Store dimension order using new "axes" spec

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

@@ -1220,7 +1220,8 @@ public void saveResolutions(int series)
           .nested(nested)
           .compressor(CompressorFactory.create(
               compressionType.toString(), compressionProperties));
-      ZarrArray.create(getRootPath().resolve(resolutionString), arrayParams);
+      ZarrArray.create(getRootPath().resolve(resolutionString),
+        arrayParams, getArrayAttributes());
 
       nTile = new AtomicInteger(0);
       tileCount = (int) Math.ceil((double) scaledWidth / tileWidth)
@@ -1472,9 +1473,10 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
    * @param resolutions Total number of resolutions from which
    *                    names will be generated.
    * @throws IOException
+   * @throws InterruptedException
    */
   private void setSeriesLevelMetadata(int series, int resolutions)
-      throws IOException
+      throws IOException, InterruptedException
   {
     LOGGER.debug("setSeriesLevelMetadata({}, {})", series, resolutions);
     String resolutionString = String.format(
@@ -1514,6 +1516,37 @@ private void setSeriesLevelMetadata(int series, int resolutions)
       datasets.add(Collections.singletonMap("path", lastPath));
     }
     multiscale.put("datasets", datasets);
+
+    String axisOrder = null;
+    if (dimensionOrder != null) {
+      axisOrder = dimensionOrder.toString();
+    }
+    else {
+      IFormatReader reader = readers.take();
+      try {
+        axisOrder = reader.getDimensionOrder();
+      }
+      finally {
+        readers.put(reader);
+      }
+    }
+    List<Map<String, String>> axes = new ArrayList<Map<String, String>>();
+    for (int i=axisOrder.length()-1; i>=0; i--) {
+      String axis = axisOrder.substring(i, i + 1).toLowerCase();
+      String type = "space";
+      if (axis.equals("t")) {
+        type = "time";
+      }
+      else if (axis.equals("c")) {
+        type = "channel";
+      }
+      Map<String, String> thisAxis = new HashMap<String, String>();
+      thisAxis.put("name", axis);
+      thisAxis.put("type", type);
+      axes.add(thisAxis);
+    }
+    multiscale.put("axes", axes);
+
     Path subGroupPath = getRootPath().resolve(seriesString);
     LOGGER.debug("  creating subgroup {}", subGroupPath);
     ZarrGroup subGroup = ZarrGroup.create(subGroupPath);
@@ -1761,6 +1794,28 @@ private Class<?> getBaseReaderClass() throws FormatException, IOException {
     }
   }
 
+  private Map<String, Object> getArrayAttributes() throws InterruptedException {
+    Map<String, Object> attrs = new HashMap<String, Object>();
+    String order = null;
+    if (dimensionOrder != null) {
+      order = dimensionOrder.toString();
+    }
+    else {
+      IFormatReader reader = readers.take();
+      try {
+        order = reader.getDimensionOrder();
+      }
+      finally {
+        readers.put(reader);
+      }
+    }
+
+    String[] axes =
+      new StringBuilder(order.toLowerCase()).reverse().toString().split("");
+    attrs.put("_ARRAY_DIMENSIONS", axes);
+    return attrs;
+  }
+
   /**
    * Check if the given metadata object contains at least one plate
    * with at least one well that links to an image.

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

@@ -260,6 +260,10 @@ public void testMultiscalesMetadata() throws Exception {
             (List<Map<String, Object>>) multiscale.get("datasets");
     assertTrue(datasets.size() > 0);
     assertEquals("0", datasets.get(0).get("path"));
+
+    List<Map<String, Object>> axes =
+      (List<Map<String, Object>>) multiscale.get("axes");
+    checkAxes(axes, "TCZYX");
   }
 
   /**
@@ -284,6 +288,15 @@ public void testSetXYCZTDimensionOrder() throws Exception {
     ZarrGroup z = ZarrGroup.open(output.toString());
     ZarrArray array = z.openArray("0/0");
     assertArrayEquals(new int[] {1, 1, 2, 512, 512}, array.getShape());
+
+    z = ZarrGroup.open(output.resolve("0").toString());
+    List<Map<String, Object>> multiscales = (List<Map<String, Object>>)
+            z.getAttributes().get("multiscales");
+    assertEquals(1, multiscales.size());
+    Map<String, Object> multiscale = multiscales.get(0);
+    List<Map<String, Object>> axes =
+      (List<Map<String, Object>>) multiscale.get("axes");
+    checkAxes(axes, "TZCYX");
   }
 
   /**
@@ -296,6 +309,15 @@ public void testSetOriginalDimensionOrder() throws Exception {
     ZarrGroup z = ZarrGroup.open(output.toString());
     ZarrArray array = z.openArray("0/0");
     assertArrayEquals(new int[] {1, 1, 2, 512, 512}, array.getShape());
+
+    z = ZarrGroup.open(output.resolve("0").toString());
+    List<Map<String, Object>> multiscales = (List<Map<String, Object>>)
+            z.getAttributes().get("multiscales");
+    assertEquals(1, multiscales.size());
+    Map<String, Object> multiscale = multiscales.get(0);
+    List<Map<String, Object>> axes =
+      (List<Map<String, Object>>) multiscale.get("axes");
+    checkAxes(axes, "TZCYX");
   }
 
   /**
@@ -1413,6 +1435,15 @@ private void checkWell(ZarrGroup wellGroup, int fieldCount)
     }
   }
 
+  private void checkAxes(List<Map<String, Object>> axes, String order) {
+    assertEquals(axes.size(), order.length());
+    for (int i=0; i<axes.size(); i++) {
+      String name = axes.get(i).get("name").toString();
+      assertEquals(name, order.toLowerCase().substring(i, i + 1));
+      assertTrue(axes.get(i).containsKey("type"));
+    }
+  }
+
   private Path getTestFile(String resourceName) throws IOException {
     try {
       return Paths.get(this.getClass().getResource(resourceName).toURI());