N5ZarrTest.java

/*-
 * #%L
 * Not HDF5
 * %%
 * Copyright (C) 2019 - 2022 Stephan Saalfeld
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 * #L%
 */
package org.janelia.saalfeldlab.n5.zarr;

import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertThrows;
import static org.junit.Assert.assertTrue;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Reader;
import java.net.URISyntaxException;
import java.nio.file.FileSystems;
import java.nio.file.Files;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;

import org.janelia.saalfeldlab.n5.AbstractN5Test;
import org.janelia.saalfeldlab.n5.Bzip2Compression;
import org.janelia.saalfeldlab.n5.Compression;
import org.janelia.saalfeldlab.n5.DataBlock;
import org.janelia.saalfeldlab.n5.DataType;
import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess;
import org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer;
import org.janelia.saalfeldlab.n5.GzipCompression;
import org.janelia.saalfeldlab.n5.KeyValueAccess;
import org.janelia.saalfeldlab.n5.LockedChannel;
import org.janelia.saalfeldlab.n5.N5Exception;
import org.janelia.saalfeldlab.n5.N5Exception.N5ClassCastException;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.N5Reader.Version;
import org.janelia.saalfeldlab.n5.N5Writer;
import org.janelia.saalfeldlab.n5.RawCompression;
import org.janelia.saalfeldlab.n5.StringDataBlock;
import org.janelia.saalfeldlab.n5.blosc.BloscCompression;
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.scicomp.n5.zstandard.ZstandardCompression;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;

import com.google.gson.GsonBuilder;
import com.google.gson.JsonElement;
import com.google.gson.JsonNull;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
import com.google.gson.reflect.TypeToken;

import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.type.numeric.IntegerType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.LongType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.integer.UnsignedIntType;
import net.imglib2.type.numeric.integer.UnsignedLongType;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.view.Views;

/**
 * @author Stephan Saalfeld <saalfelds@janelia.hhmi.org>
 */
public class N5ZarrTest extends AbstractN5Test {

	static private final String testZarrDatasetName = "test/data";

	public static KeyValueAccess createKeyValueAccess() {
		return new FileSystemKeyValueAccess(FileSystems.getDefault());
	}

	@Override
	protected String tempN5Location() {

		try {
			return Files.createTempDirectory("n5-zarr-test").toUri().getPath();
		} catch (final IOException e) {
			throw new RuntimeException(e);
		}
	}

	@Override
	protected N5Writer createN5Writer()  {

		final String testDirPath = tempN5Location();
		return new ZarrKeyValueWriter(createKeyValueAccess(), testDirPath, new GsonBuilder(), true, true, ".",false);
	}

	@Override
	protected N5Writer createN5Writer(final String location, final GsonBuilder gsonBuilder) throws IOException {

		return createTempN5Writer(location, gsonBuilder, ".", true);
	}

	protected N5Writer createTempN5Writer(final String location, final String dimensionSeparator) throws IOException {

		return createTempN5Writer(location, new GsonBuilder(), dimensionSeparator, true);
	}


	protected N5Writer createTempN5Writer(final String location, final String dimensionSeparator, final boolean cacheAttributes) throws IOException {

		return createTempN5Writer(location, new GsonBuilder(), dimensionSeparator,true, cacheAttributes);
	}

	protected N5Writer createTempN5Writer(
			final String location,
			final GsonBuilder gsonBuilder,
			final String dimensionSeparator,
			final boolean mapN5DatasetAttributes) throws IOException {

		return createTempN5Writer(location, gsonBuilder, dimensionSeparator, mapN5DatasetAttributes, false);
	}

	protected N5Writer createTempN5Writer(
			final String location,
			final GsonBuilder gsonBuilder,
			final String dimensionSeparator,
			final boolean mapN5DatasetAttributes,
			final boolean cacheAttributes) {

		final ZarrKeyValueWriter tempWriter = new ZarrKeyValueWriter(createKeyValueAccess(), location, gsonBuilder, mapN5DatasetAttributes, true, dimensionSeparator, cacheAttributes);
		tempWriters.add(tempWriter);
		return tempWriter;
	}

	@Override
	protected N5Reader createN5Reader(final String location, final GsonBuilder gson) throws IOException {

		return new ZarrKeyValueReader(createKeyValueAccess(), location, gson, true, true, false);
	}

	@Override
	protected Compression[] getCompressions() {

		return new Compression[]{
				new Bzip2Compression(),
				new GzipCompression(),
				new GzipCompression(5, true),
				new BloscCompression(),
				new BloscCompression("lz4", 6, BloscCompression.BITSHUFFLE, 0, 4),
				new ZstandardCompression(),
				new ZstandardCompression(0),
				new ZstandardCompression(-1),
				//add new compressions here
				new RawCompression()
		};
	}

