Fix problems with missing groups/metadata and sparse plates

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

@@ -627,7 +627,7 @@ public void convert()
       }
 
       if (!noHCS) {
-        scaleFormatString = "%d/%d/%d/%d";
+        scaleFormatString = "%s/%s/%d/%d";
       }
 
       for (Integer index : seriesList) {
@@ -711,8 +711,8 @@ private Object[] getScaleFormatStringArgs(
     List<Object> args = new ArrayList<Object>();
     if (!noHCS) {
       HCSIndex index = hcsIndexes.get(series);
-      args.add(index.getWellRowIndex());
-      args.add(index.getWellColumnIndex());
+      args.add(index.getRowPath());
+      args.add(index.getColumnPath());
       args.add(index.getFieldIndex());
       args.add(resolution);
     }
@@ -1331,29 +1331,36 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
     List<Map<String, Object>> rows = new ArrayList<Map<String, Object>>();
 
     // try to set plate dimensions based upon Plate.Rows/Plate.Columns
-    // if not possible, use well data later on
-    try {
-      for (int r=0; r<meta.getPlateRows(plate).getValue(); r++) {
-        Map<String, Object> row = new HashMap<String, Object>();
-        String rowName = String.valueOf(r);
-        row.put("name", rowName);
-        rows.add(row);
-        root.createSubGroup(rowName);
+    // if not possible, use well data
+    PositiveInteger plateRows =  meta.getPlateRows(plate);
+    if (plateRows == null) {
+      plateRows = new PositiveInteger(1);
+      for (int wellIndex=0; wellIndex<meta.getWellCount(plate); wellIndex++) {
+        plateRows = new PositiveInteger(Math.max(
+            meta.getWellRow(plate, wellIndex).getNumberValue().intValue(),
+            plateRows.getNumberValue().intValue()));
       }
     }
-    catch (NullPointerException e) {
-      // expected when Plate.Rows not set
+    for (int r=0; r<plateRows.getValue(); r++) {
+      Map<String, Object> row = new HashMap<String, Object>();
+      String rowName = HCSIndex.getRowName(r);
+      row.put("name", rowName);
+      rows.add(row);
     }
-    try {
-      for (int c=0; c<meta.getPlateColumns(plate).getValue(); c++) {
-        Map<String, Object> column = new HashMap<String, Object>();
-        String columnName = String.valueOf(c);
-        column.put("name", columnName);
-        columns.add(column);
+    PositiveInteger plateColumns = meta.getPlateColumns(plate);
+    if (plateColumns == null) {
+      plateColumns = new PositiveInteger(1);
+      for (int wellIndex=0; wellIndex<meta.getWellCount(plate); wellIndex++) {
+        plateColumns = new PositiveInteger(Math.max(
+            meta.getWellColumn(plate, wellIndex).getNumberValue().intValue(),
+            plateColumns.getNumberValue().intValue()));
       }
     }
-    catch (NullPointerException e) {
-      // expected when Plate.Columns not set
+    for (int c=0; c<plateColumns.getValue(); c++) {
+      Map<String, Object> column = new HashMap<String, Object>();
+      String columnName = HCSIndex.getColumnName(c);
+      column.put("name", columnName);
+      columns.add(column);
     }
 
     List<Map<String, Object>> acquisitions =
@@ -1363,7 +1370,9 @@ 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;
@@ -1377,61 +1386,66 @@ 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() &&
               field.getWellColumnIndex() == index.getWellColumnIndex())
             {
               Map<String, Object> image = new HashMap<String, Object>();
-              int plateAcq = field.getPlateAcquisitionIndex();
-              image.put("acquisition", plateAcq);
+              Integer plateAcq = field.getPlateAcquisitionIndex();
+              if (plateAcq != null) {
+                image.put("acquisition", plateAcq);
+              }
               image.put("path", String.valueOf(field.getFieldIndex()));
               imageList.add(image);
             }
           }
 
           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
-          int column = index.getWellColumnIndex();
-          int row = index.getWellRowIndex();
+          String column = index.getColumnPath();
+          String row = index.getRowPath();
 
           int columnIndex = -1;
           for (int c=0; c<columns.size(); c++) {
-            if (columns.get(c).get("name").equals(String.valueOf(column))) {
+            if (columns.get(c).get("name").equals(column)) {
               columnIndex = c;
               break;
             }
           }
           if (columnIndex < 0) {
             Map<String, Object> colMap = new HashMap<String, Object>();
-            colMap.put("name", String.valueOf(column));
+            colMap.put("name", column);
             columnIndex = columns.size();
             columns.add(colMap);
           }
 
           int rowIndex = -1;
           for (int r=0; r<rows.size(); r++) {
-            if (rows.get(r).get("name").equals(String.valueOf(row))) {
+            if (rows.get(r).get("name").equals(row)) {
               rowIndex = r;
               break;
             }
           }
           if (rowIndex < 0) {
             Map<String, Object> rowMap = new HashMap<String, Object>();
-            rowMap.put("name", String.valueOf(row));
+            rowMap.put("name", row);
             rowIndex = rows.size();
             rows.add(rowMap);
           }
 
