Fix boundary issues for ome-zarr writing

pom.xml

@@ -85,6 +85,10 @@
 
         <!-- EMBL CBA -->
         <imagej-utils.version>0.6.4</imagej-utils.version>
+
+        <!-- spim_data.version required for fix that closes xml files properly after creation - should soon be in main fiji	-->
+        <spim_data.version>2.2.5</spim_data.version>
+
         <!-- NB: Deploy releases to the SciJava Maven repository. -->
         <releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
     </properties>
@@ -148,6 +152,11 @@
             <groupId>sc.fiji</groupId>
             <artifactId>bigdataviewer_fiji</artifactId>
         </dependency>
+        <dependency>
+            <groupId>sc.fiji</groupId>
+            <artifactId>spim_data</artifactId>
+            <version>${spim_data.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.janelia.saalfeldlab</groupId>
             <artifactId>n5-aws-s3</artifactId>
@@ -203,7 +212,13 @@
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-api</artifactId>
-            <version>5.5.2</version>
+            <version>5.8.2</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <version>5.8.2</version>
             <scope>test</scope>
         </dependency>
     </dependencies>

src/main/java/org/embl/mobie/io/ome/zarr/util/N5ZarrImageReader.java

@@ -29,7 +29,6 @@ static GsonBuilder initGsonBuilder(final GsonBuilder gsonBuilder) {
 
         gsonBuilder.registerTypeAdapter(DType.class, new DType.JsonAdapter());
         gsonBuilder.registerTypeAdapter(ZarrCompressor.class, ZarrCompressor.jsonAdapter);
-        gsonBuilder.serializeNulls();
         gsonBuilder.registerTypeAdapter(ZarrAxes.class, new ZarrAxesAdapter());
         gsonBuilder.registerTypeAdapter(N5Reader.Version.class, new VersionAdapter());
         gsonBuilder.setPrettyPrinting();

src/main/java/org/embl/mobie/io/ome/zarr/writers/imgplus/WriteSequenceToN5OmeZarr.java

@@ -22,6 +22,7 @@
 import net.imglib2.util.Cast;
 import org.embl.mobie.io.n5.util.DownsampleBlock;
 import org.embl.mobie.io.n5.util.ExportScalePyramid;
+import org.embl.mobie.io.ome.zarr.util.N5OMEZarrCacheArrayLoader;
 import org.embl.mobie.io.ome.zarr.util.OmeZarrMultiscales;
 import org.embl.mobie.io.ome.zarr.util.ZarrAxes;
 import org.embl.mobie.io.ome.zarr.util.ZarrDatasetAttributes;
@@ -337,6 +338,22 @@ private long[] addSetupAndTimeToShape(long[] zyxShape) {
             return shape;
         }
 
+        private long[] removeSetupAndTimeFromShape( long[] shape ) {
+            long[] xyzShape = new long[3];
+            for (int i = 0; i < 3; i++) {
+                xyzShape[i] = shape[i];
+            }
+            return xyzShape;
+        }
+
+        private int[] removeSetupAndTimeFromShape( int[] shape ) {
+            int[] xyzShape = new int[3];
+            for (int i = 0; i < 3; i++) {
+                xyzShape[i] = shape[i];
+            }
+            return xyzShape;
+        }
+
         @Override
         public OmeZarrDataset createDataset(final int level, final long[] zyxDimensions, final int[] zyxBlockSize) throws IOException {
             // create dataset directory + metadata
@@ -370,12 +387,14 @@ public void flush(final OmeZarrDataset dataset) {
 
         @Override
         public RandomAccessibleInterval<T> getImage(final int level) throws IOException {
-            final String pathName = getPathName(level);
-            final DatasetAttributes attributes = zarrWriter.getDatasetAttributes("s" + level);
-            final long[] dimensions = attributes.getDimensions();
-            final int[] cellDimensions = attributes.getBlockSize();
+            // this needs to return the zyx image for the current timepoint and channel (as we are only chunking in zyx)
+            final String pathName = String.format("s%d", level); // only include level as rest is handled by N5OmeZarrCacheArrayLoader
+            final DatasetAttributes attributes = zarrWriter.getDatasetAttributes( pathName );
+            final long[] dimensions = removeSetupAndTimeFromShape( attributes.getDimensions() );
+            final int[] cellDimensions = removeSetupAndTimeFromShape( attributes.getBlockSize() );
             final CellGrid grid = new CellGrid(dimensions, cellDimensions);
-            final SimpleCacheArrayLoader<?> cacheArrayLoader = N5ImageLoader.createCacheArrayLoader(zarrWriter, pathName);
+            final SimpleCacheArrayLoader<?> cacheArrayLoader =
+                    new N5OMEZarrCacheArrayLoader<>( zarrWriter, pathName, setupId, timepointId, attributes, grid, axes );
             return new ReadOnlyCachedCellImgFactory().createWithCacheLoader(
                     dimensions, type,
                     key -> {

src/test/java/spimdata/OmeZarrWithWriterTest.java

@@ -1,12 +1,106 @@
 package spimdata;
 
