├── .DS_Store ├── README.md ├── nnUNet_LICENSE ├── nnunet.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── entry_points.txt ├── requires.txt └── top_level.txt ├── nnunet ├── .DS_Store ├── .idea │ ├── .gitignore │ ├── inspectionProfiles │ │ ├── Project_Default.xml │ │ └── profiles_settings.xml │ ├── misc.xml │ ├── modules.xml │ ├── nnunet.iml │ └── vcs.xml ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-38.pyc │ ├── configuration.cpython-38.pyc │ └── paths.cpython-38.pyc ├── configuration.py ├── dataset_conversion │ ├── Task017_BeyondCranialVaultAbdominalOrganSegmentation.py │ ├── Task024_Promise2012.py │ ├── Task027_AutomaticCardiacDetectionChallenge.py │ ├── Task029_LiverTumorSegmentationChallenge.py │ ├── Task032_BraTS_2018.py │ ├── Task035_ISBI_MSLesionSegmentationChallenge.py │ ├── Task037_038_Chaos_Challenge.py │ ├── Task040_KiTS.py │ ├── Task043_BraTS_2019.py │ ├── Task055_SegTHOR.py │ ├── Task056_VerSe2019.py │ ├── Task056_Verse_normalize_orientation.py │ ├── Task058_ISBI_EM_SEG.py │ ├── Task059_EPFL_EM_MITO_SEG.py │ ├── Task061_CREMI.py │ ├── Task062_NIHPancreas.py │ ├── Task064_KiTS_labelsFixed.py │ ├── Task065_KiTS_NicksLabels.py │ ├── Task069_CovidSeg.py │ ├── Task075_Fluo_C3DH_A549_ManAndSim.py │ ├── Task076_Fluo_N3DH_SIM.py │ ├── Task082_BraTS_2020.py │ ├── Task083_VerSe2020.py │ ├── Task089_Fluo-N2DH-SIM.py │ ├── Task114_heart_MNMs.py │ ├── Task115_COVIDSegChallenge.py │ ├── Task120_Massachusetts_RoadSegm.py │ ├── Task135_KiTS2021.py │ ├── Task154_RibFrac_multi_label.py │ ├── Task155_RibFrac_binary.py │ ├── Task156_RibSeg.py │ ├── Task159_MyoPS2020.py │ ├── __init__.py │ └── utils.py ├── evaluation │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── evaluator.cpython-38.pyc │ │ ├── metrics.cpython-38.pyc │ │ └── region_based_evaluation.cpython-38.pyc │ ├── add_dummy_task_with_mean_over_all_tasks.py │ ├── add_mean_dice_to_json.py │ ├── collect_results_files.py │ ├── evaluator.py │ ├── metrics.py │ ├── model_selection │ │ ├── __init__.py │ │ ├── collect_all_fold0_results_and_summarize_in_one_csv.py │ │ ├── ensemble.py │ │ ├── figure_out_what_to_submit.py │ │ ├── rank_candidates.py │ │ ├── rank_candidates_StructSeg.py │ │ ├── rank_candidates_cascade.py │ │ ├── summarize_results_in_one_json.py │ │ └── summarize_results_with_plans.py │ ├── region_based_evaluation.py │ └── surface_dice.py ├── experiment_planning │ ├── .DS_Store │ ├── DatasetAnalyzer.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── DatasetAnalyzer.cpython-38.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── change_batch_size.cpython-38.pyc │ │ ├── common_utils.cpython-38.pyc │ │ ├── experiment_planner_baseline_2DUNet.cpython-38.pyc │ │ ├── experiment_planner_baseline_2DUNet_v21.cpython-38.pyc │ │ ├── experiment_planner_baseline_3DUNet.cpython-38.pyc │ │ ├── experiment_planner_baseline_3DUNet_v21.cpython-38.pyc │ │ ├── nnUNet_convert_decathlon_task.cpython-38.pyc │ │ ├── nnUNet_plan_and_preprocess.cpython-38.pyc │ │ ├── summarize_plans.cpython-38.pyc │ │ └── utils.cpython-38.pyc │ ├── alternative_experiment_planning │ │ ├── .DS_Store │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── experiment_planner_Attention_3DUNet_v21.cpython-38.pyc │ │ │ ├── experiment_planner_SingleAttention_3DUNet_v21.cpython-38.pyc │ │ │ ├── experiment_planner_SpatialSingleAttention_3DUNet_v21.cpython-38.pyc │ │ │ ├── experiment_planner_baseline_3DUNet_v21_11GB.cpython-38.pyc │ │ │ ├── experiment_planner_baseline_3DUNet_v21_16GB.cpython-38.pyc │ │ │ ├── experiment_planner_baseline_3DUNet_v21_32GB.cpython-38.pyc │ │ │ ├── experiment_planner_baseline_3DUNet_v21_3convperstage.cpython-38.pyc │ │ │ ├── experiment_planner_baseline_3DUNet_v22.cpython-38.pyc │ │ │ ├── experiment_planner_baseline_3DUNet_v23.cpython-38.pyc │ │ │ ├── experiment_planner_dense3DUNet_v21.cpython-38.pyc │ │ │ ├── experiment_planner_generic_3DUNet_v21.cpython-38.pyc │ │ │ ├── experiment_planner_inception3DUNet_v21.cpython-38.pyc │ │ │ ├── experiment_planner_pretrained.cpython-38.pyc │ │ │ └── experiment_planner_residual3DUNet_v21.cpython-38.pyc │ │ ├── experiment_planner_ChannelSpatialAttention_3DUNet_v21.py │ │ ├── experiment_planner_SpatialMultiAttention_3DUNet_v21.py │ │ ├── experiment_planner_SpatialSingleAttention_3DUNet_v21.py │ │ ├── experiment_planner_baseline_3DUNet_v21_11GB.py │ │ ├── experiment_planner_baseline_3DUNet_v21_16GB.py │ │ ├── experiment_planner_baseline_3DUNet_v21_32GB.py │ │ ├── experiment_planner_baseline_3DUNet_v21_3convperstage.py │ │ ├── experiment_planner_baseline_3DUNet_v22.py │ │ ├── experiment_planner_baseline_3DUNet_v23.py │ │ ├── experiment_planner_dense3DUNet_v21.py │ │ ├── experiment_planner_generic_3DUNet_v21.py │ │ ├── experiment_planner_inception3DUNet_v21.py │ │ ├── experiment_planner_pretrained.py │ │ ├── experiment_planner_residual3DUNet_v21.py │ │ ├── experiment_planner_residual_3DUNet_v21.py │ │ ├── experiment_planner_residualattention3DUNet_v21.py │ │ ├── normalization │ │ │ ├── __init__.py │ │ │ ├── experiment_planner_2DUNet_v21_RGB_scaleto_0_1.py │ │ │ ├── experiment_planner_3DUNet_CT2.py │ │ │ └── experiment_planner_3DUNet_nonCT.py │ │ ├── patch_size │ │ │ ├── __init__.py │ │ │ ├── experiment_planner_3DUNet_isotropic_in_mm.py │ │ │ └── experiment_planner_3DUNet_isotropic_in_voxels.py │ │ ├── pooling_and_convs │ │ │ ├── __init__.py │ │ │ ├── experiment_planner_baseline_3DUNet_allConv3x3.py │ │ │ └── experiment_planner_baseline_3DUNet_poolBasedOnSpacing.py │ │ ├── readme.md │ │ └── target_spacing │ │ │ ├── __init__.py │ │ │ ├── experiment_planner_baseline_3DUNet_targetSpacingForAnisoAxis.py │ │ │ ├── experiment_planner_baseline_3DUNet_v21_customTargetSpacing_2x2x2.py │ │ │ └── experiment_planner_baseline_3DUNet_v21_noResampling.py │ ├── change_batch_size.py │ ├── common_utils.py │ ├── experiment_planner_baseline_2DUNet.py │ ├── experiment_planner_baseline_2DUNet_v21.py │ ├── experiment_planner_baseline_3DUNet.py │ ├── experiment_planner_baseline_3DUNet_v21.py │ ├── nnUNet_convert_decathlon_task.py │ ├── nnUNet_plan_and_preprocess.py │ ├── old │ │ ├── __init__.py │ │ └── old_plan_and_preprocess_task.py │ ├── summarize_plans.py │ └── utils.py ├── inference │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── ensemble_predictions.cpython-38.pyc │ │ ├── predict.cpython-38.pyc │ │ ├── predict_simple.cpython-38.pyc │ │ └── segmentation_export.cpython-38.pyc │ ├── change_trainer.py │ ├── ensemble_predictions.py │ ├── predict.py │ ├── predict_simple.py │ ├── pretrained_models │ │ ├── __init__.py │ │ ├── collect_pretrained_models.py │ │ └── download_pretrained_model.py │ └── segmentation_export.py ├── network_architecture │ ├── .DS_Store │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── generic_UNet.cpython-38.pyc │ │ ├── generic_UNet_DP.cpython-38.pyc │ │ ├── generic_modular_UNet.cpython-38.pyc │ │ ├── generic_modular_custom_UNet.cpython-38.pyc │ │ ├── generic_modular_residual_UNet.cpython-38.pyc │ │ ├── initialization.cpython-38.pyc │ │ └── neural_network.cpython-38.pyc │ ├── custom_modules │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── conv_blocks.cpython-38.pyc │ │ │ ├── feature_response_normalization.cpython-38.pyc │ │ │ ├── helperModules.cpython-38.pyc │ │ │ └── mish.cpython-38.pyc │ │ ├── conv_blocks.py │ │ ├── feature_response_normalization.py │ │ ├── helperModules.py │ │ └── mish.py │ ├── generic_UNet.py │ ├── generic_UNet_DP.py │ ├── generic_modular_UNet.py │ ├── generic_modular_custom_UNet.py │ ├── generic_modular_preact_residual_UNet.py │ ├── generic_modular_residual_UNet.py │ ├── initialization.py │ └── neural_network.py ├── paths.py ├── postprocessing │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── connected_components.cpython-38.pyc │ │ └── consolidate_postprocessing.cpython-38.pyc │ ├── connected_components.py │ ├── consolidate_all_for_paper.py │ ├── consolidate_postprocessing.py │ └── consolidate_postprocessing_simple.py ├── preprocessing │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── cropping.cpython-38.pyc │ │ ├── preprocessing.cpython-38.pyc │ │ └── sanity_checks.cpython-38.pyc │ ├── cropping.py │ ├── custom_preprocessors │ │ ├── __init__.py │ │ └── preprocessor_scale_RGB_to_0_1.py │ ├── preprocessing.py │ └── sanity_checks.py ├── run │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── default_configuration.cpython-38.pyc │ │ ├── load_pretrained_weights.cpython-38.pyc │ │ └── run_training.cpython-38.pyc │ ├── default_configuration.py │ ├── load_pretrained_weights.py │ ├── run_training.py │ ├── run_training_DDP.py │ └── run_training_DP.py ├── training │ ├── .DS_Store │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ └── model_restore.cpython-38.pyc │ ├── cascade_stuff │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ └── predict_next_stage.cpython-38.pyc │ │ └── predict_next_stage.py │ ├── data_augmentation │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── custom_transforms.cpython-38.pyc │ │ │ ├── data_augmentation_insaneDA.cpython-38.pyc │ │ │ ├── data_augmentation_insaneDA2.cpython-38.pyc │ │ │ ├── data_augmentation_moreDA.cpython-38.pyc │ │ │ ├── data_augmentation_noDA.cpython-38.pyc │ │ │ ├── default_data_augmentation.cpython-38.pyc │ │ │ ├── downsampling.cpython-38.pyc │ │ │ └── pyramid_augmentations.cpython-38.pyc │ │ ├── custom_transforms.py │ │ ├── data_augmentation_insaneDA.py │ │ ├── data_augmentation_insaneDA2.py │ │ ├── data_augmentation_moreDA.py │ │ ├── data_augmentation_noDA.py │ │ ├── default_data_augmentation.py │ │ ├── downsampling.py │ │ └── pyramid_augmentations.py │ ├── dataloading │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ └── dataset_loading.cpython-38.pyc │ │ └── dataset_loading.py │ ├── learning_rate │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ └── poly_lr.cpython-38.pyc │ │ └── poly_lr.py │ ├── loss_functions │ │ ├── TopK_loss.py │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── TopK_loss.cpython-38.pyc │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── crossentropy.cpython-38.pyc │ │ │ ├── deep_supervision.cpython-38.pyc │ │ │ └── dice_loss.cpython-38.pyc │ │ ├── crossentropy.py │ │ ├── deep_supervision.py │ │ ├── dice_loss.py │ │ └── focal_loss.py │ ├── model_restore.py │ ├── network_training │ │ ├── .DS_Store │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── network_trainer.cpython-38.pyc │ │ │ ├── nnUNetTrainer.cpython-38.pyc │ │ │ ├── nnUNetTrainerCascadeFullRes.cpython-38.pyc │ │ │ ├── nnUNetTrainerV2.cpython-38.pyc │ │ │ ├── nnUNetTrainerV2_CascadeFullRes.cpython-38.pyc │ │ │ ├── nnUNetTrainerV2_DDP.cpython-38.pyc │ │ │ ├── nnUNetTrainerV2_DP.cpython-38.pyc │ │ │ └── nnUNetTrainerV2_fp32.cpython-38.pyc │ │ ├── competitions_with_custom_Trainers │ │ │ ├── BraTS2020 │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── nnUNetTrainerV2BraTSRegions.cpython-38.pyc │ │ │ │ │ └── nnUNetTrainerV2BraTSRegions_moreDA.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2BraTSRegions.py │ │ │ │ └── nnUNetTrainerV2BraTSRegions_moreDA.py │ │ │ ├── MMS │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ └── nnUNetTrainerV2_MMS.cpython-38.pyc │ │ │ │ └── nnUNetTrainerV2_MMS.py │ │ │ ├── __init__.py │ │ │ └── __pycache__ │ │ │ │ └── __init__.cpython-38.pyc │ │ ├── network_trainer.py │ │ ├── nnUNetTrainer.py │ │ ├── nnUNetTrainerCascadeFullRes.py │ │ ├── nnUNetTrainerV2.py │ │ ├── nnUNetTrainerV2_CascadeFullRes.py │ │ ├── nnUNetTrainerV2_DDP.py │ │ ├── nnUNetTrainerV2_DP.py │ │ ├── nnUNetTrainerV2_fp32.py │ │ └── nnUNet_variants │ │ │ ├── .DS_Store │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── nnUNetTrainerCE.cpython-38.pyc │ │ │ └── nnUNetTrainerNoDA.cpython-38.pyc │ │ │ ├── architectural_variants │ │ │ ├── .DS_Store │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_3ConvPerStage.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_3ConvPerStage_samefilters.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_BN.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_DenseUNet.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_FRN.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_GN.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_GeLU.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_GenericAttentionUNet.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_GenericSingleAttentionUNet.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_GenericSpatialSingleAttentionUNet.