Change construction of DType

DType is constructed by a typestring and a collection of filters. In
particular, it's not directly de-serialized anymore.

src/main/java/org/janelia/saalfeldlab/n5/zarr/DType.java

@@ -32,6 +32,7 @@
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.EnumMap;
 import java.util.List;
 
@@ -76,6 +77,7 @@ public class DType {
 		typestrs.put(DataType.FLOAT32, ">f4");
 		typestrs.put(DataType.FLOAT64, ">f8");
 		typestrs.put(DataType.STRING, "|O");
+		typestrs.put(DataType.OBJECT, "|O");
 	}
 
 	public static enum Primitive {
@@ -131,7 +133,7 @@ public static Primitive fromCode(final char code) {
 	/* the closest possible N5 DataType */
 	protected final DataType dataType;
 
-	public DType(final String typestr) {
+	public DType(final String typestr, final Collection<Filter> filters) {
 
 		this.typestr = typestr;
 
@@ -217,10 +219,8 @@ public DType(final String typestr) {
 		case OBJECT:
 			nBytes = 1;
 			nBits = 0;
-			dataBlockFactory = (blockSize, gridPosition, numElements) ->
-					new ZarrCompatibleStringDataBlock(blockSize, gridPosition, new String[0]);
-			byteBlockFactory = (blockSize, gridPosition, numElements) ->
-					new ByteArrayDataBlock(blockSize, gridPosition, new byte[numElements * nBytes]);
+			dataBlockFactory = null;
+			byteBlockFactory = null;
 			break;
 //		case BOOLEAN:
 //		case OTHER:     // not sure about this
@@ -343,8 +343,8 @@ protected final static DataType getDataType(
 			default:
 				return DataType.UINT8; // fallback
 			}
-		case OBJECT: // todo: this should also depend on filters!
-			return DataType.STRING;
+		case OBJECT:
+			return DataType.OBJECT;
 		default:
 			return DataType.UINT8; // fallback
 		}
@@ -433,27 +433,6 @@ private static interface ByteBlockFactory {
 		public ByteArrayDataBlock createByteBlock(final int[] blockSize, final long[] gridPosition, final int numElements);
 	}
 
-	static public class JsonAdapter implements JsonDeserializer<DType>, JsonSerializer<DType> {
-
-		@Override
-		public DType deserialize(
-				final JsonElement json,
-				final Type typeOfT,
-				final JsonDeserializationContext context) throws JsonParseException {
-
-			return new DType(json.getAsString());
-		}
-
-		@Override
-		public JsonElement serialize(
-				final DType src,
-				final Type typeOfSrc,
-				final JsonSerializationContext context) {
-
-			return new JsonPrimitive(src.toString());
-		}
-	}
-
 	public ByteOrder getOrder() {
 
 		return order;

src/main/java/org/janelia/saalfeldlab/n5/zarr/N5ZarrReader.java

@@ -80,7 +80,6 @@ public N5ZarrReader(final String basePath,
 				new FileSystemKeyValueAccess(FileSystems.getDefault()),
 				basePath,
 				gsonBuilder
-					.registerTypeAdapter(DType.class, new DType.JsonAdapter())
 					.registerTypeAdapter(ZarrCompressor.class, ZarrCompressor.jsonAdapter),
 				mapN5DatasetAttributes,
 				mergeAttributes,

src/main/java/org/janelia/saalfeldlab/n5/zarr/ZArrayAttributes.java

@@ -215,16 +215,20 @@ public ZArrayAttributes deserialize(JsonElement json, Type typeOfT, JsonDeserial
 			final JsonObject obj = json.getAsJsonObject();
 			final JsonElement sepElem = obj.get("dimension_separator");
 			try {
+				final Collection<Filter> filters = context.deserialize(obj.get("filters"), TypeToken.getParameterized(Collection.class, Filter.class).getType());
+				final String typestr = context.deserialize(obj.get("dtype"), String.class);
+				final DType dType = new DType(typestr, filters);
+
 				return new ZArrayAttributes(
 						obj.get("zarr_format").getAsInt(),
 						context.deserialize( obj.get("shape"), long[].class),
 						context.deserialize( obj.get("chunks"), int[].class),
-						context.deserialize( obj.get("dtype"), DType.class), // fix
+						dType, // fix
 						context.deserialize( obj.get("compressor"), ZarrCompressor.class), // fix
 						obj.get("fill_value").getAsString(),
 						obj.get("order").getAsCharacter(),
 						sepElem != null ? sepElem.getAsString() : ".",
-						context.deserialize( obj.get("filters"), TypeToken.getParameterized(Collection.class, Filter.class).getType()));
+						filters);
 			} catch (Exception e) {
 				return null;
 			}

src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueReader.java

@@ -836,7 +836,6 @@ static Gson registerGson(final GsonBuilder gsonBuilder) {
 
 	protected static GsonBuilder addTypeAdapters(final GsonBuilder gsonBuilder) {
 
-		gsonBuilder.registerTypeAdapter(DType.class, new DType.JsonAdapter());
 		gsonBuilder.registerTypeAdapter(DataType.class, new DataType.JsonAdapter());
 		gsonBuilder.registerTypeAdapter(ZarrCompressor.class, ZarrCompressor.jsonAdapter);
 		gsonBuilder.registerTypeHierarchyAdapter(Compression.class, CompressionAdapter.getJsonAdapter());

src/test/java/org/janelia/saalfeldlab/n5/zarr/N5ZarrTest.java

@@ -46,6 +46,7 @@
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -800,7 +801,9 @@ public void testAttributeMapping() throws IOException {
 			int[] blkN5 = n5.getAttribute(datasetName, DatasetAttributes.BLOCK_SIZE_KEY, int[].class);
 			assertArrayEquals(blkZarr, blkN5);
 
-			DType dtype = n5.getAttribute(datasetName, ZArrayAttributes.dTypeKey, DType.class);
+			String typestr = n5.getAttribute(datasetName, ZArrayAttributes.dTypeKey, String.class);
+			Collection<Filter> filters = n5.getAttribute(datasetName, ZArrayAttributes.filtersKey, TypeToken.getParameterized(Collection.class, Filter.class).getType());
+			DType dtype = new DType(typestr, filters);
 			// read to a string because zarr may not have the N5 DataType deserializer
 			DataType n5DataType = DataType.fromString(n5.getAttribute(datasetName, DatasetAttributes.DATA_TYPE_KEY, String.class));
 			assertEquals(dtype.getDataType(), n5DataType);
@@ -828,7 +831,9 @@ public void testAttributeMapping() throws IOException {
 
 			n5.setAttribute(datasetName, DatasetAttributes.DATA_TYPE_KEY, newDtype.toString());
 
-			dtype = n5.getAttribute(datasetName, ZArrayAttributes.dTypeKey, DType.class);
+			typestr = n5.getAttribute(datasetName, ZArrayAttributes.dTypeKey, String.class);
+			filters = n5.getAttribute(datasetName, ZArrayAttributes.filtersKey, TypeToken.getParameterized(Collection.class, Filter.class).getType());
+			dtype = new DType(typestr, filters);
 			n5DataType = DataType.fromString(n5.getAttribute(datasetName, DatasetAttributes.DATA_TYPE_KEY, String.class));
 			assertEquals(newDtype, dtype.getDataType());
 			assertEquals(newDtype, n5DataType);