bug fix: channelIndex -> channel

src/main/java/org/embl/mobie/MoBIE.java

@@ -728,17 +728,17 @@ private void initDataSource( DataSource dataSource, String log )
 			{
 				// the whole plate is already initialised as one big SpimData
 				// note that channel <=> setupID
-				return new SpimDataImage( site.getSpimData(), site.channelIndex, name, settings.values.getRemoveSpatialCalibration() );
+				return new SpimDataImage( site.getSpimData(), site.channel, name, settings.values.getRemoveSpatialCalibration() );
 			}
 
 			if ( site.getImageDataFormat().equals( ImageDataFormat.OmeZarr ) )
 			{
-				return new SpimDataImage( ImageDataFormat.OmeZarr, site.absolutePath, site.channelIndex, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
+				return new SpimDataImage( ImageDataFormat.OmeZarr, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
 			}
 
 			if ( site.getImageDataFormat().equals( ImageDataFormat.OmeZarrS3 ) )
 			{
-				return new SpimDataImage( ImageDataFormat.OmeZarrS3, site.absolutePath, site.channelIndex, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
+				return new SpimDataImage( ImageDataFormat.OmeZarrS3, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration() );
 			}
 
 			return new SpimDataImage( site, name, ThreadHelper.sharedQueue, settings.values.getRemoveSpatialCalibration()  );

src/main/java/org/embl/mobie/lib/hcs/Plate.java

@@ -291,7 +291,7 @@ private void buildPlateMap( List< String > imagePaths )
 				if ( hcsPattern.equals( hcsPattern.OMEZarr ) )
 				{
 					site.absolutePath = imagePath;
-					site.channelIndex = channel.getChannelIndex();
+					site.channel = channel.getChannelIndex();
 				}
 				else
 				{

src/main/java/org/embl/mobie/lib/hcs/Site.java

@@ -56,15 +56,15 @@ public Site( String id, ImageDataFormat imageDataFormat )
 	{
 		this.id = id;
 		this.imageDataFormat = imageDataFormat;
-		this.channelIndex = 0;
+		this.channel = 0;
 	}
 
 	public Site( String id, ImageDataFormat imageDataFormat, AbstractSpimData< ? > spimData, int imageIndex )
 	{
 		this.id = id;
 		this.imageDataFormat = imageDataFormat;
 		this.spimData = spimData;
-		this.channelIndex = imageIndex;
+		this.channel = imageIndex;
 	}
 
 	public String getId()

src/main/java/org/embl/mobie/lib/io/StorageLocation.java

@@ -83,15 +83,15 @@ public class StorageLocation
 	// historically, we only had fluorescence channels,
 	// and thus the name of the variable is "channel" and cannot
 	// readily be changed because we use in the MoBIE JSON spec
-	public Integer channelIndex; // only for images, will default to zero if not set
+	public Integer channel; // only for images, will default to zero if not set
 
 	public Integer getChannel()
 	{
-		return channelIndex == null ? 0 : channelIndex;
+		return channel == null ? 0 : channel;
 	}
 
 	public void setChannel( Integer channel )
 	{
-		this.channelIndex = channel;
+		this.channel = channel;
 	}
 }

src/test/java/projects/jonas/OpenLocalJonas.java

@@ -0,0 +1,50 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2023 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package projects.jonas;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.MoBIE;
+import org.embl.mobie.MoBIESettings;
+import org.embl.mobie.lib.io.DataFormats;
+
+import java.io.IOException;
+
+public class OpenLocalJonas
+{
+	public static void main( String[] args ) throws IOException
+	{
+		final ImageJ imageJ = new ImageJ();
+		imageJ.ui().showUI();
+
+		MoBIESettings settings = new MoBIESettings();
+		settings.preferentialDataLocation( DataFormats.Location.Local );
+		settings.view( "5488_5533" );
+		final MoBIE moBIE = new MoBIE( "/Volumes/kreshuk/hellgoth/mobie_project_shared/culture-collections/data/", settings);
+	}
+}