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_GenericUNet.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_GenericUNet_noDeepSupervision.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_InceptionUNet.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_LReLU_slope_2en1.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_Mish.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_NoNormalization.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_NoNormalization_lr1en3.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_ReLU.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_ReLU_biasInSegOutput.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_ReLU_convReLUIN.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_ResencUNet.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_ResencUNet_DA3.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_ResencUNet_DA3_BN.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_ResidualAttentionUNet.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_ResidualUNet.cpython-38.pyc │ │ │ │ └── nnUNetTrainerV2_noDeepSupervision.cpython-38.pyc │ │ │ ├── nnUNetTrainerV2_3ConvPerStage.py │ │ │ ├── nnUNetTrainerV2_3ConvPerStage_samefilters.py │ │ │ ├── nnUNetTrainerV2_BN.py │ │ │ ├── nnUNetTrainerV2_DenseUNet.py │ │ │ ├── nnUNetTrainerV2_FRN.py │ │ │ ├── nnUNetTrainerV2_GN.py │ │ │ ├── nnUNetTrainerV2_GeLU.py │ │ │ ├── nnUNetTrainerV2_GenericChannelSpatialAttentionUNet.py │ │ │ ├── nnUNetTrainerV2_GenericSpatialMultiAttentionUNet.py │ │ │ ├── nnUNetTrainerV2_GenericSpatialSingleAttentionUNet.py │ │ │ ├── nnUNetTrainerV2_GenericUNet.py │ │ │ ├── nnUNetTrainerV2_GenericUNet_noDeepSupervision.py │ │ │ ├── nnUNetTrainerV2_InceptionUNet.py │ │ │ ├── nnUNetTrainerV2_LReLU_slope_2en1.py │ │ │ ├── nnUNetTrainerV2_Mish.py │ │ │ ├── nnUNetTrainerV2_NoNormalization.py │ │ │ ├── nnUNetTrainerV2_NoNormalization_lr1en3.py │ │ │ ├── nnUNetTrainerV2_ReLU.py │ │ │ ├── nnUNetTrainerV2_ReLU_biasInSegOutput.py │ │ │ ├── nnUNetTrainerV2_ReLU_convReLUIN.py │ │ │ ├── nnUNetTrainerV2_ResencUNet.py │ │ │ ├── nnUNetTrainerV2_ResencUNet_DA3.py │ │ │ ├── nnUNetTrainerV2_ResencUNet_DA3_BN.py │ │ │ ├── nnUNetTrainerV2_ResidualAttentionUNet.py │ │ │ ├── nnUNetTrainerV2_ResidualUNet.py │ │ │ ├── nnUNetTrainerV2_allConv3x3.py │ │ │ ├── nnUNetTrainerV2_lReLU_biasInSegOutput.py │ │ │ ├── nnUNetTrainerV2_lReLU_convlReLUIN.py │ │ │ ├── nnUNetTrainerV2_noDeepSupervision.py │ │ │ └── nnUNetTrainerV2_softDeepSupervision.py │ │ │ ├── benchmarking │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerV2_2epochs.py │ │ │ └── nnUNetTrainerV2_dummyLoad.py │ │ │ ├── cascade │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerV2CascadeFullRes_DAVariants.py │ │ │ ├── nnUNetTrainerV2CascadeFullRes_lowerLR.py │ │ │ ├── nnUNetTrainerV2CascadeFullRes_shorter.py │ │ │ └── nnUNetTrainerV2CascadeFullRes_shorter_lowerLR.py │ │ │ ├── copies │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainerV2_copies.py │ │ │ ├── data_augmentation │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── nnUNetTrainerV2_DA3.cpython-38.pyc │ │ │ │ └── nnUNetTrainerV2_insaneDA.cpython-38.pyc │ │ │ ├── nnUNetTrainerV2_DA2.py │ │ │ ├── nnUNetTrainerV2_DA3.py │ │ │ ├── nnUNetTrainerV2_DA5.py │ │ │ ├── nnUNetTrainerV2_independentScalePerAxis.py │ │ │ ├── nnUNetTrainerV2_insaneDA.py │ │ │ ├── nnUNetTrainerV2_noDA.py │ │ │ └── nnUNetTrainerV2_noMirroring.py │ │ │ ├── loss_function │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerV2_ForceBD.py │ │ │ ├── nnUNetTrainerV2_ForceSD.py │ │ │ ├── nnUNetTrainerV2_Loss_CE.py │ │ │ ├── nnUNetTrainerV2_Loss_CEGDL.py │ │ │ ├── nnUNetTrainerV2_Loss_Dice.py │ │ │ ├── nnUNetTrainerV2_Loss_DiceCE_noSmooth.py │ │ │ ├── nnUNetTrainerV2_Loss_DiceTopK10.py │ │ │ ├── nnUNetTrainerV2_Loss_Dice_lr1en3.py │ │ │ ├── nnUNetTrainerV2_Loss_Dice_squared.py │ │ │ ├── nnUNetTrainerV2_Loss_MCC.py │ │ │ ├── nnUNetTrainerV2_Loss_TopK10.py │ │ │ ├── nnUNetTrainerV2_focalLoss.py │ │ │ └── nnUNetTrainerV2_graduallyTransitionFromCEToDice.py │ │ │ ├── miscellaneous │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainerV2_fullEvals.py │ │ │ ├── nnUNetTrainerCE.py │ │ │ ├── nnUNetTrainerNoDA.py │ │ │ ├── optimizer_and_lr │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerV2_Adam.py │ │ │ ├── nnUNetTrainerV2_Adam_ReduceOnPlateau.py │ │ │ ├── nnUNetTrainerV2_Adam_lr_3en4.py │ │ │ ├── nnUNetTrainerV2_Ranger_lr1en2.py │ │ │ ├── nnUNetTrainerV2_Ranger_lr3en3.py │ │ │ ├── nnUNetTrainerV2_Ranger_lr3en4.py │ │ │ ├── nnUNetTrainerV2_SGD_ReduceOnPlateau.py │ │ │ ├── nnUNetTrainerV2_SGD_fixedSchedule.py │ │ │ ├── nnUNetTrainerV2_SGD_fixedSchedule2.py │ │ │ ├── nnUNetTrainerV2_SGD_lrs.py │ │ │ ├── nnUNetTrainerV2_cycleAtEnd.py │ │ │ ├── nnUNetTrainerV2_fp16.py │ │ │ ├── nnUNetTrainerV2_momentum09.py │ │ │ ├── nnUNetTrainerV2_momentum095.py │ │ │ ├── nnUNetTrainerV2_momentum098.py │ │ │ ├── nnUNetTrainerV2_momentum09in2D.py │ │ │ ├── nnUNetTrainerV2_reduceMomentumDuringTraining.py │ │ │ └── nnUNetTrainerV2_warmup.py │ │ │ └── resampling │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainerV2_resample33.py │ └── optimizer │ │ ├── __init__.py │ │ └── ranger.py └── utilities │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-38.pyc │ ├── distributed.cpython-38.pyc │ ├── file_endings.cpython-38.pyc │ ├── nd_softmax.cpython-38.pyc │ ├── one_hot_encoding.cpython-38.pyc │ ├── random_stuff.cpython-38.pyc │ ├── sitk_stuff.cpython-38.pyc │ ├── task_name_id_conversion.cpython-38.pyc │ ├── tensor_utilities.cpython-38.pyc │ └── to_torch.cpython-38.pyc │ ├── distributed.py │ ├── file_conversions.py │ ├── file_endings.py │ ├── folder_names.py │ ├── image_reorientation.py │ ├── nd_softmax.py │ ├── one_hot_encoding.py │ ├── overlay_plots.py │ ├── random_stuff.py │ ├── recursive_delete_npz.py │ ├── recursive_rename_taskXX_to_taskXXX.py │ ├── set_n_proc_DA.py │ ├── sitk_stuff.py │ ├── task_name_id_conversion.py │ ├── tensor_utilities.py │ └── to_torch.py ├── scratch.py ├── setup.cfg └── setup.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/niccolo246/Advanced_nnUNet/HEAD/.DS_Store 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