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move the namespace of ome to dev.zarr.zarrjava.experimental.ome
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Lines changed: 874 additions & 874 deletions

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‎USERGUIDE-OME-ZARR.md‎

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## Scope and supported versions
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`dev.zarr.zarrjava.ome` supports:
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`dev.zarr.zarrjava.experimental.ome` supports:
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- v0.4 (Zarr v2 layout)
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- v0.5 (Zarr v3 layout)
@@ -64,7 +64,7 @@ If you need the raw version-specific metadata model instead of normalized `Multi
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## v0.6 Scene metadata
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Scene roots (groups with `ome.scene`) are supported via `dev.zarr.zarrjava.ome.v0_6.Scene`:
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Scene roots (groups with `ome.scene`) are supported via `dev.zarr.zarrjava.experimental.ome.v0_6.Scene`:
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- `Scene.openScene(StoreHandle)` / `Scene.open(StoreHandle)`
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- `Scene.createScene(StoreHandle, SceneMetadata)` / `Scene.create(...)`
@@ -79,9 +79,9 @@ Notes:
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## Read example
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```java
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import dev.zarr.zarrjava.ome.MultiscaleImage;
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import dev.zarr.zarrjava.ome.Plate;
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import dev.zarr.zarrjava.ome.Well;
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import dev.zarr.zarrjava.experimental.ome.MultiscaleImage;
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import dev.zarr.zarrjava.experimental.ome.Plate;
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import dev.zarr.zarrjava.experimental.ome.Well;
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import dev.zarr.zarrjava.store.FilesystemStore;
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import dev.zarr.zarrjava.store.StoreHandle;
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@@ -90,7 +90,7 @@ MultiscaleImage image = MultiscaleImage.open(imageHandle);
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int scaleCount = image.getScaleLevelCount();
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java.util.List<String> axisNames = image.getAxisNames();
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dev.zarr.zarrjava.ome.metadata.MultiscalesEntry entry0 = image.getMultiscaleNode(0);
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dev.zarr.zarrjava.experimental.ome.metadata.MultiscalesEntry entry0 = image.getMultiscaleNode(0);
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dev.zarr.zarrjava.core.Array s0 = image.openScaleLevel(0);
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ucar.ma2.Array full = s0.read();
@@ -112,9 +112,9 @@ MultiscaleImage wellImage = well.openImage("0");
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Creation is version-specific, but the pattern is the same: create node with version metadata, then append levels/datasets with scale transforms. For example, for v0.5:
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```java
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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.experimental.ome.metadata.Axis;
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import dev.zarr.zarrjava.experimental.ome.metadata.CoordinateTransformation;
117+
import dev.zarr.zarrjava.experimental.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;
@@ -128,7 +128,7 @@ MultiscalesEntry ms = new MultiscalesEntry(
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Arrays.asList(new Axis("y", "space", "micrometer"), new Axis("x", "space", "micrometer")),
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Collections.<Dataset>emptyList());
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);
131-
dev.zarr.zarrjava.ome.v0_5.MultiscaleImage written = dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.create(out, ms);
131+
dev.zarr.zarrjava.experimental.ome.v0_5.MultiscaleImage written = dev.zarr.zarrjava.experimental.ome.v0_5.MultiscaleImage.create(out, ms);
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written.createScaleLevel(
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"s0",

src/main/java/dev/zarr/zarrjava/ome/MultiscaleImage.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/MultiscaleImage.java

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@@ -1,8 +1,8 @@
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package dev.zarr.zarrjava.ome;
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package dev.zarr.zarrjava.experimental.ome;
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import dev.zarr.zarrjava.ZarrException;
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import dev.zarr.zarrjava.core.Node;
5-
import dev.zarr.zarrjava.ome.metadata.MultiscalesEntry;
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import dev.zarr.zarrjava.experimental.ome.metadata.MultiscalesEntry;
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import dev.zarr.zarrjava.store.StoreHandle;
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import dev.zarr.zarrjava.utils.Utils;
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@@ -43,7 +43,7 @@ public interface MultiscaleImage {
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default List<String> getAxisNames() throws ZarrException {
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MultiscalesEntry entry = getMultiscaleNode(0);
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List<String> names = new ArrayList<>();
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for (dev.zarr.zarrjava.ome.metadata.Axis axis : entry.axes) {
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for (dev.zarr.zarrjava.experimental.ome.metadata.Axis axis : entry.axes) {
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names.add(axis.name);
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}
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return names;
@@ -115,9 +115,9 @@ static MultiscaleImage open(StoreHandle storeHandle) throws IOException, ZarrExc
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com.fasterxml.jackson.databind.JsonNode omeNode = attrs.get("ome");
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String version = omeNode.has("version") ? omeNode.get("version").asText() : "";
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if (version.startsWith("0.6")) {
118-
return dev.zarr.zarrjava.ome.v0_6.MultiscaleImage.openMultiscaleImage(storeHandle);
118+
return dev.zarr.zarrjava.experimental.ome.v0_6.MultiscaleImage.openMultiscaleImage(storeHandle);
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}
120-
return dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.openMultiscaleImage(storeHandle);
120+
return dev.zarr.zarrjava.experimental.ome.v0_5.MultiscaleImage.openMultiscaleImage(storeHandle);
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}
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}
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@@ -128,7 +128,7 @@ static MultiscaleImage open(StoreHandle storeHandle) throws IOException, ZarrExc
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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")) {
131-
return dev.zarr.zarrjava.ome.v0_4.MultiscaleImage.openMultiscaleImage(storeHandle);
131+
return dev.zarr.zarrjava.experimental.ome.v0_4.MultiscaleImage.openMultiscaleImage(storeHandle);
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}
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}
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src/main/java/dev/zarr/zarrjava/ome/MultiscalesMetadataImage.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/MultiscalesMetadataImage.java

