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] 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);