Merge branch 'Project-MONAI:dev' into 4980-get-wsi-at-mpp

Author: NikolasSchmitz

docs/source/networks.rst

@@ -109,6 +109,16 @@ Blocks
 .. autoclass:: SABlock
     :members:
 
+`CABlock Block`
+~~~~~~~~~~~~~~~
+.. autoclass:: CABlock
+    :members:
+
+`FeedForward Block`
+~~~~~~~~~~~~~~~~~~~
+.. autoclass:: FeedForward
+    :members:
+
 `Squeeze-and-Excitation`
 ~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: ChannelSELayer
@@ -173,6 +183,16 @@ Blocks
 .. autoclass:: Subpixelupsample
 .. autoclass:: SubpixelUpSample
 
+`Downsampling`
+~~~~~~~~~~~~~~
+.. autoclass:: DownSample
+    :members:
+.. autoclass:: Downsample
+.. autoclass:: SubpixelDownsample
+    :members:
+.. autoclass:: Subpixeldownsample
+.. autoclass:: SubpixelDownSample
+
 `Registration Residual Conv Block`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: RegistrationResidualConvBlock
@@ -625,6 +645,11 @@ Nets
 .. autoclass:: ViT
   :members:
 
+`Restormer`
+~~~~~~~~~~~
+.. autoclass:: restormer
+  :members:
+
 `ViTAutoEnc`
 ~~~~~~~~~~~~
 .. autoclass:: ViTAutoEnc

monai/networks/blocks/__init__.py

@@ -15,12 +15,13 @@
 from .activation import GEGLU, MemoryEfficientSwish, Mish, Swish
 from .aspp import SimpleASPP
 from .backbone_fpn_utils import BackboneWithFPN
+from .cablock import CABlock, FeedForward
 from .convolutions import Convolution, ResidualUnit
 from .crf import CRF
 from .crossattention import CrossAttentionBlock
 from .denseblock import ConvDenseBlock, DenseBlock
 from .dints_block import ActiConvNormBlock, FactorizedIncreaseBlock, FactorizedReduceBlock, P3DActiConvNormBlock
-from .downsample import MaxAvgPool
+from .downsample import DownSample, Downsample, MaxAvgPool, SubpixelDownsample, SubpixelDownSample, Subpixeldownsample
 from .dynunet_block import UnetBasicBlock, UnetOutBlock, UnetResBlock, UnetUpBlock, get_output_padding, get_padding
 from .encoder import BaseEncoder
 from .fcn import FCN, GCN, MCFCN, Refine

monai/networks/blocks/cablock.py

@@ -0,0 +1,182 @@
+# 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 __future__ import annotations
+
+from typing import cast
+
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+
+from monai.networks.blocks.convolutions import Convolution
+from monai.utils import optional_import
+
+rearrange, _ = optional_import("einops", name="rearrange")
+
+__all__ = ["FeedForward", "CABlock"]
+
+
+class FeedForward(nn.Module):
+    """Gated-DConv Feed-Forward Network (GDFN) that controls feature flow using gating mechanism.
+    Uses depth-wise convolutions for local context mixing and GELU-activated gating for refined feature selection.
+
+    Args:
+        spatial_dims: Number of spatial dimensions (2D or 3D)
+        dim: Number of input channels
+        ffn_expansion_factor: Factor to expand hidden features dimension
+        bias: Whether to use bias in convolution layers
+    """
+
+    def __init__(self, spatial_dims: int, dim: int, ffn_expansion_factor: float, bias: bool):
+        super().__init__()
+        hidden_features = int(dim * ffn_expansion_factor)
+
+        self.project_in = Convolution(
+            spatial_dims=spatial_dims,
+            in_channels=dim,
+            out_channels=hidden_features * 2,
+            kernel_size=1,
+            bias=bias,
+            conv_only=True,
+        )
+
+        self.dwconv = Convolution(
+            spatial_dims=spatial_dims,
+            in_channels=hidden_features * 2,
+            out_channels=hidden_features * 2,
+            kernel_size=3,
+            strides=1,
+            padding=1,
+            groups=hidden_features * 2,
+            bias=bias,
+            conv_only=True,
+        )
+
+        self.project_out = Convolution(
+            spatial_dims=spatial_dims,
+            in_channels=hidden_features,
+            out_channels=dim,
+            kernel_size=1,
+            bias=bias,
+            conv_only=True,
+        )
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        x = self.project_in(x)
+        x1, x2 = self.dwconv(x).chunk(2, dim=1)
+        return cast(torch.Tensor, self.project_out(F.gelu(x1) * x2))
+
+
+class CABlock(nn.Module):
+    """Multi-DConv Head Transposed Self-Attention (MDTA): Differs from standard self-attention
