Merge pull request #156 from melissalinkert/metadataonly

Add MetadataOnly to METADATA.ome.xml
glencoesoftware · May 19, 2022 · 6ee2587 · 6ee2587
2 parents c267819 + 748b06e
commit 6ee2587
Show file tree

Hide file tree

Showing 2 changed files with 16 additions and 3 deletions.
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -632,7 +632,13 @@ public void convert()
         }
 
         if (!noOMEMeta) {
-          String xml = getService().getOMEXML(meta);
+          OMEXMLService service = getService();
+          service.removeBinData((OMEXMLMetadata) meta);
+          service.removeTiffData((OMEXMLMetadata) meta);
+          for (int s=0; s<meta.getImageCount(); s++) {
+            service.addMetadataOnly((OMEXMLMetadata) meta, s, s == 0);
+          }
+          String xml = service.getOMEXML(meta);
 
           // write the original OME-XML to a file
           Path metadataPath = getRootPath().resolve("OME");

diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -445,6 +445,12 @@ public void testMultiSeries() throws Exception {
     series1.read(tile, shape);
     seriesPlaneNumberZCT = FakeReader.readSpecialPixels(tile);
     assertArrayEquals(new int[] {1, 0, 0, 0, 0}, seriesPlaneNumberZCT);
+
+    OME ome = getOMEMetadata();
+    assertEquals(2, ome.sizeOfImageList());
+    for (int i=0; i<ome.sizeOfImageList(); i++) {
+      assertNotNull(ome.getImage(i).getPixels().getMetadataOnly());
+    }
   }
 
   /**
@@ -1768,7 +1774,8 @@ private OME getOMEMetadata() throws Exception {
     Path xml = output.resolve("OME").resolve("METADATA.ome.xml");
     ServiceFactory sf = new ServiceFactory();
     OMEXMLService xmlService = sf.getInstance(OMEXMLService.class);
-    return (OME) xmlService.createOMEXMLRoot(
-      new String(Files.readAllBytes(xml), StandardCharsets.UTF_8));
+    String omexml = new String(Files.readAllBytes(xml), StandardCharsets.UTF_8);
+    assertTrue(xmlService.validateOMEXML(omexml));
+    return (OME) xmlService.createOMEXMLRoot(omexml);
   }
 }