Add group path to series index mapping in root attributes

Fixes glencoesoftware#126.

The root level attributes (if they are written) will now contain
a "groups" dictionary that maps each group with multiscales metadata
to the corresponding Bio-Formats series index (== Image index in METADATA.ome.xml).

Author: melissalinkert

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

@@ -665,6 +665,32 @@ public void convert()
         scaleFormatString = "%s/%s/%d/%d";
       }
 
+      // fileset level metadata
+      if (!noRootGroup) {
+        final ZarrGroup root = ZarrGroup.create(getRootPath());
+        Map<String, Object> attributes = new HashMap<String, Object>();
+        attributes.put("bioformats2raw.layout", LAYOUT);
+
+        // record the path to each series (multiscales) and the corresponding
+        // series (OME-XML Image) index
+        // using the index as the key would mean that the index is stored
+        // as a string instead of an integer
+        Map<String, Integer> groupMap = new HashMap<String, Integer>();
+        for (Integer index : seriesList) {
+          String resolutionString = String.format(
+                  scaleFormatString, getScaleFormatStringArgs(index, 0));
+          String seriesString = "";
+          if (resolutionString.indexOf('/') >= 0) {
+            seriesString = resolutionString.substring(0,
+                resolutionString.lastIndexOf('/'));
+          }
+          groupMap.put(seriesString, index);
+        }
+        attributes.put("groups", groupMap);
+
+        root.writeAttributes(attributes);
+      }
+
       for (Integer index : seriesList) {
         try {
           write(index);
@@ -1215,14 +1241,6 @@ public void saveResolutions(int series)
         sizeX, tileWidth, sizeY, tileHeight, sizeZ, chunkDepth, imageCount
     );
 
-    // fileset level metadata
-    if (!noRootGroup) {
-      final ZarrGroup root = ZarrGroup.create(getRootPath());
-      Map<String, Object> attributes = new HashMap<String, Object>();
-      attributes.put("bioformats2raw.layout", LAYOUT);
-      root.writeAttributes(attributes);
-    }
-
     // series level metadata
     setSeriesLevelMetadata(series, resolutions);
 

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

@@ -210,6 +210,13 @@ public void testAdditionalScaleFormatStringArgs() throws Exception {
     series0.openArray("0");
     series0 = ZarrGroup.open(output.resolve("ghi/999/1").toString());
     series0.openArray("0");
+
+    ZarrGroup z = ZarrGroup.open(output.toString());
+    Map<String, Integer> groupMap =
+      (Map<String, Integer>) z.getAttributes().get("groups");
+    assertEquals(groupMap.size(), 2);
+    assertEquals(groupMap.get("abc/888/0"), 0);
+    assertEquals(groupMap.get("ghi/999/1"), 1);
   }
 
   /**
@@ -240,6 +247,12 @@ public void testDefaultLayoutIsSetAndIsNested() throws Exception {
     ZarrGroup z = ZarrGroup.open(output.toString());
     Integer layout = (Integer)
         z.getAttributes().get("bioformats2raw.layout");
+
+    Map<String, Integer> groupMap =
+      (Map<String, Integer>) z.getAttributes().get("groups");
+    assertEquals(groupMap.size(), 1);
+    assertEquals(groupMap.get("0"), 0);
+
     ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0");
 
     // no getter for DimensionSeparator in ZarrArray
@@ -428,6 +441,12 @@ public void testMultiSeries() throws Exception {
     assertTool();
     ZarrGroup z = ZarrGroup.open(output.toString());
 
+    Map<String, Integer> groupMap =
+      (Map<String, Integer>) z.getAttributes().get("groups");
+    assertEquals(groupMap.size(), 2);
+    assertEquals(groupMap.get("0"), 0);
+    assertEquals(groupMap.get("1"), 1);
+
     // Check series 0 dimensions and special pixels
     ZarrArray series0 = z.openArray("0/0");
     assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getShape());
@@ -461,6 +480,10 @@ public void testSingleBeginningSeries() throws Exception {
     input = fake("series", "2");
     assertTool("-s", "0");
     ZarrGroup z = ZarrGroup.open(output.toString());
+    Map<String, Integer> groupMap =
+      (Map<String, Integer>) z.getAttributes().get("groups");
+    assertEquals(groupMap.size(), 1);
+    assertEquals(groupMap.get("0"), 0);
 
     // Check series 0 dimensions and special pixels
     ZarrArray series0 = z.openArray("0/0");
@@ -488,6 +511,10 @@ public void testSingleEndSeries() throws Exception {
     input = fake("series", "2");
     assertTool("-s", "1");
     ZarrGroup z = ZarrGroup.open(output.toString());
+    Map<String, Integer> groupMap =
+      (Map<String, Integer>) z.getAttributes().get("groups");
+    assertEquals(groupMap.size(), 1);
+    assertEquals(groupMap.get("0"), 1);
 
     // Check series 1 dimensions and special pixels
     ZarrArray series0 = z.openArray("0/0");
@@ -515,6 +542,10 @@ public void testSingleMiddleSeries() throws Exception {
     input = fake("series", "3");
     assertTool("-s", "1");
     ZarrGroup z = ZarrGroup.open(output.toString());
+    Map<String, Integer> groupMap =
+      (Map<String, Integer>) z.getAttributes().get("groups");
+    assertEquals(groupMap.size(), 1);
+    assertEquals(groupMap.get("0"), 1);
 
     // Check series 1 dimensions and special pixels
     ZarrArray series0 = z.openArray("0/0");
@@ -911,6 +942,12 @@ public void testNoHCSOption() throws Exception {
     assertTool("--no-hcs");
 
     ZarrGroup z = ZarrGroup.open(output);
+    Map<String, Integer> groupMap =
+      (Map<String, Integer>) z.getAttributes().get("groups");
+    assertEquals(groupMap.size(), 12);
+    for (int i=0; i<12; i++) {
+      assertEquals(groupMap.get(String.valueOf(i)), i);
+    }
 
     // Check dimensions and block size
     ZarrArray series0 = z.openArray("0/0");
@@ -952,6 +989,20 @@ public void testHCSMetadata() throws Exception {
     int rowCount = 2;
     int colCount = 3;
     int fieldCount = 2;
+
+    Map<String, Integer> groupMap =
+      (Map<String, Integer>) z.getAttributes().get("groups");
+    assertEquals(groupMap.size(), 12);
+    int index = 0;
+    for (int r=0; r<rowCount; r++) {
+      for (int c=0; c<colCount; c++) {
+        for (int f=0; f<fieldCount; f++) {
+          String groupPath = (char) (r + 'A') + "/" + (c + 1) + "/" + f;
+          assertEquals(groupMap.get(groupPath), index++);
+        }
+      }
+    }
+
     Map<String, List<String>> plateMap = new HashMap<String, List<String>>();
     plateMap.put("A", Arrays.asList("1", "2", "3"));
     plateMap.put("B", Arrays.asList("1", "2", "3"));