Add "row_index" and "column_index" for each well

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

@@ -1199,7 +1199,6 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
 
           Map<String, Object> well = new HashMap<String, Object>();
           well.put("path", wellPath);
-          wells.add(well);
 
           List<Map<String, Object>> imageList =
             new ArrayList<Map<String, Object>>();
@@ -1228,31 +1227,37 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
           int column = index.getWellColumnIndex();
           int row = index.getWellRowIndex();
 
-          boolean foundColumn = false;
-          for (Map<String, Object> colMap : columns) {
-            if (colMap.get("name").equals(String.valueOf(column))) {
-              foundColumn = true;
+          int columnIndex = -1;
+          for (int c=0; c<columns.size(); c++) {
+            if (columns.get(c).get("name").equals(String.valueOf(column))) {
+              columnIndex = c;
               break;
             }
           }
-          if (!foundColumn) {
+          if (columnIndex < 0) {
             Map<String, Object> colMap = new HashMap<String, Object>();
             colMap.put("name", String.valueOf(column));
+            columnIndex = columns.size();
             columns.add(colMap);
           }
 
-          boolean foundRow = false;
-          for (Map<String, Object> rowMap : rows) {
-            if (rowMap.get("name").equals(String.valueOf(row))) {
-              foundRow = true;
+          int rowIndex = -1;
+          for (int r=0; r<rows.size(); r++) {
+            if (rows.get(r).get("name").equals(String.valueOf(row))) {
+              rowIndex = r;
               break;
             }
           }
-          if (!foundRow) {
+          if (rowIndex < 0) {
             Map<String, Object> rowMap = new HashMap<String, Object>();
             rowMap.put("name", String.valueOf(row));
+            rowIndex = rows.size();
             rows.add(rowMap);
           }
+
+          well.put("row_index", rowIndex);
+          well.put("column_index", columnIndex);
+          wells.add(well);
         }
 
         maxField = (int) Math.max(maxField, index.getFieldIndex());

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

@@ -793,31 +793,15 @@ public void testHCSMetadata() throws IOException {
 
     ZarrGroup z = ZarrGroup.open(output);
 
-    // check valid group layout
-    // METADATA.ome.xml, .zattrs (Plate), .zgroup (Plate) and 2 rows
-    assertEquals(5, Files.list(output).toArray().length);
-    for (int row=0; row<2; row++) {
-      Path rowPath = output.resolve(Integer.toString(row));
-      // .zgroup (Row) and 3 columns
-      assertEquals(4, Files.list(rowPath).toArray().length);
-      for (int col=0; col<3; col++) {
-        Path colPath = rowPath.resolve(Integer.toString(col));
-        ZarrGroup colGroup = ZarrGroup.open(colPath);
-        // .zattrs (Column/Image), .zgroup (Column/Image) and 2 fields
-        assertEquals(4, Files.list(colPath).toArray().length);
-        for (int field=0; field<2; field++) {
-          // append resolution index
-          ZarrArray series0 = colGroup.openArray(field + "/0");
-          assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getShape());
-          assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getChunks());
-        }
-      }
-    }
+    int rowCount = 2;
+    int colCount = 3;
+    int fieldCount = 2;
+    checkPlateGroupLayout(output, rowCount, colCount, fieldCount, 512, 512);
 
     // check plate/well level metadata
     Map<String, Object> plate =
         (Map<String, Object>) z.getAttributes().get("plate");
-    assertEquals(2, ((Number) plate.get("field_count")).intValue());
+    assertEquals(fieldCount, ((Number) plate.get("field_count")).intValue());
 
     List<Map<String, Object>> acquisitions =
       (List<Map<String, Object>>) plate.get("acquisitions");
@@ -831,15 +815,8 @@ public void testHCSMetadata() throws IOException {
     assertEquals(1, acquisitions.size());
     assertEquals("0", acquisitions.get(0).get("id"));
 
-    assertEquals(2, rows.size());
-    for (int row=0; row<rows.size(); row++) {
-      assertEquals(String.valueOf(row), rows.get(row).get("name"));
-    }
-
-    assertEquals(3, columns.size());
-    for (int col=0; col<columns.size(); col++) {
-      assertEquals(String.valueOf(col), columns.get(col).get("name"));
-    }
+    checkDimension(rows, rowCount);
+    checkDimension(columns, colCount);
 
