├── .gitignore ├── .mdai ├── README.md ├── config.yaml ├── custom_gradcam.py ├── helper.py ├── mdai_deploy.py └── requirements.txt ├── README.md ├── args ├── __init__.py ├── base_arg_parser.py ├── test_arg_parser.py └── train_arg_parser.py ├── cams ├── __init__.py ├── base_cam.py ├── get_cams_intermountain.sh ├── grad_cam.py └── guided_backprop.py ├── ct ├── __init__.py ├── ct_pe.py ├── ct_pe_constants.py ├── ct_series.py └── ct_series_intermountain.py ├── data_loader ├── __init__.py ├── ct_data_loader.py ├── kinetics_data_loader.py ├── padded_inputs.py └── sorted_sampler.py ├── datasets ├── __init__.py ├── base_ct_dataset.py ├── ct_pe_dataset_3d.py └── kinetics_dataset.py ├── environment.yml ├── evaluator ├── __init__.py ├── model_evaluator.py └── output_aggregator.py ├── get_cams.py ├── get_cams.sh ├── img └── grad_cam.gif ├── intermountain ├── __init__.py ├── create_hdf5_intermountain.py ├── create_series_list_intermountain.py ├── parse_raw_dicom.py ├── parse_raw_dicom.sh └── test_intermountain.py ├── logger ├── __init__.py ├── base_logger.py ├── test_logger.py └── train_logger.py ├── models ├── __init__.py ├── activation │ ├── __init__.py │ └── swish.py ├── layers │ ├── __init__.py │ └── penet │ │ ├── __init__.py │ │ ├── gap_linear.py │ │ ├── penet_asp_pool.py │ │ ├── penet_bottleneck.py │ │ ├── penet_decoder.py │ │ ├── penet_encoder.py │ │ ├── penet_lateral.py │ │ └── se_block.py ├── loss │ ├── __init__.py │ ├── focal_loss.py │ ├── hybrid_loss.py │ └── lovasz_hinge_loss.py ├── penet.py └── penet_classifier.py ├── requirements.txt ├── run_test_intermountain.sh ├── saver ├── __init__.py └── model_saver.py ├── scripts ├── .ipynb_checkpoints │ └── Model Statistics-checkpoint.ipynb ├── Model Statistics.ipynb ├── __init__.py ├── convert_masks.py ├── create_hdf5.py ├── create_pe_hdf5.py ├── create_pe_hdf5_update.py ├── create_series_list.py ├── generate_nifti.py ├── get_cams.py ├── get_gpu_stats.py ├── get_mean_voxel.py ├── get_series_numbers.py ├── get_subset_stats.py ├── kinetics │ ├── __init__.py │ ├── fps.py │ ├── kinetics_json.py │ ├── n_frames_kinetics.py │ ├── video_jpg.py │ └── video_jpg_kinetics.py ├── merge_converted.py ├── merge_pe.py ├── move_masks.py ├── restructure_normals.py ├── run_args.py ├── run_xgboost.py └── write_csv.py ├── series_list.pkl ├── test.py ├── test.sh ├── test_from_dicom.py ├── test_from_dicom.sh ├── train.py ├── train.sh └── util ├── __init__.py ├── eval_util.py ├── hdf5 ├── create_pe_hdf5.sh ├── create_pe_hdf5_intermountain.py └── create_pe_hdf5_stanford.py ├── image_util.py ├── io_util.py ├── optim_util.py ├── single_study_util.py └── transforms ├── __init__.py ├── spatial_transforms.py ├── target_transforms.py └── temporal_transforms.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marshuang80/penet/HEAD/.gitignore -------------------------------------------------------------------------------- /.mdai/README.md: 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