# ------------------------------------------------------------------------------------------- # Copyright (c) Microsoft Corporation. All rights reserved. # Licensed under the MIT License (MIT). See LICENSE in the repo root for license information. # ------------------------------------------------------------------------------------------- import math from dataclasses import dataclass from functools import partial from typing import Any, Callable, Optional, Set, Tuple import torch import torch.nn as nn from timm.models.layers import DropPath, Mlp, trunc_normal_ def torch_int_div(tensor1, tensor2): """ A function that performs integer division across different versions of PyTorch. """ return torch.div(tensor1, tensor2, rounding_mode="floor") @dataclass class MultiHeadAttentionOutput: mha_output: torch.Tensor attention: Optional[torch.Tensor] = None class VisionTransformerPooler(nn.Module): """ :param input_dim: Input feature dimension (i.e., channels in old CNN terminology) :param grid_shape: Shape of the grid of patches per image :param num_heads: Number of self-attention heads within the MHA block :param num_blocks: Number of blocks per attention layer :param norm_layer: Normalisation layer `self.type_embed`: Is used to characterise prior and current scans, and create permutation variance across modalities/series. """ def __init__(self, input_dim: int, grid_shape: Tuple[int, int], num_heads: int = 8, num_blocks: int = 3, norm_layer: Any = partial(nn.LayerNorm, eps=1e-6)): super().__init__() block_kwargs = dict(dim=input_dim, num_heads=num_heads, mlp_ratio=1., drop=0.10, attn_drop=0.10, drop_path=0.25, act_layer=nn.GELU, norm_layer=norm_layer) self.blocks = nn.ModuleList([Block(**block_kwargs) for _ in range(num_blocks)]) self.norm_post = norm_layer(input_dim) self.grid_shape = grid_shape self.num_patches = grid_shape[0] * grid_shape[1] self.num_blocks = num_blocks # Temporal positional embeddings num_series: int = 2 self.type_embed = nn.Parameter(torch.zeros(num_series, 1, input_dim)) trunc_normal_(self.type_embed, std=.02) # Positional embeddings 1 x L x C (L: Sequence length, C: Feature dimension) self.pos_drop = nn.Dropout(p=0.10) pos_embed_class = SinePositionEmbedding(embedding_dim=input_dim // 2, normalize=True) pos_embed = pos_embed_class(mask=torch.ones([1, grid_shape[0], grid_shape[1]])) # 1 x L x C self.register_buffer("pos_embed", pos_embed, persistent=False) # Initialisation self.apply(self._init_weights) def no_weight_decay(self) -> Set[str]: return {'type_embed'} def forward(self, current_image: torch.Tensor, previous_image: Optional[torch.Tensor] = None) -> torch.Tensor: B, C, H, W = current_image.shape assert H == self.grid_shape[0] and W == self.grid_shape[1], "Input and grid shapes do not match" # Flatten patch embeddings to have shape (B x L x C), L = H * W if previous_image is not None: assert previous_image.shape == current_image.shape, "current_image and previous_image shapes do not match" previous_image = previous_image.view(B, C, H * W).transpose(1, 2) current_image = current_image.view(B, C, H * W).transpose(1, 2) pos_embed = self.pos_embed.repeat(B, 1, 1) # type: ignore # Final token activations (B x 2L x C) token_features = self.forward_after_reshape(x=current_image, pos_embed=pos_embed, x_previous=previous_image) # Extract the patch features of current image cur_img_token_id = 0 current_token_features = token_features[:, cur_img_token_id:self.num_patches+cur_img_token_id] current_patch_features = current_token_features.transpose(1, 2).view(B, C, H, W) return current_patch_features def forward_after_reshape(self, x: torch.Tensor, pos_embed: torch.Tensor) -> torch.Tensor: B, L, _ = x.shape # Batch, Sequence length, Feature dimension # Positional and type embeddings type_embed = self.type_embed[0].expand(B, L, -1) # Add positional and type embeddings (used in query and key matching) pos_and_type_embed = pos_embed + type_embed # Positional dropout x = self.pos_drop(x) # Multihead attention followed by MLP for block in self.blocks: x = block(x=x, pos_and_type_embed=pos_and_type_embed) x = self.norm_post(x) return x def _init_weights(self, m: nn.Module) -> None: if isinstance(m, nn.Linear): trunc_normal_(m.weight, std=.02) if isinstance(m, nn.Linear) and m.bias is not None: nn.init.constant_(m.bias, 0) elif isinstance(m, nn.LayerNorm): nn.init.constant_(m.bias, 0) nn.init.constant_(m.weight, 1.0) class MultiHeadAttentionLayer(nn.Module): """ Multi-head self attention module The content builds on top of the TIMM library (vision_transformer.py) and differs by the following: - Defines a custom `MultiHeadAttentionLayer` which does not only apply `self-attention` but it can be generalised to arbitrary (query, key, value) input tuples. This feature can be valuable to process more than 2 scans at a time. - `Self-attention` specific use-case can still be invoked by calling the `forward_as_mhsa` method. """ def __init__(self, dim: int, num_heads: int = 8, qkv_bias: bool = False, attn_drop: float = 0., proj_drop: float = 0.) -> None: super().