(3):
layer = Dense(
feature_size,
activation=activation,
use_bias=True,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(layer)
return Model(inputs=input_, outputs=layer)
def make_one_level_model(feature_shape: Tuple, params: Dict):
feature_size = reduce(mul, feature_shape)
activation = get_activation(params["activation"])
bias_initializer = get_initializer(params["bias_initializer"])
kernel_initializer = get_initializer(params["kernel_initializer"])
inputs = [
Input(shape=[feature_size]),
Input(shape=[feature_size]),
]
prev_block, new_block = inputs
dense_in = Dense(
feature_size,
activation=None,
use_bias=False,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(new_block)
layer = Dense(
feature_size,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(prev_block)
layer = Add()([dense_in, layer])
layer = activation(layer)
layer = Dense(
feature_size,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(layer)
layer = Add()([layer, prev_block]) # residual connection
layer = activation(layer)
return Model(inputs=inputs, outputs=layer)
def make_model(params: Dict):
feature_shape = tuple(params["feature_shape"])
levels = params["scale_levels"]
activation = get_activation(params["activation"])
bias_initializer = get_initializer(params["bias_initializer"])
kernel_initializer = get_initializer(params["kernel_initializer"])
input_ = Input(shape=(len(levels), ) + feature_shape)
combined_input = input_
if params.get("preprocess_channel", {}).get("enabled", False):
conf = params.get("preprocess_channel", {})
input_preprocess = InputPreprocessChannel(
polynom2_initializers=conf.get("polynom2_initializers",
[0.00, -0.1]),
polynom1_initializers=conf.get("polynom1_initializers",
[0.0, 2.05]),
bias_initializers=conf.get("bias_initializers", [0.47, -0.42]),
mask_channel=feature_shape[-1] == 3,
)
combined_input = input_preprocess(combined_input)
feature_shape = input_preprocess.compute_output_shape(feature_shape)
input_levels = [
Lambda(lambda x: x[:, i, :, :, :, :])(combined_input)
for i in range(len(levels))
]
feature_size = reduce(mul, feature_shape)
level_block = make_one_level_model(feature_shape, params)
blocks = []
for idx, scale_level in enumerate(levels):
if len(blocks) == 0:
zero_layer = Lambda(lambda x: K.zeros_like(x))(input_levels[idx])
zero_layer = Reshape([
feature_size,
])(zero_layer)
prev_block = zero_layer
else:
prev_block = blocks[-1]
assert scale_level[0] == scale_level[1]
multiplier = scale_level[0] / 64
multiplier = [multiplier, multiplier] + [
1,
] * (input_levels[idx].shape[-1] - 2)
new_level = Lambda(lambda x: x * multiplier,
name="input_density_mult_{}".format(idx))(
input_levels[idx])
new_level = Reshape([
feature_size,
])(new_level)
layer = level_block([prev_block, new_level])
blocks.append(layer)
prev_layer = blocks[-1]
for i in range(3):
output_size = 1 if i == 2 else feature_size
prev_layer = Dense(
output_size,
activation=activation,
use_bias=True,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(prev_layer)
sum_layer = Lambda(lambda x: K.sum(x, axis=1, keepdims=True),
name="FinalOutputLayer")(prev_layer)
return Model(inputs=input_, outputs=sum_layer)
def make_model(params: Dict):
feature_shape = tuple(params["feature_shape"])
levels = len(params["scale_levels"])
activation = get_activation(params["activation"])
bias_initializer = get_initializer(params["bias_initializer"])
kernel_initializer = get_initializer(params["kernel_initializer"])
input_ = Input(shape=(levels, ) + feature_shape)
combined_input = input_
if params.get("preprocess_channel", {}).get("enabled", False):
conf = params.get("preprocess_channel", {})
input_preprocess = InputPreprocessChannel(
polynom2_initializers=conf.get("polynom2_initializers",
[0.00, -0.1]),
polynom1_initializers=conf.get("polynom1_initializers",
[0.0, 2.05]),
bias_initializers=conf.get("bias_initializers", [0.47, -0.42]),
mask_channel=feature_shape[-1] == 3,
)
combined_input = input_preprocess(combined_input)
