diff --git a/.gitignore b/.gitignore index c7bb7ca..9d60c97 100644 --- a/.gitignore +++ b/.gitignore @@ -1,8 +1,6 @@ .venv/ .mypy_cache/ __pycache__/ - -checkpoints/ wandb/ -INTERRUPTED.pth +*.pth diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 0000000..f7a9165 --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,22 @@ +{ + // Use IntelliSense to learn about possible attributes. + // Hover to view descriptions of existing attributes. + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 + "version": "0.2.0", + "configurations": [ + { + "name": "Python: Current File", + "type": "python", + "request": "launch", + "program": "${file}", + "console": "integratedTerminal", + "args": [ + "--input", + "SM.png", + "--output", + "test.png", + ], + "justMyCode": true + } + ] +} diff --git a/SM.png.REMOVED.git-id b/SM.png.REMOVED.git-id new file mode 100644 index 0000000..21a947e --- /dev/null +++ b/SM.png.REMOVED.git-id @@ -0,0 +1 @@ +c6d08aa612451072cfe32a3ee086d08342ed9dd9 \ No newline at end of file diff --git a/src/predict.py b/src/predict.py index c1a445c..587e11e 100755 --- a/src/predict.py +++ b/src/predict.py @@ -1,16 +1,13 @@ import argparse import logging -import os +import albumentations as A import numpy as np import torch -import torch.nn.functional as F +from albumentations.pytorch import ToTensorV2 from PIL import Image -from torchvision import transforms -from src.utils.dataset import BasicDataset from unet import UNet -from utils.utils import plot_img_and_mask def get_args(): @@ -20,7 +17,7 @@ def get_args(): parser.add_argument( "--model", "-m", - default="MODEL.pth", + default="model.pth", metavar="FILE", help="Specify the file in which the model is stored", ) @@ -28,7 +25,6 @@ def get_args(): "--input", "-i", metavar="INPUT", - nargs="+", help="Filenames of input images", required=True, ) @@ -36,108 +32,62 @@ def get_args(): "--output", "-o", metavar="OUTPUT", - nargs="+", help="Filenames of output images", ) parser.add_argument( - "--viz", - "-v", - action="store_true", - help="Visualize the images as they are processed", - ) - parser.add_argument( - "--no-save", - "-n", - action="store_true", - help="Do not save the output masks", - ) - parser.add_argument( - "--mask-threshold", + "--threshold", "-t", type=float, default=0.5, help="Minimum probability value to consider a mask pixel white", ) - parser.add_argument( - "--scale", - "-s", - type=float, - default=0.5, - help="Scale factor for the input images", - ) return parser.parse_args() -def predict_img(net, full_img, device, scale_factor=1, out_threshold=0.5): - net.eval() - img = torch.from_numpy(BasicDataset.preprocess(full_img, scale_factor, is_mask=False)) +def predict_img(net, img, device, threshold): img = img.unsqueeze(0) img = img.to(device=device, dtype=torch.float32) + net.eval() with torch.inference_mode(): output = net(img) + preds = torch.sigmoid(output)[0] + full_mask = preds.cpu().squeeze() - probs = torch.sigmoid(output)[0] - - tf = transforms.Compose( - [transforms.ToPILImage(), transforms.Resize((full_img.size[1], full_img.size[0])), transforms.ToTensor()] - ) - - full_mask = tf(probs.cpu()).squeeze() - - if net.n_classes == 1: - return (full_mask > out_threshold).numpy() - else: - return F.one_hot(full_mask.argmax(dim=0), net.n_classes).permute(2, 0, 1).numpy() - - -def get_output_filenames(args): - def _generate_name(fn): - split = os.path.splitext(fn) - return f"{split[0]}_OUT{split[1]}" - - return args.output or list(map(_generate_name, args.input)) - - -def mask_to_image(mask: np.ndarray): - if mask.ndim == 2: - return Image.fromarray((mask * 255).astype(np.uint8)) - elif mask.ndim == 3: - return Image.fromarray((np.argmax(mask, axis=0) * 255 / mask.shape[0]).astype(np.uint8)) + return np.asarray(full_mask > threshold) if __name__ == "__main__": args = get_args() - in_files = args.input - out_files = get_output_filenames(args) - net = UNet(n_channels=3, n_classes=2) + net = UNet(n_channels=3, n_classes=1) device = torch.device("cuda" if torch.cuda.is_available() else "cpu") - logging.info(f"Loading model {args.model}") logging.info(f"Using device {device}") + logging.info("Transfering model to device") net.to(device=device) + + logging.info(f"Loading model {args.model}") net.load_state_dict(torch.load(args.model, map_location=device)) - logging.info("Model loaded!") + logging.info(f"Loading image {args.input}") + img = Image.open(args.input).convert("RGB") - for i, filename in enumerate(in_files): + logging.info(f"Preprocessing image {args.input}") + tf = A.Compose( + [ + A.ToFloat(max_value=255), + ToTensorV2(), + ], + ) + aug = tf(image=np.asarray(img)) + img = aug["image"] - logging.info(f"\nPredicting image {filename} ...") - img = Image.open(filename) + logging.info(f"Predicting image {args.input}") + mask = predict_img(net=net, img=img, threshold=args.threshold, device=device) - mask = predict_img( - net=net, full_img=img, scale_factor=args.scale, out_threshold=args.mask_threshold, device=device - ) - - if not args.no_save: - out_filename = out_files[i] - result = mask_to_image(mask) - result.save(out_filename) - logging.info(f"Mask saved to {out_filename}") - - if args.viz: - logging.info(f"Visualizing results for image {filename}, close to continue...") - plot_img_and_mask(img, mask) + logging.info(f"Saving prediction to {args.output}") + mask = Image.fromarray(mask) + mask.write(args.output) diff --git a/src/train.py b/src/train.py index 1fd7468..4f56bde 100644 --- a/src/train.py +++ b/src/train.py @@ -105,6 +105,9 @@ def main(): net.load_state_dict(torch.load(args.load, map_location=device)) logging.info(f"Model loaded from {args.load}") + # save initial model.pth + torch.save(net.state_dict(), "model.pth") + # transfer network to device net.to(device=device) @@ -146,7 +149,7 @@ def main(): criterion = nn.BCEWithLogitsLoss() # setup wandb - wandb.init( + run = wandb.init( project="U-Net-tmp", config=dict( epochs=args.epochs, @@ -156,6 +159,9 @@ def main(): ), ) wandb.watch(net, log_freq=100) + # artifact = wandb.Artifact("model", type="model") + # artifact.add_file("model.pth") + # run.log_artifact(artifact) logging.info( f"""Starting training: @@ -222,9 +228,11 @@ def main(): print(f"Train Loss: {train_loss:.3f}, Valid Score: {val_score:3f}") # save weights when epoch end - Path(CHECKPOINT_DIR).mkdir(parents=True, exist_ok=True) - torch.save(net.state_dict(), str(CHECKPOINT_DIR / "checkpoint_epoch{}.pth".format(epoch))) - logging.info(f"Checkpoint {epoch} saved!") + # torch.save(net.state_dict(), "model.pth") + # run.log_artifact(artifact) + logging.info(f"model saved!") + + run.finish() except KeyboardInterrupt: torch.save(net.state_dict(), "INTERRUPTED.pth") diff --git a/test.png b/test.png new file mode 100644 index 0000000..a0cad88 Binary files /dev/null and b/test.png differ