├── .gitignore ├── LICENSE ├── README.md ├── experiments ├── cnn.py ├── lstm.py └── mtms_tcn.py ├── hparams ├── bern_by70 │ └── series_01 │ │ ├── CNN │ │ ├── h001.yaml │ │ ├── h002.yaml │ │ └── h003.yaml │ │ ├── MTMS_TCN │ │ ├── h001.yaml │ │ ├── h002.yaml │ │ └── h003.yaml │ │ └── MT_LSTM │ │ ├── h001.yaml │ │ ├── h002.yaml │ │ └── h003.yaml ├── multi_by140 │ └── series_01 │ │ ├── CNN │ │ ├── h001.yaml │ │ ├── h002.yaml │ │ └── h003.yaml │ │ ├── MTMS_TCN │ │ ├── h001.yaml │ │ ├── h002.yaml │ │ └── h003.yaml │ │ └── MT_LSTM │ │ ├── h001.yaml │ │ ├── h002.yaml │ │ └── h003.yaml └── stras_by70 │ └── series_01 │ ├── CNN │ ├── h001.yaml │ ├── h002.yaml │ └── h003.yaml │ ├── MTMS_TCN │ ├── h001.yaml │ ├── h002.yaml │ └── h003.yaml │ └── MT_LSTM │ ├── h001.yaml │ ├── h002.yaml │ └── h003.yaml ├── jobs ├── bern_by70 │ └── series_01 │ │ ├── CNN │ │ ├── s001.sh │ │ ├── s002.sh │ │ └── s003.sh │ │ ├── MTMS_TCN │ │ ├── s001.sh │ │ ├── s002.sh │ │ └── s003.sh │ │ └── MT_LSTM │ │ ├── s001.sh │ │ ├── s002.sh │ │ └── s003.sh ├── multi_by140 │ └── series_01 │ │ ├── CNN │ │ ├── s001.sh │ │ ├── s002.sh │ │ └── s003.sh │ │ ├── MTMS_TCN │ │ ├── s001.sh │ │ ├── s002.sh │ │ └── s003.sh │ │ └── MT_LSTM │ │ ├── s001.sh │ │ ├── s002.sh │ │ └── s003.sh └── stras_by70 │ └── series_01 │ ├── CNN │ ├── s001.sh │ ├── s002.sh │ └── s003.sh │ ├── MTMS_TCN │ ├── s001.sh │ ├── s002.sh │ └── s003.sh │ └── MT_LSTM │ ├── s001.sh │ ├── s002.sh │ └── s003.sh ├── labels ├── bern │ ├── avg_img_bby70.png │ ├── labels_by70 │ │ ├── BBP01.mp4.json │ │ ├── BBP02.mp4.json │ │ ├── BBP03.mp4.json │ │ ├── BBP04.mp4.json │ │ ├── BBP05.mp4.json │ │ ├── BBP06.mp4.json │ │ ├── BBP07.mp4.json │ │ ├── BBP08.mp4.json │ │ ├── BBP09.mp4.json │ │ ├── BBP10.mp4.json │ │ ├── BBP11.mp4.json │ │ ├── BBP12.mp4.json │ │ ├── BBP13.mp4.json │ │ ├── BBP14.mp4.json │ │ ├── BBP15.mp4.json │ │ ├── BBP16.mp4.json │ │ ├── BBP17.mp4.json │ │ ├── BBP18.mp4.json │ │ ├── BBP19.mp4.json │ │ ├── BBP20.mp4.json │ │ ├── BBP21.mp4.json │ │ ├── BBP22.mp4.json │ │ ├── BBP23.mp4.json │ │ ├── BBP24.mp4.json │ │ ├── BBP25.mp4.json │ │ ├── BBP26.mp4.json │ │ ├── BBP27.mp4.json │ │ ├── BBP28.mp4.json │ │ ├── BBP29.mp4.json │ │ ├── BBP30.mp4.json │ │ ├── BBP31.mp4.json │ │ ├── BBP32.mp4.json │ │ ├── BBP33.mp4.json │ │ ├── BBP34.mp4.json │ │ ├── BBP35.mp4.json │ │ ├── BBP36.mp4.json │ │ ├── BBP37.mp4.json │ │ ├── BBP38.mp4.json │ │ ├── BBP39.mp4.json │ │ ├── BBP40.mp4.json │ │ ├── BBP41.mp4.json │ │ ├── BBP42.mp4.json │ │ ├── BBP43.mp4.json │ │ ├── BBP44.mp4.json │ │ ├── BBP45.mp4.json │ │ ├── BBP46.mp4.json │ │ ├── BBP47.mp4.json │ │ ├── BBP48.mp4.json │ │ ├── BBP49.mp4.json │ │ ├── BBP50.mp4.json │ │ ├── BBP51.mp4.json │ │ ├── BBP52.mp4.json │ │ ├── BBP53.mp4.json │ │ ├── BBP54.mp4.json │ │ ├── BBP55.mp4.json │ │ ├── BBP56.mp4.json │ │ ├── BBP57.mp4.json │ │ ├── BBP58.mp4.json │ │ ├── BBP59.mp4.json │ │ ├── BBP60.mp4.json │ │ ├── BBP61.mp4.json │ │ ├── BBP62.mp4.json │ │ ├── BBP63.mp4.json │ │ ├── BBP64.mp4.json │ │ ├── BBP65.mp4.json │ │ ├── BBP66.mp4.json │ │ ├── BBP67.mp4.json │ │ ├── BBP68.mp4.json │ │ ├── BBP69.mp4.json │ │ └── BBP70.mp4.json │ └── labels_by70_splits │ │ └── labels │ │ ├── test │ │ ├── 1fps_0.pickle │ │ ├── 1fps_1.pickle │ │ ├── 1fps_2.pickle │ │ ├── 1fps_3.pickle │ │ └── 1fps_4.pickle │ │ ├── train │ │ ├── 1fps_100_0.pickle │ │ ├── 1fps_100_1.pickle │ │ ├── 1fps_100_2.pickle │ │ ├── 1fps_100_3.pickle │ │ └── 1fps_100_4.pickle │ │ └── val │ │ ├── 1fps_0.pickle │ │ ├── 1fps_1.pickle │ │ ├── 1fps_2.pickle │ │ ├── 1fps_3.pickle │ │ └── 1fps_4.pickle └── strasbourg │ ├── avg_img_sby70.png │ ├── labels_by70 │ ├── SBP01.mp4.json │ ├── SBP02.mp4.json │ ├── SBP03.mp4.json │ ├── SBP04.mp4.json │ ├── SBP05.mp4.json │ ├── SBP06.mp4.json │ ├── SBP07.mp4.json │ ├── SBP08.mp4.json │ ├── SBP09.mp4.json │ ├── SBP10.mp4.json │ ├── SBP11.mp4.json │ ├── SBP12.mp4.json │ ├── SBP13.mp4.json │ ├── SBP14.mp4.json │ ├── SBP15.mp4.json │ ├── SBP16.mp4.json │ ├── SBP17.mp4.json │ ├── SBP18.mp4.json │ ├── SBP19.mp4.json │ ├── SBP20.mp4.json │ ├── SBP21.mp4.json │ ├── SBP22.mp4.json │ ├── SBP23.mp4.json │ ├── SBP24.mp4.json │ ├── SBP25.mp4.json │ ├── SBP26.mp4.json │ ├── SBP27.mp4.json │ ├── SBP28.mp4.json │ ├── SBP29.mp4.json │ ├── SBP30.mp4.json │ ├── SBP31.mp4.json │ ├── SBP32.mp4.json │ ├── SBP33.mp4.json │ ├── SBP34.mp4.json │ ├── SBP35.mp4.json │ ├── SBP36.mp4.json │ ├── SBP37.mp4.json │ ├── SBP38.mp4.json │ ├── SBP39.mp4.json │ ├── SBP40.mp4.json │ ├── SBP41.mp4.json │ ├── SBP42.mp4.json │ ├── SBP43.mp4.json │ ├── SBP44.mp4.json │ ├── SBP45.mp4.json │ ├── SBP46.mp4.json │ ├── SBP47.mp4.json │ ├── SBP48.mp4.json │ ├── SBP49.mp4.json │ ├── SBP50.mp4.json │ ├── SBP51.mp4.json │ ├── SBP52.mp4.json │ ├── SBP53.mp4.json │ ├── SBP54.mp4.json │ ├── SBP55.mp4.json │ ├── SBP56.mp4.json │ ├── SBP57.mp4.json │ ├── SBP58.mp4.json │ ├── SBP59.mp4.json │ ├── SBP60.mp4.json │ ├── SBP61.mp4.json │ ├── SBP62.mp4.json │ ├── SBP63.mp4.json │ ├── SBP64.mp4.json │ ├── SBP65.mp4.json │ ├── SBP66.mp4.json │ ├── SBP67.mp4.json │ ├── SBP68.mp4.json │ ├── SBP69.mp4.json │ └── SBP70.mp4.json │ └── labels_by70_splits │ └── labels │ ├── test │ ├── 1fps_0.pickle │ ├── 1fps_1.pickle │ ├── 1fps_2.pickle │ ├── 1fps_3.pickle │ └── 1fps_4.pickle │ ├── train │ ├── 1fps_100_0.pickle │ ├── 1fps_100_1.pickle │ ├── 1fps_100_2.pickle │ ├── 1fps_100_3.pickle │ └── 1fps_100_4.pickle │ └── val │ ├── 1fps_0.pickle │ ├── 1fps_1.pickle │ ├── 1fps_2.pickle │ ├── 1fps_3.pickle │ └── 1fps_4.pickle ├── loaders ├── data_loader_cnn.py └── data_loader_temp.py ├── main_cnn.py ├── main_temp.py ├── requirements.txt ├── static ├── camma_logo_tr.png └── hierarchy.jpg ├── tables ├── phase.csv └── step.csv └── util ├── data_reader.py ├── extract_frames.py ├── results_collator.