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b/train_dtc.py |
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import os |
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import sys |
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from tqdm import tqdm |
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from tensorboardX import SummaryWriter |
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import argparse |
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import logging |
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import time |
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import random |
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import numpy as np |
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import torch |
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import torch.optim as optim |
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from torchvision import transforms |
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import torch.nn.functional as F |
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import torch.backends.cudnn as cudnn |
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import torch.nn as nn |
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from torch.nn import BCEWithLogitsLoss, MSELoss |
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from torch.utils.data import DataLoader |
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from networks.vnet_sdf import VNet |
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from utils import ramps, losses |
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from dataloaders.la_heart import * |
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from dataloaders.utils import compute_sdf |
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parser = argparse.ArgumentParser() |
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parser.add_argument('--dataset_name', type=str, default='LA', help='dataset_name') |
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parser.add_argument('--root_path', type=str, default='/data/omnisky/postgraduate/Yb/data_set/LASet/data', help='Name of Experiment') |
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parser.add_argument('--exp', type=str, default='vnet', help='model_name') |
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parser.add_argument('--model', type=str, default='DTC', help='model_name') |
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parser.add_argument('--max_iterations', type=int, default=6000, help='maximum epoch number to train') |
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parser.add_argument('--batch_size', type=int, default=4, help='batch_size per gpu') |
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parser.add_argument('--labeled_bs', type=int, default=2, help='labeled_batch_size per gpu') |
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parser.add_argument('--base_lr', type=float, default=0.01, help='maximum epoch number to train') |
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parser.add_argument('--D_lr', type=float, default=1e-4, help='maximum discriminator learning rate to train') |
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parser.add_argument('--deterministic', type=int, default=1, help='whether use deterministic training') |
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parser.add_argument('--labelnum', type=int, default=25, help='num of labeled samples') |
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parser.add_argument('--max_samples', type=int, default=123, help='all samples') |
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parser.add_argument('--seed', type=int, default=1337, help='random seed') |
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parser.add_argument('--consistency_weight', type=float, default=0.1, help='balance factor to control supervised loss and consistency loss') |
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parser.add_argument('--gpu', type=str, default='1', help='GPU to use') |
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parser.add_argument('--beta', type=float, default=0.3, help='balance factor to control regional and sdm loss') |
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parser.add_argument('--gamma', type=float, default=0.5, help='balance factor to control supervised and consistency loss') |
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# costs |
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parser.add_argument('--consistency', type=float, default=1.0, help='consistency') |
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parser.add_argument('--consistency_rampup', type=float, default=40.0, help='consistency_rampup') |
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args = parser.parse_args() |
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train_data_path = args.root_path |
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snapshot_path = "model/{}_{}_{}_labeled/{}".format(args.dataset_name, args.exp, args.labelnum, args.model) |
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os.environ['CUDA_VISIBLE_DEVICES'] = args.gpu |
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batch_size = args.batch_size * len(args.gpu.split(',')) |
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max_iterations = args.max_iterations |
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base_lr = args.base_lr |
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labeled_bs = args.labeled_bs |
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if not args.deterministic: |
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cudnn.benchmark = True |
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cudnn.deterministic = False |
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else: |
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cudnn.benchmark = False # True # |
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cudnn.deterministic = True # False # |
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random.seed(args.seed) |
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np.random.seed(args.seed) |
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torch.manual_seed(args.seed) |
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torch.cuda.manual_seed(args.seed) |
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num_classes = 2 |
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patch_size = (112, 112, 80) |
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def cal_dice(output, target, eps=1e-3): |
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output = torch.sigmoid(output) |
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output = (output>0.5).float() |
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output = torch.squeeze(output) |
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inter = torch.sum(output * target) + eps |
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union = torch.sum(output) + torch.sum(target) + eps * 2 |
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dice = 2 * inter / union |
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return dice |
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def get_current_consistency_weight(epoch): |
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# Consistency ramp-up from https://arxiv.org/abs/1610.02242 |
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return args.consistency * ramps.sigmoid_rampup(epoch, args.consistency_rampup) |
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if __name__ == "__main__": |
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# make logger file |
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if not os.path.exists(snapshot_path): |
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os.makedirs(snapshot_path) |
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logging.basicConfig(filename=snapshot_path+"/log.txt", level=logging.INFO, |
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format='[%(asctime)s.%(msecs)03d] %(message)s', datefmt='%H:%M:%S') |
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logging.getLogger().addHandler(logging.StreamHandler(sys.stdout)) |
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logging.info(str(args)) |
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def create_model(ema=False): |
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# Network definition |
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net = VNet(n_channels=1, n_classes=num_classes-1, |
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normalization='batchnorm', has_dropout=True) |
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model = net.cuda() |
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if ema: |
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for param in model.parameters(): |
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param.detach_() |
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return model |
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model = create_model() |
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db_train = LAHeart(base_dir=train_data_path, |
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split='train', # train/val split |
