diff --git a/osrt/encoder.py b/osrt/encoder.py
index 2c49b92820d75229d028b9ce8c354e24891e6735..a121d0f98ce89680a9f40c1fc0459a4779653f55 100644
--- a/osrt/encoder.py
+++ b/osrt/encoder.py
@@ -16,12 +16,12 @@ from osrt.layers import RayEncoder, Transformer, SlotAttention
from osrt.utils.common import batch_iterator, MaskData, calculate_stability_score, get_indices_sorted_pos, get_positional_embedding, create_points_grid, rotation_matrix_to_euler_angles
from osrt.utils.nerf import get_extrinsic
-from segment_anything import sam_model_registry
-from segment_anything.modeling.image_encoder import ImageEncoderViT
-from segment_anything.modeling.mask_decoder import MaskDecoder
-from segment_anything.modeling.prompt_encoder import PromptEncoder
-from segment_anything.utils.transforms import ResizeLongestSide
-from segment_anything.utils.amg import batched_mask_to_box, remove_small_regions, mask_to_rle_pytorch, area_from_rle
+from sam import sam_model_registry
+from sam.image_encoder import ImageEncoderViT
+from sam.mask_decoder import MaskDecoder
+from sam.prompt_encoder import PromptEncoder
+from sam.utils.transforms import ResizeLongestSide
+from sam.utils.amg import batched_mask_to_box, remove_small_regions, mask_to_rle_pytorch, area_from_rle
from torch.nn.utils.rnn import pad_sequence
diff --git a/osrt/sam/__init__.py b/osrt/sam/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..93e458e4b70b5bf24898fc926d5d1cabe793f88c
--- /dev/null
+++ b/osrt/sam/__init__.py
@@ -0,0 +1,18 @@
+# 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.
+
+from .sam import Sam
+from .image_encoder import ImageEncoderViT
+from .mask_decoder import MaskDecoder
+from .prompt_encoder import PromptEncoder
+from .transformer import TwoWayTransformer
+from .build_sam import (
+ build_sam,
+ build_sam_vit_h,
+ build_sam_vit_l,
+ build_sam_vit_b,
+ sam_model_registry,
+)
\ No newline at end of file
diff --git a/osrt/sam/build_sam.py b/osrt/sam/build_sam.py
new file mode 100644
index 0000000000000000000000000000000000000000..f23f46d54397a156b83462ffabc9febfcb6d80ae
--- /dev/null
+++ b/osrt/sam/build_sam.py
@@ -0,0 +1,108 @@
+# 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 torch
+
+from functools import partial
+
+from . import ImageEncoderViT, MaskDecoder, PromptEncoder, Sam, TwoWayTransformer
+
+
+def build_sam_vit_h(checkpoint=None):
+ return _build_sam(
+ encoder_embed_dim=1280,
+ encoder_depth=32,
+ encoder_num_heads=16,
+ encoder_global_attn_indexes=[7, 15, 23, 31],
+ checkpoint=checkpoint,
+ )
+
+
+build_sam = build_sam_vit_h
+
+
+def build_sam_vit_l(checkpoint=None):
+ return _build_sam(
+ encoder_embed_dim=1024,
+ encoder_depth=24,
+ encoder_num_heads=16,
+ encoder_global_attn_indexes=[5, 11, 17, 23],
+ checkpoint=checkpoint,
+ )
+
+
+def build_sam_vit_b(checkpoint=None):
+ return _build_sam(
+ encoder_embed_dim=768,
+ encoder_depth=12,
+ encoder_num_heads=12,
+ encoder_global_attn_indexes=[2, 5, 8, 11],
+ checkpoint=checkpoint,
+ )
+
+
+
+sam_model_registry = {
+ "default": build_sam_vit_h,
+ "vit_h": build_sam_vit_h,
+ "vit_l": build_sam_vit_l,
+ "vit_b": build_sam_vit_b,
+}
+
+
+def _build_sam(
+ encoder_embed_dim,
+ encoder_depth,
+ encoder_num_heads,
+ encoder_global_attn_indexes,
+ checkpoint=None,
+):
+ prompt_embed_dim = 256
+ image_size = 1024
+ vit_patch_size = 16
+ image_embedding_size = image_size // vit_patch_size
+ sam = Sam(
+ image_encoder=ImageEncoderViT(
+ depth=encoder_depth,
+ embed_dim=encoder_embed_dim,
+ img_size=image_size,
+ mlp_ratio=4,
+ norm_layer=partial(torch.nn.LayerNorm, eps=1e-6),
+ num_heads=encoder_num_heads,
+ patch_size=vit_patch_size,
+ qkv_bias=True,
+ use_rel_pos=True,
+ global_attn_indexes=encoder_global_attn_indexes,
+ window_size=14,
+ out_chans=prompt_embed_dim,
+ ),
+ prompt_encoder=PromptEncoder(
+ embed_dim=prompt_embed_dim,
+ image_embedding_size=(image_embedding_size, image_embedding_size),
+ input_image_size=(image_size, image_size),
+ mask_in_chans=16,
+ ),
+ mask_decoder=MaskDecoder(
+ num_multimask_outputs=3,
+ transformer=TwoWayTransformer(
+ depth=2,
+ embedding_dim=prompt_embed_dim,
+ mlp_dim=2048,
+ num_heads=8,
+ ),
+ transformer_dim=prompt_embed_dim,
+ iou_head_depth=3,
+ iou_head_hidden_dim=256,
+ ),
+ pixel_mean=[123.675, 116.28, 103.53],
+ pixel_std=[58.395, 57.12, 57.375],
+ )
+ sam.eval()
+ if checkpoint is not None:
+ with open(checkpoint, "rb") as f:
+ state_dict = torch.load(f)
+ sam.load_state_dict(state_dict)
+ return sam
diff --git a/osrt/sam/common.py b/osrt/sam/common.py
new file mode 100644
index 0000000000000000000000000000000000000000..2bf15236a3eb24d8526073bc4fa2b274cccb3f96
--- /dev/null
+++ b/osrt/sam/common.py
@@ -0,0 +1,43 @@
+# 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 torch
+import torch.nn as nn
+
+from typing import Type
+
+
+class MLPBlock(nn.Module):
+ def __init__(
+ self,
+ embedding_dim: int,
+ mlp_dim: int,
+ act: Type[nn.Module] = nn.GELU,
+ ) -> None:
+ super().__init__()
+ self.lin1 = nn.Linear(embedding_dim, mlp_dim)
+ self.lin2 = nn.Linear(mlp_dim, embedding_dim)
+ self.act = act()
+
+ def forward(self, x: torch.Tensor) -> torch.Tensor:
+ return self.lin2(self.act(self.lin1(x)))
+
+
+# From https://github.com/facebookresearch/detectron2/blob/main/detectron2/layers/batch_norm.py # noqa
+# Itself from https://github.com/facebookresearch/ConvNeXt/blob/d1fa8f6fef0a165b27399986cc2bdacc92777e40/models/convnext.py#L119 # noqa
+class LayerNorm2d(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] * x + self.bias[:, None, None]
+ return x
diff --git a/osrt/sam/image_encoder.py b/osrt/sam/image_encoder.py
new file mode 100644
index 0000000000000000000000000000000000000000..528e4e010214eb59192ec4ca99fb44e440fac6d5
--- /dev/null
+++ b/osrt/sam/image_encoder.py
@@ -0,0 +1,396 @@
+# 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 torch
+import torch.nn as nn
+import torch.nn.functional as F
+
+from typing import Optional, Tuple, Type
+
+from .common import LayerNorm2d, MLPBlock
+
+
+# This class and its supporting functions below lightly adapted from the ViTDet backbone available at: https://github.com/facebookresearch/detectron2/blob/main/detectron2/modeling/backbone/vit.py # noqa
+class ImageEncoderViT(nn.Module):
+ def __init__(
+ self,
+ img_size: int = 1024,
+ patch_size: int = 16,
+ in_chans: int = 3,
+ embed_dim: int = 768,
+ depth: int = 12,
+ num_heads: int = 12,
+ mlp_ratio: float = 4.0,
+ out_chans: int = 256,
+ qkv_bias: bool = True,
+ norm_layer: Type[nn.Module] = nn.LayerNorm,
+ act_layer: Type[nn.Module] = nn.GELU,
+ use_abs_pos: bool = True,
+ use_rel_pos: bool = False,
+ rel_pos_zero_init: bool = True,
+ window_size: int = 0,
+ global_attn_indexes: Tuple[int, ...] = (),
+ ) -> None:
+ """
+ Args:
+ img_size (int): Input image size.
+ patch_size (int): Patch size.
+ in_chans (int): Number of input image channels.
+ embed_dim (int): Patch embedding dimension.
+ depth (int): Depth of ViT.
+ num_heads (int): Number of attention heads in each ViT block.
+ mlp_ratio (float): Ratio of mlp hidden dim to embedding dim.
+ qkv_bias (bool): If True, add a learnable bias to query, key, value.
+ norm_layer (nn.Module): Normalization layer.
+ act_layer (nn.Module): Activation layer.
+ use_abs_pos (bool): If True, use absolute positional embeddings.
+ use_rel_pos (bool): If True, add relative positional embeddings to the attention map.
