Commit
·
373b8b8
1
Parent(s):
8f0bd34
dump
Browse files- config.yaml +15 -0
- loss.py +50 -0
- mae_modules.py +272 -0
- mae_utils.py +64 -0
- masking.py +46 -0
- vit.py +284 -0
config.yaml
ADDED
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loss:
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_target_: torch.nn.MSELoss # combine with fourier loss weighted at 0.01 mixing factor for best results
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reduction: none
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optimizer:
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_target_: timm.optim.lion.Lion
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_partial_: true
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lr: *lr 1e-4 # 1e-4 for <= ViT-B, and 3e-5 for ViT-L
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weight_decay: 0.05
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betas: [0.9, 0.95]
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lr_scheduler:
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_target_: torch.optim.lr_scheduler.OneCycleLR
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_partial_: true
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max_lr: @lr
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pct_start: 0.1
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anneal_strategy: cos
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loss.py
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import torch
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import torch.nn as nn
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class FourierLoss(nn.Module):
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def __init__(
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self,
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use_l1_loss: bool = True,
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num_multimodal_modalities: int = 1, # set to 1 for vanilla MAE, 6 for channel-agnostic MAE
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) -> None:
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"""
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Fourier transform loss is only sound when using L1 or L2 loss to compare the frequency domains
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between the images / their radial histograms.
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We will always set `reduction="none"` and enforce that the computation of any reductions from the
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output of this loss be managed by the model under question.
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"""
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super().__init__()
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self.loss = nn.L1Loss(reduction="none") if use_l1_loss else nn.MSELoss(reduction="none")
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self.num_modalities = num_multimodal_modalities
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def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
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# input = reconstructed image, target = original image
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# flattened images from MAE are (B, H*W, C), so, here we convert to B x C x H x W (note we assume H == W)
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flattened_images = len(input.shape) == len(target.shape) == 3
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if flattened_images:
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B, H_W, C = input.shape
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H_W = H_W // self.num_modalities
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four_d_shape = (B, C * self.num_modalities, int(H_W**0.5), int(H_W**0.5))
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input = input.view(*four_d_shape)
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target = target.view(*four_d_shape)
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else:
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B, C, h, w = input.shape
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H_W = h * w
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if len(input.shape) != len(target.shape) != 4:
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raise ValueError(f"Invalid input shape: got {input.shape} and {target.shape}.")
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fft_reconstructed = torch.fft.fft2(input)
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fft_original = torch.fft.fft2(target)
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magnitude_reconstructed = torch.abs(fft_reconstructed)
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magnitude_original = torch.abs(fft_original)
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loss_tensor: torch.Tensor = self.loss(magnitude_reconstructed, magnitude_original)
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if flattened_images and not self.num_bins: # then output loss should be reshaped
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loss_tensor = loss_tensor.reshape(B, H_W * self.num_modalities, C)
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return loss_tensor
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mae_modules.py
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from functools import partial
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| 2 |
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from typing import Tuple, Union
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| 3 |
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| 4 |
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import torch
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| 5 |
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import torch.nn as nn
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| 6 |
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from timm.models.helpers import checkpoint_seq
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| 7 |
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from timm.models.vision_transformer import Block, Mlp, VisionTransformer
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| 8 |
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| 9 |
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from .masking import transformer_random_masking
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| 10 |
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from .vit import channel_agnostic_vit
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| 11 |
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| 12 |
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# If interested in training new MAEs, combine an encoder and decoder into a new module, and you should
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| 13 |
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# leverage the flattening and unflattening utilities as needed from mae_utils.py.
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| 14 |
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# Be sure to use an encoder-decoder Linear projection layer to match encoder dims with decoder dimensions.
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| 15 |
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# As described in the paper, images are self-standardized at the start.
