src/models/prompt_encoder.py

# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.

# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.

import numpy as np
import torch
from torch import nn
from .transformer import TwoWayTransformer3D
from typing import Any, Optional, Tuple, Type

class LayerNorm3d(nn.Module):
    def __init__(self, num_channels: int, eps: float = 1e-6) -> None:
        super().__init__()
        self.weight = nn.Parameter(torch.ones(num_channels))
        self.bias = nn.Parameter(torch.zeros(num_channels))
        self.eps = eps

    def forward(self, x: torch.Tensor) -> torch.Tensor:
        u = x.mean(1, keepdim=True)
        s = (x - u).pow(2).mean(1, keepdim=True)
        x = (x - u) / torch.sqrt(s + self.eps)
        x = self.weight[:, None, None, None] * x + self.bias[:, None, None, None]
        return x


class PromptEncoder3D(nn.Module):
    def __init__(
        self,
        embed_dim: int,
        image_embedding_size: Tuple[int, int, int],
        input_image_size: Tuple[int, int, int],
        mask_in_chans: int,
        # transformer_dim: int,
        num_multiple_outputs: int = 3,
        activation: Type[nn.Module] = nn.GELU,
        multiple_outputs: bool = False,
    ) -> None:
        """
        Encodes prompts for input to SAM's mask decoder.

        Arguments:
          embed_dim (int): The prompts' embedding dimension
          image_embedding_size (tuple(int, int)): The spatial size of the
            image embedding, as (H, W).
          input_image_size (int): The padded size of the image as input
            to the image encoder, as (H, W).
          mask_in_chans (int): The number of hidden channels used for
            encoding input masks.
          activation (nn.Module): The activation to use when encoding
            input masks.
        """
        super().__init__()
        self.embed_dim = embed_dim
        self.input_image_size = input_image_size
        self.image_embedding_size = image_embedding_size
        self.pe_layer = PositionEmbeddingRandom3D(embed_dim // 3)

        self.num_point_embeddings: int = 4  # pos/neg point + 2 box corners
        point_embeddings = [nn.Embedding(1, embed_dim) for i in range(self.num_point_embeddings)]
        self.point_embeddings = nn.ModuleList(point_embeddings)
        self.not_a_point_embed = nn.Embedding(1, embed_dim)

        self.mask_input_size = (image_embedding_size[0], image_embedding_size[1], image_embedding_size[2])
        self.mask_downscaling = nn.Sequential(
            nn.Conv3d(1, mask_in_chans // 4, kernel_size=2, stride=2),
            LayerNorm3d(mask_in_chans // 4),
            activation(),
            # nn.Conv3d(mask_in_chans // 4, mask_in_chans // 2, kernel_size=2, stride=2),
            # LayerNorm3d(mask_in_chans // 2),
            # activation(),
            nn.Conv3d(mask_in_chans // 4, mask_in_chans, kernel_size=2, stride=2),
            LayerNorm3d(mask_in_chans),
            activation(),
            nn.Conv3d(mask_in_chans, embed_dim, kernel_size=1),
        )

        self.no_mask_embed = nn.Embedding(1, embed_dim)

        self.transformer_dim = embed_dim
        self.transformer = TwoWayTransformer3D(
                depth=2,
                embedding_dim=self.transformer_dim,
                mlp_dim=2048,
                num_heads=8,
            )
        self.multiple_outputs = multiple_outputs

        self.mask_tokens = nn.Embedding(num_multiple_outputs + 1, embed_dim)
        self.iou_token = nn.Embedding(1, embed_dim)
        #self.iou_token = nn.Embedding(1, embed_dim) if multiple_outputs else None

    def forward(
        self,
        points: Optional[Tuple[torch.Tensor, torch.Tensor]],
        boxes: Optional[torch.Tensor],
        masks: Optional[torch.Tensor],
        image_embeddings: torch.Tensor,
    ) -> Tuple[torch.Tensor, torch.Tensor]:
        """
        Embeds different types of prompts, returning both sparse and dense
        embeddings.

