def main(): args = get_arguments() #os.environ["CUDA_VISIBLE_DEVICES"] = "0" ## FOR REPRODUCIBILITY OF RESULTS seed = 1777777 utils.reproducibility(args, seed) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets( args, path='.././datasets') model, optimizer = medzoo.create_model(args) # criterion = DiceLoss(classes=args.classes) # # ## TODO LOAD PRETRAINED MODEL print(affine.shape) # #model.restore_checkpoint(args.pretrained) if args.cuda: model = model.cuda() full_volume = full_volume.cuda() print("Model transferred in GPU.....") x = torch.randn(3, 156, 240, 240).cuda() output = non_overlap_padding(args, x, model, criterion, kernel_dim=(32, 32, 32))
def main(): args = get_arguments() utils.reproducibility(args, seed) utils.make_dirs(args.save) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets( args, path='/home/mulns/My_project/VV/MedicalZooPytorch/datasets') model, optimizer = medzoo.create_model(args) criterion = DiceLoss(classes=args.classes) if args.cuda: # model=torch.nn.DataParallel(model) model = model.cuda() print("Model transferred in GPU.....") trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator, lr_scheduler=None) print("START TRAINING...") trainer.training()
def main(): args = get_arguments() os.environ["CUDA_VISIBLE_DEVICES"] = "0" ## FOR REPRODUCIBILITY OF RESULTS seed = 1777777 utils.reproducibility(args, seed) utils.make_dirs(args.save) utils.save_arguments(args, args.save) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets( args, path='.././datasets') model, optimizer = medzoo.create_model(args) criterion = create_loss('CrossEntropyLoss') criterion = DiceLoss(classes=args.classes, weight=torch.tensor([0.1, 1, 1, 1]).cuda()) if args.cuda: model = model.cuda() print("Model transferred in GPU.....") trainer = Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator, lr_scheduler=None) print("START TRAINING...") trainer.training()
def main(): args = get_arguments() utils.reproducibility(args, seed) # utils.make_dirs(args.save) if not os.path.exists(args.save): os.makedirs(args.save) # training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args, training_generator, val_generator, full_volume, affine, dataset = medical_loaders.generate_datasets(args, path='/data/hejy/MedicalZooPytorch_2cls/datasets') model, optimizer = medzoo.create_model(args) criterion = DiceLoss(classes=2, skip_index_after=args.classes, weight = torch.tensor([1, 1]).cuda(), sigmoid_normalization=True) # criterion = WeightedCrossEntropyLoss() if args.cuda: model = model.cuda() # model.restore_checkpoint(args.pretrained) dataloader_train = MICCAI2020_RIBFRAC_DataLoader3D(dataset, args.batchSz, args.dim, num_threads_in_multithreaded=2) tr_transforms = get_train_transform(args.dim) training_generator_aug = SingleThreadedAugmenter(dataloader_train, tr_transforms,) trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator, lr_scheduler=None, dataset = dataset, train_data_loader_aug=training_generator_aug) trainer.training()
def main(): args = get_arguments() utils.reproducibility(args, seed) utils.make_dirs(args.save) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args, path='.././datasets')
def main(): args = get_arguments() utils.reproducibility(args, seed) # utils.make_dirs(args.save) if not os.path.exists(args.save): os.makedirs(args.save) training_generator, val_generator, full_volume, affine, dataset = medical_loaders.generate_datasets( args, path='/data/hejy/MedicalZooPytorch_2cls/datasets') model, optimizer = medzoo.create_model(args) criterion = DiceLoss(classes=2, skip_index_after=args.classes, weight=torch.tensor([1, 1]).cuda(), sigmoid_normalization=True) # criterion = WeightedCrossEntropyLoss() if args.cuda: model = model.cuda() # model.restore_checkpoint(args.pretrained) trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator, lr_scheduler=None) trainer.training()
def main(): args = get_arguments() utils.reproducibility(args, seed) utils.make_dirs(args.save) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets( args, path='.././datasets') model, optimizer = medzoo.create_model(args) criterion = DiceLoss(classes=args.classes) if args.cuda: model = model.cuda() print("Model transferred in GPU.....") trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator, lr_scheduler=None) print("START TRAINING...") trainer.training() visualize_3D_no_overlap_new(args, full_volume, affine, model, 10, args.dim)
