Multiscale metadata

By listing pyramids in the group attributes which contain
the pyramids, clients can lookup the number of resolutions
without needing to know beforehand or perform a directory
listing.

see: zarr-developers/zarr-specs#50

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

@@ -13,7 +13,10 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.concurrent.ArrayBlockingQueue;
 import java.util.concurrent.BlockingQueue;
 import java.util.concurrent.Callable;
@@ -848,10 +851,14 @@ public void saveResolutions(int series)
     Compression compression = N5Compression.getCompressor(compressionType,
             compressionParameter);
 
+    // fileset level metadata
     final String pyramidPath = outputPath.resolve(pyramidName).toString();
     final N5Writer n5 = fileType.writer(pyramidPath);
     n5.setAttribute("/", "bioformats2raw.layout", LAYOUT);
 
+    // series level metadata
+    setSeriesLevelMetadata(series, resolutions, n5);
+
     for (int resCounter=0; resCounter<resolutions; resCounter++) {
       final int resolution = resCounter;
       int scale = (int) Math.pow(PYRAMID_SCALE, resolution);
@@ -870,6 +877,9 @@ public void saveResolutions(int series)
         activeTileHeight = scaledHeight;
       }
 
+      String resolutionString = "/" +  String.format(
+              scaleFormatString, getScaleFormatStringArgs(series, resolution));
+
       n5.createDataset(
           "/" +  String.format(
               scaleFormatString, getScaleFormatStringArgs(series, resolution)),
@@ -928,6 +938,37 @@ scaleFormatString, getScaleFormatStringArgs(series, resolution)),
 
   }
 
+  /**
+   * Use {@link N5Writer#setAttribute(String, String, Object)} to attach the multiscales
+   * metadata to the group containing the pyramids.
+   *
+   * @param series
+   * @param resolutions
+   * @param n5
+   * @throws IOException
+   */
+  private void setSeriesLevelMetadata(int series, int resolutions, N5Writer n5) throws IOException {
+    String resolutionString = "/" +  String.format(
+            scaleFormatString, getScaleFormatStringArgs(series, 0));
+    String seriesString = resolutionString.substring(0,
+            resolutionString.lastIndexOf('/'));
+    List<Map<String, Object>> multiscales =
+            new ArrayList<Map<String, Object>>();
+    Map<String, Object> multiscale = new HashMap<String, Object>();
+    multiscale.put("version", "0.1");
+    multiscales.add(multiscale);
+    List<Map<String, String>> datasets = new ArrayList<Map<String, String>>();
+    for (int r = 0; r < resolutions; r++) {
+      resolutionString = "/" +  String.format(
+              scaleFormatString, getScaleFormatStringArgs(series, r));
+      String lastPath = resolutionString.substring(resolutionString.lastIndexOf('/'+1));
+      datasets.add(Collections.singletonMap("path", lastPath));
+    }
+    multiscale.put("datasets", datasets);
+    n5.createGroup(seriesString);
+    n5.setAttribute(seriesString, "multiscales", multiscales);
+  }
+
   /**
    * Takes exception from asynchronous execution and re-throw known exception
    * types. If the end is reached with no known exception detected, either the

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

@@ -191,6 +191,27 @@ public void testDefaultLayoutIsSet() throws Exception {
     Assert.assertEquals(Converter.LAYOUT, layout);
   }
 
+  /**
+   * Test that multiscales metadata is present.
+   */
+  @Test
+  public void testMultiscalesMetadata() throws Exception {
+    input = fake();
+    assertTool();
+    N5ZarrReader z =
+            new N5ZarrReader(output.resolve("data.zarr").toString());
+    //
+    List<Map<String, Object>> multiscales =
+            z.getAttribute("/0", "multiscales", List.class);
+    Assert.assertEquals(1, multiscales.size());
+    Map<String, Object> multiscale = multiscales.get(0);
+    Assert.assertEquals("0.1", multiscale.get("version"));
+    List<Map<String, Object>> datasets =
+            (List<Map<String, Object>>) multiscale.get("datasets");
+    Assert.assertTrue(datasets.size() > 0);
+    Assert.assertEquals("0", datasets.get(0).get("path"));
+  }
+
   /**
    * Test alternative dimension order.
    */