| import os, sys
|
|
|
| ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
|
| sys.path.append(ROOT_DIR)
|
|
|
| import gc
|
| import torch
|
| import torchvision
|
| from torch import nn
|
| from torchvision.utils import save_image
|
| from torch.utils.data import DataLoader
|
|
|
| from torch.optim import Adam, SGD
|
| from Diffusion.diffuser import DeformDDPM
|
| from Diffusion.networks import get_net, STN
|
| from torchvision.transforms import Lambda
|
| import torch.nn.functional as F
|
| import Diffusion.losses as losses
|
| import random
|
| import glob
|
| import numpy as np
|
| import utils
|
| from tqdm import tqdm
|
|
|
| from Dataloader.dataloader0 import get_dataloader
|
| from Dataloader.dataLoader import *
|
|
|
| from Dataloader.dataloader_utils import thresh_img
|
| import yaml
|
| import argparse
|
|
|
|
|
| try:
|
| import intel_extension_for_pytorch as ipex
|
| except ImportError:
|
| ipex = None
|
| try:
|
| import oneccl_bindings_for_pytorch
|
| except (ImportError, Exception) as e:
|
| print(f"WARNING: Failed to import oneccl_bindings_for_pytorch: {e}")
|
|
|
|
|
| import torch.multiprocessing as mp
|
| from torch.utils.data.distributed import DistributedSampler
|
| from torch.nn.parallel import DistributedDataParallel as DDP
|
| import torch.distributed as dist
|
|
|
|
|
| def _device_available(device_type):
|
| if device_type == 'xpu':
|
| return hasattr(torch, 'xpu') and torch.xpu.is_available()
|
| return torch.cuda.is_available()
|
|
|
| def _device_count(device_type):
|
| if device_type == 'xpu':
|
| return torch.xpu.device_count() if hasattr(torch, 'xpu') else 0
|
| return torch.cuda.device_count()
|
|
|
| def _set_device(rank, device_type):
|
| if device_type == 'xpu':
|
| torch.xpu.set_device(rank)
|
| else:
|
| torch.cuda.set_device(rank)
|
|
|
| def _empty_cache(device_type):
|
| if device_type == 'xpu' and hasattr(torch, 'xpu'):
|
| torch.xpu.empty_cache()
|
| elif torch.cuda.is_available():
|
| torch.cuda.empty_cache()
|
|
|
| def ddp_setup(rank, world_size):
|
| """
|
| Args:
|
| rank: Unique identifier of each process (local_rank when launched by torchrun)
|
| world_size: Total number of processes
|
| """
|
| backend = "ccl" if DEVICE_TYPE == "xpu" else "nccl"
|
| if "LOCAL_RANK" in os.environ:
|
|
|
| dist.init_process_group(backend=backend)
|
| _set_device(int(os.environ["LOCAL_RANK"]), DEVICE_TYPE)
|
| else:
|
|
|
| os.environ["MASTER_ADDR"] = "localhost"
|
| os.environ["MASTER_PORT"] = "12355"
|
| dist.init_process_group(backend=backend, rank=rank, world_size=world_size)
|
| _set_device(rank, DEVICE_TYPE)
|
|
|
| EPS = 1e-5
|
| MSK_EPS = 0.01
|
| TEXT_EMBED_PROB = 0.5
|
| AUG_RESAMPLE_PROB = 0.5
|
| LOSS_WEIGHTS_DIFF = [2.0, 1.0, 4.0]
|
|
|
| LOSS_WEIGHTS_REGIST = [1.0, 0.01, 1e2]
|
| DIFF_REG_BATCH_RATIO = 2
|
| LOSS_WEIGHT_CONTRASTIVE = 0.001
|
| REGISTRATION_STEP_RATIO = 1
|
| CONTRASTIVE_STEP_RATIO = 1
|
|
|
|
|
|
|
| parser = argparse.ArgumentParser()
|
|
|
|
|
| parser.add_argument(
|
| "--config",
|
| "-C",
|