def main(): args = get_arguments() os.environ["CUDA_VISIBLE_DEVICES"] = "0,2" ## FOR REPRODUCIBILITY OF RESULTS seed = 1777777 utils.reproducibility(args, seed) utils.make_dirs(args.save) name_model = args.model + "_" + args.dataset_name + "_" + utils.datestr() # TODO visual3D_temp.Basewriter package writer = SummaryWriter(log_dir='../runs/' + name_model, comment=name_model) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets( args, path='.././datasets') model, optimizer = medzoo.create_model(args) if args.cuda: model = model.cuda() print("Model transferred in GPU.....") print("START TRAINING...") for epoch in range(1, args.nEpochs + 1): train(args, model, training_generator, optimizer, epoch, writer) val_metrics, confusion_matrix = validation(args, model, val_generator, epoch, writer)
def main(): args = get_arguments() utils.reproducibility(args, seed) utils.make_dirs(args.save) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args, path='.././datasets') model, optimizer = medzoo.create_model(args) criterion = DiceLoss(classes=args.classes) if args.cuda: model = model.cuda() trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator) trainer.training()
def main(): args = get_arguments() utils.reproducibility(args, seed) utils.make_dirs(args.save) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args, path='.././datasets') model, optimizer = medzoo.create_model(args) criterion = DiceLoss(classes=args.classes) # ,skip_index_after=2,weight=torch.tensor([0.00001,1,1,1]).cuda()) if args.cuda: model = model.cuda() print("Model transferred in GPU.....") trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator) print("START TRAINING...") trainer.training()
def main(): args = get_arguments() if args.distributed: torch.cuda.set_device(args.local_rank) torch.distributed.init_process_group(backend='nccl', init_method='env://') args.world_size = torch.distributed.get_world_size() assert torch.backends.cudnn.enabled, "Amp requires cudnn backend to be enabled." torch.backends.cudnn.benchmark = True utils.reproducibility(args, seed) # utils.make_dirs(args.save) if not os.path.exists(args.save): os.makedirs(args.save) training_generator, val_generator, full_volume, affine, dataset = medical_loaders.generate_datasets( args, path='/data/hejy/MedicalZooPytorch_2cls/datasets') model, optimizer = medzoo.create_model(args) if args.sync_bn: model = apex.parallel.convert_syncbn_model(model) criterion = DiceLoss(classes=2, skip_index_after=args.classes, weight=torch.tensor([1, 1]).cuda(), sigmoid_normalization=True) # criterion = WeightedCrossEntropyLoss() if args.cuda: model = model.cuda() if args.distributed: model = DDP(model, delay_allreduce=True) # model.restore_checkpoint(args.pretrained) trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator, lr_scheduler=None) trainer.training()
def main(): args = get_arguments() utils.reproducibility(args, seed) utils.make_dirs(args.save) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets(args, path='./datasets') model, optimizer = medzoo.create_model(args) criterion = DiceLoss(classes=args.classes) # print("training_generator shape:", training_generator.dim()) # print("val_generator shape:", val_generator.dim()) if args.cuda: model = model.cuda() print("start training...") # torch.save(training_generator, "training_generator.tch") # torch.save(val_generator, "val_generator.tch") trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator) trainer.training()
def main(): args = get_arguments() if args.distributed: torch.distributed.init_process_group(backend='nccl', init_method='env://') args.world_size = torch.distributed.get_world_size() assert torch.backends.cudnn.enabled, "Amp requires cudnn backend to be enabled." #1 torch.backends.cudnn.benchmark = True utils.reproducibility(args, seed) utils.make_dirs(args.save) training_generator, val_generator, full_volume, affine = medical_loaders.generate_datasets( args, path='.././datasets') model, optimizer = medzoo.create_model(args) criterion = DiceLoss(classes=11, skip_index_after=args.classes) if args.sync_bn: model = apex.parallel.convert_syncbn_model(model) if args.cuda: model = model.cuda() print("Model transferred in GPU.....") if args.distributed: model = DDP(model, delay_allreduce=True) trainer = train.Trainer(args, model, criterion, optimizer, train_data_loader=training_generator, valid_data_loader=val_generator, lr_scheduler=None) print("START TRAINING...") trainer.training()