From 112d546e71fa0e0a2129050f50a190a8cd78b8e9 Mon Sep 17 00:00:00 2001
From: Christian Tischer <christian.tischer@embl.de>
Date: Thu, 26 Oct 2023 19:42:13 +0200
Subject: [PATCH] Compiles

---
 src/main/java/org/embl/mobie/MoBIE.java        | 18 ++++++++++++++++--
 .../java/org/embl/mobie/lib/MoBIEHelper.java   | 15 +++++++++++++++
 .../java/org/embl/mobie/lib/hcs/Plate.java     |  2 ++
 3 files changed, 33 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/embl/mobie/MoBIE.java b/src/main/java/org/embl/mobie/MoBIE.java
index d7bfc0a9b..21d5ca0fc 100644
--- a/src/main/java/org/embl/mobie/MoBIE.java
+++ b/src/main/java/org/embl/mobie/MoBIE.java
@@ -744,9 +744,23 @@ private void initDataSource( DataSource dataSource, String log )
 			return new CachedCellImage<>( name, storageLocation.absolutePath, storageLocation.getChannel(), imageDataFormat, ThreadHelper.sharedQueue );
 		}
 
-		if ( storageLocation instanceof Site )
+		if ( storageLocation instanceof Site ) // HCS data
 		{
-			return new SpimDataImage( ( Site ) storageLocation, name, ThreadHelper.sharedQueue );
+			final Site site = ( Site ) storageLocation;
+
+			if ( site.getImageDataFormat().equals( ImageDataFormat.SpimData ) )
+			{
+				// the whole plate is already initialised as one big SpimData
+				// note that channel <=> setupID
+				return new SpimDataImage( site.getSpimData(), site.channel, name, false );
+			}
+
+			if ( site.getImageDataFormat().equals( ImageDataFormat.OmeZarr ) )
+			{
+				return new SpimDataImage( ImageDataFormat.OmeZarr, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, false );
+			}
+
+			return new SpimDataImage( site, name, ThreadHelper.sharedQueue );
 		}
 
 		final String imagePath = getImageLocation( imageDataFormat, storageLocation );
diff --git a/src/main/java/org/embl/mobie/lib/MoBIEHelper.java b/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
index 6873b692b..e76170bf1 100644
--- a/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
+++ b/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
@@ -253,6 +253,21 @@ public static Metadata getMetadataFromSource( ImageDataSource imageDataSource )
 		return metadata;
 	}
 
+	public static ImagePlus openOMEZarrAsImagePlus( String path, int setupID )
+	{
+		try
+		{
+			AbstractSpimData< ? > spimData = new SpimDataOpener().open( path, ImageDataFormat.OmeZarr );
+			final SpimSource< ? > spimSource = new SpimSource( spimData, setupID, "" );
+			final ImagePlus imagePlus = new SourceToImagePlusConverter<>( spimSource ).getImagePlus( 0 );
+			return imagePlus;
+		} catch ( SpimDataException e )
+		{
+			e.printStackTrace();
+			throw new RuntimeException( e );
+		}
+	}
+
 	public static String createAbsolutePath( String rootFolder, String fileName, String folderName )
 	{
 		// The "root" is AutoMic table specific
diff --git a/src/main/java/org/embl/mobie/lib/hcs/Plate.java b/src/main/java/org/embl/mobie/lib/hcs/Plate.java
index b8b39d9b8..df9237634 100644
--- a/src/main/java/org/embl/mobie/lib/hcs/Plate.java
+++ b/src/main/java/org/embl/mobie/lib/hcs/Plate.java
@@ -41,6 +41,7 @@
 import org.embl.mobie.io.ImageDataFormat;
 import org.embl.mobie.io.SpimDataOpener;
 import org.embl.mobie.io.toml.TPosition;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.color.ColorHelper;
 
 import ch.epfl.biop.bdv.img.bioformats.entity.SeriesIndex;
@@ -174,6 +175,7 @@ private void buildPlateMap( List< String > paths )
 					channel = new Channel( channelName );
 					channelWellSites.put( channel, new HashMap<>() );
 
+					// FIXME Replace with MoBIEHelper.getMetadataFromImageFile
 					ImagePlus singleChannelImagePlus = operettaMetadata == null ? openImagePlus( path, channelName ) : null;
 
 					// set channel metadata