     assertEquals(rows.size() * columns.size(), wells.size());
     for (int row=0; row<rows.size(); row++) {
@@ -856,21 +833,155 @@ public void testHCSMetadata() throws IOException {
         String columnName = (String) column.get("name");
         ZarrGroup wellGroup = ZarrGroup.open(
             output.resolve(rowName).resolve(columnName));
-        Map<String, Object> well =
-            (Map<String, Object>) wellGroup.getAttributes().get("well");
-        List<Map<String, Object>> images =
-            (List<Map<String, Object>>) well.get("images");
-        assertEquals(2, images.size());
-        Map<String, Object> field1 = images.get(0);  // Field 1
-        assertEquals(field1.get("path"), "0");
-        assertEquals(0, field1.get("acquisition"));
-        Map<String, Object> field2 = images.get(1);  // Field 2
-        assertEquals(field2.get("path"), "1");
-        assertEquals(0, field2.get("acquisition"));
+        checkWell(wellGroup, fieldCount);
       }
     }
   }
 
+  /**
+   * 96 well plate with only well E6.
+   */
+  @Test
+  public void testSingleWell() throws IOException {
+    input = getTestFile("E6-only.ome.xml");
+    assertTool();
+
+    ZarrGroup z = ZarrGroup.open(output);
+
+    int rowCount = 8;
+    int colCount = 12;
+    int fieldCount = 1;
+
+    // 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>> acquisitions =
+      (List<Map<String, Object>>) plate.get("acquisitions");
+    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");
+
+    assertEquals(1, acquisitions.size());
+    assertEquals("0", acquisitions.get(0).get("id"));
+
+    checkDimension(rows, rowCount);
+    checkDimension(columns, colCount);
+
+    assertEquals(1, wells.size());
+    Map<String, Object> well = wells.get(0);
+    String wellPath = (String) well.get("path");
+    assertEquals("4/5", wellPath);
+    assertEquals(4, ((Number) well.get("row_index")).intValue());
+    assertEquals(5, ((Number) well.get("column_index")).intValue());
+
+    // check well metadata
+    ZarrGroup wellGroup = ZarrGroup.open(output.resolve(wellPath));
+    checkWell(wellGroup, fieldCount);
+  }
+
+  /**
+   * 96 well plate with only wells C4 and H2.
+   */
+  @Test
+  public void testTwoWells() throws IOException {
+    input = getTestFile("C4-H2-only.ome.xml");
+    assertTool();
+
+    ZarrGroup z = ZarrGroup.open(output);
+
+    int rowCount = 8;
+    int colCount = 12;
+    int fieldCount = 1;
+
+    // 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>> acquisitions =
+      (List<Map<String, Object>>) plate.get("acquisitions");
+    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");
+
+    assertEquals(1, acquisitions.size());
+    assertEquals("0", acquisitions.get(0).get("id"));
+
+    checkDimension(rows, rowCount);
+    checkDimension(columns, colCount);
+
+    assertEquals(2, wells.size());
+    Map<String, Object> well = wells.get(0);
+    String wellPath = (String) well.get("path");
+    assertEquals("2/3", wellPath);
+    assertEquals(2, ((Number) well.get("row_index")).intValue());
+    assertEquals(3, ((Number) well.get("column_index")).intValue());
+    ZarrGroup wellGroup = ZarrGroup.open(output.resolve(wellPath));
+    checkWell(wellGroup, fieldCount);
+
+    well = wells.get(1);
+    wellPath = (String) well.get("path");
+    assertEquals("7/1", wellPath);
+    assertEquals(7, ((Number) well.get("row_index")).intValue());
+    assertEquals(1, ((Number) well.get("column_index")).intValue());
+    wellGroup = ZarrGroup.open(output.resolve(wellPath));
+    checkWell(wellGroup, fieldCount);
+  }
+
+  /**
+   * 96 well plate with all wells in row F.
+   */
+  @Test
+  public void testOnePlateRow() throws IOException {
+    input = getTestFile("row-F-only.ome.xml");
+    assertTool();
+
+    ZarrGroup z = ZarrGroup.open(output);
+
+    int rowCount = 8;
+    int colCount = 12;
+    int fieldCount = 1;
+
+    // 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>> acquisitions =
+      (List<Map<String, Object>>) plate.get("acquisitions");
+    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");
+
+    assertEquals(1, acquisitions.size());
+    assertEquals("0", acquisitions.get(0).get("id"));
+
+    checkDimension(rows, rowCount);
+    checkDimension(columns, colCount);
+
+    assertEquals(colCount, wells.size());
+    for (int col=0; col<wells.size(); col++) {
+      Map<String, Object> well = wells.get(col);
+      String wellPath = (String) well.get("path");
+      assertEquals("5/" + col, wellPath);
+      assertEquals(5, ((Number) well.get("row_index")).intValue());
+      assertEquals(col, ((Number) well.get("column_index")).intValue());
+      ZarrGroup wellGroup = ZarrGroup.open(output.resolve(wellPath));
+      checkWell(wellGroup, fieldCount);
+    }
+  }
+
   /**
    * Convert an RGB image.  Ensure that the Channels are correctly split.
    */
@@ -889,7 +1000,6 @@ public void testRGBChannelSeparator() throws Exception {
     assertEquals(3, pixels.sizeOfChannelList());
   }
 
