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	diff --git a/DeconvolutionLab2/DeconvolutionLab2.config b/DeconvolutionLab2/DeconvolutionLab2.config
	index d929b86..48b59a1 100644
	--- a/DeconvolutionLab2/DeconvolutionLab2.config
	+++ b/DeconvolutionLab2/DeconvolutionLab2.config
	@@ -1,80 +1,82 @@
	#DeconvolutionLab2 [Beta 1]
	#DeconvolutionLab2 [Beta 1]
	-#Thu Feb 02 15:10:59 CET 2017
	+#Fri Feb 03 08:33:07 CET 2017
	Algorithm.FISTA.iterations=10
	Algorithm.FISTA.reg=0.1
	Algorithm.FISTA.scale=3
	Algorithm.FISTA.step=1.0
	Algorithm.FISTA.wavelets=Haar
	Algorithm.ICTM.iterations=10
	Algorithm.ICTM.reg=0.1
	Algorithm.ICTM.step=1.0
	Algorithm.ISTA.iterations=10
	Algorithm.ISTA.reg=0.1
	Algorithm.ISTA.scale=3
	Algorithm.ISTA.step=1.0
	Algorithm.ISTA.wavelets=Haar
	Algorithm.LW+.iterations=10
	Algorithm.LW+.step=1.0
	Algorithm.LW.iterations=10
	Algorithm.LW.step=1.0
	Algorithm.RIF.reg=0.1
	Algorithm.RL.iterations=10
	Algorithm.RLTV.reg=0.1
	Algorithm.SIM.gaussian.mean=0.0
	Algorithm.SIM.gaussian.stdev=1.0
	Algorithm.SIM.poisson=0.0
	Algorithm.TM.iterations=10
	Algorithm.TM.reg=0.1
	Algorithm.TM.step=1.0
	Algorithm.TRIF.reg=0.1
	Algorithm.VC.iterations=10
	Algorithm.VC.step=1.0
	-Algorithm.algorithm=Regularized Inverse Filter
	+Algorithm.algorithm=Landweber
	Border.apoxy=Uniform
	Border.apoz=Uniform
	Border.extxy=0
	Border.extz=0
	Border.normalization=1
	Border.padxy=None
	Border.padz=None
	Controller.constraint.enable=false
	Controller.constraint.snapshot=1
	Controller.constraint.value=No
	Controller.reference.enable=false
	Controller.reference.snapshot=1
	Controller.reference.value=
	Controller.residu.enable=false
	Controller.residu.snapshot=1
	Controller.residu.value=0.01
	Controller.savestats.enable=false
	Controller.savestats.snapshot=1
	Controller.savestats.value=Stats
	Controller.showstats.enable=false
	Controller.showstats.snapshot=1
	Controller.showstats.value=Stats
	DeconvolutionLab.MainDialog.location.h=579
	DeconvolutionLab.MainDialog.location.w=573
	-DeconvolutionLab.MainDialog.location.x=5
	-DeconvolutionLab.MainDialog.location.y=23
	+DeconvolutionLab.MainDialog.location.x=124
	+DeconvolutionLab.MainDialog.location.y=52
	Fourier.dim=XYZ
	Fourier.epsilon=1E-6
	Fourier.fft=Academic
	Image.image.row0=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;null
	Image.image.row1=resolution;directory;/Users/dsage/Desktop/DeconvolutionLab2-Course/resolution;null
	Image.image.selected=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;null
	Language.headless=Run (Headless)
	-Language.language=Command line
	-Monitor.disable.console=false
	-Monitor.disable.display=false
	-Monitor.disable.multithreading=false
	-Monitor.disable.table=false
	-Monitor.path=/Users/dsage/git/deconvolution/DeconvolutionLab2
	-Monitor.time.value=3600
	-Monitor.time=No time limitation
	-Monitor.verbose=Verbose\: log
	-Output.output.row0=ortho;Noname;;;;\u2713;\u2713;null
	-Output.output.selected=ortho;Noname;;;;\u2713;\u2713;null
	-PSF.psf.row0=Airy;synthetic;Airy 100.0 0.0 1.0 size 128 128 32 ;null
	-PSF.psf.row1=Defocus;synthetic;Defocus 100.0 0.0 3.0 10.0 10.0 size 3 3 100 ;null
	-PSF.psf.selected=Airy;synthetic;Airy 100.0 0.0 1.0 size 128 128 32 ;null
	+Language.job=Job
	+Language.language=ImageJ Macro
	+Output.output.row0=mip @1;MI1;;;;\u2713;null;null
	+Output.output.selected=mip @1;MI1;;;;\u2713;null;null
	+PSF.psf.row0=MotionBlur;synthetic;MotionBlur 100.0 0.0 3.0 30.0 3.0 size 128 128 32 ;
	+PSF.psf.row1=Airy;synthetic;Airy 100.0 0.0 1.0 size 128 128 32 ;null
	+PSF.psf.row2=Defocus;synthetic;Defocus 100.0 0.0 3.0 10.0 10.0 size 3 3 100 ;null
	+PSF.psf.selected=MotionBlur;synthetic;MotionBlur 100.0 0.0 3.0 30.0 3.0 size 128 128 32 ;
	+Watcher.disable.console=false
	+Watcher.disable.display=false
	+Watcher.disable.multithreading=false
	+Watcher.disable.table=false
	+Watcher.path=/Users/dsage/git/deconvolution/DeconvolutionLab2
	+Watcher.time.value=3600
	+Watcher.time=No time limitation
	+Watcher.verbose=Verbose\: log
	diff --git a/DeconvolutionLab2/src/deconvolution/DeconvolutionListener.java b/DeconvolutionLab2/src/deconvolution/DeconvolutionListener.java
	new file mode 100644
	index 0000000..fe4542b
	--- /dev/null
	+++ b/DeconvolutionLab2/src/deconvolution/DeconvolutionListener.java
	@@ -0,0 +1,7 @@
	+package deconvolution;
	+
	+public interface DeconvolutionListener {
	+
	+ public abstract void started();
	+ public abstract void finish();
	+}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java b/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	index f7859cd..5c6a7bb 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	@@ -1,381 +1,381 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package deconvolution.algorithm;

	import java.util.Timer;
	import java.util.TimerTask;

	import deconvolution.Deconvolution;
	import deconvolutionlab.Lab;
	import deconvolutionlab.OutputCollection;
	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.FFT;
	import lab.system.SystemUsage;
	import lab.tools.NumFormat;
	import signal.Assessment;
	import signal.ComplexSignal;
	import signal.Constraint;
	import signal.RealSignal;
	import signal.Signal;

	public class Controller {

	private int iterationsMax = 100;
	private double timeMax = 1000;
	private double residuMin = -1;

	private boolean doResidu = false;
	private boolean doTime = false;
	private boolean doReference = false;
	private boolean doConstraint = false;
	private boolean doShowStats = false;
	private boolean doSaveStats = false;
	private boolean abort = false;

	private int snapshotResidu = 0;
	private int snapshotReference = 0;
	private int snapshotConstraint = 0;
	private int snapshotSaveStats = 0;
	private int snapshotShowStats = 0;

	private double timeStarting = 0;
	private double memoryStarting = 0;
	private double residu = Double.MAX_VALUE;
	private int iterations = 0;
	private double memoryPeak = 0;
	private double snr = 0;
	private double psnr = 0;

	private Constraint.Mode constraint = Constraint.Mode.NO;
	private OutputCollection outs = null;
	private String referenceName = "";
	private String showstatsName = "";
	private String savestatsName = "";
	private RealSignal refImage;
	private RealSignal prevImage;
	private RealSignal x;

	private Timer timer;
	private AbstractFFT fft;

	private String algo = "";
	private float statsInput[];

	private Monitors monitors = new Monitors();

	public Controller() {
	constraint = Constraint.Mode.NO;
	doResidu = false;
	doTime = false;
	doReference = false;
	doConstraint = false;
	doShowStats = false;
	doSaveStats = false;
	}

	public void setMonitors(Monitors monitors) {
	this.monitors = monitors;
	}

	public void setAlgorithm(String algo) {
	this.algo = algo;
	}

	public void setFFT(AbstractFFT fft) {
	this.fft = fft;
	}

	public void abort() {
	this.abort = true;
	}

	public int getIterationMax() {
	return iterationsMax;
	}

	public void setIterationMax(int iterationsMax) {
	this.iterationsMax = iterationsMax;
	}

	public void setTimeStop(double timeMax) {
	this.doTime = true;
	this.timeMax = timeMax * 1e9;
	}

	public void setResiduStop(int snapshot, double residuMin) {
	this.doResidu = true;
	this.snapshotResidu = snapshot;
	this.residuMin = residuMin;
	}

	public void setReference(int snapshot, String referenceName) {
	this.doReference = true;
	this.snapshotReference = snapshot;
	this.referenceName = referenceName;
	}

	public void setConstraint(int snapshot, Constraint.Mode constraint) {
	this.doConstraint = true;
	this.snapshotConstraint = snapshot;
	this.constraint = constraint;
	}

	public void setSaveStats(int snapshot, String name) {
	this.doSaveStats = true;
	this.snapshotSaveStats = snapshot;
	this.savestatsName = name;
	}

	public void setShowStats(int snapshot, String name) {
	this.doShowStats = true;
	this.snapshotShowStats = snapshot;
	this.showstatsName = name;
	}

	public void setOutputs(OutputCollection outs) {
	this.outs = outs;
	}

	public void start(RealSignal x) {
	this.x = x;
	statsInput = x.getStats();
	iterations = 0;
	timer = new Timer();
	timer.schedule(new Updater(), 0, 100);
	timeStarting = System.nanoTime();
	memoryStarting = SystemUsage.getHeapUsed();
	Signal.bytes = 0;

	if (doConstraint && x != null)
	Constraint.setModel(x);

	if (doReference && snapshotReference >= 1) {
	refImage = new Deconvolution("-image file " + referenceName).openImage();
	if (refImage == null)
	monitors.error("Impossible to load the reference image " + referenceName);
	else
	monitors.log("Reference image loaded");
	}

	if (doShowStats \|\| doSaveStats)
	if (monitors != null)
	Lab.firstStats(monitors, showstatsName, this, doShowStats, doSaveStats);
	this.prevImage = x;
	}

