├── Dockerfile ├── LICENSE ├── README.md ├── assets ├── efficiency.png └── pipeline.png ├── inputs └── .keepgit ├── model ├── dataset.json ├── dataset_fingerprint.json ├── fold_all │ ├── debug.json │ ├── progress.png │ └── training_log_2023_8_14_15_25_22.txt └── plans.json ├── nnunetv2 ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-310.pyc │ ├── __init__.cpython-311.pyc │ ├── configuration.cpython-310.pyc │ ├── configuration.cpython-311.pyc │ ├── paths.cpython-310.pyc │ └── paths.cpython-311.pyc ├── batch_running │ ├── __init__.py │ ├── benchmarking │ │ ├── __init__.py │ │ ├── generate_benchmarking_commands.py │ │ └── summarize_benchmark_results.py │ ├── collect_results_custom_Decathlon.py │ ├── collect_results_custom_Decathlon_2d.py │ ├── generate_lsf_runs_customDecathlon.py │ └── release_trainings │ │ ├── __init__.py │ │ └── nnunetv2_v1 │ │ ├── __init__.py │ │ ├── collect_results.py │ │ └── generate_lsf_commands.py ├── configuration.py ├── dataset_conversion │ ├── Dataset027_ACDC.py │ ├── Dataset073_Fluo_C3DH_A549_SIM.py │ ├── Dataset120_RoadSegmentation.py │ ├── Dataset137_BraTS21.py │ ├── Dataset218_Amos2022_task1.py │ ├── Dataset219_Amos2022_task2.py │ ├── Dataset220_KiTS2023.py │ ├── Dataset988_dummyDataset4.py │ ├── __init__.py │ ├── convert_MSD_dataset.py │ ├── convert_raw_dataset_from_old_nnunet_format.py │ ├── datasets_for_integration_tests │ │ ├── Dataset996_IntegrationTest_Hippocampus_regions_ignore.py │ │ ├── Dataset997_IntegrationTest_Hippocampus_regions.py │ │ ├── Dataset998_IntegrationTest_Hippocampus_ignore.py │ │ ├── Dataset999_IntegrationTest_Hippocampus.py │ │ └── __init__.py │ └── generate_dataset_json.py ├── ensembling │ ├── __init__.py │ └── ensemble.py ├── evaluation │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-311.pyc │ │ ├── evaluate_predictions.cpython-310.pyc │ │ └── evaluate_predictions.cpython-311.pyc │ ├── accumulate_cv_results.py │ ├── evaluate_predictions.py │ └── find_best_configuration.py ├── experiment_planning │ ├── __init__.py │ ├── dataset_fingerprint │ │ ├── __init__.py │ │ └── fingerprint_extractor.py │ ├── experiment_planners │ │ ├── __init__.py │ │ ├── default_experiment_planner.py │ │ ├── network_topology.py │ │ ├── readme.md │ │ └── resencUNet_planner.py │ ├── plan_and_preprocess_api.py │ ├── plan_and_preprocess_entrypoints.py │ ├── plans_for_pretraining │ │ ├── __init__.py │ │ └── move_plans_between_datasets.py │ └── verify_dataset_integrity.py ├── imageio │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-311.pyc │ │ ├── base_reader_writer.cpython-310.pyc │ │ ├── base_reader_writer.cpython-311.pyc │ │ ├── natural_image_reager_writer.cpython-310.pyc │ │ ├── natural_image_reager_writer.cpython-311.pyc │ │ ├── nibabel_reader_writer.cpython-310.pyc │ │ ├── nibabel_reader_writer.cpython-311.pyc │ │ ├── reader_writer_registry.cpython-310.pyc │ │ ├── reader_writer_registry.cpython-311.pyc │ │ ├── simpleitk_reader_writer.cpython-310.pyc │ │ ├── simpleitk_reader_writer.cpython-311.pyc │ │ ├── tif_reader_writer.cpython-310.pyc │ │ └── tif_reader_writer.cpython-311.pyc │ ├── base_reader_writer.py │ ├── natural_image_reager_writer.py │ ├── nibabel_reader_writer.py │ ├── reader_writer_registry.py │ ├── readme.md │ ├── simpleitk_reader_writer.py │ └── tif_reader_writer.py ├── inference │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-311.pyc │ │ ├── data_iterators.cpython-310.pyc │ │ ├── data_iterators.cpython-311.pyc │ │ ├── export_prediction.cpython-310.pyc │ │ ├── export_prediction.cpython-311.pyc │ │ ├── predict_from_raw_data.cpython-310.pyc │ │ ├── predict_from_raw_data.cpython-311.pyc │ │ ├── sliding_window_prediction.cpython-310.pyc │ │ └── sliding_window_prediction.cpython-311.pyc │ ├── data_iterators.py │ ├── examples.py │ ├── export_prediction.py │ ├── nnUNet_predict_fast.py │ ├── predict_from_raw_data.py │ ├── readme.md │ └── sliding_window_prediction.py ├── model_sharing │ ├── __init__.py │ ├── entry_points.py │ ├── model_download.py │ ├── model_export.py │ └── model_import.py ├── paths.py ├── postprocessing │ ├── __init__.py │ └── remove_connected_components.py ├── preprocessing │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ └── __init__.cpython-311.pyc │ ├── cropping │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── cropping.cpython-310.pyc │ │ │ └── cropping.cpython-311.pyc │ │ └── cropping.py │ ├── normalization │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── default_normalization_schemes.cpython-310.pyc │ │ │ ├── default_normalization_schemes.cpython-311.pyc │ │ │ ├── map_channel_name_to_normalization.cpython-310.pyc │ │ │ └── map_channel_name_to_normalization.cpython-311.pyc │ │ ├── default_normalization_schemes.py │ │ ├── map_channel_name_to_normalization.py │ │ └── readme.md │ ├── preprocessors │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── default_preprocessor.cpython-310.pyc │ │ │ └── default_preprocessor.cpython-311.pyc │ │ └── default_preprocessor.py │ └── resampling │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-311.pyc │ │ ├── default_resampling.cpython-310.pyc │ │ ├── default_resampling.cpython-311.pyc │ │ ├── utils.cpython-310.pyc │ │ └── utils.cpython-311.pyc │ │ ├── default_resampling.py │ │ └── utils.py ├── run │ ├── __init__.py │ ├── load_pretrained_weights.py │ └── run_training.py ├── tests │ ├── __init__.py │ └── integration_tests │ │ ├── __init__.py │ │ ├── add_lowres_and_cascade.py │ │ ├── cleanup_integration_test.py │ │ ├── lsf_commands.sh │ │ ├── prepare_integration_tests.sh │ │ ├── readme.md │ │ ├── run_integration_test.sh │ │ ├── run_integration_test_bestconfig_inference.py │ │ └── run_integration_test_trainingOnly_DDP.sh ├── training │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ └── __init__.cpython-311.pyc │ ├── data_augmentation │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── compute_initial_patch_size.cpython-310.pyc │ │ │ └── compute_initial_patch_size.cpython-311.pyc │ │ ├── compute_initial_patch_size.py │ │ └── custom_transforms │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── cascade_transforms.cpython-310.pyc │ │ │ ├── cascade_transforms.cpython-311.pyc │ │ │ ├── deep_supervision_donwsampling.cpython-310.pyc │ │ │ ├── deep_supervision_donwsampling.cpython-311.pyc │ │ │ ├── limited_length_multithreaded_augmenter.cpython-310.pyc │ │ │ ├── limited_length_multithreaded_augmenter.cpython-311.pyc │ │ │ ├── masking.cpython-310.pyc │ │ │ ├── masking.cpython-311.pyc │ │ │ ├── region_based_training.cpython-310.pyc │ │ │ ├── region_based_training.cpython-311.pyc │ │ │ ├── transforms_for_dummy_2d.cpython-310.pyc │ │ │ └── transforms_for_dummy_2d.cpython-311.pyc │ │ │ ├── cascade_transforms.py │ │ │ ├── deep_supervision_donwsampling.py │ │ │ ├── limited_length_multithreaded_augmenter.py │ │ │ ├── manipulating_data_dict.py │ │ │ ├── masking.py │ │ │ ├── region_based_training.py │ │ │ └── transforms_for_dummy_2d.py │ ├── dataloading │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── base_data_loader.cpython-310.pyc │ │ │ ├── base_data_loader.cpython-311.pyc │ │ │ ├── data_loader_2d.cpython-310.pyc │ │ │ ├── data_loader_2d.cpython-311.pyc │ │ │ ├── data_loader_3d.cpython-310.pyc │ │ │ ├── data_loader_3d.cpython-311.pyc │ │ │ ├── nnunet_dataset.cpython-310.pyc │ │ │ ├── nnunet_dataset.cpython-311.pyc │ │ │ ├── utils.cpython-310.pyc │ │ │ └── utils.cpython-311.pyc │ │ ├── base_data_loader.py │ │ ├── data_loader_2d.py │ │ ├── data_loader_3d.py │ │ ├── nnunet_dataset.py │ │ └── utils.py │ ├── logging │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── nnunet_logger.cpython-310.pyc │ │ │ └── nnunet_logger.cpython-311.pyc │ │ └── nnunet_logger.py │ ├── loss │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── compound_losses.cpython-310.pyc │ │ │ ├── compound_losses.cpython-311.pyc │ │ │ ├── deep_supervision.cpython-310.pyc │ │ │ ├── deep_supervision.cpython-311.pyc │ │ │ ├── dice.cpython-310.pyc │ │ │ ├── dice.cpython-311.pyc │ │ │ ├── robust_ce_loss.cpython-310.pyc │ │ │ └── robust_ce_loss.cpython-311.pyc │ │ ├── compound_losses.py │ │ ├── deep_supervision.py │ │ ├── dice.py │ │ └── robust_ce_loss.py │ ├── lr_scheduler │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── polylr.cpython-310.pyc │ │ │ └── polylr.cpython-311.pyc │ │ └── polylr.py │ └── nnUNetTrainer │ │ ├── STUNetTrainer.py │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── STUNetTrainer.cpython-310.pyc │ │ ├── STUNetTrainer.cpython-311.pyc │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-311.pyc │ │ ├── nnUNetTrainer.cpython-310.pyc │ │ └── nnUNetTrainer.cpython-311.pyc │ │ ├── nnUNetTrainer.py │ │ └── variants │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ └── __init__.cpython-311.pyc │ │ ├── benchmarking │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── nnUNetTrainerBenchmark_5epochs.cpython-310.pyc │ │ │ ├── nnUNetTrainerBenchmark_5epochs.cpython-311.pyc │ │ │ ├── nnUNetTrainerBenchmark_5epochs_noDataLoading.cpython-310.pyc │ │ │ └── nnUNetTrainerBenchmark_5epochs_noDataLoading.cpython-311.pyc │ │ ├── nnUNetTrainerBenchmark_5epochs.py │ │ └── nnUNetTrainerBenchmark_5epochs_noDataLoading.py │ │ ├── data_augmentation │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── nnUNetTrainerDA5.cpython-310.pyc │ │ │ ├── nnUNetTrainerDA5.cpython-311.pyc │ │ │ ├── nnUNetTrainerDAOrd0.cpython-310.pyc │ │ │ ├── nnUNetTrainerDAOrd0.cpython-311.pyc │ │ │ ├── nnUNetTrainerNoDA.cpython-310.pyc │ │ │ ├── nnUNetTrainerNoDA.cpython-311.pyc │ │ │ ├── nnUNetTrainerNoMirroring.cpython-310.pyc │ │ │ └── nnUNetTrainerNoMirroring.cpython-311.pyc │ │ ├── nnUNetTrainerDA5.py │ │ ├── nnUNetTrainerDAOrd0.py │ │ ├── nnUNetTrainerNoDA.py │ │ └── nnUNetTrainerNoMirroring.py │ │ ├── loss │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── nnUNetTrainerCELoss.cpython-310.pyc │ │ │ ├── nnUNetTrainerCELoss.cpython-311.pyc │ │ │ ├── nnUNetTrainerDiceLoss.cpython-310.pyc │ │ │ ├── nnUNetTrainerDiceLoss.cpython-311.pyc │ │ │ ├── nnUNetTrainerTopkLoss.cpython-310.pyc │ │ │ └── nnUNetTrainerTopkLoss.cpython-311.pyc │ │ ├── nnUNetTrainerCELoss.py │ │ ├── nnUNetTrainerDiceLoss.py │ │ └── nnUNetTrainerTopkLoss.py │ │ ├── lr_schedule │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── nnUNetTrainerCosAnneal.cpython-310.pyc │ │ │ └── nnUNetTrainerCosAnneal.cpython-311.pyc │ │ └── nnUNetTrainerCosAnneal.py │ │ ├── network_architecture │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── nnUNetTrainerBN.cpython-310.pyc │ │ │ ├── nnUNetTrainerBN.cpython-311.pyc │ │ │ ├── nnUNetTrainerNoDeepSupervision.cpython-310.pyc │ │ │ └── nnUNetTrainerNoDeepSupervision.cpython-311.pyc │ │ ├── nnUNetTrainerBN.py │ │ └── nnUNetTrainerNoDeepSupervision.py │ │ ├── optimizer │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── nnUNetTrainerAdam.cpython-310.pyc │ │ │ ├── nnUNetTrainerAdam.cpython-311.pyc │ │ │ ├── nnUNetTrainerAdan.cpython-310.pyc │ │ │ └── nnUNetTrainerAdan.cpython-311.pyc │ │ ├── nnUNetTrainerAdam.py │ │ └── nnUNetTrainerAdan.py │ │ ├── sampling │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── nnUNetTrainer_probabilisticOversampling.cpython-310.pyc │ │ │ └── nnUNetTrainer_probabilisticOversampling.cpython-311.pyc │ │ └── nnUNetTrainer_probabilisticOversampling.py │ │ └── training_length │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-311.pyc │ │ ├── nnUNetTrainer_Xepochs.cpython-310.pyc │ │ ├── nnUNetTrainer_Xepochs.cpython-311.pyc │ │ ├── nnUNetTrainer_Xepochs_NoMirroring.cpython-310.pyc │ │ └── nnUNetTrainer_Xepochs_NoMirroring.cpython-311.pyc │ │ ├── nnUNetTrainer_Xepochs.py │ │ └── nnUNetTrainer_Xepochs_NoMirroring.py └── utilities │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-310.pyc │ ├── __init__.cpython-311.pyc │ ├── collate_outputs.cpython-310.pyc │ ├── collate_outputs.cpython-311.pyc │ ├── dataset_name_id_conversion.cpython-310.pyc │ ├── dataset_name_id_conversion.cpython-311.pyc │ ├── ddp_allgather.cpython-310.pyc │ ├── ddp_allgather.cpython-311.pyc │ ├── default_n_proc_DA.cpython-310.pyc │ ├── default_n_proc_DA.cpython-311.pyc │ ├── file_path_utilities.cpython-310.pyc │ ├── file_path_utilities.cpython-311.pyc │ ├── find_class_by_name.cpython-310.pyc │ ├── find_class_by_name.cpython-311.pyc │ ├── get_network_from_plans.cpython-310.pyc │ ├── get_network_from_plans.cpython-311.pyc │ ├── helpers.cpython-310.pyc │ ├── helpers.cpython-311.pyc │ ├── json_export.cpython-310.pyc │ ├── json_export.cpython-311.pyc │ ├── network_initialization.cpython-310.pyc │ ├── network_initialization.cpython-311.pyc │ ├── tensor_utilities.cpython-310.pyc │ ├── tensor_utilities.cpython-311.pyc │ ├── utils.cpython-310.pyc │ └── utils.cpython-311.pyc │ 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