        Arguments:
          points (tuple(torch.Tensor, torch.Tensor) or none): point coordinates
            and labels to embed.
          boxes (torch.Tensor or none): boxes to embed
          masks (torch.Tensor or none): masks to embed

        Returns:
          torch.Tensor: sparse embeddings for the points and boxes, with shape
            BxNx(embed_dim), where N is determined by the number of input points
            and boxes.
          torch.Tensor: dense embeddings for the masks, in the shape
            Bx(embed_dim)x(embed_H)x(embed_W)
        """
        bs = self._get_batch_size(points, boxes, masks)
        sparse_embeddings = torch.empty((bs, 0, self.embed_dim), device=self._get_device())
        if points is not None:
            coords, labels = points
            point_embeddings = self._embed_points(coords, labels, pad=(boxes is None))
            sparse_embeddings = torch.cat([sparse_embeddings, point_embeddings], dim=1)
        if boxes is not None:
            box_embeddings = self._embed_boxes(boxes)
            sparse_embeddings = torch.cat([sparse_embeddings, box_embeddings], dim=1)

        if masks is not None:
            dense_embeddings = self._embed_masks(masks)
        else:
            dense_embeddings = self.no_mask_embed.weight.reshape(1, -1, 1, 1, 1).expand(
                bs, -1, self.image_embedding_size[0], self.image_embedding_size[1], self.image_embedding_size[2]
            )

        new_prompt_embeddings, new_image_embeddings = self._two_way_transformer(
            image_embeddings=image_embeddings,
            image_pe=self.get_dense_pe(),
            sparse_prompt_embeddings=sparse_embeddings, # sparse_embeddings --> (B, 2, embed_dim) 2 represents concat of coordination and its label
            dense_prompt_embeddings=dense_embeddings, # dense_embeddings --> (B, embed_dim, W, H, D), whd values are customized
        )
        # new_prompt_embedding --> [b, self.num_mask_tokens, c], new_image_embedding --> [b, c, low_res / 4, low_res / 4, low_res / 4]
        # new_image_embedding --> [b, c, low_res / 4, low_res / 4, low_res / 4]
        # return sparse_embeddings, dense_embeddings
        return new_prompt_embeddings, new_image_embeddings


    def _two_way_transformer(
        self,
        image_embeddings: torch.Tensor,
        image_pe: torch.Tensor,
        sparse_prompt_embeddings: torch.Tensor,
        dense_prompt_embeddings: torch.Tensor,
    ) -> Tuple[torch.Tensor, torch.Tensor]:
        """Predicts masks. See 'forward' for more details."""
        # Concatenate output tokens
        # if self.multiple_outputs:
        #     output_tokens = torch.cat([self.iou_token.weight, self.mask_tokens.weight], dim=0)
        # else:
        #     output_tokens = self.mask_tokens.weight

        output_tokens = torch.cat([self.iou_token.weight, self.mask_tokens.weight], dim=0)
        output_tokens = output_tokens.unsqueeze(0).expand(sparse_prompt_embeddings.size(0), -1, -1)
        tokens = torch.cat((output_tokens, sparse_prompt_embeddings), dim=1)

        # Expand per-image data in batch direction to be per-mask
        if image_embeddings.shape[0] != tokens.shape[0]:
            src = torch.repeat_interleave(image_embeddings, tokens.shape[0], dim=0)
        else:
            src = image_embeddings
        src = src + dense_prompt_embeddings
        b, c, x, y, z = src.shape
        if image_pe.shape[0] != tokens.shape[0]:
            pos_src = torch.repeat_interleave(image_pe, tokens.shape[0], dim=0)
        else:
            pos_src = image_pe
        # token size [batch, tokens, embedding dim]
        # embedding dim = 384, tokens = number points + box + 3 multiple outputs + 1 iou
        new_point_embedding, new_image_embedding = self.transformer(src, pos_src, tokens) # hidden state and src
        return new_point_embedding, new_image_embedding.transpose(1, 2).view(b, c, x, y, z)
        # else:
        #     return new_point_embedding[:, 0, :].unsqueeze(1), new_image_embedding.transpose(1, 2).view(b, c, x, y, z)

        #
        #
        # a = new_sparse.shape[1]
        # if new_sparse.shape[1] != 1:
        #     return self.output_sparse_mlps(new_sparse.transpose(1, 2)).transpose(1, 2), new_dense
        # else:
        #     return new_sparse, new_dense


    def get_dense_pe(self) -> torch.Tensor:
        """
        Returns the positional encoding used to encode point prompts,
        applied to a dense set of points the shape of the image encoding.

