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	diff --git a/DeconvolutionLab2/DeconvolutionLab2.config b/DeconvolutionLab2/DeconvolutionLab2.config
	index 0341ed5..fa32aa7 100644
	--- a/DeconvolutionLab2/DeconvolutionLab2.config
	+++ b/DeconvolutionLab2/DeconvolutionLab2.config
	@@ -1,83 +1,84 @@
	#DeconvolutionLab2 [Beta 1]
	#DeconvolutionLab2 [Beta 1]
	-#Sun Feb 05 16:18:49 CET 2017
	+#Tue Feb 07 19:01:05 CET 2017
	Algorithm.FISTA.iterations=10
	Algorithm.FISTA.reg=0.1
	Algorithm.FISTA.scale=3
	Algorithm.FISTA.step=1.0
	Algorithm.FISTA.wavelets=Haar
	Algorithm.ICTM.iterations=10
	Algorithm.ICTM.reg=0.1
	Algorithm.ICTM.step=1.0
	Algorithm.ISTA.iterations=10
	Algorithm.ISTA.reg=0.1
	Algorithm.ISTA.scale=3
	Algorithm.ISTA.step=1.0
	Algorithm.ISTA.wavelets=Haar
	Algorithm.LW+.iterations=10
	Algorithm.LW+.step=1.0
	Algorithm.LW.iterations=10
	Algorithm.LW.step=1.0
	Algorithm.RIF.reg=0.1
	Algorithm.RL.iterations=10
	Algorithm.RLTV.reg=0.1
	Algorithm.SIM.gaussian.mean=0.0
	Algorithm.SIM.gaussian.stdev=1.0
	Algorithm.SIM.poisson=0.0
	Algorithm.TM.iterations=10
	Algorithm.TM.reg=0.1
	Algorithm.TM.step=1.0
	Algorithm.TRIF.reg=0.1
	Algorithm.VC.iterations=10
	Algorithm.VC.step=1.0
	-Algorithm.algorithm=Iterative Contraint Tikhonov-Miller
	+Algorithm.algorithm=Richardson-Lucy
	Border.apoxy=Uniform
	Border.apoz=Uniform
	Border.extxy=0
	Border.extz=0
	Border.normalization=1
	Border.padxy=None
	Border.padz=None
	Controller.constraint.enable=false
	Controller.constraint.snapshot=1
	Controller.constraint.value=No
	Controller.reference.enable=false
	Controller.reference.snapshot=1
	Controller.reference.value=
	Controller.residu.enable=false
	Controller.residu.snapshot=1
	Controller.residu.value=0.01
	Controller.savestats.enable=false
	Controller.savestats.snapshot=1
	Controller.savestats.value=Stats
	Controller.showstats.enable=false
	Controller.showstats.snapshot=1
	Controller.showstats.value=Stats
	DeconvolutionLab.MainDialog.location.h=608
	DeconvolutionLab.MainDialog.location.w=502
	-DeconvolutionLab.MainDialog.location.x=372
	-DeconvolutionLab.MainDialog.location.y=70
	+DeconvolutionLab.MainDialog.location.x=337
	+DeconvolutionLab.MainDialog.location.y=53
	Fourier.dim=XYZ
	Fourier.epsilon=1E-6
	Fourier.fft=Academic
	Image.image.row0=RandomLines;synthetic;RandomLines 100.0 0.0 300.0 size 300 300 32 ;null
	Image.image.row1=logo-h360.png;file;/Users/dsage/Desktop/logo-h360.png;null
	Image.image.row2=logo-psf.png;file;/Users/dsage/Desktop/logo-psf.png;null
	Image.image.selected=RandomLines;synthetic;RandomLines 100.0 0.0 300.0 size 300 300 32 ;null
	Language.headless=Run (Headless)
	Language.job=Job
	Language.language=Command line
	-PSF.psf.row0=AirySimulated;synthetic;AirySimulated 100.0 0.0 10.0 size 128 128 32 ;null
	-PSF.psf.row1=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;null
	-PSF.psf.row2=AirySimulated;synthetic;AirySimulated 100.0 0.0 10.0 10.0 size 128 128 32 ;null