	public boolean ends(ComplexSignal X) {
	boolean res = doResidu && snapshotResidu >= 1 ? (iterations % snapshotResidu == 0) : false;
	boolean con = doConstraint && snapshotConstraint >= 1 ? (iterations % snapshotConstraint == 0) : false;
	boolean ref = doReference && snapshotReference >= 1 ? (iterations % snapshotReference == 0) : false;
	boolean sav = doSaveStats && snapshotSaveStats >= 1 ? (iterations % snapshotSaveStats == 0) : false;
	boolean shw = doShowStats && snapshotShowStats >= 1 ? (iterations % snapshotShowStats == 0) : false;
	boolean out = outs == null ? false : outs.hasShow(iterations);

	if (con \|\| res \|\| ref \|\| sav \|\| shw \|\| out) {
	if (fft == null)
	fft = FFT.createDefaultFFT(monitors, X.nx, X.ny, X.nz);
	x = new RealSignal(X.nx, X.ny, X.nz, false);
	fft.inverse(X, x);
	return ends(x);
	}

	return ends((RealSignal) null);
	}

	public boolean ends(RealSignal x) {
	this.x = x;
	boolean res = doResidu && snapshotResidu >= 1 ? (iterations % snapshotResidu == 0) : false;
	boolean con = doConstraint && snapshotConstraint >= 1 ? (iterations % snapshotConstraint == 0) : false;
	boolean ref = doReference && snapshotReference >= 1 ? (iterations % snapshotReference == 0) : false;
	boolean sav = doSaveStats && snapshotSaveStats >= 1 ? (iterations % snapshotSaveStats == 0) : false;
	boolean shw = doShowStats && snapshotShowStats >= 1 ? (iterations % snapshotShowStats == 0) : false;

	if (con \|\| res \|\| ref)
	compute(iterations, x, con, res, ref);

	if (sav \|\| shw)
	Lab.nextStats(monitors, showstatsName, this, sav, shw);

	if (outs != null)
	- outs.executeIterative(monitors, x, this);
	+ outs.executeIterative(monitors, x, iterations, this);

	iterations++;
	double p = iterations * 100.0 / iterationsMax;
	monitors.progress("Iterative " + iterations + "/" + iterationsMax, p);
	double timeElapsed = getTimeNano();
	boolean stopIter = (iterations >= iterationsMax);
	boolean stopTime = doTime && (timeElapsed >= timeMax);
	boolean stopResd = doResidu && (residu <= residuMin);
	monitors.log("@" + iterations + " Time: " + NumFormat.seconds(timeElapsed) + " Memory: " + NumFormat.bytes(Signal.bytes));

	String prefix = "Stopped>> by ";
	if (abort)
	monitors.log(prefix + "abort");
	if (stopIter)
	monitors.log(prefix + "iteration " + iterations + " > " + iterationsMax);
	if (stopTime)
	monitors.log(prefix + "time " + timeElapsed + " > " + timeMax);
	if (stopResd)
	monitors.log(prefix + "residu " + NumFormat.nice(residu) + " < " + NumFormat.nice(residuMin));

	return abort \| stopIter \| stopTime \| stopResd;
	}

	public void finish(RealSignal x) {
	this.x = x;

	boolean ref = doReference;
	boolean con = doConstraint;
	boolean res = doResidu;
	if (con \|\| res \|\| ref)
	compute(iterations, x, con, res, ref);

	if (doShowStats \|\| doSaveStats)
	Lab.lastStats(monitors, savestatsName, this, doShowStats, doSaveStats);

	monitors.log("Time: " + NumFormat.seconds(getTimeNano()) + " Peak:" + getMemoryAsString());
	if (timer != null)
	timer.cancel();
	}

	private void compute(int iterations, RealSignal x, boolean con, boolean res, boolean ref) {
	if (x == null)
	return;

	if (con && constraint != null)
	new Constraint(monitors).apply(x, constraint);

	if (ref && refImage != null) {
	String s = "";
	psnr = Assessment.psnr(x, refImage);
	snr = Assessment.snr(x, refImage);
	s += " PSNR: " + NumFormat.nice(psnr);
	s += " SNR: " + NumFormat.nice(snr);
	monitors.log("@" + iterations + " " + s);
	}

	residu = Double.MAX_VALUE;
	if (res && prevImage != null) {
	residu = Assessment.relativeResidu(x, prevImage);
	prevImage = x.duplicate();
	monitors.log("@" + iterations + " Residu: " + NumFormat.nice(residu));
	}

	}

	public String[] stats(String name) {
	float params[] = null;
	if (x != null)
	params = x.getStats();
	String[] row = new String[15];
	row[0] = name;
	row[1] = algo;
	row[2] = "" + iterations;
	row[3] = (params == null ? "-" : "" + params[0]);
	row[4] = (params == null ? "-" : "" + params[1]);
	row[5] = (params == null ? "-" : "" + params[2]);
	row[6] = (params == null ? "-" : "" + params[3]);
	row[7] = (params == null ? "-" : "" + params[4]);
	row[8] = (params == null ? "-" : "" + params[5]);
	row[9] = NumFormat.seconds(getTimeNano());
	row[10] = NumFormat.bytes(SystemUsage.getHeapUsed());
	row[11] = NumFormat.bytes(memoryPeak);
	row[12] = doReference ? NumFormat.nice(psnr) : "n/a";
	row[13] = doReference ? NumFormat.nice(snr) : "n/a";
	row[14] = doResidu ? NumFormat.nice(residu) : "n/a";
	return row;
	}

	public double getTimeNano() {
	return (System.nanoTime() - timeStarting);
	}

	public Constraint.Mode getConstraint() {
	return constraint;
	}

	public String getConstraintAsString() {
	if (!doConstraint)
	return "no";
	if (constraint == Constraint.Mode.NO)
	return "no";
	else
	return constraint.name().toLowerCase();
	}

	public String getReference() {
	return doReference ? referenceName : "no ground-truth";
	}

	public String getShowStats() {
	return doShowStats ? showstatsName : "no stats";
	}

	public String getSaveStats() {
	return doSaveStats ? savestatsName : "no stats";
	}

	public String getStoppingCriteria(AbstractAlgorithm algo) {
	String stop = algo.isIterative() ? " iterations limit=" + getIterationMax() + " " : ", ";
	stop += doTime ? ", time limit=" + NumFormat.nice(timeMax * 1e-9) : " no time limit" + ", ";
	stop += doResidu ? ", residu limit=" + NumFormat.nice(residuMin) : " no residu limit";
	return stop;
	}

	public float[] getStatsInput() {
	return statsInput;
	}

	public double getMemory() {
	return memoryPeak - memoryStarting;
	}

	public String getMemoryAsString() {
	return NumFormat.bytes(getMemory());
	}

	public int getIterations() {
	return iterations;
	}

	private void update() {
	memoryPeak = Math.max(memoryPeak, SystemUsage.getHeapUsed());
	}

	private class Updater extends TimerTask {
	@Override
	public void run() {
	update();
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/Lab.java b/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	index 895597e..2d2504b 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	@@ -1,359 +1,363 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package deconvolutionlab;

	-import imagej.IJImager;
	-
	import java.io.File;
	import java.util.ArrayList;
	import java.util.regex.Pattern;

	import javax.swing.JFrame;

	+import deconvolution.algorithm.Controller;
	+import deconvolutionlab.PlatformImager.ContainerImage;
	+import deconvolutionlab.monitor.Monitors;
	+import fft.AbstractFFT;
	+import fft.AbstractFFTLibrary;
	+import fft.FFT;
	+import imagej.IJImager;
	import lab.component.CustomizedColumn;
	import lab.component.CustomizedTable;
	import lab.tools.NumFormat;
	import lab.tools.WebBrowser;
	import plugins.sage.deconvolutionlab.IcyImager;
	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;
	import signal.factory.Sphere;
	-import deconvolution.algorithm.Controller;
	-import deconvolutionlab.monitor.ConsoleMonitor;
	-import deconvolutionlab.monitor.Monitors;
	-import fft.AbstractFFT;
	-import fft.AbstractFFTLibrary;
	-import fft.FFT;

	public class Lab {

	private static PlatformImager imager;
	private static Lab instance = null;
	private static Platform platform = Platform.IMAGEJ;

	private static CustomizedTable tableStats = null;
	private static JFrame frameStats = null;

	static {
	imager = new IJImager();
	createStats();
	}

	private static void createStats() {

	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Name", String.class, 100, false));
	columns.add(new CustomizedColumn("Algorithm", String.class, 100, false));
	columns.add(new CustomizedColumn("Iterations", String.class, 100, false));
	columns.add(new CustomizedColumn("Image Mean", String.class, 100, false));
	columns.add(new CustomizedColumn("Image Minimum", String.class, 100, false));
	columns.add(new CustomizedColumn("Image Maximum", String.class, 100, false));
	columns.add(new CustomizedColumn("Image Stdev", String.class, 100, false));
	columns.add(new CustomizedColumn("Image norm1", String.class, 100, false));
	columns.add(new CustomizedColumn("Image norm2", String.class, 100, false));
	columns.add(new CustomizedColumn("Time", String.class, 100, false));
	columns.add(new CustomizedColumn("Memory", String.class, 100, false));
	columns.add(new CustomizedColumn("Peak", String.class, 100, false));
	columns.add(new CustomizedColumn("PSNR", String.class, 100, false));
	columns.add(new CustomizedColumn("SNR", String.class, 100, false));
	columns.add(new CustomizedColumn("Residu", String.class, 100, false));
	tableStats = new CustomizedTable(columns, true);

	}

	public static Platform getPlatform() {
	return platform;
	}

	public static void getInstance(Platform p) {
	platform = p;
	if (instance == null) {
	instance = new Lab();
	switch (p) {
	case STANDALONE:
	imager = new LabImager();
	break;
	case IMAGEJ:
	imager = new IJImager();
	break;
	case ICY:
	imager = new IcyImager();
	break;
	default:
	imager = new LabImager();
	break;
	}
	}
	}

	public static void help() {
	WebBrowser.open(Constants.url);
	}

	public static void checkFFT(Monitors monitors) {

	ArrayList<AbstractFFTLibrary> libraries = FFT.getInstalledLibraries();
	for (int k = 1; k <= 3; k++)
	for (AbstractFFTLibrary library : libraries) {
	RealSignal y = new Sphere(3, 1).generate(40, 30, 20);
	double chrono = System.nanoTime();
	AbstractFFT fft = FFT.createDefaultFFT(monitors, y.nx, y.ny, y.nz);
	RealSignal x = fft.inverse(fft.transform(y));
	chrono = System.nanoTime() - chrono;
	double residu = y.getEnergy() - x.getEnergy();
	monitors.log(fft.getName() + " Test " + k);
	monitors.log("\t residu of reconstruction: " + residu);
	monitors.log("\t computation time (" + x.nx + "x" + x.ny + "x" + x.nz + ") " + NumFormat.time(chrono));
	}
	}

