Image Segmentation
Transformers
PyTorch
repcontur
feature-extraction
medical
radiology
ct
3d
tumor-segmentation
referring-segmentation
report-generation
visual-question-answering
custom_code
Instructions to use Oncosoft-Research/RepConTUR with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use Oncosoft-Research/RepConTUR with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("image-segmentation", model="Oncosoft-Research/RepConTUR", trust_remote_code=True)# pip install -U transformers accelerate # Load model directly from transformers import AutoModel model = AutoModel.from_pretrained("Oncosoft-Research/RepConTUR", trust_remote_code=True, device_map="auto") - Notebooks
- Google Colab
- Kaggle
File size: 16,829 Bytes
c6be546 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 | from pathlib import Path
import copy
import math
from functools import wraps
import torch
import torch.nn.functional as F
from torch import nn, einsum
from torch.autograd import grad as torch_grad
from torchvision import transforms as T, utils
import torchvision
from einops import rearrange, repeat, pack, unpack
from einops.layers.torch import Rearrange
from vector_quantize_pytorch import VectorQuantize
from .attention import Attention, Transformer, ContinuousPositionBias
# helpers
def exists(val):
return val is not None
def default(val, d):
return val if exists(val) else d
def divisible_by(numer, denom):
return (numer % denom) == 0
def leaky_relu(p = 0.1):
return nn.LeakyReLU(p)
def remove_vgg(fn):
@wraps(fn)
def inner(self, *args, **kwargs):
has_vgg = hasattr(self, 'vgg')
if has_vgg:
vgg = self.vgg
delattr(self, 'vgg')
out = fn(self, *args, **kwargs)
if has_vgg:
self.vgg = vgg
return out
return inner
def pair(val):
ret = (val, val) if not isinstance(val, tuple) else val
assert len(ret) == 2
return ret
def cast_tuple(val, l = 1):
return val if isinstance(val, tuple) else (val,) * l
def gradient_penalty(images, output, weight = 10):
batch_size = images.shape[0]
device=torch.device('cuda')
gradients = torch_grad(
outputs = output,
inputs = images,
grad_outputs = torch.ones(output.size(), device = device),
create_graph = True,
retain_graph = True,
only_inputs = True
)[0]
gradients = rearrange(gradients, 'b ... -> b (...)')
return weight * ((gradients.norm(2, dim = 1) - 1) ** 2).mean()
def l2norm(t):
return F.normalize(t, dim = -1)
def leaky_relu(p = 0.1):
return nn.LeakyReLU(p)
def safe_div(numer, denom, eps = 1e-8):
return numer / (denom + eps)
# gan losses
def hinge_discr_loss(fake, real):
return (F.relu(1 + fake) + F.relu(1 - real)).mean()
def hinge_gen_loss(fake):
return -fake.mean()
def bce_discr_loss(fake, real):
return (-log(1 - torch.sigmoid(fake)) - log(torch.sigmoid(real))).mean()
def bce_gen_loss(fake):
return -log(torch.sigmoid(fake)).mean()
def grad_layer_wrt_loss(loss, layer):
return torch_grad(
outputs = loss,
inputs = layer,
grad_outputs = torch.ones_like(loss),
retain_graph = True
)[0].detach()
# ctvit - 3d ViT with factorized spatial and temporal attention made into an vqgan-vae autoencoder
def pick_video_frame(video, frame_indices):
batch, device = video.shape[0], video.device
video = rearrange(video, 'b c f ... -> b f c ...')
device=torch.device('cuda')
batch_indices = torch.arange(batch, device = device)
batch_indices = rearrange(batch_indices, 'b -> b 1')
images = video[batch_indices, frame_indices]
images = rearrange(images, 'b 1 c ... -> b c ...')
return images
class CTViT(nn.Module):
def __init__(
self,
*,
dim,
codebook_size,
image_size,
patch_size,
temporal_patch_size,
spatial_depth,
temporal_depth,
discr_base_dim = 16,
dim_head = 64,
heads = 8,
channels = 1,
use_vgg_and_gan = True,
vgg = None,
discr_attn_res_layers = (16,),
use_hinge_loss = True,
attn_dropout = 0.,
ff_dropout = 0.
