Update OMEZarrWriterTest

mobie · May 14, 2024 · 16a5cb2 · 16a5cb2
1 parent 44fab8a
commit 16a5cb2
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Showing 3 changed files with 34 additions and 18 deletions.
diff --git a/src/main/java/org/embl/mobie/io/OMEZarrWriter.java b/src/main/java/org/embl/mobie/io/OMEZarrWriter.java
@@ -34,9 +34,12 @@
 import ij.ImagePlus;
 import mpicbg.spim.data.generic.sequence.BasicViewSetup;
 import org.embl.mobie.io.util.IOHelper;
+import org.janelia.saalfeldlab.n5.N5URI;
 import org.janelia.saalfeldlab.n5.ij.N5Importer;
 import org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter;
 
+import java.net.URISyntaxException;
+
 import static org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter.GZIP_COMPRESSION;
 import static org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter.ZARR_FORMAT;
 
@@ -57,9 +60,37 @@ public static void write( ImagePlus imp, String uri, ImageType imageType, boolea
 
         String chunkSizeArg = imp.getNSlices() == 1 ?  "1024,1024,1,1,1" : "96,96,1,96,1"; // X,Y,C,Z,T
 
+
+        try
+        {
+            N5URI n5URI = new N5URI( uri );
+            String containerPath = n5URI.getContainerPath();
+            String groupPath = n5URI.getGroupPath();
+            int a = 1;
+
+            N5ScalePyramidExporter exporter = new N5ScalePyramidExporter(
+                    imp,
+                    containerPath,
+                    groupPath,
+                    ZARR_FORMAT,
+                    chunkSizeArg,
+                    true,
+                    downsampleMethod,
+                    N5Importer.MetadataOmeZarrKey,
+                    GZIP_COMPRESSION
+            );
+
+            exporter.setOverwrite( overwrite );
+            exporter.run();
+        }
+        catch ( URISyntaxException e )
+        {
+            throw new RuntimeException( e );
+        }
+
         // TODO: If we want to give the dataset a name we also have to
         //       update how we refer to such an image or segmentation in the dataset.JSON
-        String n5Dataset = "";
+        //       String n5Dataset = "";
 //        String n5Dataset = imageType.equals( ImageType.Labels ) ? "labels" : "intensities";
 //        if ( imageType.equals( ImageType.Labels ) )
 //        {
@@ -69,22 +100,6 @@ public static void write( ImagePlus imp, String uri, ImageType imageType, boolea
 //        {
 //            uri = IOHelper.combinePath( uri, "intensities" );
 //        }
-
-        N5ScalePyramidExporter exporter = new N5ScalePyramidExporter(
-                imp,
-                uri,
-                n5Dataset,
-                ZARR_FORMAT,
-                chunkSizeArg,
-                true,
-                downsampleMethod,
-                N5Importer.MetadataOmeZarrKey,
-                GZIP_COMPRESSION
-        );
-
-        exporter.setOverwrite( overwrite );
-
-        exporter.run();
     }
 
 }
diff --git a/src/main/java/org/embl/mobie/io/imagedata/N5ImageData.java b/src/main/java/org/embl/mobie/io/imagedata/N5ImageData.java
@@ -20,6 +20,7 @@
 import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;

diff --git a/src/test/java/org/embl/mobie/io/OMEZarrWriterTest.java b/src/test/java/org/embl/mobie/io/OMEZarrWriterTest.java
@@ -13,7 +13,7 @@ public void writeAndReadOMEZarr()
     {
         ImagePlus imp = IJ.createImage( "test", "8-bit ramp", 186, 226, 27 );
 
-        String uri = "src/test/tmp/test.zarr";
+        String uri = "src/test/tmp/test.zarr/image";
 
         OMEZarrWriter.write( imp,
                 uri,