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| 16 |
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| 17 |
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class SelfStandardize(nn.Module):
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| 19 |
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def __init__(self) -> None:
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| 20 |
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super().__init__()
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| 21 |
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self.self_standardize = nn.LazyInstanceNorm2d(
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| 22 |
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affine=False, track_running_stats=False
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)
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| 24 |
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| 25 |
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def forward(self, pixels: torch.Tensor) -> torch.Tensor:
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| 26 |
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x = pixels.float() / 255.0
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| 27 |
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return self.self_standardize(x)
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| 28 |
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| 29 |
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| 30 |
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class MAEEncoder(nn.Module):
|
| 31 |
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def __init__(
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| 32 |
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self,
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vit_backbone: VisionTransformer,
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max_in_chans: int = 6,
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| 35 |
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channel_agnostic: bool = False,
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| 36 |
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) -> None:
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| 37 |
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super().__init__()
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| 38 |
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if channel_agnostic:
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| 39 |
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self.vit_backbone = channel_agnostic_vit(
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| 40 |
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vit_backbone, max_in_chans=max_in_chans
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| 41 |
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)
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| 42 |
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else:
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| 43 |
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self.vit_backbone = vit_backbone
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| 44 |
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self.max_in_chans = max_in_chans
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| 45 |
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self.channel_agnostic = channel_agnostic
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| 46 |
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| 47 |
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@property
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| 48 |
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def embed_dim(self) -> int:
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| 49 |
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return int(self.vit_backbone.embed_dim)
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| 50 |
+
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| 51 |
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def forward(self, x: torch.Tensor) -> torch.Tensor:
|
| 52 |
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x = self.vit_backbone.forward_features(x)
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| 53 |
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x = self.vit_backbone.forward_head(x)
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| 54 |
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return x # type: ignore[no-any-return]
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| 55 |
+
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| 56 |
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def forward_masked(
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| 57 |
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self,
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| 58 |
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x: torch.Tensor,
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| 59 |
+
mask_ratio: float,
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| 60 |
+
constant_noise: Union[torch.Tensor, None] = None,
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| 61 |
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) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
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| 62 |
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x = self.vit_backbone.patch_embed(x)
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| 63 |
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x = self.vit_backbone._pos_embed(x) # adds class token
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| 64 |
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x_ = x[:, 1:, :] # no class token
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| 65 |
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x_, mask, ind_restore = transformer_random_masking(
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| 66 |
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x_, mask_ratio, constant_noise
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)
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| 68 |
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x = torch.cat([x[:, :1, :], x_], dim=1) # add class token
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| 69 |
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x = self.vit_backbone.norm_pre(x)
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| 70 |
+
|
| 71 |
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if self.vit_backbone.grad_checkpointing and not torch.jit.is_scripting():
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| 72 |
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x = checkpoint_seq(self.vit_backbone.blocks, x)
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| 73 |
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else:
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| 74 |
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x = self.vit_backbone.blocks(x)
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| 75 |