__init__() self.num_heads = num_heads assert dim % num_heads == 0, f"The embedding dim ({dim}) must be divisible by the number of heads ({num_heads})" head_dim = dim // num_heads self.scale = head_dim ** -0.5 self.return_attention = False self.proj_q = nn.Linear(dim, dim, bias=qkv_bias) self.proj_k = nn.Linear(dim, dim, bias=qkv_bias) self.proj_v = nn.Linear(dim, dim, bias=qkv_bias) self.attn_drop = nn.Dropout(attn_drop) self.proj = nn.Linear(dim, dim) self.proj_drop = nn.Dropout(proj_drop) def forward(self, k: torch.Tensor, q: torch.Tensor, v: torch.Tensor) -> MultiHeadAttentionOutput: B, N, C = v.shape assert C % self.num_heads == 0, \ f"The embedding dim ({C}) must be divisible by the number of heads ({self.num_heads})" w_q = self.proj_q(q).reshape(B, N, self.num_heads, C // self.num_heads).permute(0, 2, 1, 3) w_k = self.proj_k(k).reshape(B, N, self.num_heads, C // self.num_heads).permute(0, 2, 1, 3) w_v = self.proj_v(v).reshape(B, N, self.num_heads, C // self.num_heads).permute(0, 2, 1, 3) attn = (w_q @ w_k.transpose(-2, -1)) * self.scale attn = attn.softmax(dim=-1) attn = self.attn_drop(attn) o = (attn @ w_v).transpose(1, 2).reshape(B, N, C) o = self.proj(o) o = self.proj_drop(o) attention_output = attn if self.return_attention else None return MultiHeadAttentionOutput(mha_output=o, attention=attention_output) def forward_as_mhsa(self, input: torch.Tensor) -> MultiHeadAttentionOutput: return self(k=input, q=input, v=input) class Block(nn.Module): """ Encapsulates multi-layer perceptron and multi-head self attention modules into a block. The content builds on top of the TIMM library (vision_transformer.py) and differs by the following: - This implementation uses spatio-temporal positional embeddings instead of 2D positional embeddings only, and they are taken into account within the forward pass of each ViT block. - Utilises the custom defined `MultiHeadAttentionLayer` which does not apply `self-attention` only but can be generalised to arbitrary (query, key, value) tuples. This can be valuable to process more than 2 scans. Positional and type embeddings are handled in a similar fashion as DETR object localisation paper https://alcinos.github.io/detr_page/, where a fixed set of sine/cos positional embeddings are used in an additive manner to Q and K tensors. """ def __init__(self, dim: int, num_heads: int, mlp_ratio: float = 1., qkv_bias: bool = False, drop: float = 0., attn_drop: float = 0., drop_path: float = 0., act_layer: Callable = nn.GELU, norm_layer: Callable = nn.LayerNorm) -> None: super().__init__() self.norm1 = norm_layer(dim) self.attn = MultiHeadAttentionLayer(dim=dim, num_heads=num_heads, qkv_bias=qkv_bias, attn_drop=attn_drop, proj_drop=drop) self.drop_path = DropPath(drop_path) if drop_path > 0. else nn.Identity() self.norm2 = norm_layer(dim) mlp_hidden_dim = int(dim * mlp_ratio) self.mlp = Mlp(in_features=dim, hidden_features=mlp_hidden_dim, act_layer=act_layer, drop=drop) def with_pos_and_type_embed(self, tensor: torch.Tensor, emb: Optional[torch.Tensor]) -> torch.Tensor: # Add positional embeddings to key and query tensors return tensor if emb is None else tensor + emb def forward(self, x: torch.Tensor, pos_and_type_embed: Optional[torch.Tensor]) -> torch.Tensor: x_with_emb = self.with_pos_and_type_embed(self.norm1(x), emb=pos_and_type_embed) x = x + self.drop_path(self.attn.forward_as_mhsa(x_with_emb).mha_output) x = x + self.drop_path(self.mlp(self.norm2(x))) return x class SinePositionEmbedding(): """ This is a more standard version of the position embedding, very similar to the one used by the Attention is all you need paper, generalized to work on images. """ def __init__(self, embedding_dim: int = 64, temperature: int = 10000, normalize: bool = False, scale: float = None) -> None: super().__init__() self.embedding_dim = embedding_dim self.temperature = temperature self.normalize = normalize if scale is not None and normalize is False: raise ValueError("normalize should be True if scale is passed") if scale is None: scale = 2 * math.pi self.scale = scale def __call__(self, mask: torch.Tensor) -> torch.Tensor: assert mask is not None, "No pixel mask provided" B, H, W = mask.shape y_embed = mask.cumsum(1, dtype=torch.float32) x_embed = mask.cumsum(2, dtype=torch.float32) if self.normalize: y_embed = y_embed / (y_embed[:, -1:, :] + 1e-6) * self.scale x_embed = x_embed / (x_embed[:, :, -1:] + 1e-6) * self.scale dim_t = torch.arange(self.embedding_dim, dtype=torch.float32) dim_t = self.temperature ** (2 * torch_int_div(dim_t, 2) / self.embedding_dim) pos_x = x_embed[:, :, :, None] / dim_t pos_y = y_embed[:, :, :, None] / dim_t pos_x = torch.stack((pos_x[:, :, :, 0::2].sin(), pos_x[:, :, :, 1::2].cos()), dim=4).flatten(3) pos_y = torch.stack((pos_y[:, :, :, 0::2].sin(), pos_y[:, :, :, 1::2].cos()), dim=4).flatten(3) pos = torch.cat((pos_y, pos_x), dim=3).view(B, H * W, self.embedding_dim * 2) return pos