Some small debugging and text corrections

main_process_mating.py

@@ -10,10 +10,8 @@ start = time.time()
 xyz_path = os.path.join(os.getcwd(),
                         'data/examples/mosquito_escapes/calib/to_delete/xyz_calibration_device_small.csv')
 #xy_path = os.path.join(os.getcwd(), 'data/calib/20200615_xypts-rot.csv')
-xy_path = os.path.join(os.getcwd(),
-                       'data/examples/mosquito_escapes/calib/to_delete/20200615_xypts.csv')
-dlt_path = os.path.join(os.getcwd(),
-                        'data/examples/mosquito_escapes/calib/to_delete/20200615_DLTcoefs-py.csv')
+xy_path = os.path.join(os.getcwd(), 'data/examples/mosquito_escapes/calib/to_delete/20200615_xypts.csv')
+dlt_path = os.path.join(os.getcwd(), 'data/examples/mosquito_escapes/calib/to_delete/20200615_DLTcoefs-py.csv')
 dlc_cfg_path = '/home/user/Desktop/Antoine/_DLC/config.yaml'
 
 img_size = (896, 896)

process/batch_processing.py

@@ -624,9 +624,6 @@ class BatchProcessing:
             show_plot:
         """
 
-        # TODO check parameter needed for fit_skeleton
-        # csv_path=csv_wings_geo_path, body_param_names=body_param_names, wing_param_names=wing_param_names,
-
         kwargs['animal_name'] = animal_name
         kwargs['model_name'] = model_name
         kwargs['res_method'], kwargs['opt_method'] = res_method, opt_method

process/dlc_postprocessing.py

@@ -403,7 +403,7 @@ def save_stroboscopic_images(image_sequence: MultiImageSequence, frames: List[in
 #                                                 'y': np.nan * np.ones(np.size(skeleton2d[obj_name]['frames'])),
 #                                                 'z': np.nan * np.ones(np.size(skeleton2d[obj_name]['frames']))}
 #
-#         # Compute angles btw the right and left wing/bodyparts
+#         # Compute angles btw the right and left limb/bodyparts
 #         angles, angles_out, mean_angles = {}, {}, {}
 #         for i, camn in enumerate(range(1, nb_cam + 1)):
 #             angles[camn], angles_out[camn] = {}, {}
@@ -448,7 +448,7 @@ def save_stroboscopic_images(image_sequence: MultiImageSequence, frames: List[in
 #
 #         if show_plot:
 #             fig1, axs1 = plt.subplots(nb_cam, 1)
-#             fig1.suptitle('Angle of the line btw right and left wing part - Before unscrambling')
+#             fig1.suptitle('Angle of the line btw right and left limb part - Before unscrambling')
 #             for i, camn in enumerate(range(1, nb_cam + 1)):
 #                 axs1[i].clear()
 #                 for label_right in label_names_right:
@@ -637,7 +637,7 @@ def save_stroboscopic_images(image_sequence: MultiImageSequence, frames: List[in
 #
 #         if show_plot:
 #             fig2, axs2 = plt.subplots(nb_cam, 1)
-#             fig2.suptitle('Angle of the line btw right and left wing part - After unscrambling')
+#             fig2.suptitle('Angle of the line btw right and left limb part - After unscrambling')
 #             for i, camn in enumerate(range(1, nb_cam + 1)):
 #                 axs2[i].clear()
 #                 for label_right in label_names_right:

skeleton_fitter/modules/limbs/insect_wings_flat.py

@@ -238,8 +238,9 @@ def estimate_params_from_skeleton3d(wing_skeleton3d_world: Dict[str, List[float]
     r_world2stroke = Rotation.from_euler('xyz', [- body_params['roll_a'], - body_params['pitch_a'], - body_params['yaw_a']], degrees=True)
 
     for label in wing_skeleton_stroke.keys():
-        wing_skeleton_stroke[label] = r_world2stroke.inv().apply(wing_skeleton_stroke[label])
-        wing_skeleton_stroke[label] = r_stroke2body.inv().apply(wing_skeleton_stroke[label])
+        if not any(np.isnan(wing_skeleton_stroke[label])):
+            wing_skeleton_stroke[label] = r_world2stroke.inv().apply(wing_skeleton_stroke[label])
+            wing_skeleton_stroke[label] = r_stroke2body.inv().apply(wing_skeleton_stroke[label])
 
     # Vectors along the span and chord
     span_v = wing_skeleton_stroke['tip'] - wing_skeleton_stroke['hinge']

skeleton_fitter/utils.py

@@ -79,26 +79,26 @@ def distance_btw_pts(pt1, pt2):
     return length_from_vector(pt2 - pt1)
 
 
-def load_body_params_from_csv(path, labels):
+def load_body_params_from_csv(path, param_names):
     body_params = {}
     params_csv = np.genfromtxt(path, delimiter=',', skip_header=0, names=True)
 
-    for body_param_name in labels:
+    for body_param_name in param_names:
         body_params[body_param_name] = params_csv[body_param_name]
 
     return body_params
 
 
-def load_limbs_params_from_csv(path, body_labels, limb_labels):
+def load_limbs_params_from_csv(path, body_param_names, limb_labels):
     limbs_params = {}
     params_csv = np.genfromtxt(path, delimiter=',', skip_header=0, names=True)
 
     for side in ['right', 'left']:
         limbs_params[side] = {}
-        for wing_param_name in limb_labels:
-            if wing_param_name in body_labels:
-                limbs_params[side][wing_param_name] = params_csv[wing_param_name]
+        for limb_param_name in limb_labels:
+            if limb_param_name in body_param_names:
+                limbs_params[side][limb_param_name] = params_csv[limb_param_name]
             else:
-                limbs_params[side][wing_param_name] = params_csv[wing_param_name + '_' + side]
+                limbs_params[side][limb_param_name] = params_csv[limb_param_name + '_' + side]
 
     return limbs_params
\ No newline at end of file