├── .DS_Store ├── .gitignore ├── 0_inference.py ├── 1_rename_mri_data.py ├── 2_preprocessing_mri.py ├── 3_train.py ├── 4_predict.py ├── 5_compute_metrics.py ├── README.md ├── causal-conv1d ├── .DS_Store ├── 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 ├── images ├── data_structure.jpg ├── method_figure.jpg ├── modules.jpg └── segmamba_ablation.jpg ├── light_training ├── .DS_Store ├── augment │ ├── multi_processor.py │ └── train_augment.py ├── dataloading │ ├── __init__.py │ ├── base_data_loader.py │ ├── dataset.py │ ├── dataset_sdm_edge.py │ ├── get_train_val_test_datalist.py │ └── utils.py ├── dataloading_global │ ├── __init__.py │ ├── dataset.py │ └── utils.py ├── evaluation │ └── metric.py ├── examples │ ├── 1_rename_mri_data_BraTS2023.py │ ├── 2_preprocessing_AIIB23.py │ ├── 2_preprocessing_BraTS2023.py │ ├── AbdomenAtlas1.0Mini │ │ ├── 2_preprocessing_AbdomenAtlas1_0Mini.py │ │ ├── 3_train_diffunet.py │ │ ├── 3_train_diffunet_train_all.py │ │ └── 4_predict_diffunet.py │ ├── liver2017 │ │ └── 2_preprocessing_liver2017.py │ └── read_pickle.py ├── launch.py ├── loss │ ├── __init__.py │ ├── compound_losses.py │ ├── ddp_allgather.py │ ├── deepsupervision.py │ ├── dice.py │ ├── helpers.py │ ├── robust_ce_loss.py │ └── tensor_utilities.py ├── prediction.py ├── prediction_fp32.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 │ │ ├── default_preprocessor_AbdomenAtlas1_0Mini.py │ │ ├── default_preprocessor_liver_2017.py │ │ ├── preprocessor_brats23_global.py │ │ ├── preprocessor_mri.py │ │ ├── preprocessor_multiinput_and_region.py │ │ ├── preprocessor_multiinput_and_region_01norm_first.py │ │ └── preprocessor_multiinput_mrinorm_noresample_nocrop.py │ └── resampling │ │ ├── __init__.py │ │ └── default_resampling.py ├── process_framework │ ├── norm.py │ └── process.py ├── sampler.py ├── trainer.py ├── trainer_fp32.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 │ ├── tensor_utilities.py │ └── utils.py └── utils │ ├── files_helper.py │ ├── log_image.py │ └── lr_scheduler.py ├── mamba ├── .DS_Store ├── .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 │ ├── .DS_Store │ ├── __init__.py │ ├── models │ │ ├── __init__.py │ │ └── mixer_seq_simple.py │ ├── modules │ │ ├── __init__.py │ │ └── mamba_simple.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 ├── model_segmamba └── segmamba.py └── monai ├── .DS_Store ├── README.md ├── __init__.py ├── _extensions ├── __init__.py ├── gmm │ ├── gmm.cpp │ ├── gmm.h │ ├── gmm_cpu.cpp │ ├── gmm_cuda.cu │ └── gmm_cuda_linalg.cuh └── loader.py ├── _version.py ├── apps ├── __init__.py ├── auto3dseg │ ├── __init__.py │ ├── __main__.py │ ├── auto_runner.py │ ├── bundle_gen.py │ ├── data_analyzer.py │ ├── ensemble_builder.py │ ├── hpo_gen.py │ ├── transforms.py │ └── utils.py ├── datasets.py ├── deepedit │ ├── __init__.py │ ├── interaction.py │ └── transforms.py ├── deepgrow │ ├── __init__.py │ ├── dataset.py │ ├── interaction.py │ └── transforms.py ├── detection │ ├── __init__.py │ ├── metrics │ │ ├── __init__.py │ │ ├── coco.py │ │ └── matching.py │ ├── networks │ │ ├── __init__.py │ │ ├── retinanet_detector.py │ │ └── retinanet_network.py │ ├── transforms │ │ ├── __init__.py │ │ ├── array.py │ │ ├── box_ops.py │ │ └── dictionary.py │ └── utils │ │ ├── ATSS_matcher.py │ │ ├── __init__.py │ │ ├── anchor_utils.py │ │ ├── box_coder.py │ │ ├── box_selector.py │ │ ├── detector_utils.py │ │ ├── hard_negative_sampler.py │ │ └── predict_utils.py ├── mmars │ ├── __init__.py │ ├── mmars.py │ └── model_desc.py ├── nnunet │ ├── __init__.py │ ├── __main__.py │ ├── nnunetv2_runner.py │ └── utils.py ├── nuclick │ ├── __init__.py │ └── transforms.py ├── pathology │ ├── __init__.py │ ├── engines │ │ ├── __init__.py │ │ └── utils.py │ ├── handlers │ │ ├── __init__.py │ │ └── utils.py │ ├── inferers │ │ ├── __init__.py │ │ └── inferer.py │ ├── losses │ │ ├── __init__.py │ │ └── hovernet_loss.py │ ├── metrics │ │ ├── __init__.py │ │ └── lesion_froc.py │ ├── transforms │ │ ├── __init__.py │ │ ├── post │ │ │ ├── __init__.py │ │ │ ├── array.py │ │ │ └── dictionary.py │ │ └── stain │ │ │ ├── __init__.py │ │ │ ├── array.py │ │ │ └── dictionary.py │ └── utils.py ├── reconstruction │ ├── __init__.py │ ├── complex_utils.py │ ├── fastmri_reader.py │ ├── mri_utils.py │ ├── networks │ │ ├── __init__.py │ │ ├── blocks │ │ │ ├── __init__.py │ │ │ └── varnetblock.py │ │ └── nets │ │ │ ├── __init__.py │ │ │ ├── coil_sensitivity_model.py │ │ │ ├── complex_unet.py │ │ │ ├── utils.py │ │ │ └── varnet.py │ └── transforms │ │ ├── __init__.py │ │ ├── array.py │ │ └── dictionary.py ├── tcia │ ├── __init__.py │ ├── label_desc.py │ └── utils.py └── utils.py ├── auto3dseg ├── __init__.py ├── algo_gen.py ├── analyzer.py ├── operations.py ├── seg_summarizer.py └── utils.py ├── bundle ├── __init__.py ├── __main__.py ├── config_item.py ├── config_parser.py ├── properties.py ├── reference_resolver.py ├── scripts.py ├── utils.py └── workflows.py ├── config ├── __init__.py ├── deviceconfig.py └── type_definitions.py ├── csrc ├── ext.cpp ├── filtering │ ├── bilateral │ │ ├── bilateral.cpp │ │ ├── bilateral.h │ │ ├── bilateralfilter_cpu.cpp │ │ ├── bilateralfilter_cpu_phl.cpp │ │ ├── bilateralfilter_cuda.cu │ │ └── bilateralfilter_cuda_phl.cu │ ├── filtering.h │ ├── permutohedral │ │ ├── hash_table.cuh │ │ ├── permutohedral.cpp │ │ ├── permutohedral.h │ │ ├── permutohedral_cpu.cpp │ │ └── permutohedral_cuda.cu │ ├── trainable_bilateral │ │ ├── bf_layer_cpu_backward.cpp │ │ ├── bf_layer_cpu_forward.cpp │ │ ├── bf_layer_gpu_backward.cu │ │ ├── bf_layer_gpu_forward.cu │ │ ├── trainable_bilateral.cpp │ │ └── trainable_bilateral.h │ └── trainable_joint_bilateral │ │ ├── jbf_layer_cpu_backward.cpp │ │ ├── jbf_layer_cpu_forward.cpp │ │ ├── jbf_layer_gpu_backward.cu │ │ ├── jbf_layer_gpu_forward.cu │ │ ├── trainable_joint_bilateral.cpp │ │ └── trainable_joint_bilateral.h ├── lltm │ ├── lltm.h │ ├── lltm_cpu.cpp │ └── lltm_cuda.cu ├── resample │ ├── bounds_common.h │ ├── interpolation_common.h │ ├── pushpull.h │ ├── pushpull_cpu.cpp │ └── pushpull_cuda.cu └── utils │ ├── common_utils.h │ ├── meta_macros.h │ ├── resample_utils.h │ ├── tensor_description.h │ └── tensor_indexing.h ├── data ├── __init__.py ├── box_utils.py ├── csv_saver.py ├── dataloader.py ├── dataset.py ├── dataset_summary.py ├── decathlon_datalist.py ├── fft_utils.py ├── folder_layout.py ├── grid_dataset.py ├── image_dataset.py ├── image_reader.py ├── image_writer.py ├── iterable_dataset.py ├── itk_torch_bridge.py ├── meta_obj.py ├── meta_tensor.py ├── samplers.py ├── synthetic.py ├── test_time_augmentation.py ├── thread_buffer.py ├── torchscript_utils.py ├── ultrasound_confidence_map.py ├── utils.py ├── video_dataset.py ├── wsi_datasets.py └── wsi_reader.py ├── engines ├── __init__.py ├── evaluator.py ├── trainer.py ├── utils.py └── workflow.py ├── fl ├── __init__.py ├── client │ ├── __init__.py │ ├── client_algo.py │ └── monai_algo.py └── utils │ ├── __init__.py │ ├── constants.py │ ├── exchange_object.py │ └── filters.py ├── handlers ├── __init__.py ├── checkpoint_loader.py ├── checkpoint_saver.py ├── classification_saver.py ├── clearml_handlers.py ├── confusion_matrix.py ├── decollate_batch.py ├── earlystop_handler.py ├── garbage_collector.py ├── hausdorff_distance.py ├── ignite_metric.py ├── logfile_handler.py ├── lr_schedule_handler.py ├── mean_dice.py ├── mean_iou.py ├── metric_logger.py ├── metrics_reloaded_handler.py ├── metrics_saver.py ├── mlflow_handler.py ├── nvtx_handlers.py ├── panoptic_quality.py ├── parameter_scheduler.py ├── postprocessing.py ├── probability_maps.py ├── regression_metrics.py ├── roc_auc.py ├── smartcache_handler.py ├── stats_handler.py ├── surface_distance.py ├── tensorboard_handlers.py ├── utils.py └── validation_handler.py ├── inferers ├── __init__.py ├── inferer.py ├── merger.py ├── splitter.py └── utils.py ├── losses ├── __init__.py ├── adversarial_loss.py ├── barlow_twins.py ├── cldice.py ├── contrastive.py ├── deform.py ├── dice.py ├── ds_loss.py ├── focal_loss.py ├── giou_loss.py ├── hausdorff_loss.py ├── image_dissimilarity.py ├── multi_scale.py ├── perceptual.py ├── spatial_mask.py ├── spectral_loss.py ├── ssim_loss.py ├── sure_loss.py ├── tversky.py └── unified_focal_loss.py ├── metrics ├── __init__.py ├── active_learning_metrics.py ├── confusion_matrix.py ├── cumulative_average.py ├── f_beta_score.py ├── fid.py ├── froc.py ├── generalized_dice.py ├── hausdorff_distance.py ├── loss_metric.py ├── meandice.py ├── meaniou.py ├── metric.py ├── mmd.py ├── panoptic_quality.py ├── regression.py ├── rocauc.py ├── surface_dice.py ├── surface_distance.py ├── utils.py └── wrapper.py ├── networks ├── __init__.py ├── blocks │ ├── __init__.py │ ├── acti_norm.py │ ├── activation.py │ ├── aspp.py │ ├── backbone_fpn_utils.py │ ├── convolutions.py │ ├── crf.py │ ├── denseblock.py │ ├── dints_block.py │ ├── downsample.py │ ├── dynunet_block.py │ ├── encoder.py │ ├── fcn.py │ ├── feature_pyramid_network.py │ ├── fft_utils_t.py │ ├── localnet_block.py │ ├── mlp.py │ ├── patchembedding.py │ ├── pos_embed_utils.py │ ├── regunet_block.py │ ├── segresnet_block.py │ ├── selfattention.py │ ├── squeeze_and_excitation.py │ ├── text_embedding.py │ ├── transformerblock.py │ ├── unetr_block.py │ ├── upsample.py │ └── warp.py ├── layers │ ├── __init__.py │ ├── conjugate_gradient.py │ ├── convutils.py │ ├── drop_path.py │ ├── factories.py │ ├── filtering.py │ ├── gmm.py │ ├── simplelayers.py │ ├── spatial_transforms.py │ ├── utils.py │ └── weight_init.py ├── nets │ ├── __init__.py │ ├── ahnet.py │ ├── attentionunet.py │ ├── autoencoder.py │ ├── basic_unet.py │ ├── basic_unetplusplus.py │ ├── classifier.py │ ├── daf3d.py │ ├── densenet.py │ ├── dints.py │ ├── dynunet.py │ ├── efficientnet.py │ ├── flexible_unet.py │ ├── fullyconnectednet.py │ ├── generator.py │ ├── highresnet.py │ ├── hovernet.py │ ├── milmodel.py │ ├── netadapter.py │ ├── quicknat.py │ ├── regressor.py │ ├── regunet.py │ ├── resnet.py │ ├── segresnet.py │ ├── segresnet_ds.py │ ├── senet.py │ ├── swin_unetr.py │ ├── torchvision_fc.py │ ├── transchex.py │ ├── unet.py │ ├── unetr.py │ ├── varautoencoder.py │ ├── vit.py │ ├── vitautoenc.py │ ├── vnet.py │ └── voxelmorph.py └── utils.py ├── optimizers ├── __init__.py ├── lr_finder.py ├── lr_scheduler.py ├── novograd.py └── utils.py ├── py.typed ├── transforms ├── __init__.py ├── adaptors.py ├── compose.py ├── croppad │ ├── __init__.py │ ├── array.py │ ├── batch.py │ ├── dictionary.py │ └── functional.py ├── intensity │ ├── __init__.py │ ├── array.py │ └── dictionary.py ├── inverse.py ├── inverse_batch_transform.py ├── io │ ├── __init__.py │ ├── array.py │ └── dictionary.py ├── lazy │ ├── __init__.py │ ├── array.py │ ├── dictionary.py │ ├── functional.py │ └── utils.py ├── meta_utility │ ├── __init__.py │ └── dictionary.py ├── nvtx.py ├── post │ ├── __init__.py │ ├── array.py │ └── dictionary.py ├── regularization │ ├── __init__.py │ ├── array.py │ └── dictionary.py ├── signal 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