	@Override
	@Test
	public void testCreateDataset()  {

		final DatasetAttributes info;
		try (N5Writer n5 = createTempN5Writer()) {
			n5.createDataset(datasetName, dimensions, blockSize, DataType.UINT64, getCompressions()[0]);

			assertTrue("Dataset does not exist", n5.exists(datasetName));

			info = n5.getDatasetAttributes(datasetName);
			assertArrayEquals(dimensions, info.getDimensions());
			assertArrayEquals(blockSize, info.getBlockSize());
			assertEquals(DataType.UINT64, info.getDataType());
			assertEquals(getCompressions()[0].getClass(), info.getCompression().getClass());

			final JsonElement elem = n5.getAttribute(datasetName, "/", JsonElement.class);
			assertTrue(elem.getAsJsonObject().get("fill_value").getAsJsonPrimitive().isNumber());
		}
	}

	@Test
	public void testCreateNestedDataset() throws IOException {

		final String datasetName = "/test/nested/data";

		final String testDirPath = tempN5Location();
		final ZarrKeyValueWriter n5Nested = (ZarrKeyValueWriter) createTempN5Writer(testDirPath, "/");

		n5Nested.createDataset(datasetName, dimensions, blockSize, DataType.UINT64, getCompressions()[0]);
		assertEquals("/", n5Nested.getZArrayAttributes(datasetName).getDimensionSeparator());

		// TODO test that parents of nested dataset are groups
	}

	@Test
	public void testCreateDatasetNameEmpty()  {

		final String testDirPath = tempN5Location();
		final N5Writer n5 = createTempN5Writer(testDirPath);
		n5.createDataset("", dimensions, blockSize, DataType.UINT64, getCompressions()[0]);
	}

	@Test
	public void testCreateDatasetNameSlash()  {

		try (final N5Writer n5 = createTempN5Writer()) {
			n5.createDataset("", dimensions, blockSize, DataType.UINT64, getCompressions()[0]);
		}
	}

	@Test
	public void testGetDatasetAttributesNull()  {

		try (final N5Writer n5 = createTempN5Writer()) {
			final DatasetAttributes attributes = n5.getDatasetAttributes("");
			assertNull(attributes);
		}
	}

	@Test
	public void testPadCrop() {

		final byte[] src = new byte[]{1, 1, 1, 1}; // 2x2
		final int[] srcBlockSize = new int[]{2, 2};
		final int[] dstBlockSize = new int[]{3, 3};
		final int nBytes = 1;
		final int nBits = 0;
		final byte[] fillValue = new byte[]{0};

		final byte[] dst = N5ZarrWriter.padCrop(src, srcBlockSize, dstBlockSize, nBytes, nBits, fillValue);
		assertArrayEquals(new byte[]{1, 1, 0, 1, 1, 0, 0, 0, 0}, dst);
	}

	@Override
	@Test
	public void testVersion() throws NumberFormatException, IOException, URISyntaxException {

		try (final N5Writer writer = createTempN5Writer()) {

			final ZarrKeyValueWriter zarr = (ZarrKeyValueWriter)writer;
			final Version n5Version = writer.getVersion();
			assertEquals(n5Version, N5ZarrReader.VERSION);

			final JsonObject bumpVersion = new JsonObject();
			bumpVersion.add(N5ZarrReader.ZARR_FORMAT_KEY, new JsonPrimitive(N5ZarrReader.VERSION.getMajor() + 1));
			zarr.writeZGroup("", bumpVersion);

			final Version version = writer.getVersion();
			assertFalse(N5ZarrReader.VERSION.isCompatible(version));

			// check that writer creation fails for incompatible version
			assertThrows(N5Exception.N5IOException.class, () -> createTempN5Writer(writer.getURI().toString()));

			//			final Version compatibleVersion = new Version(N5ZarrReader.VERSION.getMajor(), N5ZarrReader.VERSION.getMinor(), N5Reader.VERSION.getPatch());
			//			writer.setAttribute("/", ZarrUtils.ZARR_FORMAT_KEY, compatibleVersion.toString());
		}
	}

	@Test
	@Override
	public void testReaderCreation() throws IOException, URISyntaxException {

		final String canonicalPath = tempN5Location();
		try (N5Writer writer = createTempN5Writer(canonicalPath)) {

			final N5Reader n5r = createN5Reader(canonicalPath);
			assertNotNull(n5r);

