Merge pull request #9 from periakiva/check_feature_vector

Check feature vector

configs/experiment/m3/feat_v6.yaml

@@ -38,7 +38,7 @@ model:
     dim: 188 # length of feature vector
 
 data:
-  num_classes: 9 # activities: includes background
+  num_classes: 6 # activities: includes background
   batch_size: 512
   num_workers: 0
   epoch_length: 20000
@@ -51,12 +51,12 @@ data:
 
     MoveCenterPts:
         feat_version: 6
-        num_obj_classes: 9 # not including background
+        num_obj_classes: 4 # not including background
     NormalizeFromCenter:
       feat_version: 6
     NormalizePixelPts:
       feat_version: 6
-      num_obj_classes: 9 # not including background
+      num_obj_classes: 4 # not including background
 
 data_gen:
   reshuffle_datasets: true

configs/experiment/r18/feat_v6.yaml

@@ -14,7 +14,8 @@ defaults:
 # all parameters below will be merged with parameters from default configurations set above
 # this allows you to overwrite only specified parameters
 # exp_name: "p_m2_tqt_data_test_feat_v6_with_pose" #[_v2_aug_False]
-exp_name: "p_r18_feat_v6_with_pose_v3_aug_False_reshuffle_True" #[_v2_aug_False]
+# exp_name: "p_r18_feat_v6_with_pose_v3_aug_False_reshuffle_True" #[_v2_aug_False]
+exp_name: "p_r18_feat_v6_with_pose_v3_aug_False_reshuffle_True_bbn" #[_v2_aug_False]
 # exp_name: "p_m2_tqt_data_test_feat_v6_with_pose_v2_aug_False_reshuffle_False" #[_v2_aug_False]
 # exp_name: "p_m2_tqt_data_test_feat_v6_with_pose_v2_aug_True_reshuffle_True" #[_v2_aug_False]
 # exp_name: "p_m2_tqt_data_test_feat_v6_with_pose_v2_aug_True_reshuffle_False" #[_v2_aug_False]
@@ -70,14 +71,20 @@ data_gen:
   val_vid_ids: [3, 7, 10, 18, 27, 32, 41]
   test_vid_ids: [50, 13, 47, 25]
 
+  train_vid_ids_bbn: [1, 2, 3, 4, 5, 6, 7, 8]
+  val_vid_ids_bbn: [9]
+  test_vid_ids_bbn: [10]
+
 paths:
-  data_dir: "/data/PTG/TCN_data/r18/p_r18_feat_v6_with_pose_v3_aug_False_reshuffle_True" #[_v2_aug_False]
+  # data_dir: "/data/PTG/TCN_data/r18/p_r18_feat_v6_with_pose_v3_aug_False_reshuffle_True" #[_v2_aug_False]
+  data_dir: "/data/PTG/TCN_data/r18/p_r18_feat_v6_with_pose_v3_aug_False_reshuffle_True_bbn" #[_v2_aug_False]
   # data_dir: "/data/PTG/TCN_data/m2/p_m2_tqt_data_test_feat_v6_with_pose_v2_aug_False_reshuffle_False" #[_v2_aug_False]
   # data_dir: "/data/PTG/TCN_data/m2/p_m2_tqt_data_test_feat_v6_with_pose_v2_aug_True_reshuffle_True" #[_v2_aug_False]
   # data_dir: "/data/PTG/TCN_data/m2/p_m2_tqt_data_test_feat_v6_with_pose_v2_aug_True_reshuffle_False" #[_v2_aug_False]
   # root_dir: "/data/PTG/medical/training/activity_classifier/TCN_HPL"
   root_dir: "/data/users/peri.akiva/PTG/medical/training/activity_classifier/TCN_HPL"
   dataset_kwcoco: "/data/users/peri.akiva/datasets/ptg/r18_all_all_obj_results_with_dets_and_pose.mscoco.json"
+  dataset_kwcoco_lab: "/data/users/peri.akiva/datasets/ptg/r18_all_bbn_lab_data_all_obj_results_with_dets_and_pose.mscoco.json"
   activity_config_root: "/home/local/KHQ/peri.akiva/projects/angel_system/config/activity_labels"
   activity_config_fn: "${paths.activity_config_root}/${task}"
   ptg_root: "/home/local/KHQ/peri.akiva/angel_system"

