Further improve annotation overlay performance

mobie · Oct 30, 2024 · fdfed71 · fdfed71
1 parent 4854704
commit fdfed71
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Showing 4 changed files with 57 additions and 47 deletions.
diff --git a/src/main/java/org/embl/mobie/lib/bdv/overlay/AnnotatedRegionsOverlay.java b/src/main/java/org/embl/mobie/lib/bdv/overlay/AnnotatedRegionsOverlay.java
@@ -99,7 +99,7 @@ protected synchronized void draw( Graphics2D g )
 		start = System.currentTimeMillis();
 		for ( OverlayItem overlayItem : overlayItems )
 		{
-			OverlayHelper.drawTextWithBackground( g, overlayItem );
+			OverlayHelper.drawTextWithBackground( g, overlayItem, false );
 		}
 //		System.out.println( "drawn " + overlayItems.size() +  " overlay items in [ms] " + ( System.currentTimeMillis() - start ) );
 	}
@@ -118,14 +118,14 @@ private void updateOverlayItems( Graphics2D g )
 				final RealMaskRealInterval mask = annotatedRegion.getMask();
 				FinalRealInterval bounds = viewerTransform.estimateBounds( mask );
 
-				OverlayItem overlayItem = OverlayHelper.itemFromBounds(
+				OverlayItem newItem = OverlayHelper.itemFromBounds(
 						g,
 						bounds,
 						annotatedRegion.getValue( annotationColumn ).toString(),
 						font
 				);
 
-				overlayItems.add( overlayItem );
+				overlayItems.add( newItem );
 			}
 		}
 	}

diff --git a/src/main/java/org/embl/mobie/lib/bdv/overlay/ImageNameOverlay.java b/src/main/java/org/embl/mobie/lib/bdv/overlay/ImageNameOverlay.java
@@ -28,11 +28,7 @@
  */
 package org.embl.mobie.lib.bdv.overlay;
 
-import bdv.util.BdvFunctions;
-import bdv.util.BdvHandle;
-import bdv.util.BdvOptions;
-import bdv.util.BdvOverlay;
-import bdv.util.BdvOverlaySource;
+import bdv.util.*;
 import bdv.viewer.SourceAndConverter;
 import bdv.viewer.TransformListener;
 import bdv.viewer.ViewerState;
@@ -52,9 +48,7 @@
 import java.awt.*;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
-import java.util.concurrent.ConcurrentHashMap;
 
 public class ImageNameOverlay extends BdvOverlay implements TransformListener< AffineTransform3D >
 {
@@ -136,10 +130,9 @@ private void updateOverlayItems( Graphics2D g )
 
 			if ( image instanceof RegionAnnotationImage )
 			{
-				continue;
+				// Do nothing
 			}
-
-			if ( image instanceof StitchedImage )
+			else if ( image instanceof StitchedImage )
 			{
 				final List< ? extends Image< ? > > tileImages = ( ( StitchedImage< ?, ? > ) image ).getTileImages();
 
@@ -149,35 +142,43 @@ private void updateOverlayItems( Graphics2D g )
 					final FinalRealInterval intersect = Intervals.intersect( viewerInterval, imageMask );
 					if ( ! Intervals.isEmpty( intersect ) )
 					{
-						overlayItems.add(
-								OverlayHelper.itemFromBounds(
-										g,
-										viewerTransform.estimateBounds( imageMask ),
-										image.getName(),
-										font )
-						);
+						createAndAddNewOverlayItem( g, viewerTransform, imageMask, image );
 					}
 				}
-				continue;
 			}
+			else
+			{
+				final RealMaskRealInterval imageMask = image.getMask();
+				final FinalRealInterval intersect = Intervals.intersect( viewerInterval, imageMask );
+				if ( !Intervals.isEmpty( intersect ) )
+				{
+					createAndAddNewOverlayItem( g, viewerTransform, imageMask, image );
+				}
+			}
+		}
+	}
 