			// existing directory without attributes is okay;
			// Remove and create to remove attributes store
			writer.remove("/");
			writer.createGroup("/");
			final N5Reader na = createN5Reader(canonicalPath);
			assertNotNull(na);

			// existing location with attributes, but no version
			writer.remove("/");
			writer.createGroup("/");
			writer.setAttribute("/", "mystring", "ms");
			final N5Reader wa = createN5Reader(canonicalPath);
			assertNotNull(wa);

			// non-existent directory should fail
			writer.remove("/");
			assertThrows(
					"Non-existant location throws error",
					N5Exception.N5IOException.class,
					() -> {
						final N5Reader test = createN5Reader(canonicalPath);
						test.list("/");
					});
		}
	}

	@Override
	@Test
	public void testExists()  {

		final String groupName2 = groupName + "-2";
		final String datasetName2 = datasetName + "-2";
		final String notExists = groupName + "-notexists";

		try (N5Writer n5 = createTempN5Writer()) {

			n5.createDataset(datasetName2, dimensions, blockSize, DataType.UINT64, getCompressions()[0]);
			assertTrue(n5.exists(datasetName2));
			assertTrue(n5.datasetExists(datasetName2));

			n5.createGroup(groupName2);
			assertTrue(n5.exists(groupName2));
			assertFalse(n5.datasetExists(groupName2));

			assertFalse(n5.exists(notExists));
			assertFalse(n5.datasetExists(notExists));

			assertTrue(n5.remove(datasetName2));
			assertTrue(n5.remove(groupName2));
		}
	}

	@Override
	@Test
	public void testListAttributes()  {

		final String groupName2 = groupName + "-2";
		final String datasetName2 = datasetName + "-2";

		try (N5Writer n5 = createTempN5Writer()) {

			n5.createDataset(datasetName2, dimensions, blockSize, DataType.UINT64, getCompressions()[0]);
			n5.setAttribute(datasetName2, "attr1", new double[]{1, 2, 3});
			n5.setAttribute(datasetName2, "attr2", new String[]{"a", "b", "c"});
			n5.setAttribute(datasetName2, "attr3", 1.0);
			n5.setAttribute(datasetName2, "attr4", "a");
			n5.setAttribute(datasetName2, "attr5", 5.4);

			Map<String, Class<?>> attributesMap = n5.listAttributes(datasetName2);
			assertSame(attributesMap.get("attr1"), long[].class);
			assertSame(attributesMap.get("attr2"), String[].class);
			assertSame(attributesMap.get("attr3"), long.class);
			assertSame(attributesMap.get("attr4"), String.class);
			assertSame(attributesMap.get("attr5"), double.class);

			n5.createGroup(groupName2);
			n5.setAttribute(groupName2, "attr1", new double[]{1, 2, 3});
			n5.setAttribute(groupName2, "attr2", new String[]{"a", "b", "c"});
			n5.setAttribute(groupName2, "attr3", 1.0);
			n5.setAttribute(groupName2, "attr4", "a");
			n5.setAttribute(groupName2, "attr5", 5.4);

			attributesMap = n5.listAttributes(datasetName2);
			assertSame(attributesMap.get("attr1"), long[].class);
			assertSame(attributesMap.get("attr2"), String[].class);
			assertSame(attributesMap.get("attr3"), long.class);
			assertSame(attributesMap.get("attr4"), String.class);
			assertSame(attributesMap.get("attr5"), double.class);
		}
	}

	@Override
	@Test
	@Ignore("Zarr does not currently support mode 1 data blocks.")
	public void testMode1WriteReadByteBlock() {

	}

	@Override
	@Test
	@Ignore("Zarr does not currently support mode 2 data blocks and serialized objects.")
	public void testWriteReadSerializableBlock() {

	}

	@Test
	@Override
	public void testWriteReadStringBlock()  {
		final DataType dataType = DataType.STRING;
		final int[] blockSize = new int[]{3, 2, 1};
		final String[] stringBlock = new String[]{"", "a", "bc", "de", "fgh", ":-þ"};
		final Compression[] compressions = this.getCompressions();

		for (final Compression compression : compressions) {

			try (final N5Writer n5 = createTempN5Writer()) {
				n5.createDataset("/test/group/dataset", dimensions, blockSize, dataType, compression);
				final DatasetAttributes attributes = n5.getDatasetAttributes("/test/group/dataset");
				final StringDataBlock dataBlock = new ZarrStringDataBlock(blockSize, new long[]{0L, 0L, 0L}, stringBlock);
				n5.writeBlock("/test/group/dataset", attributes, dataBlock);
				final DataBlock<?> loadedDataBlock = n5.readBlock("/test/group/dataset", attributes, 0L, 0L, 0L);
				assertArrayEquals(stringBlock, (String[])loadedDataBlock.getData());
				assertTrue(n5.remove("/test/group/dataset"));
			}
		}
	}

	private boolean runPythonTest(final String script, final String containerPath) throws InterruptedException {

		try {
			final Process process = Runtime.getRuntime().exec("poetry run python src/test/python/" + script + " " + containerPath);
			final int exitCode = process.waitFor();
			new BufferedReader(new InputStreamReader(process.getErrorStream())).lines().forEach(System.out::println);
			process.destroy();
			return (exitCode == 0);
		} catch (final IOException e) {
			return false;
		}

