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	diff --git a/DeconvolutionLab2.config b/DeconvolutionLab2.config
	new file mode 100644
	index 0000000..67086af
	--- /dev/null
	+++ b/DeconvolutionLab2.config
	@@ -0,0 +1,58 @@
	+#DeconvolutionLab2 [Beta 2]
	+#DeconvolutionLab2 [Beta 2]
	+#Sun Feb 26 14:32:31 CET 2017
	+Algorithm.I.gaussian.mean=0.0
	+Algorithm.I.gaussian.stdev=1.0
	+Algorithm.I.iterations=10
	+Algorithm.I.poisson=0.0
	+Algorithm.I.reg=0.1
	+Algorithm.I.scale=3
	+Algorithm.I.step=1.0
	+Algorithm.I.wavelets=Haar
	+Algorithm.algorithm=Regularized Inverse Filter [RIF \| LRIF]
	+Border.apoxy=Uniform
	+Border.apoz=Uniform
	+Border.extxy=0
	+Border.extz=0
	+Border.padxy=None
	+Border.padz=None
	+Computation.dim=XYZ
	+Computation.epsilon=1E-6
	+Computation.fft=Fastest
	+Computation.normalization=1
	+Controller.constraint.enable=false
	+Controller.constraint.value=no
	+Controller.itmax.enable=true
	+Controller.reference.enable=false
	+Controller.reference.value=
	+Controller.residu.enable=false
	+Controller.residu.value=0.01
	+Controller.time.enable=false
	+Controller.time.value=3600
	+DeconvolutionLab.DeconvolutionDialog.location.h=400
	+DeconvolutionLab.DeconvolutionDialog.location.w=600
	+DeconvolutionLab.DeconvolutionDialog.location.x=802
	+DeconvolutionLab.DeconvolutionDialog.location.y=266
	+DeconvolutionLab.MainDialog.location.h=511
	+DeconvolutionLab.MainDialog.location.w=593
	+DeconvolutionLab.MainDialog.location.x=181
	+DeconvolutionLab.MainDialog.location.y=298
	+Image.image.row0=Cell7.tif;file;/Users/dsage/Desktop/Maria Azevedo/Cell7.tif;
	+Image.image.selected=Cell7.tif;file;/Users/dsage/Desktop/Maria Azevedo/Cell7.tif;
	+Language.headless=Run (Headless)
	+Language.job=Job
	+Language.language=Command line
	+PSF.psf.row0=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;
	+PSF.psf.selected=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;
	+Running.Directory=/Users/dsage/git/deconvolution
	+Running.Display=yes
	+Running.Monitor=console table
	+Running.Multithreading=yes
	+Running.Path=current
	+Running.Stats=no
	+Running.System=yes
	+Running.Verbose=log
	+System.Frame.location.h=313
	+System.Frame.location.w=637
	+System.Frame.location.x=0
	+System.Frame.location.y=23
	diff --git a/DeconvolutionLab2/DeconvolutionLab2.config b/DeconvolutionLab2/DeconvolutionLab2.config
	index cab7984..192c0b8 100644
	--- a/DeconvolutionLab2/DeconvolutionLab2.config
	+++ b/DeconvolutionLab2/DeconvolutionLab2.config
	@@ -1,80 +1,89 @@
	#DeconvolutionLab2 [Beta 2]
	#DeconvolutionLab2 [Beta 2]
	-#Sun Mar 26 18:45:42 CEST 2017
	+#Thu Apr 20 22:35:15 CEST 2017
	Algorithm.BVLS.iterations=10
	Algorithm.BVLS.step=1.0
	Algorithm.FISTA.iterations=10
	Algorithm.FISTA.reg=0.1
	Algorithm.FISTA.scale=3
	Algorithm.FISTA.step=1.0
	Algorithm.FISTA.wavelets=Haar
	Algorithm.ICTM.iterations=10
	Algorithm.ICTM.reg=0.1
	Algorithm.ICTM.step=1.0
	Algorithm.ISTA.iterations=10
	Algorithm.ISTA.reg=0.1
	Algorithm.ISTA.scale=3
	Algorithm.ISTA.step=1.0
	Algorithm.ISTA.wavelets=Haar
	Algorithm.LW.iterations=10
	Algorithm.LW.step=1.0
	Algorithm.NNLS.iterations=10
	Algorithm.NNLS.step=1.0
	Algorithm.RIF.reg=0.1
	Algorithm.RL.iterations=10
	Algorithm.RLTV.reg=1.000E-18
	Algorithm.SIM.gaussian.mean=0.0
	Algorithm.SIM.gaussian.stdev=1.0
	Algorithm.SIM.poisson=0.0
	Algorithm.TM.iterations=10
	Algorithm.TM.reg=0.1
	Algorithm.TM.step=1.0
	Algorithm.TRIF.reg=0.1
	Algorithm.VC.iterations=10
	Algorithm.VC.step=1.0
	-Algorithm.algorithm=Regularized Inverse Filter
	+Algorithm.algorithm=Richardson-Lucy
	Border.apoxy=Hamming
	Border.apoz=Uniform
	-Border.extxy=1
	+Border.extxy=6
	Border.extz=0
	Border.padxy=None
	Border.padz=None
	-Computation.dim=XYZ
	+Computation.display=yes
	Computation.epsilon=1E-6
	Computation.fft=Fastest
	+Computation.multithreading=yes
	Computation.normalization=1
	-Controller.constraint.enable=false
	-Controller.constraint.value=no
	-Controller.itmax.enable=true
	+Computation.system=no
	+Controller.constraint=no
	+Controller.monitor=console
	Controller.reference.enable=false
	Controller.reference.value=
	Controller.residu.enable=false
	Controller.residu.value=0.01
	+Controller.stats=show
	Controller.time.enable=false
	-Controller.time.value=3600
	-DeconvolutionLab.MainDialog.location.h=780
	+Controller.time.value=1
	+Controller.verbose=log
	+DeconvolutionLab.MainDialog.location.h=626
	DeconvolutionLab.MainDialog.location.w=500
	-DeconvolutionLab.MainDialog.location.x=141
	-DeconvolutionLab.MainDialog.location.y=51
	-Image.image.row0=active;platform;active;\u232B
	-Image.image.row1=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
	-Image.image.row2=Applications;directory;/users/dsage/Applications;\u232B
	-Image.image.row3=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
	-Image.image.row4=lib;directory;/Users/dsage/git/deconvolution/DeconvolutionLab2/lib;\u232B
	-Image.image.selected=active;platform;active;\u232B
	+DeconvolutionLab.MainDialog.location.x=896
	+DeconvolutionLab.MainDialog.location.y=23
	+Image.image.row0=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
	+Image.image.row10=Applications;directory;/users/dsage/Applications;\u232B
	+Image.image.row11=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
	+Image.image.row12=lib;directory;/Users/dsage/git/deconvolution/DeconvolutionLab2/lib;\u232B
	+Image.image.row1=20170302_AIDE-MEMOIRE.pdf;file;/Users/dsage/Desktop/20170302_AIDE-MEMOIRE.pdf;null
	+Image.image.row2=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
	+Image.image.row3=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
	+Image.image.row4=20170302_AIDE-MEMOIRE.pdf;file;/Users/dsage/Desktop/20170302_AIDE-MEMOIRE.pdf;null
	+Image.image.row5=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
	+Image.image.row6=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
	+Image.image.row7=RandomLines;synthetic;RandomLines 100.0 size 128 128 32 intensity 255.0 ;\u232B
	+Image.image.row8=active;platform;active;\u232B
	+Image.image.row9=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
	+Image.image.selected=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
	Language.headless=Run (Headless)
	Language.job=Job
	Language.language=Java
	-Output.output.row0=ortho;OR2;;;;\u2713;\u2713;\u232B
	-Output.output.selected=ortho;OR2;;;;\u2713;\u2713;\u232B
	-PSF.psf.row0=Chrome Apps.localized;directory;/users/dsage/applications/Chrome Apps.localized;\u232B
	-PSF.psf.row1=FI1.tif;file;/Users/dsage/git/deconvolution/DeconvolutionLab2/FI1.tif;\u232B
	-PSF.psf.selected=FI1.tif;file;/Users/dsage/git/deconvolution/DeconvolutionLab2/FI1.tif;\u232B
	-Running.Directory=/Users/dsage/Applications
	-Running.Display=no
	-Running.Monitor=console table
	-Running.Multithreading=yes
	+Output.output.row0=mip;MI1;rescaled;;;\u2713;\u2713;\u232B
	+Output.output.selected=mip;MI1;rescaled;;;\u2713;\u2713;\u232B
	+PSF.psf.row0=Double-Helix;synthetic;Double-Helix 3.0 30.0 10.0 size 128 128 32 intensity 255.0 ;null
	+PSF.psf.row1=Sinc;synthetic;Sinc 3.0 3.0 3.0 size 100 128 200 intensity 255.0 ;null
	+PSF.psf.selected=Double-Helix;synthetic;Double-Helix 3.0 30.0 10.0 size 128 128 32 intensity 255.0 ;null
	+Path.current=Current
	+Path.path=/Users/dsage/git/deconvolution/DeconvolutionLab2
	+Running.Directory=/Users/dsage/git/deconvolution/DeconvolutionLab2
	+Running.Monitor=table
	Running.Path=specify
	-Running.Stats=show
	-Running.System=no
	-Running.Verbose=log
	+Running.Verbose=quiet
	diff --git a/DeconvolutionLab2/build.xml b/DeconvolutionLab2/build.xml
	index c512b7d..21ed668 100644
	--- a/DeconvolutionLab2/build.xml
	+++ b/DeconvolutionLab2/build.xml
	@@ -1,51 +1,49 @@
	<?xml version="1.0" encoding="UTF-8"?>
	<project name="DeconvolutionLab2" default="build" basedir=".">

	<property name="imagej" location="${user.home}/Desktop/ImageJ/plugins" />
	<property name="fiji" location="${user.home}/Desktop/Fiji-deconv.app/plugins" />
	<property name="matlab" location="/Applications/MATLAB_R2014b.app/java/" />
	<property name="doc" location="${user.home}/Desktop/doc/" />

	<property name="javadoc.header" value="<h3>DeconvolutionLab2</h3> v1.0" />
	<property name="javadoc.footer" value="<h4>DeconvolutionLab2</h4> <script> var tStamp=new Date(); document.write(tStamp.toUTCString()); </script>" />
	<property name="javadoc.bottom" value='Copyright &copy; <script> var currYear=new Date(); document.write(currYear.getFullYear()); </script>, Biomedical Imaging Group, EPFL, Lausanne, Switzerland. All rights reserved.' />

	<target name="build">
	<mkdir dir="${doc}" />
	<mkdir dir="bin" />
	<copy todir="bin">
	<fileset dir="ij">
	</fileset>
	</copy>
	<copy file="plugins.config" toDir="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>
	<javadoc destdir="${doc}"
	author="true"
	version="true"
	overview="${basedir}/overview.html"
	windowtitle="DeconvolutionLab2">
	<fileset dir="src">
	<include name="*/.java" />
	<exclude name="/fft/" />
	<exclude name="/jfftw/" />
	</fileset>
	<header><![CDATA[${javadoc.header}]]></header>
	<footer><![CDATA[${javadoc.footer}]]></footer>
	<bottom><![CDATA[${javadoc.bottom}]]></bottom>
	-
	</javadoc>
	<copy toDir="${fiji}" file="../DeconvolutionLab_2.jar" />
	<copy toDir="${matlab}" file="../DeconvolutionLab_2.jar" />
	-
	<copy toDir="${imagej}" file="../DeconvolutionLab_2.jar" />

	</target>
	</project>
	diff --git a/DeconvolutionLab2/src/DeconvolutionLab2.java b/DeconvolutionLab2/src/DeconvolutionLab2.java
	index e854461..cdfffc5 100644
	--- a/DeconvolutionLab2/src/DeconvolutionLab2.java
	+++ b/DeconvolutionLab2/src/DeconvolutionLab2.java
	@@ -1,133 +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/>.
	*/

	import java.io.File;

	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Imager;
	import deconvolutionlab.Imager.Platform;
	import deconvolutionlab.Lab;
	import deconvolutionlab.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.init(Platform.STANDALONE);

	if (arg.length == 0) {
	System.out.println("Starting lab");
	lab(arg);
	return;
	}