):
"""
einstein notations:
b - batch
c - channels
t - time
d - feature dimension
p1, p2, pt - image patch sizes and then temporal patch size
"""
super().__init__()
self.image_size = pair(image_size)
self.patch_size = pair(patch_size)
patch_height, patch_width = self.patch_size
self.temporal_patch_size = temporal_patch_size
self.spatial_rel_pos_bias = ContinuousPositionBias(dim = dim, heads = heads)
image_height, image_width = self.image_size
assert (image_height % patch_height) == 0 and (image_width % patch_width) == 0
self.to_patch_emb_first_frame = nn.Sequential(
Rearrange('b c 1 (h p1) (w p2) -> b 1 h w (c p1 p2)', p1 = patch_height, p2 = patch_width),
nn.LayerNorm(channels * patch_width * patch_height),
nn.Linear(channels * patch_width * patch_height, dim),
nn.LayerNorm(dim)
)
self.to_patch_emb = nn.Sequential(
Rearrange('b c (t pt) (h p1) (w p2) -> b t h w (c pt p1 p2)', p1 = patch_height, p2 = patch_width, pt = temporal_patch_size),
nn.LayerNorm(channels * patch_width * patch_height * temporal_patch_size),
nn.Linear(channels * patch_width * patch_height * temporal_patch_size, dim),
nn.LayerNorm(dim)
)
transformer_kwargs = dict(
dim = dim,
dim_head = dim_head,
heads = heads,
attn_dropout = attn_dropout,
ff_dropout = ff_dropout,
peg = True,
peg_causal = True,
)
self.enc_spatial_transformer = Transformer(depth = spatial_depth, **transformer_kwargs)
self.enc_temporal_transformer = Transformer(depth = temporal_depth, **transformer_kwargs)
self.vq = VectorQuantize(dim = dim, codebook_size = codebook_size, use_cosine_sim = True)
self.vq.float() # VQ must stay in float32 for compatibility
self.to_pixels_first_frame = nn.Sequential(
nn.Linear(dim, channels * patch_width * patch_height),
Rearrange('b 1 h w (c p1 p2) -> b c 1 (h p1) (w p2)', p1 = patch_height, p2 = patch_width)
)
self.to_pixels = nn.Sequential(
nn.Linear(dim, channels * patch_width * patch_height * temporal_patch_size),
Rearrange('b t h w (c pt p1 p2) -> b c (t pt) (h p1) (w p2)', p1 = patch_height, p2 = patch_width, pt = temporal_patch_size),
)
self.gen_loss = hinge_gen_loss if use_hinge_loss else bce_gen_loss
def _apply(self, fn):
# Override _apply to keep VQ module in float32
# This catches to(), half(), bfloat16(), cuda(), etc.
super()._apply(fn)
self.vq.float()
return self
def calculate_video_token_mask(self, videos, video_frame_mask):
*_, h, w = videos.shape
ph, pw = self.patch_size
first_frame_mask, rest_frame_mask = video_frame_mask[:, :1], video_frame_mask[:, 1:]
rest_vq_mask = rearrange(rest_frame_mask, 'b (f p) -> b f p', p = self.temporal_patch_size)
video_mask = torch.cat((first_frame_mask, rest_vq_mask.any(dim = -1)), dim = -1)
return repeat(video_mask, 'b f -> b (f hw)', hw = (h // ph) * (w // pw))
def get_video_patch_shape(self, num_frames, include_first_frame = True):
patch_frames = 0
if include_first_frame:
num_frames -= 1
patch_frames += 1
patch_frames += (num_frames // self.temporal_patch_size)
return (patch_frames, *self.patch_height_width)
@property
def image_num_tokens(self):
return int(self.image_size[0] / self.patch_size[0]) * int(self.image_size[1] / self.patch_size[1])
def frames_per_num_tokens(self, num_tokens):
tokens_per_frame = self.image_num_tokens
assert (num_tokens % tokens_per_frame) == 0, f'number of tokens must be divisible by number of tokens per frame {tokens_per_frame}'
assert (num_tokens > 0)
pseudo_frames = num_tokens // tokens_per_frames
return (pseudo_frames - 1) * self.temporal_patch_size + 1
def num_tokens_per_frames(self, num_frames, include_first_frame = True):
image_num_tokens = self.image_num_tokens
total_tokens = 0
if include_first_frame:
