Apply an Affine transform to the current image in QuPath v0.2.0 and write this as a pyramidal OME-TIFF file

QuPath-Export transformed image.groovy

/**
 * Apply an Affine transform to the current image in QuPath,
 * and write this as a pyramidal TIFF file.
 *
 * Note: Be careful with the pixel size! In v0.2.0 this is not automatically 
 * updated (later versions might correct this issue).
 *
 * @author Pete Bankhead
 */

import org.locationtech.jts.geom.util.AffineTransformation
import qupath.lib.gui.dialogs.Dialogs
import qupath.lib.images.servers.TransformedServerBuilder
import qupath.lib.roi.GeometryTools

import static qupath.lib.gui.scripting.QPEx.*

// Define transform
def transform = GeometryTools.convertTransform(
        new AffineTransformation([2, 0, 0,
                                  0, 4, 0] as double[]))

// May or may not need to create an inverse transform (depending upon what was defined)
// - remove this line if it isn't needed
transform = transform.createInverse()


def server = getCurrentServer()

def serverTransformed = new TransformedServerBuilder(server)
        .transform(transform)
        .build()

def file = Dialogs.promptToSaveFile("Save transformed image", null, null, "OME-TIFF", "ome.tiff")
if (file)
    writeImage(serverTransformed, file.getAbsolutePath())