Support for Zarr v3 (resp NGFF 0.5)

build.gradle

@@ -8,8 +8,16 @@ plugins {
 group = 'com.glencoesoftware.omero'
 version = '0.6.0-SNAPSHOT'
 
-sourceCompatibility = 1.11
-targetCompatibility = 1.11
+// Java 11 compatibility configuration
+java {
+    sourceCompatibility = JavaVersion.VERSION_11
+    targetCompatibility = JavaVersion.VERSION_11
+}
+
+// Ensure UTF-8 encoding for compilation
+tasks.withType(JavaCompile) {
+    options.encoding = 'UTF-8'
+}
 
 repositories {
     mavenCentral()
@@ -31,14 +39,47 @@ repositories {
     }
 }
 
+configurations.all {
+    resolutionStrategy {
+        // Force all Jackson dependencies to version 2.14.2
+        eachDependency { DependencyResolveDetails details ->
+            if (details.requested.group == 'com.fasterxml.jackson.core' ||
+                details.requested.group == 'com.fasterxml.jackson.dataformat' ||
+                details.requested.group == 'com.fasterxml.jackson.datatype' ||
+                details.requested.group == 'com.fasterxml.jackson.module' ||
+                details.requested.group == 'com.fasterxml.jackson.jr') {
+                details.useVersion '2.14.2'
+            }
+        }
+
+        // Explicit force for common Jackson modules
+        force 'com.fasterxml.jackson.core:jackson-core:2.14.2'
+        force 'com.fasterxml.jackson.core:jackson-databind:2.14.2'
+        force 'com.fasterxml.jackson.core:jackson-annotations:2.14.2'
+    }
+}
+
 dependencies {
     api 'org.openmicroscopy:omero-blitz:5.8.3'
+
     implementation 'com.github.ben-manes.caffeine:caffeine:3.1.8'
     implementation 'dev.zarr:jzarr:0.4.2'
     implementation 'org.lasersonlab:s3fs:2.2.3'
     implementation 'com.amazonaws:aws-java-sdk-s3:1.12.659'
     implementation 'org.apache.tika:tika-core:1.28.5'
+    implementation 'net.java.dev.jna:jna:5.10.0'
+    implementation 'ome:formats-gpl:7.3.1'
+    implementation 'info.picocli:picocli:4.7.5'
+    implementation 'com.univocity:univocity-parsers:2.8.4'
+    implementation 'dev.zarr:zarr-java:0.0.4'
+    implementation 'javax.xml.bind:jaxb-api:2.3.0'
+    implementation group: 'ch.qos.logback', name: 'logback-classic', version: '1.3.14'
+    implementation group: 'ch.qos.logback', name: 'logback-core', version: '1.3.14'
+    implementation 'org.apache.maven:maven-artifact:3.9.4'
 
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.14.2'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.14.2'
+
     testImplementation 'info.picocli:picocli:4.7.5'
     testImplementation 'com.glencoesoftware:bioformats2raw:0.11.0'
 }

src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java

@@ -18,16 +18,15 @@
 
 package com.glencoesoftware.omero.zarr;
 
-import com.bc.zarr.DataType;
-import com.bc.zarr.ZarrArray;
 import com.github.benmanes.caffeine.cache.AsyncLoadingCache;
 import com.github.benmanes.caffeine.cache.Caffeine;
+import com.glencoesoftware.omero.zarr.compat.ZArray;
+import com.glencoesoftware.omero.zarr.compat.ZarrPath;
 import java.awt.Dimension;
 import java.io.IOException;
 import java.nio.BufferOverflowException;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
-import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -56,7 +55,7 @@ public class ZarrPixelBuffer implements PixelBuffer {
     private final Pixels pixels;
 
     /** Root of the OME-NGFF multiscale we are operating on. */
-    private final Path root;
+    private final ZarrPath root;
 
     /** Requested resolution level. */
     private int resolutionLevel;
@@ -74,7 +73,7 @@ public class ZarrPixelBuffer implements PixelBuffer {
     private final Map<String, Object> rootGroupAttributes;
 
     /** Zarr array corresponding to the current resolution level. */
-    private ZarrArray array;
+    private ZArray array;
 
