Source code for monai.networks.nets.unetr

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from __future__ import annotations

from import Sequence

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 <>" """
[docs] def __init__( self, in_channels: int, out_channels: int, img_size: 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: tuple | str = "instance", conv_block: bool = True, res_block: bool = True, dropout_rate: float = 0.0, spatial_dims: int = 3, qkv_bias: bool = False, save_attn: 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. Defaults to 16. hidden_size: dimension of hidden layer. Defaults to 768. mlp_dim: dimension of feedforward layer. Defaults to 3072. num_heads: number of attention heads. Defaults to 12. pos_embed: position embedding layer type. Defaults to "conv". norm_name: feature normalization type and arguments. Defaults to "instance". conv_block: if convolutional block is used. Defaults to True. res_block: if residual block is used. Defaults to True. dropout_rate: fraction of the input units to drop. Defaults to 0.0. spatial_dims: number of spatial dims. Defaults to 3. qkv_bias: apply the bias term for the qkv linear layer in self attention block. Defaults to False. save_attn: to make accessible the attention in self attention block. Defaults to False. 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, save_attn=save_attn, ) 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)