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.DS_Store 2 | datasets/ 3 | datasets/* 4 | **__pycache__** 5 | **/frames 6 | **/frames/** 7 | models/ 8 | models/* 9 | mvenv/ 10 | mvenv/* 11 | -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/CNN/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_BBY70_s01_CNN_phase_100_0 4 | method : CNN 5 | dataset : bern_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/CNN/run_001 50 | run_dir : bern_by70/series_01/CNN/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/CNN/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_BBY70_s01_CNN_step_100_0 4 | method : CNN 5 | dataset : bern_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/CNN/run_002 50 | run_dir : bern_by70/series_01/CNN/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/CNN/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_BBY70_s01_CNN_phase_step_100_0 4 | method : CNN 5 | dataset : bern_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/CNN/run_003 50 | run_dir : bern_by70/series_01/CNN/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/MTMS_TCN/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_BBY70_s01_MTMS_TCN_phase_100_0 4 | method : MTMS_TCN 5 | dataset : bern_bypass70 6 | pkl_path : bern_by70/series_01/CNN/run_001 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/MTMS_TCN/run_001 50 | run_dir : bern_by70/series_01/MTMS_TCN/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/MTMS_TCN/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_BBY70_s01_MTMS_TCN_step_100_0 4 | method : MTMS_TCN 5 | dataset : bern_bypass70 6 | pkl_path : bern_by70/series_01/CNN/run_002 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/MTMS_TCN/run_002 50 | run_dir : bern_by70/series_01/MTMS_TCN/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/MTMS_TCN/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_BBY70_s01_MTMS_TCN_phase_step_100_0 4 | method : MTMS_TCN 5 | dataset : bern_bypass70 6 | pkl_path : bern_by70/series_01/CNN/run_003 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/MTMS_TCN/run_003 50 | run_dir : bern_by70/series_01/MTMS_TCN/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/MT_LSTM/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_BBY70_s01_MT_LSTM_phase_100_0 4 | method : MT_LSTM 5 | dataset : bern_bypass70 6 | pkl_path : bern_by70/series_01/CNN/run_001 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/MT_LSTM/run_001 50 | run_dir : bern_by70/series_01/MT_LSTM/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/MT_LSTM/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_BBY70_s01_MT_LSTM_step_100_0 4 | method : MT_LSTM 5 | dataset : bern_bypass70 6 | pkl_path : bern_by70/series_01/CNN/run_002 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/MT_LSTM/run_002 50 | run_dir : bern_by70/series_01/MT_LSTM/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/bern_by70/series_01/MT_LSTM/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_BBY70_s01_MT_LSTM_phase_step_100_0 4 | method : MT_LSTM 5 | dataset : bern_bypass70 6 | pkl_path : bern_by70/series_01/CNN/run_003 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : bern_by70/series_01/MT_LSTM/run_003 50 | run_dir : bern_by70/series_01/MT_LSTM/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/CNN/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_BS_BY70_s01_CNN_phase_100_0 4 | method : CNN 5 | dataset : bern_stras_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/CNN/run_001 50 | run_dir : multi_by140/series_01/CNN/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/CNN/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_BS_BY70_s01_CNN_step_100_0 4 | method : CNN 5 | dataset : bern_stras_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/CNN/run_002 50 | run_dir : multi_by140/series_01/CNN/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/CNN/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_BS_BY70_s01_CNN_phase_step_100_0 4 | method : CNN 5 | dataset : bern_stras_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/CNN/run_003 50 | run_dir : multi_by140/series_01/CNN/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/MTMS_TCN/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_BS_BY70_s01_MTMS_TCN_phase_100_0 4 | method : MTMS_TCN 5 | dataset : bern_stras_bypass70 6 | pkl_path : multi_by140/series_01/CNN/run_001 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/MTMS_TCN/run_001 50 | run_dir : multi_by140/series_01/MTMS_TCN/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/MTMS_TCN/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_BS_BY70_s01_MTMS_TCN_step_100_0 4 | method : MTMS_TCN 5 | dataset : bern_stras_bypass70 6 | pkl_path : multi_by140/series_01/CNN/run_002 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/MTMS_TCN/run_002 50 | run_dir : multi_by140/series_01/MTMS_TCN/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/MTMS_TCN/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_BS_BY70_s01_MTMS_TCN_phase_step_100_0 4 | method : MTMS_TCN 5 | dataset : bern_stras_bypass70 6 | pkl_path : multi_by140/series_01/CNN/run_003 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/MTMS_TCN/run_003 50 | run_dir : multi_by140/series_01/MTMS_TCN/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/MT_LSTM/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_BS_BY70_s01_MT_LSTM_phase_100_0 4 | method : MT_LSTM 5 | dataset : bern_stras_bypass70 6 | pkl_path : multi_by140/series_01/CNN/run_001 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/MT_LSTM/run_001 50 | run_dir : multi_by140/series_01/MT_LSTM/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/MT_LSTM/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_BS_BY70_s01_MT_LSTM_step_100_0 4 | method : MT_LSTM 5 | dataset : bern_stras_bypass70 6 | pkl_path : multi_by140/series_01/CNN/run_002 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/MT_LSTM/run_002 50 | run_dir : multi_by140/series_01/MT_LSTM/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/multi_by140/series_01/MT_LSTM/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_BS_BY70_s01_MT_LSTM_phase_step_100_0 4 | method : MT_LSTM 5 | dataset : bern_stras_bypass70 6 | pkl_path : multi_by140/series_01/CNN/run_003 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : multi_by140/series_01/MT_LSTM/run_003 50 | run_dir : multi_by140/series_01/MT_LSTM/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/CNN/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_SBY70_s01_CNN_phase_100_0 4 | method : CNN 5 | dataset : stras_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/CNN/run_001 50 | run_dir : stras_by70/series_01/CNN/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/CNN/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_SBY70_s01_CNN_step_100_0 4 | method : CNN 5 | dataset : stras_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/CNN/run_002 50 | run_dir : stras_by70/series_01/CNN/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/CNN/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_SBY70_s01_CNN_phase_step_100_0 4 | method : CNN 5 | dataset : stras_bypass70 6 | pkl_path : None 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : None 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/CNN/run_003 50 | run_dir : stras_by70/series_01/CNN/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : None 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/MTMS_TCN/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_SBY70_s01_MTMS_TCN_phase_100_0 4 | method : MTMS_TCN 5 | dataset : stras_bypass70 6 | pkl_path : stras_by70/series_01/CNN/run_001 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/MTMS_TCN/run_001 50 | run_dir : stras_by70/series_01/MTMS_TCN/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/MTMS_TCN/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_SBY70_s01_MTMS_TCN_step_100_0 4 | method : MTMS_TCN 5 | dataset : stras_bypass70 6 | pkl_path : stras_by70/series_01/CNN/run_002 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/MTMS_TCN/run_002 50 | run_dir : stras_by70/series_01/MTMS_TCN/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/MTMS_TCN/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_SBY70_s01_MTMS_TCN_phase_step_100_0 4 | method : MTMS_TCN 5 | dataset : stras_bypass70 6 | pkl_path : stras_by70/series_01/CNN/run_003 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MTMS_TCN 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/MTMS_TCN/run_003 50 | run_dir : stras_by70/series_01/MTMS_TCN/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/MT_LSTM/h001.