     /**
      * Mapping of Z plane indexes in full resolution to
@@ -90,10 +89,10 @@ public class ZarrPixelBuffer implements PixelBuffer {
 
     /** Root path vs. metadata cache. */
     private final
-        AsyncLoadingCache<Path, Map<String, Object>> zarrMetadataCache;
+        AsyncLoadingCache<ZarrPath, Map<String, Object>> zarrMetadataCache;
 
-    /** Array path vs. ZarrArray cache. */
-    private final AsyncLoadingCache<Path, ZarrArray> zarrArrayCache;
+    /** Array path vs. ZArray cache */
+    private final AsyncLoadingCache<ZarrPath, ZArray> zarrArrayCache;
 
     /** Supported axes, X and Y are essential. */
     public enum Axis {
@@ -109,10 +108,10 @@ public enum Axis {
      * @param pixels Pixels metadata for the pixel buffer
      * @param root The root of this buffer
      */
-    public ZarrPixelBuffer(Pixels pixels, Path root, Integer maxPlaneWidth,
+    public ZarrPixelBuffer(Pixels pixels, ZarrPath root, Integer maxPlaneWidth,
             Integer maxPlaneHeight,
-            AsyncLoadingCache<Path, Map<String, Object>> zarrMetadataCache,
-            AsyncLoadingCache<Path, ZarrArray> zarrArrayCache)
+            AsyncLoadingCache<ZarrPath, Map<String, Object>> zarrMetadataCache,
+            AsyncLoadingCache<ZarrPath, ZArray> zarrArrayCache)
             throws IOException {
         log.info("Creating ZarrPixelBuffer");
         this.pixels = pixels;
@@ -121,7 +120,13 @@ public ZarrPixelBuffer(Pixels pixels, Path root, Integer maxPlaneWidth,
         this.zarrArrayCache = zarrArrayCache;
         this.isRemote = root.toString().startsWith("s3://") ? true : false;
         try {
-            rootGroupAttributes = this.zarrMetadataCache.get(this.root).get();
+            Map<String, Object> tmp = this.zarrMetadataCache.get(this.root).get();
+            if (tmp.containsKey("ome")) { 
+                // for ngff challenge data attr are often nested within "ome" key
+                rootGroupAttributes = (Map<String, Object>) tmp.get("ome");
+            } else {
+                rootGroupAttributes = tmp;
+            }
         } catch (ExecutionException | InterruptedException e) {
             throw new IOException(e);
         }
@@ -158,36 +163,6 @@ public ZarrPixelBuffer(Pixels pixels, Path root, Integer maxPlaneWidth,
                 });
     }
 
