├── .gitignore ├── LICENSE ├── MedLAM ├── Anatomy_detection.py ├── Cal_support_feature.py ├── Predic_corner_cor.py └── detection_functions.py ├── MedLAM_Inference.py ├── MedLSAM_SPL_Inference.py ├── MedLSAM_WPL_Inference.py ├── MedSAM ├── auto_pre_CT.py ├── segment_anything │ ├── __init__.py │ ├── automatic_mask_generator.py │ ├── build_sam.py │ ├── modeling │ │ ├── __init__.py │ │ ├── common.py │ │ ├── image_encoder.py │ │ ├── mask_decoder.py │ │ ├── prompt_encoder.py │ │ ├── sam.py │ │ └── transformer.py │ ├── predictor.py │ └── utils │ │ ├── __init__.py │ │ ├── amg.py │ │ ├── onnx.py │ │ └── transforms.py ├── setup.py └── utils │ ├── SurfaceDice.py │ └── precompute_img_embed.py ├── MedSAM_Inference.py ├── checkpoint └── .md ├── config ├── data │ ├── StructSeg_HaN │ │ ├── query_image.txt │ │ ├── query_label.txt │ │ ├── support_image.txt │ │ └── support_label.txt │ └── WORD │ │ ├── query_image.txt │ │ ├── query_label.txt │ │ ├── support_image.txt │ │ └── support_label.txt └── test_config │ ├── test_structseg_medlam.txt │ ├── test_structseg_medlam_spl_medsam.txt │ ├── test_structseg_medlam_spl_sam.txt │ ├── test_structseg_medlam_wpl_medsam.txt │ ├── test_structseg_medlam_wpl_sam.txt │ ├── test_word_medlam.txt │ ├── test_word_medlam_spl_medsam.txt │ ├── test_word_medlam_spl_sam.txt │ ├── test_word_medlam_wpl_medsam.txt │ └── test_word_medlam_wpl_sam.txt ├── data_process ├── Create_file_ls.py ├── Create_file_ls_total.py └── data_process_func.py ├── fig ├── dsc.png ├── iou.png ├── medlsam.jpg └── wpl_spl.png ├── networks ├── NetFactory.py ├── layers.py └── medlam.py ├── readme.md ├── result_analysis ├── draw_vio_structseg.py ├── draw_vio_word.py ├── output.csv └── table_latex2excel.py ├── setup.py ├── total_test.sh ├── train ├── checkpoint │ └── .md ├── config │ ├── ori_nii.txt │ ├── pre_nii.txt │ └── train_position_full_size_with_fc.txt ├── dataloaders │ └── Position_dataloader.py ├── dataset_preprocess.py ├── extract_weights.py ├── losses │ ├── EmbFCLoss.py │ └── __init__.py ├── readme.md └── train_position_full_size_with_fc.py └── util ├── evaluation_index.py ├── load_save_model.py ├── logger.py ├── parse_config.py └── util_func.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/LICENSE -------------------------------------------------------------------------------- /MedLAM/Anatomy_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedLAM/Anatomy_detection.py -------------------------------------------------------------------------------- /MedLAM/Cal_support_feature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedLAM/Cal_support_feature.py -------------------------------------------------------------------------------- /MedLAM/Predic_corner_cor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedLAM/Predic_corner_cor.py -------------------------------------------------------------------------------- /MedLAM/detection_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedLAM/detection_functions.py -------------------------------------------------------------------------------- /MedLAM_Inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedLAM_Inference.py -------------------------------------------------------------------------------- /MedLSAM_SPL_Inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedLSAM_SPL_Inference.py -------------------------------------------------------------------------------- /MedLSAM_WPL_Inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedLSAM_WPL_Inference.py -------------------------------------------------------------------------------- /MedSAM/auto_pre_CT.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/auto_pre_CT.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/__init__.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/automatic_mask_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/automatic_mask_generator.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/build_sam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/build_sam.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/modeling/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/modeling/__init__.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/modeling/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/modeling/common.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/modeling/image_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/modeling/image_encoder.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/modeling/mask_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/modeling/mask_decoder.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/modeling/prompt_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/modeling/prompt_encoder.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/modeling/sam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/modeling/sam.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/modeling/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/modeling/transformer.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/predictor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/predictor.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/utils/__init__.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/utils/amg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/utils/amg.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/utils/onnx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/utils/onnx.py -------------------------------------------------------------------------------- /MedSAM/segment_anything/utils/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/segment_anything/utils/transforms.py -------------------------------------------------------------------------------- /MedSAM/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/setup.py -------------------------------------------------------------------------------- /MedSAM/utils/SurfaceDice.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/utils/SurfaceDice.py -------------------------------------------------------------------------------- /MedSAM/utils/precompute_img_embed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM/utils/precompute_img_embed.py -------------------------------------------------------------------------------- /MedSAM_Inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/MedSAM_Inference.py -------------------------------------------------------------------------------- /checkpoint/.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config/data/StructSeg_HaN/query_image.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/data/StructSeg_HaN/query_image.txt -------------------------------------------------------------------------------- /config/data/StructSeg_HaN/query_label.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/data/StructSeg_HaN/query_label.txt -------------------------------------------------------------------------------- /config/data/StructSeg_HaN/support_image.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/data/StructSeg_HaN/support_image.txt -------------------------------------------------------------------------------- /config/data/StructSeg_HaN/support_label.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/data/StructSeg_HaN/support_label.txt -------------------------------------------------------------------------------- /config/data/WORD/query_image.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/data/WORD/query_image.txt -------------------------------------------------------------------------------- /config/data/WORD/query_label.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/data/WORD/query_label.txt -------------------------------------------------------------------------------- /config/data/WORD/support_image.