add OmeZarrUserGuideExamplesTest

Author: brokkoli71

USERGUIDE-OME-ZARR.md

@@ -52,7 +52,7 @@ Navigation:
 - `Plate.openWell(String rowColPath)` (for example `"A/1"`)
 - `Well.openImage(String path)` (for example `"0"`)
 
-## Version-specific typed metadata (when needed)
+## Version-specific typed metadata
 
 If you need the raw version-specific metadata model instead of normalized `MultiscalesEntry`:
 
@@ -72,7 +72,6 @@ import dev.zarr.zarrjava.store.StoreHandle;
 StoreHandle imageHandle = new FilesystemStore("/data/ome/image.zarr").resolve();
 MultiscaleImage image = MultiscaleImage.open(imageHandle);
 
-// Drive viewer model
 int scaleCount = image.getScaleLevelCount();
 java.util.List<String> axisNames = image.getAxisNames();
 dev.zarr.zarrjava.ome.metadata.MultiscalesEntry entry0 = image.getMultiscaleNode(0);
@@ -89,7 +88,7 @@ if (!labels.isEmpty()) {
 StoreHandle plateHandle = new FilesystemStore("/data/ome/plate.zarr").resolve();
 Plate plate = Plate.open(plateHandle);
 Well well = plate.openWell("A/1");
-MultiscaleImage fov = well.openImage("0");
+MultiscaleImage wellImage = well.openImage("0");
 ```
 
 ## Write example
@@ -111,7 +110,7 @@ import java.util.Collections;
 StoreHandle out = new FilesystemStore("/tmp/ome_v05.zarr").resolve();
 MultiscalesEntry ms = new MultiscalesEntry(
     Arrays.asList(new Axis("y", "space", "micrometer"), new Axis("x", "space", "micrometer")),
-    Collections.emptyList()
+    Collections.<Dataset>emptyList());
 );
 dev.zarr.zarrjava.ome.v0_5.MultiscaleImage written = dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.create(out, ms);
 

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

@@ -0,0 +1,90 @@
+package dev.zarr.zarrjava.ome;
+
+import dev.zarr.zarrjava.ZarrTest;
+import dev.zarr.zarrjava.ome.metadata.Axis;
+import dev.zarr.zarrjava.ome.metadata.CoordinateTransformation;
+import dev.zarr.zarrjava.ome.metadata.Dataset;
+import dev.zarr.zarrjava.ome.metadata.MultiscalesEntry;
+import dev.zarr.zarrjava.store.FilesystemStore;
+import dev.zarr.zarrjava.store.StoreHandle;
+import dev.zarr.zarrjava.v3.Array;
+import dev.zarr.zarrjava.v3.DataType;
+import org.junit.jupiter.api.Test;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class OmeZarrUserGuideExamplesTest extends ZarrTest {
+
+    private StoreHandle storeHandle(java.nio.file.Path path) throws Exception {
+        return new FilesystemStore(path).resolve();
+    }
+
+    @Test
+    void userGuideReadingExampleWorks() throws Exception {
+        StoreHandle imageHandle = storeHandle(TESTDATA.resolve("ome/v0.5"));
+        MultiscaleImage image = MultiscaleImage.open(imageHandle);
+
+        int scaleCount = image.getScaleLevelCount();
+        List<String> axisNames = image.getAxisNames();
+        dev.zarr.zarrjava.ome.metadata.MultiscalesEntry entry0 = image.getMultiscaleNode(0);
+
+        dev.zarr.zarrjava.core.Array s0 = image.openScaleLevel(0);
+        ucar.ma2.Array full = s0.read();
+        ucar.ma2.Array subset = s0.read(new long[]{0, 0, 0, 0, 0}, new long[]{1, 1, 4, 8, 8});
+
+        assertTrue(scaleCount > 0);
+        assertFalse(axisNames.isEmpty());
+        assertNotNull(entry0);
+        assertArrayEquals(new int[]{1, 2, 8, 16, 16}, full.getShape());
+        assertArrayEquals(new int[]{1, 1, 4, 8, 8}, subset.getShape());
+
+        List<String> labels = image.getLabels();
+        assertEquals(Collections.singletonList("nuclei"), labels);
+        MultiscaleImage labelImage = image.openLabel(labels.get(0));
+        assertEquals(Arrays.asList("z", "y", "x"), labelImage.getAxisNames());
+
+        StoreHandle plateHandle = storeHandle(TESTDATA.resolve("ome/v0.5_hcs"));
+        Plate plate = Plate.open(plateHandle);
+        Well well = plate.openWell("A/1");
+        MultiscaleImage wellImage = well.openImage("0");
+        assertEquals(Arrays.asList("t", "c", "z", "y", "x"), wellImage.getAxisNames());
+    }
+
+    @Test
+    void userGuideWritingExampleWorks() throws Exception {
+        StoreHandle out = storeHandle(TESTOUTPUT.resolve("ome_userguide_v05.zarr"));
+        MultiscalesEntry ms = new MultiscalesEntry(
+                Arrays.asList(new Axis("y", "space", "micrometer"), new Axis("x", "space", "micrometer")),
+                Collections.<Dataset>emptyList());
+        dev.zarr.zarrjava.ome.v0_5.MultiscaleImage written = dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.create(out, ms);
+
+        written.createScaleLevel(
+                "s0",
+                Array.metadataBuilder()
+                        .withShape(1024, 1024)
+                        .withChunkShape(256, 256)
+                        .withDataType(DataType.UINT16)
+                        .build(),
+                Collections.singletonList(CoordinateTransformation.scale(Arrays.asList(1.0, 1.0))));
+        written.createScaleLevel(
+                "s1",
+                Array.metadataBuilder()
+                        .withShape(512, 512)
+                        .withChunkShape(256, 256)
+                        .withDataType(DataType.UINT16)
+                        .build(),
+                Collections.singletonList(CoordinateTransformation.scale(Arrays.asList(2.0, 2.0))));
+
+        MultiscaleImage reopened = MultiscaleImage.open(out);
+        assertInstanceOf(dev.zarr.zarrjava.ome.v0_5.MultiscaleImage.class, reopened);
+        assertEquals(2, reopened.getScaleLevelCount());
+        assertEquals("s0", reopened.getMultiscaleNode(0).datasets.get(0).path);
+        assertEquals("s1", reopened.getMultiscaleNode(0).datasets.get(1).path);
+        assertEquals(Arrays.asList(2.0, 2.0),
+                reopened.getMultiscaleNode(0).datasets.get(1).coordinateTransformations.get(0).scale);
+    }
+}