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 1 3 | tag : SL_SBY70_s01_MT_LSTM_phase_100_0 4 | method : MT_LSTM 5 | dataset : stras_bypass70 6 | pkl_path : stras_by70/series_01/CNN/run_001 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : False 22 | phases_weighted : True 23 | steps_weighted : False 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/MT_LSTM/run_001 50 | run_dir : stras_by70/series_01/MT_LSTM/run_001 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/MT_LSTM/h002.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 2 3 | tag : SL_SBY70_s01_MT_LSTM_step_100_0 4 | method : MT_LSTM 5 | dataset : stras_bypass70 6 | pkl_path : stras_by70/series_01/CNN/run_002 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : False 21 | add_steps : True 22 | phases_weighted : False 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/MT_LSTM/run_002 50 | run_dir : stras_by70/series_01/MT_LSTM/run_002 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /hparams/stras_by70/series_01/MT_LSTM/h003.yaml: -------------------------------------------------------------------------------- 1 | default : &DEFAULT 2 | id : 3 3 | tag : SL_SBY70_s01_MT_LSTM_phase_step_100_0 4 | method : MT_LSTM 5 | dataset : stras_bypass70 6 | pkl_path : stras_by70/series_01/CNN/run_003 7 | read_pkl : True 8 | pretrain_model : "./models/resnet50-19c8e357.pth" # ImageNet pretrained 9 | xml_dir : "raw/" 10 | phases_file : "tables/phases_order.csv" 11 | steps_file : "tables/steps_order.csv" 12 | gpu_devices : [0, 1] 13 | sample_frequency : 1 14 | model : resnet_50 15 | temporal_model : MT_LSTM 16 | num_sup_videos : -1 17 | num_weak_sup_vids : 0 18 | random_seed : 99765 19 | pretained_model : True 20 | add_phases : True 21 | add_steps : True 22 | phases_weighted : True 23 | steps_weighted : True 24 | loss_type : cross_entropy 25 | focal_gamma : 0.7 26 | mse_loss : True 27 | n_cnn_outputs : 2048 28 | id_split : 0 29 | num_stages : 1 30 | num_layers : 10 31 | num_f_maps : 64 32 | no_drop : 1 33 | n_batch : 1 34 | n_minibatch : 64 35 | n_phases : 13 36 | n_steps : 46 37 | n_epochs : 30 38 | n_epochs_temp_model : 200 39 | n_resize : 224 40 | aug_rot_angle : 30 41 | aug_n_offset : 0 42 | saturate_level : 3 43 | bright_level : 0.4 44 | n_parallel : 8 45 | n_prefetch : 4 46 | ini_fc : 0.1 47 | eval_mode : True 48 | augment_funcs : ["flip", "saturate", "rotate"] 49 | weights_init : stras_by70/series_01/MT_LSTM/run_003 50 | run_dir : stras_by70/series_01/MT_LSTM/run_003 51 | weight_decay : 0.0005 52 | learning_rate : 0.00001 53 | temporal_lr : 0.0003 54 | resume_training : True 55 | use_amp : True -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/CNN/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/bern_by70/series_01/CNN/h001.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s001__SL_BBY70_s01_CNN_phase_100_0.log 11 | 12 | python main_cnn.py -hp hparams/bern_by70/series_01/CNN/h001.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_BBY70_s01_CNN_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/CNN/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/bern_by70/series_01/CNN/h002.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s002__SL_BBY70_s01_CNN_step_100_0.log 11 | 12 | python main_cnn.py -hp hparams/bern_by70/series_01/CNN/h002.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_BBY70_s01_CNN_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/CNN/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/bern_by70/series_01/CNN/h003.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s003__SL_BBY70_s01_CNN_phase_step_100_0.log 11 | 12 | python main_cnn.py -hp hparams/bern_by70/series_01/CNN/h003.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_BBY70_s01_CNN_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/MTMS_TCN/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/bern_by70/series_01/MTMS_TCN/h001.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s001__SL_BBY70_s01_MTMS_TCN_phase_100_0.log 11 | 12 | python main_temp.py -hp hparams/bern_by70/series_01/MTMS_TCN/h001.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_BBY70_s01_MTMS_TCN_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/MTMS_TCN/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/bern_by70/series_01/MTMS_TCN/h002.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s002__SL_BBY70_s01_MTMS_TCN_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/bern_by70/series_01/MTMS_TCN/h002.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_BBY70_s01_MTMS_TCN_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/MTMS_TCN/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/bern_by70/series_01/MTMS_TCN/h003.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s003__SL_BBY70_s01_MTMS_TCN_phase_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/bern_by70/series_01/MTMS_TCN/h003.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_BBY70_s01_MTMS_TCN_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/MT_LSTM/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/bern_by70/series_01/MT_LSTM/h001.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s001__SL_BBY70_s01_MT_LSTM_phase_100_0.log 11 | 12 | python main_temp.py -hp hparams/bern_by70/series_01/MT_LSTM/h001.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_BBY70_s01_MT_LSTM_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/MT_LSTM/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/bern_by70/series_01/MT_LSTM/h002.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s002__SL_BBY70_s01_MT_LSTM_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/bern_by70/series_01/MT_LSTM/h002.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_BBY70_s01_MT_LSTM_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/bern_by70/series_01/MT_LSTM/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/bern_by70/series_01/MT_LSTM/h003.