| help="Path for the config file",
|
| type=str,
|
|
|
|
|
| default="Config/config_all.yaml",
|
| required=False,
|
| )
|
| parser.add_argument("--batchsize", type=int, default=0, help="Override batch size from config (0=use config value)")
|
| args = parser.parse_args()
|
|
|
|
|
| with open(args.config, 'r') as _f:
|
| _cfg = yaml.safe_load(_f)
|
| DEVICE_TYPE = _cfg.get('device', 'cuda')
|
|
|
|
|
| use_distributed = _device_available(DEVICE_TYPE) and _device_count(DEVICE_TYPE) > 1
|
|
|
|
|
|
|
|
|
|
|
| def main_train(rank=0,world_size=1,train_mode_ratio=1,thresh_imgsim=0.01):
|
| if use_distributed:
|
| ddp_setup(rank,world_size)
|
|
|
| if torch.distributed.is_initialized() and rank == 0:
|
| print(f"World size: {torch.distributed.get_world_size()}")
|
| print(f"Communication backend: {torch.distributed.get_backend()}")
|
|
|
| if "RANK" in os.environ:
|
| gpu_id = int(os.environ["RANK"])
|
| rank = int(os.environ["LOCAL_RANK"])
|
| else:
|
| gpu_id = rank
|
|
|
|
|
| with open(args.config, 'r') as file:
|
| hyp_parameters = yaml.safe_load(file)
|
| if args.batchsize > 0:
|
| hyp_parameters['batchsize'] = args.batchsize
|
| if gpu_id == 0:
|
| print(hyp_parameters)
|
|
|
|
|
| epoch_per_save=hyp_parameters['epoch_per_save']
|
|
|
| data_name=hyp_parameters['data_name']
|
| net_name = hyp_parameters['net_name']
|
|
|
| Net=get_net(net_name)
|
|
|
| suffix_pth=f'_{data_name}_{net_name}.pth'
|
| model_save_path = os.path.join('Models',f'{data_name}_{net_name}/')
|
| model_dir=model_save_path
|
| transformer=utils.get_transformer(img_sz=hyp_parameters["ndims"]*[hyp_parameters['img_size']])
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| dataset = OMDataset_indiv(transform=None)
|
|
|
| datasetp = OMDataset_pair(transform=None)
|
|
|
| if use_distributed:
|
| sampler = DistributedSampler(dataset, shuffle=True)
|
| sampler_p = DistributedSampler(datasetp, shuffle=True)
|
| else:
|
| sampler = None
|
| sampler_p = None
|
|
|
| train_loader = DataLoader(
|
| dataset,
|
| batch_size=hyp_parameters['batchsize'],
|
| shuffle=(sampler is None),
|
| drop_last=True,
|
| sampler=sampler,
|
| )
|
| train_loader_p = DataLoader(
|
| datasetp,
|
| batch_size=max(1, hyp_parameters['batchsize']//DIFF_REG_BATCH_RATIO),
|
| shuffle=(sampler_p is None),
|
| drop_last=True,
|
| sampler=sampler_p,
|
| )
|
|
|
|
|
|
|
| Deformddpm = DeformDDPM(
|
| network=Net(
|
| n_steps=hyp_parameters["timesteps"],
|
| ndims=hyp_parameters["ndims"],
|
| num_input_chn = hyp_parameters["num_input_chn"],
|
| res = hyp_parameters['img_size']
|
| ),
|
| n_steps=hyp_parameters["timesteps"],
|
| image_chw=[1] + [hyp_parameters["img_size"]]*hyp_parameters["ndims"],
|
| device=hyp_parameters["device"],
|
| batch_size=hyp_parameters["batchsize"],
|
| img_pad_mode=hyp_parameters["img_pad_mode"],
|
| v_scale=hyp_parameters["v_scale"],
|
| )
|
|
|
|
|
| ddf_stn = STN(
|
| img_sz=hyp_parameters["img_size"],
|
| ndims=hyp_parameters["ndims"],
|
|
|
| padding_mode=hyp_parameters["padding_mode"],
|