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x = self.vit_backbone.norm(x)
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| 76 |
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return x, mask, ind_restore
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| 77 |
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|
| 78 |
+
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| 79 |
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class MAEDecoder(nn.Module):
|
| 80 |
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def __init__(
|
| 81 |
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self,
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| 82 |
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embed_dim: int = 512,
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| 83 |
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depth: int = 8,
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| 84 |
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num_heads: int = 16,
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| 85 |
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mlp_ratio: float = 4,
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| 86 |
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qkv_bias: bool = True,
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| 87 |
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norm_layer: nn.Module = partial(nn.LayerNorm, eps=1e-6), # type: ignore[assignment]
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| 88 |
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) -> None:
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| 89 |
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super().__init__()
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| 90 |
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self.embed_dim = embed_dim
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| 91 |
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self.pos_embeddings = None # to be overwritten by MAE class
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| 92 |
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self.mask_token = nn.Parameter(torch.zeros(1, 1, embed_dim))
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| 93 |
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self.blocks = nn.Sequential(
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| 94 |
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*[
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| 95 |
+
Block(
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| 96 |
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embed_dim,
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| 97 |
+
num_heads,
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| 98 |
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mlp_ratio,
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| 99 |
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qkv_bias=qkv_bias,
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| 100 |
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norm_layer=norm_layer,
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| 101 |
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)
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| 102 |
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for i in range(depth)
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| 103 |
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]
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| 104 |
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)
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| 105 |
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self.norm = norm_layer(embed_dim)
|
| 106 |
+
|
| 107 |
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def forward(self, x: torch.Tensor) -> torch.Tensor:
|
| 108 |
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x = x + self.pos_embeddings
|
| 109 |
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x = self.blocks(x)
|
| 110 |
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x = self.norm(x)
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| 111 |
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return x # type: ignore[no-any-return]
|
| 112 |
+
|
| 113 |
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def forward_masked(
|
| 114 |
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self, x: torch.Tensor, ind_restore: torch.Tensor
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| 115 |
+
) -> torch.Tensor:
|
| 116 |
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mask_tokens = self.mask_token.repeat(
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| 117 |
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x.shape[0], ind_restore.shape[1] + 1 - x.shape[1], 1
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| 118 |
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)
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| 119 |
+
x_ = torch.cat([x[:, 1:, :], mask_tokens], dim=1) # remove class token
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| 120 |
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x_ = torch.gather(
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| 121 |
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x_, dim=1, index=ind_restore.unsqueeze(-1).repeat(1, 1, x.shape[2])
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| 122 |
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) # unshuffle
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| 123 |
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x = torch.cat([x[:, :1, :], x_], dim=1) # add class token
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| 124 |
+
|
| 125 |
+
x = x + self.pos_embeddings
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| 126 |
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x = self.blocks(x)
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| 127 |
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x = self.norm(x)
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| 128 |
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return x # type: ignore[no-any-return]
|
| 129 |
+
|
| 130 |
+
|
| 131 |
+
class CrossAttention(nn.Module):
|
| 132 |
+
def __init__(
|
| 133 |
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self, embed_dim, num_heads=8, qkv_bias=False, attn_drop=0.0, proj_drop=0.0
|
| 134 |
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):
|
| 135 |
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super().__init__()
|
| 136 |
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self.num_heads = num_heads
|
| 137 |
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head_dim = embed_dim // num_heads
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| 138 |
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self.scale = head_dim**-0.5
|
| 139 |
+
|
| 140 |
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self.q = nn.Linear(embed_dim, embed_dim, bias=qkv_bias)
|
| 141 |
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self.kv = nn.Linear(embed_dim, embed_dim * 2, bias=qkv_bias)
