3.0.2

mobie · Jul 10, 2024 · fa26773 · fa26773
1 parent fc0bc6b
commit fa26773
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Showing 3 changed files with 47 additions and 6 deletions.
diff --git a/src/main/java/org/embl/mobie/io/OMEZarrWriter.java b/src/main/java/org/embl/mobie/io/OMEZarrWriter.java
@@ -41,6 +41,7 @@
 import org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter;
 import org.jetbrains.annotations.NotNull;
 
+import java.lang.reflect.Field;
 import java.net.URISyntaxException;
 import java.sql.Array;
 import java.util.ArrayList;
@@ -65,18 +66,16 @@ public static void write( ImagePlus imp, String uri, ImageType imageType, boolea
 
         // TODO: https://github.com/saalfeldlab/n5-ij/issues/82
         String chunkSizeArg = getChunkSizeArg( imp );
-        IJ.log("Using chunk sizes: " + chunkSizeArg );
+
+        IJ.log("Writing data to: " + uri );
+        IJ.log("Chunking: " + chunkSizeArg );
 
         try
         {
             N5URI n5URI = new N5URI( uri );
             String containerPath = n5URI.getContainerPath();
             String groupPath = n5URI.getGroupPath();
 
-            // TODO: set number of threads!
-            //    https://github.com/saalfeldlab/n5-ij/issues/83
-            //    we could do it now with reflection...
-
             N5ScalePyramidExporter exporter = new N5ScalePyramidExporter(
                     imp,
                     containerPath,
@@ -88,13 +87,29 @@ public static void write( ImagePlus imp, String uri, ImageType imageType, boolea
                     N5Importer.MetadataOmeZarrKey,
                     GZIP_COMPRESSION
             );
+
+            // TODO: https://github.com/saalfeldlab/n5-ij/issues/83
+            Field nThreads = N5ScalePyramidExporter.class.getDeclaredField( "nThreads" );
+            nThreads.setAccessible( true );
+            nThreads.setInt( exporter, Runtime.getRuntime().availableProcessors() - 1 );
+
             exporter.setOverwrite( overwrite );
+
+            // TODO: Log progress: https://github.com/saalfeldlab/n5-ij/issues/84
             exporter.run();
         }
         catch ( URISyntaxException e )
         {
             throw new RuntimeException( e );
         }
+        catch ( NoSuchFieldException e )
+        {
+            throw new RuntimeException( e );
+        }
+        catch ( IllegalAccessException e )
+        {
+            throw new RuntimeException( e );
+        }
 
         // TODO: If we wanted to give the dataset a name we also have to
         //       update how we refer to such an image or segmentation in the dataset.JSON

diff --git a/src/test/java/develop/WriteOMEZarr.java b/src/test/java/develop/WriteOMEZarr.java
@@ -14,7 +14,7 @@
 import static org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter.GZIP_COMPRESSION;
 import static org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter.ZARR_FORMAT;
 
-public class WriteOMEZarr
+public class  WriteOMEZarr
 {
     public static void main( String[] args )
     {

diff --git a/src/test/java/examples/SaveOMEZarrExample.java b/src/test/java/examples/SaveOMEZarrExample.java
@@ -0,0 +1,26 @@
+package examples;
+
+import bdv.cache.SharedQueue;
+import bdv.util.BdvFunctions;
+import ij.IJ;
+import ij.ImagePlus;
+import net.imagej.ImageJ;
+import org.embl.mobie.io.OMEZarrWriter;
+import org.embl.mobie.io.imagedata.N5ImageData;
+
+public class SaveOMEZarrExample
+{
+    public static void main( String[] args )
+    {
+        new ImageJ().ui().showUI(); // initialise services such that progress bar can be shown
+
+        ImagePlus imp = IJ.createImage( "image", 500, 500, 500, 8 );
+
+        long start = System.currentTimeMillis();
+        OMEZarrWriter.write( imp,
+                "/Users/tischer/Desktop/zarr-test",
+                OMEZarrWriter.ImageType.Intensities,
+                true );
+        System.out.println("Saving time [ms]: " + ( System.currentTimeMillis() - start ));
+    }
+}