Add a propagate button to copy the (warped) contours from the template image to the selected overlay one

src/main/java/qupath/ext/align/gui/ImageAlignmentPane.java

@@ -114,6 +114,7 @@
 import qupath.lib.objects.PathObject;
 import qupath.lib.objects.classes.PathClass;
 import qupath.lib.objects.classes.PathClassFactory;
+import qupath.lib.objects.hierarchy.PathObjectHierarchy;
 import qupath.lib.projects.Project;
 import qupath.lib.projects.ProjectImageEntry;
 import qupath.lib.regions.RegionRequest;
@@ -406,6 +407,77 @@ public ImageAlignmentPane(final QuPathGUI qupath) {
 			content.putString(s);
 			Clipboard.getSystemClipboard().setContent(content);
 		});
+		Button btnImport = new Button("Propagate");
+		btnImport.setOnAction(e -> {
+			ImageData<BufferedImage> imageDataBase = viewer.getImageData();
+			ImageData<BufferedImage> imageDataSelected = selectedImageData.get();
+			if (imageDataBase == null) {
+				Dialogs.showNoImageError("Auto-alignment");
+				return;
+			}
+			if (imageDataSelected == null) {
+				Dialogs.showErrorMessage("Auto-alignment", "Please ensure an image overlay is selected!");
+				return;
+			}
+			if (imageDataBase == imageDataSelected) {
+				Dialogs.showErrorMessage("Auto-alignment", "Please select an image overlay, not the 'base' image from the viewer!");
+				return;
+			}
+
+			var overlay = getSelectedOverlay();
+			var transform = overlay == null ? null : overlay.getTransform();
+
+			if (transform == null) {
+				logger.warn("No transform found, can't import transformed annotations!");
+				return;
+			}
+
+			var hierarchy = imageDataBase.getHierarchy();
+
+			Project<BufferedImage> project = qupath.getProject();
+			ProjectImageEntry<BufferedImage> selectedEntry = project.getEntry(imageDataSelected);
+			var otherHierarchy = imageDataSelected.getHierarchy(); //selectedEntry.readImageData().getHierarchy(); //readHierarchy();
+
+			for (var pathObject : otherHierarchy.getAnnotationObjects() ) {
+				logger.info("Destination: "+pathObject.getName());
+			}
+
+			//these are the annotations in the source
+			logger.info("Importing from "+imageDataBase.getServer().getPath());
+			//logger.info("Destination to "+selectedEntry.getImageName());
+
+			List<PathObject> newObjects = new ArrayList<>();
+			for (var pathObject : hierarchy.getAnnotationObjects() ) {
+				logger.info("Importing: "+pathObject.getName());
+				//Transform ROI (via conversion to Java AWT shape)
+				newObjects.add(overlay.transformObject(pathObject));
+
+				//otherHierarchy.addPathObject(pathObject);
+				//otherHierarchy.addPathObject(newObject);
+			}
+			if (otherHierarchy != null) {
+				logger.info("Adding objects!");
+				otherHierarchy.addPathObjects(newObjects);
+				try {
+					selectedEntry.saveImageData(imageDataSelected);
+				} catch (IOException e1) {
+					logger.error("Error saving hieararchy! "+ e1.getLocalizedMessage(), e1);
+				}
+			}
+
+			for (var pathObject : otherHierarchy.getAnnotationObjects() ) {
+				logger.info("Destination: "+pathObject.getName());
+			}
+
+
+			/*
+			for (var pathObject : otherHierarchy.getAnnotationObjects() ) {
+				logger.info("Destination: "+pathObject.getName());
+			}
+			*/
+			logger.info("Importing done!");
+		});
+
 		btnReset.disableProperty().bind(noOverlay);
 		btnReset.setTooltip(new Tooltip("Reset the transform"));
 		btnInvert.disableProperty().bind(noOverlay);
@@ -414,8 +486,10 @@ public ImageAlignmentPane(final QuPathGUI qupath) {
 		btnUpdate.setTooltip(new Tooltip("Update the transform using the current text"));
 		btnCopy.disableProperty().bind(noOverlay);
 		btnCopy.setTooltip(new Tooltip("Copy the current transform to clipboard"));
+		btnImport.disableProperty().bind(noOverlay);
+		btnImport.setTooltip(new Tooltip("Propagate annotations from base image to selected"));
 		textArea.editableProperty().bind(noOverlay.not());
-		paneTransform.add(PaneTools.createColumnGridControls(btnUpdate, btnInvert, btnReset, btnCopy), 0, row++);
+		paneTransform.add(PaneTools.createColumnGridControls(btnUpdate, btnInvert, btnReset, btnCopy, btnImport), 0, row++);
 		PaneTools.setFillWidth(Boolean.TRUE, paneTransform.getChildren().toArray(Node[]::new));
 		PaneTools.setHGrowPriority(Priority.ALWAYS, paneTransform.getChildren().toArray(Node[]::new));
 		paneTransform.setVgap(5.0);