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package dev.zarr.zarrjava.ome;
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package dev.zarr.zarrjava.experimental.ome;
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import dev.zarr.zarrjava.ZarrException;
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import dev.zarr.zarrjava.ome.metadata.transform.CoordinateTransformation;
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import dev.zarr.zarrjava.ome.metadata.MultiscalesEntry;
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import dev.zarr.zarrjava.experimental.ome.metadata.transform.CoordinateTransformation;
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import dev.zarr.zarrjava.experimental.ome.metadata.MultiscalesEntry;
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import java.io.IOException;
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import java.util.List;

src/main/java/dev/zarr/zarrjava/ome/OmeObjectMappers.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/OmeObjectMappers.java

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package dev.zarr.zarrjava.ome;
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package dev.zarr.zarrjava.experimental.ome;
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import com.fasterxml.jackson.core.JsonParser;
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import com.fasterxml.jackson.databind.DeserializationContext;

src/main/java/dev/zarr/zarrjava/ome/OmeV2Group.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/OmeV2Group.java

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package dev.zarr.zarrjava.ome;
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package dev.zarr.zarrjava.experimental.ome;
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import com.fasterxml.jackson.core.type.TypeReference;
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import dev.zarr.zarrjava.ZarrException;

src/main/java/dev/zarr/zarrjava/ome/OmeV3Group.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/OmeV3Group.java

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package dev.zarr.zarrjava.ome;
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package dev.zarr.zarrjava.experimental.ome;
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import com.fasterxml.jackson.core.type.TypeReference;
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import dev.zarr.zarrjava.ZarrException;

src/main/java/dev/zarr/zarrjava/ome/Plate.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/Plate.java

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package dev.zarr.zarrjava.ome;
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package dev.zarr.zarrjava.experimental.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.ome.metadata.PlateMetadata;
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import dev.zarr.zarrjava.experimental.ome.metadata.PlateMetadata;
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import dev.zarr.zarrjava.store.StoreHandle;
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import dev.zarr.zarrjava.utils.Utils;
88

@@ -43,9 +43,9 @@ static Plate open(StoreHandle storeHandle) throws IOException, ZarrException {
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com.fasterxml.jackson.databind.JsonNode omeNode = attrs.get("ome");
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String version = omeNode.has("version") ? omeNode.get("version").asText() : "";
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if (version.startsWith("0.6")) {
46-
return dev.zarr.zarrjava.ome.v0_6.Plate.openPlate(storeHandle);
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return dev.zarr.zarrjava.experimental.ome.v0_6.Plate.openPlate(storeHandle);
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}
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return dev.zarr.zarrjava.ome.v0_5.Plate.openPlate(storeHandle);
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return dev.zarr.zarrjava.experimental.ome.v0_5.Plate.openPlate(storeHandle);
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}
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}
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@@ -56,7 +56,7 @@ static Plate open(StoreHandle storeHandle) throws IOException, ZarrException {
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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("plate")) {
59-
return dev.zarr.zarrjava.ome.v0_4.Plate.openPlate(storeHandle);
59+
return dev.zarr.zarrjava.experimental.ome.v0_4.Plate.openPlate(storeHandle);
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}
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}
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src/main/java/dev/zarr/zarrjava/ome/Well.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/Well.java

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package dev.zarr.zarrjava.ome;
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package dev.zarr.zarrjava.experimental.ome;
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import dev.zarr.zarrjava.ZarrException;
44
import dev.zarr.zarrjava.core.Node;
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import dev.zarr.zarrjava.ome.metadata.WellMetadata;
5+
import dev.zarr.zarrjava.experimental.ome.metadata.WellMetadata;
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import dev.zarr.zarrjava.store.StoreHandle;
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import dev.zarr.zarrjava.utils.Utils;
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@@ -43,9 +43,9 @@ static Well open(StoreHandle storeHandle) throws IOException, ZarrException {
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com.fasterxml.jackson.databind.JsonNode omeNode = attrs.get("ome");
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String version = omeNode.has("version") ? omeNode.get("version").asText() : "";
4545
if (version.startsWith("0.6")) {
46-
return dev.zarr.zarrjava.ome.v0_6.Well.openWell(storeHandle);
46+
return dev.zarr.zarrjava.experimental.ome.v0_6.Well.openWell(storeHandle);
4747
}
48-
return dev.zarr.zarrjava.ome.v0_5.Well.openWell(storeHandle);
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return dev.zarr.zarrjava.experimental.ome.v0_5.Well.openWell(storeHandle);
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}
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}
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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("well")) {
59-
return dev.zarr.zarrjava.ome.v0_4.Well.openWell(storeHandle);
59+
return dev.zarr.zarrjava.experimental.ome.v0_4.Well.openWell(storeHandle);
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}
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}
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src/main/java/dev/zarr/zarrjava/ome/metadata/Acquisition.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/metadata/Acquisition.java

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package dev.zarr.zarrjava.ome.metadata;
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package dev.zarr.zarrjava.experimental.ome.metadata;
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import com.fasterxml.jackson.annotation.JsonCreator;
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import com.fasterxml.jackson.annotation.JsonInclude;

src/main/java/dev/zarr/zarrjava/ome/metadata/Axis.java renamed to src/main/java/dev/zarr/zarrjava/experimental/ome/metadata/Axis.java

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package dev.zarr.zarrjava.ome.metadata;
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package dev.zarr.zarrjava.experimental.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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