def __init__(
self,
dimensions: int,
in_channels: int,
out_channels: int,
strides=1,
kernel_size=3,
act=Act.PRELU,
norm=Norm.INSTANCE,
dropout=None,
dilation=1,
bias: bool = True,
conv_only: bool = False,
is_transposed: bool = False,
) -> None:
super().__init__()
self.dimensions = dimensions
self.in_channels = in_channels
self.out_channels = out_channels
self.is_transposed = is_transposed
padding = same_padding(kernel_size, dilation)
conv_type = Conv[Conv.CONVTRANS if is_transposed else Conv.CONV, dimensions]
# define the normalisation type and the arguments to the constructor
norm_name, norm_args = split_args(norm)
norm_type = Norm[norm_name, dimensions]
# define the activation type and the arguments to the constructor
if act is not None:
act_name, act_args = split_args(act)
act_type = Act[act_name]
else:
act_type = act_args = None
if dropout:
# if dropout was specified simply as a p value, use default name and make a keyword map with the value
if isinstance(dropout, (int, float)):
drop_name = Dropout.DROPOUT
drop_args = {"p": dropout}
else:
drop_name, drop_args = split_args(dropout)
drop_type = Dropout[drop_name, dimensions]
if is_transposed:
conv = conv_type(in_channels, out_channels, kernel_size, strides, padding, strides - 1, 1, bias, dilation)
else:
conv = conv_type(in_channels, out_channels, kernel_size, strides, padding, dilation, bias=bias)
self.add_module("conv", conv)
if not conv_only:
self.add_module("norm", norm_type(out_channels, **norm_args))
if dropout:
self.add_module("dropout", drop_type(**drop_args))
if act is not None:
self.add_module("act", act_type(**act_args))
def __init__(
self,
ordering: str = "NDA",
in_channels: Optional[int] = None,
act: Optional[Union[Tuple, str]] = "RELU",
norm: Optional[Union[Tuple, str]] = None,
norm_dim: Optional[int] = None,
dropout: Optional[Union[Tuple, str, float]] = None,
dropout_dim: Optional[int] = None,
) -> None:
super().__init__()
op_dict = {"A": None, "D": None, "N": None}
# define the normalization type and the arguments to the constructor
if norm is not None:
if norm_dim is None and dropout_dim is None:
raise ValueError(
"norm_dim or dropout_dim needs to be specified.")
norm_name, norm_args = split_args(norm)
norm_type = Norm[norm_name, norm_dim or dropout_dim]
kw_args = dict(norm_args)
if has_option(norm_type,
"num_features") and "num_features" not in kw_args:
kw_args["num_features"] = in_channels
if has_option(norm_type,
"num_channels") and "num_channels" not in kw_args:
kw_args["num_channels"] = in_channels
op_dict["N"] = norm_type(**kw_args)
# define the activation type and the arguments to the constructor
if act is not None:
act_name, act_args = split_args(act)
act_type = Act[act_name]
op_dict["A"] = act_type(**act_args)
if dropout is not None:
# if dropout was specified simply as a p value, use default name and make a keyword map with the value
if isinstance(dropout, (int, float)):
drop_name = Dropout.DROPOUT
drop_args = {"p": float(dropout)}
else:
drop_name, drop_args = split_args(dropout)
if norm_dim is None and dropout_dim is None:
raise ValueError(
"norm_dim or dropout_dim needs to be specified.")
drop_type = Dropout[drop_name, dropout_dim or norm_dim]
op_dict["D"] = drop_type(**drop_args)
for item in ordering.upper():
if item not in op_dict:
raise ValueError(
f"ordering must be a string of {op_dict}, got {item} in it."
)
if op_dict[item] is not None:
self.add_module(item, op_dict[item]) # type: ignore
def __init__(
self,
spatial_dims: int,
in_channels: int,
r: int = 2,
acti_type_1: Union[Tuple[str, Dict], str] = ("relu", {
"inplace": True
}),
acti_type_2: Union[Tuple[str, Dict], str] = "sigmoid",
add_residual: bool = False,
) -> None:
"""
Args:
spatial_dims: number of spatial dimensions, could be 1, 2, or 3.
in_channels: number of input channels.
r: the reduction ratio r in the paper. Defaults to 2.
acti_type_1: activation type of the hidden squeeze layer. Defaults to ``("relu", {"inplace": True})``.
acti_type_2: activation type of the output squeeze layer. Defaults to "sigmoid".
Raises:
ValueError: When ``r`` is nonpositive or larger than ``in_channels``.
