find_beads: handle failure to estimate background

changelog.md

@@ -30,6 +30,7 @@
 #### Bug fixes
 
 * Ensure that operators such as (e.g. `+`, `-`, `/`) work on [`Slice`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.channel.Slice.html) with all types that are convertible to scalars. Previously these failed with zero dimensional numpy arrays and other convertible objects.
+* Fixed a bug where bead edge determination could fail with an unhandled exception when determining the background failed rather than issued the expected `RuntimeError`.
 
 ## v1.5.3 | 2024-10-29
 

lumicks/pylake/detail/bead_cropping.py

@@ -5,7 +5,11 @@ def _guess_background(data):
     """Determine background level by determining most prominent mode"""
     import scipy.stats
 
-    kde_estimate = scipy.stats.gaussian_kde(data, 0.02)
+    try:
+        kde_estimate = scipy.stats.gaussian_kde(data, 0.02)
+    except np.linalg.LinAlgError:
+        return np.median(data)  # Use the median count as fallback
+
     interpolated_kde = np.arange(min(data), np.max(data))
     return interpolated_kde[np.argmax(kde_estimate.pdf(interpolated_kde))]
 

lumicks/pylake/detail/tests/test_bead_crop.py

@@ -46,7 +46,10 @@ def test_bead_cropping_allow_negative_beads(filename, ref_edges, ref_edges_no_ne
 
 def test_bead_cropping_failure():
     mock = np.zeros((100, 1))
-    mock[50] = 1  # Standard deviation of the data should not be zero or the KDE estimate fails.
+    with pytest.raises(RuntimeError, match="Did not find two beads"):
+        find_beads_brightness(mock, bead_diameter_pixels=1, plot=True)
+
+    mock[50] = 1
     with pytest.raises(RuntimeError, match="Did not find two beads"):
         find_beads_brightness(mock, bead_diameter_pixels=1, plot=True)