        Returns:
          torch.Tensor: Positional encoding with shape
            1x(embed_dim)x(embedding_h)x(embedding_w)
        """
        return self.pe_layer(self.image_embedding_size).unsqueeze(0)  # 1xXxYxZ

    def _embed_points(
        self,
        points: torch.Tensor,
        labels: torch.Tensor,
        pad: bool,
    ) -> torch.Tensor:
        """Embeds point prompts."""
        points = points + 0.5  # Shift to center of pixel
        if pad:
            padding_point = torch.zeros((points.shape[0], 1, 3), device=points.device)
            padding_label = -torch.ones((labels.shape[0], 1), device=labels.device)
            points = torch.cat([points, padding_point], dim=1)
            labels = torch.cat([labels, padding_label], dim=1)
        point_embedding = self.pe_layer.forward_with_coords(points, self.input_image_size)
        point_embedding[labels == -1] = 0.0
        point_embedding[labels == -1] += self.not_a_point_embed.weight
        point_embedding[labels == 0] += self.point_embeddings[0].weight
        point_embedding[labels == 1] += self.point_embeddings[1].weight
        return point_embedding

    def _embed_boxes(self, boxes: torch.Tensor) -> torch.Tensor: # XYWH format https://github.com/facebookresearch/segment-anything/blob/main/segment_anything/automatic_mask_generator.py
        """Embeds box prompts."""
        boxes = boxes + 0.5  # Shift to center of pixel
        coords = boxes.reshape(-1, 2, 3)
        corner_embedding = self.pe_layer.forward_with_coords(coords, self.input_image_size)
        corner_embedding[:, 0, :] += self.point_embeddings[2].weight
        corner_embedding[:, 1, :] += self.point_embeddings[3].weight
        return corner_embedding

    def _embed_masks(self, masks: torch.Tensor) -> torch.Tensor:
        """Embeds mask inputs."""
        mask_embedding = self.mask_downscaling(masks)
        return mask_embedding

    def _get_batch_size(
        self,
        points: Optional[Tuple[torch.Tensor, torch.Tensor]],
        boxes: Optional[torch.Tensor],
        masks: Optional[torch.Tensor],
    ) -> int:
        """
        Gets the batch size of the output given the batch size of the input prompts.
        """
        if points is not None:
            return points[0].shape[0]
        elif boxes is not None:
            return boxes.shape[0]
        elif masks is not None:
            return masks.shape[0]
        else:
            return 1

    def _get_device(self) -> torch.device:
        return self.point_embeddings[0].weight.device




class PositionEmbeddingRandom3D(nn.Module):
    """
    Positional encoding using random spatial frequencies.
    """

    def __init__(self, num_pos_feats: int = 64, scale: Optional[float] = None) -> None:
        super().__init__()
        if scale is None or scale <= 0.0:
            scale = 1.0
        self.register_buffer(
            "positional_encoding_gaussian_matrix",
            scale * torch.randn((3, num_pos_feats)),
        )

    def _pe_encoding(self, coords: torch.Tensor) -> torch.Tensor:
        """Positionally encode points that are normalized to [0,1]."""
        # assuming coords are in [0, 1]^2 square and have d_1 x ... x d_n x 2 shape
        coords = 2 * coords - 1
        coords = coords @ self.positional_encoding_gaussian_matrix
        coords = 2 * np.pi * coords
        # outputs d_1 x ... x d_n x C shape
        return torch.cat([torch.sin(coords), torch.cos(coords), torch.sin(coords)], dim=-1)

    def forward(self, size: Tuple[int, int, int]) -> torch.Tensor:
        """Generate positional encoding for a grid of the specified size."""
        x, y, z = size
        device: Any = self.positional_encoding_gaussian_matrix.device
        grid = torch.ones((x, y, z), device=device, dtype=torch.float32)
        y_embed = grid.cumsum(dim=0) - 0.5
        x_embed = grid.cumsum(dim=1) - 0.5
        z_embed = grid.cumsum(dim=2) - 0.5
        y_embed = y_embed / y
        x_embed = x_embed / x
        z_embed = z_embed / z

        pe = self._pe_encoding(torch.stack([x_embed, y_embed, z_embed], dim=-1))
        return pe.permute(3, 0, 1, 2)  # C x X x Y x Z

    def forward_with_coords(
        self, coords_input: torch.Tensor, image_size: Tuple[int, int, int]
    ) -> torch.Tensor:
        """Positionally encode points that are not normalized to [0,1]."""
        coords = coords_input.clone()
        coords[:, :, 0] = coords[:, :, 0] / image_size[0]
        coords[:, :, 1] = coords[:, :, 1] / image_size[1]
        coords[:, :, 2] = coords[:, :, 2] / image_size[2]
        return self._pe_encoding(coords.to(torch.float))  # B x N x C