MCP-MedSAM / models /prompt_encoder.py
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# -*- coding: utf-8 -*-
# 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
import torch.nn.functional as F
from typing import Any, Optional, Tuple, Type
from .common import LayerNorm2d
class PositionEmbeddingRandom(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((2, 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)], dim=-1)
def forward(self, size: Tuple[int, int]) -> torch.Tensor:
"""Generate positional encoding for a grid of the specified size."""
h, w = size
device: Any = self.positional_encoding_gaussian_matrix.device
grid = torch.ones((h, w), device=device, dtype=torch.float32)
y_embed = grid.cumsum(dim=0) - 0.5
x_embed = grid.cumsum(dim=1) - 0.5
y_embed = y_embed / h
x_embed = x_embed / w
pe = self._pe_encoding(torch.stack([x_embed, y_embed], dim=-1))
return pe.permute(2, 0, 1) # C x H x W
def forward_with_coords(
self, coords_input: torch.Tensor, image_size: Tuple[int, int]
) -> torch.Tensor:
"""Positionally encode points that are not normalized to [0,1]."""
coords = coords_input.clone()
coords[:, :, 0] = coords[:, :, 0] / image_size[1]
coords[:, :, 1] = coords[:, :, 1] / image_size[0]
return self._pe_encoding(coords.to(torch.float)) # B x N x C
class Block(nn.Module):
def __init__(self, in_channels, out_channels, i_downsample=None, stride=1):
super(Block, self).__init__()
self.conv1 = nn.Conv2d(in_channels, out_channels, kernel_size=3, padding=1, stride=stride, bias=False)
self.batch_norm1 = nn.BatchNorm2d(out_channels)
self.conv2 = nn.Conv2d(out_channels, out_channels, kernel_size=3, padding=1, stride=stride, bias=False)
self.batch_norm2 = nn.BatchNorm2d(out_channels)
self.i_downsample = i_downsample
self.stride = stride
self.relu = nn.LeakyReLU(negative_slope=0.1, inplace=True)
def forward(self, x):
identity = x.clone()
x = self.relu(self.batch_norm1(self.conv1(x)))
x = self.batch_norm2(self.conv2(x))
if self.i_downsample is not None:
identity = self.i_downsample(identity)
x += identity
x = self.relu(x)
return x
class Crop_Net_New(nn.Module):
def __init__(self, dim):
super().__init__()
self.conv = nn.Conv2d(3, dim, 3, 1, 1)
self.conv1 = Block(dim, dim)
self.conv2 = Block(dim, dim)
self.conv3 = Block(dim, dim)
self.conv4 = nn.Conv2d(dim, dim, 5, 1, 2)
def forward(self, x):
x = self.conv(x)
x = self.conv1(x)
x = self.conv2(x)
x = self.conv3(x)
return self.conv4(x)
class Mlp(nn.Module):
def __init__(self, in_dim, hid_dim=None, out_dim=None, act=nn.GELU, drop=0.):
super().__init__()
out_dim = out_dim or in_dim
hid_dim = hid_dim or in_dim
self.fc1 = nn.Linear(in_dim, hid_dim)
self.act = act()
self.fc2 = nn.Linear(hid_dim, out_dim)
self.drop = nn.Dropout(drop)
def forward(self, x):
x = self.fc1(x)
x = self.act(x)
x = self.drop(x)
x = self.fc2(x)
x = self.drop(x)
return x
class PromptEncoder(nn.Module):
def __init__(
self,
embed_dim: int,
image_embedding_size: Tuple[int, int],
input_image_size: Tuple[int, int],
mask_in_chans: int,
activation: Type[nn.Module] = nn.GELU,
) -> 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 = PositionEmbeddingRandom(embed_dim // 2)
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 = (
4 * image_embedding_size[0],
4 * image_embedding_size[1],
)
self.no_mask_embed = nn.Embedding(1, embed_dim)
self.crop_nets = Crop_Net_New(embed_dim)
self.clip_img_mlp = Mlp(in_dim=512, hid_dim=256, out_dim=256)
self.clip_text_mlp = Mlp(in_dim=512, hid_dim=256, out_dim=256)
self.mlps = Mlp(in_dim=512, hid_dim=512, out_dim=256)
self.categories = nn.Embedding(11, 256)
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)
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, 2), 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:
"""Embeds box prompts."""
boxes = boxes + 0.5 # Shift to center of pixel
coords = boxes.reshape(-1, 2, 2)
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 tokens is not None:
# return tokens.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
def forward(
self,
points: Optional[Tuple[torch.Tensor, torch.Tensor]],
boxes: Optional[torch.Tensor],
masks,
features,
crops,
text_features,
category_idx
) -> 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 features is not None:
clip_embeddings = self.clip_img_mlp(features)
sparse_embeddings = torch.cat([sparse_embeddings, clip_embeddings], dim=1)
if category_idx is not None:
text_embeddings = self.clip_text_mlp(text_features)
category_embeddings = torch.zeros((bs, 1, 256)).to(boxes.device)
for i in range(bs):
category_embeddings[i,0,:] = self.categories(category_idx[i].long())
modality_embeddings = torch.cat((text_embeddings, category_embeddings), dim=-1)
text_embeddings = self.mlps(modality_embeddings)
sparse_embeddings = torch.cat([sparse_embeddings, text_embeddings], dim=1)
if crops is not None:
dense_embeddings = self.crop_nets(crops)
else:
dense_embeddings = self.no_mask_embed.weight.reshape(1, -1, 1, 1).expand(
bs, -1, self.image_embedding_size[0], self.image_embedding_size[1]
)
return sparse_embeddings, dense_embeddings