From 153a466deb98f698d1b8b581d9e25043e2c51292 Mon Sep 17 00:00:00 2001
From: David Gault <d.gault@dundee.ac.uk>
Date: Thu, 8 Feb 2024 17:50:13 +0000
Subject: [PATCH 1/3] Reduce number of fields in memo file

---
 src/loci/formats/in/ZarrReader.java | 35 ++++++++++++++++-------------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/src/loci/formats/in/ZarrReader.java b/src/loci/formats/in/ZarrReader.java
index 450706c..21abcde 100644
--- a/src/loci/formats/in/ZarrReader.java
+++ b/src/loci/formats/in/ZarrReader.java
@@ -99,15 +99,18 @@ public class ZarrReader extends FormatReader {
   public static final boolean INCLUDE_LABELS_DEFAULT = false;
   protected transient ZarrService zarrService;
   private ArrayList<String> arrayPaths = new ArrayList<String>();
-  private ArrayList<String> groupKeys = new ArrayList<String>();
-  private HashMap<Integer, ArrayList<String>> resSeries = new HashMap<Integer, ArrayList<String>>();
-  private HashMap<String, Integer> resCounts = new HashMap<String, Integer>();
-  private HashSet<Integer> uniqueResCounts = new HashSet<Integer>();
-  private HashMap<String, Integer> resIndexes = new HashMap<String, Integer>();
+  
+  // The below fields are only required for initialization and are not required to be serialized
+  private transient ArrayList<String> groupKeys = new ArrayList<String>(); 
+  private transient HashMap<Integer, ArrayList<String>> resSeries = new HashMap<Integer, ArrayList<String>>(); // can be removed
+  private transient HashMap<String, Integer> resCounts = new HashMap<String, Integer>(); // can be removed
+  private transient HashSet<Integer> uniqueResCounts = new HashSet<Integer>(); // can be removed
+  private transient HashMap<String, Integer> resIndexes = new HashMap<String, Integer>(); // can be removed
+  private transient HashMap<String, ArrayList<String>> pathArrayDimensions = new HashMap<String, ArrayList<String>>(); // can be removed
+  
   private String dimensionOrder = "XYZCT";
   private int wellCount = 0;
   private int wellSamplesCount = 0;
-  private HashMap<String, ArrayList<String>> pathArrayDimensions = new HashMap<String, ArrayList<String>>();
   private boolean planesPrePopulated = false;
   private boolean hasSPW = false;
   private transient int currentOpenZarr = -1;
@@ -200,15 +203,17 @@ protected void initFile(String id) throws FormatException, IOException {
     if (attr != null && !attr.isEmpty()) {
       parseResolutionCount(zarrRootPath, "", attr);
       parseOmeroMetadata(zarrRootPath, attr);
-      String jsonAttr;
-      try {
-        jsonAttr = ZarrUtils.toJson(attr, true);
-        store.setXMLAnnotationValue(jsonAttr, attrIndex);
-        String xml_id = MetadataTools.createLSID("Annotation", attrIndex);
-        store.setXMLAnnotationID(xml_id, attrIndex);
-      } catch (JZarrException e) {
-        LOGGER.warn("Failed to convert attributes to JSON");
-        e.printStackTrace();
+      if (saveAnnotations()) {
+        String jsonAttr;
+        try {
+          jsonAttr = ZarrUtils.toJson(attr, true);
+          store.setXMLAnnotationValue(jsonAttr, attrIndex);
+          String xml_id = MetadataTools.createLSID("Annotation", attrIndex);
+          store.setXMLAnnotationID(xml_id, attrIndex);
+        } catch (JZarrException e) {
+          LOGGER.warn("Failed to convert attributes to JSON");
+          e.printStackTrace();
+        }
       }
     }
     generateGroupKeys(attr, canonicalPath);

From 0130777e5ec5b63a9004116ceba47282d1290dca Mon Sep 17 00:00:00 2001
From: David Gault <d.gault@dundee.ac.uk>
Date: Sun, 11 Feb 2024 23:26:27 +0000
Subject: [PATCH 2/3] Don't populate originalMetadata by default

---
 src/loci/formats/in/ZarrReader.java | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/loci/formats/in/ZarrReader.java b/src/loci/formats/in/ZarrReader.java
index 21abcde..21ab8b5 100644
--- a/src/loci/formats/in/ZarrReader.java
+++ b/src/loci/formats/in/ZarrReader.java
@@ -966,8 +966,10 @@ private void parseOMEXML(Location omeMetaFile, MetadataStore store, ArrayList<St
     {
       service = new ServiceFactory().getInstance( OMEXMLService.class );
       omexmlMeta = service.createOMEXMLMetadata( xml );
-      Hashtable originalMetadata = service.getOriginalMetadata(omexmlMeta);
-      if (originalMetadata != null) metadata = originalMetadata;
+      if (saveAnnotations()) {
+        Hashtable originalMetadata = service.getOriginalMetadata(omexmlMeta);
+        if (originalMetadata != null) metadata = originalMetadata;
+      }
       planesPrePopulated = true;
     }
     catch (DependencyException | ServiceException | NullPointerException e1 )

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 3/3] 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