	String flag = arg[0].trim().toLowerCase();
	if (flag.equalsIgnoreCase("help")) {
	System.out.println("Starting help");
	help();
	return;
	}

	else if (flag.equalsIgnoreCase("lab")) {
	System.out.println("Starting lab");
	lab(arg);
	}

	else if (flag.equalsIgnoreCase("fft")) {
	System.out.println("Starting fft");
	Lab.checkFFT(Monitors.createDefaultMonitor());
	}

	else if (flag.equalsIgnoreCase("run")) {
	System.out.println("Starting run");
	String cmd = "";
	for (int i = 1; i < arg.length; i++)
	cmd += arg[i] + " ";
	new Deconvolution("Run", cmd, Deconvolution.Finish.KILL).deconvolve();
	}

	else if (flag.equalsIgnoreCase("launch")) {
	System.out.println("Starting launch");
	String cmd = "";
	for (int i = 1; i < arg.length; i++)
	cmd += arg[i] + " ";
	new Deconvolution("Launch", cmd, Deconvolution.Finish.KILL).launch();
	}
	else
	System.out.println("" + flag + " command not found");

	}

	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;
	}
	Lab.init(Platform.STANDALONE, config);
	LabDialog dialog = new LabDialog();
	dialog.setVisible(true);
	}

	public static void help() {
	System.out.println("More info:" + Constants.url);
	System.out.println("Syntax:");
	System.out.println("java -jar DeconvolutionLab_2.jar lab");
	System.out.println("java -jar DeconvolutionLab_2.jar run {command} ...");
	System.out.println("java -jar DeconvolutionLab_2.jar launch {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.println("Keywords of {command}: ");
	for (String keyword : Command.keywords)
	System.out.println("\t" + keyword);
	-
	}

	public DeconvolutionLab2(String cmd) {
	System.out.println("cmd: " + cmd);
	Lab.init(Imager.Platform.STANDALONE, System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config");
	new Deconvolution("CommandLine", cmd).deconvolve();
	}
	-
	-
	}
	diff --git a/DeconvolutionLab2/src/Display_FactorySignals.java b/DeconvolutionLab2/src/Display_FactorySignals.java
	new file mode 100644
	index 0000000..57e2c07
	--- /dev/null
	+++ b/DeconvolutionLab2/src/Display_FactorySignals.java
	@@ -0,0 +1,254 @@
	+import java.io.File;
	+import java.util.ArrayList;
	+
	+import bilib.table.CustomizedTable;
	+import bilib.tools.Files;
	+import deconvolution.algorithm.Convolution;
	+import deconvolutionlab.Lab;
	+import deconvolutionlab.monitor.Monitors;
	+import fft.AbstractFFT;
	+import fft.FFT;
	+import ij.plugin.PlugIn;
	+import signal.ComplexSignal;
	+import signal.RealSignal;
	+import signal.factory.SignalFactory;
	+import signal.factory.Sphere;
	+import signal.factory.complex.ComplexSignalFactory;
	+
	+public class Display_FactorySignals implements PlugIn {
	+
	+ private String path = Files.getDesktop() + File.separator + "Deconvolution" + File.separator + "Signals" + File.separator;
	+
	+ @Override
	+ public void run(String arg0) {
	+ }
	+
	+ public static void main(String arg[]) {
	+ new Display_FactorySignals();
	+ }
	+
	+ public Display_FactorySignals() {
	+ new File(path).mkdir();
	+ int nx = 128;
	+ int ny = 96;
	+ int nz = 100;
	+
	+ ArrayList<SignalFactory> factories = SignalFactory.getAll();
	+ RealSignal image = new Sphere(20, 0.5).generate(nx, ny, nz);
	+ Monitors monitors = Monitors.createDefaultMonitor();
	+ CustomizedTable table = new CustomizedTable(new String[] {"Name", "mean", "min", "max"}, true);
	+ table.show("Stats", 500, 500);
	+ for(SignalFactory factory : factories) {
	+ RealSignal psf = factory.intensity(133).generate(nx, ny, nz);
	+ Lab.show(psf);
	+ float s[] = psf.getStats();
	+ table.append(new String[] {factory.getName(), ""+s[0], ""+s[1], ""+s[2]});
	+ Lab.showOrthoview(psf);
	+ Lab.save(monitors, psf, path + psf.name + ".tif");
	+ Lab.save(monitors, psf.createMIP(), path + "mip-" + psf.name + ".tif");
	+ Lab.save(monitors, psf.createOrthoview(), path + "ortho-" + psf.name + ".tif");
	+ Convolution convolution = new Convolution();
	+ RealSignal a = convolution.run(image, psf);
	+ Lab.showMIP(monitors, a, "conv " + factory.getName());
	+ Lab.save(monitors, a, path + "conv-"+psf.name + ".tif");
	+ Lab.save(monitors, a.createMIP(), path + "conv-mip-" + psf.name + ".tif");
	+ Lab.save(monitors, a.createOrthoview(), path + "conv-ortho-" + psf.name + ".tif");
	+ }
	+ }
	+
	+ public void d() {
	+ int nx = 150;
	+ int ny = 128;
	+ int nz = 100;
	+ int xsize = nx / 2;
	+ int ysize = ny / 2;
	+ int zsize = nz / 2;
	+ double wx, wy, wz;
	+ RealSignal psf = new RealSignal("psf", nx, ny, nz);
	+ AbstractFFT fft = FFT.getFastestFFT().getDefaultFFT();
	+ fft.init(Monitors.createDefaultMonitor(), nx, ny, 1);
	+ double pupil = 10;
	+ double defocus = 10;
	+ double wave = 2;
	+
	+ double defocusTop = 2.0Math.PI / (defocusdefocus*pupil);
	+ double defocusCen = 2.0*Math.PI / pupil;
	+
	+ for (int z = 0; z <= zsize; z++) {
	+ float[][][] real = new float[xsize + 1][ysize + 1][1];
	+ float[][][] imag = new float[xsize + 1][ysize + 1][1];
	+ wz = wave(z-zsize)2.0*Math.PI / zsize;
	+ double cosz = Math.cos(wz);
	+ double sinz = Math.sin(wz);
	+ double fcz = z * Math.abs(defocusTop-defocusCen) / zsize+ defocusTop;
	+ for (int y = 0; y <= ysize; y++)
	+ for (int x = 0; x <= xsize; x++) {
	+ wx = Math.PI * x / xsize;
	+ wy = Math.PI * y / ysize;
	+ double g = wywy+wxwx >= fcz*fcz ? 0 : 1;
	+ real[x][y][0] = (float) (g * cosz);
	+ imag[x][y][0] = (float) (g * sinz);
	+ }
	+ ComplexSignal c = ComplexSignalFactory.createHermitian(""+z, nx, ny, 1, real, imag);
	+ RealSignal pz = fft.inverse(c).circular();
	+
	+ //pz.plus(1);
	+ //pz.normalize(1);
	+ psf.setXY(z, pz.getXY(0));
	+ psf.setXY(nz-1-z, pz.duplicate().getXY(0));
	+ }
	+ //psf = new Gaussian(3,4,4).generate(nx, ny, nz);
	+ float min = psf.getExtrema()[0];
	+ psf.minus(min);
	+ float max = psf.getExtrema()[1];
	+ psf.times(1/max);
	+ float aft[] = psf.getExtrema();
	+ System.out.println(" // " + aft[0] + " // " + aft[1]);
	+ psf.normalize(1);
	+ Lab.show(psf);
	+ Lab.showOrthoview(psf);
	+ Lab.save(Monitors.createDefaultMonitor(), psf, "psfdiffraction.tif");
	+ /*
	+ fft.init(Monitors.createDefaultMonitor(), nx, ny, nz);
	+ ComplexSignal otf = fft.transform(psf);
	+ Lab.show(otf.getModule().circular().log());
	+ Lab.showOrthoview(otf.getModule().circular().log());
	+
	+
	+ RealSignal r = new Cube(30, 1).generate(nx, ny, nz);
	+ RealSignal a = new Convolution().run(r, psf);
	+ Lab.showOrthoview(a);
	+ */
	+ }
	+ public void c() {
	+ int nx = 128;
	+ int ny = 128;
	+ int nz = 128;
	+ RealSignal otf = new RealSignal("psf", nx, ny, nz);
	+
	+ int cx = nx/2;
	+ int cy = ny/2;
	+ int cz = nz/2;
	+ double pi = Math.PI;
	+ double periodTop = 5;
	+ double periodCenter = 15;
	+ double attenuation = 10;
	+ double aperture = 60;
	+ double apernorm = (2.0*aperture)/(nx+ny);
	+ double diag = Math.sqrt(nxnx+nyny+nz*nz);
	+ double step = (periodCenter-periodTop)/nz;
	+ for(int i=0; i<nx; i++)
	+ for(int j=0; j<ny; j++) {
	+ double r = Math.sqrt((i-cx)(i-cx)+(j-cy)(j-cy));
	+ for(int k=0; k<nx; k++) {
	+ double z = Math.abs(k-cz);
	+ double p = Math.sqrt(rr + zz)/diag;
	+ double period = Math.max(1, periodCenter-step*z);
	+ double sz = apernormz + period0.25;
	+ double s1 = 1.0 / (1.0+Math.exp(-(r+sz)));
	+ double s2 = 1.0 / (1.0+Math.exp(-(r-sz)));
	+ double s = Math.cos(2pi(r-apernorm*z)/period);
	+ double g = (attenuation*p+1);
	+ otf.data[k][i+jnx] = (float)((s1-s2)s*s/g);
	+ }
	+ }
	+ Lab.show(otf);
	+ Lab.showOrthoview(otf, "out", cx, cy, cz);
	+ float[] stats = otf.getStats();
	+ for(float s : stats)
	+ System.out.println("" + s);
	+
	+ AbstractFFT fft = FFT.getFastestFFT().getDefaultFFT();
	+ fft.init(Monitors.createDefaultMonitor(), nx, ny, nz);
	+ ComplexSignal psf = fft.transform(otf);
	+ float[] stats1 = psf.getModule().getStats();
	+ for(float s : stats1)
	+ System.out.println("PSF " + s);
	+ Lab.show(psf.getModule().circular().log());
	+ Lab.showOrthoview(psf.getModule().circular().log(), "out", cx, cy, cz);
	+ }
	+
	+ public void b() {
	+ int nx = 128;
	+ int ny = 128;
	+ int nz = 128;
	+ RealSignal otf = new RealSignal("psf", nx, ny, nz);
	+
	+ int cx = nx/2;
	+ int cy = ny/2;
	+ int cz = nz/2;
	+
	+ for(int i=0; i<nx; i++)
	+ for(int j=0; j<ny; j++) {
	+ double r = Math.sqrt((i-cx)(i-cx)+(j-cy)(j-cy));
	+ for(int k=0; k<nx; k++) {
	+ double df = Math.abs(k-cz);
	+ double dd = df - 6;
	+ double sig = 3 + df * 0.2;
	+ double sigd = 0.1 + dd * 0.2;
	+ double norm = 1.0 / (Math.PIsigsig);
	+ double g = norm * Math.exp(-rr/(2.0sig*sig));
	+ double gd = (dd < 0 ? 0 : norm * Math.exp(-rr/(2sigd*sigd)));
	+ otf.data[k][i+jnx] = (float)(g-gd); //(Math.exp(-r0.1));
	+ }
	+ }
	+ Lab.show(otf);
	+ Lab.showOrthoview(otf, "out", cx, cy, cz);
	+
	+ float[] stats = otf.getStats();
	+ for(float s : stats)
	+ System.out.println("" + s);
	+
	+ AbstractFFT fft = FFT.getFastestFFT().getDefaultFFT();
	+ fft.init(Monitors.createDefaultMonitor(), nx, ny, nz);
	+ ComplexSignal psf = fft.transform(otf);
	+ float[] stats1 = psf.getModule().getStats();
	+ for(float s : stats1)
	+ System.out.println("PSF " + s);
	+ Lab.show(Monitors.createDefaultMonitor(), psf.getModule().circular(), "psf");
	+ }
	+
	+ public void va() {
	+ int nx = 128;
	+ int ny = 128;
	+ int nz = 128;
	+ RealSignal otf = new RealSignal("psf", nx, ny, nz);
	+
	+ int cx = nx/2;
	+ int cy = ny/2;
	+ int cz = nz/2;
	+ double p = 1.3;
	+ for(int i=0; i<nx; i++)
	+ for(int j=0; j<ny; j++) {
	+ double d = Math.sqrt((i-cx)(i-cx) + (j-cy)(j-cy));
	+ double v = (p-Math.exp(-d*0.1));
	+ for(int k=0; k<nx; k++) {
	+ double dz = ((double)Math.abs(k-cz))/nz;
	+ double g = Math.exp(-dzdz2*nx);
	+ double vz = gvMath.cos(dMath.PI2/nx);
	+ if (vz > 0) {
	+ double r = Math.sqrt((i-cx)(i-cx) + (j-cy)(j-cy) + (k-cz)*(k-cz));
	+ if (r < cx)
	+ otf.data[k][i+jnx] = (float)vz; //(Math.exp(-r0.1));
	+
	+ }
	+ }
	+ }
	+ Lab.show(otf);
	+ Lab.showOrthoview(otf, "out", cx, cy, cz);
	+
	+ float[] stats = otf.getStats();
	+ for(float s : stats)
	+ System.out.println("" + s);
	+
	+ AbstractFFT fft = FFT.getFastestFFT().getDefaultFFT();
	+ fft.init(Monitors.createDefaultMonitor(), nx, ny, nz);
	+ ComplexSignal psf = fft.transform(otf);
	+ float[] stats1 = psf.getModule().getStats();
	+ for(float s : stats1)
	+ System.out.println("PSF " + s);
	+ Lab.show(Monitors.createDefaultMonitor(), psf.getModule().circular(), "psf");
	+
	+ }
	+
	+}
	diff --git a/DeconvolutionLab2/src/bilib/component/BorderToggledButton.java b/DeconvolutionLab2/src/bilib/component/BorderToggledButton.java
	index 5e1b91e..18997b6 100644
	--- a/DeconvolutionLab2/src/bilib/component/BorderToggledButton.java
	+++ b/DeconvolutionLab2/src/bilib/component/BorderToggledButton.java
	@@ -1,22 +1,51 @@
	+/*
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	+ *
	+ * 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.
	+ */
	+
	+/*
	+ * 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 bilib.component;