+ rel_pos_zero_init (bool): If True, zero initialize relative positional parameters.
+ window_size (int): Window size for window attention blocks.
+ global_attn_indexes (list): Indexes for blocks using global attention.
+ """
+ super().__init__()
+ self.img_size = img_size
+
+ self.patch_embed = PatchEmbed(
+ kernel_size=(patch_size, patch_size),
+ stride=(patch_size, patch_size),
+ in_chans=in_chans,
+ embed_dim=embed_dim,
+ )
+
+ self.pos_embed: Optional[nn.Parameter] = None
+ if use_abs_pos:
+ # Initialize absolute positional embedding with pretrain image size.
+ self.pos_embed = nn.Parameter(
+ torch.zeros(1, img_size // patch_size, img_size // patch_size, embed_dim)
+ )
+
+ self.blocks = nn.ModuleList()
+ for i in range(depth):
+ block = Block(
+ dim=embed_dim,
+ num_heads=num_heads,
+ mlp_ratio=mlp_ratio,
+ qkv_bias=qkv_bias,
+ norm_layer=norm_layer,
+ act_layer=act_layer,
+ use_rel_pos=use_rel_pos,
+ rel_pos_zero_init=rel_pos_zero_init,
+ window_size=window_size if i not in global_attn_indexes else 0,
+ input_size=(img_size // patch_size, img_size // patch_size),
+ )
+ self.blocks.append(block)
+
+ self.neck = nn.Sequential(
+ nn.Conv2d(
+ embed_dim,
+ out_chans,
+ kernel_size=1,
+ bias=False,
+ ),
+ LayerNorm2d(out_chans),
+ nn.Conv2d(
+ out_chans,
+ out_chans,
+ kernel_size=3,
+ padding=1,
+ bias=False,
+ ),
+ LayerNorm2d(out_chans),
+ )
+ def forward(self, x: torch.Tensor, before_channel_reduc=False) -> torch.Tensor:
+
+ x = self.patch_embed(x)
+
+ if self.pos_embed is not None:
+ x = x + self.pos_embed
+
+ for blk in self.blocks:
+ x = blk(x)
+
+ embed_no_reduc = x
+ x = self.neck(x.permute(0, 3, 1, 2))
+
+ # Extract image embedding before channel reduction, cf. https://github.com/facebookresearch/segment-anything/issues/283
+ if before_channel_reduc:
+ return x, embed_no_reduc
+
+ return x
+
+
+class Block(nn.Module):
+ """Transformer blocks with support of window attention and residual propagation blocks"""
+
+ def __init__(
+ self,
+ dim: int,
+ num_heads: int,
+ mlp_ratio: float = 4.0,
+ qkv_bias: bool = True,
+ norm_layer: Type[nn.Module] = nn.LayerNorm,
+ act_layer: Type[nn.Module] = nn.GELU,
+ use_rel_pos: bool = False,
+ rel_pos_zero_init: bool = True,
+ window_size: int = 0,
+ input_size: Optional[Tuple[int, int]] = None,
+ ) -> None:
+ """
+ Args:
+ dim (int): Number of input channels.
+ num_heads (int): Number of attention heads in each ViT block.
+ mlp_ratio (float): Ratio of mlp hidden dim to embedding dim.
+ qkv_bias (bool): If True, add a learnable bias to query, key, value.
+ norm_layer (nn.Module): Normalization layer.
+ act_layer (nn.Module): Activation layer.
+ use_rel_pos (bool): If True, add relative positional embeddings to the attention map.
+ rel_pos_zero_init (bool): If True, zero initialize relative positional parameters.
+ window_size (int): Window size for window attention blocks. If it equals 0, then
+ use global attention.
+ input_size (tuple(int, int) or None): Input resolution for calculating the relative
+ positional parameter size.
+ """
+ super().__init__()
+ self.norm1 = norm_layer(dim)
+ self.attn = Attention(
+ dim,
+ num_heads=num_heads,
+ qkv_bias=qkv_bias,
+ use_rel_pos=use_rel_pos,
+ rel_pos_zero_init=rel_pos_zero_init,
+ input_size=input_size if window_size == 0 else (window_size, window_size),
+ )
+
+ self.norm2 = norm_layer(dim)
+ self.mlp = MLPBlock(embedding_dim=dim, mlp_dim=int(dim * mlp_ratio), act=act_layer)
+
+ self.window_size = window_size
+
+ def forward(self, x: torch.Tensor) -> torch.Tensor:
+ shortcut = x
+ x = self.norm1(x)
+ # Window partition
+ if self.window_size > 0:
+ H, W = x.shape[1], x.shape[2]
+ x, pad_hw = window_partition(x, self.window_size)
+
+ x = self.attn(x)
+
+ # Reverse window partition
+ if self.window_size > 0:
+ x = window_unpartition(x, self.window_size, pad_hw, (H, W))
+ torch.cuda.empty_cache()
+
+ x = shortcut + x
+ x = x + self.mlp(self.norm2(x))
+
+ return x
+
+
+class Attention(nn.Module):
+ """Multi-head Attention block with relative position embeddings."""
+
+ def __init__(
+ self,
+ dim: int,
+ num_heads: int = 8,
+ qkv_bias: bool = True,
+ use_rel_pos: bool = False,
+ rel_pos_zero_init: bool = True,
+ input_size: Optional[Tuple[int, int]] = None,
+ ) -> None:
+ """
+ Args:
+ dim (int): Number of input channels.
+ num_heads (int): Number of attention heads.
+ qkv_bias (bool): If True, add a learnable bias to query, key, value.
+ rel_pos (bool): If True, add relative positional embeddings to the attention map.
+ rel_pos_zero_init (bool): If True, zero initialize relative positional parameters.
+ input_size (tuple(int, int) or None): Input resolution for calculating the relative
+ positional parameter size.
+ """
+ super().__init__()
+ self.num_heads = num_heads
+ head_dim = dim // num_heads
+ self.scale = head_dim**-0.5
+ self.qkv = nn.Linear(dim, dim * 3, bias=qkv_bias)
+ self.proj = nn.Linear(dim, dim)
+
+ self.use_rel_pos = use_rel_pos
+ if self.use_rel_pos:
+ assert (
+ input_size is not None
+ ), "Input size must be provided if using relative positional encoding."
+ # initialize relative positional embeddings
+ self.rel_pos_h = nn.Parameter(torch.zeros(2 * input_size[0] - 1, head_dim))
+ self.rel_pos_w = nn.Parameter(torch.zeros(2 * input_size[1] - 1, head_dim))
+
+ def forward(self, x: torch.Tensor) -> torch.Tensor:
+ B, H, W, _ = x.shape
+ # qkv with shape (3, B, nHead, H * W, C)
+ qkv = self.qkv(x).reshape(B, H * W, 3, self.num_heads, -1).permute(2, 0, 3, 1, 4)
+ # q, k, v with shape (B * nHead, H * W, C)
+ q, k, v = qkv.reshape(3, B * self.num_heads, H * W, -1).unbind(0)
+ x = (q * self.scale) @ k.transpose(-2, -1)
+ if self.use_rel_pos:
+ x = add_decomposed_rel_pos(x, q, self.rel_pos_h, self.rel_pos_w, (H, W), (H, W))
+ x = x.softmax(dim=-1)
+ x = (x @ v).view(B, self.num_heads, H, W, -1).permute(0, 2, 3, 1, 4).reshape(B, H, W, -1)
+ x = self.proj(x)
+
+ return x
+
+
+def window_partition(x: torch.Tensor, window_size: int) -> Tuple[torch.Tensor, Tuple[int, int]]:
+ """
+ Partition into non-overlapping windows with padding if needed.
+ Args:
+ x (tensor): input tokens with [B, H, W, C].
+ window_size (int): window size.
+
+ Returns:
+ windows: windows after partition with [B * num_windows, window_size, window_size, C].
+ (Hp, Wp): padded height and width before partition
+ """
+ B, H, W, C = x.shape
+
+ pad_h = (window_size - H % window_size) % window_size
+ pad_w = (window_size - W % window_size) % window_size
+ if pad_h > 0 or pad_w > 0:
+ x = F.pad(x, (0, 0, 0, pad_w, 0, pad_h))
+ Hp, Wp = H + pad_h, W + pad_w
+ x = x.view(B, Hp // window_size, window_size, Wp // window_size, window_size, C)
+ x = x.permute(0, 1, 3, 2, 4, 5).contiguous().view(-1, window_size, window_size, C)
+ return x, (Hp, Wp)
+
+
+def window_unpartition(
+ windows: torch.Tensor, window_size: int, pad_hw: Tuple[int, int], hw: Tuple[int, int]
+) -> torch.Tensor:
+ """
+ Window unpartition into original sequences and removing padding.
+ Args:
+ windows (tensor): input tokens with [B * num_windows, window_size, window_size, C].
+ window_size (int): window size.
+ pad_hw (Tuple): padded height and width (Hp, Wp).
+ hw (Tuple): original height and width (H, W) before padding.
+
+ Returns:
+ x: unpartitioned sequences with [B, H, W, C].
