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	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_JavaCoding.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_JavaCoding.java
	index bdb1d9b..2a46496 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_JavaCoding.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_JavaCoding.java
	@@ -1,78 +1,68 @@
	/*
	* 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 course;

	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

	-import deconvolution.algorithm.Convolution;
	+import deconvolution.algorithm.Simulation;
	import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.Monitors;
	import ij.plugin.PlugIn;
	import signal.RealSignal;

	public class DeconvolutionLab2_JavaCoding implements PlugIn {

	- private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop";
	- private String root = desktop + File.separator + "Deconvolution" + File.separator;
	- private String res = root + "results" + File.separator + "bigradient" + File.separator;
	- private String data = root + "data" + File.separator + "bigradient" + File.separator;
	+ private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop" + File.separator;

	public DeconvolutionLab2_JavaCoding() {
	-
	+ String path = desktop + "Deconvolution" + File.separator + "data" + File.separator + "bars" + File.separator;
	Monitors monitors = new Monitors();
	+ RealSignal image = Lab.openFile(monitors, path + "bars.tif");
	+ RealSignal psf = Lab.openFile(monitors, path + "psf.tif");

	- RealSignal image = Lab.openFile(filename);
	-
	- Convolution convolution = new Convolution();
	-
	-
	- RealSignal a = convolution.run(monitors, image, psf, fftlib, pad, apo, norm, threaded);
	-
	- }
	-
	- private static String out(String root, String name) {
	- return "out stats " + root + name +
	- " -out stack " + root + name + "_32 -out stack " + root + name + "_8 rescaled byte noshow";
	+ Simulation convolution = new Simulation(100, 100, 10);
	+ RealSignal a = convolution.run(image, psf);
	+ Lab.showMIP(monitors, a, "a");
	}

	public static void main(String arg[]) {
	new DeconvolutionLab2_JavaCoding();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_JavaCoding();
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/Command.java b/DeconvolutionLab2/src/deconvolution/Command.java
	index 04b0d54..fbf999e 100644
	--- a/DeconvolutionLab2/src/deconvolution/Command.java
	+++ b/DeconvolutionLab2/src/deconvolution/Command.java
	@@ -1,457 +1,456 @@
	/*
	* 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;

	import java.util.ArrayList;
	import java.util.Collections;
	import java.util.regex.Matcher;
	import java.util.regex.Pattern;

	import bilib.tools.NumFormat;
	import deconvolution.algorithm.AbstractAlgorithm;
	import deconvolution.algorithm.Algorithm;
	import deconvolution.algorithm.Controller;
	import deconvolutionlab.Output;
	import deconvolutionlab.OutputCollection;
	import deconvolutionlab.Output.View;
	import deconvolutionlab.modules.AbstractModule;
	import deconvolutionlab.modules.CommandModule;
	import deconvolutionlab.monitor.Verbose;
	import fft.AbstractFFT;
	import fft.AbstractFFTLibrary;
	import fft.FFT;
	import signal.Constraint;
	import signal.Operations;
	import signal.apodization.AbstractApodization;
	import signal.apodization.Apodization;
	import signal.apodization.UniformApodization;
	import signal.padding.AbstractPadding;
	import signal.padding.NoPadding;
	import signal.padding.Padding;
	import wavelets.Wavelets;

	public class Command {

	public static String keywords[] = { "-image", "-psf", "-algorithm", "-path", "-disable", "-verbose", "-monitor", "-display", "-multithreading", "-system", "-stats", "-constraint", "-time", "-residu", "-reference", "-out", "-pad", "-apo", "-norm", "-fft", "-epsilon" };

	private static AbstractModule modules[];
	private static CommandModule command;

	public static void active(AbstractModule[] m, CommandModule c) {
	modules = m;
	command = c;
	}

	public static String command() {
	if (modules == null)
	return "";
	String cmd = "";

	for (AbstractModule m : modules)
	cmd += m.getCommand() + " ";

	if (command != null)
	command.setCommand(cmd);

	return cmd;
	}

	public static void decode(String command, Deconvolution deconvolution) {

	AbstractAlgorithm algo = Algorithm.getDefaultAlgorithm();
	boolean flagSystem = true;
	boolean flagDisplay = true;
	boolean flagMultithreading = true;
	int monitor = 3;
	int stats = 0;
	Verbose verbose = Verbose.Log;
	String path = System.getProperty("user.dir");
	Controller controller = new Controller();
	OutputCollection outs = new OutputCollection();
	Padding pad = new Padding();
	Apodization apo = new Apodization();
	double norm = 1.0;
	AbstractFFTLibrary fft = FFT.getFastestFFT();

	ArrayList<Token> tokens = parse(command);
	for (Token token : tokens) {
	if (token.keyword.equalsIgnoreCase("-algorithm"))
	algo = Command.decodeAlgorithm(token, controller);

	if (token.keyword.equalsIgnoreCase("-path") && !token.parameters.equalsIgnoreCase("current"))
	path = token.parameters;

	if (token.keyword.equalsIgnoreCase("-monitor"))
	monitor = decodeMonitor(token);
	if (token.keyword.equalsIgnoreCase("-stats"))
	stats = decodeStats(token);
	if (token.keyword.equalsIgnoreCase("-system"))
	flagSystem = decodeSystem(token);

	if (token.keyword.equalsIgnoreCase("-display"))
	flagDisplay = decodeDisplay(token);

	if (token.keyword.equalsIgnoreCase("-multithreading"))
	flagMultithreading = decodeMultithreading(token);

	if (token.keyword.equalsIgnoreCase("-verbose"))
	verbose = Verbose.getByName(token.parameters);

	if (token.keyword.equalsIgnoreCase("-fft"))
	fft = FFT.getLibraryByName(token.parameters);

	if (token.keyword.equalsIgnoreCase("-pad"))
	pad = decodePadding(token);

	if (token.keyword.equalsIgnoreCase("-apo"))
	apo = decodeApodization(token);

	if (token.keyword.equalsIgnoreCase("-norm"))
	norm = decodeNormalization(token);

	if (token.keyword.equalsIgnoreCase("-constraint"))
	decodeController(token, controller);

	if (token.keyword.equalsIgnoreCase("-time"))
	decodeController(token, controller);

	if (token.keyword.equalsIgnoreCase("-residu"))
	decodeController(token, controller);

	if (token.keyword.equalsIgnoreCase("-reference"))
	decodeController(token, controller);

	if (token.keyword.equalsIgnoreCase("-epsilon"))
	Operations.epsilon = NumFormat.parseNumber(token.parameters, 1e-6);

	if (token.keyword.equals("-out")) {
	Output out = decodeOut(token);
	if (out != null)
	outs.add(out);
	}
	}

	deconvolution.setAlgorithm(algo, controller);
	deconvolution.setPath(path);
	deconvolution.setNormalization(norm);
	deconvolution.setPadding(pad);
	deconvolution.setApodization(apo);
	deconvolution.setOutput(outs);
	deconvolution.setVerbose(verbose);
	deconvolution.setFFT(fft);
	deconvolution.setMonitor(monitor);
	deconvolution.setStats(stats);
	deconvolution.setFlags(flagDisplay, flagMultithreading, flagSystem);
	}

	/**
	* This methods first segments the command line, then create all the tokens
	* of the command line
	*
	* @param command
	* Command line
	* @return the list of tokens extracted from the command line
	*/
	public static ArrayList<Token> parse(String command) {

	ArrayList<CommandSegment> segments = new ArrayList<CommandSegment>();
	for (String keyword : keywords)
	segments.addAll(findSegment(command, keyword));
	Collections.sort(segments);

	ArrayList<Token> tokens = new ArrayList<Token>();
	for (int i = 0; i < segments.size(); i++) {
	String keyword = segments.get(i).keyword;
	int begin = segments.get(i).index + keyword.length() + 1;
	int end = (i < segments.size() - 1 ? segments.get(i + 1).index : command.length());
	Token token = new Token(keyword, command, begin, end);
	tokens.add(token);
	}
	return tokens;
	}

	public static Token extract(String command, String keyword) {
	ArrayList<Token> tokens = parse(command);
	for (Token token : tokens)
	if (token.keyword.equalsIgnoreCase(keyword))
	return token;
	return (Token) null;
	}

	public static double[] parseNumeric(String line) {
	ArrayList<String> num = new ArrayList<String>();
	Pattern p = Pattern.compile("[-+]?[0-9]+[.]?[0-9]*([eE][-+]?[0-9]+)?");
	Matcher m = p.matcher(line);
	while (m.find()) {
	num.add(m.group());
	}
	double number[] = new double[num.size()];
	for (int i = 0; i < num.size(); i++)
	number[i] = Double.parseDouble(num.get(i));
	return number;
	}

	public static ArrayList<CommandSegment> findSegment(String command, String keyword) {
	ArrayList<CommandSegment> segments = new ArrayList<CommandSegment>();
	String regex = "(?<!\\w)" + keyword + "(?!\\w)";
	if (command == null)
	return segments;
	Matcher matcher = Pattern.compile(regex).matcher(command);
	while (matcher.find()) {
	segments.add(new CommandSegment(keyword, matcher.start()));
	}
	return segments;
	}

	public static String extractOptions(String command) {
	ArrayList<CommandSegment> segments = new ArrayList<CommandSegment>();
	for (String keyword : keywords)
	segments.addAll(findSegment(command, keyword));
	Collections.sort(segments);

	String options = "";
	for (int i = 0; i < segments.size(); i++) {
	String keyword = segments.get(i).keyword;
	int begin = segments.get(i).index + keyword.length() + 1;
	int end = (i < segments.size() - 1 ? segments.get(i + 1).index : command.length());
	if (keyword != "-image" && keyword != "-psf" && keyword != "-algorithm")
	options += keyword + " " + command.substring(begin, end);
	}
	return options;
	}

	public static AbstractAlgorithm decodeAlgorithm(Token token, Controller controller) {

	String option = token.option;

	AbstractAlgorithm algo = Algorithm.createAlgorithm(option);
	- algo.setShortname(option);
	double params[] = parseNumeric(token.parameters);
	if (params != null) {
	algo.setParameters(params);
	if (algo.isIterative() && params.length >= 1)
	controller.setIterationMax((int)params[0]);
	}

	if (algo.isWaveletsBased()) {
	for (String wavelet : Wavelets.getWaveletsAsArray()) {
	int pos = token.parameters.toLowerCase().indexOf(wavelet.toLowerCase());
	if (pos >= 0)
	algo.setWavelets(wavelet);
	}
	}
	return algo;
	}

	public static Output decodeOut(Token token) {
	int freq = 0;
	String line = token.parameters;
	String parts[] = token.parameters.split(" ");
	for (int i = 0; i < Math.min(2, parts.length); i++) {
	if (parts[i].startsWith("@"))
	freq = (int) NumFormat.parseNumber(parts[i], 0);
	}

	String p = token.parameters.toLowerCase();
	Output out = null;
	if (p.startsWith("stack"))
	out = new Output(View.STACK, freq, line.substring("stack".length(), line.length()));
	if (p.startsWith("series"))
	out = new Output(View.SERIES, freq, line.substring("series".length(), line.length()));
	if (p.startsWith("mip"))
	out = new Output(View.MIP, freq, line.substring("mip".length(), line.length()));
	if (p.startsWith("ortho"))
	out = new Output(View.ORTHO, freq, line.substring("ortho".length(), line.length()));
	if (p.startsWith("figure"))
	out = new Output(View.FIGURE, freq, line.substring("figure".length(), line.length()));
	if (p.startsWith("planar"))
	out = new Output(View.PLANAR, freq, line.substring("planar".length(), line.length()));

	return out;
	}

	public static void decodeController(Token token, Controller controller) {
	String line = token.parameters;
	if (token.parameters.startsWith("@")) {
	String parts[] = token.parameters.split(" ");
	if (parts.length >= 1) {
	line = token.parameters.substring(parts[0].length(), token.parameters.length()).trim();
	}
	}

	if (token.keyword.equals("-constraint"))
	controller.setConstraint(Constraint.getByName(line.trim()));
	else if (token.keyword.equals("-residu"))
	controller.setResiduStop(NumFormat.parseNumber(line, -1));
	else if (token.keyword.equals("-reference"))
	controller.setReference(line);
	else if (token.keyword.equals("-time"))
	controller.setTimeStop(NumFormat.parseNumber(line, Double.MAX_VALUE));

	}

	public static double decodeNormalization(Token token) {
	if (token.parameters.toLowerCase().endsWith("no"))
	return 0;
	else
	return NumFormat.parseNumber(token.parameters, 1);
	}

	public static int decodeMonitor(Token token) {
	String parts[] = token.parameters.toLowerCase().split(" ");
	int m = 0;
	for(String p : parts) {
	if (p.startsWith("no"))
	return 0;
	if (p.equals("false"))
	return 0;
	if (p.equals("0"))
	return 0;
	if (p.equals("1"))
	return 1;
	if (p.equals("2"))
	return 2;
	if (p.equals("3"))
	return 3;
	if (p.equals("console"))
	m += 1;
	if (p.equals("table"))
	m += 2;
	}
	return m;
	}

	public static int decodeStats(Token token) {
	String parts[] = token.parameters.toLowerCase().split(" ");
	int m = 0;
	for(String p : parts) {
	if (p.startsWith("no"))
	return 0;
	if (p.equals("false"))
	return 0;
	if (p.equals("0"))
	return 0;
	if (p.equals("1"))
	return 1;
	if (p.equals("2"))
	return 2;
	if (p.equals("3"))
	return 3;
	if (p.equals("show"))
	m += 1;
	if (p.equals("save"))
	m += 2;
	}
	return m;
	}

	public static boolean decodeSystem(Token token) {
	String p = token.parameters.toLowerCase();
	if (p.startsWith("no"))
	return false;
	if (p.equals("0"))
	return false;
	if (p.equals("false"))
	return false;
	return true;
	}

	public static boolean decodeDisplay(Token token) {
	String p = token.parameters.toLowerCase();
	if (p.startsWith("no"))
	return false;
	if (p.equals("0"))
	return false;
	if (p.equals("false"))
	return false;
	return true;
	}

	public static boolean decodeMultithreading(Token token) {
	String p = token.parameters.toLowerCase();
	if (p.startsWith("no"))
	return false;
	if (p.equals("0"))
	return false;
	if (p.equals("false"))
	return false;
	if (p.startsWith("dis"))
	return false;
	return true;
	}

	public static Padding decodePadding(Token token) {
	AbstractPadding padXY = new NoPadding();
	AbstractPadding padZ = new NoPadding();
	int extXY = 0;
	int extZ = 0;