	import java.awt.Insets;

	import javax.swing.JButton;

	public class BorderToggledButton extends JButton {

	private String text = "";
	public BorderToggledButton(String text) {
	super(text);
	this.text = text;
	setMargin(new Insets(1, 1, 1, 1));
	}

	public void setSelected(boolean selected) {
	if (selected)
	setText("<html><b>" + text + "</b></html>");
	else
	setText(text);
	}
	}
	diff --git a/DeconvolutionLab2/src/bilib/component/GridPanel.java b/DeconvolutionLab2/src/bilib/component/GridPanel.java
	index 0f89435..f0fec94 100644
	--- a/DeconvolutionLab2/src/bilib/component/GridPanel.java
	+++ b/DeconvolutionLab2/src/bilib/component/GridPanel.java
	@@ -1,200 +1,198 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.component;

	import java.awt.GridBagConstraints;
	import java.awt.GridBagLayout;
	import java.awt.Insets;

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

	/**
	* This class extends the JPanel to create grid panel given the possibility to
	* place Java components in an organized manner in the dialog box.
	*
	* @author Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland.
	*
	*/
	public class GridPanel extends JPanel {

	private static final long serialVersionUID = 1L;
	private GridBagLayout layout = new GridBagLayout();
	private GridBagConstraints constraint = new GridBagConstraints();
	private int defaultSpace = 3;

	/**
	* Constructor.
	*/
	public GridPanel() {
	super();
	setLayout(layout);
	setBorder(BorderFactory.createEtchedBorder());
	}

	/**
	* Constructor.
	*/
	public GridPanel(int defaultSpace) {
	super();
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	setBorder(BorderFactory.createEtchedBorder());
	}

	/**
	* Constructor.
	*/
	public GridPanel(boolean border) {
	super();
	setLayout(layout);
	if (border) {
	setBorder(BorderFactory.createEtchedBorder());
	}
	}

	/**
	* Constructor.
	*/
	public GridPanel(String title) {
	super();
	setLayout(layout);
	setBorder(BorderFactory.createTitledBorder(title));
	}

	/**
	* Constructor.
	*/
	public GridPanel(boolean border, int defaultSpace) {
	super();
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	if (border) {
	setBorder(BorderFactory.createEtchedBorder());
	}
	}

	/**
	* Constructor.
	*/
	public GridPanel(String title, int defaultSpace) {
	super();
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	setBorder(BorderFactory.createTitledBorder(title));
	}

	/**
	* Specify the defaultSpace.
	*/
	public void setSpace(int defaultSpace) {
	this.defaultSpace = defaultSpace;
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, String label) {
	place(row, col, 1, 1, defaultSpace, new JLabel(label));
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int space, String label) {
	place(row, col, 1, 1, space, new JLabel(label));
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int width, int height, String label) {
	place(row, col, width, height, defaultSpace, new JLabel(label));
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, JComponent comp) {
	place(row, col, 1, 1, defaultSpace, comp);
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int space, JComponent comp) {
	place(row, col, 1, 1, space, comp);
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int width, int height, JComponent comp) {
	place(row, col, width, height, defaultSpace, comp);
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int width, int height, int space, JComponent comp) {
	if (comp == null)
	return;
	constraint.gridx = col;
	constraint.gridy = row;
	constraint.gridwidth = width;
	constraint.gridheight = height;
	constraint.anchor = GridBagConstraints.NORTHWEST;
	constraint.insets = new Insets(space, space, space, space);
	constraint.fill = GridBagConstraints.HORIZONTAL;
	layout.setConstraints(comp, constraint);
	add(comp);
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int width, int height, int spaceHorizontal, int spaceVertical, JComponent comp) {
	if (comp == null)
	return;
	constraint.gridx = col;
	constraint.gridy = row;
	constraint.gridwidth = width;
	constraint.gridheight = height;
	constraint.anchor = GridBagConstraints.NORTHWEST;
	constraint.insets = new Insets(spaceVertical, spaceHorizontal, spaceHorizontal, spaceVertical);
	constraint.fill = GridBagConstraints.HORIZONTAL;
	layout.setConstraints(comp, constraint);
	add(comp);
	}
	}
	diff --git a/DeconvolutionLab2/src/bilib/component/GridToolbar.java b/DeconvolutionLab2/src/bilib/component/GridToolbar.java
	index 721e775..d37aa43 100644
	--- a/DeconvolutionLab2/src/bilib/component/GridToolbar.java
	+++ b/DeconvolutionLab2/src/bilib/component/GridToolbar.java
	@@ -1,246 +1,244 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.component;

	import java.awt.GridBagConstraints;
	import java.awt.GridBagLayout;
	import java.awt.Insets;

	import javax.swing.BorderFactory;
	import javax.swing.JComponent;
	import javax.swing.JLabel;
	import javax.swing.JToolBar;

	/**
	* This class extends the JToolbar to create grid panel given the possibility to
	* place Java components in an organized manner in the dialog box.
	*
	* @author Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland.
	*
	*/
	public class GridToolbar extends JToolBar {

	private GridBagLayout layout = new GridBagLayout();
	private GridBagConstraints constraint = new GridBagConstraints();
	private int defaultSpace = 3;

	/**
	* Constructor.
	*/
	public GridToolbar() {
	super("Control");
	setLayout(layout);
	setBorder(BorderFactory.createEtchedBorder());
	setFloatable(false);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(boolean border) {
	super("Control");
	setLayout(layout);
	if (border) {
	setBorder(BorderFactory.createEtchedBorder());
	}
	setFloatable(false);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(String title) {
	super(title);
	setLayout(layout);
	setBorder(BorderFactory.createTitledBorder(title));
	setFloatable(false);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(int defaultSpace) {
	super("Control");
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	setBorder(BorderFactory.createEtchedBorder());
	setFloatable(false);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(boolean border, int defaultSpace) {
	super("Control");
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	if (border) {
	setBorder(BorderFactory.createEtchedBorder());
	}
	setFloatable(false);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(boolean border, int defaultSpace, boolean floatable) {
	super("Control");
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	if (border) {
	setBorder(BorderFactory.createEtchedBorder());
	}
	setFloatable(floatable);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(boolean border, boolean floatable) {
	super("Control");
	setLayout(layout);
	if (border) {
	setBorder(BorderFactory.createEtchedBorder());
	}
	setFloatable(floatable);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(String title, boolean floatable) {
	super(title);
	setLayout(layout);
	setBorder(BorderFactory.createTitledBorder(title));
	setFloatable(floatable);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(int defaultSpace, boolean floatable) {
	super("Control");
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	setBorder(BorderFactory.createEtchedBorder());
	setFloatable(floatable);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(String title, int defaultSpace) {
	super(title);
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	setBorder(BorderFactory.createTitledBorder(title));
	setFloatable(false);
	}

	/**
	* Constructor.
	*/
	public GridToolbar(String title, int defaultSpace, boolean floatable) {
	super(title);
	setLayout(layout);
	this.defaultSpace = defaultSpace;
	setBorder(BorderFactory.createTitledBorder(title));
	setFloatable(floatable);
	}

	/**
	* Specify the defaultSpace.
	*/
	public void setSpace(int defaultSpace) {
	this.defaultSpace = defaultSpace;
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, String label) {
	place(row, col, 1, 1, defaultSpace, new JLabel(label));
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int space, String label) {
	place(row, col, 1, 1, space, new JLabel(label));
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int width, int height, String label) {
	place(row, col, width, height, defaultSpace, new JLabel(label));
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, JComponent comp) {
	place(row, col, 1, 1, defaultSpace, comp);
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int space, JComponent comp) {
	place(row, col, 1, 1, space, comp);
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int width, int height, JComponent comp) {
	place(row, col, width, height, defaultSpace, comp);
	}

	/**
	* Place a component in the northwest of the cell.
	*/
	public void place(int row, int col, int width, int height, int space, JComponent comp) {
	if (comp == null)
	return;
	constraint.gridx = col;
	constraint.gridy = row;
	constraint.gridwidth = width;
	constraint.gridheight = height;
	constraint.anchor = GridBagConstraints.NORTHWEST;
	constraint.insets = new Insets(space, space, space, space);
	constraint.fill = GridBagConstraints.HORIZONTAL;
	layout.setConstraints(comp, constraint);
	add(comp);
	}

	}
	diff --git a/DeconvolutionLab2/src/bilib/component/HTMLPane.java b/DeconvolutionLab2/src/bilib/component/HTMLPane.java
	index 49a0c9e..db5e904 100644
	--- a/DeconvolutionLab2/src/bilib/component/HTMLPane.java
	+++ b/DeconvolutionLab2/src/bilib/component/HTMLPane.java
	@@ -1,141 +1,139 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.component;

	import java.awt.Dimension;

	import javax.swing.JEditorPane;
	import javax.swing.JScrollPane;
	import javax.swing.text.BadLocationException;
	import javax.swing.text.Document;

	/**
	* This class extends the Java JEditorPane to make a easy to use panel to
	* display HTML information.
	*
	* @author Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland.
	*
	*/
	public class HTMLPane extends JEditorPane {

	private String html = "";
	private String header = "";
	private String footer = "";
	private Dimension dim;
	private String font = "verdana";
	private String color = "#222222";
	private String background = "#f8f8f8";

	public HTMLPane() {
	create();
	}

	public HTMLPane(String font) {
	this.font = font;
	create();
	}

	public HTMLPane(int width, int height) {
	this.dim = new Dimension(width, height);
	create();
	}

	public HTMLPane(String font, int width, int height) {
	this.font = font;
	this.dim = new Dimension(width, height);
	create();
	}

	public HTMLPane(String font, String color, String background, int width, int height) {
	this.font = font;
	this.dim = new Dimension(width, height);
	this.color = color;
	this.background = background;
	create();
	}

	@Override
	public String getText() {
	Document doc = this.getDocument();
	try {
	return doc.getText(0, doc.getLength());
	}
	catch (BadLocationException e) {
	e.printStackTrace();
	return getText();
	}
	}

	public void clear() {
	html = "";
	append("");
	}

	private void create() {
	header += "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">\n";
	header += "<html><head>\n";
	header += "<style>body {background-color:" + background + "; color:" + color + "; font-family: " + font + ";margin:4px}</style>\n";
	header += "<style>h1 {color:#555555; font-size:1.0em; font-weight:bold; padding:1px; margin:1px;}</style>\n";
	header += "<style>h2 {color:#333333; font-size:0.9em; font-weight:bold; padding:1px; margin:1px;}</style>\n";
	header += "<style>h3 {color:#000000; font-size:0.9em; font-weight:italic; padding:1px; margin:1px;}</style>\n";
	header += "<style>p {color:" + color + "; font-size:0.9em; padding:1px; margin:0px;}</style>\n";
	header += "</head>\n";
	header += "<body>\n";
	footer += "</body></html>\n";
	setEditable(false);
	setContentType("text/html; charset=ISO-8859-1");
	}

	public void append(String content) {
	html += content;
	setText(header + html + footer);
	if (dim != null) {
	setPreferredSize(dim);
	}
	setCaretPosition(0);
	}

	public void append(String tag, String content) {
	html += "<" + tag + ">" + content + "</" + tag + ">";
	setText(header + html + footer);
	if (dim != null) {
	setPreferredSize(dim);
	}
	setCaretPosition(0);
	}

	public JScrollPane getPane() {
	JScrollPane scroll = new JScrollPane(this, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
	scroll.setPreferredSize(dim);
	return scroll;
	}
	}
	diff --git a/DeconvolutionLab2/src/bilib/component/PanelImage.java b/DeconvolutionLab2/src/bilib/component/PanelImage.java
	index 304113f..2abb46a 100644
	--- a/DeconvolutionLab2/src/bilib/component/PanelImage.java
	+++ b/DeconvolutionLab2/src/bilib/component/PanelImage.java
	@@ -1,64 +1,92 @@
	+/*
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	+ *
	+ * 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.
	+ */
	+
	+/*
	+ * 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 bilib.component;

	import java.awt.Color;
	import java.awt.Graphics;
	import java.awt.Image;
	import java.awt.image.BufferedImage;
	-
	import javax.swing.JPanel;