	- public static void appendShowLive(Monitors monitors, String key, RealSignal signal, String title, String code) {
	- imager.appendShowLive(key, signal, title);
	+ public static ContainerImage createContainer(Monitors monitors, String title) {
	+ monitors.log("Create Live Real Signal " + title);
	+ return imager.createContainer(title);
	+ }
	+
	+ public static void append(Monitors monitors, ContainerImage container, RealSignal signal, String title) {
	+ imager.append(container, signal, title);
	monitors.log("Add Live Real Signal " + title);
	}

	- public static void appendShowLive(Monitors monitors, String key, RealSignal signal, String title, PlatformImager.Type type) {
	- imager.appendShowLive(key, signal, title, type);
	+ public static void append(Monitors monitors, ContainerImage container, RealSignal signal, String title, PlatformImager.Type type) {
	+ imager.append(container, signal, title, type);
	monitors.log("Add Live Real Signal " + title);
	}

	public static void show(Monitors monitors, ComplexSignal signal, String title) {
	if (signal == null) {
	monitors.error("Show " + title + " this image does not exist.");
	return;
	}
	monitors.log("Show Real Signal " + title);
	imager.show(signal, title);
	}

	public static void show(Monitors monitors, ComplexSignal signal, String title, ComplexComponent complex) {
	if (signal == null) {
	monitors.error("Show " + title + " this image does not exist.");
	return;
	}
	monitors.log("Show Real Signal " + title);
	imager.show(signal, title, complex);
	}

	public static void show(Monitors monitors, RealSignal signal, String title) {
	if (signal == null) {
	monitors.error("Show " + title + " this image does not exist.");
	return;
	}
	monitors.log("Show Real Signal " + title);
	imager.show(signal, title);
	}

	public static void show(Monitors monitors, RealSignal signal, String title, PlatformImager.Type type) {
	if (signal == null) {
	monitors.error("Show " + title + " this image does not exist.");
	return;
	}
	monitors.log("Show Real Signal " + title);
	imager.show(signal, title, type);
	}

	public static void show(Monitors monitors, RealSignal signal, String title, PlatformImager.Type type, int z) {
	if (signal == null) {
	monitors.error("Show " + title + " this image does not exist.");
	return;
	}
	monitors.log("Show Real Signal " + title);
	imager.show(signal, title, type);
	}

	public static void save(Monitors monitors, RealSignal signal, String filename) {
	imager.save(signal, filename);
	monitors.log("Save Real Signal " + filename);
	}

	public static void save(Monitors monitors, RealSignal signal, String filename, PlatformImager.Type type) {
	imager.save(signal, filename, type);
	monitors.log("Save Real Signal " + filename);
	}

	public static void firstStats(Monitors monitors, String name, Controller controller, boolean show, boolean save) {
	if (controller == null)
	return;

	Lab.createStats();

	if (show) {
	frameStats = new JFrame(name);
	frameStats.getContentPane().add(tableStats.getPane(600, 200));
	frameStats.pack();
	frameStats.setVisible(true);
	}
	nextStats(monitors, "Start", controller, show, save);
	}

	public static void nextStats(Monitors monitors, String name, Controller controller, boolean show, boolean save) {
	if (tableStats == null)
	return;
	if (controller == null)
	return;
	tableStats.append(controller.stats(name));
	monitors.log("Stats " + name);
	if (show && frameStats != null) {
	if (!frameStats.isVisible())
	frameStats.setVisible(true);
	frameStats.requestFocus();
	}
	}

	public static void lastStats(Monitors monitors, String filename, Controller controller, boolean show, boolean save) {
	if (controller == null)
	return;
	if (tableStats == null)
	return;
	nextStats(monitors, "End", controller, show, save);
	if (save) {
	monitors.log("Stats " + filename);
	tableStats.saveCSV(filename + ".csv");
	}
	}

	public static RealSignal open(Monitors monitors, String filename) {
	RealSignal signal = imager.open(filename);
	if (signal == null)
	monitors.error("Unable to open " + filename);
	else
	monitors.log("Load " + filename);
	return signal;
	}

	public static RealSignal openDir(Monitors monitors, String path) {

	String parts[] = path.split(" pattern ");
	String dirname = path;
	String regex = "";
	if (parts.length == 2) {
	dirname = parts[0].trim();
	regex = parts[1].trim();
	}

	File file = new File(dirname + File.separator);

	if (!file.isDirectory()) {
	monitors.error("Dir " + dirname + " is not a directory.");
	return null;
	}
	String[] list = file.list();
	ArrayList<RealSignal> slices = new ArrayList<RealSignal>();
	int nx = 0;
	int ny = 0;
	Pattern pattern = Pattern.compile(regex);
	for (String filename : list) {
	if (pattern.matcher(filename).find()) {
	RealSignal slice = imager.open(dirname + File.separator + filename);
	if (slice != null) {
	slices.add(slice);
	nx = Math.max(nx, slice.nx);
	ny = Math.max(ny, slice.ny);
	monitors.log("Image " + path + File.separator + filename + " is loaded.");
	}
	}
	else {
	monitors.error("Error in loading image " + path + File.separator + filename);
	}
	}
	int nz = slices.size();
	if (nz <= 0) {
	monitors.error("Dir " + path + " do no contain valid images.");
	return null;
	}
	RealSignal signal = new RealSignal(nx, ny, nz);
	for (int z = 0; z < slices.size(); z++)
	signal.setSlice(z, slices.get(z));
	return signal;
	}

	public static void showOrthoview(Monitors monitors, RealSignal signal, String title, int hx, int hy, int hz) {
	if (signal == null) {
	monitors.error("Show Orthoview " + title + " this image does not exist.");
	return;
	}
	imager.show(signal.createOrthoview(hx, hy, hz), title);
	}

	public static void showOrthoview(Monitors monitors, RealSignal signal, String title) {
	if (signal == null) {
	monitors.error("Show Orthoview " + title + " this image does not exist.");
	return;
	}
	int hx = signal.nx / 2;
	int hy = signal.ny / 2;
	int hz = signal.nz / 2;
	imager.show(signal.createOrthoview(hx, hy, hz), title);
	}

	public static void showMIP(Monitors monitors, RealSignal signal, String title) {
	if (signal == null) {
	monitors.error("Show MIP " + title + " this image does not exist.");
	return;
	}
	imager.show(signal.createMIP(), title);
	}

	public static void showMontage(Monitors monitors, RealSignal signal, String title) {
	if (signal == null) {
	monitors.error("Show Montage " + title + " this image does not exist.");
	return;
	}
	imager.show(signal.createMontage(), title);
	}

	public static RealSignal create(Monitors monitors, String name) {
	RealSignal signal = imager.create(name);
	if (signal != null)
	monitors.log("Created the real signal " + name + " " + signal.toString());
	else
	monitors.error("Impossible to create the real signal " + name);
	return signal;
	}

	public static RealSignal create(Monitors monitors) {
	RealSignal signal = imager.create();
	if (signal != null)
	monitors.log("Created the real signal from the active window " + signal.toString());
	else
	monitors.error("Impossible to create the real signal from the active window");
	return signal;
	}

	public static PlatformImager getImager() {
	return imager;
	}


	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/LabImager.java b/DeconvolutionLab2/src/deconvolutionlab/LabImager.java
	index c796f02..2667f60 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/LabImager.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/LabImager.java
	@@ -1,214 +1,214 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package deconvolutionlab;

	import ij.ImagePlus;
	import ij.ImageStack;
	import ij.WindowManager;
	import ij.io.FileSaver;
	import ij.io.Opener;
	import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;
	-
	-import java.util.HashMap;
	-
	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class LabImager extends PlatformImager {

	- private static HashMap<String, ImageStack> stacks = new HashMap<String, ImageStack>();
	- private static HashMap<String, ImagePlus> images = new HashMap<String, ImagePlus>();
	-
	public static RealSignal create(ImagePlus imp) {
	int nx = imp.getWidth();
	int ny = imp.getHeight();
	int nz = imp.getStackSize();
	RealSignal signal = new RealSignal(nx, ny, nz);
	for (int k = 0; k < nz; k++) {
	ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
	signal.setXY(k, (float[]) ip.getPixels());
	}
	return signal;
	- }
	+ }

	@Override
	public RealSignal create() {
	return build(WindowManager.getCurrentImage());
	}

	@Override
	public RealSignal create(String name) {
	ImagePlus imp = WindowManager.getImage(name);
	if (imp == null)
	imp = WindowManager.getCurrentImage();
	return build(imp);
	}

	@Override
	public RealSignal open(String filename) {
	Opener opener = new Opener();
	ImagePlus imp = opener.openImage(filename);
	return build(imp);
	}
	-
	+
	@Override
	public void show(RealSignal signal, String title) {
	show(signal, title, PlatformImager.Type.FLOAT);
	}

	@Override
	public void show(RealSignal signal, String title, PlatformImager.Type type) {
	- show(signal, title, type, signal.nz/2);
	+ show(signal, title, type, signal.nz / 2);
	}

	@Override
	public void show(RealSignal signal, String title, PlatformImager.Type type, int z) {
	ImagePlus imp = build(signal, type);
	if (imp != null) {
	imp.setTitle(title);
	int nz = imp.getStackSize();
	imp.show();
	imp.setSlice(Math.max(1, Math.min(nz, z)));
	imp.getProcessor().resetMinAndMax();
	}
	}
	-
	+
	+ public ContainerImage createContainer(String title) {
	+ return new ContainerImage();
	+ }
	+
	@Override
	- public void appendShowLive(String key, RealSignal signal, String title) {
	- appendShowLive(key, signal, title, PlatformImager.Type.FLOAT);
	+ public void append(ContainerImage container, RealSignal signal, String title) {
	+ append(container, signal, title, PlatformImager.Type.FLOAT);
	}