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s003__SL_BBY70_s01_MT_LSTM_phase_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/bern_by70/series_01/MT_LSTM/h003.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_BBY70_s01_MT_LSTM_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/CNN/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/multi_by140/series_01/CNN/h001.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s001__SL_MBY140_s01_CNN_phase_100_0.log 11 | 12 | python main_cnn.py -hp hparams/multi_by140/series_01/CNN/h001.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_MBY140_s01_CNN_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/CNN/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/multi_by140/series_01/CNN/h002.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s002__SL_MBY140_s01_CNN_step_100_0.log 11 | 12 | python main_cnn.py -hp hparams/multi_by140/series_01/CNN/h002.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_MBY140_s01_CNN_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/CNN/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/multi_by140/series_01/CNN/h003.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s003__SL_MBY140_s01_CNN_phase_step_100_0.log 11 | 12 | python main_cnn.py -hp hparams/multi_by140/series_01/CNN/h003.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_MBY140_s01_CNN_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/MTMS_TCN/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/multi_by140/series_01/MTMS_TCN/h001.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s001__SL_MBY140_s01_MTMS_TCN_phase_100_0.log 11 | 12 | python main_temp.py -hp hparams/multi_by140/series_01/MTMS_TCN/h001.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_MBY140_s01_MTMS_TCN_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/MTMS_TCN/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/multi_by140/series_01/MTMS_TCN/h002.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s002__SL_MBY140_s01_MTMS_TCN_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/multi_by140/series_01/MTMS_TCN/h002.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_MBY140_s01_MTMS_TCN_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/MTMS_TCN/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/multi_by140/series_01/MTMS_TCN/h003.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s003__SL_MBY140_s01_MTMS_TCN_phase_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/multi_by140/series_01/MTMS_TCN/h003.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_MBY140_s01_MTMS_TCN_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/MT_LSTM/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/multi_by140/series_01/MT_LSTM/h001.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s001__SL_MBY140_s01_MT_LSTM_phase_100_0.log 11 | 12 | python main_temp.py -hp hparams/multi_by140/series_01/MT_LSTM/h001.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_MBY140_s01_MT_LSTM_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/MT_LSTM/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/multi_by140/series_01/MT_LSTM/h002.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s002__SL_MBY140_s01_MT_LSTM_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/multi_by140/series_01/MT_LSTM/h002.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_MBY140_s01_MT_LSTM_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/multi_by140/series_01/MT_LSTM/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/multi_by140/series_01/MT_LSTM/h003.yaml \ 9 | -p models \ 10 | -d labels/bern/labels_by70_splits/ | tee $sdir/s003__SL_MBY140_s01_MT_LSTM_phase_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/multi_by140/series_01/MT_LSTM/h003.yaml \ 13 | -p models \ 14 | -d labels/bern/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_MBY140_s01_MT_LSTM_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/CNN/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/stras_by70/series_01/CNN/h001.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s001__SL_SBY70_s01_CNN_phase_100_0.log 11 | 12 | python main_cnn.py -hp hparams/stras_by70/series_01/CNN/h001.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_SBY70_s01_CNN_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/CNN/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/stras_by70/series_01/CNN/h002.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s002__SL_SBY70_s01_CNN_step_100_0.log 11 | 12 | python main_cnn.py -hp hparams/stras_by70/series_01/CNN/h002.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_SBY70_s01_CNN_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/CNN/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_cnn.py -hp hparams/stras_by70/series_01/CNN/h003.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s003__SL_SBY70_s01_CNN_phase_step_100_0.log 11 | 12 | python main_cnn.py -hp hparams/stras_by70/series_01/CNN/h003.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_SBY70_s01_CNN_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/MTMS_TCN/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/stras_by70/series_01/MTMS_TCN/h001.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s001__SL_SBY70_s01_MTMS_TCN_phase_100_0.log 11 | 12 | python main_temp.py -hp hparams/stras_by70/series_01/MTMS_TCN/h001.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_SBY70_s01_MTMS_TCN_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/MTMS_TCN/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/stras_by70/series_01/MTMS_TCN/h002.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s002__SL_SBY70_s01_MTMS_TCN_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/stras_by70/series_01/MTMS_TCN/h002.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_SBY70_s01_MTMS_TCN_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/MTMS_TCN/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/stras_by70/series_01/MTMS_TCN/h003.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s003__SL_SBY70_s01_MTMS_TCN_phase_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/stras_by70/series_01/MTMS_TCN/h003.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_SBY70_s01_MTMS_TCN_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/MT_LSTM/s001.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/stras_by70/series_01/MT_LSTM/h001.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s001__SL_SBY70_s01_MT_LSTM_phase_100_0.log 11 | 12 | python main_temp.py -hp hparams/stras_by70/series_01/MT_LSTM/h001.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s001__SL_SBY70_s01_MT_LSTM_phase_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/MT_LSTM/s002.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/stras_by70/series_01/MT_LSTM/h002.