Handle calibration files with extra cameras

Pose2Sim/common.py

@@ -251,7 +251,7 @@ def bounding_boxes(js_file, margin_percent=0.1, around='extremities'):
     return bounding_boxes   
 
 
-def retrieve_calib_params(calib_file):
+def retrieve_calib_params(calib_file, json_pose_dirs_names=None):
     '''
     Compute projection matrices from toml calibration file.
 
@@ -273,22 +273,35 @@ def retrieve_calib_params(calib_file):
     cal_keys = [c for c in calib.keys() 
                 if c not in ['metadata', 'capture_volume', 'charuco', 'checkerboard'] 
                 and isinstance(calib[c],dict)]
+
+    if json_pose_dirs_names is None:
+        pose_keys = cal_keys
+    else:
+        pose_keys = [name.replace('_json', '') for name in json_pose_dirs_names]
+        missing_cams = [cam for cam in pose_keys if cam not in cal_keys]
+        if missing_cams:
+            logging.error(f"The following cameras are present in the pose folders but missing in the calibration file: {missing_cams}.")
+            raise ValueError(f"The following cameras are present in the pose folders but missing in the calibration file: {missing_cams}.")
+
+
     S, K, dist, optim_K, inv_K, R, R_mat, T = [], [], [], [], [], [], [], []
-    for c, cam in enumerate(cal_keys):
+    for cam in list(cal_keys):
+        if cam not in pose_keys:
+            continue
         S.append(np.array(calib[cam]['size']))
         K.append(np.array(calib[cam]['matrix']))
         dist.append(np.array(calib[cam]['distortions']))
-        optim_K.append(cv2.getOptimalNewCameraMatrix(K[c], dist[c], [int(s) for s in S[c]], 1, [int(s) for s in S[c]])[0])
-        inv_K.append(np.linalg.inv(K[c]))
+        optim_K.append(cv2.getOptimalNewCameraMatrix(K[-1], dist[-1], [int(s) for s in S[-1]], 1, [int(s) for s in S[-1]])[0])
+        inv_K.append(np.linalg.inv(K[-1]))
         R.append(np.array(calib[cam]['rotation']))
-        R_mat.append(cv2.Rodrigues(R[c])[0])
+        R_mat.append(cv2.Rodrigues(R[-1])[0])
         T.append(np.array(calib[cam]['translation']))
     calib_params = {'S': S, 'K': K, 'dist': dist, 'inv_K': inv_K, 'optim_K': optim_K, 'R': R, 'R_mat': R_mat, 'T': T}
 
     return calib_params
 
 
-def computeP(calib_file, undistort=False):
+def computeP(calib_file, json_pose_dirs_names=None, undistort=False):
     '''
     Compute projection matrices from toml calibration file.
 
@@ -305,8 +318,20 @@ def computeP(calib_file, undistort=False):
     cal_keys = [c for c in calib.keys() 
                 if c not in ['metadata', 'capture_volume', 'charuco', 'checkerboard'] 
                 and isinstance(calib[c],dict)]
+
+    if json_pose_dirs_names is None:
+        pose_keys = cal_keys
+    else:
+        pose_keys = [name.replace('_json', '') for name in json_pose_dirs_names]
+        missing_cams = [cam for cam in pose_keys if cam not in cal_keys]
+        if missing_cams:
+            logging.error(f"The following cameras are present in the pose folders but missing in the calibration file: {missing_cams}.")
+            raise ValueError(f"The following cameras are present in the pose folders but missing in the calibration file: {missing_cams}.")
+
     P = []
     for cam in list(cal_keys):
+        if cam not in pose_keys:
+            continue
         K = np.array(calib[cam]['matrix'])
         if undistort:
             S = np.array(calib[cam]['size'])

Pose2Sim/personAssociation.py

@@ -659,10 +659,6 @@ def associate_all(config_dict):
     pose_dir = os.path.join(project_dir, 'pose')
     poseSync_dir = os.path.join(project_dir, 'pose-sync')
     poseTracked_dir = os.path.join(project_dir, 'pose-associated')
-
-    # projection matrix from toml calibration file
-    P_all = computeP(calib_file, undistort=undistort_points)
-    calib_params = retrieve_calib_params(calib_file)
 
