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brokkoli71brokkoli71
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add ome v0.4 and v0.5 implementation
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‎src/main/java/dev/zarr/zarrjava/ome/MultiscaleImage.java‎

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package dev.zarr.zarrjava.ome;
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import dev.zarr.zarrjava.ZarrException;
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import dev.zarr.zarrjava.core.Node;
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import dev.zarr.zarrjava.store.StoreHandle;
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import dev.zarr.zarrjava.utils.Utils;
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import java.io.IOException;
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import java.nio.ByteBuffer;
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import java.util.List;
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/**
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* Unified interface for reading OME-Zarr multiscale images across Zarr format versions.
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*/
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public interface MultiscaleImage {
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/**
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* Returns the multiscale node descriptor at index {@code i}.
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*/
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UnifiedMultiscaleNode getMultiscaleNode(int i) throws ZarrException;
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/**
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* Opens the scale level array at index {@code i} within the first multiscale entry.
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*/
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dev.zarr.zarrjava.core.Array openScaleLevel(int i) throws IOException, ZarrException;
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/**
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* Returns the number of scale levels in the first multiscale entry.
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*/
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int getScaleLevelCount() throws ZarrException;
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/**
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* Returns the axis names of the first multiscale entry.
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*/
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default List<String> getAxisNames() throws ZarrException {
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UnifiedMultiscaleNode node = getMultiscaleNode(0);
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List<String> names = new java.util.ArrayList<>();
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for (dev.zarr.zarrjava.ome.metadata.Axis axis : node.axes) {
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names.add(axis.name);
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}
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return names;
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}
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/**
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* Opens an OME-Zarr multiscale image at the given store handle, auto-detecting the Zarr version.
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*
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* <p>Tries v0.5 (zarr.json with "ome" key) first, then v0.4 (.zattrs with "multiscales" key).
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*/
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static MultiscaleImage open(StoreHandle storeHandle) throws IOException, ZarrException {
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// Try v0.5: zarr.json with "ome" key
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StoreHandle zarrJson = storeHandle.resolve(Node.ZARR_JSON);
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if (zarrJson.exists()) {
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com.fasterxml.jackson.databind.ObjectMapper mapper = dev.zarr.zarrjava.v3.Node.makeObjectMapper();
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byte[] bytes = Utils.toArray(zarrJson.readNonNull());
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com.fasterxml.jackson.databind.JsonNode root = mapper.readTree(bytes);
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com.fasterxml.jackson.databind.JsonNode attrs = root.get("attributes");
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if (attrs != null && attrs.has("ome")) {
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return dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.openMultiscaleImage(storeHandle);
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}
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}
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// Try v0.4: .zattrs with "multiscales" key
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StoreHandle zattrs = storeHandle.resolve(Node.ZATTRS);
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if (zattrs.exists()) {
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com.fasterxml.jackson.databind.ObjectMapper mapper = dev.zarr.zarrjava.v2.Node.makeObjectMapper();
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byte[] bytes = Utils.toArray(zattrs.readNonNull());
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com.fasterxml.jackson.databind.JsonNode root = mapper.readTree(bytes);
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if (root.has("multiscales")) {
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return dev.zarr.zarrjava.ome.v0_4.MultiscaleImage.openMultiscaleImage(storeHandle);
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}
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}
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throw new ZarrException("No OME-Zarr multiscale metadata found at " + storeHandle);
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}
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}

‎src/main/java/dev/zarr/zarrjava/ome/MultiscalesMetadataImage.java‎

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package dev.zarr.zarrjava.ome;
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import dev.zarr.zarrjava.ZarrException;
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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 java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Extension of {@link MultiscaleImage} that provides typed access to OME-Zarr multiscales metadata
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* and supports creating new scale levels.
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*
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* @param <M> the concrete multiscales entry type
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*/
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public interface MultiscalesMetadataImage<M extends MultiscalesEntry> extends MultiscaleImage {
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/**
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* Returns the raw multiscales entry at index {@code i}.
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*/
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M getMultiscalesEntry(int i) throws ZarrException;
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/**
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* Creates a new scale level array at {@code path} with the given metadata and coordinate transformations,
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* then registers it in the multiscales metadata.
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*/
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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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@Override
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default UnifiedMultiscaleNode getMultiscaleNode(int i) throws ZarrException {
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M entry = getMultiscalesEntry(i);
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List<UnifiedSinglescaleNode> nodes = new ArrayList<>();
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for (dev.zarr.zarrjava.ome.metadata.Dataset dataset : entry.datasets) {
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nodes.add(new UnifiedSinglescaleNode(dataset.path, dataset.coordinateTransformations));
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}
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return new UnifiedMultiscaleNode(entry.name, entry.axes, nodes);
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}
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}

