Merge pull request #4141 from melissalinkert/gh-4103

CZI: fix image naming, especially for attachments
ome · Jan 19, 2024 · 40dbbfd · 40dbbfd
2 parents 077ed12 + 53cdef0
commit 40dbbfd
Showing 1 changed file with 19 additions and 9 deletions.
diff --git a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
@@ -1406,14 +1406,9 @@ else if (positions == 1) {
           }
         }
       }
-      else if (extraIndex == 0) {
-        store.setImageName("label image", i);
-      }
-      else if (extraIndex == 1) {
-        store.setImageName("macro image", i);
-      }
-      else {
-        store.setImageName("thumbnail image", i);
+      else if (extraIndex >= 0 && extraIndex < extraImages.size()) {
+        AttachmentEntry entry = extraImages.get(extraIndex).attachment;
+        store.setImageName(entry.getNormalizedName(), i);
       }
 
       // remaining acquisition settings (esp. channels) do not apply to
@@ -3392,7 +3387,8 @@ private void translateExperiment(Element root) throws FormatException {
                   platePositions.add(value);
                 }
                 String name = well.getAttribute("Name");
-                for (int f=0; f<well.getElementsByTagName("SingleTileRegion").getLength(); f++) {
+                int tileRegionCount = (int) Math.max(1, well.getElementsByTagName("SingleTileRegion").getLength());
+                for (int f=0; f<tileRegionCount; f++) {
                   imageNames.add(name);
                 }
               }
@@ -4556,6 +4552,20 @@ public String toString() {
         ", filePart = " + filePart + ", contentGUID = " + contentGUID +
         ", contentFileType = " + contentFileType;
     }
+
+    public String getNormalizedName() {
+      if (name == null) {
+        return "";
+      }
+      String n = name.trim();
+      if (n.toLowerCase().startsWith("label")) {
+        return "label image";
+      }
+      else if (n.toLowerCase().startsWith("slidepreview")) {
+        return "macro image";
+      }
+      return n;
+    }
   }
 
   static class Channel {