LICENSE
pyproject.toml
readme.md
setup.py
nnunetv2/__init__.py
nnunetv2/configuration.py
nnunetv2/paths.py
nnunetv2.egg-info/PKG-INFO
nnunetv2.egg-info/SOURCES.txt
nnunetv2.egg-info/dependency_links.txt
nnunetv2.egg-info/entry_points.txt
nnunetv2.egg-info/requires.txt
nnunetv2.egg-info/top_level.txt
nnunetv2/batch_running/__init__.py
nnunetv2/batch_running/collect_results_custom_Decathlon.py
nnunetv2/batch_running/collect_results_custom_Decathlon_2d.py
nnunetv2/batch_running/generate_lsf_runs_customDecathlon.py
nnunetv2/batch_running/benchmarking/__init__.py
nnunetv2/batch_running/benchmarking/generate_benchmarking_commands.py
nnunetv2/batch_running/benchmarking/summarize_benchmark_results.py
nnunetv2/batch_running/release_trainings/__init__.py
nnunetv2/batch_running/release_trainings/nnunetv2_v1/__init__.py
nnunetv2/batch_running/release_trainings/nnunetv2_v1/collect_results.py
nnunetv2/batch_running/release_trainings/nnunetv2_v1/generate_lsf_commands.py
nnunetv2/dataset_conversion/Dataset027_ACDC.py
nnunetv2/dataset_conversion/Dataset042_BraTS18.py
nnunetv2/dataset_conversion/Dataset043_BraTS19.py
nnunetv2/dataset_conversion/Dataset073_Fluo_C3DH_A549_SIM.py
nnunetv2/dataset_conversion/Dataset114_MNMs.py
nnunetv2/dataset_conversion/Dataset115_EMIDEC.py
nnunetv2/dataset_conversion/Dataset120_RoadSegmentation.py
nnunetv2/dataset_conversion/Dataset137_BraTS21.py
nnunetv2/dataset_conversion/Dataset218_Amos2022_task1.py
nnunetv2/dataset_conversion/Dataset219_Amos2022_task2.py
nnunetv2/dataset_conversion/Dataset220_KiTS2023.py
nnunetv2/dataset_conversion/Dataset221_AutoPETII_2023.py
nnunetv2/dataset_conversion/Dataset223_AMOS2022postChallenge.py
nnunetv2/dataset_conversion/Dataset224_AbdomenAtlas1.0.py
nnunetv2/dataset_conversion/Dataset988_dummyDataset4.py
nnunetv2/dataset_conversion/__init__.py
nnunetv2/dataset_conversion/convert_MSD_dataset.py
nnunetv2/dataset_conversion/convert_raw_dataset_from_old_nnunet_format.py
nnunetv2/dataset_conversion/generate_dataset_json.py
nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset996_IntegrationTest_Hippocampus_regions_ignore.py
nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset997_IntegrationTest_Hippocampus_regions.py
nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset998_IntegrationTest_Hippocampus_ignore.py
nnunetv2/dataset_conversion/datasets_for_integration_tests/Dataset999_IntegrationTest_Hippocampus.py
nnunetv2/dataset_conversion/datasets_for_integration_tests/__init__.py
nnunetv2/ensembling/__init__.py
nnunetv2/ensembling/ensemble.py
nnunetv2/evaluation/__init__.py
nnunetv2/evaluation/accumulate_cv_results.py
nnunetv2/evaluation/evaluate_predictions.py
nnunetv2/evaluation/find_best_configuration.py
nnunetv2/experiment_planning/__init__.py
nnunetv2/experiment_planning/plan_and_preprocess_api.py
nnunetv2/experiment_planning/plan_and_preprocess_entrypoints.py
nnunetv2/experiment_planning/verify_dataset_integrity.py
nnunetv2/experiment_planning/dataset_fingerprint/__init__.py
nnunetv2/experiment_planning/dataset_fingerprint/fingerprint_extractor.py
nnunetv2/experiment_planning/experiment_planners/__init__.py
nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py