	}

	private static <T extends IntegerType<T>> void assertIsSequence(
			final RandomAccessibleInterval<T> source,
			final T ref) {

		ref.setZero();
		for (final T t : Views.flatIterable(source)) {

			if (!t.valueEquals(ref))
				throw new AssertionError("values not equal: expected " + ref + ", actual " + t);
			ref.inc();
		}
	}

	private static <T extends RealType<T>> void assertIsSequence(
			final RandomAccessibleInterval<T> source,
			final T ref) {

		ref.setReal(0);
		for (final T t : Views.flatIterable(source)) {

			if (!t.valueEquals(ref))
				throw new AssertionError("values not equal: expected " + ref + ", actual " + t);
			ref.inc();
		}
	}

	@SuppressWarnings("unchecked")
	@Test
	public void testReadZarrPython() throws IOException, InterruptedException {

		final String testZarrDirPath = tempN5Location();

		/* create test data with python */
		if (!runPythonTest("zarr-test.py", testZarrDirPath)) {
			System.out.println("Couldn't run Python test, skipping compatibility test with Python.");
			return;
		}

		final ZarrKeyValueWriter n5Zarr = (ZarrKeyValueWriter)createTempN5Writer(testZarrDirPath, ".");
		final ZarrKeyValueWriter n5ZarrWithoutMapping = (ZarrKeyValueWriter)createTempN5Writer(testZarrDirPath, new GsonBuilder(), ".", false);

		/* groups */
		assertTrue(n5Zarr.exists(testZarrDatasetName) && !n5Zarr.datasetExists(testZarrDatasetName));

		/* array parameters */
		final DatasetAttributes datasetAttributesC = n5Zarr.getDatasetAttributes(testZarrDatasetName + "/3x2_c_i8");
		assertArrayEquals(datasetAttributesC.getDimensions(), new long[]{3, 2});
		assertArrayEquals(datasetAttributesC.getBlockSize(), new int[]{3, 2});
		assertEquals(DataType.INT64, datasetAttributesC.getDataType());

		final DatasetAttributes datasetAttributesF = n5Zarr.getDatasetAttributes(testZarrDatasetName + "/3x2_f_i8");
		assertArrayEquals(datasetAttributesF.getDimensions(), new long[]{2, 3});
		assertArrayEquals(datasetAttributesF.getBlockSize(), new int[]{2, 3});
		assertEquals(DataType.INT64, datasetAttributesF.getDataType());

		/* N5 array parameter mapping */
		assertArrayEquals(
				n5Zarr.getAttribute(testZarrDatasetName + "/3x2_c_i8", "dimensions", long[].class),
				new long[]{3, 2});
		assertArrayEquals(
				n5Zarr.getAttribute(testZarrDatasetName + "/3x2_c_i8", "blockSize", int[].class),
				new int[]{3, 2});
		assertEquals(
				n5Zarr.getAttribute(testZarrDatasetName + "/3x2_c_i8", "dataType", DataType.class),
				DataType.INT64);

		assertNull(n5ZarrWithoutMapping.getAttribute(testZarrDatasetName + "/3x2_c_i8", "dimensions", long[].class));
		assertNull(n5ZarrWithoutMapping.getAttribute(testZarrDatasetName + "/3x2_c_i8", "blockSize", int[].class));
		assertNull(n5ZarrWithoutMapping.getAttribute(testZarrDatasetName + "/3x2_c_i8", "dataType", DataType.class));

		/* LE uint8 in C and F order */
		final UnsignedByteType refUnsignedByte = new UnsignedByteType();

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_c_u1"), refUnsignedByte);
		assertIsSequence(
			Views.permute(
				(RandomAccessibleInterval<UnsignedByteType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_f_u1"),
				0,
				1),
			refUnsignedByte);

		/* LE int64 in C and F order */
		final LongType refLong = new LongType();

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_c_i8"), refLong);
		assertIsSequence(
				Views.permute(
					(RandomAccessibleInterval<LongType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_f_i8"),
					0,
					1),
				refLong);

