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brokkoli71brokkoli71
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add v0.4zarr3
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‎src/main/java/dev/zarr/zarrjava/ome/MultiscaleImage.java‎

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@@ -120,6 +120,9 @@ static MultiscaleImage open(StoreHandle storeHandle) throws IOException, ZarrExc
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}
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throw new ZarrException("v1.0 store at " + storeHandle + " is a Collection, not a MultiscaleImage. Use v1_0.Collection.openCollection() instead.");
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}
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if (version.startsWith("0.4-zarr3")) {
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return dev.zarr.zarrjava.ome.v0_4_zarr3.MultiscaleImage.openMultiscaleImage(storeHandle);
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}
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if (version.startsWith("0.6")) {
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return dev.zarr.zarrjava.ome.v0_6.MultiscaleImage.openMultiscaleImage(storeHandle);
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}

‎src/main/java/dev/zarr/zarrjava/ome/v0_4_zarr3/MultiscaleImage.java‎

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package dev.zarr.zarrjava.ome.v0_4_zarr3;
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import dev.zarr.zarrjava.ZarrException;
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import dev.zarr.zarrjava.ome.MultiscalesMetadataImage;
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import dev.zarr.zarrjava.ome.OmeV3Group;
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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.store.StoreHandle;
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import dev.zarr.zarrjava.v3.Array;
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import dev.zarr.zarrjava.v3.Group;
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import dev.zarr.zarrjava.v3.GroupMetadata;
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import javax.annotation.Nonnull;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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/**
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* OME-Zarr v0.4-zarr3 compatibility image reader backed by a Zarr v3 group.
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*/
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public final class MultiscaleImage extends OmeV3Group
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implements MultiscalesMetadataImage<dev.zarr.zarrjava.ome.v0_6.metadata.MultiscalesEntry> {
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private dev.zarr.zarrjava.ome.v0_6.metadata.OmeMetadata omeMetadata;
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private MultiscaleImage(
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@Nonnull StoreHandle storeHandle,
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@Nonnull GroupMetadata groupMetadata,
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@Nonnull dev.zarr.zarrjava.ome.v0_6.metadata.OmeMetadata omeMetadata
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) throws IOException {
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super(storeHandle, groupMetadata);
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this.omeMetadata = omeMetadata;
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}
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public static MultiscaleImage openMultiscaleImage(@Nonnull StoreHandle storeHandle)
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throws IOException, ZarrException {
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Group group = Group.open(storeHandle);
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dev.zarr.zarrjava.ome.v0_6.metadata.OmeMetadata omeMetadata = readOmeAttribute(
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group.metadata.attributes, storeHandle, dev.zarr.zarrjava.ome.v0_6.metadata.OmeMetadata.class);
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if (!omeMetadata.version.startsWith("0.4-zarr3")) {
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throw new ZarrException(
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"Expected OME-Zarr version '0.4-zarr3', got '" + omeMetadata.version + "' at " + storeHandle);
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}
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return new MultiscaleImage(storeHandle, group.metadata, omeMetadata);
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}
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@Override
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public StoreHandle getStoreHandle() {
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return this.storeHandle;
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}
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@Override
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public dev.zarr.zarrjava.ome.v0_6.metadata.MultiscalesEntry getMultiscalesEntry(int i) throws ZarrException {
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return omeMetadata.multiscales.get(i);
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}
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@Override
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public dev.zarr.zarrjava.core.Array openScaleLevel(int i) throws IOException, ZarrException {
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String path = getMultiscalesEntry(0).datasets.get(i).path;
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return Array.open(storeHandle.resolve(path));
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}
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@Override
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public int getScaleLevelCount() throws ZarrException {
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return getMultiscalesEntry(0).datasets.size();
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}
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@Override
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public void createScaleLevel(
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String path,
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dev.zarr.zarrjava.core.ArrayMetadata arrayMetadata,
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List<CoordinateTransformation> coordinateTransformations
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) throws IOException, ZarrException {
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throw new ZarrException("OME-Zarr v0.4-zarr3 create/write is not supported by this compatibility reader");
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}
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@Override
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public dev.zarr.zarrjava.ome.metadata.MultiscalesEntry getMultiscaleNode(int i) throws ZarrException {
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dev.zarr.zarrjava.ome.v0_6.metadata.MultiscalesEntry entry = getMultiscalesEntry(i);
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List<dev.zarr.zarrjava.ome.metadata.Dataset> mappedDatasets = new ArrayList<>();
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for (dev.zarr.zarrjava.ome.v0_6.metadata.Dataset ds : entry.datasets) {
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List<CoordinateTransformation> mapped = new ArrayList<>();
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for (dev.zarr.zarrjava.ome.v0_6.metadata.CoordinateTransformation ct : ds.coordinateTransformations) {
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mapped.add(new CoordinateTransformation(ct.type, ct.scale, ct.translation, ct.path));
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}
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mappedDatasets.add(new dev.zarr.zarrjava.ome.metadata.Dataset(ds.path, mapped));
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}
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List<Axis> axes = entry.axes;
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if ((axes == null || axes.isEmpty()) && entry.coordinateSystems != null && !entry.coordinateSystems.isEmpty()) {
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axes = entry.coordinateSystems.get(0).axes;
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}
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return new dev.zarr.zarrjava.ome.metadata.MultiscalesEntry(
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axes != null ? axes : Collections.<Axis>emptyList(),
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mappedDatasets,
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null,
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entry.name,
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null,
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null,
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"0.4-zarr3");
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}
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}

