From a6ed52c6891af9be400b7ca8ad1faacb06c65a2c Mon Sep 17 00:00:00 2001
From: Christian Tischer <christian.tischer@embl.de>
Date: Thu, 25 Jul 2024 11:47:36 +0200
Subject: [PATCH] Fixes https://github.com/mobie/mobie-viewer-fiji/issues/1181

---
 .../embl/mobie/io/imagedata/N5ImageData.java  |  5 +--
 .../java/org/embl/mobie/io/util/S3Utils.java  |  2 ++
 .../develop/LazyConvertAndSaveOMEZarr.java    | 32 +++++++++++++++++++
 .../OpenOMEZarrFromS3WithCredentials.java     | 24 ++++++++++++++
 4 files changed, 59 insertions(+), 4 deletions(-)
 create mode 100644 src/test/java/develop/LazyConvertAndSaveOMEZarr.java
 create mode 100644 src/test/java/develop/OpenOMEZarrFromS3WithCredentials.java

diff --git a/src/main/java/org/embl/mobie/io/imagedata/N5ImageData.java b/src/main/java/org/embl/mobie/io/imagedata/N5ImageData.java
index 538e2d3..e152d95 100644
--- a/src/main/java/org/embl/mobie/io/imagedata/N5ImageData.java
+++ b/src/main/java/org/embl/mobie/io/imagedata/N5ImageData.java
@@ -16,6 +16,7 @@
 import net.imglib2.util.ValuePair;
 import org.embl.mobie.io.ngff.Labels;
 import org.embl.mobie.io.util.IOHelper;
+import org.embl.mobie.io.util.S3Utils;
 import org.janelia.saalfeldlab.n5.*;
 import org.janelia.saalfeldlab.n5.bdv.N5Viewer;
 import org.janelia.saalfeldlab.n5.ui.DataSelection;
@@ -150,10 +151,6 @@ private synchronized void open()
             {
                 n5Factory = n5Factory.s3UseCredentials( new BasicAWSCredentials( s3AccessAndSecretKey[ 0 ], s3AccessAndSecretKey[ 1 ] ) );
             }
-            else
-            {
-                n5Factory = n5Factory.s3UseCredentials( new AnonymousAWSCredentials() );
-            }
 
             N5Reader n5 = n5Factory.openReader( containerPath );
             String rootGroup = n5URI.getGroupPath() != null ? n5URI.getGroupPath() : "/";
diff --git a/src/main/java/org/embl/mobie/io/util/S3Utils.java b/src/main/java/org/embl/mobie/io/util/S3Utils.java
index 27b68b3..8fc72df 100644
--- a/src/main/java/org/embl/mobie/io/util/S3Utils.java
+++ b/src/main/java/org/embl/mobie/io/util/S3Utils.java
@@ -51,11 +51,13 @@ public abstract class S3Utils
     private static boolean useCredentialsChain;
 
     // FIXME: We should remove this!
+    @Deprecated // instead use ImageDataFormat.setS3AccessAndSecretKey
     public static void setS3AccessAndSecretKey( String[] s3AccessAndSecretKey ) {
         S3Utils.s3AccessAndSecretKey = s3AccessAndSecretKey;
     }
 
     // FIXME: We should remove this!
+    @Deprecated
     public static String[] getS3AccessAndSecretKey()
     {
         return s3AccessAndSecretKey;
diff --git a/src/test/java/develop/LazyConvertAndSaveOMEZarr.java b/src/test/java/develop/LazyConvertAndSaveOMEZarr.java
new file mode 100644
index 0000000..22b3169
--- /dev/null
+++ b/src/test/java/develop/LazyConvertAndSaveOMEZarr.java
@@ -0,0 +1,32 @@
+package develop;
+
+import ij.IJ;
+import ij.ImagePlus;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.converter.Converters;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+import net.imglib2.type.numeric.real.FloatType;
+import org.embl.mobie.io.OMEZarrWriter;
+
+public class LazyConvertAndSaveOMEZarr
+{
+    public static void main( String[] args )
+    {
+        // Open
+        ImagePlus floatImp = IJ.openVirtual("/Users/tischer/Desktop/blobs-float.tif");
+
+        // Lazy convert from float to short
+        float min = 0.0F;
+        float max = 255.0F;
+        float scale = 65535 / ( max - min);
+        RandomAccessibleInterval< FloatType > floatTypes = ImageJFunctions.wrapFloat( floatImp );
+        RandomAccessibleInterval< UnsignedShortType > shortTypes =
+                Converters.convert( floatTypes, ( floatType, shortType )
+                    -> shortType.setReal( scale * ( floatType.get() - min ) ), new UnsignedShortType() );
+        ImagePlus shortImp = ImageJFunctions.wrap( shortTypes, "converted image" );
+
+        // Save
+        OMEZarrWriter.write( shortImp, "/Users/tischer/Desktop/test.zarr", OMEZarrWriter.ImageType.Intensities, true );
+    }
+}
diff --git a/src/test/java/develop/OpenOMEZarrFromS3WithCredentials.java b/src/test/java/develop/OpenOMEZarrFromS3WithCredentials.java
new file mode 100644
index 0000000..c9375b8
--- /dev/null
+++ b/src/test/java/develop/OpenOMEZarrFromS3WithCredentials.java
@@ -0,0 +1,24 @@
+package develop;
+
+import bdv.cache.SharedQueue;
+import org.embl.mobie.io.ImageDataFormat;
+import org.embl.mobie.io.ImageDataOpener;
+import org.embl.mobie.io.imagedata.ImageData;
+
+import java.util.Arrays;
+
+public class OpenOMEZarrFromS3WithCredentials
+{
+    public static void main( String[] args )
+    {
+        ImageDataFormat omeZarr = ImageDataFormat.OmeZarr;
+        // If the below is commented it will look in ~/.aws/credentials
+        //omeZarr.setS3SecretAndAccessKey( new String[]{"tr4UedW5", "XfECV2scqKkpAM"} );
+        ImageData< ? > imageData = ImageDataOpener.open(
+                "https://s3.embl.de/wsi-unihd/mitosis-5D.ome.zarr",
+                omeZarr,
+                new SharedQueue( 4 ) );
+        long[] dimensions = imageData.getSourcePair( 0 ).getA().getSource( 0, 0 ).dimensionsAsLongArray();
+        System.out.println( Arrays.toString( dimensions ));
+    }
+}