Exporter plugin: remove any extra Channel elements

Fixes ome#3539.
melissalinkert · Aug 9, 2023 · 10980fe · 10980fe
1 parent 19d7fb9
commit 10980fe
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/components/bio-formats-plugins/src/loci/plugins/out/Exporter.java b/components/bio-formats-plugins/src/loci/plugins/out/Exporter.java
@@ -446,6 +446,15 @@ else if (store.getImageCount() > 1) {
             store.setPixelsSizeC(new PositiveInteger(channels*imp.getNChannels()), 0);
             store.setPixelsSizeT(new PositiveInteger(imp.getNFrames()), 0);
 
+            try {
+              // if a subset of the data was opened, the number of Channels
+              // in the OME-XML may not match the ImagePlus channel count
+              // channel count mismatches can cause problems when actually writing pixels
+              service.removeChannels(service.getOMEMetadata(store), 0, imp.getNChannels());
+            }
+            catch (ServiceException e) {
+            }
+
             if (store.getImageID(0) == null) {
                 store.setImageID(MetadataTools.createLSID("Image", 0), 0);
             }