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| 142 |
+
|
| 143 |
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self.attn_drop = nn.Dropout(attn_drop)
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| 144 |
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self.proj = nn.Linear(embed_dim, embed_dim)
|
| 145 |
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self.proj_drop = nn.Dropout(proj_drop)
|
| 146 |
+
|
| 147 |
+
def forward(self, x, context):
|
| 148 |
+
B, N, C = x.shape
|
| 149 |
+
_, M, _ = context.shape
|
| 150 |
+
|
| 151 |
+
q = (
|
| 152 |
+
self.q(x)
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| 153 |
+
.reshape(B, N, self.num_heads, C // self.num_heads)
|
| 154 |
+
.permute(0, 2, 1, 3)
|
| 155 |
+
)
|
| 156 |
+
kv = (
|
| 157 |
+
self.kv(context)
|
| 158 |
+
.reshape(B, M, 2, self.num_heads, C // self.num_heads)
|
| 159 |
+
.permute(2, 0, 3, 1, 4)
|
| 160 |
+
)
|
| 161 |
+
k, v = kv[0], kv[1]
|
| 162 |
+
|
| 163 |
+
attn = (q @ k.transpose(-2, -1)) * self.scale
|
| 164 |
+
attn = attn.softmax(dim=-1)
|
| 165 |
+
attn = self.attn_drop(attn)
|
| 166 |
+
|
| 167 |
+
x = (attn @ v).transpose(1, 2).reshape(B, N, -1)
|
| 168 |
+
x = self.proj(x)
|
| 169 |
+
x = self.proj_drop(x)
|
| 170 |
+
return x
|
| 171 |
+
|
| 172 |
+
|
| 173 |
+
class CAMAEDecoder(nn.Module):
|
| 174 |
+
def __init__(
|
| 175 |
+
self,
|
| 176 |
+
num_modalities: int = 6,
|
| 177 |
+
tokens_per_modality: int = 256,
|
| 178 |
+
embed_dim: int = 256,
|
| 179 |
+
depth: int = 2,
|
| 180 |
+
num_heads: int = 16,
|
| 181 |
+
mlp_ratio: float = 4,
|
| 182 |
+
qkv_bias: bool = True,
|
| 183 |
+
norm_layer: nn.Module = partial(nn.LayerNorm, eps=1e-6), # type: ignore[assignment]
|
| 184 |
+
) -> None:
|
| 185 |
+
super().__init__()
|
| 186 |
+
self.num_modalities = num_modalities
|
| 187 |
+
self.tokens_per_modality = tokens_per_modality
|
| 188 |
+
self.embed_dim = embed_dim
|
| 189 |
+
self.pos_embeddings = None # to be overwritten by MAE class
|
| 190 |
+
self.mask_token = nn.Parameter(torch.zeros(1, 1, embed_dim))
|
| 191 |
+
self.placeholder = nn.Parameter(
|
| 192 |
+
torch.zeros(1, 1, embed_dim), requires_grad=False
|
| 193 |
+
)
|
| 194 |
+
self.modality_tokens = nn.ParameterList(
|
| 195 |
+
[
|
| 196 |
+
nn.Parameter(torch.zeros(1, 1, self.embed_dim))
|
| 197 |
+
for modality in range(self.num_modalities)
|
| 198 |
+
]
|
| 199 |
+
)
|
| 200 |
+
|
| 201 |
+
self.cross_attention = CrossAttention(embed_dim=self.embed_dim)
|
| 202 |
+
self.mlp = Mlp(self.embed_dim, hidden_features=int(self.embed_dim * mlp_ratio))
|
| 203 |
+
|
| 204 |
+
self.decoders = nn.ModuleList(
|
| 205 |
+
[
|
| 206 |
+
nn.Sequential(
|
| 207 |
+
*[
|
| 208 |
+
Block(
|
| 209 |
+
embed_dim,
|
| 210 |
+
num_heads,
|
| 211 |
+
mlp_ratio,
|
| 212 |
+
qkv_bias=qkv_bias,
|
| 213 |
+
norm_layer=norm_layer,
|
| 214 |
+
)
|
| 215 |
+
for i in range(depth)
|
| 216 |
+
]
|
| 217 |
+
)
|
| 218 |
+
for modality in range(self.num_modalities)
|
| 219 |
+
]
|
| 220 |
+
)
|
| 221 |
+
# self.norm = norm_layer(embed_dim) # we decided to drop the last layer norm
|
| 222 |
+
self.context_norm = norm_layer(embed_dim)
|
| 223 |
+
self.query_norm = norm_layer(embed_dim)
|
| 224 |
+
self.out_norm = norm_layer(embed_dim)
|
| 225 |
+
|
| 226 |
+
def forward(self, x: torch.Tensor) -> torch.Tensor:
|
| 227 |
+
x_m_s = []
|
| 228 |
+
|
| 229 |
+
modality_tokens_concat = torch.cat(
|
| 230 |
+
[
|
| 231 |
+
self.placeholder,
|
| 232 |
+
] # placeholder for class token
|
| 233 |
+
+ [
|
| 234 |
+
m_t.repeat(1, self.tokens_per_modality, 1)
|
| 235 |
+
for m_t in self.modality_tokens
|
| 236 |
+
],
|
| 237 |
+
dim=1,
|
| 238 |
+
)
|
| 239 |
+
|
| 240 |
+
x = (
|
| 241 |
+
x + self.pos_embeddings + modality_tokens_concat
|
| 242 |
+
) # add pos and tiled modality tokens
|
| 243 |
+
x_ = x[:, 1:, :] # no class token
|
| 244 |
+
for m, decoder in enumerate(
|
| 245 |
+
self.decoders
|
| 246 |
+
): # iterate through modalities and decoders
|
| 247 |
+
x_m = x_[
|
| 248 |
+
:, m * self.tokens_per_modality : (m + 1) * self.tokens_per_modality, :
|
| 249 |
+
]
|
| 250 |
+
x_m = self.cross_attention(self.query_norm(x_m), self.context_norm(x_))
|
| 251 |
+
x_m = x_m + self.mlp(self.out_norm(x_m))
|
| 252 |
+
x_m = decoder(x_m)
|
| 253 |
+
x_m_s.append(x_m)
|
| 254 |
+
x_m_s = torch.cat(x_m_s, dim=1) # concat all tokens
|
| 255 |
+
# x_m_s = self.norm(x_m_s) # we decided to drop the last layer norm
|
| 256 |
+
x_m_s = torch.cat([x[:, :1, :], x_m_s], dim=1) # add back class token
|
| 257 |
+
|
| 258 |
+
return x_m_s
|
| 259 |
+
|
| 260 |
+
def forward_masked(
|
| 261 |
+
self, x: torch.Tensor, ind_restore: torch.Tensor
|
| 262 |
+
) -> torch.Tensor:
|
| 263 |
+
mask_tokens = self.mask_token.repeat(
|
| 264 |
+
x.shape[0], ind_restore.shape[1] + 1 - x.shape[1], 1
|
| 265 |
+
)
|
| 266 |
+
x_ = torch.cat([x[:, 1:, :], mask_tokens], dim=1) # remove class token
|
| 267 |
+
x_ = torch.gather(
|
| 268 |
+
x_, dim=1, index=ind_restore.unsqueeze(-1).repeat(1, 1, x.shape[2])
|
| 269 |
+
) # unshuffle
|
| 270 |
+
x = torch.cat([x[:, :1, :], x_], dim=1) # add class token
|
| 271 |
+
x = self.forward(x)
|
| 272 |
+
return x
|
mae_utils.py
ADDED
|
@@ -0,0 +1,64 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import math
|
| 2 |
+
|
| 3 |
+
import torch
|
| 4 |
+
|
| 5 |
+
|
| 6 |
+
def flatten_images(img: torch.Tensor, patch_size: int, channel_agnostic: bool = False) -> torch.Tensor:
|
| 7 |
+
"""
|
| 8 |
+
Flattens 2D images into tokens with the same pixel values
|
| 9 |
+
|
| 10 |
+
Parameters
|
| 11 |
+
----------
|
| 12 |
+
img : input image tensor (N, C, H, W)
|
| 13 |
+
|
| 14 |
+
Returns
|
| 15 |
+
-------
|
| 16 |
+
flattened_img: flattened image tensor (N, L, patch_size**2 * C)
|
| 17 |
+
"""
|
| 18 |
+
|
| 19 |
+
if (img.shape[2] != img.shape[3]) or (img.shape[2] % patch_size != 0):
|
| 20 |
+
raise ValueError("image H must equal image W and be divisible by patch_size")
|
| 21 |
+
in_chans = img.shape[1]
|
| 22 |
+
|
| 23 |
+
h = w = int(img.shape[2] // patch_size)
|
| 24 |
+
x = img.reshape(shape=(img.shape[0], in_chans, h, patch_size, w, patch_size))
|
| 25 |
+
|
| 26 |
+
if channel_agnostic:
|
| 27 |
+
x = torch.permute(x, (0, 1, 2, 4, 3, 5)) # NCHPWQ -> NCHWPQ
|
| 28 |
+
x = x.reshape(shape=(img.shape[0], in_chans * h * w, int(patch_size**2)))
|
| 29 |
+
else:
|
| 30 |
+
x = torch.permute(x, (0, 2, 4, 3, 5, 1)) # NCHPWQ -> NHWPQC
|
| 31 |
+
x = x.reshape(shape=(img.shape[0], h * w, int(patch_size**2 * in_chans)))
|
| 32 |
+
return x
|
| 33 |
+
|
| 34 |
+
|
| 35 |
+
def unflatten_tokens(
|
| 36 |
+
tokens: torch.Tensor, patch_size: int, num_modalities: int = 1, channel_agnostic: bool = False
|
| 37 |
+
) -> torch.Tensor:
|
| 38 |
+
"""
|
| 39 |
+
Unflattens tokens (N,L,patch_size**2 * C) into image tensor (N,C,H,W) with the pixel values
|
| 40 |
+
|
| 41 |
+
Parameters
|
| 42 |
+
----------
|
| 43 |
+
tokens : input token tensor (N,L,patch_size**2 * C)
|
| 44 |
+
|
| 45 |
+
Returns
|
| 46 |
+
-------
|
| 47 |
+
img: image tensor (N,C,H,W)
|
| 48 |
+
"""
|
| 49 |
+
if num_modalities > 1 and not channel_agnostic:
|
| 50 |
+
raise ValueError("Multiple modalities requires channel agnostic unflattening.")
