from pathlib import Path from tqdm import trange import torch import monai from monai.data import ThreadDataLoader from monai.networks.nets import FlexibleUNet from surg_seg.Datasets.ImageDataset import ImageSegmentationDataset from surg_seg.Datasets.VideoDatasets import CombinedVidDataset from surg_seg.Trainers.Trainer import ModelTrainer def create_FlexibleUnet(device, pretrained_weights_path: Path, out_channels: int): model = FlexibleUNet( in_channels=3, out_channels=out_channels, backbone="efficientnet-b0", pretrained=True, is_pad=False, ).to(device) pretrained_weights = monai.bundle.load( name="endoscopic_tool_segmentation", bundle_dir=pretrained_weights_path, version="0.2.0" ) model_weight = model.state_dict() weights_no_head = {k: v for k, v in pretrained_weights.items() if not "segmentation_head" in k} model_weight.update(weights_no_head) model.load_state_dict(model_weight) return model def train_with_video_dataset(): device = "cpu" vid_root = Path("/home/juan1995/research_juan/accelnet_grant/data/rec01/") vid_filepath = vid_root / "raw/rec01_seg_raw.avi" seg_filepath = vid_root / "annotation2colors/rec01_seg_annotation2colors.avi" ds = CombinedVidDataset(vid_filepath, seg_filepath) dl = ThreadDataLoader(ds, batch_size=4, num_workers=0, shuffle=True) pretrained_weigths_path = Path("./assets/weights/trained-weights.pt") model = create_FlexibleUnet(device, pretrained_weigths_path, ds.label_channels) optimizer = torch.optim.Adam(model.parameters(), 1e-2) trainer = ModelTrainer(device=device, max_epochs=2) model, training_stats = trainer.train_model(model, optimizer, dl) training_stats.plot_stats() model_path = "./assets/weights/myweights_video" torch.save(model.state_dict(), model_path) training_stats.to_pickle(model_path) def train_with_image_dataset(): device = "cpu" root = Path("/home/juan1995/research_juan/accelnet_grant/data") train_dirs = [root / "rec01", root / "rec03", root / "rec05"] val_dirs = [root / "rec02", root / "rec04"] ds = ImageSegmentationDataset(train_dirs, "5colors") dl = ThreadDataLoader(ds, batch_size=4, num_workers=0, shuffle=True) val_ds = ImageSegmentationDataset(val_dirs, "5colors") val_dl = ThreadDataLoader(val_ds, batch_size=4, num_workers=0, shuffle=True) print(f"Training dataset size: {len(ds)}") print(f"Validation dataset size: {len(val_ds)}") pretrained_weigths_path = Path("./assets/weights/pretrained-weights") model = create_FlexibleUnet(device, pretrained_weigths_path, ds.label_channels) optimizer = torch.optim.Adam(model.parameters(), 1e-2) trainer = ModelTrainer(device=device, max_epochs=2) model, training_stats = trainer.train_model(model, optimizer, dl, validation_dl=val_dl) model_path = Path("./assets/weights/myweights_image") model_path.mkdir(exist_ok=True) torch.save(model.state_dict(), model_path / "myweights.pt") training_stats.to_pickle(model_path) training_stats.plot_stats(file_path=model_path) print(f"Last train IOU {training_stats.iou_list[-1]}") print(f"Last validation IOU {training_stats.validation_iou_list[-1]}") def main(): # train_with_video_dataset() train_with_image_dataset() if __name__ == "__main__": main()