apply-aligned-overlapping-projects_russell.bsh

/**
 * Applies a previously estimated rigid transformation to a series of
 * overlapping projects and updates their bounding boxes accordingly
 * Call
 *
 * xvfb-run ./ImageJ-linux64 -Ddir=<projects directory> -Dstart=<first index> -Dend=<last index> -Doverlap=<overlap size>  -- --no-splash apply-aligned-overlapping-projects.bsh
 *
 TODO this has very specific directory structure requirements:
 ./chunkstart-chunkend/rigid.txt
 * @author Stephan Saalfeld <saalfeld@mpi-cbg.de>
 * modified by Yang Li
 * Russel Torres
 * Sharmishtaa Seshamani
 */

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.BufferedReader;
import java.io.FileReader;
import java.util.ArrayList;
import mpicbg.trakem2.transform.RigidModel2D;
import mpicbg.trakem2.transform.TranslationModel2D;
import mpicbg.trakem2.util.Pair;


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 initTransform(path, transform) {
	try {
		reader = new BufferedReader(new FileReader(path));
		transform.init(reader.readLine());
		reader.close();
		return true;
	}
	catch (e) {
		return false;
	}
}

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

dir = System.getProperty("dir");
start = Integer.parseInt(System.getProperty("start"));
end = Integer.parseInt(System.getProperty("end"));
overlap = Integer.parseInt(System.getProperty("overlap"));

ControlWindow.setGUIEnabled(false);

range = start + "-" + (start + 2* overlap );
project1 = null;
project2 = tryOpenProject(dir + "/" + range + "/intersection_Affine.xml");
layerset1;
layerset2 = project2.getRootLayerSet();


/* initialize ranges and transformation models */
ranges = new ArrayList();
ranges.add(range);
models = new ArrayList();
models.add(new RigidModel2D());

box = layerset2.get2DBounds();

for (int a = start+overlap ; a < end ; a += overlap) {
	System.out.println( "range1: " + range );
	if ((a + 2* overlap - 1) > end) {
	  range = a + "-" + end;
  }
	else {
	range = a + "-" + (a + 2 * overlap );
  }
	ranges.add(range);
	System.out.println("range2: " + range);

	/* flip and load new project */
	if (project1 != null)
		project1.destroy();
	project1 = project2;
	project2 = tryOpenProject(dir + "/" + range + "/intersection_Affine.xml");
	layerset1 = layerset2;
	layerset2 = project2.getRootLayerSet();

	/* load pairwise transformation model */
	model = new RigidModel2D();
	if (!initTransform(dir + "/" + range + "/rigid.txt", model))
		System.out.println("Failed loading transformation.");

	/* accumulate transformation model */

	model.preConcatenate(models.get(models.size() - 1));


	/* store transformation model */
	models.add(model);

	/* estimate local bounds after transformation */
	box2 = layerset2.get2DBounds();
	min = new double[]{box2.x, box2.y};
	max = new double[]{box2.x + box2.width - 1, box2.y + box2.height - 1};
	model.estimateBounds(min, max);

	/* accumulate bounds */
	box = box.union(new Rectangle(
			(int)Math.floor(min[0]),
			(int)Math.floor(min[1]),
			(int)Math.ceil(max[0] + 1) - (int)Math.floor(min[0]),
			(int)Math.ceil(max[1] + 1) - (int)Math.floor(min[1])));

	System.out.println(model.toString());
	System.out.println(box.toString());
}

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




/* re-box and apply transformation models */
for (int i = 0; i < ranges.size(); ++i) {
	affine = models.get(i).createAffine();

	project = tryOpenProject(dir + "/" + ranges.get(i) + "/intersection_Affine.xml");
	System.out.println("final:"+affine.toString()+","+ranges.get(i));

	layerset = project.getRootLayerSet();
	for (patch : layerset.getDisplayables(Patch.class)) {
		patch.getAffineTransform().preConcatenate(affine);
		patch.updateInDatabase("transform");
		patch.updateBucket();
	}
	layerset.setDimensions(box.x, box.y, box.width, box.height);

	project.save();
	project.destroy();
}


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