align-overlapping-projects-pair.bsh

/**
 * Aligns a pair of overlapping projects 
 * Call
 *
 * xvfb-run ./ImageJ-linux64 -Ddir1=<project1 directory> -Ddir2=<project2 directory> -- --no-splash align-overlaping-projects.bsh
 * 
 * @author Stephan Saalfeld <saalfeld@mpi-cbg.de>
 */

import ini.trakem2.ControlWindow;
import ini.trakem2.Project;
import ini.trakem2.display.Layer;
import ini.trakem2.display.Patch;
import ij.IJ;
import ij.ImagePlus;
import ij.process.ImageProcessor;
import java.awt.geom.AffineTransform;
import java.io.FileOutputStream;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
import mpicbg.ij.TransformMeshMapping;
import mpicbg.models.CoordinateTransformMesh;
import mpicbg.models.InterpolatedCoordinateTransform;
import mpicbg.models.Point;
import mpicbg.models.PointMatch;
import mpicbg.trakem2.transform.RigidModel2D;
import mpicbg.trakem2.transform.TranslationModel2D;
import mpicbg.trakem2.util.Pair;

double sampleSpacing = 100.0;

Project tryOpenProject(path) {
	Exception f = null;
	for (int i = 0; i < 10; ++i) {
		try {
			project = Project.openFSProject(path, false);
			if (project != null)
				return project;
		}
		catch (e) {
			f = e;
			f.printStackTrace();
		}
		System.out.println("Trial " + i + ", failed to open project \"" + path + "\".");
		Thread.sleep(1000);
	}
	if (f == null)
		return null;
	else
		throw f;
}

boolean saveTransform(path, transform) {
	try {
		fos = new FileOutputStream(path);
		out = new OutputStreamWriter(fos, "UTF-8");
		dataString = transform.toDataString();
		out.write(dataString, 0, dataString.length() );
		out.close();
		return true;
	}
	catch (e) {
		return false;
	}
}

runtime = Runtime.getRuntime();
System.out.println(runtime.availableProcessors() + " cores available for multi-threading");

dir1 = System.getProperty("dir1");
dir2 = System.getProperty("dir2");

ControlWindow.setGUIEnabled(false);

project1 = tryOpenProject(dir1 + "/project.xml");
project2 = tryOpenProject(dir2 + "/project.xml");
layerset1 = project1.getRootLayerSet();
layerset2 = project2.getRootLayerSet();

/* put corresponding layers into a list of Pairs */
pairs = new ArrayList();
for (layer1 : layerset1.getLayers()) {
	for (layer2 : layerset2.getLayers()) {
		if (layer1.getZ() == layer2.getZ()) {
			pairs.add(new Pair(layer1, layer2));
			break;
		}
	}
}
	
/* sample point matches */
/* TODO do it for more than a single patch per layer */
matches = new ArrayList();
for (pair : pairs) {
	System.out.println("layer " + pair.a.getZ());
	/* corresponding patches */
	p1 = pair.a.getDisplayables(Patch.class).get(0);
	p2 = pair.b.getDisplayables(Patch.class).get(0);
	
	/* all inclusive CoordinateTransform */
	ct1 = p1.getFullCoordinateTransform();
	ct2 = p2.getFullCoordinateTransform();
	
	/* generate samples */
	w = p1.getOWidth();
	h = p1.getOHeight();
	for (double y = 0; y < h; y += sampleSpacing) {
		for (double x = 0; x < w; x += sampleSpacing) {
			p = new Point(new double[]{(double)x, (double)y });
			pw = p.getW();
			p.apply(ct1);
			p1 = new Point(new double[]{pw[0], pw[1]});
			p.apply(ct2);
			p2 = new Point(new double[]{pw[0], pw[1]});
			matches.add(new PointMatch(p2, p1));
		}
	}
}
	
/* estimate pairwise transformation model */
model = new RigidModel2D();
//model = new TranslationModel2D();
model.fit(matches);

/* try to save transform */
for (i = 0; i < 10 && !saveTransform(dir2 + "/rigid.txt", model); ++i)
	Thread.sleep(1000);

project1.destroy();
project2.destroy();


/* shutdown */
runtime.exit(0);