Metadata-Version: 2.1
Name: pyra-pytorch
Version: 0.0.5
Summary: Pyramid Focus Augmentation: Medical Image Segmentation with Step Wise Focus
Home-page: https://github.com/vlbthambawita/pyra-pytorch
Author: Vajira Thambawita
Author-email: vlbthambawita@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: Pillow

# 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](https://arxiv.org/pdf/2012.07430v1.pdf)) and the original github repository: [PYRA](https://vlbthambawita.github.io/PYRA/).





```latex
@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,
```bash
pip install pyra-pytorch
```

### Creating a PYRA augmented dataset:

```python
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](https://github.com/vlbthambawita/pyra-pytorch/blob/main/tutorial/load_data_with_PYRA.ipynb)


# Contact us:

vajira@simula.no | michael@simula.no


