Region Attention Transformer for Medical Image Restoration (RAT)

PyTorch implementation for Region Attention Transformer for Medical Image Restoration (MICCAI 2024).

Network Architecture

Visual Comparison

Getting Started with Model Inference

RAT has two inputs: the input image and the indexed mask obtained from post-processing the SAM output mask. The example input image is located at “./example_img/input_img.png", and the resulting indexed mask can be found at “./example_img/indexed_mask.nii”.

Next, we will first explain how to obtain the indexed mask using SAM, followed by an introduction to the final model inference.

• Mask Prediction & Postprocess

  First, you can obtain region partitioning masks with the Segment Anything Model (SAM) as follows:

  from segment_anything import SamAutomaticMaskGenerator, sam_model_registry
  sam = sam_model_registry["<model_type>"](checkpoint = "<path/to/checkpoint>")
  mask_generator = SamAutomaticMaskGenerator(sam)
  masks = mask_generator.generate(<your_image>) 
  #<your_image>: Load the input image at "./example_img/input_img.png"

  !!!!! It is now recommended to employ advanced models such as Efficient-SAM, and RWKV-SAM, as they provide superior efficiency and effectiveness over the conventional SAM model.

  Then, you need to post-process the masks to obtain an indexed mask, which can be then used for compact region partitioning during the downsampling process.

  import numpy as np
  def toSegMap(masks): 
      result = np.zeros(masks[0]['segmentation'].shape)
      for i in range(len(masks)): 
          result[masks[i]['segmentation']] = (i+1) 
      result[result==0] = len(masks) + 1
      return result
  masks = sorted(masks, key = itemgetter('area'), reverse = True) 
  indexed_mask = toSegMap(masks) # Output at "./example_img/indexed_mask.nii"

  The resultant indexed mask is available at "./example_img/indexed_mask.nii". You can use AMIDE or ITK-SNAP softwares to visualize the ".nii" file. To facilitate understanding, a toy example of the indexed mask is displayed below:

  

• RAT Inference

  With the input image and its resultant indexed mask, the output of RAT can be obtained as follows:

  from Model_RAT import RAT
  model = RAT()
  output_img = model(input_img, indexed_mask) 
  # lr_img shape: [B, C, H, W] 
  # indexed_mask shape: [B, H, W]

Citation

If you find RAT useful in your research, please consider citing:

@inproceedings{yang2024rat,
  title={Region Attention Transformer for Medical Image Restoration},
  author={Yang, Zhiwen and Chen, Haowei and Qian, Ziniu and Zhou, Yang and Zhang, Hui and Zhao, Dan and Wei, Bingzheng and Xu, Yan},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={603--613},
  year={2024},
  organization={Springer}
}