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	diff --git a/DeconvolutionLab2/.classpath b/DeconvolutionLab2/.classpath
	index 5aa6316..da27baf 100644
	--- a/DeconvolutionLab2/.classpath
	+++ b/DeconvolutionLab2/.classpath
	@@ -1,9 +1,9 @@
	<?xml version="1.0" encoding="UTF-8"?>
	<classpath>
	<classpathentry kind="src" path="src"/>
	<classpathentry kind="var" path="ICY_HOME/icy.jar"/>
	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
	<classpathentry kind="lib" path="ij"/>
	- <classpathentry kind="lib" path="lib/JTransforms.jar"/>
	+ <classpathentry kind="lib" path="lib/jtransforms.jar"/>
	<classpathentry kind="output" path="bin"/>
	</classpath>
	diff --git a/DeconvolutionLab2/DeconvolutionLab2.config b/DeconvolutionLab2/DeconvolutionLab2.config
	index 06d248e..47aa668 100644
	--- a/DeconvolutionLab2/DeconvolutionLab2.config
	+++ b/DeconvolutionLab2/DeconvolutionLab2.config
	@@ -1,63 +1,81 @@
	#DeconvolutionLab2 [Beta 2]
	#DeconvolutionLab2 [Beta 2]
	-#Sat Mar 18 22:03:52 CET 2017
	-Algorithm.I.gaussian.mean=0.0
	-Algorithm.I.gaussian.stdev=1.0
	-Algorithm.I.iterations=10
	-Algorithm.I.poisson=0.0
	-Algorithm.I.reg=0.1
	-Algorithm.I.scale=3
	-Algorithm.I.step=1.0
	-Algorithm.I.wavelets=Haar
	-Algorithm.algorithm=Landweber [LW \|\u00A0LLS]
	+#Mon Mar 20 09:47:20 CET 2017
	+Algorithm.BVLS.iterations=10
	+Algorithm.BVLS.step=1.0
	+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.NNLS.iterations=10
	+Algorithm.NNLS.step=1.0
	+Algorithm.RIF.reg=0.1
	+Algorithm.RL.iterations=10
	+Algorithm.RLTV.reg=1.000E-18
	+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=Fast Iterative Shrinkage-Thresholding [FISTA]
	Border.apoxy=Hamming
	Border.apoz=Uniform
	Border.extxy=1
	Border.extz=0
	Border.padxy=None
	Border.padz=None
	Computation.dim=XYZ
	Computation.epsilon=1E-6
	Computation.fft=Fastest
	Computation.normalization=1
	Controller.constraint.enable=false
	Controller.constraint.value=no
	Controller.itmax.enable=true
	Controller.reference.enable=false
	Controller.reference.value=
	Controller.residu.enable=false
	Controller.residu.value=0.01
	Controller.time.enable=false
	Controller.time.value=3600
	-DeconvolutionLab.MainDialog.location.h=597
	+DeconvolutionLab.MainDialog.location.h=780
	DeconvolutionLab.MainDialog.location.w=500
	-DeconvolutionLab.MainDialog.location.x=72
	-DeconvolutionLab.MainDialog.location.y=33
	-Image.image.row0=Cell7.tif;file;/Users/dsage/Desktop/Maria Azevedo/Cell7.tif;null
	+DeconvolutionLab.MainDialog.location.x=141
	+DeconvolutionLab.MainDialog.location.y=51
	+Image.image.row0=active;platform;active;\u232B
	Image.image.row1=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
	-Image.image.row2=DoG;synthetic;DoG 100.0 0.0 3.0 35.0 size 128 128 32 ;\u232B
	+Image.image.row2=Applications;directory;/users/dsage/Applications;\u232B
	Image.image.row3=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
	-Image.image.row4=RandomLines;synthetic;RandomLines 100.0 0.0 300.0 size 512 512 32 ;\u232B
	-Image.image.row5=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
	-Image.image.row6=Applications;platform;Applications;\u232B
	-Image.image.row7=Applications;directory;/users/dsage/Applications;\u232B
	-Image.image.row8=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
	-Image.image.row9=lib;directory;/Users/dsage/git/deconvolution/DeconvolutionLab2/lib;\u232B
	-Image.image.selected=Cell7.tif;file;/Users/dsage/Desktop/Maria Azevedo/Cell7.tif;null
	+Image.image.row4=lib;directory;/Users/dsage/git/deconvolution/DeconvolutionLab2/lib;\u232B
	+Image.image.selected=active;platform;active;\u232B
	Language.headless=Run (Headless)
	Language.job=Job
	-Language.language=Command line
	+Language.language=Java
	Output.output.row0=ortho;OR2;;;;\u2713;\u2713;\u232B
	Output.output.selected=ortho;OR2;;;;\u2713;\u2713;\u232B
	PSF.psf.row0=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;null
	PSF.psf.row1=Chrome Apps.localized;directory;/users/dsage/applications/Chrome Apps.localized;\u232B
	PSF.psf.row2=FI1.tif;file;/Users/dsage/git/deconvolution/DeconvolutionLab2/FI1.tif;\u232B
	PSF.psf.selected=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;null
	Running.Directory=/Users/dsage/Applications
	Running.Display=no
	Running.Monitor=console table
	Running.Multithreading=yes
	Running.Path=specify
	Running.Stats=show
	Running.System=no
	Running.Verbose=log
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_JavaCoding.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_JavaCoding.java
	index 2a46496..91bb4ca 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_JavaCoding.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_JavaCoding.java
	@@ -1,68 +1,67 @@
	/*
	* 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.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" + File.separator;

