No OneTemporary
Actions

Subscribers

None

File Metadata

Created: Thu, Dec 19, 09:09

View Options

This file is larger than 256 KB, so syntax highlighting was skipped.

	diff --git a/DeconvolutionLab2/DeconvolutionLab2.config b/DeconvolutionLab2/DeconvolutionLab2.config
	index 94713ca..f98f514 100644
	--- a/DeconvolutionLab2/DeconvolutionLab2.config
	+++ b/DeconvolutionLab2/DeconvolutionLab2.config
	@@ -1,77 +1,77 @@
	-#DeconvolutionLab2
	-#DeconvolutionLab2
	-#Wed Feb 01 12:36:36 CET 2017
	+#DeconvolutionLab2 [Beta 1]
	+#DeconvolutionLab2 [Beta 1]
	+#Wed Feb 01 21:16:58 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=Convolution
	+Algorithm.algorithm=Regularized Inverse Filter
	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=Non-negativity
	+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=737
	-DeconvolutionLab.MainDialog.location.w=453
	-DeconvolutionLab.MainDialog.location.x=39
	-DeconvolutionLab.MainDialog.location.y=67
	+DeconvolutionLab.MainDialog.location.h=579
	+DeconvolutionLab.MainDialog.location.w=573
	+DeconvolutionLab.MainDialog.location.x=5
	+DeconvolutionLab.MainDialog.location.y=23
	Fourier.dim=XYZ
	Fourier.epsilon=1E-6
	-Fourier.fft=JTransforms
	-Image.image.row0=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;null
	-Image.image.selected=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;null
	-Language.headless=Launch (with control panel)
	+Fourier.fft=Academic
	+Image.image.row0=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;
	+Image.image.row1=resolution;directory;/Users/dsage/Desktop/DeconvolutionLab2-Course/resolution;
	+Image.image.selected=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;
	+Language.headless=Run (Headless)
	Language.language=Command line
	-Main.path=/Users/sage/Desktop
	-Monitoring.monitor=console
	-Monitoring.path=current
	-Monitoring.time.value=3600
	-Monitoring.time=no limit
	-Monitoring.verbose=log
	-Output.output.row0=mip;Noname;;;;\u2713;\u2713;null
	-Output.output.row1=ortho @2;Noname;;;;\u2713;\u2713;null
	-Output.output.selected=ortho @2;Noname;;;;\u2713;\u2713;null
	-PSF.psf.row0=DoG;synthetic;DoG 100.0 0.0 3.0 4.0 size 128 128 32 ;null
	-PSF.psf.selected=DoG;synthetic;DoG 100.0 0.0 3.0 4.0 size 128 128 32 ;null
	+Monitor.monitor=console table
	+Monitor.path=/Users/dsage/git/deconvolution/DeconvolutionLab2
	+Monitor.time.value=3600
	+Monitor.time=no limit
	+Monitor.verbose=log
	+Output.output.row0=ortho;Noname;;;;\u2713;\u2713;
	+Output.output.selected=ortho;Noname;;;;\u2713;\u2713;
	+PSF.psf.row0=Airy;synthetic;Airy 100.0 0.0 1.0 size 128 128 32 ;
	+PSF.psf.row1=Defocus;synthetic;Defocus 100.0 0.0 3.0 10.0 10.0 size 3 3 100 ;
	+PSF.psf.selected=Airy;synthetic;Airy 100.0 0.0 1.0 size 128 128 32 ;
	diff --git a/DeconvolutionLab2/build.xml b/DeconvolutionLab2/build.xml
	index f0514fb..f2d1dd2 100644
	--- a/DeconvolutionLab2/build.xml
	+++ b/DeconvolutionLab2/build.xml
	@@ -1,27 +1,26 @@
	<?xml version="1.0" encoding="UTF-8"?>
	<project name="DeconvolutionLab2" default="build" basedir=".">

	<property name="imagej" location="../../ImageJ/plugins"/>
	<property name="fiji" location="../../Fiji-deconv.app/plugins"/>

	<target name="build">
	<mkdir dir="bin"/>
	<copy todir="bin"><fileset dir="ij"></fileset></copy>
	<copy file="plugins.config" toDir="bin" />

	- <mkdir dir="dist"/>
	- <zip destfile="dist/DeconvolutionLab2-src.zip" basedir="src" />
	- <zip destfile="dist/DeconvolutionLab2-cls.zip" basedir="bin" />
	- <jar destfile="dist/DeconvolutionLab_2.jar" basedir="bin">
	+ <zip destfile="../DeconvolutionLab2-src.zip" basedir="src" />
	+ <zip destfile="../DeconvolutionLab2-cls.zip" basedir="bin" />
	+ <jar destfile="../DeconvolutionLab_2.jar" basedir="bin">
	<manifest>
	<attribute name="Main-Class" value="DeconvolutionLab2"/>
	<attribute name="Class-Path" value="ij.jar jtransforms.jar"/>
	</manifest>
	</jar>

	- <copy toDir="${fiji}" file="dist/DeconvolutionLab_2.jar" />
	+ <copy toDir="${fiji}" file="../DeconvolutionLab_2.jar" />

	- <copy toDir="${imagej}" file="dist/DeconvolutionLab_2.jar" />
	+ <copy toDir="${imagej}" file="../DeconvolutionLab_2.jar" />

	</target>
	</project>
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/dist/DeconvolutionLab2-cls.zip b/DeconvolutionLab2/dist/DeconvolutionLab2-cls.zip
	index 1c9b469..72c7d52 100644
	Binary files a/DeconvolutionLab2/dist/DeconvolutionLab2-cls.zip and b/DeconvolutionLab2/dist/DeconvolutionLab2-cls.zip differ
	diff --git a/DeconvolutionLab2/dist/DeconvolutionLab2-src.zip b/DeconvolutionLab2/dist/DeconvolutionLab2-src.zip
	index 274d0aa..5d6208e 100644
	Binary files a/DeconvolutionLab2/dist/DeconvolutionLab2-src.zip and b/DeconvolutionLab2/dist/DeconvolutionLab2-src.zip differ
	diff --git a/DeconvolutionLab2/dist/DeconvolutionLab_2.jar b/DeconvolutionLab2/dist/DeconvolutionLab_2.jar
	index a596be2..6d7c2fc 100644
	Binary files a/DeconvolutionLab2/dist/DeconvolutionLab_2.jar and b/DeconvolutionLab2/dist/DeconvolutionLab_2.jar differ
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2.java b/DeconvolutionLab2/src/DeconvolutionLab2.java
	index 493db2b..dc11b21 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2.java
	@@ -1,96 +1,93 @@
	import java.io.File;

	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	-import deconvolutionlab.dialog.MainDialog;
	+import deconvolutionlab.dialog.LabDialog;
	import deconvolutionlab.monitor.Monitors;

	public class DeconvolutionLab2 {

	public static String ack = Constants.name + " " + Constants.version + " " + Constants.copyright;

	public static void main(String arg[]) {

	System.out.println(ack);
	Lab.getInstance(Platform.STANDALONE);

	if (arg.length == 0) {
	lab(arg);
	return;
	}

	String flag = arg[0].trim().toLowerCase();
	- if (flag.equals("help")) {
	+ if (flag.equalsIgnoreCase("help")) {
	help();
	return;
	}

	- if (flag.toLowerCase().equals("lab")) {
	+ if (flag.equalsIgnoreCase("lab")) {
	lab(arg);
	}

	- if (flag.toLowerCase().equals("fft")) {
	+ if (flag.equalsIgnoreCase("fft")) {
	Lab.checkFFT(Monitors.createDefaultMonitor());
	}

	- if (flag.toLowerCase().equals("run")) {
	+ if (flag.equalsIgnoreCase("run")) {
	String cmd = "";
	for (int i = 1; i < arg.length; i++)
	cmd += arg[i] + " ";
	- new Deconvolution(cmd).deconvolve();
	+ new Deconvolution(cmd).deconvolve(true);
	}

	- if (flag.toLowerCase().equals("launch")) {
	+ if (flag.equalsIgnoreCase("launch")) {
	String cmd = "";
	for (int i = 1; i < arg.length; i++)
	cmd += arg[i] + " ";
	- new Deconvolution(cmd).launch("");
	+ new Deconvolution(cmd).launch("", true);
	}
	-
	- System.exit(0);
	-
	}

	private static void lab(String arg[]) {
	String config = System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config";
	if (arg.length >= 2) {
	String filename = arg[1].trim();
	File file = new File(filename);
	if (file.exists())
	if (file.isFile())
	if (file.canRead())
	config = filename;
	}
	Config.getInstance(config);
	- MainDialog dialog = new MainDialog();
	+ LabDialog dialog = new LabDialog();
	dialog.setVisible(true);
	}

	private static void help() {
	System.out.println("More info:" + Constants.url);
	System.out.println("Syntax:");
	System.out.println("java -jar DeconvolutionLab_2.jar lab [config.txt]");
	System.out.println("java -jar DeconvolutionLab_2.jar run {command} ...");
	System.out.println("java -jar DeconvolutionLab_2.jar {command} ...");
	System.out.println("java -jar DeconvolutionLab_2.jar fft");
	System.out.println("java -jar DeconvolutionLab_2.jar info");
	System.out.println("java -jar DeconvolutionLab_2.jar help");
	System.out.println("{command} is the full command line for running a deconvolution");
	System.out.print("Keywords of {command}: ");
	for (String keyword : Command.keywords)
	System.out.print(keyword + " ");

	}

	public DeconvolutionLab2(String cmd) {
	System.out.println("cmd: " + cmd);
	deconvolutionlab.Lab.getInstance(Platform.STANDALONE);
	String config = System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config";
	Config.getInstance(config);
	- new Deconvolution(cmd).deconvolve();
	+ new Deconvolution(cmd).deconvolve(false);
	}
	}
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2_Launch.java b/DeconvolutionLab2/src/DeconvolutionLab2_Launch.java
	index fe8b70c..33a8d1c 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2_Launch.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_Launch.java
	@@ -1,24 +1,24 @@
	import java.io.File;

	import deconvolution.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	-import deconvolutionlab.dialog.MainDialog;
	+import deconvolutionlab.dialog.LabDialog;
	import ij.IJ;
	import ij.Macro;
	import ij.plugin.PlugIn;

	public class DeconvolutionLab2_Launch implements PlugIn {

	@Override
	public void run(String arg) {
	Lab.getInstance(Platform.IMAGEJ);
	String config = IJ.getDirectory("plugins") + File.separator + "DeconvolutionLab2.config";
	Config.getInstance(config);
	if (Macro.getOptions() == null)
	- new MainDialog().setVisible(true);
	+ new LabDialog().setVisible(true);
	else
	- new Deconvolution(Macro.getOptions()).launch("");
	+ new Deconvolution(Macro.getOptions()).launch("", false);
	}
	}
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2_Run.java b/DeconvolutionLab2/src/DeconvolutionLab2_Run.java
	index 086fd20..0462b41 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2_Run.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2_Run.java
	@@ -1,24 +1,24 @@
	import java.io.File;

	import deconvolution.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Platform;
	-import deconvolutionlab.dialog.MainDialog;
	+import deconvolutionlab.dialog.LabDialog;
	import ij.IJ;
	import ij.Macro;
	import ij.plugin.PlugIn;

	public class DeconvolutionLab2_Run implements PlugIn {

	@Override
	public void run(String arg) {
	Lab.getInstance(Platform.IMAGEJ);
	String config = IJ.getDirectory("plugins") + File.separator + "DeconvolutionLab2.config";
	Config.getInstance(config);
	if (Macro.getOptions() == null)
	- new MainDialog().setVisible(true);
	+ new LabDialog().setVisible(true);
	else
	- new Deconvolution(Macro.getOptions()).deconvolve();
	+ new Deconvolution(Macro.getOptions()).deconvolve(false);
	}
	}
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Bigradient.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Bigradient.java
	index a89fa89..f25419c 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Bigradient.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Bigradient.java
	@@ -1,94 +1,94 @@
	package course;
	import ij.plugin.PlugIn;

	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

	import deconvolution.Deconvolution;
	import deconvolutionlab.monitor.Monitors;


	public class DeconvolutionLab2_Course_Bigradient implements PlugIn {

	private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop";
	private String root = desktop + File.separator + "DeconvolutionLab2-Course" + File.separator;
	private String res = root + "Results" + File.separator + "bigradient" + File.separator;
	private String data = root + "Data" + File.separator + "bigradient" + File.separator;

	public DeconvolutionLab2_Course_Bigradient() {

	new File(res).mkdir();
	System.setProperty("user.dir", res);

	new File(res + "TRIF").mkdir();
	new File(res + "RIF").mkdir();
	new File(res + "LW").mkdir();
	new File(res + "LW-ITER").mkdir();
	new File(res + "LW+").mkdir();
	new File(res + "LW+-ITER").mkdir();
	new File(res + "RL").mkdir();
	new File(res + "RL-ITER").mkdir();
	new File(res + "RLTV").mkdir();
	new File(res + "RLTV-ITER").mkdir();
	new File(res + "FISTA").mkdir();
	new File(res + "FISTA-ITER").mkdir();

	String psf = " -psf file " + data + "psf.tif -reference " + data + "ref.tif ";
	String noisy = " -image file convnoise.tif";

	- new Deconvolution("-image file " + data + "ref.tif" + psf + " -algorithm SIM 0 1 1 -out stack convnoise -out stack conbnoise_8 rescaled byte noshow").deconvolve();
	+ new Deconvolution("-image file " + data + "ref.tif" + psf + " -algorithm SIM 0 1 1 -out stack convnoise -out stack conbnoise_8 rescaled byte noshow").deconvolve(false);

	- new Deconvolution(noisy + psf + " -algorithm NIF -out stack NIF").deconvolve();
	- new Deconvolution(noisy + psf + " -algorithm DIV -out stack DIV").deconvolve();
	+ new Deconvolution(noisy + psf + " -algorithm NIF -out stack NIF").deconvolve(false);
	+ new Deconvolution(noisy + psf + " -algorithm DIV -out stack DIV").deconvolve(false);

	for(int i=0; i<=3; i++) {
	double p = Math.pow(5, i-10);
	String name = "RIF" + String.format("%02d", i);
	- new Deconvolution(noisy + psf + " -algorithm RIF " + p + out("RIF" + File.separator, name)).deconvolve();
	+ new Deconvolution(noisy + psf + " -algorithm RIF " + p + out("RIF" + File.separator, name)).deconvolve(false);
	}
	for(int i=0; i<=3; i++) {
	double p = Math.pow(5, i-10);
	String name = "TRIF" + String.format("%02d", i);
	- new Deconvolution(noisy + psf + " -algorithm TRIF " + p + out("TRIF" + File.separator, name)).deconvolve();
	+ new Deconvolution(noisy + psf + " -algorithm TRIF " + p + out("TRIF" + File.separator, name)).deconvolve(false);
	}

	String lw = " -algorithm LW 20 1 -out mip @2 LW-ITER/I -showstats @1 LW";
	- new Deconvolution(noisy + psf + lw).deconvolve();
	+ new Deconvolution(noisy + psf + lw).deconvolve(false);
	new File(res + "LW-ITER/I.tif").delete();


	String lwp = " -algorithm LW+ 20 1 -out mip @2 LW+-ITER/I -showstats @1 LW+";
	- new Deconvolution(noisy + psf + lwp).deconvolve();
	+ new Deconvolution(noisy + psf + lwp).deconvolve(false);
	new File(res + "LW+-ITER/I.tif").delete();


	String rl = " -algorithm RL 20 -out mip @2 RL-ITER/I -showstats @1 RL";
	- new Deconvolution(noisy + psf + rl).deconvolve();
	+ new Deconvolution(noisy + psf + rl).deconvolve(false);
	new File(res + "RL-ITER/I.tif").delete();

	String rltv = " -algorithm RLRV 20 10 -out mip @2 RLTV-ITER/I -showstats @1 RLTV";
	- new Deconvolution(noisy + psf + rltv).deconvolve();
	+ new Deconvolution(noisy + psf + rltv).deconvolve(false);
	new File(res + "RLTV-ITER/I.tif").delete();

	String fista = " -algorithm FISTA 20 1 1 Spline3 3 -mip @2 FISTA-ITER/I -showstats @1 FISTA";
	- new Deconvolution(noisy + psf + fista).deconvolve();
	+ new Deconvolution(noisy + psf + fista).deconvolve(false);
	new File(res + "FISTA-ITER/I.tif").delete();

	}

	private static String out(String root, String name) {
	return "showstats " + root + name + " -savestats " + root + name +
	" -out stack " + root + name + "_32 -out stack " + root + name + "_8 rescaled byte noshow";
	}

	public static void main(String arg[]) {
	new DeconvolutionLab2_Course_Bigradient();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_Course_Bigradient();
	}

	}
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Border.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Border.java
	index 871d82d..d9eb32d 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Border.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Border.java
	@@ -1,108 +1,108 @@
	package course;
	// Course Version 2

	import ij.plugin.PlugIn;

	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

	import signal.RealSignal;
	import signal.factory.Cube;
	import signal.factory.Gaussian;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.Monitors;

	public class DeconvolutionLab2_Course_Border implements PlugIn {

	private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop";
	private String root = desktop + File.separator + "DeconvolutionLab2-Course" + File.separator;
	private String res = root + "Results" + File.separator + "border" + File.separator;

	public DeconvolutionLab2_Course_Border() {

	Monitors monitors = Monitors.createDefaultMonitor();
	new File(res).mkdir();
	System.setProperty("user.dir", res);

	int nx = 200;
	int ny = 200;
	int nz = 40;

	RealSignal im = new Cube(22, .1).intensity(0, 100).center(0.25, 0.00, 0.05).generate(nx, ny, nz);
	RealSignal i0 = new Cube(22, .1).intensity(0, 100).center(0.25, 0.05, 0.05).generate(nx, ny, nz);
	RealSignal i1 = new Cube(22, .1).intensity(0, 100).center(0.25, 0.10, 0.05).generate(nx, ny, nz);
	RealSignal i2 = new Cube(22, .1).intensity(0, 100).center(0.25, 0.15, 0.05).generate(nx, ny, nz);
	im.max(i1.max(i2).max(i0));

	RealSignal g = new Gaussian(10, 10, 10).intensity(0, 101).generate(nx, ny, nz);

	Lab.save(monitors, im, res + "ref.tif");
	Lab.save(monitors, g, res + "psf.tif");

	String psf = " -psf file " + "psf.tif";
	String ref = " -image file " + "ref.tif";
	String cst = " -image synthetic constant 250 0 size 200 200 40";

	String algo = " -algorithm CONV -out ortho REFo (64,32,16)";
	- new Deconvolution(ref + " -psf synthetic impulse " + algo).deconvolve();
	+ new Deconvolution(ref + " -psf synthetic impulse " + algo).deconvolve(false);

	algo = " -algorithm CONV -stack CONV -out ortho CONVo rescaled byte (64,32,16) -out mip CONVp rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -pad NO NO 200 200 -out ortho PADo200 rescaled byte (64,32,16) -out mip PADp200 rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -pad NO NO 100 100 -out ortho PADo100 rescaled byte (64,32,16) -out mip PADp100 rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -pad NO NO 40 40 -out ortho PADo40 rescaled byte (64,32,16) -out mip PADp40 rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -pad NO NO 20 20 -out ortho PADo20 rescaled byte (64,32,16) -out mip PADp20 rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -pad NO NO 10 10 -out ortho PADo10 rescaled byte (64,32,16) -out mip PADp10 rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -pad NO NO 5 5 -out ortho PADo2 rescaled byte (64,32,16) -out mip PADp2 rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -apo HANN HANN -out ortho HANNo rescaled byte (64,32,16) -out mip HANNp rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -apo TUKEY TUKEY -out ortho TUKEYo rescaled byte (64,32,16) -out mip TUKEYp rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);

	algo = " -algorithm CONV --pad NO NO 8 8 apo HANN HANN -out ortho PAD8_HANNo rescaled byte (64,32,16) -out mip PAD8_HANNp rescaled byte";
	- new Deconvolution(ref + psf + algo).deconvolve();
	+ new Deconvolution(ref + psf + algo).deconvolve(false);


	algo = " -algorithm CONV -apo HANN HANN -out ortho HANN_CSTo rescaled byte -out mip HANN_CSTp rescaled byte";
	- new Deconvolution(cst + psf + algo).deconvolve();
	+ new Deconvolution(cst + psf + algo).deconvolve(false);

	algo = " -algorithm CONV -apo TUKEY TUKEY -out ortho TUKEY_CSTo rescaled byte -out mip TUKEY_CSTp rescaled byte";
	- new Deconvolution(cst + psf + algo).deconvolve();
	+ new Deconvolution(cst + psf + algo).deconvolve(false);


	algo = " -algorithm CONV -pad E2 E2 -out ortho PADpPower2FFTW rescaled byte (64,32,16) -out mip PADpPower2FFTW rescaled byte";


	- new Deconvolution(cst + psf + algo + " -fft FFTW2 ").deconvolve();
	- new Deconvolution(cst + psf + algo + " -fft Academic ").deconvolve();
	- new Deconvolution(cst + psf + algo+ " -fft JTransforms ").deconvolve();
	+ new Deconvolution(cst + psf + algo + " -fft FFTW2 ").deconvolve(false);
	+ new Deconvolution(cst + psf + algo + " -fft Academic ").deconvolve(false);
	+ new Deconvolution(cst + psf + algo + " -fft JTransforms ").deconvolve(false);

	}

	public static void main(String arg[]) {
	new DeconvolutionLab2_Course_Border();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_Course_Border();
	}


	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Resolution.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Resolution.java
	index 19ca6bb..d47a9b4 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Resolution.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Resolution.java
	@@ -1,81 +1,81 @@
	package course;
	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

	import deconvolution.Deconvolution;
	import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.Monitors;
	import ij.plugin.PlugIn;
	import signal.RealSignal;
	import signal.factory.GridSpots;

	public class DeconvolutionLab2_Course_Resolution implements PlugIn {

	private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop";
	private String root = desktop + File.separator + "DeconvolutionLab2-Course" + File.separator;
	private String res = root + "Results" + File.separator + "resolution" + File.separator;

	public DeconvolutionLab2_Course_Resolution() {

	Monitors monitors = Monitors.createDefaultMonitor();
	new File(res).mkdir();
	System.setProperty("user.dir", res);

	new File(res + "RIF").mkdir();
	new File(res + "LW").mkdir();
	new File(res + "LW+").mkdir();

	int nx = 128;
	int ny = 128;
	int nz = 128;
	int spacing = 16;

	RealSignal x = new GridSpots(3, 1, spacing).intensity(0, 10).generate(nx, ny, nz);
	Lab.show(monitors, x, "reference");
	Lab.save(monitors, x, res + "reference.tif");

	String algo = " ";
	String ground = " -image file reference.tif ";
	String psf = " -psf file ../../Data/resolution/psf-bw-500.tif ";
	//String psf = " -psf synthetic gaussian 100.0 0.0 1 1 1 size " + nx + " " + ny + " " + nz;
	String signal = " -image file signal.tif -reference reference.tif -monitor table";

	String paramout = " intact float (" + spacing + "," + spacing + "," + spacing + ")";

	algo = " -algorithm CONV -showstats @3 PR -out stack PR -out ortho PRo ";
	- new Deconvolution(ground + "-reference reference.tif -psf synthetic impulse 100 0 size 128 128 128 " + algo).deconvolve();
	+ new Deconvolution(ground + "-reference reference.tif -psf synthetic impulse 100 0 size 128 128 128 " + algo).deconvolve(false);

	algo = " -algorithm SIM 0 0.1 0 -showstats @3 SIM -out stack SIGNAL -out ortho SIGNALo ";
	- new Deconvolution(ground + psf + algo).deconvolve();
	+ new Deconvolution(ground + psf + algo).deconvolve(false);

	algo = " -algorithm NIF -out ortho NIF " + paramout;
	- new Deconvolution(signal + psf + algo).deconvolve();
	+ new Deconvolution(signal + psf + algo).deconvolve(false);

	algo = " -algorithm LW+ 17 1 -showstats @3 LW -out ortho @10 LW+/LW+" + paramout;
	- new Deconvolution(signal + psf + algo).deconvolve();
	+ new Deconvolution(signal + psf + algo).deconvolve(false);

	for(int i=0; i<=15; i++) {
	double p = Math.pow(10, i-15);
	algo = " -algorithm RIF " + p + " -out ortho RIF/RIF" + String.format("%02d", i) + paramout;
	- new Deconvolution(signal + psf + algo).deconvolve();
	+ new Deconvolution(signal + psf + algo).deconvolve(false);
	}


	algo = " -algorithm LW 11 1 -showstats @3 LW -out ortho @10 LW/LW" + paramout;
	- new Deconvolution(signal + psf + algo).deconvolve();
	+ new Deconvolution(signal + psf + algo).deconvolve(false);


	}

	public static void main(String arg[]) {
	new DeconvolutionLab2_Course_Resolution();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_Course_Resolution();
	}


	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_SpectralAnaylsis.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_SpectralAnaylsis.java
	index fb46d9a..bdbc99e 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_SpectralAnaylsis.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_SpectralAnaylsis.java
	@@ -1,159 +1,159 @@
	package course;
	import ij.plugin.PlugIn;

	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

	import signal.ComplexSignal;
	import signal.Operations;
	import signal.RealSignal;
	import signal.factory.DoG;
	import signal.factory.Gaussian;
	import signal.factory.complex.ComplexSignalFactory;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Lab;
	import deconvolutionlab.PlatformImager;
	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.FFT;

	public class DeconvolutionLab2_Course_SpectralAnaylsis implements PlugIn {

	private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop";
	private String root = desktop + File.separator + "DeconvolutionLab2-Course" + File.separator;
	private String res = root + "Results" + File.separator + "star" + File.separator;
	private String data = root + "Data" + File.separator + "star" + File.separator;

	public DeconvolutionLab2_Course_SpectralAnaylsis() {

	new File(res).mkdir();
	System.setProperty("user.dir", res);

	new File(res + "TRIF").mkdir();
	new File(res + "TRIF-FILTER").mkdir();
	new File(res + "RIF").mkdir();
	new File(res + "RIF-FILTER").mkdir();
	new File(res + "LW").mkdir();
	new File(res + "LW-ITER").mkdir();
	new File(res + "LW+").mkdir();
	new File(res + "LW+-ITER").mkdir();
	new File(res + "RL").mkdir();
	new File(res + "RL-ITER").mkdir();
	new File(res + "NOISELESS").mkdir();
	new File(res + "PERTURBATION").mkdir();
	new File(res + "SIMULATION").mkdir();
	new File(res + "ICTM").mkdir();
	new File(res + "ICTM-ITER").mkdir();

