remove anchor

src/vame/preprocessing/clean_timeseries.py

@@ -18,6 +18,9 @@ def clean_timeseries(
     pos = [0]
     pos_temp = 0
 
+    pose_ref_1 = config["pose_ref_1"]
+    pose_ref_2 = config["pose_ref_2"]
+
     session_names = config["session_names"]
     for session in session_names:
         logger.info("z-scoring of session %s" % session)
@@ -27,7 +30,7 @@ def clean_timeseries(
 
         path_to_file = Path(config["project_path"]) / "data" / "processed" / session / session + "-aligned.nc"
         ds = load_vame_dataset(path_to_file)
-        X = ds.position_aligned.sel(individuals="individual_0").values
+        X = ds.position_aligned.sel(individuals="individual_0").drop_sel(keypoints=pose_ref_1).values
 
         # Standardize data
         X_mean = np.mean(X, axis=0)
@@ -53,25 +56,3 @@ def clean_timeseries(
         X_all_sessions.append(X_z)
 
     X_all_sessions = np.concatenate(X_all_sessions, axis=0)
-
-    # Detect and delete anchors
-    detect_anchors = np.std(X_all_sessions, axis=0)
-    sort_anchors = np.sort(detect_anchors)
-    if sort_anchors[0] == sort_anchors[1]:
-        anchors = np.where(detect_anchors == sort_anchors[0])[0]
-        anchor_1_temp = anchors[0]
-        anchor_2_temp = anchors[1]
-    else:
-        anchor_1_temp = int(np.where(detect_anchors == sort_anchors[0])[0])
-        anchor_2_temp = int(np.where(detect_anchors == sort_anchors[1])[0])
-
-    if anchor_1_temp > anchor_2_temp:
-        anchor_1 = anchor_1_temp
-        anchor_2 = anchor_2_temp
-    else:
-        anchor_1 = anchor_2_temp
-        anchor_2 = anchor_1_temp
-
-    X = np.delete(X, anchor_1, 1)
-    X = np.delete(X, anchor_2, 1)
-    X = X.T