From d3b1ddd2b8924bc99e8b7203b42cff792596cebd Mon Sep 17 00:00:00 2001
From: kapoorlab <randomaccessiblekapoor@gmail.com>
Date: Fri, 3 Nov 2023 18:25:43 +0100
Subject: [PATCH] handle empty clusters

---
 src/napatrackmater/Trackvector.py | 9 +++++++++
 src/napatrackmater/_version.py    | 4 ++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/napatrackmater/Trackvector.py b/src/napatrackmater/Trackvector.py
index 5ae503bf..c513a3d4 100644
--- a/src/napatrackmater/Trackvector.py
+++ b/src/napatrackmater/Trackvector.py
@@ -907,6 +907,15 @@ def unsupervised_clustering(
             track_arrays_array.index(track_arrays)
         ]
         shape_dynamic_cosine_distance = pdist(clusterable_track_array, metric=metric)
+        if (
+            np.isnan(shape_dynamic_cosine_distance).any()
+            or np.isinf(shape_dynamic_cosine_distance).any()
+        ):
+            print(
+                "Cosine distance matrix contains NaN or infinite values. Returning an empty linkage matrix."
+            )
+            return
+
         shape_dynamic_linkage_matrix = linkage(
             shape_dynamic_cosine_distance, method=method
         )
diff --git a/src/napatrackmater/_version.py b/src/napatrackmater/_version.py
index d71742ca..17532934 100644
--- a/src/napatrackmater/_version.py
+++ b/src/napatrackmater/_version.py
@@ -1,2 +1,2 @@
-__version__ = version = "4.4.1"
-__version_tuple__ = version_tuple = (4, 4, 1)
+__version__ = version = "4.4.2"
+__version_tuple__ = version_tuple = (4, 4, 2)