correctview.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-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.BufferedReader;
import java.io.FileReader;
import java.util.ArrayList;
import mpicbg.trakem2.transform.RigidModel2D;
import mpicbg.trakem2.transform.AffineModel2D;
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"));

ControlWindow.setGUIEnabled(false);

/* initialize project */

project2 = tryOpenProject(dir + "/100-199/project.xml");
layerset2 = project2.getRootLayerSet();

/* initialize ranges and transformation models */

models = new ArrayList();
models.add(new AffineModel2D());
box = layerset2.get2DBounds();
	
/* load transformation model */
model = new AffineModel2D();
if (!initTransform(dir + "/100-199/rigidnew.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};

System.out.println("Min and Max.");	
System.out.println(min[0]);
System.out.println(min[1]);
System.out.println(max[0]);
System.out.println(max[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());

project2.destroy();

/* re-box and apply transformation models */

//affine = models.get(0).createAffine();


//System.out.println(affine[0])

//affine = models.get(0);
affine = model.createAffine();

project = tryOpenProject(dir + "/100-199/project.xml");
System.out.println("final:"+affine.toString()+", 100-199");
layerset = project.getRootLayerSet();

allpatches = layerset.getDisplayables(Patch.class);
affine0= allpatches.get(0).getAffineTransform();
affine = affine0.createInverse();

for (patch : layerset.getDisplayables(Patch.class)) {
	patch.getAffineTransform().preConcatenate(affine);
	patch.updateInDatabase("transform");
	patch.updateBucket();
}

layerset.setMinimumDimensions();
//layerset.setDimensions(box.x, box.y, box.width, box.height);
	
System.out.println("final:"+affine.toString()+", 100-199");

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

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