	Monitors monitors = Monitors.createDefaultMonitor();
	int nx = 256;
	int ny = 256;
	int nz = 1;
	String size = " size " + nx + " " + ny + " " + nz;
	double noise = 0.04;
	double poisson = 0.01;
	double wiener = Math.sqrt(noise * 2.0 / Math.PI);
	System.out.println("Wiener value " + wiener);
	AbstractFFT fft = FFT.createDefaultFFT(monitors, nx, ny, nz);
	ComplexSignal L = ComplexSignalFactory.laplacian(nx, ny, nz);
	RealSignal laplacian = fft.inverse(L).circular().rescale(monitors);
	Lab.save(monitors, laplacian, res + "laplacian.tif", PlatformImager.Type.BYTE);

	RealSignal h = new DoG(2, 3.6).generate(nx, ny, nz);
	h.times(0.7f);
	h.plus(new Gaussian(1.5, 1.5, 1.5).generate(nx, ny, nz));
	Lab.save(monitors, h, res + "psf.tif");

	h.plus(new Gaussian(0.5, 0.5, 0.5).generate(nx, ny, nz));
	Lab.save(monitors, h, res + "psfPerturbated.tif");

	String psf = " -psf file psf.tif -fft FFTW2";
	String impulse = " -psf synthetic impulse 100.0 0.0 " + size;
	String image = " -image file " + data + "ref.tif";
	String constant = " -image constant 0 0 " + size;

	// Simulation
	String algo = " -algorithm CONV " + out("CONV");
	- new Deconvolution(psf + image + algo).deconvolve();
	+ new Deconvolution(psf + image + algo).deconvolve(false);

	algo = " -algorithm CONV " + out("CONV-PERTURBATED");
	- new Deconvolution(psf + image + algo).deconvolve();
	+ new Deconvolution(psf + image + algo).deconvolve(false);
	ComplexSignal H = fft.transform(h);
	ComplexSignal H2 = Operations.multiply(H, H);
	ComplexSignal LP = ComplexSignalFactory.laplacian(nx, ny, nz);

	algo = " -algorithm SIM " + (6*noise) + " " + noise + " " + poisson + " " + out("SIM");
	- new Deconvolution(psf + image + algo).deconvolve();
	+ new Deconvolution(psf + image + algo).deconvolve(false);

	algo = " -algorithm SIM " + (6*noise) + " " + noise + " " + poisson + " " + out("NOISE");
	- new Deconvolution(impulse + constant + algo).deconvolve();
	+ new Deconvolution(impulse + constant + algo).deconvolve(false);

	// No Noise
	String nonoise = " -image file CONV.tif -psf file psfPerturbated.tif";
	- new Deconvolution(nonoise + " -algorithm TRIF " + wiener + out("NOISELESS/WIF")).deconvolve();
	- new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E0 " + out("NOISELESS/NIF0")).deconvolve();
	- new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E-3 " + out("NOISELESS/NIF-1")).deconvolve();
	- new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E-6 " + out("NOISELESS/NIF-6")).deconvolve();
	- new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E-9 " + out("NOISELESS/NIF-9")).deconvolve();
	- new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E-12 " + out("NOISELESS/NIF-12")).deconvolve();
	- new Deconvolution(nonoise + " -algorithm DIV " + out("NOISELESS/DIV")).deconvolve();
	+ new Deconvolution(nonoise + " -algorithm TRIF " + wiener + out("NOISELESS/WIF")).deconvolve(false);
	+ new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E0 " + out("NOISELESS/NIF0")).deconvolve(false);
	+ new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E-3 " + out("NOISELESS/NIF-1")).deconvolve(false);
	+ new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E-6 " + out("NOISELESS/NIF-6")).deconvolve(false);
	+ new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E-9 " + out("NOISELESS/NIF-9")).deconvolve(false);
	+ new Deconvolution(nonoise + " -algorithm NIF -epsilon 1E-12 " + out("NOISELESS/NIF-12")).deconvolve(false);
	+ new Deconvolution(nonoise + " -algorithm DIV " + out("NOISELESS/DIV")).deconvolve(false);

	// Pertubatation
	String pertubation = " -image file CONV.tif -psf file psfPerturbated.tif";
	- new Deconvolution(pertubation + " -algorithm TRIF " + wiener + out("PERTURBATION/WIF")).deconvolve();
	- new Deconvolution(pertubation + " -algorithm NIF " + out("PERTURBATION/NIF")).deconvolve();
	- new Deconvolution(pertubation + " -algorithm DIV " + out("PERTURBATION/DIV")).deconvolve();
	+ new Deconvolution(pertubation + " -algorithm TRIF " + wiener + out("PERTURBATION/WIF")).deconvolve(false);
	+ new Deconvolution(pertubation + " -algorithm NIF " + out("PERTURBATION/NIF")).deconvolve(false);
	+ new Deconvolution(pertubation + " -algorithm DIV " + out("PERTURBATION/DIV")).deconvolve(false);

	// Noisy
	String simulation = " -image file SIM.tif " + psf;

	- new Deconvolution(simulation + " -algorithm TRIF " + wiener + out("SIMULATION/WIF")).deconvolve();
	- new Deconvolution(simulation + " -algorithm NIF "+ out("SIMULATION/NIF")).deconvolve();
	- new Deconvolution(simulation + " -algorithm DIV" + out("SIMULATION/DIV")).deconvolve();
	+ new Deconvolution(simulation + " -algorithm TRIF " + wiener + out("SIMULATION/WIF")).deconvolve(false);
	+ new Deconvolution(simulation + " -algorithm NIF "+ out("SIMULATION/NIF")).deconvolve(false);
	+ new Deconvolution(simulation + " -algorithm DIV" + out("SIMULATION/DIV")).deconvolve(false);

	algo = " -algorithm LW+ 100 0.5 -out mip @1 LW+-ITER/I ";
	- new Deconvolution(simulation + algo + out("LW+/LW+")).deconvolve();
	+ new Deconvolution(simulation + algo + out("LW+/LW+")).deconvolve(false);
	new File(res + "LW+-ITER/I.tif").delete();

	for(int i=0; i<=20; i++) {
	double p = Math.pow(5, i-12);
	String name = "RIF/RIF" + String.format("%02d", i);
	- new Deconvolution(simulation + " -algorithm RIF " + p + out(name)).deconvolve();
	+ new Deconvolution(simulation + " -algorithm RIF " + p + out(name)).deconvolve(false);
	RealSignal fa = fft.inverse(Operations.add(H2, Operations.multiply(p, LP, LP))).circular();
	Lab.save(monitors, fa, res + "RIF-FILTER/RIF" + String.format("%02d", i) + ".tif");
	}

	for(int i=0; i<=20; i++) {
	double p = Math.pow(5, i-12);
	String name = "TRIF/TRIF" + String.format("%02d", i);
	- new Deconvolution(simulation + " -algorithm TRIF " + p + out(name)).deconvolve();
	+ new Deconvolution(simulation + " -algorithm TRIF " + p + out(name)).deconvolve(false);
	RealSignal fa = fft.inverse(Operations.add(H2, Operations.multiply(p, LP, LP))).circular();
	Lab.save(monitors, fa, res + "TRIF-FILTER/RIF" + String.format("%02d", i) + ".tif");
	}


	algo = " -algorithm RL 100 -out mip @1 RL-ITER/I ";
	- new Deconvolution(simulation + algo + out("RL/RL")).deconvolve();
	+ new Deconvolution(simulation + algo + out("RL/RL")).deconvolve(false);
	new File(res + "RL-ITER/I.tif").delete();

	algo = " -algorithm ICTM 100 1.5 0.001 -out mip @1 ICTM-ITER/I ";
	- new Deconvolution(simulation + algo + out("ICTM/ICTM")).deconvolve();
	+ new Deconvolution(simulation + algo + out("ICTM/ICTM")).deconvolve(false);
	new File(res + "ICTM-ITER/I.tif").delete();
	}

	private static String out(String name) {
	return " -out stack " + name +
	" -out stack " + name + "-BYTE rescaled byte noshow";
	}

	public static void main(String arg[]) {
	new DeconvolutionLab2_Course_SpectralAnaylsis();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_Course_SpectralAnaylsis();
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/Deconvolution.java b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	index 5d97694..8dfbc8a 100644
	--- a/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	+++ b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	@@ -1,572 +1,607 @@
	/*
	* 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 javax.swing.JFrame;
	+import javax.swing.JTabbedPane;

	-import lab.tools.NumFormat;
	-import signal.RealSignal;
	-import signal.apodization.AbstractApodization;
	-import signal.apodization.Apodization;
	-import signal.apodization.UniformApodization;
	-import signal.factory.SignalFactory;
	-import signal.padding.Padding;
	import deconvolution.algorithm.AbstractAlgorithm;
	import deconvolution.algorithm.Controller;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Output;
	import deconvolutionlab.OutputCollection;
	import deconvolutionlab.monitor.AbstractMonitor;
	import deconvolutionlab.monitor.Monitors;
	import deconvolutionlab.monitor.TableMonitor;
	import deconvolutionlab.monitor.Verbose;
	import fft.AbstractFFT;
	import fft.AbstractFFTLibrary;
	import fft.FFT;
	+import lab.tools.NumFormat;
	+import signal.RealSignal;
	+import signal.apodization.AbstractApodization;
	+import signal.apodization.Apodization;
	+import signal.apodization.UniformApodization;
	+import signal.factory.SignalFactory;
	+import signal.padding.Padding;

	public class Deconvolution implements Runnable {

	- private AbstractAlgorithm algo = null;
	+ private AbstractAlgorithm algo = null;

	- private String path;
	- private Monitors monitors = Monitors.createDefaultMonitor();
	- private Verbose verbose = Verbose.Log;
	- private Controller controller;
	+ private String path;
	+ private Monitors monitors = Monitors.createDefaultMonitor();
	+ private Verbose verbose = Verbose.Log;
	+ private Controller controller;
	private OutputCollection outs;

	- private Padding padding = new Padding();
	- private Apodization apodization = new Apodization();
	- private double factorNormalization = 1.0;
	+ private Padding padding = new Padding();
	+ private Apodization apodization = new Apodization();
	+ private double factorNormalization = 1.0;
	private AbstractFFTLibrary fftlib;

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

	- private ArrayList<String> results = new ArrayList<String>();
	+ private ArrayList<String> results = new ArrayList<String>();

	- private String name = "";
	+ private String name = "";
	+ private boolean exit = false;

	public Deconvolution(String command) {
	super();
	monitors = Monitors.createDefaultMonitor();
	this.command = command;
	decode();
	}

	public void setCommand(String command) {
	this.command = command;
	decode();
	}

	public String getCommand() {
	return command;
	}

	public Monitors getMonitors() {
	if (monitors == null)
	return Monitors.createDefaultMonitor();
	return monitors;
	}

	- public void deconvolve() {
	+ /**
	+ * This method runs the deconvolution without graphical user interface.
	+ *
	+ * @param exit
	+ * System.exit call is true
	+ */
	+ public void deconvolve(boolean exit) {
	+ this.exit = exit;
	+
	+ for (AbstractMonitor monitor : monitors) {
	+ if (monitor instanceof TableMonitor) {
	+ String t = algo == null ? "Monitor " + name : name + " " + algo.getName();
	+ JFrame frame = new JFrame(t);
	+ frame.add(((TableMonitor) monitor).getPanel());
	+ frame.pack();
	+ frame.setVisible(true);
	+ }
	+ }

	if (fftlib == null) {
	run();
	return;
	}
	if (!fftlib.isMultithreadable()) {
	run();
	return;
	}
	-
	Thread thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}

	- public String getName() {
	- return name;
	- }
	-
	- public void launch(String job) {
	+ /**
	+ * This method runs the deconvolution with a graphical user interface.
	+ *
	+ * @param job
	+ * Name of the job of deconvolution
	+ * @param exit
	+ * System.exit call is true
	+ */
	+ public void launch(String job, boolean exit) {
	this.name = job;
	- new DeconvolutionDialog(this);
	- }
	-
	- public ArrayList<String> getDeconvolutionResults() {
	- return results;
	+ this.exit = exit;
	+ DeconvolutionDialog d = new DeconvolutionDialog(this);
	+ for (AbstractMonitor monitor : monitors) {
	+ if (monitor instanceof TableMonitor) {
	+ String t = algo == null ? "Monitor " + name : name + " " + algo.getName();
	+ d.addTableMonitor(t, ((TableMonitor) monitor));
	+ }
	+ }
	}

	public void decode() {

	algo = null;

	path = System.getProperty("user.dir");
	monitors = Monitors.createDefaultMonitor();
	verbose = Verbose.Log;

	controller = new Controller();
	outs = new OutputCollection();

	padding = new Padding();
	apodization = new Apodization();
	factorNormalization = 1.0;
	fftlib = FFT.getLibraryByName("Academic");

	live = false;

	results = new ArrayList<String>();

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

	if (token.keyword.equalsIgnoreCase("-monitor"))
	monitors = Command.decodeMonitors(token);

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

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

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

	if (token.keyword.equalsIgnoreCase("-pad"))
	padding = Command.decodePadding(token);
	if (token.keyword.equalsIgnoreCase("-apo"))
	apodization = Command.decodeApodization(token);
	if (token.keyword.equalsIgnoreCase("-norm"))
	factorNormalization = Command.decodeNormalization(token);
	if (token.keyword.equalsIgnoreCase("-constraint"))
	Command.decodeController(token, controller);
	if (token.keyword.equalsIgnoreCase("-time"))
	Command.decodeController(token, controller);
	if (token.keyword.equalsIgnoreCase("-residu"))
	Command.decodeController(token, controller);
	if (token.keyword.equalsIgnoreCase("-reference"))
	Command.decodeController(token, controller);
	if (token.keyword.equalsIgnoreCase("-savestats"))
	Command.decodeController(token, controller);
	if (token.keyword.equalsIgnoreCase("-showstats"))
	Command.decodeController(token, controller);

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

	if (name.equals("") && algo != null)
	name = algo.getShortname();
	+
	}

	public void setApodization(ArrayList<AbstractApodization> apos) {
	AbstractApodization apoXY = new UniformApodization();
	AbstractApodization apoZ = new UniformApodization();
	if (apos.size() >= 1)
	apoXY = apos.get(0);
	if (apos.size() >= 2)
	apoZ = apos.get(1);
	this.apodization = new Apodization(apoXY, apoXY, apoZ);
	}

	@Override
	public void run() {
	live = true;
	- ArrayList<JFrame> frames = new ArrayList<JFrame>();
	- if (monitors != null) {
	+ if (monitors != null)
	monitors.setVerbose(verbose);
	- for (AbstractMonitor monitor : monitors) {
	- if (monitor instanceof TableMonitor) {
	- JFrame frame = new JFrame("Monitor");
	- frame.add(((TableMonitor) monitor).getPanel());
	- frame.pack();
	- frame.setVisible(true);
	- frames.add(frame);
	- }
	- }
	- }
	+
	results.add("Path: " + checkPath(path));
	-
	monitors.log("Path: " + checkPath(path));
	+
	RealSignal image = openImage();

	if (image == null) {
	monitors.error("Image: Not valid " + command);
	+ if (exit)
	+ System.exit(-101);
	return;
	}
	monitors.log("Image: " + image.nx + " x " + image.ny + " x " + image.nz);
	RealSignal y = padding.pad(monitors, getApodization().apodize(monitors, image));

	RealSignal psf = openPSF();
	if (psf == null) {
	monitors.error("PSF: not valid");
	+ if (exit)
	+ System.exit(-102);
	return;
	}

	monitors.log("PSF: " + psf.nx + " x " + psf.ny + " x " + psf.nz);
	monitors.log("PSF: normalization " + (factorNormalization <= 0 ? "no" : factorNormalization));
	RealSignal h = psf.changeSizeAs(y).normalize(factorNormalization);

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

	if (controller == null) {
	monitors.error("Controller: not valid");
	+ if (exit)
	+ System.exit(-104);
	return;
	}

	- for (JFrame frame : frames)
	- frame.setTitle(name + " (" + algo.getName() + ") ");
	-
	AbstractFFT fft;
	if (fftlib != null)
	fft = FFT.createFFT(monitors, fftlib, image.nx, image.ny, image.nz);
	else
	fft = FFT.createDefaultFFT(monitors, image.nx, image.ny, image.nz);
	algo.setFFT(fft);
	controller.setFFT(fft);

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

	monitors.log("Algorithm: " + algo.getName());

	RealSignal x = algo.run(monitors, y, h, true);

	RealSignal result = padding.crop(monitors, x);

	if (outs != null)
	outs.executeFinal(monitors, result, controller);

	live = false;
	+
	+ if (exit) {
	+ System.out.println("End");
	+ System.exit(0);
	+ }
	+
	}

	public ArrayList<String> recap() {
	ArrayList<String> lines = new ArrayList<String>();
	Token image = Command.extract(command, "-image");
	if (image == null)
	lines.add("<b>Image</b>: <span color=\"red\">keyword -image not found</span>");
	else
	lines.add("<b>Image</b>: " + image.parameters);

	String norm = (factorNormalization < 0 ? " (no normalization)" : " (normalization to " + factorNormalization + ")");
	Token psf = Command.extract(command, "-psf");
	if (psf == null)
	lines.add("<b>PSF</b>: <span color=\"red\">keyword -psf not found</span>");
	else
	lines.add("<b>PSF</b>: " + psf.parameters + norm);

	if (algo == null) {
	lines.add("<b>Algorithm</b>: <span color=\"red\">not valid</span>");
	}
	else {
	Controller controller = algo.getController();
	String con = ", " + controller.getConstraintAsString() + " constraint";
	lines.add("<b>Algorithm</b>: " + algo.toString() + con);
	lines.add("<b>Stopping Criteria</b>: " + controller.getStoppingCriteria(algo));
	lines.add("<b>Reference</b>: " + controller.getReference());
	lines.add("<b>Stats</b>: " + controller.getShowStats() + " " + controller.getSaveStats());
	lines.add("<b>Padding</b>: " + padding.toString());
	lines.add("<b>Apodization</b>: " + apodization.toString());
	if (algo.getFFT() != null)
	lines.add("<b>FFT</b>: " + algo.getFFT().getName());
	}
	lines.add("<b>Path</b>: " + path);

	String m = "";
	if (monitors != null) {
	for (AbstractMonitor monitor : monitors)
	m += monitor.getName() + " ";
	}
	String v = "";
	if (verbose != null)
	v = "(" + verbose.name().toLowerCase() + ")";
	lines.add("<b>Monitor</b>:" + m + " " + v);

	if (outs == null)
	lines.add("<b>Outputs</b>: not valid");
	else
	lines.addAll(outs.getInformation());
	return lines;
	}

	public ArrayList<String> checkAlgo() {
	ArrayList<String> lines = new ArrayList<String>();
	RealSignal image = openImage();
	if (image == null) {
	lines.add("No valid input image");
	return lines;
	}
	if (padding == null) {
	lines.add("No valid padding");
	return lines;
	}
	if (apodization == null) {
	lines.add("No valid apodization");
	return lines;
	}
	RealSignal psf = openPSF();
	if (psf == null) {
	lines.add("No valid PSF");
	return lines;
	}
	if (algo == null) {
	lines.add("No valid algorithm");
	return lines;
	}

	Controller controller = algo.getController();
	RealSignal y = padding.pad(monitors, getApodization().apodize(monitors, image));
	RealSignal h = psf.changeSizeAs(y).normalize(factorNormalization);

	int iter = controller.getIterationMax();
	algo.getController().setIterationMax(1);
	RealSignal x = algo.run(monitors, y, h, true);
	Lab.show(monitors, x, "Estimate after 1 iteration");
	lines.add("Time: " + NumFormat.seconds(controller.getTimeNano()));
	lines.add("Peak Memory: " + controller.getMemoryAsString());
	controller.setIterationMax(iter);
	return lines;
	}

	public ArrayList<String> checkImage() {
	ArrayList<String> lines = new ArrayList<String>();
	RealSignal image = openImage();
	if (image == null) {
	lines.add("No valid input image");
	return lines;
	}
	if (padding == null) {
	lines.add("No valid padding");
	return lines;
	}
	if (apodization == null) {
	lines.add("No valid apodization");
	return lines;
	}

	RealSignal signal = padding.pad(monitors, getApodization().apodize(monitors, image));
	lines.add("<b>Image</b>");
	lines.add("Original size " + image.dimAsString() + " padded to " + signal.dimAsString());
	lines.add("Original: " + formatStats(image));
	lines.add("Preprocessing: " + formatStats(signal));

	Lab.show(monitors, signal, "Image");
	return lines;
	}

	public ArrayList<String> checkPSF() {
	ArrayList<String> lines = new ArrayList<String>();
	RealSignal image = openImage();
	if (image == null) {
	lines.add("No valid input image");
	return lines;
	}
	if (padding == null) {
	lines.add("No valid padding");
	return lines;
	}
	if (apodization == null) {
	lines.add("No valid apodization");
	return lines;
	}

	RealSignal psf = openPSF();
	if (psf == null) {
	lines.add("No valid PSF");
	return lines;
	}

	RealSignal signal = padding.pad(monitors, getApodization().apodize(monitors, image));
	RealSignal h = psf.changeSizeAs(signal);
	lines.add("<b>PSF</b>");
	lines.add("Original size " + psf.dimAsString() + " padded to " + h.dimAsString());

	String e = NumFormat.nice(h.getEnergy());

	h.normalize(factorNormalization);
	lines.add("Original: " + formatStats(psf));
	lines.add("Preprocessing: " + formatStats(h));
	lines.add("Energy = " + e + " and after normalization=" + NumFormat.nice(h.getEnergy()));
	Lab.show(monitors, h, "Padded and Normalized PSF");
	return lines;
	}

	+ public ArrayList<String> getDeconvolutionResults() {
	+ return results;
	+ }
	+
	+ public String getName() {
	+ return name;
	+ }
	+
	public boolean isLive() {
	return live;
	}

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

	public Padding getPadding1() {
	return padding;
	}

	public Apodization getApodization() {
	return apodization;
	}

	public OutputCollection getOuts() {
	return outs;
	}

	public AbstractAlgorithm getAlgo() {
	return algo;
	}

	public String getPath() {
	return path;
	}

	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;
	return getImage(monitors, token);
	}

	public RealSignal openPSF() {
	Token token = Command.extract(command, "-psf");
	if (token == null)
	return null;
	return getImage(monitors, token);
	}

	private RealSignal getImage(Monitors monitors, Token token) {
	String arg = token.option.trim();
	String cmd = token.parameters.substring(arg.length(), token.parameters.length()).trim();

	if (arg.equalsIgnoreCase("synthetic")) {
	String parts[] = cmd.split(" ");
	if (parts.length <= 0)
	return null;
	String shape = parts[0];
	for (String name : SignalFactory.getAllName()) {
	if (shape.equalsIgnoreCase(name.toLowerCase())) {
	double params[] = Command.parseNumeric(cmd);
	SignalFactory factory = SignalFactory.getFactoryByName(shape);
	if (factory == null)
	return null;
	double amplitude = params.length > 0 ? params[0] : 1;
	double background = params.length > 1 ? params[1] : 0;
	factory.intensity(background, amplitude);
	int np = factory.getParameters().length;
	double[] features = new double[np];
	for (int i = 0; i < Math.min(np, params.length); i++)
	features[i] = params[i + 2];
	factory.setParameters(features);
	int nx = params.length > np + 2 ? (int) Math.round(params[np + 2]) : 128;
	int ny = params.length > np + 3 ? (int) Math.round(params[np + 3]) : 128;
	int nz = params.length > np + 4 ? (int) Math.round(params[np + 4]) : 128;
	double cx = params.length > np + 5 ? params[np + 5] : 0.5;
	double cy = params.length > np + 6 ? params[np + 6] : 0.5;
	double cz = params.length > np + 7 ? params[np + 7] : 0.5;
	factory = factory.center(cx, cy, cz);
	RealSignal x = factory.generate(nx, ny, nz);
	return x;
	}
	}
	}
	if (arg.equalsIgnoreCase("file") \|\| arg.equalsIgnoreCase("dir") \|\| arg.equalsIgnoreCase("directory")) {
	RealSignal signal = null;
	File file = new File(path + File.separator + cmd);
	if (file != null) {
	if (file.isFile())
	signal = Lab.open(monitors, path + File.separator + cmd);
	if (file.isDirectory())
	signal = Lab.openDir(monitors, path + File.separator + cmd);
	}
	if (signal == null) {
	File local = new File(cmd);
	if (local != null) {
	if (local.isFile())
	signal = Lab.open(monitors, cmd);
	if (local.isDirectory())
	signal = Lab.openDir(monitors, cmd);
	}
	}
	return signal;

	}

	if (arg.equalsIgnoreCase("platform")) {
	return Lab.getImager().create(cmd);
	}

	return null;
	}

	private static String formatStats(RealSignal x) {
	float stats[] = x.getStats();
	String s = " mean=" + NumFormat.nice(stats[0]);
	s += " stdev=" + NumFormat.nice(stats[1]);
	s += " min=" + NumFormat.nice(stats[3]);
	s += " max=" + NumFormat.nice(stats[2]);
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java b/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
	index 9cb9d33..0eaa65e 100644
	--- a/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
	+++ b/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
	@@ -1,265 +1,271 @@
	/*
	* 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 ij.gui.GUI;
	-
	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.KeyEvent;
	import java.awt.event.KeyListener;
	import java.text.SimpleDateFormat;
	import java.util.ArrayList;
	import java.util.Date;

	import javax.swing.BorderFactory;
	import javax.swing.BoxLayout;
	import javax.swing.JButton;
	import javax.swing.JDialog;
	import javax.swing.JFrame;
	import javax.swing.JLabel;
	import javax.swing.JPanel;
	import javax.swing.JProgressBar;
	+import javax.swing.JTabbedPane;
	import javax.swing.JToolBar;
	import javax.swing.text.BadLocationException;

	-import lab.component.HTMLPane;
	-import lab.system.SystemBar;
	import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.StatusMonitor;
	+import deconvolutionlab.monitor.TableMonitor;
	+import ij.gui.GUI;
	+import lab.component.HTMLPane;
	+import lab.system.SystemBar;

	public class DeconvolutionDialog extends JDialog implements ActionListener, Runnable, KeyListener {

	- private JButton bnStart = new JButton("Run");
	- private JButton bnQuit = new JButton("Quit");
	- private JButton bnRecap = new JButton("Recap");
	- private JButton bnImage = new JButton("Check Image");
	- private JButton bnPSF = new JButton("Check PSF");
	- private JButton bnAlgo = new JButton("Check Algo");
	- private JButton bnHelp = new JButton("Help");
	- // private JTabbedPane tab = new JTabbedPane();
	+ private JButton bnStart = new JButton("Run");
	+ private JButton bnQuit = new JButton("Quit");
	+ private JButton bnRecap = new JButton("Recap");
	+ private JButton bnImage = new JButton("Check Image");
	+ private JButton bnPSF = new JButton("Check PSF");
	+ private JButton bnAlgo = new JButton("Check Algo");
	+ private JButton bnHelp = new JButton("Help");
	+ private JTabbedPane tab = new JTabbedPane();

	private HTMLPane pnCommand;
	private HTMLPane pnResume;