src/main/java/qupath/ext/align/gui/ImageServerOverlay.java

@@ -25,6 +25,7 @@
 import java.awt.RenderingHints;
 import java.awt.geom.AffineTransform;
 import java.awt.geom.NoninvertibleTransformException;
+import java.awt.geom.Point2D;
 import java.awt.image.BufferedImage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -41,6 +42,22 @@
 import qupath.lib.images.servers.ImageServer;
 import qupath.lib.regions.ImageRegion;
 
+import qupath.lib.roi.RoiTools;
+import qupath.lib.roi.PointsROI;
+import qupath.lib.roi.ROIs;
+import qupath.lib.objects.PathObject;
+import qupath.lib.objects.PathObjects;
+import qupath.lib.roi.interfaces.ROI;
+
+
+import qupath.lib.objects.PathTileObject;
+import qupath.lib.objects.PathCellObject;
+import qupath.lib.objects.PathDetectionObject;
+import java.util.List;
+import java.util.Arrays;
+import java.util.ArrayList;
+import qupath.lib.geom.Point2;
+
 /**
  * A {@link PathOverlay} implementation capable of painting one image on top of another, 
  * including an optional affine transformation.
@@ -116,6 +133,15 @@ public Affine getAffine() {
 		return affine;
 	}
 
+	/**
+	 * Get the affine transform applied to the overlay image.
+	 * Making changes here will trigger repaints in the viewer.
+	 * @return
+	 */
+	public AffineTransform getTransform() {
+		return transform;
+	}
+
 	private void updateTransform() {
 		transform.setTransform(
 			affine.getMxx(),
@@ -158,5 +184,62 @@ public void paintOverlay(Graphics2D g2d, ImageRegion imageRegion, double downsam
 		gCopy.dispose();
 
 	}
+
+	/**
+	 * Transform object, recursively transforming all child objects
+	 *
+	 * @param pathObject
+	 * @return
+	 */
+	public PathObject transformObject(PathObject pathObject) {
+		// Create a new object with the converted ROI
+		var roi = pathObject.getROI();
+		var roi2 = this.transformROI(roi, transform);
+
+		PathObject newObject = null;
+
+		newObject = PathObjects.createAnnotationObject(roi2, pathObject.getPathClass(), pathObject.getMeasurementList());
+		newObject.setName(pathObject.getName());
+
+		return newObject;
+	}
+
+	/**
+	 * Transform ROI (via conversion to Java AWT shape)
+	 *
+	 * @param roi
+	 * @param transform
+	 * @return
+	 */
+	private ROI transformROI(ROI roi, AffineTransform transform) {
+		if (roi.getRoiType() == ROI.RoiType.POINT) {
+			List<Point2> points = roi.getAllPoints();
+			var nPoints = points.size();
+
+			// Convert List<Point2> to Point2D[]
+			Point2D[] pointsArray = points.stream()
+                              .map(point -> new Point2D.Double(point.getX(), point.getY()))
+                              .toArray(Point2D[]::new);
+
+			Point2D[] points2 = new Point2D[nPoints];
+			transform.transform(pointsArray,0,points2,0,nPoints);
+
+			// Create a list to store Point2 objects
+			List<Point2> pointsList = new ArrayList<>(nPoints);
+
+			// Add Point2 objects to the list
+			for (int i = 0; i < nPoints; i++) {
+				Point2D point = points2[i];
+				// Create a new Point2 object and add it to the list
+				pointsList.add(new Point2(point.getX(), point.getY()));
+			}
+			return ROIs.createPointsROI(pointsList, roi.getImagePlane());
+		} else {
+			var shape = RoiTools.getShape(roi); // Should be able to use roi.getShape() - but there's currently a bug in it for rectangles/ellipses!
+			var shape2 = transform.createTransformedShape(shape);
+			var roi2 = RoiTools.getShapeROI(shape2, roi.getImagePlane(), 0.5);
+			return roi2;
+		}
+	}
+}
 
-}