	@Override
	- public void appendShowLive(String key, RealSignal signal, String title, PlatformImager.Type type) {
	- ImagePlus imp = build(signal, type);
	- ImagePlus image = images.get(key);
	- ImageStack stack = stacks.get(key);
	- if (image == null \|\| stack == null) {
	- stack = new ImageStack(signal.nx, signal.ny);
	- stack.addSlice(imp.getProcessor());
	- image = new ImagePlus(title, stack);
	- image.show();
	- images.put(key, image);
	- stacks.put(key, stack);
	+ public void append(ContainerImage container, RealSignal signal, String title, PlatformImager.Type type) { ImagePlus cont = (ImagePlus) container.object;
	+ if (container.object == null) {
	+ ImageStack stack = new ImageStack(signal.nx, signal.ny);
	+ stack.addSlice(build(signal, type).getProcessor());
	+ stack.addSlice(build(signal, type).getProcessor());
	+ container.object = new ImagePlus(title, stack);
	+ ((ImagePlus)container.object).show();
	}
	else {
	- stack.addSlice(imp.getProcessor());
	- image.setStack(stack);
	+ cont.getStack().addSlice(build(signal, type).getProcessor());
	+ cont.setSlice(cont.getStack().getSize());
	+ cont.updateAndDraw();
	+ cont.getProcessor().resetMinAndMax();
	}
	- image.updateAndDraw();
	- image.setSlice(image.getStack().getSize());
	- image.getProcessor().resetMinAndMax();
	}

	@Override
	public void save(RealSignal signal, String filename) {
	save(signal, filename, PlatformImager.Type.FLOAT);
	}

	@Override
	public void save(RealSignal signal, String filename, PlatformImager.Type type) {
	ImagePlus imp = build(signal, type);
	if (imp != null) {
	if (imp.getStackSize() == 1) {
	new FileSaver(imp).saveAsTiff(filename);
	}
	else {
	new FileSaver(imp).saveAsTiffStack(filename);
	}
	}
	}

	@Override
	- public void show(ComplexSignal signal, String title) {
	+ public void show(ComplexSignal signal, String title) {
	show(signal, title, ComplexComponent.MODULE);
	}
	-
	+
	@Override
	- public void show(ComplexSignal signal, String title, ComplexComponent complex) {
	+ public void show(ComplexSignal signal, String title, ComplexComponent complex) {
	ImageStack stack = new ImageStack(signal.nx, signal.ny);
	for (int k = 0; k < signal.nz; k++) {
	float[] plane = null;
	- switch(complex) {
	- case REAL: plane = signal.getRealXY(k); break;
	- case IMAGINARY: plane = signal.getImagXY(k); break;
	- case MODULE: plane = signal.getModuleXY(k); break;
	- default: plane = signal.getModuleXY_dB(k);
	+ switch (complex) {
	+ case REAL:
	+ plane = signal.getRealXY(k);
	+ break;
	+ case IMAGINARY:
	+ plane = signal.getImagXY(k);
	+ break;
	+ case MODULE:
	+ plane = signal.getModuleXY(k);
	+ break;
	+ default:
	+ plane = signal.getModuleXY_dB(k);
	}
	stack.addSlice(new FloatProcessor(signal.nx, signal.ny, plane));
	}
	new ImagePlus(title, stack).show();
	}
	-
	+
	private RealSignal build(ImagePlus imp) {
	if (imp == null)
	return null;
	int nx = imp.getWidth();
	int ny = imp.getHeight();
	int nz = imp.getStackSize();
	RealSignal signal = new RealSignal(nx, ny, nz);
	for (int k = 0; k < nz; k++) {
	ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
	signal.setXY(k, (float[]) ip.getPixels());
	}
	return signal;
	}
	-
	+
	private ImagePlus build(RealSignal signal, PlatformImager.Type type) {
	if (signal == null)
	return null;
	-
	+
	ImageStack stack = new ImageStack(signal.nx, signal.ny);
	for (int k = 0; k < signal.nz; k++) {
	ImageProcessor ip = new FloatProcessor(signal.nx, signal.ny, signal.getXY(k));
	- switch(type) {
	- case BYTE:
	- stack.addSlice(ip.convertToByteProcessor(false));
	- break;
	- case SHORT:
	- stack.addSlice(ip.convertToShortProcessor(false));
	- break;
	- case FLOAT:
	- stack.addSlice(ip);
	- default:
	- break;
	+ switch (type) {
	+ case BYTE:
	+ stack.addSlice(ip.convertToByteProcessor(false));
	+ break;
	+ case SHORT:
	+ stack.addSlice(ip.convertToShortProcessor(false));
	+ break;
	+ case FLOAT:
	+ stack.addSlice(ip);
	+ default:
	+ break;
	}
	}
	return new ImagePlus("", stack);
	}
	-
	+
	@Override
	public String getName() {
	return "ImageJ";
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/Output.java b/DeconvolutionLab2/src/deconvolutionlab/Output.java
	index 41e5c88..7cb9c24 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/Output.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/Output.java
	@@ -1,335 +1,353 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package deconvolutionlab;

	import java.io.File;

	import deconvolution.algorithm.Controller;
	+import deconvolutionlab.PlatformImager.ContainerImage;
	import deconvolutionlab.monitor.Monitors;
	import lab.tools.NumFormat;
	import signal.Constraint;
	import signal.RealSignal;

	public class Output {

	public enum View {
	STACK, SERIES, ORTHO, MIP, PLANAR, FIGURE
	};

	public enum Dynamic {
	INTACT, RESCALED, NORMALIZED, CLIPPED
	};

	+ private ContainerImage container = null;
	private int px = 0;
	private int py = 0;
	private int pz = 0;
	private boolean center = true;

	private String name = "";
	private boolean save = true;
	private boolean show = true;

	private View view = View.STACK;
	private PlatformImager.Type type = PlatformImager.Type.FLOAT;
	private Dynamic dynamic = Dynamic.INTACT;

	private int frequency = 0;
	private String path = "";

	public Output(View view, int frequency, String param) {
	String[] tokens = param.trim().split(" ");
	this.view = view;
	this.frequency = frequency;
	this.name = "";
	this.center = true;
	this.save = true;
	this.show = true;
	+ this.container = Lab.createContainer(Monitors.createDefaultMonitor(), "");
	for (int i = 0; i < tokens.length; i++) {
	boolean found = false;
	String p = tokens[i].trim().toLowerCase();

	if (p.startsWith("@")) {
	found = true;
	}

	if (p.startsWith("noshow")) {
	show = false;
	found = true;
	}

	if (p.startsWith("nosave")) {
	save = false;
	found = true;
	}

	for (Dynamic d : Dynamic.values()) {
	if (p.toLowerCase().equals(d.name().toLowerCase())) {
	dynamic = d;
	found = true;
	}
	}
	for (View v : View.values()) {
	if (p.toLowerCase().equals(v.name().toLowerCase())) {
	view = v;
	found = true;
	}
	}
	for (PlatformImager.Type t : PlatformImager.Type.values()) {
	if (p.toLowerCase().equals(t.name().toLowerCase())) {
	type = t;
	found = true;
	}
	}
	if (p.startsWith("(") && p.endsWith(")")) {
	double pos[] = NumFormat.parseNumbers(p);
	if (pos.length > 0)
	px = (int) Math.round(pos[0]);
	if (pos.length > 1)
	py = (int) Math.round(pos[1]);
	if (pos.length > 2)
	pz = (int) Math.round(pos[2]);
	found = true;
	center = false;
	}
	if (!found)
	name += tokens[i] + " ";
	name = name.trim();
	}
	}

	public Output(View view, boolean show, boolean save, int frequency, String name, Dynamic dynamic, PlatformImager.Type type, boolean center) {
	this.name = name;
	this.show = show;
	this.save = save;
	this.view = view;
	this.type = type;
	this.dynamic = dynamic;
	this.center = center;
	this.frequency = frequency;
	}

	public Output(View view, boolean show, boolean save, int frequency, String name, Dynamic dynamic, PlatformImager.Type type, int px, int py, int pz) {
	this.name = name;
	this.show = show;
	this.save = save;
	this.view = view;
	this.type = type;
	this.dynamic = dynamic;
	this.center = false;
	this.px = px;
	this.py = py;
	this.pz = pz;
	this.frequency = frequency;
	}

	public boolean is(int iterations) {
	if (frequency == 0)
	return false;
	return iterations % frequency == 0;
	}

	public View getView() {
	return view;
	}

	public String getName() {
	return name;
	}

	- public void setPath1(String path) {
	+ public void setPath(String path) {
	this.path = path;
	}

	public int extractFrequency(String param) {
	String line = param.trim();
	if (!line.startsWith("@"))
	line = "@0 " + line;
	String parts[] = line.split(" ");
	if (parts.length >= 1) {
	return (int) Math.round(NumFormat.parseNumber(parts[0], 0));
	}
	return 0;
	}

	public void setKeypoint(int px, int py, int pz) {
	this.px = px;
	this.py = py;
	this.pz = pz;
	this.center = false;
	}

	public String[] getAsString() {
	String t = (type == PlatformImager.Type.FLOAT ? "" : type.name().toLowerCase());
	String d = (dynamic == Dynamic.INTACT ? "" : dynamic.name().toLowerCase());
	String k = "";
	if (!center)
	k = " (" + px + "," + py + "," + pz + ")";
	else
	k = "";
	String sa = save ? "\u2713" : "";
	String sh = show ? "\u2713" : "";
	String fr = frequency > 0 ? " @" + frequency : "";
	return new String[] { view.name().toLowerCase() + fr, name, d, t, k, sh, sa, "" };
	}

	- public void execute(Monitors monitors, RealSignal signal, Controller controller, boolean live) {
	+ public void execute(Monitors monitors, RealSignal signal, Controller controller, int iter, boolean live) {
	if (signal == null)
	return;
	String title = name;
	+ if (live)
	+ if (!is(iter))
	+ return;
	+
	if (controller != null && live) {
	if (controller.getIterations() > 0) {
	title += "@" + controller.getIterations();
	}
	}
	RealSignal x = null;
	Constraint constraint = new Constraint(monitors);
	+
	switch (dynamic) {
	case RESCALED:
	x = signal.duplicate();
	constraint.rescaled(x, 0, 255);
	break;
	case CLIPPED:
	x = signal.duplicate();
	float[] stats = controller.getStatsInput();
	if (stats != null)
	constraint.clipped(x, stats[1], stats[2]);
	break;
	case NORMALIZED:
	x = signal.duplicate();
	float[] stats1 = controller.getStatsInput();
	if (stats1 != null)
	constraint.normalized(x, stats1[0], stats1[3]);
	break;
	default:
	x = signal;
	}
	String filename = path + File.separator + title + ".tif";
	- String key = name + "-" + type.name() + "-" + view.name() + "-" + dynamic.name() + "-" + (px + py + pz);
	+
	switch (view) {
	case STACK:
	if (show && !live)
	Lab.show(monitors, x, title, type, (center ? x.nz / 2 : pz));
	if (save && !live)
	Lab.save(monitors, x, filename, type);
	break;
	case SERIES:
	for (int k = 0; k < x.nz; k++) {
	RealSignal slice = x.getSlice(k);
	if (show && !live)
	Lab.show(monitors, slice, title, type);
	if (save && !live)
	Lab.save(monitors, slice, filename, type);
	}
	break;
	case ORTHO:
	- orthoview(monitors, x, title, filename, live, key);
	+ orthoview(monitors, x, title, filename, live);
	break;
	case FIGURE:
	- figure(monitors, x, title, filename, live, key);
	+ figure(monitors, x, title, filename, live);
	break;
	case MIP:
	- mip(monitors, x, title, filename, live, key);
	+ mip(monitors, x, title, filename, live);
	break;
	case PLANAR:
	- planar(monitors, x, title, filename, live, key);
	+ planar(monitors, x, title, filename, live);
	break;
	default:
	break;
	}
	}

