Effectively don't use Display.sourceAndConverters() anymore

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.0.6</version>
+    <version>5.0.7</version>
 
     <!-- force javadoc generation to fetch errors:    -->
     <!-- mvn javadoc:javadoc | grep error -->

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

@@ -213,7 +213,7 @@ private void openImagesAndLabels( List< ImageFileSources > images, List< LabelFi
 
 		new FileSourcesDataSetter( images, labels, regionTable ).addDataAndDisplaysAndViews( dataset );
 
-		initUIandShowView( null ); //dataset.views().keySet().iterator().next() );
+		initUiAndShowView( null ); //dataset.views().keySet().iterator().next() );
 	}
 
 	public MoBIE( String projectName, ImageData< ? > imageData, ImageData< ? > labelData, @Nullable StorageLocation tableStorageLocation, @Nullable TableDataFormat tableDataFormat )
@@ -230,7 +230,7 @@ public MoBIE( String projectName, ImageData< ? > imageData, ImageData< ? > label
 				tableStorageLocation,
 				tableDataFormat ).addData( dataset, settings );
 
-		initUIandShowView( null );
+		initUiAndShowView( null );
 	}
 
 	private void initImageJAndMoBIE()
@@ -260,10 +260,10 @@ private void openHCSDataset( double wellMargin, double siteMargin, @Nullable Vox
 		initProject( "HCS" );
 		final Plate plate = new Plate( projectLocation, voxelDimensions );
 		new HCSPlateAdder( plate, wellMargin, siteMargin ).addPlateToDataset( dataset );
-		initUIandShowView( dataset.views().keySet().iterator().next() );
+		initUiAndShowView( dataset.views().keySet().iterator().next() );
 	}
 
-	private void initUIandShowView( @Nullable String view )
+	private void initUiAndShowView( @Nullable String view )
 	{
 		buildUI();
 

src/main/java/org/embl/mobie/command/context/SourcesInfoCommand.java

@@ -70,7 +70,7 @@ public void run()
             IJ.log( "Voxel size: " + Arrays.toString( source.getVoxelDimensions().dimensionsAsDoubleArray() ) );
 
             Image< ? > image = DataStore.sourceToImage().get( sac );
-            ArrayList< Transformation > transformations = TransformHelper.fetchAllTransformations( image );
+            ArrayList< Transformation > transformations = TransformHelper.fetchAllImageTransformations( image );
 
             transformations.forEach( transformation ->
             {

src/main/java/org/embl/mobie/lib/bdv/view/AbstractSliceView.java

@@ -61,7 +61,6 @@ public void close( boolean closeImgLoader )
 			moBIE.closeSourceAndConverter( sourceAndConverter, closeImgLoader );
 		}
 		display.images().clear();
-		display.sourceAndConverters().clear();
 
 		sliceViewer.updateTimepointSlider();
 	}

src/main/java/org/embl/mobie/lib/bdv/view/SliceViewer.java

@@ -30,6 +30,7 @@
 
 import bdv.util.BdvHandle;
 import bdv.viewer.SourceAndConverter;
+import ij.IJ;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.embl.mobie.DataStore;
 import org.embl.mobie.command.context.*;
@@ -205,7 +206,12 @@ public static BdvHandle createBdv( boolean is2D, String frameTitle )
 		final MobieSerializableBdvOptions sOptions = new MobieSerializableBdvOptions();
 		sOptions.is2D = is2D;
 		sOptions.frameTitle = frameTitle;
-		sOptions.interpolate = !is2D;
+		sOptions.interpolate = false;
+		IJ.log("BigDataViewer (BDV) initialised.");
+		IJ.log("BDV navigation mode: " + ( is2D ? "2D" : "3D" ));
+		IJ.log("BDV interpolation: Nearest neighbour (Press \"I\" in BDV window to change this)" );
+		IJ.log("" );
+
 		IBdvSupplier bdvSupplier = new MobieBdvSupplier( sOptions );
 		//SourceAndConverterServices.getBdvDisplayService().setDefaultBdvSupplier( bdvSupplier );
 		//BdvHandle bdvHandle = SourceAndConverterServices.getBdvDisplayService().getNewBdv();
@@ -217,13 +223,12 @@ public Window getWindow()
 		return SwingUtilities.getWindowAncestor( bdvHandle.getViewerPanel() );
 	}
 