|
| 51 |
+
|
| 52 |
+
h = w = int(math.sqrt(tokens.shape[1] // num_modalities))
|
| 53 |
+
if h * w != (tokens.shape[1] // num_modalities):
|
| 54 |
+
raise ValueError("sqrt of number of tokens not integer")
|
| 55 |
+
|
| 56 |
+
if channel_agnostic:
|
| 57 |
+
x = tokens.reshape(shape=(tokens.shape[0], -1, h, w, patch_size, patch_size))
|
| 58 |
+
x = torch.permute(x, (0, 1, 2, 4, 3, 5)) # NCHWPQ -> NCHPWQ
|
| 59 |
+
else:
|
| 60 |
+
x = tokens.reshape(shape=(tokens.shape[0], h, w, patch_size, patch_size, -1))
|
| 61 |
+
x = torch.permute(x, (0, 5, 1, 3, 2, 4)) # NHWPQC -> NCHPWQ
|
| 62 |
+
img = x.reshape(shape=(x.shape[0], -1, h * patch_size, h * patch_size))
|
| 63 |
+
|
| 64 |
+
return img
|
masking.py
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from typing import Tuple, Union
|
| 2 |
+
|
| 3 |
+
import torch
|
| 4 |
+
|
| 5 |
+
|
| 6 |
+
def transformer_random_masking(
|
| 7 |
+
x: torch.Tensor, mask_ratio: float, constant_noise: Union[torch.Tensor, None] = None
|
| 8 |
+
) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
|
| 9 |
+
"""
|
| 10 |
+
Random mask patches per sample
|
| 11 |
+
|
| 12 |
+
Parameters
|
| 13 |
+
----------
|
| 14 |
+
x : token tensor (N, L, D)
|
| 15 |
+
mask_ratio: float - ratio of image to mask
|
| 16 |
+
constant_noise: None, if provided should be a tensor of shape (N, L) to produce consistent masks
|
| 17 |
+
|
| 18 |
+
Returns
|
| 19 |
+
-------
|
| 20 |
+
x_masked : sub-sampled version of x ( int(mask_ratio * N), L, D)
|
| 21 |
+
mask : binary mask indicated masked tokens (1 where masked) (N, L)
|
| 22 |
+
ind_restore : locations of masked tokens, needed for decoder
|
| 23 |
+
"""
|
| 24 |
+
|
| 25 |
+
N, L, D = x.shape # batch, length, dim
|
| 26 |
+
len_keep = int(L * (1 - mask_ratio))
|
| 27 |
+
|
| 28 |
+
# use random noise to generate batch based random masks
|
| 29 |
+
if constant_noise is not None:
|
| 30 |
+
noise = constant_noise
|
| 31 |
+
else:
|
| 32 |
+
noise = torch.rand(N, L, device=x.device)
|
| 33 |
+
|
| 34 |
+
shuffled_tokens = torch.argsort(noise, dim=1) # shuffled index
|
| 35 |
+
ind_restore = torch.argsort(shuffled_tokens, dim=1) # unshuffled index
|
| 36 |
+
|
| 37 |
+
# get masked input
|
| 38 |
+
tokens_to_keep = shuffled_tokens[:, :len_keep] # keep the first len_keep indices
|
| 39 |
+
x_masked = torch.gather(x, dim=1, index=tokens_to_keep.unsqueeze(-1).repeat(1, 1, D))
|
| 40 |
+
|
| 41 |
+
# get binary mask used for loss masking: 0 is keep, 1 is remove
|
| 42 |
+
mask = torch.ones([N, L], device=x.device)
|
| 43 |
+
mask[:, :len_keep] = 0
|
| 44 |
+
mask = torch.gather(mask, dim=1, index=ind_restore) # unshuffle to get the binary mask
|
| 45 |
+
|
| 46 |
+
return x_masked, mask, ind_restore
|
vit.py
ADDED
|
@@ -0,0 +1,284 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
|
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|
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|
|
|
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|
| 1 |
+
import timm.models.vision_transformer as vit
|
| 2 |
+
import torch
|
| 3 |
+
|
| 4 |
+
|
| 5 |
+
def generate_2d_sincos_pos_embeddings(
|
| 6 |
+
embedding_dim: int, length: int, scale: float = 10000.0, use_class_token: bool = True, num_modality: int = 1
|
| 7 |
+
) -> torch.nn.Parameter:
|
| 8 |
+
"""
|
| 9 |
+
Generate 2Dimensional sin/cosine positional embeddings
|
| 10 |
+
|
| 11 |
+
Parameters
|
| 12 |
+
----------
|
| 13 |
+
embedding_dim : int
|
| 14 |
+
embedding dimension used in vit
|
| 15 |
+
length : int
|
| 16 |
+
number of tokens along height or width of image after patching (assuming square)
|
| 17 |
+
scale : float
|
| 18 |
+
scale for sin/cos functions
|
| 19 |
+
use_class_token : bool
|
| 20 |
+
True - add zero vector to be added to class_token, False - no vector added
|
| 21 |
+
num_modality: number of modalities. If 0, a single modality is assumed.