See also:
:py:class:`monai.networks.layers.Act`
"""
super(ChannelSELayer, self).__init__()
self.add_residual = add_residual
pool_type = Pool[Pool.ADAPTIVEAVG, spatial_dims]
self.avg_pool = pool_type(1) # spatial size (1, 1, ...)
channels = int(in_channels // r)
if channels <= 0:
raise ValueError(
f"r must be positive and smaller than in_channels, got r={r} in_channels={in_channels}."
)
act_1, act_1_args = split_args(acti_type_1)
act_2, act_2_args = split_args(acti_type_2)
self.fc = nn.Sequential(
nn.Linear(in_channels, channels, bias=True),
Act[act_1](**act_1_args),
nn.Linear(channels, in_channels, bias=True),
Act[act_2](**act_2_args),
)
def get_norm_layer(name: Union[Tuple, str],
spatial_dims: Optional[int] = 1,
channels: Optional[int] = 1):
"""
Create a normalization layer instance.
For example, to create normalization layers:
.. code-block:: python
from monai.networks.layers import get_norm_layer
g_layer = get_norm_layer(name=("group", {"num_groups": 1}))
n_layer = get_norm_layer(name="instance", spatial_dims=2)
Args:
name: a normalization type string or a tuple of type string and parameters.
spatial_dims: number of spatial dimensions of the input.
channels: number of features/channels when the normalization layer requires this parameter
but it is not specified in the norm parameters.
"""
norm_name, norm_args = split_args(name)
norm_type = Norm[norm_name, spatial_dims]
kw_args = dict(norm_args)
if has_option(norm_type, "num_features") and "num_features" not in kw_args:
kw_args["num_features"] = channels
if has_option(norm_type, "num_channels") and "num_channels" not in kw_args:
kw_args["num_channels"] = channels
return norm_type(**kw_args)
def get_dropout_layer(name: Union[Tuple, str, float, int],
dropout_dim: Optional[int] = 1):
"""
Create a dropout layer instance.
For example, to create dropout layers:
.. code-block:: python
from monai.networks.layers import get_dropout_layer
d_layer = get_dropout_layer(name="dropout")
a_layer = get_dropout_layer(name=("alphadropout", {"p": 0.25}))
Args:
name: a dropout ratio or a tuple of dropout type and parameters.
dropout_dim: the spatial dimension of the dropout operation.
"""
if isinstance(name, (int, float)):
# if dropout was specified simply as a p value, use default name and make a keyword map with the value
drop_name = Dropout.DROPOUT
drop_args = {"p": float(name)}
else:
drop_name, drop_args = split_args(name)
drop_type = Dropout[drop_name, dropout_dim]
return drop_type(**drop_args)
def build_net():
from init import Options
opt = Options().parse()
from monai.networks.layers import Norm
from monai.networks.layers.factories import split_args
act_type, args = split_args("RELU")
# # create Unet
# Unet = monai.networks.nets.UNet(
# dimensions=3,
# in_channels=opt.in_channels,
# out_channels=opt.out_channels,
# channels=(64, 128, 256, 512, 1024),
# strides=(2, 2, 2, 2),
# act=act_type,
# num_res_units=3,
# dropout=0.2,
# norm=Norm.BATCH,
#
# )
# create nn-Unet
if opt.resolution is None:
sizes, spacings = opt.patch_size, opt.spacing
else:
sizes, spacings = opt.patch_size, opt.resolution
strides, kernels = [], []
while True:
spacing_ratio = [sp / min(spacings) for sp in spacings]
stride = [
2 if ratio <= 2 and size >= 8 else 1
for (ratio, size) in zip(spacing_ratio, sizes)
]
kernel = [3 if ratio <= 2 else 1 for ratio in spacing_ratio]
if all(s == 1 for s in stride):
break
sizes = [i / j for i, j in zip(sizes, stride)]
spacings = [i * j for i, j in zip(spacings, stride)]
kernels.append(kernel)
strides.append(stride)
strides.insert(0, len(spacings) * [1])
kernels.append(len(spacings) * [3])
nn_Unet = monai.networks.nets.DynUNet(
spatial_dims=3,
in_channels=opt.in_channels,
out_channels=opt.out_channels,
kernel_size=kernels,
strides=strides,
upsample_kernel_size=strides[1:],
res_block=True,
)
init_weights(nn_Unet, init_type='normal')
return nn_Unet
def __init__(
self,
spatial_dims: int,
in_channels: int,
r: int = 2,
acti_type_1=("relu", {
"inplace": True
}),
acti_type_2="sigmoid",
) -> None:
"""
Args:
spatial_dims: number of spatial dimensions, could be 1, 2, or 3.
in_channels: number of input channels.
r: the reduction ratio r in the paper. Defaults to 2.
acti_type_1: activation type of the hidden squeeze layer. Defaults to ``("relu", {"inplace": True})``.
acti_type_2: activation type of the output squeeze layer. Defaults to "sigmoid".