nnunetv2/experiment_planning/experiment_planners/network_topology.py
nnunetv2/experiment_planning/experiment_planners/resencUNet_planner.py
nnunetv2/experiment_planning/experiment_planners/resampling/__init__.py
nnunetv2/experiment_planning/experiment_planners/resampling/resample_with_torch.py
nnunetv2/experiment_planning/experiment_planners/residual_unets/__init__.py
nnunetv2/experiment_planning/experiment_planners/residual_unets/residual_encoder_unet_planners.py
nnunetv2/experiment_planning/plans_for_pretraining/__init__.py
nnunetv2/experiment_planning/plans_for_pretraining/move_plans_between_datasets.py
nnunetv2/imageio/__init__.py
nnunetv2/imageio/base_reader_writer.py
nnunetv2/imageio/natural_image_reader_writer.py
nnunetv2/imageio/nibabel_reader_writer.py
nnunetv2/imageio/reader_writer_registry.py
nnunetv2/imageio/simpleitk_reader_writer.py
nnunetv2/imageio/tif_reader_writer.py
nnunetv2/inference/JHU_inference.py
nnunetv2/inference/__init__.py
nnunetv2/inference/data_iterators.py
nnunetv2/inference/examples.py
nnunetv2/inference/export_prediction.py
nnunetv2/inference/predict_from_raw_data.py
nnunetv2/inference/sliding_window_prediction.py
nnunetv2/model_sharing/__init__.py
nnunetv2/model_sharing/entry_points.py
nnunetv2/model_sharing/model_download.py
nnunetv2/model_sharing/model_export.py
nnunetv2/model_sharing/model_import.py
nnunetv2/postprocessing/__init__.py
nnunetv2/postprocessing/remove_connected_components.py
nnunetv2/preprocessing/__init__.py
nnunetv2/preprocessing/cropping/__init__.py
nnunetv2/preprocessing/cropping/cropping.py
nnunetv2/preprocessing/normalization/__init__.py
nnunetv2/preprocessing/normalization/default_normalization_schemes.py
nnunetv2/preprocessing/normalization/map_channel_name_to_normalization.py
nnunetv2/preprocessing/preprocessors/__init__.py
nnunetv2/preprocessing/preprocessors/default_preprocessor.py
nnunetv2/preprocessing/resampling/__init__.py
nnunetv2/preprocessing/resampling/default_resampling.py
nnunetv2/preprocessing/resampling/resample_torch.py
nnunetv2/preprocessing/resampling/utils.py
nnunetv2/run/__init__.py
nnunetv2/run/load_pretrained_weights.py
nnunetv2/run/run_training.py
nnunetv2/tests/__init__.py
nnunetv2/tests/integration_tests/__init__.py
nnunetv2/tests/integration_tests/add_lowres_and_cascade.py
nnunetv2/tests/integration_tests/cleanup_integration_test.py
nnunetv2/tests/integration_tests/run_integration_test_bestconfig_inference.py
nnunetv2/training/__init__.py
nnunetv2/training/data_augmentation/__init__.py
nnunetv2/training/data_augmentation/compute_initial_patch_size.py
nnunetv2/training/data_augmentation/custom_transforms/__init__.py
nnunetv2/training/data_augmentation/custom_transforms/cascade_transforms.py
nnunetv2/training/data_augmentation/custom_transforms/deep_supervision_donwsampling.py
nnunetv2/training/data_augmentation/custom_transforms/masking.py
nnunetv2/training/data_augmentation/custom_transforms/region_based_training.py
nnunetv2/training/data_augmentation/custom_transforms/transforms_for_dummy_2d.py
nnunetv2/training/dataloading/__init__.py
nnunetv2/training/dataloading/base_data_loader.py
nnunetv2/training/dataloading/data_loader_2d.py
nnunetv2/training/dataloading/data_loader_3d.py
