A library for chest X-ray datasets and models. Including pre-trainined models.
This code is still under development
pip install torchxrayvision
import torchxrayvision as xrv
These are default pathologies:
xrv.datasets.default_pathologies
['Atelectasis',
'Consolidation',
'Infiltration',
'Pneumothorax',
'Edema',
'Emphysema',
'Fibrosis',
'Effusion',
'Pneumonia',
'Pleural_Thickening',
'Cardiomegaly',
'Nodule',
'Mass',
'Hernia',
'Lung Lesion',
'Fracture',
'Lung Opacity',
'Enlarged Cardiomediastinum']
Specify weights for pretrained models (currently all DenseNet121)
model = xrv.models.DenseNet(weights="all")
model = xrv.models.DenseNet(weights="kaggle")
model = xrv.models.DenseNet(weights="nih")
model = xrv.models.DenseNet(weights="chex")
model = xrv.models.DenseNet(weights="minix_nb")
model = xrv.models.DenseNet(weights="minix_ch")
transform = torchvision.transforms.Compose([xrv.datasets.XRayCenterCrop(),
xrv.datasets.XRayResizer(224)])
d_kaggle = xrv.datasets.Kaggle_Dataset(imgpath="path to stage_2_train_images_jpg",
transform=transform)
d_chex = xrv.datasets.CheX_Dataset(imgpath="path to CheXpert-v1.0-small",
csvpath="path to CheXpert-v1.0-small/train.csv",
transform=transform)
d_nih = xrv.datasets.NIH_Dataset(imgpath="path to NIH images")
d_nih2 = xrv.datasets.NIH_Google_Dataset(imgpath="path to NIH images")
d_pc = xrv.datasets.PC_Dataset(imgpath="path to image folder")
d_covid19 = xrv.datasets.COVID19_Dataset() # specify imgpath and csvpath for the dataset
relabel_dataset will align labels to have the same order as the pathologies argument.
xrv.datasets.relabel_dataset(xrv.datasets.default_pathologies , d_nih) # has side effects
Joseph Paul Cohen, Joseph Viviano, Mohammad Hashir, and Hadrien Bertrand.
TorchXrayVision: A library of chest X-ray datasets and models.
https://github.com/mlmed/torchxrayvision, 2020
and
Cohen, J. P., Hashir, M., Brooks, R., & Bertrand, H.
On the limits of cross-domain generalization in automated X-ray prediction. 2020
arXiv preprint [https://arxiv.org/abs/2002.02497](https://arxiv.org/abs/2002.02497)
@article{cohen2020limits,
title={On the limits of cross-domain generalization in automated X-ray prediction},
author={Cohen, Joseph Paul and Hashir, Mohammad and Brooks, Rupert and Bertrand, Hadrien},
journal={arXiv preprint arXiv:2002.02497},
year={2020}
}