See also:
:py:class:`monai.networks.layers.Act`
Raises:
ValueError: r must be a positive number smaller than `in_channels`.
"""
super(ChannelSELayer, self).__init__()
pool_type = Pool[Pool.ADAPTIVEAVG, spatial_dims]
self.avg_pool = pool_type(1) # spatial size (1, 1, ...)
channels = int(in_channels // r)
if channels <= 0:
raise ValueError(
"r must be a positive number smaller than `in_channels`.")
act_1, act_1_args = split_args(acti_type_1)
act_2, act_2_args = split_args(acti_type_2)
self.fc = nn.Sequential(
nn.Linear(in_channels, channels, bias=True),
Act[act_1](**act_1_args),
nn.Linear(channels, in_channels, bias=True),
Act[act_2](**act_2_args),
)
def get_act_layer(name: Union[Tuple, str]):
"""
Create an activation layer instance.
For example, to create activation layers:
.. code-block:: python
from monai.networks.layers import get_act_layer
s_layer = get_act_layer(name="swish")
p_layer = get_act_layer(name=("prelu", {"num_parameters": 1, "init": 0.25}))
Args:
name: an activation type string or a tuple of type string and parameters.
"""
act_name, act_args = split_args(name)
act_type = Act[act_name]
return act_type(**act_args)
def get_pool_layer(name: Union[Tuple, str], spatial_dims: Optional[int] = 1):
"""
Create a pooling layer instance.
For example, to create adaptiveavg layer:
.. code-block:: python
from monai.networks.layers import get_pool_layer
pool_layer = get_pool_layer(("adaptiveavg", {"output_size": (1, 1, 1)}), spatial_dims=3)
Args:
name: a pooling type string or a tuple of type string and parameters.
spatial_dims: number of spatial dimensions of the input.
"""
pool_name, pool_args = split_args(name)
pool_type = Pool[pool_name, spatial_dims]
return pool_type(**pool_args)
def __init__(
self,
in_shape: Sequence[int],
classes: int,
channels: Sequence[int],
strides: Sequence[int],
kernel_size: Union[Sequence[int], int] = 3,
num_res_units: int = 2,
act=Act.PRELU,
norm=Norm.INSTANCE,
dropout: Optional[float] = None,
bias: bool = True,
last_act: Optional[str] = None,
) -> None:
super().__init__(in_shape, (classes,), channels, strides, kernel_size, num_res_units, act, norm, dropout, bias)
if last_act is not None:
last_act_name, last_act_args = split_args(last_act)
last_act_type = Act[last_act_name]
self.final.add_module("lastact", last_act_type(**last_act_args))
def __init__(
self,
in_shape,
classes,
channels,
strides,
kernel_size=3,
num_res_units=2,
act=Act.PRELU,
norm=Norm.INSTANCE,
dropout=None,
bias=True,
last_act=None,
):
super().__init__(in_shape, (classes,), channels, strides, kernel_size, num_res_units, act, norm, dropout, bias)
if last_act is not None:
last_act_name, last_act_args = split_args(last_act)
last_act_type = Act[last_act_name]
self.final.add_module("lastact", last_act_type(**last_act_args))
def __init__(
self,
in_shape: Sequence[int],
classes: int,
channels: Sequence[int],
strides: Sequence[int],
kernel_size: Union[Sequence[int], int] = 3,
num_res_units: int = 2,
act=Act.PRELU,
norm=Norm.INSTANCE,
dropout: Optional[float] = None,
bias: bool = True,
last_act: Optional[str] = None,
) -> None:
"""
Args:
in_shape: tuple of integers stating the dimension of the input tensor (minus batch dimension)
classes: integer stating the dimension of the final output tensor
channels: tuple of integers stating the output channels of each convolutional layer
strides: tuple of integers stating the stride (downscale factor) of each convolutional layer
kernel_size: integer or tuple of integers stating size of convolutional kernels
num_res_units: integer stating number of convolutions in residual units, 0 means no residual units
act: name or type defining activation layers
norm: name or type defining normalization layers
