├── .DS_Store ├── 2d_train.sh ├── LICENSE ├── README.md ├── Tim ├── .gitignore ├── README.md ├── causal-conv1d │ ├── AUTHORS │ ├── LICENSE │ ├── README.md │ ├── causal_conv1d │ │ ├── __init__.py │ │ └── causal_conv1d_interface.py │ ├── csrc │ │ ├── causal_conv1d.cpp │ │ ├── causal_conv1d.h │ │ ├── causal_conv1d_bwd.cu │ │ ├── causal_conv1d_common.h │ │ ├── causal_conv1d_fwd.cu │ │ ├── causal_conv1d_update.cu │ │ └── static_switch.h │ ├── setup.py │ └── tests │ │ └── test_causal_conv1d.py ├── mamba │ ├── .gitmodules │ ├── AUTHORS │ ├── LICENSE │ ├── README.md │ ├── assets │ │ └── selection.png │ ├── benchmarks │ │ └── benchmark_generation_mamba_simple.py │ ├── csrc │ │ └── selective_scan │ │ │ ├── reverse_scan.cuh │ │ │ ├── selective_scan.cpp │ │ │ ├── selective_scan.h │ │ │ ├── selective_scan_bwd_bf16_complex.cu │ │ │ ├── selective_scan_bwd_bf16_real.cu │ │ │ ├── selective_scan_bwd_fp16_complex.cu │ │ │ ├── selective_scan_bwd_fp16_real.cu │ │ │ ├── selective_scan_bwd_fp32_complex.cu │ │ │ ├── selective_scan_bwd_fp32_real.cu │ │ │ ├── selective_scan_bwd_kernel.cuh │ │ │ ├── selective_scan_common.h │ │ │ ├── selective_scan_fwd_bf16.cu │ │ │ ├── selective_scan_fwd_fp16.cu │ │ │ ├── selective_scan_fwd_fp32.cu │ │ │ ├── selective_scan_fwd_kernel.cuh │ │ │ ├── static_switch.h │ │ │ └── uninitialized_copy.cuh │ ├── evals │ │ └── lm_harness_eval.py │ ├── mamba_ssm │ │ ├── __init__.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ └── mixer_seq_simple.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── mamba_simple.py │ │ │ └── mamba_simple_fft.py │ │ ├── ops │ │ │ ├── __init__.py │ │ │ ├── selective_scan_interface.py │ │ │ └── triton │ │ │ │ ├── __init__.py │ │ │ │ ├── layernorm.py │ │ │ │ └── selective_state_update.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── generation.py │ │ │ └── hf.py │ ├── setup.py │ ├── test_mamba_module.py │ └── tests │ │ └── ops │ │ ├── test_selective_scan.py │ │ └── triton │ │ └── test_selective_state_update.py └── vim │ ├── .gitignore │ ├── LICENSE │ ├── augment.py │ ├── datasets.py │ ├── engine.py │ ├── hubconf.py │ ├── losses.py │ ├── main.py │ ├── models_mamba.py │ ├── rope.py │ ├── run_with_submitit.py │ ├── samplers.py │ ├── scripts │ └── pt-vim-t.sh │ ├── utils.py │ └── vim_requirements.txt ├── datasets ├── .DS_Store ├── CBCT_data_visualization.py ├── README.md ├── chect_mask.py ├── compute_draw_GSM_weights.py ├── draw_TED3_gt_edge.py ├── draw_TED3_gt_mask.py ├── draw_TED3_mask_ratio.py ├── draw_img_w_h.py └── see_mask_value.py ├── images ├── 3D_CBCT_Tooth_samples.jpg ├── 3D_CBCT_Tooth_segmentation.jpg ├── README.md └── T-Mamba-logo.png ├── infer.sh ├── infer_2d.sh ├── infer_3d.sh ├── inference.py ├── kill ├── lib ├── .DS_Store ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-310.pyc │ └── __init__.cpython-39.pyc ├── dataloaders │ ├── ISIC2018Dataset.py │ ├── MMOTUDataset.py │ ├── ToothDataset.py │ ├── __init__.py │ └── __pycache__ │ │ ├── ISIC2018Dataset.cpython-39.pyc │ │ ├── MMOTUDataset.cpython-39.pyc │ │ ├── ToothDataset.cpython-39.pyc │ │ └── __init__.cpython-39.pyc ├── losses │ ├── DiceLoss.py │ ├── __init__.py │ └── __pycache__ │ │ ├── DiceLoss.cpython-39.pyc │ │ └── __init__.cpython-39.pyc ├── metrics │ ├── ISIC2018 │ │ ├── ACC.py │ │ ├── DICE.py │ │ ├── IoU.py │ │ ├── JI.py │ │ ├── __init__.py │ │ └── __pycache__ │ │ │ ├── ACC.cpython-39.pyc │ │ │ ├── DICE.cpython-39.pyc │ │ │ ├── IoU.cpython-39.pyc │ │ │ ├── JI.cpython-39.pyc │ │ │ └── __init__.cpython-39.pyc │ ├── MMOTU │ │ ├── DICE.py │ │ ├── IoU.py │ │ ├── __init__.py │ │ └── __pycache__ │ │ │ ├── DICE.cpython-39.pyc │ │ │ ├── IoU.cpython-39.pyc │ │ │ └── __init__.cpython-39.pyc │ ├── Tooth │ │ ├── ASSD.py │ │ ├── DICE.py │ │ ├── HD.py │ │ ├── IoU.py │ │ ├── SD.py │ │ ├── SO.py │ │ ├── __init__.py │ │ └── __pycache__ │ │ │ ├── ASSD.cpython-39.pyc │ │ │ ├── DICE.cpython-39.pyc │ │ │ ├── HD.cpython-39.pyc │ │ │ ├── IoU.cpython-39.pyc │ │ │ ├── SD.cpython-39.pyc │ │ │ ├── SO.cpython-39.pyc │ │ │ └── __init__.cpython-39.pyc │ ├── __init__.py │ └── __pycache__ │ │ └── __init__.cpython-39.pyc ├── models │ ├── AttU_Net.py │ ├── AttentionUNet3D.py │ ├── BCDUNet.py │ ├── BiSeNetV2.py │ ├── CANet.py │ ├── CENet.py │ ├── CKDNet.py │ ├── CPFNet.py │ ├── DANet.py │ ├── DenseASPPUNet.py │ ├── DenseVNet.py │ ├── DenseVNet.py.our.vim │ ├── DenseVNet.py.ours.wofreq │ ├── DenseVNet.py.umamba │ ├── DenseVNet.py.vmamba │ ├── DenseVNet.py.wopos │ ├── DenseVNet2D.py │ ├── DenseVoxelNet.py │ ├── HighResNet3D.py │ ├── MedT.py │ ├── MobileNetV2.py │ ├── MsRED.py │ ├── MultiResUNet3D.py │ ├── PMFSNet.py │ ├── PSPNet.py │ ├── R2AttentionUNet.py │ ├── R2UNet.py │ ├── SegFormer.py │ ├── Swin-UMamba-main │ │ ├── .gitignore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── assets │ │ │ ├── abdomenmr.png │ │ │ ├── endoscopy.png │ │ │ ├── microscopy.png │ │ │ └── swin-umamba.png │ │ ├── data │ │ │ ├── nnUNet_raw │ │ │ │ ├── Dataset702_AbdomenMR │ │ │ │ │ └── dataset.json │ │ │ │ ├── Dataset703_NeurIPSCell │ │ │ │ │ └── dataset.json │ │ │ │ └── Dataset704_Endovis17 │ │ │ │ │ └── dataset.json │ │ │ └── pretrained │ │ │ │ └── vmamba │ │ │ │ └── .gitignore │ │ ├── evaluation │ │ │ ├── SurfaceDice.py │ │ │ ├── abdomen_DSC_Eval.py │ │ │ ├── abdomen_NSD_Eval.py │ │ │ ├── compute_cell_metric.py │ │ │ ├── endoscopy_DSC_Eval.py │ │ │ └── endoscopy_NSD_Eval.py │ │ ├── scripts │ │ │ ├── train_AbdomenMR.sh │ │ │ ├── train_Endoscopy.sh │ │ │ └── train_Microscopy.sh │ │ └── swin_umamba │ │ │ ├── .gitignore │ │ │ ├── LICENSE │ │ │ ├── nnunetv2 │ │ │ ├── __init__.py │ │ │ ├── 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 │ │ │ │ ├── Dataset114_MNMs.py │ │ │ │ ├── Dataset115_EMIDEC.py │ │ │ │ ├── Dataset120_RoadSegmentation.py │ │ │ │ ├── Dataset137_BraTS21.py │ │ │ │ ├── Dataset218_Amos2022_task1.py │ │ │ │ ├── Dataset219_Amos2022_task2.py │ │ │ │ ├── Dataset220_KiTS2023.py │ │ │ │ ├── Dataset221_AutoPETII_2023.