+import ij.IJ;
+import ij.ImagePlus;
+import mpicbg.spim.data.SpimDataException;
+import net.imglib2.realtransform.AffineTransform3D;
+import org.embl.mobie.io.ImageDataFormat;
+import org.embl.mobie.io.SpimDataOpener;
+import org.embl.mobie.io.n5.util.DownsampleBlock;
+import org.embl.mobie.io.n5.writers.WriteImgPlusToN5;
+import org.embl.mobie.io.ome.zarr.writers.imgplus.WriteImgPlusToN5BdvOmeZarr;
+import org.embl.mobie.io.ome.zarr.writers.imgplus.WriteImgPlusToN5OmeZarr;
+import org.janelia.saalfeldlab.n5.Compression;
+import org.janelia.saalfeldlab.n5.GzipCompression;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+
+import static org.apache.commons.io.FilenameUtils.removeExtension;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
 public class OmeZarrWithWriterTest {
-//    public static void main( String[] args ) {
-//        ImagePlus imp = IJ.openImage("");
-//        new WriteImgPlusToN5OmeZarr().export(imp, "src/test/resources/zyx.ome.zarr",
-//                DownsampleBlock.DownsamplingMethod.Average, new GzipCompression());
-//
-//        new WriteImgPlusToN5BdvOmeZarr().export(imp, "src/test/resources/writingTest.xml",
-//                DownsampleBlock.DownsamplingMethod.Average, new GzipCompression());
-//    }
+
+    private String imageName;
+    private AffineTransform3D sourceTransform;
+    private File tempDir;
+
+    @BeforeEach
+    void setUp( @TempDir Path tempDir ) throws IOException {
+        this.tempDir = tempDir.toFile();
+        imageName = "testImage";
+        sourceTransform = new AffineTransform3D();
+    }
+
+    public static ImagePlus makeImage( String imageName ) {
+        // make an image with random values, same size as the imagej sample head image
+        return IJ.createImage(imageName, "8-bit noise", 186, 226, 27);
+    }
+
+    String writeImageAndGetPath( ImageDataFormat imageDataFormat ) {
+        ImagePlus imp = makeImage( imageName );
+        DownsampleBlock.DownsamplingMethod downsamplingMethod = DownsampleBlock.DownsamplingMethod.Average;
+        Compression compression = new GzipCompression();
+        String filePath;
+
+        // gzip compression by default
+        switch( imageDataFormat ) {
+            case BdvN5:
+                filePath = new File(tempDir, imageName + ".xml").getAbsolutePath();
+                new WriteImgPlusToN5().export(imp, filePath, sourceTransform, downsamplingMethod,
+                        compression, new String[]{imageName} );
+                break;
+
+            case BdvOmeZarr:
+                filePath = new File(tempDir, imageName + ".xml").getAbsolutePath();
+                new WriteImgPlusToN5BdvOmeZarr().export(imp, filePath, sourceTransform,
+                        downsamplingMethod, compression, new String[]{imageName} );
+                break;
+
+            case OmeZarr:
+                filePath = new File(tempDir, imageName + ".ome.zarr").getAbsolutePath();
+                new WriteImgPlusToN5OmeZarr().export(imp, filePath, sourceTransform,
+                        downsamplingMethod, compression, new String[]{imageName});
+                break;
+
+            default:
+                throw new UnsupportedOperationException();
+
+        }
+
+        return filePath;
+    }
+
+    @Test
+    void writeAndReadImageBdvN5() throws SpimDataException {
+        ImageDataFormat format = ImageDataFormat.BdvN5;
+        String xmlPath = writeImageAndGetPath( format );
+        assertTrue( new File(xmlPath).exists() );
+        assertTrue( new File(removeExtension(xmlPath) + ".n5").exists() );
+
+        new SpimDataOpener().openSpimData( xmlPath, format );
+    }
+
+    @Test
+    void writeAndReadImageOmeZarr() throws SpimDataException {
+        ImageDataFormat format = ImageDataFormat.OmeZarr;
+        String zarrPath = writeImageAndGetPath( ImageDataFormat.OmeZarr );
+        assertTrue( new File(zarrPath).exists() );
+
+        new SpimDataOpener().openSpimData( zarrPath, format );
+    }
+
+    @Test
+    void writeAndReadImageBdvOmeZarr() throws SpimDataException {
+        ImageDataFormat format = ImageDataFormat.BdvOmeZarr;
+        String xmlPath = writeImageAndGetPath( ImageDataFormat.BdvOmeZarr );
+        assertTrue( new File(xmlPath).exists() );
+        assertTrue( new File(removeExtension(xmlPath) + ".ome.zarr").exists() );
+
+        new SpimDataOpener().openSpimData( xmlPath, format );
+    }
 }