	- private JButton job = null;
	- private Thread thread = null;
	+ private JButton job = null;
	+ private Thread thread = null;

	private Deconvolution deconvolution;

	public DeconvolutionDialog(Deconvolution deconvolution) {
	super(new JFrame(), deconvolution.getName() + " " + new SimpleDateFormat("dd/MM/yy HH:m:s").format(new Date()));

	this.deconvolution = deconvolution;
	JProgressBar status = new JProgressBar();
	deconvolution.getMonitors().add(new StatusMonitor(status));

	pnCommand = new HTMLPane("Monaco", 100, 100);
	pnCommand.append("p", deconvolution.getCommand());
	pnResume = new HTMLPane("Verdana", 600, 150);

	+ tab.add("Resume", pnResume.getPane());
	+
	pnCommand.setEditable(true);
	pnCommand.addKeyListener(this);
	JPanel bn = new JPanel();
	bn.setLayout(new GridLayout(1, 5));
	bn.setBorder(BorderFactory.createEtchedBorder());
	bn.add(bnRecap);
	bn.add(bnImage);
	bn.add(bnPSF);
	bn.add(bnAlgo);
	bn.add(bnStart);

	status.setAlignmentX(JLabel.CENTER_ALIGNMENT);
	status.setBorder(BorderFactory.createLoweredBevelBorder());
	JToolBar statusBar = new JToolBar();
	statusBar.setBorder(BorderFactory.createLoweredBevelBorder());
	statusBar.setFloatable(false);
	statusBar.setLayout(new BorderLayout());
	statusBar.add(bnHelp, BorderLayout.WEST);
	statusBar.add(status, BorderLayout.CENTER);
	statusBar.add(bnQuit, BorderLayout.EAST);

	JPanel bottom = new JPanel();
	bottom.setLayout(new BoxLayout(bottom, BoxLayout.PAGE_AXIS));
	bottom.add(bn);
	bottom.add(new SystemBar(200));
	bottom.add(statusBar);

	JPanel panel = new JPanel();
	panel.setLayout(new BorderLayout());
	panel.add(pnCommand.getPane(), BorderLayout.NORTH);
	panel.add(bottom, BorderLayout.SOUTH);
	- panel.add(pnResume.getPane(), BorderLayout.CENTER);
	+ panel.add(tab, BorderLayout.CENTER);

	add(panel);
	bnQuit.addActionListener(this);
	bnStart.addActionListener(this);
	bnPSF.addActionListener(this);
	bnImage.addActionListener(this);
	bnAlgo.addActionListener(this);
	bnRecap.addActionListener(this);
	bnHelp.addActionListener(this);

	setMinimumSize(new Dimension(200, 400));
	pack();
	GUI.center(this);
	setVisible(true);

	print(deconvolution.recap());
	}

	@Override
	public void actionPerformed(ActionEvent e) {

	if (e.getSource() == bnStart) {
	if (thread == null) {
	job = bnStart;
	thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}
	else {
	- if (deconvolution != null) deconvolution.abort();
	+ if (deconvolution != null)
	+ deconvolution.abort();
	}
	}
	else if (e.getSource() == bnRecap) {
	if (thread == null) {
	job = bnRecap;
	thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}
	}
	else if (e.getSource() == bnImage) {
	if (thread == null) {
	job = bnImage;
	thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}
	}
	else if (e.getSource() == bnPSF) {
	if (thread == null) {
	job = bnPSF;
	thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}
	}
	else if (e.getSource() == bnAlgo) {
	if (thread == null) {
	job = bnAlgo;
	thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}
	}

	else if (e.getSource() == bnQuit) {
	dispose();
	}
	- else if (e.getSource() == bnHelp) Lab.help();
	+ else if (e.getSource() == bnHelp)
	+ Lab.help();
	}

	@Override
	public void run() {
	bnRecap.setEnabled(false);
	bnAlgo.setEnabled(false);
	bnPSF.setEnabled(false);
	bnImage.setEnabled(false);
	bnStart.setText("Stop");
	String command = pnCommand.getText();
	- System.out.println(">>> " + command);
	deconvolution.setCommand(command);
	if (job == bnStart) {
	- // tab.setSelectedIndex(1);
	+ // tab.setSelectedIndex(1);
	print(deconvolution.recap());
	deconvolution.run();
	print(deconvolution.getDeconvolutionResults());
	}
	else if (job == bnRecap) {
	- // tab.setSelectedIndex(0);
	+ tab.setSelectedIndex(0);
	print(deconvolution.recap());
	}
	else if (job == bnImage) {
	- // tab.setSelectedIndex(0);
	+ tab.setSelectedIndex(0);
	print(deconvolution.checkImage());
	}
	else if (job == bnPSF) {
	- // tab.setSelectedIndex(0);
	+ tab.setSelectedIndex(0);
	print(deconvolution.checkPSF());
	}
	else if (job == bnAlgo) {
	- // tab.setSelectedIndex(0);
	+ tab.setSelectedIndex(0);
	print(deconvolution.checkAlgo());
	}
	bnRecap.setEnabled(true);
	bnAlgo.setEnabled(true);
	bnPSF.setEnabled(true);
	bnImage.setEnabled(true);
	bnStart.setText("Start");
	thread = null;
	}

	private void print(ArrayList<String> lines) {
	pnResume.clear();
	for (String line : lines)
	pnResume.append("p", line);
	}

	+ public void addTableMonitor(String title, TableMonitor tm) {
	+ tab.add(title, tm.getPanel());
	+ }
	+
	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	try {
	int len = pnCommand.getDocument().getLength();
	- String command;
	- command = pnCommand.getDocument().getText(0, len);
	- System.out.println(">>> " + command);
	+ String command = pnCommand.getDocument().getText(0, len);
	deconvolution.setCommand(command);
	print(deconvolution.recap());
	}
	catch (BadLocationException e1) {
	e1.printStackTrace();
	}
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	index 9847abd..7a8c629 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	@@ -1,172 +1,181 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;
	import java.util.concurrent.ExecutionException;
	import java.util.concurrent.ExecutorService;
	import java.util.concurrent.Executors;
	import java.util.concurrent.Future;

	-import signal.Operations;
	-import signal.RealSignal;
	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.FFT;
	+import signal.Operations;
	+import signal.RealSignal;

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

	- protected RealSignal y = null;
	- protected RealSignal h = null;
	+ protected RealSignal y = null;
	+ protected RealSignal h = null;
	protected RealSignal reference = null;

	protected Controller controller = null;
	- protected AbstractFFT fft = null;
	-
	+ protected AbstractFFT fft = null;
	+
	public AbstractAlgorithm() {
	this.controller = new Controller();
	}

	public abstract String getName();
	+
	public abstract String getShortname();
	+
	public abstract boolean isRegularized();
	+
	public abstract boolean isStepControllable();
	+
	public abstract boolean isIterative();
	+
	public abstract boolean isWaveletsBased();
	+
	public abstract void setParameters(double[] params);
	+
	public abstract double getRegularizationFactor();
	+
	public abstract double getStepFactor();
	+
	public abstract double[] getParameters();
	+
	public abstract double[] getDefaultParameters();

	public RealSignal run(Monitors monitors, RealSignal image, RealSignal psf, boolean threaded) {

	String iterations = (isIterative() ? controller.getIterationMax() + " iterations" : "direct");
	monitors.log(getShortname() + " is starting (" + iterations + ")");
	y = image.duplicate();
	h = psf.duplicate();
	controller.setMonitors(monitors);
	controller.start(y);
	h = Operations.circularShift(h);
	if (fft == null)
	fft = FFT.createDefaultFFT(monitors, y.nx, y.ny, y.nz);
	else
	fft.init(monitors, y.nx, y.ny, y.nz);
	monitors.log(getShortname() + " data ready");
	-
	+
	double params[] = getParameters();
	if (params != null) {
	if (params.length > 0) {
	String s = " ";
	for (double param : params)
	s += "" + param + " ";
	monitors.log(getShortname() + s);
	}
	}
	RealSignal x = null;
	try {
	if (threaded == true) {
	ExecutorService pool = Executors.newSingleThreadExecutor();
	Future<RealSignal> future = pool.submit(this);
	x = future.get();
	}
	else {
	x = call();
	}
	}
	catch (InterruptedException ex) {
	ex.printStackTrace();
	x = y.duplicate();
	}
	catch (ExecutionException ex) {
	ex.printStackTrace();
	x = y.duplicate();
	}
	catch (Exception e) {
	e.printStackTrace();
	x = y.duplicate();
	}

	controller.finish(x);
	monitors.log(getName() + " is finished");
	return x;
	}

	public AbstractFFT getFFT() {
	return fft;
	}

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

	public Controller getController() {
	return controller;
	}

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

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

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

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

	- public void setWavelets(String waveletsName) {
	+ public void setWavelets(String waveletsName) {
	}

	-
	@Override
	public String toString() {
	String s = "";
	s += getName();
	s += (isIterative() ? ", " + controller.getIterationMax() + " iterations" : " (direct)");
	- s += (isRegularized() ? ", &lambda=" + getRegularizationFactor() : "") ;
	- s += (isStepControllable() ? ", &gamma=" + getStepFactor() : "") ;
	+ s += (isRegularized() ? ", &lambda=" + getRegularizationFactor() : "");
	+ s += (isStepControllable() ? ", &gamma=" + getStepFactor() : "");
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithmPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithmPanel.java
	index d964304..5c6b1b1 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithmPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithmPanel.java
	@@ -1,25 +1,56 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import javax.swing.JPanel;

	public abstract class AbstractAlgorithmPanel {

	public abstract JPanel getPanelParameters();

	public abstract String getCommand();

	public abstract String getName();

	public abstract String getShortname();

	public abstract String getDocumentation();

	public boolean isNamed(String name) {
	if (name.equals(getShortname().toLowerCase()))
	return true;
	if (name.equals(getName().toLowerCase()))
	return true;
	return false;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java b/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
	index f655e53..632ec12 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Algorithm.java
	@@ -1,135 +1,135 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.ArrayList;

	public class Algorithm {

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

	public static AbstractAlgorithm getDefaultAlgorithm() {
	return new Identity();
	}
	-
	+
	public static AbstractAlgorithm createAlgorithm(String name) {
	if (name == null)
	return getDefaultAlgorithm();
	String n = name.trim().toLowerCase();
	int i = 0;
	-
	+
	if (list.get(i++).isNamed(n))
	return new RegularizedInverseFilter(0.1);
	if (list.get(i++).isNamed(n))
	return new TikhonovRegularizationInverseFilter(1.0);
	if (list.get(i++).isNamed(n))
	return new NaiveInverseFilter();
	if (list.get(i++).isNamed(n))
	return new FISTA(10, 1, 1, "Haar", 3);
	if (list.get(i++).isNamed(n))
	return new ISTA(10, 1, 1, "Haar", 3);
	if (list.get(i++).isNamed(n))
	return new Landweber(10, 1);
	if (list.get(i++).isNamed(n))
	return new LandweberPositivity(10, 1);
	if (list.get(i++).isNamed(n))
	return new RichardsonLucy(10);
	if (list.get(i++).isNamed(n))
	return new RichardsonLucyTV(10, 1);
	if (list.get(i++).isNamed(n))
	return new TikhonovMiller(10, 1, 0.1);
	if (list.get(i++).isNamed(n))
	return new ICTM(10, 1, 0.1);
	if (list.get(i++).isNamed(n))
	return new VanCittert(10, 1);
	if (list.get(i++).isNamed(n))
	return new Identity();
	if (list.get(i++).isNamed(n))
	return new Convolution();
	if (list.get(i++).isNamed(n))
	return new Simulation(0, 1, 0);
	if (list.get(i++).isNamed(n))
	return new NonStabilizedDivision();
	return getDefaultAlgorithm();
	}

	- public static AbstractAlgorithmPanel getPanel(String name) {
	+ public static AbstractAlgorithmPanel getPanel(String name) {
	for (AbstractAlgorithmPanel panel : getAvailableAlgorithms()) {
	if (panel.getShortname().equals(name.trim()))
	return panel;
	if (panel.getName().equals(name.trim()))
	return panel;
	-
	+
	}
	return null;
	}

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

	public static String getDocumentation(String name) {
	for (AbstractAlgorithmPanel algo : getAvailableAlgorithms()) {
	if (name.equals(algo.getName()))
	return algo.getDocumentation();
	}
	return "Unknown Algorithm";
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java b/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	index eb04bd4..f7859cd 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	@@ -1,381 +1,381 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

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

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

	public class Controller {

	- private int iterationsMax = 100;
	- private double timeMax = 1000;
	- private double residuMin = -1;
	-
	- private boolean doResidu = false;
	- private boolean doTime = false;
	- private boolean doReference = false;
	- private boolean doConstraint = false;
	- private boolean doShowStats = false;
	- private boolean doSaveStats = false;
	- private boolean abort = false;
	-
	- private int snapshotResidu = 0;
	- private int snapshotReference = 0;
	- private int snapshotConstraint = 0;
	- private int snapshotSaveStats = 0;
	- private int snapshotShowStats = 0;
	-
	- private double timeStarting = 0;
	- private double memoryStarting = 0;
	- private double residu = Double.MAX_VALUE;
	- private int iterations = 0;
	- private double memoryPeak = 0;
	- private double snr = 0;
	- private double psnr = 0;
	-
	- private Constraint.Mode constraint = Constraint.Mode.NO;
	- private OutputCollection outs = null;
	- private String referenceName = "";
	- private String showstatsName = "";
	- private String savestatsName = "";
	- private RealSignal refImage;
	- private RealSignal prevImage;
	- private RealSignal x;
	-
	- private Timer timer;
	- private AbstractFFT fft;
	-
	- private String algo = "";
	- private float statsInput[];
	-
	- private Monitors monitors = new Monitors();
	+ private int iterationsMax = 100;
	+ private double timeMax = 1000;
	+ private double residuMin = -1;
	+
	+ private boolean doResidu = false;
	+ private boolean doTime = false;
	+ private boolean doReference = false;
	+ private boolean doConstraint = false;
	+ private boolean doShowStats = false;
	+ private boolean doSaveStats = false;
	+ private boolean abort = false;
	+
	+ private int snapshotResidu = 0;
	+ private int snapshotReference = 0;
	+ private int snapshotConstraint = 0;
	+ private int snapshotSaveStats = 0;
	+ private int snapshotShowStats = 0;
	+
	+ private double timeStarting = 0;
	+ private double memoryStarting = 0;
	+ private double residu = Double.MAX_VALUE;
	+ private int iterations = 0;
	+ private double memoryPeak = 0;
	+ private double snr = 0;
	+ private double psnr = 0;
	+
	+ private Constraint.Mode constraint = Constraint.Mode.NO;
	+ private OutputCollection outs = null;
	+ private String referenceName = "";
	+ private String showstatsName = "";
	+ private String savestatsName = "";
	+ private RealSignal refImage;
	+ private RealSignal prevImage;
	+ private RealSignal x;
	+
	+ private Timer timer;
	+ private AbstractFFT fft;
	+
	+ private String algo = "";
	+ private float statsInput[];
	+
	+ private Monitors monitors = new Monitors();

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

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

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

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

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

	public int getIterationMax() {
	return iterationsMax;
	}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

	return ends((RealSignal) null);
	}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

	}

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

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

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

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

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

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

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

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

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

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

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

	public int getIterations() {
	return iterations;
	}

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

	private class Updater extends TimerTask {
	@Override
	public void run() {
	update();
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Convolution.java b/DeconvolutionLab2/src/deconvolution/algorithm/Convolution.java
	index ac32605..1317644 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Convolution.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Convolution.java
	@@ -1,110 +1,109 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class Convolution extends AbstractAlgorithm implements Callable<RealSignal> {

	public Convolution() {
	super();
	}

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

	@Override
	public String getName() {
	return "Convolution";
	}
	-
	+
	@Override
	public String getShortname() {
	return "CONV";
	}
	-
	+
	@Override
	public boolean isRegularized() {
	return false;
	}

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

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

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

	@Override
	public void setParameters(double[] params) {
	}
	-
	+
	@Override
	public double[] getParameters() {
	return new double[] {};
	}
	-
	+
	@Override
	public double[] getDefaultParameters() {
	return new double[] {};
	}
	-
	-
	+
	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}
	-
	+
	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ConvolutionPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/ConvolutionPanel.java
	index cd1453a..90294ef 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ConvolutionPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ConvolutionPanel.java
	@@ -1,41 +1,72 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import javax.swing.JPanel;

	import lab.component.GridPanel;

	public class ConvolutionPanel extends AbstractAlgorithmPanel {
	-
	+
	private Convolution algo = new Convolution();
	-
	+
	@Override
	public JPanel getPanelParameters() {
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\">No parameters</span></html>");
	return pn;
	}
	-
	+
	@Override
	public String getCommand() {
	return "";
	}
	-
	+
	@Override
	public String getName() {
	return algo.getName();
	}

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

	@Override
	public String getDocumentation() {
	- String s = "";
	+ String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>This algorithm is only used for simulation. It convolves the input image with the PSF.</p>";
	return s;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java b/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	index 463a8ec..acfcbca 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	@@ -1,169 +1,169 @@
	/*
	* 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 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;
	-
	+
	+ 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);
	-
	+
	ComplexSignal Z = G.duplicate();
	- RealSignal x = fft.inverse(G);
	+ RealSignal x = fft.inverse(G);
	RealSignal s = x.duplicate();
	RealSignal z = x.duplicate();
	-
	- RealSignal xprev = fft.inverse(G);
	+
	+ RealSignal xprev = fft.inverse(G);
	float pk1 = 1f;
	float pk0 = 1f;
	- float threshold = (float)(lambdagamma0.5);
	+ float threshold = (float) (lambda * gamma * 0.5);
	RealSignal buffer = y.duplicate();
	- while(!controller.ends(x)) {
	+ 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 + 4fpk0pk0)) * 0.5f;
	- update(xprev, x, (pk0-1f)/pk1, s);
	+ pk1 = (1f + (float) Math.sqrt(1f + 4f * pk0 * pk0)) * 0.5f;
	+ update(xprev, x, (pk0 - 1f) / pk1, s);
	}
	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;
	- }
	+ 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 "FISTA";
	}

	@Override
	public String getShortname() {
	return "FISTA";
	}

	@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) {
	+ 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]));
	+ controller.setIterationMax((int) Math.round(params[0]));
	if (params.length > 1)
	- gamma = (float)params[1];
	+ gamma = (float) params[1];
	if (params.length > 2)
	- lambda = (float)params[2];
	+ lambda = (float) params[2];
	if (params.length > 3)
	- scale = (int)params[3];
	+ scale = (int) params[3];
	}
	-
	+
	@Override
	public double[] getDefaultParameters() {
	- return new double[] {10, 1, 0.1};
	+ return new double[] { 10, 1, 0.1 };
	}
	-
	+
	@Override
	public double[] getParameters() {
	- return new double[] {controller.getIterationMax(), gamma, lambda};
	+ 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 86d0e31..271d542 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/FISTAPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/FISTAPanel.java
	@@ -1,136 +1,165 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import java.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 deconvolution.Command;
	+import deconvolutionlab.Config;
	+import deconvolutionlab.Constants;
	import lab.component.GridPanel;
	import lab.component.RegularizationPanel;
	import lab.component.SpinnerRangeDouble;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	import wavelets.AbstractWavelets;
	import wavelets.Wavelets;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;
	-import deconvolutionlab.Constants;

	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 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);

	- private FISTA algo = new FISTA(10, 1, 0.1, "Haar", 3);
	-
	@Override
	public JPanel getPanelParameters() {
	AbstractWavelets wavdef = Wavelets.getDefaultWavelets();
	- double[] params = algo.getDefaultParameters();
	-
	+ double[] params = algo.getDefaultParameters();
	+
	reg = new RegularizationPanel(params[2]);
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	cmbWav.setPreferredSize(Constants.dimParameters);
	cmbScale.setPreferredSize(Constants.dimParameters);
	-
	+
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);
	-
	+
	pn.place(2, 0, 5, 1, reg);
	-
	+
	pn.place(5, 0, "<html><span \"nowrap\"><b>Wavelets</b></span></html>");
	pn.place(5, 2, cmbWav);
	pn.place(5, 3, "<html>Scale</html>");
	pn.place(5, 4, cmbScale);
	-
	+
	Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	Config.register("Algorithm." + algo.getShortname(), "wavelets", cmbWav, wavdef.getName());
	Config.register("Algorithm." + algo.getShortname(), "scale", cmbScale, wavdef.getScales());
	Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	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 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;
	+ String waveletsName = (String) cmbWav.getSelectedItem();
	+ int scale = Integer.parseInt((String) cmbScale.getSelectedItem());
	+ return iter + " " + NumFormat.nice(gamma) + " " + NumFormat.nice(lambda) + " " + waveletsName + " " + scale;
	}
	-
	+
	@Override
	public void actionPerformed(ActionEvent e) {
	Command.command();
	- }
	-
	+ }
	+
	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

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

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

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

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

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java b/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	index 10b47fb..7e7a7b8 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	@@ -1,136 +1,135 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class ICTM extends AbstractAlgorithm implements Callable<RealSignal> {
	-
	- private double gamma = 1.0;
	- private double lambda = 1.0;
	-
	+
	+ private double gamma = 1.0;
	+ private double lambda = 1.0;
	+
	public ICTM(int iter, double gamma, double lambda) {
	super();
	controller.setIterationMax(iter);
	controller.setConstraint(1, Constraint.Mode.NONNEGATIVE);
	this.gamma = gamma;
	this.lambda = lambda;
	}

	@Override
	public RealSignal call() throws Exception {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal A = Operations.delta(gamma, H);
	ComplexSignal L = ComplexSignalFactory.laplacian(Y.nx, Y.ny, Y.nz);
	- ComplexSignal L2 = Operations.multiplyConjugate(lambda*gamma, L, L);
	+ ComplexSignal L2 = Operations.multiplyConjugate(lambda * gamma, L, L);
	A.minus(L2);
	ComplexSignal G = Operations.multiplyConjugate(gamma, H, Y);
	ComplexSignal X = G.duplicate();
	controller.setConstraint(1, Constraint.Mode.NONNEGATIVE);
	- while(!controller.ends(X)) {
	+ while (!controller.ends(X)) {
	X.times(A);
	X.plus(G);
	}
	RealSignal x = fft.inverse(X);
	return x;
	}
	-
	+
	@Override
	public String getName() {
	return "Iterative Contraint Tikhonov-Miller";
	}

	@Override
	public String getShortname() {
	return "ICTM";
	}

	@Override
	public boolean isRegularized() {
	return true;
	}
	-
	+
	@Override
	public boolean isStepControllable() {
	return true;
	}
	-
	+
	@Override
	public boolean isIterative() {
	return true;
	}
	-
	+
	@Override
	public boolean isWaveletsBased() {
	return false;
	}
	-
	+
	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	- controller.setIterationMax((int)Math.round(params[0]));
	+ controller.setIterationMax((int) Math.round(params[0]));
	if (params.length > 1)
	- gamma = (float)params[1];
	+ gamma = (float) params[1];
	if (params.length > 2)
	- lambda = (float)params[2];
	+ lambda = (float) params[2];
	}
	-
	+
	@Override
	public double[] getDefaultParameters() {
	- return new double[] {10, 1, 0.1};
	+ return new double[] { 10, 1, 0.1 };
	}
	-
	+
	@Override
	public double[] getParameters() {
	- return new double[] {controller.getIterationMax(), gamma, lambda};
	+ return new double[] { controller.getIterationMax(), gamma, lambda };
	}

	-
	@Override
	public double getRegularizationFactor() {
	return lambda;
	}
	-
	+
	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ICTMPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/ICTMPanel.java
	index 185733b..7f210c3 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ICTMPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ICTMPanel.java
	@@ -1,114 +1,143 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

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

	+import deconvolution.Command;
	+import deconvolutionlab.Config;
	+import deconvolutionlab.Constants;
	import lab.component.GridPanel;
	import lab.component.RegularizationPanel;
	import lab.component.SpinnerRangeDouble;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;
	-import deconvolutionlab.Constants;

	public class ICTMPanel extends AbstractAlgorithmPanel implements KeyListener, ActionListener, ChangeListener {
	-
	+
	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	private SpinnerRangeDouble spnStep = new SpinnerRangeDouble(1, 0, 2, 0.1, "#.#");
	- private RegularizationPanel reg;
	+ private RegularizationPanel reg;
	+
	+ private ICTM algo = new ICTM(10, 0.1, 1);

	- private ICTM algo = new ICTM(10, 0.1, 1);
	-
	@Override
	public JPanel getPanelParameters() {
	- double[] params = algo.getDefaultParameters();
	+ double[] params = algo.getDefaultParameters();
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	reg = new RegularizationPanel(params[2]);
	-
	+
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);
	-
	+
	pn.place(2, 0, 5, 1, reg);
	-
	+
	Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

	-
	@Override
	public String getCommand() {
	- double gamma = spnStep.get();
	+ double gamma = spnStep.get();
	double lambda = reg.getValue();
	return spnIter.get() + " " + NumFormat.nice(gamma) + " " + NumFormat.nice(lambda);
	}
	-
	+
	@Override
	public void actionPerformed(ActionEvent e) {
	Command.command();
	- }
	-
	+ }
	+
	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}
	-
	+
	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

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

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

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ISTAPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/ISTAPanel.java
	index 7b56017..8ffd206 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ISTAPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ISTAPanel.java
	@@ -1,134 +1,165 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import java.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 deconvolution.Command;
	+import deconvolutionlab.Config;
	+import deconvolutionlab.Constants;
	import lab.component.GridPanel;
	import lab.component.RegularizationPanel;
	import lab.component.SpinnerRangeDouble;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	import wavelets.AbstractWavelets;
	import wavelets.Wavelets;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;
	-import deconvolutionlab.Constants;

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

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

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

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

	reg = new RegularizationPanel(params[2]);

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

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

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

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

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

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

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

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

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

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

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/IdentityPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/IdentityPanel.java
	index 58007d3..d90764a 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/IdentityPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/IdentityPanel.java
	@@ -1,41 +1,72 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import javax.swing.JPanel;

	import lab.component.GridPanel;

	public class IdentityPanel extends AbstractAlgorithmPanel {
	-
	+
	private Identity algo = new Identity();
	-
	+
	@Override
	public JPanel getPanelParameters() {
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\">No parameters</span></html>");
	return pn;
	}
	-
	+
	@Override
	public String getCommand() {
	return "";
	}
	-
	+
	@Override
	public String getName() {
	return algo.getName();
	}