-    /**
-     * Get Bio-Formats/OMERO pixels type for buffer.
-     *
-     * @return See above.
-     */
-    public int getPixelsType() {
-        DataType dataType = array.getDataType();
-        switch (dataType) {
-            case u1:
-                return FormatTools.UINT8;
-            case i1:
-                return FormatTools.INT8;
-            case u2:
-                return FormatTools.UINT16;
-            case i2:
-                return FormatTools.INT16;
-            case u4:
-                return FormatTools.UINT32;
-            case i4:
-                return FormatTools.INT32;
-            case f4:
-                return FormatTools.FLOAT;
-            case f8:
-                return FormatTools.DOUBLE;
-            default:
-                throw new IllegalArgumentException(
-                        "Data type " + dataType + " not supported");
-        }
-    }
-
     /**
      * Calculates the pixel length of a given NumPy like "shape".
      *
@@ -223,43 +198,43 @@ private void read(byte[] buffer, int[] shape, int[] offset)
         }
         try {
             ByteBuffer asByteBuffer = ByteBuffer.wrap(buffer);
-            DataType dataType = array.getDataType();
+            int dataType = array.getPixelsType();
             for (int z = 0; z < planes; z++) {
                 if (axesOrder.containsKey(Axis.Z)) {
                     offset[axesOrder.get(Axis.Z)] = zIndexMap.get(originalZIndex + z);
                 }
                 switch (dataType) {
-                    case u1:
-                    case i1:
+                    case FormatTools.UINT8:
+                    case FormatTools.INT8:
                         array.read(buffer, shape, offset);
                         break;
-                    case u2:
-                    case i2:
+                    case FormatTools.UINT16:
+                    case FormatTools.INT16:
                     {
                         short[] data = (short[]) array.read(shape, offset);
                         asByteBuffer.asShortBuffer().put(data);
                         break;
                     }
-                    case u4:
-                    case i4:
+                    case FormatTools.UINT32:
+                    case FormatTools.INT32:
                     {
                         int[] data = (int[]) array.read(shape, offset);
                         asByteBuffer.asIntBuffer().put(data);
                         break;
                     }
-                    case i8:
-                    {
-                        long[] data = (long[]) array.read(shape, offset);
-                        asByteBuffer.asLongBuffer().put(data);
-                        break;
-                    }
-                    case f4:
+                    // case FormatTools.INT64:
+                    // {
+                    //     long[] data = (long[]) array.read(shape, offset);
+                    //     asByteBuffer.asLongBuffer().put(data);
+                    //     break;
+                    // }
+                    case FormatTools.FLOAT:
                     {
                         float[] data = (float[]) array.read(shape, offset);
                         asByteBuffer.asFloatBuffer().put(data);
                         break;
                     }
-                    case f8:
+                    case FormatTools.DOUBLE:
                     {
                         double[] data = (double[]) array.read(shape, offset);
                         asByteBuffer.asDoubleBuffer().put(data);
@@ -284,7 +259,7 @@ private PixelData toPixelData(byte[] buffer) {
             return null;
         }
         PixelData d = new PixelData(
-                FormatTools.getPixelTypeString(getPixelsType()),
+                FormatTools.getPixelTypeString(array.getPixelsType()),
                 ByteBuffer.wrap(buffer));
         d.setOrder(ByteOrder.BIG_ENDIAN);
         return d;
@@ -300,8 +275,8 @@ public int[][] getChunks() throws IOException {
         List<Map<String, String>> datasets = getDatasets();
         List<int[]> chunks = new ArrayList<int[]>();
         for (Map<String, String> dataset : datasets) {
-            ZarrArray resolutionArray = ZarrArray.open(
-                    root.resolve(dataset.get("path")));
+            ZarrPath dsPath = root.resolve(dataset.get("path"));
+            ZArray resolutionArray = dsPath.getArray();
             int[] shape = resolutionArray.getChunks();
             chunks.add(shape);
         }
@@ -843,17 +818,17 @@ public byte[] calculateMessageDigest() throws IOException {
 
     @Override
     public int getByteWidth() {
-        return FormatTools.getBytesPerPixel(getPixelsType());
+        return FormatTools.getBytesPerPixel(array.getPixelsType());
     }
 
     @Override
     public boolean isSigned() {
-        return FormatTools.isSigned(getPixelsType());
+        return FormatTools.isSigned(array.getPixelsType());
     }
 
     @Override
     public boolean isFloat() {
-        return FormatTools.isFloatingPoint(getPixelsType());
+        return FormatTools.isFloatingPoint(array.getPixelsType());
     }
 
     @Override
@@ -925,6 +900,10 @@ public int getResolutionLevel() {
                 resolutionLevel - (resolutionLevels - 1));
     }
 
+    public int getPixelsType() {
+        return array.getPixelsType();
+    }
+
     @Override
     public void setResolutionLevel(int resolutionLevel) {
         if (resolutionLevel >= resolutionLevels) {
@@ -945,10 +924,9 @@ public void setResolutionLevel(int resolutionLevel) {
             zIndexMap.clear();
         }
         try {
-            array = zarrArrayCache.get(
-                    root.resolve(Integer.toString(this.resolutionLevel))).get();
-
-            ZarrArray fullResolutionArray = zarrArrayCache.get(
+            ZarrPath p = root.resolve(Integer.toString(this.resolutionLevel));
+            array = zarrArrayCache.get(p).get(); 
+            ZArray fullResolutionArray = zarrArrayCache.get(
                     root.resolve("0")).get();
 
             if (axesOrder.containsKey(Axis.Z)) {