From fc0bc6b2e39f41835f4b847aee20f79cbd7ca433 Mon Sep 17 00:00:00 2001
From: Christian Tischer <christian.tischer@embl.de>
Date: Sat, 6 Jul 2024 09:39:48 +0200
Subject: [PATCH] Add examples for opening OMEZarr

---
 src/test/java/develop/OMEZarrSavingSpeed.java |  2 +-
 src/test/java/examples/N5ViewerExample.java   | 12 +++++++
 .../java/examples/OpenOMEZarrExample.java     | 32 +++++++++++++++++++
 3 files changed, 45 insertions(+), 1 deletion(-)
 create mode 100644 src/test/java/examples/N5ViewerExample.java
 create mode 100644 src/test/java/examples/OpenOMEZarrExample.java

diff --git a/src/test/java/develop/OMEZarrSavingSpeed.java b/src/test/java/develop/OMEZarrSavingSpeed.java
index 0ac9a23..15f7e5e 100644
--- a/src/test/java/develop/OMEZarrSavingSpeed.java
+++ b/src/test/java/develop/OMEZarrSavingSpeed.java
@@ -8,7 +8,7 @@ public class OMEZarrSavingSpeed
 {
     public static void main( String[] args )
     {
-        int size = 100;
+        int size = 100; // => 2 s
         ImagePlus imp = IJ.createImage( "image", size, size, size, 8 );
 
         long start = System.currentTimeMillis();
diff --git a/src/test/java/examples/N5ViewerExample.java b/src/test/java/examples/N5ViewerExample.java
new file mode 100644
index 0000000..aa242f3
--- /dev/null
+++ b/src/test/java/examples/N5ViewerExample.java
@@ -0,0 +1,12 @@
+package examples;
+
+import org.janelia.saalfeldlab.n5.bdv.N5Viewer;
+
+public class N5ViewerExample
+{
+    public static void main( String[] args )
+    {
+        String uri = "/Users/tischer/Downloads/20240524_1_s2.zarr";
+        N5Viewer.show( uri );
+    }
+}
diff --git a/src/test/java/examples/OpenOMEZarrExample.java b/src/test/java/examples/OpenOMEZarrExample.java
new file mode 100644
index 0000000..1b567bb
--- /dev/null
+++ b/src/test/java/examples/OpenOMEZarrExample.java
@@ -0,0 +1,32 @@
+package examples;
+
+import bdv.cache.SharedQueue;
+import bdv.util.BdvFunctions;
+import bdv.viewer.SourceAndConverter;
+import org.embl.mobie.io.imagedata.N5ImageData;
+import org.jruby.RubyProcess;
+
+import java.util.List;
+
+public class OpenOMEZarrExample
+{
+    public static void main( String[] args )
+    {
+        //String uri = "https://s3.embl.de/imatrec/IMATREC_HiTT_20240414_AS/TAL_20to200_20230627_NA_01_epo_05.ome.zarr";
+        String uri = "/Users/tischer/Downloads/20240524_1_s2.zarr";
+
+        long start = System.currentTimeMillis();
+        N5ImageData< ? > imageData = new N5ImageData<>(
+                uri,
+                new SharedQueue( Math.max( 1, Runtime.getRuntime().availableProcessors() / 2 ) )
+        );
+        imageData.getSourcesAndConverters(); // triggers actual opening of the data
+        System.out.println("Opened " + uri );
+        System.out.println("Opening time [ms]: " + (System.currentTimeMillis() - start ) );
+
+        BdvFunctions.show(
+                imageData.getSourcesAndConverters(),
+                imageData.getNumTimepoints(),
+                imageData.getBdvOptions());
+    }
+}