| device=hyp_parameters["device"],
|
| )
|
|
|
|
|
| if use_distributed:
|
| device = f"{DEVICE_TYPE}:{rank}"
|
| Deformddpm.to(device)
|
| Deformddpm = DDP(Deformddpm, device_ids=[rank])
|
| ddf_stn.to(device)
|
| else:
|
| Deformddpm.to(hyp_parameters["device"])
|
| ddf_stn.to(hyp_parameters["device"])
|
|
|
|
|
|
|
|
|
|
|
|
|
| loss_reg = losses.Grad(penalty=['l1', 'negdetj', 'range'], ndims=hyp_parameters["ndims"],outrange_thresh=0.2,outrange_weight=1e3)
|
| loss_reg1 = losses.Grad(penalty=['l1', 'negdetj', 'range'], ndims=hyp_parameters["ndims"],outrange_thresh=0.6,outrange_weight=1e3)
|
|
|
| loss_dist = losses.MRSE(img_sz=hyp_parameters["img_size"])
|
|
|
| loss_ang = losses.NCC(img_sz=hyp_parameters["img_size"])
|
| loss_imgsim = losses.MSLNCC()
|
| loss_imgmse = losses.LMSE()
|
|
|
| optimizer = Adam(Deformddpm.parameters(), lr=hyp_parameters["lr"])
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| if not os.path.exists(model_dir):
|
| os.makedirs(model_dir, exist_ok=True)
|
| model_files = glob.glob(os.path.join(model_dir, "*.pth"))
|
| model_files.sort()
|
| if model_files:
|
| if gpu_id == 0:
|
| print(model_files)
|
| initial_epoch, Deformddpm, optimizer = ddp_load_dict(gpu_id, Deformddpm, optimizer, model_files[-1], use_distributed=use_distributed)
|
| else:
|
| initial_epoch = 0
|
|
|
| if gpu_id == 0:
|
| print('len_train_data: ',len(dataset))
|
|
|
| for epoch in range(initial_epoch,hyp_parameters["epoch"]):
|
| if use_distributed and sampler is not None:
|
| sampler.set_epoch(epoch)
|
| sampler_p.set_epoch(epoch)
|
|
|
| epoch_loss_tot = 0.0
|
| epoch_loss_gen_d = 0.0
|
| epoch_loss_gen_a = 0.0
|
| epoch_loss_reg = 0.0
|
| epoch_loss_regist = 0.0
|
| epoch_loss_imgsim = 0.0
|
| epoch_loss_imgmse = 0.0
|
| epoch_loss_ddfreg = 0.0
|
| epoch_loss_contrastive = 0.0
|
|
|
| Deformddpm.train()
|
|
|
| loss_nan_step = 0
|
|
|
| total = min(len(train_loader), len(train_loader_p))
|
| total_reg = total // REGISTRATION_STEP_RATIO
|
|
|
|
|
|
|
| for step, (batch, batch_p) in tqdm(enumerate(zip(train_loader, train_loader_p)), total=total):
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| [x0,embd] = batch
|
| x0 = x0.to(hyp_parameters["device"]).type(torch.float32)
|
|
|
| embd_dev = embd.to(hyp_parameters["device"]).type(torch.float32)
|
| if np.random.uniform(0,1)<TEXT_EMBED_PROB:
|
| embd_in = embd_dev
|
| else:
|
| embd_in = None
|
|
|
|
|
|
|
| n = x0.size()[0]
|
| x0 = x0.to(hyp_parameters["device"])
|
|
|
| blind_mask = utils.get_random_deformed_mask(x0.shape[2:],apply_possibility=0.6).to(hyp_parameters["device"])
|
|
|
|
|
| if hyp_parameters["ndims"]>2:
|
| if np.random.uniform(0,1)<AUG_RESAMPLE_PROB:
|
| x0 = utils.random_resample(x0, deform_scale=0)
|
|
|
| else:
|
| [x0] = utils.random_permute([x0], select_dims=[-1,-2,-3])
|
|
|
| if hyp_parameters['noise_scale']>0:
|
| if np.random.uniform(0,1)<AUG_RESAMPLE_PROB:
|
| x0 = thresh_img(x0, [0, 2*hyp_parameters['noise_scale']])
|