     # selection of tracked keypoint id
     try: # from skeletons.py
@@ -709,11 +705,9 @@ def associate_all(config_dict):
     f_range = [[0,max([len(j) for j in json_files_names])] if frame_range in ('all', 'auto', []) else frame_range][0]
     n_cams = len(json_dirs_names)
 
-    # Check that camera number is consistent between calibration file and pose folders
-    if n_cams != len(P_all):
-        raise Exception(f'Error: The number of cameras is not consistent:\
-                    Found {len(P_all)} cameras in the calibration file,\
-                    and {n_cams} cameras based on the number of pose folders.')
+    # projection matrix from toml calibration file
+    P = computeP(calib_file, json_dirs_names, undistort=undistort_points)
+    calib_params = retrieve_calib_params(calib_file, json_dirs_names)
 
     if not multi_person:
         logging.info('\nSingle-person analysis selected.')
@@ -744,12 +738,12 @@ def associate_all(config_dict):
             personsIDs_comb = persons_combinations(json_files_f) 
 
             # choose persons of interest and exclude cameras with bad pose estimation
-            error_proposals, proposals, Q_kpt = best_persons_and_cameras_combination(config_dict, json_files_f, personsIDs_comb, P_all, tracked_keypoint_id, calib_params)
+            error_proposals, proposals, Q_kpt = best_persons_and_cameras_combination(config_dict, json_files_f, personsIDs_comb, P, tracked_keypoint_id, calib_params)
 
             if not np.isinf(error_proposals):
                 error_min_tot.append(np.nanmean(error_proposals))
             cameras_off_count = np.count_nonzero([np.isnan(comb) for comb in proposals]) / len(proposals)
-            cameras_off_tot.append(cameras_off_count)            
+            cameras_off_tot.append(cameras_off_count)
 
         else:
             # read data

Pose2Sim/triangulation.py

@@ -698,7 +698,7 @@ def triangulate_all(config_dict):
     try:
         calib_dir = [os.path.join(session_dir, c) for c in os.listdir(session_dir) if os.path.isdir(os.path.join(session_dir, c)) and  'calib' in c.lower()][0]
     except:
-        raise Exception(f'No .toml calibration direcctory found.')
+        raise Exception(f'No .toml calibration directory found.')
     try:
         calib_files = glob.glob(os.path.join(calib_dir, '*.toml'))
         calib_file = max(calib_files, key=os.path.getctime) # lastly created calibration file
@@ -707,10 +707,6 @@ def triangulate_all(config_dict):
     pose_dir = os.path.join(project_dir, 'pose')
     poseSync_dir = os.path.join(project_dir, 'pose-sync')
     poseTracked_dir = os.path.join(project_dir, 'pose-associated')
-
-    # Projection matrix from toml calibration file
-    P = computeP(calib_file, undistort=undistort_points)
-    calib_params = retrieve_calib_params(calib_file)
 
     # Retrieve keypoints from model
     try: # from skeletons.py
@@ -774,10 +770,10 @@ def triangulate_all(config_dict):
     # frame range selection
     f_range = [[0,min([len(j) for j in json_files_names])] if frame_range in ('all', 'auto', []) else frame_range][0]
     frame_nb = f_range[1] - f_range[0]
-    
-    # Check that camera number is consistent between calibration file and pose folders
-    if n_cams != len(P):
-        raise Exception(f'Error: The number of cameras is not consistent: Found {len(P)} cameras in the calibration file, and {n_cams} cameras based on the number of pose folders.')
+
+    # Projection matrix from toml calibration file
+    P = computeP(calib_file, json_dirs_names, undistort=undistort_points)
+    calib_params = retrieve_calib_params(calib_file, json_dirs_names)
 
     # Triangulation
     if multi_person: