reset-project-bounding-boxes.bsh

/**
 * Call
 *
 * xvfb-run -a ./ImageJ-linux64 -Ddir=<project directory> -- --no-splash reset-project-bounding-boxes.bsh
 *
 * on the cluster with absolute paths, e.g.
 *
 * ${HOME}/bin/xvfb-run -a ${HOME}/packages/Fiji.app/fiji-linux64 \
 *   -Xms10g -Xmx10g -Ddir=${HOME}/AL-FIB-Z0712-12/0-99 \
 *   -Dfile=${HOME}/AL-FIB-Z0712-12/0-99/import.txt  -- --no-splash \
 *   ${HOME}/AL-FIB-Z0712-12/AL-FIB-Z0712-12/import-and-align.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 ini.trakem2.utils.Filter;
import ij.ImagePlus;
import java.lang.Runtime;
import java.util.ArrayList;
import java.util.HashSet;
import mpicbg.trakem2.align.ElasticLayerAlignment;
import mpicbg.trakem2.align.RegularizedAffineLayerAlignment;

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;
}

try {
	runtime = Runtime.getRuntime();
	System.out.println( runtime.availableProcessors() + " cores available for multi-threading" );
	
	dir = System.getProperty("dir");
	
	ControlWindow.setGUIEnabled(false);
    project = tryOpenProject(dir + "/project.xml");
	loader = project.getLoader();
	layerset = project.getRootLayerSet();
	layerset.setMinimumDimensions();
		
	/* save the project */
	project.saveAs(dir + "/project_up.xml", true);
}
catch (e) {
	e.printStackTrace();
}

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