configs/model/ptg.yaml

@@ -3,7 +3,7 @@ _target_: tcn_hpl.models.ptg_module.PTGLitModule
 optimizer:
   _target_: torch.optim.Adam
   _partial_: true
-  lr: 0.0001
+  lr: 0.000001
   weight_decay: 0.0001
 
 scheduler:

tcn_hpl/data/utils/pose_generation/configs/main.yaml

@@ -1,4 +1,5 @@
 task: r18
+data_type: bbn #[bbn, gyges]
 root: /data/PTG/medical/bbn_data/Release_v0.5/v0.52/M2_Tourniquet/Data
 img_save_path: /data/users/peri.akiva/datasets/m2_tourniquet/imgs
 pose_model_config: /home/local/KHQ/peri.akiva/projects/TCN_HPL/tcn_hpl/data/utils/pose_generation/configs/ViTPose_base_medic_casualty_256x192.py
@@ -20,3 +21,6 @@ data:
   m5: /data/PTG/medical/training/yolo_object_detector/detect//m5_all/m5_all_all_obj_results.mscoco.json
   r18: /data/PTG/medical/training/yolo_object_detector/detect//r18_all/r18_all_all_obj_results.mscoco.json
   save_root: /data/users/peri.akiva/datasets/ptg
+bbn_lab:
+  r18: /data/PTG/medical/training/yolo_object_detector/detect//r18_all_bbn_lab_data/r18_all_bbn_lab_data_all_obj_results.mscoco.json
+  save_root: /data/users/peri.akiva/datasets/ptg

tcn_hpl/data/utils/pose_generation/generate_pose_data.py

@@ -43,10 +43,16 @@ def __init__(self, config: dict) -> None:
         self.config = config
         self.root_path = config['root']
 
-        self.dataset = kwcoco.CocoDataset(config['data'][config['task']])
+        if config['data_type'] == "bbn":
+            self.config_data_key = "bbn_lab"
+        else:
+            self.config_data_key = "data"
+
+        self.dataset = kwcoco.CocoDataset(config[self.config_data_key][config['task']])
         self.patient_cid = self.dataset.add_category('patient')
         self.user_cid = self.dataset.add_category('user')
 
+
         self.keypoints_cats = [
                         "nose", "mouth", "throat","chest","stomach","left_upper_arm",
                         "right_upper_arm","left_lower_arm","right_lower_arm","left_wrist",
@@ -59,7 +65,7 @@ def __init__(self, config: dict) -> None:
 
         self.dataset.dataset['keypoint_categories'] = self.keypoints_cats_dset
 
-        self.dataset_path_name = self.config['data'][self.config['task']][:-12].split('/')[-1] #remove .mscoco.json
+        self.dataset_path_name = self.config[self.config_data_key][self.config['task']][:-12].split('/')[-1] #remove .mscoco.json
 
         self.args = get_parser(self.config['detection_model_config']).parse_args()
         detecron_cfg = setup_detectron_cfg(self.args)
@@ -257,13 +263,13 @@ def generate_bbs_and_pose(self, dset: kwcoco.CocoDataset, save_intermediate: boo
             # import matplotlib.pyplot as plt
             # image_show = dset.draw_image(gid=img_id)
             # plt.imshow(image_show)
-            # plt.savefig(f"myfig_{self.config['task']}_{index}.png")
+            # plt.savefig(f"figs/myfig_{self.config['task']}_{index}.png")
             # if index >= 20:
             #     exit()
 
             if save_intermediate:
                 if (index % 45000) == 0:
-                    dset_inter_name = f"{self.config['data']['save_root']}/{self.dataset_path_name}_{index}_with_dets_and_pose.mscoco.json"
+                    dset_inter_name = f"{self.config[self.config_data_key]['save_root']}/{self.dataset_path_name}_{index}_with_dets_and_pose.mscoco.json"
                     self.dataset.dump(dset_inter_name, newlines=True)
                     print(f"Saved intermediate dataset at index {index} to: {dset_inter_name}")
 
@@ -293,7 +299,7 @@ def run(self) -> None:
         """
         self.dataset = self.generate_bbs_and_pose(self.dataset)
 
-        dataset_path_with_pose = f"{self.config['data']['save_root']}/{self.dataset_path_name}_with_dets_and_pose.mscoco.json"        
+        dataset_path_with_pose = f"{self.config[self.config_data_key]['save_root']}/{self.dataset_path_name}_with_dets_and_pose.mscoco.json"        
         self.dataset.dump(dataset_path_with_pose, newlines=True)
         print(f"Saved test dataset to: {dataset_path_with_pose}")
         return