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

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

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java b/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	index 7aac84c..693166d 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	@@ -1,129 +1,130 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class Landweber extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

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

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

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

	@Override
	public String getShortname() {
	return "LW";
	}

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

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

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

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

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

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 10, 1 };
	}
	-
	+
	@Override
	public double[] getParameters() {
	- return new double[] {controller.getIterationMax(), gamma};
	+ return new double[] { controller.getIterationMax(), gamma };
	}
	+
	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}
	-
	+
	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPanel.java
	index fc3f87e..66af4d4 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPanel.java
	@@ -1,78 +1,109 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

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

	+import deconvolution.Command;
	+import deconvolutionlab.Config;
	+import deconvolutionlab.Constants;
	import lab.component.GridPanel;
	import lab.component.SpinnerRangeDouble;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;
	-import deconvolutionlab.Constants;

	-public class LandweberPanel extends AbstractAlgorithmPanel implements ChangeListener{
	+public class LandweberPanel extends AbstractAlgorithmPanel implements ChangeListener {

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

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	-
	+
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);
	-
	+
	pn.place(2, 0, "<html><span \"nowrap\"><b>Regularization</b></span></html>");
	pn.place(2, 1, 4, 1, "<html><span \"nowrap\">No regularization</i></span></html>");
	-
	+
	Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

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

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	- }
	-
	+ }
	+
	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	index d00878c..4c888cf 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	@@ -1,133 +1,133 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class LandweberPositivity extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

	public LandweberPositivity(int iter, double gamma) {
	super();
	controller.setIterationMax(iter);
	controller.setConstraint(1, Constraint.Mode.NONNEGATIVE);
	this.gamma = gamma;
	}

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

	@Override
	public String getName() {
	return "Landweber+Positivity";
	}

	@Override
	public String getShortname() {
	return "LW+";
	}

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

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

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

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

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

	@Override
	public double[] getDefaultParameters() {
	return new double[] { 10, 1 };
	}
	-
	+
	@Override
	public double[] getParameters() {
	- return new double[] {controller.getIterationMax(), gamma};
	+ return new double[] { controller.getIterationMax(), gamma };
	}
	-
	+
	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}
	-
	+
	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivityPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivityPanel.java
	index 658a33e..cc103bc 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivityPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivityPanel.java
	@@ -1,79 +1,109 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

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

	+import deconvolution.Command;
	+import deconvolutionlab.Config;
	+import deconvolutionlab.Constants;
	import lab.component.GridPanel;
	import lab.component.SpinnerRangeDouble;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;
	-import deconvolutionlab.Constants;

	public class LandweberPositivityPanel extends AbstractAlgorithmPanel implements ChangeListener {

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

	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	-
	+
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);

	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);
	-
	+
	pn.place(2, 0, "<html><span \"nowrap\"><b>Regularization</b></span></html>");
	pn.place(2, 1, 4, 1, "<html><span \"nowrap\">No regularization</i></span></html>");
	-
	+
	Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

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

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	- }
	-
	+ }
	+
	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilter.java b/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilter.java
	index 200e329..089b7c2 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilter.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilter.java
	@@ -1,109 +1,109 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class NaiveInverseFilter extends AbstractAlgorithm implements Callable<RealSignal> {

	public NaiveInverseFilter() {
	super();
	}
	-
	+
	@Override
	public RealSignal call() {
	ComplexSignal Y = fft.transform(y);
	ComplexSignal H = fft.transform(h);
	ComplexSignal X = Operations.divideStabilized(Y, H);
	RealSignal x = fft.inverse(X);
	return x;
	}
	-
	+
	@Override
	public String getShortname() {
	return "NIF";
	}

	@Override
	public String getName() {
	return "Naive Inverse Filter";
	}

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

	@Override
	public boolean isStepControllable() {
	return false;
	}
	-
	+
	@Override
	public boolean isIterative() {
	return false;
	}
	-
	+
	@Override
	public boolean isWaveletsBased() {
	return false;
	}
	-
	+
	@Override
	public void setParameters(double[] params) {
	}
	-
	+
	@Override
	public double[] getDefaultParameters() {
	return new double[] {};
	}
	-
	+
	@Override
	public double[] getParameters() {
	return new double[] {};
	}
	-
	+
	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}
	-
	+
	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilterPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilterPanel.java
	index 7ac093c..aad48fe 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilterPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NaiveInverseFilterPanel.java
	@@ -1,46 +1,76 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import javax.swing.JPanel;

	import lab.component.GridPanel;

	public class NaiveInverseFilterPanel extends AbstractAlgorithmPanel {
	-
	+
	private NaiveInverseFilter algo = new NaiveInverseFilter();
	-
	+
	@Override
	public JPanel getPanelParameters() {
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\">No parameters</span></html>");
	return pn;
	}
	-
	+
	@Override
	public String getCommand() {
	return "";
	}
	-
	+
	@Override
	public String getName() {
	return algo.getName();
	}

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

	-
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	index 141acde..94c4421 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	@@ -1,109 +1,109 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class NonStabilizedDivision extends AbstractAlgorithm implements Callable<RealSignal> {

	public NonStabilizedDivision() {
	super();
	}

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

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

	@Override
	public String getShortname() {
	return "DIV";
	}

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

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

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

	@Override
	public boolean isWaveletsBased() {
	return false;
	}
	-
	+
	@Override
	public void setParameters(double[] params) {
	}
	-
	+
	@Override
	public double[] getDefaultParameters() {
	return new double[] {};
	}
	-
	+
	@Override
	public double[] getParameters() {
	return new double[] {};
	}
	-
	+
	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}
	-
	+
	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivisionPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivisionPanel.java
	index 775db9a..40cd77e 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivisionPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivisionPanel.java
	@@ -1,46 +1,76 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import javax.swing.JPanel;

	import lab.component.GridPanel;

	public class NonStabilizedDivisionPanel extends AbstractAlgorithmPanel {

	private NonStabilizedDivision algo = new NonStabilizedDivision();
	-
	+
	@Override
	public JPanel getPanelParameters() {
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\">No parameters</span></html>");
	return pn;
	}
	-
	+
	@Override
	public String getCommand() {
	return "";
	}
	-
	+
	@Override
	public String getName() {
	return algo.getName();
	}

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

	-
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilter.java b/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilter.java
	index db028b1..16211c6 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilter.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilter.java
	@@ -1,123 +1,122 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class RegularizedInverseFilter extends AbstractAlgorithm implements Callable<RealSignal> {

	private double lambda = 0.001;
	-
	+
	public RegularizedInverseFilter(double lambda) {
	super();
	this.lambda = lambda;
	}

	@Override
	public RealSignal call() {
	- ComplexSignal Y = fft.transform(y);
	- ComplexSignal H = fft.transform(h);
	+ ComplexSignal Y = fft.transform(y);
	+ ComplexSignal H = fft.transform(h);
	ComplexSignal H2 = Operations.multiply(H, H);
	- ComplexSignal L = ComplexSignalFactory.laplacian(Y.nx, Y.ny, Y.nz);
	+ ComplexSignal L = ComplexSignalFactory.laplacian(Y.nx, Y.ny, Y.nz);
	ComplexSignal L2 = Operations.multiply(lambda, L, L);
	ComplexSignal FA = Operations.add(H2, L2);
	- ComplexSignal FT = Operations.divideStabilized(H, FA);
	- ComplexSignal X = Operations.multiply(Y, FT);
	+ ComplexSignal FT = Operations.divideStabilized(H, FA);
	+ ComplexSignal X = Operations.multiply(Y, FT);
	RealSignal x = fft.inverse(X);
	return x;
	}
	-
	+
	@Override
	public String getName() {
	return "Regularized Inverse Filter";
	}

	@Override
	public String getShortname() {
	return "RIF";
	}
	-
	+
	@Override
	public boolean isRegularized() {
	return true;
	}

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

	@Override
	public boolean isIterative() {
	return false;
	}
	-
	+
	@Override
	public boolean isWaveletsBased() {
	return false;
	}
	-
	+
	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	- lambda = (float)params[0];
	+ lambda = (float) params[0];
	}
	-
	+
	@Override
	public double[] getDefaultParameters() {
	- return new double[] {0.1};
	+ return new double[] { 0.1 };
	}
	-
	+
	@Override
	public double[] getParameters() {
	- return new double[] {lambda};
	+ return new double[] { lambda };
	}
	-
	-
	+
	@Override
	public double getRegularizationFactor() {
	return lambda;
	}
	-
	+
	@Override
	public double getStepFactor() {
	return 0;
	}
	-
	+
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilterPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilterPanel.java
	index 1e7a7d0..826279b 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilterPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RegularizedInverseFilterPanel.java
	@@ -1,84 +1,115 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

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

	+import deconvolution.Command;
	+import deconvolutionlab.Config;
	import lab.component.GridPanel;
	import lab.component.RegularizationPanel;
	import lab.tools.NumFormat;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;

	public class RegularizedInverseFilterPanel extends AbstractAlgorithmPanel implements KeyListener, ChangeListener {
	-
	- private RegularizationPanel reg;
	- private RegularizedInverseFilter algo = new RegularizedInverseFilter(0.1);
	-
	+
	+ private RegularizationPanel reg;
	+ private RegularizedInverseFilter algo = new RegularizedInverseFilter(0.1);
	+
	@Override
	public JPanel getPanelParameters() {
	- double[] params = algo.getDefaultParameters();
	+ double[] params = algo.getDefaultParameters();
	reg = new RegularizationPanel(params[0]);
	GridPanel pn = new GridPanel(false);
	pn.place(0, 0, reg);
	Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	return pn;
	}
	-
	+
	@Override
	public String getCommand() {
	return NumFormat.nice(reg.getValue());
	}
	-
	+
	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}
	-
	+
	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

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

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

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

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	index 5b7ba9d..b98a130 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	@@ -1,126 +1,126 @@
	/*
	* 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;

	public class RichardsonLucy extends AbstractAlgorithm implements Callable<RealSignal> {

	public RichardsonLucy(int iter) {
	super();
	controller.setIterationMax(iter);
	}
	-
	+
	// x(k+1) = x(k) . Hconj ( y /. H x(k))
	@Override
	public RealSignal call() {
	ComplexSignal H = fft.transform(h);
	ComplexSignal U = new ComplexSignal(y.nx, y.ny, y.nz);
	RealSignal x = y.duplicate();
	RealSignal p = y.duplicate();
	RealSignal u = y.duplicate();
	- while(!controller.ends(x)) {
	+ while (!controller.ends(x)) {
	fft.transform(x, U);
	U.times(H);
	fft.inverse(U, u);
	Operations.divide(y, u, p);
	fft.transform(p, U);
	U.timesConjugate(H);
	fft.inverse(U, u);
	- x.times(u);
	+ x.times(u);
	}
	return x;
	}
	-
	+
	@Override
	public String getName() {
	return "Richardson-Lucy";
	}
	-
	+
	@Override
	public String getShortname() {
	return "RL";
	}

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

	@Override
	public boolean isStepControllable() {
	return false;
	}
	-
	+
	@Override
	public boolean isIterative() {
	return true;
	}
	-
	+
	@Override
	public boolean isWaveletsBased() {
	return false;
	}
	-
	+
	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	- controller.setIterationMax((int)Math.round(params[0]));
	+ controller.setIterationMax((int) Math.round(params[0]));
	}
	-
	+
	@Override
	public double[] getDefaultParameters() {
	- return new double[] {10};
	+ return new double[] { 10 };
	}
	-
	+
	@Override
	public double[] getParameters() {
	- return new double[] {controller.getIterationMax()};
	+ return new double[] { controller.getIterationMax() };
	}
	-
	+
	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}
	-
	+
	@Override
	public double getStepFactor() {
	return 0;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyPanel.java
	index 54a78fd..f15c342 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyPanel.java
	@@ -1,61 +1,92 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

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

	-import lab.component.GridPanel;
	-import lab.component.SpinnerRangeInteger;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	+import lab.component.GridPanel;
	+import lab.component.SpinnerRangeInteger;

	public class RichardsonLucyPanel extends AbstractAlgorithmPanel implements ChangeListener {
	-
	+
	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);

	- private RichardsonLucy algo = new RichardsonLucy(10);
	-
	+ private RichardsonLucy algo = new RichardsonLucy(10);
	+
	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	spnIter.addChangeListener(this);
	return pn;
	}

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

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	}
	-
	+
	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTVPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTVPanel.java
	index 70d89d8..a4fbe82 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTVPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTVPanel.java
	@@ -1,99 +1,129 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

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

	+import deconvolution.Command;
	+import deconvolutionlab.Config;
	import lab.component.GridPanel;
	import lab.component.RegularizationPanel;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;

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

	private SpinnerRangeInteger spnIter = new SpinnerRangeInteger(10, 1, 99999, 1);
	- private RegularizationPanel reg;
	+ private RegularizationPanel reg;
	+
	+ private RichardsonLucyTV algo = new RichardsonLucyTV(10, 0.1);

	- private RichardsonLucyTV algo = new RichardsonLucyTV(10, 0.1);
	-
	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	- reg = new RegularizationPanel(params[1]);
	+ reg = new RegularizationPanel(params[1]);
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	- pn.place(1, 2, spnIter);
	- pn.place(2, 0, 3, 1, reg);
	+ pn.place(1, 2, spnIter);
	+ pn.place(2, 0, 3, 1, reg);
	Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	spnIter.addChangeListener(this);
	return pn;
	}
	-
	+
	@Override
	public String getCommand() {
	double lambda = reg.getValue();
	return spnIter.get() + " " + NumFormat.nice(lambda);
	}
	-
	+
	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

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

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

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

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

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/SimulationPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/SimulationPanel.java
	index 8e82648..19dce0f 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/SimulationPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/SimulationPanel.java
	@@ -1,84 +1,113 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

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

	-import lab.component.GridPanel;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	+import lab.component.GridPanel;

	public class SimulationPanel extends AbstractAlgorithmPanel implements KeyListener {
	-
	+
	private JTextField txtMean;
	private JTextField txtStdev;
	private JTextField txtPoisson;

	- private Simulation algo = new Simulation(0, 0, 0);
	-
	+ private Simulation algo = new Simulation(0, 0, 0);
	+
	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	- txtMean = new JTextField(""+ params[0], 5);
	- txtStdev = new JTextField(""+ params[1], 5);
	- txtPoisson = new JTextField(""+ params[2], 5);
	-
	+ txtMean = new JTextField("" + params[0], 5);
	+ txtStdev = new JTextField("" + params[1], 5);
	+ txtPoisson = new JTextField("" + params[2], 5);
	+
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html>Gaussian (Mean)</html>");
	pn.place(1, 2, txtMean);
	pn.place(2, 0, "<html>Gaussian (Stdev)</html>");
	pn.place(2, 2, txtStdev);
	pn.place(3, 0, "<html>Poisson</html>");
	pn.place(3, 2, txtPoisson);
	txtMean.addKeyListener(this);
	txtStdev.addKeyListener(this);
	txtPoisson.addKeyListener(this);
	Config.register("Algorithm." + algo.getShortname(), "gaussian.mean", txtMean, params[0]);
	Config.register("Algorithm." + algo.getShortname(), "gaussian.stdev", txtStdev, params[1]);
	Config.register("Algorithm." + algo.getShortname(), "poisson", txtPoisson, params[2]);
	return pn;
	}
	-
	+
	@Override
	public String getCommand() {
	- return txtMean.getText() + " " + txtStdev.getText() + " " + txtPoisson.getText();
	+ return txtMean.getText() + " " + txtStdev.getText() + " " + txtPoisson.getText();
	}

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

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

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

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

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	- String s = "";
	+ String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>This algorithm is only used for simulation. It convolves the input image with the PSF and adds some noise.</p>";
	return s;
	}

	-
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMillerPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMillerPanel.java
	index 117ef36..62179db 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMillerPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMillerPanel.java
	@@ -1,113 +1,142 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

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

	+import deconvolution.Command;
	+import deconvolutionlab.Config;
	+import deconvolutionlab.Constants;
	import lab.component.GridPanel;
	import lab.component.RegularizationPanel;
	import lab.component.SpinnerRangeDouble;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;
	-import deconvolutionlab.Constants;

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

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

	- private TikhonovMiller algo = new TikhonovMiller(10, 1, 0.1);
	-
	@Override
	public JPanel getPanelParameters() {
	- double[] params = algo.getDefaultParameters();
	+ double[] params = algo.getDefaultParameters();
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	reg = new RegularizationPanel(params[2]);
	-
	+
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);
	pn.place(2, 0, 5, 1, reg);
	-
	+
	Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

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

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

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

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

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

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilterPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilterPanel.java
	index fa85274..ff6c72d 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilterPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovRegularizationInverseFilterPanel.java
	@@ -1,92 +1,123 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

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

	+import deconvolution.Command;
	+import deconvolutionlab.Config;
	import lab.component.GridPanel;
	import lab.component.RegularizationPanel;
	import lab.tools.NumFormat;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;

	public class TikhonovRegularizationInverseFilterPanel extends AbstractAlgorithmPanel implements ActionListener, ChangeListener, KeyListener {
	-
	- private RegularizationPanel reg;
	- private TikhonovRegularizationInverseFilter algo = new TikhonovRegularizationInverseFilter(0.1);
	-
	+
	+ private RegularizationPanel reg;
	+ private TikhonovRegularizationInverseFilter algo = new TikhonovRegularizationInverseFilter(0.1);
	+
	@Override
	public JPanel getPanelParameters() {
	- double[] params = algo.getDefaultParameters();
	+ double[] params = algo.getDefaultParameters();
	reg = new RegularizationPanel(params[0]);
	GridPanel pn = new GridPanel(false);
	pn.place(0, 0, reg);
	-
	+
	Config.register("Algorithm." + algo.getShortname(), "reg", reg.getText(), "0.1");
	reg.getText().addKeyListener(this);
	reg.getSlider().addChangeListener(this);
	return pn;

	}
	-
	+
	@Override
	public String getCommand() {
	return NumFormat.nice(reg.getValue());
	}
	-
	+
	@Override
	public void stateChanged(ChangeEvent e) {
	reg.getText().removeKeyListener(this);
	reg.updateFromSlider();
	Command.command();
	reg.getText().addKeyListener(this);
	}

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

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

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

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

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/VanCittertPanel.java b/DeconvolutionLab2/src/deconvolution/algorithm/VanCittertPanel.java
	index ec2ff25..996b573 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/VanCittertPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/VanCittertPanel.java
	@@ -1,75 +1,106 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution.algorithm;

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

	+import deconvolution.Command;
	+import deconvolutionlab.Config;
	+import deconvolutionlab.Constants;
	import lab.component.GridPanel;
	import lab.component.SpinnerRangeDouble;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	-import deconvolution.Command;
	-import deconvolutionlab.Config;
	-import deconvolutionlab.Constants;

	public class VanCittertPanel extends AbstractAlgorithmPanel implements ChangeListener {

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

	- private VanCittert algo = new VanCittert(10, 1);
	-
	+ private VanCittert algo = new VanCittert(10, 1);
	+
	@Override
	public JPanel getPanelParameters() {
	double[] params = algo.getDefaultParameters();
	-
	+
	spnIter.setPreferredSize(Constants.dimParameters);
	spnStep.setPreferredSize(Constants.dimParameters);
	GridPanel pn = new GridPanel(false);
	pn.place(1, 0, "<html><span \"nowrap\"><b>Iterations</b></span></html>");
	pn.place(1, 1, "<html><span \"nowrap\"><i>N</i></span></html>");
	pn.place(1, 2, spnIter);
	pn.place(1, 3, "<html><span \"nowrap\">Step <i>γ</i></span></html>");
	pn.place(1, 4, spnStep);
	-
	+
	Config.register("Algorithm." + algo.getShortname(), "iterations", spnIter, params[0]);
	Config.register("Algorithm." + algo.getShortname(), "step", spnStep, params[1]);
	spnIter.addChangeListener(this);
	spnStep.addChangeListener(this);
	return pn;
	}

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

	@Override
	public void stateChanged(ChangeEvent e) {
	Command.command();
	- }
	-
	+ }
	+
	@Override
	public String getName() {
	return algo.getName();
	}

	@Override
	public String getShortname() {
	return algo.getShortname();
	}
	-
	+
	@Override
	public String getDocumentation() {
	String s = "";
	s += "<h1>" + getName() + "</h1>";
	s += "<p>Iterative: " + algo.isIterative() + "</p>";
	s += "<p>Step controllable: " + algo.isStepControllable() + "</p>";
	s += "<p>Regularization: " + algo.isRegularized() + "</p>";
	s += "<p>Wavelet-base: " + algo.isWaveletsBased() + "</p>";
	s += "<p>Shortname: " + getShortname() + "</p>";
	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/Constants.java b/DeconvolutionLab2/src/deconvolutionlab/Constants.java
	index faf23f5..97dc944 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/Constants.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/Constants.java
	@@ -1,65 +1,65 @@
	/*
	* 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.awt.Dimension;

	public class Constants {

	- public static String name = "DeconvolutionLab2";
	+ public static String name = "DeconvolutionLab2 [Beta 1]";
	public static String copyright = "\u00A9 2010-2017. Biomedical Imaging Group, EPFL.";

	public static String url = "http://bigwww.epfl.ch/deconvolution/";
	public static String reference =
	"D. Sage, L. Donati, F. Soulez, D. Fortun, A. Seitz, R. Guiet, C. Vonesch, M Unser " +
	"DeconvolutionLab2 : An open-source software for deconvolution microscopy " +
	"Methods, 2017.";

	public static String version = "(Beta 24.01.2017)";

	public static String authors =
	"Daniel Sage, " +
	"Cédric Vonesch, " +
	"Guillaume Schmit, " +
	"Pierre Besson, " +
	"Raquel Terrés Cristofani, " +
	"Alessandra Griffa";

	public static String help =
	"<h1>" + name + "</h1>" +
	"<h2>" + version + "</h2>";

	public static int widthGUI = 500;
	public static Dimension dimParameters = new Dimension(88, 25);


	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/LabImageSelector.java b/DeconvolutionLab2/src/deconvolutionlab/LabImageSelector.java
	index 185d73b..cd5d8c9 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/LabImageSelector.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/LabImageSelector.java
	@@ -1,140 +1,147 @@
	package deconvolutionlab;

	-import ij.ImagePlus;
	-import ij.WindowManager;
	-import ij.gui.GUI;
	-
	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 ij.ImagePlus;
	+import ij.WindowManager;
	+import ij.gui.GUI;
	+
	public class LabImageSelector extends PlatformImageSelector {

	@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();
	- DefaultListModel listModel = new DefaultListModel();
	- if (list != null)
	+
	+ 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 = new JList(listModel);
	- list.setSelectionMode(ListSelectionModel.SINGLE_INTERVAL_SELECTION);
	- JScrollPane listScroller = new JScrollPane(list);
	- listScroller.setPreferredSize(new Dimension(250, 80));
	- JPanel bn = new JPanel(new GridLayout(1, 2));
	- bn.add(bnCancel);
	- bn.add(bnOK);
	- JPanel panel = new JPanel(new BorderLayout());
	- panel.add(listScroller, BorderLayout.CENTER);
	+ 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(5, 5, 5, 5));
	+ 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) {
	}

	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/Output.java b/DeconvolutionLab2/src/deconvolutionlab/Output.java
	index 3b662a2..41e5c88 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/Output.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/Output.java
	@@ -1,311 +1,335 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab;

	import java.io.File;

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

	public class Output {

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

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

	private int px = 0;
	private int py = 0;
	private int pz = 0;
	private boolean center = true;

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

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

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

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

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

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

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

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

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

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

	public View getView() {
	return view;
	}

	public String getName() {
	return name;
	}
	-
	+
	public void setPath1(String path) {
	this.path = path;
	}

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

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

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

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

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

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

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

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

	@Override
	public String toString() {
	String t = type.name().toLowerCase();
	String v = view.name().toLowerCase();
	String d = dynamic.name().toLowerCase();
	String f = frequency > 0 ? " every " + frequency + " iterations" : "";
	String k = (center ? "" : " keypoint = (" + px + "," + py + "," + pz + ")");
	return v + " " + name + " format = (" + d + ", " + t + ") " + k + f;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java b/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java
	index 884d38b..65a34a8 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java
	@@ -1,86 +1,86 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab;

	import java.util.ArrayList;

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

	public class OutputCollection {
	-
	+
	private ArrayList<Output> list = new ArrayList<Output>();
	-
	+
	public void setPath(String path) {
	- for(Output out : list)
	+ for (Output out : list)
	out.setPath1(path);
	}
	-
	+
	public void add(Output out) {
	if (out != null) {
	list.add(out);
	}
	}
	-
	+
	public boolean hasShow(int iterations) {
	boolean flag = false;
	for (Output out : list)
	flag = flag \| out.is(iterations);
	return flag;
	}
	-
	+
	public void executeFinal(Monitors monitors, RealSignal signal, Controller controller) {
	- for(Output out : list)
	+ for (Output out : list)
	if (out != null)
	out.execute(monitors, signal, controller, false);
	}
	-
	+
	public void executeIterative(Monitors monitors, RealSignal signal, Controller controller) {
	- for(Output out : list)
	+ for (Output out : list)
	if (out != null)
	out.execute(monitors, signal, controller, true);
	}

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

	}
	-
	+
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/Platform.java b/DeconvolutionLab2/src/deconvolutionlab/Platform.java
	index 45dec63..52df21f 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/Platform.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/Platform.java
	@@ -1,76 +1,74 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab;

	-import imagej.IJImager;
	-
	import java.util.ArrayList;

	+import imagej.IJImager;
	import plugins.sage.deconvolutionlab.IcyImager;
	-import deconvolutionlab.monitor.Monitors;

	public enum Platform {
	-
	+
	IMAGEJ, ICY, STANDALONE, MATLAB;
	-
	+
	public static ArrayList<PlatformImager> getImagers() {
	ArrayList<PlatformImager> imagers = new ArrayList<PlatformImager>();
	try {
	PlatformImager imager = new IJImager();
	if (imager != null) {
	imagers.add(imager);
	}
	}
	- catch(NoClassDefFoundError ex) {
	+ catch (NoClassDefFoundError ex) {
	}

	try {
	PlatformImager imager = new IcyImager();
	if (imager != null) {
	imagers.add(imager);
	}
	}
	- catch(NoClassDefFoundError ex) {
	+ catch (NoClassDefFoundError ex) {
	}
	-
	+
	imagers.add(new LabImager());
	return imagers;
	}
	-
	+
	public static ArrayList<String> getNameImagers() {
	ArrayList<PlatformImager> imagers = getImagers();
	ArrayList<String> names = new ArrayList<String>();
	- for(PlatformImager imager : imagers)
	+ for (PlatformImager imager : imagers)
	names.add(imager.getName());
	return names;
	}
	};
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/PlatformImageSelector.java b/DeconvolutionLab2/src/deconvolutionlab/PlatformImageSelector.java
	index d8a746d..279a9de 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/PlatformImageSelector.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/PlatformImageSelector.java
	@@ -1,7 +1,39 @@
	+/*
	+ * 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;

	public abstract class PlatformImageSelector {
	-
	+
	public abstract String getSelectedImage();
	+
	public abstract boolean isSelectable();
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/dialog/BatchDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/BatchDialog.java
	index b5f8e74..ad5bec2 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/BatchDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/BatchDialog.java
	@@ -1,158 +1,156 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.dialog;