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_c_i8"), refLong);
		assertIsSequence(
				Views.permute(
					(RandomAccessibleInterval<LongType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_f_i8"),
					0,
					1),
				refLong);

		/* BE int32 in C and F order */
		final UnsignedIntType refUnsignedInt = new UnsignedIntType();

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_c_u4"), refUnsignedInt);
		assertIsSequence(
			Views.permute(
				(RandomAccessibleInterval<UnsignedIntType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_f_u4"),
				0,
				1),
			refUnsignedInt);

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_c_u4"), refUnsignedInt);
		assertIsSequence(
			Views.permute(
				(RandomAccessibleInterval<UnsignedIntType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_f_u4"),
				0,
				1),
			refUnsignedInt);

		/* LE float64 in C and F order */
		final DoubleType refDouble = new DoubleType();

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_c_f8"), refDouble);
		assertIsSequence(
			Views.permute(
					(RandomAccessibleInterval<DoubleType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_f_f8"),
					0,
					1),
			refDouble);

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_c_f8"), refDouble);
		assertIsSequence(
			Views.permute(
				(RandomAccessibleInterval<DoubleType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_f_f8"),
				0,
				1),
			refDouble);

		/* BE float32 in C and F order */
		final FloatType refFloat = new FloatType();

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_c_f4"), refFloat);
		assertIsSequence(
			Views.permute(
				(RandomAccessibleInterval<FloatType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_f_f4"),
				0,
				1),
			refFloat);

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_c_f4"), refFloat);
		assertIsSequence(
			Views.permute(
				(RandomAccessibleInterval<FloatType>)N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_f_f4"),
				0,
				1),
			refFloat);

		/* compressors */
		final UnsignedLongType refUnsignedLong = new UnsignedLongType();

		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_c_u8_zlib"), refUnsignedLong);
		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_c_u8_gzip"), refUnsignedLong);
		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/30x20_c_u8_bz2"), refUnsignedLong);

		/* fill value 1 */
		String datasetName = testZarrDatasetName + "/3x2_c_u4_f1";

		final RandomAccessibleInterval<UnsignedIntType> a3x2_c_bu4_f1 = N5Utils.open(n5Zarr, datasetName);
		assertIsSequence(a3x2_c_bu4_f1, refUnsignedInt);

		DatasetAttributes attributes = n5Zarr.getDatasetAttributes(datasetName);
		final long[] shape = attributes.getDimensions();
		Arrays.setAll(shape, i -> shape[i] + 5);
		n5Zarr.setAttribute(datasetName, "dimensions", shape);

		final RandomAccessibleInterval<UnsignedIntType> a3x2_c_bu4_f1_after = N5Utils.open(n5Zarr, datasetName);
		assertIsSequence(Views.interval(a3x2_c_bu4_f1_after, a3x2_c_bu4_f1), refUnsignedInt);
		final RandomAccess<UnsignedIntType> ra = a3x2_c_bu4_f1_after.randomAccess();
		final int fill_value = Integer.parseInt(n5Zarr.getZArrayAttributes(datasetName).getFillValue());
		ra.setPosition(shape[0] - 5, 0);
		assertEquals(fill_value, ra.get().getInteger());
		ra.setPosition(shape[1] - 5, 1);
		assertEquals(fill_value, ra.get().getInteger());

		/* fill value NaN */
		datasetName = testZarrDatasetName + "/3x2_c_f4_fnan";

		final RandomAccessibleInterval<FloatType> a3x2_c_lf4_fnan = N5Utils.open(n5Zarr, datasetName);
		assertIsSequence(a3x2_c_lf4_fnan, refFloat);

		attributes = n5Zarr.getDatasetAttributes(datasetName);
		final long[] shapef = attributes.getDimensions();
		Arrays.setAll(shapef, i -> shapef[i] + 5);
		n5Zarr.setAttribute(datasetName, "dimensions", shapef);

		final RandomAccessibleInterval<FloatType> a3x2_c_lf4_fnan_after = N5Utils.open(n5Zarr, datasetName);
		assertIsSequence(Views.interval(a3x2_c_lf4_fnan_after, a3x2_c_lf4_fnan), refFloat);
		final RandomAccess<FloatType> raf = a3x2_c_lf4_fnan_after.randomAccess();
		raf.setPosition(shapef[0] - 5, 0);
		assertTrue(Float.isNaN(raf.get().getRealFloat()));
		raf.setPosition(shapef[1] - 5, 1);
		assertTrue(Float.isNaN(raf.get().getRealFloat()));

