From 75814b4205fc5b7cfa92a28d5542a57dd71c0faa Mon Sep 17 00:00:00 2001
From: David Gault <d.gault@dundee.ac.uk>
Date: Sun, 11 Feb 2024 23:37:54 +0000
Subject: [PATCH] Don't copy over any original annotations

---
 src/loci/formats/in/ZarrReader.java | 38 +++++++++++++++++------------
 1 file changed, 23 insertions(+), 15 deletions(-)

diff --git a/src/loci/formats/in/ZarrReader.java b/src/loci/formats/in/ZarrReader.java
index 21ab8b5..5bfc736 100644
--- a/src/loci/formats/in/ZarrReader.java
+++ b/src/loci/formats/in/ZarrReader.java
@@ -1041,24 +1041,32 @@ private void parseOMEXML(Location omeMetaFile, MetadataStore store, ArrayList<St
     }
     setSeries(oldSeries);
 
-    // Remove old PyramidResolution annotations
     OME root = (OME) omexmlMeta.getRoot();
-    StructuredAnnotations annotations = root.getStructuredAnnotations();
-    if (annotations != null) {
-      int numMapAnnotations = annotations.sizeOfMapAnnotationList();
-      int index = 0;
-      for (int i = 0; i < numMapAnnotations; i++) {
-        MapAnnotation mapAnnotation = annotations.getMapAnnotation(index);
-        String namespace = mapAnnotation.getNamespace();
-        if (namespace != null && namespace.toLowerCase().contains("pyramidresolution")) {
-          annotations.removeMapAnnotation(mapAnnotation);
-        }
-        else {
-          index++;
+    
+    // Optionally remove all annotations
+    if (!saveAnnotations()) {
+      root.setStructuredAnnotations(null);
+      omexmlMeta.setRoot((MetadataRoot) root);
+    }
+    else {
+      // Remove old PyramidResolution annotations
+      StructuredAnnotations annotations = root.getStructuredAnnotations();
+      if (annotations != null) {
+        int numMapAnnotations = annotations.sizeOfMapAnnotationList();
+        int index = 0;
+        for (int i = 0; i < numMapAnnotations; i++) {
+          MapAnnotation mapAnnotation = annotations.getMapAnnotation(index);
+          String namespace = mapAnnotation.getNamespace();
+          if (namespace != null && namespace.toLowerCase().contains("pyramidresolution")) {
+            annotations.removeMapAnnotation(mapAnnotation);
+          }
+          else {
+            index++;
+          }
         }
+        root.setStructuredAnnotations(annotations);
+        omexmlMeta.setRoot((MetadataRoot) root);
       }
-      root.setStructuredAnnotations(annotations);
-      omexmlMeta.setRoot((MetadataRoot) root);
     }
     
     // Remove old Screen and Plate metadata