	-import deconvolutionlab.splash.ImageLoader;
	+import resources.ImageLoader;

	public class PanelImage extends JPanel {

	private Image image;
	private int w = -1;
	private int h = -1;

	public PanelImage() {
	super();
	}

	public PanelImage(String filename) {
	super();
	image = ImageLoader.get(filename);
	}

	public PanelImage(int w, int h) {
	super();
	image = null;
	this.w = w;
	this.h = h;
	}

	public PanelImage(String filename, int w, int h) {
	super();
	image = ImageLoader.get(filename);
	this.w = w;
	this.h = h;
	}

	public void setImage(BufferedImage image) {
	this.image = image;
	repaint();
	}

	@Override
	protected void paintComponent(Graphics g) {
	super.paintComponent(g);
	if (image != null) {
	if (w < 0)
	g.drawImage(image, 0, 0, getWidth(), getHeight(), null);
	else {
	g.setColor(Color.WHITE);
	g.fillRect(0, 0, getWidth(), getHeight());
	g.drawImage(image, (getWidth()-w)/2, 0, w, h, null);
	}
	}
	else {
	g.setColor(Color.DARK_GRAY);
	g.fillRect(0, 0, getWidth(), getHeight());
	}
	}

	}
	diff --git a/DeconvolutionLab2/src/bilib/component/SpinnerRangeDouble.java b/DeconvolutionLab2/src/bilib/component/SpinnerRangeDouble.java
	index 73a1401..74e1fd0 100644
	--- a/DeconvolutionLab2/src/bilib/component/SpinnerRangeDouble.java
	+++ b/DeconvolutionLab2/src/bilib/component/SpinnerRangeDouble.java
	@@ -1,197 +1,195 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.component;

	import javax.swing.JFormattedTextField;
	import javax.swing.JSpinner;
	import javax.swing.SpinnerNumberModel;

	/**
	* This class extends the Java Swing JSpinner to make a easy to use spinner for
	* double. It handles double type. The size can be control by the number of
	* visible chars or by a specific format (NumberEditor).
	*
	* @author Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland.
	*
	*/
	public class SpinnerRangeDouble extends JSpinner {

	private SpinnerNumberModel model;

	private double defValue;
	private double minValue;
	private double maxValue;
	private double incValue;

	/**
	* Constructor.
	*/
	public SpinnerRangeDouble(double defValue, double minValue, double maxValue, double incValue) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Double def = new Double(defValue);
	Double min = new Double(minValue);
	Double max = new Double(maxValue);
	Double inc = new Double(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(7);
	}

	/**
	* Constructor.
	*/
	public SpinnerRangeDouble(double defValue, double minValue, double maxValue, double incValue, String format) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Double def = new Double(defValue);
	Double min = new Double(minValue);
	Double max = new Double(maxValue);
	Double inc = new Double(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	setEditor(new JSpinner.NumberEditor(this, format));
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(7);
	}

	/**
	* Constructor.
	*/
	public SpinnerRangeDouble(double defValue, double minValue, double maxValue, double incValue, int visibleChars) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Double def = new Double(defValue);
	Double min = new Double(minValue);
	Double max = new Double(maxValue);
	Double inc = new Double(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(visibleChars);
	}

	/**
	* Set the format of the numerical value.
	*/
	public void setFormat(String format) {
	setEditor(new JSpinner.NumberEditor(this, format));
	}

	/**
	* Set the minimal and the maximal limit.
	*/
	public void setLimit(double minValue, double maxValue) {
	this.minValue = minValue;
	this.maxValue = maxValue;
	double value = get();
	Double min = new Double(minValue);
	Double max = new Double(maxValue);
	Double inc = new Double(incValue);
	defValue = (value > maxValue ? maxValue : (value < minValue ? minValue : value));
	Double def = new Double(defValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	}

	/**
	* Set the incremental step.
	*/
	public void setIncrement(double incValue) {
	this.incValue = incValue;
	Double def = (Double) getModel().getValue();
	Double min = new Double(minValue);
	Double max = new Double(maxValue);
	Double inc = new Double(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	}

	/**
	* Returns the incremental step.
	*/
	public double getIncrement() {
	return incValue;
	}

	/**
	* Set the value in the JSpinner with clipping in the range [min..max].
	*/
	public void set(double value) {
	value = (value > maxValue ? maxValue : (value < minValue ? minValue : value));
	model.setValue(new Double(value));
	}

	/**
	* Return the value with clipping the value in the range [min..max].
	*/
	public double get() {
	if (model.getValue() instanceof Integer) {
	Integer i = (Integer) model.getValue();
	double ii = i.intValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	else if (model.getValue() instanceof Double) {
	Double i = (Double) model.getValue();
	double ii = i.doubleValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	else if (model.getValue() instanceof Float) {
	Float i = (Float) model.getValue();
	double ii = i.floatValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	return 0.0;
	}

	public double getRangeMaximum() {
	return maxValue;
	}

	public double getRangeMinimum() {
	return minValue;
	}

	}
	diff --git a/DeconvolutionLab2/src/bilib/component/SpinnerRangeFloat.java b/DeconvolutionLab2/src/bilib/component/SpinnerRangeFloat.java
	index 0d59520..a211630 100644
	--- a/DeconvolutionLab2/src/bilib/component/SpinnerRangeFloat.java
	+++ b/DeconvolutionLab2/src/bilib/component/SpinnerRangeFloat.java
	@@ -1,197 +1,195 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.component;

	import javax.swing.JFormattedTextField;
	import javax.swing.JSpinner;
	import javax.swing.SpinnerNumberModel;

	/**
	* This class extends the Java Swing JSpinner to make a easy to use spinner for
	* float. It handles float type. The size can be control by the number of
	* visible chars or by a specific format (NumberEditor).
	*
	* @author Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland.
	*
	*/
	public class SpinnerRangeFloat extends JSpinner {

	private SpinnerNumberModel model;

	private float defValue;
	private float minValue;
	private float maxValue;
	private float incValue;

	/**
	* Constructor.
	*/
	public SpinnerRangeFloat(float defValue, float minValue, float maxValue, float incValue) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Float def = new Float(defValue);
	Float min = new Float(minValue);
	Float max = new Float(maxValue);
	Float inc = new Float(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(7);
	}

	/**
	* Constructor.
	*/
	public SpinnerRangeFloat(float defValue, float minValue, float maxValue, float incValue, String format) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Double def = new Double(defValue);
	Double min = new Double(minValue);
	Double max = new Double(maxValue);
	Double inc = new Double(incValue);
	this.model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	setEditor(new JSpinner.NumberEditor(this, format));
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(7);
	}

	/**
	* Constructor.
	*/
	public SpinnerRangeFloat(float defValue, float minValue, float maxValue, float incValue, int visibleChars) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Float def = new Float(defValue);
	Float min = new Float(minValue);
	Float max = new Float(maxValue);
	Float inc = new Float(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(visibleChars);
	}

	/**
	* Set the format of the numerical value.
	*/
	public void setFormat(String format) {
	setEditor(new JSpinner.NumberEditor(this, format));
	}

	/**
	* Set the minimal and the maximal limit.
	*/
	public void setLimit(float minValue, float maxValue) {
	this.minValue = minValue;
	this.maxValue = maxValue;
	float value = get();
	Float min = new Float(minValue);
	Float max = new Float(maxValue);
	Float inc = new Float(incValue);
	defValue = (value > maxValue ? maxValue : (value < minValue ? minValue : value));
	Float def = new Float(defValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	}

	/**
	* Set the incremental step.
	*/
	public void setIncrement(float incValue) {
	this.incValue = incValue;
	Float def = (Float) getModel().getValue();
	Float min = new Float(minValue);
	Float max = new Float(maxValue);
	Float inc = new Float(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	}

	/**
	* Returns the incremental step.
	*/
	public float getIncrement() {
	return incValue;
	}

	/**
	* Set the value in the JSpinner with clipping in the range [min..max].
	*/
	public void set(float value) {
	value = (value > maxValue ? maxValue : (value < minValue ? minValue : value));
	model.setValue(new Float(value));
	}

	/**
	* Return the value without clipping the value in the range [min..max].
	*/
	public float get() {
	if (model.getValue() instanceof Integer) {
	Integer i = (Integer) model.getValue();
	float ii = (float) i.intValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	else if (model.getValue() instanceof Double) {
	Double i = (Double) model.getValue();
	float ii = (float) i.doubleValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	else if (model.getValue() instanceof Float) {
	Float i = (Float) model.getValue();
	float ii = i.floatValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	return 0f;
	}

	public float getRangeMaximum() {
	return maxValue;
	}

	public float getRangeMinimum() {
	return minValue;
	}

	}
	diff --git a/DeconvolutionLab2/src/bilib/component/SpinnerRangeInteger.java b/DeconvolutionLab2/src/bilib/component/SpinnerRangeInteger.java
	index 9c5558c..a258627 100644
	--- a/DeconvolutionLab2/src/bilib/component/SpinnerRangeInteger.java
	+++ b/DeconvolutionLab2/src/bilib/component/SpinnerRangeInteger.java
	@@ -1,196 +1,194 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.component;

	import javax.swing.JFormattedTextField;
	import javax.swing.JSpinner;
	import javax.swing.SpinnerNumberModel;

	/**
	* This class extends the Java Swing JSpinner to make a easy to use spinner for
	* integer. It handles int type. The size can be control by the number of
	* visible chars or by a specific format (NumberEditor).
	*
	* @author Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland.
	*
	*/
	public class SpinnerRangeInteger extends JSpinner {

	private SpinnerNumberModel model;

	private int defValue;
	private int minValue;
	private int maxValue;
	private int incValue;

	/**
	* Constructor.
	*/
	public SpinnerRangeInteger(int defValue, int minValue, int maxValue, int incValue) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Integer def = new Integer(defValue);
	Integer min = new Integer(minValue);
	Integer max = new Integer(maxValue);
	Integer inc = new Integer(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(7);
	}

	/**
	* Constructor.
	*/
	public SpinnerRangeInteger(int defValue, int minValue, int maxValue, int incValue, String format) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Integer def = new Integer(defValue);
	Integer min = new Integer(minValue);
	Integer max = new Integer(maxValue);
	Integer inc = new Integer(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	setEditor(new JSpinner.NumberEditor(this, format));
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(format.length());
	}

	/**
	* Constructor.
	*/
	public SpinnerRangeInteger(int defValue, int minValue, int maxValue, int incValue, int visibleChars) {
	super();
	this.defValue = defValue;
	this.minValue = minValue;
	this.maxValue = maxValue;
	this.incValue = incValue;

	Integer def = new Integer(defValue);
	Integer min = new Integer(minValue);
	Integer max = new Integer(maxValue);
	Integer inc = new Integer(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	JFormattedTextField tf = ((JSpinner.DefaultEditor) getEditor()).getTextField();
	tf.setColumns(visibleChars);
	}

	/**
	* Set the format of the numerical value.
	*/
	public void setFormat(String format) {
	setEditor(new JSpinner.NumberEditor(this, format));
	}

	/**
	* Set the minimal and the maximal limit.
	*/
	public void setLimit(int minValue, int maxValue) {
	this.minValue = minValue;
	this.maxValue = maxValue;
	int value = get();
	Integer min = new Integer(minValue);
	Integer max = new Integer(maxValue);
	Integer inc = new Integer(incValue);
	defValue = (value > maxValue ? maxValue : (value < minValue ? minValue : value));
	Integer def = new Integer(defValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	}