‎src/main/java/dev/zarr/zarrjava/ome/UnifiedMultiscaleNode.java‎

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package dev.zarr.zarrjava.ome;
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import dev.zarr.zarrjava.ome.metadata.Axis;
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import javax.annotation.Nullable;
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import java.util.List;
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/** A multiscale image node, using v1.0 RFC-8 terminology ("nodes" not "datasets"). */
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public final class UnifiedMultiscaleNode {
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@Nullable
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public final String name;
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public final List<Axis> axes;
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public final List<UnifiedSinglescaleNode> nodes;
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public UnifiedMultiscaleNode(@Nullable String name, List<Axis> axes, List<UnifiedSinglescaleNode> nodes) {
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this.name = name;
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this.axes = axes;
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this.nodes = nodes;
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}
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}

‎src/main/java/dev/zarr/zarrjava/ome/UnifiedSinglescaleNode.java‎

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package dev.zarr.zarrjava.ome;
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import dev.zarr.zarrjava.ome.metadata.CoordinateTransformation;
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import java.util.List;
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/** A single scale level within a multiscale image, using v1.0 RFC-8 terminology. */
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public final class UnifiedSinglescaleNode {
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public final String path;
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public final List<CoordinateTransformation> coordinateTransformations;
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public UnifiedSinglescaleNode(String path, List<CoordinateTransformation> coordinateTransformations) {
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this.path = path;
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this.coordinateTransformations = coordinateTransformations;
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}
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}

‎src/main/java/dev/zarr/zarrjava/ome/metadata/Axis.java‎

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package dev.zarr.zarrjava.ome.metadata;
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import com.fasterxml.jackson.annotation.JsonCreator;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import javax.annotation.Nullable;
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@JsonInclude(JsonInclude.Include.NON_NULL)
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public final class Axis {
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public final String name;
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@Nullable
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public final String type;
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@Nullable
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public final String unit;
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@Nullable
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public final Boolean discrete;
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@Nullable
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@JsonProperty("long_name")
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public final String longName;
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@JsonCreator(mode = JsonCreator.Mode.PROPERTIES)
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public Axis(
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@JsonProperty(value = "name", required = true) String name,
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@Nullable @JsonProperty("type") String type,
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@Nullable @JsonProperty("unit") String unit,
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@Nullable @JsonProperty("discrete") Boolean discrete,
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@Nullable @JsonProperty("long_name") String longName
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) {
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this.name = name;
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this.type = type;
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this.unit = unit;
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this.discrete = discrete;
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this.longName = longName;
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}
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public Axis(String name, @Nullable String type, @Nullable String unit) {
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this(name, type, unit, null, null);
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}
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}

‎src/main/java/dev/zarr/zarrjava/ome/metadata/CoordinateTransformation.java‎

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package dev.zarr.zarrjava.ome.metadata;
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import com.fasterxml.jackson.annotation.JsonCreator;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import javax.annotation.Nullable;
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import java.util.List;
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@JsonInclude(JsonInclude.Include.NON_NULL)
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public final class CoordinateTransformation {
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public final String type;
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@Nullable
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public final List<Double> scale;
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@Nullable
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public final List<Double> translation;
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@Nullable
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public final String path;
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@JsonCreator(mode = JsonCreator.Mode.PROPERTIES)
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public CoordinateTransformation(
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@JsonProperty(value = "type", required = true) String type,
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@Nullable @JsonProperty("scale") List<Double> scale,
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@Nullable @JsonProperty("translation") List<Double> translation,
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@Nullable @JsonProperty("path") String path
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) {
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this.type = type;
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this.scale = scale;
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this.translation = translation;
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this.path = path;
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}
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public static CoordinateTransformation scale(List<Double> scale) {
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return new CoordinateTransformation("scale", scale, null, null);
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}
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public static CoordinateTransformation translation(List<Double> translation) {
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return new CoordinateTransformation("translation", null, translation, null);
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}
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public static CoordinateTransformation identity() {
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return new CoordinateTransformation("identity", null, null, null);
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}
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}

