filter_tracks: add option to filter by length

changelog.md

@@ -8,6 +8,7 @@
   * Shortcuts `"r"`, `"g"`, and `"b"` can now be used for plotting single color channels in addition to `"red"`, `"green"`, and `"blue"`.
   * 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).
 
 #### Improvements
 

lumicks/pylake/kymotracker/kymotracker.py

@@ -367,7 +367,7 @@ def track_lines(
     return refine_tracks_centroid(kymotrack_group, track_width=line_width, bias_correction=True)
 
 
-def filter_tracks(tracks, minimum_length):
+def filter_tracks(tracks, minimum_length, *, minimum_duration=0):
     """Remove tracks shorter than a minimum number of time points from the list.
 
     This can be used to enforce a minimum number of frames a spot has to be detected in order
@@ -379,8 +379,19 @@ def filter_tracks(tracks, minimum_length):
         Detected tracks on a kymograph.
     minimum_length : int
         Minimum length for the track to be accepted.
+    minimum_duration : seconds
+        Minimum duration for a track to be accepted.
     """
 
+    def minimum_observable_time(track, min_length, min_duration):
+        line_time = track._kymo.line_time_seconds
+        minimum_length_based = (min_length - 1) * line_time
+
+        # When we filter with a minimum duration, we lose all durations up to the next
+        # full time step.
+        minimum_duration_based = np.ceil(min_duration / line_time) * line_time
+        return max(minimum_length_based, minimum_duration_based)
+
     return KymoTrackGroup(
         [
             track._with_minimum_time(
@@ -389,11 +400,11 @@ def filter_tracks(tracks, minimum_length):
                     track._minimum_observable_duration
                     if track._minimum_observable_duration is not None
                     else 0,
-                    (minimum_length - 1) * track._kymo.line_time_seconds,
+                    minimum_observable_time(track, minimum_length, minimum_duration),
                 )
             )
             for track in tracks
-            if len(track) >= minimum_length
+            if len(track) >= minimum_length and track.duration >= minimum_duration
         ]
     )
 

lumicks/pylake/kymotracker/tests/test_refinement.py

@@ -480,6 +480,36 @@ def test_filter_tracks(blank_kymo, blank_kymo_track_args):
     )
 
 
+@pytest.mark.parametrize(
+    "minimum_duration, ref_length, ref_minimum, ref_minimum_dt2",
+    [
+        [1.0, 5, 1.0, 2.0],
+        [1.1, 4, 2.0, 2.0],  # Going over slightly bumps the minimum time to the next frame
+        [2.0, 4, 2.0, 2.0],
+        [2.1, 2, 3.0, 4.0],  # Last line gets a bigger bump in minimum time once we filter
+    ],
+)
+def test_filter_by_duration(
+    blank_kymo_track_args, minimum_duration, ref_length, ref_minimum, ref_minimum_dt2
+):
+    k1 = KymoTrack([1, 2, 3], [1, 2, 3], *blank_kymo_track_args)  # duration = 2
+    k2 = KymoTrack([2, 3], [1, 2], *blank_kymo_track_args)  # duration = 1
+    k3 = KymoTrack([2, 3, 5], [1, 2, 5], *blank_kymo_track_args)  # duration = 3
+
+    # Track with different line time. We use two line times because we want to test that the
+    # minimum observable time gets bumped correctly to the next full timestep.
+    kymo2 = _kymo_from_array(np.zeros((3, 3)), "r", line_time_seconds=2.0, pixel_size_um=50)
+    k4 = KymoTrack([2, 3], [1, 2, 5], kymo2, "red", 0)  # duration = 2
+    k5 = KymoTrack([2, 6], [1, 2, 5], kymo2, "red", 0)  # duration = 6
+
+    tracks = KymoTrackGroup([k1, k2, k3, k4, k5])
+
+    filtered = filter_tracks(tracks, 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)
+
+
 def test_empty_group():
     """Validate that the refinement methods don't fail when applied to an empty group"""
     tracks = KymoTrackGroup([])