FakeReader: add support for populating instrument metadata

This metadata is already populated in the case of SPW fake files. Adds a new boolean key withInstrument allowing to use XMLMockObjects.createInstrument() to add an instrument to the OME metadata
sbesson · Feb 6, 2025 · 0f47e17 · 0f47e17
1 parent 1f3a5e3
commit 0f47e17
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diff --git a/components/formats-bsd/src/loci/formats/in/FakeReader.java b/components/formats-bsd/src/loci/formats/in/FakeReader.java
@@ -609,6 +609,7 @@ protected void initFile(String id) throws FormatException, IOException {
     boolean metadataComplete = true;
     boolean thumbnail = false;
     boolean withMicrobeam = false;
+    boolean withInstrument = false;
 
     int seriesCount = 1;
     int resolutionCount = 1;
@@ -720,6 +721,7 @@ else if (key.equals("pixelType")) {
       else if (key.equals("fields")) fields = intValue;
       else if (key.equals("plateAcqs")) plateAcqs = intValue;
       else if (key.equals("withMicrobeam")) withMicrobeam = boolValue;
+      else if (key.equals("withInstrument")) withInstrument = boolValue;
       else if (key.equals("annLong")) annLong = intValue;
       else if (key.equals("annDouble")) annDouble = intValue;
       else if (key.equals("annMap")) annMap = intValue;
@@ -852,6 +854,8 @@ else if (dimOrder == null) {
         populateSPW(store, screens, plates, plateRows, plateCols, fields, plateAcqs, withMicrobeam);
       if (imageCount > 0) seriesCount = imageCount;
       else hasSPW = false; // failed to generate SPW metadata
+    } else if (withInstrument) {
+      populateInstrument(store);
     }
 
     // populate core metadata
@@ -1400,6 +1404,15 @@ private int populateSPW(MetadataStore store, int screens, int plates, int rows,
     return ome.sizeOfImageList();
   }
 
+  private void populateInstrument(MetadataStore store)
+  {
+    final XMLMockObjects xml = new XMLMockObjects();
+    OME ome = xml.getRoot();
+    ome.addInstrument(xml.createInstrument(true));
+    getOmeXmlMetadata().setRoot(new OMEXMLMetadataRoot(ome));
+    getOmeXmlService().convertMetadata(omeXmlMetadata, store);
+  }
+
   /** Creates a mapping between indices and color values. */
   private void createIndexMap(int num) {
     int sizeC = core.get(0).sizeC;

diff --git a/components/formats-bsd/test/loci/formats/utests/FakeReaderTest.java b/components/formats-bsd/test/loci/formats/utests/FakeReaderTest.java
@@ -761,4 +761,13 @@ public void testEmissionWavelengths() throws Exception {
     assertEquals(m.getChannelEmissionWavelength(0, 4), new Length(5020.0, UNITS.ANGSTROM));
     reader.close();
   }
+
+  @Test
+  public void testInstrument() throws Exception {
+    reader.setId("test&withInstrument=true.fake");
+    m = service.asRetrieve(reader.getMetadataStore());
+    assertTrue(service.validateOMEXML(service.getOMEXML(m)));
+    assertEquals(m.getInstrumentCount(), 1);
+    reader.close();
+  }
 }