|
| 22 |
+
Otherwise one-hot modality encoding is added and sincos encoding size is appropriately reduced.
|
| 23 |
+
|
| 24 |
+
Returns
|
| 25 |
+
-------
|
| 26 |
+
positional_encoding : torch.Tensor
|
| 27 |
+
positional encoding to add to vit patch encodings
|
| 28 |
+
[num_modality*length*length, embedding_dim] or [1+num_modality*length*length, embedding_dim]
|
| 29 |
+
(w/ or w/o cls_token)
|
| 30 |
+
"""
|
| 31 |
+
|
| 32 |
+
linear_positions = torch.arange(length, dtype=torch.float32)
|
| 33 |
+
height_mesh, width_mesh = torch.meshgrid(linear_positions, linear_positions, indexing="ij")
|
| 34 |
+
positional_dim = embedding_dim // 4 # accomodate h and w x cos and sin embeddings
|
| 35 |
+
positional_weights = torch.arange(positional_dim, dtype=torch.float32) / positional_dim
|
| 36 |
+
positional_weights = 1.0 / (scale**positional_weights)
|
| 37 |
+
|
| 38 |
+
height_weights = torch.outer(height_mesh.flatten(), positional_weights)
|
| 39 |
+
width_weights = torch.outer(width_mesh.flatten(), positional_weights)
|
| 40 |
+
|
| 41 |
+
positional_encoding = torch.cat(
|
| 42 |
+
[torch.sin(height_weights), torch.cos(height_weights), torch.sin(width_weights), torch.cos(width_weights)],
|
| 43 |
+
dim=1,
|
| 44 |
+
)[None, :, :]
|
| 45 |
+
|
| 46 |
+
# repeat positional encoding for multiple channel modalities
|
| 47 |
+
positional_encoding = positional_encoding.repeat(1, num_modality, 1)
|
| 48 |
+
|
| 49 |
+
if use_class_token:
|
| 50 |
+
class_token = torch.zeros([1, 1, embedding_dim], dtype=torch.float32)
|
| 51 |
+
positional_encoding = torch.cat([class_token, positional_encoding], dim=1)
|
| 52 |
+
|
| 53 |
+
positional_encoding = torch.nn.Parameter(positional_encoding, requires_grad=False)
|
| 54 |
+
|
| 55 |
+
return positional_encoding
|
| 56 |
+
|
| 57 |
+
|
| 58 |
+
class ChannelAgnosticPatchEmbed(vit.PatchEmbed): # type: ignore[misc]
|
| 59 |
+
def __init__(
|
| 60 |
+
self,
|
| 61 |
+
img_size: int,
|
| 62 |
+
patch_size: int,
|
| 63 |
+
embed_dim: int,
|
| 64 |
+
bias: bool = True,
|
| 65 |
+
) -> None:
|
| 66 |
+
super().__init__(
|
| 67 |
+
img_size=img_size,
|
| 68 |
+
patch_size=patch_size,
|
| 69 |
+
in_chans=1, # in_chans is used by self.proj, which we override anyway
|
| 70 |
+
embed_dim=embed_dim,
|
| 71 |
+
norm_layer=None,
|
| 72 |
+
flatten=False,
|
| 73 |
+
bias=bias,
|
| 74 |
+
)
|
| 75 |
+
# channel-agnostic MAE has a single projection for all chans
|
| 76 |
+
self.proj = torch.nn.Conv2d(1, embed_dim, kernel_size=patch_size, stride=patch_size, bias=bias)
|
| 77 |
+
|
| 78 |
+
def forward(self, x: torch.Tensor) -> torch.Tensor:
|
| 79 |
+
in_chans = x.shape[1]
|
| 80 |
+
x = torch.stack([self.proj(x[:, i : i + 1]) for i in range(in_chans)], dim=2) # single project for all chans
|
| 81 |
+
x = x.flatten(2).transpose(1, 2) # BCMHW -> BNC
|
| 82 |
+
return x
|
| 83 |
+
|
| 84 |
+
|
| 85 |
+
class ChannelAgnosticViT(vit.VisionTransformer): # type: ignore[misc]
|
| 86 |
+
def _pos_embed(self, x: torch.Tensor) -> torch.Tensor:
|
| 87 |
+
# rewrite https://github.com/huggingface/pytorch-image-models/blob/main/timm/models/vision_transformer.py#L586
|
| 88 |
+
to_cat = []
|
| 89 |
+
if self.cls_token is not None:
|
| 90 |
+
to_cat.append(self.cls_token.expand(x.shape[0], -1, -1))
|
| 91 |
+
|
| 92 |
+
# TODO: upgrade timm to get access to register tokens
|
| 93 |
+
# if self.vit_backbone.reg_token is not None:
|
| 94 |
+
# to_cat.append(self.reg_token.expand(x.shape[0], -1, -1))
|
| 95 |
+
|
| 96 |
+