dropout: optional float value in range [0, 1] stating dropout probability for layers, None for no dropout
bias: boolean stating if convolution layers should have a bias component
last_act: name defining the last activation layer
"""
super().__init__(in_shape, (classes, ), channels, strides, kernel_size,
num_res_units, act, norm, dropout, bias)
if last_act is not None:
last_act_name, last_act_args = split_args(last_act)
last_act_type = Act[last_act_name]
self.final.add_module("lastact", last_act_type(**last_act_args))
def get_acti_layer(act: Union[Tuple[str, Dict], str]):
act_name, act_args = split_args(act)
act_type = Act[act_name]
return act_type(**act_args)
def __init__(
self,
spatial_dims: int,
in_channels: int,
n_chns_1: int,
n_chns_2: int,
n_chns_3: int,
conv_param_1: Optional[Dict] = None,
conv_param_2: Optional[Dict] = None,
conv_param_3: Optional[Dict] = None,
project: Optional[Convolution] = None,
r: int = 2,
acti_type_1: Union[Tuple[str, Dict], str] = ("relu", {
"inplace": True
}),
acti_type_2: Union[Tuple[str, Dict], str] = "sigmoid",
acti_type_final: Optional[Union[Tuple[str, Dict], str]] = ("relu", {
"inplace":
True
}),
):
"""
Args:
spatial_dims: number of spatial dimensions, could be 1, 2, or 3.
in_channels: number of input channels.
n_chns_1: number of output channels in the 1st convolution.
n_chns_2: number of output channels in the 2nd convolution.
n_chns_3: number of output channels in the 3rd convolution.
conv_param_1: additional parameters to the 1st convolution.
Defaults to ``{"kernel_size": 1, "norm": Norm.BATCH, "act": ("relu", {"inplace": True})}``
conv_param_2: additional parameters to the 2nd convolution.
Defaults to ``{"kernel_size": 3, "norm": Norm.BATCH, "act": ("relu", {"inplace": True})}``
conv_param_3: additional parameters to the 3rd convolution.
Defaults to ``{"kernel_size": 1, "norm": Norm.BATCH, "act": None}``
project: in the case of residual chns and output chns doesn't match, a project
(Conv) layer/block is used to adjust the number of chns. In SENET, it is
consisted with a Conv layer as well as a Norm layer.
Defaults to None (chns are matchable) or a Conv layer with kernel size 1.
r: the reduction ratio r in the paper. Defaults to 2.
acti_type_1: activation type of the hidden squeeze layer. Defaults to "relu".
acti_type_2: activation type of the output squeeze layer. Defaults to "sigmoid".
acti_type_final: activation type of the end of the block. Defaults to "relu".
See also:
:py:class:`monai.networks.blocks.ChannelSELayer`
"""
super(SEBlock, self).__init__()
if not conv_param_1:
conv_param_1 = {
"kernel_size": 1,
"norm": Norm.BATCH,
"act": ("relu", {
"inplace": True
})
}
self.conv1 = Convolution(dimensions=spatial_dims,
in_channels=in_channels,
out_channels=n_chns_1,
**conv_param_1)
if not conv_param_2:
conv_param_2 = {
"kernel_size": 3,
"norm": Norm.BATCH,
"act": ("relu", {
"inplace": True
})
}
self.conv2 = Convolution(dimensions=spatial_dims,
in_channels=n_chns_1,
out_channels=n_chns_2,
**conv_param_2)
if not conv_param_3:
conv_param_3 = {"kernel_size": 1, "norm": Norm.BATCH, "act": None}
self.conv3 = Convolution(dimensions=spatial_dims,
in_channels=n_chns_2,
out_channels=n_chns_3,
**conv_param_3)
self.se_layer = ChannelSELayer(spatial_dims=spatial_dims,
in_channels=n_chns_3,
r=r,
acti_type_1=acti_type_1,
acti_type_2=acti_type_2)
self.project = project
if self.project is None and in_channels != n_chns_3:
self.project = Conv[Conv.CONV, spatial_dims](in_channels,
n_chns_3,
kernel_size=1)
self.act = None
if acti_type_final is not None:
act_final, act_final_args = split_args(acti_type_final)
self.act = Act[act_final](**act_final_args)
def __init__(
self,
dimensions: int,
in_channels: int,