	- private void mip(Monitors monitors, RealSignal signal, String title, String filename, boolean live, String key) {
	+ private void mip(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
	RealSignal plane = signal.createMIP();
	- if (show && live)
	- Lab.appendShowLive(monitors, key, plane, title, type);
	+ if (show && live) {
	+ Lab.append(monitors, container, plane, title, type);
	+ }
	if (show && !live)
	Lab.show(monitors, plane, title, type);
	if (save)
	Lab.save(monitors, plane, filename, type);
	}

	- private void orthoview(Monitors monitors, RealSignal signal, String title, String filename, boolean live, String key) {
	+ private void orthoview(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
	int cx = px;
	int cy = py;
	int cz = pz;
	if (center) {
	cx = signal.nx / 2;
	cy = signal.ny / 2;
	cz = signal.nz / 2;
	}
	RealSignal plane = signal.createOrthoview(cx, cy, cz);
	- if (show && live)
	- Lab.appendShowLive(monitors, key, plane, title, type);
	+ if (show && live) {
	+ if (container == null)
	+ container = Lab.createContainer(monitors, title);
	+ Lab.append(monitors, container, plane, title, type);
	+ }
	if (show && !live)
	Lab.show(monitors, plane, title, type);
	if (save)
	Lab.save(monitors, plane, filename, type);
	}

	- private void figure(Monitors monitors, RealSignal signal, String title, String filename, boolean live, String key) {
	+ private void figure(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
	int cx = px;
	int cy = py;
	int cz = pz;
	if (center) {
	cx = signal.nx / 2;
	cy = signal.ny / 2;
	cz = signal.nz / 2;
	}
	RealSignal plane = signal.createFigure(cx, cy, cz);
	- if (show && live)
	- Lab.appendShowLive(monitors, key, plane, title, type);
	+ if (show && live) {
	+ if (container == null)
	+ container = Lab.createContainer(monitors, title);
	+ Lab.append(monitors, container, plane, title, type);
	+ }
	if (show && !live)
	Lab.show(monitors, plane, title, type);
	if (save)
	Lab.save(monitors, plane, filename, type);
	}

	- private void planar(Monitors monitors, RealSignal signal, String title, String filename, boolean live, String key) {
	+ private void planar(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
	RealSignal plane = signal.createMontage();
	- if (show && live)
	- Lab.appendShowLive(monitors, key, plane, title, type);
	+ if (show && live) {
	+ if (container == null)
	+ container = Lab.createContainer(monitors, title);
	+ Lab.append(monitors, container, plane, title, type);
	+ }
	if (show && !live)
	Lab.show(monitors, plane, title, type);
	if (save)
	Lab.save(monitors, plane, filename, type);
	}

	@Override
	public String toString() {
	String t = type.name().toLowerCase();
	String v = view.name().toLowerCase();
	String d = dynamic.name().toLowerCase();
	String f = frequency > 0 ? " every " + frequency + " iterations" : "";
	String k = (center ? "" : " keypoint = (" + px + "," + py + "," + pz + ")");
	return v + " " + name + " format = (" + d + ", " + t + ") " + k + f;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java b/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java
	index 65a34a8..910648f 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java
	@@ -1,86 +1,86 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package deconvolutionlab;

	import java.util.ArrayList;

	import deconvolution.algorithm.Controller;
	import deconvolutionlab.monitor.Monitors;
	import signal.RealSignal;

	public class OutputCollection {

	private ArrayList<Output> list = new ArrayList<Output>();

	public void setPath(String path) {
	for (Output out : list)
	- out.setPath1(path);
	+ out.setPath(path);
	}

	public void add(Output out) {
	if (out != null) {
	list.add(out);
	}
	}

	public boolean hasShow(int iterations) {
	boolean flag = false;
	for (Output out : list)
	flag = flag \| out.is(iterations);
	return flag;
	}

	public void executeFinal(Monitors monitors, RealSignal signal, Controller controller) {
	for (Output out : list)
	if (out != null)
	- out.execute(monitors, signal, controller, false);
	+ out.execute(monitors, signal, controller, 0, false);
	}

	- public void executeIterative(Monitors monitors, RealSignal signal, Controller controller) {
	+ public void executeIterative(Monitors monitors, RealSignal signal, int iter, Controller controller) {
	for (Output out : list)
	if (out != null)
	- out.execute(monitors, signal, controller, true);
	+ out.execute(monitors, signal, controller, iter, true);
	}

	public ArrayList<String> getInformation() {
	ArrayList<String> lines = new ArrayList<String>();
	for (Output out : list) {
	if (out == null)
	lines.add("ERR>" + list.size());
	else
	lines.add("" + out.toString());
	}
	return lines;

	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/PlatformImager.java b/DeconvolutionLab2/src/deconvolutionlab/PlatformImager.java
	index 3dac786..5f2c155 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/PlatformImager.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/PlatformImager.java
	@@ -1,63 +1,69 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package deconvolutionlab;

	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;
	import deconvolutionlab.monitor.Monitors;

	public abstract class PlatformImager {

	+ public class ContainerImage {
	+ public Object object;
	+ }
	+
	public enum Type {FLOAT, SHORT, BYTE};

	public abstract RealSignal create();
	public abstract RealSignal create(String name);

	+ public abstract ContainerImage createContainer(String title);
	+
	public abstract void show(ComplexSignal signal, String title, ComplexComponent complex);
	public abstract void show(ComplexSignal signal, String title);

	- public abstract void appendShowLive(String key, RealSignal signal, String title);
	- public abstract void appendShowLive(String key, RealSignal signal, String title, Type type);
	+ public abstract void append(ContainerImage container, RealSignal signal, String title);
	+ public abstract void append(ContainerImage container, RealSignal signal, String title, Type type);

	public abstract void show(RealSignal signal, String title);
	public abstract void show(RealSignal signal, String title, Type type);
	public abstract void show(RealSignal signal, String title, PlatformImager.Type type, int z);

	public abstract void save(RealSignal signal, String filename);
	public abstract void save(RealSignal signal, String filename, Type type);

	public abstract RealSignal open(String filename);

	public abstract String getName();

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/dialog/OutputDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/OutputDialog.java
	index 42637fc..6a8111b 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/OutputDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/OutputDialog.java
	@@ -1,239 +1,238 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package deconvolutionlab.dialog;

	import java.awt.Component;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JCheckBox;
	import javax.swing.JComboBox;
	import javax.swing.JDialog;
	import javax.swing.JFrame;
	import javax.swing.JLabel;
	import javax.swing.JTextField;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import deconvolutionlab.Output;
	import deconvolutionlab.Output.Dynamic;
	import deconvolutionlab.Output.View;
	import deconvolutionlab.PlatformImager;
	import ij.gui.GUI;
	import lab.component.GridPanel;
	import lab.component.SpinnerRangeInteger;

	public class OutputDialog extends JDialog implements ActionListener, ChangeListener {

	private JComboBox<String> cmbDynamic = new JComboBox<String>(new String[] { "intact", "rescaled", "normalized", "clipped" });
	private JComboBox<String> cmbType = new JComboBox<String>(new String[] { "float", "short", "byte" });

	private JCheckBox chkSave = new JCheckBox("Save output", true);
	private JCheckBox chkShow = new JCheckBox("Show output", true);

	private SpinnerRangeInteger snpSnapshot = new SpinnerRangeInteger(0, 0, 99999, 1);
	private JComboBox<String> cmbSnapshot = new JComboBox<String>(new String[] { "Final Output", "Specify Iterations..." });

	private SpinnerRangeInteger spnX = new SpinnerRangeInteger(128, 0, 99999, 1);
	private SpinnerRangeInteger spnY = new SpinnerRangeInteger(128, 0, 99999, 1);
	private SpinnerRangeInteger spnZ = new SpinnerRangeInteger(32, 0, 99999, 1);
	private JTextField txtName = new JTextField("Noname", 18);

	private JCheckBox chkCenter = new JCheckBox("Center of the volume", true);
	private JButton bnOK = new JButton("OK");
	private JButton bnCancel = new JButton("Cancel");
	private boolean cancel = false;
	private JLabel lblBit = new JLabel("32-bit");
	private JLabel lblIter = new JLabel("iterations");
	private JLabel lblSnapshot = new JLabel("Snapshot");
	private Output out;
	private View view;
	private GridPanel pnOrtho;

	private static int count = 1;

	public OutputDialog(View view) {
	super(new JFrame(), "Create a new output");
	this.view = view;
	lblBit.setBorder(BorderFactory.createEtchedBorder());
	lblIter.setBorder(BorderFactory.createEtchedBorder());

	txtName.setText(view.name().substring(0, 2) + (count++));

	GridPanel pn = new GridPanel(view.name());
	pn.place(0, 0, "Name");
	pn.place(0, 1, 2, 1, txtName);
	-
	pn.place(1, 0, "Dynamic");
	pn.place(1, 1, cmbDynamic);
	pn.place(2, 0, "Type");
	pn.place(2, 1, cmbType);
	pn.place(2, 2, lblBit);

	if (view != View.SERIES && view != View.STACK) {
	pn.place(4, 0, "Snapshot");
	pn.place(4, 1, cmbSnapshot);
	pn.place(5, 0, lblSnapshot);
	pn.place(5, 1, snpSnapshot);
	pn.place(5, 2, lblIter);
	}
	pn.place(6, 0, 3, 1, chkShow);
	pn.place(7, 0, 3, 1, chkSave);

