Fix problems with missing groups/metadata and sparse plates

src/main/java/com/glencoesoftware/bioformats2raw/Converter.java

@@ -1338,7 +1338,6 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
         String rowName = String.valueOf(r);
         row.put("name", rowName);
         rows.add(row);
-        root.createSubGroup(rowName);
       }
     }
     catch (NullPointerException e) {
@@ -1363,7 +1362,9 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
       acquisition.put("id", String.valueOf(pa));
       acquisitions.add(acquisition);
     }
-    plateMap.put("acquisitions", acquisitions);
+    if (acquisitions.size() > 0) {
+      plateMap.put("acquisitions", acquisitions);
+    }
 
     List<Map<String, Object>> wells = new ArrayList<Map<String, Object>>();
     int maxField = Integer.MIN_VALUE;
@@ -1377,7 +1378,10 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
 
           List<Map<String, Object>> imageList =
             new ArrayList<Map<String, Object>>();
-          ZarrGroup wellGroup = root.createSubGroup(wellPath);
+          String rowPath = index.getRowPath();
+          ZarrGroup rowGroup = root.createSubGroup(rowPath);
+          String columnPath = index.getColumnPath();
+          ZarrGroup columnGroup = rowGroup.createSubGroup(columnPath);
           for (HCSIndex field : hcsIndexes) {
             if (field.getPlateIndex() == index.getPlateIndex() &&
               field.getWellRowIndex() == index.getWellRowIndex() &&
@@ -1393,9 +1397,9 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
 
           Map<String, Object> wellMap = new HashMap<String, Object>();
           wellMap.put("images", imageList);
-          Map<String, Object> attributes = wellGroup.getAttributes();
+          Map<String, Object> attributes = columnGroup.getAttributes();
           attributes.put("well", wellMap);
-          wellGroup.writeAttributes(attributes);
+          columnGroup.writeAttributes(attributes);
 
           // make sure the row/column indexes are added to the plate attributes
           // this is necessary when Plate.Rows or Plate.Columns is not set

src/main/java/com/glencoesoftware/bioformats2raw/HCSIndex.java

@@ -134,11 +134,25 @@ public void setFieldIndex(int fieldIndex) {
     this.field = fieldIndex;
   }
 
+  /**
+   * @return row path relative to the plate group
+   */
+  public String getRowPath() {
+    return String.format("%d", getWellRowIndex());
+  }
+
+  /**
+   * @return column path relative to the row group
+   */
+  public String getColumnPath() {
+    return String.format("%d", getWellColumnIndex());
+  }
+
   /**
    * @return well path relative to the plate group
    */
   public String getWellPath() {
-    return String.format("%d/%d", getWellRowIndex(), getWellColumnIndex());
+    return String.format("%s/%s", getRowPath(), getColumnPath());
   }
 
   @Override

src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java

@@ -42,6 +42,7 @@
 
 import static org.junit.jupiter.api.Assertions.assertArrayEquals;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -868,6 +869,65 @@ public void testHCSMetadata() throws Exception {
     assertEquals(1, ome.sizeOfPlateList());
   }
 
+  /**
+   * Convert a plate with default options.
+   * The output should be compliant with OME Zarr HCS.
+   */
+  @Test
+  public void testHCSMetadataNoAcquisitions() throws Exception {
+    input = getTestFile("C4-H2-only-no-acqs.xml");
+    assertTool();
+
+    ZarrGroup z = ZarrGroup.open(output);
+
+    int rowCount = 8;
+    int colCount = 12;
+    int fieldCount = 1;
+
+    // Only two rows are filled out with one column each (two Wells total)
+    checkPlateGroupLayout(output, 2, 1, fieldCount, 2, 2);
+
+    // check plate/well level metadata
+    Map<String, Object> plate =
+        (Map<String, Object>) z.getAttributes().get("plate");
+    assertEquals(fieldCount, ((Number) plate.get("field_count")).intValue());
+
+    List<Map<String, Object>> rows =
+      (List<Map<String, Object>>) plate.get("rows");
+    List<Map<String, Object>> columns =
+      (List<Map<String, Object>>) plate.get("columns");
+    List<Map<String, Object>> wells =
+      (List<Map<String, Object>>) plate.get("wells");
+
+    assertFalse(plate.containsKey("acquisitions"));
+
+    checkDimension(rows, rowCount);
+    checkDimension(columns, colCount);
+
+    assertEquals(rows.size() * columns.size(), wells.size());
+    for (int row=0; row<rows.size(); row++) {
+      for (int col=0; col<columns.size(); col++) {
+        int well = row * columns.size() + col;
+        assertEquals(row + "/" + col, wells.get(well).get("path"));
+      }
+    }
+
+    // check well metadata
+    for (Map<String, Object> row : rows) {
+      String rowName = (String) row.get("name");
+      for (Map<String, Object> column : columns) {
+        String columnName = (String) column.get("name");
+        ZarrGroup wellGroup = ZarrGroup.open(
+            output.resolve(rowName).resolve(columnName));
+        checkWell(wellGroup, fieldCount);
+      }
+    }
+
+    // check OME metadata
+    OME ome = getOMEMetadata();
+    assertEquals(1, ome.sizeOfPlateList());
+  }
+
   /**
    * 96 well plate with only well E6.
    */
@@ -1211,7 +1271,7 @@ private void checkPlateGroupLayout(Path root, int rowCount, int colCount,
     throws IOException
   {
     // check valid group layout
-    // OME (OME-XML metadata), .zattrs (Plate), .zgroup (Plate) and rows
+    // OME (OME-XML metadata) folder, .zattrs (Plate), .zgroup (Plate) and rows
     assertEquals(rowCount + 3, Files.list(root).toArray().length);
     for (int row=0; row<rowCount; row++) {
       Path rowPath = root.resolve(Integer.toString(row));