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s002__SL_SBY70_s01_MT_LSTM_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/stras_by70/series_01/MT_LSTM/h002.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s002__SL_SBY70_s01_MT_LSTM_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /jobs/stras_by70/series_01/MT_LSTM/s003.sh: -------------------------------------------------------------------------------- 1 | sdir="$(pwd)" 2 | cd $MBy140 3 | 4 | 5 | 6 | nvidia-smi 7 | 8 | python main_temp.py -hp hparams/stras_by70/series_01/MT_LSTM/h003.yaml \ 9 | -p models \ 10 | -d labels/strasbourg/labels_by70_splits/ | tee $sdir/s003__SL_SBY70_s01_MT_LSTM_phase_step_100_0.log 11 | 12 | python main_temp.py -hp hparams/stras_by70/series_01/MT_LSTM/h003.yaml \ 13 | -p models \ 14 | -d labels/strasbourg/labels_by70_splits/ \ 15 | -s extract_predictions | tee -a $sdir/s003__SL_SBY70_s01_MT_LSTM_phase_step_100_0.log 16 | 17 | 18 | nvidia-smi -------------------------------------------------------------------------------- /labels/bern/avg_img_bby70.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CAMMA-public/MultiBypass140/d3ace464d04ec3f4661f2f992276554e9a5b5af6/labels/bern/avg_img_bby70.png -------------------------------------------------------------------------------- /labels/bern/labels_by70/BBP01.mp4.json: -------------------------------------------------------------------------------- 1 | {"phases": [{"start": 13301, "end": 1371912, "label_name": "preparation", "label_id": 0}, {"start": 53583, "end": 75743, "label_name": "out_of_body", "label_id": 12}, {"start": 93024, "end": 125625, "label_name": "out_of_body", "label_id": 12}, {"start": 268391, "end": 270951, "label_name": "out_of_body", "label_id": 12}, {"start": 1371912, "end": 2090539, "label_name": "gastric_pouch_creation", "label_id": 1}, {"start": 1423834, "end": 1424954, "label_name": "severe_index", "label_id": 13}, {"start": 1482636, "end": 1502357, "label_name": "severe_index", "label_id": 13}, 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"s5_his_angle_dissection", "label_id": 5}, {"start": 605224, "end": 848545, "label_name": "s6_horizontal_stapling", "label_id": 6}, {"start": 848545, "end": 988706, "label_name": "s7_retrogastric_dissection", "label_id": 7}, {"start": 988706, "end": 1054346, "label_name": "s8_vertical_stapling", "label_id": 8}, {"start": 1054346, "end": 1088907, "label_name": "s7_retrogastric_dissection", "label_id": 7}, {"start": 1088907, "end": 1135067, "label_name": "s8_vertical_stapling", "label_id": 8}, {"start": 1135067, "end": 1331828, "label_name": "s11_gastric_opening", "label_id": 11}, {"start": 1331828, "end": 1382348, "label_name": "s15_treitz_angle_identification", "label_id": 15}, {"start": 1382348, "end": 1447508, "label_name": "s16_biliary_limb_measurement", "label_id": 16}, {"start": 1447508, "end": 1575029, "label_name": "s17_jejunum_opening", "label_id": 17}, {"start": 1575029, "end": 1740590, "label_name": "s18_gastrojejunal_stapling", "label_id": 18}, {"start": 1740590, "end": 2917997, "label_name": "s19_gastrojejunal_defect_closing", "label_id": 19}, {"start": 2917997, "end": 2961357, "label_name": "s27_petersen_space_exposure", "label_id": 27}, {"start": 2961357, "end": 3303279, "label_name": "s28_petersen_space_closing", "label_id": 28}, {"start": 3303279, "end": 3416359, "label_name": "s20_mesenteric_opening", "label_id": 20}, {"start": 3416359, "end": 3473720, "label_name": "s21_jejunal_section", "label_id": 21}, {"start": 3473720, "end": 3557560, "label_name": "s29_biliary_limb_opening", "label_id": 29}, {"start": 3557560, "end": 3644721, "label_name": "s30_alimentary_limb_measurement", "label_id": 30}, {"start": 3644721, "end": 3702321, "label_name": "s31_alimentary_limb_opening", "label_id": 31}, {"start": 3702321, "end": 3984042, "label_name": "s32_jejunojejunal_stapling", "label_id": 32}, {"start": 3984042, "end": 5219929, "label_name": "s33_jejunojejunal_defect_closing", "label_id": 33}, {"start": 5219929, "end": 5275530, "label_name": 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-------------------------------------------------------------------------------- /loaders/data_loader_temp.py: -------------------------------------------------------------------------------- 1 | import torch 2 | import random 3 | import pickle 4 | import logging 5 | import numpy as np 6 | 7 | class BatchGenerator(object): 8 | def __init__(self, num_phases, num_steps, datafile, sample_rate=1 9 | ): 10 | self.index = 0 11 | self.videos = list() 12 | self.num_phases = num_phases 13 | self.num_steps = num_steps 14 | self.datafile = datafile 15 | self.sample_rate = sample_rate 16 | self._read_data() 17 | 18 | def reset(self): 19 | self.index = 0 20 | random.shuffle(self.videos) 21 | 22 | def has_next(self): 23 | if self.index < len(self.videos): 24 | return True 25 | return False 26 | 27 | def next_batch(self, batch_size): 28 | video_batch = self.videos[self.index:self.index + batch_size] 29 | self.index += batch_size 30 | bsize = 1e5 31 | batch_input = [] 32 | batch_phases = [] 33 | batch_steps = [] 34 | batch_images = [] 35 | supervision_signals = [] 36 | for video in video_batch: 37 | features = np.array(video['features']).T 38 | phases = video['phase_labels'] 39 | im_files = video['images'] 40 | try: 41 | steps = video['step_labels'] 42 | except: 43 | steps = video['phase_labels'] 44 | supervision_signals.append(video['supervision']) 45 | 46 | seq_len = len(im_files) 47 | batch_images += np.array_split(im_files[:], seq_len // bsize + 1) 48 | batch_input += np.array_split(features[::self.sample_rate], seq_len // bsize + 1, 1) 49 | batch_phases += np.array_split(phases[::self.sample_rate], seq_len // bsize + 1) 50 | batch_steps += np.array_split(steps[::self.sample_rate], seq_len // bsize + 1) 51 | 52 | 53 | max_seq = np.shape(batch_input[0])[1] 54 | 55 | batch_input_tensor = torch.zeros(len(batch_input), np.shape(batch_input[0])[0], np.shape(batch_input[0])[1], dtype=torch.float) 56 | batch_phases_tensor = torch.ones(len(batch_input), max_seq, dtype=torch.long)*(-100) 57 | batch_steps_tensor = torch.ones(len(batch_input), max_seq, dtype=torch.long)*(-100) 58 | mask = torch.zeros(len(batch_input), self.num_phases, max_seq, dtype=torch.float) 59 | for i in range(len(batch_input)): 60 | batch_input_tensor[i, :, :np.shape(batch_input[i])[1]] = torch.from_numpy(batch_input[i]) 61 | batch_phases_tensor[i, :np.shape(batch_phases[i])[0]] = torch.from_numpy(batch_phases[i]) 62 | batch_steps_tensor[i, :np.shape(batch_steps[i])[0]] = torch.from_numpy(batch_steps[i]) 63 | mask[i, :, :np.shape(batch_phases[i])[0]] = torch.ones(self.num_phases, np.shape(batch_phases[i])[0]) 64 | 65 | return batch_images, batch_input_tensor, batch_phases_tensor, batch_steps_tensor, mask, supervision_signals 66 | 67 | def _read_data(self): 68 | with open(self.datafile, 'rb') as fp: 69 | self.videos = pickle.load(fp) 70 | 71 | random.shuffle(self.videos) 72 | logging.info('-' * 50) 73 | logging.info('datafile : ' + self.datafile) 74 | logging.info('No of videos loaded : ' + str(len(self.videos))) 75 | logging.info('-' * 50) 76 | -------------------------------------------------------------------------------- /main_cnn.py: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | 4 | import numpy as np 5 | from shutil import copy2 6 | 7 | from experiments.cnn import * 8 | from loaders.data_loader_cnn import * 9 | 10 | from util.utils import create_argument_parser, parse_config 11 | 12 | import torch 13 | 14 | import logging 15 | logging.basicConfig(format='%(asctime)s %(levelname)-8s: %(message)s', 16 | stream=sys.stdout, level=logging.INFO, datefmt='%d-%m-%Y %H:%M:%S') 17 | 18 | def Main(args): 19 | logging.info('\n'*5) 20 | logging.info('-'*50) 21 | logging.info('Module: CNN'.center(50)) 22 | logging.info('-'*50) 23 | hp_file = args.hyper_params 24 | hp = parse_config(hp_file).default 25 | 26 | stats = {'experiment': hp.run_dir} 27 | stats['state'] = args.state 28 | stats['dataset'] = hp.data_dir if args.dataset == '' else args.dataset 29 | stats['best_model'] = 0 # best model at epoch 0 (default) 30 | stats['latest_epoch'] = -1 # latest model at epoch -1 (default) 31 | stats['best_m_stats'] = [-1, 0.0, 0.0] 32 | stats['preload_model'] = args.load_model 33 | stats['experiment_stats'] = [] 34 | path = args.path 35 | stats['model_path'] = os.path.join(path, stats['experiment']) 36 | 37 | if not os.path.exists(stats['model_path']): 38 | os.makedirs(stats['model_path']) 39 | 40 | copy2(hp_file, stats['model_path']) 41 | 42 | seed = hp.random_seed 43 | random.seed(seed) 44 | np.random.seed(seed) 45 | torch.manual_seed(seed) 46 | torch.cuda.manual_seed_all(seed) 47 | torch.backends.cudnn.deterministic = True 48 | shuffle = True 49 | augment = True 50 | 51 | ### If 'extracted_features' then do it on the full dataset 52 | if args.state == 'extract_predictions': 53 | hp.num_weak_sup_vids = -1 54 | shuffle = False 55 | 56 | data_loader_fn = create_data_loaders 57 | assert ('bern' in stats['dataset']) or ('strasbourg' in stats['dataset']), \ 58 | f'Only bern or strasbourg data is accepted (Given {stats["dataset"]})' 59 | 60 | train_loader, valid_loader, test_loader = data_loader_fn(stats, hp, shuffle=shuffle, augment=augment) 61 | mtrainer = CNNTrainer 62 | trainer = mtrainer(stats, hp) 63 | trainer.build_model() 64 | trainer.add_data_loaders(train_loader, valid_loader, test_loader) 65 | 66 | trainer.resume_training() 67 | if args.state == "train": 68 | stats = trainer.train() 69 | elif args.state == "extract_predictions": 70 | trainer.test() 71 | 72 | return 73 | 74 | if __name__ == '__main__': 75 | parser = create_argument_parser() 76 | args = parser.parse_args() 77 | Main(args) 78 | -------------------------------------------------------------------------------- /main_temp.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python2.7 2 | import os 3 | import sys 4 | import json 5 | import torch 6 | import random 7 | 8 | from shutil import copy2 9 | 10 | from util.utils import create_argument_parser, parse_config 11 | 12 | from loaders.data_loader_temp import BatchGenerator 13 | from experiments.lstm import LSTMTrainer 14 | from experiments.mtms_tcn import TCNTrainer 15 | 16 | import logging 17 | logging.basicConfig(format='%(asctime)s %(levelname)-8s: %(message)s', 18 | stream=sys.stdout, level=logging.INFO, datefmt='%d-%m-%Y %H:%M:%S') 19 | 20 | def create_data_loaders(hp, exp_path, sample_rate=1): 21 | train_batch_gen = BatchGenerator( 22 | hp.n_phases, hp.n_steps, os.path.join(exp_path, 'train_videos.pickle'), 23 | hp.num_sup_videos, hp.num_weak_sup_vids, sample_rate=sample_rate 24 | ) 25 | 26 | valid_batch_gen = BatchGenerator( 27 | hp.n_phases, hp.n_steps, os.path.join(exp_path, 'valid_videos.pickle'), sample_rate=sample_rate 28 | ) 29 | test_batch_gen = BatchGenerator( 30 | hp.n_phases, hp.n_steps, os.path.join(exp_path, 'test_videos.pickle'), sample_rate=sample_rate 31 | ) 32 | 33 | return train_batch_gen, valid_batch_gen, test_batch_gen 34 | 35 | def Main(args): 36 | logging.info('\n'*5) 37 | logging.info('-'*50) 38 | logging.info('Module: LSTM/BiLSTM-CRF/TCN'.center(50)) 39 | logging.info('-'*50) 40 | 41 | hp_file = args.hyper_params 42 | hp = parse_config(hp_file).default 43 | 44 | exp_path = os.path.join(args.path, hp.run_dir) 45 | 46 | stats = {} 47 | stats_fp = '{}/{}/{}'.format(args.path, hp.pkl_path, 'stats_test.json') 48 | if os.path.exists(stats_fp): stats = json.load(open(stats_fp, 'r')) 49 | stats_fp = '{}/{}/{}'.format(args.path, hp.pkl_path, 'stats.json') 50 | if os.path.exists(stats_fp): stats = json.load(open(stats_fp, 'r')) 51 | 52 | stats['experiment'] = exp_path 53 | stats['preload_model'] = args.load_model 54 | stats['state'] = args.state 55 | stats['dataset'] = os.path.join(args.path, hp.pkl_path) if hp.read_pkl else args.dataset 56 | stats['model_path'] = exp_path 57 | stats['best_model'] = 0 # best model at epoch 0 (default) 58 | stats['latest_epoch'] = -1 # latest model at epoch -1 (default) 59 | stats['best_m_stats'] = [-1, 0.0, 0.0] 60 | stats['experiment_stats'] = [] 61 | 62 | if not os.path.exists(stats['model_path']): 63 | os.makedirs(stats['model_path']) 64 | 65 | copy2(hp_file, stats['model_path']) 66 | 67 | sample_rate = 1 68 | device = torch.device("cuda:" + str(hp.gpu_devices[0])) 69 | 70 | seed = hp.random_seed 71 | random.seed(seed) 72 | torch.manual_seed(seed) 73 | torch.cuda.manual_seed_all(seed) 74 | torch.backends.cudnn.deterministic = True 75 | 76 | if args.state == 'extract_predictions': 77 | hp.num_weak_sup_vids = -1 78 | 79 | Trainer = LSTMTrainer if 'LSTM' in hp.method else TCNTrainer 80 | train_batch_gen, valid_batch_gen, test_batch_gen = create_data_loaders(hp, stats['dataset'], sample_rate) 81 | trainer = Trainer(stats, hp) 82 | trainer.resume_training() 83 | 84 | if args.state == "train": 85 | stats = trainer.train( 86 | train_batch_gen, valid_batch_gen, device 87 | ) 88 | elif args.state == "extract_predictions": 89 | trainer.predict( 90 | train_batch_gen, valid_batch_gen, test_batch_gen, 91 | device, sample_rate 92 | ) 93 | return 94 | 95 | if __name__ == '__main__': 96 | parser = create_argument_parser() 97 | args = parser.parse_args() 98 | 99 | Main(args) 100 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | attrs==23.1.0 2 | certifi==2023.11.17 3 | charset-normalizer==3.3.2 4 | cmake==3.28.0 5 | cycler==0.12.1 6 | easydict==1.9 7 | filelock==3.13.1 