	/**
	* Set the incremental step.
	*/
	public void setIncrement(int incValue) {
	this.incValue = incValue;
	Integer def = (Integer) getModel().getValue();
	Integer min = new Integer(minValue);
	Integer max = new Integer(maxValue);
	Integer inc = new Integer(incValue);
	model = new SpinnerNumberModel(def, min, max, inc);
	setModel(model);
	}

	/**
	* Returns the incremental step.
	*/
	public int getIncrement() {
	return incValue;
	}

	/**
	* Set the value in the JSpinner with clipping in the range [min..max].
	*/
	public void set(int value) {
	value = (value > maxValue ? maxValue : (value < minValue ? minValue : value));
	model.setValue(new Integer(value));
	}

	/**
	* Return the value without clipping the value in the range [min..max].
	*/
	public int get() {
	if (model.getValue() instanceof Integer) {
	Integer i = (Integer) model.getValue();
	int ii = i.intValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	else if (model.getValue() instanceof Double) {
	Double i = (Double) model.getValue();
	int ii = (int) i.doubleValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	else if (model.getValue() instanceof Float) {
	Float i = (Float) model.getValue();
	int ii = (int) i.floatValue();
	return (ii > maxValue ? maxValue : (ii < minValue ? minValue : ii));
	}
	return 0;
	}

	public int getRangeMaximum() {
	return maxValue;
	}

	public int getRangeMinimum() {
	return minValue;
	}
	}
	diff --git a/DeconvolutionLab2/src/bilib/table/CustomizedColumn.java b/DeconvolutionLab2/src/bilib/table/CustomizedColumn.java
	index 43fc093..df3c3fd 100644
	--- a/DeconvolutionLab2/src/bilib/table/CustomizedColumn.java
	+++ b/DeconvolutionLab2/src/bilib/table/CustomizedColumn.java
	@@ -1,67 +1,65 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.table;

	public class CustomizedColumn {
	public Class<?> classe;
	public String header;
	public int width;
	public boolean editable;
	public String[] choices; // Combobox
	public String button; // Button
	public String tooltip;

	public CustomizedColumn(String header, Class<?> classe, int width, boolean editable) {
	this.classe = classe;
	this.header = header;
	this.width = width;
	this.editable = editable;
	}

	public CustomizedColumn(String header, Class<?> classe, int width, String[] choices, String tooltip) {
	this.classe = classe;
	this.header = header;
	this.width = width;
	this.editable = true;
	this.choices = choices;
	this.tooltip = tooltip;
	}

	public CustomizedColumn(String header, Class<?> classe, int width, String button, String tooltip) {
	this.classe = classe;
	this.header = header;
	this.width = width;
	this.editable = false;
	this.button = button;
	this.tooltip = tooltip;
	}
	}
	diff --git a/DeconvolutionLab2/src/bilib/table/CustomizedTable.java b/DeconvolutionLab2/src/bilib/table/CustomizedTable.java
	index ae916d9..c1a2859 100644
	--- a/DeconvolutionLab2/src/bilib/table/CustomizedTable.java
	+++ b/DeconvolutionLab2/src/bilib/table/CustomizedTable.java
	@@ -1,298 +1,296 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.table;

	import java.awt.Component;
	import java.awt.Dimension;
	import java.awt.Insets;
	import java.awt.Rectangle;
	import java.io.BufferedWriter;
	import java.io.File;
	import java.io.FileWriter;
	import java.io.IOException;
	import java.util.ArrayList;

	import javax.swing.DefaultCellEditor;
	import javax.swing.JButton;
	import javax.swing.JComboBox;
	import javax.swing.JFrame;
	import javax.swing.JScrollPane;
	import javax.swing.JTable;
	import javax.swing.table.DefaultTableModel;
	import javax.swing.table.TableCellRenderer;
	import javax.swing.table.TableColumn;

	public class CustomizedTable extends JTable {

	private JScrollPane pane = null;
	private ArrayList<CustomizedColumn> columns;

	public CustomizedTable(String headers[], boolean sortable) {
	ArrayList<CustomizedColumn> colums = new ArrayList<CustomizedColumn>();
	for (int i = 0; i < headers.length; i++)
	colums.add(new CustomizedColumn(headers[i], String.class, 150, false));
	create(colums);
	setAutoCreateRowSorter(sortable);
	setRowHeight(20);
	}

	public CustomizedTable(ArrayList<CustomizedColumn> columns, boolean sortable) {
	create(columns);
	setAutoCreateRowSorter(sortable);
	setRowHeight(20);
	}

	private void create(ArrayList<CustomizedColumn> column) {
	columns = column;
	DefaultTableModel model = new DefaultTableModel() {
	@Override
	public boolean isCellEditable(int row, int col) {
	return columns.get(col).editable;
	}

	@Override
	public Class<?> getColumnClass(int col) {
	return columns.get(col).classe;
	}
	};

	setModel(model);
	int n = columns.size();
	String headers[] = new String[n];
	for (int col = 0; col < n; col++)
	headers[col] = columns.get(col).header;

	model.setColumnIdentifiers(headers);
	setFillsViewportHeight(true);

	for (int col = 0; col < n; col++) {
	TableColumn tc = getColumnModel().getColumn(col);
	tc.setPreferredWidth(columns.get(col).width);

	if (columns.get(col).choices != null) {
	JComboBox<String> cmb = new JComboBox<String>();
	for (String p : columns.get(col).choices) {
	cmb.addItem(p);
	cmb.setToolTipText(columns.get(col).tooltip);
	tc.setCellEditor(new DefaultCellEditor(cmb));
	}
	}
	if (columns.get(col).button != null) {
	ButtonRenderer bn = new ButtonRenderer();
	bn.setToolTipText(columns.get(col).tooltip);
	tc.setCellRenderer(bn);
	}
	}
	getTableHeader().setReorderingAllowed(false);
	}

	public void setPreferredSize(int width, int height) {
	if (pane != null)
	pane.setPreferredSize(new Dimension(width, height));
	}

	public void removeRow(int row) {
	if (row >= 0 && row < getRowCount())
	((DefaultTableModel) getModel()).removeRow(row);
	}

	public void removeRows() {
	while(getRowCount() > 0)
	((DefaultTableModel) getModel()).removeRow(0);
	}

	public String[] getRow(int row) {
	if (row >= 0) {
	int ncol = getColumnCount();
	String items[] = new String[ncol];
	for (int col = 0; col < ncol; col++)
	items[col] = (String) getModel().getValueAt(row, col);
	return items;
	}
	return new String[1];
	}

	public String getCell(int row, int col) {
	if (row >= 0 && col >= 0) {
	return (String) getModel().getValueAt(row, col);
	}
	return "";
	}

	public void setCell(int row, int col, String value) {
	if (row >= 0 && col >= 0) {
	getModel().setValueAt(value, row, col);
	}
	}

	public String getRowCSV(int row, String seperator) {
	if (row >= 0) {
	int ncol = getColumnCount();
	String items = "";
	for (int col = 0; col < ncol - 1; col++) {
	if ((String) getModel().getValueAt(row, col) == null)
	items += "" + seperator;
	else
	items += (String) getModel().getValueAt(row, col) + seperator;
	}
	if (ncol >= 1)
	items += (String) getModel().getValueAt(row, ncol - 1);
	return items;
	}
	return "";
	}

	public void saveCSV(String filename) {
	File file = new File(filename);
	try {
	BufferedWriter buffer = new BufferedWriter(new FileWriter(file));
	int nrows = getRowCount();
	int ncols = getColumnCount();

	String row = "";
	for (int c = 0; c < columns.size(); c++)
	row += columns.get(c).header + (c == columns.size() - 1 ? "" : ", ");
	buffer.write(row + "\n");

	for (int r = 0; r < nrows; r++) {
	row = "";
	for (int c = 0; c < ncols; c++)
	row += this.getCell(r, c) + (c == ncols - 1 ? "" : ", ");
	buffer.write(row + "\n");
	}
	buffer.close();
	}
	catch (IOException ex) {
	}
	}

	public String getSelectedAtColumn(int col) {
	int row = getSelectedRow();
	if (row >= 0)
	return (String) getModel().getValueAt(row, col);
	else
	return "";
	}

	public void setSelectedAtColumn(int col, String selection) {
	int nrows = this.getRowCount();
	for (int i = 0; i < nrows; i++) {
	String name = (String) getModel().getValueAt(i, col);
	if (name.equals(selection))
	this.setRowSelectionInterval(i, i + 1);
	}
	}

	public void append(Object[] row) {
	DefaultTableModel model = (DefaultTableModel) getModel();
	int i = 0;
	try {
	model.addRow(row);
	i = getRowCount() - 1;
	if (i >= 0) {
	getSelectionModel().setSelectionInterval(i, i);
	scrollRectToVisible(new Rectangle(getCellRect(i, 0, true)));
	}
	}
	catch (Exception e) {
	}
	repaint();
	}

	public void insert(Object[] row) {
	DefaultTableModel model = (DefaultTableModel) getModel();
	int i = 0;
	try {
	model.insertRow(0, row);
	getSelectionModel().setSelectionInterval(i, i);
	scrollRectToVisible(new Rectangle(getCellRect(i, 0, true)));
	}
	catch (Exception e) {
	}
	repaint();
	}

	@Override
	public int getSelectedRow() {
	int row = super.getSelectedRow();
	if (row < 0) {
	if (getRowCount() > 0) {
	setRowSelectionInterval(0, 0);
	row = super.getSelectedRow();
	}
	return row;
	}
	return row;
	}

	public void update(ArrayList<String[]> data) {
	DefaultTableModel model = (DefaultTableModel) getModel();
	model.getDataVector().removeAllElements();
	for (String[] row : data)
	model.addRow(row);
	repaint();
	}

	public JScrollPane getPane(int width, int height) {
	setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
	setPreferredScrollableViewportSize(new Dimension(width, height));
	setFillsViewportHeight(true);
	pane = new JScrollPane(this);
	return pane;
	}

	public JScrollPane getMinimumPane(int width, int height) {
	setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
	setMinimumSize(new Dimension(width, height));
	setShowVerticalLines(true);
	setPreferredScrollableViewportSize(new Dimension(width, height));
	setFillsViewportHeight(true);
	return new JScrollPane(this);
	}

	public JFrame show(String title, int w, int h) {
	JFrame frame = new JFrame(title);
	frame.add(getPane(w, h));
	frame.pack();
	frame.setVisible(true);
	return frame;
	}
	public class ButtonRenderer extends JButton implements TableCellRenderer {
	@Override
	public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
	setText((String)value);
	setMargin(new Insets(1, 1, 1, 1));
	return this;
	}
	}

	}
	diff --git a/DeconvolutionLab2/src/bilib/tools/Bessel.java b/DeconvolutionLab2/src/bilib/tools/Bessel.java
	new file mode 100644
	index 0000000..50ca2fe
	--- /dev/null
	+++ b/DeconvolutionLab2/src/bilib/tools/Bessel.java
	@@ -0,0 +1,79 @@
	+/*
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	+ *
	+ * 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.
	+ */
	+
	+/*
	+ * 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 bilib.tools;
	+
	+public class Bessel {
	+
	+ // Returns the Bessel function J0(x) for any real x. Adapted from Computer
	+ // Approximations by Hart 1978.
	+ public static double J0(double x) {
	+ double ax, z;
	+ double xx, y, ans, ans1, ans2;
	+ if ((ax = Math.abs(x)) < 8.0) {
	+ y = x * x;
	+ ans1 = 57568490574.0 + y * (-13362590354.0 + y * (651619640.7 + y * (-11214424.18 + y * (77392.33017 + y * (-184.9052456)))));
	+ ans2 = 57568490411.0 + y * (1029532985.0 + y * (9494680.718 + y * (59272.64853 + y * (267.8532712 + y * 1.0))));
	+ ans = ans1 / ans2;
	+ }
	+ else {
	+ z = 8.0 / ax;
	+ y = z * z;
	+ xx = ax - 0.785398164;
	+ ans1 = 1.0 + y * (-0.1098628627e-2 + y * (0.2734510407e-4 + y * (-0.2073370639e-5 + y * 0.2093887211e-6)));
	+ ans2 = -0.1562499995e-1 + y * (0.1430488765e-3 + y * (-0.6911147651e-5 + y * (0.7621095161e-6 - y * 0.934945152e-7)));
	+ ans = Math.sqrt(0.636619772 / ax) * (Math.cos(xx) * ans1 - z * Math.sin(xx) * ans2);
	+ }
	+ return ans;
	+ }
	+
	+ // Returns the Bessel function J1(x) for any real x. Adapted from Computer
	+ // Approximations by Hart 1978.
	+ public static double J1(double x) {
	+ double ax, z;
	+ double xx, y, ans, ans1, ans2;
	+ if ((ax = Math.abs(x)) < 8.0) {
	+ y = x * x;
	+ ans1 = x * (72362614232.0 + y * (-7895059235.0 + y * (242396853.1 + y * (-2972611.439 + y * (15704.48260 + y * (-30.16036606))))));
	+ ans2 = 144725228442.0 + y * (2300535178.0 + y * (18583304.74 + y * (99447.43394 + y * (376.9991397 + y * 1.0))));
	+ ans = ans1 / ans2;
	+ }
	+ else {
	+ z = 8.0 / ax;
	+ y = z * z;
	+ xx = ax - 2.356194491;
	+ ans1 = 1.0 + y * (0.183105e-2 + y * (-0.3516396496e-4 + y * (0.2457520174e-5 + y * (-0.240337019e-6))));
	+ ans2 = 0.04687499995 + y * (-0.2002690873e-3 + y * (0.8449199096e-5 + y * (-0.88228987e-6 + y * 0.105787412e-6)));
	+ ans = Math.sqrt(0.636619772 / ax) * (Math.cos(xx) * ans1 - z * Math.sin(xx) * ans2);
	+ if (x < 0.0)
	+ ans = -ans;
	+ }
	+ return ans;
	+ }
	+
	+}
	diff --git a/DeconvolutionLab2/src/bilib/tools/Files.java b/DeconvolutionLab2/src/bilib/tools/Files.java
	index 423081a..f337d83 100644
	--- a/DeconvolutionLab2/src/bilib/tools/Files.java
	+++ b/DeconvolutionLab2/src/bilib/tools/Files.java
	@@ -1,71 +1,79 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.tools;