| x0 = x0 * (np.random.normal(1, hyp_parameters['noise_scale'] * 1)) + np.random.normal(0, hyp_parameters['noise_scale'] * 1)
|
|
|
|
|
| t = torch.randint(0, hyp_parameters["timesteps"], (n,)).to(
|
| hyp_parameters["device"]
|
| )
|
|
|
|
|
| proc_type = random.choice(['adding', 'downsample', 'slice', 'slice1', 'none', 'uncon', 'uncon', 'uncon'])
|
|
|
| ddpm = Deformddpm.module if use_distributed else Deformddpm
|
| cond_img, _, cond_ratio = ddpm.proc_cond_img(x0,proc_type=proc_type)
|
|
|
| pre_dvf_I,dvf_I = Deformddpm(img_org=x0, t=t, cond_imgs=cond_img, mask=blind_mask,proc_type=[],text=embd_in)
|
|
|
|
|
|
|
|
|
| loss_tot=0
|
|
|
| loss_ddf = loss_reg(pre_dvf_I,img=x0)
|
| trm_pred = ddf_stn(pre_dvf_I, dvf_I)
|
| loss_gen_d = loss_dist(pred=trm_pred,inv_lab=dvf_I,ddf_stn=None,mask=blind_mask)
|
| loss_gen_a = loss_ang(pred=trm_pred,inv_lab=dvf_I,ddf_stn=None,mask=blind_mask)
|
|
|
| loss_tot += LOSS_WEIGHTS_DIFF[0] * loss_gen_a + LOSS_WEIGHTS_DIFF[1] * loss_gen_d
|
| loss_tot += LOSS_WEIGHTS_DIFF[2] * loss_ddf
|
| loss_tot = torch.sqrt(1.+MSK_EPS-cond_ratio) * loss_tot
|
|
|
|
|
| if torch.isnan(x0).any():
|
| print(f"*** Encountered NaN in input image x0 at epoch {epoch}, step {step}.")
|
|
|
| if loss_ddf>0.001:
|
| print(f"*** High diffusion DDF loss at epoch {epoch}, step {step}: {loss_ddf.item()}.")
|
|
|
| if torch.isnan(loss_tot) or torch.isinf(loss_tot):
|
| print(f"*** Encountered NaN or Inf loss at epoch {epoch}, step {step}. Skipping this batch.")
|
| loss_nan_step += 1
|
| continue
|
| if loss_nan_step > 5:
|
| print(f"*** Too many NaN or Inf losses ({loss_nan_step} times) at epoch {epoch}, step {step}. Stopping training.")
|
| raise ValueError("Too many NaN losses detected in loss_tot. Code terminated.")
|
|
|
| optimizer.zero_grad()
|
| loss_tot.backward()
|
| optimizer.step()
|
|
|
| epoch_loss_tot += loss_tot.item() / total
|
| epoch_loss_gen_d += loss_gen_d.item() / total
|
| epoch_loss_gen_a += loss_gen_a.item() / total
|
| epoch_loss_reg += loss_ddf.item() / total
|
|
|
|
|
|
|
| loss_contra_val = None
|
| if step % CONTRASTIVE_STEP_RATIO == 0:
|
| raw_network = Deformddpm.module.network if use_distributed else Deformddpm.network
|
| n_contra = x0.size()[0]
|
| t_contra = torch.randint(0, hyp_parameters["timesteps"], (n_contra,)).to(hyp_parameters["device"])
|
| _ = raw_network(x=(x0 * blind_mask).detach(), y=cond_img.detach(), t=t_contra, text=None)
|
| if hasattr(raw_network, 'img_embd') and raw_network.img_embd is not None:
|
| img_embd = raw_network.img_embd
|
| loss_contra = LOSS_WEIGHT_CONTRASTIVE * F.relu(1 - F.cosine_similarity(img_embd, embd_dev, dim=-1).mean()-0.05)
|
|
|
| optimizer.zero_grad()
|
| loss_contra.backward()
|
| torch.nn.utils.clip_grad_norm_(Deformddpm.parameters(), max_norm=0.02)
|
| optimizer.step()
|
| loss_contra_val = loss_contra.item()
|
| epoch_loss_contrastive += loss_contra_val / total * CONTRASTIVE_STEP_RATIO
|
| else:
|
| if gpu_id == 0:
|
| print(f"*** Warning: Network does not have img_embd attribute for contrastive loss at epoch {epoch}, step {step}.")