	GridPanel main = new GridPanel(false);
	main.place(1, 0, 2, 1, pn);

	if (view == View.ORTHO \|\| view == View.FIGURE) {
	- pn.place(7, 0, 3, 1, chkCenter);
	+ pn.place(8, 0, 3, 1, chkCenter);
	pnOrtho = new GridPanel("Keypoint");
	pnOrtho.place(4, 0, "Position in X");
	pnOrtho.place(4, 1, spnX);
	pnOrtho.place(4, 2, "[pixel]");

	pnOrtho.place(5, 0, "Position in Y");
	pnOrtho.place(5, 1, spnY);
	pnOrtho.place(5, 2, "[pixel]");

	pnOrtho.place(6, 0, "Position in Z");
	pnOrtho.place(6, 1, spnZ);
	pnOrtho.place(5, 2, "[pixel]");
	main.place(2, 0, 2, 1, pnOrtho);
	}

	main.place(3, 0, bnCancel);
	main.place(3, 1, bnOK);

	cmbSnapshot.addActionListener(this);
	snpSnapshot.addChangeListener(this);
	chkCenter.addActionListener(this);
	cmbType.addActionListener(this);
	bnOK.addActionListener(this);
	bnCancel.addActionListener(this);
	add(main);
	update();
	pack();
	GUI.center(this);
	setModal(true);
	setVisible(true);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	if (e.getSource() == chkCenter) {
	update();
	}
	else if (e.getSource() == cmbSnapshot) {
	update();
	}
	else if (e.getSource() == cmbType) {
	if (cmbType.getSelectedIndex() == 0)
	lblBit.setText("32-bits");
	if (cmbType.getSelectedIndex() == 1)
	lblBit.setText("16-bits");
	if (cmbType.getSelectedIndex() == 2)
	lblBit.setText("8-bits");
	}
	else if (e.getSource() == bnCancel) {
	dispose();
	cancel = true;
	return;
	}
	else if (e.getSource() == bnOK) {
	int freq = snpSnapshot.get();
	Dynamic dynamic = Output.Dynamic.values()[cmbDynamic.getSelectedIndex()];
	PlatformImager.Type type = PlatformImager.Type.values()[cmbType.getSelectedIndex()];
	boolean show = chkShow.isSelected();
	boolean save = chkSave.isSelected();
	String name = txtName.getText();
	if (chkCenter.isSelected()) {
	out = new Output(view, show, save, freq, name, dynamic, type, true);
	}
	else {
	int px = spnX.get();
	int py = spnY.get();
	int pz = spnZ.get();
	out = new Output(view, show, save, freq, name, dynamic, type, px, py, pz);
	}
	dispose();
	cancel = false;
	}
	}

	private void update() {

	if (cmbSnapshot.getSelectedIndex() == 0) {
	snpSnapshot.set(0);
	lblSnapshot.setEnabled(false);
	lblIter.setEnabled(false);
	lblSnapshot.setEnabled(false);
	}
	else {
	lblSnapshot.setEnabled(true);
	lblIter.setEnabled(true);
	lblSnapshot.setEnabled(true);
	}
	if (snpSnapshot.get() == 0)
	lblIter.setText("at the end (default)");
	else
	lblIter.setText("every " + snpSnapshot.get() + " iterations");

	if (snpSnapshot.get() == 0)
	lblIter.setText("at the end (default)");
	else
	lblIter.setText("every " + snpSnapshot.get() + " iterations");

	boolean b = !chkCenter.isSelected();
	if (pnOrtho != null) {
	pnOrtho.setEnabled(b);
	for (Component c : pnOrtho.getComponents())
	c.setEnabled(b);
	}
	pack();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	if (e.getSource() == snpSnapshot)
	update();
	}

	public Output getOut() {
	return out;
	}

	public boolean wasCancel() {
	return cancel;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	index b7631ba..f3e67fd 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	@@ -1,163 +1,213 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.FlowLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.text.SimpleDateFormat;
	import java.util.ArrayList;
	import java.util.Date;

	import javax.swing.JComboBox;
	import javax.swing.JPanel;
	+import javax.swing.JTextField;

	import deconvolution.Command;
	import deconvolution.Token;
	import deconvolutionlab.Config;
	import lab.component.HTMLPane;

	public class LanguageModule extends AbstractModule implements ActionListener {

	private HTMLPane language;
	private JComboBox<String> cmb;
	private JComboBox<String> gui;
	+ private JTextField txt;

	public LanguageModule(boolean expanded) {
	super("Language", "", "", "", expanded);
	}

	@Override
	public JPanel buildExpandedPanel() {
	language = new HTMLPane("Monaco", 100, 100);
	cmb = new JComboBox<String>(new String[] { "Command line", "ImageJ Macro", "Java", "Matlab" });
	gui = new JComboBox<String>(new String[] { "Run (Headless)", "Launch (with control panel)" });
	+ txt = new JTextField("Job", 8);
	JPanel pn = new JPanel(new FlowLayout());
	+ pn.add(txt);
	pn.add(cmb);
	pn.add(gui);

	JPanel panel = new JPanel(new BorderLayout());
	panel.add(pn, BorderLayout.NORTH);
	panel.add(language.getPane(), BorderLayout.CENTER);
	cmb.addActionListener(this);
	gui.addActionListener(this);
	Config.register(getName(), "language", cmb, cmb.getItemAt(0));
	Config.register(getName(), "headless", gui, gui.getItemAt(0));
	+ Config.register(getName(), "job", txt, "Job");
	language.clear();
	return panel;
	}

	@Override
	public void expand() {
	super.expand();
	update();
	}

	public void update() {
	if (cmb.getSelectedIndex() == 0) {
	language.clear();
	String mode = "java -jar DeconvolutionLab_2.jar ";
	if (gui.getSelectedIndex() == 0)
	mode += " Run ";
	else
	mode += " Launch ";
	language.append("p", mode + Command.command());
	}
	else if (cmb.getSelectedIndex() == 1) {
	language.clear();
	language.append("p", imagej(gui.getSelectedIndex() == 0));
	}
	else if (cmb.getSelectedIndex() == 2) {
	language.clear();
	- String text = "Java code, not yet implemented";
	- language.append("p", text);
	+ language.append("p", java(gui.getSelectedIndex() == 0));
	}
	else if (cmb.getSelectedIndex() == 3) {
	language.clear();
	String text = "Matlab code, not yet implemented";
	language.append("p", text);
	}
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == cmb)
	update();
	if (e.getSource() == gui)
	update();
	}

	@Override
	public void close() {
	}

	@Override
	public void setCommand(String command) {
	update();
	}

	@Override
	public String getCommand() {
	return "";
	}

	private String imagej(boolean headless) {
	- String macro = "<p>// Macro generated by DeconvolutionLab2 </p>";
	+ String job = txt.getText();
	+ String macro = "<p>// Job: " + job + " </p>";
	+ macro += "<p>// Macro generated by DeconvolutionLab2 </p>";
	macro += "<p>// " + new SimpleDateFormat("dd/MM/yy HH:m:s").format(new Date()) + " </p>";
	String param = "<p>parameters = \"\"</p>";
	ArrayList<Token> tokens = Command.parse(Command.command());
	String image = "image = \" NOT DEFINED \" ";
	String psf = "psf = \" NOT DEFINED \" ";
	String algo = "algo = \" NOT DEFINED \" ";
	for (Token token : tokens) {
	if (token.keyword.equals("-image"))
	image = "<p>image = \" -image " + token.parameters.trim() + "\" </p>";
	else if (token.keyword.equals("-psf"))
	psf = "<p>psf = \" -psf " + token.parameters.trim() + "\" </p>";
	else if (token.keyword.equals("-algorithm"))
	algo = "<p>algorithm = \" -algorithm " + token.parameters.trim() + "\" </p>";
	else
	param += "<p>parameters += \" " + token.keyword + " " + token.parameters.trim() + "\" </p>";
	}

	String option = macro + image + psf + algo + param;
	String cmd = "";
	if (headless)
	cmd = "<p>run(\"DeconvolutionLab2 Run\", image + psf + algorithm + parameters)</p>";
	else
	cmd = "<p>run(\"DeconvolutionLab2 Launch\", image + psf + algorithm + parameters)</p>";

	return option + cmd;
	}
	+
	+
	+ private String java(boolean headless) {
	+ String job = txt.getText();
	+ String p = headless ? ".deconvolve(false);" : ".launch(\"" + job + "\", false);";
	+ String tab1 = "<p style=\"padding-left:10px\">";
	+ String tab2 = "<p style=\"padding-left:20px\">";
	+ String code = "";
	+ code += "<p>import deconvolution.Deconvolution;</p>";
	+ code += "<p>import ij.plugin.PlugIn;</p>";
	+ code += "<p></p>";
	+
	+ code += "<p>public class DeconvolutionLab2_" + job + " implements PlugIn {</p>";
	+ code += tab1 + "public DeconvolutionLab2_" + job + "() {</p>";
	+
	+ String param = tab2 + "String parameters = \"\";</p>";
	+ ArrayList<Token> tokens = Command.parse(Command.command());
	+ String image = tab2 + "String image = \" NOT DEFINED \";";
	+ String psf = tab2 + "String psf = \" NOT DEFINED \";";
	+ String algo = tab2 + "String algo = \" NOT DEFINED \";";
	+ for (Token token : tokens) {
	+ if (token.keyword.equals("-image"))
	+ image = tab2 + "String image = \" -image " + token.parameters.trim() + "\";</p>";
	+ else if (token.keyword.equals("-psf"))
	+ psf = tab2 + "String psf = \" -psf " + token.parameters.trim() + "\";</p>";
	+ else if (token.keyword.equals("-algorithm"))
	+ algo = tab2 + "String algorithm = \" -algorithm " + token.parameters.trim() + "\";</p>";
	+ else
	+ param += tab2 + "parameters += \" " + token.keyword + " " + token.parameters.trim() + "\";</p>";
	+ }
	+ code += image + psf + algo + param;
	+ code += tab2 + "new Deconvolution(image + psf + algorithm + parameters)" + p;
	+ code += tab1 + "}</p>";
	+
	+ code += tab1 + "<p></p>";
	+
	+ code += tab1 + "@Override</p>";
	+ code += tab1 + "public void run(String arg0) {</p>";
	+ code += tab2 + " new DeconvolutionLab2_" + job + "();</p>";
	+
	+ code += tab1 + "}</p>";
	+ code += "<p>}</p>";
	+ return code;
	+ }
	}
	diff --git a/DeconvolutionLab2/src/imagej/IJImager.java b/DeconvolutionLab2/src/imagej/IJImager.java
	index ac671b5..f60c2eb 100644
	--- a/DeconvolutionLab2/src/imagej/IJImager.java
	+++ b/DeconvolutionLab2/src/imagej/IJImager.java
	@@ -1,221 +1,218 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package imagej;

	import java.util.HashMap;

	import deconvolutionlab.PlatformImager;
	+import deconvolutionlab.PlatformImager.ContainerImage;
	import ij.ImagePlus;
	import ij.ImageStack;
	import ij.WindowManager;
	import ij.io.FileSaver;
	import ij.io.Opener;
	import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;
	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class IJImager extends PlatformImager {

