pyra-pytorch 0.0.5

Pyramid Focus Augmentation: Medical Image Segmentation with Step Wise Focus

pyra-pytorch

This is a package supporting Pytorch datasets. This implementation is based on the augmentation method discussed in the paper "Pyramid-Focus-Augmentation: Medical Image Segmentation with Step-Wise Focus" (PDF) and the original github repository: PYRA.

@article{thambawita2020pyramid,
  title={Pyramid-Focus-Augmentation: Medical Image Segmentation with Step-Wise Focus},
  author={Thambawita, Vajira and Hicks, Steven and Halvorsen, P{\aa}l and Riegler, Michael A},
  journal={arXiv preprint arXiv:2012.07430},
  year={2020}
}

How to use:

Install the package,

pip install pyra-pytorch

Creating a PYRA augmented dataset:

from pyra_pytorch import PYRADataset

dataset = PYRADataset("./image_path", # image folder
                      "./masks_path", # mask folder - files´s names of this folder should have image names as prefix to find correct image and mask pairs.
                      img_size = 256,  # height and width of image to resize
                      grid_sizes=[2,4,8,16,32,64,128,256] , # Gird sizes to use as grid augmentation. Note that, the image size after resizing ()
                      transforms = None
                      )
'''
./image_path" --> image folder

./masks_path" --> mask folder - files´s names of this folder should have image names as prefix to find correct image and mask pairs.

img_size = 256 --> height and width of image to resize

grid_sizes=[2,4,8,16,32,64,128,256]  --> Gird sizes to use as grid augmentation. Note that, the image size after resizing (in this case, it is 256) shoud be divisible by these grid sizes.

transforms = None --> Other type of transformations using in Pytorch. 

'''

Sample ipython notebook

notebook

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