+ """
+ Hp, Wp = pad_hw
+ H, W = hw
+ B = windows.shape[0] // (Hp * Wp // window_size // window_size)
+ x = windows.view(B, Hp // window_size, Wp // window_size, window_size, window_size, -1)
+ x = x.permute(0, 1, 3, 2, 4, 5).contiguous().view(B, Hp, Wp, -1)
+
+ if Hp > H or Wp > W:
+ x = x[:, :H, :W, :].contiguous()
+ return x
+
+
+def get_rel_pos(q_size: int, k_size: int, rel_pos: torch.Tensor) -> torch.Tensor:
+ """
+ Get relative positional embeddings according to the relative positions of
+ query and key sizes.
+ Args:
+ q_size (int): size of query q.
+ k_size (int): size of key k.
+ rel_pos (Tensor): relative position embeddings (L, C).
+
+ Returns:
+ Extracted positional embeddings according to relative positions.
+ """
+ max_rel_dist = int(2 * max(q_size, k_size) - 1)
+ # Interpolate rel pos if needed.
+ if rel_pos.shape[0] != max_rel_dist:
+ # Interpolate rel pos.
+ rel_pos = F.interpolate(
+ rel_pos.reshape(1, rel_pos.shape[0], -1).permute(0, 2, 1),
+ size=max_rel_dist,
+ mode="linear",
+ )
+ rel_pos = rel_pos.reshape(-1, max_rel_dist).permute(1, 0)
+
+ # Scale the coords with short length if shapes for q and k are different.
+ q_coords = torch.arange(q_size)[:, None] * max(k_size / q_size, 1.0)
+ k_coords = torch.arange(k_size)[None, :] * max(q_size / k_size, 1.0)
+ relative_coords = (q_coords - k_coords) + (k_size - 1) * max(q_size / k_size, 1.0)
+
+ return rel_pos[relative_coords.long()]
+
+
+def add_decomposed_rel_pos(
+ attn: torch.Tensor,
+ q: torch.Tensor,
+ rel_pos_h: torch.Tensor,
+ rel_pos_w: torch.Tensor,
+ q_size: Tuple[int, int],
+ k_size: Tuple[int, int],
+) -> torch.Tensor:
+ """
+ Calculate decomposed Relative Positional Embeddings from :paper:`mvitv2`.
+ https://github.com/facebookresearch/mvit/blob/19786631e330df9f3622e5402b4a419a263a2c80/mvit/models/attention.py # noqa B950
+ Args:
+ attn (Tensor): attention map.
+ q (Tensor): query q in the attention layer with shape (B, q_h * q_w, C).
+ rel_pos_h (Tensor): relative position embeddings (Lh, C) for height axis.
+ rel_pos_w (Tensor): relative position embeddings (Lw, C) for width axis.
+ q_size (Tuple): spatial sequence size of query q with (q_h, q_w).
+ k_size (Tuple): spatial sequence size of key k with (k_h, k_w).
+
+ Returns:
+ attn (Tensor): attention map with added relative positional embeddings.
+ """
+ q_h, q_w = q_size
+ k_h, k_w = k_size
+ Rh = get_rel_pos(q_h, k_h, rel_pos_h)
+ Rw = get_rel_pos(q_w, k_w, rel_pos_w)
+
+ B, _, dim = q.shape
+ r_q = q.reshape(B, q_h, q_w, dim)
+ rel_h = torch.einsum("bhwc,hkc->bhwk", r_q, Rh)
+ rel_w = torch.einsum("bhwc,wkc->bhwk", r_q, Rw)
+
+ attn = (
+ attn.view(B, q_h, q_w, k_h, k_w) + rel_h[:, :, :, :, None] + rel_w[:, :, :, None, :]
+ ).view(B, q_h * q_w, k_h * k_w)
+
+ return attn
+
+
+class PatchEmbed(nn.Module):
+ """
+ Image to Patch Embedding.
+ """
+
+ def __init__(
+ self,
+ kernel_size: Tuple[int, int] = (16, 16),
+ stride: Tuple[int, int] = (16, 16),
+ padding: Tuple[int, int] = (0, 0),
+ in_chans: int = 3,
+ embed_dim: int = 768,
+ ) -> None:
+ """
+ Args:
+ kernel_size (Tuple): kernel size of the projection layer.
+ stride (Tuple): stride of the projection layer.
+ padding (Tuple): padding size of the projection layer.
+ in_chans (int): Number of input image channels.
+ embed_dim (int): Patch embedding dimension.
+ """
+ super().__init__()
+
+ self.proj = nn.Conv2d(
+ in_chans, embed_dim, kernel_size=kernel_size, stride=stride, padding=padding
+ )
+
+ def forward(self, x: torch.Tensor) -> torch.Tensor:
+ x = self.proj(x)
+ # B C H W -> B H W C
+ x = x.permute(0, 2, 3, 1)
+ return x
diff --git a/osrt/sam/mask_decoder.py b/osrt/sam/mask_decoder.py
new file mode 100644
index 0000000000000000000000000000000000000000..347c5c5977a65c36553c487416a281e0e5694356
--- /dev/null
+++ b/osrt/sam/mask_decoder.py
@@ -0,0 +1,181 @@
+# 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 torch
+from torch import nn
+from torch.nn import functional as F
+
+from typing import List, Tuple, Type
+
+from .common import LayerNorm2d
+
+
+class MaskDecoder(nn.Module):
+ def __init__(
+ self,
+ *,
+ transformer_dim: int,
+ transformer: nn.Module,
+ num_multimask_outputs: int = 3,
+ activation: Type[nn.Module] = nn.GELU,
+ iou_head_depth: int = 3,
+ iou_head_hidden_dim: int = 256,
+ ) -> None:
+ """
+ Predicts masks given an image and prompt embeddings, using a
+ transformer architecture.
+
+ Arguments:
+ transformer_dim (int): the channel dimension of the transformer
+ transformer (nn.Module): the transformer used to predict masks
+ num_multimask_outputs (int): the number of masks to predict
+ when disambiguating masks
+ activation (nn.Module): the type of activation to use when
+ upscaling masks
+ iou_head_depth (int): the depth of the MLP used to predict
+ mask quality
+ iou_head_hidden_dim (int): the hidden dimension of the MLP
+ used to predict mask quality
+ """
+ super().__init__()
+ self.transformer_dim = transformer_dim
+ self.transformer = transformer
+
+ self.num_multimask_outputs = num_multimask_outputs
+
+ self.iou_token = nn.Embedding(1, transformer_dim)
+ self.num_mask_tokens = num_multimask_outputs + 1
+ self.mask_tokens = nn.Embedding(self.num_mask_tokens, transformer_dim)
+
+ self.output_upscaling = nn.Sequential(
+ nn.ConvTranspose2d(transformer_dim, transformer_dim // 4, kernel_size=2, stride=2),
+ LayerNorm2d(transformer_dim // 4),
+ activation(),
+ nn.ConvTranspose2d(transformer_dim // 4, transformer_dim // 8, kernel_size=2, stride=2),
+ activation(),
+ )
+ self.output_hypernetworks_mlps = nn.ModuleList(
+ [
+ MLP(transformer_dim, transformer_dim, transformer_dim // 8, 3)
+ for i in range(self.num_mask_tokens)
+ ]
+ )
+
+ self.iou_prediction_head = MLP(
+ transformer_dim, iou_head_hidden_dim, self.num_mask_tokens, iou_head_depth
+ )
+
+ def forward(
+ self,
+ image_embeddings: torch.Tensor,
+ image_pe: torch.Tensor,
+ sparse_prompt_embeddings: torch.Tensor,
+ dense_prompt_embeddings: torch.Tensor,
+ multimask_output: bool,
+ ) -> Tuple[torch.Tensor, torch.Tensor]:
+ """
+ Predict masks given image and prompt embeddings.
+
+ Arguments:
+ image_embeddings (torch.Tensor): the embeddings from the image encoder
+ image_pe (torch.Tensor): positional encoding with the shape of image_embeddings
+ sparse_prompt_embeddings (torch.Tensor): the embeddings of the points and boxes
+ dense_prompt_embeddings (torch.Tensor): the embeddings of the mask inputs
+ multimask_output (bool): Whether to return multiple masks or a single
+ mask.
