Automatically use zip storage if the .ozx output file extension is used

README.md

@@ -227,6 +227,9 @@ specification but may be suitable for other applications.
 Specifies the version of the [OME-Zarr specification](https://ngff.openmicroscopy.org/specifications/index.html)
 that should be used while writing Zarr. Current supported values are 0.4 and 0.5.
 
+If `--ngff-version 0.5` is used, and the output file name ends with `.ozx`, then a single Zip file
+will be written in accordance with [RFC-9](https://ngff.openmicroscopy.org/rfc/9/index.html).
+
 #### --pyramid-name
 
 Specifies a subdirectory of the output directory where Zarr data should be written.

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

@@ -98,7 +98,9 @@
 import dev.zarr.zarrjava.core.Attributes;
 import dev.zarr.zarrjava.core.Group;
 import dev.zarr.zarrjava.core.chunkkeyencoding.Separator;
+import dev.zarr.zarrjava.store.BufferedZipStore;
 import dev.zarr.zarrjava.store.FilesystemStore;
+import dev.zarr.zarrjava.store.Store;
 import dev.zarr.zarrjava.store.StoreHandle;
 import dev.zarr.zarrjava.utils.IndexingUtils;
 import dev.zarr.zarrjava.utils.Utils;
@@ -120,6 +122,8 @@ public class Converter implements Callable<Integer> {
    */
   private static final String METADATA_FILE = "METADATA.ome.xml";
 
+  private static final String ZIP_EXTENSION = ".ozx";
+
   /**
    * Minimum size of the largest XY dimension in the smallest resolution,
    * when calculating the number of resolutions to generate.
@@ -175,7 +179,7 @@ public class Converter implements Callable<Integer> {
 
   private volatile SupportedVersions ngffVersion = SupportedVersions.NGFF_04;
   private volatile boolean v3 = false;
-  private volatile FilesystemStore store = null;
+  private volatile Store store = null;
 
   private volatile int maxWorkers;
   private volatile int maxCachedTiles;
@@ -1505,6 +1509,7 @@ public void convert()
              EnumerationException, ZarrException
   {
     checkOutputPaths();
+    initializeStore();
 
     Cache<TilePointer, byte[]> tileCache = CacheBuilder.newBuilder()
         .maximumSize(maxCachedTiles)
@@ -1634,13 +1639,9 @@ public void convert()
           }
           String xml = service.getOMEXML(meta);
 
-          // write the original OME-XML to a file
-          Path metadataPath = getRootPath().resolve("OME");
-          if (!Files.exists(metadataPath)) {
-            Files.createDirectories(metadataPath);
-          }
-          Path omexmlFile = metadataPath.resolve(METADATA_FILE);
-          Files.write(omexmlFile, xml.getBytes(Constants.ENCODING));
+          // write the original OME-XML to the store
+          store.set(new String[] {"OME", METADATA_FILE},
+            ByteBuffer.wrap(xml.getBytes(Constants.ENCODING)));
         }
       }
       catch (ServiceException se) {
@@ -1702,6 +1703,9 @@ public void convert()
           LOGGER.error("Exception while closing reader", e);
         }
       });
+      if (store != null && store instanceof BufferedZipStore) {
+        ((BufferedZipStore) store).close();
+      }
     }
 
     // delete the memo file if it was saved and it's not explicitly kept
@@ -1713,11 +1717,19 @@ public void convert()
     }
   }
 
-  private void writeZarrMetadata() throws IOException, ZarrException {
+  private void initializeStore() throws IOException, ZarrException {
     if (store == null) {
-      store = new FilesystemStore(getRootPath());
+      Path rootPath = getRootPath();
+      if (rootPath.toString().endsWith(ZIP_EXTENSION) && getV3()) {
+        store = new BufferedZipStore(rootPath, true);
+      }
+      else {
+        store = new FilesystemStore(rootPath);
+      }
     }
+  }
 
+  private void writeZarrMetadata() throws IOException, ZarrException {
     // fileset level metadata
     if (!noRootGroup) {
       Attributes attributes = new Attributes();

src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrV3Test.java

@@ -17,6 +17,7 @@
 
 import com.scalableminds.bloscjava.Blosc;
 import dev.zarr.zarrjava.core.Attributes;
+import dev.zarr.zarrjava.store.ReadOnlyZipStore;
 import dev.zarr.zarrjava.v3.Array;
 import dev.zarr.zarrjava.v3.ArrayMetadata;
 import dev.zarr.zarrjava.v3.DataType;
@@ -118,6 +119,69 @@ public void testDefault() throws Exception {
     }
   }
 
+ /**
+   * Test basic v3 .ozx conversion.
+   */
+  @Test
+  public void testDefaultZip() throws Exception {
+    input = fake();
+    output = output.resolve("zipstore.ozx");
+    assertTool("--ngff-version", getNGFFVersion());
+
+    assertFalse(Files.exists(output.resolve("zarr.json")));
+    assertFalse(
+      Files.exists(output.resolve("OME").resolve("METADATA.ome.xml")));
+    assertTrue(Files.exists(output));
+
+    ReadOnlyZipStore zipStore = new ReadOnlyZipStore(output);
+
+    Group rootGroup = Group.open(zipStore.resolve());
+    Attributes attrs = rootGroup.metadata().attributes;
+    Attributes omeAttrs = attrs.getAttributes("ome");
+    assertEquals(getNGFFVersion(), omeAttrs.get("version"));
+    assertEquals(3, omeAttrs.get("bioformats2raw.layout"));
+
+    Array array = Array.open(zipStore.resolve("0", "0"));
+    assertArrayEquals(new long[] {1, 1, 1, 512, 512}, array.metadata().shape);
+
+    rootGroup = Group.open(zipStore.resolve("0"));
+    attrs = rootGroup.metadata().attributes;
+    omeAttrs = attrs.getAttributes("ome");
+    assertEquals("0.5", omeAttrs.get("version"));
+
+    List<Map<String, Object>> multiscales =
+      (List<Map<String, Object>>) omeAttrs.get("multiscales");
+    assertEquals(1, multiscales.size());
+    Map<String, Object> multiscale = multiscales.get(0);
+    checkMultiscale(multiscale, "image");
+
+    List<Map<String, Object>> datasets =
+      (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", null);
+
+    for (int r=0; r<datasets.size(); r++) {
+      Map<String, Object> dataset = datasets.get(r);
+      List<Map<String, Object>> transforms =
+        (List<Map<String, Object>>) dataset.get("coordinateTransformations");
+      assertEquals(1, transforms.size());
+      Map<String, Object> scale = transforms.get(0);
+      assertEquals("scale", scale.get("type"));
+      List<Double> axisValues = (List<Double>) scale.get("scale");
+
+      assertEquals(5, axisValues.size());
+      double factor = Math.pow(2, r);
+      // X and Y are the only dimensions that are downsampled,
+      // so the TCZ physical scales remain the same across all resolutions
+      assertEquals(axisValues, Arrays.asList(new Double[] {
+        1.0, 1.0, 1.0, factor, factor}));
+    }
+  }
+
   /**
    * Test HCS v3 conversion.
    */
@@ -231,8 +295,8 @@ public void testNoOMEOption() throws Exception {
     input = fake();
     assertTool("--no-ome-meta-export", "--ngff-version", getNGFFVersion());
 
-    assertTrue(
-      !Files.exists(output.resolve("OME").resolve("METADATA.ome.xml")));
+    assertFalse(
+      Files.exists(output.resolve("OME").resolve("METADATA.ome.xml")));
   }
 
   /**