Nested chunk storage

build.gradle

@@ -13,13 +13,17 @@ sourceCompatibility = 1.8
 targetCompatibility = 1.8
 
 repositories {
+    mavenLocal()
     jcenter()
     maven {
         url 'https://artifacts.glencoesoftware.com/artifactory/ome.releases'
     }
     maven {
         url 'https://repo.glencoesoftware.com/repository/n5-zarr-snapshots/'
     }
+    maven {
+        url 'https://repo.glencoesoftware.com/repository/jzarr-snapshots'
+    }
     maven {
         url 'https://maven.scijava.org/content/groups/public'
     }
@@ -37,7 +41,7 @@ dependencies {
     implementation 'ome:formats-gpl:6.5.1'
     implementation 'info.picocli:picocli:4.2.0'
     implementation 'com.univocity:univocity-parsers:2.8.4'
-    implementation 'com.bc.zarr:jzarr:0.3.2'
+    implementation 'com.bc.zarr:jzarr:0.3.3-gs-SNAPSHOT'
 
     implementation 'org.openpnp:opencv:3.4.2-1'
     implementation 'me.tongfei:progressbar:0.9.0'

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

@@ -216,6 +216,13 @@ public class Converter implements Callable<Void> {
     PyramidTiffReader.class, MiraxReader.class
   };
 
+  @Option(
+          names = "--nested", negatable=true,
+          description = "Whether to use '/' as the chunk path seprator " +
+                  "(false by default)"
+  )
+  private volatile boolean nested = false;
+
   @Option(
           names = "--pyramid-name",
           description = "Name of pyramid (default: ${DEFAULT-VALUE}) " +
@@ -1025,6 +1032,7 @@ public void saveResolutions(int series)
               workingReader, scaledWidth, scaledHeight))
           .chunks(new int[] {1, 1, 1, activeTileHeight, activeTileWidth})
           .dataType(dataType)
+          .nested(nested)
           .compressor(CompressorFactory.create(
               compressionType.toString(), compressionProperties));
       root.createArray(resolutionString, arrayParams);

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

@@ -52,6 +52,7 @@
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.EnumSource;
 import org.junit.jupiter.params.provider.MethodSource;
+import org.junit.jupiter.params.provider.ValueSource;
 import org.opencv.core.Core;
 
 public class ZarrTest {
@@ -767,6 +768,18 @@ public void testDownsampleTypes(Downsampling type) throws IOException {
     }
   }
 
+  /**
+   * Test that nested storage works equivalently.
+   *
+   * @param nested whether to use "/" or "." as the chunk separator.
+   */
+  @ParameterizedTest
+  @ValueSource(booleans = {true, false})
+  public void testNestedStorage(boolean nested) throws IOException {
+    input = fake();
+    assertTool(nested ? "--nested" : "--no-nested");
+  }
+
   /**
    * Convert a plate with the --no-hcs option.
    * The output should not be compliant with OME Zarr HCS.