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transform=transforms.Compose([ |
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RandomRotFlip(), |
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RandomCrop(patch_size), |
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ToTensor(), |
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])) |
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db_test = LAHeart(base_dir=args.root_path, |
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split='test', |
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transform=transforms.Compose([ |
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CenterCrop(patch_size), |
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ToTensor() |
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])) |
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labeled_idxs = list(range(args.labelnum)) |
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unlabeled_idxs = list(range(args.labelnum, args.max_samples)) |
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batch_sampler = TwoStreamBatchSampler(labeled_idxs, unlabeled_idxs, batch_size, batch_size-labeled_bs) |
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def worker_init_fn(worker_id): |
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random.seed(args.seed+worker_id) |
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trainloader = DataLoader(db_train, batch_sampler=batch_sampler, num_workers=4, pin_memory=True, worker_init_fn=worker_init_fn) |
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test_loader = DataLoader(db_test, batch_size=1,shuffle=False, num_workers=4, pin_memory=True) |
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model.train() |
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optimizer = optim.SGD(model.parameters(), lr=base_lr, momentum=0.9, weight_decay=0.0001) |
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ce_loss = BCEWithLogitsLoss() |
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mse_loss = MSELoss() |
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writer = SummaryWriter(snapshot_path+'/log') |
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logging.info("{} itertations per epoch".format(len(trainloader))) |
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iter_num = 0 |
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max_epoch = max_iterations//len(trainloader)+1 |
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lr_ = base_lr |
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best_dice = 0.0 |
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iterator = tqdm(range(max_epoch), ncols=70) |
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for epoch_num in iterator: |
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time1 = time.time() |
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for i_batch, sampled_batch in enumerate(trainloader): |
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time2 = time.time() |
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# print('fetch data cost {}'.format(time2-time1)) |
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volume_batch, label_batch = sampled_batch['image'], sampled_batch['label'] |
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volume_batch, label_batch = volume_batch.cuda(), label_batch.cuda() |
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outputs_tanh, outputs = model(volume_batch) |
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outputs_soft = torch.sigmoid(outputs) |
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# calculate the loss |
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with torch.no_grad(): |
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gt_dis = compute_sdf(label_batch[:].cpu().numpy(), outputs[:labeled_bs, 0, ...].shape) |
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gt_dis = torch.from_numpy(gt_dis).float().cuda() |
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loss_sdf = mse_loss(outputs_tanh[:labeled_bs, 0, ...], gt_dis) |
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loss_seg = ce_loss(outputs[:labeled_bs, 0, ...], label_batch[:labeled_bs].float()) |
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loss_seg_dice = losses.dice_loss(outputs_soft[:labeled_bs, 0, :, :, :], label_batch[:labeled_bs] == 1) |
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supervised_loss = loss_seg_dice + args.beta * loss_sdf |
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# unsupervised loss |
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dis_to_mask = torch.sigmoid(-1500*outputs_tanh) |
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consistency_loss = torch.mean((dis_to_mask - outputs_soft) ** 2) |
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consistency_weight = get_current_consistency_weight(iter_num//150) |
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loss = supervised_loss + consistency_weight * consistency_loss |
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optimizer.zero_grad() |
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loss.backward() |
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optimizer.step() |
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iter_num = iter_num + 1 |
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writer.add_scalar('lr', lr_, iter_num) |
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writer.add_scalar('loss/loss', loss, iter_num) |
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writer.add_scalar('loss/loss_seg', loss_seg, iter_num) |
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writer.add_scalar('loss/loss_dice', loss_seg_dice, iter_num) |
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writer.add_scalar('loss/loss_hausdorff', loss_sdf, iter_num) |
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writer.add_scalar('loss/consistency_weight', consistency_weight, iter_num) |
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writer.add_scalar('loss/consistency_loss', consistency_loss, iter_num) |
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logging.info('iteration %d : loss : %f, loss_consis: %f, loss_haus: %f, loss_seg: %f, loss_dice: %f' % |
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(iter_num, loss.item(), consistency_loss.item(), loss_sdf.item(), loss_seg.item(), loss_seg_dice.item())) |
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writer.add_scalar('loss/loss', loss, iter_num) |
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# logging.info('iteration %d : loss : %f' % (iter_num, loss.item())) |
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if iter_num >= 800 and iter_num % 200 == 0: |
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model.eval() |
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with torch.no_grad(): |
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dice_sample = 0 |
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for sampled_batch in test_loader: |
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img, lbl = sampled_batch['image'].cuda(), sampled_batch['label'].cuda() |
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_, outputs = model(img) |
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dice_once = cal_dice(outputs,lbl) |
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print(dice_once) |
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dice_sample += dice_once |
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dice_sample = dice_sample / len(test_loader) |
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print('Average center dice:{:.3f}'.format(dice_sample)) |
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if dice_sample > best_dice: |
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best_dice = dice_sample |
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save_mode_path = os.path.join(snapshot_path, 'iter_{}_dice_{}.pth'.format(iter_num, best_dice)) |
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save_best_path = os.path.join(snapshot_path, '{}_best_model.pth'.format(args.model)) |
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torch.save(model.state_dict(), save_mode_path) |
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torch.save(model.state_dict(), save_best_path) |
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logging.info("save best model to {}".format(save_mode_path)) |
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writer.add_scalar('Var_dice/Dice', dice_sample, iter_num) |
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writer.add_scalar('Var_dice/Best_dice', best_dice, iter_num) |
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model.train() |
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if iter_num >= max_iterations: |
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break |
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time1 = time.time() |
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if iter_num >= max_iterations: |
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iterator.close() |
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break |
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writer.close() |