├── .gitattributes ├── .github └── workflows │ ├── docker-keras-publish.yml │ ├── docker-torch-publish.yml │ └── python-app.yml ├── .gitignore ├── Dockerfile_keras ├── Dockerfile_torch ├── LICENSE ├── Makefile ├── README.md ├── docs ├── Makefile ├── commands.rst ├── conf.py ├── getting-started.rst ├── index.rst └── make.bat ├── models ├── configparams.txt ├── model_trained_keras.hdf5 ├── model_trained_torch.pt └── run_model_trained.sh ├── requirements_all.txt ├── requirements_keras.txt ├── requirements_torch.txt ├── run_docker_models.sh ├── scripts ├── launch_distributedata_cluster.sh ├── launch_predictions_full.py ├── launch_preparedata_full.py └── launch_train_cluster.sh ├── setup.py ├── src ├── common │ ├── __init__.py │ ├── constant.py │ ├── exceptionmanager.py │ ├── functionutil.py │ └── workdirmanager.py ├── dataloaders │ ├── __init__.py │ ├── batchdatagenerator.py │ ├── dataloader_manager.py │ ├── imagedataloader.py │ ├── imagefilereader.py │ ├── keras │ │ └── batchdatagenerator.py │ └── pytorch │ │ └── batchdatagenerator.py ├── imageoperators │ ├── __init__.py │ ├── boundingboxes.py │ ├── imageoperator.py │ └── maskoperator.py ├── models │ ├── __init__.py │ ├── callbacks.py │ ├── keras │ │ ├── __init__.py │ │ ├── callbacks.py │ │ ├── metrics.py │ │ ├── modeltrainer.py │ │ ├── networkchecker.py │ │ ├── networks.py │ │ └── optimizers.py │ ├── metrics.py │ ├── model_manager.py │ ├── modeltrainer.py │ ├── networkchecker.py │ ├── networks.py │ └── pytorch │ │ ├── __init__.py │ │ ├── callbacks.py │ │ ├── metrics.py │ │ ├── modeltrainer.py │ │ ├── networkchecker.py │ │ ├── networks.py │ │ └── optimizers.py ├── plotting │ ├── __init__.py │ ├── froc_util.py │ ├── histogram.py │ └── plotgeneral.py ├── postprocessing │ ├── __init__.py │ ├── imagereconstructor.py │ └── postprocessing_manager.py ├── preprocessing │ ├── __init__.py │ ├── elasticdeformimages.py │ ├── filteringbordersimages.py │ ├── imagegenerator.py │ ├── preprocessing_manager.py │ ├── randomwindowimages.py │ ├── slidingwindowimages.py │ └── transformrigidimages.py ├── scripts_evalresults │ ├── compute_result_metrics.py │ ├── compute_result_metrics_diffthres.py │ ├── compute_threshold_metric_value.py │ ├── merge_pydictionaries_preds.py │ ├── postprocess_predictions.py │ └── process_predicted_airway_tree.py ├── scripts_experiments │ ├── distribute_data.py │ ├── predict_model.py │ └── train_model.py ├── scripts_preparedata │ ├── compute_boundingbox_images.py │ ├── compute_rescalefactor_images.py │ ├── prepare_data.py │ ├── prepare_merged_data.py │ ├── prepdata_dlcst │ │ ├── check_boundingbox_cropped_images.py │ │ ├── crop_images_boundingbox.py │ │ └── extend_cropped_images_fullsize.py │ ├── visual_processed_images_batches.py │ └── visual_processed_labels_fieldview.py └── scripts_util │ ├── apply_operation_images.py │ ├── compare_images_two_dirs.py │ ├── compare_ptest_two_data.py │ ├── compute_balance_classes_masks.py │ ├── compute_mean_data_files.py │ ├── convert_images_to_nifti.py │ ├── create_homemade_mask.py │ ├── create_movie_slicesCT_with_masks.py │ ├── generate_mhd_header_files.py │ ├── get_converged_epoch_model.py │ ├── plot_data_files_csv.py │ ├── plot_loss_history.py │ ├── plot_roc_curves.py │ └── plot_stats_images.py ├── test_environment.py ├── tests ├── test_launch_preds_CFCT-DLCST.sh └── test_launch_preds_EXACT.sh └── tox.ini /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/antonioguj/bronchinet/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/docker-keras-publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/antonioguj/bronchinet/HEAD/.github/workflows/docker-keras-publish.yml -------------------------------------------------------------------------------- /.github/workflows/docker-torch-publish.yml: 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