├── .gitignore ├── README.md ├── binary-code ├── One_Binary_Compare_Bubble.jpg ├── One_Binary_Compare_Optimize.jpg ├── One_Binary_Compare_Visualization.jpg ├── analyse.py ├── config.yaml ├── experience_data.xlsx ├── images │ ├── challenging_samples │ │ ├── 00.jpg │ │ ├── 01.jpg │ │ ├── 02.jpg │ │ ├── 03.jpg │ │ ├── 10.jpg │ │ ├── 11.jpg │ │ ├── 12.jpg │ │ ├── 13.jpg │ │ ├── 20.jpg │ │ ├── 21.jpg │ │ ├── 22.jpg │ │ ├── 23.jpg │ │ ├── 30.jpg │ │ ├── 31.jpg │ │ ├── 32.jpg │ │ ├── 33.jpg │ │ └── challenging_samples.jpg │ ├── three_views │ │ ├── axial_plane.jpg │ │ ├── coronal_plane.jpg │ │ ├── sagittal_plane.jpg │ │ └── three_views_image.jpg │ └── two_stage_pictures │ │ ├── label.jpg │ │ ├── origin_image.jpg │ │ └── surface_label.jpg ├── index_to_class │ ├── class2.json │ └── class35.json ├── lib │ ├── __init__.py │ ├── dataloaders │ │ ├── BinaryToothDataset.py │ │ ├── BinaryToothSurfaceDataset.py │ │ └── __init__.py │ ├── losses │ │ ├── DiceLoss.py │ │ └── __init__.py │ ├── metrics │ │ ├── ASSD.py │ │ ├── DSC.py │ │ ├── HD.py │ │ ├── IoU.py │ │ ├── SO.py │ │ └── __init__.py │ ├── models │ │ ├── AttentionUNet3D.py │ │ ├── DenseASPPUNet.py │ │ ├── DenseVNet.py │ │ ├── DenseVoxelNet.py │ │ ├── HighResNet3D.py │ │ ├── MultiResUNet3D.py │ │ ├── PMFSNet.py │ │ ├── R2AttentionUNet.py │ │ ├── R2UNet.py │ │ ├── SwinUNETR.py │ │ ├── TransBTS.py │ │ ├── TwoStageNet.py │ │ ├── UNETR.py │ │ ├── UNet3D.py │ │ ├── UXNet_3D │ │ │ ├── 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 │ │ │ ├── LocalPMFSBlock_v1.py │ │ │ ├── LocalPMFSBlock_v2.py │ │ │ ├── LocalPMFSBlock_v3.py │ │ │ ├── PolarizedSelfAttention3d.py │ │ │ ├── PositionalEncoding.py │ │ │ ├── RecurrentResidualBlock.py │ │ │ ├── ResBlock.py │ │ │ ├── Transformer.py │ │ │ ├── UNet3D_buildingblocks.py │ │ │ ├── Unet_skipconnection.py │ │ │ ├── UpConv.py │ │ │ └── __init__.py │ │ └── nnFormer │ │ │ ├── __init__.py │ │ │ ├── generic_UNet.py │ │ │ ├── initialization.py │ │ │ ├── neural_network.py │ │ │ ├── nnFormer_acdc.py │ │ │ ├── nnFormer_seg.py │ │ │ ├── nnFormer_tumor.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 │ ├── testers │ │ ├── __init__.py │ │ └── tester.py │ ├── trainers │ │ ├── __init__.py │ │ └── trainer.py │ ├── transforms │ │ ├── __init__.py │ │ ├── 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 │ ├── utils │ │ ├── OTSU.py │ │ ├── __init__.py │ │ ├── calculate_metric.py │ │ ├── general.py │ │ ├── one_hot.py │ │ ├── preprocess.py │ │ └── weights_init_methods.py │ └── visualizations │ │ ├── AverageMeterWriter.py │ │ ├── SegmentMapDisplayer.py │ │ ├── TensorboardWriter.py │ │ └── __init__.py ├── search_space.json ├── search_space_template.json ├── test_plot.py └── train.py ├── multi-code ├── analyse.py ├── images │ ├── samples │ │ ├── 00.jpg │ │ ├── 01.jpg │ │ ├── 02.jpg │ │ ├── 10.jpg │ │ ├── 11.jpg │ │ ├── 12.jpg │ │ ├── 20.jpg │ │ ├── 21.jpg │ │ ├── 22.jpg │ │ └── Multiple_Dataset_Samples.jpg │ └── two_stage_pictures │ │ ├── centroid_label.jpg │ │ ├── label.jpg │ │ ├── origin_image.jpg │ │ └── surface_label.jpg ├── index_to_class │ ├── class2.json │ └── class35.json ├── lib │ ├── __init__.py │ ├── dataloaders │ │ ├── MultipleToothCentroidDataset.py │ │ ├── MultipleToothDataset.py │ │ ├── MultipleToothSurfaceDataset.py │ │ └── __init__.py │ ├── losses │ │ ├── DiceLoss.py │ │ └── __init__.py │ ├── metrics │ │ ├── APE.py │ │ ├── ASSD.py │ │ ├── DSC.py │ │ ├── HD.py │ │ ├── IoU.py │ │ ├── SO.py │ │ └── __init__.py │ ├── models │ │ ├── AttentionUNet3D.py │ │ ├── DenseASPPUNet.py │ │ ├── DenseVNet.py │ │ ├── DenseVoxelNet.py │ │ ├── HighResNet3D.py │ │ ├── MultiResUNet3D.py │ │ ├── PMFSNet.py │ │ ├── R2AttentionUNet.py │ │ ├── R2UNet.py │ │ ├── SwinUNETR.py │ │ ├── TransBTS.py │ │ ├── TwoStageNet.py │ │ ├── UNETR.py │ │ ├── UNet3D.py │ │ ├── UXNet_3D │ │ │ ├── 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 │ │ │ ├── LocalPMFSBlock_v1.py │ │ │ ├── LocalPMFSBlock_v2.py │ │ │ ├── LocalPMFSBlock_v3.py │ │ │ ├── PolarizedSelfAttention3d.py │ │ │ ├── PositionalEncoding.py │ │ │ ├── RecurrentResidualBlock.py │ │ │ ├── ResBlock.py │ │ │ ├── Transformer.py │ │ │ ├── UNet3D_buildingblocks.py │ │ │ ├── Unet_skipconnection.py │ │ │ ├── UpConv.py │ │ │ └── __init__.py │ │ └── nnFormer │ │ │ ├── __init__.py │ │ │ ├── generic_UNet.py │ │ │ ├── initialization.py │ │ │ ├── neural_network.py │ │ │ ├── nnFormer_acdc.py │ │ │ ├── nnFormer_seg.py │ │ │ ├── nnFormer_tumor.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 │ ├── testers │ │ ├── __init__.py │ │ └── tester.py │ ├── trainers │ │ ├── __init__.py │ │ ├── centroid_trainer.py │ │ ├── surface_trainer.py │ │ └── trainer.py │ ├── transforms │ │ ├── __init__.py │ │ ├── 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 │ ├── utils │ │ ├── OTSU.py │ │ ├── __init__.py │ │ ├── calculate_metric.py │ │ ├── general.py │ │ ├── one_hot.py │ │ ├── preprocess.py │ │ └── weights_init_methods.py │ └── visualizations │ │ ├── AverageMeterWriter.py │ │ ├── SegmentMapDisplayer.py │ │ ├── TensorboardWriter.py │ │ └── __init__.py ├── test_plot.py ├── train.py ├── train_centroid.py └── train_surface.py └── tooth_system ├── app.py ├── designer_ui ├── EmailRetrievalWindow.py ├── EmailRetrievalWindow.ui ├── LoginWindow.py ├── LoginWindow.ui ├── MainWindow.py ├── 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