Support labels in OME-Zarr HCS

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.channel, name, false );
+				return new SpimDataImage( site.getSpimData(), site.channelIndex, name, false );
 			}
 
 			if ( site.getImageDataFormat().equals( ImageDataFormat.OmeZarr ) )
 			{
-				return new SpimDataImage( ImageDataFormat.OmeZarr, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, false );
+				return new SpimDataImage( ImageDataFormat.OmeZarr, site.absolutePath, site.channelIndex, name, ThreadHelper.sharedQueue, false );
 			}
 
 			if ( site.getImageDataFormat().equals( ImageDataFormat.OmeZarrS3 ) )
 			{
-				return new SpimDataImage( ImageDataFormat.OmeZarrS3, site.absolutePath, site.channel, name, ThreadHelper.sharedQueue, false );
+				return new SpimDataImage( ImageDataFormat.OmeZarrS3, site.absolutePath, site.channelIndex, name, ThreadHelper.sharedQueue, false );
 			}
 
 			return new SpimDataImage( site, name, ThreadHelper.sharedQueue );

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

@@ -33,10 +33,12 @@ public class Channel
 	private final String name;
 	private String color;
 	private double[] contrastLimits;
+	private final int channelIndex;
 
-	public Channel( String name )
+	public Channel( String name, int channelIndex )
 	{
 		this.name = name;
+		this.channelIndex = channelIndex; // main use-case is loading from multi-channel files
 	}
 
 	public String getColor()
@@ -63,4 +65,9 @@ public String getName()
 	{
 		return name;
 	}
+
+	public int getChannelIndex()
+	{
+		return channelIndex;
+	}
 }

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

@@ -164,7 +164,7 @@ public void addData( Dataset dataset )
 					{
 						// the one site is the well
 						//
-						ImageDataSource imageDataSource = createImageDataSource( channel, site, site.getId() );
+						ImageDataSource imageDataSource = createImageDataSource( channel, site, wellID );
 						dataset.addDataSource( imageDataSource );
 					}
 				}

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

@@ -278,7 +278,7 @@ public String getZ()
 			return "1";
 	}
 
-	public void setChannels( List< String > channels )
+	public void setChannelNames( List< String > channels )
 	{
 		this.channels = channels;
 	}

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

@@ -32,17 +32,14 @@
 import ij.ImagePlus;
 import ij.io.Opener;
 import ij.measure.Calibration;
-import mpicbg.spim.data.SpimDataException;
 import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
 import mpicbg.spim.data.generic.sequence.BasicViewSetup;
 import mpicbg.spim.data.sequence.FinalVoxelDimensions;
 import mpicbg.spim.data.sequence.ViewSetup;
 import mpicbg.spim.data.sequence.VoxelDimensions;
 import mpicbg.spim.data.generic.base.Entity;
 import org.embl.mobie.DataStore;
 import org.embl.mobie.io.ImageDataFormat;
-import org.embl.mobie.io.SpimDataOpener;
 import org.embl.mobie.io.toml.TPosition;
 import org.embl.mobie.io.util.IOHelper;
 import org.embl.mobie.lib.MoBIEHelper;
@@ -63,7 +60,6 @@
 import java.util.NoSuchElementException;
 import java.util.Set;
 import java.util.stream.Collectors;
-import java.util.stream.IntStream;
 
 public class Plate
 {
@@ -110,7 +106,7 @@ public Plate( String hcsDirectory ) throws IOException
 			AbstractSpimData< ? > spimData = DataStore.fetchSpimData( firstImagePath, imageDataFormat, ThreadHelper.sharedQueue );
 			List< ViewSetup > viewSetupsOrdered = ( List< ViewSetup > ) spimData.getSequenceDescription().getViewSetupsOrdered();
 			List< String > channels = viewSetupsOrdered.stream().map( vs -> vs.getChannel().getName() ).collect( Collectors.toList() );
-			hcsPattern.setChannels( channels );
+			hcsPattern.setChannelNames( channels );
 		}
 		else
 		{
@@ -149,24 +145,22 @@ private void buildPlateMap( List< String > sitePaths )
 			hcsPattern.setMatcher( sitePath );
 
 			// some formats contain multiple channels in one file
-			List< String > channelIDs = hcsPattern.getChannels();
+			List< String > channelNames = hcsPattern.getChannels();
 
-			// FIXME: For labels, it can be that they are not present for all sites
-			//   Thus the site should not be instantiated in this case.
-			for ( String channelName : channelIDs ) // this could also be labels
+			for ( String channelName : channelNames )
 			{
 				Channel channel = getChannel( channelWellSites, channelName );
 
 				if ( channel == null )
 				{
 					// configure channel properties
 					//
-					channel = new Channel( channelName );
+					channel = new Channel( channelName, channelNames.indexOf( channelName ) );
 					channelWellSites.put( channel, new HashMap<>() );
 
 					// FIXME Replace with MoBIEHelper.getMetadataFromImageFile
 					IJ.log( "Fetching metadata for setup " + channelName + " from " + sitePath + "..." );
-					ImagePlus singleChannelImagePlus = operettaMetadata == null ? openImagePlus( sitePath, channelName ) : null;
+					ImagePlus singleChannelImagePlus = operettaMetadata == null ? openImagePlus( sitePath, channel.getChannelIndex() ) : null;
 
 					// set channel metadata
 					//
@@ -269,7 +263,7 @@ private void buildPlateMap( List< String > sitePaths )
 				if ( hcsPattern.equals( hcsPattern.OMEZarr ) )
 				{
 					site.absolutePath = sitePath;
-					site.channel = Integer.parseInt( channelName );
+					site.channelIndex = channel.getChannelIndex();
 				}
 				else
 				{
@@ -288,7 +282,7 @@ private void buildPlateMap( List< String > sitePaths )
 		IJ.log( "Channels: " + channelWellSites.keySet().size() );
 	}
 
-	private ImagePlus openImagePlus( String path, String channelName )
+	private ImagePlus openImagePlus( String path, int channelID )
 	{
 		if ( this.imageDataFormat.equals( ImageDataFormat.Tiff ) )
 		{
@@ -298,8 +292,7 @@ private ImagePlus openImagePlus( String path, String channelName )
 		else if ( this.imageDataFormat.equals( ImageDataFormat.OmeZarr )
 				|| this.imageDataFormat.equals( ImageDataFormat.OmeZarrS3 ) )
 		{
-			final int setupID = Integer.parseInt( channelName );
-			return MoBIEHelper.openAsImagePlus( path, setupID, imageDataFormat );
+			return MoBIEHelper.openAsImagePlus( path, channelID, imageDataFormat );
 		}
 		else
 		{

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

@@ -54,15 +54,15 @@ public Site( String id, ImageDataFormat imageDataFormat )
 	{
 		this.id = id;
 		this.imageDataFormat = imageDataFormat;
-		this.channel = 0;
+		this.channelIndex = 0;
 	}
 
 	public Site( String id, ImageDataFormat imageDataFormat, AbstractSpimData< ? > spimData, int imageIndex )
 	{
 		this.id = id;
 		this.imageDataFormat = imageDataFormat;
 		this.spimData = spimData;
-		this.channel = imageIndex;
+		this.channelIndex = 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 channel; // only for images, will default to zero if not set
+	public Integer channelIndex; // only for images, will default to zero if not set
 
 	public Integer getChannel()
 	{
-		return channel == null ? 0 : channel;
+		return channelIndex == null ? 0 : channelIndex;
 	}
 
 	public void setChannel( Integer channel )
 	{
-		this.channel = channel;
+		this.channelIndex = channel;
 	}
 }