From 0feec6f3b06991a29e185a5540d378b5b0aab70e Mon Sep 17 00:00:00 2001
From: David Gault <d.gault@dundee.ac.uk>
Date: Fri, 10 May 2024 13:33:51 +0100
Subject: [PATCH] Flex: add try catch for traversing parent dirs

---
 .../src/loci/formats/in/FlexReader.java         | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/components/formats-gpl/src/loci/formats/in/FlexReader.java b/components/formats-gpl/src/loci/formats/in/FlexReader.java
index 66802d98b87..38bc81bb089 100644
--- a/components/formats-gpl/src/loci/formats/in/FlexReader.java
+++ b/components/formats-gpl/src/loci/formats/in/FlexReader.java
@@ -397,6 +397,23 @@ protected void initFile(String id) throws FormatException, IOException {
     if (!dir.getName().startsWith("Meas_") || !groupPlates()) {
       runDirs.add(dir);
     }
+    else {
+      try {
+        // look for other acquisitions of the same plate
+        dir = dir.getParentFile();
+        String[] parentDirs = dir.list(true);
+        Arrays.sort(parentDirs);
+        for (String d : parentDirs) {
+          Location f = new Location(dir.getAbsoluteFile(), d);
+          if (f.isDirectory() && d.startsWith("Meas_")) {
+            runDirs.add(f);
+          }
+        }
+      }
+      catch (Exception e) {
+        LOGGER.error("Error while traversing parent directories: ", e);
+      }
+    }
     
     runCount = runDirs.size();
     if (runCount == 0) runCount = 1;