|
|
|
|
|
|
|
| if step%REGISTRATION_STEP_RATIO == 0 and loss_gen_a.item()<-0.6:
|
| [x1, y1, _, embd_y] = batch_p
|
| if np.random.uniform(0,1)<TEXT_EMBED_PROB:
|
| embd_y = embd_y.to(hyp_parameters["device"]).type(torch.float32)
|
| else:
|
| embd_y = None
|
|
|
| x1 = x1.to(hyp_parameters["device"]).type(torch.float32)
|
| y1 = y1.to(hyp_parameters["device"]).type(torch.float32)
|
| n = x1.size()[0]
|
| [x1, y1] = utils.random_permute([x1, y1], select_dims=[-1,-2,-3])
|
| if hyp_parameters['noise_scale']>0:
|
| [x1, y1] = thresh_img([x1, y1], [0, 2*hyp_parameters['noise_scale']])
|
| random_scale = np.random.normal(1, hyp_parameters['noise_scale'] * 1)
|
| random_shift = np.random.normal(0, hyp_parameters['noise_scale'] * 1)
|
| x1 = x1 * random_scale + random_shift
|
| y1 = y1 * random_scale + random_shift
|
|
|
| scale_regist = np.random.uniform(0.0,0.7)
|
| select_timestep = np.random.randint(12, 25)
|
| T_regist = sorted(random.sample(range(int(hyp_parameters["timesteps"] * scale_regist),hyp_parameters["timesteps"]), select_timestep), reverse=True)
|
|
|
| T_regist = [[t for _ in range(max(1, hyp_parameters["batchsize"]//2))] for t in T_regist]
|
|
|
| proc_type = random.choice(['downsample', 'slice', 'slice1', 'none', 'none'])
|
| ddpm_inner = Deformddpm.module if use_distributed else Deformddpm
|
| y1_proc, msk_tgt, cond_ratio = ddpm_inner.proc_cond_img(y1,proc_type=proc_type)
|
| msk_tgt = msk_tgt+MSK_EPS
|
| [ddf_comp,ddf_rand],[img_rec,img_diff,img_save],_ = Deformddpm(img_org=x1, cond_imgs=y1_proc, T=[None, T_regist], proc_type=[],text=embd_y)
|
| loss_sim = loss_imgsim(img_rec, y1, label=msk_tgt*(y1>thresh_imgsim))
|
| loss_mse = loss_imgmse(img_rec, y1, label=msk_tgt*(y1>=0.0))
|
| loss_ddf1 = loss_reg1(ddf_comp, img=y1)
|
|
|
| loss_regist = 0
|
| loss_regist += LOSS_WEIGHTS_REGIST[0] * loss_sim
|
| loss_regist += LOSS_WEIGHTS_REGIST[1] * loss_mse
|
| loss_regist += LOSS_WEIGHTS_REGIST[2] * loss_ddf1
|
|
|
|
|
| if torch.isnan(x0).any():
|
| print(f"*** Encountered NaN in input image x0 at epoch {epoch}, step {step}.")
|
|
|
| if loss_ddf1>0.002:
|
| print(f"*** High registration DDF loss at epoch {epoch}, step {step}: {loss_ddf1.item()}.")