+
+ Returns:
+ torch.Tensor: batched predicted masks
+ torch.Tensor: batched predictions of mask quality
+ """
+ masks, iou_pred = self.predict_masks(
+ image_embeddings=image_embeddings,
+ image_pe=image_pe,
+ sparse_prompt_embeddings=sparse_prompt_embeddings,
+ dense_prompt_embeddings=dense_prompt_embeddings,
+ )
+
+ # Select the correct mask or masks for output
+ if multimask_output:
+ mask_slice = slice(1, None)
+ else:
+ mask_slice = slice(0, 1)
+ masks = masks[:, mask_slice, :, :]
+ iou_pred = iou_pred[:, mask_slice]
+
+ # Prepare output
+ return masks, iou_pred
+
+ def predict_masks(
+ 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
+ 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
+
+ pos_src = torch.repeat_interleave(image_pe, tokens.shape[0], dim=0)
+ b, c, h, w = src.shape
+
+
+ # Run the transformer
+ hs, src = self.transformer(src, pos_src, tokens)
+ iou_token_out = hs[:, 0, :]
+ mask_tokens_out = hs[:, 1 : (1 + self.num_mask_tokens), :]
+
+ # Upscale mask embeddings and predict masks using the mask tokens
+ src = src.transpose(1, 2).view(b, c, h, w)
+ upscaled_embedding = self.output_upscaling(src)
+ hyper_in_list: List[torch.Tensor] = []
+ for i in range(self.num_mask_tokens):
+ hyper_in_list.append(self.output_hypernetworks_mlps[i](mask_tokens_out[:, i, :]))
+ hyper_in = torch.stack(hyper_in_list, dim=1)
+ b, c, h, w = upscaled_embedding.shape
+ masks = (hyper_in @ upscaled_embedding.view(b, c, h * w)).view(b, -1, h, w)
+
+ # Generate mask quality predictions
+ iou_pred = self.iou_prediction_head(iou_token_out)
+
+ return masks, iou_pred
+
+
+# Lightly adapted from
+# https://github.com/facebookresearch/MaskFormer/blob/main/mask_former/modeling/transformer/transformer_predictor.py # noqa
+class MLP(nn.Module):
+ def __init__(
+ self,
+ input_dim: int,
+ hidden_dim: int,
+ output_dim: int,
+ num_layers: int,
+ sigmoid_output: bool = False,
+ ) -> None:
+ super().__init__()
+ self.num_layers = num_layers
+ h = [hidden_dim] * (num_layers - 1)
+ self.layers = nn.ModuleList(
+ nn.Linear(n, k) for n, k in zip([input_dim] + h, h + [output_dim])
+ )
+ self.sigmoid_output = sigmoid_output
+
+ def forward(self, x):
+ for i, layer in enumerate(self.layers):
+ x = F.relu(layer(x)) if i < self.num_layers - 1 else layer(x)
+ if self.sigmoid_output:
+ x = F.sigmoid(x)
+ return x
diff --git a/osrt/sam/prompt_encoder.py b/osrt/sam/prompt_encoder.py
new file mode 100644
index 0000000000000000000000000000000000000000..c3143f4f8e02ddd7ca8587b40ff5d47c3a6b7ef3
--- /dev/null
+++ b/osrt/sam/prompt_encoder.py
@@ -0,0 +1,214 @@
+# 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 typing import Any, Optional, Tuple, Type
+
+from .common import LayerNorm2d
+
+
+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.mask_downscaling = nn.Sequential(
+ nn.Conv2d(1, mask_in_chans // 4, kernel_size=2, stride=2),
+ LayerNorm2d(mask_in_chans // 4),
+ activation(),
+ nn.Conv2d(mask_in_chans // 4, mask_in_chans, kernel_size=2, stride=2),
+ LayerNorm2d(mask_in_chans),
+ activation(),
+ nn.Conv2d(mask_in_chans, embed_dim, kernel_size=1),
+ )
+ self.no_mask_embed = nn.Embedding(1, embed_dim)
+
+ 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 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: Optional[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).expand(
+ bs, -1, self.image_embedding_size[0], self.image_embedding_size[1]
+ )
+
+ return sparse_embeddings, dense_embeddings
+
+
+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
diff --git a/osrt/sam/sam.py b/osrt/sam/sam.py
new file mode 100644
index 0000000000000000000000000000000000000000..8074cff6b40addc6b66f7ab4962218eef20da13c
--- /dev/null
+++ b/osrt/sam/sam.py
@@ -0,0 +1,174 @@
+# 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 torch
+from torch import nn
+from torch.nn import functional as F
+
+from typing import Any, Dict, List, Tuple
+
+from .image_encoder import ImageEncoderViT
+from .mask_decoder import MaskDecoder
+from .prompt_encoder import PromptEncoder
+
+
+class Sam(nn.Module):
+ mask_threshold: float = 0.0
+ image_format: str = "RGB"
+
+ def __init__(
+ self,
+ image_encoder: ImageEncoderViT,
+ prompt_encoder: PromptEncoder,
+ mask_decoder: MaskDecoder,
+ pixel_mean: List[float] = [123.675, 116.28, 103.53],
+ pixel_std: List[float] = [58.395, 57.12, 57.375],
+ ) -> None:
+ """
+ SAM predicts object masks from an image and input prompts.
+
+ Arguments:
+ image_encoder (ImageEncoderViT): The backbone used to encode the
+ image into image embeddings that allow for efficient mask prediction.
+ prompt_encoder (PromptEncoder): Encodes various types of input prompts.
+ mask_decoder (MaskDecoder): Predicts masks from the image embeddings
+ and encoded prompts.
+ pixel_mean (list(float)): Mean values for normalizing pixels in the input image.
+ pixel_std (list(float)): Std values for normalizing pixels in the input image.
+ """
+ super().__init__()
+ self.image_encoder = image_encoder
+ self.prompt_encoder = prompt_encoder
+ self.mask_decoder = mask_decoder
+ self.register_buffer("pixel_mean", torch.Tensor(pixel_mean).view(-1, 1, 1), False)
+ self.register_buffer("pixel_std", torch.Tensor(pixel_std).view(-1, 1, 1), False)
+
+ @property
+ def device(self) -> Any:
+ return self.pixel_mean.device
+
+ @torch.no_grad()
+ def forward(
+ self,
+ batched_input: List[Dict[str, Any]],
+ multimask_output: bool,
+ ) -> List[Dict[str, torch.Tensor]]:
+ """
+ Predicts masks end-to-end from provided images and prompts.
+ If prompts are not known in advance, using SamPredictor is
+ recommended over calling the model directly.
+
+ Arguments:
+ batched_input (list(dict)): A list over input images, each a
+ dictionary with the following keys. A prompt key can be
+ excluded if it is not present.
+ 'image': The image as a torch tensor in 3xHxW format,
+ already transformed for input to the model.
+ 'original_size': (tuple(int, int)) The original size of
+ the image before transformation, as (H, W).
+ 'point_coords': (torch.Tensor) Batched point prompts for
+ this image, with shape BxNx2. Already transformed to the
+ input frame of the model.
+ 'point_labels': (torch.Tensor) Batched labels for point prompts,
+ with shape BxN.
+ 'boxes': (torch.Tensor) Batched box inputs, with shape Bx4.
+ Already transformed to the input frame of the model.
+ 'mask_inputs': (torch.Tensor) Batched mask inputs to the model,
+ in the form Bx1xHxW.
+ multimask_output (bool): Whether the model should predict multiple
+ disambiguating masks, or return a single mask.
+
+ Returns:
+ (list(dict)): A list over input images, where each element is
+ as dictionary with the following keys.
+ 'masks': (torch.Tensor) Batched binary mask predictions,
+ with shape BxCxHxW, where B is the number of input prompts,
+ C is determined by multimask_output, and (H, W) is the
+ original size of the image.
+ 'iou_predictions': (torch.Tensor) The model's predictions
+ of mask quality, in shape BxC.
+ 'low_res_logits': (torch.Tensor) Low resolution logits with
+ shape BxCxHxW, where H=W=256. Can be passed as mask input
+ to subsequent iterations of prediction.
+ """
+ input_images = torch.stack([self.preprocess(x["image"]) for x in batched_input], dim=0)
+ image_embeddings = self.image_encoder(input_images)
+
+ outputs = []
+ for image_record, curr_embedding in zip(batched_input, image_embeddings):
+ if "point_coords" in image_record:
+ points = (image_record["point_coords"], image_record["point_labels"])
+ else:
+ points = None
+ sparse_embeddings, dense_embeddings = self.prompt_encoder(
+ points=points,
+ boxes=image_record.get("boxes", None),
+ masks=image_record.get("mask_inputs", None),
+ )
+ low_res_masks, iou_predictions = self.mask_decoder(
+ image_embeddings=curr_embedding.unsqueeze(0),
+ image_pe=self.prompt_encoder.get_dense_pe(),
+ sparse_prompt_embeddings=sparse_embeddings,
+ dense_prompt_embeddings=dense_embeddings,
+ multimask_output=multimask_output,
+ )
+ masks = self.postprocess_masks(
+ low_res_masks,
+ input_size=image_record["image"].shape[-2:],
+ original_size=image_record["original_size"],
+ )
+ masks = masks > self.mask_threshold
+ outputs.append(
+ {
+ "masks": masks,
+ "iou_predictions": iou_predictions,
+ "low_res_logits": low_res_masks,
+ }
+ )
+ return outputs
+
+ def postprocess_masks(
+ self,
+ masks: torch.Tensor,
+ input_size: Tuple[int, ...],
+ original_size: Tuple[int, ...],
+ ) -> torch.Tensor:
+ """
+ Remove padding and upscale masks to the original image size.
+
+ Arguments:
+ masks (torch.Tensor): Batched masks from the mask_decoder,
+ in BxCxHxW format.
+ input_size (tuple(int, int)): The size of the image input to the
+ model, in (H, W) format. Used to remove padding.
+ original_size (tuple(int, int)): The original size of the image
+ before resizing for input to the model, in (H, W) format.
+
+ Returns:
+ (torch.Tensor): Batched masks in BxCxHxW format, where (H, W)
+ is given by original_size.
