Proof-of-concept script showing one whole slide image as an overlay on top of another within QuPath.

QuPath-Show whole slide overlay.groovy

/**
 * Proof-of-concept script showing one whole slide image as an overlay on top
 * of another within QuPath.
 *
 * Note that this script simply overlays the *same* image that is currently open;
 * therefore it may not be immediately obvious that anything has happened.
 *
 * Uncomment the line
 *   g2d.translate(1000, 1000)
 * if you want to convince yourself that something *has* actually happened,
 * and adjust the opacity slider as required.
 *
 * In practice, it will be more useful to overlay a *different* image...
 * 
 * Note that you can also optionally bind the overlay display to the show/hide detections option.
 *
 * WARNING!  This should work in QuPath v0.1.2, and possibly v0.1.3.
 * However, the API will definitely change in the future as overlays become
 * a more important part of the software... therefore be prepared to update any
 * code based on this.
 *
 * @author Pete Bankhead
 */

import javafx.application.Platform
import qupath.lib.awt.common.AwtTools
import qupath.lib.gui.viewer.QuPathViewer
import qupath.lib.gui.viewer.overlays.AbstractImageDataOverlay
import qupath.lib.images.ImageData
import qupath.lib.images.servers.ImageServer
import qupath.lib.images.servers.ImageServerProvider
import qupath.lib.regions.ImageRegion
import qupath.lib.scripting.QPEx

import java.awt.Graphics2D
import java.awt.Shape
import java.awt.geom.AffineTransform
import java.awt.image.BufferedImage
import java.awt.image.ImageObserver


// Replace overlay in the Application thread
Platform.runLater {

    def viewer = QPEx.getCurrentViewer()
    def path = viewer.getServerPath()
    
    def overlay = new WholeSlideImageOverlay(viewer, path, false)
    
    // Remove any existing overlays of this kind (helpful during debugging...)
    viewer.getOverlayLayers().findAll({it.getClass().getName().contains('WholeSlideImageOverlay')}).each {
        viewer.removeOverlay(it)
    }

    // Add the new overlay
    viewer.addOverlay(overlay)
    print 'Done!'
}

/**
 * Create an overlay to display one whole slide image on top of another.
 */
class WholeSlideImageOverlay extends AbstractImageDataOverlay {

    private boolean initialized = false
    private QuPathViewer viewer
    private ImageServer<BufferedImage> server
    private AffineTransform transform
    private boolean bindToObjectDisplay

    public WholeSlideImageOverlay(final QuPathViewer viewer, final String path, boolean bindToObjectDisplay) {
        super(viewer.getOverlayOptions(), viewer.getImageData())
        this.viewer = viewer
        this.server = ImageServerProvider.buildServer(path, BufferedImage.class)
        this.initialized = true
        this.bindToObjectDisplay = bindToObjectDisplay
    }

    @Override
    boolean supportsImageDataChange() {
        return true
    }

    /**
     * If the ImageData for the viewer is changed, remove the overlay.
     *
     * @param imageData
     */
    @Override
    public void setImageData(final ImageData<BufferedImage> imageData) {
        if (this.imageData == imageData || !initialized)
            return
        viewer.removeOverlay(this)
        this.server.close()
    }

    @Override
    void paintOverlay(Graphics2D g2d, ImageRegion imageRegion, double downsampleFactor, ImageObserver observer, boolean paintCompletely) {
        // Don't do anything if opacity is zero
        if (getOpacity() == 0)
            return

        // If we're binding this to the display of objects, don't paint if detections aren't visible
        // (this lets us toggle the overlay on & off with the 'h' shortcut)
        if (bindToObjectDisplay && !viewer.getOverlayOptions().showObjects)
            return

        // Create a rectangle for the region
        Shape shape = AwtTools.getBounds(imageRegion)

        // Apply transform... handy if using the same image, just to check *something* happens
//        g2d.translate(1000, 1000)

        // Paint region with the help of the image region store (used for caching & painting)
        int z = viewer.getZPosition()
        int t = viewer.getTPosition()
        viewer.getImageRegionStore().paintRegion(
                server, g2d, g2d.getClip(), z, t, downsampleFactor,
                viewer.getImageRegionStore().getThumbnail(server, z, t, true),
                null, null)

    }

}