|
|
|
| loss_regist = torch.sqrt(cond_ratio+MSK_EPS) *loss_regist
|
| optimizer.zero_grad()
|
| loss_regist.backward()
|
|
|
| torch.nn.utils.clip_grad_norm_(Deformddpm.parameters(), max_norm=0.1)
|
| optimizer.step()
|
|
|
| epoch_loss_regist += loss_regist.item()
|
| epoch_loss_imgsim += loss_sim.item()
|
| epoch_loss_imgmse += loss_mse.item()
|
| epoch_loss_ddfreg += loss_ddf1.item()
|
| else:
|
| loss_sim = torch.tensor(0.0)
|
| loss_mse = torch.tensor(0.0)
|
| loss_ddf1 = torch.tensor(0.0)
|
| loss_regist = torch.tensor(0.0)
|
| if step % REGISTRATION_STEP_RATIO==0:
|
| total_reg = total_reg-1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| if gpu_id == 0:
|
| print('==================')
|
| print(epoch,':', epoch_loss_tot,'=',epoch_loss_gen_a,'+', epoch_loss_gen_d,'+',epoch_loss_reg, ' (ang+dist+regul)')
|
| print(f' loss_contrastive: {epoch_loss_contrastive}')
|
| print(f' loss_regist: {epoch_loss_regist/total_reg} = {epoch_loss_imgsim/total_reg} (imgsim) + {epoch_loss_imgmse/total_reg} (imgmse) + {epoch_loss_ddfreg/total_reg} (ddf)')
|
| print('==================')
|
|
|
|
|
| if 0 == epoch % epoch_per_save:
|
| save_dir=model_save_path + str(epoch).rjust(6, '0') + suffix_pth
|
| os.makedirs(os.path.dirname(model_save_path), exist_ok=True)
|
|
|
| if not use_distributed:
|
| print(f"saved in {save_dir}")
|
|
|
| torch.save({
|
| 'model_state_dict': Deformddpm.state_dict(),
|
| 'optimizer_state_dict': optimizer.state_dict(),
|
| 'epoch': epoch
|
| }, save_dir)
|
| elif gpu_id == 0:
|
| print(f"saved in {save_dir}")
|
|
|
| torch.save({
|
| 'model_state_dict': Deformddpm.module.state_dict(),
|
| 'optimizer_state_dict': optimizer.state_dict(),
|
| 'epoch': epoch
|
| }, save_dir)
|
|
|
|
|
| _empty_cache(DEVICE_TYPE)
|
| gc.collect()
|
| if use_distributed and dist.is_initialized():
|
| dist.destroy_process_group()
|
|
|
| def ddp_load_dict(gpu_id, Deformddpm, optimizer, model_file,use_distributed=True, load_strict=False):
|
|
|
| if gpu_id == 0:
|
|
|
| utils.print_memory_usage("Before Loading Model")
|
| gc.collect()
|
| _empty_cache(DEVICE_TYPE)
|
|
|
|
|
| checkpoint = torch.load(model_file, map_location='cpu')
|
|
|
| if use_distributed:
|
| Deformddpm.module.load_state_dict(checkpoint['model_state_dict'], strict=load_strict)
|
| else:
|
| Deformddpm.load_state_dict(checkpoint['model_state_dict'], strict=load_strict)
|
| if load_strict:
|
| optimizer.load_state_dict(checkpoint['optimizer_state_dict'])
|
| utils.print_memory_usage("After Loading Checkpoint on GPU")
|
|
|
| if use_distributed:
|
|
|
| dist.barrier()
|
| for param in Deformddpm.parameters():
|
| dist.broadcast(param.data, src=0)
|
| dist.barrier()
|
| for param_group in optimizer.param_groups:
|
| for param in param_group['params']:
|
| if param.grad is not None:
|
| dist.broadcast(param.grad, src=0)
|
|
|
|
|
|
|
| initial_epoch = int(os.path.basename(model_file).split('.')[0][:6]) + 1
|
|
|
| return initial_epoch, Deformddpm, optimizer
|
|
|
|
|
|
|
| if __name__ == "__main__":
|
| if "LOCAL_RANK" in os.environ:
|
|
|
| use_distributed = True
|
| local_rank = int(os.environ["LOCAL_RANK"])
|
| world_size = int(os.environ["WORLD_SIZE"])
|
| print(f"torchrun launch: LOCAL_RANK={local_rank}, RANK={os.environ.get('RANK')}, WORLD_SIZE={world_size}")
|
| try:
|
| main_train(local_rank, world_size)
|
| except Exception as e:
|
| import traceback
|
| print(f"\n{'='*60}\nRANK {os.environ.get('RANK')} FAILED:\n{'='*60}", flush=True)
|
| traceback.print_exc()
|
| raise
|
| elif use_distributed:
|
|
|
| world_size = _device_count(DEVICE_TYPE)
|
| print(f"Distributed {DEVICE_TYPE.upper()} device number = {world_size}")
|
| mp.spawn(main_train,args = (world_size,),nprocs = world_size)
|
| else:
|
| main_train(0,1) |