	public DeconvolutionLab2_JavaCoding() {
	String path = desktop + "Deconvolution" + File.separator + "data" + File.separator + "bars" + File.separator;
	- Monitors monitors = new Monitors();
	+ Monitors monitors = Monitors.createDefaultMonitor();
	RealSignal image = Lab.openFile(monitors, path + "bars.tif");
	RealSignal psf = Lab.openFile(monitors, path + "psf.tif");
	-
	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/Deconvolution.java b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	index 283126e..35cce6f 100644
	--- a/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	+++ b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	@@ -1,553 +1,595 @@
	/*
	* 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.factory.SignalFactory;
	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.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);

	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.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);
	+ image = 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);
	+ psf = createRealSignal(monitors, arg, cmd, path);
	return psf;
	}

	+ private static RealSignal createRealSignal(Monitors monitors, String arg, String cmd, String path) {
	+ RealSignal signal = null;
	+ if (arg.equalsIgnoreCase("synthetic")) {
	+ signal = Lab.createSynthetic(monitors, cmd);
	+ }
	+
	+ if (arg.equalsIgnoreCase("platform")) {
	+ signal = Lab.getImage(monitors, 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 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/FISTA.java b/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	index 2947d54..2454d9f 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	@@ -1,188 +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]";
	+ return "Fast Iterative Shrinkage-Thresholding";
	}

	@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 a94a846..ca37acf 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/FISTAPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/FISTAPanel.java
	@@ -1,167 +1,166 @@
	/*
	* 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.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[] getShortnames() {
	return algo.getShortnames();
	}

	@Override
	public String getDocumentation() {
	String s = "";
	- s += "<h1>" + getName() + "</h1>";
	- s += "<h2>Shortname: FISTA</h2>";
	+ s += "<h1>" + getName() + " (FISTA)</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></p>";
	s += "<h3>Reference: Beck and Teboulle, SIAM <b>2</b> 2009</h3>";
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java b/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	index 12217dc..e041133 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	@@ -1,180 +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]";
	+ return "Iterative Shrinkage-Thresholding";
	}

