# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from typing import Sequence, Tuple, Union
import torch.nn as nn
from monai.networks.blocks.dynunet_block import UnetOutBlock
from monai.networks.blocks.unetr_block import UnetrBasicBlock, UnetrPrUpBlock, UnetrUpBlock
from monai.networks.nets.vit import ViT
from monai.utils import ensure_tuple_rep
[docs]class UNETR(nn.Module):
"""
UNETR based on: "Hatamizadeh et al.,
UNETR: Transformers for 3D Medical Image Segmentation <https://arxiv.org/abs/2103.10504>"
"""
[docs] def __init__(
self,
in_channels: int,
out_channels: int,
img_size: Union[Sequence[int], int],
feature_size: int = 16,
hidden_size: int = 768,
mlp_dim: int = 3072,
num_heads: int = 12,
pos_embed: str = "conv",
norm_name: Union[Tuple, str] = "instance",
conv_block: bool = True,
res_block: bool = True,
dropout_rate: float = 0.0,
spatial_dims: int = 3,
qkv_bias: bool = False,
) -> None:
"""
Args:
in_channels: dimension of input channels.
out_channels: dimension of output channels.
img_size: dimension of input image.
feature_size: dimension of network feature size.
hidden_size: dimension of hidden layer.
mlp_dim: dimension of feedforward layer.
num_heads: number of attention heads.
pos_embed: position embedding layer type.
norm_name: feature normalization type and arguments.
conv_block: bool argument to determine if convolutional block is used.
res_block: bool argument to determine if residual block is used.
dropout_rate: faction of the input units to drop.
spatial_dims: number of spatial dims.
qkv_bias: apply the bias term for the qkv linear layer in self attention block
Examples::
# for single channel input 4-channel output with image size of (96,96,96), feature size of 32 and batch norm
>>> net = UNETR(in_channels=1, out_channels=4, img_size=(96,96,96), feature_size=32, norm_name='batch')
# for single channel input 4-channel output with image size of (96,96), feature size of 32 and batch norm
>>> net = UNETR(in_channels=1, out_channels=4, img_size=96, feature_size=32, norm_name='batch', spatial_dims=2)
# for 4-channel input 3-channel output with image size of (128,128,128), conv position embedding and instance norm
>>> net = UNETR(in_channels=4, out_channels=3, img_size=(128,128,128), pos_embed='conv', norm_name='instance')
"""
super().__init__()
if not (0 <= dropout_rate <= 1):
raise ValueError("dropout_rate should be between 0 and 1.")
if hidden_size % num_heads != 0:
raise ValueError("hidden_size should be divisible by num_heads.")
self.num_layers = 12
img_size = ensure_tuple_rep(img_size, spatial_dims)
self.patch_size = ensure_tuple_rep(16, spatial_dims)
self.feat_size = tuple(img_d // p_d for img_d, p_d in zip(img_size, self.patch_size))
self.hidden_size = hidden_size
self.classification = False
self.vit = ViT(
in_channels=in_channels,
img_size=img_size,
patch_size=self.patch_size,
hidden_size=hidden_size,
mlp_dim=mlp_dim,
num_layers=self.num_layers,
num_heads=num_heads,
pos_embed=pos_embed,
classification=self.classification,
dropout_rate=dropout_rate,
spatial_dims=spatial_dims,
qkv_bias=qkv_bias,
)
self.encoder1 = UnetrBasicBlock(
spatial_dims=spatial_dims,
in_channels=in_channels,
out_channels=feature_size,
kernel_size=3,
stride=1,
norm_name=norm_name,
res_block=res_block,
)
self.encoder2 = UnetrPrUpBlock(
spatial_dims=spatial_dims,
in_channels=hidden_size,
out_channels=feature_size * 2,
num_layer=2,
kernel_size=3,
stride=1,
upsample_kernel_size=2,
norm_name=norm_name,
conv_block=conv_block,
res_block=res_block,
)
self.encoder3 = UnetrPrUpBlock(
spatial_dims=spatial_dims,
in_channels=hidden_size,
out_channels=feature_size * 4,
num_layer=1,
kernel_size=3,
stride=1,
upsample_kernel_size=2,
norm_name=norm_name,
conv_block=conv_block,
res_block=res_block,
)
self.encoder4 = UnetrPrUpBlock(
spatial_dims=spatial_dims,
in_channels=hidden_size,
out_channels=feature_size * 8,
num_layer=0,
kernel_size=3,
stride=1,
upsample_kernel_size=2,
norm_name=norm_name,
conv_block=conv_block,
res_block=res_block,
)
self.decoder5 = UnetrUpBlock(
spatial_dims=spatial_dims,
in_channels=hidden_size,
out_channels=feature_size * 8,
kernel_size=3,
upsample_kernel_size=2,
norm_name=norm_name,
res_block=res_block,
)
self.decoder4 = UnetrUpBlock(
spatial_dims=spatial_dims,
in_channels=feature_size * 8,
out_channels=feature_size * 4,
kernel_size=3,
upsample_kernel_size=2,
norm_name=norm_name,
res_block=res_block,
)
self.decoder3 = UnetrUpBlock(
spatial_dims=spatial_dims,
in_channels=feature_size * 4,
out_channels=feature_size * 2,
kernel_size=3,
upsample_kernel_size=2,
norm_name=norm_name,
res_block=res_block,
)
self.decoder2 = UnetrUpBlock(
spatial_dims=spatial_dims,
in_channels=feature_size * 2,
out_channels=feature_size,
kernel_size=3,
upsample_kernel_size=2,
norm_name=norm_name,
res_block=res_block,
)
self.out = UnetOutBlock(spatial_dims=spatial_dims, in_channels=feature_size, out_channels=out_channels)
self.proj_axes = (0, spatial_dims + 1) + tuple(d + 1 for d in range(spatial_dims))
self.proj_view_shape = list(self.feat_size) + [self.hidden_size]
def proj_feat(self, x):
new_view = [x.size(0)] + self.proj_view_shape
x = x.view(new_view)
x = x.permute(self.proj_axes).contiguous()
return x
[docs] def forward(self, x_in):
x, hidden_states_out = self.vit(x_in)
enc1 = self.encoder1(x_in)
x2 = hidden_states_out[3]
enc2 = self.encoder2(self.proj_feat(x2))
x3 = hidden_states_out[6]
enc3 = self.encoder3(self.proj_feat(x3))
x4 = hidden_states_out[9]
enc4 = self.encoder4(self.proj_feat(x4))
dec4 = self.proj_feat(x)
dec3 = self.decoder5(dec4, enc4)
dec2 = self.decoder4(dec3, enc3)
dec1 = self.decoder3(dec2, enc2)
out = self.decoder2(dec1, enc1)
return self.out(out)