From b2c2b9c3e3fcb778990734f8065e6ae281d35edc Mon Sep 17 00:00:00 2001
From: Dominik Lindner <d.lindner@dundee.ac.uk>
Date: Tue, 29 Oct 2024 14:51:50 +0000
Subject: [PATCH] Fix issue if 'labels' part of filename

---
 src/loci/formats/in/ZarrReader.java | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/loci/formats/in/ZarrReader.java b/src/loci/formats/in/ZarrReader.java
index b4dcb00..6c2e4f6 100644
--- a/src/loci/formats/in/ZarrReader.java
+++ b/src/loci/formats/in/ZarrReader.java
@@ -1127,6 +1127,7 @@ private Double getDouble(Map<String, Object> src, String key) {
   public String[] getUsedFiles(boolean noPixels) {
     FormatTools.assertId(currentId, true, 1);
     String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr") + 5);
+    int rootPathLength = zarrRootPath.length();
     ArrayList<String> usedFiles = new ArrayList<String>();
     reloadOptionsFile(zarrRootPath);
 
@@ -1134,11 +1135,11 @@ public String[] getUsedFiles(boolean noPixels) {
     boolean includeLabels = includeLabels();
     try (Stream<Path> paths = Files.walk(Paths.get(zarrRootPath), FileVisitOption.FOLLOW_LINKS)) {
       paths.filter(Files::isRegularFile) 
-      .forEach(path -> {if ((!skipPixels && includeLabels) || 
-          (!skipPixels && !includeLabels && !path.toString().toLowerCase().contains("labels")) ||
+      .forEach(path -> { if ((!skipPixels && includeLabels) ||
+          (!skipPixels && !includeLabels && !(path.toString().toLowerCase().indexOf("labels")>=rootPathLength)) ||
           (skipPixels && includeLabels && (path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml"))) ||
-          (skipPixels && !includeLabels &&  !path.toString().toLowerCase().contains("labels") &&(path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml"))))
-        usedFiles.add(path.toFile().getAbsolutePath());
+          (skipPixels && !includeLabels &&  !(path.toString().toLowerCase().indexOf("labels")>=rootPathLength) &&(path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml"))))
+          usedFiles.add(path.toFile().getAbsolutePath());
       });
     } catch (IOException e) {
       e.printStackTrace();