	String param = token.parameters.trim();
	String[] parts = param.split(" ");
	if (parts.length > 0)
	padXY = Padding.getByShortname(parts[0].trim());
	if (parts.length > 1)
	padZ = Padding.getByShortname(parts[1].trim());
	double[] ext = NumFormat.parseNumbers(param);
	if (ext.length > 0)
	extXY = (int) Math.round(ext[0]);
	if (ext.length > 1)
	extZ = (int) Math.round(ext[1]);

	return new Padding(padXY, padXY, padZ, extXY, extXY, extZ);
	}

	public static Apodization decodeApodization(Token token) {
	AbstractApodization apoXY = new UniformApodization();
	AbstractApodization apoZ = new UniformApodization();
	String[] parts = token.parameters.trim().split(" ");
	if (parts.length >= 1)
	apoXY = Apodization.getByShortname(parts[0].trim());
	if (parts.length >= 2)
	apoZ = Apodization.getByShortname(parts[1].trim());
	return new Apodization(apoXY, apoXY, apoZ);
	}

	public static String getPath() {
	command();
	ArrayList<Token> tokens = parse(command.getCommand());
	String path = System.getProperty("user.dir");

	for (Token token : tokens)
	if (token.keyword.equalsIgnoreCase("-path") && !token.parameters.equalsIgnoreCase("current"))
	path = token.parameters;
	return path;
	}



	}
	diff --git a/DeconvolutionLab2/src/deconvolution/Deconvolution.java b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	index 20a4e98..283126e 100644
	--- a/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	+++ b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	@@ -1,550 +1,553 @@
	/*
	* 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;

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

	import bilib.tools.NumFormat;
	import deconvolution.algorithm.AbstractAlgorithm;
	import deconvolution.algorithm.Controller;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Output;
	import deconvolutionlab.OutputCollection;
	import deconvolutionlab.TableStats;
	import deconvolutionlab.monitor.ConsoleMonitor;
	import deconvolutionlab.monitor.Monitors;
	import deconvolutionlab.monitor.StatusMonitor;
	import deconvolutionlab.monitor.TableMonitor;
	import deconvolutionlab.monitor.Verbose;
	import deconvolutionlab.system.SystemInfo;
	import fft.AbstractFFTLibrary;
	import signal.RealSignal;
	import signal.SignalCollector;
	import signal.apodization.Apodization;
	import signal.padding.Padding;

	public class Deconvolution implements Runnable {

	public enum Finish {
	DIE, ALIVE, KILL
	};

	public AbstractAlgorithm algo = null;

	private String path;
	public double norm = 1.0;
	public Padding pad = new Padding();
	public Apodization apo = new Apodization();
	private OutputCollection outs;
	private Verbose verbose = Verbose.Log;
	private AbstractFFTLibrary fft;
	private int flagMonitor = 3;
	private int flagStats = 0;
	private boolean flagDisplay = true;
	private boolean flagMultithreading = true;
	private boolean flagSystem = true;

	public Monitors monitors = new Monitors();

	private String command = "";
	private boolean live = false;

	private Features report = new Features();

	private String name = "";

	private ArrayList<DeconvolutionListener> listeners = new ArrayList<DeconvolutionListener>();
	public RealSignal image;
	public RealSignal psf;
	private RealSignal deconvolvedImage;

	private Finish finish = Finish.DIE;
	private DeconvolutionDialog dialog;

	private TableStats tableStats;

	public Deconvolution(String name, String command) {
	this.name = name;
	this.finish = Finish.DIE;
	setCommand(command);
	tableStats = new TableStats(name, Constants.widthGUI, 240, path, (flagStats & 2) == 2);
	}

	public Deconvolution(String name, String command, Finish finish) {
	this.name = name;
	this.finish = finish;
	setCommand(command);
	tableStats = new TableStats(name, Constants.widthGUI, 240, path, (flagStats & 2) == 2);
	}

	public void setCommand(String command) {
	this.command = command;
	Command.decode(command, this);
	this.command = command;
	if (name.equals("") && algo != null)
	- name = algo.getShortname();
	+ name = algo.getShortnames()[0];
	live = false;
	}

	/**
	* This method runs the deconvolution without graphical user interface.
	*
	* @param exit
	* System.exit call is true
	*/
	public RealSignal deconvolve(RealSignal image, RealSignal psf) {
	this.image = image;
	this.psf = psf;
	runDeconvolve();
	return deconvolvedImage;
	}

	public RealSignal deconvolve() {
	this.image = null;
	this.psf = null;
	runDeconvolve();
	return deconvolvedImage;
	}

	/**
	* This method runs the deconvolution without graphical user interface.
	*
	* @param exit
	* System.exit call is true
	*/
	private void runDeconvolve() {
	if ((flagMonitor & 2) == 2) {
	TableMonitor tableMonitor = new TableMonitor(name , Constants.widthGUI, 240);
	monitors.add(tableMonitor);
	Lab.setVisible(tableMonitor.getPanel(), "Monitor of " + name, 10, 10);
	}

	if ((flagMonitor & 1) == 1)
	monitors.add(new ConsoleMonitor());

	if ((flagStats & 1) == 1) {
	Lab.setVisible(tableStats.getPanel(), "Stats of " + name, 50, 50);
	}

	if (fft == null) {
	run();
	return;
	}

	if (!fft.isMultithreadable()) {
	run();
	return;
	}

	if (flagMultithreading) {
	Thread thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}
	else {
	run();
	}

	}

	/**
	* This method runs the deconvolution with a graphical user interface.
	*
	* @param job
	* Name of the job of deconvolution
	*/
	public void launch() {
	monitors = new Monitors();
	TableMonitor tableMonitor = null;
	if ((flagMonitor & 2) == 2) {
	tableMonitor = new TableMonitor(name , Constants.widthGUI, 240);
	monitors.add(tableMonitor);
	}
	if ((flagMonitor & 1) == 1)
	monitors.add(new ConsoleMonitor());
	if (flagStats == 0) {
	tableStats = null;
	}

	dialog = new DeconvolutionDialog(DeconvolutionDialog.Module.ALL, this, tableMonitor, tableStats);
	monitors.add(new StatusMonitor(dialog.getProgressBar()));

	Lab.setVisible(dialog, false);
	}

	@Override
	public void run() {
	double chrono = System.nanoTime();

	if (flagSystem)
	SystemInfo.activate();

	for (DeconvolutionListener listener : listeners)
	listener.started();

	live = true;
	if (monitors != null)
	monitors.setVerbose(verbose);

	report.add("Path", checkPath(path));
	monitors.log("Path: " + checkPath(path));

	if (image == null)
	image = openImage();

	if (image == null) {
	monitors.error("Image: Not valid " + command);
	report.add("Image", "Not valid");
	if (finish == Finish.KILL)
	System.exit(-101);
	return;
	}
	report.add("Image", image.dimAsString());
	monitors.log("Image: " + image.dimAsString());

	psf = openPSF();

	if (psf == null) {
	monitors.error("PSF: not valid");
	report.add("PSF", "Not valid");
	if (finish == Finish.KILL)
	System.exit(-102);
	return;
	}
	report.add("PSF", psf.dimAsString());
	monitors.log("PSF: " + psf.dimAsString());

	if (algo == null) {
	monitors.error("Algorithm: not valid");
	if (finish == Finish.KILL)
	System.exit(-103);
	return;
	}

	Controller controller = algo.getController();
	if (controller == null) {
	monitors.error("Controller: not valid");
	if (finish == Finish.KILL)
	System.exit(-104);
	return;
	}

	if (flagStats > 0)
	controller.setTableStats(tableStats);

	report.add("FFT", fft.getLibraryName());

	if (outs != null) {
	outs.setPath(path);
	controller.setOutputs(outs);
	}

	monitors.log("Algorithm: " + algo.getName());
	report.add("Algorithm", algo.getName());
	algo.setController(controller);

	- deconvolvedImage = algo.run(monitors, image, psf, fft, pad, apo, norm, true);
	+ algo.setFFT(fft);
	+ algo.setMonitors(monitors);
	+
	+ deconvolvedImage = algo.run(image, psf, pad, apo, norm);

	live = false;
	for (DeconvolutionListener listener : listeners)
	listener.finish();

	report.add("End", NumFormat.time(System.nanoTime() - chrono));

	if (flagDisplay)
	- Lab.show(monitors, deconvolvedImage, "Result of " + algo.getShortname());
	+ Lab.show(monitors, deconvolvedImage, "Result of " + algo.getShortnames()[0]);

	if (finish == Finish.KILL) {
	System.out.println("End");
	System.exit(0);
	}

	if (finish == Finish.DIE)
	die();
	}


	public void close() {
	if (dialog != null)
	dialog.dispose();
	SignalCollector.free(image);
	SignalCollector.free(psf);
	SignalCollector.free(deconvolvedImage);
	algo = null;
	image = null;
	psf = null;
	deconvolvedImage = null;
	monitors = null;
	System.gc();
	}

	public void die() {
	SignalCollector.free(image);
	SignalCollector.free(psf);
	}


	/**
	* This methods make a recap of the deconvolution. Useful before starting
	* the processing.
	*
	* @return list of messages to print
	*/
	public Features recap() {
	Features features = new Features();
	Token image = Command.extract(command, "-image");
	features.add("Image", image == null ? "keyword -image not found" : image.parameters);

	String normf = (norm < 0 ? " (no normalization)" : " (normalization to " + norm + ")");
	Token psf = Command.extract(command, "-psf");
	features.add("PSF", psf == null ? "keyword -psf not found" : psf.parameters + " norm:" + normf);

	if (algo == null) {
	features.add("Algorithm", "not valid>");
	}
	else {
	Controller controller = algo.getController();
	features.add("Algorithm", algo.toString());
	features.add("Stopping Criteria", controller.getStoppingCriteriaAsString(algo));
	features.add("Reference", controller.getReference());
	features.add("Constraint", controller.getConstraintAsString());
	features.add("Padding", pad.toString());
	features.add("Apodization", apo.toString());
	features.add("FFT", fft == null ? "null" : fft.getLibraryName());
	}
	features.add("Path", path);

	String monitor = "";
	if (flagMonitor == 0)
	monitor = "no ";
	if (flagMonitor == 1)
	monitor = "console (" + verbose.name().toLowerCase() + ")";
	if (flagMonitor == 2)
	monitor = "table (" + verbose.name().toLowerCase() + ")";
	if (flagMonitor == 3)
	monitor = "console table (" + verbose.name().toLowerCase() + ")";
	String stats = "";
	if (flagStats == 0)
	stats = "no ";
	if (flagStats == 1)
	stats = "show ";
	if (flagStats == 2)
	stats = "save ";
	if (flagStats == 3)
	stats = "show save";
	String running = "";
	running += "multithreading: " + (flagMultithreading ? "on " : "off ");
	running += " display: " + (flagDisplay ? "on " : "off ");
	running += " system: " + (flagSystem ? "shown" : "hidden ");

	features.add("Monitor", monitor);
	features.add("Stats", stats);
	features.add("Running", running);
	if (outs == null)
	features.add("Output", "not valid");
	else
	for (Output out : outs)
	features.add("Output " + out.getName(), out.toString());
	return features;
	}


	public Features checkOutput() {
	Features features = new Features();
	if (deconvolvedImage == null) {
	features.add("Image", "No valid output image");
	return features;
	}
	float stati[] = deconvolvedImage.getStats();
	int sizi = deconvolvedImage.nx * deconvolvedImage.ny * deconvolvedImage.nz;
	float totali = stati[0] * sizi;
	features.add("<html><b>Deconvolved Image</b></html>", "");
	features.add("Size", deconvolvedImage.dimAsString() + " " + NumFormat.bytes(sizi*4));
	features.add("Mean (stdev)", NumFormat.nice(stati[0]) + " (" + NumFormat.nice(stati[3]) + ")");
	features.add("Min ... Max", NumFormat.nice(stati[1]) + " ... " + NumFormat.nice(stati[2]));
	features.add("Energy (int)", NumFormat.nice(stati[5]) + " (" + NumFormat.nice(totali) + ")");
	return features;
	}

	public boolean isLive() {
	return live;
	}

	public void abort() {
	live = false;
	algo.getController().abort();
	}

	public String checkPath(String path) {
	File dir = new File(path);
	if (dir.exists()) {
	if (dir.isDirectory()) {
	if (dir.canWrite())
	return path + " (writable)";
	else
	return path + " (non-writable)";
	}
	else {
	return path + " (non-directory)";
	}
	}
	else {
	return path + " (not-valid)";
	}
	}

	public RealSignal openImage() {
	Token token = Command.extract(command, "-image");
	if (token == null)
	return null;
	if (token.parameters.startsWith(">>>"))
	return null;
	String arg = token.option.trim();
	String cmd = token.parameters.substring(arg.length(), token.parameters.length()).trim();
	image = Lab.createRealSignal(monitors, arg, cmd, path);
	return image;
	}

	public RealSignal openPSF() {
	Token token = Command.extract(command, "-psf");
	if (token == null)
	return null;
	if (token.parameters.startsWith(">>>"))
	return null;
	String arg = token.option.trim();
	String cmd = token.parameters.substring(arg.length(), token.parameters.length()).trim();
	psf = Lab.createRealSignal(monitors, arg, cmd, path);
	return psf;
	}


	public void addDeconvolutionListener(DeconvolutionListener listener) {
	listeners.add(listener);
	}

	public OutputCollection getOuts() {
	return outs;
	}

	public void setAlgorithm(AbstractAlgorithm algo, Controller controller) {
	this.algo = algo;
	if (algo != null && controller != null) {
	algo.setController(controller);
	}
	}

	public AbstractAlgorithm getAlgo() {
	return algo;
	}

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

	public String getPath() {
	return path;
	}

	public void setNormalization(double norm) {
	this.norm = norm;
	}

	public void setPadding(Padding pad) {
	this.pad = pad;
	}

	public Padding getPadding() {
	return pad;
	}

	public RealSignal getOutput() {
	return deconvolvedImage;
	}

	public RealSignal getImage() {
	return image;
	}

	public RealSignal getPSF() {
	return psf;
	}

	public Features getDeconvolutionReports() {
	return report;
	}

	public String getName() {
	return name;
	}

	public void setApodization(Apodization apo) {
	this.apo = apo;
	}

	public Apodization getApodization() {
	return apo;
	}

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

	public void setVerbose(Verbose verbose) {
	this.verbose = verbose;
	}

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

	public void setMonitor(int flagMonitor) {
	this.flagMonitor = flagMonitor;
	}

	public void setStats(int flagStats) {
	this.flagStats = flagStats;
	}

	public void setFlags(boolean flagDisplay, boolean flagMultithreading, boolean flagSystem) {
	this.flagDisplay = flagDisplay;
	this.flagMultithreading = flagMultithreading;
	this.flagSystem = flagSystem;
	}

	public String getCommand() {
	return command;
	}


	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	index becc3da..bdfa307 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	@@ -1,240 +1,268 @@
	/*
	* 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.concurrent.Callable;
	import java.util.concurrent.ExecutionException;
	import java.util.concurrent.ExecutorService;
	import java.util.concurrent.Executors;
	import java.util.concurrent.Future;

	import bilib.tools.NumFormat;
	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.AbstractFFTLibrary;
	import fft.FFT;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;
	import signal.apodization.Apodization;
	import signal.padding.Padding;

