added padding to handle missing instances

added functionality to remove body parts not used in SIMBA

Author: JensBlack

experiments/custom/experiments.py

@@ -422,10 +422,10 @@ def _trials(self):
         Defining the trials
         """
         identification_dict = dict(active={'animal': 1
-                                            , 'bp': ['bp0']
+                                            , 'bp': ['bp2']
                                            }
                                 ,passive = {'animal': 0
-                                            , 'bp': ['bp2']
+                                            , 'bp': ['bp6']
                                                 }
                                 )
 

experiments/custom/stimulus_process.py

@@ -74,7 +74,6 @@ def example_protocol_run(condition_q: mp.Queue):
         if condition_q.full():
             current_trial = condition_q.get()
         if current_trial is not None:
-            print('IM HEEEEERE!')
             show_visual_stim_img(type=current_trial, name='DlStream')
             #dmod_device.toggle()
         else:

experiments/custom/triggers.py

@@ -589,7 +589,13 @@ def __init__(self,prob_threshold: float, class_process_pool, debug: bool = False
 
     def fill_time_window(self,skeleton: dict):
         """Transforms skeleton input into flat numpy array of coordinates to pass to feature extraction"""
-        flat_values = transform_2pose(skeleton).flatten()
+        #todo: remove bodyparts that are not used automatically
+        key_selection = {'0_tail_tip','1_tail_tip'}
+        skeleton_selection = {k: skeleton[k] for k in skeleton.keys() if k not in key_selection}
+        flat_values = transform_2pose(skeleton_selection).flatten()
+        # if not enough animals are present, padd the rest with default value "0,0"
+        if flat_values.shape[0] < 28:
+            flat_values = np.pad(flat_values, (0, 28-flat_values.shape[0]), 'constant', constant_values=0)
         # this appends the new row to the deque time_window, which will drop the "oldest" entry due to a maximum
         # length of time_window_len
         self._time_window.append(flat_values)

utils/configloader.py

@@ -35,7 +35,7 @@ def get_script_path():
 model_path_string = [str(part).strip() for part in dsc_config['Pose Estimation'].get('MODEL_PATH').split(',')]
 MODEL_PATH = model_path_string[0] if len(model_path_string) <= 1 else model_path_string
 MODEL_NAME = dsc_config['Pose Estimation'].get('MODEL_NAME')
-ALL_BODYPARTS = tuple(part for part in dsc_config['Pose Estimation'].get('ALL_BODYPARTS').split(','))
+ALL_BODYPARTS = tuple(part.strip() for part in dsc_config['Pose Estimation'].get('ALL_BODYPARTS').split(','))
 
 # Streaming items