-
   /**
    * Check that a root group and attributes are created and populated.
    */
@@ -914,4 +1024,65 @@ public void testNoRootGroupOption() throws Exception {
     assertTrue(!Files.exists(output.resolve(".zattrs")));
     assertTrue(!Files.exists(output.resolve(".zgroup")));
   }
+
+  private void checkPlateGroupLayout(Path root, int rowCount, int colCount,
+    int fieldCount, int x, int y)
+    throws IOException
+  {
+    // check valid group layout
+    // METADATA.ome.xml, .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));
+      // .zgroup (Row) and columns
+      assertEquals(colCount + 1, Files.list(rowPath).toArray().length);
+      for (int col=0; col<colCount; col++) {
+        Path colPath = rowPath.resolve(Integer.toString(col));
+        ZarrGroup colGroup = ZarrGroup.open(colPath);
+        // .zattrs (Column/Image), .zgroup (Column/Image) and fields
+        assertEquals(fieldCount + 2, Files.list(colPath).toArray().length);
+        for (int field=0; field<fieldCount; field++) {
+          // append resolution index
+          ZarrArray series0 = colGroup.openArray(field + "/0");
+          assertArrayEquals(new int[] {1, 1, 1, y, x}, series0.getShape());
+          assertArrayEquals(new int[] {1, 1, 1, y, x}, series0.getChunks());
+        }
+      }
+    }
+  }
+
+  private void checkDimension(List<Map<String, Object>> dims, int dimCount)
+    throws IOException
+  {
+    assertEquals(dimCount, dims.size());
+    for (int dim=0; dim<dims.size(); dim++) {
+      assertEquals(String.valueOf(dim), dims.get(dim).get("name"));
+    }
+  }
+
+  private void checkWell(ZarrGroup wellGroup, int fieldCount)
+    throws IOException
+  {
+    Map<String, Object> well =
+        (Map<String, Object>) wellGroup.getAttributes().get("well");
+    List<Map<String, Object>> images =
+        (List<Map<String, Object>>) well.get("images");
+    assertEquals(fieldCount, images.size());
+
+    for (int i=0; i<fieldCount; i++) {
+      Map<String, Object> field = images.get(i);
+      assertEquals(field.get("path"), String.valueOf(i));
+      assertEquals(0, field.get("acquisition"));
+    }
+  }
+
+  private Path getTestFile(String resourceName) throws IOException {
+    try {
+      return Paths.get(this.getClass().getResource(resourceName).toURI());
+    }
+    catch (Exception e) {
+      throw new IOException(e);
+    }
+  }
+
 }

src/test/resources/com/glencoesoftware/bioformats2raw/test/C4-H2-only.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" 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="3" ExternalDescription="External Description" ExternalIdentifier="External Identifier" ID="Well:0_0_0_0" Row="2" 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="1" ExternalDescription="External Description" ExternalIdentifier="External Identifier" ID="Well:0_0_1_0" Row="7" 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>
+<PlateAcquisition EndTime="2006-05-04T18:13:51" ID="PlateAcquisition:0" Name="PlateAcquisition Name 0" StartTime="2006-05-04T18:13:51">
+<Description>PlateAcquisition 0 of 1</Description>
+<WellSampleRef ID="WellSample:0_0_0_0_0_0"></WellSampleRef>
+<WellSampleRef ID="WellSample:0_0_1_0_0_0"></WellSampleRef></PlateAcquisition></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>

src/test/resources/com/glencoesoftware/bioformats2raw/test/E6-only.ome.xml

@@ -0,0 +1,16 @@
+<?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="5" ExternalDescription="External Description" ExternalIdentifier="External Identifier" ID="Well:0_0_0_0" Row="4" 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>
+<PlateAcquisition EndTime="2006-05-04T18:13:51" ID="PlateAcquisition:0" Name="PlateAcquisition Name 0" StartTime="2006-05-04T18:13:51">
+<Description>PlateAcquisition 0 of 1</Description>
+<WellSampleRef ID="WellSample:0_0_0_0_0_0"></WellSampleRef></PlateAcquisition></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></OME>