From d7f80b810be20afa7bbe3cf247f6d047a6b16a90 Mon Sep 17 00:00:00 2001
From: espg <refuge@rocktalus.com>
Date: Tue, 17 Jun 2025 16:18:44 -0600
Subject: [PATCH] basic check to prevent 'orphan' clusters during prune

---
 pgamit/cluster.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pgamit/cluster.py b/pgamit/cluster.py
index 615fa669..29c0deae 100644
--- a/pgamit/cluster.py
+++ b/pgamit/cluster.py
@@ -50,8 +50,12 @@ def prune(OC, central_points, method='minsize'):
         counts = mod.sum(axis=0)
         problems = np.sum(counts == 0)
         if problems == 0:
-            subset.append(i)
-            OC[i, :] = np.zeros(rowlength)
+            for row in mod:
+                if np.sum(row) > 0:
+                    problems += ~(np.max(mod[:,row].sum(axis=0)) >= 2)
+            if problems == 0:
+                subset.append(i)
+                OC[i, :] = np.zeros(rowlength)
     # Cast subset list to pandas index
     dfIndex = pd.Index(subset)
     # Cast OC to pandas dataframe