import-and-align.bsh

/**
 * Call
 *
 * xvfb-run -a ./ImageJ-linux64 -Ddir=<project directory> -Dfile=<import file>  -- --no-splash import-and-align.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;

try {
	runtime = Runtime.getRuntime();
	System.out.println( runtime.availableProcessors() + " cores available for multi-threading" );
	//System.getProperties().setProperty("plugins.dir","/home/sharmishtaas/packages/Fiji.app/plugins");
	//System.getProperties().setProperty("ij1.plugins.dir", "/home/sharmishtaas/packages/Fiji.app/plugins/");
	dir = System.getProperty("dir");
	file = System.getProperty("file");
	
	ControlWindow.setGUIEnabled(false);
	project = Project.newFSProject("blank", null, dir, false);
	loader = project.getLoader();
	layerset = project.getRootLayerSet();
	layerset.setSnapshotsMode(1);
	
	/* add a reference layer (pointless gymnastik) */
	layer = new Layer(project, 0, 1, layerset);
	layerset.add(layer);
	layer.recreateBuckets();
	
	/* import images */
	task = loader.importImages(
			layerset.getLayer(0),	// the first layer
			file,					// the absolute file path to the text file with absolute image file paths
			" ",					// the column separator  <path> <x> <y> <section index>
			1.0,					// section thickness, defaults to 1
			1.0,					// calibration, defaults to 1
			false,					// whether to homogenize contrast, avoid
			1.0f,					// scaling factor, default to 1
			0);						// border width
	
	/* wait until all images have been imported */
	task.join();
	
//	/* wait until all mipmaps are generated */
//	futures = new ArrayList();
//	for (p : layerset.getDisplayables(Patch.class))
//		futures.add(p.updateMipMaps());
//	for (f : futures)
//		f.get();

	/* delete reference layer if it was not part of the import range */
	l0 = layerset.getLayer(0);
	if (l0.getDisplayables(Patch.class).size() == 0)
		layerset.remove(l0);
	

	/* save the project */
		project.saveAs(dir + "/project.xml", false);
	
	/* prepare alignment */
	layerRange = layerset.getLayers();
	fixedLayers = new HashSet();

	emptyLayers = new HashSet();
	
	filter = new Filter() {
		public boolean accept(Patch patch) {
			return patch.isVisible();
			}
		};
	
	/* affine alignment */
	paramAffine = new RegularizedAffineLayerAlignment.Param();
	
	paramAffine.ppm.sift.initialSigma = 1.6f;
	paramAffine.ppm.sift.steps = 3;
	paramAffine.ppm.sift.minOctaveSize = 200;
	paramAffine.ppm.sift.maxOctaveSize = 2048;
	paramAffine.ppm.sift.fdSize = 4;
	paramAffine.ppm.sift.fdBins = 8;
	paramAffine.ppm.rod = 0.92f;
	paramAffine.ppm.clearCache = true;
	paramAffine.ppm.maxNumThreadsSift = runtime.availableProcessors();
	
	paramAffine.maxEpsilon = 20.0f;
	paramAffine.minInlierRatio = 0.1f;
	paramAffine.minNumInliers = 50;
	
	//model indices, 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();
	
	//model indices, 0=translation, 1=rigid, 2=similarity, 3=affine
	paramAffine.desiredModelIndex = 3;
	
	paramAffine.regularize = true;
	paramAffine.maxIterationsOptimize = 200;
	paramAffine.maxPlateauwidthOptimize = 2000;
	
	//model indices, 0=translation, 1=rigid, 2=similarity, 3=affine
	paramAffine.regularizerIndex = 1;
	paramAffine.visualize = false;
	
	paramAffine.lambda = 0.1f;
	
	new RegularizedAffineLayerAlignment().exec(
			paramAffine,
			layerRange,	
			fixedLayers,
			emptyLayers,
			layerset.get2DBounds(),
			false,
			false,
			filter);
	
	paramAffine.lambda = 0.01f;
	
	layerset.setMinimumDimensions();
	
	new RegularizedAffineLayerAlignment().exec(
			paramAffine,
			layerRange,	
			fixedLayers,
			emptyLayers,
			layerset.get2DBounds(),
			false,
			false,
			filter);
	

	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();
		
	/* save the project */
	project.saveAs(dir + "/project.xml", true);

	/* elastic alignment */
	paramElastic = new ElasticLayerAlignment.Param();
	
	paramElastic.layerScale = 0.25f;
	paramElastic.searchRadius = 25;
	//paramElastic.blockRadius = 200;
	paramElastic.blockRadius = 128;
	paramElastic.resolutionSpringMesh = (int)Math.ceil((double)layerset.get2DBounds().width / 400);
	
	paramElastic.minR = 0.4f;
	paramElastic.maxCurvatureR = 10.0f;
	paramElastic.rodR = 0.9f;
	
	paramElastic.useLocalSmoothnessFilter = true;
	paramElastic.localModelIndex = 1;
	paramElastic.localRegionSigma = 400.0f;
	paramElastic.maxLocalEpsilon = 25.0f;
	paramElastic.maxLocalTrust = 4.0f;
	
	paramElastic.isAligned = true;
	paramElastic.maxNumFailures = 3;
	paramElastic.maxNumNeighbors = 10;
	paramElastic.maxNumThreads = 8;
	
	paramElastic.desiredModelIndex = 1;
	paramElastic.maxIterationsOptimize = 1000;
	paramElastic.maxPlateauwidthOptimize = 200;

	//paramElastic.stiffnessSpringMesh = 0.25f; //original
	paramElastic.stiffnessSpringMesh = 0.1f;
	paramElastic.maxStretchSpringMesh = 2000.0f;
	paramElastic.maxIterationsSpringMesh = 5000;
	paramElastic.maxPlateauwidthSpringMesh = 1000;
	paramElastic.dampSpringMesh = 0.9f;
	paramElastic.useLegacyOptimizer = false;

	new ElasticLayerAlignment().exec(
		paramElastic,
		project,
		layerRange,
		fixedLayers,
		emptyLayers,
		layerset.get2DBounds(),
		false,
		false,
		filter);
	
	/* wait until all mipmaps are generated */
	futures = new ArrayList();
	for (p : layerset.getDisplayables(Patch.class))
		futures.add(p.updateMipMaps());
	for (f : futures)
		f.get();
		
	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(); 
		
	/* save the project */
	project.saveAs(dir + "/project.xml", true); 
}
catch (e) {
	e.printStackTrace();
}

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