	-import ij.gui.GUI;
	-
	import java.awt.BorderLayout;
	import java.awt.Dimension;
	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.JButton;
	import javax.swing.JDialog;
	import javax.swing.JFrame;
	import javax.swing.JPanel;
	import javax.swing.JTextField;

	-import lab.component.GridPanel;
	-import lab.component.HTMLPane;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.modules.BatchModule;
	+import ij.gui.GUI;
	+import lab.component.GridPanel;
	+import lab.component.HTMLPane;

	public class BatchDialog extends JDialog implements ActionListener, WindowListener {

	- private JTextField txt = new JTextField("job", 10);
	+ private JTextField txt = new JTextField("job", 10);
	private HTMLPane pnCommand;

	- private JButton bnAdd = new JButton("Add Job");
	- private JButton bnCancel = new JButton("Cancel");
	+ private JButton bnAdd = new JButton("Add Job");
	+ private JButton bnCancel = new JButton("Cancel");

	private BatchModule module;

	public BatchDialog(BatchModule module) {
	super(new JFrame(), "Batch");
	-
	+
	this.module = module;
	-
	+
	txt.setText("job" + module.getCountJob());
	-
	+
	Deconvolution deconvolution = new Deconvolution(Command.command());
	pnCommand = new HTMLPane("Monaco", 300, 100);
	pnCommand.append("p", deconvolution.getCommand());
	pnCommand.setEditable(true);
	-
	+
	GridPanel pn = new GridPanel(true, 5);
	pn.place(1, 0, "Job Name");
	pn.place(1, 1, txt);
	-
	+
	GridPanel bn = new GridPanel(false);
	bn.place(11, 0, bnCancel);
	bn.place(11, 1, bnAdd);
	pn.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));

	JPanel panel = new JPanel();
	panel.setLayout(new BorderLayout());
	panel.add(pn, BorderLayout.NORTH);
	panel.add(pnCommand.getPane(), BorderLayout.CENTER);
	panel.add(bn, BorderLayout.SOUTH);

	bnAdd.addActionListener(this);
	bnCancel.addActionListener(this);
	-
	+
	add(panel);
	- pack();
	+ pack();
	addWindowListener(this);
	GUI.center(this);
	setModal(true);
	setVisible(true);
	setMinimumSize(new Dimension(400, 300));
	-
	+
	}

	private void addJob() {
	module.addJob(txt.getText(), pnCommand.getText());
	}
	-
	+
	@Override
	public void actionPerformed(ActionEvent e) {
	if (e.getSource() == bnAdd) {
	addJob();
	bnAdd.removeActionListener(this);
	bnCancel.removeActionListener(this);
	dispose();
	return;
	}
	else if (e.getSource() == bnCancel) {
	bnAdd.removeActionListener(this);
	bnCancel.removeActionListener(this);
	dispose();
	}
	}

	@Override
	public void windowOpened(WindowEvent e) {
	}

	@Override
	public void windowClosing(WindowEvent e) {
	addJob();
	dispose();
	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) {
	}

	-
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/dialog/MainDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/LabDialog.java
	similarity index 91%
	rename from DeconvolutionLab2/src/deconvolutionlab/dialog/MainDialog.java
	rename to DeconvolutionLab2/src/deconvolutionlab/dialog/LabDialog.java
	index 833b3bc..2652188 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/MainDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/LabDialog.java
	@@ -1,384 +1,365 @@
	/*
	* 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.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.JLabel;
	import javax.swing.JPanel;
	-import javax.swing.JProgressBar;
	import javax.swing.JTabbedPane;
	-import javax.swing.JTextField;
	-import javax.swing.JToolBar;
	import javax.swing.border.Border;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	-import lab.component.PanelImage;
	-import lab.system.SystemPanel;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	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.MonitoringModule;
	import deconvolutionlab.modules.OutputModule;
	import deconvolutionlab.modules.PSFModule;
	-import deconvolutionlab.monitor.AbstractMonitor;
	-import deconvolutionlab.monitor.StatusMonitor;
	+import lab.component.PanelImage;
	+import lab.system.SystemPanel;

	-public class MainDialog extends JDialog implements ComponentListener, ActionListener, ChangeListener, WindowListener {
	+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 MonitoringModule monitoring;

	private ControllerModule controller;

	private GroupedModulePanel panelDeconv;
	private GroupedModulePanel panelAdvanc;
	private GroupedModulePanel panelProgra;
	private GroupedModulePanel panelAbout;
	- //private JProgressBar status = new JProgressBar();
	-
	private AbstractModule modules[];

	- public MainDialog() {
	+ 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();
	monitoring = new MonitoringModule(false);

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

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

	addWindowListener(this);
	addComponentListener(this);
	((GroupedModulePanel) tab.getSelectedComponent()).organize();
	- setMinimumSize(new Dimension(400, 400));
	+ 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);
	panelProgra = new GroupedModulePanel(buildProgrammingPanel(), this);
	panelAbout = new GroupedModulePanel(buildAboutPanel(), this);
	PanelImage bottom = new PanelImage("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);
	- /*
	- status.setAlignmentX(JLabel.CENTER_ALIGNMENT);
	- status.setBorder(BorderFactory.createLoweredBevelBorder());
	- JToolBar statusBar = new JToolBar();
	- statusBar.setBorder(BorderFactory.createEmptyBorder());
	- statusBar.setFloatable(false);
	- statusBar.setLayout(new BorderLayout());
	- statusBar.add(bnHelp, BorderLayout.WEST);
	- statusBar.add(status, BorderLayout.CENTER);
	- statusBar.add(bnQuit, BorderLayout.EAST);
	- */

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

	JPanel base = new JPanel(new BorderLayout());
	base.add(bottom, BorderLayout.CENTER);
	//base.add(statusBar, BorderLayout.SOUTH);

	add(tab, BorderLayout.CENTER);
	add(base, BorderLayout.SOUTH);

	bnBatch.addActionListener(this);
	bnRun.addActionListener(this);
	bnLaunch.addActionListener(this);
	bnClose.addActionListener(this);
	bnHelp.addActionListener(this);
	bnQuit.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();
	close();
	dispose();
	}
	else if (e.getSource() == bnQuit) {
	close();
	dispose();
	}
	else if (e.getSource() == bnBatch) {
	tab.setSelectedIndex(2);
	batch.expand();
	new BatchDialog(batch);
	}
	else if (e.getSource() == bnLaunch) {
	- new Deconvolution(Command.command()).launch("");
	+ new Deconvolution(Command.command()).launch("", false);
	}
	else if (e.getSource() == bnRun) {
	- new Deconvolution(Command.command()).deconvolve();
	+ 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(monitoring);
	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(command);
	list.add(language);
	list.add(batch);
	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();
	close();
	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);
	bnQuit.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) {
	}

	@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(panelProgra);
	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/dialog/OutputDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/OutputDialog.java
	index 17bf32d..73a8615 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/OutputDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/OutputDialog.java
	@@ -1,236 +1,235 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.dialog;

	-import ij.gui.GUI;
	-
	import java.awt.Component;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;

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

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

	public class OutputDialog extends JDialog implements ActionListener, ChangeListener {

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

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

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

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

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

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

	GridPanel pn = new GridPanel(view.name());
	pn.place(0, 0, "Name");
	pn.place(0, 1, 2, 1, txtName);

	pn.place(1, 0, "Dynamic");
	pn.place(1, 1, cmbDynamic);
	pn.place(2, 0, "Type");
	pn.place(2, 1, cmbType);
	pn.place(2, 2, lblBit);

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

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

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

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

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

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

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

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

	private void update() {

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

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

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

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

	public Output getOut() {
	return out;
	}

	public boolean wasCancel() {
	return cancel;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/dialog/PatternDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/PatternDialog.java
	index cbd334e..a936e05 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/PatternDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/PatternDialog.java
	@@ -1,227 +1,226 @@
	/*
	* 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 ij.gui.GUI;
	-
	import java.awt.BorderLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;
	import java.awt.event.WindowEvent;
	import java.awt.event.WindowListener;
	import java.io.File;
	import java.util.regex.Pattern;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JDialog;
	import javax.swing.JFrame;
	import javax.swing.JLabel;
	import javax.swing.JPanel;
	import javax.swing.JTextField;

	+import ij.gui.GUI;
	import lab.component.GridPanel;

	public class PatternDialog extends JDialog implements ActionListener, WindowListener, KeyListener {

	- private JTextField txt = new JTextField("");
	- private JLabel lblDir = new JLabel("");
	- private JLabel lbl1 = new JLabel(".tif (only tif files)");
	- private JLabel lbl2 = new JLabel("Empty to take all files");
	- private JLabel lblCount = new JLabel("count files");
	+ private JTextField txt = new JTextField("");
	+ private JLabel lblDir = new JLabel("");
	+ private JLabel lbl1 = new JLabel(".tif (only tif files)");
	+ private JLabel lbl2 = new JLabel("Empty to take all files");
	+ private JLabel lblCount = new JLabel("count files");

	- private JButton bnCount = new JButton("Count");
	- private JButton bnOK = new JButton("OK");
	- private JButton bnCancel = new JButton("Cancel");
	- private boolean cancel = false;
	+ private JButton bnCount = new JButton("Count");
	+ private JButton bnOK = new JButton("OK");
	+ private JButton bnCancel = new JButton("Cancel");
	+ private boolean cancel = false;

	- private File file;
	- private String command = "";
	- private String name = "";
	+ private File file;
	+ private String command = "";
	+ private String name = "";

	public PatternDialog(File file) {
	super(new JFrame(), "Pattern");
	lblDir.setText(file.getAbsolutePath());
	lblDir.setBorder(BorderFactory.createEtchedBorder());
	lbl1.setBorder(BorderFactory.createEtchedBorder());
	lbl2.setBorder(BorderFactory.createEtchedBorder());
	lblCount.setBorder(BorderFactory.createEtchedBorder());
	this.file = file;
	GridPanel pn = new GridPanel(true, 5);
	pn.place(0, 0, "Directory");
	pn.place(0, 1, lblDir);
	pn.place(1, 0, "Pattern");
	pn.place(1, 1, txt);
	pn.place(2, 0, "Example 1");
	pn.place(2, 1, lbl1);
	pn.place(3, 0, "Example 2");
	pn.place(3, 1, lbl2);
	pn.place(4, 0, "Count");
	pn.place(4, 1, lblCount);

	GridPanel bn = new GridPanel(false);
	bn.place(11, 0, bnCancel);
	bn.place(11, 1, bnCount);
	bn.place(11, 2, bnOK);

	pn.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));

	bnCount.addActionListener(this);
	bnOK.addActionListener(this);
	bnCancel.addActionListener(this);
	txt.addKeyListener(this);
	JPanel panel = new JPanel(new BorderLayout());
	panel.add(pn, BorderLayout.CENTER);
	panel.add(bn, BorderLayout.SOUTH);
	add(panel);
	pack();
	update();
	-
	+
	addWindowListener(this);
	GUI.center(this);
	setModal(true);
	-
	+
	}

	private void update() {
	command = "";
	name = "";
	if (file == null)
	return;
	if (!file.exists())
	return;
	if (!file.isDirectory())
	return;

	String list[] = file.list();
	int count = 0;
	int n = list.length;
	String regex = txt.getText().trim();
	Pattern pattern = Pattern.compile(regex);
	for (int i = 0; i < n; i++)
	if (pattern.matcher(list[i]).find())
	count++;
	if (!regex.trim().equals(""))
	- command = file.getAbsolutePath() + " pattern " + regex;
	- else
	+ command = file.getAbsolutePath() + " pattern " + regex;
	+ else
	command = file.getAbsolutePath();
	name = file.getName();
	lblCount.setText("" + n + " files in dir, " + count + " matched files");
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	if (e.getSource() == bnCount) {
	update();
	}
	else if (e.getSource() == bnCancel) {
	bnCount.removeActionListener(this);
	bnOK.removeActionListener(this);
	bnCancel.removeActionListener(this);
	txt.removeKeyListener(this);
	dispose();
	cancel = true;
	command = "";
	name = "";
	-
	+
	return;
	}
	else if (e.getSource() == bnOK) {
	update();
	bnCount.removeActionListener(this);
	bnOK.removeActionListener(this);
	bnCancel.removeActionListener(this);
	txt.removeKeyListener(this);
	dispose();
	cancel = false;
	}
	}

	public String getCommand() {
	return command;
	}
	-
	+
	public String getDirName() {
	return name;
	}

	public boolean wasCancel() {
	return cancel;
	}

	@Override
	public void windowOpened(WindowEvent e) {
	}

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

	@Override
	- public void keyTyped(KeyEvent e) {
	- }
	+ public void keyTyped(KeyEvent e) {
	+ }

	@Override
	- public void keyPressed(KeyEvent e) {
	- }
	+ public void keyPressed(KeyEvent e) {
	+ }

	@Override
	- public void keyReleased(KeyEvent e) {
	- update();
	- }
	+ public void keyReleased(KeyEvent e) {
	+ update();
	+ }
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/dialog/SyntheticDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/SyntheticDialog.java
	index 06f86b1..bf68e73 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/SyntheticDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/SyntheticDialog.java
	@@ -1,313 +1,312 @@
	/*
	* 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 ij.gui.GUI;
	-
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	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.JComboBox;
	import javax.swing.JDialog;
	import javax.swing.JFrame;
	import javax.swing.JLabel;

	import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.Monitors;
	+import ij.gui.GUI;
	import lab.component.GridPanel;
	import lab.component.SpinnerRangeDouble;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	import signal.RealSignal;
	import signal.factory.SignalFactory;

	public class SyntheticDialog extends JDialog implements ActionListener, WindowListener {

	private SpinnerRangeDouble spnSignal = new SpinnerRangeDouble(100, -999999, 999999, 1);
	private SpinnerRangeDouble spnBackground = new SpinnerRangeDouble(0, -999999, 999999, 1);

	private SpinnerRangeInteger spnWidth = new SpinnerRangeInteger(128, 1, 9999, 1);
	private SpinnerRangeInteger spnHeight = new SpinnerRangeInteger(128, 1, 9999, 1);
	private SpinnerRangeInteger spnSlices = new SpinnerRangeInteger(32, 1, 9999, 1);

	private SpinnerRangeDouble spnCenterX = new SpinnerRangeDouble(0.5, -10, 10, 0.05);
	private SpinnerRangeDouble spnCenterY = new SpinnerRangeDouble(0.5, -10, 10, 0.05);
	private SpinnerRangeDouble spnCenterZ = new SpinnerRangeDouble(0.5, -10, 10, 0.05);

	private SpinnerRangeDouble spnParameter1 = new SpinnerRangeDouble(10, -9999, 9999, 1);
	private SpinnerRangeDouble spnParameter2 = new SpinnerRangeDouble(10, -9999, 9999, 1);
	private SpinnerRangeDouble spnParameter3 = new SpinnerRangeDouble(10, -9999, 9999, 1);

	private JLabel lbl1 = new JLabel("Parameters 1 of the shape");
	private JLabel lbl2 = new JLabel("Parameters 2 of the shape");
	private JLabel lbl3 = new JLabel("Parameters 3 of the shape");

	private JComboBox<String> cmbShapes;
	private JButton bnShow = new JButton("Show");
	private JButton bnOK = new JButton("OK");
	private JButton bnCancel = new JButton("Cancel");
	private boolean cancel = false;

	private String shape;
	private String command;

	public SyntheticDialog(ArrayList<SignalFactory> list) {
	super(new JFrame(), "Synthetic");
	String[] cmb = new String[list.size()];
	for (int i = 0; i < list.size(); i++) {
	cmb[i] = list.get(i).getName();
	}
	cmbShapes = new JComboBox<String>(cmb);
	-
	+
	GridPanel pnIntensity = new GridPanel("Intensity", 3);
	pnIntensity.place(1, 0, "Signal Intensity");
	pnIntensity.place(1, 1, spnSignal);
	pnIntensity.place(2, 0, "Background Intensity");
	pnIntensity.place(2, 1, spnBackground);
	-
	+
	GridPanel pnSize = new GridPanel("Dimension", 3);
	pnSize.place(1, 0, "Width [pixels] (nx)");
	pnSize.place(1, 1, spnWidth);
	pnSize.place(2, 0, "Height [pixels] (ny)");
	pnSize.place(2, 1, spnHeight);
	pnSize.place(3, 0, "Number of Slices (nz)");
	pnSize.place(3, 1, spnSlices);

	GridPanel pnCenter = new GridPanel("Center", 3);
	pnCenter.place(4, 0, "Center [% of nx] (cx)");
	pnCenter.place(4, 1, spnCenterX);
	pnCenter.place(5, 0, "Center [% of ny] (cy)");
	pnCenter.place(5, 1, spnCenterY);
	pnCenter.place(7, 0, "Center [% of nz] (cz)");
	pnCenter.place(7, 1, spnCenterZ);

	GridPanel pnParams = new GridPanel("Specific Parameters", 3);
	pnParams.place(8, 0, lbl1);
	pnParams.place(8, 1, spnParameter1);
	pnParams.place(9, 0, lbl2);
	pnParams.place(9, 1, spnParameter2);
	pnParams.place(10, 0, lbl3);
	pnParams.place(10, 1, spnParameter3);

	- GridPanel pn = new GridPanel(false);
	+ GridPanel pn = new GridPanel(false);
	pn.place(0, 0, 3, 1, cmbShapes);
	pn.place(1, 0, 3, 1, pnIntensity);
	pn.place(2, 0, 3, 1, pnParams);
	pn.place(3, 0, 3, 1, pnSize);
	pn.place(4, 0, 3, 1, pnCenter);
	pn.place(11, 0, bnCancel);
	pn.place(11, 1, bnShow);
	pn.place(11, 2, bnOK);
	-
	+
	pn.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));

	bnShow.addActionListener(this);
	bnOK.addActionListener(this);
	bnCancel.addActionListener(this);
	cmbShapes.addActionListener(this);
	add(pn);
	pack();
	updateInterface();
	addWindowListener(this);
	GUI.center(this);
	setModal(true);
	}

	private void updateInterface() {
	- SignalFactory factory = SignalFactory.get((String)cmbShapes.getSelectedItem());
	+ SignalFactory factory = SignalFactory.get((String) cmbShapes.getSelectedItem());
	String labels[] = factory.getParametersName();
	lbl1.setVisible(false);
	lbl2.setVisible(false);
	lbl3.setVisible(false);
	if (labels.length >= 1) {
	lbl1.setVisible(true);
	lbl1.setText(labels[0]);
	}
	if (labels.length >= 2) {
	lbl2.setVisible(true);
	lbl2.setText(labels[1]);
	}
	if (labels.length >= 3) {
	lbl3.setVisible(true);
	lbl3.setText(labels[2]);
	}
	double params[] = factory.getParameters();
	spnParameter1.setVisible(false);
	spnParameter2.setVisible(false);
	spnParameter3.setVisible(false);
	if (params.length >= 1) {
	spnParameter1.setVisible(true);
	spnParameter1.set(params[0]);
	}
	if (params.length >= 2) {
	spnParameter2.setVisible(true);
	spnParameter2.set(params[1]);
	}
	if (params.length >= 3) {
	spnParameter3.setVisible(true);
	spnParameter3.set(params[2]);
	}
	pack();
	-
	+
	}
	-
	+
	@Override
	public void actionPerformed(ActionEvent e) {
	if (e.getSource() == bnShow) {
	- SignalFactory factory = SignalFactory.get((String)cmbShapes.getSelectedItem());
	+ SignalFactory factory = SignalFactory.get((String) cmbShapes.getSelectedItem());
	double params[] = factory.getParameters();
	factory.setParameters(params);
	factory.center(spnCenterX.get(), spnCenterX.get(), spnCenterX.get());
	RealSignal signal = factory.generate(spnWidth.get(), spnWidth.get(), spnWidth.get());
	Lab.show(Monitors.createDefaultMonitor(), signal, factory.getName());
	}
	if (e.getSource() == cmbShapes) {
	updateInterface();
	}
	if (e.getSource() == bnCancel) {
	dispose();
	cancel = true;
	shape = "";
	command = "";
	return;
	}
	if (e.getSource() == bnOK) {
	int nx = spnWidth.get();
	int ny = spnHeight.get();
	int nz = spnSlices.get();
	- shape = (String)cmbShapes.getSelectedItem();
	+ shape = (String) cmbShapes.getSelectedItem();
	command = shape + " " + spnSignal.get() + " " + spnBackground.get() + " ";
	SignalFactory factory = SignalFactory.get(shape);
	int n = factory.getParameters().length;
	if (n >= 1) {
	command += "" + spnParameter1.get();
	if (n >= 2)
	command += " " + spnParameter2.get();
	if (n >= 3)
	command += " " + spnParameter3.get();
	command += " ";
	}
	command += " size " + nx + " " + ny + " " + nz + " ";
	if (spnCenterX.get() != 0.5 \|\| spnCenterY.get() != 0.5 \|\| spnCenterZ.get() != 0.5) {
	double cx = Math.round(spnCenterX.get() * 1000000) / 1000000.0;
	double cy = Math.round(spnCenterY.get() * 1000000) / 1000000.0;
	double cz = Math.round(spnCenterZ.get() * 1000000) / 1000000.0;
	- command += " center " + cx + " " + cy + " " + cz + " ";
	+ command += " center " + cx + " " + cy + " " + cz + " ";
	}
	dispose();
	cancel = false;
	}
	}

	public void setParameters(String name, String parameters) {
	double params[] = NumFormat.parseNumbers(parameters);
	cmbShapes.setSelectedItem(name);
	SignalFactory factory = SignalFactory.getFactoryByName(name);
	if (factory == null)
	return;
	int np = factory.getParameters().length;
	if (params.length > 0)
	spnSignal.set(params[0]);
	if (params.length > 1)
	spnBackground.set(params[1]);
	- if (params.length > 2+np)
	- spnWidth.set((int)params[2+np]);
	- if (params.length > 3+np)
	- spnHeight.set((int)params[3+np]);
	- if (params.length > 4+np)
	- spnSlices.set((int)params[4+np]);
	- if (params.length > 5+np)
	- spnCenterX.set(params[5+np]);
	- if (params.length > 6+np)
	- spnCenterY.set(params[6+np]);
	- if (params.length > 7+np)
	- spnCenterZ.set(params[7+np]);
	-
	- if (np >= 1 && params.length > 2+np)
	+ if (params.length > 2 + np)
	+ spnWidth.set((int) params[2 + np]);
	+ if (params.length > 3 + np)
	+ spnHeight.set((int) params[3 + np]);
	+ if (params.length > 4 + np)
	+ spnSlices.set((int) params[4 + np]);
	+ if (params.length > 5 + np)
	+ spnCenterX.set(params[5 + np]);
	+ if (params.length > 6 + np)
	+ spnCenterY.set(params[6 + np]);
	+ if (params.length > 7 + np)
	+ spnCenterZ.set(params[7 + np]);
	+
	+ if (np >= 1 && params.length > 2 + np)
	spnParameter1.set(params[2]);
	- if (np >= 2 && params.length > 3+np)
	+ if (np >= 2 && params.length > 3 + np)
	spnParameter2.set(params[3]);
	- if (np >= 3 && params.length > 4+np)
	+ if (np >= 3 && params.length > 4 + np)
	spnParameter3.set(params[4]);

	}
	-
	+
	public String getShapeName() {
	return shape;
	}

	public String getCommand() {
	return command;
	}

	public boolean wasCancel() {
	return cancel;
	}

	@Override
	public void windowOpened(WindowEvent e) {
	}

	@Override
	public void windowClosing(WindowEvent e) {
	dispose();
	cancel = true;
	shape = "";
	command = "";
	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) {
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/AboutModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/AboutModule.java
	index 5793445..ca832f1 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AboutModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/AboutModule.java
	@@ -1,78 +1,78 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.event.ActionEvent;

	import javax.swing.JPanel;

	import lab.component.HTMLPane;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Lab;

	public class AboutModule extends AbstractModule {

	public AboutModule(boolean expanded) {
	super("About", "", "Help", "", expanded);
	}

	@Override
	public String getCommand() {
	return "DeconvolutionLab2 " + Constants.version;
	}
	-
	+
	@Override
	public JPanel buildExpandedPanel() {
	JPanel panel = new JPanel(new BorderLayout());
	HTMLPane html = new HTMLPane("verdana", 200, 200);
	html.append("h1", "DeconvolutionLab2 " + Constants.version);
	html.append("p", Constants.copyright);
	html.append("p", "<b>Reference:</b> " + Constants.reference);
	html.append("h3", "<b>Authors:</b> " + Constants.authors);
	panel.add(html.getPane(), BorderLayout.CENTER);
	getAction1Button().addActionListener(this);
	return panel;
	}
	-
	+
	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (getAction1Button() == e.getSource())
	Lab.help();
	}
	-
	+
	@Override
	public void close() {
	getAction1Button().removeActionListener(this);
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/AbstractModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/AbstractModule.java
	index a70fa0f..7fc18a6 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AbstractModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/AbstractModule.java
	@@ -1,219 +1,221 @@
	/*
	* 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.Dimension;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JLabel;
	import javax.swing.JPanel;
	import javax.swing.SwingConstants;

	public abstract class AbstractModule extends JPanel implements ActionListener {
	private JButton bnTitle;
	private JButton bnSynopsis;
	- private JButton bnAction1 = new JButton();
	- private JButton bnAction2 = new JButton();
	+ private JButton bnAction1 = new JButton();
	+ private JButton bnAction2 = new JButton();
	private JLabel lblCommand;

	private JButton bnExpand;
	private CardLayout card = new CardLayout();
	private JPanel space = new JPanel(card);
	private boolean expanded = false;
	private GroupedModulePanel mpns;
	private JPanel pnExpanded;
	private JPanel pnCollapsed;
	private String name;
	private String key;

	public AbstractModule(String name, String key, String action1, String action2, boolean expanded) {
	this.name = name;
	this.key = key;
	pnCollapsed = buildCollapsedPanel();
	pnExpanded = buildExpandedPanel();
	setLayout(new BorderLayout());
	this.expanded = expanded;
	bnTitle = new JButton("<html><b>" + name + "</b></html>");
	bnTitle.setHorizontalAlignment(SwingConstants.LEFT);
	- bnTitle.setPreferredSize(new Dimension(180, 20));
	+ bnTitle.setPreferredSize(new Dimension(160, 20));
	bnTitle.setMaximumSize(new Dimension(250, 20));
	bnTitle.setMinimumSize(new Dimension(120, 20));
	bnTitle.addActionListener(this);

	bnSynopsis = new JButton("");
	bnSynopsis.setHorizontalAlignment(SwingConstants.LEFT);
	bnSynopsis.setPreferredSize(new Dimension(200, 20));
	bnSynopsis.addActionListener(this);

	bnExpand = new JButton("\u25BA");
	bnExpand.setPreferredSize(new Dimension(40, 20));
	bnExpand.setMaximumSize(new Dimension(40, 20));
	bnExpand.setMinimumSize(new Dimension(40, 20));
	bnExpand.addActionListener(this);