	@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/deconvolutionlab/Lab.java b/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	index dd28e3f..44433ba 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/Lab.java
	@@ -1,378 +1,354 @@
	/*
	* 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);
	- }
	- }
	- }
	+ public static RealSignal createSynthetic(Monitors monitors, String cmd) {
	+ RealSignal signal = SignalFactory.createFromCommand(cmd);
	+ if (signal == null)
	+ monitors.error("Unable to create " + cmd);
	+ else
	+ monitors.log("Create " + cmd);
	+ return signal;
	+ }
	+
	+ public static RealSignal getImage(Monitors monitors, String name) {
	+ RealSignal signal = getImager().create(name);
	+ if (signal == null)
	+ monitors.error("Unable to get " + name);
	+ else
	+ monitors.log("Load " + name);
	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 0750aed..62230dc 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	@@ -1,153 +1,155 @@
	/*
	* 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.getShortnames()[0] + " " + algo.getCommand();
	- String synopsis = name;
	+ String synopsis = algo.getShortnames()[0] + " " + algo.getCommand();
	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));
	+ cards.setBorder(BorderFactory.createEtchedBorder());
	+
	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/monitor/Message.java b/DeconvolutionLab2/src/deconvolutionlab/monitor/Message.java
	index 8d3ced9..5c54494 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/monitor/Message.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/monitor/Message.java
	@@ -1,82 +1,85 @@
	/*
	* 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.monitor;

	import bilib.tools.NumFormat;
	import deconvolutionlab.system.SystemUsage;

	public class Message {

	private static long id = 0;
	private double chrono;
	private String mem;
	private Verbose level;
	private String message;
	private double progress;

	public Message(Verbose level, String message, double chrono, double progress) {
	id = id+1;
	this.chrono = chrono;
	this.mem = SystemUsage.getMemoryMB();
	this.message = message;
	this.level = level;
	this.progress = progress;
	}

	public long getID() {
	return id;
	}

	public String getMessage() {
	return message;
	}

	public Verbose getLevel() {
	return level;
	}

	public double getProgress() {
	return progress;
	}

	public String formatProgress() {
	return NumFormat.time(chrono) + " \t " + message + " (" + progress + "%)";
	}

	public String formatTab() {
	- return level.name() + " \t " + NumFormat.time(chrono) + " \t " + mem + " \t " + message;
	+ if (level.name().equalsIgnoreCase("quiet"))
	+ return "Error" + " \t " + NumFormat.time(chrono) + " \t " + mem + " \t " + message;
	+ else
	+ return "Log " + " \t " + NumFormat.time(chrono) + " \t " + mem + " \t " + message;
	}

	public String[] formatArray() {
	return new String[] {NumFormat.time(chrono), mem, message};
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/monitor/Monitors.java b/DeconvolutionLab2/src/deconvolutionlab/monitor/Monitors.java
	index 0db6c4c..6d18f26 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/monitor/Monitors.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/monitor/Monitors.java
	@@ -1,100 +1,100 @@
	/*
	* 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.monitor;

	import java.util.ArrayList;

	public class Monitors extends ArrayList<AbstractMonitor> {

	private double start;
	private Verbose verbose;
	private double progress;

	public Monitors() {
	super();
	start = System.nanoTime();
	verbose = Verbose.Log;
	progress = 0;
	}

	public void setVerbose(Verbose v) {
	verbose = v;
	}

	public Verbose getVerbose() {
	return verbose;
	}

	public static Monitors createDefaultMonitor() {
	Monitors monitors = new Monitors();
	monitors.add(new ConsoleMonitor());
	return monitors;
	}

	public static Monitors create(AbstractMonitor monitor) {
	Monitors monitors = new Monitors();
	monitors.add(new ConsoleMonitor());
	monitors.add(monitor);
	return monitors;
	}

	public void detail(String msg) {
	if (verbose.ordinal() >= Verbose.Prolix.ordinal())
	sendMessage(new Message(Verbose.Prolix, msg, System.nanoTime() - start, 0));
	}

	public void progress(String msg, double p) {
	progress = Math.max(0, Math.min(100, p));
	sendProgress(new Message(Verbose.Prolix, msg, System.nanoTime() - start, progress));
	}

	public void log(String msg) {
	if (verbose.ordinal() >= Verbose.Log.ordinal())
	sendMessage(new Message(Verbose.Log, msg, System.nanoTime() - start, progress));
	}

	public void error(String msg) {
	if (verbose.ordinal() >= Verbose.Quiet.ordinal())
	sendMessage(new Message(Verbose.Quiet, msg, System.nanoTime() - start, 0));
	}