+ """
+ masks = F.interpolate(
+ masks,
+ (self.image_encoder.img_size, self.image_encoder.img_size),
+ mode="bilinear",
+ align_corners=False,
+ )
+ masks = masks[..., : input_size[0], : input_size[1]]
+ masks = F.interpolate(masks, original_size, mode="bilinear", align_corners=False)
+ return masks
+
+ def preprocess(self, x: torch.Tensor) -> torch.Tensor:
+ """Normalize pixel values and pad to a square input."""
+ # Normalize colors
+ x = (x - self.pixel_mean) / self.pixel_std
+
+ # Pad
+ h, w = x.shape[-2:]
+ padh = self.image_encoder.img_size - h
+ padw = self.image_encoder.img_size - w
+ x = F.pad(x, (0, padw, 0, padh))
+ return x
diff --git a/osrt/sam/transformer.py b/osrt/sam/transformer.py
new file mode 100644
index 0000000000000000000000000000000000000000..28fafea52288603fea275f3a100790471825c34a
--- /dev/null
+++ b/osrt/sam/transformer.py
@@ -0,0 +1,240 @@
+# 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 torch
+from torch import Tensor, nn
+
+import math
+from typing import Tuple, Type
+
+from .common import MLPBlock
+
+
+class TwoWayTransformer(nn.Module):
+ def __init__(
+ self,
+ depth: int,
+ embedding_dim: int,
+ num_heads: int,
+ mlp_dim: int,
+ activation: Type[nn.Module] = nn.ReLU,
+ attention_downsample_rate: int = 2,
+ ) -> None:
+ """
+ A transformer decoder that attends to an input image using
+ queries whose positional embedding is supplied.
+
+ Args:
+ depth (int): number of layers in the transformer
+ embedding_dim (int): the channel dimension for the input embeddings
+ num_heads (int): the number of heads for multihead attention. Must
+ divide embedding_dim
+ mlp_dim (int): the channel dimension internal to the MLP block
+ activation (nn.Module): the activation to use in the MLP block
+ """
+ super().__init__()
+ self.depth = depth
+ self.embedding_dim = embedding_dim
+ self.num_heads = num_heads
+ self.mlp_dim = mlp_dim
+ self.layers = nn.ModuleList()
+
+ for i in range(depth):
+ self.layers.append(
+ TwoWayAttentionBlock(
+ embedding_dim=embedding_dim,
+ num_heads=num_heads,
+ mlp_dim=mlp_dim,
+ activation=activation,
+ attention_downsample_rate=attention_downsample_rate,
+ skip_first_layer_pe=(i == 0),
+ )
+ )
+
+ self.final_attn_token_to_image = Attention(
+ embedding_dim, num_heads, downsample_rate=attention_downsample_rate
+ )
+ self.norm_final_attn = nn.LayerNorm(embedding_dim)
+
+ def forward(
+ self,
+ image_embedding: Tensor,
+ image_pe: Tensor,
+ point_embedding: Tensor,
+ ) -> Tuple[Tensor, Tensor]:
+ """
+ Args:
+ image_embedding (torch.Tensor): image to attend to. Should be shape
+ B x embedding_dim x h x w for any h and w.
+ image_pe (torch.Tensor): the positional encoding to add to the image. Must
+ have the same shape as image_embedding.
+ point_embedding (torch.Tensor): the embedding to add to the query points.
+ Must have shape B x N_points x embedding_dim for any N_points.
+
+ Returns:
+ torch.Tensor: the processed point_embedding
+ torch.Tensor: the processed image_embedding
+ """
+ # BxCxHxW -> BxHWxC == B x N_image_tokens x C
+ bs, c, h, w = image_embedding.shape
+ image_embedding = image_embedding.flatten(2).permute(0, 2, 1)
+ image_pe = image_pe.flatten(2).permute(0, 2, 1)
+
+ # Prepare queries
+ queries = point_embedding
+ keys = image_embedding
+
+ # Apply transformer blocks and final layernorm
+ for layer in self.layers:
+ queries, keys = layer(
+ queries=queries,
+ keys=keys,
+ query_pe=point_embedding,
+ key_pe=image_pe,
+ )
+
+ # Apply the final attention layer from the points to the image
+ q = queries + point_embedding
+ k = keys + image_pe
+ attn_out = self.final_attn_token_to_image(q=q, k=k, v=keys)
+ queries = queries + attn_out
+ queries = self.norm_final_attn(queries)
+
+ return queries, keys
+
+
+class TwoWayAttentionBlock(nn.Module):
+ def __init__(
+ self,
+ embedding_dim: int,
+ num_heads: int,
+ mlp_dim: int = 2048,
+ activation: Type[nn.Module] = nn.ReLU,
+ attention_downsample_rate: int = 2,
+ skip_first_layer_pe: bool = False,
+ ) -> None:
+ """
+ A transformer block with four layers: (1) self-attention of sparse
+ inputs, (2) cross attention of sparse inputs to dense inputs, (3) mlp
+ block on sparse inputs, and (4) cross attention of dense inputs to sparse
+ inputs.
+
+ Arguments:
+ embedding_dim (int): the channel dimension of the embeddings
+ num_heads (int): the number of heads in the attention layers
+ mlp_dim (int): the hidden dimension of the mlp block
+ activation (nn.Module): the activation of the mlp block
+ skip_first_layer_pe (bool): skip the PE on the first layer
+ """
+ super().__init__()
+ self.self_attn = Attention(embedding_dim, num_heads)
+ self.norm1 = nn.LayerNorm(embedding_dim)
+
+ self.cross_attn_token_to_image = Attention(
+ embedding_dim, num_heads, downsample_rate=attention_downsample_rate
+ )
+ self.norm2 = nn.LayerNorm(embedding_dim)
+
+ self.mlp = MLPBlock(embedding_dim, mlp_dim, activation)
+ self.norm3 = nn.LayerNorm(embedding_dim)
+
+ self.norm4 = nn.LayerNorm(embedding_dim)
+ self.cross_attn_image_to_token = Attention(
+ embedding_dim, num_heads, downsample_rate=attention_downsample_rate
+ )
+
+ self.skip_first_layer_pe = skip_first_layer_pe
+
+ def forward(
+ self, queries: Tensor, keys: Tensor, query_pe: Tensor, key_pe: Tensor
+ ) -> Tuple[Tensor, Tensor]:
+ # Self attention block
+ if self.skip_first_layer_pe:
+ queries = self.self_attn(q=queries, k=queries, v=queries)
+ else:
+ q = queries + query_pe
+ attn_out = self.self_attn(q=q, k=q, v=queries)
+ queries = queries + attn_out
+ queries = self.norm1(queries)
+
+ # Cross attention block, tokens attending to image embedding
+ q = queries + query_pe
+ k = keys + key_pe
+ attn_out = self.cross_attn_token_to_image(q=q, k=k, v=keys)
+ queries = queries + attn_out
+ queries = self.norm2(queries)
+
+ # MLP block
+ mlp_out = self.mlp(queries)
+ queries = queries + mlp_out
+ queries = self.norm3(queries)
+
+ # Cross attention block, image embedding attending to tokens
+ q = queries + query_pe
+ k = keys + key_pe
+ attn_out = self.cross_attn_image_to_token(q=k, k=q, v=queries)
+ keys = keys + attn_out
+ keys = self.norm4(keys)
+
+ return queries, keys
+
+
+class Attention(nn.Module):
+ """
+ An attention layer that allows for downscaling the size of the embedding
+ after projection to queries, keys, and values.
+ """
+
+ def __init__(
+ self,
+ embedding_dim: int,
+ num_heads: int,
+ downsample_rate: int = 1,
+ ) -> None:
+ super().__init__()
+ self.embedding_dim = embedding_dim
+ self.internal_dim = embedding_dim // downsample_rate
+ self.num_heads = num_heads
+ assert self.internal_dim % num_heads == 0, "num_heads must divide embedding_dim."
+
+ self.q_proj = nn.Linear(embedding_dim, self.internal_dim)
+ self.k_proj = nn.Linear(embedding_dim, self.internal_dim)
+ self.v_proj = nn.Linear(embedding_dim, self.internal_dim)
+ self.out_proj = nn.Linear(self.internal_dim, embedding_dim)
+
+ def _separate_heads(self, x: Tensor, num_heads: int) -> Tensor:
+ b, n, c = x.shape
+ x = x.reshape(b, n, num_heads, c // num_heads)
+ return x.transpose(1, 2) # B x N_heads x N_tokens x C_per_head
+
+ def _recombine_heads(self, x: Tensor) -> Tensor:
+ b, n_heads, n_tokens, c_per_head = x.shape
+ x = x.transpose(1, 2)
+ return x.reshape(b, n_tokens, n_heads * c_per_head) # B x N_tokens x C
+
+ def forward(self, q: Tensor, k: Tensor, v: Tensor) -> Tensor:
+ # Input projections
+ q = self.q_proj(q)
+ k = self.k_proj(k)
+ v = self.v_proj(v)
+
+ # Separate into heads
+ q = self._separate_heads(q, self.num_heads)
+ k = self._separate_heads(k, self.num_heads)
+ v = self._separate_heads(v, self.num_heads)
+
+ # Attention
+ _, _, _, c_per_head = q.shape
+ attn = q @ k.permute(0, 1, 3, 2) # B x N_heads x N_tokens x N_tokens
+ attn = attn / math.sqrt(c_per_head)
+ attn = torch.softmax(attn, dim=-1)
+
+ # Get output
+ out = attn @ v
+ out = self._recombine_heads(out)
+ out = self.out_proj(out)
+
+ return out
diff --git a/osrt/sam/utils/__init__.py b/osrt/sam/utils/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..5277f46157403e47fd830fc519144b97ef69d4ae
--- /dev/null
+++ b/osrt/sam/utils/__init__.py
@@ -0,0 +1,5 @@
+# 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.
diff --git a/osrt/sam/utils/amg.py b/osrt/sam/utils/amg.py
new file mode 100644
index 0000000000000000000000000000000000000000..b114d37a3f7acae1b2cef8f6724f48b5950c4cbe
--- /dev/null
+++ b/osrt/sam/utils/amg.py
@@ -0,0 +1,347 @@
+# 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
+
+import math
+from copy import deepcopy
+from itertools import product
+from typing import Any, Dict, Generator, ItemsView, List, Tuple
+
+
+class MaskData:
+ """
+ A structure for storing masks and their related data in batched format.