		/* strings */
		String[] expected = {"", "a", "bc", "de", "fgh", ":-þ"}; // C-order
		datasetName = testZarrDatasetName + "/3x2_c_str";
		DatasetAttributes strAttributes = n5Zarr.getDatasetAttributes(datasetName);
		DataBlock<?> loadedDataBlock = n5Zarr.readBlock(datasetName, strAttributes, 0L, 0L);
		assertArrayEquals(expected, ((String[])loadedDataBlock.getData()));

		expected = new String[] {"", "de", "a", "fgh", "bc", ":-þ"}; // F-order
		datasetName = testZarrDatasetName + "/3x2_f_str";
		strAttributes = n5Zarr.getDatasetAttributes(datasetName);
		loadedDataBlock = n5Zarr.readBlock(datasetName, strAttributes, 0L, 0L);
		assertArrayEquals(expected, ((String[])loadedDataBlock.getData()));

		expected = new String[] {"bc", "", ":-þ", ""}; // chunked and compressed (second chunk)
		datasetName = testZarrDatasetName + "/3x2_c_str_bz2";
		strAttributes = n5Zarr.getDatasetAttributes(datasetName);
		loadedDataBlock = n5Zarr.readBlock(datasetName, strAttributes, 1L, 0L);
		assertArrayEquals(expected, ((String[])loadedDataBlock.getData()));
	}

	@Test
	public void testReadZarrNestedPython() throws IOException, InterruptedException {

		final String testZarrNestedDirPath = tempN5Location();

		/* create test data with python */
		if (!runPythonTest("zarr-nested-test.py", testZarrNestedDirPath)) {
			System.out.println("Couldn't run Python test, skipping compatibility test with Python.");
			return;
		}

		final ZarrKeyValueWriter n5Zarr = (ZarrKeyValueWriter) createTempN5Writer(testZarrNestedDirPath, ".", true);

		/* groups */
		assertTrue(n5Zarr.exists(testZarrDatasetName) && !n5Zarr.datasetExists(testZarrDatasetName));

		/* array parameters */
		final DatasetAttributes datasetAttributesC = n5Zarr.getDatasetAttributes(testZarrDatasetName + "/3x2_c_u1");
		assertArrayEquals(datasetAttributesC.getDimensions(), new long[]{3, 2});
		assertArrayEquals(datasetAttributesC.getBlockSize(), new int[]{3, 2});
		assertEquals(datasetAttributesC.getDataType(), DataType.UINT8);
		assertEquals(n5Zarr.getZArrayAttributes(testZarrDatasetName + "/3x2_c_u1").getDimensionSeparator(), "/");

		final UnsignedByteType refUnsignedByte = new UnsignedByteType();
		assertIsSequence(N5Utils.open(n5Zarr, testZarrDatasetName + "/3x2_c_u1"), refUnsignedByte);
	}

	@Test
	public void testRawCompressorNullInZarray() throws IOException, ParseException, URISyntaxException {

		final GsonKeyValueN5Writer n5 = (GsonKeyValueN5Writer) createTempN5Writer();
		n5.createDataset(
				testZarrDatasetName,
				new long[]{1, 2, 3},
				new int[]{1, 2, 3},
				DataType.UINT16,
				new RawCompression());
		final String zarrayLocation = n5.getKeyValueAccess().compose(n5.getURI(), testZarrDatasetName, ".zarray");
		final LockedChannel zarrayChannel = n5.getKeyValueAccess().lockForReading(zarrayLocation);
		final JSONParser jsonParser = new JSONParser();
		try (Reader reader = zarrayChannel.newReader()) {
			final JSONObject zarray = (JSONObject)jsonParser.parse(reader);
			final JSONObject compressor = (JSONObject)zarray.get("compressor");
			assertNull(compressor);
		}
	}

	@Test
	@Override
	public void testAttributes()  {

		try (final N5Writer n5 = createTempN5Writer()) {
			n5.createGroup(groupName);

			n5.setAttribute(groupName, "key1", "value1");
			// length 2 because it includes "zarr_version"
			Assert.assertEquals(2, n5.listAttributes(groupName).size());
			/* class interface */
			Assert.assertEquals("value1", n5.getAttribute(groupName, "key1", String.class));
			/* type interface */
			Assert.assertEquals("value1", n5.getAttribute(groupName, "key1", new TypeToken<String>() {

			}.getType()));

			final Map<String, String> newAttributes = new HashMap<>();
			newAttributes.put("key2", "value2");
			newAttributes.put("key3", "value3");
			n5.setAttributes(groupName, newAttributes);

