Test Fiji / Elastix bridge of BigDataViewer-Playground

TestRegister.groovy

/**
 * BIOP, EPFL, Nicolas Chiaruttini, 18th April 2021
 * Simple script for a simple registration test
 */

import ij.IJ
import ch.epfl.biop.wrappers.elastix.ij2commands.Elastix_Register
import ch.epfl.biop.wrappers.transformix.ij2commands.Transformix_TransformImgPlus
import ij.gui.WaitForUserDialog

#@CommandService cs

(new WaitForUserDialog(
	"The PTBIOP update site should be enabled.\n"+
	"Elastix and Transformix should be installed and work in a command line interface.")).show();
(new WaitForUserDialog("Set the location of elastix and transformix executable file")).show();
// IJ.run("Set and Check Wrappers","");

// Test images : blobs and rotated blobs
(new WaitForUserDialog("Click 'OK' to start a registration test, which should take about 10 seconds ...")).show();
IJ.run("Blobs (25K)");
IJ.run("Duplicate...", "title=blobs-rot15.gif");
IJ.run("Rotate... ", "angle=8 grid=1 interpolation=Bilinear");

// Get transformation
rh = cs.run(Elastix_Register.class, true,
		"moving_image", "blobs.gif",
		"fixed_image", "blobs-rot15.gif",
		"rigid",false,
		"fast_affine",true,
		"affine",false,
		"spline",false,
		"spline_grid_spacing",40
).get().getOutput("rh")

// Transform image
transformed_image = cs.run(Transformix_TransformImgPlus.class, true,
		"img_in", "blobs.gif",
		"rh", rh
).get().getOutput("img_out")

transformed_image.show()

IJ.run("Tile");
(new WaitForUserDialog("The test is successful if the last and the next-to.last images look identical.")).show();