-	public void show( Image< ? > image, SourceAndConverter< ? > sourceAndConverter, AbstractDisplay display )
+	public void show( Image< ? > image, SourceAndConverter< ? > sourceAndConverter, AbstractDisplay< ? > display )
 	{
-		// register
+		// register sac
 		SourceAndConverterServices.getSourceAndConverterService().register( sourceAndConverter );
-		display.sourceAndConverters().add( sourceAndConverter );
 
-		// link to image
+		// link sac to image
 		DataStore.sourceToImage().forcePut( sourceAndConverter, image );
 
 		// blending mode
@@ -248,7 +253,7 @@ public void updateTimepointSlider()
 		if ( bdvHandle.getViewerPanel().state()	 == null ) return;
 
 		final List< SourceAndConverter< ? > > sacs = bdvHandle.getViewerPanel().state().getSources();
-		if ( sacs.size() == 0 ) return;
+		if ( sacs.isEmpty() ) return;
 
 		int maxNumTimePoints = 1;
 		for ( SourceAndConverter< ? > sac : sacs )
@@ -257,8 +262,8 @@ public void updateTimepointSlider()
 			if ( image instanceof RegionAnnotationImage )
 				continue; // https://github.com/mobie/mobie-viewer-fiji/issues/975
 
-			int numTimepoints = SourceHelper.getNumTimePoints( sac.getSpimSource() );
-			if ( numTimepoints > maxNumTimePoints ) maxNumTimePoints = numTimepoints;
+			int numTimePoints = SourceHelper.getNumTimePoints( sac.getSpimSource() );
+			if ( numTimePoints > maxNumTimePoints ) maxNumTimePoints = numTimePoints;
 		}
 		bdvHandle.getViewerPanel().state().setNumTimepoints( maxNumTimePoints );
 	}

src/main/java/org/embl/mobie/lib/serialize/display/AbstractDisplay.java

@@ -29,12 +29,15 @@
 package org.embl.mobie.lib.serialize.display;
 
 import bdv.viewer.SourceAndConverter;
+import org.embl.mobie.DataStore;
 import org.embl.mobie.lib.bdv.blend.BlendingMode;
 import org.embl.mobie.lib.bdv.view.SliceViewer;
 import org.embl.mobie.lib.image.Image;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
+import java.util.stream.Collectors;
 
 public abstract class AbstractDisplay< T > implements Display< T >
 {
@@ -45,8 +48,7 @@ public abstract class AbstractDisplay< T > implements Display< T >
 	protected BlendingMode blendingMode; // Do not set default to avoid serialisation for AnnotationDisplays
 
 	// Runtime
-	private transient List< Image< T > > images = new ArrayList<>();
-	private transient List< SourceAndConverter< T > > sourceAndConverters = new ArrayList<>();
+	private final transient List< Image< T > > images = new ArrayList<>();
 	public transient SliceViewer sliceViewer;
 
 	@Override
@@ -79,7 +81,9 @@ public List< Image< T > > images()
 	@Override
 	public List< SourceAndConverter< T > > sourceAndConverters()
 	{
-		return sourceAndConverters;
+		return Collections.unmodifiableList( ( List ) images.stream()
+				.map( image -> DataStore.sourceToImage().inverse().get( image ) )
+				.collect( Collectors.toList() ) );
 	}
 
 	public void setOpacity( double opacity )

src/main/java/org/embl/mobie/lib/serialize/display/Display.java

@@ -40,7 +40,7 @@
  * with shared display settings.
  *
  * Currently, everything that we display in MoBIE
- * is a display. This implies that it must be
+ * is a Display. This implies that it must be
  * modelled as an Image, which essentially is a Source.
  * This is in line with BDV, which internally also
  * models everything as a Source.
@@ -58,6 +58,8 @@ public interface Display< T >
 	BlendingMode getBlendingMode();
 	double getOpacity();
 	boolean isVisible();
+
+	// TODO: https://github.com/mobie/mobie-viewer-fiji/issues/1162
 	List< Image< T > > images();
 	List< SourceAndConverter< T > > sourceAndConverters();
 }

src/main/java/org/embl/mobie/lib/transform/TransformHelper.java

@@ -389,7 +389,7 @@ else if ( numDimensions == 3 )
 		}
 	}
 
-	public static ArrayList< Transformation > fetchAllTransformations( Image< ? > image )
+	public static ArrayList< Transformation > fetchAllImageTransformations( Image< ? > image )
 	{
 		ArrayList< Transformation > transformations = new ArrayList<>();
 		collectTransformations( image, transformations );
@@ -419,14 +419,14 @@ private static void collectTransformations( Image< ? > image, Collection< Transf
 	}
 
