kymotracking: add KymoTrackGroup.filter()

changelog.md

@@ -9,6 +9,7 @@
   * Two-channel visualizations can be plotted using `"rg"`, `"gb"`, or `"rb"`.
 * Added `duration` property to `KymoTrack` which returns the duration (in seconds) that the track was observed.
 * Added option to filter tracks with `lk.filter_tracks(tracks, minimum_duration=duration_in_seconds)` by track duration (in seconds).
+* Added `KymoTrackGroup.filter()` to filter tracks by duration or length (number of identified track points) in-place.
 
 #### Improvements
 

lumicks/pylake/kymotracker/kymotrack.py

@@ -1276,6 +1276,22 @@ def remove_tracks_in_rect(self, rect, all_points=False):
 
         self._src = [track for track in self._src if not track.in_rect(rect, all_points)]
 
+    def filter(self, *, minimum_length=1, minimum_duration=0):
+        """Remove tracks shorter than a minimum number of time points from the list.
+
+        Parameters
+        ----------
+        minimum_length : int, optional
+            Minimum length for the track to be accepted (default: 1).
+        minimum_duration : seconds, optional
+            Minimum duration for a track to be accepted (default: 0).
+        """
+        from .kymotracker import filter_tracks  # local import to avoid circular import
+
+        self._src = filter_tracks(
+            self, minimum_length=minimum_length, minimum_duration=minimum_duration
+        )._src
+
     def __repr__(self):
         return f"{self.__class__.__name__}(N={len(self)})"
 

lumicks/pylake/kymotracker/tests/test_refinement.py

@@ -505,9 +505,17 @@ def test_filter_by_duration(
     tracks = KymoTrackGroup([k1, k2, k3, k4, k5])
 
     filtered = filter_tracks(tracks, minimum_length=0, minimum_duration=minimum_duration)
-    assert len(filtered) == ref_length
-    np.testing.assert_allclose(filtered[0]._minimum_observable_duration, ref_minimum)
-    np.testing.assert_allclose(filtered[-1]._minimum_observable_duration, ref_minimum_dt2)
+    assert len(tracks) == 5  # return new instance
+
+    tracks.filter(minimum_length=0, minimum_duration=minimum_duration)
+    assert len(tracks) == ref_length  # in-place modification
+
+    for filtered_tracks in (filtered, tracks):
+        assert len(filtered_tracks) == ref_length
+        np.testing.assert_allclose(filtered_tracks[0]._minimum_observable_duration, ref_minimum)
+        np.testing.assert_allclose(
+            filtered_tracks[-1]._minimum_observable_duration, ref_minimum_dt2
+        )
 
 
 def test_empty_group():