	/**
	* This class is the common part of every algorithm of deconvolution.
	*
	* @author Daniel Sage
	*
	*/
	public abstract class AbstractAlgorithm implements Callable<RealSignal> {

	- /** y is the input signal of the deconvolution. */
	- protected RealSignal y = null;
	-
	- /** h is the PSF signal for the deconvolution. */
	- protected RealSignal h = null;
	-
	- /** The controller takes the control of the algorithm, in
	- * particular to do some operations at the starting,
	- * at every iteration and at the end. */
	- protected Controller controller = null;
	-
	+ /** y is the input signal of the deconvolution. */
	+ protected RealSignal y;
	+
	+ /** h is the PSF signal for the deconvolution. */
	+ protected RealSignal h;
	+
	+ /**
	+ * The controller takes the control of the algorithm, in particular to do
	+ * some operations at the starting, at every iteration and at the end.
	+ */
	+ protected Controller controller;
	+
	/** This is the FFT used. */
	- protected AbstractFFT fft = null;
	+ protected AbstractFFT fft ;

	- /** Shortname of the algorithm given by the user, useful in particular to deal with the synonym. */
	- protected String shortname = "I";
	+ protected Monitors monitors;
	+ protected AbstractFFTLibrary fftlib;
	+ protected boolean threaded;

	/** Optimized implementation in term of memory footprint */
	- protected boolean optimizedMemoryFootprint = true;
	+ protected boolean optimizedMemoryFootprint;

	public AbstractAlgorithm() {
	this.controller = new Controller();
	- }
	-
	- public void setShortname(String shortname) {
	- this.shortname = shortname;
	- }
	-
	- public String getShortname() {
	- return shortname;
	+ monitors = Monitors.createDefaultMonitor();
	+ fftlib = FFT.getFastestFFT();
	+ optimizedMemoryFootprint = true;
	+ threaded = true;
	}

	public void setOptimizedMemoryFootprint(boolean optimizedMemoryFootprint) {
	this.optimizedMemoryFootprint = optimizedMemoryFootprint;
	}
	-
	+
	public abstract String getName();
	+ public abstract String[] getShortnames();
	+
	public abstract double getMemoryFootprintRatio();
	+
	public abstract int getComplexityNumberofFFT();
	+
	public abstract boolean isRegularized();
	+
	public abstract boolean isStepControllable();
	+
	public abstract boolean isIterative();
	+
	public abstract boolean isWaveletsBased();
	+
	public abstract void setParameters(double[] params);
	+
	public abstract double getRegularizationFactor();
	+
	public abstract double getStepFactor();
	+
	public abstract double[] getParameters();
	+
	public abstract double[] getDefaultParameters();

	- public RealSignal run(Monitors monitors,
	- RealSignal image, RealSignal psf,
	- AbstractFFTLibrary fftlib, Padding pad, Apodization apo, double norm, boolean threaded) {
	+ public RealSignal run(RealSignal image, RealSignal psf) {
	+ return run(image, psf, new Padding(), new Apodization(), 1);
	+ }
	+
	+ public RealSignal run(RealSignal image, RealSignal psf, Padding pad, Apodization apo) {
	+ return run(image, psf, pad, apo, 1);
	+ }
	+
	+ public RealSignal run(RealSignal image, RealSignal psf, Padding pad, Apodization apo, double norm) {

	if (image == null)
	return null;
	if (psf == null)
	return null;
	-
	+
	if (fftlib != null)
	fft = FFT.createFFT(monitors, fftlib, image.nx, image.ny, image.nz);
	else
	fft = FFT.createDefaultFFT(monitors, image.nx, image.ny, image.nz);
	controller.setFFT(fft);
	-
	+
	y = pad.pad(monitors, image);
	y.setName("y");
	apo.apodize(monitors, y);
	monitors.log("Input: " + y.dimAsString());
	-
	+
	h = psf.changeSizeAs(y);
	h.setName("h");
	- h.normalize(norm);
	+ h.normalize(norm);
	monitors.log("PSF: " + h.dimAsString() + " normalized " + (norm <= 0 ? "no" : norm));

	String iterations = (isIterative() ? controller.getIterationMax() + " iterations" : "direct");
	- monitors.log(getShortname() + " is starting (" + iterations + ")");
	+ monitors.log(getShortnames()[0] + " is starting (" + iterations + ")");
	controller.setMonitors(monitors);
	controller.start(y);

	h.circular();
	if (fft == null)
	fft = FFT.createDefaultFFT(monitors, y.nx, y.ny, y.nz);
	else
	fft.init(monitors, y.nx, y.ny, y.nz);
	- monitors.log(getShortname() + " data ready");
	+ monitors.log(getShortnames()[0] + " data ready");

	double params[] = getParameters();
	if (params != null) {
	if (params.length > 0) {
	String s = " ";
	for (double param : params)
	s += "" + param + " ";
	- monitors.log(getShortname() + s);
	+ monitors.log(getShortnames()[0] + s);
	}
	}
	RealSignal x = null;

	try {
	if (threaded == true) {
	ExecutorService pool = Executors.newSingleThreadExecutor();
	Future<RealSignal> future = pool.submit(this);
	x = future.get();
	}
	else {
	x = call();
	}
	}
	catch (InterruptedException ex) {
	ex.printStackTrace();
	x = y.duplicate();
	}
	catch (ExecutionException ex) {
	ex.printStackTrace();
	x = y.duplicate();
	}
	catch (Exception e) {
	e.printStackTrace();
	x = y.duplicate();
	}
	x.setName("x");
	controller.finish(x);
	monitors.log(getName() + " is finished");
	SignalCollector.free(y);
	SignalCollector.free(h);

	RealSignal result = pad.crop(monitors, x);
	SignalCollector.free(x);
	return result;
	}

	+ public Monitors getMonitors() {
	+ return monitors;
	+ }
	+
	+ public void setMonitors(Monitors monitors) {
	+ this.monitors = monitors;
	+ }
	+
	public AbstractFFT getFFT() {
	return fft;
	}

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

	+ public void setFFT(AbstractFFTLibrary fftlib) {
	+ this.fftlib = fftlib;
	+ }
	+
	public Controller getController() {
	return controller;
	}

	public void setController(Controller controller) {
	this.controller = controller;
	}

	public int getIterations() {
	return controller.getIterations();
	}

	public double getTime() {
	return controller.getTimeNano();
	}

	public double getMemory() {
	return controller.getMemory();
	}

	public void setWavelets(String waveletsName) {
	}

	@Override
	public String toString() {
	String s = "";
	s += getName();
	s += (isIterative() ? ", " + controller.getIterationMax() + " iterations" : " (direct)");
	s += (isRegularized() ? ", &lambda=" + NumFormat.nice(getRegularizationFactor()) : "");
	s += (isStepControllable() ? ", &gamma=" + NumFormat.nice(getStepFactor()) : "");
	return s;
	}
	-
	+
	public String getParametersAsString() {
	double p[] = getParameters();
	- String param = "";
	- for(int i=0; i<p.length; i++)
	- if (i==p.length-1)
	+ String param = "";
	+ for (int i = 0; i < p.length; i++)
	+ if (i == p.length - 1)
	param += p[i];
	else
	param += p[i] + ", ";
	return param;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithmPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithmPanel.java
	index 491076f..15eafef 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithmPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithmPanel.java
	@@ -1,58 +1,58 @@
	/*
	* 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 javax.swing.JPanel;

	public abstract class AbstractAlgorithmPanel {

	public abstract JPanel getPanelParameters();

	public abstract String getCommand();

	public abstract String getName();

	- public abstract String[] getShortname();
	+ public abstract String[] getShortnames();

	public abstract String getDocumentation();

	public boolean isNamed(String name) {
	- for(String sn : getShortname()) {
	+ for(String sn : getShortnames()) {
	if (name.equals(sn.toLowerCase()))
	return true;
	if (name.equals(getName().toLowerCase()))
	return true;
	}
	return false;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java b/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
	index 9ec9346..ff39c53 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
	@@ -1,158 +1,156 @@
	/*
	* 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.ArrayList;

	public class Algorithm {

	/** This is the static list of all available algorithms. */
	private static ArrayList<AbstractAlgorithmPanel> list;

	static {
	list = new ArrayList<AbstractAlgorithmPanel>();
	list.add(new RegularizedInverseFilterPanel());
	list.add(new TikhonovRegularizationInverseFilterPanel());
	list.add(new NaiveInverseFilterPanel());
	list.add(new FISTAPanel());
	list.add(new ISTAPanel());
	list.add(new LandweberPanel());
	list.add(new LandweberPositivityPanel());
	list.add(new StarkParkerPanel());
	list.add(new RichardsonLucyPanel());
	list.add(new RichardsonLucyTVPanel());
	list.add(new TikhonovMillerPanel());
	list.add(new ICTMPanel());
	list.add(new VanCittertPanel());
	list.add(new IdentityPanel());
	list.add(new ConvolutionPanel());
	list.add(new SimulationPanel());
	list.add(new NonStabilizedDivisionPanel());
	}

	public static ArrayList<AbstractAlgorithmPanel> getAvailableAlgorithms() {
	return list;
	}

	public static AbstractAlgorithm getDefaultAlgorithm() {
	return new Identity();
	}

	/**
	* This static method return the algorithm specify by one of its shortname,
	*
	* @param shortname
	* @return an algorithm
	*/
	public static AbstractAlgorithm createAlgorithm(String shortname) {
	AbstractAlgorithm algo = getDefaultAlgorithm();
	String n = shortname.trim().toLowerCase();
	int i = 0;

	if (list.get(i++).isNamed(n))
	algo = new RegularizedInverseFilter(0.1);
	else if (list.get(i++).isNamed(n))
	algo = new TikhonovRegularizationInverseFilter(1.0);
	else if (list.get(i++).isNamed(n))
	algo = new NaiveInverseFilter();
	else if (list.get(i++).isNamed(n))
	algo = new FISTA(10, 1, 1, "Haar", 3);
	else if (list.get(i++).isNamed(n))
	algo = new ISTA(10, 1, 1, "Haar", 3);
	else if (list.get(i++).isNamed(n))
	algo = new Landweber(10, 1);
	else if (list.get(i++).isNamed(n))
	algo = new LandweberPositivity(10, 1);
	else if (list.get(i++).isNamed(n))
	algo = new StarkParker(10, 1);
	else if (list.get(i++).isNamed(n))
	algo = new RichardsonLucy(10);
	else if (list.get(i++).isNamed(n))
	algo = new RichardsonLucyTV(10, 1);
	else if (list.get(i++).isNamed(n))
	algo = new TikhonovMiller(10, 1, 0.1);
	else if (list.get(i++).isNamed(n))
	algo = new ICTM(10, 1, 0.1);
	else if (list.get(i++).isNamed(n))
	algo = new VanCittert(10, 1);
	else if (list.get(i++).isNamed(n))
	algo = new Identity();
	else if (list.get(i++).isNamed(n))
	algo = new Convolution();
	else if (list.get(i++).isNamed(n))
	algo = new Simulation(0, 1, 0);
	else if (list.get(i++).isNamed(n))
	algo = new NonStabilizedDivision();
	else
	algo = getDefaultAlgorithm();

	- if (algo != null)
	- algo.setShortname(shortname);
	return algo;
	}

	/**
	* This static method return the panel associated with
	* the algorithm specify by one of its shortname,
	*
	* @param shortname
	* @return an algorithm's panel
	*/
	public static AbstractAlgorithmPanel getPanel(String shortname) {
	for (AbstractAlgorithmPanel panel : getAvailableAlgorithms()) {
	- for(String sn : panel.getShortname())
	+ for(String sn : panel.getShortnames())
	if (sn.equals(shortname.trim()))
	return panel;
	if (panel.getName().equals(shortname.trim()))
	return panel;

	}
	return null;
	}

	public static ArrayList<String> getShortnames() {
	ArrayList<String> list = new ArrayList<String>();
	for (AbstractAlgorithmPanel algo : getAvailableAlgorithms()) {
	- for(String sn : algo.getShortname())
	+ for(String sn : algo.getShortnames())
	list.add(sn);
	}
	return list;
	}

	public static String getDocumentation(String name) {
	for (AbstractAlgorithmPanel algo : getAvailableAlgorithms()) {
	if (name.equals(algo.getName()))
	return algo.getDocumentation();
	}
	return "Unknown Algorithm";
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Convolution.java b/DeconvolutionLab2/src/deconvolution/algorithm/Convolution.java
	index 0970991..b4e49cf 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Convolution.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Convolution.java
	@@ -1,118 +1,122 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class Convolution extends AbstractAlgorithm implements Callable<RealSignal> {

	public Convolution() {
	super();
	}

	@Override
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal X = Operations.multiply(H, Y);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	@Override
	public String getName() {
	- return "Convolution Noiseless [CONV]";
	+ return "Convolution Noiseless";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"CONV"};
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3;
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 8.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return false;
	}

	@Override
	public boolean isIterative() {
	return false;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	}

	@Override
	public double[] getParameters() {
	return new double[] {};
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {};
	}

	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return 0;
	}
	-
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ConvolutionPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/ConvolutionPanel.java
	index 4a93291..0679d91 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ConvolutionPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ConvolutionPanel.java
	@@ -1,72 +1,72 @@
	/*
	* 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 javax.swing.JPanel;

	import bilib.component.GridPanel;

	public class ConvolutionPanel extends AbstractAlgorithmPanel {

	private Convolution algo = new Convolution();

	@Override
	public JPanel getPanelParameters() {
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\">No parameters</span></html>");
	return pn;
	}

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

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"CONV"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>This algorithm is only used for simulation. It make a pure convolution of the input image with the PSF in the Fourier domain.</p>";
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java b/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	index 657f0c0..2947d54 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	@@ -1,183 +1,188 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;
	import wavelets.AbstractWavelets;
	import wavelets.Wavelets;

	public class FISTA extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;
	private double lambda = 0.1;
	private String waveletsName = "Haar";
	private int scale = 3;

	public FISTA(int iter, double gamma, double lambda, String waveletsName, int scale) {
	super();
	controller.setIterationMax(iter);
	this.gamma = gamma;
	this.lambda = lambda;
	this.waveletsName = waveletsName;
	this.scale = scale;
	}