 
-	@Deprecated // use fetchAllTransformations( Image< ? > image ) instead
-	public static ArrayList< Transformation > fetchAllTransformations( Source< ? > source )
-	{
-		ArrayList< Transformation > transformations = new ArrayList<>();
-		collectTransformations( source, transformations );
-		Collections.reverse( transformations ); // first transformation first
-		return transformations;
-	}
+//	@Deprecated // use fetchAllTransformations( Image< ? > image ) instead
+//	public static ArrayList< Transformation > fetchAllSourceTransformations( Source< ? > source )
+//	{
+//		ArrayList< Transformation > transformations = new ArrayList<>();
+//		collectTransformations( source, transformations );
+//		Collections.reverse( transformations ); // first transformation first
+//		return transformations;
+//	}
 
 	private static void collectTransformations( Source< ? > source, Collection< Transformation > transformations )
 	{
@@ -487,19 +487,21 @@ else if ( source instanceof RealTransformedSource )
 		}
 	}
 
-	public static ArrayList< Transformation > fetchAddedTransformations( Image< ? > image )
+	public static ArrayList< Transformation > fetchAddedImageTransformations( Image< ? > image )
 	{
-		ArrayList< Transformation > allTransformations = fetchAllTransformations( image );
+		ArrayList< Transformation > allTransformations = fetchAllImageTransformations( image );
 		allTransformations.remove( 0 ); // in MoBIE this is part of the raw image itself
 		return allTransformations;
 	}
 
-	public static ArrayList< Transformation > fetchAddedTransformations( Source< ? > source )
-	{
-		ArrayList< Transformation > allTransformations = fetchAllTransformations( source );
-		allTransformations.remove( 0 ); // in MoBIE this is part of the raw image itself
-		return allTransformations;
-	}
+//	@Deprecated
+//	public static ArrayList< Transformation > fetchAddedSourceTransformations( Source< ? > source )
+//	{
+//		ArrayList< Transformation > allTransformations = fetchAllSourceTransformations( source );
+//		if ( ! allTransformations.isEmpty() )
+//			allTransformations.remove( 0 ); // in MoBIE this is part of the raw image itself
+//		return allTransformations;
+//	}
 
 	// Wrap the input sourcePair into new TransformedSources,
 	// because otherwise, if the incremental transformations of the input TransformedSources

src/main/java/org/embl/mobie/lib/transform/viewer/MoBIEViewerTransformAdjuster.java

@@ -36,6 +36,7 @@
 import net.imglib2.RealInterval;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.util.LinAlgHelpers;
+import org.embl.mobie.DataStore;
 import org.embl.mobie.lib.serialize.display.Display;
 import org.embl.mobie.lib.transform.TransformHelper;
 
@@ -48,6 +49,7 @@ public class MoBIEViewerTransformAdjuster {
 
 	public MoBIEViewerTransformAdjuster( BdvHandle bdvHandle, Display< ? > display) {
 		this.bdvHandle = bdvHandle;
+		// TODO: It may be better to use display.images() here instead, but not sure
 		this.sources = display.sourceAndConverters().stream().map( sac -> sac.getSpimSource() ).collect( Collectors.toList() );
 	}
 

src/main/java/org/embl/mobie/lib/view/ViewManager.java

@@ -109,7 +109,7 @@ public static View createTransformedImageView(
 			Transformation transformation,
 			String viewDescription )
 	{
-		ArrayList< Transformation > transformations = TransformHelper.fetchAddedTransformations( image );
+		ArrayList< Transformation > transformations = TransformHelper.fetchAddedImageTransformations( image );
 		transformations.add( transformation );
 
 		Display< ? > display;
@@ -138,34 +138,34 @@ public static View createTransformedImageView(
 		return view;
 	}
 
