kaggle project: https://www.kaggle.com/c/hubmap-kidney-segmentation/
developed using pytorch 1.5.0, CUDA 10.1
the train script is at train/train_v1.py and this works with a configuration file where a sample can be found in train/config/train_v1_config/train_v1.sample.yaml.
copy the sample config and adjust the options to fit your needs.
then run the train script from bash command like:
$ python train_v1.py path/to/config
the outputs will be saved in an automatically created directory under train/ckpt/train_v1
to run inference on a slice image, setup config file from sample in predict/config/predict_config/sample.yaml and run with the following command
$ cd predict
$ python predict.py /config/file/path
this will save output mask images.
to run evaluation on slice image, setup config file from sample in predict/config/eval_config/sample.yaml and run with the following command
$ cd predcit
$ python eval.py /config/file/path
this will save outputs including overlayed images and save dice values.
data preparation scripts are under data_prep/. these scripts are mainly slicing raw data, splitting, restructuring dataset structure, etc.
a pretrained model and trained config file is zipped and available here
when using this for prediction, please adjust prediction config appropriately to match pretrained model's config, such as resize_w and resize_h.