	@Override
	public RealSignal call() throws Exception {
	AbstractWavelets wavelets = Wavelets.getWaveletsByName(waveletsName);
	wavelets.setScale(scale);
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta(gamma, H);
	ComplexSignal G = Operations.multiplyConjugate(gamma, H, Y);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	ComplexSignal Z = G.duplicate();
	RealSignal x = fft.inverse(G);
	RealSignal s = x.duplicate();
	RealSignal z = x.duplicate();

	RealSignal xprev = fft.inverse(G);
	float pk1 = 1f;
	float pk0 = 1f;
	float threshold = (float) (lambda * gamma * 0.5);
	RealSignal buffer = y.duplicate();
	while (!controller.ends(x)) {
	fft.transform(s, Z);
	Z.times(A);
	Z.plus(G);
	fft.inverse(Z, z);
	wavelets.shrinkage(threshold, z, x, buffer);
	pk0 = pk1;
	pk1 = (1f + (float) Math.sqrt(1f + 4f * pk0 * pk0)) * 0.5f;
	update(xprev, x, (pk0 - 1f) / pk1, s);
	}
	SignalCollector.free(A);
	SignalCollector.free(Z);
	SignalCollector.free(G);
	SignalCollector.free(s);
	SignalCollector.free(z);
	SignalCollector.free(xprev);
	SignalCollector.free(buffer);
	return x;
	}

	public void update(RealSignal xprev, RealSignal x, double w, RealSignal s) {
	int nxy = x.nx * x.ny;
	for (int k = 0; k < x.nz; k++)
	for (int i = 0; i < nxy; i++) {
	float vx = x.data[k][i];
	s.data[k][i] = (float) (vx + w * (vx - xprev.data[k][i]));
	xprev.data[k][i] = vx;
	}
	}

	@Override
	public String getName() {
	return "Fast Iterative Shrinkage-Thresholding [FISTA]";
	}
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"FISTA"};
	+ }

	@Override
	public int getComplexityNumberofFFT() {
	return 4 + 4 * controller.getIterationMax();
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 15.0;
	}

	@Override
	public boolean isRegularized() {
	return true;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return true;
	}

	@Override
	public void setWavelets(String waveletsName) {
	this.waveletsName = waveletsName;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int) Math.round(params[0]));
	if (params.length > 1)
	gamma = (float) params[1];
	if (params.length > 2)
	lambda = (float) params[2];
	if (params.length > 3)
	scale = (int) params[3];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 10, 1, 0.1 };
	}

	@Override
	public double[] getParameters() {
	return new double[] { controller.getIterationMax(), gamma, lambda };
	}

	@Override
	public double getRegularizationFactor() {
	return lambda;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/FISTAPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/FISTAPanel.java
	index a96e210..a94a846 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/FISTAPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/FISTAPanel.java
	@@ -1,167 +1,167 @@
	/*
	* 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.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import javax.swing.JComboBox;
	import javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.RegularizationPanel;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import wavelets.AbstractWavelets;
	import wavelets.Wavelets;

	public class FISTAPanel extends AbstractAlgorithmPanel implements KeyListener, ActionListener, ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1, "#.#");
	private RegularizationPanel reg;
	private JComboBox<String> cmbWav = new JComboBox<String>(Wavelets.getWaveletsAsArray());
	private JComboBox<String> cmbScale = new JComboBox<String>(new String[] { "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" });

	private FISTA algo = new FISTA(10, 1, 0.1, "Haar", 3);

	@Override
	public JPanel getPanelParameters() {
	AbstractWavelets wavdef = Wavelets.getDefaultWavelets();
	double[] params = algo.getDefaultParameters();

	reg = new RegularizationPanel(params[2]);
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	cmbWav.setPreferredSize(Constants.dimParameters);
	cmbScale.setPreferredSize(Constants.dimParameters);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);

	pn.place(2, 0, 5, 1, reg);

	pn.place(5, 0, "<html><span \"nowrap\"><b>Wavelets</b></span></html>");
	pn.place(5, 2, cmbWav);
	pn.place(5, 3, "<html>Scale</html>");
	pn.place(5, 4, cmbScale);

	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	- Config.register("Algorithm." + algo.getShortname(), "wavelets", cmbWav, wavdef.getName());
	- Config.register("Algorithm." + algo.getShortname(), "scale", cmbScale, wavdef.getScales());
	- Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "step", spnStep, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "wavelets", cmbWav, wavdef.getName());
	+ Config.register("Algorithm." + algo.getShortnames()[0], "scale", cmbScale, wavdef.getScales());
	+ Config.register("Algorithm." + algo.getShortnames()[0], "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	cmbWav.addActionListener(this);
	cmbScale.addActionListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	int iter = spnIter.get();
	double gamma = spnStep.get();
	double lambda = reg.getValue();
	String waveletsName = (String) cmbWav.getSelectedItem();
	int scale = Integer.parseInt((String) cmbScale.getSelectedItem());
	return iter + " " + NumFormat.nice(gamma) + " " + NumFormat.nice(lambda) + " " + waveletsName + " " + scale;
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	Command.command();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	reg.getSlider().removeChangeListener(this);
	reg.updateFromText();
	Command.command();
	reg.getSlider().addChangeListener(this);
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"FISTA"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<h2>Shortname: FISTA</h2>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p></p>";
	s += "<h3>Reference: Beck and Teboulle, SIAM <b>2</b> 2009</h3>";
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java b/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	index cec5094..1f051ab 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	@@ -1,148 +1,153 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Constraint;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;
	import signal.factory.complex.ComplexSignalFactory;

	public class ICTM extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;
	private double lambda = 1.0;

	public ICTM(int iter, double gamma, double lambda) {
	super();
	controller.setIterationMax(iter);
	controller.setConstraint(Constraint.Mode.NONNEGATIVE);
	this.gamma = gamma;
	this.lambda = lambda;
	}

	@Override
	public RealSignal call() throws Exception {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta(gamma, H);
	ComplexSignal L = ComplexSignalFactory.laplacian(Y.nx, Y.ny, Y.nz);
	ComplexSignal L2 = Operations.multiplyConjugate(lambda * gamma, L, L);
	SignalCollector.free(L);
	A.minus(L2);
	SignalCollector.free(L2);
	ComplexSignal G = Operations.multiplyConjugate(gamma, H, Y);
	SignalCollector.free(H);
	SignalCollector.free(Y);
	ComplexSignal X = G.duplicate();
	controller.setConstraint(Constraint.Mode.NONNEGATIVE);
	while (!controller.ends(X)) {
	X.times(A);
	X.plus(G);
	}
	SignalCollector.free(A);
	SignalCollector.free(G);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	@Override
	public String getName() {
	- return "Iterative Contraint Tikhonov-Miller [ICTM]";
	+ return "Iterative Contraint Tikhonov-Miller";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"ICTM"};
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3 + controller.getIterationMax() * 2;
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 10.0;
	}

	@Override
	public boolean isRegularized() {
	return true;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int) Math.round(params[0]));
	if (params.length > 1)
	gamma = (float) params[1];
	if (params.length > 2)
	lambda = (float) params[2];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 10, 1, 0.1 };
	}

	@Override
	public double[] getParameters() {
	return new double[] { controller.getIterationMax(), gamma, lambda };
	}

	@Override
	public double getRegularizationFactor() {
	return lambda;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ICTMPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/ICTMPanel.java
	index 8952d5e..01c1f54 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ICTMPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ICTMPanel.java
	@@ -1,144 +1,146 @@
	/*
	* 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.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.RegularizationPanel;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;

	public class ICTMPanel extends AbstractAlgorithmPanel implements KeyListener, ActionListener, ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1, "#.#");
	private RegularizationPanel reg;

	private ICTM algo = new ICTM(10, 0.1, 1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	reg = new RegularizationPanel(params[2]);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);

	pn.place(2, 0, 5, 1, reg);

	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	- Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "step", spnStep, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	double gamma = spnStep.get();
	double lambda = reg.getValue();
	return spnIter.get() + " " + NumFormat.nice(gamma) + " " + NumFormat.nice(lambda);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	Command.command();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	reg.getSlider().removeChangeListener(this);
	reg.updateFromText();
	Command.command();
	reg.getSlider().addChangeListener(this);
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"ICTM"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	-
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	- s += "<p>Shortname: " + getShortname() + "</p>";
	+ String shortname = "<p>Shortname: ";
	+ for(String name : getShortnames())
	+ shortname += name + " ";
	+ s += shortname + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java b/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	index d37c909..12217dc 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	@@ -1,174 +1,180 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;
	import wavelets.AbstractWavelets;
	import wavelets.Wavelets;

	public class ISTA extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;
	private double lambda = 1.0;
	private String waveletsName = "Haar";
	private int scale = 3;

	public ISTA(int iter, double gamma, double lambda, String waveletsName, int scale) {
	super();
	controller.setIterationMax(iter);
	this.gamma = gamma;
	this.lambda = lambda;
	this.waveletsName = waveletsName;
	this.scale = scale;
	}

	@Override
	public RealSignal call() throws Exception {
	AbstractWavelets wavelets = Wavelets.getWaveletsByName(waveletsName);
	wavelets.setScale(scale);

	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta(gamma, H);
	ComplexSignal G = Operations.multiplyConjugate(gamma, H, Y);
	SignalCollector.free(Y);
	SignalCollector.free(H);

	ComplexSignal Z = G.duplicate();
	RealSignal x = fft.inverse(G);
	RealSignal z = x.duplicate();
	float threshold = (float)(lambdagamma0.5);
	RealSignal buffer = y.duplicate();
	while(!controller.ends(x)) {
	fft.transform(x, Z);
	Z.times(A);
	Z.plus(G);
	fft.inverse(Z, z);
	wavelets.shrinkage(threshold, z, x, buffer);
	}
	SignalCollector.free(A);
	SignalCollector.free(Z);
	SignalCollector.free(G);
	SignalCollector.free(z);
	SignalCollector.free(buffer);
	return x;
	}

	public void update(RealSignal xprev, RealSignal x, double w, RealSignal s) {
	int nxy = x.nx * x.ny;
	for(int k=0; k<x.nz; k++)
	for(int i=0; i< nxy; i++) {
	float vx = x.data[k][i];
	s.data[k][i] = (float)(vx + w*(vx - xprev.data[k][i]));
	xprev.data[k][i] = vx;
	}
	}

	@Override
	public String getName() {
	return "Iterative Shrinkage-Thresholding [ISTA]";
	}
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"ISTA"};
	+ }
	+

	@Override
	public int getComplexityNumberofFFT() {
	return 3 + 4 * controller.getIterationMax();
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 13.0;
	}

	@Override
	public boolean isRegularized() {
	return true;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return true;
	}

	@Override
	public void setWavelets(String waveletsName) {
	this.waveletsName = waveletsName;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int)Math.round(params[0]));
	if (params.length > 1)
	gamma = (float)params[1];
	if (params.length > 2)
	lambda = (float)params[2];
	if (params.length > 3)
	scale = (int)params[3];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {10, 1, 0.1};
	}

	@Override
	public double[] getParameters() {
	return new double[] {controller.getIterationMax(), gamma, lambda};
	}

	@Override
	public double getRegularizationFactor() {
	return lambda;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ISTAPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/ISTAPanel.java
	index 6d52d27..8b6d089 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ISTAPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ISTAPanel.java
	@@ -1,165 +1,168 @@
	/*
	* 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.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import javax.swing.JComboBox;
	import javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.RegularizationPanel;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import wavelets.AbstractWavelets;
	import wavelets.Wavelets;

	public class ISTAPanel extends AbstractAlgorithmPanel implements KeyListener, ActionListener, ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1);
	private RegularizationPanel reg;
	private JComboBox<String> cmbWav = new JComboBox<String>(Wavelets.getWaveletsAsArray());
	private JComboBox<String> cmbScale = new JComboBox<String>(new String[] { "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12" });

	private ISTA algo = new ISTA(0, 1, 0.1, "Haar", 3);

	@Override
	public JPanel getPanelParameters() {
	AbstractWavelets wavdef = Wavelets.getDefaultWavelets();
	double[] params = algo.getDefaultParameters();

	reg = new RegularizationPanel(params[2]);

	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	cmbWav.setPreferredSize(Constants.dimParameters);
	cmbScale.setPreferredSize(Constants.dimParameters);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);

	pn.place(2, 0, 5, 1, reg);

	pn.place(5, 0, "<html><span \"nowrap\"><b>Wavelets</b></span></html>");
	pn.place(5, 2, cmbWav);
	pn.place(5, 3, "<html>Scale</html>");
	pn.place(5, 4, cmbScale);

	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	- Config.register("Algorithm." + algo.getShortname(), "wavelets", cmbWav, wavdef.getName());
	- Config.register("Algorithm." + algo.getShortname(), "scale", cmbScale, wavdef.getScales());
	- Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "step", spnStep, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "wavelets", cmbWav, wavdef.getName());
	+ Config.register("Algorithm." + algo.getShortnames()[0], "scale", cmbScale, wavdef.getScales());
	+ Config.register("Algorithm." + algo.getShortnames()[0], "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	cmbWav.addActionListener(this);
	cmbScale.addActionListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	int iter = spnIter.get();
	double gamma = spnStep.get();
	double lambda = reg.getValue();
	String waveletsName = (String) cmbWav.getSelectedItem();
	int scale = Integer.parseInt((String) cmbScale.getSelectedItem());
	return iter + " " + NumFormat.nice(gamma) + " " + NumFormat.nice(lambda) + " " + waveletsName + " " + scale;
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	Command.command();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	reg.getSlider().removeChangeListener(this);
	reg.updateFromText();
	Command.command();
	reg.getSlider().addChangeListener(this);
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"ISTA"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	- s += "<p>Shortname: " + getShortname() + "</p>";
	+ String shortname = "<p>Shortname: ";
	+ for(String name : getShortnames())
	+ shortname += name + " ";
	+ s += shortname + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Identity.java b/DeconvolutionLab2/src/deconvolution/algorithm/Identity.java
	index 194d690..e2fc317 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Identity.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Identity.java
	@@ -1,109 +1,114 @@
	/*
	* 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.concurrent.Callable;

	import signal.RealSignal;

	public class Identity extends AbstractAlgorithm implements Callable<RealSignal> {

	public Identity() {
	super();
	}

	@Override
	public RealSignal call() {
	return y.duplicate();
	}

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

	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"I"};
	+ }
	+
	@Override
	public double getMemoryFootprintRatio() {
	return 5.0;
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 1;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return false;
	}

	@Override
	public boolean isIterative() {
	return false;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	}

	@Override
	public double[] getParameters() {
	return new double[] {};
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {};
	}


	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/IdentityPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/IdentityPanel.java
	index e6836c8..dbcc779 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/IdentityPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/IdentityPanel.java
	@@ -1,72 +1,72 @@
	/*
	* 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 javax.swing.JPanel;

	import bilib.component.GridPanel;

	public class IdentityPanel extends AbstractAlgorithmPanel {

	private Identity algo = new Identity();