			Assert.assertEquals(4, n5.listAttributes(groupName).size());
			/* class interface */
			Assert.assertEquals("value1", n5.getAttribute(groupName, "key1", String.class));
			Assert.assertEquals("value2", n5.getAttribute(groupName, "key2", String.class));
			Assert.assertEquals("value3", n5.getAttribute(groupName, "key3", String.class));
			/* type interface */
			Assert.assertEquals("value1", n5.getAttribute(groupName, "key1", new TypeToken<String>() {

			}.getType()));
			Assert.assertEquals("value2", n5.getAttribute(groupName, "key2", new TypeToken<String>() {

			}.getType()));
			Assert.assertEquals("value3", n5.getAttribute(groupName, "key3", new TypeToken<String>() {

			}.getType()));

			n5.setAttribute(groupName, "key1", 1);
			n5.setAttribute(groupName, "key2", 2);

			Assert.assertEquals(4, n5.listAttributes(groupName).size());
			/* class interface */
			Assert.assertEquals(new Integer(1), n5.getAttribute(groupName, "key1", Integer.class));
			Assert.assertEquals(new Integer(2), n5.getAttribute(groupName, "key2", Integer.class));
			Assert.assertEquals("value3", n5.getAttribute(groupName, "key3", String.class));
			/* type interface */
			Assert
					.assertEquals(
							new Integer(1),
							n5.getAttribute(groupName, "key1", new TypeToken<Integer>() {

							}.getType()));
			Assert
					.assertEquals(
							new Integer(2),
							n5.getAttribute(groupName, "key2", new TypeToken<Integer>() {

							}.getType()));
			Assert.assertEquals("value3", n5.getAttribute(groupName, "key3", new TypeToken<String>() {

			}.getType()));

			n5.removeAttribute(groupName, "key1");
			n5.removeAttribute(groupName, "key2");
			n5.removeAttribute(groupName, "key3");
			Assert.assertEquals(1, n5.listAttributes(groupName).size());
		}
	}

	@Test
	public void testAttributeMapping()  {

		// attribute mapping on by default
		try (final N5Writer n5 = createTempN5Writer(tempN5Location(), new GsonBuilder().serializeNulls())) {

			n5.createDataset(datasetName, dimensions, blockSize, DataType.UINT64, getCompressions()[0]);

			long[] dimsZarr = n5.getAttribute(datasetName, ZArrayAttributes.shapeKey, long[].class);
			long[] dimsN5 = n5.getAttribute(datasetName, DatasetAttributes.DIMENSIONS_KEY, long[].class);
			assertArrayEquals(dimsZarr, dimsN5);

			int[] blkZarr = n5.getAttribute(datasetName, ZArrayAttributes.chunksKey, int[].class);
			int[] blkN5 = n5.getAttribute(datasetName, DatasetAttributes.BLOCK_SIZE_KEY, int[].class);
			assertArrayEquals(blkZarr, blkN5);

			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);

			ZarrCompressor zarrCompression = n5.getAttribute(datasetName, ZArrayAttributes.compressorKey, ZarrCompressor.class);
			Compression n5Compression = n5.getAttribute(datasetName, DatasetAttributes.COMPRESSION_KEY, Compression.class);
			assertEquals(zarrCompression.getCompression(), n5Compression);

			final long[] newDims = new long[]{30, 40, 50};
			final int[] newBlk = new int[]{30, 40, 50};
			final DataType newDtype = DataType.FLOAT64;

			// ensure variables can be set through the n5 variables as well
			n5.setAttribute(datasetName, DatasetAttributes.DIMENSIONS_KEY, newDims);
			dimsZarr = n5.getAttribute(datasetName, ZArrayAttributes.shapeKey, long[].class);
			dimsN5 = n5.getAttribute(datasetName, DatasetAttributes.DIMENSIONS_KEY, long[].class);
			assertArrayEquals(newDims, dimsZarr);
			assertArrayEquals(newDims, dimsN5);

			n5.setAttribute(datasetName, DatasetAttributes.BLOCK_SIZE_KEY, newBlk);
			blkZarr = n5.getAttribute(datasetName, ZArrayAttributes.shapeKey, int[].class);
			blkN5 = n5.getAttribute(datasetName, DatasetAttributes.BLOCK_SIZE_KEY, int[].class);
			assertArrayEquals(newBlk, blkZarr);
			assertArrayEquals(newBlk, blkN5);

			n5.setAttribute(datasetName, DatasetAttributes.DATA_TYPE_KEY, newDtype.toString());

