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add ome v0.4 and v0.5 tests
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‎src/test/java/dev/zarr/zarrjava/OmeZarrTest.java‎

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package dev.zarr.zarrjava;
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import dev.zarr.zarrjava.ome.MultiscaleImage;
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import dev.zarr.zarrjava.ome.MultiscalesMetadataImage;
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import dev.zarr.zarrjava.ome.UnifiedMultiscaleNode;
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import dev.zarr.zarrjava.ome.UnifiedSinglescaleNode;
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import dev.zarr.zarrjava.ome.metadata.Axis;
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import dev.zarr.zarrjava.ome.metadata.CoordinateTransformation;
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import dev.zarr.zarrjava.ome.metadata.MultiscalesEntry;
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import dev.zarr.zarrjava.store.FilesystemStore;
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import dev.zarr.zarrjava.store.StoreHandle;
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import dev.zarr.zarrjava.v3.Array;
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import dev.zarr.zarrjava.v3.DataType;
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import org.junit.jupiter.api.Test;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import static org.junit.jupiter.api.Assertions.*;
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public class OmeZarrTest extends ZarrTest {
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private StoreHandle storeHandle(java.nio.file.Path path) throws Exception {
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return new FilesystemStore(path).resolve();
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}
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// ── v0.5 read tests ──────────────────────────────────────────────────────
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@Test
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void readV05_axesAndDatasets() throws Exception {
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MultiscaleImage image = MultiscaleImage.open(storeHandle(TESTDATA.resolve("ome/v0.5")));
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assertInstanceOf(dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.class, image);
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UnifiedMultiscaleNode node = image.getMultiscaleNode(0);
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assertEquals("test_image", node.name);
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assertEquals(5, node.axes.size());
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assertEquals(2, node.nodes.size());
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List<String> axisNames = Arrays.asList("t", "c", "z", "y", "x");
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for (int i = 0; i < axisNames.size(); i++) {
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assertEquals(axisNames.get(i), node.axes.get(i).name);
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}
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List<String> axisTypes = Arrays.asList("time", "channel", "space", "space", "space");
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for (int i = 0; i < axisTypes.size(); i++) {
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assertEquals(axisTypes.get(i), node.axes.get(i).type);
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}
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UnifiedSinglescaleNode scaleNode0 = node.nodes.get(0);
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assertEquals("0", scaleNode0.path);
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assertEquals("scale", scaleNode0.coordinateTransformations.get(0).type);
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}
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@Test
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void readV04_axesAndDatasets() throws Exception {
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MultiscaleImage image = MultiscaleImage.open(storeHandle(TESTDATA.resolve("ome/v0.4")));
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assertInstanceOf(dev.zarr.zarrjava.ome.v0_4.MultiscaleImage.class, image);
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UnifiedMultiscaleNode node = image.getMultiscaleNode(0);
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assertEquals("test_image", node.name);
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assertEquals(5, node.axes.size());
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assertEquals(2, node.nodes.size());
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List<String> axisNames = Arrays.asList("t", "c", "z", "y", "x");
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for (int i = 0; i < axisNames.size(); i++) {
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assertEquals(axisNames.get(i), node.axes.get(i).name);
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}
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List<String> axisTypes = Arrays.asList("time", "channel", "space", "space", "space");
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for (int i = 0; i < axisTypes.size(); i++) {
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assertEquals(axisTypes.get(i), node.axes.get(i).type);
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}
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UnifiedSinglescaleNode scaleNode0 = node.nodes.get(0);
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assertEquals("0", scaleNode0.path);
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assertEquals("scale", scaleNode0.coordinateTransformations.get(0).type);
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}
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@Test
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void readV05_getAxisNames() throws Exception {
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MultiscaleImage image = MultiscaleImage.open(storeHandle(TESTDATA.resolve("ome/v0.5")));
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assertEquals(Arrays.asList("t", "c", "z", "y", "x"), image.getAxisNames());
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}
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@Test
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void readV05_openScaleLevel() throws Exception {
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MultiscaleImage image = MultiscaleImage.open(storeHandle(TESTDATA.resolve("ome/v0.5")));
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dev.zarr.zarrjava.core.Array level0 = image.openScaleLevel(0);
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assertArrayEquals(new long[]{1, 2, 8, 16, 16}, level0.metadata().shape);
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dev.zarr.zarrjava.core.Array level1 = image.openScaleLevel(1);
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assertArrayEquals(new long[]{1, 2, 4, 8, 8}, level1.metadata().shape);
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}
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@Test
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void readV04_openScaleLevel() throws Exception {
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MultiscaleImage image = MultiscaleImage.open(storeHandle(TESTDATA.resolve("ome/v0.4")));
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dev.zarr.zarrjava.core.Array level0 = image.openScaleLevel(0);
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assertArrayEquals(new long[]{1, 2, 8, 16, 16}, level0.metadata().shape);
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dev.zarr.zarrjava.core.Array level1 = image.openScaleLevel(1);
