Read input files with unflattened resolutions (i.e. keep pyramid hierarchy)

This better matches what bioformats2raw would have produced.

Author: melissalinkert

src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java

@@ -965,6 +965,7 @@ else if (layoutVersion != 3) {
       else if (imageFile != null && !imageFile.isEmpty()) {
         try (ChannelSeparator imageReader = new ChannelSeparator()) {
           IMetadata srcMetadata = service.createOMEXMLMetadata();
+          imageReader.setFlattenedResolutions(false);
           imageReader.setMetadataStore(srcMetadata);
           imageReader.setId(imageFile);
           xml = service.getOMEXML(srcMetadata);