			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);

			final RawCompression rawCompression = new RawCompression();
			n5.setAttribute(datasetName, DatasetAttributes.COMPRESSION_KEY, rawCompression);
			zarrCompression = n5.getAttribute(datasetName, ZArrayAttributes.compressorKey, ZarrCompressor.class);
			n5Compression = n5.getAttribute(datasetName, DatasetAttributes.COMPRESSION_KEY, Compression.class);
			assertEquals(rawCompression, zarrCompression.getCompression());
			assertEquals(rawCompression, n5Compression);

			final GzipCompression gzipCompression = new GzipCompression();
			n5.setAttribute(datasetName, DatasetAttributes.COMPRESSION_KEY, gzipCompression);
			zarrCompression = n5.getAttribute(datasetName, ZArrayAttributes.compressorKey, ZarrCompressor.class);
			n5Compression = n5.getAttribute(datasetName, DatasetAttributes.COMPRESSION_KEY, Compression.class);
			assertEquals(gzipCompression, zarrCompression.getCompression());
			assertEquals(gzipCompression, n5Compression);
		}
	}

	@Test
	public void testNullFillValue() {

		final String key = ZArrayAttributes.fillValueKey;
		final JsonNull jsonNull = JsonNull.INSTANCE;
		final byte[] zero = new byte[8];

		try (final N5Writer n5 = createTempN5Writer(tempN5Location(), new GsonBuilder().serializeNulls())) {

			n5.createDataset(datasetName, dimensions, blockSize, DataType.UINT64, getCompressions()[0]);
			n5.setAttribute(datasetName, key, jsonNull);

			assertEquals(jsonNull, n5.getAttribute(datasetName, key, JsonElement.class));
			assertTrue(n5.datasetExists(datasetName));

			final ZarrDatasetAttributes dsetAttrs = (ZarrDatasetAttributes) n5.getDatasetAttributes(datasetName);
			assertArrayEquals(zero, dsetAttrs.getFillBytes());
		}
	}

	@Test
	@Override
	@Ignore
	public void testNullAttributes()  {

		// serializeNulls must be on for Zarr to be able to write datasets with raw compression

		/* serializeNulls*/
		try (N5Writer writer = createTempN5Writer(tempN5Location(), new GsonBuilder().serializeNulls())) {

			writer.createGroup(groupName);
			writer.setAttribute(groupName, "nullValue", null);
			assertNull(writer.getAttribute(groupName, "nullValue", Object.class));
			assertEquals(JsonNull.INSTANCE, writer.getAttribute(groupName, "nullValue", JsonElement.class));
			final HashMap<String, Object> nulls = new HashMap<>();
			nulls.put("anotherNullValue", null);
			nulls.put("structured/nullValue", null);
			nulls.put("implicitNulls[3]", null);
			writer.setAttributes(groupName, nulls);

			assertNull(writer.getAttribute(groupName, "anotherNullValue", Object.class));
			assertEquals(JsonNull.INSTANCE, writer.getAttribute(groupName, "anotherNullValue", JsonElement.class));

			assertNull(writer.getAttribute(groupName, "structured/nullValue", Object.class));
			assertEquals(JsonNull.INSTANCE, writer.getAttribute(groupName, "structured/nullValue", JsonElement.class));

			assertNull(writer.getAttribute(groupName, "implicitNulls[3]", Object.class));
			assertEquals(JsonNull.INSTANCE, writer.getAttribute(groupName, "implicitNulls[3]", JsonElement.class));

			assertNull(writer.getAttribute(groupName, "implicitNulls[1]", Object.class));
			assertEquals(JsonNull.INSTANCE, writer.getAttribute(groupName, "implicitNulls[1]", JsonElement.class));

			/* Negative test; a value that truly doesn't exist will still return `null` but will also return `null` when querying as a `JsonElement` */
			assertNull(writer.getAttribute(groupName, "implicitNulls[10]", Object.class));
			assertNull(writer.getAttribute(groupName, "implicitNulls[10]", JsonElement.class));

			assertNull(writer.getAttribute(groupName, "keyDoesn'tExist", Object.class));
			assertNull(writer.getAttribute(groupName, "keyDoesn'tExist", JsonElement.class));

			/* check existing value gets overwritten */
			writer.setAttribute(groupName, "existingValue", 1);
			assertEquals((Integer)1, writer.getAttribute(groupName, "existingValue", Integer.class));
			writer.setAttribute(groupName, "existingValue", null);
			assertThrows(N5ClassCastException.class, () -> writer.getAttribute(groupName, "existingValue", Integer.class));
			assertEquals(JsonNull.INSTANCE, writer.getAttribute(groupName, "existingValue", JsonElement.class));
		}
	}

	@Test
	@Override
	@Ignore
	public void testRootLeaves() {

		// This tests serializing primitives, and arrays at the root of an n5's attributes,
		// since .zattrs must be a json object, this would test invalide behavior for zarr,
		// therefore this test is ignored.
	}
}