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assertArrayEquals(new long[]{1, 2, 4, 8, 8}, level1.metadata().shape);
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}
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@Test
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void readV05_scaleLevelCount() throws Exception {
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MultiscaleImage image = MultiscaleImage.open(storeHandle(TESTDATA.resolve("ome/v0.5")));
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assertEquals(2, image.getScaleLevelCount());
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}
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// ── v0.5 write tests ─────────────────────────────────────────────────────
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@Test
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void writeV05_createAndReopen() throws Exception {
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List<Axis> axes = Arrays.asList(
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new Axis("z", "space", "micrometer"),
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new Axis("y", "space", "micrometer")
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);
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MultiscalesEntry entry = new MultiscalesEntry(axes, Collections.emptyList());
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StoreHandle handle = storeHandle(TESTOUTPUT.resolve("ome_v05_create"));
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dev.zarr.zarrjava.ome.v0_5.MultiscaleImage created =
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dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.create(handle, entry);
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dev.zarr.zarrjava.v3.ArrayMetadata arrayMetadata = Array.metadataBuilder()
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.withShape(16, 16)
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.withChunkShape(16, 16)
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.withDataType(DataType.FLOAT32)
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.build();
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List<CoordinateTransformation> transforms =
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Collections.singletonList(CoordinateTransformation.scale(Arrays.asList(0.5, 0.5)));
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created.createScaleLevel("0", arrayMetadata, transforms);
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MultiscaleImage reopened = MultiscaleImage.open(handle);
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assertInstanceOf(dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.class, reopened);
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assertEquals(Arrays.asList("z", "y"), reopened.getAxisNames());
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assertEquals(1, reopened.getScaleLevelCount());
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assertEquals("0", reopened.getMultiscaleNode(0).nodes.get(0).path);
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}
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// ── v0.4 write tests ─────────────────────────────────────────────────────
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@Test
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void writeV04_createAndReopen() throws Exception {
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List<Axis> axes = Arrays.asList(
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new Axis("z", "space", "micrometer"),
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new Axis("y", "space", "micrometer")
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);
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MultiscalesEntry entry = new MultiscalesEntry(axes, Collections.emptyList());
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StoreHandle handle = storeHandle(TESTOUTPUT.resolve("ome_v04_create"));
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dev.zarr.zarrjava.ome.v0_4.MultiscaleImage created =
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dev.zarr.zarrjava.ome.v0_4.MultiscaleImage.create(handle, entry);
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dev.zarr.zarrjava.v2.ArrayMetadata arrayMetadata = new dev.zarr.zarrjava.v2.ArrayMetadata(
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2,
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new long[]{16, 16},
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new int[]{16, 16},
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dev.zarr.zarrjava.v2.DataType.FLOAT32,
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0,
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dev.zarr.zarrjava.v2.Order.C,
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null,
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null,
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null
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);
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List<CoordinateTransformation> transforms =
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Collections.singletonList(CoordinateTransformation.scale(Arrays.asList(0.5, 0.5)));
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created.createScaleLevel("0", arrayMetadata, transforms);
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MultiscaleImage reopened = MultiscaleImage.open(handle);
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assertInstanceOf(dev.zarr.zarrjava.ome.v0_4.MultiscaleImage.class, reopened);
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assertEquals(Arrays.asList("z", "y"), reopened.getAxisNames());
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assertEquals(1, reopened.getScaleLevelCount());
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assertEquals("0", reopened.getMultiscaleNode(0).nodes.get(0).path);
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}
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// ── typed metadata tests ─────────────────────────────────────────────────
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@Test
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void readV05_typedMetadata() throws Exception {
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MultiscalesMetadataImage<?> image =
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(MultiscalesMetadataImage<?>) MultiscaleImage.open(storeHandle(TESTDATA.resolve("ome/v0.5")));
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MultiscalesEntry entry = image.getMultiscalesEntry(0);
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assertEquals("test_image", entry.name);
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assertNull(entry.version);
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List<Double> expectedScale = Arrays.asList(1.0, 1.0, 0.5, 0.5, 0.5);
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assertEquals(expectedScale, entry.datasets.get(0).coordinateTransformations.get(0).scale);
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}
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@Test
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void readV04_entryHasVersion() throws Exception {
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MultiscalesMetadataImage<?> image =
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(MultiscalesMetadataImage<?>) MultiscaleImage.open(storeHandle(TESTDATA.resolve("ome/v0.4")));
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MultiscalesEntry entry = image.getMultiscalesEntry(0);
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assertEquals("0.4", entry.version);
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}
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}

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