	@Override
	public JPanel getPanelParameters() {
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\">No parameters</span></html>");
	return pn;
	}

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

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"I", "ID"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>This algorithm does nothing. It returns the input image.</p>";
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java b/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	index d353893..9592e83 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	@@ -1,142 +1,147 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class Landweber extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

	public Landweber(int iter, double gamma) {
	super();
	controller.setIterationMax(iter);
	this.gamma = gamma;
	}

	@Override
	// Landweber algorithm
	// X(n+1) = X(n) + gH(Y-H*X(n))
	// => X(n+1) = X(n) - gHHX(n) + gH*Y
	// => X(n+1) = X(n) * (I-gHH) + gHY
	// => pre-compute: A = (I-gHH) and G = gHY
	// => Iteration : X(n+1) = X(n) * A + G with F(0) = G
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta(gamma, H);
	ComplexSignal G = Operations.multiplyConjugate(gamma, H, Y);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	ComplexSignal X = G.duplicate();
	X.setName("X");
	while (!controller.ends(X)) {
	X.times(A);
	X.plus(G);
	}
	SignalCollector.free(A);
	SignalCollector.free(G);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	@Override
	public String getName() {
	- return "Landweber [LW \| LLS]";
	+ return "Landweber";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"LW", "LLS"};
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3 + (controller.needSpatialComputation() ? 2 * controller.getIterationMax() : 0);
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 9.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int) Math.round(params[0]));
	if (params.length > 1)
	gamma = (float) params[1];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 10, 1 };
	}

	@Override
	public double[] getParameters() {
	return new double[] { controller.getIterationMax(), gamma };
	}

	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPanel.java
	index 865687a..50bf183 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPanel.java
	@@ -1,109 +1,112 @@
	/*
	* 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 javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;

	public class LandweberPanel extends AbstractAlgorithmPanel implements ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1);
	private Landweber algo = new Landweber(10, 1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();

	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);

	pn.place(2, 0, "<html><span \"nowrap\"><b>Regularization</b></span></html>");
	pn.place(2, 1, 4, 1, "<html><span \"nowrap\">No regularization</i></span></html>");

	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "step", spnStep, params[1]);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	int iter = spnIter.get();
	double gamma = spnStep.get();
	return iter + " " + NumFormat.nice(gamma);
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"LW", "LLS"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	- s += "<p>Shortname: " + getShortname() + "</p>";
	+ String shortname = "<p>Shortname: ";
	+ for(String name : getShortnames())
	+ shortname += name + " ";
	+ s += shortname + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	index 34cafe1..1110ba6 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	@@ -1,144 +1,149 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Constraint;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class LandweberPositivity extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

	public LandweberPositivity(int iter, double gamma) {
	super();
	controller.setIterationMax(iter);
	controller.setConstraint(Constraint.Mode.NONNEGATIVE);
	this.gamma = gamma;
	}

	@Override
	// Landweber algorithm
	// X(n+1) = X(n) + gH(Y-H*X(n))
	// => X(n+1) = X(n) - gHHX(n) + gH*Y
	// => X(n+1) = X(n) * (I-gHH) + gHY
	// => pre-compute: A = (I-gHH) and G = gHY
	// => Iteration : X(n+1) = X(n) * A + G with F(0) = G
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta(gamma, H);
	ComplexSignal G = Operations.multiplyConjugate(gamma, H, Y);
	ComplexSignal X = G.duplicate();
	controller.setConstraint(Constraint.Mode.NONNEGATIVE);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	while (!controller.ends(X)) {
	X.times(A);
	X.plus(G);
	}
	SignalCollector.free(A);
	SignalCollector.free(G);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	@Override
	public String getName() {
	- return "Non-Negative Least-Square [NNLS \| LW+]";
	+ return "Non-Negative Least-Square";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"NNLS", "LW+"};
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3 + controller.getIterationMax() * 2;
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 10.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int) Math.round(params[0]));
	if (params.length > 1)
	gamma = (float) params[1];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 10, 1 };
	}

	@Override
	public double[] getParameters() {
	return new double[] { controller.getIterationMax(), gamma };
	}

	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivityPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivityPanel.java
	index 8ca1655..49c6d3c 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivityPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivityPanel.java
	@@ -1,109 +1,112 @@
	/*
	* 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 javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;

	public class LandweberPositivityPanel extends AbstractAlgorithmPanel implements ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1);
	private LandweberPositivity algo = new LandweberPositivity(10, 1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();

	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);

	pn.place(2, 0, "<html><span \"nowrap\"><b>Regularization</b></span></html>");
	pn.place(2, 1, 4, 1, "<html><span \"nowrap\">No regularization</i></span></html>");

	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "step", spnStep, params[1]);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	int iter = spnIter.get();
	double gamma = spnStep.get();
	return iter + " " + NumFormat.nice(gamma);
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"NLLS", "LW+"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	- s += "<p>Shortname: " + getShortname() + "</p>";
	+ String shortname = "<p>Shortname: ";
	+ for(String name : getShortnames())
	+ shortname += name + " ";
	+ s += shortname + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilter.java b/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilter.java
	index f2bbf6d..53314be 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilter.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilter.java
	@@ -1,118 +1,123 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class NaiveInverseFilter extends AbstractAlgorithm implements Callable<RealSignal> {

	public NaiveInverseFilter() {
	super();
	}

	@Override
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal X = Operations.divideStabilized(Y, H);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	@Override
	public String getName() {
	- return "Naive Inverse Filter [NIF \| IF]";
	+ return "Naive Inverse Filter";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"NIF", "IF"};
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3;
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 8.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return false;
	}

	@Override
	public boolean isIterative() {
	return false;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {};
	}

	@Override
	public double[] getParameters() {
	return new double[] {};
	}

	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilterPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilterPanel.java
	index 7fa81fc..d79e65f 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilterPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilterPanel.java
	@@ -1,75 +1,75 @@
	/*
	* 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 javax.swing.JPanel;

	import bilib.component.GridPanel;

	public class NaiveInverseFilterPanel extends AbstractAlgorithmPanel {

	private NaiveInverseFilter algo = new NaiveInverseFilter();

	@Override
	public JPanel getPanelParameters() {
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\">No parameters</span></html>");
	return pn;
	}

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

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"NIF", "IF"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<h3>Shortname: NIF or IF</p>";
	s += "<p>This is the classical inverse filter.</p>";
	s += "<p>This algorithm only performs a stabilized division in the Fourier domain.</p>";
	s += "<p>The stabilization is controlled by the machine epsilon parameter Ε set by default at 1E-6.</p>";
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	index f89e80f..bf806d6 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	@@ -1,118 +1,123 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class NonStabilizedDivision extends AbstractAlgorithm implements Callable<RealSignal> {

	public NonStabilizedDivision() {
	super();
	}

	@Override
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal X = Operations.divideNotStabilized(Y, H);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	@Override
	public String getName() {
	return "Non Stablized Division [DIV]";
	}

	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"DIV"};
	+ }
	+
	@Override
	public int getComplexityNumberofFFT() {
	return 3;
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 8.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return false;
	}

	@Override
	public boolean isIterative() {
	return false;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {};
	}

	@Override
	public double[] getParameters() {
	return new double[] {};
	}

	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivisionPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivisionPanel.java
	index 39ed17a..e3484bf 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivisionPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivisionPanel.java
	@@ -1,76 +1,79 @@
	/*
	* 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 javax.swing.JPanel;

	import bilib.component.GridPanel;

	public class NonStabilizedDivisionPanel extends AbstractAlgorithmPanel {

	private NonStabilizedDivision algo = new NonStabilizedDivision();

	@Override
	public JPanel getPanelParameters() {
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\">No parameters</span></html>");
	return pn;
	}

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

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"DIV"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	- s += "<p>Shortname: " + getShortname() + "</p>";
	+ String shortname = "<p>Shortname: ";
	+ for(String name : getShortnames())
	+ shortname += name + " ";
	+ s += shortname + "</p>";
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilter.java b/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilter.java
	index d334dcd..a74440a 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilter.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilter.java
	@@ -1,185 +1,189 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;
	import signal.factory.complex.ComplexSignalFactory;

	public class RegularizedInverseFilter extends AbstractAlgorithm implements Callable<RealSignal> {

	private double lambda = 0.001;

	public RegularizedInverseFilter(double lambda) {
	super();
	this.lambda = lambda;
	}

	@Override
	public RealSignal call() {
	if (optimizedMemoryFootprint)
	return runOptimizedMemoryFootprint();
	else
	return runTextBook();
	}

	public RealSignal runTextBook() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal H2 = Operations.multiply(H, H);
	ComplexSignal L = ComplexSignalFactory.laplacian(Y.nx, Y.ny, Y.nz);
	ComplexSignal L2 = Operations.multiply(lambda, L, L);
	ComplexSignal FA = Operations.add(H2, L2);
	ComplexSignal FT = Operations.divideStabilized(H, FA);
	ComplexSignal X = Operations.multiply(Y, FT);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(FT);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	SignalCollector.free(FA);
	SignalCollector.free(L);
	SignalCollector.free(H2);
	SignalCollector.free(L2);
	SignalCollector.free(X);
	return x;
	}

	public RealSignal runOptimizedMemoryFootprint() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal X = filter(Y, H);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	public ComplexSignal filter(ComplexSignal Y, ComplexSignal H) {
	ComplexSignal X = ComplexSignalFactory.laplacian(Y.nx, Y.ny, Y.nz);
	X.setName("X");
	int nx = X.nx;
	int ny = X.ny;
	int nz = X.nz;
	float la, lb, ha, hb, fa, fb, ta, tb, ya, yb;
	int nxy = nx * ny * 2;
	float w = (float) lambda;
	float epsilon = (float) Operations.epsilon;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i += 2) {
	la = X.data[k][i];
	lb = X.data[k][i + 1];
	ha = H.data[k][i];
	hb = H.data[k][i + 1];
	fa = w * (la * la - lb * lb) + (ha * ha - hb * hb);
	fb = w * (2f * la * lb) + (2f * ha * hb);
	float mag = Math.max(epsilon, fa * fa + fb * fb);
	ta = (ha * fa + hb * fb) / mag;
	tb = (hb * fa - ha * fb) / mag;
	ya = Y.data[k][i];
	yb = Y.data[k][i + 1];
	X.data[k][i] = ya * ta - yb * tb;
	X.data[k][i + 1] = ya * tb + ta * yb;
	}
	// SignalCollector.free(L);
	return X;
	}

	-
	@Override
	public String getName() {
	- return "Regularized Inverse Filter [RIF \| LRIF]";
	+ return "Regularized Inverse Filter";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"RIF", "LRIF"};
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3;
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 8.0;
	}

	@Override
	public boolean isRegularized() {
	return true;
	}

	@Override
	public boolean isStepControllable() {
	return false;
	}

	@Override
	public boolean isIterative() {
	return false;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	lambda = (float) params[0];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 0.1 };
	}

	@Override
	public double[] getParameters() {
	return new double[] { lambda };
	}

	@Override
	public double getRegularizationFactor() {
	return lambda;
	}

	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilterPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilterPanel.java
	index d1c3ec2..0de764e 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilterPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilterPanel.java
	@@ -1,115 +1,115 @@
	/*
	* 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.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.RegularizationPanel;
	import deconvolutionlab.Config;

	public class RegularizedInverseFilterPanel extends AbstractAlgorithmPanel implements KeyListener, ChangeListener {

	private RegularizationPanel reg;
	private RegularizedInverseFilter algo = new RegularizedInverseFilter(0.1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	reg = new RegularizationPanel(params[0]);
	GridPanel pn = new GridPanel(false);
	pn.place(0, 0, reg);
	- Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	+ Config.register("Algorithm." + algo.getShortnames()[0], "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	return NumFormat.nice(reg.getValue());
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	reg.getSlider().removeChangeListener(this);
	reg.updateFromText();
	Command.command();
	reg.getSlider().addChangeListener(this);
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"RIF", "LRIF"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<h2>Shortname RIF or LRIF</h2>";
	s += "<p>Laplacian Regularized Inverse Filter</p>";
	s += "<p>This is a inverse filter with a Laplacian regularization that tends to have an effect on high frequency</p>";
	s += "<p>It is very fast, non-iterative algorithm</p>";
	s += "<p>The regularization blurs the noise and the image. It is controlled by λ</p>";
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	index 2c66b08..3d149e8 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	@@ -1,136 +1,141 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class RichardsonLucy extends AbstractAlgorithm implements Callable<RealSignal> {

	public RichardsonLucy(int iter) {
	super();
	controller.setIterationMax(iter);
	}

	// x(k+1) = x(k) . Hconj ( y /. H x(k))
	@Override
	public RealSignal call() {
	ComplexSignal H = fft.transform(h);
	ComplexSignal U = new ComplexSignal("RL-U", y.nx, y.ny, y.nz);
	RealSignal x = y.duplicate();
	RealSignal p = y.duplicate();
	RealSignal u = y.duplicate();
	while (!controller.ends(x)) {
	fft.transform(x, U);
	U.times(H);
	fft.inverse(U, u);
	Operations.divide(y, u, p);
	fft.transform(p, U);
	U.timesConjugate(H);
	fft.inverse(U, u);
	x.times(u);
	}
	SignalCollector.free(H);
	SignalCollector.free(p);
	SignalCollector.free(u);
	SignalCollector.free(U);
	return x;
	}

	@Override
	public String getName() {
	- return "Richardson-Lucy [RL]";
	+ return "Richardson-Lucy";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"RL"};
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 1 + 5 * controller.getIterationMax();
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 9.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return false;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int) Math.round(params[0]));
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 10 };
	}

	@Override
	public double[] getParameters() {
	return new double[] { controller.getIterationMax() };
	}

	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyPanel.java
	index 47d0a6c..dc2ce21 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyPanel.java
	@@ -1,94 +1,94 @@
	/*
	* 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 javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeInteger;
	import deconvolution.Command;
	import deconvolutionlab.Config;

	public class RichardsonLucyPanel extends AbstractAlgorithmPanel implements ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);

	private RichardsonLucy algo = new RichardsonLucy(10);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	spnIter.addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	return "" + spnIter.get();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"RL"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<h2> Shortname: RL</h2>";

	s += "<p>This is the well-known Richardson-Lucy algorithm.</p>";
	s += "<p>It is an iterative with a slow convergence, it has only one parameter to tune: the maximum number of iterations</p>";
	s += "<p>RL is well appropiate for dominant Poison noise.</p>";
	s += "<p>It is a maximum likelihood estimator (MLE).</p>";
	s += "<p>Warning: the input image should have only positive values</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTV.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTV.java
	index 0d7654d..479af1c 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTV.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTV.java
	@@ -1,230 +1,235 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class RichardsonLucyTV extends AbstractAlgorithm implements Callable<RealSignal> {

	private double lambda = 0.1;

	public RichardsonLucyTV(int iter, double lambda) {
	super();
	controller.setIterationMax(iter);
	this.lambda = lambda;
	}

