Ome zarr followup (#68)

* add unified getOmeroMetadata and getBioformats2rawLayout for all versions

* change type of consolidated_metadata to Object

* improve performance on Array.read (less allocation and memory overhead)

* fix test openSceneExample1AffinePathBetweenInstruments

Author: brokkoli71

src/main/java/dev/zarr/zarrjava/core/Array.java

@@ -396,6 +396,10 @@ public ucar.ma2.Array read(final long[] offset, final long[] shape, final boolea
 
         final ucar.ma2.Array outputArray = ucar.ma2.Array.factory(metadata.dataType().getMA2DataType(),
                 Utils.toIntArray(shape));
+        final Object parsedFillValue = metadata.parsedFillValue();
+        if (parsedFillValue != null) {
+            MultiArrayUtils.fill(outputArray, parsedFillValue);
+        }
         Stream<long[]> chunkStream = Arrays.stream(IndexingUtils.computeChunkCoords(metadata.shape, chunkShape, offset, shape));
         if (parallel) {
             chunkStream = chunkStream.parallel();
@@ -408,17 +412,13 @@ public ucar.ma2.Array read(final long[] offset, final long[] shape, final boolea
                                         shape
                                 );
 
-                        if (chunkIsInArray(chunkCoords)) {
-                            MultiArrayUtils.copyRegion(metadata.allocateFillValueChunk(),
-                                    chunkProjection.chunkOffset, outputArray, chunkProjection.outOffset,
-                                    chunkProjection.shape
-                            );
-                        }
-
                         final String[] chunkKeys = metadata.chunkKeyEncoding().encodeChunkKey(chunkCoords);
                         final StoreHandle chunkHandle = storeHandle.resolve(chunkKeys);
 
                         if (codecPipeline.supportsPartialDecode()) {
+                            if (!chunkHandle.exists()) {
+                                return;
+                            }
                             final ucar.ma2.Array chunkArray = codecPipeline.decodePartial(chunkHandle,
                                     Utils.toLongArray(chunkProjection.chunkOffset), chunkProjection.shape);
                             MultiArrayUtils.copyRegion(chunkArray, new int[metadata.ndim()], outputArray,

src/main/java/dev/zarr/zarrjava/experimental/ome/MultiscaleImage.java

@@ -3,9 +3,11 @@
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.core.Node;
 import dev.zarr.zarrjava.experimental.ome.metadata.MultiscalesEntry;
+import dev.zarr.zarrjava.experimental.ome.metadata.OmeroMetadata;
 import dev.zarr.zarrjava.store.StoreHandle;
 import dev.zarr.zarrjava.utils.Utils;
 
+import javax.annotation.Nullable;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -37,6 +39,18 @@ public interface MultiscaleImage {
      */
     int getScaleLevelCount() throws ZarrException;
 
+    /**
+     * Returns the OmeroMetadata if present, or null if not.
+     */
+    @Nullable
+    OmeroMetadata getOmeroMetadata();
+
+    /**
+     * Returns the bioformats2raw.layout property if present, or null if not
+     */
+    @Nullable
+    Integer getBioformats2rawLayout();
+
     /**
      * Returns the axis names of the first multiscale entry.
      */

src/main/java/dev/zarr/zarrjava/experimental/ome/v0_4/MultiscaleImage.java

@@ -30,7 +30,7 @@ public final class MultiscaleImage extends OmeV2Group implements MultiscalesMeta
     @Nullable
     private OmeroMetadata omeroMetadata;
     @Nullable
-    private Integer bioformats2rawLayout;
+    private final Integer bioformats2rawLayout;
 
     private MultiscaleImage(
             @Nonnull StoreHandle storeHandle,
@@ -83,6 +83,7 @@ public dev.zarr.zarrjava.store.StoreHandle getStoreHandle() {
         return this.storeHandle;
     }
 
+    @Override
     @Nullable
     public OmeroMetadata getOmeroMetadata() {
         return omeroMetadata;
@@ -93,6 +94,7 @@ public void setOmeroMetadata(@Nullable OmeroMetadata omeroMetadata) throws IOExc
         persistAttributes();
     }
 
+    @Override
     @Nullable
     public Integer getBioformats2rawLayout() {
         return bioformats2rawLayout;

src/main/java/dev/zarr/zarrjava/experimental/ome/v0_5/MultiscaleImage.java

@@ -13,6 +13,7 @@
 import dev.zarr.zarrjava.v3.GroupMetadata;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.io.IOException;
 import java.util.Collections;
 import java.util.List;
@@ -68,12 +69,14 @@ public MultiscalesEntry getMultiscalesEntry(int i) throws ZarrException {
         return omeMetadata.multiscales.get(i);
     }
 
-    @javax.annotation.Nullable
+    @Override
+    @Nullable
     public dev.zarr.zarrjava.experimental.ome.metadata.OmeroMetadata getOmeroMetadata() {
         return omeMetadata.omero;
     }
 
-    @javax.annotation.Nullable
+    @Override
+    @Nullable
     public Integer getBioformats2rawLayout() {
         return omeMetadata.bioformats2rawLayout;
     }

src/main/java/dev/zarr/zarrjava/experimental/ome/v0_6/MultiscaleImage.java

@@ -18,6 +18,7 @@
 import dev.zarr.zarrjava.v3.GroupMetadata;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -85,12 +86,14 @@ public MultiscalesEntry getMultiscalesEntry(int i) throws ZarrException {
         return omeMetadata.multiscales.get(i);
     }
 
-    @javax.annotation.Nullable
+    @Override
+    @Nullable
     public dev.zarr.zarrjava.experimental.ome.metadata.OmeroMetadata getOmeroMetadata() {
         return omeMetadata.omero;
     }
 
-    @javax.annotation.Nullable
+    @Override
+    @Nullable
     public Integer getBioformats2rawLayout() {
         return omeMetadata.bioformats2rawLayout;
     }

src/main/java/dev/zarr/zarrjava/v3/GroupMetadata.java

@@ -17,7 +17,7 @@ public final class GroupMetadata extends dev.zarr.zarrjava.core.GroupMetadata {
     @JsonProperty("node_type")
     public final String nodeType = "group";
     @JsonProperty("consolidated_metadata")
-    public final String consolidatedMetadata = null;
+    public final Object consolidatedMetadata = null;
 
     @Nullable
     public final Attributes attributes;

src/test/java/dev/zarr/zarrjava/experimental/ome/OmeZarrSceneV06Test.java

@@ -144,7 +144,7 @@ void createAndReopenScene() throws Exception {
     void openSceneExample1AffinePathBetweenInstruments() throws Exception {
         dev.zarr.zarrjava.experimental.ome.v0_6.Scene scene =
                 dev.zarr.zarrjava.experimental.ome.v0_6.Scene.openScene(new FilesystemStore(V06_SCENE_EXAMPLE1).resolve());
-        assertEquals(Arrays.asList("sampleA_instrument1", "sampleA_instrument2"), scene.listImageNodes());
+        assertEquals(new HashSet<>(Arrays.asList("sampleA_instrument1", "sampleA_instrument2")), new HashSet<>(scene.listImageNodes()));
         assertEquals(1, scene.getSceneMetadata().coordinateTransformations.size());
         dev.zarr.zarrjava.experimental.ome.v0_6.metadata.transform.CoordinateTransformation ct =
                 scene.getSceneMetadata().coordinateTransformations.get(0);