	-PSF.psf.row3=Airy;synthetic;Airy 100.0 0.0 10.0 10.0 size 128 128 32 ;null
	-PSF.psf.row4=Airy;synthetic;Airy 100.0 0.0 1.0 size 128 128 32 ;null
	-PSF.psf.selected=AirySimulated;synthetic;AirySimulated 100.0 0.0 10.0 10.0 size 128 128 32 ;null
	+PSF.psf.row0=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;
	+PSF.psf.row1=AirySimulated;synthetic;AirySimulated 100.0 0.0 10.0 size 128 128 32 ;null
	+PSF.psf.row2=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;null
	+PSF.psf.row3=AirySimulated;synthetic;AirySimulated 100.0 0.0 10.0 10.0 size 128 128 32 ;null
	+PSF.psf.row4=Airy;synthetic;Airy 100.0 0.0 10.0 10.0 size 128 128 32 ;null
	+PSF.psf.row5=Airy;synthetic;Airy 100.0 0.0 1.0 size 128 128 32 ;null
	+PSF.psf.selected=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;
	Watcher.disable.console=false
	Watcher.disable.display=false
	Watcher.disable.multithreading=false
	Watcher.disable.table=false
	Watcher.path=/Users/dsage/git/deconvolution/DeconvolutionLab2
	Watcher.time.value=3600
	Watcher.time=No time limitation
	Watcher.verbose=Verbose\: log
	diff --git a/DeconvolutionLab2/src/TestRegex.java b/DeconvolutionLab2/src/TestRegex.java
	deleted file mode 100644
	index fcb071a..0000000
	--- a/DeconvolutionLab2/src/TestRegex.java
	+++ /dev/null
	@@ -1,23 +0,0 @@
	-import java.util.regex.Matcher;
	-import java.util.regex.Pattern;
	-
	-public class TestRegex {
	-
	- public static void main(String[] args) {
	- // TODO Auto-generated method stub
	- String c = "-image -image -- image image -image \t language -image";
	- String regex = "\bimage\b";
	- Pattern p = Pattern.compile(regex);
	-
	- // Check each entry of list to find the correct value
	- Matcher matcher = p.matcher(c);
	-
	- while (matcher.find())
	- {
	- System.out.print("Start index: " + matcher.start());
	- System.out.print(" End index: " + matcher.end() + " ");
	- System.out.println(matcher.group());
	- }
	- }
	-
	-}
	diff --git a/DeconvolutionLab2/src/deconvolution/Command.java b/DeconvolutionLab2/src/deconvolution/Command.java
	index 3ee918d..7c82eed 100644
	--- a/DeconvolutionLab2/src/deconvolution/Command.java
	+++ b/DeconvolutionLab2/src/deconvolution/Command.java
	@@ -1,286 +1,299 @@
	/*
	* 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 lab.tools.NumFormat;
	import signal.Constraint;
	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;
	import deconvolution.algorithm.AbstractAlgorithm;
	import deconvolution.algorithm.Algorithm;
	import deconvolution.algorithm.Controller;
	import deconvolutionlab.Output;
	import deconvolutionlab.Output.View;
	import deconvolutionlab.modules.AbstractModule;
	import deconvolutionlab.modules.CommandModule;
	import deconvolutionlab.modules.LanguageModule;
	import deconvolutionlab.monitor.ConsoleMonitor;
	import deconvolutionlab.monitor.Monitors;
	import deconvolutionlab.monitor.TableMonitor;