# MAIN DIFFERENCE with Timm - we DYNAMICALLY ADDING POS EMBEDDINGS based on shape of inputs
|
| 97 |
+
# this supports having CA-MAEs actually be channel-agnostic at inference time
|
| 98 |
+
if self.no_embed_class:
|
| 99 |
+
x = x + self.pos_embed[:, : x.shape[1]]
|
| 100 |
+
if to_cat:
|
| 101 |
+
x = torch.cat(to_cat + [x], dim=1)
|
| 102 |
+
else:
|
| 103 |
+
if to_cat:
|
| 104 |
+
x = torch.cat(to_cat + [x], dim=1)
|
| 105 |
+
x = x + self.pos_embed[:, : x.shape[1]]
|
| 106 |
+
return self.pos_drop(x) # type: ignore[no-any-return]
|
| 107 |
+
|
| 108 |
+
|
| 109 |
+
def channel_agnostic_vit(vit_backbone: vit.VisionTransformer, max_in_chans: int) -> vit.VisionTransformer:
|
| 110 |
+
# replace patch embedding with channel-agnostic version
|
| 111 |
+
vit_backbone.patch_embed = ChannelAgnosticPatchEmbed(
|
| 112 |
+
img_size=vit_backbone.patch_embed.img_size[0],
|
| 113 |
+
patch_size=vit_backbone.patch_embed.patch_size[0],
|
| 114 |
+
embed_dim=vit_backbone.embed_dim,
|
| 115 |
+
)
|
| 116 |
+
|
| 117 |
+
# replace positional embedding with channel-agnostic version
|
| 118 |
+
vit_backbone.pos_embed = generate_2d_sincos_pos_embeddings(
|
| 119 |
+
embedding_dim=vit_backbone.embed_dim,
|
| 120 |
+
length=vit_backbone.patch_embed.grid_size[0],
|
| 121 |
+
use_class_token=vit_backbone.cls_token is not None,
|
| 122 |
+
num_modality=max_in_chans,
|
| 123 |
+
)
|
| 124 |
+
|
| 125 |
+
# change the class to be ChannelAgnostic so that it actually uses the new _pos_embed
|
| 126 |
+
vit_backbone.__class__ = ChannelAgnosticViT
|
| 127 |
+
return vit_backbone
|
| 128 |
+
|
| 129 |
+
|
| 130 |
+
def sincos_positional_encoding_vit(
|
| 131 |
+
vit_backbone: vit.VisionTransformer, scale: float = 10000.0
|
| 132 |
+
) -> vit.VisionTransformer:
|
| 133 |
+
"""Attaches no-grad sin-cos positional embeddings to a pre-constructed ViT backbone model.
|
| 134 |
+
|
| 135 |
+
Parameters
|
| 136 |
+
----------
|
| 137 |
+
vit_backbone : timm.models.vision_transformer.VisionTransformer
|
| 138 |
+
the constructed vision transformer from timm
|
| 139 |
+
scale : float (default 10000.0)
|
| 140 |
+
hyperparameter for sincos positional embeddings, recommend keeping at 10,000
|
| 141 |
+
|
| 142 |
+
Returns
|
| 143 |
+
-------
|
| 144 |
+
timm.models.vision_transformer.VisionTransformer
|
| 145 |
+
the same ViT but with fixed no-grad positional encodings to add to vit patch encodings
|
| 146 |
+
"""
|
| 147 |
+
# length: number of tokens along height or width of image after patching (assuming square)
|
| 148 |
+
length = vit_backbone.patch_embed.img_size[0] // vit_backbone.patch_embed.patch_size[0]
|
| 149 |
+
pos_embeddings = generate_2d_sincos_pos_embeddings(
|
| 150 |
+
vit_backbone.embed_dim, length=length, scale=scale, use_class_token=vit_backbone.cls_token is not None
|
| 151 |
+
)
|
| 152 |
+
# note, if the model had weight_init == 'skip', this might get overwritten
|
| 153 |
+
vit_backbone.pos_embed = pos_embeddings
|
| 154 |
+
return vit_backbone
|
| 155 |
+
|
| 156 |
+
|
| 157 |
+
def vit_small_patch16_256(**kwargs):
|
| 158 |
+
default_kwargs = dict(
|
| 159 |
+
img_size=256,
|
| 160 |
+
in_chans=6,
|
| 161 |
+
num_classes=0,
|
| 162 |
+
fc_norm=None,
|
| 163 |
+
class_token=True,
|
| 164 |
+
drop_path_rate=0.1,
|
| 165 |
+
init_values=0.0001,
|
| 166 |
+
block_fn=vit.ParallelScalingBlock,
|
| 167 |
+
qkv_bias=False,
|
| 168 |
+
qk_norm=True,
|
| 169 |
+
)
|
| 170 |
+
for k, v in kwargs.items():
|
| 171 |
+
default_kwargs[k] = v
|
| 172 |