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/data/WORD/support_image.txt -------------------------------------------------------------------------------- /config/data/WORD/support_label.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/data/WORD/support_label.txt -------------------------------------------------------------------------------- /config/test_config/test_structseg_medlam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_structseg_medlam.txt -------------------------------------------------------------------------------- /config/test_config/test_structseg_medlam_spl_medsam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_structseg_medlam_spl_medsam.txt -------------------------------------------------------------------------------- /config/test_config/test_structseg_medlam_spl_sam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_structseg_medlam_spl_sam.txt -------------------------------------------------------------------------------- /config/test_config/test_structseg_medlam_wpl_medsam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_structseg_medlam_wpl_medsam.txt -------------------------------------------------------------------------------- /config/test_config/test_structseg_medlam_wpl_sam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_structseg_medlam_wpl_sam.txt -------------------------------------------------------------------------------- /config/test_config/test_word_medlam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_word_medlam.txt -------------------------------------------------------------------------------- /config/test_config/test_word_medlam_spl_medsam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_word_medlam_spl_medsam.txt -------------------------------------------------------------------------------- /config/test_config/test_word_medlam_spl_sam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_word_medlam_spl_sam.txt -------------------------------------------------------------------------------- /config/test_config/test_word_medlam_wpl_medsam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_word_medlam_wpl_medsam.txt -------------------------------------------------------------------------------- /config/test_config/test_word_medlam_wpl_sam.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/config/test_config/test_word_medlam_wpl_sam.txt -------------------------------------------------------------------------------- /data_process/Create_file_ls.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/data_process/Create_file_ls.py -------------------------------------------------------------------------------- /data_process/Create_file_ls_total.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/data_process/Create_file_ls_total.py -------------------------------------------------------------------------------- /data_process/data_process_func.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/data_process/data_process_func.py -------------------------------------------------------------------------------- /fig/dsc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/fig/dsc.png -------------------------------------------------------------------------------- /fig/iou.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/fig/iou.png -------------------------------------------------------------------------------- /fig/medlsam.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/fig/medlsam.jpg -------------------------------------------------------------------------------- /fig/wpl_spl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/fig/wpl_spl.png -------------------------------------------------------------------------------- /networks/NetFactory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/networks/NetFactory.py -------------------------------------------------------------------------------- /networks/layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/networks/layers.py -------------------------------------------------------------------------------- /networks/medlam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/networks/medlam.py -------------------------------------------------------------------------------- /readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/readme.md -------------------------------------------------------------------------------- /result_analysis/draw_vio_structseg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/result_analysis/draw_vio_structseg.py -------------------------------------------------------------------------------- /result_analysis/draw_vio_word.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/result_analysis/draw_vio_word.py -------------------------------------------------------------------------------- /result_analysis/output.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/result_analysis/output.csv -------------------------------------------------------------------------------- /result_analysis/table_latex2excel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/result_analysis/table_latex2excel.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/setup.py -------------------------------------------------------------------------------- /total_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/total_test.sh -------------------------------------------------------------------------------- /train/checkpoint/.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /train/config/ori_nii.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /train/config/pre_nii.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /train/config/train_position_full_size_with_fc.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/train/config/train_position_full_size_with_fc.txt -------------------------------------------------------------------------------- /train/dataloaders/Position_dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/train/dataloaders/Position_dataloader.py -------------------------------------------------------------------------------- /train/dataset_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/train/dataset_preprocess.py -------------------------------------------------------------------------------- /train/extract_weights.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/train/extract_weights.py -------------------------------------------------------------------------------- /train/losses/EmbFCLoss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/train/losses/EmbFCLoss.py -------------------------------------------------------------------------------- /train/losses/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /train/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/train/readme.md -------------------------------------------------------------------------------- /train/train_position_full_size_with_fc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/train/train_position_full_size_with_fc.py -------------------------------------------------------------------------------- /util/evaluation_index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/util/evaluation_index.py -------------------------------------------------------------------------------- /util/load_save_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/util/load_save_model.py -------------------------------------------------------------------------------- /util/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/util/logger.py -------------------------------------------------------------------------------- /util/parse_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/util/parse_config.py -------------------------------------------------------------------------------- /util/util_func.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openmedlab/MedLSAM/HEAD/util/util_func.py --------------------------------------------------------------------------------