+    by operating on feature channels instead of spatial dimensions. Incorporates depth-wise
+    convolutions for local mixing before attention, achieving linear complexity vs quadratic
+    in vanilla attention. Based on SW Zamir, et al., 2022 <https://arxiv.org/abs/2111.09881>
+
+    Args:
+        spatial_dims: Number of spatial dimensions (2D or 3D)
+        dim: Number of input channels
+        num_heads: Number of attention heads
+        bias: Whether to use bias in convolution layers
+        flash_attention: Whether to use flash attention optimization. Defaults to False.
+
+    Raises:
+        ValueError: If flash attention is not available in current PyTorch version
+        ValueError: If spatial_dims is greater than 3
+    """
+
+    def __init__(self, spatial_dims, dim: int, num_heads: int, bias: bool, flash_attention: bool = False):
+        super().__init__()
+        if flash_attention and not hasattr(F, "scaled_dot_product_attention"):
+            raise ValueError("Flash attention not available")
+        if spatial_dims > 3:
+            raise ValueError(f"Only 2D and 3D inputs are supported. Got spatial_dims={spatial_dims}")
+        self.spatial_dims = spatial_dims
+        self.num_heads = num_heads
+        self.temperature = nn.Parameter(torch.ones(num_heads, 1, 1))
+        self.flash_attention = flash_attention
+
+        self.qkv = Convolution(
+            spatial_dims=spatial_dims, in_channels=dim, out_channels=dim * 3, kernel_size=1, bias=bias, conv_only=True
+        )
+
+        self.qkv_dwconv = Convolution(
+            spatial_dims=spatial_dims,
+            in_channels=dim * 3,
+            out_channels=dim * 3,
+            kernel_size=3,
+            strides=1,
+            padding=1,
+            groups=dim * 3,
+            bias=bias,
+            conv_only=True,
+        )
+
+        self.project_out = Convolution(
+            spatial_dims=spatial_dims, in_channels=dim, out_channels=dim, kernel_size=1, bias=bias, conv_only=True
+        )
+
+        self._attention_fn = self._get_attention_fn()
+
+    def _get_attention_fn(self):
+        if self.flash_attention:
+            return self._flash_attention
+        return self._normal_attention
+
+    def _flash_attention(self, q, k, v):
+        """Flash attention implementation using scaled dot-product attention."""
+        scale = float(self.temperature.mean())
+        out = F.scaled_dot_product_attention(q, k, v, scale=scale, dropout_p=0.0, is_causal=False)
+        return out
+
+    def _normal_attention(self, q, k, v):
+        """Attention matrix multiplication with depth-wise convolutions."""
+        attn = (q @ k.transpose(-2, -1)) * self.temperature
+        attn = attn.softmax(dim=-1)
+        return attn @ v
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        """Forward pass for MDTA attention.
+        1. Apply depth-wise convolutions to Q, K, V
+        2. Reshape Q, K, V for multi-head attention
+        3. Compute attention matrix using flash or normal attention
+        4. Reshape and project out attention output"""
+        spatial_dims = x.shape[2:]
+
+        # Project and mix
+        qkv = self.qkv_dwconv(self.qkv(x))
+        q, k, v = qkv.chunk(3, dim=1)
+
+        # Select attention
+        if self.spatial_dims == 2:
+            qkv_to_multihead = "b (head c) h w -> b head c (h w)"
+            multihead_to_qkv = "b head c (h w) -> b (head c) h w"
+        else:  # dims == 3
+            qkv_to_multihead = "b (head c) d h w -> b head c (d h w)"
+            multihead_to_qkv = "b head c (d h w) -> b (head c) d h w"
+
+        # Reconstruct and project feature map
+        q = rearrange(q, qkv_to_multihead, head=self.num_heads)
+        k = rearrange(k, qkv_to_multihead, head=self.num_heads)
+        v = rearrange(v, qkv_to_multihead, head=self.num_heads)
+
+        q = torch.nn.functional.normalize(q, dim=-1)
+        k = torch.nn.functional.normalize(k, dim=-1)
+
+        out = self._attention_fn(q, k, v)
+        out = rearrange(
+            out,
+            multihead_to_qkv,
+            head=self.num_heads,
+            **dict(zip(["h", "w"] if self.spatial_dims == 2 else ["d", "h", "w"], spatial_dims)),
+        )
+
+        return cast(torch.Tensor, self.project_out(out))