+ Implements basic filtering and concatenation.
+ """
+
+ def __init__(self, **kwargs) -> None:
+ for v in kwargs.values():
+ assert isinstance(
+ v, (list, np.ndarray, torch.Tensor)
+ ), "MaskData only supports list, numpy arrays, and torch tensors."
+ self._stats = dict(**kwargs)
+
+ def __setitem__(self, key: str, item: Any) -> None:
+ assert isinstance(
+ item, (list, np.ndarray, torch.Tensor)
+ ), "MaskData only supports list, numpy arrays, and torch tensors."
+ self._stats[key] = item
+
+ def __delitem__(self, key: str) -> None:
+ del self._stats[key]
+
+ def __getitem__(self, key: str) -> Any:
+ return self._stats[key]
+
+ def items(self) -> ItemsView[str, Any]:
+ return self._stats.items()
+
+ def filter(self, keep: torch.Tensor) -> None:
+ for k, v in self._stats.items():
+ if v is None:
+ self._stats[k] = None
+ elif isinstance(v, torch.Tensor):
+ self._stats[k] = v[torch.as_tensor(keep, device=v.device)]
+ elif isinstance(v, np.ndarray):
+ self._stats[k] = v[keep.detach().cpu().numpy()]
+ elif isinstance(v, list) and keep.dtype == torch.bool:
+ self._stats[k] = [a for i, a in enumerate(v) if keep[i]]
+ elif isinstance(v, list):
+ self._stats[k] = [v[i] for i in keep]
+ else:
+ raise TypeError(f"MaskData key {k} has an unsupported type {type(v)}.")
+
+
+ def cat(self, new_stats: "MaskData") -> None:
+ for k, v in new_stats.items():
+ if k not in self._stats or self._stats[k] is None:
+ self._stats[k] = deepcopy(v)
+ elif isinstance(v, torch.Tensor):
+ self._stats[k] = torch.cat([self._stats[k], v], dim=0)
+ elif isinstance(v, np.ndarray):
+ self._stats[k] = np.concatenate([self._stats[k], v], axis=0)
+ elif isinstance(v, list):
+ self._stats[k] = self._stats[k] + deepcopy(v)
+ else:
+ raise TypeError(f"MaskData key {k} has an unsupported type {type(v)}.")
+
+ def to_numpy(self) -> None:
+ for k, v in self._stats.items():
+ if isinstance(v, torch.Tensor):
+ self._stats[k] = v.detach().cpu().numpy()
+
+
+def is_box_near_crop_edge(
+ boxes: torch.Tensor, crop_box: List[int], orig_box: List[int], atol: float = 20.0
+) -> torch.Tensor:
+ """Filter masks at the edge of a crop, but not at the edge of the original image."""
+ crop_box_torch = torch.as_tensor(crop_box, dtype=torch.float, device=boxes.device)
+ orig_box_torch = torch.as_tensor(orig_box, dtype=torch.float, device=boxes.device)
+ boxes = uncrop_boxes_xyxy(boxes, crop_box).float()
+ near_crop_edge = torch.isclose(boxes, crop_box_torch[None, :], atol=atol, rtol=0)
+ near_image_edge = torch.isclose(boxes, orig_box_torch[None, :], atol=atol, rtol=0)
+ near_crop_edge = torch.logical_and(near_crop_edge, ~near_image_edge)
+ return torch.any(near_crop_edge, dim=1)
+
+
+def box_xyxy_to_xywh(box_xyxy: torch.Tensor) -> torch.Tensor:
+ box_xywh = deepcopy(box_xyxy)
+ box_xywh[2] = box_xywh[2] - box_xywh[0]
+ box_xywh[3] = box_xywh[3] - box_xywh[1]
+ return box_xywh
+
+
+def batch_iterator(batch_size: int, *args) -> Generator[List[Any], None, None]:
+ assert len(args) > 0 and all(
+ len(a) == len(args[0]) for a in args
+ ), "Batched iteration must have inputs of all the same size."
+ n_batches = len(args[0]) // batch_size + int(len(args[0]) % batch_size != 0)
+ for b in range(n_batches):
+ yield [arg[b * batch_size : (b + 1) * batch_size] for arg in args]
+
+
+def mask_to_rle_pytorch(tensor: torch.Tensor) -> List[Dict[str, Any]]:
+ """
+ Encodes masks to an uncompressed RLE, in the format expected by
+ pycoco tools.
+ """
+ # Put in fortran order and flatten h,w
+ b, h, w = tensor.shape
+ tensor = tensor.permute(0, 2, 1).flatten(1)
+
+ # Compute change indices
+ diff = tensor[:, 1:] ^ tensor[:, :-1]
+ change_indices = diff.nonzero()
+
+ # Encode run length
+ out = []
+ for i in range(b):
+ cur_idxs = change_indices[change_indices[:, 0] == i, 1]
+ cur_idxs = torch.cat(
+ [
+ torch.tensor([0], dtype=cur_idxs.dtype, device=cur_idxs.device),
+ cur_idxs + 1,
+ torch.tensor([h * w], dtype=cur_idxs.dtype, device=cur_idxs.device),
+ ]
+ )
+ btw_idxs = cur_idxs[1:] - cur_idxs[:-1]
+ counts = [] if tensor[i, 0] == 0 else [0]
+ counts.extend(btw_idxs.detach().cpu().tolist())
+ out.append({"size": [h, w], "counts": counts})
+ return out
+
+
+def rle_to_mask(rle: Dict[str, Any]) -> np.ndarray:
+ """Compute a binary mask from an uncompressed RLE."""
+ h, w = rle["size"]
+ mask = np.empty(h * w, dtype=bool)
+ idx = 0
+ parity = False
+ for count in rle["counts"]:
+ mask[idx : idx + count] = parity
+ idx += count
+ parity ^= True
+ mask = mask.reshape(w, h)
+ return mask.transpose() # Put in C order
+
+
+def area_from_rle(rle: Dict[str, Any]) -> int:
+ return sum(rle["counts"][1::2])
+
+
+def calculate_stability_score(
+ masks: torch.Tensor, mask_threshold: float, threshold_offset: float
+) -> torch.Tensor:
+ """
+ Computes the stability score for a batch of masks. The stability
+ score is the IoU between the binary masks obtained by thresholding
+ the predicted mask logits at high and low values.
+ """
+ # One mask is always contained inside the other.
+ # Save memory by preventing unnecessary cast to torch.int64
+ intersections = (
+ (masks > (mask_threshold + threshold_offset))
+ .sum(-1, dtype=torch.int16)
+ .sum(-1, dtype=torch.int32)
+ )
+ unions = (
+ (masks > (mask_threshold - threshold_offset))
+ .sum(-1, dtype=torch.int16)
+ .sum(-1, dtype=torch.int32)
+ )
+ return intersections / unions
+
+
+def build_point_grid(n_per_side: int) -> np.ndarray:
+ """Generates a 2D grid of points evenly spaced in [0,1]x[0,1]."""
+ offset = 1 / (2 * n_per_side)
+ points_one_side = np.linspace(offset, 1 - offset, n_per_side)
+ points_x = np.tile(points_one_side[None, :], (n_per_side, 1))
+ points_y = np.tile(points_one_side[:, None], (1, n_per_side))
+ points = np.stack([points_x, points_y], axis=-1).reshape(-1, 2)
+ return points
+
+
+def build_all_layer_point_grids(
+ n_per_side: int, n_layers: int, scale_per_layer: int
+) -> List[np.ndarray]:
+ """Generates point grids for all crop layers."""
+ points_by_layer = []
+ for i in range(n_layers + 1):
+ n_points = int(n_per_side / (scale_per_layer**i))
+ points_by_layer.append(build_point_grid(n_points))
+ return points_by_layer
+
+
+def generate_crop_boxes(
+ im_size: Tuple[int, ...], n_layers: int, overlap_ratio: float
+) -> Tuple[List[List[int]], List[int]]:
+ """
+ Generates a list of crop boxes of different sizes. Each layer
+ has (2**i)**2 boxes for the ith layer.