feature_shape = input_preprocess.compute_output_shape(feature_shape)
input_levels = [
Lambda(lambda x: x[:, i, :, :, :, :])(combined_input)
for i in range(levels)
]
y_half_dim = feature_shape[1] // 2 + feature_shape[1] % 2
x_half_dim = feature_shape[2] // 2 + feature_shape[2] % 2
symmetrical_block_shape = (feature_shape[0], y_half_dim, x_half_dim,
feature_shape[3])
q1, q2, q3, q4 = get_quadrants(input_levels[0])
sym_block = make_symmetrical_block(symmetrical_block_shape, params)
r1 = sym_block(q1)
r2 = sym_block(q2)
r3 = sym_block(q3)
r4 = sym_block(q4)
start_block = Concatenate(axis=1)([r1, r2, r3, r4])
block_dimension = int(start_block.shape[1])
blocks = [start_block]
for i in range(1, levels):
q1, q2, q3, q4 = get_quadrants(input_levels[i])
sym_block = make_symmetrical_block(symmetrical_block_shape, params)
r1 = sym_block(q1)
r2 = sym_block(q2)
r3 = sym_block(q3)
r4 = sym_block(q4)
dense_in = Concatenate(axis=1)([r1, r2, r3, r4])
layer = Dense(
block_dimension,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(blocks[i - 1])
layer = Add()([dense_in, layer])
layer = activation(layer)
layer = Dense(
block_dimension,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(layer)
layer = Add()([layer, blocks[i - 1]]) # residual connection
layer = activation(layer)
blocks.append(layer)
prev_layer = blocks[-1]
quadrant_size = int(r1.shape[1])
sym_end_block = make_symmetrical_end_block(quadrant_size, params)
quadrants = []
for idx in range(4):
quadrant = Lambda(lambda x: x[:, quadrant_size * idx:quadrant_size *
(idx + 1)])(prev_layer)
quadrants.append(sym_end_block(quadrant))
quadrants = Concatenate(axis=1)(quadrants)
sum_layer = Lambda(lambda x: K.sum(x, axis=1, keepdims=True),
name="FinalOutputLayer")(quadrants)
return Model(inputs=input_, outputs=sum_layer)
def make_model(params: Dict):
feature_shape = tuple(params["feature_shape"])
levels = len(params["scale_levels"])
activation = get_activation(params["activation"])
bias_initializer = get_initializer(params["bias_initializer"])
kernel_initializer = get_initializer(params["kernel_initializer"])
input_ = Input(shape=(levels, ) + feature_shape)
combined_input = input_
if params.get("preprocess_channel", {}).get("enabled", False):
conf = params.get("preprocess_channel", {})
input_preprocess = InputPreprocessChannel(
polynom2_initializers=conf.get("polynom2_initializers",
[0.00, -0.1]),
polynom1_initializers=conf.get("polynom1_initializers",
[0.0, 2.05]),
bias_initializers=conf.get("bias_initializers", [0.47, -0.42]),
mask_channel=feature_shape[-1] == 3,
)
combined_input = input_preprocess(combined_input)
feature_shape = input_preprocess.compute_output_shape(feature_shape)
if params.get("euclidian_distance_channel", {}).get("enabled", False):
conf = params.get("euclidian_distance_channel", {})
distance_channel = EuclidianDistanceChannel(
scale_levels=params["scale_levels"],
patch_size=params["patch_size"],
voxel_size=params["voxel_size"],
add_voxel_volume_channel=conf.get("add_voxel_volume_channel",
False),
)
combined_input = distance_channel(combined_input)
feature_shape = distance_channel.compute_output_shape(feature_shape)
if params.get("channel_crossing", {}).get("enabled", False):
conf = params.get("preprocess_channel", {})
channel_crossing = ChannelCrossing(
conf.get("output_channels", feature_shape[-1]))
combined_input = channel_crossing(combined_input)
feature_shape = channel_crossing.compute_output_shape(feature_shape)
input_levels = [
Lambda(lambda x: x[:, i, :, :, :, :])(combined_input)
for i in range(levels)
]
z_half_dim = feature_shape[0] // 2 + feature_shape[0] % 2
y_half_dim = feature_shape[1] // 2 + feature_shape[1] % 2
x_half_dim = feature_shape[2] // 2 + feature_shape[2] % 2
symmetrical_block_shape = (z_half_dim, y_half_dim, x_half_dim,
feature_shape[3])
oct1, oct2, oct3, oct4, oct5, oct6, oct7, oct8 = get_octants(
input_levels[0])
sym_block = make_symmetrical_block(symmetrical_block_shape, params)
