import os import torch from desam import sam_model_registry from desam.training import run_training, run_testing import argparse import monai from torch.utils.data import DataLoader from utils.utils import Logger, split_prostatedataset from utils.datasets import ProstateDataset import torch.cuda.amp parser = argparse.ArgumentParser() parser.add_argument('--gpuid', type=int, default=0) parser.add_argument('--seed', type=int, default=0) parser.add_argument('--center', type=int, default=3) parser.add_argument('--model_type', type=str, default='vit_h') parser.add_argument('--work_dir', type=str, default='E:/DeSAMData') parser.add_argument('--epoch', type=int, default=50) parser.add_argument('--neg_points', type=int, default=1) parser.add_argument('--grid', type=int, default=9) parser.add_argument('--batch_size', type=int, default=8) parser.add_argument('--lr', type=float, default=0.0001) parser.add_argument('--iou_thresh', type=float, default=0.5) parser.add_argument('--mse', type=bool, default=False) parser.add_argument('--sgd', type=bool, default=False) parser.add_argument('--pred_embedding', type=bool, default=False) parser.add_argument('--test_only', type=bool, default=False) parser.add_argument('--random_validation', type=bool, default=False) parser.add_argument('--mixprecision', type=bool, default=False) ''' GPU info with mix precision: bs=1 | bs=2 | bs=4 | bs=8 | bs=16 4.1GB | 4.8GB | 5.7GB | 7.8GB | 11.6GB without mix precision: bs=8 10.9GB ''' args = parser.parse_args() os.environ["CUDA_VISIBLE_DEVICES"] = str(args.gpuid) # prepare data path work_dir = args.work_dir os.makedirs(work_dir, exist_ok=True) data_root = os.path.join(work_dir, 'image_embeddings', 'npz_files_{}').format(args.model_type) if not os.path.exists(data_root): print('no precomputed image embeddings! please run precompute_embeddings.py first.') raise task_name = 'desam_prostate_gridpoints_center{}'.format(args.center) patientid_path = os.path.join(work_dir, 'raw_data', 'prostate_patientid.csv') model_save_path = os.path.join(work_dir, 'results_folder', task_name) os.makedirs(model_save_path, exist_ok=True) logger = Logger(output_folder=model_save_path) # prepare SAM model model_zoo = { 'vit_h': os.path.join(work_dir, 'checkpoint/sam_vit_h_4b8939.pth'), 'vit_l': os.path.join(work_dir, 'checkpoint/sam_vit_l_0b3195.pth'), 'vit_b': os.path.join(work_dir, 'checkpoint/sam_vit_b_01ec64.pth'), } device = 'cuda' checkpoint = model_zoo[args.model_type] desam = sam_model_registry[args.model_type](checkpoint=checkpoint) desam.to(device) # dataset split train_patientid, val_patientid, test_patientid = split_prostatedataset( data_root=data_root, patientid_path=patientid_path, center=args.center, seed=args.center, random_validation=args.random_validation ) # Set up the optimizer, hyperparameter tuning will improve performance here if args.sgd: optimizer = torch.optim.SGD(desam.mask_decoder.parameters(), lr=args.lr, weight_decay=0, momentum=0.99) else: optimizer = torch.optim.Adam(desam.mask_decoder.parameters(), lr=args.lr, weight_decay=0) if args.mse: iou_loss = torch.nn.MSELoss(size_average=None, reduce=None, reduction='mean') else: iou_loss = torch.nn.L1Loss(size_average=None, reduce=None, reduction='mean') dicece_loss = monai.losses.DiceCELoss(sigmoid=True, squared_pred=True, reduction='mean') scaler = torch.cuda.amp.GradScaler(enabled=args.mixprecision) # prepare dataloader train_dataset = ProstateDataset(data_root, train_patientid, args.neg_points) train_dataloader = DataLoader(train_dataset, batch_size=args.batch_size, shuffle=True) val_dataset = ProstateDataset(data_root, val_patientid, args.neg_points) val_dataloader = DataLoader(val_dataset, batch_size=1, shuffle=False) desam.train() # train, validation and test if args.test_only: if not os.path.exists(os.path.join(model_save_path, 'desam_model_best.pth')): print('use test_only after training!') raise desam = sam_model_registry[args.model_type](checkpoint=os.path.join(model_save_path, 'desam_model_best.pth')) desam.to(device=device) run_testing( model=desam, data_root=data_root, model_save_path=model_save_path, iou_thresh=args.iou_thresh, ood_patientid=test_patientid, grid=args.grid, logger=logger, pred_embedding=args.pred_embedding, device=device ) else: run_training( model=desam, max_num_epochs=args.epoch, logger=logger, model_save_path=model_save_path, optimizer=optimizer, initial_lr=args.lr, train_dataloader=train_dataloader, val_dataloader=val_dataloader, scaler=scaler, dicece_loss=dicece_loss, iou_loss=iou_loss, device=device, is_mixprecision=args.mixprecision ) desam = sam_model_registry[args.model_type](checkpoint=os.path.join(model_save_path, 'desam_model_best.pth')) desam.to(device=device) run_testing( model=desam, data_root=data_root, model_save_path=model_save_path, iou_thresh=args.iou_thresh, ood_patientid=test_patientid, grid=args.grid, logger=logger, pred_embedding=args.pred_embedding, device=device )