out_channels: int,
strides: int = 1,
kernel_size: Union[Sequence[int], int] = 3,
act: Optional[Union[Tuple, str]] = Act.PRELU,
norm: Union[Tuple, str] = Norm.INSTANCE,
dropout: Optional[Union[Tuple, str, float]] = None,
dropout_dim: int = 1,
dilation: Union[Sequence[int], int] = 1,
groups: int = 1,
bias: bool = True,
conv_only: bool = False,
is_transposed: bool = False,
) -> None:
super().__init__()
self.dimensions = dimensions
self.in_channels = in_channels
self.out_channels = out_channels
self.is_transposed = is_transposed
padding = same_padding(kernel_size, dilation)
conv_type = Conv[Conv.CONVTRANS if is_transposed else Conv.CONV, dimensions]
# define the normalisation type and the arguments to the constructor
if norm is not None:
norm_name, norm_args = split_args(norm)
norm_type = Norm[norm_name, dimensions]
else:
norm_type = norm_args = None
# define the activation type and the arguments to the constructor
if act is not None:
act_name, act_args = split_args(act)
act_type = Act[act_name]
else:
act_type = act_args = None
if dropout:
# if dropout was specified simply as a p value, use default name and make a keyword map with the value
if isinstance(dropout, (int, float)):
drop_name = Dropout.DROPOUT
drop_args = {"p": dropout}
else:
drop_name, drop_args = split_args(dropout)
if dropout_dim > dimensions:
raise ValueError(
f"dropout_dim should be no larger than dimensions, got dropout_dim={dropout_dim} and dimensions={dimensions}."
)
drop_type = Dropout[drop_name, dropout_dim]
if is_transposed:
conv = conv_type(
in_channels,
out_channels,
kernel_size=kernel_size,
stride=strides,
padding=padding,
output_padding=strides - 1,
groups=groups,
bias=bias,
dilation=dilation,
)
else:
conv = conv_type(
in_channels,
out_channels,
kernel_size=kernel_size,
stride=strides,
padding=padding,
dilation=dilation,
groups=groups,
bias=bias,
)
self.add_module("conv", conv)
if not conv_only:
if norm is not None:
self.add_module("norm", norm_type(out_channels, **norm_args))
if dropout:
self.add_module("dropout", drop_type(**drop_args))
if act is not None:
self.add_module("act", act_type(**act_args))
def get_acti_layer(act: Union[Tuple[str, Dict], str], nchan: int = 0):
if act == "prelu":
act = ("prelu", {"num_parameters": nchan})
act_name, act_args = split_args(act)
act_type = Act[act_name]
return act_type(**act_args)
def build_net():
from init import Options
opt = Options().parse()
from monai.networks.layers import Norm
from monai.networks.layers.factories import split_args
act_type, args = split_args("RELU")
# create Unet
Unet = monai.networks.nets.UNet(
dimensions=3,
in_channels=opt.in_channels,
out_channels=opt.out_channels,
channels=(32, 64, 128, 256, 512),
strides=(2, 2, 2, 2),
act=act_type,
num_res_units=3,
dropout=0.2,
norm=Norm.BATCH,
)
class UNet_David(Module):
# __ __
# 1|__ ________________ __|1
# 2|__ ____________ __|2
# 3|__ ______ __|3
# 4|__ __ __|4
# The convolution operations on either side are residual subject to 1*1 Convolution for channel homogeneity
def __init__(self, feat_channels=[32, 64, 128, 256, 512], residual='conv'):
# residual: conv for residual input x through 1*1 conv across every layer for downsampling, None for removal of residuals
super(UNet_David, self).__init__()
class Conv3D_Block(Module):
def __init__(self, inp_feat, out_feat, kernel=3, stride=1, padding=1, residual=None):
super(Conv3D_Block, self).__init__()
self.conv1 = Sequential(
Conv3d(inp_feat, out_feat, kernel_size=kernel,
stride=stride, padding=padding, bias=True),
BatchNorm3d(out_feat),
ReLU())
self.conv2 = Sequential(
Conv3d(out_feat, out_feat, kernel_size=kernel,
stride=stride, padding=padding, bias=True),
BatchNorm3d(out_feat),
ReLU())