	public class Command {

	- public static String keywords[] = {
	- "-image", "-psf", "-algorithm",
	- "-path", "-disable", "-verbose", "-time",
	- "-constraint", "-residu", "-reference", "-savestats", "-showstats",
	- "-out", "-pad", "-apo", "-norm", "-fft"
	- };
	+ public static String keywords[] = { "-image", "-psf", "-algorithm", "-path", "-disable", "-verbose", "-time", "-constraint", "-residu", "-reference", "-savestats", "-showstats", "-out", "-pad", "-apo", "-norm", "-fft" };

	private static AbstractModule modules[];
	- private static CommandModule command;
	+ 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;
	}

	/**
	- * This methods first segments the command line, then create all the tokens of the command line
	+ * This methods first segments the command line, then create all the tokens
	+ * of the command line
	*
	- * @param command 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) {
	+ 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);
	+ }
	+
	+ /*
	for (int i = 0; i < segments.size(); i++) {
	CommandSegment segment = segments.get(i);
	String next = (i + 1 < segments.size() ? segments.get(i + 1).keyword : "");
	int end = (i + 1 < segments.size() ? segments.get(i + 1).index - next.length() : command.length());
	tokens.add(new Token(segment.keyword, command, segment.index, end));
	}
	+ */
	+
	return tokens;
	}

	public static Token extract(String command, String keyword) {
	ArrayList<Token> tokens = parse(command);
	- for(Token token : tokens)
	+ for (Token token : tokens)
	if (token.keyword.equalsIgnoreCase(keyword))
	return token;
	- return (Token)null;
	+ 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 key) {
	- int index = -1;
	+
	+ public static ArrayList<CommandSegment> findSegment(String command, String keyword) {
	ArrayList<CommandSegment> segments = new ArrayList<CommandSegment>();
	- do {
	- index = command.indexOf(key, index + 1);
	- if (index >= 0) {
	- segments.add(new CommandSegment(key, index + key.length()));
	- }
	+ String regex = "(?<!\\w)" + keyword + "(?!\\w)";
	+ Matcher matcher = Pattern.compile(regex).matcher(command);
	+
	+ while (matcher.find()) {
	+ segments.add(new CommandSegment(keyword, matcher.start()));
	+ System.out.println(" " + "," + matcher.end() + " " + matcher.group());
	}
	- while (index >= 0);
	+
	+ Collections.sort(segments);
	return segments;
	}
	-
	+ /*
	+ * public static ArrayList<CommandSegment> findSegment(String command,
	+ * String key) { int index = -1; ArrayList<CommandSegment> segments = new
	+ * ArrayList<CommandSegment>(); do { index = command.indexOf(key, index +
	+ * 1); if (index >= 0) { segments.add(new CommandSegment(key, index +
	+ * key.length())); } } while (index >= 0); return segments; }
	+ */

	public static AbstractAlgorithm decodeAlgorithm(Token token, Controller controller) {
	-
	+
	String option = token.option;

	AbstractAlgorithm algo = Algorithm.createAlgorithm(option);
	double params[] = parseNumeric(token.parameters);
	if (params != null) {
	algo.setParameters(params);
	if (algo.isIterative())
	controller.setIterationMax(algo.getController().getIterationMax());
	}
	-
	+
	if (algo.isWaveletsBased()) {
	- for(String wavelet : Wavelets.getWaveletsAsArray()) {
	+ for (String wavelet : Wavelets.getWaveletsAsArray()) {
	int pos = token.parameters.toLowerCase().indexOf(wavelet.toLowerCase());
	if (pos >= 0)
	- algo.setWavelets(wavelet);
	+ 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++) {
	+ for (int i = 0; i < Math.min(2, parts.length); i++) {
	if (parts[i].startsWith("@"))
	- freq = (int)NumFormat.parseNumber(parts[i], 0);
	+ 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) {
	-
	+
	int freq = 1;
	String line = token.parameters;
	if (token.parameters.startsWith("@")) {
	String parts[] = token.parameters.split(" ");
	if (parts.length >= 1) {
	- freq = (int)NumFormat.parseNumber(parts[0], 1);
	+ freq = (int) NumFormat.parseNumber(parts[0], 1);
	line = token.parameters.substring(parts[0].length(), token.parameters.length()).trim();
	}
	}

	if (token.keyword.equals("-constraint")) {
	controller.setConstraint(freq, Constraint.getByName(line.trim()));
	}
	-
	+
	else if (token.keyword.equals("-residu")) {
	double stop = NumFormat.parseNumber(line, -1);
	- controller.setResiduStop(freq, stop);
	+ controller.setResiduStop(freq, stop);
	}
	-
	+
	else if (token.keyword.equals("-reference")) {
	controller.setReference(freq, line);
	}