	// x(k+1) = x(k) . Hconj ( y /. H x(k))
	@Override
	public RealSignal call() {
	ComplexSignal H = fft.transform(h);
	ComplexSignal U = new ComplexSignal("RLTV-U",y.nx, y.ny, y.nz);
	RealSignal x = y.duplicate();
	RealSignal gx = y.duplicate();
	RealSignal gy = y.duplicate();
	RealSignal gz = y.duplicate();
	RealSignal ggx = y.duplicate();
	RealSignal ggy = y.duplicate();
	RealSignal ggz = y.duplicate();

	RealSignal u = gx; // resued memory
	RealSignal p = gy; // resued memory
	RealSignal tv = gz; // resued memory

	while(!controller.ends(x)) {
	gradientX(x, gx);
	gradientY(x, gy);
	gradientZ(x, gz);
	normalize(gx, gy, gz);
	gradientX(gx, ggx);
	gradientY(gy, ggy);
	gradientZ(gz, ggz);
	compute((float)lambda, ggx, ggy, ggz, tv);
	fft.transform(x, U);
	U.times(H);
	fft.inverse(U, u);
	Operations.divide(y, u, p);
	fft.transform(p, U);
	U.timesConjugate(H);
	fft.inverse(U, u);
	x.times(u);
	x.times(tv);
	}
	SignalCollector.free(H);
	SignalCollector.free(U);
	SignalCollector.free(ggx);
	SignalCollector.free(ggy);
	SignalCollector.free(ggz);
	SignalCollector.free(tv);
	SignalCollector.free(u);
	SignalCollector.free(p);
	return x;
	}

	private void compute(float lambda, RealSignal gx, RealSignal gy, RealSignal gz, RealSignal tv) {
	int nxy = gx.nx * gy.ny;
	for(int k=0; k<gx.nz; k++)
	for(int i=0; i< nxy; i++) {
	double dx = gx.data[k][i];
	double dy = gy.data[k][i];
	double dz = gz.data[k][i];
	tv.data[k][i] = (float)(1.0 / ( (dx+dy+dz) * lambda + 1.0));
	}
	}

	public void gradientX(RealSignal signal, RealSignal output) {
	int nx = signal.nx;
	int ny = signal.ny;
	int nz = signal.nz;
	for(int k=0; k<nz; k++)
	for(int j=0; j<ny; j++)
	for(int i=0; i<nx-1; i++) {
	int index = i + signal.nx*j;
	output.data[k][index] = signal.data[k][index] - signal.data[k][index+1];
	}
	}

	public void gradientY(RealSignal signal, RealSignal output) {
	int nx = signal.nx;
	int ny = signal.ny;
	int nz = signal.nz;
	for(int k=0; k<nz; k++)
	for(int j=0; j<ny-1; j++)
	for(int i=0; i<nx; i++) {
	int index = i + signal.nx*j;
	output.data[k][index] = signal.data[k][index] - signal.data[k][index+nx];
	}
	}

	public void gradientZ(RealSignal signal, RealSignal output) {
	int nx = signal.nx;
	int ny = signal.ny;
	int nz = signal.nz;
	for(int k=0; k<nz-1; k++)
	for(int j=0; j<ny; j++)
	for(int i=0; i<nx; i++) {
	int index = i + signal.nx*j;
	output.data[k][index] = signal.data[k][index] - signal.data[k+1][index];
	}
	}

	public void normalize(RealSignal x, RealSignal y, RealSignal z) {
	int nx = x.nx;
	int ny = y.ny;
	int nz = z.nz;
	float e = (float) Operations.epsilon;
	for(int k=0; k<nz; k++)
	for(int i=0; i<nx*ny; i++) {
	double norm = Math.sqrt(x.data[k][i] * x.data[k][i] + y.data[k][i] * y.data[k][i] + z.data[k][i] * z.data[k][i]);
	if (norm < e) {
	x.data[k][i] = e;
	y.data[k][i] = e;
	z.data[k][i] = e;
	}
	else {
	x.data[k][i] /= norm;
	y.data[k][i] /= norm;
	z.data[k][i] /= norm;
	}
	}
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 1 + 7 * controller.getIterationMax();
	}

	@Override
	public String getName() {
	- return "Richardson-Lucy Total Variation [RLTV]";
	+ return "Richardson-Lucy Total Variation";
	}
	-
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"RLTV"};
	+ }
	+
	@Override
	public double getMemoryFootprintRatio() {
	return 13.0;
	}

	@Override
	public boolean isRegularized() {
	return true;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int)Math.round(params[0]));
	if (params.length > 1)
	lambda = (float)params[1];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {10, 0.1};
	}

	@Override
	public double[] getParameters() {
	return new double[] {controller.getIterationMax(), lambda};
	}

	@Override
	public double getRegularizationFactor() {
	return lambda;
	}

	@Override
	public double getStepFactor() {
	return 0.0;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTVPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTVPanel.java
	index 11982b3..5fb9be6 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTVPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTVPanel.java
	@@ -1,130 +1,130 @@
	/*
	* 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.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.RegularizationPanel;
	import deconvolutionlab.Config;

	public class RichardsonLucyTVPanel extends AbstractAlgorithmPanel implements KeyListener, ActionListener, ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);
	private RegularizationPanel reg;

	private RichardsonLucyTV algo = new RichardsonLucyTV(10, 0.1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	reg = new RegularizationPanel(params[1]);
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(2, 0, 3, 1, reg);
	- Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	+ Config.register("Algorithm." + algo.getShortnames()[0], "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	spnIter.addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	double lambda = reg.getValue();
	return spnIter.get() + " " + NumFormat.nice(lambda);
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	Command.command();
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	reg.getSlider().removeChangeListener(this);
	reg.updateFromText();
	Command.command();
	reg.getSlider().addChangeListener(this);
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"RLTV"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<h2> Shortname: RLTV</h2>";
	s += "<p>This algorithm is a combinaison of the Richardson–Lucy algorithm with a regularization constraint based on Total Variation, which tends to reduce unstable oscillations while preserving object edges.</p>";
	s += "<p>It is a iterative algorithm, relative slow to compute the Total Variation at every iteration.s</p>";
	s += "<p>It has a weighted parameter &lamdba; to control the effect of the total variation.</p>";
	s += "<p></p>";
	- s += "<h3>Reference: Dey et al., Microscopy Research and Technics, 2006 " + getShortname() + "</p>";
	+ s += "<h3>Reference: Dey et al., Microscopy Research and Technics, 2006.</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Simulation.java b/DeconvolutionLab2/src/deconvolution/algorithm/Simulation.java
	index 4faaaf2..912e708 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Simulation.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Simulation.java
	@@ -1,159 +1,165 @@
	/*
	* 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.concurrent.Callable;

	import bilib.tools.PsRandom;
	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class Simulation extends AbstractAlgorithm implements Callable<RealSignal> {

	private static PsRandom rand = new PsRandom(1234);

	private double mean = 0.0;
	private double stdev = 10.0;
	private double poisson = 0.0;

	public Simulation(double mean, double stdev, double poisson) {
	super();
	this.mean = mean;
	this.stdev = stdev;
	this.poisson = poisson;
	}

	@Override
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal X = Operations.multiply(H, Y);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	gaussian(x, mean, stdev);
	poisson(x, poisson);
	return x;
	}

	public void gaussian(RealSignal x, double mean, double sd) {
	for (int k = 0; k < x.nz; k++) {
	float[] slice = x.getXY(k);
	for (int j = 0; j < x.ny * x.nx; j++)
	slice[j] += (float) rand.nextGaussian(mean, sd);
	}
	}

	public void poisson(RealSignal x, double factor) {
	if (factor < Operations.epsilon)
	return;
	double f = 1.0/(factor);
	for (int k = 0; k < x.nz; k++) {
	float[] slice = x.getXY(k);
	for (int j = 0; j < x.ny * x.nx; j++)
	if (slice[j] > Operations.epsilon) {
	slice[j] = (float)(rand.nextPoissonian(f(slice[j])) factor);
	}
	}
	}

	@Override
	public String getName() {
	- return "Simulation with noise [SIM]";
	+ return "Simulation with noise";
	}
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"SIM", "SIMU"};
	+ }
	+

	@Override
	public int getComplexityNumberofFFT() {
	return 3;
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 8.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return false;
	}

	@Override
	public boolean isIterative() {
	return false;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	mean = params[0];
	if (params.length > 1)
	stdev = params[1];
	if (params.length > 2)
	poisson = params[2];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {0, 1, 0};
	}

	@Override
	public double[] getParameters() {
	return new double[] {mean, stdev, poisson};
	}

	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/SimulationPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/SimulationPanel.java
	index d0bf53b..8f721c1 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/SimulationPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/SimulationPanel.java
	@@ -1,114 +1,114 @@
	/*
	* 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.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import javax.swing.JPanel;
	import javax.swing.JTextField;

	import bilib.component.GridPanel;
	import deconvolution.Command;
	import deconvolutionlab.Config;

	public class SimulationPanel extends AbstractAlgorithmPanel implements KeyListener {

	private JTextField txtMean;
	private JTextField txtStdev;
	private JTextField txtPoisson;

	private Simulation algo = new Simulation(0, 0, 0);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	txtMean = new JTextField("" + params[0], 5);
	txtStdev = new JTextField("" + params[1], 5);
	txtPoisson = new JTextField("" + params[2], 5);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html>Gaussian (Mean)</html>");
	pn.place(1, 2, txtMean);
	pn.place(2, 0, "<html>Gaussian (Stdev)</html>");
	pn.place(2, 2, txtStdev);
	pn.place(3, 0, "<html>Poisson</html>");
	pn.place(3, 2, txtPoisson);
	txtMean.addKeyListener(this);
	txtStdev.addKeyListener(this);
	txtPoisson.addKeyListener(this);
	- Config.register("Algorithm." + algo.getShortname(), "gaussian.mean", txtMean, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "gaussian.stdev", txtStdev, params[1]);
	- Config.register("Algorithm." + algo.getShortname(), "poisson", txtPoisson, params[2]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "gaussian.mean", txtMean, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "gaussian.stdev", txtStdev, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "poisson", txtPoisson, params[2]);
	return pn;
	}

	@Override
	public String getCommand() {
	return txtMean.getText() + " " + txtStdev.getText() + " " + txtPoisson.getText();
	}

	@Override
	public void keyTyped(KeyEvent e) {
	Command.command();
	}

	@Override
	public void keyPressed(KeyEvent e) {
	Command.command();
	}

	@Override
	public void keyReleased(KeyEvent e) {
	Command.command();
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	- @Override
	- public String[] getShortname() {
	- return new String[] {"SIM", "SIMU"};
	- }
	-
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>This algorithm is only used for simulation. It convolves the input image with the PSF and adds some noise.</p>";
	s += "<p>The noise has a Gaussian distribution (mean, stdev) and a Poisson distribution (poisson).</p>";
	return s;
	}

	+ @Override
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	+ }
	+
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/StarkParker.java b/DeconvolutionLab2/src/deconvolution/algorithm/StarkParker.java
	index 5acfb8e..794d5c2 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/StarkParker.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/StarkParker.java
	@@ -1,143 +1,148 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Constraint;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class StarkParker extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

	public StarkParker(int iter, double gamma) {
	super();
	controller.setIterationMax(iter);
	this.gamma = gamma;
	}

	@Override
	// Landweber algorithm
	// X(n+1) = X(n) + gH(Y-H*X(n))
	// => X(n+1) = X(n) - gHHX(n) + gH*Y
	// => X(n+1) = X(n) * (I-gHH) + gHY
	// => pre-compute: A = (I-gHH) and G = gHY
	// => Iteration : X(n+1) = X(n) * A + G with F(0) = G
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta(gamma, H);
	ComplexSignal G = Operations.multiplyConjugate(gamma, H, Y);
	SignalCollector.free(H);
	SignalCollector.free(Y);
	ComplexSignal X = G.duplicate();
	controller.setConstraint(Constraint.Mode.CLIPPED);
	while (!controller.ends(X)) {
	X.times(A);
	X.plus(G);
	}
	SignalCollector.free(A);
	SignalCollector.free(G);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	@Override
	public String getName() {
	- return "Bounded-Variable Least Squares [BVLS \| SP]";
	+ return "Bounded-Variable Least Squares";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"BVLS", "SP"};
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3 + controller.getIterationMax() * 2;
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 9.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int) Math.round(params[0]));
	if (params.length > 1)
	gamma = (float) params[1];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 10, 1 };
	}

	@Override
	public double[] getParameters() {
	return new double[] { controller.getIterationMax(), gamma };
	}

	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/StarkParkerPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/StarkParkerPanel.java
	index d36bd80..6009cc6 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/StarkParkerPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/StarkParkerPanel.java
	@@ -1,110 +1,110 @@
	/*
	* 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 javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;

	public class StarkParkerPanel extends AbstractAlgorithmPanel implements ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1);
	private StarkParker algo = new StarkParker(10, 1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();

	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);

	pn.place(2, 0, "<html><span \"nowrap\"><b>Regularization</b></span></html>");
	pn.place(2, 1, 4, 1, "<html><span \"nowrap\">No regularization</i></span></html>");

	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "step", spnStep, params[1]);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	int iter = spnIter.get();
	double gamma = spnStep.get();
	return iter + " " + NumFormat.nice(gamma);
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] { "BVLS", "SP" };
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<h1>Stark-Parker Algorithm</p>";
	s += "<h2>Shortname: BVLS or SP</p>";
	s += "<p>This algorithm also known as Stark-Parker algorithm is a least squares variant with a bounded-variable constraint.</p>";
	s += "<p>In this implementation, the bounds are the bounds of the input image.</p>";
	s += "<p></p>";
	s += "<p>Reference: Stark and Parker, Computational Statistics <b>10</b>, 1995.</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMiller.java b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMiller.java
	index a4dfc20..350c3e2 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMiller.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMiller.java
	@@ -1,146 +1,151 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;
	import signal.factory.complex.ComplexSignalFactory;

	public class TikhonovMiller extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;
	private double lambda = 1.0;

	public TikhonovMiller(int iter, double gamma, double lambda) {
	super();
	controller.setIterationMax(iter);
	this.gamma = gamma;
	this.lambda = lambda;
	}

