updates

Author: yeshaokai

amadeusgpt/analysis_objects/animal.py

@@ -92,12 +92,16 @@ def get_path(self, ind):
         codes, verts = zip(*path_data)
         return mpath.Path(verts, codes)
 
-    def get_keypoints(self, average_keypoints=False) -> ndarray:
-        if average_keypoints:
-            return np.nanmedian(self.keypoints, axis=1)
+    def get_keypoints(self) -> ndarray:
+        # the shape should be (n_frames, n_keypoints, 2)
+        # extending to 3D?
+        assert len(self.keypoints.shape) == 3, f"keypoints shape is {self.keypoints.shape}"
         return self.keypoints
 
     def get_center(self):
+        """
+        median is more robust than mean
+        """
         return np.nanmedian(self.keypoints, axis=1).squeeze()
 
     def get_xmin(self):
@@ -222,3 +226,9 @@ def calc_head_cs(self):
 
 
 
+if __name__ == "__main__":
+    # unit testing the shape of kinematics data
+    # acceleration, acceleration_mag, velocity, speed, and keypoints
+
+
+