	JPanel tool0 = new JPanel(new BorderLayout());
	JPanel tool1 = new JPanel(new BorderLayout());
	tool1.add(bnExpand, BorderLayout.WEST);
	tool1.add(bnTitle, BorderLayout.EAST);
	tool0.add(tool1, BorderLayout.WEST);
	tool0.add(bnSynopsis, BorderLayout.CENTER);

	JPanel toola = null;
	if (!action1.equals("")) {
	bnAction1.setText(action1);
	bnAction1.setPreferredSize(new Dimension(50, 20));
	if (toola == null)
	toola = new JPanel(new BorderLayout());
	toola.add(bnAction1, BorderLayout.WEST);
	}
	if (!action2.equals("")) {
	bnAction2.setText(action2);
	bnAction2.setPreferredSize(new Dimension(50, 20));
	if (toola == null)
	toola = new JPanel(new BorderLayout());
	toola.add(bnAction2, BorderLayout.EAST);
	}

	- if (toola != null)
	+ if (toola != null)
	tool0.add(toola, BorderLayout.EAST);
	-
	+
	space.add(pnExpanded, "expand");
	space.add(pnCollapsed, "collapse");
	add(tool0, BorderLayout.NORTH);
	add(space, BorderLayout.CENTER);
	setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
	if (expanded)
	expand();
	else
	collapse();
	setPreferredSize(pnCollapsed.getPreferredSize());
	}

	public JPanel buildCollapsedPanel() {
	JPanel panel = new JPanel(new BorderLayout());
	lblCommand = new JLabel("");
	lblCommand.setBorder(BorderFactory.createEtchedBorder());
	lblCommand.setHorizontalAlignment(SwingConstants.LEFT);
	lblCommand.setPreferredSize(new Dimension(500, 30));
	panel.add(lblCommand, BorderLayout.NORTH);
	return panel;
	}

	public abstract JPanel buildExpandedPanel();
	+
	public abstract String getCommand();
	+
	public abstract void close();
	-
	+
	public JButton getAction1Button() {
	return bnAction1;
	}

	public JButton getAction2Button() {
	return bnAction2;
	}

	@Override
	public String getName() {
	return name;
	}
	-
	+
	public String getKey() {
	return key;
	}

	public String getTitle() {
	return bnTitle.getText();
	}

	public void setCommand(String command) {
	lblCommand.setText("<html><p style=\"font-family: monospace\"><small>" + command + "</small></p></html>");
	}
	-
	+
	public void setSynopsis(String synopsis) {
	bnSynopsis.setText(synopsis);
	}

	public JPanel getCollapsedPanel() {
	return pnCollapsed;
	}

	public JPanel getExpandedPanel() {
	return pnExpanded;
	}

	public void setMultipleModulePanel(GroupedModulePanel mpns) {
	this.mpns = mpns;
	}

	@Override
	public Dimension getPreferredSize() {
	if (expanded)
	return pnExpanded.getPreferredSize();
	else
	return pnCollapsed.getPreferredSize();
	}

	public boolean isExpanded() {
	return expanded;
	}

	public void collapse() {
	expanded = false;
	card.show(space, "collapse");
	bnExpand.setText("\u25BA");
	}

	public void expand() {
	expanded = true;
	card.show(space, "expand");
	bnExpand.setText("\u25BC");
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	if (e.getSource() == bnTitle \|\| e.getSource() == bnExpand \|\| e.getSource() == bnSynopsis) {
	if (expanded) {
	collapse();
	}
	else {
	for (AbstractModule module : mpns.getModules())
	module.collapse();
	expand();
	}
	mpns.organize();
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	index 9b83f24..4e2162e 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	@@ -1,143 +1,143 @@
	/*
	* 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 lab.component.HTMLPane;
	import deconvolution.Command;
	import deconvolution.algorithm.AbstractAlgorithmPanel;
	import deconvolution.algorithm.Algorithm;
	import deconvolutionlab.Config;

	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", "", "", expanded);
	ArrayList<AbstractAlgorithmPanel> panels = Algorithm.getAvailableAlgorithms();
	for (AbstractAlgorithmPanel panel : panels)
	cmb.addItem(panel.getName());
	cmb.addActionListener(this);
	}

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

	@Override
	public JPanel buildExpandedPanel() {
	cmb = new JComboBox<String>();
	JPanel pnc = new JPanel();
	pnc.add(cmb);
	doc = new HTMLPane(100, 1000);
	cards = new JPanel(new CardLayout());
	ArrayList<AbstractAlgorithmPanel> panels = Algorithm.getAvailableAlgorithms();
	- for (AbstractAlgorithmPanel panel : panels) {
	+ for (AbstractAlgorithmPanel panel : panels) {
	JScrollPane scroll = new JScrollPane(panel.getPanelParameters());
	scroll.setBorder(BorderFactory.createEmptyBorder());
	scroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
	scroll.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
	cards.add(panel.getName(), scroll);
	}
	cmb.setMaximumRowCount(panels.size());

	JPanel control = new JPanel();
	control.setLayout(new BoxLayout(control, BoxLayout.PAGE_AXIS));
	Border b1 = BorderFactory.createEtchedBorder();
	Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);
	control.setBorder(BorderFactory.createCompoundBorder(b1, b2));
	control.add(cmb);
	control.add(cards);
	-
	+
	doc.append("h1", "Documentation");
	-
	+
	JPanel panel = new JPanel(new BorderLayout());
	panel.add(control, BorderLayout.NORTH);
	panel.add(doc.getPane(), BorderLayout.CENTER);
	- //cmb.addActionListener(this);
	+ // cmb.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);
	}
	setSynopsis((String) cmb.getSelectedItem());
	setCommand(getCommand());
	Command.command();
	}

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

	@Override
	public void close() {
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java
	index f366b99..7e08089 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java
	@@ -1,190 +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 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 lab.component.CustomizedColumn;
	-import lab.component.CustomizedTable;
	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;
	+ 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;
	}

	@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");
	+ 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) {
	if (e.getSource() == bnRunJob) {
	int rows[] = table.getSelectedRows();
	- for(int row : rows) {
	- new Deconvolution(table.getCell(row, 1)).deconvolve();
	- }
	+ 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));
	- }
	+ 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();
	- }
	+ 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));
	- }
	+ 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);
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/BorderModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/BorderModule.java
	index ad7b25c..18bf0ac 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/BorderModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/BorderModule.java
	@@ -1,304 +1,304 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.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 deconvolution.Command;
	+import deconvolution.Deconvolution;
	+import deconvolutionlab.Config;
	import lab.component.GridPanel;
	import lab.component.HTMLPane;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.NumFormat;
	import signal.RealSignal;
	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 deconvolution.Command;
	-import deconvolution.Deconvolution;
	-import deconvolutionlab.Config;

	public class BorderModule extends AbstractModule implements ActionListener, ChangeListener {

	private JComboBox<String> cmbNormalization;
	private JComboBox<String> cmbPadXY;
	private JComboBox<String> cmbPadZ;
	private JComboBox<String> cmbApoXY;
	private JComboBox<String> cmbApoZ;
	private SpinnerRangeInteger spnExtensionXY;
	private SpinnerRangeInteger spnExtensionZ;
	private HTMLPane info;

	private boolean build = false;

	public BorderModule(boolean expanded) {
	super("Border", "", "Test", "Default", expanded);
	}

	@Override
	public String getCommand() {
	AbstractPadding pxy = Padding.getByName((String) cmbPadXY.getSelectedItem());
	AbstractPadding paz = Padding.getByName((String) cmbPadZ.getSelectedItem());
	AbstractApodization axy = Apodization.getByName((String) cmbApoXY.getSelectedItem());
	AbstractApodization apz = Apodization.getByName((String) cmbApoZ.getSelectedItem());
	boolean ext = spnExtensionXY.get() + spnExtensionZ.get() > 0;
	String extXY = (ext ? "" + spnExtensionXY.get() : "") + " ";
	String extZ = ext ? "" + spnExtensionZ.get() : "";
	String cmd = "";
	if (!(pxy instanceof NoPadding) \|\| !(paz instanceof NoPadding) \|\| spnExtensionXY.get() > 0 \|\| spnExtensionZ.get() > 0)
	cmd += " -pad " + pxy.getShortname() + " " + paz.getShortname() + " " + extXY + extZ;
	if (!(axy instanceof UniformApodization) \|\| !(apz instanceof UniformApodization))
	cmd += " -apo " + axy.getShortname() + " " + apz.getShortname() + " ";
	if (cmbNormalization.getSelectedIndex() != 0)
	cmd += " -norm " + NumFormat.parseNumber((String)cmbNormalization.getSelectedItem(), 1);
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {
	info = new HTMLPane(100, 100);

	cmbPadXY = new JComboBox<String>(Padding.getPaddingsAsArray());
	cmbPadZ = new JComboBox<String>(Padding.getPaddingsAsArray());
	cmbApoXY = new JComboBox<String>(Apodization.getApodizationsAsArray());
	cmbApoZ = new JComboBox<String>(Apodization.getApodizationsAsArray());
	spnExtensionXY = new SpinnerRangeInteger(0, 0, 99999, 1);
	spnExtensionZ = new SpinnerRangeInteger(0, 0, 99999, 1);
	cmbNormalization = new JComboBox<String>(new String[] { "1", "10", "1000", "1E+6", "1E+9", "no" });

	GridPanel pnBorder = new GridPanel("Border Artifact Cancelation", 3);
	pnBorder.place(0, 2, "Lateral (XY)");
	pnBorder.place(0, 4, "Axial (Z)");
	pnBorder.place(2, 0, "Apodization");
	pnBorder.place(2, 2, cmbApoXY);
	pnBorder.place(2, 4, cmbApoZ);

	pnBorder.place(3, 0, "Padding Extension");
	pnBorder.place(3, 2, spnExtensionXY);
	pnBorder.place(3, 4, spnExtensionZ);

	pnBorder.place(4, 0, "Padding Constraint");
	pnBorder.place(4, 2, cmbPadXY);
	pnBorder.place(4, 4, cmbPadZ);

	pnBorder.place(5, 0, "PSF Normalization");
	pnBorder.place(5, 2, cmbNormalization);
	pnBorder.place(5, 4, "1, recommended");

	JScrollPane scroll1 = new JScrollPane(pnBorder);
	scroll1.setBorder(BorderFactory.createEmptyBorder());
	scroll1.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
	scroll1.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);

	JPanel control = new JPanel();
	control.setLayout(new BoxLayout(control, BoxLayout.PAGE_AXIS));
	Border b1 = BorderFactory.createEtchedBorder();
	Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);
	control.setBorder(BorderFactory.createCompoundBorder(b1, b2));
	control.add(scroll1);
	control.add(info.getPane());

	JPanel panel = new JPanel(new BorderLayout());
	panel.add(control, BorderLayout.CENTER);

	Config.register(getName(), "padxy", cmbPadXY, Padding.getDefault().getName());
	Config.register(getName(), "padz", cmbPadZ, Padding.getDefault().getName());
	Config.register(getName(), "apoxy", cmbApoXY, Apodization.getDefault().getName());
	Config.register(getName(), "apoz", cmbApoZ, Apodization.getDefault().getName());
	Config.register(getName(), "extxy", spnExtensionXY, "0");
	Config.register(getName(), "extz", spnExtensionZ, "0");
	Config.register(getName(), "normalization", cmbNormalization, cmbNormalization.getItemAt(0));

	cmbNormalization.addActionListener(this);
	spnExtensionXY.addChangeListener(this);
	spnExtensionZ.addChangeListener(this);
	cmbPadXY.addActionListener(this);
	cmbPadZ.addActionListener(this);
	cmbApoXY.addActionListener(this);
	cmbApoZ.addActionListener(this);

	getAction1Button().addActionListener(this);
	getAction2Button().addActionListener(this);
	build = true;
	return panel;
	}

	private void update() {
	setCommand(getCommand());
	boolean ext = spnExtensionXY.get() + spnExtensionZ.get() > 0;
	boolean pad = cmbPadXY.getSelectedIndex() + cmbPadZ.getSelectedIndex() > 0;
	boolean apo = cmbApoXY.getSelectedIndex() + cmbApoZ.getSelectedIndex() > 0;
	if (pad \|\| apo \|\| ext) {
	setSynopsis("" + " " + (pad ? "Padding" : "") + " " + (ext ? "Extension" : "") + " " + (apo ? "Apodization" : ""));
	}
	else {
	setSynopsis("Default options");
	}

	Command.command();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	testInfo();
	update();
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == getAction2Button()) {
	cmbPadXY.removeActionListener(this);
	cmbPadZ.removeActionListener(this);
	cmbApoXY.removeActionListener(this);
	cmbApoZ.removeActionListener(this);
	cmbPadXY.setSelectedIndex(0);
	cmbPadZ.setSelectedIndex(0);
	cmbApoXY.setSelectedIndex(0);
	cmbApoZ.setSelectedIndex(0);
	spnExtensionXY.set(0);
	spnExtensionZ.set(0);
	cmbNormalization.setSelectedIndex(0);
	cmbPadXY.addActionListener(this);
	cmbPadZ.addActionListener(this);
	cmbApoXY.addActionListener(this);
	cmbApoZ.addActionListener(this);
	update();
	return;
	}
	if (e.getSource() == getAction1Button()) {
	Thread thread = new Thread(new Runnable() {
	@Override
	public void run() {
	getAction1Button().setEnabled(false);
	getAction2Button().setEnabled(false);
	info.clear();
	info.append("p", "Test running...");
	info.clear();
	ArrayList<String> lines = new Deconvolution(Command.command()).checkImage();
	for (String line : lines)
	info.append("p", line);
	ArrayList<String> linesPSF = new Deconvolution(Command.command()).checkPSF();
	for (String line : linesPSF)
	info.append("p", line);
	getAction1Button().setEnabled(true);
	getAction2Button().setEnabled(true);
	}
	});
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	return;
	}
	testInfo();
	update();
	}

	@Override
	public void close() {
	cmbNormalization.removeActionListener(this);
	cmbPadXY.removeActionListener(this);
	cmbPadZ.removeActionListener(this);
	cmbApoXY.removeActionListener(this);
	cmbApoZ.removeActionListener(this);
	getAction1Button().removeActionListener(this);
	getAction2Button().removeActionListener(this);
	spnExtensionXY.removeChangeListener(this);
	spnExtensionZ.removeChangeListener(this);
	}

	private void testInfo() {
	Thread thread = new Thread(new Runnable() {
	@Override
	public void run() {
	if (build)
	info();
	}
	});
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}

	private Padding getPadding() {
	AbstractPadding padXY = Padding.getByName((String) cmbPadXY.getSelectedItem());
	AbstractPadding padZ = Padding.getByName((String) cmbPadZ.getSelectedItem());
	int extXY = spnExtensionXY.get();
	int extZ = spnExtensionZ.get();
	return new Padding(padXY, padXY, padZ, extXY, extXY, extZ);
	}

	private Apodization getApodization() {
	AbstractApodization apoXY = Apodization.getByName((String) cmbApoXY.getSelectedItem());
	AbstractApodization apoZ = Apodization.getByName((String) cmbApoZ.getSelectedItem());
	return new Apodization(apoXY, apoXY, apoZ);
	}

	private void info() {
	int nx = 600;
	int ny = 400;
	int nz = 100;
	RealSignal image = new Deconvolution(Command.command()).openImage();
	if (image != null) {
	nx = image.nx;
	ny = image.ny;
	nz = image.nz;
	}
	try {
	info.clear();
	}
	catch (Exception ex) {
	}
	int[] p = getPadding().pad(nx, ny, nz);
	String in = "[" + nx + " x" + ny + " x " + nz + "]";
	String out = "[" + p[0] + " x" + p[1] + " x " + p[2] + "]";
	String bin = NumFormat.bytes(nx * ny * nz * 4);
	String pout = NumFormat.bytes(p[0] * p[1] * p[2] * 4);
	if (info != null) {
	info.append("p", "Input size: " + in + " (" + bin + ")");
	info.append("p", "Padded size: " + out + " (" + pout + ")");
	double lost = getApodization().estimateLostEnergy(10);
	info.append("p", "Estimation of lost energy by apodization: " + (lost * 100) + "%");
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/ConfigModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/ConfigModule.java
	index c3c8978..f1d9ee4 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/ConfigModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/ConfigModule.java
	@@ -1,124 +1,124 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.FlowLayout;
	import java.awt.event.ActionListener;
	import java.io.BufferedReader;
	import java.io.File;
	import java.io.FileReader;
	import java.io.IOException;
	import java.util.ArrayList;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JLabel;
	import javax.swing.JPanel;

	-import lab.component.CustomizedColumn;
	-import lab.component.CustomizedTable;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	+import lab.component.CustomizedColumn;
	+import lab.component.CustomizedTable;
	public class ConfigModule extends AbstractModule implements ActionListener {

	private JButton bnLoad;
	private JButton bnSave;
	private CustomizedTable table;
	private JLabel lblDefault;

	public ConfigModule(boolean expanded) {
	super("Config", "", "", "", expanded);
	}

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

	@Override
	public JPanel buildExpandedPanel() {

	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Key", String.class, 180, false));
	columns.add(new CustomizedColumn("Value", String.class, Constants.widthGUI - 80, true));
	table = new CustomizedTable(columns, true);

	read();
	lblDefault = new JLabel(Config.getFilename());
	bnLoad = new JButton("Load");
	bnSave = new JButton("Save");
	lblDefault.setBorder(BorderFactory.createEtchedBorder());

	JPanel button = new JPanel();
	button.setLayout(new FlowLayout());
	button.add(bnLoad);
	button.add(bnSave);

	JPanel panel = new JPanel(new BorderLayout());
	panel.add(lblDefault, BorderLayout.NORTH);
	panel.add(table.getMinimumPane(100, 100), BorderLayout.CENTER);

	bnLoad.addActionListener(this);
	bnSave.addActionListener(this);
	return panel;
	}

	private void read() {
	String filename = Config.getFilename();
	File file = new File(filename);
	if (file.exists()) {
	try {
	BufferedReader br = new BufferedReader(new FileReader(file));
	String line;
	while ((line = br.readLine()) != null) {
	String entry = line.trim();
	if (!entry.startsWith("#")) {
	String[] parts = entry.split("=");
	if (parts.length == 2)
	table.append(parts);
	}
	}
	br.close();
	}
	catch (IOException e) {
	e.printStackTrace();
	}
	}
	}

	@Override
	public void close() {
	bnLoad.removeActionListener(this);
	bnSave.removeActionListener(this);
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/ControllerModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/ControllerModule.java
	index fb5da06..cc09c44 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/ControllerModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/ControllerModule.java
	@@ -1,308 +1,308 @@
	/*
	* 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.Dimension;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;
	import java.io.File;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JCheckBox;
	import javax.swing.JComboBox;
	import javax.swing.JPanel;
	import javax.swing.JScrollPane;
	import javax.swing.JTextField;
	import javax.swing.border.Border;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	+import deconvolution.Command;
	+import deconvolution.Deconvolution;
	+import deconvolutionlab.Config;
	import lab.component.GridPanel;
	import lab.component.SpinnerRangeInteger;
	import lab.tools.Files;
	import signal.Constraint;
	-import deconvolution.Command;
	-import deconvolution.Deconvolution;
	-import deconvolutionlab.Config;

	public class ControllerModule extends AbstractModule implements ActionListener, ChangeListener, KeyListener {

	private JButton bnBrowse;

	private JTextField txtReference;
	private JTextField txtResidu;
	private JTextField txtSaveStats;
	private JTextField txtShowStats;
	private JComboBox<String> cmbConstraint;

	private JCheckBox chkResidu;
	private JCheckBox chkReference;
	private JCheckBox chkConstraint;
	private JCheckBox chkSaveStats;
	private JCheckBox chkShowStats;

	private SpinnerRangeInteger snapshotResidu;
	private SpinnerRangeInteger snapshotConstraint;
	private SpinnerRangeInteger snapshotReference;
	private SpinnerRangeInteger snapshotSaveStats;
	private SpinnerRangeInteger snapshotShowStats;

	public ControllerModule(boolean expanded) {
	super("Controller", "", "Default", "", expanded);
	}

	@Override
	public String getCommand() {
	String cmd = "";
	int sr = snapshotResidu.get();
	int sc = snapshotConstraint.get();
	int sg = snapshotReference.get();
	int ss = snapshotSaveStats.get();
	int sd = snapshotShowStats.get();

	if (chkConstraint.isSelected())
	cmd += "-constraint " + (sc > 1 ? "@" + sc + " ": "") + cmbConstraint.getSelectedItem() + " ";
	if (chkReference.isSelected())
	cmd += "-reference " + (sg > 1 ? "@" + sg + " " : "") + txtReference.getText() + " ";
	if (chkResidu.isSelected())
	cmd += "-residu " + (sr > 1 ? "@" + sr + " " : "") + txtResidu.getText() + " ";
	if (chkSaveStats.isSelected())
	cmd += "-savestats " + (ss > 1 ? "@" + ss + " " : "") + txtSaveStats.getText() + " ";
	if (chkShowStats.isSelected())
	cmd += "-showstats " + (sd > 1 ? "@" + sd + " " : "") + txtShowStats.getText() + " ";
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {

	snapshotResidu = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	snapshotConstraint = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	snapshotReference = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	snapshotSaveStats = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	snapshotShowStats = new SpinnerRangeInteger(10, 1, 99999, 1, "###");
	chkConstraint = new JCheckBox("Constraint");
	chkResidu = new JCheckBox("Residu Minimun");
	chkReference = new JCheckBox("Reference");
	chkSaveStats = new JCheckBox("Save Stats");
	chkShowStats = new JCheckBox("Show Stats");

	bnBrowse = new JButton("Browse");
	txtReference = new JTextField("");
	txtResidu = new JTextField("0.01");
	txtSaveStats = new JTextField("stats");
	txtShowStats = new JTextField("stats");

	cmbConstraint = new JComboBox<String>(Constraint.getContraintsAsArray());
	txtReference.setPreferredSize(new Dimension(200, 20));

	GridPanel pn = new GridPanel(true);

	pn.place(1, 0, chkResidu);
	pn.place(1, 1, txtResidu);
	pn.place(1, 2, snapshotResidu);

	pn.place(4, 0, chkConstraint);
	pn.place(4, 1, cmbConstraint);
	pn.place(4, 2, snapshotConstraint);

	pn.place(5, 0, chkSaveStats);
	pn.place(5, 1, txtSaveStats);
	pn.place(5, 2, snapshotSaveStats);

	pn.place(6, 0, chkShowStats);
	pn.place(6, 1, txtShowStats);
	pn.place(6, 2, snapshotShowStats);

	pn.place(7, 0, chkReference);
	pn.place(7, 1, txtReference);
	pn.place(7, 2, snapshotReference);
	pn.place(8, 0, "Ground-truth file");
	pn.place(8, 1, bnBrowse);

	Border b1 = BorderFactory.createEtchedBorder();
	Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);
	pn.setBorder(BorderFactory.createCompoundBorder(b1, b2));

	JScrollPane scroll = new JScrollPane(pn);
	scroll.setBorder(BorderFactory.createEmptyBorder());
	scroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
	scroll.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);

	JPanel panel = new JPanel(new BorderLayout());
	panel.setBorder(BorderFactory.createEtchedBorder());
	panel.add(scroll, BorderLayout.NORTH);

	bnBrowse.addActionListener(this);

	chkResidu.addChangeListener(this);
	chkReference.addChangeListener(this);
	chkConstraint.addChangeListener(this);
	chkSaveStats.addChangeListener(this);
	chkShowStats.addChangeListener(this);

	snapshotResidu.addChangeListener(this);
	snapshotConstraint.addChangeListener(this);
	snapshotReference.addChangeListener(this);
	snapshotShowStats.addChangeListener(this);
	snapshotSaveStats.addChangeListener(this);

	txtResidu.addKeyListener(this);
	txtReference.addKeyListener(this);
	txtSaveStats.addKeyListener(this);
	txtShowStats.addKeyListener(this);
	cmbConstraint.addActionListener(this);
	getAction1Button().addActionListener(this);

	Config.register(getName(), "residu.enable", chkResidu, false);
	Config.register(getName(), "reference.enable", chkReference, false);
	Config.register(getName(), "constraint.enable", chkConstraint, false);
	Config.register(getName(), "showstats.enable", chkShowStats, false);
	Config.register(getName(), "savestats.enable", chkSaveStats, false);

	Config.register(getName(), "reference.value", txtReference, "");
	Config.register(getName(), "residu.value", txtResidu, "0.01");
	Config.register(getName(), "showstats.value", txtShowStats, "Stats");
	Config.register(getName(), "savestats.value", txtSaveStats, "Stats");
	Config.register(getName(), "constraint.value", cmbConstraint, "No");