	- private static HashMap<String, ImagePlus> images = new HashMap<String, ImagePlus>();
	- private static HashMap<String, ImageStack> stacks = new HashMap<String, ImageStack>();
	-
	public static RealSignal create(ImagePlus imp) {
	int nx = imp.getWidth();
	int ny = imp.getHeight();
	int nz = imp.getStackSize();
	RealSignal signal = new RealSignal(nx, ny, nz);
	for (int k = 0; k < nz; k++) {
	ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
	signal.setXY(k, (float[]) ip.getPixels());
	}
	return signal;
	}

	@Override
	public RealSignal create() {
	return build(WindowManager.getCurrentImage());
	}

	@Override
	public RealSignal create(String name) {
	ImagePlus imp = WindowManager.getImage(name);
	if (imp == null)
	imp = WindowManager.getCurrentImage();
	return build(imp);
	}

	@Override
	public RealSignal open(String filename) {
	Opener opener = new Opener();
	ImagePlus imp = opener.openImage(filename);
	return build(imp);
	}

	@Override
	public void show(RealSignal signal, String title) {
	show(signal, title, PlatformImager.Type.FLOAT);
	}

	@Override
	public void show(RealSignal signal, String title, PlatformImager.Type type) {
	show(signal, title, type, signal.nz / 2);
	}

	@Override
	public void show(RealSignal signal, String title, PlatformImager.Type type, int z) {
	ImagePlus imp = build(signal, type);
	if (imp != null) {
	imp.setTitle(title);
	int nz = imp.getStackSize();
	imp.show();
	imp.setSlice(Math.max(1, Math.min(nz, z)));
	imp.getProcessor().resetMinAndMax();
	}
	}

	+ public ContainerImage createContainer(String title) {
	+ return new ContainerImage();
	+ }
	+
	@Override
	- public void appendShowLive(String key, RealSignal signal, String title) {
	- appendShowLive(key, signal, title, PlatformImager.Type.FLOAT);
	+ public void append(ContainerImage container, RealSignal signal, String title) {
	+ append(container, signal, title, PlatformImager.Type.FLOAT);
	}

	@Override
	- public void appendShowLive(String key, RealSignal signal, String title, PlatformImager.Type type) {
	- ImagePlus imp = build(signal, type);
	- ImagePlus image = images.get(key);
	- ImageStack stack = stacks.get(key);
	- if (image == null \|\| stack == null) {
	- stack = new ImageStack(signal.nx, signal.ny);
	- stack.addSlice(imp.getProcessor());
	- image = new ImagePlus(key, stack);
	- image.show();
	- images.put(key, image);
	- stacks.put(key, stack);
	+ public void append(ContainerImage container, RealSignal signal, String title, PlatformImager.Type type) { ImagePlus cont = (ImagePlus) container.object;
	+ if (container.object == null) {
	+ ImageStack stack = new ImageStack(signal.nx, signal.ny);
	+ stack.addSlice(build(signal, type).getProcessor());
	+ stack.addSlice(build(signal, type).getProcessor());
	+ container.object = new ImagePlus(title, stack);
	+ ((ImagePlus)container.object).show();
	}
	else {
	- stack.addSlice(imp.getProcessor());
	- image.setStack(stack);
	+ cont.getStack().addSlice(build(signal, type).getProcessor());
	+ cont.setSlice(cont.getStack().getSize());
	+ cont.updateAndDraw();
	+ cont.getProcessor().resetMinAndMax();
	}
	- image.updateAndDraw();
	- image.setSlice(image.getStack().getSize());
	- image.getProcessor().resetMinAndMax();
	}

	@Override
	public void save(RealSignal signal, String filename) {
	save(signal, filename, PlatformImager.Type.FLOAT);
	}

	@Override
	public void save(RealSignal signal, String filename, PlatformImager.Type type) {
	ImagePlus imp = build(signal, type);
	if (imp != null) {
	if (imp.getStackSize() == 1) {
	new FileSaver(imp).saveAsTiff(filename);
	}
	else {
	new FileSaver(imp).saveAsTiffStack(filename);
	}
	}
	}

	@Override
	public void show(ComplexSignal signal, String title) {
	show(signal, title, ComplexComponent.MODULE);
	}

	@Override
	public void show(ComplexSignal signal, String title, ComplexComponent complex) {
	ImageStack stack = new ImageStack(signal.nx, signal.ny);
	for (int k = 0; k < signal.nz; k++) {
	float[] plane = null;
	switch (complex) {
	case REAL:
	plane = signal.getRealXY(k);
	break;
	case IMAGINARY:
	plane = signal.getImagXY(k);
	break;
	case MODULE:
	plane = signal.getModuleXY(k);
	break;
	default:
	plane = signal.getModuleXY_dB(k);
	}
	stack.addSlice(new FloatProcessor(signal.nx, signal.ny, plane));
	}
	new ImagePlus(title, stack).show();
	}

	private RealSignal build(ImagePlus imp) {
	if (imp == null)
	return null;
	int nx = imp.getWidth();
	int ny = imp.getHeight();
	int nz = imp.getStackSize();
	RealSignal signal = new RealSignal(nx, ny, nz);
	for (int k = 0; k < nz; k++) {
	ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
	signal.setXY(k, (float[]) ip.getPixels());
	}
	return signal;
	}

	private ImagePlus build(RealSignal signal, PlatformImager.Type type) {
	if (signal == null)
	return null;

	ImageStack stack = new ImageStack(signal.nx, signal.ny);
	for (int k = 0; k < signal.nz; k++) {
	ImageProcessor ip = new FloatProcessor(signal.nx, signal.ny, signal.getXY(k));
	switch (type) {
	case BYTE:
	stack.addSlice(ip.convertToByteProcessor(false));
	break;
	case SHORT:
	stack.addSlice(ip.convertToShortProcessor(false));
	break;
	case FLOAT:
	stack.addSlice(ip);
	default:
	break;
	}
	}
	return new ImagePlus("", stack);
	}

	@Override
	public String getName() {
	return "ImageJ";
	}
	}
	diff --git a/DeconvolutionLab2/src/plugins/sage/deconvolutionlab/IcyImager.java b/DeconvolutionLab2/src/plugins/sage/deconvolutionlab/IcyImager.java
	index 90064b6..db2a17c 100644
	--- a/DeconvolutionLab2/src/plugins/sage/deconvolutionlab/IcyImager.java
	+++ b/DeconvolutionLab2/src/plugins/sage/deconvolutionlab/IcyImager.java
	@@ -1,204 +1,210 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package plugins.sage.deconvolutionlab;

	import icy.file.Saver;
	import icy.image.IcyBufferedImage;
	import icy.imagej.ImageJUtil;
	import icy.main.Icy;
	import icy.sequence.Sequence;
	import icy.type.DataType;
	import icy.type.collection.array.Array1DUtil;
	import ij.ImagePlus;
	import ij.io.Opener;

	import java.io.File;
	import java.util.ArrayList;

	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;
	import deconvolutionlab.PlatformImager;
	import deconvolutionlab.monitor.Monitors;

	public class IcyImager extends PlatformImager {


	public static RealSignal create(Sequence seq) {
	int nx = seq.getSizeX();
	int ny = seq.getSizeY();
	int nz = seq.getSizeZ();
	RealSignal signal = new RealSignal(nx, ny, nz);
	for (int k = 0; k < nz; k++) {
	float pixels[] = new float[nx * ny];
	Array1DUtil.arrayToFloatArray(seq.getDataXY(0, k, 0), pixels, seq.isSignedDataType());
	signal.setXY(k, pixels);
	}
	return signal;
	}

	@Override
	public RealSignal create() {
	return build(Icy.getMainInterface().getActiveSequence());
	}

	@Override
	public RealSignal create(String name) {
	ArrayList<Sequence> sequences = Icy.getMainInterface().getSequences(name);
	for(Sequence sequence : sequences)
	if (sequence.getName().equals(name))
	return build(sequence);
	return null;
	}

	@Override
	public RealSignal open(String filename) {
	//File file = new File(filename);
	//return build(Loader.loadSequence(file, 0, false));
	Opener opener = new Opener();
	ImagePlus imp = opener.openImage(filename);
	Sequence seq = ImageJUtil.convertToIcySequence(imp, null);
	return build(seq);
	}

	@Override
	public void show(RealSignal signal, String title) {
	show(signal, title, PlatformImager.Type.FLOAT);
	}

	@Override
	public void show(RealSignal signal, String title, PlatformImager.Type type) {
	Sequence sequence = build(signal, type);
	Icy.getMainInterface().addSequence(sequence);
	}

	@Override
	public void show(ComplexSignal signal, String title, ComplexComponent complex) {
	Sequence sequence = new Sequence();
	for (int k = 0; k < signal.nz; k++) {
	float[] plane = null;
	switch(complex) {
	case REAL: plane = signal.getRealXY(k); break;
	case IMAGINARY: plane = signal.getImagXY(k); break;
	case MODULE: plane = signal.getModuleXY(k); break;
	default: plane = signal.getModuleXY_dB(k);
	}
	IcyBufferedImage image = new IcyBufferedImage(signal.nx, signal.ny, 1, DataType.FLOAT);
	Array1DUtil.floatArrayToSafeArray(plane, image.getDataXY(0), image.isSignedDataType());
	image.dataChanged();
	sequence.setImage(0, k, image);
	}
	sequence.setName(title);
	Icy.getMainInterface().addSequence(sequence);
	}

	@Override
	public void save(RealSignal signal, String filename) {
	save(signal, filename, PlatformImager.Type.FLOAT);
	}