‎src/test/java/dev/zarr/zarrjava/ome/OmeZarrV04Zarr3Test.java‎

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package dev.zarr.zarrjava.ome;
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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 org.junit.jupiter.api.Test;
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import java.util.Arrays;
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import static org.junit.jupiter.api.Assertions.assertArrayEquals;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertInstanceOf;
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public class OmeZarrV04Zarr3Test extends OmeZarrBaseTest {
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@Override
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StoreHandle imageStoreHandle() throws Exception {
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return new FilesystemStore(TESTDATA.resolve("l4_sample").resolve("color")).resolve();
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}
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@Override
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Class<?> expectedConcreteClass() {
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return dev.zarr.zarrjava.ome.v0_4_zarr3.MultiscaleImage.class;
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}
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@Override
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int expectedScaleLevelCount() {
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return 5;
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}
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@Override
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long[] expectedLevel0Shape() {
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return new long[]{1, 4096, 4096, 2048};
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}
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@Override
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java.util.List<String> expectedAxisNames() {
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return Arrays.asList("c", "x", "y", "z");
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}
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@Test
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void openL4SampleSegmentation() throws Exception {
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StoreHandle segmentation = new FilesystemStore(TESTDATA.resolve("l4_sample").resolve("segmentation")).resolve();
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MultiscaleImage image = MultiscaleImage.open(segmentation);
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assertInstanceOf(dev.zarr.zarrjava.ome.v0_4_zarr3.MultiscaleImage.class, image);
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assertEquals(5, image.getScaleLevelCount());
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assertEquals(Arrays.asList("c", "x", "y", "z"), image.getAxisNames());
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assertArrayEquals(new long[]{1, 4096, 4096, 2048}, image.openScaleLevel(0).metadata().shape);
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}
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@Test
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void normalizedEntryCarriesCompatibilityVersion() throws Exception {
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MultiscaleImage image = MultiscaleImage.open(imageStoreHandle());
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dev.zarr.zarrjava.ome.metadata.MultiscalesEntry entry = image.getMultiscaleNode(0);
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assertEquals("0.4-zarr3", entry.version);
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assertEquals("1", entry.datasets.get(0).path);
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assertEquals("16-16-4", entry.datasets.get(entry.datasets.size() - 1).path);
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assertEquals("scale", entry.datasets.get(0).coordinateTransformations.get(0).type);
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}
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}

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