	Config.register(getName(), "residu.snapshot", snapshotResidu, "1");
	Config.register(getName(), "reference.snapshot", snapshotConstraint, "1");
	Config.register(getName(), "constraint.snapshot", snapshotReference, "1");
	Config.register(getName(), "showstats.snapshot", snapshotShowStats, "1");
	Config.register(getName(), "savestats.snapshot", snapshotSaveStats, "1");
	return panel;
	}

	private void update() {
	setCommand(getCommand());
	int count = 0;
	count += (chkResidu.isSelected() ? 1 : 0);
	count += (chkReference.isSelected() ? 1 : 0);
	count += (chkConstraint.isSelected() ? 1 : 0);
	count += (chkSaveStats.isSelected() ? 1 : 0);
	count += (chkShowStats.isSelected() ? 1 : 0);
	setSynopsis("" + count + (count >= 2 ? " controls" : " control "));
	Command.command();
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnBrowse) {
	Deconvolution deconvolution = new Deconvolution(Command.command());
	File file = Files.browseFile(deconvolution.getPath());
	if (file != null)
	txtReference.setText(file.getAbsolutePath());
	}
	if (e.getSource() == getAction1Button()) {
	chkResidu.removeChangeListener(this);
	chkReference.removeChangeListener(this);
	chkConstraint.removeChangeListener(this);
	chkSaveStats.removeChangeListener(this);
	chkShowStats.removeChangeListener(this);

	snapshotResidu.removeChangeListener(this);
	snapshotConstraint.removeChangeListener(this);
	snapshotReference.removeChangeListener(this);
	snapshotShowStats.removeChangeListener(this);
	snapshotSaveStats.removeChangeListener(this);

	chkResidu.setSelected(false);
	chkReference.setSelected(false);
	chkConstraint.setSelected(false);
	chkShowStats.setSelected(false);
	chkSaveStats.setSelected(false);

	txtReference.setText("");
	txtResidu.setText("0.01");
	txtShowStats.setText("Stats");
	txtSaveStats.setText("Stats");
	cmbConstraint.setSelectedIndex(0);

	snapshotResidu.set(1);
	snapshotConstraint.set(1);
	snapshotReference.set(1);
	snapshotShowStats.set(1);
	snapshotSaveStats.set(1);

	chkResidu.addChangeListener(this);
	chkReference.addChangeListener(this);
	chkConstraint.addChangeListener(this);
	chkSaveStats.addChangeListener(this);
	chkShowStats.addChangeListener(this);

	snapshotResidu.addChangeListener(this);
	snapshotConstraint.addChangeListener(this);
	snapshotReference.addChangeListener(this);
	snapshotShowStats.addChangeListener(this);
	snapshotSaveStats.addChangeListener(this);

	}
	update();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	update();
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	update();
	}

	@Override
	public void close() {
	bnBrowse.removeActionListener(this);
	chkReference.removeChangeListener(this);
	chkResidu.removeChangeListener(this);
	chkConstraint.removeChangeListener(this);
	chkShowStats.removeChangeListener(this);
	chkSaveStats.removeChangeListener(this);
	getAction1Button().removeChangeListener(this);
	}


	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java
	index 018934b..3dc93d5 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java
	@@ -1,197 +1,199 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.util.ArrayList;

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

	import lab.component.CustomizedColumn;
	import lab.component.CustomizedTable;
	import lab.component.GridPanel;
	import lab.component.HTMLPane;
	import lab.tools.NumFormat;
	import signal.Signal;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolution.algorithm.Algorithm;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import fft.AbstractFFTLibrary;
	import fft.FFT;

	public class FFTModule extends AbstractModule implements ActionListener, ChangeListener {

	- private HTMLPane info;
	+ private HTMLPane info;

	private JComboBox<String> cmbFFT;
	private JComboBox<String> cmbType;
	private JComboBox<String> cmbSep;
	private JComboBox<String> cmbEpsilon;
	-
	+
	private CustomizedTable table;
	-
	+
	public FFTModule(boolean expanded) {
	super("Fourier", "", "", "Default", expanded);
	}

	@Override
	public String getCommand() {
	String cmd = "";
	if (cmbFFT.getSelectedIndex() != 0)
	cmd += " -fft " + (String) cmbFFT.getSelectedItem();
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {
	-
	+
	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Name", String.class, 120, false));
	columns.add(new CustomizedColumn("Installed", String.class, 120, false));
	columns.add(new CustomizedColumn("Location", String.class, Constants.widthGUI, false));
	table = new CustomizedTable(columns, true);
	table.setRowSelectionAllowed(false);
	-
	+
	info = new HTMLPane(100, 100);
	cmbFFT = new JComboBox<String>(FFT.getLibrariesAsArray());
	cmbType = new JComboBox<String>(new String[] { "float" });
	cmbSep = new JComboBox<String>(new String[] { "XYZ" });
	- cmbEpsilon = new JComboBox<String>(new String[] { "1E-0", "1E-1", "1E-2", "1E-3", "1E-4", "1E-5", "1E-6", "1E-7", "1E-8", "1E-9", "1E-10", "1E-11", "1E-12"});
	+ cmbEpsilon = new JComboBox<String>(new String[] { "1E-0", "1E-1", "1E-2", "1E-3", "1E-4", "1E-5", "1E-6", "1E-7", "1E-8", "1E-9", "1E-10", "1E-11", "1E-12" });
	cmbEpsilon.setSelectedItem("1E-6");

	GridPanel pnNumeric = new GridPanel(false, 3);
	pnNumeric.place(3, 0, new JLabel("FFT Fourier Library"));
	pnNumeric.place(3, 1, cmbFFT);
	pnNumeric.place(6, 0, new JLabel("FFT Dimension"));
	pnNumeric.place(6, 1, cmbSep);
	pnNumeric.place(7, 0, new JLabel("<html>Machine Epsilon ε</html>"));
	pnNumeric.place(7, 1, cmbEpsilon);
	pnNumeric.place(8, 0, new JLabel("Data Type"));
	pnNumeric.place(8, 1, cmbType);

	JScrollPane scroll2 = new JScrollPane(pnNumeric);
	scroll2.setBorder(BorderFactory.createEmptyBorder());
	scroll2.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
	scroll2.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);

	JPanel control = new JPanel(new BorderLayout());
	Border b1 = BorderFactory.createEtchedBorder();
	Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);
	-
	+
	control.setBorder(BorderFactory.createCompoundBorder(b1, b2));
	control.add(scroll2, BorderLayout.NORTH);
	control.add(info.getPane(), BorderLayout.CENTER);
	control.add(table.getPane(80, 80), BorderLayout.SOUTH);

	JPanel panel = new JPanel(new BorderLayout());
	panel.add(control, BorderLayout.CENTER);
	-
	+
	Config.register(getName(), "epsilon", cmbEpsilon, "1E-6");
	Config.register(getName(), "fft", cmbFFT, Algorithm.getDefaultAlgorithm());
	Config.register(getName(), "dim", cmbSep, "XYZ");

	cmbFFT.addActionListener(this);
	cmbType.addActionListener(this);
	cmbEpsilon.addActionListener(this);

	getAction1Button().addActionListener(this);
	getAction2Button().addActionListener(this);
	fillInstallation();
	return panel;
	}

	private void fillInstallation() {
	-
	+
	ArrayList<AbstractFFTLibrary> libs = FFT.getLibraries();
	- for(AbstractFFTLibrary lib : libs) {
	+ for (AbstractFFTLibrary lib : libs) {
	String name = lib.getLibraryName();
	String installed = lib.isInstalled() ? " Yes" : "No";
	String location = lib.getLocation();
	- table.append(new String[] {name, installed, location});
	+ table.append(new String[] { name, installed, location });
	}
	+ AbstractFFTLibrary fftlib = FFT.getLibraryByName((String) cmbFFT.getSelectedItem());
	+ info.clear();
	+ info.append("p", fftlib.getLicence());
	}
	-
	+
	private void update() {
	setCommand(getCommand());
	- Signal.epsilon = NumFormat.parseNumber( (String) cmbEpsilon.getSelectedItem(), 1e-6);
	-
	+ Signal.epsilon = NumFormat.parseNumber((String) cmbEpsilon.getSelectedItem(), 1e-6);
	Command.command();
	}

	@Override
	public void stateChanged(ChangeEvent e) {
	update();
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == cmbFFT \|\| e.getSource() == cmbSep) {
	AbstractFFTLibrary fftlib = FFT.getLibraryByName((String) cmbFFT.getSelectedItem());
	info.clear();
	info.append("p", fftlib.getLicence());
	}
	-
	+
	if (e.getSource() == getAction1Button()) {
	cmbFFT.removeActionListener(this);
	cmbType.removeActionListener(this);
	cmbEpsilon.removeActionListener(this);
	cmbFFT.setSelectedIndex(0);
	cmbType.setSelectedIndex(0);
	cmbEpsilon.setSelectedIndex(0);
	cmbFFT.addActionListener(this);
	cmbType.addActionListener(this);
	cmbEpsilon.addActionListener(this);
	}
	update();
	}

	@Override
	public void close() {
	getAction1Button().removeActionListener(this);
	getAction2Button().removeActionListener(this);
	cmbFFT.removeActionListener(this);
	cmbType.removeActionListener(this);
	cmbEpsilon.removeActionListener(this);
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/GroupedModulePanel.java b/DeconvolutionLab2/src/deconvolutionlab/modules/GroupedModulePanel.java
	index 63c5da7..3281aa1 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/GroupedModulePanel.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/GroupedModulePanel.java
	@@ -1,102 +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 deconvolutionlab.modules;

	import java.awt.Dimension;
	import java.util.ArrayList;

	import javax.swing.BorderFactory;
	import javax.swing.BoxLayout;
	import javax.swing.JPanel;

	-import deconvolutionlab.dialog.MainDialog;
	+import deconvolutionlab.dialog.LabDialog;

	public class GroupedModulePanel extends JPanel {
	private ArrayList<AbstractModule> modules;
	- private MainDialog parent;
	+ private LabDialog parent;
	private Dimension min;

	- public GroupedModulePanel(ArrayList<AbstractModule> modules, MainDialog parent) {
	+ public GroupedModulePanel(ArrayList<AbstractModule> modules, LabDialog parent) {
	this.modules = modules;
	this.parent = parent;

	setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
	setLayout(new BoxLayout(this, BoxLayout.PAGE_AXIS));
	int minWidth = 0;
	int minHeight = 0;
	for (AbstractModule mpn : modules) {
	mpn.setMultipleModulePanel(this);
	add(mpn);
	Dimension dim = mpn.getCollapsedPanel().getPreferredSize();
	minWidth = Math.max(minWidth, dim.width);
	minHeight += dim.height;
	}
	min = new Dimension(minWidth, minHeight);
	}

	public Dimension getMinimumSize() {
	return min;
	}

	public void organize() {
	parent.sizeModule();
	}

	public ArrayList<AbstractModule> getModules() {
	return modules;
	}

	public Dimension getVisibleSize(Dimension goal) {
	int height = 0;
	for (AbstractModule mpn : modules) {
	height += mpn.getPreferredSize().height;
	}
	if (height > goal.height) {
	return new Dimension(goal.width, height);
	}
	else {
	ArrayList<AbstractModule> visibles = new ArrayList<AbstractModule>();
	for (AbstractModule mpn : modules) {
	if (mpn.isExpanded())
	visibles.add(mpn);
	}
	if (visibles.size() > 0) {
	int supp = (goal.height - height) / visibles.size();
	for (AbstractModule mpn : modules) {
	Dimension dim = mpn.getPreferredSize();
	mpn.setPreferredSize(new Dimension(dim.width, dim.height + supp));
	}
	}
	return new Dimension(goal.width, goal.height);
	}
	}
	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
	index 9f481b8..d3a6253 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
	@@ -1,339 +1,339 @@
	/*
	* 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.datatransfer.DataFlavor;
	import java.awt.datatransfer.Transferable;
	import java.awt.datatransfer.UnsupportedFlavorException;
	import java.awt.dnd.DnDConstants;
	import java.awt.dnd.DropTarget;
	import java.awt.dnd.DropTargetDropEvent;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.MouseEvent;
	import java.awt.event.MouseListener;
	import java.io.File;
	import java.io.IOException;
	import java.util.ArrayList;
	import java.util.List;

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

	-import lab.component.CustomizedColumn;
	-import lab.component.CustomizedTable;
	-import lab.tools.Files;
	-import signal.RealSignal;
	-import signal.factory.SignalFactory;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.ImageSelector;
	import deconvolutionlab.Lab;
	import deconvolutionlab.PlatformImageSelector;
	import deconvolutionlab.dialog.PatternDialog;
	import deconvolutionlab.dialog.SyntheticDialog;
	import deconvolutionlab.monitor.Monitors;
	+import lab.component.CustomizedColumn;
	+import lab.component.CustomizedTable;
	+import lab.tools.Files;
	+import signal.RealSignal;
	+import signal.factory.SignalFactory;

	public class ImageModule extends AbstractModule implements ActionListener, MouseListener {

	private CustomizedTable table;
	private JButton bnFile;
	private JButton bnDirectory;
	private JButton bnSynthetic;
	private JButton bnPlatform;

	public ImageModule(boolean expanded) {
	- super("Image", "-image", "Open", "Show", expanded);
	+ super("Image", "-image", "Select", "Show", expanded);
	}

	@Override
	public String getCommand() {
	int row = table.getSelectedRow();
	if (row < 0)
	return "";
	return "-image " + table.getCell(row, 1) + " " + table.getCell(row, 2);
	}

	@Override
	public JPanel buildExpandedPanel() {

	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Name", String.class, 100, false));
	columns.add(new CustomizedColumn("Source", String.class, 100, false));
	columns.add(new CustomizedColumn("Command", String.class, Constants.widthGUI - 200, true));
	columns.add(new CustomizedColumn("", String.class, 30, "\u232B", "Delete this image source"));

	table = new CustomizedTable(columns, true);
	table.getColumnModel().getColumn(3).setMaxWidth(30);
	table.getColumnModel().getColumn(3).setMinWidth(30);
	table.addMouseListener(this);

	bnFile = new JButton("\u2295 file");
	bnDirectory = new JButton("\u2295 directory");
	bnSynthetic = new JButton("\u2295 synthetic");
	bnPlatform = new JButton("\u2295 platform");

	JToolBar pn = new JToolBar("Controls Image");
	pn.setBorder(BorderFactory.createEmptyBorder());
	pn.setLayout(new GridLayout(1, 5));
	pn.setFloatable(false);
	pn.add(bnFile);
	pn.add(bnDirectory);
	pn.add(bnSynthetic);
	pn.add(bnPlatform);

	JPanel panel = new JPanel();
	panel.setBorder(BorderFactory.createEtchedBorder());
	panel.setLayout(new BorderLayout());
	panel.add(pn, BorderLayout.SOUTH);
	panel.add(table.getMinimumPane(100, 100), BorderLayout.CENTER);

	table.setDropTarget(new LocalDropTarget());
	getCollapsedPanel().setDropTarget(new LocalDropTarget());
	-
	+
	bnFile.addActionListener(this);
	bnDirectory.addActionListener(this);
	bnSynthetic.addActionListener(this);
	bnPlatform.addActionListener(this);
	getAction1Button().addActionListener(this);
	getAction2Button().addActionListener(this);

	Config.registerTable(getName(), "image", table);

	return panel;
	}

	public void update() {
	int row = table.getSelectedRow();
	if (row >= 0) {
	setCommand(getCommand());
	setSynopsis(table.getCell(row, 0));
	Command.command();
	}
	- else
	+ else
	setSynopsis("");
	getAction2Button().setEnabled(table.getRowCount() > 0);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnFile) {
	- Deconvolution deconvolution = new Deconvolution(Command.command());
	+ Deconvolution deconvolution = new Deconvolution(Command.command());
	file(deconvolution.getPath());
	}
	else if (e.getSource() == bnDirectory) {
	- Deconvolution deconvolution = new Deconvolution(Command.command());
	+ Deconvolution deconvolution = new Deconvolution(Command.command());
	dir(deconvolution.getPath());
	}
	else if (e.getSource() == bnSynthetic)
	synthetic(false);
	else if (e.getSource() == bnPlatform)
	platform();
	else if (e.getSource() == getAction1Button())
	platform();
	else if (e.getSource() == getAction2Button())
	display();
	update();
	}

	public void platform() {
	PlatformImageSelector selector = new ImageSelector(Lab.getPlatform()).getImageSelector();
	String name = selector.getSelectedImage();
	if (name != null)
	if (name != "")
	- table.insert(new String[] {name, "platform", name, "" });
	+ table.insert(new String[] { name, "platform", name, "" });
	}
	-
	+
	private void file(String path) {
	File file = Files.browseFile(path);
	- if (file == null)
	+ if (file == null)
	return;
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	}

	private void dir(String path) {
	File file = Files.browseDirectory(path);
	- if (file == null)
	+ if (file == null)
	return;
	PatternDialog dlg = new PatternDialog(file);
	dlg.setVisible(true);
	if (dlg.wasCancel())
	return;
	table.insert(new String[] { dlg.getDirName(), "directory", dlg.getCommand(), "" });
	}

	private void synthetic(boolean edit) {
	ArrayList<SignalFactory> list = SignalFactory.getImages();
	SyntheticDialog dlg = new SyntheticDialog(list);
	if (edit) {
	int row = table.getSelectedRow();
	if (row >= 0) {
	dlg.setParameters(table.getCell(row, 0), table.getCell(row, 1));
	}
	}
	dlg.setVisible(true);
	if (dlg.wasCancel())
	return;
	if (edit) {
	int row = table.getSelectedRow();
	if (row <= 0)
	table.removeRow(row);
	}
	table.insert(new String[] { dlg.getShapeName(), "synthetic", dlg.getCommand(), "" });
	}

	private void edit() {
	int row = table.getSelectedRow();
	-
	+
	if (row < 0)
	return;
	String name = table.getCell(row, 0).trim();
	System.out.println("edit " + row + " " + name);
	- for(SignalFactory factory : SignalFactory.getAll()) {
	+ for (SignalFactory factory : SignalFactory.getAll()) {
	if (name.equals(factory.getName().trim()))
	synthetic(true);
	- return;
	+ return;
	}
	String filename = table.getCell(row, 1).trim();
	- System.out.println("edit " + row + " " + filename + " " + new File(filename).exists() + " " +new File(filename).isDirectory());
	+ System.out.println("edit " + row + " " + filename + " " + new File(filename).exists() + " " + new File(filename).isDirectory());
	File file = new File(filename);
	if (!file.exists())
	return;
	if (file.isFile())
	file(table.getCell(row, 21));
	else
	dir(table.getCell(row, 1));
	}

	private void display() {
	int row = table.getSelectedRow();
	if (row < 0)
	return;
	Thread thread = new Thread(new Runnable() {
	@Override
	public void run() {
	int row = table.getSelectedRow();
	RealSignal x = new Deconvolution(getCommand()).openImage();
	if (x != null)
	Lab.show(Monitors.createDefaultMonitor(), x, table.getCell(row, 0));
	}
	});
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}

	@Override
	public void mouseClicked(MouseEvent e) {
	if (e.getSource() == table) {
	int row = table.getSelectedRow();
	if (row < 0)
	return;
	if (table.getSelectedColumn() == 3) {
	table.removeRow(row);
	if (table.getRowCount() > 0)
	table.setRowSelectionInterval(0, 0);
	}
	update();
	if (e.getClickCount() == 2) {
	edit();
	}
	}
	}

	@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() {
	bnFile.removeActionListener(this);
	bnDirectory.removeActionListener(this);
	bnSynthetic.removeActionListener(this);
	bnPlatform.removeActionListener(this);
	}

	public class LocalDropTarget extends DropTarget {
	-
	+
	@Override
	public void drop(DropTargetDropEvent e) {
	e.acceptDrop(DnDConstants.ACTION_COPY);
	e.getTransferable().getTransferDataFlavors();
	Transferable transferable = e.getTransferable();
	DataFlavor[] flavors = transferable.getTransferDataFlavors();
	for (DataFlavor flavor : flavors) {
	if (flavor.isFlavorJavaFileListType()) {
	try {
	List<File> files = (List<File>) transferable.getTransferData(flavor);
	for (File file : files) {
	if (file.isDirectory()) {
	table.insert(new String[] { file.getName(), "directory", file.getAbsolutePath(), "" });
	table.setRowSelectionInterval(0, 0);
	update();
	}
	if (file.isFile()) {
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	update();
	}
	}
	}
	catch (UnsupportedFlavorException ex) {
	ex.printStackTrace();
	}
	catch (IOException ex) {
	ex.printStackTrace();
	}
	}
	}
	e.dropComplete(true);
	super.drop(e);
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	index 76bd47d..b7631ba 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	@@ -1,163 +1,163 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

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

	import javax.swing.JComboBox;
	import javax.swing.JPanel;

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

	public class LanguageModule extends AbstractModule implements ActionListener {

	private HTMLPane language;
	private JComboBox<String> cmb;
	private JComboBox<String> gui;

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

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

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

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

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

	@Override
	public void close() {
	}

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

	@Override
	public String getCommand() {
	return "";
	}
	-
	+
	private String imagej(boolean headless) {
	String macro = "<p>// Macro generated by DeconvolutionLab2 </p>";
	macro += "<p>// " + new SimpleDateFormat("dd/MM/yy HH:m:s").format(new Date()) + " </p>";
	String param = "<p>parameters = \"\"</p>";
	ArrayList<Token> tokens = Command.parse(Command.command());
	String image = "image = \" NOT DEFINED \" ";
	String psf = "psf = \" NOT DEFINED \" ";
	String algo = "algo = \" NOT DEFINED \" ";
	for (Token token : tokens) {
	if (token.keyword.equals("-image"))
	image = "<p>image = \" -image " + token.parameters.trim() + "\" </p>";
	else if (token.keyword.equals("-psf"))
	psf = "<p>psf = \" -psf " + token.parameters.trim() + "\" </p>";
	else if (token.keyword.equals("-algorithm"))
	algo = "<p>algorithm = \" -algorithm " + token.parameters.trim() + "\" </p>";
	else
	param += "<p>parameters += \" " + token.keyword + " " + token.parameters.trim() + "\" </p>";
	}
	-
	+
	String option = macro + image + psf + algo + param;
	String cmd = "";
	- if (headless)
	+ if (headless)
	cmd = "<p>run(\"DeconvolutionLab2 Run\", image + psf + algorithm + parameters)</p>";
	else
	cmd = "<p>run(\"DeconvolutionLab2 Launch\", image + psf + algorithm + parameters)</p>";
	-
	+
	return option + cmd;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/LicenceModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/LicenceModule.java
	index dc66ac8..7176066 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/LicenceModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/LicenceModule.java
	@@ -1,88 +1,88 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

	import java.awt.BorderLayout;
	import java.awt.event.ActionEvent;

	import javax.swing.JPanel;

	-import lab.component.HTMLPane;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Lab;
	+import lab.component.HTMLPane;

	public class LicenceModule extends AbstractModule {

	public LicenceModule(boolean expanded) {
	super("Licence", "", "", "", expanded);
	}

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

	@Override
	public JPanel buildExpandedPanel() {
	JPanel panel = new JPanel(new BorderLayout());
	HTMLPane html = new HTMLPane("verdana", 200, 200);
	html.append("h1", "DeconvolutionLab2 " + Constants.version);
	html.append("p",
	"DeconvolutionLab2 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.");
	html.append("p",
	"DeconvolutionLab2 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.");
	html.append("p",
	"You should have received a copy of the GNU General Public License along with " +
	"DeconvolutionLab2. If not, see http://www.gnu.org/licenses/.");
	panel.add(html.getPane(), BorderLayout.CENTER);
	getAction1Button().addActionListener(this);
	return panel;
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (getAction1Button() == e.getSource())
	Lab.help();
	}

	@Override
	public void close() {
	getAction1Button().removeActionListener(this);
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/MonitoringModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/MonitoringModule.java
	index 86d2a00..e167fa8 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/MonitoringModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/MonitoringModule.java
	@@ -1,199 +1,211 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolutionlab.modules;

	-import java.awt.BorderLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;
	import java.io.File;

	import javax.swing.BoxLayout;
	import javax.swing.JButton;
	+import javax.swing.JCheckBox;
	import javax.swing.JComboBox;
	-import javax.swing.JLabel;
	import javax.swing.JPanel;
	import javax.swing.JTextField;

	-import lab.component.GridPanel;
	-import lab.tools.Files;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	-import deconvolutionlab.Lab;
	+import lab.component.GridPanel;
	+import lab.tools.Files;

	public class MonitoringModule extends AbstractModule implements ActionListener, KeyListener {

	- private JTextField txtTime;
	- private JTextField txtPath;
	- private JButton bnBrowse;
	- private JLabel lblTime;
	- private JLabel lblPath;
	+ private JTextField txtTime;
	+ private JTextField txtPath;
	+ private JButton bnBrowse;
	private JComboBox<String> cmbTime;
	private JComboBox<String> cmbPath;
	private JComboBox<String> cmbVerbose;
	- private JComboBox<String> cmbMonitor;
	+ private JCheckBox chkDisableTable;
	+ private JCheckBox chkDisableConsole;
	+ private JCheckBox chkDisableDisplay;
	+ private JCheckBox chkDisableMultithreading;

	public MonitoringModule(boolean expanded) {
	super("Monitor", "", "", "", expanded);
	}

	@Override
	public String getCommand() {
	String cmd = "";
	+ boolean t = chkDisableTable.isSelected();
	+ boolean c = chkDisableConsole.isSelected();
	+ boolean d = chkDisableDisplay.isSelected();
	+ boolean m = chkDisableMultithreading.isSelected();
	if (cmbPath.getSelectedIndex() != 0)
	cmd += " -path " + txtPath.getText();
	if (cmbTime.getSelectedIndex() != 0)
	cmd += " -time " + txtTime.getText();
	- if (cmbMonitor.getSelectedIndex() != 0)
	- cmd += " -monitor " + cmbMonitor.getSelectedItem();
	- if (cmbVerbose.getSelectedIndex() != 0)
	- cmd += " -verbose " + cmbVerbose.getSelectedItem();
	+ if (c \|\| t \|\| d \|\| m)
	+ cmd += " -disable " + (t ? "monitor " : "") +
	+ (c ? "console " : "") + (d ? "display " : "") + (m ? "multithreading " : "");
	+ if (cmbVerbose.getSelectedIndex() != 0) {
	+ String parts[] = ((String)cmbVerbose.getSelectedItem()).split(" ");
	+ cmd += " -verbose " + parts[1];
	+ }
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {

	- cmbTime = new JComboBox<String>(new String[] { "no limit", "specify ..." });
	- cmbPath = new JComboBox<String>(new String[] { "current", "specify ..." });
	- cmbVerbose = new JComboBox<String>(new String[] { "log", "quiet ", "prolix", "mute" });
	- cmbMonitor = new JComboBox<String>(new String[] { "console", "table ", "console table", "no" });
	+ cmbTime = new JComboBox<String>(new String[] { "No time limitation", "Specify limit (s) ..." });
	+ cmbPath = new JComboBox<String>(new String[] { "Current", "Specify ..." });
	+ cmbVerbose = new JComboBox<String>(new String[] { "Verbose: log", "Verbose: quiet ", "Verbose: prolix", "Verbose: mute" });
	+ chkDisableTable = new JCheckBox("Monitor");
	+ chkDisableConsole = new JCheckBox("Console");
	+ chkDisableDisplay = new JCheckBox("Display");
	+ chkDisableMultithreading = new JCheckBox("Multithreading");

	- lblTime = new JLabel("seconds");
	- lblPath = new JLabel("Working directory");
	txtTime = new JTextField("3600");
	txtPath = new JTextField("...", 30);
	bnBrowse = new JButton("Browse");