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 │ │ │ │ ├── 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 │ │ │ │ ├── base_reader_writer.py │ │ │ │ ├── natural_image_reader_writer.py │ │ │ │ ├── nibabel_reader_writer.py │ │ │ │ ├── reader_writer_registry.py │ │ │ │ ├── readme.md │ │ │ │ ├── simpleitk_reader_writer.py │ │ │ │ └── tif_reader_writer.py │ │ │ ├── inference │ │ │ │ ├── __init__.py │ │ │ │ ├── data_iterators.py │ │ │ │ ├── examples.py │ │ │ │ ├── export_prediction.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 │ │ │ ├── nets │ │ │ │ ├── SwinUMamba.py │ │ │ │ └── SwinUMambaD.py │ │ │ ├── paths.py │ │ │ ├── postprocessing │ │ │ │ ├── __init__.py │ │ │ │ └── remove_connected_components.py │ │ │ ├── preprocessing │ │ │ │ ├── __init__.py │ │ │ │ ├── cropping │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── cropping.py │ │ │ │ ├── normalization │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── default_normalization_schemes.py │ │ │ │ │ ├── map_channel_name_to_normalization.py │ │ │ │ │ └── readme.md │ │ │ │ ├── preprocessors │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── default_preprocessor.py │ │ │ │ └── resampling │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── 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 │ │ │ │ ├── data_augmentation │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── compute_initial_patch_size.py │ │ │ │ │ └── custom_transforms │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── 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 │ │ │ │ │ ├── base_data_loader.py │ │ │ │ │ ├── data_loader_2d.py │ │ │ │ │ ├── data_loader_3d.py │ │ │ │ │ ├── nnunet_dataset.py │ │ │ │ │ └── utils.py │ │ │ │ ├── logging │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── nnunet_logger.py │ │ │ │ ├── loss │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── compound_losses.py │ │ │ │ │ ├── deep_supervision.py │ │ │ │ │ ├── dice.py │ │ │ │ │ └── robust_ce_loss.py │ │ │ │ ├── lr_scheduler │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── polylr.py │ │ │ │ └── nnUNetTrainer │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainer.py │ │ │ │ │ ├── nnUNetTrainerSwinUMamba.py │ │ │ │ │ ├── nnUNetTrainerSwinUMambaD.py │ │ │ │ │ ├── nnUNetTrainerSwinUMambaDScratch.py │ │ │ │ │ ├── nnUNetTrainerSwinUMambaScratch.py │ │ │ │ │ └── variants │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── benchmarking │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerBenchmark_5epochs.py │ │ │ │ │ └── nnUNetTrainerBenchmark_5epochs_noDataLoading.py │ │ │ │ │ ├── data_augmentation │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerDA5.py │ │ │ │ │ ├── nnUNetTrainerDAOrd0.py │ │ │ │ │ ├── nnUNetTrainerNoDA.py │ │ │ │ │ └── nnUNetTrainerNoMirroring.py │ │ │ │ │ ├── loss │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerCELoss.py │ │ │ │ │ ├── nnUNetTrainerDiceLoss.py │ │ │ │ │ └── nnUNetTrainerTopkLoss.py │ │ │ │ │ ├── lr_schedule │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── nnUNetTrainerCosAnneal.py │ │ │ │ │ ├── network_architecture │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerBN.py │ │ │ │ │ └── nnUNetTrainerNoDeepSupervision.py │ │ │ │ │ ├── optimizer │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerAdam.py │ │ │ │ │ └── nnUNetTrainerAdan.py │ │ │ │ │ ├── sampling │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── nnUNetTrainer_probabilisticOversampling.py │ │ │ │ │ └── training_length │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainer_Xepochs.py │ │ │ │ │ └── nnUNetTrainer_Xepochs_NoMirroring.py │ │ │ └── utilities │ │ │ │ ├── __init__.py │ │ │ │ ├── collate_outputs.py │ │ │ │ ├── dataset_name_id_conversion.py │ │ │ │ ├── ddp_allgather.py │ │ │ │ ├── default_n_proc_DA.py │ │ │ │ ├── file_path_utilities.py │ │ │ │ ├── find_class_by_name.py │ │ │ │ ├── get_network_from_plans.py │ │ │ │ ├── helpers.py │ │ │ │ ├── json_export.py │ │ │ │ ├── label_handling │ │ │ │ ├── __init__.py │ │ │ │ └── label_handling.py │ │ │ │ ├── network_initialization.py │ │ │ │ ├── overlay_plots.py │ │ │ │ ├── plans_handling │ │ │ │ ├── __init__.py │ │ │ │ └── plans_handler.py │ │ │ │ └── utils.py │ │ │ └── setup.py │ ├── SwinUMamba.py │ ├── TMamba2D.py │ ├── TMamba3D.py │ ├── TransBTS.py │ ├── TransUNet.py │ ├── UNet.py │ ├── UNet3D.py │ ├── UXNet_3D │ │ ├── __pycache__ │ │ │ ├── module_helper.cpython-39.pyc │ │ │ ├── network_backbone.cpython-39.pyc │ │ │ └── uxnet_encoder.cpython-39.pyc │ │ ├── extensions │ │ │ ├── __init__.py │ │ │ ├── cc_attention │ │ │ │ ├── __init__.py │ │ │ │ ├── _ext │ │ │ │ │ └── __init__.py │ │ │ │ ├── build.py │ │ │ │ ├── build.sh │ │ │ │ ├── functions.py │ │ │ │ └── src │ │ │ │ │ ├── ca.cu │ │ │ │ │ ├── ca.h │ │ │ │ │ ├── common.h │ │ │ │ │ ├── lib_cffi.cpp │ │ │ │ │ └── lib_cffi.h │ │ │ ├── crf │ │ │ │ └── dense_crf.py │ │ │ ├── dcn │ │ │ │ ├── README.md │ │ │ │ ├── __init__.py │ │ │ │ ├── _ext │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── deform_conv │ │ │ │ │ │ └── __init__.py │ │ │ │ │ └── modulated_dcn │ │ │ │ │ │ └── __init__.py │ │ │ │ ├── build.py │ │ │ │ ├── build_modulated.py │ │ │ │ ├── functions │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── deform_conv.py │ │ │ │ │ └── modulated_dcn_func.py │ │ │ │ ├── make.sh │ │ │ │ ├── make_p100.sh │ │ │ │ ├── modules │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── deform_conv.py │ │ │ │ │ └── modulated_dcn.py │ │ │ │ ├── src │ │ │ │ │ ├── cuda │ │ │ │ │ │ ├── deform_psroi_pooling_cuda.cu │ │ │ │ │ │ ├── deform_psroi_pooling_cuda.h │ │ │ │ │ │ ├── modulated_deform_im2col_cuda.cu │ │ │ │ │ │ └── modulated_deform_im2col_cuda.h │ │ │ │ │ ├── deform_conv.c │ │ │ │ │ ├── deform_conv.h │ │ │ │ │ ├── deform_conv_cuda.c │ │ │ │ │ ├── deform_conv_cuda.h │ │ │ │ │ ├── deform_conv_cuda_kernel.cu │ │ │ │ │ ├── deform_conv_cuda_kernel.h │ │ │ │ │ ├── modulated_dcn.c │ │ │ │ │ ├── modulated_dcn.h │ │ │ │ │ ├── modulated_dcn_cuda.c │ │ │ │ │ └── modulated_dcn_cuda.h │ │ │ │ ├── test.py │ │ │ │ └── test_modulated.py │ │ │ ├── frn │ │ │ │ ├── __init__.py │ │ │ │ └── frn.py │ │ │ ├── inplace_abn │ │ │ │ ├── __init__.py │ │ │ │ ├── bn.py │ │ │ │ ├── functions.py │ │ │ │ └── src │ │ │ │ │ ├── common.h │ │ │ │ │ ├── inplace_abn.cpp │ │ │ │ │ ├── inplace_abn.h │ │ │ │ │ ├── inplace_abn_cpu.cpp │ │ │ │ │ └── inplace_abn_cuda.cu │ │ │ ├── inplace_abn_1 │ │ │ │ ├── __init__.py │ │ │ │ ├── bn.py │ │ │ │ ├── functions.py │ │ │ │ ├── misc.py │ │ │ │ └── src │ │ │ │ │ ├── checks.h │ │ │ │ │ ├── inplace_abn.cpp │ │ │ │ │ ├── inplace_abn.h │ │ │ │ │ ├── inplace_abn_cpu.cpp │ │ │ │ │ ├── inplace_abn_cuda.cu │ │ │ │ │ ├── inplace_abn_cuda_half.cu │ │ │ │ │ └── utils │ │ │ │ │ ├── checks.h │ │ │ │ │ ├── common.h │ │ │ │ │ └── cuda.cuh │ │ │ ├── pacnet │ │ │ │ ├── __init__.py │ │ │ │ ├── pac.py │ │ │ │ ├── paccrf.py │ │ │ │ └── test_pac.py │ │ │ ├── parallel │ │ │ │ ├── __init__.py │ │ │ │ ├── _functions.py │ │ │ │ ├── data_container.py │ │ │ │ ├── data_parallel.py │ │ │ │ ├── distributed.py │ │ │ │ └── scatter_gather.py │ │ │ ├── switchablenorms │ │ │ │ ├── __init__.py │ │ │ │ └── switchable_norm.py │ │ │ └── syncbn │ │ │ │ ├── __init__.py │ │ │ │ ├── allreduce.py │ │ │ │ ├── comm.py │ │ │ │ ├── module.py │ │ │ │ └── src │ │ │ │ ├── common.h │ │ │ │ ├── device_tensor.h │ │ │ │ ├── operator.cpp │ │ │ │ ├── operator.h │ │ │ │ ├── syncbn_cpu.cpp │ │ │ │ └── syncbn_kernel.cu │ │ ├── module_helper.py │ │ ├── network_backbone.py │ │ └── uxnet_encoder.py │ ├── VNet.py │ ├── __init__.py │ ├── modules │ │ ├── ConvBlock.py │ │ ├── GlobalPMFSBlock.py │ │ ├── GridAttentionGate3d.py │ │ ├── LocalPMFSBlock.py │ │ ├── PositionalEncoding.py │ │ ├── RecurrentResidualBlock.py │ │ ├── ResBlock.py │ │ ├── Transformer.py │ │ ├── UNet3D_buildingblocks.py │ │ ├── Unet_skipconnection.py │ │ ├── UpConv.py │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── ConvBlock.cpython-39.pyc │ │ │ ├── GlobalPMFSBlock.cpython-39.pyc │ │ │ ├── GridAttentionGate3d.cpython-39.pyc │ │ │ ├── LocalPMFSBlock.cpython-39.pyc │ │ │ ├── PositionalEncoding.cpython-39.pyc │ │ │ ├── RecurrentResidualBlock.cpython-39.pyc │ │ │ ├── ResBlock.cpython-39.pyc │ │ │ ├── Transformer.cpython-39.pyc │ │ │ ├── UNet3D_buildingblocks.cpython-39.pyc │ │ │ ├── Unet_skipconnection.cpython-39.pyc │ │ │ ├── UpConv.cpython-39.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── backbone.cpython-39.pyc │ │ │ ├── channel_attention_layer.cpython-39.pyc │ │ │ ├── extractors.cpython-39.pyc │ │ │ ├── grid_attention_layer.cpython-39.pyc │ │ │ ├── modules.cpython-39.pyc │ │ │ ├── nonlocal_layer.cpython-39.pyc │ │ │ ├── resnet.cpython-39.pyc │ │ │ ├── resnet_CKDNet.cpython-39.pyc │ │ │ ├── scale_attention_layer.cpython-39.pyc │ │ │ ├── scale_attention_layer_softpool.cpython-39.pyc │ │ │ ├── vgg.cpython-39.pyc │ │ │ ├── vit_seg_configs.cpython-39.pyc │ │ │ └── vit_seg_modeling_resnet_skip.cpython-39.pyc │ │ ├── backbone.py │ │ ├── channel_attention_layer.py │ │ ├── extractors.py │ │ ├── grid_attention_layer.py │ │ ├── modules.py │ │ ├── nonlocal_layer.py │ │ ├── resnet.py │ │ ├── resnet_CKDNet.py │ │ ├── scale_attention_layer.py │ │ ├── scale_attention_layer_softpool.py │ │ ├── vgg.py │ │ ├── vit_seg_configs.py │ │ └── vit_seg_modeling_resnet_skip.py │ ├── nnFormer │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── initialization.cpython-39.pyc │ │ │ ├── neural_network.cpython-39.pyc │ │ │ └── nnFormer_seg.cpython-39.pyc │ │ ├── generic_UNet.py │ │ ├── initialization.py │ │ ├── neural_network.py │ │ ├── nnFormer_acdc.py │ │ ├── nnFormer_seg.py │ │ ├── nnFormer_tumor.py │ │ └── utilities │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── nd_softmax.cpython-39.pyc │ │ │ ├── random_stuff.cpython-39.pyc │ │ │ └── to_torch.cpython-39.pyc │ │ │ ├── distributed.py │ │ │ ├── file_conversions.py │ │ │ ├── file_endings.py │ │ │ ├── folder_names.py │ │ │ ├── nd_softmax.py │ │ │ ├── one_hot_encoding.py │ │ │ ├── overlay_plots.py │ │ │ ├── random_stuff.py │ │ │ ├── recursive_delete_npz.py │ │ │ ├── recursive_rename_taskXX_to_taskXXX.py │ │ │ ├── sitk_stuff.py │ │ │ ├── task_name_id_conversion.py │ │ │ ├── tensor_utilities.py │ │ │ └── to_torch.py │ └── nnunetv2 │ │ ├── __init__.py │ │ ├── __pycache__ │ │ └── __init__.cpython-39.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 │ │ ├── Dataset114_MNMs.py │ │ ├── Dataset115_EMIDEC.py │ │ ├── Dataset120_RoadSegmentation.py │ │ ├── Dataset137_BraTS21.py │ │ ├── Dataset218_Amos2022_task1.py │ │ ├── Dataset219_Amos2022_task2.py │ │ ├── Dataset220_KiTS2023.py │ │ ├── Dataset221_AutoPETII_2023.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 │ │ ├── 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-39.pyc │ │ │ ├── base_reader_writer.cpython-39.pyc │ │ │ ├── natural_image_reader_writer.cpython-39.pyc │ │ │ ├── nibabel_reader_writer.cpython-39.pyc │ │ │ ├── reader_writer_registry.cpython-39.pyc │ │ │ ├── simpleitk_reader_writer.cpython-39.pyc │ │ │ └── tif_reader_writer.cpython-39.pyc │ │ ├── base_reader_writer.py │ │ ├── natural_image_reader_writer.py │ │ ├── nibabel_reader_writer.py │ │ ├── reader_writer_registry.py │ │ ├── readme.md │ │ ├── simpleitk_reader_writer.py │ │ └── tif_reader_writer.py │ │ ├── inference │ │ ├── __init__.py │ │ ├── data_iterators.py │ │ ├── examples.py │ │ ├── export_prediction.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 │ │ ├── nets │ │ ├── SwinUMamba.py │ │ └── SwinUMambaD.py │ │ ├── paths.py │ │ ├── postprocessing │ │ ├── __init__.py │ │ └── remove_connected_components.py │ │ ├── preprocessing │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ └── __init__.cpython-39.pyc │ │ ├── cropping │ │ │ ├── __init__.py │ │ │ └── cropping.py │ │ ├── normalization │ │ │ ├── __init__.py │ │ │ ├── default_normalization_schemes.py │ │ │ ├── map_channel_name_to_normalization.py │ │ │ └── readme.md │ │ ├── preprocessors │ │ │ ├── __init__.py │ │ │ └── default_preprocessor.py │ │ └── resampling │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.