‎src/main/java/dev/zarr/zarrjava/ome/metadata/Dataset.java‎

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package dev.zarr.zarrjava.ome.metadata;
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import com.fasterxml.jackson.annotation.JsonCreator;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import java.util.List;
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public final class Dataset {
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public final String path;
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@JsonProperty("coordinateTransformations")
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public final List<CoordinateTransformation> coordinateTransformations;
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@JsonCreator(mode = JsonCreator.Mode.PROPERTIES)
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public Dataset(
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@JsonProperty(value = "path", required = true) String path,
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@JsonProperty(value = "coordinateTransformations", required = true)
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List<CoordinateTransformation> coordinateTransformations
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) {
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this.path = path;
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this.coordinateTransformations = coordinateTransformations;
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}
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}

‎src/main/java/dev/zarr/zarrjava/ome/metadata/MultiscalesEntry.java‎

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package dev.zarr.zarrjava.ome.metadata;
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import com.fasterxml.jackson.annotation.JsonCreator;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import javax.annotation.Nullable;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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@JsonInclude(JsonInclude.Include.NON_NULL)
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public final class MultiscalesEntry {
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public final List<Axis> axes;
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public final List<Dataset> datasets;
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@Nullable
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@JsonProperty("coordinateTransformations")
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public final List<CoordinateTransformation> coordinateTransformations;
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@Nullable
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public final String name;
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@Nullable
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public final String type;
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@Nullable
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public final Map<String, Object> metadata;
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@Nullable
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public final String version;
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@JsonCreator(mode = JsonCreator.Mode.PROPERTIES)
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public MultiscalesEntry(
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@JsonProperty(value = "axes", required = true) List<Axis> axes,
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@JsonProperty(value = "datasets", required = true) List<Dataset> datasets,
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@Nullable @JsonProperty("coordinateTransformations") List<CoordinateTransformation> coordinateTransformations,
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@Nullable @JsonProperty("name") String name,
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@Nullable @JsonProperty("type") String type,
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@Nullable @JsonProperty("metadata") Map<String, Object> metadata,
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@Nullable @JsonProperty("version") String version
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) {
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this.axes = axes;
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this.datasets = datasets;
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this.coordinateTransformations = coordinateTransformations;
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this.name = name;
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this.type = type;
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this.metadata = metadata;
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this.version = version;
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}
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public MultiscalesEntry(List<Axis> axes, List<Dataset> datasets) {
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this(axes, datasets, null, null, null, null, null);
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}
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/** Returns a new MultiscalesEntry with the given dataset appended. */
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public MultiscalesEntry withDataset(Dataset dataset) {
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List<Dataset> updated = new ArrayList<>(this.datasets);
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updated.add(dataset);
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return new MultiscalesEntry(axes, updated, coordinateTransformations, name, type, metadata, version);
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}
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}

‎src/main/java/dev/zarr/zarrjava/ome/metadata/OmeMetadata.java‎

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package dev.zarr.zarrjava.ome.metadata;
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import com.fasterxml.jackson.annotation.JsonCreator;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import java.util.List;
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/** OME-Zarr metadata stored under {@code attributes["ome"]} (v0.5). */
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public final class OmeMetadata {
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public final String version;
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public final List<MultiscalesEntry> multiscales;
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@JsonCreator(mode = JsonCreator.Mode.PROPERTIES)
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public OmeMetadata(
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@JsonProperty(value = "version", required = true) String version,
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@JsonProperty(value = "multiscales", required = true) List<MultiscalesEntry> multiscales
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) {
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this.version = version;
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this.multiscales = multiscales;
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}
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}

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