num_frames -= 1
total_tokens += image_num_tokens
assert (num_frames % self.temporal_patch_size) == 0
return total_tokens + int(num_frames / self.temporal_patch_size) * image_num_tokens
def copy_for_eval(self):
device = next(self.parameters()).device
device=torch.device('cuda')
vae_copy = copy.deepcopy(self.cpu())
if vae_copy.use_vgg_and_gan:
del vae_copy.discr
del vae_copy.vgg
vae_copy.eval()
return vae_copy.to(device)
#@remove_vgg
def state_dict(self, *args, **kwargs):
return super().state_dict(*args, **kwargs)
#@remove_vgg
def load_state_dict(self, *args, **kwargs):
return super().load_state_dict(*args, **kwargs)
def load(self, path):
path = Path(path)
assert path.exists()
pt = torch.load(str(path))
self.load_state_dict(pt)
def decode_from_codebook_indices(self, indices):
codes = self.vq.codebook[indices]
return self.decode(codes)
@property
def patch_height_width(self):
return self.image_size[0] // self.patch_size[0], self.image_size[1] // self.patch_size[1]
def encode(
self,
tokens
):
b = tokens.shape[0]
h, w = self.patch_height_width
video_shape = tuple(tokens.shape[:-1])
tokens = rearrange(tokens, 'b t h w d -> (b t) (h w) d')
device=torch.device('cuda')
attn_bias = self.spatial_rel_pos_bias(h, w, device = device)
tokens = self.enc_spatial_transformer(tokens, attn_bias = attn_bias, video_shape = video_shape)
tokens = rearrange(tokens, '(b t) (h w) d -> b t h w d', b = b, h = h , w = w)
# encode - temporal
tokens = rearrange(tokens, 'b t h w d -> (b h w) t d')
tokens = self.enc_temporal_transformer(tokens, video_shape = video_shape)
tokens = rearrange(tokens, '(b h w) t d -> b t h w d', b = b, h = h, w = w)
return tokens
def decode(
self,
tokens
):
b = tokens.shape[0]
h, w = self.patch_height_width
if tokens.ndim == 3:
tokens = rearrange(tokens, 'b (t h w) d -> b t h w d', h = h, w = w)
video_shape = tuple(tokens.shape[:-1])
# decode - temporal
tokens = rearrange(tokens, 'b t h w d -> (b h w) t d')
tokens = self.dec_temporal_transformer(tokens, video_shape = video_shape)
tokens = rearrange(tokens, '(b h w) t d -> b t h w d', b = b, h = h, w = w)
# decode - spatial
tokens = rearrange(tokens, 'b t h w d -> (b t) (h w) d')
device=torch.device('cuda')
attn_bias = self.spatial_rel_pos_bias(h, w, device = device)
tokens = self.dec_spatial_transformer(tokens, attn_bias = attn_bias, video_shape = video_shape)
tokens = rearrange(tokens, '(b t) (h w) d -> b t h w d', b = b, h = h , w = w)
# to pixels
#first_frame_token, rest_frames_tokens = tokens[:, :1], tokens[:, 1:]
#first_frame = self.to_pixels_first_frame(first_frame_token)
#rest_frames = self.to_pixels(rest_frames_tokens)
recon_video = self.to_pixels(tokens)
#recon_video = torch.cat((first_frame, rest_frames), dim = 2)
return recon_video
def forward(
self,
video,
mask = None,
return_recons = False,
return_recons_only = False,
return_discr_loss = False,
apply_grad_penalty = True,
return_only_codebook_ids = False,
return_encoded_tokens=False
):
assert video.ndim in {4, 5}
is_image = video.ndim == 4
#print(video.shape)
if is_image:
video = rearrange(video, 'b c h w -> b c 1 h w')
assert not exists(mask)
b, c, f, *image_dims, device = *video.shape, video.device
device=torch.device('cuda')
assert tuple(image_dims) == self.image_size
assert not exists(mask) or mask.shape[-1] == f
first_frame, rest_frames = video[:, :, :1], video[:, :, 1:]
# derive patches
#first_frame_tokens = self.to_patch_emb_first_frame(first_frame)
#rest_frames_tokens = self.to_patch_emb(rest_frames)
#tokens = torch.cat((first_frame_tokens, rest_frames_tokens), dim = 1)
tokens = self.to_patch_emb(video)
# save height and width in
shape = tokens.shape