self.residual = residual
if self.residual is not None:
self.residual_upsampler = Conv3d(inp_feat, out_feat, kernel_size=1, bias=False)
def forward(self, x):
res = x
if not self.residual:
return self.conv2(self.conv1(x))
else:
return self.conv2(self.conv1(x)) + self.residual_upsampler(res)
class Deconv3D_Block(Module):
def __init__(self, inp_feat, out_feat, kernel=3, stride=2, padding=1):
super(Deconv3D_Block, self).__init__()
self.deconv = Sequential(
ConvTranspose3d(inp_feat, out_feat, kernel_size=(kernel, kernel, kernel),
stride=(stride, stride, stride), padding=(padding, padding, padding),
output_padding=1, bias=True),
ReLU())
def forward(self, x):
return self.deconv(x)
class ChannelPool3d(AvgPool1d):
def __init__(self, kernel_size, stride, padding):
super(ChannelPool3d, self).__init__(kernel_size, stride, padding)
self.pool_1d = AvgPool1d(self.kernel_size, self.stride, self.padding, self.ceil_mode)
def forward(self, inp):
n, c, d, w, h = inp.size()
inp = inp.view(n, c, d * w * h).permute(0, 2, 1)
pooled = self.pool_1d(inp)
c = int(c / self.kernel_size[0])
return inp.view(n, c, d, w, h)
# Encoder downsamplers
self.pool1 = MaxPool3d((2, 2, 2))
self.pool2 = MaxPool3d((2, 2, 2))
self.pool3 = MaxPool3d((2, 2, 2))
self.pool4 = MaxPool3d((2, 2, 2))
# Encoder convolutions
self.conv_blk1 = Conv3D_Block(opt.in_channels, feat_channels[0], residual=residual)
self.conv_blk2 = Conv3D_Block(feat_channels[0], feat_channels[1], residual=residual)
self.conv_blk3 = Conv3D_Block(feat_channels[1], feat_channels[2], residual=residual)
self.conv_blk4 = Conv3D_Block(feat_channels[2], feat_channels[3], residual=residual)
self.conv_blk5 = Conv3D_Block(feat_channels[3], feat_channels[4], residual=residual)
# Decoder convolutions
self.dec_conv_blk4 = Conv3D_Block(2 * feat_channels[3], feat_channels[3], residual=residual)
self.dec_conv_blk3 = Conv3D_Block(2 * feat_channels[2], feat_channels[2], residual=residual)
self.dec_conv_blk2 = Conv3D_Block(2 * feat_channels[1], feat_channels[1], residual=residual)
self.dec_conv_blk1 = Conv3D_Block(2 * feat_channels[0], feat_channels[0], residual=residual)
# Decoder upsamplers
self.deconv_blk4 = Deconv3D_Block(feat_channels[4], feat_channels[3])
self.deconv_blk3 = Deconv3D_Block(feat_channels[3], feat_channels[2])
self.deconv_blk2 = Deconv3D_Block(feat_channels[2], feat_channels[1])
self.deconv_blk1 = Deconv3D_Block(feat_channels[1], feat_channels[0])
# Final 1*1 Conv Segmentation map
self.one_conv = Conv3d(feat_channels[0], opt.out_channels, kernel_size=1, stride=1, padding=0, bias=True)
def forward(self, x):
# Encoder part
x1 = self.conv_blk1(x)
x_low1 = self.pool1(x1)
x2 = self.conv_blk2(x_low1)
x_low2 = self.pool2(x2)
x3 = self.conv_blk3(x_low2)
x_low3 = self.pool3(x3)
x4 = self.conv_blk4(x_low3)
x_low4 = self.pool4(x4)
base = self.conv_blk5(x_low4)
# Decoder part
d4 = torch.cat([self.deconv_blk4(base), x4], dim=1)
d_high4 = self.dec_conv_blk4(d4)
d3 = torch.cat([self.deconv_blk3(d_high4), x3], dim=1)
d_high3 = self.dec_conv_blk3(d3)
d_high3 = Dropout3d(p=0.5)(d_high3)
d2 = torch.cat([self.deconv_blk2(d_high3), x2], dim=1)
d_high2 = self.dec_conv_blk2(d2)
d_high2 = Dropout3d(p=0.5)(d_high2)
d1 = torch.cat([self.deconv_blk1(d_high2), x1], dim=1)
d_high1 = self.dec_conv_blk1(d1)
seg = self.one_conv(d_high1)
return seg
# create HighResNet
HighResNet = monai.networks.nets.HighResNet(
spatial_dims=3,
in_channels=opt.in_channels,
out_channels=opt.out_channels,
)
if opt.net == 'Unet_Monai':
network = Unet
elif opt.net == 'HighResNet':
network = HighResNet
elif opt.net == 'Unet_David':
network = UNet_David(residual='pool')
else:
raise NotImplementedError
init_weights(network, init_type='normal')
return network