├── .gitignore ├── DEMO ├── Orbitrap_XL_untarget │ ├── 0_pc_extraction.py │ └── 1_peak_detection.py ├── QE_HF_target │ ├── 0_pc_extraction.py │ └── 1_peak_detection.py ├── QE_HF_untarget │ ├── 0_pc_extraction.py │ └── 1_peak_detection.py ├── TripleTOF_6600_target │ ├── 0_pc_extraction.py │ └── 1_peak_detection.py └── TripleTOF_6600_untarget │ ├── 0_pc_extraction.py │ └── 1_peak_detection.py ├── LICENSE ├── README.md ├── config └── msnet_default.yaml ├── cuda ├── setup.py └── src │ ├── ball_query.cpp │ ├── ball_query2.cpp │ ├── ball_query2_gpu.cu │ ├── ball_query2_gpu.h │ ├── ball_query_gpu.cu │ ├── ball_query_gpu.h │ ├── bilinear_interpolate.cpp │ ├── bilinear_interpolate_gpu.cu │ ├── bilinear_interpolate_gpu.h │ ├── cuda_utils.h │ ├── extract_features.cpp │ ├── extract_features_gpu.cu │ ├── extract_features_gpu.h │ ├── extract_pc.cpp │ ├── extract_pc_gpu.cu │ ├── extract_pc_gpu.h │ ├── group_points.cpp │ ├── group_points_gpu.cu │ ├── group_points_gpu.h │ ├── interpolate.cpp │ ├── interpolate_gpu.cu │ ├── interpolate_gpu.h │ ├── match_features.cpp │ ├── match_features_gpu.cu │ ├── match_features_gpu.h │ ├── ms_query.cpp │ ├── ms_query_gpu.cu │ ├── ms_query_gpu.h │ ├── msnet_api.cpp │ ├── sampling.cpp │ ├── sampling_gpu.cu │ └── sampling_gpu.h ├── experiment ├── msnet_20220215_143158 │ ├── backbone_300.pth │ ├── box_center_net_300.pth │ ├── polar_mask_net_300.pth │ └── sem_net_300.pth └── msnet_20220427_141044 │ ├── backbone_1000.pth │ ├── box_center_net_1000.pth │ ├── polar_mask_net_1000.pth │ └── sem_net_1000.pth ├── model ├── main_msnet.py ├── msnet_model.py ├── msnet_modules.py ├── msnet_utils.py └── pytorch_utils.py ├── requirements.txt ├── third-party └── pyvenn │ ├── LICENSE │ ├── README.md │ ├── __init__.py │ ├── demo.py │ └── venn.py ├── utils ├── config.py ├── log.py ├── ms_compatibility.py ├── polar_mask.py └── visualize.py └── workflow ├── predict ├── main_eval.py └── point_cloud_extractor.py └── train ├── dataset_generator.py ├── dataset_loader.py └── main_train.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/.gitignore -------------------------------------------------------------------------------- /DEMO/Orbitrap_XL_untarget/0_pc_extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/Orbitrap_XL_untarget/0_pc_extraction.py -------------------------------------------------------------------------------- /DEMO/Orbitrap_XL_untarget/1_peak_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/Orbitrap_XL_untarget/1_peak_detection.py -------------------------------------------------------------------------------- /DEMO/QE_HF_target/0_pc_extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/QE_HF_target/0_pc_extraction.py -------------------------------------------------------------------------------- /DEMO/QE_HF_target/1_peak_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/QE_HF_target/1_peak_detection.py -------------------------------------------------------------------------------- /DEMO/QE_HF_untarget/0_pc_extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/QE_HF_untarget/0_pc_extraction.py -------------------------------------------------------------------------------- /DEMO/QE_HF_untarget/1_peak_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/QE_HF_untarget/1_peak_detection.py -------------------------------------------------------------------------------- /DEMO/TripleTOF_6600_target/0_pc_extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/TripleTOF_6600_target/0_pc_extraction.py -------------------------------------------------------------------------------- /DEMO/TripleTOF_6600_target/1_peak_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/TripleTOF_6600_target/1_peak_detection.py -------------------------------------------------------------------------------- /DEMO/TripleTOF_6600_untarget/0_pc_extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/TripleTOF_6600_untarget/0_pc_extraction.py -------------------------------------------------------------------------------- /DEMO/TripleTOF_6600_untarget/1_peak_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/DEMO/TripleTOF_6600_untarget/1_peak_detection.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/README.md -------------------------------------------------------------------------------- /config/msnet_default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/config/msnet_default.yaml -------------------------------------------------------------------------------- /cuda/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/setup.py -------------------------------------------------------------------------------- /cuda/src/ball_query.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ball_query.cpp -------------------------------------------------------------------------------- /cuda/src/ball_query2.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ball_query2.cpp -------------------------------------------------------------------------------- /cuda/src/ball_query2_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ball_query2_gpu.cu -------------------------------------------------------------------------------- /cuda/src/ball_query2_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ball_query2_gpu.h -------------------------------------------------------------------------------- /cuda/src/ball_query_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ball_query_gpu.cu -------------------------------------------------------------------------------- /cuda/src/ball_query_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ball_query_gpu.h -------------------------------------------------------------------------------- /cuda/src/bilinear_interpolate.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/bilinear_interpolate.cpp -------------------------------------------------------------------------------- /cuda/src/bilinear_interpolate_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/bilinear_interpolate_gpu.cu -------------------------------------------------------------------------------- /cuda/src/bilinear_interpolate_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/bilinear_interpolate_gpu.h -------------------------------------------------------------------------------- /cuda/src/cuda_utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/cuda_utils.h -------------------------------------------------------------------------------- /cuda/src/extract_features.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/extract_features.cpp -------------------------------------------------------------------------------- /cuda/src/extract_features_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/extract_features_gpu.cu -------------------------------------------------------------------------------- /cuda/src/extract_features_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/extract_features_gpu.h -------------------------------------------------------------------------------- /cuda/src/extract_pc.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/extract_pc.cpp -------------------------------------------------------------------------------- /cuda/src/extract_pc_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/extract_pc_gpu.cu -------------------------------------------------------------------------------- /cuda/src/extract_pc_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/extract_pc_gpu.h -------------------------------------------------------------------------------- /cuda/src/group_points.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/group_points.cpp -------------------------------------------------------------------------------- /cuda/src/group_points_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/group_points_gpu.cu -------------------------------------------------------------------------------- /cuda/src/group_points_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/group_points_gpu.h -------------------------------------------------------------------------------- /cuda/src/interpolate.