1. added sample.py to sample from a trained model.

2. --num_ens sets the number of ensembles. --save_uncertainty to save the std of the ensembles

Author: Aaron

driver.py

@@ -48,7 +48,7 @@ def parse_args():
     parser.add_argument('-bs', '--batch_size', type=int, default=8, help='batch size to train on (default: 8)')
     parser.add_argument('--timesteps', type=int, default=1000, help='number of timesteps (default: 1000)')
     parser.add_argument('-ds', '--dataset', default='generic', help='Dataset to use')
-    parser.add_argument('--save_every', type=int, default=100, help='save_every n rpochs (default: 100)')
+    parser.add_argument('--save_every', type=int, default=100, help='save_every n epochs (default: 100)')
     parser.add_argument('--load_model_from', default=None, help='path to pt file to load from')
     return parser.parse_args()
 

med_seg_diff_pytorch/dataset.py

@@ -66,11 +66,11 @@ def __init__(self, directory: str, transform, test_flag: bool = True):
         self.directory = os.path.expanduser(directory)
         self.transform = transform
         self.test_flag = test_flag
-        self.filenames = [os.path.join(self.directory, x) for x in os.listdir(self.directory) if x.endswith('.npy')]
+        self.filenames = [x for x in os.listdir(self.directory) if x.endswith('.npy')]
 
     def __getitem__(self, x: int):
         fname = self.filenames[x]
-        npy_img = np.load(fname)
+        npy_img = np.load(os.path.join(self.directory, fname))
         img = npy_img[:, :, :1]
         img = torch.from_numpy(img).permute(2, 0, 1)
         mask = npy_img[:, :, 1:]
@@ -84,7 +84,8 @@ def __getitem__(self, x: int):
             image = self.transform(image)
             torch.set_rng_state(state)
             mask = self.transform(mask)
-
+        if self.test_flag:
+            return image, mask, fname
         return image, mask
 
     def __len__(self) -> int:

sample.py

@@ -0,0 +1,117 @@
+import os
+import argparse
+from tqdm import tqdm
+import torch
+import torchvision.transforms as transforms
+from med_seg_diff_pytorch import Unet, MedSegDiff
+from med_seg_diff_pytorch.dataset import ISICDataset, GenericNpyDataset
+from accelerate import Accelerator
+import skimage.io as io
+
+
+
+## Parse CLI arguments ##
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-od', '--output_dir', type=str, default="output", help="Output dir.")
+    parser.add_argument('-ld', '--logging_dir', type=str, default="logs", help="Logging dir.")
+    parser.add_argument('-mp', '--mixed_precision', type=str, default="no", choices=["no", "fp16", "bf16"],
+                        help="Whether to do mixed precision")
+    parser.add_argument('-img', '--img_folder', type=str, default='ISBI2016_ISIC_Part3B_Training_Data',
+                        help='The image file path from data_path')
+    parser.add_argument('-csv', '--csv_file', type=str, default='ISBI2016_ISIC_Part3B_Training_GroundTruth.csv',
+                        help='The csv file to load in from data_path')
+    parser.add_argument('-sc', '--self_condition', action='store_true', help='Whether to do self condition')
+    parser.add_argument('-ic', '--mask_channels', type=int, default=1, help='input channels for training (default: 3)')
+    parser.add_argument('-c', '--input_img_channels', type=int, default=3,
+                        help='output channels for training (default: 3)')
+    parser.add_argument('-is', '--image_size', type=int, default=128, help='input image size (default: 128)')
+    parser.add_argument('-dd', '--data_path', default='./data', help='directory of input image')
+    parser.add_argument('-d', '--dim', type=int, default=64, help='dim (default: 64)')
+    parser.add_argument('-e', '--epochs', type=int, default=10000, help='number of epochs (default: 10000)')
+    parser.add_argument('-bs', '--batch_size', type=int, default=8, help='batch size to train on (default: 8)')
+    parser.add_argument('--timesteps', type=int, default=1000, help='number of timesteps (default: 1000)')
+    parser.add_argument('-ds', '--dataset', default='generic', help='Dataset to use')
+    parser.add_argument('--save_every', type=int, default=100, help='save_every n epochs (default: 100)')
+    parser.add_argument('--num_ens', type=int, default=5,
+                        help='number of times to sample to make an ensable of predictions like in the paper (default: 5)')
+    parser.add_argument('--load_model_from', default=None, help='path to pt file to load from')
+    parser.add_argument('--save_uncertainty', action='store_true',
+                        help='Whether to store the uncertainty in predictions (only works for ensablmes)')
+
+    return parser.parse_args()
+
+
+def load_data(args):
+    # Load dataset
+    if args.dataset == 'ISIC':
+        transform_list = [transforms.Resize((args.image_size, args.image_size)), transforms.ToTensor(), ]
+        transform_train = transforms.Compose(transform_list)
+        dataset = ISICDataset(args.data_path, args.csv_file, args.img_folder, transform=transform_train, training=False,
+                              flip_p=0.5)
+    elif args.dataset == 'generic':
+        transform_list = [transforms.ToPILImage(), transforms.Resize(args.image_size), transforms.ToTensor()]
+        transform_train = transforms.Compose(transform_list)
+        dataset = GenericNpyDataset(args.data_path, transform=transform_train, test_flag=True)
+    else:
+        raise NotImplementedError(f"Your dataset {args.dataset} hasn't been implemented yet.")
+
+    ## Define PyTorch data generator
+    training_generator = torch.utils.data.DataLoader(
+        dataset,
+        batch_size=args.batch_size,
+        shuffle=False)
+
+    return training_generator
+
+
+def main():
+    args = parse_args()
+    logging_dir = os.path.join(args.output_dir, args.logging_dir)
+    inference_dir = os.path.join(args.output_dir, 'inference')
+    os.makedirs(inference_dir, exist_ok=True)
+    accelerator = Accelerator(
+        mixed_precision=args.mixed_precision,
+    )
+    # if accelerator.is_main_process:
+    #     accelerator.init_trackers("med-seg-diff", config=vars(args))
+
+    ## DEFINE MODEL ##
+    model = Unet(
+        dim=args.dim,
+        image_size=args.image_size,
+        dim_mults=(1, 2, 4, 8),
+        mask_channels=args.mask_channels,
+        input_img_channels=args.input_img_channels,
+        self_condition=args.self_condition
+    )
+
+    ## LOAD DATA ##
+    data_loader = load_data(args)
+
+    diffusion = MedSegDiff(
+        model,
+        timesteps=args.timesteps
+    ).to(accelerator.device)
+
+    if args.load_model_from is not None:
+        save_dict = torch.load(args.load_model_from)
+        diffusion.model.load_state_dict(save_dict['model_state_dict'])
+
+    for (imgs, masks, fnames) in tqdm(data_loader):
+        # pre allocate preds
+        preds = torch.zeros((imgs.shape[0], args.num_ens, imgs.shape[2], imgs.shape[3]))
+        for i in range(args.num_ens):
+            preds[:, i:i+1, :, :] = diffusion.sample(imgs).cpu().detach()
+        preds_mean = preds.mean(dim=1)
+        preds_std = preds.std(dim=1)
+
+        for idx in range(preds.shape[0]):
+            io.imsave(os.path.join(inference_dir, fnames[idx].replace('.npy', '.png')), preds_mean[idx, :, :])
+            if args.save_uncertainty:
+                io.imsave(os.path.join(inference_dir, fnames[idx].replace('.npy', '_std.png')), preds_std[idx, :, :])
+
+
+
+if __name__ == '__main__':
+    main()