	import java.io.File;

	import javax.swing.JFileChooser;
	+import javax.swing.filechooser.FileSystemView;

	public class Files {

	+ public static String getHome() {
	+ return FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath();
	+
	+ }
	+
	+ public static String getDesktop() {
	+ return getHome() + File.separator + "Desktop";
	+ }
	+
	public static File browseFile(String path) {
	JFileChooser fc = new JFileChooser();
	fc.setFileSelectionMode(JFileChooser.FILES_ONLY);
	File dir = new File(path);
	if (dir.exists())
	fc.setCurrentDirectory(dir);

	int ret = fc.showOpenDialog(null);
	if (ret == JFileChooser.APPROVE_OPTION) {
	File file = new File(fc.getSelectedFile().getAbsolutePath());
	if (file.exists())
	return file;
	}
	return null;
	}

	public static File browseDirectory(String path) {
	JFileChooser fc = new JFileChooser();
	fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
	File dir = new File(path);
	if (dir.exists())
	fc.setCurrentDirectory(dir);

	int ret = fc.showOpenDialog(null);
	if (ret == JFileChooser.APPROVE_OPTION) {
	File file = new File(fc.getSelectedFile().getAbsolutePath());
	if (file.exists())
	return file;
	}
	return null;
	}
	}
	diff --git a/DeconvolutionLab2/src/bilib/tools/NumFormat.java b/DeconvolutionLab2/src/bilib/tools/NumFormat.java
	index 912a246..65235c1 100644
	--- a/DeconvolutionLab2/src/bilib/tools/NumFormat.java
	+++ b/DeconvolutionLab2/src/bilib/tools/NumFormat.java
	@@ -1,129 +1,135 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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 bilib.tools;

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

	public class NumFormat {

	public static double parseNumber(String line, double def) {
	double[] numbers = parseNumbers(line);
	if (numbers.length >= 1)
	return numbers[0];
	else
	return def;
	}

	+ public static double[] parseNumbersAfter(String keyword, String line) {
	+ String parts[] = line.trim().toLowerCase().split(keyword.toLowerCase());
	+ if (parts.length == 2)
	+ return parseNumbers(parts[1]);
	+ else
	+ return new double[0];
	+ }
	+
	public static double[] parseNumbers(String line) {
	ArrayList<String> num = new ArrayList<String>();
	Pattern p = Pattern.compile("[-+]?[0-9]+[.]?[0-9]*([eE][-+]?[0-9]+)?");
	Matcher m = p.matcher(line);
	while (m.find()) {
	num.add(m.group());
	}
	double number[] = new double[num.size()];
	for (int i = 0; i < num.size(); i++)
	number[i] = Double.parseDouble(num.get(i));
	return number;
	}

	public static String nice(double a) {
	double b = Math.abs(a);
	- String n = a < 0 ? "-" : " ";
	+ String n = a < 0 ? "-" : "";
	if (a == 0)
	return "0.0";
	if (b > 3000.0)
	return String.format(n + "%6.3E", b);
	if (b > 300.0)
	return String.format(n + "%4.1f", b);
	if (b > 30.0)
	return String.format(n + "%3.2f", b);
	if (b > 3.0)
	return String.format(n + "%2.4f", b);
	if (b > 0.003)
	return String.format(n + "%1.4f", b);

	return String.format(n + "%6.3E", b).trim();
	}

	public static String seconds(double ns) {
	return String.format("%5.1f s", ns * 1e-9);
	}

	public static String time(double ns) {
	if (ns < 3000.0)
	return String.format("%3.2f ns", ns);
	ns *= 0.001;
	if (ns < 3000.0)
	return String.format("%3.2f us", ns);
	ns *= 0.001;
	if (ns < 3000.0)
	return String.format("%3.2f ms", ns);
	ns *= 0.001;
	if (ns < 3600.0 * 3)
	return String.format("%3.2f s", ns);
	ns /= 3600;
	return String.format("%3.2f h", ns);
	}

	public static String bytes(double bytes) {
	if (bytes < 3000)
	return String.format("%3.0f", bytes);
	bytes /= 1024.0;
	if (bytes < 3000)
	return String.format("%3.1f Kb", bytes);
	bytes /= 1024.0;
	if (bytes < 3000)
	return String.format("%3.1f Mb", bytes);
	bytes /= 1024.0;
	if (bytes < 3000)
	return String.format("%3.1f Gb", bytes);
	bytes /= 1024.0;
	return String.format("%3.1f Tb", bytes);
	}

	public static String toPercent(String value) {
	try {
	return toPercent(Double.parseDouble(value));
	}
	catch (Exception ex) {
	}
	return value;
	}

	public static String toPercent(double value) {
	return String.format("%5.3f", value * 100) + "%";
	}

	}
	diff --git a/DeconvolutionLab2/src/bilib/tools/WebBrowser.java b/DeconvolutionLab2/src/bilib/tools/WebBrowser.java
	index e516788..ad9655f 100644
	--- a/DeconvolutionLab2/src/bilib/tools/WebBrowser.java
	+++ b/DeconvolutionLab2/src/bilib/tools/WebBrowser.java
	@@ -1,61 +1,90 @@
	/*
	* 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/>.
	*/

	+/*
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	+ *
	+ * 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.
	+ */
	+
	+/*
	+ * 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 bilib.tools;

	import java.awt.Desktop;
	import java.net.URL;

	import javax.swing.JFrame;
	import javax.swing.JLabel;

	public class WebBrowser {

	public static boolean open(String url) {
	Desktop desktop = Desktop.isDesktopSupported() ? Desktop.getDesktop() : null;
	if (desktop != null && desktop.isSupported(Desktop.Action.BROWSE)) {
	try {
	desktop.browse(new URL(url).toURI());
	return true;
	}
	catch (Exception e) {
	e.printStackTrace();
	}
	}
	JFrame frame = new JFrame("Help");
	JLabel lbl = new JLabel(url);
	frame.add(lbl);
	frame.pack();
	frame.setVisible(true);
	return false;
	}

	}
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Bigradient.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Bigradient.java
	index 198952e..0bbc747 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Bigradient.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Bigradient.java
	@@ -1,123 +1,123 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package course;

	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

	+import bilib.tools.Files;
	import deconvolution.Deconvolution;
	import ij.plugin.PlugIn;

	public class DeconvolutionLab2_Course_Bigradient implements PlugIn {

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

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

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

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

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


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


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

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

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

	}

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

	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 e82fddb..441d0b4 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Border.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Border.java
	@@ -1,138 +1,138 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package course;

	import 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 + "Deconvolution" + 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);
	+ RealSignal im = new Cube(22, .1).intensity(100).center(0.25, 0.00, 0.05).generate(nx, ny, nz);
	+ RealSignal i0 = new Cube(22, .1).intensity(100).center(0.25, 0.05, 0.05).generate(nx, ny, nz);
	+ RealSignal i1 = new Cube(22, .1).intensity(100).center(0.25, 0.10, 0.05).generate(nx, ny, nz);
	+ RealSignal i2 = new Cube(22, .1).intensity(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);
	+ RealSignal g = new Gaussian(10, 10, 10).intensity(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("run", ref + " -psf synthetic impulse " + algo).deconvolve();

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

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

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

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

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

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

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

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

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

	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("run", ref + psf + algo).deconvolve();


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

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


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


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

	}

	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_Noise.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Noise.java
	index 4672d13..a2c2354 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Noise.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Noise.java
	@@ -1,98 +1,98 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

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

	public class DeconvolutionLab2_Course_Noise implements PlugIn {

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

	public DeconvolutionLab2_Course_Noise() {

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

	int nx = 560;
	int ny = 120;
	int nz = 1;
	String size = " size " + nx + " " + ny + " " + nz;

	- RealSignal im = new Cube(50, 0.25).intensity(0, 100).center(0.2, 0.5, 0).generate(nx, ny, nz);
	- RealSignal i1 = new Cube(50, 0.25).intensity(0, 70).center(0.4, 0.5, 0).generate(nx, ny, nz);
	- RealSignal i2 = new Cube(50, 0.25).intensity(0, 40).center(0.6, 0.5, 0).generate(nx, ny, nz);
	- RealSignal i3 = new Cube(50, 0.25).intensity(0, 10).center(0.8, 0.5, 0).generate(nx, ny, nz);
	+ RealSignal im = new Cube(50, 0.25).intensity(100).center(0.2, 0.5, 0).generate(nx, ny, nz);
	+ RealSignal i1 = new Cube(50, 0.25).intensity(70).center(0.4, 0.5, 0).generate(nx, ny, nz);
	+ RealSignal i2 = new Cube(50, 0.25).intensity(40).center(0.6, 0.5, 0).generate(nx, ny, nz);
	+ RealSignal i3 = new Cube(50, 0.25).intensity(10).center(0.8, 0.5, 0).generate(nx, ny, nz);
	im.plus(i1);
	im.plus(i2);
	im.plus(i3);
	Lab.show(monitors, im, "im.tif");
	Lab.save(monitors, im, res + "im.tif");

	String psf = " -psf synthetic impulse 1 0 " + size;
	String image = " -image file im.tif";

	// Simulation
	String name = "SIM m 0 s 50 p 0";
	String out = " -stack " + name + " -out stack " + name + "-BYTE rescaled byte noshow";
	new Deconvolution("noise", psf + image + " -algorithm " + name + out).run();

	name = "SIM m 0 s 00 p 150";
	out = " -stack " + name + " -out stack " + name + "-BYTE rescaled byte noshow";
	new Deconvolution("noise", psf + image + " -algorithm " + name + out).run();

	name = "SIM m 0 s 15 p 30";
	out = " -stack " + name + " -out stack " + name + "-BYTE rescaled byte noshow";
	new Deconvolution("noise", psf + image + " -algorithm " + name + out).run();
	}


	public static void main(String arg[]) {
	new DeconvolutionLab2_Course_Noise();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_Course_Noise();
	}

	}
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Piecewise.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Piecewise.java
	index 5c1b8f5..8f2e87e 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Piecewise.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Piecewise.java
	@@ -1,116 +1,116 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package course;

	import java.io.File;
	import java.util.Random;

	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.Constant;
	import signal.factory.Cube;

	public class DeconvolutionLab2_Course_Piecewise implements PlugIn {

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

	public DeconvolutionLab2_Course_Piecewise() {

	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();
	new File(res + "RL").mkdir();
	new File(res + "RLTV").mkdir();
	new File(res + "ISTA").mkdir();
	new File(res + "FISTA").mkdir();