	private void sendMessage(Message message) {
	for (AbstractMonitor monitor : this)
	- monitor.add(message);
	+ monitor.add(message);
	}

	private void sendProgress(Message message) {
	for (AbstractMonitor monitor : this)
	if (monitor instanceof StatusMonitor)
	monitor.add(message);
	}
	}
	diff --git a/DeconvolutionLab2/src/fft/jtransforms/JTransforms.java b/DeconvolutionLab2/src/fft/jtransforms/JTransforms.java
	index 98f47b4..ff5719b 100644
	--- a/DeconvolutionLab2/src/fft/jtransforms/JTransforms.java
	+++ b/DeconvolutionLab2/src/fft/jtransforms/JTransforms.java
	@@ -1,89 +1,89 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package fft.jtransforms;

	+import signal.ComplexSignal;
	+import signal.RealSignal;
	import deconvolutionlab.monitor.Monitors;
	-import org.jtransforms.fft.FloatFFT_2D;
	-import org.jtransforms.fft.FloatFFT_3D;
	+import edu.emory.mathcs.jtransforms.fft.FloatFFT_2D;
	+import edu.emory.mathcs.jtransforms.fft.FloatFFT_3D;
	import fft.AbstractFFT;
	import fft.Separability;
	-import signal.ComplexSignal;
	-import signal.RealSignal;

	public class JTransforms extends AbstractFFT {

	private FloatFFT_3D fftXYZ = null;
	private FloatFFT_2D fftXY = null;

	public JTransforms() {
	super(Separability.XYZ);
	}

	@Override
	public void init(Monitors monitors, int nx, int ny, int nz) {
	super.init(monitors, nx, ny, nz);
	try {
	if (nz > 1)
	fftXYZ = new FloatFFT_3D(nz, ny, nx);
	else
	fftXY = new FloatFFT_2D(ny, nx);
	}
	catch (Exception ex) {
	System.out.println("check " + ex + ". " + nx + " " + ny + " " + nz);
	}
	}

	@Override
	public void transformInternal(RealSignal x, ComplexSignal X) {
	float[] interleave = x.getInterleaveXYZAtReal();
	if (fftXYZ != null)
	fftXYZ.complexForward(interleave);
	if (fftXY != null)
	fftXY.complexForward(interleave);
	X.setInterleaveXYZ(interleave);
	}

	@Override
	public void inverseInternal(ComplexSignal X, RealSignal x) {
	float[] interleave = X.getInterleaveXYZ();
	if (fftXYZ != null)
	fftXYZ.complexInverse(interleave, true);
	if (fftXY != null)
	fftXY.complexInverse(interleave, true);
	x.setInterleaveXYZAtReal(interleave);
	}

	@Override
	public String getName() {
	return "JTransforms";
	}
	}
	diff --git a/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XYZ.java b/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XYZ.java
	index 5982742..da8d8c6 100644
	--- a/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XYZ.java
	+++ b/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XYZ.java
	@@ -1,89 +1,89 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package fft.jtransforms;

	+import signal.ComplexSignal;
	+import signal.RealSignal;
	import deconvolutionlab.monitor.Monitors;
	-import org.jtransforms.fft.FloatFFT_2D;
	-import org.jtransforms.fft.FloatFFT_3D;
	+import edu.emory.mathcs.jtransforms.fft.FloatFFT_2D;
	+import edu.emory.mathcs.jtransforms.fft.FloatFFT_3D;
	import fft.AbstractFFT;
	import fft.Separability;
	-import signal.ComplexSignal;
	-import signal.RealSignal;

	public class JTransformsFFT_XYZ extends AbstractFFT {

	private FloatFFT_3D fftXYZ = null;
	private FloatFFT_2D fftXY = null;

	public JTransformsFFT_XYZ() {
	super(Separability.XYZ);
	}

	@Override
	public void init(Monitors monitors, int nx, int ny, int nz) {
	super.init(monitors, nx, ny, nz);
	try {
	if (nz > 1)
	fftXYZ = new FloatFFT_3D(nz, ny, nx);
	else
	fftXY = new FloatFFT_2D(ny, nx);
	}
	catch (Exception ex) {
	System.out.println("check " + ex + ". " + nx + " " + ny + " " + nz);
	}
	}

