Fix min_time_point with link metadata

jvzonlab · Nov 25, 2024 · 5f6faaa · 5f6faaa
1 parent 5f8aa54
commit 5f6faaa
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Showing 2 changed files with 33 additions and 8 deletions.
diff --git a/organoid_tracker/imaging/io.py b/organoid_tracker/imaging/io.py
@@ -310,22 +310,23 @@ def _parse_tracks_and_meta_format(experiment: Experiment, tracks_json: List[Dict
 
         coords_xyz_px = track_json["coords_xyz_px"]
         positions_of_track = list()
-        for i, raw_position in enumerate(coords_xyz_px):
-            time_point_number = time_point_number_start + i
-            if time_point_number < min_time_point or time_point_number > max_time_point:
-                continue
-            position_previous_track = Position(*raw_position, time_point_number=time_point_number_start + i)
-            positions_of_track.append(position_previous_track)
+        min_index = max(0, min_time_point - time_point_number_start)
+        max_index = min(len(coords_xyz_px), max_time_point - time_point_number_start)
+        for i in range(min_index, max_index):
+            position = Position(*coords_xyz_px[i], time_point_number=time_point_number_start + i)
+            positions_of_track.append(position)
         track = LinkingTrack(positions_of_track)
         links.add_track(track)
 
         # Handle link metadata
         if "link_meta" in track_json:
             for metadata_key, metadata_values in track_json["link_meta"].items():
-                for i, value in enumerate(metadata_values):
+                for i in range(min_index, max_index - 1):
+                    value = metadata_values[i]
                     if value is None:
                         continue
-                    link_data.set_link_data(positions_of_track[i], positions_of_track[i + 1], metadata_key, value)
+
+                    link_data.set_link_data(positions_of_track[i - min_index], positions_of_track[i - min_index + 1], metadata_key, value)
 
         # Handle lineage metadata
         if "lineage_meta" in track_json:
@@ -337,6 +338,8 @@ def _parse_tracks_and_meta_format(experiment: Experiment, tracks_json: List[Dict
         if "coords_xyz_px_before" not in track_json:
             continue
         time_point_number_start = track_json["time_point_start"]
+        if min_time_point >= time_point_number_start:
+            continue  # Ignore tracks that start at/after the minimum time point - can't add metadata to before
 
         position_first = Position(*track_json["coords_xyz_px"][0], time_point_number=time_point_number_start)
         metadata = track_json.get("link_meta_before")

diff --git a/tests/test_io.py b/tests/test_io.py
@@ -160,3 +160,25 @@ def test_loading_old_format(self):
             # Link meta
             self.assertEqual(4, experiment.link_data.get_link_data(Position(4, 5, 6, time_point_number=2),
                                                                    Position(7, 8, 9, time_point_number=3), "test_key"))
+
+    def test_loading_with_min_time_point(self):
+        experiment = Experiment()
+        position_1 = Position(1, 2, 3, time_point_number=1)
+        position_2 = Position(4, 5, 6, time_point_number=2)
+        position_3 = Position(7, 8, 9, time_point_number=3)
+        experiment.positions.add(position_1)
+        experiment.positions.add(position_2)
+        experiment.positions.add(position_3)
+        experiment.links.add_link(position_1, position_2)
+        experiment.links.add_link(position_2, position_3)
+        experiment.link_data.set_link_data(position_1, position_2, "test_key", 1)
+        experiment.link_data.set_link_data(position_2, position_3, "test_key", 2)
+
+        with TemporaryDirectory() as directory:
+            file = os.path.join(directory, "test." + io.FILE_EXTENSION)
+            io.save_data_to_json(experiment, file, write_new_format=True)
+
+            experiment = io.load_data_file(file, min_time_point=2)
+            self.assertEqual(2, len(experiment.positions))
+            self.assertEqual(1, len(experiment.links))
+            self.assertEqual(2, experiment.link_data.get_link_data(position_2, position_3, "test_key"))