r1 = sym_block(oct1)
r2 = sym_block(oct2)
r3 = sym_block(oct3)
r4 = sym_block(oct4)
r5 = sym_block(oct5)
r6 = sym_block(oct6)
r7 = sym_block(oct7)
r8 = sym_block(oct8)
start_block = Concatenate(axis=1)([r1, r2, r3, r4, r5, r6, r7, r8])
block_dimension = int(start_block.shape[1])
blocks = [start_block]
for i in range(1, levels):
oct1, oct2, oct3, oct4, oct5, oct6, oct7, oct8 = get_octants(
input_levels[i])
sym_block = make_symmetrical_block(symmetrical_block_shape, params)
r1 = sym_block(oct1)
r2 = sym_block(oct2)
r3 = sym_block(oct3)
r4 = sym_block(oct4)
r5 = sym_block(oct5)
r6 = sym_block(oct6)
r7 = sym_block(oct7)
r8 = sym_block(oct8)
dense_in = Concatenate(axis=1)([r1, r2, r3, r4, r5, r6, r7, r8])
layer = Dense(
block_dimension,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(blocks[i - 1])
layer = Add()([dense_in, layer])
layer = activation(layer)
layer = Dense(
block_dimension,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(layer)
layer = Add()([layer, blocks[i - 1]]) # residual connection
layer = activation(layer)
blocks.append(layer)
prev_layer = blocks[-1]
octant_size = int(r1.shape[1])
sym_end_block = make_symmetrical_end_block(octant_size, params)
octants = []
for idx in range(8):
octant = Lambda(lambda x: x[:, octant_size * idx:octant_size *
(idx + 1)])(prev_layer)
octants.append(sym_end_block(octant))
octants = Concatenate(axis=1)(octants)
sum_layer = Lambda(lambda x: K.sum(x, axis=1, keepdims=True),
name="FinalOutputLayer")(octants)
return Model(inputs=input_, outputs=sum_layer)
def make_model(params: Dict):
feature_shape = tuple(params["feature_shape"])
levels = len(params["scale_levels"])
feature_size = reduce(mul, feature_shape)
activation = get_activation(params["activation"])
bias_initializer = get_initializer(params["bias_initializer"])
kernel_initializer = get_initializer(params["kernel_initializer"])
inputs = [Input(shape=(reduce(mul, feature_shape), ))]
start_block = inputs[0]
# optional input preprocess channel
if params.get("preprocess_channel", {}).get("enabled", False):
conf = params.get("preprocess_channel", {})
input_preprocess = InputPreprocessChannel(
polynom2_initializers=conf.get("polynom2_initializers",
[0.00, -0.1]),
polynom1_initializers=conf.get("polynom1_initializers",
[0.0, 2.05]),
bias_initializers=conf.get("bias_initializers", [0.47, -0.42]),
mask_channel=feature_shape[-1] == 3,
)
start_block = input_preprocess(start_block)
new_feature_shape = input_preprocess.compute_output_shape(
feature_shape)
feature_size = reduce(mul, new_feature_shape)
start_block = Dense(
feature_size,
activation=activation,
use_bias=True,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(start_block)
start_block = Dense(
feature_size,
activation=activation,
use_bias=True,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(start_block)
blocks = [start_block]
for i in range(1, levels):
inputs.append(Input(shape=(reduce(mul, feature_shape), )))
dense_in = inputs[i]
if params.get("preprocess_channel", {}).get("enabled", False):
dense_in = input_preprocess(dense_in)
dense_in = Dense(
feature_size,
activation=None,
use_bias=False,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(dense_in)
layer = Dense(
feature_size,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(blocks[i - 1])
layer = Add()([dense_in, layer])
layer = activation(layer)
layer = Dense(
feature_size,
activation=None,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(layer)
layer = Add()([layer, blocks[i - 1]]) # residual connection
layer = activation(layer)
blocks.append(layer)
prev_layer = blocks[-1]
for i in range(3):
output_size = 1 if i == 2 else feature_size
prev_layer = Dense(
output_size,
activation=activation,
use_bias=True,
kernel_initializer=kernel_initializer,
bias_initializer=bias_initializer,
)(prev_layer)
sum_layer = Lambda(lambda x: K.sum(x, axis=1, keepdims=True),
name="FinalOutputLayer")(prev_layer)
return Model(inputs=inputs, outputs=sum_layer)