	@Override
	public void transformInternal(RealSignal x, ComplexSignal X) {
	float[] interleave = x.getInterleaveXYZAtReal();
	if (fftXYZ != null)
	fftXYZ.complexForward(interleave);
	if (fftXY != null)
	fftXY.complexForward(interleave);
	X.setInterleaveXYZ(interleave);
	}

	@Override
	public void inverseInternal(ComplexSignal X, RealSignal x) {
	float[] interleave = X.getInterleaveXYZ();
	if (fftXYZ != null)
	fftXYZ.complexInverse(interleave, true);
	if (fftXY != null)
	fftXY.complexInverse(interleave, true);
	x.setInterleaveXYZAtReal(interleave);
	}

	@Override
	public String getName() {
	return "JTransforms XYZ";
	}
	}
	diff --git a/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XY_Z.java b/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XY_Z.java
	index 8403988..5f02651 100644
	--- a/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XY_Z.java
	+++ b/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XY_Z.java
	@@ -1,103 +1,102 @@
	/*
	* 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 fft.jtransforms;

	-import org.jtransforms.fft.FloatFFT_1D;
	-import org.jtransforms.fft.FloatFFT_2D;
	-
	+import signal.ComplexSignal;
	+import signal.RealSignal;
	import deconvolutionlab.monitor.Monitors;
	+import edu.emory.mathcs.jtransforms.fft.FloatFFT_1D;
	+import edu.emory.mathcs.jtransforms.fft.FloatFFT_2D;
	import fft.AbstractFFT;
	import fft.Separability;
	-import signal.ComplexSignal;
	-import signal.RealSignal;

	public class JTransformsFFT_XY_Z extends AbstractFFT {

	private FloatFFT_2D fftXY = null;
	private FloatFFT_1D fftZ = null;

	public JTransformsFFT_XY_Z() {
	super(Separability.XY_Z);
	}

	@Override
	public void init(Monitors monitors, int nx, int ny, int nz) {
	super.init(monitors, nx, ny, nz);
	try {
	fftXY = new FloatFFT_2D(ny, nx);
	if (nz > 1)
	fftZ = new FloatFFT_1D(nz);
	}
	catch (Exception ex) {
	}
	}

	@Override
	public void transformInternal(RealSignal x, ComplexSignal X) {
	for (int k = 0; k < nz; k++) {
	float interleave[] = x.getInterleaveXYAtReal(k);
	fftXY.complexForward(interleave);
	X.setInterleaveXY(k, interleave);
	}
	if (fftZ == null)
	return;
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	float interleave[] = X.getInterleaveZ(i, j);
	fftZ.complexForward(interleave);
	X.setInterleaveZ(i, j, interleave);
	}
	}

	@Override
	public void inverseInternal(ComplexSignal X, RealSignal x) {
	for (int k = 0; k < nz; k++) {
	float interleave[] = X.getInterleaveXY(k);
	fftXY.complexInverse(interleave, true);
	X.setInterleaveXY(k, interleave);
	}
	if (fftZ != null) {
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	float interleave[] = X.getInterleaveZ(i, j);
	fftZ.complexInverse(interleave, true);
	X.setInterleaveZ(i, j, interleave);
	}
	}
	x = X.getRealSignal();
	}

	@Override
	public String getName() {
	return "JTransforms XY_Z";
	}
	}
	diff --git a/DeconvolutionLab2/src/imagej/IJImager.java b/DeconvolutionLab2/src/imagej/IJImager.java
	index 88caaaf..e20549c 100644
	--- a/DeconvolutionLab2/src/imagej/IJImager.java
	+++ b/DeconvolutionLab2/src/imagej/IJImager.java
	@@ -1,348 +1,350 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package imagej;

	import java.awt.BorderLayout;
	import java.awt.Dimension;
	import java.awt.GridLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.WindowEvent;
	import java.awt.event.WindowListener;

	import javax.swing.BorderFactory;
	import javax.swing.DefaultListModel;
	import javax.swing.JButton;
	import javax.swing.JDialog;
	import javax.swing.JFrame;
	import javax.swing.JLabel;
	import javax.swing.JList;
	import javax.swing.JPanel;
	import javax.swing.JScrollPane;
	import javax.swing.ListSelectionModel;

	import deconvolutionlab.Imaging;
	import ij.ImagePlus;
	import ij.ImageStack;
	import ij.WindowManager;
	import ij.gui.GUI;
	import ij.io.FileSaver;
	import ij.io.Opener;
	import ij.process.FloatProcessor;
	import ij.process.ImageProcessor;
	import signal.ComplexComponent;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class IJImager extends Imaging {