+ """
+ crop_boxes, layer_idxs = [], []
+ im_h, im_w = im_size
+ short_side = min(im_h, im_w)
+
+ # Original image
+ crop_boxes.append([0, 0, im_w, im_h])
+ layer_idxs.append(0)
+
+ def crop_len(orig_len, n_crops, overlap):
+ return int(math.ceil((overlap * (n_crops - 1) + orig_len) / n_crops))
+
+ for i_layer in range(n_layers):
+ n_crops_per_side = 2 ** (i_layer + 1)
+ overlap = int(overlap_ratio * short_side * (2 / n_crops_per_side))
+
+ crop_w = crop_len(im_w, n_crops_per_side, overlap)
+ crop_h = crop_len(im_h, n_crops_per_side, overlap)
+
+ crop_box_x0 = [int((crop_w - overlap) * i) for i in range(n_crops_per_side)]
+ crop_box_y0 = [int((crop_h - overlap) * i) for i in range(n_crops_per_side)]
+
+ # Crops in XYWH format
+ for x0, y0 in product(crop_box_x0, crop_box_y0):
+ box = [x0, y0, min(x0 + crop_w, im_w), min(y0 + crop_h, im_h)]
+ crop_boxes.append(box)
+ layer_idxs.append(i_layer + 1)
+
+ return crop_boxes, layer_idxs
+
+
+def uncrop_boxes_xyxy(boxes: torch.Tensor, crop_box: List[int]) -> torch.Tensor:
+ x0, y0, _, _ = crop_box
+ offset = torch.tensor([[x0, y0, x0, y0]], device=boxes.device)
+ # Check if boxes has a channel dimension
+ if len(boxes.shape) == 3:
+ offset = offset.unsqueeze(1)
+ return boxes + offset
+
+
+def uncrop_points(points: torch.Tensor, crop_box: List[int]) -> torch.Tensor:
+ x0, y0, _, _ = crop_box
+ offset = torch.tensor([[x0, y0]], device=points.device)
+ # Check if points has a channel dimension
+ if len(points.shape) == 3:
+ offset = offset.unsqueeze(1)
+ return points + offset
+
+
+def uncrop_masks(
+ masks: torch.Tensor, crop_box: List[int], orig_h: int, orig_w: int
+) -> torch.Tensor:
+ x0, y0, x1, y1 = crop_box
+ if x0 == 0 and y0 == 0 and x1 == orig_w and y1 == orig_h:
+ return masks
+ # Coordinate transform masks
+ pad_x, pad_y = orig_w - (x1 - x0), orig_h - (y1 - y0)
+ pad = (x0, pad_x - x0, y0, pad_y - y0)
+ return torch.nn.functional.pad(masks, pad, value=0)
+
+
+def remove_small_regions(
+ mask: np.ndarray, area_thresh: float, mode: str
+) -> Tuple[np.ndarray, bool]:
+ """
+ Removes small disconnected regions and holes in a mask. Returns the
+ mask and an indicator of if the mask has been modified.
+ """
+ import cv2 # type: ignore
+
+ assert mode in ["holes", "islands"]
+ correct_holes = mode == "holes"
+ working_mask = (correct_holes ^ mask).astype(np.uint8)
+ n_labels, regions, stats, _ = cv2.connectedComponentsWithStats(working_mask, 8)
+ sizes = stats[:, -1][1:] # Row 0 is background label
+ small_regions = [i + 1 for i, s in enumerate(sizes) if s < area_thresh]
+ if len(small_regions) == 0:
+ return mask, False
+ fill_labels = [0] + small_regions
+ if not correct_holes:
+ fill_labels = [i for i in range(n_labels) if i not in fill_labels]
+ # If every region is below threshold, keep largest
+ if len(fill_labels) == 0:
+ fill_labels = [int(np.argmax(sizes)) + 1]
+ mask = np.isin(regions, fill_labels)
+ return mask, True
+
+
+def coco_encode_rle(uncompressed_rle: Dict[str, Any]) -> Dict[str, Any]:
+ from pycocotools import mask as mask_utils # type: ignore
+
+ h, w = uncompressed_rle["size"]
+ rle = mask_utils.frPyObjects(uncompressed_rle, h, w)
+ rle["counts"] = rle["counts"].decode("utf-8") # Necessary to serialize with json
+ return rle
+
+
+def batched_mask_to_box(masks: torch.Tensor) -> torch.Tensor:
+ """
+ Calculates boxes in XYXY format around masks. Return [0,0,0,0] for
+ an empty mask. For input shape C1xC2x...xHxW, the output shape is C1xC2x...x4.
+ """
+ # torch.max below raises an error on empty inputs, just skip in this case
+ if torch.numel(masks) == 0:
+ return torch.zeros(*masks.shape[:-2], 4, device=masks.device)
+
+ # Normalize shape to CxHxW
+ shape = masks.shape
+ h, w = shape[-2:]
+ if len(shape) > 2:
+ masks = masks.flatten(0, -3)
+ else:
+ masks = masks.unsqueeze(0)
+
+ # Get top and bottom edges
+ in_height, _ = torch.max(masks, dim=-1)
+ in_height_coords = in_height * torch.arange(h, device=in_height.device)[None, :]
+ bottom_edges, _ = torch.max(in_height_coords, dim=-1)
+ in_height_coords = in_height_coords + h * (~in_height)
+ top_edges, _ = torch.min(in_height_coords, dim=-1)
+
+ # Get left and right edges
+ in_width, _ = torch.max(masks, dim=-2)
+ in_width_coords = in_width * torch.arange(w, device=in_width.device)[None, :]
+ right_edges, _ = torch.max(in_width_coords, dim=-1)
+ in_width_coords = in_width_coords + w * (~in_width)
+ left_edges, _ = torch.min(in_width_coords, dim=-1)
+
+ # If the mask is empty the right edge will be to the left of the left edge.
+ # Replace these boxes with [0, 0, 0, 0]
+ empty_filter = (right_edges < left_edges) | (bottom_edges < top_edges)
+ out = torch.stack([left_edges, top_edges, right_edges, bottom_edges], dim=-1)
+ out = out * (~empty_filter).unsqueeze(-1)
+
+ # Return to original shape
+ if len(shape) > 2:
+ out = out.reshape(*shape[:-2], 4)
+ else:
+ out = out[0]
+
+ return out
diff --git a/osrt/sam/utils/onnx.py b/osrt/sam/utils/onnx.py
new file mode 100644
index 0000000000000000000000000000000000000000..3196bdf4b782e6eeb3da4ad66ef3c7b1741535fe
--- /dev/null
+++ b/osrt/sam/utils/onnx.py
@@ -0,0 +1,144 @@
+# 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 torch
+import torch.nn as nn
+from torch.nn import functional as F
+
+from typing import Tuple
+
+from ..modeling import Sam
+from .amg import calculate_stability_score
+
+
+class SamOnnxModel(nn.Module):
+ """
+ This model should not be called directly, but is used in ONNX export.
+ It combines the prompt encoder, mask decoder, and mask postprocessing of Sam,
+ with some functions modified to enable model tracing. Also supports extra
+ options controlling what information. See the ONNX export script for details.
+ """
+
+ def __init__(
+ self,
+ model: Sam,
+ return_single_mask: bool,
+ use_stability_score: bool = False,
+ return_extra_metrics: bool = False,
+ ) -> None:
+ super().__init__()
+ self.mask_decoder = model.mask_decoder
+ self.model = model
+ self.img_size = model.image_encoder.img_size
+ self.return_single_mask = return_single_mask
+ self.use_stability_score = use_stability_score
+ self.stability_score_offset = 1.0
+ self.return_extra_metrics = return_extra_metrics
+
+ @staticmethod
+ def resize_longest_image_size(
+ input_image_size: torch.Tensor, longest_side: int
+ ) -> torch.Tensor:
+ input_image_size = input_image_size.to(torch.float32)
+ scale = longest_side / torch.max(input_image_size)
+ transformed_size = scale * input_image_size
+ transformed_size = torch.floor(transformed_size + 0.5).to(torch.int64)
+ return transformed_size
+
+ def _embed_points(self, point_coords: torch.Tensor, point_labels: torch.Tensor) -> torch.Tensor:
+ point_coords = point_coords + 0.5
+ point_coords = point_coords / self.img_size
+ point_embedding = self.model.prompt_encoder.pe_layer._pe_encoding(point_coords)
+ point_labels = point_labels.unsqueeze(-1).expand_as(point_embedding)
+
+ point_embedding = point_embedding * (point_labels != -1)
+ point_embedding = point_embedding + self.model.prompt_encoder.not_a_point_embed.weight * (
+ point_labels == -1
+ )
+
+ for i in range(self.model.prompt_encoder.num_point_embeddings):
+ point_embedding = point_embedding + self.model.prompt_encoder.point_embeddings[
+ i
+ ].weight * (point_labels == i)
+
+ return point_embedding
+
+ def _embed_masks(self, input_mask: torch.Tensor, has_mask_input: torch.Tensor) -> torch.Tensor:
+ mask_embedding = has_mask_input * self.model.prompt_encoder.mask_downscaling(input_mask)
+ mask_embedding = mask_embedding + (
+ 1 - has_mask_input
+ ) * self.model.prompt_encoder.no_mask_embed.weight.reshape(1, -1, 1, 1)
+ return mask_embedding
+
+ def mask_postprocessing(self, masks: torch.Tensor, orig_im_size: torch.Tensor) -> torch.Tensor:
+ masks = F.interpolate(
+ masks,
+ size=(self.img_size, self.img_size),
+ mode="bilinear",
+ align_corners=False,
+ )
+
+ prepadded_size = self.resize_longest_image_size(orig_im_size, self.img_size).to(torch.int64)
+ masks = masks[..., : prepadded_size[0], : prepadded_size[1]] # type: ignore
+
+ orig_im_size = orig_im_size.to(torch.int64)
+ h, w = orig_im_size[0], orig_im_size[1]
+ masks = F.interpolate(masks, size=(h, w), mode="bilinear", align_corners=False)
+ return masks
+
+ def select_masks(
+ self, masks: torch.Tensor, iou_preds: torch.Tensor, num_points: int
+ ) -> Tuple[torch.Tensor, torch.Tensor]:
+ # Determine if we should return the multiclick mask or not from the number of points.