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/interpolate.cpp -------------------------------------------------------------------------------- /cuda/src/interpolate_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/interpolate_gpu.cu -------------------------------------------------------------------------------- /cuda/src/interpolate_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/interpolate_gpu.h -------------------------------------------------------------------------------- /cuda/src/match_features.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/match_features.cpp -------------------------------------------------------------------------------- /cuda/src/match_features_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/match_features_gpu.cu -------------------------------------------------------------------------------- /cuda/src/match_features_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/match_features_gpu.h -------------------------------------------------------------------------------- /cuda/src/ms_query.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ms_query.cpp -------------------------------------------------------------------------------- /cuda/src/ms_query_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ms_query_gpu.cu -------------------------------------------------------------------------------- /cuda/src/ms_query_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/ms_query_gpu.h -------------------------------------------------------------------------------- /cuda/src/msnet_api.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/msnet_api.cpp -------------------------------------------------------------------------------- /cuda/src/sampling.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/sampling.cpp -------------------------------------------------------------------------------- /cuda/src/sampling_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/sampling_gpu.cu -------------------------------------------------------------------------------- /cuda/src/sampling_gpu.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/cuda/src/sampling_gpu.h -------------------------------------------------------------------------------- /experiment/msnet_20220215_143158/backbone_300.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/experiment/msnet_20220215_143158/backbone_300.pth -------------------------------------------------------------------------------- /experiment/msnet_20220215_143158/box_center_net_300.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/experiment/msnet_20220215_143158/box_center_net_300.pth -------------------------------------------------------------------------------- /experiment/msnet_20220215_143158/polar_mask_net_300.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/experiment/msnet_20220215_143158/polar_mask_net_300.pth -------------------------------------------------------------------------------- /experiment/msnet_20220215_143158/sem_net_300.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/experiment/msnet_20220215_143158/sem_net_300.pth -------------------------------------------------------------------------------- /experiment/msnet_20220427_141044/backbone_1000.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/experiment/msnet_20220427_141044/backbone_1000.pth -------------------------------------------------------------------------------- /experiment/msnet_20220427_141044/box_center_net_1000.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/experiment/msnet_20220427_141044/box_center_net_1000.pth -------------------------------------------------------------------------------- /experiment/msnet_20220427_141044/polar_mask_net_1000.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/experiment/msnet_20220427_141044/polar_mask_net_1000.pth -------------------------------------------------------------------------------- /experiment/msnet_20220427_141044/sem_net_1000.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/experiment/msnet_20220427_141044/sem_net_1000.pth -------------------------------------------------------------------------------- /model/main_msnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/model/main_msnet.py -------------------------------------------------------------------------------- /model/msnet_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/model/msnet_model.py -------------------------------------------------------------------------------- /model/msnet_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/model/msnet_modules.py -------------------------------------------------------------------------------- /model/msnet_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/model/msnet_utils.py -------------------------------------------------------------------------------- /model/pytorch_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/model/pytorch_utils.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/requirements.txt -------------------------------------------------------------------------------- /third-party/pyvenn/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/third-party/pyvenn/LICENSE -------------------------------------------------------------------------------- /third-party/pyvenn/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/third-party/pyvenn/README.md -------------------------------------------------------------------------------- /third-party/pyvenn/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /third-party/pyvenn/demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/third-party/pyvenn/demo.py -------------------------------------------------------------------------------- /third-party/pyvenn/venn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/third-party/pyvenn/venn.py -------------------------------------------------------------------------------- /utils/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/utils/config.py -------------------------------------------------------------------------------- /utils/log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/utils/log.py -------------------------------------------------------------------------------- /utils/ms_compatibility.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/utils/ms_compatibility.py -------------------------------------------------------------------------------- /utils/polar_mask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/utils/polar_mask.py -------------------------------------------------------------------------------- /utils/visualize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/utils/visualize.py -------------------------------------------------------------------------------- /workflow/predict/main_eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/workflow/predict/main_eval.py -------------------------------------------------------------------------------- /workflow/predict/point_cloud_extractor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/workflow/predict/point_cloud_extractor.py -------------------------------------------------------------------------------- /workflow/train/dataset_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/workflow/train/dataset_generator.py -------------------------------------------------------------------------------- /workflow/train/dataset_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/workflow/train/dataset_loader.py -------------------------------------------------------------------------------- /workflow/train/main_train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSi-Studio/3D-MSNet/HEAD/workflow/train/main_train.py --------------------------------------------------------------------------------