-	@Deprecated // use createTransformedImageView instead
-	public static void createTransformedSourceView(
-			SourceAndConverter< ? > sac,
-			String imageName,
-			Transformation transformation,
-			String viewDescription )
-	{
-		// TODO: Use TransformHelper.fetchAddedTransformations( Image<?> image ) instead
-		// TODO: Make this work for label images https://github.com/mobie/mobie-viewer-fiji/issues/1126
-		ArrayList< Transformation > transformations = TransformHelper.fetchAddedTransformations( sac.getSpimSource() );
-		transformations.add( transformation );
-
-		ImageDisplay< ? > imageDisplay = new ImageDisplay<>( imageName, imageName );
-		imageDisplay.setDisplaySettings( sac );
-
-		View view = new View(
-				imageName,
-				null, // to be determined by the user in below dialog
-				Collections.singletonList( imageDisplay ),
-				transformations,
-				null,
-				false,
-				viewDescription );
-
-		MoBIE.getInstance().getViewManager().getViewsSaver().saveViewDialog( view );
-
-		MoBIE.getInstance().getViewManager().show( view );
-	}
+//	@Deprecated // use createTransformedImageView instead
+//	public static void createTransformedSourceView(
+//			SourceAndConverter< ? > sac,
+//			String imageName,
+//			Transformation transformation,
+//			String viewDescription )
+//	{
+//		// TODO: Use TransformHelper.fetchAddedTransformations( Image<?> image ) instead
+//		// TODO: Make this work for label images https://github.com/mobie/mobie-viewer-fiji/issues/1126
+//		ArrayList< Transformation > transformations = TransformHelper.fetchAddedSourceTransformations( sac.getSpimSource() );
+//		transformations.add( transformation );
+//
+//		ImageDisplay< ? > imageDisplay = new ImageDisplay<>( imageName, imageName );
+//		imageDisplay.setDisplaySettings( sac );
+//
+//		View view = new View(
+//				imageName,
+//				null, // to be determined by the user in below dialog
+//				Collections.singletonList( imageDisplay ),
+//				transformations,
+//				null,
+//				false,
+//				viewDescription );
+//
+//		MoBIE.getInstance().getViewManager().getViewsSaver().saveViewDialog( view );
+//
+//		MoBIE.getInstance().getViewManager().show( view );
+//	}
 
 	private void initScatterPlotView( AbstractAnnotationDisplay< ? > display )
 	{
@@ -193,14 +193,14 @@ public SliceViewer getSliceViewer()
 
 	public ViewSaver getViewsSaver() { return viewSaver; }
 
-	private void addImageTransforms( List< Transformation > transformations, List< ? extends SourceAndConverter< ? >> sourceAndConverters )
+	private void addImageTransforms( List< Transformation > transformations,
+									 List< ? extends Image< ? > > images )
 	{
-		for ( SourceAndConverter< ? > sourceAndConverter : sourceAndConverters )
+		images.forEach( image ->
 		{
-			Source< ? > source = sourceAndConverter.getSpimSource();
-			ArrayList< Transformation > fetchedTransformations = TransformHelper.fetchAddedTransformations( source );
-			transformations.addAll( fetchedTransformations );
-        }
+			ArrayList< Transformation > imageTransformations = TransformHelper.fetchAddedImageTransformations( image );
+			transformations.addAll( imageTransformations );
+		});
     }
 
 	public View createViewFromCurrentState()
@@ -221,7 +221,8 @@ else if ( display instanceof SpotDisplay )
 			else
 				throw new UnsupportedOperationException( "Serialisation of a " + display.getClass().getName() + " is not yet supported." );
 
-			addImageTransforms( transformations, display.sourceAndConverters() );
+
+			addImageTransforms( transformations, display.images() );
 		}
 
 		// the parameters that are null must be later set via the view's setter methods

src/main/java/org/embl/mobie/lib/view/save/ViewSaver.java

@@ -88,15 +88,15 @@ public boolean saveViewDialog( View view )
         final GenericDialog gd = new GenericDialog("Save view " + ( view.getName() == null ? "" : view.getName()) );
 
         gd.addChoice("Save to", new String[]{ FileLocation.CurrentProject.toString(), FileLocation.ExternalJSONFile.toString() }, saveToProjectOrFile );
-        gd.addFileField( "External JSON file", externalJsonPath, 70 );
+        gd.addFileField( "( External JSON file )", externalJsonPath, 70 );
         gd.addMessage( "" );
         if ( view.getName() == null )
             gd.addStringField("View name", "my-new-view-name", 35 );
         gd.addStringField( "View description", view.getDescription() != null ? view.getDescription() : "My view description....", 70 );
         gd.addCheckbox("Make view exclusive", view.isExclusive() != null ? view.isExclusive() : false );
         gd.addMessage( "" );
         gd.addChoice("Selection group", getSelectionGroupChoices(), uiSelectionChoice );
-        gd.addStringField("New selection group", "my-new-group", 30 );
+        gd.addStringField("( New selection group )", "my-new-group", 30 );
 
         gd.showDialog();