-          well.put("row_index", rowIndex);
-          well.put("column_index", columnIndex);
+          well.put("rowIndex", rowIndex);
+          well.put("columnIndex", columnIndex);
           wells.add(well);
         }
 

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

@@ -11,11 +11,11 @@
 
 public class HCSIndex {
 
-  private int plate = -1;
-  private int plateAcquisition = -1;
-  private int wellRow = -1;
-  private int wellColumn = -1;
-  private int field = -1;
+  private final int plate;
+  private final Integer plateAcquisition;
+  private final int wellRow;
+  private final int wellColumn;
+  private final int field;
 
   /**
    * Construct an HCSIndex object representing an Image/series,
@@ -25,6 +25,7 @@ public class HCSIndex {
    * @param series OME Image/Bio-Formats series index
    */
   public HCSIndex(IMetadata meta, int series) {
+    Integer thePlateAcquisition = null;
     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++) {
@@ -39,19 +40,22 @@ public HCSIndex(IMetadata meta, int series) {
               for (int s=0; s<meta.getWellSampleRefCount(p, pa); s++) {
                 String refID = meta.getPlateAcquisitionWellSampleRef(p, pa, s);
                 if (id.equals(refID)) {
-                  plateAcquisition = pa;
+                  thePlateAcquisition = pa;
                   break;
                 }
               }
-              if (plateAcquisition >= 0) {
+              if (thePlateAcquisition >= 0) {
                 break;
               }
             }
+            plateAcquisition = thePlateAcquisition;
             return;
           }
         }
       }
     }
+    throw new IllegalArgumentException(
+        "Series " + series + " not present in metadata!");
   }
 
   /**
@@ -62,46 +66,20 @@ public int getPlateIndex() {
   }
 
   /**
-   * Set plate index.
-   *
-   * @param plateIndex plate index
-   */
-  public void setPlateIndex(int plateIndex) {
-    this.plate = plateIndex;
-  }
-
-  /**
-   * @return plate acquisition index
+   * @return plate acquisition index or <code>null</code> if no related plate
+   * acquisition can be found
    */
-  public int getPlateAcquisitionIndex() {
+  public Integer getPlateAcquisitionIndex() {
     return plateAcquisition;
   }
 
-  /**
-   * Set plate acquisition index.
-   *
-   * @param plateAcquisitionIndex plate acquisition index
-   */
-  public void setPlateAcquisitionIndex(int plateAcquisitionIndex) {
-    this.plateAcquisition = plateAcquisitionIndex;
-  }
-
   /**
    * @return well row index
    */
   public int getWellRowIndex() {
     return wellRow;
   }
 
-  /**
-   * Set well row index.
-   *
-   * @param wellRowIndex well row index
-   */
-  public void setWellRowIndex(int wellRowIndex) {
-    this.wellRow = wellRowIndex;
-  }
-
   /**
    * @return well column index
    */
@@ -110,35 +88,31 @@ public int getWellColumnIndex() {
   }
 
   /**
-   * Set well column index.
-   *
-   * @param wellColumnIndex well column index
+   * @return field index
    */
-  public void setWellColumnIndex(int wellColumnIndex) {
-    this.wellColumn = wellColumnIndex;
+  public int getFieldIndex() {
+    return field;
   }
 
   /**
-   * @return field index
+   * @return row path relative to the plate group
    */
-  public int getFieldIndex() {
-    return field;
+  public String getRowPath() {
+    return getRowName(getWellRowIndex());
   }
 
   /**
-   * Set field (well sample) index.
-   *
-   * @param fieldIndex field index
+   * @return column path relative to the row group
    */
-  public void setFieldIndex(int fieldIndex) {
-    this.field = fieldIndex;
+  public String getColumnPath() {
+    return getColumnName(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
@@ -151,4 +125,33 @@ public String toString() {
       getFieldIndex());
   }
 
+  /**
+   * Get a row name for the specified 0-based row index.
+   * The name is a single upper-case letter starting with A
+   * if the row index is less than 26, and two upper-case letters
+   * starting with AA for indexes greater than or equal to 26.
+   *
+   * @param rowIndex row index
+   * @return row name
+   */
+  public static String getRowName(int rowIndex) {
+    String name = String.valueOf((char) ('A' + (rowIndex % 26)));
+    if (rowIndex >= 26) {
+      name = (char) ('A' + ((rowIndex / 26) - 1)) + name;
+    }
+    return name;
+  }
+
+  /**
+   * Get a column name for the specified 0-based column index.
+   * The name is a string representation of the corresponding
+   * 1-based index.
+   *
+   * @param colIndex column index
+   * @return column name
+   */
+  public static String getColumnName(int colIndex) {
+    return String.format("%d", colIndex + 1);
+  }
+
 }