align3d_affine.bsh

/**
 * Call
 *
 * xvfb-run -a ./ImageJ-linux64 -Dproj=<trakem2 XML> -Doutdir=<out directory> -- --no-splash intersection_AffineAlign.bsh
 *
 * @author Stephan Saalfeld <saalfeld@mpi-cbg.de>
 * modified by Russel Torres
 * modified by Sharmishtaa Seshamani
 */

import ini.trakem2.ControlWindow;
import ini.trakem2.Project;
import ini.trakem2.display.Layer;
import ini.trakem2.display.Patch;
import ini.trakem2.utils.Filter;
/* import ini.trakem2.utils.Montage; */
import ini.trakem2.imaging.filters.NormalizeLocalContrast;
import ini.trakem2.imaging.filters.IFilter;
import ij.ImagePlus;
import java.lang.Runtime;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.regex;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import mpicbg.trakem2.align.Align;
import mpicbg.trakem2.align.AlignTask;
import mpicbg.trakem2.align.RegularizedAffineLayerAlignment;

Project cloneProject(origProj, newdir) {
	/*
	clone all layers in project, generating project with new unuid,
		and thus temporary directories
	*/

	check = new File(newdir).isDirectory();
	fileobj = new File(newdir);

	newProj = Project.newFSProject("blank", null, newdir, false);
	System.out.println( "After opening second one..." );
	

	newloader = newProj.getLoader();
	newloader.setMipMapsRegeneration(false);

	newlayerset = newProj.getRootLayerSet();
	newlayerset.setSnapshotsMode(1);

	origLayerSet = origProj.getRootLayerSet();
	for (l: origLayerSet.getLayers()) {
		newlayerset.add(l.clone(newProj, newlayerset, l.getMinimalBoundingBox(Patch.class), false, false));
	}

	newlayerset.setMinimumDimensions();
	return newProj;
}


try {
  runtime = Runtime.getRuntime();
  proj = System.getProperty("proj");

  dir = System.getProperty("outdir"); // TODO better handling
  ControlWindow.setGUIEnabled(false);
  project = cloneProject(Project.openFSProject(proj, false), dir);
  layerset = project.getRootLayerSet();
  layerset.setSnapshotsMode(1);

  // prepare inter-section alignment
	layerRange = layerset.getLayers();
	fixedLayers = new HashSet();
	emptyLayers = new HashSet();


  // use visible patches only
	filter = new Filter() {
		public boolean accept(Patch patch) {
			return patch.isVisible();
			}
		};


	/* affine alignment */
	System.out.println( "Inter-section affine alignment starting..." );

	paramAffine = new RegularizedAffineLayerAlignment.Param();

	paramAffine.ppm.sift.initialSigma 	= 1.6f;
	paramAffine.ppm.sift.steps 		= 9;
	paramAffine.ppm.sift.minOctaveSize 	= 200;
	paramAffine.ppm.sift.maxOctaveSize 	= 2048;
	paramAffine.ppm.sift.fdSize 		= 8;
	paramAffine.ppm.sift.fdBins 		= 8;
	paramAffine.ppm.rod 			= 0.92f;
	paramAffine.ppm.clearCache 		= true;
	paramAffine.ppm.maxNumThreadsSift 	= runtime.availableProcessors() - 1;//24;

	paramAffine.maxEpsilon 			= 40.0f;
	paramAffine.minInlierRatio 		= 0.10f;
	paramAffine.minNumInliers 		= 20;
	      /*  ModelIndex 0 = "Translation", 1 = "Rigid", 2 = "Similarity", 3 = "Affine" */
	paramAffine.expectedModelIndex 		= 1;
	paramAffine.multipleHypotheses 		= true;
	paramAffine.rejectIdentity 		= false;
	paramAffine.identityTolerance 		= 0.0f;
	paramAffine.maxNumNeighbors 		= 10;
	paramAffine.maxNumFailures 		= 3;
	paramAffine.maxNumThreads 		= runtime.availableProcessors(); //runtime.availableProcessors(); TODO what is this value?

	paramAffine.desiredModelIndex 		= 3; /* affine */
	paramAffine.regularize 			= true;
	paramAffine.maxIterationsOptimize 	= 2000;
	paramAffine.maxPlateauwidthOptimize 	= 1000;
	paramAffine.regularizerIndex 		= 1;
	paramAffine.visualize 			= false;


  /* affine regularized by 0.10 rigid */
	paramAffine.lambda 			= 0.1f;
	new RegularizedAffineLayerAlignment().exec(
			paramAffine,
			layerRange,
			fixedLayers,
			emptyLayers,
			layerset.get2DBounds(),
      false,
      false,
			filter);

	layerset.setMinimumDimensions();

	/* save the project */
	project.saveAs(dir + "/intersection_Affine.xml", true);
}
catch (e) {
	e.printStackTrace();
}

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