nnunetv2/training/dataloading/nnunet_dataset.py
nnunetv2/training/dataloading/utils.py
nnunetv2/training/logging/__init__.py
nnunetv2/training/logging/nnunet_logger.py
nnunetv2/training/loss/__init__.py
nnunetv2/training/loss/compound_losses.py
nnunetv2/training/loss/deep_supervision.py
nnunetv2/training/loss/dice.py
nnunetv2/training/loss/robust_ce_loss.py
nnunetv2/training/lr_scheduler/__init__.py
nnunetv2/training/lr_scheduler/polylr.py
nnunetv2/training/nnUNetTrainer/__init__.py
nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py
nnunetv2/training/nnUNetTrainer/variants/__init__.py
nnunetv2/training/nnUNetTrainer/variants/benchmarking/__init__.py
nnunetv2/training/nnUNetTrainer/variants/benchmarking/nnUNetTrainerBenchmark_5epochs.py
nnunetv2/training/nnUNetTrainer/variants/benchmarking/nnUNetTrainerBenchmark_5epochs_noDataLoading.py
nnunetv2/training/nnUNetTrainer/variants/data_augmentation/__init__.py
nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDA5.py
nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDAOrd0.py
nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoDA.py
nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoMirroring.py
nnunetv2/training/nnUNetTrainer/variants/loss/__init__.py
nnunetv2/training/nnUNetTrainer/variants/loss/nnUNetTrainerCELoss.py
nnunetv2/training/nnUNetTrainer/variants/loss/nnUNetTrainerDiceLoss.py
nnunetv2/training/nnUNetTrainer/variants/loss/nnUNetTrainerTopkLoss.py
nnunetv2/training/nnUNetTrainer/variants/lr_schedule/__init__.py
nnunetv2/training/nnUNetTrainer/variants/lr_schedule/nnUNetTrainerCosAnneal.py
nnunetv2/training/nnUNetTrainer/variants/network_architecture/__init__.py
nnunetv2/training/nnUNetTrainer/variants/network_architecture/nnUNetTrainerBN.py
nnunetv2/training/nnUNetTrainer/variants/network_architecture/nnUNetTrainerNoDeepSupervision.py
nnunetv2/training/nnUNetTrainer/variants/optimizer/__init__.py
nnunetv2/training/nnUNetTrainer/variants/optimizer/nnUNetTrainerAdam.py
nnunetv2/training/nnUNetTrainer/variants/optimizer/nnUNetTrainerAdan.py
nnunetv2/training/nnUNetTrainer/variants/sampling/__init__.py
nnunetv2/training/nnUNetTrainer/variants/sampling/nnUNetTrainer_probabilisticOversampling.py
nnunetv2/training/nnUNetTrainer/variants/training_length/__init__.py
nnunetv2/training/nnUNetTrainer/variants/training_length/nnUNetTrainer_Xepochs.py
nnunetv2/training/nnUNetTrainer/variants/training_length/nnUNetTrainer_Xepochs_NoMirroring.py
nnunetv2/utilities/__init__.py
nnunetv2/utilities/collate_outputs.py
nnunetv2/utilities/crossval_split.py
nnunetv2/utilities/dataset_name_id_conversion.py
nnunetv2/utilities/ddp_allgather.py
nnunetv2/utilities/default_n_proc_DA.py
nnunetv2/utilities/file_path_utilities.py
nnunetv2/utilities/find_class_by_name.py
nnunetv2/utilities/get_network_from_plans.py
nnunetv2/utilities/helpers.py
nnunetv2/utilities/json_export.py
nnunetv2/utilities/network_initialization.py
nnunetv2/utilities/overlay_plots.py
nnunetv2/utilities/utils.py
nnunetv2/utilities/label_handling/__init__.py
nnunetv2/utilities/label_handling/label_handling.py
nnunetv2/utilities/plans_handling/__init__.py
nnunetv2/utilities/plans_handling/plans_handler.py