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

	Random rand = new Random(1234);
	- RealSignal x = new Constant().intensity(0, 10).generate(nx, ny, nz);
	+ RealSignal x = new Constant().intensity(10).generate(nx, ny, nz);
	for(int i = 0; i< 12; i++) {
	double xc = (rand.nextDouble()*0.6 + 0.2);
	double yc = (rand.nextDouble()*0.6 + 0.2);
	double zc = (rand.nextDouble()*0.6 + 0.2);
	double size = 15 + (rand.nextDouble()*30);
	double ampl = (rand.nextDouble()+0.5)*10;
	- x.plus(new Cube(size, 0.1).intensity(0, ampl).center(xc, yc, zc).generate(nx, ny, nz));
	+ x.plus(new Cube(size, 0.1).intensity(ampl).center(xc, yc, zc).generate(nx, ny, nz));
	}
	Lab.show(monitors, x, "reference");
	Lab.save(monitors, x, res + "ref.tif");

	String algo = " ";
	String ground = " -image file " + res + "ref.tif ";
	//String psf = " -psf file ../../Data/resolution/psfgl.tif";
	String psf = " -psf synthetic gaussian 100.0 0.0 1.2 1.2 3.6 size ";
	// nx + " " + ny + " " + nz;
	String signal = " -image file signal.tif -reference " + res + "ref.tif -disable monitor";

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

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

	algo = " -algorithm SIM 0 1 1 -out stats @3 SIM nosave -out stack signal -out ortho SIGNALo ";
	new Deconvolution("run", ground + psf + algo).deconvolve();

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

	algo = " -algorithm RLTV 15 0.01 -out stats @1 RLTV nosave -out ortho @1 RLTV/RLTV" + paramout;
	new Deconvolution("run", signal + psf + algo).deconvolve();
	}

	public static void main(String arg[]) {
	new DeconvolutionLab2_Course_Piecewise();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_Course_Piecewise();
	}

	}
	diff --git a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Resolution.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Resolution.java
	index 2aaefc6..72a1933 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Resolution.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Resolution.java
	@@ -1,107 +1,154 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package course;
	import java.io.File;

	import javax.swing.filechooser.FileSystemView;

	import deconvolution.Deconvolution;
	+import deconvolution.Stats;
	+import deconvolution.algorithm.Controller;
	+import deconvolution.algorithm.Convolution;
	import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.Monitors;
	import ij.plugin.PlugIn;
	import signal.RealSignal;
	-import signal.factory.GridSpots;
	+import signal.factory.Airy;
	+import signal.factory.CubeSphericalBeads;

	public class DeconvolutionLab2_Course_Resolution implements PlugIn {

	private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop";
	private String root = desktop + File.separator + "Deconvolution" + File.separator;
	private String res = root + "results" + File.separator + "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();
	new File(res + "RL").mkdir();

	int nx = 128;
	- int ny = 128;
	- int nz = 128;
	- int spacing = 16;
	+ int ny = 120;
	+ int nz = 122;
	+ int spacing = 12;
	+ int border = 6;

	- RealSignal x = new GridSpots(3, 0.1, spacing).intensity(0, 255).generate(nx, ny, nz);
	- Lab.show(monitors, x, "reference");
	- Lab.save(monitors, x, res + "ref.tif");
	+ RealSignal x = new CubeSphericalBeads(4, 0.1, spacing, border).intensity(400).generate(nx, ny, nz);
	+ //RealSignal x = new Sphere(30, 1).generate(nx, ny, nz);
	+ //RealSignal x = new Constant().intensity(0, 255).generate(nx, ny, nz);
	+ //Lab.show(monitors, x, "reference");
	+ //Lab.showOrthoview(x);
	+ //Lab.showMIP(x);
	+ //Lab.save(monitors, x, res + "ref.tif");
	+
	+ //RealSignal h = new Gaussian(3, 3, 1).generate(nx, ny, nz);
	+ RealSignal h = new Airy(100, 50, 0.5, 0.1).generate(nx, ny, nz);
	+ Lab.show(monitors, h, "psf");
	+ Lab.showOrthoview(h);
	+ Lab.showMIP(h);
	+ Lab.save(monitors, h, res + "psf.tif");
	+ Lab.save(monitors, h.createOrthoview(), res + "psfo.tif");
	+ Lab.save(monitors, h.createMIP(), res + "psfp.tif");

	String algo = " ";
	- String ground = " -image file " + res + "ref.tif ";
	- //String psf = " -psf file ../../Data/resolution/psfgl.tif";
	- String psf = " -psf synthetic gaussian 100.0 0.0 1.2 1.2 3.6 size " + nx + " " + ny + " " + nz;
	- String signal = " -image file signal.tif -reference " + res + "ref.tif -disable monitor";
	+ String param = " -reference " + res + "ref.tif -stats show -display no -monitor no -system no";
	+ String conv = " -image file " + res + "conv.tif ";
	+ String ref = " -image file " + res + "ref.tif ";
	+ String psf = " -psf file " + res + "psf.tif ";
	+
	+ Controller controller = new Controller();
	+ controller.setSystem(true);
	+ controller.setReference(res + "ref.tif");
	+ controller.setStatsMode(Stats.Mode.SHOW);

	- String paramout = " intact float (" + spacing + "," + spacing + "," + spacing + ")";
	+ Convolution convo = new Convolution();
	+ convo.setController(controller);
	+ RealSignal y = convo.run(x, h);
	+ Lab.show(y);
	+ /*
	+ algo = " -algorithm NIF -out mip NIFp ";
	+ new Deconvolution("nif", conv + psf + algo + param).deconvolve();
	+/*
	+// algo = " -algorithm TRIF 10e-5 -pad NO NO 0 32 -out mip trifppad -out ortho trifopad ";
	+// new Deconvolution("trif", conv + psf + algo + param).deconvolve();
	+
	+ algo = " -algorithm TRIF 10e-5 -out mip TRIFo ";
	+ new Deconvolution("trif", conv + psf + algo + param).deconvolve();

	- algo = " -algorithm CONV -out stats @3 PR -out stack PR -out ortho PRo ";
	- new Deconvolution("run", ground + "-reference reference.tif -psf synthetic impulse 100 0 size 128 128 128 " + algo).deconvolve();
	+ algo = " -algorithm TRIF 10e-5 -pad NO NO 100 100 -out mip TRIFoapo ";
	+ new Deconvolution("TRIF apo", conv + psf + algo + param).deconvolve();

	- algo = " -algorithm SIM 0 1.5 0 -out stats @3 SIM -out stack signal -out ortho SIGNALo ";
	- new Deconvolution("run", ground + psf + algo).deconvolve();

	- algo = " -algorithm NIF -out ortho NIF " + paramout;
	- new Deconvolution("run", signal + psf + algo).deconvolve();
	+// algo = " -algorithm TRIF 10e-4 -pad NO NO 0 20 -out mip trif_ppad -out ortho trif_opad";
	+// new Deconvolution("trif", conv + psf + algo + param).deconvolve();
	+
	+ //algo = " -algorithm TRIF 10e-6 -out mip trif_p -out ortho trif_o -stats show";
	+ //new Deconvolution("trif", conv + psf + algo + param).deconvolve();
	+ /*

	+ for(int i=-8; i<=-2; i+=20) {
	+ algo = " -algorithm TRIF " + Math.pow(10, i) + " -out mip nifp" + i + " -out ortho nifo" + i + " -stats show";
	+ new Deconvolution("trif", conv + psf + algo + param).deconvolve();
	+ }
	+
	+ algo = " -algorithm SIM 0 1 0 -out ortho simo -system no -monitor no";
	+ new Deconvolution("run", ref + psf + algo).deconvolve();
	+
	+ algo = " -algorithm NIF -out ortho nifo -system -monitor";
	+ new Deconvolution("run", signal + psf + algo).deconvolve();
	for(int i=0; i<=24; i++) {
	double p = Math.pow(10, i-18);
	algo = " -algorithm RIF " + p + " -out ortho @5 RIF/RIF" + i + paramout;
	new Deconvolution("run", signal + psf + algo).deconvolve();
	}
	-
	- algo = " -algorithm LW+ 305 1 -out stats @3 LW+ nosave -out ortho @25 LW+/LW+" + paramout;
	+ algo = " -algorithm LW+ 30 1 -out stats @3 LW+ nosave -out ortho @s5 LW+/LW+" + paramout;
	new Deconvolution("run", signal + psf + algo).deconvolve();
	+ */
	}

	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_MemoryFootprint.java b/DeconvolutionLab2/src/course/DeconvolutionLab2_MemoryFootprint.java
	index 6bc3659..aa43077 100644
	--- a/DeconvolutionLab2/src/course/DeconvolutionLab2_MemoryFootprint.java
	+++ b/DeconvolutionLab2/src/course/DeconvolutionLab2_MemoryFootprint.java
	@@ -1,103 +1,103 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	import bilib.table.CustomizedTable;
	import bilib.tools.NumFormat;
	import deconvolution.Deconvolution;
	import ij.plugin.PlugIn;
	import signal.SignalCollector;

	public class DeconvolutionLab2_MemoryFootprint implements PlugIn {

	public DeconvolutionLab2_MemoryFootprint() {

	CustomizedTable table = new CustomizedTable(new String[] { "Name", "Algo", "Optimized", "Time", "Energy", "Peak Count", "Peak Bytes", "End Count", "End Byte", "Ratio" }, true);
	table.show("Memory Footprint", 1100, 300);

	run(table, "CONV");
	run(table, "FISTA 10 1 1");
	run(table, "ICTM 10 1 0.1");
	run(table, "I");
	run(table, "ISTA 10 1 1");
	run(table, "LW 10 1");
	run(table, "LLS 10 1");
	run(table, "NLLS 10 1");
	run(table, "NIF");
	run(table, "DIV");
	run(table, "RIF 1");
	run(table, "RL 10");
	run(table, "RLTV 10 1");
	run(table, "SIM 1 1 1");
	run(table, "BVLS 10 1");
	run(table, "TM 10 1 0.1");
	run(table, "TRIF 1");
	run(table, "VC 10 1");
	}

	private void run(CustomizedTable table, String cmd) {
	int nx = 64;
	int ny = 32;
	int nz = 12;
	String size = " size " + nx + " " + ny + " " + nz;
	String image = " -image synthetic Cross 110 0 1 1 80.0 " + size;
	String psf = " -psf synthetic Double-Helix 100 0 3 10 10 " + size;

	for (int i = 0; i <= 1; i++) {
	SignalCollector.resetSignals();
	SignalCollector.clear();
	Deconvolution d = new Deconvolution("noise", " -algorithm " + cmd + psf + image + " -display no");
	boolean optimized = i == 1;
	- d.getAlgo().setOptimizedMemoryFootprint(optimized);
	- String n = d.getAlgo().getName();
	+ d.getAlgorithm().setOptimizedMemoryFootprint(optimized);
	+ String n = d.getAlgorithm().getName();
	double chrono = System.nanoTime();
	d.run();
	String energy = "" + d.getOutput().getEnergy();
	String time = NumFormat.time(System.nanoTime() - chrono);
	int cp = SignalCollector.getCountPeakSignals();
	int cs = SignalCollector.getCountSignals();
	long bp = SignalCollector.getBytesPeakSignals();
	long bs = SignalCollector.getBytesSignals();
	double ratio = (bp + bs) / (nx * ny * nz * 4);
	table.append(new String[] { n, cmd, "" + optimized, time, energy, "" + cp, NumFormat.bytes(bp), "" + cs, NumFormat.bytes(bs), NumFormat.nice(ratio) });
	}
	}

	public static void main(String arg[]) {
	new DeconvolutionLab2_MemoryFootprint();
	}

	@Override
	public void run(String arg) {
	new DeconvolutionLab2_MemoryFootprint();
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/Command.java b/DeconvolutionLab2/src/deconvolution/Command.java
	index fbf999e..8dc0a8e 100644
	--- a/DeconvolutionLab2/src/deconvolution/Command.java
	+++ b/DeconvolutionLab2/src/deconvolution/Command.java
	@@ -1,456 +1,425 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution;

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

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

	public class Command {

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

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

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

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

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

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

	return cmd;
	}
	-
	- public static void decode(String command, Deconvolution deconvolution) {
	-
	- AbstractAlgorithm algo = Algorithm.getDefaultAlgorithm();
	- boolean flagSystem = true;
	- boolean flagDisplay = true;
	- boolean flagMultithreading = true;
	- int monitor = 3;
	- int stats = 0;
	- Verbose verbose = Verbose.Log;
	- String path = System.getProperty("user.dir");
	- Controller controller = new Controller();
	- OutputCollection outs = new OutputCollection();
	- Padding pad = new Padding();
	- Apodization apo = new Apodization();
	- double norm = 1.0;
	- AbstractFFTLibrary fft = FFT.getFastestFFT();

