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Pseudo-Label Guided Image Synthesis for Semi-Supervised COVID-19 Pneumonia Infection Segmentation.

Implementation of Pseudo-Label Guided Image Synthesis for Semi-Supervised COVID-19 Pneumonia Infection Segmentation.

Implementation

1. Installation

pytorch==1.9.0

2. Datset Preparation

├── COVID249
│   ├── NII (Original dataset in NIFTI)
│   ├── PNG (Pre-processed dataset in PNG)
│   ├── train_0.1_l.xlsx (datasplit for 10% setting)
│   ├── train_0.1_u.xlsx (datasplit for 10% setting)
│   ├── train_0.2_l.xlsx (datasplit for 20% setting)
│   ├── train_0.2_u.xlsx (datasplit for 20% setting)
│   ├── train_0.3_l.xlsx (datasplit for 30% setting)
│   ├── train_0.3_u.xlsx (datasplit for 30% setting)
│   ├── test_slice.xlsx (datasplit for testing)
│   ├── val_slice.xlsx (datasplit for validation)
├── MOS1000
│   ├── NII (Original dataset in NIFTI)
│   ├── PNG (Pre-processed dataset in PNG)
│   ├── train_slice_label.xlsx (datasplit)
│   ├── train_slice_unlabel.xlsx (datasplit)
│   ├── test_slice.xlsx (datasplit for testing)
│   ├── val_slice.xlsx (datasplit for validation)

• Convert the nifti images to int32 png format, then subtract 32768 from the pixel intensities to obtain the original Hounsfield unit (HU) values, saved in Image folder, similar to the processing steps in Deeplesion.
• The lung regions can be extracted by a leading lung segmentation model provided by JoHof.
• Pre-processed COVID249 can be downloaded from the link. MOS1000 can be processed using the same steps, we do not provide all the processed images due to its large dataset size.
• You can train SEAN models following SEAN , or download our pre-trained checkpoints from the link.

3. Training Our Models

python train_SACPS.py
python train_SAST.py

4. Training Other Models

We have provided a template for training other models, where we have implemented the dataloader, optimizer, etc. The core codes are shown as below:

for epoch in range(max_epoch):
    print("Start epoch ", epoch+1, "!")

    tbar = tqdm(range(len(unlabeled_dataloader)), ncols=70)
    labeled_dataloader_iter = iter(labeled_dataloader)
    unlabeled_dataloader_iter = iter(unlabeled_dataloader)

    for batch_idx in tbar:
        try:
            input_l, target_l, file_name_l , lung_l = labeled_dataloader_iter.next()
        except StopIteration:
            labeled_dataloader_iter = iter(labeled_dataloader)
            input_l, target_l, file_name_l , lung_l = labeled_dataloader_iter.next()

        # load data
        input_ul, target_ul, file_name_ul , lung_ul = unlabeled_dataloader_iter.next()
        input_ul, target_ul, lung_ul = input_ul.cuda(non_blocking=True), target_ul.cuda(non_blocking=True), lung_ul.cuda(non_blocking=True)
        input_l, target_l, lung_l = input_l.cuda(non_blocking=True), target_l.cuda(non_blocking=True), lung_l.cuda(non_blocking=True)


        # Add impelmentation here: the training process
        #-------------------------------------------------------------
        #*************************************************************
        #-------------------------------------------------------------


        optimizer.zero_grad()
        loss.backward()
        optimizer.step()
        lr_ = base_lr * (1.0 - iter_num / max_iterations) ** 0.9
        for param_group in optimizer.param_groups:
            param_group['lr'] = lr_

        iter_num = iter_num + 1
        writer.add_scalar('info/lr', lr_, iter_num)
        writer.add_scalar('info/total_loss', loss, iter_num)
        logging.info('iteration %d : loss : %f' % (iter_num, loss.item()))
writer.close()

5. Testing

python segment_test.py

def test(args, snapshot_path):
    model = net_factory(net_type=args.model)
    model.load_state_dict(torch.load(args.model_path))
    model.eval()

    nsd, dice = get_model_metric(args = args, model = model, snapshot_path=snapshot_path, model_name='model', mode='test')
    print('nsd : %f dice : %f ' % (nsd, dice))

• snapshot_path: folder for saving results.
• args.model: model type.
• args.model_path: trained model path.
• get_model_metric(): which includes prediction, png2nifti, calculate_nsd_dsc.

Suplementary information

1. Statistics of the datasets.

Descriptive statistics, including x-, y- and z-spacing, of both datasets are shown as follow.

2. Links for competing methods.

• [Self-Ensembling]: JBHI 2021; code
• [Cross Pseudo Supervision]: CVPR 2021; code
• [Uncertainty-Aware Mean-Teacher]: CVPR 2021; code
• [Cross-Consistency Training]: CVPR 2020; code
• [Uncertainty-guided Dual-Consistency]: MICCAI 2021; code
• [SemiInfNet]: TMI 2020; code
• [Self-Training]: NeurIPS 2020; code

Citation

If you find this repository useful for your research, please cite the following:

@ARTICLE{9931157,
  author={Lyu, Fei and Ye, Mang and Carlsen, Jonathan Frederik and Erleben, Kenny and Darkner, Sune and Yuen, Pong C.},
  journal={IEEE Transactions on Medical Imaging}, 
  title={Pseudo-Label Guided Image Synthesis for Semi-Supervised COVID-19 Pneumonia Infection Segmentation}, 
  year={2022},
  volume={},
  number={},
  pages={1-1},
  doi={10.1109/TMI.2022.3217501}}

Acknowledgments

We thank Luo, Xiangde for sharing his codes, our code borrows heavily from https://github.com/HiLab-git/SSL4MIS.