	else if (token.keyword.equals("-savestats")) {
	controller.setSaveStats(freq, line);
	}

	else if (token.keyword.equals("-showstats")) {
	controller.setShowStats(freq, line);
	}

	else if (token.keyword.equals("-time")) {
	double stop = NumFormat.parseNumber(line, Double.MAX_VALUE);
	controller.setTimeStop(stop);
	}
	}
	-
	+
	public static double decodeNormalization(Token token) {
	- if (token.parameters.toLowerCase().endsWith("no"))
	+ if (token.parameters.toLowerCase().endsWith("no"))
	return 0;
	else
	- return NumFormat.parseNumber(token.parameters, 1);
	+ return NumFormat.parseNumber(token.parameters, 1);
	}

	public static boolean decodeDisable(Token token, String word) {
	String p = token.parameters.toLowerCase();
	String parts[] = p.split(" ");
	- for(String part : parts) {
	+ for (String part : parts) {
	if (part.trim().equals(word))
	return false;
	}
	- return true;
	+ 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]);
	+ extXY = (int) Math.round(ext[0]);
	if (ext.length > 1)
	- extZ = (int)Math.round(ext[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);
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/dialog/LabDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/LabDialog.java
	index 75a8e26..5b8d8e8 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/LabDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/LabDialog.java
	@@ -1,368 +1,369 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.dialog;

	import java.awt.BorderLayout;
	import java.awt.Dimension;
	import java.awt.GridLayout;
	import java.awt.Point;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.ComponentEvent;
	import java.awt.event.ComponentListener;
	import java.awt.event.WindowEvent;
	import java.awt.event.WindowListener;
	import java.util.ArrayList;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JDialog;
	import javax.swing.JFrame;
	import javax.swing.JPanel;
	import javax.swing.JTabbedPane;
	import javax.swing.border.Border;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolution.DeconvolutionDialog;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	import deconvolutionlab.modules.AboutModule;
	import deconvolutionlab.modules.AbstractModule;
	import deconvolutionlab.modules.AlgorithmModule;
	import deconvolutionlab.modules.BatchModule;
	import deconvolutionlab.modules.BorderModule;
	import deconvolutionlab.modules.CommandModule;
	import deconvolutionlab.modules.ConfigModule;
	import deconvolutionlab.modules.ControllerModule;
	import deconvolutionlab.modules.FFTModule;
	import deconvolutionlab.modules.GroupedModulePanel;
	import deconvolutionlab.modules.ImageModule;
	import deconvolutionlab.modules.LanguageModule;
	import deconvolutionlab.modules.LicenceModule;
	import deconvolutionlab.modules.OutputModule;
	import deconvolutionlab.modules.PSFModule;
	import deconvolutionlab.modules.WatcherModule;
	import lab.component.JPanelImage;
	import lab.system.SystemPanel;

	public class LabDialog extends JDialog implements ComponentListener, ActionListener, ChangeListener, WindowListener {

	private JTabbedPane tab = new JTabbedPane();
	private JButton bnHelp = new JButton("Help");
	private JButton bnClose = new JButton("Close");
	private JButton bnQuit = new JButton("Quit");
	private JButton bnBatch = new JButton("Batch");
	private JButton bnRun = new JButton("Run");
	private JButton bnLaunch = new JButton("Launch");
	private JButton bnSystem = new JButton("System");

	private ImageModule image;
	private PSFModule psf;
	private AlgorithmModule algo;
	private AboutModule about;
	private LicenceModule licence;
	private OutputModule output;
	private FFTModule fourier;
	private BorderModule border;
	private ConfigModule config;
	private BatchModule batch;
	private LanguageModule language;
	private CommandModule command;
	private WatcherModule watcher;

	private ControllerModule controller;

	private GroupedModulePanel panelDeconv;
	private GroupedModulePanel panelAdvanc;
	private GroupedModulePanel panelScript;
	private GroupedModulePanel panelAbout;
	private AbstractModule modules[];

