Allow OME Zarr group

See glencoesoftware/bioformats2raw#157
melissalinkert · Jul 6, 2022 · b976226 · b976226
1 parent 9afcdc2
commit b976226
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java b/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
@@ -18,6 +18,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.Set;
 import java.util.concurrent.BlockingQueue;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutorService;
@@ -508,7 +509,9 @@ private int getSubgroupCount(String path) throws IOException {
    * @return number of series
    */
   private int getSeriesCount() throws IOException {
-    int groupKeyCount = reader.getGroupKeys().size();
+    Set<String> groupKeys = reader.getGroupKeys();
+    groupKeys.remove("OME");
+    int groupKeyCount = groupKeys.size();
     LOG.debug("getSeriesCount:");
     LOG.debug("  plateData = {}", plateData);
     LOG.debug("  group key count = {}", groupKeyCount);