├── .gitignore ├── 2D ├── LICENSE ├── README.md ├── copy_model_weights.py ├── datasets │ ├── README.md │ └── dataset_synapse.py ├── deformable_LKA │ ├── LKA.py │ ├── LKA3d.py │ ├── deform_conv_speed.py │ ├── deformable_2d_convolution_alternative.py │ ├── deformable_2dconvolution.py │ ├── deformable_3dconvolution.py │ ├── deformable_LKA.py │ ├── deformable_LKA3d.py │ └── test_deformable_conv.py ├── lists │ └── lists_Synapse │ │ ├── all.lst │ │ ├── test_vol.txt │ │ └── train.txt ├── loader.py ├── mmcv_custom │ ├── __init__.py │ ├── apex_runner │ │ └── checkpoint.py │ ├── checkpoint.py │ ├── customized_text.py │ ├── layer_decay_optimizer_constructor.py │ ├── resize_transform.py │ └── train_api.py ├── networks │ ├── BiEncoderDAEDecoder.py │ ├── DAEEncoder_LKADecoder.py │ ├── DAEFormer.py │ ├── DAT │ │ ├── configs │ │ │ ├── dat_base.yaml │ │ │ ├── dat_base_384.yaml │ │ │ ├── dat_small.yaml │ │ │ └── dat_tiny.yaml │ │ ├── dat.py │ │ ├── dat_4out.py │ │ └── dat_blocks.py │ ├── DAT_LKA_Decoder.py │ ├── MaxViT_LKA_Decoder.py │ ├── MaxViT_deform_LKA.py │ ├── STViTEncoder_LKADecoder.py │ ├── STViTLayers.py │ ├── STViTSegmentation.py │ ├── _common.py │ ├── merit_lib │ │ ├── decoders.py │ │ ├── maxxvit_4out.py │ │ ├── models_timm │ │ │ ├── convnext.py │ │ │ ├── factory.py │ │ │ ├── features.py │ │ │ ├── fx_features.py │ │ │ ├── helpers.py │ │ │ ├── hub.py │ │ │ ├── layers │ │ │ │ ├── __init__.py │ │ │ │ ├── activations.py │ │ │ │ ├── activations_jit.py │ │ │ │ ├── activations_me.py │ │ │ │ ├── adaptive_avgmax_pool.py │ │ │ │ ├── attention_pool2d.py │ │ │ │ ├── blur_pool.py │ │ │ │ ├── bottleneck_attn.py │ │ │ │ ├── cbam.py │ │ │ │ ├── classifier.py │ │ │ │ ├── cond_conv2d.py │ │ │ │ ├── config.py │ │ │ │ ├── conv2d_same.py │ │ │ │ ├── conv_bn_act.py │ │ │ │ ├── create_act.py │ │ │ │ ├── create_attn.py │ │ │ │ ├── create_conv2d.py │ │ │ │ ├── create_norm.py │ │ │ │ ├── create_norm_act.py │ │ │ │ ├── drop.py │ │ │ │ ├── eca.py │ │ │ │ ├── evo_norm.py │ │ │ │ ├── fast_norm.py │ │ │ │ ├── filter_response_norm.py │ │ │ │ ├── gather_excite.py │ │ │ │ ├── global_context.py │ │ │ │ ├── halo_attn.py │ │ │ │ ├── helpers.py │ │ │ │ ├── inplace_abn.py │ │ │ │ ├── lambda_layer.py │ │ │ │ ├── linear.py │ │ │ │ ├── median_pool.py │ │ │ │ ├── mixed_conv2d.py │ │ │ │ ├── ml_decoder.py │ │ │ │ ├── mlp.py │ │ │ │ ├── non_local_attn.py │ │ │ │ ├── norm.py │ │ │ │ ├── norm_act.py │ │ │ │ ├── padding.py │ │ │ │ ├── patch_embed.py │ │ │ │ ├── pool2d_same.py │ │ │ │ ├── pos_embed.py │ │ │ │ ├── selective_kernel.py │ │ │ │ ├── separable_conv.py │ │ │ │ ├── space_to_depth.py │ │ │ │ ├── split_attn.py │ │ │ │ ├── split_batchnorm.py │ │ │ │ ├── squeeze_excite.py │ │ │ │ ├── std_conv.py │ │ │ │ ├── test_time_pool.py │ │ │ │ ├── trace_utils.py │ │ │ │ └── weight_init.py │ │ │ ├── levit.py │ │ │ ├── maxxvit.py │ │ │ ├── mlp_mixer.py │ │ │ ├── registry.py │ │ │ └── vision_transformer_relpos.py │ │ └── networks.py │ ├── mvit_LKA_Decoder.py │ ├── mvit_attention.py │ ├── mvit_common.py │ ├── mvit_model.py │ ├── mvit_model_object_4out.py │ ├── mvit_utils.py │ ├── segformer.py │ ├── swinunet.py │ └── swinunet_seg.py ├── requirements.txt ├── skin_code │ ├── Prepare_ISIC2017.py │ ├── Prepare_ISIC2018.py │ ├── Prepare_ph2.py │ ├── README.md │ ├── evaluate_skin.ipynb │ ├── load_ph2_npy.py │ ├── loader.py │ ├── model │ │ ├── MaxViT_LKA_Decoder.py │ │ ├── MaxViT_deform_LKA.py │ │ ├── __init__.py │ │ ├── deformable_LKA │ │ │ ├── LKA.py │ │ │ ├── LKA3d.py │ │ │ ├── deform_conv_speed.py │ │ │ ├── deformable_2d_convolution_alternative.py │ │ │ ├── deformable_2dconvolution.py │ │ │ ├── deformable_3dconvolution.py │ │ │ ├── deformable_LKA.py │ │ │ ├── deformable_LKA3d.py │ │ │ └── test_deformable_conv.py │ │ ├── hiformer │ │ │ ├── Decoder.py │ │ │ ├── Encoder.py │ │ │ ├── HiFormer.py │ │ │ ├── HiFormer_configs.py │ │ │ └── utils.py │ │ ├── merit_lib │ │ │ ├── decoders.py │ │ │ ├── maxxvit_4out.py │ │ │ ├── models_timm │ │ │ │ ├── convnext.py │ │ │ │ ├── factory.py │ │ │ │ ├── features.py │ │ │ │ ├── fx_features.py │ │ │ │ ├── helpers.py │ │ │ │ ├── hub.py │ │ │ │ ├── layers │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── activations.py │ │ │ │ │ ├── activations_jit.py │ │ │ │ │ ├── activations_me.py │ │ │ │ │ ├── adaptive_avgmax_pool.py │ │ │ │ │ ├── attention_pool2d.py │ │ │ │ │ ├── blur_pool.py │ │ │ │ │ ├── bottleneck_attn.py │ │ │ │ │ ├── cbam.py │ │ │ │ │ ├── classifier.py │ │ │ │ │ ├── cond_conv2d.py │ │ │ │ │ ├── config.py │ │ │ │ │ ├── conv2d_same.py │ │ │ │ │ ├── conv_bn_act.py │ │ │ │ │ ├── create_act.py │ │ │ │ │ ├── create_attn.py │ │ │ │ │ ├── create_conv2d.py │ │ │ │ │ ├── create_norm.py │ │ │ │ │ ├── create_norm_act.py │ │ │ │ │ ├── drop.py │ │ │ │ │ ├── eca.py │ │ │ │ │ ├── evo_norm.py │ │ │ │ │ ├── fast_norm.py │ │ │ │ │ ├── filter_response_norm.py │ │ │ │ │ ├── gather_excite.py │ │ │ │ │ ├── global_context.py │ │ │ │ │ ├── halo_attn.py │ │ │ │ │ ├── helpers.py │ │ │ │ │ ├── inplace_abn.py │ │ │ │ │ ├── lambda_layer.py │ │ │ │ │ ├── linear.py │ │ │ │ │ ├── median_pool.py │ │ │ │ │ ├── mixed_conv2d.py │ │ │ │ │ ├── ml_decoder.py │ │ │ │ │ ├── mlp.py │ │ │ │ │ ├── non_local_attn.py │ │ │ │ │ ├── norm.py │ │ │ │ │ ├── norm_act.py │ │ │ │ │ ├── padding.py │ │ │ │ │ ├── patch_embed.py │ │ │ │ │ ├── pool2d_same.py │ │ │ │ │ ├── pos_embed.py │ │ │ │ │ ├── selective_kernel.py │ │ │ │ │ ├── separable_conv.py │ │ │ │ │ ├── space_to_depth.py │ │ │ │ │ ├── split_attn.py │ │ │ │ │ ├── split_batchnorm.py │ │ │ │ │ ├── squeeze_excite.py │ │ │ │ │ ├── std_conv.py │ │ │ │ │ ├── test_time_pool.py │ │ │ │ │ ├── trace_utils.py │ │ │ │ │ └── weight_init.py │ │ │ │ ├── levit.py │ │ │ │ ├── maxxvit.py │ │ │ │ ├── mlp_mixer.py │ │ │ │ ├── registry.py │ │ │ │ └── vision_transformer_relpos.py │ │ │ └── networks.py │ │ ├── segformer.py │ │ ├── swinunet │ │ │ ├── config.py │ │ │ ├── configs │ │ │ │ └── swin_tiny_patch4_window7_224_lite.yaml │ │ │ ├── swin_transformer_unet_skip_expand_decoder_sys.py │ │ │ └── vision_transformer.py │ │ ├── vit_seg_configs.py │ │ ├── vit_seg_modeling.py │ │ └── vit_seg_modeling_resnet_skip.py │ ├── plot_skin.ipynb │ ├── plot_skin_with_contour.py │ ├── single_image_performance_comparison.py │ ├── train_256_ph2.py │ ├── train_LKA_ph2.py │ ├── train_ph2.py │ ├── train_skin.ipynb │ ├── train_skin.py │ ├── train_skinLKA2017.py │ ├── train_skinLKA2018.py │ ├── train_skin_2017.py │ ├── train_skin_HiFormer.py │ └── train_skin_SwinUnet.py ├── test.py ├── test_inference_speed.py ├── train.py ├── train_LKA.py ├── train_MaxViT_deform_LKA.py ├── trainer.py ├── trainer_LKA.py ├── trainer_MaxViT_LKA.py ├── trainer_MaxViT_deform_LKA.py └── utils.py ├── 3D ├── LICENSE ├── README.md ├── change_plans.py ├── d_lka_former │ ├── __init__.py │ ├── configuration.py │ ├── evaluation │ │ ├── __init__.py │ │ ├── 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 │ │ ├── unetr_pp_acdc_checkpoint │ │ │ └── unetr_pp │ │ │ │ └── 3d_fullres │ │ │ │ └── Task001_ACDC │ │ │ │ └── unetr_pp_trainer_acdc__unetr_pp_Plansv2.1 │ │ │ │ └── fold_0 │ │ │ │ └── .gitignore │ │ └── unetr_pp_synapse_checkpoint │ │ │ └── unetr_pp │ │ │ └── 3d_fullres │ │ │ └── Task002_Synapse │ │ │ └── unetr_pp_trainer_synapse__unetr_pp_Plansv2.1 │ │ │ └── fold_0 │ │ │ └── .gitignore │ ├── experiment_planning │ │ ├── DatasetAnalyzer.py │ │ ├── __init__.py │ │ ├── alternative_experiment_planning │ │ │ ├── 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_residual_3DUNet_v21.py │ │ │ ├── normalization │ │ │ │ ├── experiment_planner_2DUNet_v21_RGB_scaleto_0_1.py │ │ │ │ ├── experiment_planner_3DUNet_CT2.py │ │ │ │ └── experiment_planner_3DUNet_nonCT.py │ │ │ ├── patch_size │ │ │ │ ├── experiment_planner_3DUNet_isotropic_in_mm.py │ │ │ │ └── experiment_planner_3DUNet_isotropic_in_voxels.py │ │ │ ├── pooling_and_convs │ │ │ │ ├── experiment_planner_baseline_3DUNet_allConv3x3.py │ │ │ │ └── experiment_planner_baseline_3DUNet_poolBasedOnSpacing.py │ │ │ └── target_spacing │ │ │ │ ├── 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 │ │ ├── nnFormer_convert_decathlon_task.py │ │ ├── nnFormer_plan_and_preprocess.py │ │ ├── summarize_plans.py │ │ └── utils.py │ ├── inference │ │ ├── __init__.py │ │ ├── inferTs │ │ │ └── swin_nomask_2 │ │ │ │ └── plans.pkl │ │ ├── predict.py │ │ ├── predict_simple.py │ │ └── segmentation_export.py │ ├── inference_acdc.py │ ├── inference_synapse.py │ ├── network_architecture │ │ ├── README.md │ │ ├── __init__.py │ │ ├── acdc │ │ │ ├── __init__.py │ │ │ ├── d_lka_former_acdc.py │ │ │ ├── model_components.py │ │ │ └── transformerblock.py │ │ ├── dynunet_block.py │ │ ├── generic_UNet.py │ │ ├── initialization.py │ │ ├── layers.py │ │ ├── neural_network.py │ │ └── synapse │ │ │ ├── __init__.py │ │ │ ├── d_lka_former_synapse.py │ │ │ ├── deform_conv.py │ │ │ ├── deform_conv_func.py │ │ │ ├── model_components.py │ │ │ ├── test_deform_conv_speed.py │ │ │ └── transformerblock.py │ ├── paths.py │ ├── postprocessing │ │ ├── connected_components.py │ │ ├── consolidate_all_for_paper.py │ │ ├── consolidate_postprocessing.py │ │ └── consolidate_postprocessing_simple.py │ ├── preprocessing │ │ ├── cropping.py │ │ ├── custom_preprocessors │ │ │ └── preprocessor_scale_RGB_to_0_1.py │ │ ├── preprocessing.py │ │ └── sanity_checks.py │ ├── run │ │ ├── __init__.py │ │ ├── default_configuration.py │ │ └── run_training.py │ ├── training │ │ ├── __init__.py │ │ ├── cascade_stuff │ │ │ ├── __init__.py │ │ │ └── predict_next_stage.py │ │ ├── data_augmentation │ │ │ ├── __init__.py │ │ │ ├── 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 │ │ │ └── dataset_loading.py │ │ ├── learning_rate │ │ │ └── poly_lr.py │ │ ├── loss_functions │ │ │ ├── TopK_loss.py │ │ │ ├── __init__.py │ │ │ ├── crossentropy.py │ │ │ ├── deep_supervision.py │ │ │ └── dice_loss.py │ │ ├── model_restore.py │ │ ├── network_training │ │ │ ├── Trainer_acdc.py │ │ │ ├── Trainer_synapse.py │ │ │ ├── d_lka_former_trainer_acdc.py │ │ │ ├── d_lka_former_trainer_synapse.py │ │ │ ├── network_trainer_acdc.py │ │ │ └── network_trainer_synapse.py │ │ └── optimizer │ │ │ └── ranger.py │ └── utilities │ │ ├── __init__.py │ │ ├── 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 ├── dcn │ ├── D3D.egg-info │ │ ├── PKG-INFO │ │ ├── SOURCES.txt │ │ ├── dependency_links.txt │ │ └── top_level.txt │ ├── build │ │ ├── lib.linux-x86_64-cpython-38 │ │ │ ├── D3D.cpython-38-x86_64-linux-gnu.so │ │ │ ├── functions │ │ │ │ ├── __init__.py │ │ │ │ └── deform_conv_func.py │ │ │ └── modules │ │ │ │ ├── __init__.py │ │ │ │ └── deform_conv.py │ │ └── temp.linux-x86_64-cpython-38 │ │ │ └── home │ │ │ └── leon │ │ │ └── repos │ │ │ └── D3Dnet │ │ │ └── code │ │ │ └── dcn │ │ │ └── src │ │ │ ├── cpu │ │ │ └── deform_cpu.o │ │ │ ├── cuda │ │ │ └── deform_conv_cuda.o │ │ │ └── vision.o │ ├── dist │ │ └── D3D-1.0-py3.8-linux-x86_64.egg │ ├── functions │ │ ├── __init__.py │ │ └── deform_conv_func.py │ ├── make.bat │ ├── make.sh │ ├── modules │ │ ├── __init__.py │ │ └── deform_conv.py │ ├── setup.py │ ├── src │ │ ├── cpu │ │ │ ├── deform_conv_cpu.h │ │ │ └── deform_cpu.cpp │ │ ├── cuda │ │ │ ├── deform_conv_cuda.cu │ │ │ ├── deform_conv_cuda.h │ │ │ └── deform_im2col_cuda.cuh │ │ ├── deform_conv.h │ │ └── vision.cpp │ ├── test.py │ ├── test_3d_deform_conv_params.py │ └── test_deform_conv_speed.py ├── pancreas_code │ ├── README.md │ ├── dataloaders │ │ ├── __init__.py │ │ ├── la_heart.py │ │ ├── la_heart_processing.py │ │ └── utils.py │ ├── dataset_pancreas │ │ └── Pancreas │ │ │ └── Flods │ │ │ ├── test0.list │ │ │ ├── test1.list │ │ │ ├── test2.list │ │ │ ├── test3.list │ │ │ ├── train0.list │ │ │ ├── train1.list │ │ │ ├── train2.list │ │ │ └── train3.list │ ├── model │ │ └── pancreas1 │ │ │ ├── log.txt │ │ │ └── log │ │ │ ├── events.out.tfevents.1692809073.Leon │ │ │ ├── events.out.tfevents.1692809233.Leon │ │ │ └── events.out.tfevents.1692809394.Leon │ ├── networks │ │ ├── ResNet34.py │ │ ├── __init__.py │ │ ├── d_lka_former │ │ │ ├── __init__.py │ │ │ ├── d_lka_net_synapse.py │ │ │ ├── deform_conv.py │ │ │ ├── deform_conv_func.py │ │ │ ├── model_components.py │ │ │ ├── test_deform_conv_speed.py │ │ │ └── transformerblock.py │ │ ├── dynunet_block.py │ │ ├── generic_UNet.py │ │ ├── initialization.py │ │ ├── layers.py │ │ ├── neural_network.py │ │ ├── paths.py │ │ ├── resnet.py │ │ ├── unetr.py │ │ ├── utilities │ │ │ ├── __init__.py │ │ │ ├── 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 │ │ └── vnet.py │ ├── test_pancreas.py │ ├── test_util.py │ ├── train_pancreas.py │ └── utils │ │ ├── __init__.py │ │ ├── losses.py │ │ ├── opt_utils.py │ │ ├── ramps.py │ │ ├── ssim.py │ │ └── util.py ├── rename_layers.py ├── requirements.txt ├── run_evaluation_synapse.sh └── run_training_synapse.sh ├── README.md └── images ├── Synapse_2D.png ├── Synapse_3D.png └── Visualization.png /.gitignore: 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