Improved painting of detections (& subcellular detections)

qupath · Dec 30, 2016 · 197965c · 197965c
1 parent 0b7bc4d
commit 197965c
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Showing 3 changed files with 9 additions and 5 deletions.
diff --git a/qupath-gui-fx/src/main/java/qupath/lib/gui/viewer/PathHierarchyPaintingHelper.java b/qupath-gui-fx/src/main/java/qupath/lib/gui/viewer/PathHierarchyPaintingHelper.java
@@ -39,7 +39,6 @@
 import java.awt.geom.AffineTransform;
 import java.awt.geom.Ellipse2D;
 import java.awt.geom.Line2D;
-import java.awt.geom.Line2D.Double;
 import java.awt.geom.Path2D;
 import java.awt.geom.Point2D;
 import java.awt.geom.Rectangle2D;
@@ -356,8 +355,9 @@ else if (pathObject instanceof PathCellObject && overlayOptions.getShowCellBound
 //									colorFill = ColorToolsAwt.getTranslucentColor(colorFill);
 //								else
 									colorFill = ColorToolsAwt.getMoreTranslucentColor(colorFill);
-							}
-							else if (pathObject instanceof PathTileObject && pathClass == null && color !=null && color.getRGB() == PathPrefs.getTileColor()) {
+							} else if (pathObject.getParent() instanceof PathDetectionObject) {
+								colorFill = ColorToolsAwt.getTranslucentColor(colorFill);
+							} else if (pathObject instanceof PathTileObject && pathClass == null && color !=null && color.getRGB() == PathPrefs.getTileColor()) {
 								// Don't fill in empty, unclassified tiles
 								colorFill = null; //DisplayHelpers.getMoreTranslucentColor(colorFill);
 							}

diff --git a/qupath-gui-fx/src/main/java/qupath/lib/gui/viewer/overlays/HierarchyOverlay.java b/qupath-gui-fx/src/main/java/qupath/lib/gui/viewer/overlays/HierarchyOverlay.java
@@ -214,7 +214,7 @@ public boolean supportsImageDataChange() {
 	 * Comparator that makes use of levels, not only location.
 	 *
 	 */
-	static class DetectionComparator implements Comparator<PathObject> {
+	public static class DetectionComparator implements Comparator<PathObject> {
 
 		private Comparator<PathObject> baseComparator = DefaultPathObjectComparator.getInstance();
 

diff --git a/qupath-gui-fx/src/main/java/qupath/lib/images/servers/PathHierarchyImageServer.java b/qupath-gui-fx/src/main/java/qupath/lib/images/servers/PathHierarchyImageServer.java
@@ -29,6 +29,7 @@
 import java.awt.Transparency;
 import java.awt.image.BufferedImage;
 import java.io.File;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
@@ -39,6 +40,7 @@
 import qupath.lib.common.ColorTools;
 import qupath.lib.gui.viewer.OverlayOptions;
 import qupath.lib.gui.viewer.PathHierarchyPaintingHelper;
+import qupath.lib.gui.viewer.overlays.HierarchyOverlay;
 import qupath.lib.images.ImageData;
 import qupath.lib.images.PathImage;
 import qupath.lib.objects.DefaultPathObjectConnectionGroup;
@@ -228,14 +230,16 @@ public BufferedImage readBufferedImage(RegionRequest request) {
 		Object o = options.getShowConnections() ? imageData.getProperty(DefaultPathObjectConnectionGroup.KEY_OBJECT_CONNECTIONS) : null;
 		PathObjectConnections connections = (o instanceof PathObjectConnections) ? (PathObjectConnections)o : null;
 
-		Collection<PathObject> pathObjects = getObjectsToPaint(request);
+		List<PathObject> pathObjects = new ArrayList<>(getObjectsToPaint(request));
 		if (pathObjects == null || pathObjects.isEmpty()) {
 			// We can only return null if no connections - otherwise we might still need to draw something
 			if (connections == null) {
 				return null;
 			}
 		}
 
+		Collections.sort(pathObjects, new HierarchyOverlay.DetectionComparator());
+
 		GraphicsConfiguration gc = GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice().getDefaultConfiguration();
 		double downsampleFactor = request.getDownsample();
 		int width = (int)(request.getWidth() / downsampleFactor);