Add automated spot radius configuring

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

@@ -697,7 +697,6 @@ private void initDataSource( DataSource dataSource, String log )
 
 		if ( dataSource instanceof SpotDataSource )
 		{
-
 			// build spots image from spots table
 			final SpotImageCreator spotImageCreator = new SpotImageCreator( ( SpotDataSource ) dataSource, this );
 			DataStore.addImage( spotImageCreator.get() );

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

@@ -73,7 +73,13 @@ private void initSpotRadiusItem()
 		for ( SourceAndConverter sourceAndConverter : sourceAndConverters )
 		{
 			final SpotAnnotationImage spotAnnotationImage = ( SpotAnnotationImage ) DataStore.sourceToImage().get( sourceAndConverter );
-			spotRadiusItem.setValue( this, spotAnnotationImage.getRadius() );
+
+			Double radius = spotAnnotationImage.getRadius();
+			if ( radius != null )
+				spotRadiusItem.setValue( this, radius );
+			else
+				spotRadiusItem.setValue( this, 1.0D );
+
 			return;
 		}
 	}

src/main/java/org/embl/mobie/lib/SpotImageCreator.java

@@ -76,7 +76,12 @@ public SpotAnnotationImage< AnnotatedSpot > get()
 
 			final DefaultAnnData< AnnotatedSpot > spotAnnData = new DefaultAnnData<>( tableModel );
 
-			spotAnnotationImage = new SpotAnnotationImage( spotDataSource.getName(), spotAnnData, 1.0, spotDataSource.boundingBoxMin, spotDataSource.boundingBoxMax );
+			spotAnnotationImage = new SpotAnnotationImage(
+					spotDataSource.getName(),
+					spotAnnData,
+					null,
+					spotDataSource.boundingBoxMin,
+					spotDataSource.boundingBoxMax );
 		}
 
 		return spotAnnotationImage;

src/main/java/org/embl/mobie/lib/image/SpotAnnotationImage.java

@@ -59,14 +59,19 @@ public class SpotAnnotationImage< AS extends AnnotatedSpot > implements Annotati
 	private Source< ? extends Volatile< UnsignedIntType > > volatileSource = null;
 	private KDTree< AS > kdTree;
 	private RealMaskRealInterval mask;
-	private double radius;
+	private Double radius;
 	private double[] boundingBoxMin;
 	private double[] boundingBoxMax;
 	private AffineTransform3D affineTransform3D;
 	private Source< AnnotationType< AS > > source;
 	private TransformedSource< AnnotationType< AS > > transformedSource;
 
-	public SpotAnnotationImage( String name, DefaultAnnData< AS > annData, double radius, @Nullable double[] boundingBoxMin, @Nullable double[] boundingBoxMax )
+	public SpotAnnotationImage(
+			String name,
+			DefaultAnnData< AS > annData,
+			@Nullable Double radius,
+			@Nullable double[] boundingBoxMin,
+			@Nullable double[] boundingBoxMax )
 	{
 		this.name = name;
 		this.annData = annData;
@@ -77,14 +82,17 @@ public SpotAnnotationImage( String name, DefaultAnnData< AS > annData, double ra
 		createImage();
 	}
 
-	public double getRadius()
+	public Double getRadius()
 	{
 		return radius;
 	}
 
-	public void setRadius( double radius )
+	public void setRadius( Double radius )
 	{
-		this.radius = radius;
+		if ( radius != null )
+		{
+			this.radius = radius;
+		}
 	}
 
 	private void createImage()
@@ -107,6 +115,16 @@ private void createImage()
 
 		mask = GeomMasks.closedBox( boundingBoxMin, boundingBoxMax );
 
+		if ( radius == null)
+		{
+			// Assign each spot an area that is a fraction of the total
+			// covered area divided by the number of spots.
+			// A = Pi R^2 => R ~ Sqrt( A )
+			double area = ( mask.realMax( 0 ) - mask.realMin( 0 ) )
+					* ( mask.realMax( 1 ) - mask.realMin( 1 ) );
+			radius = Math.sqrt( area / annotations.size() ) / 10.0;
+		}
+
 		// TODO: code duplication with RegionLabelImage
 		final ArrayList< Integer > timePoints = configureTimePoints();
 		final Interval interval = Intervals.smallestContainingInterval( getMask() );

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

@@ -48,7 +48,7 @@ public class SpotDisplay< AR extends AnnotatedRegion > extends AbstractAnnotatio
 
 	private Set< String > selectedSpotIds;
 
-	public double spotRadius = 1.0D;
+	public Double spotRadius;
 
 	// Runtime