From 1ea047db60ea4ad28bd5338d40f2b4b387fefe4e Mon Sep 17 00:00:00 2001
From: roomrys <38435167+roomrys@users.noreply.github.com>
Date: Wed, 24 May 2023 17:26:23 -0700
Subject: [PATCH] Add back instances that were not tracked

---
 sleap/nn/tracking.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/sleap/nn/tracking.py b/sleap/nn/tracking.py
index fedc3597d..eacb55e6a 100644
--- a/sleap/nn/tracking.py
+++ b/sleap/nn/tracking.py
@@ -1190,20 +1190,26 @@ def run_tracker(frames: List[LabeledFrame], tracker: BaseTracker) -> List[Labele
             inst.track = None
 
         # Prefer user instances over predicted instances
-        untracked_instances = (
-            lf.user_instances if lf.has_user_instances else lf.predicted_instances
-        )
-        track_args = {"untracked_instances": untracked_instances}
+        instances = []
+        if lf.has_user_instances:
+            instances_to_track = lf.user_instances
+            if lf.has_predicted_instances:
+                instances = lf.predicted_instances
+        else:
+            instances_to_track = lf.predicted_instances
+
+        track_args = {"untracked_instances": instances_to_track}
 
         if tracker.uses_image:
             track_args["img"] = lf.video[lf.frame_idx]
         else:
             track_args["img"] = None
 
+        instances.extend(tracker.track(**track_args))
         new_lf = LabeledFrame(
             frame_idx=lf.frame_idx,
             video=lf.video,
-            instances=tracker.track(**track_args),
+            instances=instances,
         )
         new_lfs.append(new_lf)