	public LabDialog() {
	super(new JFrame(), Constants.name);
	image = new ImageModule(false);
	psf = new PSFModule(false);
	algo = new AlgorithmModule(true);
	output = new OutputModule(true);
	fourier = new FFTModule(false);
	border = new BorderModule(false);
	controller = new ControllerModule(false);
	batch = new BatchModule(false);
	language = new LanguageModule(false);
	about = new AboutModule(true);
	licence = new LicenceModule(false);
	config = new ConfigModule(false);
	command = new CommandModule();
	watcher = new WatcherModule(false);

	doDialog();
	modules = new AbstractModule[] { image, psf, algo, output, controller, border, fourier, watcher, batch };

	Command.active(modules, command);
	Command.command();

	addWindowListener(this);
	addComponentListener(this);
	((GroupedModulePanel) tab.getSelectedComponent()).organize();
	setMinimumSize(new Dimension(500, 500));
	Config.registerFrame("DeconvolutionLab", "MainDialog", this);

	pack();
	setVisible(true);
	Config.load();
	sizeModule();
	Command.command();
	image.update();
	psf.update();
	output.update();
	}

	private void doDialog() {

	panelDeconv = new GroupedModulePanel(buildDeconvolutionPanel(), this);
	panelAdvanc = new GroupedModulePanel(buildAdvancedPanel(), this);
	panelScript = new GroupedModulePanel(buildProgrammingPanel(), this);
	panelAbout = new GroupedModulePanel(buildAboutPanel(), this);
	JPanelImage bottom = new JPanelImage("celegans.jpg");
	bottom.setLayout(new GridLayout(1, 7));
	Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);
	bottom.setBorder(b2);

	bottom.add(bnHelp);
	bottom.add(bnSystem);
	bottom.add(bnQuit);
	bottom.add(bnClose);
	bottom.add(bnBatch);
	bottom.add(bnRun);
	bottom.add(bnLaunch);

	tab.add("Deconvolution", panelDeconv);
	tab.add("Advanced", panelAdvanc);
	tab.add("Scripting", panelScript);
	tab.add("About", panelAbout);
	tab.addChangeListener(this);

	JPanel base = new JPanel(new BorderLayout());
	base.add(bottom, BorderLayout.CENTER);
	//base.add(statusBar, BorderLayout.SOUTH);
	//PanelImage pi = new PanelImage("logo.png", 380, 75);
	//pi.setPreferredSize(new Dimension(400, 75));
	//add(pi, BorderLayout.NORTH);
	add(tab, BorderLayout.CENTER);
	add(base, BorderLayout.SOUTH);

	bnBatch.addActionListener(this);
	bnRun.addActionListener(this);
	bnLaunch.addActionListener(this);
	bnClose.addActionListener(this);
	+ bnQuit.addActionListener(this);
	bnHelp.addActionListener(this);
	bnSystem.addActionListener(this);

	}

	@Override
	public void actionPerformed(ActionEvent e) {

	if (e.getSource() == bnHelp) {
	Lab.help();
	}
	else if (e.getSource() == bnSystem) {
	SystemPanel.show(400, 400);
	}
	else if (e.getSource() == bnClose) {
	Config.store();
	dispose();
	}
	- else if (e.getSource() == bnClose) {
	+ else if (e.getSource() == bnQuit) {
	dispose();
	}
	else if (e.getSource() == bnBatch) {
	tab.setSelectedIndex(2);
	batch.expand();
	sizeModule();
	new BatchDialog(batch);
	}
	else if (e.getSource() == bnLaunch) {
	new Deconvolution(Command.command()).launch("", false);
	}
	else if (e.getSource() == bnRun) {
	new Deconvolution(Command.command()).deconvolve(false);
	}
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	((GroupedModulePanel) tab.getSelectedComponent()).organize();
	Command.command();
	}

	private ArrayList<AbstractModule> buildDeconvolutionPanel() {
	ArrayList<AbstractModule> list = new ArrayList<AbstractModule>();
	list.add(image);
	list.add(psf);
	list.add(algo);
	list.add(watcher);
	return list;
	}

