From 4f15c0d94bf76e1da1c22addd1857144e57f2f48 Mon Sep 17 00:00:00 2001
From: Yoshihiro OKUMURA <orrisroot@gmail.com>
Date: Tue, 12 Jul 2022 18:28:51 +0900
Subject: [PATCH] disabled to output metadata of empty annotations.

---
 .../neurodata/tools/BioFormatsImageInfo.java     | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java b/src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java
index f0ee980..2f3073f 100644
--- a/src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java
+++ b/src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java
@@ -33,14 +33,13 @@ public class BioFormatsImageInfo {
     MetadataStore ms = reader.getMetadataStore();
     MetadataRetrieve mr = ms instanceof MetadataRetrieve ? (MetadataRetrieve) ms : null;
     for (int j = 0; j < seriesCount; j++) {
+
+      // read basic metadata for series #j
       reader.setSeries(j);
       Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
 
-      // read basic metadata for series #j
       int imageCount = reader.getImageCount();
       int resolutionCount = reader.getResolutionCount();
-
-      // output basic metadata for series #i
       String seriesName = mr == null ? null : mr.getImageName(j);
       if (seriesName != null) {
         seriesMetadata.put("name", seriesName);
@@ -174,8 +173,8 @@ public class BioFormatsImageInfo {
     return ret;
   }
 
-  protected static LinkedHashMap<String, Object> makeRectangle(int width, int height) {
-    LinkedHashMap<String, Object> ret = new LinkedHashMap<String, Object>();
+  protected static Map<String, Object> makeRectangle(int width, int height) {
+    Map<String, Object> ret = new LinkedHashMap<String, Object>();
     ret.put("width", width);
     ret.put("height", height);
     return ret;
@@ -185,8 +184,8 @@ public class BioFormatsImageInfo {
     ObjectMapper mapper = new ObjectMapper();
     String json = null;
     try {
-      json = mapper.writeValueAsString(map);
       // json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
+      json = mapper.writeValueAsString(map);
     } catch (Exception e) {
       // return "null" if conversion error occured
       json = "null";
@@ -223,7 +222,10 @@ public class BioFormatsImageInfo {
       reader.setResolution(0);
       // info.printGlobalMetadata();
       // info.printOriginalMetadata();
-      metadata.put("annotations", readAnnotations(reader));
+      Map<String, Object> annotations = readAnnotations(reader);
+      if (!annotations.isEmpty()) {
+        metadata.put("annotations", annotations);
+      }
     } catch (Exception e) {
       throw new BioFormatsImageException(e);
     } finally {