+
return vit.vit_small_patch16_224(**default_kwargs)
|
| 173 |
+
|
| 174 |
+
|
| 175 |
+
def vit_small_patch32_512(**kwargs):
|
| 176 |
+
default_kwargs = dict(
|
| 177 |
+
img_size=512,
|
| 178 |
+
in_chans=6,
|
| 179 |
+
num_classes=0,
|
| 180 |
+
fc_norm=None,
|
| 181 |
+
class_token=True,
|
| 182 |
+
drop_path_rate=0.1,
|
| 183 |
+
init_values=0.0001,
|
| 184 |
+
block_fn=vit.ParallelScalingBlock,
|
| 185 |
+
qkv_bias=False,
|
| 186 |
+
qk_norm=True,
|
| 187 |
+
)
|
| 188 |
+
for k, v in kwargs.items():
|
| 189 |
+
default_kwargs[k] = v
|
| 190 |
+
return vit.vit_small_patch32_384(**default_kwargs)
|
| 191 |
+
|
| 192 |
+
|
| 193 |
+
def vit_base_patch8_256(**kwargs):
|
| 194 |
+
default_kwargs = dict(
|
| 195 |
+
img_size=256,
|
| 196 |
+
in_chans=6,
|
| 197 |
+
num_classes=0,
|
| 198 |
+
fc_norm=None,
|
| 199 |
+
class_token=True,
|
| 200 |
+
drop_path_rate=0.1,
|
| 201 |
+
init_values=0.0001,
|
| 202 |
+
block_fn=vit.ParallelScalingBlock,
|
| 203 |
+
qkv_bias=False,
|
| 204 |
+
qk_norm=True,
|
| 205 |
+
)
|
| 206 |
+
for k, v in kwargs.items():
|
| 207 |
+
default_kwargs[k] = v
|
| 208 |
+
return vit.vit_base_patch8_224(**default_kwargs)
|
| 209 |
+
|
| 210 |
+
|
| 211 |
+
def vit_base_patch16_256(**kwargs):
|
| 212 |
+
default_kwargs = dict(
|
| 213 |
+
img_size=256,
|
| 214 |
+
in_chans=6,
|
| 215 |
+
num_classes=0,
|
| 216 |
+
fc_norm=None,
|
| 217 |
+
class_token=True,
|
| 218 |
+
drop_path_rate=0.1,
|
| 219 |
+
init_values=0.0001,
|
| 220 |
+
block_fn=vit.ParallelScalingBlock,
|
| 221 |
+
qkv_bias=False,
|
| 222 |
+
qk_norm=True,
|
| 223 |
+
)
|
| 224 |
+
for k, v in kwargs.items():
|
| 225 |
+
default_kwargs[k] = v
|
| 226 |
+
return vit.vit_base_patch16_224(**default_kwargs)
|
| 227 |
+
|
| 228 |
+
|
| 229 |
+
def vit_base_patch32_512(**kwargs):
|
| 230 |
+
default_kwargs = dict(
|
| 231 |
+
img_size=512,
|
| 232 |
+
in_chans=6,
|
| 233 |
+
num_classes=0,
|
| 234 |
+
fc_norm=None,
|
| 235 |
+
class_token=True,
|
| 236 |
+
drop_path_rate=0.1,
|
| 237 |
+
init_values=0.0001,
|
| 238 |
+
block_fn=vit.ParallelScalingBlock,
|
| 239 |
+
qkv_bias=False,
|
| 240 |
+
qk_norm=True,
|
| 241 |
+
)
|
| 242 |
+
for k, v in kwargs.items():
|
| 243 |
+
default_kwargs[k] = v
|
| 244 |
+
return vit.vit_base_patch32_384(**default_kwargs)
|
| 245 |
+
|
| 246 |
+
|
| 247 |
+
def vit_large_patch8_256(**kwargs):
|
| 248 |
+
default_kwargs = dict(
|
| 249 |
+
img_size=256,
|
| 250 |
+
in_chans=6,
|
| 251 |
+
num_classes=0,
|
| 252 |
+
fc_norm=None,
|
| 253 |
+
class_token=True,
|
| 254 |
+
patch_size=8,
|
| 255 |
+
embed_dim=1024,
|
| 256 |
+
depth=24,
|
| 257 |
+
num_heads=16,
|
| 258 |
+
drop_path_rate=0.3,
|
| 259 |
+
init_values=0.0001,
|
| 260 |
+
block_fn=vit.ParallelScalingBlock,
|
| 261 |
+
qkv_bias=False,
|
| 262 |
+
qk_norm=True,
|
| 263 |
+
)
|
| 264 |
+
for k, v in kwargs.items():
|
| 265 |
+
default_kwargs[k] = v
|
| 266 |
+
return vit.VisionTransformer(**default_kwargs)
|
| 267 |
+
|
| 268 |
+
|
| 269 |
+
def vit_large_patch16_256(**kwargs):
|
| 270 |
+
default_kwargs = dict(
|
| 271 |
+
img_size=256,
|
| 272 |
+
in_chans=6,
|
| 273 |
+
num_classes=0,
|
| 274 |
+
fc_norm=None,
|
| 275 |
+
class_token=True,
|
| 276 |
+
drop_path_rate=0.3,
|
| 277 |
+
init_values=0.0001,
|
| 278 |
+
block_fn=vit.ParallelScalingBlock,
|
| 279 |
+
qkv_bias=False,
|
| 280 |
+
qk_norm=True,
|
| 281 |
+
)
|
| 282 |
+
for k, v in kwargs.items():
|
| 283 |
+
default_kwargs[k] = v
|
| 284 |
+
return vit.vit_large_patch16_384(**default_kwargs)
|