	private ArrayList<AbstractModule> buildAdvancedPanel() {
	ArrayList<AbstractModule> list = new ArrayList<AbstractModule>();
	list.add(output);
	list.add(controller);
	list.add(border);
	list.add(fourier);
	return list;
	}

	private ArrayList<AbstractModule> buildProgrammingPanel() {
	ArrayList<AbstractModule> list = new ArrayList<AbstractModule>();
	list.add(batch);
	list.add(command);
	list.add(language);
	return list;
	}

	private ArrayList<AbstractModule> buildAboutPanel() {
	ArrayList<AbstractModule> list = new ArrayList<AbstractModule>();
	list.add(about);
	list.add(licence);
	list.add(config);
	return list;
	}

	@Override
	public void windowOpened(WindowEvent e) {
	}

	@Override
	public void windowClosing(WindowEvent e) {
	Config.store();
	dispose();
	}

	@Override
	public void windowClosed(WindowEvent e) {
	}

	@Override
	public void windowIconified(WindowEvent e) {
	}

	@Override
	public void windowDeiconified(WindowEvent e) {
	}

	@Override
	public void windowActivated(WindowEvent e) {
	}

	@Override
	public void windowDeactivated(WindowEvent e) {
	}

	private void close() {
	for (AbstractModule module : modules)
	module.close();
	bnLaunch.removeActionListener(this);
	bnRun.removeActionListener(this);
	bnBatch.removeActionListener(this);
	bnClose.removeActionListener(this);
	bnHelp.removeActionListener(this);
	removeWindowListener(this);
	}

	@Override
	public void dispose() {
	super.dispose();
	if (Lab.getPlatform() == Platform.STANDALONE) System.exit(0);
	}

	@Override
	public void componentResized(ComponentEvent e) {
	sizeModule();
	}

	@Override
	public void componentMoved(ComponentEvent e) {
	Point p = this.getLocation();
	p.x += this.getWidth();
	DeconvolutionDialog.setLocationLaunch(p);
	}

	@Override
	public void componentShown(ComponentEvent e) {
	sizeModule();
	}

	@Override
	public void componentHidden(ComponentEvent e) {
	}

	public void sizeModule() {
	if (tab.getSelectedIndex() == 0) sizePanel(panelDeconv);
	if (tab.getSelectedIndex() == 1) sizePanel(panelAdvanc);
	if (tab.getSelectedIndex() == 2) sizePanel(panelScript);
	if (tab.getSelectedIndex() == 3) sizePanel(panelAbout);
	}

	private void sizePanel(GroupedModulePanel panel) {
	Dimension dim = getSize();
	int hpc = 60;
	int npc = hpc * panel.getModules().size();
	Dimension small = new Dimension(dim.width, hpc);
	Dimension large = new Dimension(dim.width, dim.height - npc);
	for (AbstractModule module : panel.getModules()) {
	if (module.isExpanded()) {
	module.setPreferredSize(large);
	module.setMaximumSize(large);
	module.setMinimumSize(small);
	module.getExpandedPanel().setPreferredSize(large);
	module.getExpandedPanel().setMaximumSize(large);
	module.getExpandedPanel().setMinimumSize(small);

	}
	else {
	module.setPreferredSize(small);
	module.setMaximumSize(small);
	module.setMinimumSize(small);
	module.getCollapsedPanel().setPreferredSize(small);
	module.getCollapsedPanel().setMaximumSize(small);
	module.getCollapsedPanel().setMinimumSize(small);
	}
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java
	index e68c434..81f4650 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java
	@@ -1,189 +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 deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.GridLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.MouseEvent;
	import java.awt.event.MouseListener;
	import java.util.ArrayList;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JPanel;
	import javax.swing.JToolBar;
	import javax.swing.ListSelectionModel;

	import deconvolution.Deconvolution;
	import deconvolutionlab.Constants;
	import lab.component.CustomizedColumn;
	import lab.component.CustomizedTable;

	public class BatchModule extends AbstractModule implements MouseListener, ActionListener {

	private CustomizedTable table;
	private JButton bnScript;
	private JButton bnRunAll;
	private JButton bnRunJob;
	private JButton bnLaunchAll;
	private JButton bnLaunchJob;

	public BatchModule(boolean expanded) {
	super("Batch", "", "", "", expanded);
	}

	@Override
	public String getCommand() {
	- return "DeconvolutionLab2 " + Constants.version;
	+ return "";
	}