	- GridPanel pn = new GridPanel(true, 3);
	- pn.place(0, 0, "Path");
	+ GridPanel pn = new GridPanel("Output Directory", 3);
	pn.place(0, 1, cmbPath);
	pn.place(0, 2, bnBrowse);
	pn.place(1, 0, 4, 1, txtPath);
	-
	- GridPanel pn2 = new GridPanel(true, 3);
	- pn2.place(3, 0, "Time");
	- pn2.place(3, 1, cmbTime);
	- pn2.place(3, 2, txtTime);
	- pn2.place(3, 3, "seconds");
	-
	- pn2.place(4, 0, "Monitor");
	- pn2.place(4, 1, cmbMonitor);
	-
	- pn2.place(4, 2, "Verbose");
	- pn2.place(4, 3, cmbVerbose);

	+ GridPanel pn2 = new GridPanel("Settings", 3);
	+ pn2.place(2, 0, cmbTime);
	+ pn2.place(2, 1, txtTime);
	+ pn2.place(2, 3, cmbVerbose);
	+
	+ GridPanel pn3 = new GridPanel("Disable", 3);
	+ pn3.place(4, 0, chkDisableTable);
	+ pn3.place(4, 1, chkDisableConsole);
	+ pn3.place(4, 2, chkDisableDisplay);
	+ pn3.place(4, 3, chkDisableMultithreading);
	+
	JPanel panel = new JPanel();
	panel.setLayout(new BoxLayout(panel, BoxLayout.PAGE_AXIS));
	panel.add(pn);
	panel.add(pn2);
	-
	+ panel.add(pn3);

	Config.register(getName(), "verbose", cmbVerbose, cmbVerbose.getItemAt(0));
	Config.register(getName(), "path", cmbPath, cmbPath.getItemAt(0));
	- Config.register(getName(), "monitor", cmbMonitor, cmbMonitor.getItemAt(0));
	Config.register(getName(), "time", cmbTime, cmbTime.getItemAt(0));
	Config.register(getName(), "time.value", txtTime, "3600");
	Config.register(getName(), "path", txtPath, new File(System.getProperty("user.dir")).getAbsolutePath());
	+ Config.register(getName(), "disable.table", chkDisableTable, "false");
	+ Config.register(getName(), "disable.console", chkDisableConsole, "false");
	+ Config.register(getName(), "disable.display", chkDisableDisplay, "false");
	+ Config.register(getName(), "disable.multithreading", chkDisableMultithreading, "false");

	cmbVerbose.addActionListener(this);
	cmbPath.addActionListener(this);
	- cmbMonitor.addActionListener(this);
	cmbTime.addActionListener(this);
	+ chkDisableTable.addActionListener(this);
	+ chkDisableConsole.addActionListener(this);
	+ chkDisableDisplay.addActionListener(this);
	+ chkDisableMultithreading.addActionListener(this);

	txtTime.addKeyListener(this);
	bnBrowse.addActionListener(this);
	txtPath.addKeyListener(this);

	return panel;
	}

	private void update() {
	setCommand(getCommand());
	setSynopsis(txtPath.getText());
	if (cmbPath != null) {
	boolean b = cmbPath.getSelectedIndex() != 0;
	bnBrowse.setEnabled(b);
	txtPath.setEnabled(b);
	- lblPath.setEnabled(b);
	}
	if (txtTime != null) {
	boolean b = cmbTime.getSelectedIndex() != 0;
	txtTime.setEnabled(b);
	- lblTime.setEnabled(b);
	}
	Command.command();
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnBrowse) {
	File f = Files.browseDirectory(txtPath.getText());
	if (f != null) {
	txtPath.setText(f.getAbsolutePath());
	}
	}
	if (e.getSource() == cmbPath) {
	if (cmbPath.getSelectedIndex() == 0) {
	File f = new File(System.getProperty("user.dir"));
	txtPath.setText(f.getAbsolutePath());
	}
	-
	+
	}
	update();
	}

	@Override
	public void close() {
	- cmbMonitor.removeActionListener(this);
	+ chkDisableTable.removeActionListener(this);
	+ chkDisableConsole.removeActionListener(this);
	+ chkDisableDisplay.removeActionListener(this);
	+ chkDisableMultithreading.removeActionListener(this);
	cmbVerbose.removeActionListener(this);
	cmbTime.removeActionListener(this);
	txtTime.removeActionListener(this);
	txtPath.removeKeyListener(this);
	bnBrowse.removeActionListener(this);
	}

	@Override
	public void keyTyped(KeyEvent e) {
	}

	@Override
	public void keyPressed(KeyEvent e) {
	}

	@Override
	public void keyReleased(KeyEvent e) {
	update();
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java b/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
	index 2934399..fde611d 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
	@@ -1,341 +1,341 @@
	/*
	* 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.datatransfer.DataFlavor;
	import java.awt.datatransfer.Transferable;
	import java.awt.datatransfer.UnsupportedFlavorException;
	import java.awt.dnd.DnDConstants;
	import java.awt.dnd.DropTarget;
	import java.awt.dnd.DropTargetDropEvent;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.awt.event.MouseEvent;
	import java.awt.event.MouseListener;
	import java.io.File;
	import java.io.IOException;
	import java.util.ArrayList;
	import java.util.List;

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

	import lab.component.CustomizedColumn;
	import lab.component.CustomizedTable;
	import lab.tools.Files;
	import signal.RealSignal;
	import signal.factory.SignalFactory;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.ImageSelector;
	import deconvolutionlab.Lab;
	import deconvolutionlab.PlatformImageSelector;
	import deconvolutionlab.dialog.PatternDialog;
	import deconvolutionlab.dialog.SyntheticDialog;
	import deconvolutionlab.monitor.Monitors;

	public class PSFModule extends AbstractModule implements ActionListener, MouseListener {

	private CustomizedTable table;
	private JButton bnFile;
	private JButton bnDirectory;
	private JButton bnSynthetic;
	private JButton bnPlatform;

	public PSFModule(boolean expanded) {
	- super("PSF", "-psf", "Open", "Show", expanded);
	+ super("PSF", "-psf", "Select", "Show", expanded);
	}

	@Override
	public String getCommand() {
	int row = table.getSelectedRow();
	if (row < 0)
	return "";
	return "-psf " + table.getCell(row, 1) + " " + table.getCell(row, 2);
	}

	@Override
	public JPanel buildExpandedPanel() {

	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Name", String.class, 100, false));
	columns.add(new CustomizedColumn("Source", String.class, 100, false));
	columns.add(new CustomizedColumn("Command", String.class, Constants.widthGUI - 200, true));
	columns.add(new CustomizedColumn("", String.class, 30, "\u232B", "Delete this PSF source"));

	table = new CustomizedTable(columns, true);
	table.getColumnModel().getColumn(3).setMaxWidth(30);
	table.getColumnModel().getColumn(3).setMinWidth(30);
	table.addMouseListener(this);

	bnFile = new JButton("\u2295 file");
	bnDirectory = new JButton("\u2295 directory");
	bnSynthetic = new JButton("\u2295 synthetic");
	bnPlatform = new JButton("\u2295 platform");

	JToolBar pn = new JToolBar("Controls PSF");
	pn.setBorder(BorderFactory.createEmptyBorder());
	pn.setLayout(new GridLayout(1, 5));
	pn.setFloatable(false);
	pn.add(bnFile);
	pn.add(bnDirectory);
	pn.add(bnSynthetic);
	pn.add(bnPlatform);

	JPanel panel = new JPanel();
	panel.setBorder(BorderFactory.createEtchedBorder());
	panel.setLayout(new BorderLayout());
	panel.add(pn, BorderLayout.SOUTH);
	panel.add(table.getMinimumPane(100, 100), BorderLayout.CENTER);

	table.setDropTarget(new LocalDropTarget());
	getCollapsedPanel().setDropTarget(new LocalDropTarget());

	bnFile.addActionListener(this);
	bnDirectory.addActionListener(this);
	bnSynthetic.addActionListener(this);
	bnPlatform.addActionListener(this);
	getAction1Button().addActionListener(this);
	getAction2Button().addActionListener(this);

	Config.registerTable(getName(), "psf", table);

	return panel;
	}

	public void update() {
	int row = table.getSelectedRow();
	if (row >= 0) {
	setCommand(getCommand());
	setSynopsis(table.getCell(row, 0));
	Command.command();
	}
	else
	setSynopsis("");
	getAction2Button().setEnabled(table.getRowCount() > 0);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnFile) {
	Deconvolution deconvolution = new Deconvolution(Command.command());
	file(deconvolution.getPath());
	}
	else if (e.getSource() == bnDirectory) {
	Deconvolution deconvolution = new Deconvolution(Command.command());
	dir(deconvolution.getPath());
	}
	else if (e.getSource() == bnSynthetic)
	synthetic(false);
	else if (e.getSource() == bnPlatform)
	platform();
	else if (e.getSource() == getAction1Button())
	platform();
	else if (e.getSource() == getAction2Button())
	display();
	update();
	}

	public void platform() {
	PlatformImageSelector selector = new ImageSelector(Lab.getPlatform()).getImageSelector();
	String name = selector.getSelectedImage();
	if (name != null)
	if (name != "")
	table.insert(new String[] {name, "platform", name, "" });
	}

	private void file(String path) {
	File file = Files.browseFile(path);
	if (file == null)
	return;
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	}

	private void dir(String path) {
	File file = Files.browseDirectory(path);
	if (file == null)
	return;
	PatternDialog dlg = new PatternDialog(file);
	dlg.setVisible(true);
	if (dlg.wasCancel())
	return;
	table.insert(new String[] { dlg.getDirName(), "directory", dlg.getCommand(), "" });
	}

	private void synthetic(boolean edit) {
	ArrayList<SignalFactory> list = SignalFactory.getPSF();
	SyntheticDialog dlg = new SyntheticDialog(list);
	if (edit) {
	int row = table.getSelectedRow();
	if (row >= 0) {
	dlg.setParameters(table.getCell(row, 0), table.getCell(row, 1));
	}
	}
	dlg.setVisible(true);

	if (dlg.wasCancel())
	return;

	if (edit) {
	int row = table.getSelectedRow();
	if (row <= 0)
	table.removeRow(row);
	}
	table.insert(new String[] { dlg.getShapeName(), "synthetic", dlg.getCommand(), "" });
	}

	private void edit() {
	int row = table.getSelectedRow();

	if (row < 0)
	return;
	String name = table.getCell(row, 0).trim();
	System.out.println("edit " + row + " " + name);
	for(SignalFactory factory : SignalFactory.getAll()) {
	if (name.equals(factory.getName().trim()))
	synthetic(true);
	return;
	}
	String filename = table.getCell(row, 1).trim();
	System.out.println("edit " + row + " " + filename + " " + new File(filename).exists() + " " +new File(filename).isDirectory());
	File file = new File(filename);
	if (!file.exists())
	return;
	if (file.isFile())
	file(table.getCell(row, 21));
	else
	dir(table.getCell(row, 1));
	}

	private void display() {
	int row = table.getSelectedRow();
	if (row < 0)
	return;
	Thread thread = new Thread(new Runnable() {
	@Override
	public void run() {
	int row = table.getSelectedRow();
	RealSignal x = new Deconvolution(getCommand() + " -nodisplay -nomonitor").openImage();
	if (x != null)
	Lab.show(Monitors.createDefaultMonitor(), x, table.getCell(row, 0));
	}
	});
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}

	@Override
	public void mouseClicked(MouseEvent e) {
	if (e.getSource() == table) {
	int row = table.getSelectedRow();
	if (row < 0)
	return;
	if (table.getSelectedColumn() == 3) {
	table.removeRow(row);
	if (table.getRowCount() > 0)
	table.setRowSelectionInterval(0, 0);
	}
	update();
	if (e.getClickCount() == 2) {
	edit();
	}
	}
	}

	@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() {
	bnFile.removeActionListener(this);
	bnDirectory.removeActionListener(this);
	bnSynthetic.removeActionListener(this);
	bnPlatform.removeActionListener(this);
	}

	public class LocalDropTarget extends DropTarget {

	@Override
	public void drop(DropTargetDropEvent e) {
	e.acceptDrop(DnDConstants.ACTION_COPY);
	e.getTransferable().getTransferDataFlavors();
	Transferable transferable = e.getTransferable();
	DataFlavor[] flavors = transferable.getTransferDataFlavors();
	for (DataFlavor flavor : flavors) {
	if (flavor.isFlavorJavaFileListType()) {
	try {
	List<File> files = (List<File>) transferable.getTransferData(flavor);
	for (File file : files) {
	if (file.isDirectory()) {
	table.insert(new String[] { file.getName(), "directory", file.getAbsolutePath(), "" });
	table.setRowSelectionInterval(0, 0);
	update();
	}
	if (file.isFile()) {
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	update();
	}
	}
	}
	catch (UnsupportedFlavorException ex) {
	ex.printStackTrace();
	}
	catch (IOException ex) {
	ex.printStackTrace();
	}
	}
	}
	e.dropComplete(true);
	super.drop(e);
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/monitor/TableMonitor.java b/DeconvolutionLab2/src/deconvolutionlab/monitor/TableMonitor.java
	index 298e4c5..2206ae1 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/monitor/TableMonitor.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/monitor/TableMonitor.java
	@@ -1,179 +1,179 @@
	/*
	* 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.awt.BorderLayout;
	import java.awt.Color;
	import java.awt.Component;
	import java.awt.Dimension;
	import java.awt.GridLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.ActionListener;
	import java.util.ArrayList;
	import java.util.HashMap;

	import javax.swing.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JFrame;
	import javax.swing.JLabel;
	import javax.swing.JPanel;
	import javax.swing.JScrollPane;
	import javax.swing.JTable;
	import javax.swing.JToolBar;
	import javax.swing.table.DefaultTableCellRenderer;
	import javax.swing.table.DefaultTableModel;

	import lab.component.CustomizedColumn;
	import lab.component.CustomizedTable;

	public class TableMonitor implements AbstractMonitor, ActionListener {

	private CustomizedTable table;
	private JButton bnClear = new JButton("Clear");
	private JButton bnProlix = new JButton("Prolix");
	private JButton bnVerbose = new JButton("verbose");
	private JButton bnQuiet = new JButton("Quiet");
	private JButton bnMute = new JButton("Mute");
	private HashMap<Long, Color> colors = new HashMap<Long, Color>();
	private JPanel panel;

	public TableMonitor(int width, int height) {
	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("#", Long.class, 60, false));
	columns.add(new CustomizedColumn("Time", String.class, 100, false));
	columns.add(new CustomizedColumn("Memory", String.class, 100, false));
	columns.add(new CustomizedColumn("Message", String.class, Math.max(60, width - 3 * 60), false));

	table = new CustomizedTable(columns, true);
	table.getColumnModel().getColumn(0).setMinWidth(60);
	table.getColumnModel().getColumn(0).setMaxWidth(60);
	table.getColumnModel().getColumn(1).setMaxWidth(100);
	table.getColumnModel().getColumn(1).setMinWidth(100);
	table.getColumnModel().getColumn(2).setMaxWidth(100);
	table.getColumnModel().getColumn(2).setMinWidth(100);

	RowRenderer renderer = new RowRenderer();
	for (int i = 0; i < 4; i++)
	table.getColumnModel().getColumn(i).setCellRenderer(renderer);

	JScrollPane scroll = new JScrollPane(table);
	scroll.setPreferredSize(new Dimension(width, height));
	-
	+ /*
	JToolBar tool = new JToolBar();
	tool.setFloatable(false);
	tool.setLayout(new GridLayout(1, 3));
	tool.add(bnClear);
	tool.add(new JLabel(""));
	tool.add(new JLabel(""));
	tool.add(bnProlix);
	tool.add(bnVerbose);
	tool.add(bnQuiet);
	tool.add(bnMute);
	-
	+ */
	JPanel main = new JPanel(new BorderLayout());

	- main.add(tool, BorderLayout.NORTH);
	+ //main.add(tool, BorderLayout.NORTH);
	main.add(scroll, BorderLayout.CENTER);
	bnClear.addActionListener(this);
	bnVerbose.addActionListener(this);
	bnQuiet.addActionListener(this);
	bnProlix.addActionListener(this);
	bnMute.addActionListener(this);
	panel = new JPanel(new BorderLayout());
	panel.add(main);
	panel.setBorder(BorderFactory.createEtchedBorder());
	}

	public JPanel getPanel() {
	return panel;
	}

	public void show(String title) {
	JFrame frame = new JFrame(title);
	frame.getContentPane().add(panel);
	frame.pack();
	frame.setVisible(true);
	}

	@Override
	public void clear() {
	DefaultTableModel model = (DefaultTableModel) table.getModel();
	model.setRowCount(0);
	}

	@Override
	public void add(Message message) {
	String msg[] = message.formatArray();
	int n = msg.length;
	Object[] row = new Object[n + 1];
	row[0] = message.getID();
	for (int i = 0; i < n; i++)
	row[i + 1] = msg[i];
	table.append(row);

	Verbose level = message.getLevel();
	Color c = new Color(0, 0, 0);
	if (level == Verbose.Prolix)
	c = new Color(255, 0, 0);
	else if (level == Verbose.Quiet)
	c = new Color(200, 200, 0);
	colors.put(new Long(message.getID()), c);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	if (e.getSource() == bnClear) {
	DefaultTableModel model = (DefaultTableModel) table.getModel();
	model.setRowCount(0);
	}
	}

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

	class RowRenderer extends DefaultTableCellRenderer {
	@Override
	public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
	DefaultTableModel model = (DefaultTableModel) table.getModel();
	Component c = super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
	if (row >= 0) {
	Long id = (Long) model.getValueAt(row, 0);
	Color color = colors.get(id);
	c.setForeground(color);
	}
	return c;
	}
	}

	}
	diff --git a/DeconvolutionLab2/src/fft/jtransforms/JTransformsLibrary.java b/DeconvolutionLab2/src/fft/jtransforms/JTransformsLibrary.java
	index 568d428..51829bb 100644
	--- a/DeconvolutionLab2/src/fft/jtransforms/JTransformsLibrary.java
	+++ b/DeconvolutionLab2/src/fft/jtransforms/JTransformsLibrary.java
	@@ -1,79 +1,79 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package fft.jtransforms;

	import fft.AbstractFFTLibrary;

	public class JTransformsLibrary extends AbstractFFTLibrary {

	public JTransformsLibrary() {
	try {
	Class.forName("edu.emory.mathcs.jtransforms.fft.FloatFFT_3D");
	Class.forName("edu.emory.mathcs.jtransforms.fft.FloatFFT_1D");
	Class.forName("edu.emory.mathcs.jtransforms.fft.FloatFFT_2D");
	installed = true;
	}
	catch (ClassNotFoundException ex) {
	installed = false;
	}
	if (installed) {
	ffts.add(new JTransforms());
	ffts.add(new JTransformsFFT_XYZ());
	ffts.add(new JTransformsFFT_XY_Z());
	}
	}

	@Override
	public String getLocation() {
	return JTransformsLibrary.class.getCanonicalName();
	}

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

	@Override
	public String getCredit() {
	return "JTransforms of Piotr Wendykier";
	}

	@Override
	public String getLibraryName() {
	return "JTransforms";
	}

	@Override
	public String getLicence() {
	- return "<h1>JTransforms of Piotr Wendykier" + "<p>https://sites.google.com/site/piotrwendykier/software/jtransforms" + "<p>JTransforms is distributed under the terms of the BSD-2-Clause license." + "<p>THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS " + "AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT " + "LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS" + "FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT " + "HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, " + "SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED " + "TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; " + "OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, " + "WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR " + "OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED " + "OF THE POSSIBILITY OF SUCH DAMAGE.";
	+ return "<h1>JTransforms of Piotr Wendykier</h1>" + "<p>https://sites.google.com/site/piotrwendykier/software/jtransforms" + "<p>JTransforms is distributed under the terms of the BSD-2-Clause license." + "<p>THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS " + "AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT " + "LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS" + "FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT " + "HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, " + "SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED " + "TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; " + "OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, " + "WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR " + "OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED " + "OF THE POSSIBILITY OF SUCH DAMAGE.";
	}
	}
	diff --git a/DeconvolutionLab2/src/imagej/IJImageSelector.java b/DeconvolutionLab2/src/imagej/IJImageSelector.java
	index f2ad068..14e6f6f 100644
	--- a/DeconvolutionLab2/src/imagej/IJImageSelector.java
	+++ b/DeconvolutionLab2/src/imagej/IJImageSelector.java
	@@ -1,140 +1,147 @@
	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.PlatformImageSelector;
	import ij.ImagePlus;
	import ij.WindowManager;
	import ij.gui.GUI;

	public class IJImageSelector extends PlatformImageSelector {

	@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();
	- DefaultListModel listModel = new DefaultListModel();
	- if (list != null)
	+
	+ 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 = new JList(listModel);
	- list.setSelectionMode(ListSelectionModel.SINGLE_INTERVAL_SELECTION);
	- JScrollPane listScroller = new JScrollPane(list);
	- listScroller.setPreferredSize(new Dimension(250, 80));
	- JPanel bn = new JPanel(new GridLayout(1, 2));
	- bn.add(bnCancel);
	- bn.add(bnOK);
	- JPanel panel = new JPanel(new BorderLayout());
	- panel.add(listScroller, BorderLayout.CENTER);
	+ 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(5, 5, 5, 5));
	+ 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) {
	}
	}

	}
	diff --git a/DeconvolutionLab2/src/imagej/IJImager.java b/DeconvolutionLab2/src/imagej/IJImager.java
	index f2dedd1..ac671b5 100644
	--- a/DeconvolutionLab2/src/imagej/IJImager.java
	+++ b/DeconvolutionLab2/src/imagej/IJImager.java
	@@ -1,215 +1,221 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package imagej;

	-import java.util.ArrayList;
	import java.util.HashMap;

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

	public class IJImager extends PlatformImager {

	- private static HashMap<String, ImagePlus> images = new HashMap<String, ImagePlus>();
	- private static HashMap<String, ImageStack> stacks = new HashMap<String, ImageStack>();
	+ private static HashMap<String, ImagePlus> images = new HashMap<String, ImagePlus>();
	+ private static HashMap<String, ImageStack> stacks = new HashMap<String, ImageStack>();

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

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

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

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

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

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

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

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

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

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

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

	@Override
	- public void show(ComplexSignal signal, String title, ComplexComponent complex) {
	+ public void show(ComplexSignal signal, String title, ComplexComponent complex) {
	ImageStack stack = new ImageStack(signal.nx, signal.ny);
	for (int k = 0; k < signal.nz; k++) {
	float[] plane = null;
	- switch(complex) {
	- case REAL: plane = signal.getRealXY(k); break;
	- case IMAGINARY: plane = signal.getImagXY(k); break;
	- case MODULE: plane = signal.getModuleXY(k); break;
	- default: plane = signal.getModuleXY_dB(k);
	+ switch (complex) {
	+ case REAL:
	+ plane = signal.getRealXY(k);
	+ break;
	+ case IMAGINARY:
	+ plane = signal.getImagXY(k);
	+ break;
	+ case MODULE:
	+ plane = signal.getModuleXY(k);
	+ break;
	+ default:
	+ plane = signal.getModuleXY_dB(k);
	}
	stack.addSlice(new FloatProcessor(signal.nx, signal.ny, plane));
	}
	new ImagePlus(title, stack).show();
	}
	-
	+
	private RealSignal build(ImagePlus imp) {
	if (imp == null)
	return null;
	int nx = imp.getWidth();
	int ny = imp.getHeight();
	int nz = imp.getStackSize();
	RealSignal signal = new RealSignal(nx, ny, nz);
	for (int k = 0; k < nz; k++) {
	ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
	signal.setXY(k, (float[]) ip.getPixels());
	}
	return signal;
	}
	-
	+
	private ImagePlus build(RealSignal signal, PlatformImager.Type type) {
	if (signal == null)
	return null;
	-
	+
	ImageStack stack = new ImageStack(signal.nx, signal.ny);
	for (int k = 0; k < signal.nz; k++) {
	ImageProcessor ip = new FloatProcessor(signal.nx, signal.ny, signal.getXY(k));
	- switch(type) {
	- case BYTE:
	- stack.addSlice(ip.convertToByteProcessor(false));
	- break;
	- case SHORT:
	- stack.addSlice(ip.convertToShortProcessor(false));
	- break;
	- case FLOAT:
	- stack.addSlice(ip);
	- default:
	- break;
	+ switch (type) {
	+ case BYTE:
	+ stack.addSlice(ip.convertToByteProcessor(false));
	+ break;
	+ case SHORT:
	+ stack.addSlice(ip.convertToShortProcessor(false));
	+ break;
	+ case FLOAT:
	+ stack.addSlice(ip);
	+ default:
	+ break;
	}
	}
	return new ImagePlus("", stack);
	}
	-
	+
	@Override
	public String getName() {
	return "ImageJ";
	}
	}
	diff --git a/DeconvolutionLab2/src/lab/system/SystemBar.java b/DeconvolutionLab2/src/lab/system/SystemBar.java
	index 117f72d..6a47847 100644
	--- a/DeconvolutionLab2/src/lab/system/SystemBar.java
	+++ b/DeconvolutionLab2/src/lab/system/SystemBar.java
	@@ -1,88 +1,88 @@
	/*
	* 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 lab.system;

	import java.awt.BorderLayout;
	import java.util.Timer;
	import java.util.TimerTask;

	import javax.swing.BoxLayout;
	import javax.swing.JToolBar;

	public class SystemBar extends JToolBar {

	private Timer timer = new Timer();
	private TimerTask updater = new Updater();

	private SystemHeap heap;
	private SystemCPU load;

	public SystemBar(int refreshTime) {
	super("System Bar");
	setFloatable(false);
	heap = new SystemHeap();
	load = new SystemCPU();
	restart(refreshTime);
	setLayout(new BorderLayout());
	setFloatable(true);
	- setLayout(new BoxLayout(this, BoxLayout.PAGE_AXIS));
	- add(heap);
	- add(load);
	+ setLayout(new BorderLayout());
	+ add(heap, BorderLayout.CENTER);
	+ add(load, BorderLayout.EAST);
	}

	public void update() {
	heap.repaint();
	load.repaint();
	}

	public void restart(int refreshTime) {
	if (updater != null) {
	updater.cancel();
	updater = null;
	}
	updater = new Updater();
	timer.schedule(updater, 0, refreshTime);
	}

	public void close() {
	timer.cancel();
	timer = null;
	}

	private class Updater extends TimerTask {
	@Override
	public void run() {
	update();
	}
	}

	}

No OneTemporaryActions

File Metadata

View Options

Event Timeline

No OneTemporary
Actions