Add vista network (#7987)

Fixes # .

### Description

Add VISTA3D model architecture to MONAI core

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: heyufan1995 <[email protected]>
Signed-off-by: Yufan He <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Yiheng Wang <[email protected]>
Co-authored-by: Yiheng Wang <[email protected]>
Co-authored-by: YunLiu <[email protected]>

Author: 4 people

docs/source/networks.rst

@@ -481,6 +481,11 @@ Nets
 .. autoclass:: SegResNetDS
   :members:
 
+`SegResNetDS2`
+~~~~~~~~~~~~~~
+.. autoclass:: SegResNetDS2
+  :members:
+
 `SegResNetVAE`
 ~~~~~~~~~~~~~~
 .. autoclass:: SegResNetVAE
@@ -556,6 +561,11 @@ Nets
 .. autoclass:: UNETR
     :members:
 
+`VISTA3D`
+~~~~~~~~~
+.. autoclass:: VISTA3D
+    :members:
+
 `SwinUNETR`
 ~~~~~~~~~~~
 .. autoclass:: SwinUNETR

monai/networks/nets/__init__.py

@@ -76,7 +76,7 @@
     resnet200,
 )
 from .segresnet import SegResNet, SegResNetVAE
-from .segresnet_ds import SegResNetDS
+from .segresnet_ds import SegResNetDS, SegResNetDS2
 from .senet import (
     SENet,
     SEnet,
@@ -118,6 +118,7 @@
 from .unet import UNet, Unet
 from .unetr import UNETR
 from .varautoencoder import VarAutoEncoder
+from .vista3d import VISTA3D, vista3d132
 from .vit import ViT
 from .vitautoenc import ViTAutoEnc
 from .vnet import VNet

monai/networks/nets/segresnet_ds.py

@@ -11,6 +11,7 @@
 
 from __future__ import annotations
 
+import copy
 from collections.abc import Callable
 from typing import Union
 
@@ -23,7 +24,7 @@
 from monai.networks.layers.utils import get_act_layer, get_norm_layer
 from monai.utils import UpsampleMode, has_option
 
-__all__ = ["SegResNetDS"]
+__all__ = ["SegResNetDS", "SegResNetDS2"]
 
 
 def scales_for_resolution(resolution: tuple | list, n_stages: int | None = None):
@@ -425,3 +426,128 @@ def _forward(self, x: torch.Tensor) -> Union[None, torch.Tensor, list[torch.Tens
 
     def forward(self, x: torch.Tensor) -> Union[None, torch.Tensor, list[torch.Tensor]]:
         return self._forward(x)
+
+
+class SegResNetDS2(SegResNetDS):
+    """
+    SegResNetDS2 adds an additional decorder branch to SegResNetDS and is the image encoder of VISTA3D
+     <https://arxiv.org/abs/2406.05285>`_.
+
+    Args:
+        spatial_dims: spatial dimension of the input data. Defaults to 3.
+        init_filters: number of output channels for initial convolution layer. Defaults to 32.
+        in_channels: number of input channels for the network. Defaults to 1.
+        out_channels: number of output channels for the network. Defaults to 2.
+        act: activation type and arguments. Defaults to ``RELU``.
+        norm: feature normalization type and arguments. Defaults to ``BATCH``.
+        blocks_down: number of downsample blocks in each layer. Defaults to ``[1,2,2,4]``.
+        blocks_up: number of upsample blocks (optional).
+        dsdepth: number of levels for deep supervision. This will be the length of the list of outputs at each scale level.
+                 At dsdepth==1,only a single output is returned.
+        preprocess: optional callable function to apply before the model's forward pass
+        resolution: optional input image resolution. When provided, the network will first use non-isotropic kernels to bring
+                    image spacing into an approximately isotropic space.
+                    Otherwise, by default, the kernel size and downsampling is always isotropic.
+
+    """
+
+    def __init__(
+        self,
+        spatial_dims: int = 3,
+        init_filters: int = 32,
+        in_channels: int = 1,
+        out_channels: int = 2,
+        act: tuple | str = "relu",
+        norm: tuple | str = "batch",
+        blocks_down: tuple = (1, 2, 2, 4),
+        blocks_up: tuple | None = None,
+        dsdepth: int = 1,
+        preprocess: nn.Module | Callable | None = None,
+        upsample_mode: UpsampleMode | str = "deconv",
+        resolution: tuple | None = None,
+    ):
+        super().__init__(
+            spatial_dims=spatial_dims,
+            init_filters=init_filters,
+            in_channels=in_channels,
+            out_channels=out_channels,
+            act=act,
+            norm=norm,
+            blocks_down=blocks_down,
+            blocks_up=blocks_up,
+            dsdepth=dsdepth,
+            preprocess=preprocess,
+            upsample_mode=upsample_mode,
+            resolution=resolution,
+        )
+
+        self.up_layers_auto = nn.ModuleList([copy.deepcopy(layer) for layer in self.up_layers])
+
+    def forward(  # type: ignore
+        self, x: torch.Tensor, with_point: bool = True, with_label: bool = True
+    ) -> tuple[Union[None, torch.Tensor, list[torch.Tensor]], Union[None, torch.Tensor, list[torch.Tensor]]]:
+        """
+        Args:
+            x: input tensor.
+            with_point: if true, return the point branch output.
+            with_label: if true, return the label branch output.
+        """
+        if self.preprocess is not None:
+            x = self.preprocess(x)
+
+        if not self.is_valid_shape(x):
+            raise ValueError(f"Input spatial dims {x.shape} must be divisible by {self.shape_factor()}")
+
+        x_down = self.encoder(x)
+
+        x_down.reverse()
+        x = x_down.pop(0)
+
+        if len(x_down) == 0:
+            x_down = [torch.zeros(1, device=x.device, dtype=x.dtype)]
+
+        outputs: list[torch.Tensor] = []
+        outputs_auto: list[torch.Tensor] = []
+        x_ = x.clone()
+        if with_point:
+            i = 0
+            for level in self.up_layers:
+                x = level["upsample"](x)
+                x = x + x_down[i]
+                x = level["blocks"](x)
+
+                if len(self.up_layers) - i <= self.dsdepth:
+                    outputs.append(level["head"](x))
+                i = i + 1
+
+            outputs.reverse()
+        x = x_
+        if with_label:
+            i = 0
+            for level in self.up_layers_auto:
+                x = level["upsample"](x)
+                x = x + x_down[i]
+                x = level["blocks"](x)
+
+                if len(self.up_layers) - i <= self.dsdepth:
+                    outputs_auto.append(level["head"](x))
+                i = i + 1
+
+            outputs_auto.reverse()
+
+        return outputs[0] if len(outputs) == 1 else outputs, outputs_auto[0] if len(outputs_auto) == 1 else outputs_auto
+
+    def set_auto_grad(self, auto_freeze=False, point_freeze=False):
+        """
+        Args:
+            auto_freeze: if true, freeze the image encoder and the auto-branch.
+            point_freeze: if true, freeze the image encoder and the point-branch.
+        """
+        for param in self.encoder.parameters():
+            param.requires_grad = (not auto_freeze) and (not point_freeze)
+
+        for param in self.up_layers_auto.parameters():
+            param.requires_grad = not auto_freeze
+
+        for param in self.up_layers.parameters():
+            param.requires_grad = not point_freeze