	@Override
	public void save(RealSignal signal, String filename, PlatformImager.Type type) {
	Sequence sequence = build(signal, type);
	File file = new File(filename);
	Saver.save(sequence, file, false, true);
	}

	private RealSignal build(Sequence sequence) {
	int nx = sequence.getSizeX();
	int ny = sequence.getSizeY();
	int nz = sequence.getSizeZ();
	RealSignal signal = new RealSignal(nx, ny, nz);
	for (int k = 0; k < nz; k++) {
	float pixels[] = new float[nx * ny];
	Array1DUtil.arrayToFloatArray(sequence.getDataXY(0, k, 0), pixels, sequence.isSignedDataType());
	signal.setXY(k, pixels);
	}
	return signal;
	}

	private Sequence build(RealSignal signal, PlatformImager.Type type) {
	Sequence sequence = new Sequence();
	for (int k = 0; k < signal.nz; k++) {
	float[] plane = signal.getXY(k);
	IcyBufferedImage image = null;
	switch(type) {
	case BYTE:
	byte[] b = Array1DUtil.arrayToByteArray(plane);
	image = new IcyBufferedImage(signal.nx, signal.ny, 1, DataType.BYTE);
	Array1DUtil.byteArrayToArray(b, image.getDataXY(0), image.isSignedDataType());
	break;
	case SHORT:
	short[] s = Array1DUtil.arrayToShortArray(plane, false);
	image = new IcyBufferedImage(signal.nx, signal.ny, 1, DataType.SHORT);
	Array1DUtil.shortArrayToArray(s, image.getDataXY(0), image.isSignedDataType());
	break;
	default:
	image = new IcyBufferedImage(signal.nx, signal.ny, 1, DataType.FLOAT);
	Array1DUtil.floatArrayToArray(signal.data[k], image.getDataXY(0));
	break;
	}
	image.dataChanged();
	sequence.setImage(0, k, image);
	}
	return sequence;
	}

	@Override
	public String getName() {
	return "Icy";
	}

	@Override
	- public void appendShowLive(String key, RealSignal signal, String title) {
	- // TODO Auto-generated method stub
	-
	+ public void show(RealSignal signal, String title, Type type, int z) {
	+ // TODO Auto-generated method stub
	+ }
	+
	+ @Override
	+ public void show(ComplexSignal signal, String title) {
	+ // TODO Auto-generated method stub
	}

	@Override
	- public void appendShowLive(String key, RealSignal signal, String title, Type type) {
	+ public ContainerImage createContainer(String title) {
	// TODO Auto-generated method stub
	-
	+ return null;
	}

	@Override
	- public void show(RealSignal signal, String title, Type type, int z) {
	- // TODO Auto-generated method stub
	+ public void append(ContainerImage container, RealSignal signal, String title) {
	+ // TODO Auto-generated method stub
	+
	}
	-
	+
	@Override
	- public void show(ComplexSignal signal, String title) {
	- // TODO Auto-generated method stub
	+ public void append(ContainerImage container, RealSignal signal, String title, Type type) {
	+ // TODO Auto-generated method stub
	+
	}


	}
	diff --git a/DeconvolutionLab2/src/signal/factory/MotionBlur.java b/DeconvolutionLab2/src/signal/factory/MotionBlur.java
	new file mode 100644
	index 0000000..59a0bbf
	--- /dev/null
	+++ b/DeconvolutionLab2/src/signal/factory/MotionBlur.java
	@@ -0,0 +1,89 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	+package signal.factory;
	+
	+import signal.RealSignal;
	+
	+public class MotionBlur extends SignalFactory {
	+
	+ private double sigma = 3.0;
	+ private double direction = 30.0;
	+ private double elongation = 3.0;
	+
	+ public MotionBlur(double sigma, double direction, double elongation) {
	+ super(new double[] {sigma, direction, elongation});
	+ }
	+
	+ @Override
	+ public String getName() {
	+ return "MotionBlur";
	+ }
	+
	+ @Override
	+ public String[] getParametersName() {
	+ return new String[] {"Sigma", "Direction", "Elongation"};
	+ }
	+
	+ @Override
	+ public void setParameters(double[] parameters) {
	+ if (parameters.length >= 1)
	+ this.sigma = parameters[0];
	+ if (parameters.length >= 2)
	+ this.direction = parameters[1];
	+ if (parameters.length >= 3)
	+ this.elongation = parameters[2];
	+ }
	+
	+ @Override
	+ public double[] getParameters() {
	+ return new double[] {sigma, direction, elongation};
	+ }
	+
	+ @Override
	+ public void fill(RealSignal signal) {
	+ double K1 = 0.5 / (sigma*sigma);
	+ double K2 = 0.5 / (sigmasigmaelongation*elongation);
	+ double cosa = Math.cos(Math.toRadians(direction));
	+ double sina = Math.sin(Math.toRadians(direction));
	+ for(int x=0; x<nx; x++)
	+ for(int y=0; y<ny; y++) {
	+ double dx = (x-xc);
	+ double dy = (y-yc);
	+ //double ps = (1.0 + (dxcosa + dysina)/(dxdx + dydy)) * 0.5;
	+ double K = K1 + dx * K2 /(dxdx + dydy);
	+ double r2 = (x-xc)(x-xc) + (y-yc)(y-yc);
	+ for(int z=0; z<nz; z++) {
	+ signal.data[z][x+nxy] = (float)((amplitude-background) Math.exp(-r2*K) + background);
	+ }
	+ }
	+ }
	+}
	diff --git a/DeconvolutionLab2/src/signal/factory/SignalFactory.java b/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	index 1935fbd..b9aee46 100644
	--- a/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	+++ b/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	@@ -1,211 +1,213 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

	/*
	* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	*
	* This file is part of DeconvolutionLab2 (DL2).
	*
	* DL2 is free software: you can redistribute it and/or modify it under the
	* terms of the GNU General Public License as published by the Free Software
	* Foundation, either version 3 of the License, or (at your option) any later
	* version.
	*
	* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License along with
	* DL2. If not, see <http://www.gnu.org/licenses/>.
	*/

	package signal.factory;

	import java.util.ArrayList;

	import javax.swing.SwingWorker;

	import deconvolutionlab.monitor.Monitors;
	import signal.RealSignal;

	public abstract class SignalFactory {

	protected double fractXC = 0.5;
	protected double fractYC = 0.5;
	protected double fractZC = 0.5;
	protected double background = 0.0;
	protected double amplitude = 1.0;
	protected double xc;
	protected double yc;
	protected double zc;
	protected int nx;
	protected int ny;
	protected int nz;


	public SignalFactory() {
	}

	public SignalFactory(double[] parameters) {
	setParameters(parameters);
	}

	public static SignalFactory get(String name) {
	ArrayList<SignalFactory> list = getAll();
	for (SignalFactory factory : list) {
	if (factory.getName().equals(name))
	return factory;
	}
	return null;
	}

	public static ArrayList<String> getAllName() {
	ArrayList<String> list = new ArrayList<String>();
	for (SignalFactory factory : getAll()) {
	list.add(factory.getName());
	}
	return list;
	}

	public static ArrayList<SignalFactory> getAll() {
	ArrayList<SignalFactory> list = new ArrayList<SignalFactory>();
	list.add(new Airy(1));
	list.add(new Astigmatism(3, 0.2));
	list.add(new Constant());
	list.add(new Cross(1, 1, 30));
	list.add(new Cube(10 ,1));
	list.add(new Defocus(3, 10, 10));
	list.add(new DoG(3, 4));
	list.add(new DoubleHelix(3, 10, 10));
	list.add(new Gaussian(3, 3, 3));
	list.add(new GridSpots(3, 1, 10));
	list.add(new Impulse());
	+ list.add(new MotionBlur(3, 30, 3));
	list.add(new Ramp(1, 0, 0));
	list.add(new RandomLines(3));
	list.add(new Sinc(3, 3, 3));
	list.add(new Sphere(10, 1));
	list.add(new Torus(10));
	return list;
	}

	public static ArrayList<SignalFactory> getImages() {
	ArrayList<SignalFactory> list = new ArrayList<SignalFactory>();
	list.add(new Cube(10, 1));
	list.add(new Sphere(10, 1));
	list.add(new GridSpots(3, 1, 10));
	list.add(new Constant());
	list.add(new Cross(1, 1, 30));
	list.add(new DoG(3, 4));
	list.add(new Gaussian(3, 3, 3));
	list.add(new Impulse());
	list.add(new Ramp(1, 0, 0));
	list.add(new RandomLines(3));
	list.add(new Torus(10));
	return list;
	}

	public static ArrayList<SignalFactory> getPSF() {
	ArrayList<SignalFactory> list = new ArrayList<SignalFactory>();
	list.add(new Airy(1));
	list.add(new Astigmatism(3, 0.2));
	list.add(new Cross(3, 1, 10));
	list.add(new Cube(10, 1));
	list.add(new Defocus(3, 10, 10));
	list.add(new DoG(3, 4));
	list.add(new DoubleHelix(3, 10, 10));
	list.add(new Gaussian(3, 3, 3));
	+ list.add(new MotionBlur(3, 30, 3));
	list.add(new Impulse());
	list.add(new Sinc(3, 3, 3));
	list.add(new Sphere(10, 1));
	list.add(new RandomLines(3));
	list.add(new Torus(10));
	return list;
	}

	public static SignalFactory getFactoryByName(String name) {
	ArrayList<SignalFactory> list = getAll();
	for (SignalFactory factory : list)
	if (name.toLowerCase().equals(factory.getName().toLowerCase())) {
	return factory;
	}
	return null;
	}

	public SignalFactory center(double fractXC, double fractYC, double fractZC) {
	this.fractXC = fractXC;
	this.fractYC = fractYC;
	this.fractZC = fractZC;
	return this;
	}

	public SignalFactory intensity(double background, double amplitude) {
	this.background = background;
	this.amplitude = amplitude;
	return this;
	}

	public String params() {
	String name[] = getParametersName();
	double params[] = getParameters();
	if (params.length == 1)
	return name[0] + "=" + params[0];
	else if (params.length == 2)
	return name[0] + "=" + params[0] + " " + name[1] + "=" + params[1];
	else
	return name[0] + "=" + params[0] + " " + name[1] + "=" + params[2] + " " + name[2] + "=" + params[2];
	}

	public RealSignal generate(int nx, int ny, int nz) {
	this.nx = nx;
	this.ny = ny;
	this.nz = nz;
	xc = fractXC * nx;
	yc = fractYC * ny;
	zc = fractZC * nz;
	RealSignal signal = new RealSignal(nx, ny, nz);
	fill(signal);

	return signal;
	}

	public abstract String getName();

	public abstract void setParameters(double[] parameters);

	public abstract double[] getParameters();

	public abstract String[] getParametersName();

	public abstract void fill(RealSignal signal);

	public class Worker extends SwingWorker<RealSignal, String> {
	private RealSignal signal;
	public boolean done=false;
	public Worker(RealSignal signal) {
	this.signal = signal;
	done = false;
	}

	protected RealSignal doInBackground() throws Exception {
	fill(signal);
	done = true;
	return signal;
	}

	protected void done() {
	System.out.println("Done");
	done = true;
	}

	}
	}

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