src/test/resources/com/glencoesoftware/bioformats2raw/test/C4-H2-only-no-acqs.xml

@@ -0,0 +1,23 @@
+<?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" Creator="OME Bio-Formats 6.6.1-SNAPSHOT" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+<Plate ColumnNamingConvention="number" Columns="12" ExternalIdentifier="External Identifier" ID="Plate:0" Name="Plate Name 0" RowNamingConvention="letter" Rows="8" Status="Plate status" WellOriginX="0.0" WellOriginXUnit="µm" WellOriginY="1.0" WellOriginYUnit="µm">
+<Description>Plate 0 of 1</Description>
+<Well Color="255" Column="0" ExternalDescription="External Description" ExternalIdentifier="External Identifier" ID="Well:0_0_0_0" Row="0" Type="Transfection: done">
+<WellSample ID="WellSample:0_0_0_0_0_0" Index="0" PositionX="0.0" PositionXUnit="reference frame" PositionY="1.0" PositionYUnit="reference frame" Timepoint="2006-05-04T18:13:51">
+<ImageRef ID="Image:0"></ImageRef></WellSample></Well>
+<Well Color="255" Column="0" ExternalDescription="External Description" ExternalIdentifier="External Identifier" ID="Well:0_0_1_0" Row="1" Type="Transfection: done">
+<WellSample ID="WellSample:0_0_1_0_0_0" Index="1" PositionX="0.0" PositionXUnit="reference frame" PositionY="1.0" PositionYUnit="reference frame" Timepoint="2006-05-04T18:13:51">
+<ImageRef ID="Image:1"></ImageRef></WellSample></Well>
+</Plate>
+<Image ID="Image:0" Name="test">
+<Description>Image Description 0</Description>
+<Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="1.0" PhysicalSizeXUnit="µm" PhysicalSizeY="1.0" PhysicalSizeYUnit="µm" PhysicalSizeZ="1.0" PhysicalSizeZUnit="µm" SignificantBits="8" SizeC="1" SizeT="1" SizeX="2" SizeY="2" SizeZ="1" Type="uint8">
+<Channel AcquisitionMode="FluorescenceLifetime" Color="1687603455" ContrastMethod="Brightfield" EmissionWavelength="300.3" EmissionWavelengthUnit="nm" ExcitationWavelength="400.3" ExcitationWavelengthUnit="nm" Fluor="Fluor" ID="Channel:0:0" IlluminationType="Oblique" NDFilter="1.0" Name="Name" PinholeSize="0.5" PinholeSizeUnit="µm" PockelCellSetting="0" SamplesPerPixel="1"/>
+<Plane DeltaT="0.1" DeltaTUnit="s" ExposureTime="10.0" ExposureTimeUnit="s" PositionX="1.0" PositionXUnit="reference frame" PositionY="1.0" PositionYUnit="reference frame" PositionZ="1.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
+<BinData xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" Length="4" BigEndian="false">AAAAAA==</BinData></Pixels></Image>
+<Image ID="Image:1" Name="test 2">
+<Description>Image Description 1</Description>
+<Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:1" Interleaved="false" PhysicalSizeX="1.0" PhysicalSizeXUnit="µm" PhysicalSizeY="1.0" PhysicalSizeYUnit="µm" PhysicalSizeZ="1.0" PhysicalSizeZUnit="µm" SignificantBits="8" SizeC="1" SizeT="1" SizeX="2" SizeY="2" SizeZ="1" Type="uint8">
+<Channel AcquisitionMode="FluorescenceLifetime" Color="1687603455" ContrastMethod="Brightfield" EmissionWavelength="300.3" EmissionWavelengthUnit="nm" ExcitationWavelength="400.3" ExcitationWavelengthUnit="nm" Fluor="Fluor" ID="Channel:1:0" IlluminationType="Oblique" NDFilter="1.0" Name="Name" PinholeSize="0.5" PinholeSizeUnit="µm" PockelCellSetting="0" SamplesPerPixel="1"/>
+<Plane DeltaT="0.1" DeltaTUnit="s" ExposureTime="10.0" ExposureTimeUnit="s" PositionX="1.0" PositionXUnit="reference frame" PositionY="1.0" PositionYUnit="reference frame" PositionZ="1.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
+<BinData xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" Length="4" BigEndian="false">AQEBAQ==</BinData></Pixels></Image></OME>