-			final RealMaskRealInterval imageMask = image.getMask();
-			final FinalRealInterval intersect = Intervals.intersect( viewerInterval, imageMask );
-			if ( ! Intervals.isEmpty( intersect ) )
+	private void createAndAddNewOverlayItem( Graphics2D g, AffineTransform3D viewerTransform, RealMaskRealInterval imageMask, Image< ? > image )
+	{
+		OverlayItem newItem = OverlayHelper.itemFromBounds(
+				g,
+				viewerTransform.estimateBounds( imageMask ),
+				image.getName(),
+				font );
+
+		boolean addItem = true;
+		for ( OverlayItem item : overlayItems )
+		{
+			// TODO: This could be changed such that small overlaps are tolerated
+			if ( ! Intervals.isEmpty( Intervals.intersect( item.interval, newItem.interval ) ) )
 			{
-				// TODO: This will be slow if there are many
-				//   Consider simplification, e.g. do not paint the black background
-				//	 But rather exclude over-painting by checking overlap with already existing
-				//   overlay Items
-				overlayItems.add(
-						OverlayHelper.itemFromBounds(
-							g,
-							viewerTransform.estimateBounds( imageMask ),
-							image.getName(),
-							font )
-				);
+				addItem = false;
+				break;
 			}
 		}
+
+		if ( addItem )
+			overlayItems.add( newItem );
 	}
 
 	@Override
@@ -191,11 +192,7 @@ protected synchronized void draw( Graphics2D g )
 
 		for ( OverlayItem overlayItem : overlayItems )
 		{
-			// TODO: This will be slow if there are many
-			//   Consider simplification, e.g. do not paint the black background
-			//	 But rather exclude over-painting by checking overlap with already existing
-			//   overlay Items
-			OverlayHelper.drawTextWithBackground( g, overlayItem );
+			OverlayHelper.drawTextWithBackground( g, overlayItem, false );
 		}
 	}
 

diff --git a/src/main/java/org/embl/mobie/lib/bdv/overlay/OverlayHelper.java b/src/main/java/org/embl/mobie/lib/bdv/overlay/OverlayHelper.java
@@ -1,21 +1,25 @@
 package org.embl.mobie.lib.bdv.overlay;
 
+import net.imglib2.FinalInterval;
 import net.imglib2.FinalRealInterval;
 
 import java.awt.*;
 
 public class OverlayHelper
 {
-    public static void drawTextWithBackground( Graphics2D g, OverlayItem item )
+    public static void drawTextWithBackground( Graphics2D g, OverlayItem item, final boolean drawBackground )
     {
         // draw background (this helps with https://github.com/mobie/mobie-viewer-fiji/issues/1013)
         // but this is slow, if there are many annotations
-        g.setColor( Color.BLACK );
-        g.fillRect(
-                item.x,
-                item.y - item.height + g.getFontMetrics().getDescent(),
-                item.width,
-                item.height );
+        if ( drawBackground )
+        {
+            g.setColor( Color.BLACK );
+            g.fillRect(
+                    ( int ) item.interval.min( 0 ),
+                    ( int ) item.interval.min( 1 ),
+                    ( int ) item.interval.dimension( 0 ),
+                    ( int ) item.interval.dimension( 1 ) );
+        }
 
         // draw text
         g.setColor( Color.WHITE );
@@ -45,6 +49,12 @@ public static OverlayItem itemFromBounds(
         item.height = g.getFontMetrics().getHeight();
         item.x = (int) ( center - item.width / 2.0 );
         item.y = (int) ( bounds.realMax( 1 ) + 1.1F * finalFont.getSize() );
+        item.interval = FinalInterval.createMinSize(
+                item.x,
+                item.y - item.height + g.getFontMetrics().getDescent(),
+                item.width,
+                item.height );
+
         return item;
     }
 

diff --git a/src/main/java/org/embl/mobie/lib/bdv/overlay/OverlayItem.java b/src/main/java/org/embl/mobie/lib/bdv/overlay/OverlayItem.java
@@ -1,5 +1,7 @@
 package org.embl.mobie.lib.bdv.overlay;
 
+import net.imglib2.FinalInterval;
+
 import java.awt.*;
 
 public class OverlayItem
@@ -10,4 +12,5 @@ public class OverlayItem
     public int width;
     public int height;
     public Font font;
+    public FinalInterval interval;
 }