Merge pull request #118 from melissalinkert/plates

Fix plate detection to ignore empty plates
glencoesoftware · Dec 22, 2021 · b2c30c5 · b2c30c5
2 parents b2b2395 + afb5f88
commit b2c30c5
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Showing 3 changed files with 73 additions and 1 deletion.
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -561,7 +561,7 @@ public void convert()
         ((OMEXMLMetadata) meta).resolveReferences();
 
         if (!noHCS) {
-          noHCS = meta.getPlateCount() == 0;
+          noHCS = !hasValidPlate(meta);
         }
         else {
           ((OMEXMLMetadata) meta).resolveReferences();
@@ -1761,6 +1761,31 @@ private Class<?> getBaseReaderClass() throws FormatException, IOException {
     }
   }
 
+  /**
+   * Check if the given metadata object contains at least one plate
+   * with at least one well that links to an image.
+   *
+   * @param meta metadata object
+   * @return true if a valid plate exists, false otherwise
+   */
+  private boolean hasValidPlate(IMetadata meta) {
+    List<String> images = new ArrayList<String>();
+    for (int i=0; i<meta.getImageCount(); i++) {
+      images.add(meta.getImageID(i));
+    }
+    for (int p=0; p<meta.getPlateCount(); p++) {
+      for (int w=0; w<meta.getWellCount(p); w++) {
+        for (int ws=0; ws<meta.getWellSampleCount(p, w); ws++) {
+          if (images.contains(meta.getWellSampleImageRef(p, w, ws))) {
+            return true;
+          }
+        }
+      }
+      LOGGER.warn("Encountered invalid plate #{}", p);
+    }
+    return false;
+  }
+
   private int calculateResolutions(int width, int height) {
     int resolutions = 1;
     while (width > minSize || height > minSize) {

diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -879,6 +879,27 @@ public void testHCSMetadata() throws Exception {
     assertEquals(1, ome.sizeOfPlateList());
   }
 
+  /**
+   * Plate defined with no linked images.
+   */
+  @Test
+  public void testEmptyPlate() throws Exception {
+    input = getTestFile("empty-plate.ome.xml");
+    assertTool();
+
+    ZarrGroup z = ZarrGroup.open(output);
+
+    // Check dimensions and block size for consistency
+    // with non-HCS layout
+    ZarrArray series0 = z.openArray("0/0");
+    assertArrayEquals(new int[] {1, 1, 1, 4, 6}, series0.getShape());
+    assertArrayEquals(new int[] {1, 1, 1, 4, 6}, series0.getChunks());
+
+    // Check OME metadata to make sure the empty plate was preserved
+    OME ome = getOMEMetadata();
+    assertEquals(1, ome.sizeOfPlateList());
+  }
+
   /**
    * 96 well plate with only well E6.
    */

diff --git a/src/test/resources/com/glencoesoftware/bioformats2raw/test/empty-plate.ome.xml b/src/test/resources/com/glencoesoftware/bioformats2raw/test/empty-plate.ome.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"
+     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+     xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06
+                         http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+  <Plate
+     ID="Plate:1"
+     Name="Control Platedasd"
+     ColumnNamingConvention="letter"
+     RowNamingConvention="number"
+     Columns="12"
+     Rows="8"
+     >
+  </Plate>
+
+  <Image ID="Image:0" Name="6x6x1x8-swatch.tif">
+    <AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
+    <Pixels DimensionOrder="XYCZT" ID="Pixels:0:0" PhysicalSizeX="10000.0"
+            PhysicalSizeY="10000.0" Type="uint8" SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
+      <Channel Color="-2147483648" ID="Channel:0"/>
+      <BinData BigEndian="false" Length="32"
+                   >/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
+    </Pixels>
+  </Image>
+
+</OME>