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,
) -> 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.
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,
)
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)
def get_output_block(self, idx: int):
return UnetOutBlock(self.spatial_dims, self.filters[idx], self.out_channels, dropout=self.dropout)