*_, h, w, _ = shape
# encode - spatial
tokens = self.encode(tokens)
# quantize
tokens, packed_fhw_shape = pack([tokens], 'b * d')
vq_mask = None
if exists(mask):
vq_mask = self.calculate_video_token_mask(video, mask)
# VQ stays in float32 - convert input/output only
tokens_dtype = tokens.dtype
tokens = tokens.float()
tokens, indices, commit_loss = self.vq(tokens, mask = vq_mask)
tokens = tokens.to(tokens_dtype)
if return_only_codebook_ids:
indices, = unpack(indices, packed_fhw_shape, 'b *')
return indices
tokens = rearrange(tokens, 'b (t h w) d -> b t h w d', h = h, w = w)
if return_encoded_tokens:
return tokens
recon_video = self.decode(tokens)
returned_recon = rearrange(recon_video, 'b c 1 h w -> b c h w') if is_image else recon_video.clone()
if return_recons_only:
return returned_recon
if exists(mask):
# variable lengthed video / images training
recon_loss = F.mse_loss(video, recon_video, reduction = 'none')
recon_loss = recon_loss[repeat(mask, 'b t -> b c t', c = c)]
recon_loss = recon_loss.mean()
else:
recon_loss = F.mse_loss(video, recon_video)
# prepare a random frame index to be chosen for discriminator and perceptual loss
pick_frame_logits = torch.randn(b, f)
if exists(mask):
mask_value = -torch.finfo(pick_frame_logits.dtype).max
pick_frame_logits = pick_frame_logits.masked_fill(~mask, mask_value)
frame_indices = pick_frame_logits.topk(1, dim = -1).indices
# whether to return discriminator loss
if return_discr_loss:
assert exists(self.discr), 'discriminator must exist to train it'
video = pick_video_frame(video, frame_indices)
recon_video = pick_video_frame(recon_video, frame_indices)
recon_video = recon_video.detach()
video.requires_grad_()
transform = T.Compose([T.Resize(256)])
recon_video = transform(recon_video)
video = transform(video)
#print("TEST")
#print(recon_video.shape)
recon_video_discr_logits, video_discr_logits = map(self.discr, (recon_video, video))
discr_loss = self.discr_loss(recon_video_discr_logits, video_discr_logits)
if apply_grad_penalty:
gp = gradient_penalty(video, video_discr_logits)
loss = discr_loss + gp
if return_recons:
return loss, returned_recon
return loss
# early return if training on grayscale
if not self.use_vgg_and_gan:
if return_recons:
return recon_loss, returned_recon
return recon_loss
# perceptual loss
input_vgg_input = pick_video_frame(video, frame_indices)
recon_vgg_input = pick_video_frame(recon_video, frame_indices)
transform = T.Compose([T.Resize(256)])
input_vgg_input = transform(input_vgg_input)
recon_vgg_input=transform(recon_vgg_input)
# handle grayscale for vgg
if video.shape[1] == 1:
input_vgg_input2, recon_vgg_input2 = map(lambda t: repeat(t, 'b 1 ... -> b c ...', c = 3), (input_vgg_input, recon_vgg_input))
transform = T.Compose([T.Resize(256)])
input_vgg_input2 = transform(input_vgg_input2)
recon_vgg_input2 = transform(recon_vgg_input2)
input_vgg_feats = self.vgg(input_vgg_input2)
recon_vgg_feats = self.vgg(recon_vgg_input2)
perceptual_loss = F.mse_loss(input_vgg_feats, recon_vgg_feats)
# generator loss
gen_loss = self.gen_loss(self.discr(recon_vgg_input))
# calculate adaptive weight
last_dec_layer = self.to_pixels[0].weight
norm_grad_wrt_gen_loss = grad_layer_wrt_loss(gen_loss, last_dec_layer).norm(p = 2)
norm_grad_wrt_perceptual_loss = grad_layer_wrt_loss(perceptual_loss, last_dec_layer).norm(p = 2)
adaptive_weight = safe_div(norm_grad_wrt_perceptual_loss, norm_grad_wrt_gen_loss)
adaptive_weight.clamp_(max = 1e4)
# combine losses
loss = recon_loss + perceptual_loss + commit_loss + adaptive_weight * gen_loss
if return_recons:
return loss, returned_recon
return loss
|