	@Override
	public JPanel buildExpandedPanel() {

	bnScript = new JButton("Create Script (not yet implemented)");
	bnRunAll = new JButton("Run All Jobs");
	bnRunJob = new JButton("Run Selected Jobs");
	bnLaunchAll = new JButton("Launch All Jobs");
	bnLaunchJob = new JButton("Launch Selected Jobs");

	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Job", String.class, 120, false));
	columns.add(new CustomizedColumn("Command", String.class, Constants.widthGUI, false));
	columns.add(new CustomizedColumn("", String.class, 30, "\u232B", "Delete this job"));

	table = new CustomizedTable(columns, true);
	table.getColumnModel().getColumn(2).setMaxWidth(30);
	table.getColumnModel().getColumn(2).setMinWidth(30);
	table.addMouseListener(this);
	table.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);

	JToolBar pn = new JToolBar("Controls Batch");
	pn.setBorder(BorderFactory.createEmptyBorder());
	pn.setLayout(new GridLayout(1, 5));
	pn.setFloatable(false);
	pn.add(bnScript);
	pn.add(bnRunAll);
	pn.add(bnRunJob);
	pn.add(bnLaunchAll);
	pn.add(bnLaunchJob);

	JPanel panel = new JPanel(new BorderLayout());
	panel.add(table.getPane(100, 100), BorderLayout.CENTER);
	panel.add(pn, BorderLayout.SOUTH);
	getAction1Button().addActionListener(this);

	bnScript.addActionListener(this);
	bnRunAll.addActionListener(this);
	bnRunJob.addActionListener(this);
	bnLaunchAll.addActionListener(this);
	bnLaunchJob.addActionListener(this);
	return panel;
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnRunJob) {
	int rows[] = table.getSelectedRows();
	for (int row : rows) {
	new Deconvolution(table.getCell(row, 1)).deconvolve(false);
	}
	}
	else if (e.getSource() == bnLaunchJob) {
	int rows[] = table.getSelectedRows();
	for (int row : rows) {
	new Deconvolution(table.getCell(row, 1)).launch(table.getCell(row, 0), false);
	}
	}
	else if (e.getSource() == bnRunAll) {
	for (int row = 0; row < table.getRowCount(); row++) {
	new Deconvolution(table.getCell(row, 1)).deconvolve(false);
	}
	}
	else if (e.getSource() == bnLaunchAll) {
	for (int row = 0; row < table.getRowCount(); row++) {
	new Deconvolution(table.getCell(row, 1)).launch(table.getCell(row, 0), false);
	}
	}
	}

	private void update() {
	setSynopsis("" + table.getRowCount() + " jobs");
	}

	public int getCountJob() {
	return table.getRowCount();
	}

	public void addJob(String name, String command) {
	table.append(new String[] { name, command, "" });
	update();
	}

	@Override
	public void mouseClicked(MouseEvent e) {
	if (e.getSource() == table) {
	int row = table.getSelectedRow();
	if (row < 0)
	return;
	if (table.getSelectedColumn() == 2) {
	table.removeRow(row);
	if (table.getRowCount() > 0)
	table.setRowSelectionInterval(0, 0);
	}
	}
	update();
	}

	@Override
	public void mousePressed(MouseEvent e) {
	}

	@Override
	public void mouseReleased(MouseEvent e) {
	}

	@Override
	public void mouseEntered(MouseEvent e) {
	}

	@Override
	public void mouseExited(MouseEvent e) {
	}

	@Override
	public void close() {
	getAction1Button().removeActionListener(this);
	}
	}

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