OME-TIFF: remove extra Channels all at once

components/formats-api/src/loci/formats/services/OMEXMLService.java

@@ -267,6 +267,16 @@ public void convertMetadata(String xml, MetadataStore dest)
    */
   public void removeTiffData(OMEXMLMetadata omexmlMeta);
 
+  /**
+   * Remove all but the first SizeC valid Channel elements from all
+   * Image elements in the OME-XML metadata object. The "SizeC" attribute
+   * on each Image's Pixels must be set to the number of Channel elements
+   * to preserve for that Image.
+   * This is a bulk removal method which minimizes the number of calls
+   * to OMEXMLMetadata.setRoot(...).
+   */
+  public void removeChannels(OMEXMLMetadata omexmlMeta);
+
   /**
    * Remove all but the first sizeC valid Channel elements from the given
    * OME-XML metadata object.

components/formats-api/src/loci/formats/services/OMEXMLServiceImpl.java

@@ -957,6 +957,25 @@ public void removeTiffData(OMEXMLMetadata omexmlMeta) {
     omexmlMeta.setRoot(root);
   }
 
+  /** @see OMEXMLService#removeChannels(OMEXMLMetadata) */
+  @Override
+  public void removeChannels(OMEXMLMetadata omexmlMeta) {
+    omexmlMeta.resolveReferences();
+    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
+    for (int image=0; image<root.sizeOfImageList(); image++) {
+      Pixels img = root.getImage(image).getPixels();
+      int sizeC = img.getSizeC().getNumberValue().intValue();
+      List<Channel> channels = img.copyChannelList();
+      for (int c=0; c<channels.size(); c++) {
+        Channel channel = channels.get(c);
+        if (channel.getID() == null || c >= sizeC) {
+          img.removeChannel(channel);
+        }
+      }
+    }
+    omexmlMeta.setRoot(root);
+  }
+
   /** @see OMEXMLService#removeChannels(OMEXMLMetadata, int, int) */
   @Override
   public void removeChannels(OMEXMLMetadata omexmlMeta, int image, int sizeC) {

components/formats-bsd/src/loci/formats/in/OMETiffReader.java

@@ -576,11 +576,7 @@
     }
 
     hasSPW = meta.getPlateCount() > 0;
-
-    for (int i=0; i<meta.getImageCount(); i++) {
-      int sizeC = meta.getPixelsSizeC(i).getValue();
-      service.removeChannels(meta, i, sizeC);
-    }
+    service.removeChannels(meta);
 
     // if flattened resolutions are requested, remove resolution annotations
     // otherwise, MetadataStore and reader metadata will be inconsistent
@@ -1384,7 +1380,7 @@
    * @return the metadata store.
    * @deprecated Use the general {@link SubResolutionFormatReader#getMetadataStore()} method.
    */
   public MetadataStore getMetadataStoreForDisplay() {
     return getMetadataStore();
   }
 
@@ -1402,7 +1398,7 @@
    * @return the metadata store.
    * @deprecated Use the general {@link SubResolutionFormatReader#getMetadataStore()} method.
    */
   public MetadataStore getMetadataStoreForConversion() {
     return getMetadataStore();
   }