8 | hparams==0.3.0 9 | idna==3.6 10 | imageio==2.9.0 11 | importlib-metadata==7.0.0 12 | Jinja2==2.11.3 13 | joblib==1.3.2 14 | json5==0.9.4 15 | jsonschema==3.2.0 16 | kiwisolver==1.4.5 17 | lit==17.0.6 18 | Markdown==3.1.1 19 | MarkupSafe==1.1.1 20 | mat4py==0.4.2 21 | matplotlib==3.1.2 22 | mistune==0.8.4 23 | more-itertools==8.0.2 24 | mpmath==1.3.0 25 | networkx==3.1 26 | numpy==1.24.4 27 | nvidia-cublas-cu11==11.10.3.66 28 | nvidia-cuda-cupti-cu11==11.7.101 29 | nvidia-cuda-nvrtc-cu11==11.7.99 30 | nvidia-cuda-runtime-cu11==11.7.99 31 | nvidia-cudnn-cu11==8.5.0.96 32 | nvidia-cufft-cu11==10.9.0.58 33 | nvidia-curand-cu11==10.2.10.91 34 | nvidia-cusolver-cu11==11.4.0.1 35 | nvidia-cusparse-cu11==11.7.4.91 36 | nvidia-nccl-cu11==2.14.3 37 | nvidia-nvtx-cu11==11.7.91 38 | opencv-python==4.1.2.30 39 | pandas==2.0.3 40 | Pillow==6.2.1 41 | progress==1.5 42 | pyparsing==3.1.1 43 | pyrsistent==0.20.0 44 | python-dateutil==2.8.2 45 | pytz==2023.3.post1 46 | PyWavelets==1.4.1 47 | PyYAML==6.0 48 | requests==2.31.0 49 | ruamel.yaml==0.16.6 50 | ruamel.yaml.clib==0.2.0 51 | scikit-image==0.17.2 52 | scikit-learn==1.3.0 53 | scipy==1.10.1 54 | seaborn==0.10.0 55 | six==1.16.0 56 | sympy==1.12 57 | tabulate==0.8.7 58 | threadpoolctl==3.2.0 59 | tifffile==2023.7.10 60 | torch==2.0.1 61 | torch-summary==1.4.5 62 | torchaudio==2.0.2 63 | torchvision==0.15.2 64 | tornado==6.0.3 65 | tqdm==4.66.0 66 | triton==2.0.0 67 | typeguard==4.1.5 68 | typing_extensions==4.9.0 69 | tzdata==2023.3 70 | urllib3==1.25.9 71 | xmltodict==0.12.0 72 | zipp==3.17.0 73 | -------------------------------------------------------------------------------- /static/camma_logo_tr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CAMMA-public/MultiBypass140/d3ace464d04ec3f4661f2f992276554e9a5b5af6/static/camma_logo_tr.png -------------------------------------------------------------------------------- /static/hierarchy.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CAMMA-public/MultiBypass140/d3ace464d04ec3f4661f2f992276554e9a5b5af6/static/hierarchy.jpg -------------------------------------------------------------------------------- /tables/phase.csv: -------------------------------------------------------------------------------- 1 | id, name 2 | 0, preparation 3 | 1, gastric_pouch_creation 4 | 2, omentum_division 5 | 3, gastrojejunal_anastomosis 6 | 4, anastomosis_test 7 | 5, jejunal_separation 8 | 6, closure_petersen_space 9 | 7, jejunojejunal_anastomosis 10 | 8, closure_mesenteric_defect 11 | 9, cleaning_coagulation 12 | 10, disassembling 13 | 11, other_intervention 14 | 12, out_of_body 15 | 13, severe_index -------------------------------------------------------------------------------- /tables/step.csv: -------------------------------------------------------------------------------- 1 | id, name 2 | 0, s0_null_step 3 | 1, s1_cavity_exploration 4 | 2, s2_trocar_placement 5 | 3, s3_retractor_placement 6 | 4, s4_crura_dissection 7 | 5, s5_his_angle_dissection 8 | 6, s6_horizontal_stapling 9 | 7, s7_retrogastric_dissection 10 | 8, s8_vertical_stapling 11 | 9, s9_gastric_remnant_reinforcement 12 | 10, s10_gastric_pouch_reinforcement 13 | 11, s11_gastric_opening 14 | 12, s12_omental_lifting 15 | 13, s13_omental_section 16 | 14, s14_adhesiolysis 17 | 15, s15_treitz_angle_identification 18 | 16, s16_biliary_limb_measurement 19 | 17, s17_jejunum_opening 20 | 18, s18_gastrojejunal_stapling 21 | 19, s19_gastrojejunal_defect_closing 22 | 20, s20_mesenteric_opening 23 | 21, s21_jejunal_section 24 | 22, s22_gastric_tube_placement 25 | 23, s23_jejunal_clamping 26 | 24, s24_ink_injection 27 | 25, s25_visual_assessment 28 | 26, s26_gastrojejunal_anastomosis_reinforcement 29 | 27, s27_petersen_space_exposure 30 | 28, s28_petersen_space_closing 31 | 29, s29_biliary_limb_opening 32 | 30, s30_alimentary_limb_measurement 33 | 31, s31_alimentary_limb_opening 34 | 32, s32_jejunojejunal_stapling 35 | 33, s33_jejunojejunal_defect_closing 36 | 34, s34_jejunojejunal_anastomosis_reinforcement 37 | 35, s35_staple_line_reinforcement 38 | 36, s36_mesenteric_defect_exposure 39 | 37, s37_mesenteric_defect_closing 40 | 38, s38_anastomosis_fixation 41 | 39, s39_coagulation 42 | 40, s40_irrigation_aspiration 43 | 41, s41_parietal_closure 44 | 42, s42_trocar_removal 45 | 43, s43_calibration 46 | 44, s44_drainage_insertion 47 | 45, s45_specimen_retrieval -------------------------------------------------------------------------------- /util/data_reader.py: -------------------------------------------------------------------------------- 1 | import os 2 | import pickle 3 | import logging 4 | 5 | def read_pkl_data(pkl_path, img_path): 6 | logging.info('reading pickle file: '+ pkl_path) 7 | with open(pkl_path, "rb") as fp: 8 | data = pickle.load(fp) 9 | fp.close() 10 | 11 | root_dir = img_path 12 | if not os.path.exists(root_dir): 13 | root_dir = root_dir.replace('train', '').replace('val', '').replace('test', '') 14 | imgs, phases, steps = [], [], [] 15 | for vid_name in sorted(data.keys()): 16 | paths = [ 17 | os.path.join(root_dir, vid_name, f"{item['Frame_id']}.jpg") 18 | for item in data[vid_name] 19 | ] 20 | imgs.append(paths) 21 | phases.append([item['Phase_gt'] for item in data[vid_name]]) 22 | steps.append([item['Step_gt'] for item in data[vid_name]]) 23 | 24 | return imgs, phases, steps 25 | 26 | -------------------------------------------------------------------------------- /util/extract_frames.py: -------------------------------------------------------------------------------- 1 | import os 2 | import argparse 3 | from tqdm import tqdm 4 | from pathlib import Path 5 | 6 | 7 | def videos_to_imgs(input_path="/Videos/input", 8 | output_path="/Videos/output", 9 | fps=1, 10 | pattern="*.mp4"): 11 | 12 | output_path = Path(output_path) 13 | input_path = Path(input_path) 14 | 15 | output_path.mkdir(exist_ok=True) 16 | 17 | dirs = list(input_path.glob(pattern)) 18 | dirs.sort() 19 | 20 | for i, vid_path in enumerate(tqdm(dirs)): 21 | file_name = vid_path.stem 22 | out_folder = output_path / file_name.split('-')[0] 23 | out_folder.mkdir(exist_ok=True) 24 | 25 | # os.system(command) method executes the command (a string) in a subshell; here, the command converts each video into images, by filtering 26 | os.system(f'ffmpeg -i {vid_path} -vf "fps={fps}" {out_folder/file_name}_%08d.jpg') 27 | print("Done extracting: {}".format(i + 1)) 28 | 29 | if __name__ == "__main__": 30 | """ 31 | Parse command line arguments 32 | """ 33 | parser = argparse.ArgumentParser( 34 | description="Utility to download annotations on DONE videos in MOSaiC ext stack" 35 | ) 36 | parser.add_argument( 37 | "--video_path", 38 | required=True, 39 | type=str, 40 | help="Define input video dir", 41 | ) 42 | parser.add_argument( 43 | "--output", 44 | required=True, 45 | type=str, 46 | help="Define output dir to save frames extracted", 47 | ) 48 | parser.add_argument( 49 | "--fps", 50 | required=False, 51 | type=int, 52 | default=1, 53 | help="Define fps for frames extraction", 54 | ) 55 | arguments = parser.parse_args() 56 | 57 | videos_to_imgs(input_path=arguments.video_path, output_path=arguments.output, fps=arguments.fps) 58 | -------------------------------------------------------------------------------- /util/results_collator.py: -------------------------------------------------------------------------------- 1 | import os 2 | import argparse 3 | import numpy as np 4 | from pathlib import Path 5 | 6 | from sklearn.metrics import precision_recall_fscore_support as score 7 | 8 | results_root = 'results/' 9 | filename = 'results.csv' 10 | header = 'no.,mode,task,acc,pr,re,f1,support\n' 11 | modes = ['train', 'valid', 'test'] 12 | tasks = ['phase', 'step'] 13 | 14 | def compute_metrics(labels, preds): 15 | pred_labels = np.argmax(preds, axis=1) if preds.ndim > 1 else preds 16 | 17 | acc = np.sum(labels == pred_labels) * 100 / len(labels) 18 | acc = np.around(acc, 2) 19 | 20 | scores = score(labels, pred_labels) 21 | mean = np.mean(np.vstack(scores).T, axis=0) 22 | mean[:-1] *= 100 23 | mean = [acc] + np.around(mean, 2).tolist() 24 | 25 | std = np.std(np.vstack(scores).T, axis=0) 26 | std[:-1] *= 100 27 | std = [0.0] + np.around(std, 2).tolist() 28 | 29 | return mean, std 30 | 31 | def compute_video_metrics(inds, preds, targets, score_fn): 32 | if len(preds) == 0: return [-1] * 5, [-1] * 5 33 | v_ids = np.array(list(map(lambda x: x.split('/')[-2], inds))) 34 | videos = np.unique(v_ids) 35 | vscores = [] 36 | for vid in videos: 37 | idxs = np.argwhere(v_ids == vid).flatten() 38 | mean, _ = score_fn(np.array(targets)[idxs], np.array(preds)[idxs]) 39 | vscores.append(mean[:]) 40 | vmean = np.around(np.mean(vscores, axis=0), 2).tolist() 41 | vstd = np.around(np.std(vscores, axis=0), 2).tolist() 42 | return vmean, vstd 43 | 44 | 45 | def generate_results(root_path, metrics='video'): 46 | for i, path in enumerate(sorted(Path(root_path).rglob('*.yaml'), key=lambda p: str(p))): 47 | exp_dir = path.parent 48 | results_file = os.path.join(results_root, str(exp_dir).split('models/')[-1], filename) 49 | print('computing results from:', exp_dir) 50 | results = header 51 | for j, mode in enumerate(modes): 52 | for task in tasks: 53 | re = [mode] 54 | re.append(task) 55 | try: 56 | inds = np.load(os.path.join(exp_dir, '_'.join([mode, 'imgs.npy']))) 57 | labels = np.load(os.path.join(exp_dir, '_'.join([mode, task, 'labels.npy']))) 58 | preds = np.load(os.path.join(exp_dir, '_'.join([mode, task, 'preds.npy']))) 59 | if metrics == 'image': mean, std = compute_metrics(labels, preds) 60 | if metrics == 'video': mean, std = compute_video_metrics(inds, labels, preds, compute_metrics) 61 | re += [ '$ ' +' \pm '.join([str(m), str(std[k])]) + ' $' for k, m in enumerate(mean)] 62 | except Exception as e: 63 | re += ['-1.00 \pm -1.00'] * 5 64 | results += ','.join(map(str, [j] + re)) + '\n' 65 | if not os.path.exists(os.path.dirname(results_file)): 66 | os.makedirs(os.path.dirname(results_file)) 67 | with open(results_file, 'w') as fp: 68 | fp.write(results) 69 | print('computing results: done!!!') 70 | return 71 | 72 | 73 | def Main(args): 74 | print('*'*50) 75 | print('search folder :', args.experiment) 76 | print('collecting metrics:', args.metrics) 77 | print('*'*50) 78 | 79 | generate_results(args.experiment, metrics=args.metrics) 80 | return 81 | 82 | 83 | if __name__ == '__main__': 84 | parser = argparse.ArgumentParser(description='Parse model training options') 85 | parser.add_argument('-e', '--experiment', default='', 86 | help='Root path to experiments folder') 87 | 88 | parser.add_argument('-m', '--metrics', default='video', 89 | help='type of metrics to compute: image/video') 90 | 91 | args = parser.parse_args() 92 | Main(args) 93 | -------------------------------------------------------------------------------- /util/utils.py: -------------------------------------------------------------------------------- 1 | import argparse 2 | import numpy as np 3 | import torch.nn as nn 4 | 5 | import yaml 6 | from easydict import EasyDict as edict 7 | 8 | ## Median weighting 9 | def compute_class_weights(classes, n_classes=13): 10 | labels, counts = np.unique(classes, return_counts=True) 11 | median = np.median(counts) 12 | weights = median/counts 13 | exp_labels = np.array(range(n_classes)) 14 | 15 | missing = [idx for idx in exp_labels if idx not in labels] 16 | for miss in missing: 17 | weights = np.insert(weights, miss, 1.0) 18 | 19 | return weights.tolist() 20 | 21 | 22 | def parse_config(config_file): 23 | with open(config_file) as f: 24 | config = edict(yaml.load(f, Loader=yaml.FullLoader)) 25 | return config 26 | 27 | 28 | def init_classification_loss( 29 | name='cross_entropy', weights=None, gamma=0.7, ignore_index=-100 30 | ): 31 | assert np.any([name == 'cross_entropy', name == 'focal_loss']), f'loss function {name} not implemented!' 32 | if name == 'cross_entropy': 33 | loss = nn.CrossEntropyLoss(weight=weights, ignore_index=ignore_index) 34 | elif name == 'focal_loss': 35 | raise Exception('Focal loss not implemented!') 36 | return loss 37 | #------------------------------------------------------------------------------------------ 38 | # Argument parser 39 | def create_argument_parser(): 40 | parser = argparse.ArgumentParser(description='Parse model training options') 41 | parser.add_argument('-d', '--dataset', default='', 42 | help='Dataset to use for training/testing.\n Options: (/mnt/data/bypass40/)') 43 | 44 | parser.add_argument('-s', '--state', default='train', 45 | help='State of the model.\n Options: train, test, features') 46 | 47 | parser.add_argument('-lm', '--load_model', default='models/resnet_v2_50_2017_04_14/resnet_v2_50.ckpt', 48 | help='path to model file to be loaded during initialization.\n') 49 | 50 | parser.add_argument('-pt', '--pretrain', default='True', 51 | help='Loading pretrained model of resnet.\n Options: True, False') 52 | 53 | parser.add_argument('-hp', '--hyper_params', default='hparams/hp_225_bypass.yaml', 54 | help='Path to the hyper parameters config file.\n') 55 | 56 | parser.add_argument('-e', '--experiment_name', default='cnn_exp', 57 | help='Name of the experiment.\n') 58 | 59 | parser.add_argument('-p', '--path', default='models', 60 | help='Path tp save the experiment.\n') 61 | 62 | parser.add_argument('--local_rank', type=int, default=-1, metavar='N', help='Local process rank.') 63 | return parser 64 | --------------------------------------------------------------------------------