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 │ │ ├── data_augmentation │ │ │ ├── __init__.py │ │ │ ├── compute_initial_patch_size.py │ │ │ └── custom_transforms │ │ │ │ ├── __init__.py │ │ │ │ ├── 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 │ │ │ ├── base_data_loader.py │ │ │ ├── data_loader_2d.py │ │ │ ├── data_loader_3d.py │ │ │ ├── nnunet_dataset.py │ │ │ └── utils.py │ │ ├── logging │ │ │ ├── __init__.py │ │ │ └── nnunet_logger.py │ │ ├── loss │ │ │ ├── __init__.py │ │ │ ├── compound_losses.py │ │ │ ├── deep_supervision.py │ │ │ ├── dice.py │ │ │ └── robust_ce_loss.py │ │ ├── lr_scheduler │ │ │ ├── __init__.py │ │ │ └── polylr.py │ │ └── nnUNetTrainer │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainer.py │ │ │ ├── nnUNetTrainerSwinUMamba.py │ │ │ ├── nnUNetTrainerSwinUMambaD.py │ │ │ ├── nnUNetTrainerSwinUMambaDScratch.py │ │ │ ├── nnUNetTrainerSwinUMambaScratch.py │ │ │ └── variants │ │ │ ├── __init__.py │ │ │ ├── benchmarking │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerBenchmark_5epochs.py │ │ │ └── nnUNetTrainerBenchmark_5epochs_noDataLoading.py │ │ │ ├── data_augmentation │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerDA5.py │ │ │ ├── nnUNetTrainerDAOrd0.py │ │ │ ├── nnUNetTrainerNoDA.py │ │ │ └── nnUNetTrainerNoMirroring.py │ │ │ ├── loss │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerCELoss.py │ │ │ ├── nnUNetTrainerDiceLoss.py │ │ │ └── nnUNetTrainerTopkLoss.py │ │ │ ├── lr_schedule │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainerCosAnneal.py │ │ │ ├── network_architecture │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerBN.py │ │ │ └── nnUNetTrainerNoDeepSupervision.py │ │ │ ├── optimizer │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerAdam.py │ │ │ └── nnUNetTrainerAdan.py │ │ │ ├── sampling │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainer_probabilisticOversampling.py │ │ │ └── training_length │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainer_Xepochs.py │ │ │ └── nnUNetTrainer_Xepochs_NoMirroring.py │ │ └── utilities │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── find_class_by_name.cpython-39.pyc │ │ └── helpers.cpython-39.pyc │ │ ├── collate_outputs.py │ │ ├── dataset_name_id_conversion.py │ │ ├── ddp_allgather.py │ │ ├── default_n_proc_DA.py │ │ ├── file_path_utilities.py │ │ ├── find_class_by_name.py │ │ ├── get_network_from_plans.py │ │ ├── helpers.py │ │ ├── json_export.py │ │ ├── label_handling │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── label_handling.cpython-39.pyc │ │ └── label_handling.py │ │ ├── network_initialization.py │ │ ├── overlay_plots.py │ │ ├── plans_handling │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── plans_handler.cpython-39.pyc │ │ └── plans_handler.py │ │ └── utils.py ├── testers │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── isic_2018_tester.cpython-39.pyc │ │ ├── mmotu_tester.cpython-39.pyc │ │ └── tooth_tester.cpython-39.pyc │ ├── isic_2018_tester.py │ ├── mmotu_tester.py │ └── tooth_tester.py ├── trainers │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── isic_2018_trainer.cpython-39.pyc │ │ ├── mmotu_trainer.cpython-39.pyc │ │ └── tooth_trainer.cpython-39.pyc │ ├── isic_2018_trainer.py │ ├── mmotu_trainer.py │ └── tooth_trainer.py ├── transforms │ ├── __init__.py │ ├── __pycache__ │ │ └── __init__.cpython-39.pyc │ ├── three │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── clip_and_shift.cpython-39.pyc │ │ │ ├── elastic_deform.cpython-39.pyc │ │ │ ├── gaussian_noise.cpython-39.pyc │ │ │ ├── normalize.cpython-39.pyc │ │ │ ├── random_crop.cpython-39.pyc │ │ │ ├── random_flip.cpython-39.pyc │ │ │ ├── random_rescale.cpython-39.pyc │ │ │ ├── random_rotate.cpython-39.pyc │ │ │ ├── random_shift.cpython-39.pyc │ │ │ └── to_tensor.cpython-39.pyc │ │ ├── clip_and_shift.py │ │ ├── elastic_deform.py │ │ ├── gaussian_noise.py │ │ ├── normalize.py │ │ ├── random_crop.py │ │ ├── random_flip.py │ │ ├── random_rescale.py │ │ ├── random_rotate.py │ │ ├── random_shift.py │ │ └── to_tensor.py │ └── two │ │ ├── ColorJitter.py │ │ ├── Compose.py │ │ ├── Cutout.py │ │ ├── Normalize.py │ │ ├── RandomGaussianNoise.py │ │ ├── RandomHorizontalFlip.py │ │ ├── RandomResizedCrop.py │ │ ├── RandomRotation.py │ │ ├── RandomVerticalFlip.py │ │ ├── Resize.py │ │ ├── ToTensor.py │ │ ├── __init__.py │ │ └── __pycache__ │ │ ├── ColorJitter.cpython-39.pyc │ │ ├── Compose.cpython-39.pyc │ │ ├── Cutout.cpython-39.pyc │ │ ├── Normalize.cpython-39.pyc │ │ ├── RandomGaussianNoise.cpython-39.pyc │ │ ├── RandomHorizontalFlip.cpython-39.pyc │ │ ├── RandomResizedCrop.cpython-39.pyc │ │ ├── RandomRotation.cpython-39.pyc │ │ ├── RandomVerticalFlip.cpython-39.pyc │ │ ├── Resize.cpython-39.pyc │ │ ├── ToTensor.cpython-39.pyc │ │ └── __init__.cpython-39.pyc └── utils │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-310.pyc │ ├── __init__.cpython-39.pyc │ ├── calculate_metric.cpython-39.pyc │ ├── general.cpython-310.pyc │ ├── general.cpython-39.pyc │ ├── official_metrics.cpython-39.pyc │ ├── one_hot.cpython-39.pyc │ ├── preprocess.cpython-310.pyc │ ├── preprocess.cpython-39.pyc │ └── weights_init_methods.cpython-39.pyc │ ├── calculate_metric.py │ ├── general.py │ ├── official_metrics.py │ ├── one_hot.py │ ├── preprocess.py │ └── weights_init_methods.py ├── pretrain └── README.md ├── requirements.txt ├── selective_scan ├── csrc │ └── selective_scan │ │ ├── reverse_scan.cuh │ │ ├── selective_scan.cpp │ │ ├── selective_scan.h │ │ ├── selective_scan_bwd_kernel.cuh │ │ ├── selective_scan_common.h │ │ ├── selective_scan_core.cu │ │ ├── selective_scan_fwd_kernel.cuh │ │ ├── static_switch.h │ │ └── uninitialized_copy.cuh ├── readme.md ├── 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