+ # The reweighting is used to avoid control flow.
+ score_reweight = torch.tensor(
+ [[1000] + [0] * (self.model.mask_decoder.num_mask_tokens - 1)]
+ ).to(iou_preds.device)
+ score = iou_preds + (num_points - 2.5) * score_reweight
+ best_idx = torch.argmax(score, dim=1)
+ masks = masks[torch.arange(masks.shape[0]), best_idx, :, :].unsqueeze(1)
+ iou_preds = iou_preds[torch.arange(masks.shape[0]), best_idx].unsqueeze(1)
+
+ return masks, iou_preds
+
+ @torch.no_grad()
+ def forward(
+ self,
+ image_embeddings: torch.Tensor,
+ point_coords: torch.Tensor,
+ point_labels: torch.Tensor,
+ mask_input: torch.Tensor,
+ has_mask_input: torch.Tensor,
+ orig_im_size: torch.Tensor,
+ ):
+ sparse_embedding = self._embed_points(point_coords, point_labels)
+ dense_embedding = self._embed_masks(mask_input, has_mask_input)
+
+ masks, scores = self.model.mask_decoder.predict_masks(
+ image_embeddings=image_embeddings,
+ image_pe=self.model.prompt_encoder.get_dense_pe(),
+ sparse_prompt_embeddings=sparse_embedding,
+ dense_prompt_embeddings=dense_embedding,
+ )
+
+ if self.use_stability_score:
+ scores = calculate_stability_score(
+ masks, self.model.mask_threshold, self.stability_score_offset
+ )
+
+ if self.return_single_mask:
+ masks, scores = self.select_masks(masks, scores, point_coords.shape[1])
+
+ upscaled_masks = self.mask_postprocessing(masks, orig_im_size)
+
+ if self.return_extra_metrics:
+ stability_scores = calculate_stability_score(
+ upscaled_masks, self.model.mask_threshold, self.stability_score_offset
+ )
+ areas = (upscaled_masks > self.model.mask_threshold).sum(-1).sum(-1)
+ return upscaled_masks, scores, stability_scores, areas, masks
+
+ return upscaled_masks, scores, masks
diff --git a/osrt/sam/utils/transforms.py b/osrt/sam/utils/transforms.py
new file mode 100644
index 0000000000000000000000000000000000000000..e801bdf1a342f509c0a32d92b032ad369f0e2908
--- /dev/null
+++ b/osrt/sam/utils/transforms.py
@@ -0,0 +1,105 @@
+# 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.nn import functional as F
+from torchvision.transforms.functional import resize, to_pil_image # type: ignore
+
+from copy import deepcopy
+from typing import Tuple
+
+
+class ResizeLongestSide:
+ """
+ Resizes images to the longest side 'target_length', as well as provides
+ methods for resizing coordinates and boxes. Provides methods for
+ transforming both numpy array and batched torch tensors.
+ """
+
+ def __init__(self, target_length: int) -> None:
+ self.target_length = target_length
+
+ def apply_image(self, image: np.ndarray) -> np.ndarray:
+ """
+ Expects a numpy array with shape HxWxC in uint8 format.
+ """
+ target_size = self.get_preprocess_shape(image.shape[0], image.shape[1], self.target_length)
+ # TODO : change this part to accept Tensors
+ if torch.is_tensor(image):
+ return np.array(resize(to_pil_image(image.permute(2, 0, 1)), target_size))
+ return np.array(resize(to_pil_image(image), target_size))
+
+ def apply_coords(self, coords: np.ndarray, original_size: Tuple[int, ...]) -> np.ndarray:
+ """
+ Expects a numpy array of length 2 in the final dimension. Requires the
+ original image size in (H, W) format.
+ """
+ old_h, old_w = original_size
+ new_h, new_w = self.get_preprocess_shape(
+ original_size[0], original_size[1], self.target_length
+ )
+ coords = deepcopy(coords).astype(float)
+ coords[..., 0] = coords[..., 0] * (new_w / old_w)
+ coords[..., 1] = coords[..., 1] * (new_h / old_h)
+ return coords
+
+ def apply_boxes(self, boxes: np.ndarray, original_size: Tuple[int, ...]) -> np.ndarray:
+ """
+ Expects a numpy array shape Bx4. Requires the original image size
+ in (H, W) format.
+ """
+ boxes = self.apply_coords(boxes.reshape(-1, 2, 2), original_size)
+ return boxes.reshape(-1, 4)
+
+ def apply_image_torch(self, image: torch.Tensor) -> torch.Tensor:
+ """
+ Expects batched images with shape BxCxHxW and float format. This
+ transformation may not exactly match apply_image. apply_image is
+ the transformation expected by the model.
+ """
+ # Expects an image in BCHW format. May not exactly match apply_image.
+ target_size = self.get_preprocess_shape(image.shape[2], image.shape[3], self.target_length)
+ return F.interpolate(
+ image, target_size, mode="bilinear", align_corners=False, antialias=True
+ )
+
+ def apply_coords_torch(
+ self, coords: torch.Tensor, original_size: Tuple[int, ...]
+ ) -> torch.Tensor:
+ """
+ Expects a torch tensor with length 2 in the last dimension. Requires the
+ original image size in (H, W) format.
+ """
+ old_h, old_w = original_size
+ new_h, new_w = self.get_preprocess_shape(
+ original_size[0], original_size[1], self.target_length
+ )
+ coords = deepcopy(coords).to(torch.float)
+ coords[..., 0] = coords[..., 0] * (new_w / old_w)
+ coords[..., 1] = coords[..., 1] * (new_h / old_h)
+ return coords
+
+ def apply_boxes_torch(
+ self, boxes: torch.Tensor, original_size: Tuple[int, ...]
+ ) -> torch.Tensor:
+ """
+ Expects a torch tensor with shape Bx4. Requires the original image
+ size in (H, W) format.
+ """
+ boxes = self.apply_coords_torch(boxes.reshape(-1, 2, 2), original_size)
+ return boxes.reshape(-1, 4)
+
+ @staticmethod
+ def get_preprocess_shape(oldh: int, oldw: int, long_side_length: int) -> Tuple[int, int]:
+ """
+ Compute the output size given input size and target long side length.
+ """
+ scale = long_side_length * 1.0 / max(oldh, oldw)
+ newh, neww = oldh * scale, oldw * scale
+ neww = int(neww + 0.5)
+ newh = int(newh + 0.5)
+ return (newh, neww)
diff --git a/osrt/utils/visualize.py b/osrt/utils/visualize.py
index 2bdf364d79ca3359905adc2a8699462491db0265..53c59485edf7584ef3ef822b94903d7bd9f49f20 100644
--- a/osrt/utils/visualize.py
+++ b/osrt/utils/visualize.py
@@ -29,7 +29,7 @@ def get_clustering_colors(num_colors):
colors = [(0., 0., 0.)]
for i in range(num_colors):
colors.append(hsv_to_rgb(i / num_colors, 0.45, 0.8))
- colors = np.array(colors.cpu())
+ colors = np.array(colors)
return colors
diff --git a/runs/clevr3d/osrt/config_ds.json b/runs/clevr3d/osrt/config_ds.json
index 9e96b5ef35f5de375fccb63cb221a0fe6bf3c9b4..f25876b8556371265b538fef5604b6f121498842 100644
--- a/runs/clevr3d/osrt/config_ds.json
+++ b/runs/clevr3d/osrt/config_ds.json
@@ -31,17 +31,23 @@
"max_it": 333000000,
"decay_it": 4000000,
"lr_warmup": 5000,
- "precision": "32"
+ "precision": "16-mixed"
},
"strategy": {
"deepspeed": {
+ "fp16": {
+ "enabled": true,
+ "auto_cast": true
+ },
"zero_optimization": {
- "stage": 2,
- "contiguous_gradients": true,
+ "stage": 3,
"overlap_comm": true,
"allgather_bucket_size": 2e8,
"reduce_bucket_size": 2e8
},
+ "activation_checkpointing": {
+ "partition_activations": true
+ },
"zero_allow_untested_optimizer": true
}
}
diff --git a/segment-anything b/segment-anything
deleted file mode 160000
index f7b29ba9df1496489af8c71a4bdabed7e8b017b1..0000000000000000000000000000000000000000
--- a/segment-anything
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit f7b29ba9df1496489af8c71a4bdabed7e8b017b1