	@Override
	public RealSignal call() throws Exception {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta(gamma, H);
	ComplexSignal L = ComplexSignalFactory.laplacian(Y.nx, Y.ny, Y.nz);
	ComplexSignal L2 = Operations.multiplyConjugate(lambda*gamma, L, L);
	SignalCollector.free(L);
	A.minus(L2);
	SignalCollector.free(L2);
	ComplexSignal G = Operations.multiplyConjugate(gamma, H, Y);
	SignalCollector.free(H);
	SignalCollector.free(Y);
	ComplexSignal X = G.duplicate();
	while(!controller.ends(X)) {
	X.times(A);
	X.plus(G);
	}
	SignalCollector.free(A);
	SignalCollector.free(G);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);

	return x;
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3 + (controller.needSpatialComputation() ? 2 * controller.getIterationMax() : 0);
	}

	@Override
	public String getName() {
	- return "Tikhonov-Miller [TM]";
	+ return "Tikhonov-Miller";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"TM"};
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 10.0;
	}

	@Override
	public boolean isRegularized() {
	return true;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int)Math.round(params[0]));
	if (params.length > 1)
	gamma = (float)params[1];
	if (params.length > 2)
	lambda = (float)params[2];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {10, 1, 0.1};
	}

	@Override
	public double[] getParameters() {
	return new double[] {controller.getIterationMax(), gamma, lambda};
	}

	@Override
	public double getRegularizationFactor() {
	return lambda;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMillerPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMillerPanel.java
	index e41b095..8b5ef79 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMillerPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMillerPanel.java
	@@ -1,142 +1,146 @@
	/*
	* 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.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.RegularizationPanel;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;

	public class TikhonovMillerPanel extends AbstractAlgorithmPanel implements KeyListener, ActionListener, ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1, "#.#");
	private RegularizationPanel reg;

	private TikhonovMiller algo = new TikhonovMiller(10, 1, 0.1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	reg = new RegularizationPanel(params[2]);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);
	pn.place(2, 0, 5, 1, reg);

	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	- Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "step", spnStep, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	double gamma = spnStep.get();
	double lambda = reg.getValue();
	return spnIter.get() + " " + NumFormat.nice(gamma) + " " + NumFormat.nice(lambda);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	Command.command();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	reg.getSlider().removeChangeListener(this);
	reg.updateFromText();
	Command.command();
	reg.getSlider().addChangeListener(this);
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"TM"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	- s += "<p>Shortname: " + getShortname() + "</p>";
	+ String shortname = "<p>Shortname: ";
	+ for(String name : getShortnames())
	+ shortname += name + " ";
	+ s += shortname + "</p>";
	+
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilter.java b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilter.java
	index efce317..09cca2c 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilter.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilter.java
	@@ -1,178 +1,184 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;
	import signal.factory.complex.ComplexSignalFactory;

	public class TikhonovRegularizationInverseFilter extends AbstractAlgorithm implements Callable<RealSignal> {

	private double lambda = 0.1;

	public TikhonovRegularizationInverseFilter(double lambda) {
	super();
	this.lambda = lambda;
	}

	@Override
	public RealSignal call() {
	if (optimizedMemoryFootprint)
	return runOptimizedMemoryFootprint();
	else
	return runTextBook();
	}

	public RealSignal runTextBook() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal H2 = Operations.multiply(H, H);
	ComplexSignal I = ComplexSignalFactory.identity(Y.nx, Y.ny, Y.nz);
	I.times((float)lambda);
	ComplexSignal FA = Operations.add(H2, I);
	ComplexSignal FT = Operations.divideStabilized(H, FA);
	ComplexSignal X = Operations.multiply(Y, FT);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(FT);
	SignalCollector.free(Y);
	SignalCollector.free(H);
	SignalCollector.free(FA);
	SignalCollector.free(I);
	SignalCollector.free(H2);
	SignalCollector.free(X);
	return x;
	}

	public RealSignal runOptimizedMemoryFootprint() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal X = filter(Y, H);
	SignalCollector.free(H);
	SignalCollector.free(Y);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	private ComplexSignal filter(ComplexSignal Y, ComplexSignal H) {
	int nx = H.nx;
	int ny = H.ny;
	int nz = H.nz;
	int nxy = nx * ny*2;
	float ya, yb, ha, hb, fa, fb, mag, ta, tb;
	float epsilon2 = (float)(Operations.epsilon * Operations.epsilon);
	ComplexSignal result = new ComplexSignal("TRIF", nx, ny, nz);
	float l = (float)lambda;
	for(int k=0; k<nz; k++)
	for(int i=0; i< nxy; i+=2) {
	ha = H.data[k][i];
	hb = H.data[k][i+1];
	ya = Y.data[k][i];
	yb = Y.data[k][i+1];
	fa = haha - hbhb + l;
	fb = 2f * ha * hb;
	mag = fafa + fbfb;
	ta = (hafa + hbfb) / (mag >= epsilon2 ? mag : epsilon2);
	tb = (hbfa - hafb) / (mag >= epsilon2 ? mag : epsilon2);
	result.data[k][i] = yata - ybtb;
	result.data[k][i+1] = yatb + tayb;
	}
	return result;
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3;
	}

	@Override
	public String getName() {
	- return "Tikhonov Regularization [TRIF]";
	+ return "Tikhonov Regularization";
	}
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"TRIF"};
	+ }
	+

	@Override
	public double getMemoryFootprintRatio() {
	return 8.0;
	}

	@Override
	public boolean isRegularized() {
	return true;
	}

	@Override
	public boolean isStepControllable() {
	return false;
	}

	@Override
	public boolean isIterative() {
	return false;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	lambda = (float)params[0];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {0.1};
	}

	@Override
	public double[] getParameters() {
	return new double[] {lambda};
	}

	@Override
	public double getRegularizationFactor() {
	return lambda;
	}

	@Override
	public double getStepFactor() {
	return 0.0;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilterPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilterPanel.java
	index 55feebe..1f1ac0a 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilterPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilterPanel.java
	@@ -1,123 +1,123 @@
	/*
	* 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.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.RegularizationPanel;
	import deconvolutionlab.Config;

	public class TikhonovRegularizationInverseFilterPanel extends AbstractAlgorithmPanel implements ActionListener, ChangeListener, KeyListener {

	private RegularizationPanel reg;
	private TikhonovRegularizationInverseFilter algo = new TikhonovRegularizationInverseFilter(0.1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	reg = new RegularizationPanel(params[0]);
	GridPanel pn = new GridPanel(false);
	pn.place(0, 0, reg);

	- Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	+ Config.register("Algorithm." + algo.getShortnames()[0], "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	return pn;

	}

	@Override
	public String getCommand() {
	return NumFormat.nice(reg.getValue());
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	Command.command();
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	reg.getSlider().removeChangeListener(this);
	reg.updateFromText();
	Command.command();
	reg.getSlider().addChangeListener(this);
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"TRIF"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<h2>Shortname TRIF</h2>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/VanCittert.java b/DeconvolutionLab2/src/deconvolution/algorithm/VanCittert.java
	index 0985224..11c33fa 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/VanCittert.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/VanCittert.java
	@@ -1,140 +1,145 @@
	/*
	* 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.concurrent.Callable;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class VanCittert extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

	public VanCittert(int iter, double gamma) {
	super();
	controller.setIterationMax(iter);
	this.gamma = gamma;
	}

	@Override
	// VAnCitter algorithm
	// X(n+1) = X(n) + g(Y-HX(n))
	// => X(n+1) = X(n) - gHX(n) + g*Y
	// => X(n+1) = X(n) * (I-gH) + gY
	// => pre-compute: A = (I-gH) and G = gY
	// => Iteration : X(n+1) = X(n) * A + G with F(0) = G
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta1(gamma, H);
	SignalCollector.free(H);
	ComplexSignal G = Operations.multiply(gamma, Y);
	SignalCollector.free(Y);
	ComplexSignal X = G.duplicate();
	while(!controller.ends(X)) {
	X.times(A);
	X.plus(G);
	}
	SignalCollector.free(G);
	SignalCollector.free(A);
	RealSignal x = fft.inverse(X);
	SignalCollector.free(X);
	return x;
	}

	@Override
	public int getComplexityNumberofFFT() {
	return 3 + (controller.needSpatialComputation() ? 2 * controller.getIterationMax() : 0);
	}

	@Override
	public String getName() {
	- return "Van Cittert [VC]";
	+ return "Van Cittert";
	+ }
	+
	+ @Override
	+ public String[] getShortnames() {
	+ return new String[] {"VC"};
	}

	@Override
	public double getMemoryFootprintRatio() {
	return 8.0;
	}

	@Override
	public boolean isRegularized() {
	return false;
	}

	@Override
	public boolean isStepControllable() {
	return true;
	}

	@Override
	public boolean isIterative() {
	return true;
	}

	@Override
	public boolean isWaveletsBased() {
	return false;
	}

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	controller.setIterationMax((int)Math.round(params[0]));
	if (params.length > 1)
	gamma = (float)params[1];
	}

	@Override
	public double[] getDefaultParameters() {
	return new double[] {10, 1};
	}

	@Override
	public double[] getParameters() {
	return new double[] {controller.getIterationMax(), gamma};
	}
	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/VanCittertPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/VanCittertPanel.java
	index 499ebb5..fd2551c 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/VanCittertPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/VanCittertPanel.java
	@@ -1,106 +1,109 @@
	/*
	* 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 javax.swing.JPanel;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;

	public class VanCittertPanel extends AbstractAlgorithmPanel implements ChangeListener {

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1);

	private VanCittert algo = new VanCittert(10, 1);

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();

	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);

	- Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	- Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "iterations", spnIter, params[0]);
	+ Config.register("Algorithm." + algo.getShortnames()[0], "step", spnStep, params[1]);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

	@Override
	public String getCommand() {
	int iter = spnIter.get();
	double gamma = spnStep.get();
	return iter + " " + NumFormat.nice(gamma);
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	}

	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	- public String[] getShortname() {
	- return new String[] {"VC"};
	+ public String[] getShortnames() {
	+ return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	- s += "<p>Shortname: " + getShortname() + "</p>";
	+ String shortname = "<p>Shortname: ";
	+ for(String name : getShortnames())
	+ shortname += name + " ";
	+ s += shortname + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/modules/AlgorithmDModule.java b/DeconvolutionLab2/src/deconvolution/modules/AlgorithmDModule.java
	index 7983173..0415057 100644
	--- a/DeconvolutionLab2/src/deconvolution/modules/AlgorithmDModule.java
	+++ b/DeconvolutionLab2/src/deconvolution/modules/AlgorithmDModule.java
	@@ -1,153 +1,153 @@
	package deconvolution.modules;

	import javax.swing.JSplitPane;

	import bilib.component.HTMLPane;
	import bilib.table.CustomizedTable;
	import bilib.tools.NumFormat;
	import deconvolution.Deconvolution;
	import deconvolution.Features;
	import deconvolution.algorithm.AbstractAlgorithm;
	import deconvolution.algorithm.AbstractAlgorithmPanel;
	import deconvolution.algorithm.Algorithm;
	import deconvolution.algorithm.Controller;
	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.FFT;
	import signal.ComplexSignal;
	import signal.RealSignal;
	import signal.SignalCollector;

	public class AlgorithmDModule extends AbstractDModule implements Runnable {

	private CustomizedTable table;
	private HTMLPane doc;

	public AlgorithmDModule(Deconvolution deconvolution) {
	super(deconvolution);
	doc = new HTMLPane(100, 1000);
	table = new CustomizedTable(new String[] { "Features", "Values" }, false);
	split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, table.getPane(200, 200), doc.getPane());
	}

	public void update() {
	if (doc == null)
	return;
	if (table == null)
	return;

	table.removeRows();
	table.append(new String[] { "PSF", "Waiting for loading ..." });
	Thread thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	split.setDividerLocation(300);
	}

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

	@Override
	public void run() {
	Features features = new Features();

	if (deconvolution.algo == null) {
	features.add("Algorithm", "No valid algorithm");
	return;
	}
	AbstractAlgorithm algo = deconvolution.algo;
	doc.clear();
	- String name = algo.getShortname();
	+ String name = algo.getShortnames()[0];
	AbstractAlgorithmPanel algoPanel = Algorithm.getPanel(name);
	if (algoPanel != null)
	doc.append(algoPanel.getDocumentation());

	if (deconvolution.image == null) {
	startAsynchronousTimer("Open image", 200);
	deconvolution.image = deconvolution.openImage();
	stopAsynchronousTimer();
	}

	if (deconvolution.image == null) {
	features.add("Image", "No valid input image");
	return;
	}
	if (deconvolution.pad == null) {
	features.add("Padding", "No valid padding");
	return;
	}
	if (deconvolution.apo == null) {
	features.add("Apodization", "No valid apodization");
	return;
	}

	if (deconvolution.psf == null) {
	startAsynchronousTimer("Open PSF", 200);
	deconvolution.psf = deconvolution.openPSF();
	stopAsynchronousTimer();
	}

	if (deconvolution.psf == null) {
	features.add("Image", "No valid PSF");
	return;
	}

	Controller controller = deconvolution.algo.getController();
	if (controller == null) {
	features.add("Controller", "No valid controller");
	return;
	}

	startAsynchronousTimer("Run FFT", 200);
	deconvolution.algo.setController(controller);
	AbstractFFT f = FFT.getFastestFFT().getDefaultFFT();
	double Q = Math.sqrt(2);
	if (deconvolution.image != null) {
	int mx = deconvolution.image.nx;
	int my = deconvolution.image.ny;
	int mz = deconvolution.image.nz;

	while (mx * my * mz > Math.pow(2, 15)) {
	mx = (int)(mx / Q);
	my = (int)(my / Q);
	mz = (int)(mz / Q);
	}
	double N = deconvolution.image.nx * deconvolution.image.ny * deconvolution.image.nz;
	double M = mx * my * mz;
	double ratio = 1;
	if (M != 0)
	ratio = (N * Math.log(N)) / (M * Math.log(M));

	double chrono = System.nanoTime();
	RealSignal x = new RealSignal("test", mx, my, mz);
	ComplexSignal c = new ComplexSignal("test", mx, my, mz);
	f.init(Monitors.createDefaultMonitor(), mx, my, mz);
	f.transform(x, c);
	SignalCollector.free(x);
	SignalCollector.free(c);

	chrono = (System.nanoTime() - chrono);
	features.add("Tested on", mx + "x" + my + "x" + mz);
	features.add("Estimated Time on small", NumFormat.time(chrono) );

	chrono = chrono * ratio * algo.getComplexityNumberofFFT();

	int n = algo.isIterative() ? controller.getIterationMax() : 1;
	features.add("Estimated Time", NumFormat.time(chrono) );
	features.add("Estimated Number of FFT / Transform", ""+algo.getComplexityNumberofFFT());
	}
	else
	features.add("Estimated Time", "Error" );
	double mem = (algo.getMemoryFootprintRatio() * deconvolution.image.nx * deconvolution.image.ny * deconvolution.image.nz * 4);
	features.add("Estimated Memory", NumFormat.bytes(mem));
	features.add("Iterative", algo.isIterative() ? "" + controller.getIterationMax() : "Direct");

	table.removeRows();
	for (String[] feature : features)
	table.append(feature);
	stopAsynchronousTimer();
	}