	@Override
	public Platform getPlatform() {
	return Imaging.Platform.IMAGEJ;
	}

	@Override
	public void setVisible(JDialog dialog, boolean modal) {
	if (modal) {
	dialog.setModal(modal);
	GUI.center(dialog);
	}
	dialog.pack();
	dialog.setVisible(true);
	}

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

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

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

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

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

	public ContainerImage createContainer(String title) {
	return new ContainerImage();
	}

	@Override
	public void append(ContainerImage container, RealSignal signal, String title, Imaging.Type type) { ImagePlus cont = (ImagePlus) container.object;
	if (container.object == null) {
	ImageStack stack = new ImageStack(signal.nx, signal.ny);
	stack.addSlice(build(signal, type).getProcessor());
	stack.addSlice(build(signal, type).getProcessor());
	container.object = new ImagePlus(title, stack);
	((ImagePlus)container.object).show();
	}
	else {
	cont.getStack().addSlice(build(signal, type).getProcessor());
	cont.setSlice(cont.getStack().getSize());
	cont.updateAndDraw();
	cont.getProcessor().resetMinAndMax();
	}
	}

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

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

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

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

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

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

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

	@Override
	public String getSelectedImage() {
	Dialog dialog = new Dialog();
	dialog.setVisible(true);
	if (dialog.wasCancel())
	return "";
	return dialog.getName();
	}

	public class Dialog extends JDialog implements ActionListener, WindowListener {

	private JList<String> list;
	private JButton bnOK = new JButton("OK");
	private JButton bnCancel = new JButton("Cancel");
	private boolean cancel = false;
	private String name = "";

	public Dialog() {
	super(new JFrame(), "Image Selection");

	JPanel bn = new JPanel(new GridLayout(1, 2));
	bn.add(bnCancel);
	bn.add(bnOK);

	JPanel panel = new JPanel(new BorderLayout());
	int[] ids = WindowManager.getIDList();

	if (ids != null) {
	DefaultListModel listModel = new DefaultListModel();
	list = new JList(listModel);
	for (int id : ids) {
	ImagePlus idp = WindowManager.getImage(id);
	if (idp != null) {
	((DefaultListModel) listModel).addElement(idp.getTitle());
	}
	}
	list.setSelectionMode(ListSelectionModel.SINGLE_INTERVAL_SELECTION);
	JScrollPane listScroller = new JScrollPane(list);
	listScroller.setPreferredSize(new Dimension(250, 80));
	panel.add(listScroller, BorderLayout.CENTER);
	}
	else {
	panel.add(new JLabel("No open images."));
	}
	panel.add(bn, BorderLayout.SOUTH);
	panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
	bnOK.addActionListener(this);
	bnCancel.addActionListener(this);
	add(panel);
	pack();
	addWindowListener(this);
	GUI.center(this);
	setModal(true);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	bnOK.removeActionListener(this);
	bnCancel.removeActionListener(this);
	if (e.getSource() == bnCancel) {
	cancel = true;
	name = "";
	dispose();
	return;
	}
	else if (e.getSource() == bnOK) {
	cancel = false;
	name = (String) list.getSelectedValue();
	dispose();
	}
	}

	public String getName() {
	return name;
	}

	public boolean wasCancel() {
	return cancel;
	}

	@Override
	public void windowOpened(WindowEvent e) {
	}

	@Override
	public void windowClosing(WindowEvent e) {
	dispose();
	cancel = true;
	name = "";
	return;
	}

	@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) {
	}
	}

	}

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