	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/Lab.java b/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	index e1ce296..dd28e3f 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	@@ -1,379 +1,378 @@
	/*
	* 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 java.util.ArrayList;
	import java.util.regex.Pattern;

	import javax.swing.JDialog;
	import javax.swing.JFrame;
	import javax.swing.JPanel;

	import bilib.tools.NumFormat;
	import bilib.tools.WebBrowser;
	import deconvolutionlab.Imaging.ContainerImage;
	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.AbstractFFTLibrary;
	import fft.FFT;
	import imagej.IJImager;
	import plugins.sage.deconvolutionlab.IcyImager;
	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;
	import signal.factory.SignalFactory;
	import signal.factory.Sphere;

	public class Lab {

	private static Imaging imaging;
	private static ArrayList<JFrame> frames;
	private static ArrayList<JDialog> dialogs;

	static {
	frames = new ArrayList<JFrame>();
	dialogs = new ArrayList<JDialog>();
	imaging = new IJImager();
	Config.init(System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config");
	}

	public static Imaging.Platform getPlatform() {
	return imaging.getPlatform();
	}

	public static void init(Imaging.Platform p) {
	init(p, System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config");
	}

	public static void init(Imaging.Platform platform, String config) {
	switch (platform) {
	case IMAGEJ:
	imaging = new IJImager();
	break;
	case ICY:
	imaging = new IcyImager();
	break;
	default:
	imaging = new IJImager();
	break;
	}

	Config.init(System.getProperty("user.dir")+File.separator+"DeconvolutionLab2.config");
	}

	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 = library.getDefaultFFT();
	fft.init(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 ContainerImage createContainer(Monitors monitors, String title) {
	monitors.log("Create Live Real Signal " + title);
	return imaging.createContainer(title);
	}

	public static void append(Monitors monitors, ContainerImage container, RealSignal signal, String title) {
	imaging.append(container, signal, title, Imaging.Type.FLOAT);
	monitors.log("Add Live Real Signal " + title);
	}

	public static void append(Monitors monitors, ContainerImage container, RealSignal signal, String title, Imaging.Type type) {
	imaging.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);
	imaging.show(signal, title, ComplexComponent.MODULE);
	}

	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);
	imaging.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);
	imaging.show(signal, title, Imaging.Type.FLOAT, signal.nz / 2);
	}

	public static void show(Monitors monitors, RealSignal signal, String title, Imaging.Type type) {
	if (signal == null) {
	monitors.error("Show " + title + " this image does not exist.");
	return;
	}
	monitors.log("Show Real Signal " + title);
	imaging.show(signal, title, type, signal.nz / 2);
	}

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

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

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

	public static RealSignal createRealSignal(Monitors monitors, String arg, String cmd, String path) {

	RealSignal signal = null;
	if (arg.equalsIgnoreCase("synthetic")) {
	signal = SignalFactory.createFromCommand(cmd);
	}

	if (arg.equalsIgnoreCase("platform")) {
	signal = getImager().create(cmd);
	}

	if (arg.equalsIgnoreCase("file")) {
	File file = new File(path + File.separator + cmd);
	if (file != null) {
	if (file.isFile())
	signal = Lab.openFile(monitors, path + File.separator + cmd);
	}
	if (signal == null) {
	File local = new File(cmd);
	if (local != null) {
	if (local.isFile())
	signal = Lab.openFile(monitors, cmd);
	}
	}
	}

	if (arg.equalsIgnoreCase("dir") \|\| arg.equalsIgnoreCase("directory")) {
	File file = new File(path + File.separator + cmd);
	if (file != null) {
	if (file.isDirectory())
	signal = Lab.openDir(monitors, path + File.separator + cmd);
	}
	if (signal == null) {
	File local = new File(cmd);
	if (local != null) {
	if (local.isDirectory())
	signal = Lab.openDir(monitors, cmd);
	}
	}
	}
	return signal;
	}

	public static RealSignal openFile(Monitors monitors, String filename) {
	RealSignal signal = imaging.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 = imaging.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(file.getName(), 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;
	}
	imaging.show(signal.createOrthoview(hx, hy, hz), title, Imaging.Type.FLOAT, 0);
	}

	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;
	imaging.show(signal.createOrthoview(hx, hy, hz), title, Imaging.Type.FLOAT, 0);
	}

	public static void showMIP(Monitors monitors, RealSignal signal, String title) {
	if (signal == null) {
	monitors.error("Show MIP " + title + " this image does not exist.");
	return;
	}
	imaging.show(signal.createMIP(), title, Imaging.Type.FLOAT, 0);
	}

	public static void showMontage(Monitors monitors, RealSignal signal, String title) {
	if (signal == null) {
	monitors.error("Show Montage " + title + " this image does not exist.");
	return;
	}
	imaging.show(signal.createMontage(), title, Imaging.Type.FLOAT, 0);
	}

	public static RealSignal create(Monitors monitors, String name) {
	RealSignal signal = imaging.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 = imaging.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 Imaging getImager() {
	return imaging;
	}

	public static String getActiveImage() {
	if (imaging.isSelectable())
	return imaging.getSelectedImage();
	return "";
	}

	public static void setVisible(JDialog dialog, boolean modal) {
	if (dialog == null)
	return;
	dialogs.add(dialog);
	imaging.setVisible(dialog, modal);
	}

	public static void setVisible(JPanel panel, String name, int x, int y) {
	JFrame frame = new JFrame(name);
	frame.getContentPane().add(panel);
	frame.pack();
	frame.setLocation(x, y);
	frame.setVisible(true);
	frames.add(frame);
	}

	public static void setVisible(JFrame frame) {
	frames.add(frame);
	frame.setVisible(true);
	}

	public static void close() {
	for(JFrame frame : frames)
	if (frame != null)
	frame.dispose();
	for(JDialog dialog : dialogs)
	if (dialog != null)
	dialog.dispose();
	}




	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	index c61d1ba..0750aed 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	@@ -1,153 +1,153 @@
	/*
	* 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.CardLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.util.ArrayList;

	import javax.swing.BorderFactory;
	import javax.swing.BoxLayout;
	import javax.swing.JComboBox;
	import javax.swing.JPanel;
	import javax.swing.JScrollPane;
	import javax.swing.border.Border;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.HTMLPane;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolution.DeconvolutionDialog;
	import deconvolution.algorithm.AbstractAlgorithmPanel;
	import deconvolution.algorithm.Algorithm;
	import deconvolutionlab.Config;
	import deconvolutionlab.Lab;

	public class AlgorithmModule extends AbstractModule implements ActionListener, ChangeListener {

	private JComboBox<String> cmb;
	private HTMLPane doc;
	private JPanel cards;

	public AlgorithmModule(boolean expanded) {
	super("Algorithm", "-algorithm", "", "Check", expanded);
	ArrayList<AbstractAlgorithmPanel> deconv = Algorithm.getAvailableAlgorithms();
	for (AbstractAlgorithmPanel panel : deconv)
	cmb.addItem(panel.getName());
	cmb.addActionListener(this);
	}

	@Override
	public String getCommand() {
	String name = (String) cmb.getSelectedItem();
	AbstractAlgorithmPanel algo = Algorithm.getPanel(name);
	- String cmd = "-algorithm " + algo.getShortname()[0] + " " + algo.getCommand();
	+ String cmd = "-algorithm " + algo.getShortnames()[0] + " " + algo.getCommand();
	String synopsis = name;
	setSynopsis(synopsis);
	setCommand(cmd);
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {
	cmb = new JComboBox<String>();
	JPanel pnc = new JPanel();
	pnc.add(cmb);
	doc = new HTMLPane(100, 1000);
	cards = new JPanel(new CardLayout());
	ArrayList<AbstractAlgorithmPanel> panels = Algorithm.getAvailableAlgorithms();

	for (AbstractAlgorithmPanel panel : panels) {
	JScrollPane scroll = new JScrollPane(panel.getPanelParameters());
	scroll.setBorder(BorderFactory.createEmptyBorder());
	scroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
	scroll.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
	cards.add(panel.getName(), scroll);
	}
	cmb.setMaximumRowCount(panels.size());

	JPanel control = new JPanel();
	control.setLayout(new BoxLayout(control, BoxLayout.PAGE_AXIS));
	Border b1 = BorderFactory.createEtchedBorder();
	Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);
	control.setBorder(BorderFactory.createCompoundBorder(b1, b2));
	control.add(cmb);
	control.add(cards);

	doc.append("h1", "Documentation");

	JPanel panel = new JPanel(new BorderLayout());
	panel.add(control, BorderLayout.NORTH);
	panel.add(doc.getPane(), BorderLayout.CENTER);
	// cmb.addActionListener(this);
	getAction2Button().setToolTipText("Human readable of the command line");
	getAction2Button().addActionListener(this);
	Config.register(getName(), "algorithm", cmb, Algorithm.getDefaultAlgorithm());
	panel.setBorder(BorderFactory.createEtchedBorder());
	return panel;
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == cmb) {
	doc.clear();
	String name = (String) cmb.getSelectedItem();
	AbstractAlgorithmPanel algo = Algorithm.getPanel(name);
	doc.append(algo.getDocumentation());
	CardLayout cl = (CardLayout) (cards.getLayout());
	cl.show(cards, name);
	}
	if (e.getSource() == getAction2Button()) {
	Deconvolution deconvolution = new Deconvolution("Check Algorithm", Command.command());
	DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.ALGO, deconvolution, null, null);
	Lab.setVisible(d, false);
	}
	setSynopsis((String) cmb.getSelectedItem());
	setCommand(getCommand());
	Command.command();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	setSynopsis((String) cmb.getSelectedItem());
	setCommand(getCommand());
	Command.command();
	}

	@Override
	public void close() {
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	index 21ebb6f..b6eca9e 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	@@ -1,251 +1,251 @@
	/*
	* 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.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 bilib.component.HTMLPane;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolution.Token;
	import deconvolution.algorithm.AbstractAlgorithm;
	import deconvolutionlab.Config;

	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);
	}

	public String getJobName() {
	if (txt != null)
	return txt.getText();
	return "";
	}
	@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 BorderLayout());
	pn.add(cmb, BorderLayout.WEST);
	pn.add(txt, BorderLayout.CENTER);
	pn.add(gui, BorderLayout.EAST);

	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 run = gui.getSelectedIndex() == 0 ? " Run " : " Launch ";
	language.append("p", "java -jar DeconvolutionLab_2.jar " + run + Command.command());
	language.append("p", "");
	language.append("p", "java -cp JTransforms.jar:DeconvolutionLab_2.jar DeconvolutionLab2 "+ run + Command.command());
	}
	else if (cmb.getSelectedIndex() == 1) {
	language.clear();
	language.append("p", imagej(gui.getSelectedIndex() == 0));
	}
	else if (cmb.getSelectedIndex() == 2) {
	language.clear();
	language.append("p", java(gui.getSelectedIndex() == 0));
	}
	else if (cmb.getSelectedIndex() == 3) {
	language.clear();
	language.append("p", matlab());
	}
	}

	@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 matlab() {
	String job = txt.getText();

	String script = "";
	String cmd = Command.command();
	Deconvolution d = new Deconvolution("Matlab", cmd);
	String options = Command.extractOptions(cmd);
	AbstractAlgorithm algo = d.getAlgo();
	if (algo == null)
	return "ERROR";
	- String s = algo.getShortname();
	+ String s = algo.getShortnames()[0];
	String param = algo.getParametersAsString();
	script += p("% this function returns the deconvolved image as an 3D matrix");
	script += p("% image is a 3D matrix containing the image");
	script += p("% psf is a 3D matrix containing the PSF");

	script += p("function result = " + job + "(image, psf)");
	script += p1("% Install first DeconvolutionLab_2.jar into the java directory of Matlab");
	script += p1("javaaddpath([matlabroot filesep 'java' filesep 'DeconvolutionLab_2.jar'])");
	script += p1("% Run the deconvolution\n");
	script += p1("result = DL2." + s + "(image, psf, " + param +" , '" + options +"');");
	script += p("end");
	return script;
	}


	private String imagej(boolean headless) {
	String job = txt.getText();
	String macro = p("// Job: " + job + " ");
	macro += p("// Macro generated by DeconvolutionLab2 ");
	macro += p("// " + new SimpleDateFormat("dd/MM/yy HH:m:s").format(new Date()) + " ");
	String param = p("parameters = \"\" ");
	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() + "\" ");
	else if (token.keyword.equals("-psf"))
	psf = p("psf = \" -psf " + token.parameters.trim() + "\" ");
	else if (token.keyword.equals("-algorithm"))
	algo = p("algorithm = \" -algorithm " + token.parameters.trim() + "\" ");
	else
	param += p("parameters += \" " + token.keyword + " " + token.parameters.trim() + "\"");
	}

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

	return option + cmd;
	}


	private String java(boolean headless) {
	String job = txt.getText();
	String code = "";
	code += p("import deconvolution.Deconvolution;");
	code += p("import ij.plugin.PlugIn;");
	code += p("");

	code += p("public class DeconvolutionLab2_" + job + " implements PlugIn {");
	code += p1("public DeconvolutionLab2_" + job + "() {");

	String param = p2("String parameters = \"\";");
	ArrayList<Token> tokens = Command.parse(Command.command());
	String image = p2("String image = \" NOT DEFINED \";");
	String psf = p2("String psf = \" NOT DEFINED \";");
	String algo = p2("String algo = \" NOT DEFINED \";");
	for (Token token : tokens) {
	if (token.keyword.equals("-image"))
	image = p2("String image = \" -image " + token.parameters.trim() + "\";");
	else if (token.keyword.equals("-psf"))
	psf = p2("String psf = \" -psf " + token.parameters.trim() + "\";");
	else if (token.keyword.equals("-algorithm"))
	algo = p2("String algorithm = \" -algorithm " + token.parameters.trim() + "\";");
	else
	param += p2("parameters += \" " + token.keyword + " " + token.parameters.trim() + "\";");
	}
	code += image + psf + algo + param;
	code += p2("new Deconvolution(image + psf + algorithm + parameters)");
	code += p1("}");

	code += p1("");

	code += p1("@Override");
	code += p1("public void run(String arg0) {");
	code += p2(" new DeconvolutionLab2_" + job + "();");

	code += p1("}");
	code += p("}");
	return code;
	}

	private String p(String content) {
	return "<p>" + content + "</p>";
	}

	private String p1(String content) {
	return "<p style=\"padding-left:10px\">" + content + "</p>";
	}

	private String p2(String content) {
	return "<p style=\"padding-left:20px\">" + content + "</p>";
	}
	}

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