	+ public static Controller decodeController(String command) {
	+
	+ Controller controller = new Controller();
	+
	ArrayList<Token> tokens = parse(command);
	for (Token token : tokens) {
	- if (token.keyword.equalsIgnoreCase("-algorithm"))
	- algo = Command.decodeAlgorithm(token, controller);
	-
	if (token.keyword.equalsIgnoreCase("-path") && !token.parameters.equalsIgnoreCase("current"))
	- path = token.parameters;
	+ controller.setPath(token.parameters);

	if (token.keyword.equalsIgnoreCase("-monitor"))
	- monitor = decodeMonitor(token);
	- if (token.keyword.equalsIgnoreCase("-stats"))
	- stats = decodeStats(token);
	- if (token.keyword.equalsIgnoreCase("-system"))
	- flagSystem = decodeSystem(token);
	+ controller.setMonitors(decodeMonitors(token.parameters));
	+
	+ if (token.keyword.equalsIgnoreCase("-verbose"))
	+ controller.setVerbose(Verbose.getByName(token.parameters));

	- if (token.keyword.equalsIgnoreCase("-display"))
	- flagDisplay = decodeDisplay(token);
	-
	- if (token.keyword.equalsIgnoreCase("-multithreading"))
	- flagMultithreading = decodeMultithreading(token);
	+ if (token.keyword.equalsIgnoreCase("-system"))
	+ controller.setSystem(decodeBoolean(token.parameters));

	- if (token.keyword.equalsIgnoreCase("-verbose"))
	- verbose = Verbose.getByName(token.parameters);
	+ if (token.keyword.equalsIgnoreCase("-multithreading"))
	+ controller.setMultithreading(decodeBoolean(token.parameters));

	- if (token.keyword.equalsIgnoreCase("-fft"))
	- fft = FFT.getLibraryByName(token.parameters);
	+ if (token.keyword.equalsIgnoreCase("-display"))
	+ controller.setDisplayFinal(decodeBoolean(token.parameters));
	+
	+ if (token.keyword.equalsIgnoreCase("-stats"))
	+ controller.setStats(decodeStats(token));

	- if (token.keyword.equalsIgnoreCase("-pad"))
	- pad = decodePadding(token);
	-
	- if (token.keyword.equalsIgnoreCase("-apo"))
	- apo = decodeApodization(token);
	-
	- if (token.keyword.equalsIgnoreCase("-norm"))
	- norm = decodeNormalization(token);
	-
	if (token.keyword.equalsIgnoreCase("-constraint"))
	- decodeController(token, controller);
	-
	+ controller.setConstraint(decodeConstraint(token));
	+
	if (token.keyword.equalsIgnoreCase("-time"))
	- decodeController(token, controller);
	-
	+ controller.setTimeLimit(decodeTimeLimit(token));
	+
	if (token.keyword.equalsIgnoreCase("-residu"))
	- decodeController(token, controller);
	-
	+ controller.setResiduMin(decodeResidu(token));
	+
	if (token.keyword.equalsIgnoreCase("-reference"))
	- decodeController(token, controller);
	+ controller.setReference(token.parameters);
	+
	+ if (token.keyword.equalsIgnoreCase("-pad"))
	+ controller.setPadding(decodePadding(token));
	+
	+ if (token.keyword.equalsIgnoreCase("-apo"))
	+ controller.setApodization(decodeApodization(token));
	+
	+ if (token.keyword.equalsIgnoreCase("-norm"))
	+ controller.setNormalizationPSF(decodeNormalization(token));
	+
	+ if (token.keyword.equalsIgnoreCase("-epsilon"))
	+ Operations.epsilon = NumFormat.parseNumber(token.parameters, 1e-6);
	+
	+ if (token.keyword.equalsIgnoreCase("-fft"))
	+ controller.setFFT(FFT.getLibraryByName(token.parameters).getDefaultFFT());

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

	if (token.keyword.equals("-out")) {
	Output out = decodeOut(token);
	if (out != null)
	- outs.add(out);
	+ controller.addOutput(out);
	}
	}
	-
	- deconvolution.setAlgorithm(algo, controller);
	- deconvolution.setPath(path);
	- deconvolution.setNormalization(norm);
	- deconvolution.setPadding(pad);
	- deconvolution.setApodization(apo);
	- deconvolution.setOutput(outs);
	- deconvolution.setVerbose(verbose);
	- deconvolution.setFFT(fft);
	- deconvolution.setMonitor(monitor);
	- deconvolution.setStats(stats);
	- deconvolution.setFlags(flagDisplay, flagMultithreading, flagSystem);
	+ return controller;
	}
	-
	+
	+ public static AbstractAlgorithm decodeAlgorithm(String command) {
	+ AbstractAlgorithm algo = Algorithm.getDefaultAlgorithm();
	+ ArrayList<Token> tokens = parse(command);
	+ for (Token token : tokens) {
	+ if (token.keyword.equalsIgnoreCase("-algorithm"))
	+ algo = Command.decodeAlgorithm(token);
	+ }
	+ return algo;
	+ }
	+
	/**
	* This methods first segments the command line, then create all the tokens
	* of the command line
	*
	* @param command
	* Command line
	* @return the list of tokens extracted from the command line
	*/
	public static ArrayList<Token> parse(String command) {

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

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

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

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

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

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

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

	- public static AbstractAlgorithm decodeAlgorithm(Token token, Controller controller) {
	-
	+ public static AbstractAlgorithm decodeAlgorithm(Token token) {
	String option = token.option;
	-
	AbstractAlgorithm algo = Algorithm.createAlgorithm(option);
	double params[] = parseNumeric(token.parameters);
	+
	if (params != null) {
	algo.setParameters(params);
	- if (algo.isIterative() && params.length >= 1)
	- controller.setIterationMax((int)params[0]);
	}

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

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

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

	return out;
	}

	- public static void decodeController(Token token, Controller controller) {
	- String line = token.parameters;
	- if (token.parameters.startsWith("@")) {
	- String parts[] = token.parameters.split(" ");
	- if (parts.length >= 1) {
	- line = token.parameters.substring(parts[0].length(), token.parameters.length()).trim();
	- }
	- }
	-
	- if (token.keyword.equals("-constraint"))
	- controller.setConstraint(Constraint.getByName(line.trim()));
	- else if (token.keyword.equals("-residu"))
	- controller.setResiduStop(NumFormat.parseNumber(line, -1));
	- else if (token.keyword.equals("-reference"))
	- controller.setReference(line);
	- else if (token.keyword.equals("-time"))
	- controller.setTimeStop(NumFormat.parseNumber(line, Double.MAX_VALUE));
	-
	- }
	-
	public static double decodeNormalization(Token token) {
	if (token.parameters.toLowerCase().endsWith("no"))
	return 0;
	else
	return NumFormat.parseNumber(token.parameters, 1);
	}

	- public static int decodeMonitor(Token token) {
	- String parts[] = token.parameters.toLowerCase().split(" ");
	- int m = 0;
	- for(String p : parts) {
	- if (p.startsWith("no"))
	- return 0;
	- if (p.equals("false"))
	- return 0;
	- if (p.equals("0"))
	- return 0;
	- if (p.equals("1"))
	- return 1;
	- if (p.equals("2"))
	- return 2;
	- if (p.equals("3"))
	- return 3;
	- if (p.equals("console"))
	- m += 1;
	- if (p.equals("table"))
	- m += 2;
	- }
	- return m;
	- }
	-
	- public static int decodeStats(Token token) {
	+ public static Stats decodeStats(Token token) {
	String parts[] = token.parameters.toLowerCase().split(" ");
	int m = 0;
	- for(String p : parts) {
	- if (p.startsWith("no"))
	- return 0;
	- if (p.equals("false"))
	- return 0;
	- if (p.equals("0"))
	- return 0;
	+ for (String p : parts) {
	+ if (p.startsWith("no") \|\| p.equals("false") \|\| p.equals("0"))
	+ return new Stats(Stats.Mode.NO);
	if (p.equals("1"))
	- return 1;
	+ return new Stats(Stats.Mode.SHOW);
	if (p.equals("2"))
	- return 2;
	+ return new Stats(Stats.Mode.SAVE);
	if (p.equals("3"))
	- return 3;
	+ return new Stats(Stats.Mode.SHOWSAVE);
	if (p.equals("show"))
	m += 1;
	if (p.equals("save"))
	m += 2;
	}
	- return m;
	- }
	+ if (m==1)
	+ return new Stats(Stats.Mode.SHOW);
	+ if (m==2)
	+ return new Stats(Stats.Mode.SAVE);
	+ if (m==3)
	+ return new Stats(Stats.Mode.SHOWSAVE);
	+ return new Stats(Stats.Mode.NO);

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

	- public static boolean decodeDisplay(Token token) {
	+ public static Constraint.Mode decodeConstraint(Token token) {
	String p = token.parameters.toLowerCase();
	+ if (p.startsWith("non"))
	+ return Constraint.Mode.NONNEGATIVE;
	if (p.startsWith("no"))
	- return false;
	+ return Constraint.Mode.NO;
	+ if (p.startsWith("clip"))
	+ return Constraint.Mode.CLIPPED;
	if (p.equals("0"))
	- return false;
	- if (p.equals("false"))
	- return false;
	- return true;
	+ return Constraint.Mode.NO;
	+ return Constraint.Mode.NO;
	}

	- public static boolean decodeMultithreading(Token token) {
	- String p = token.parameters.toLowerCase();
	- if (p.startsWith("no"))
	- return false;
	- if (p.equals("0"))
	- return false;
	- if (p.equals("false"))
	- return false;
	- if (p.startsWith("dis"))
	- return false;
	- return true;
	+ public static double decodeResidu(Token token) {
	+ if (token.parameters.toLowerCase().endsWith("no"))
	+ return -1;
	+ else
	+ return NumFormat.parseNumber(token.parameters, 1);
	+ }
	+
	+ public static double decodeTimeLimit(Token token) {
	+ if (token.parameters.toLowerCase().endsWith("no"))
	+ return -1;
	+ else
	+ return NumFormat.parseNumber(token.parameters, 1);
	}

	public static Padding decodePadding(Token token) {
	AbstractPadding padXY = new NoPadding();
	AbstractPadding padZ = new NoPadding();
	- int extXY = 0;
	- int extZ = 0;
	-
	String param = token.parameters.trim();
	String[] parts = param.split(" ");
	if (parts.length > 0)
	padXY = Padding.getByShortname(parts[0].trim());
	if (parts.length > 1)
	padZ = Padding.getByShortname(parts[1].trim());
	double[] ext = NumFormat.parseNumbers(param);
	+ int extXY = 0;
	if (ext.length > 0)
	extXY = (int) Math.round(ext[0]);
	+ int extZ = 0;
	if (ext.length > 1)
	extZ = (int) Math.round(ext[1]);

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

	public static Apodization decodeApodization(Token token) {
	AbstractApodization apoXY = new UniformApodization();
	AbstractApodization apoZ = new UniformApodization();
	String[] parts = token.parameters.trim().split(" ");
	if (parts.length >= 1)
	apoXY = Apodization.getByShortname(parts[0].trim());
	if (parts.length >= 2)
	apoZ = Apodization.getByShortname(parts[1].trim());
	return new Apodization(apoXY, apoXY, apoZ);
	}
	-
	+
	public static String getPath() {
	command();
	ArrayList<Token> tokens = parse(command.getCommand());
	String path = System.getProperty("user.dir");
	-
	for (Token token : tokens)
	if (token.keyword.equalsIgnoreCase("-path") && !token.parameters.equalsIgnoreCase("current"))
	path = token.parameters;
	return path;
	}
	-
	-
	+
	+ public static Monitors decodeMonitors(String cmd) {
	+ String parts[] = cmd.toLowerCase().split(" ");
	+ Monitors monitors = new Monitors();
	+ for (String p : parts) {
	+ if (p.equals("0") \|\| p.startsWith("no"))
	+ monitors.clear();
	+ if (p.equals("1") \|\| p.startsWith("console"))
	+ monitors.add(new ConsoleMonitor());
	+ if (p.equals("2"))
	+ monitors.add(new TableMonitor("Monitor", Constants.widthGUI, 240));
	+ if (p.equals("3")) {
	+ monitors.add(new ConsoleMonitor());
	+ monitors.add(new TableMonitor("Monitor", Constants.widthGUI, 240));
	+ }
	+ if (p.equals("console"))
	+ monitors.add(new ConsoleMonitor());
	+ if (p.equals("table"))
	+ monitors.add(new TableMonitor("Monitor", Constants.widthGUI, 240));
	+ }
	+ return monitors;
	+ }
	+
	+ public static boolean decodeBoolean(String cmd) {
	+ String p = cmd.toLowerCase();
	+ if (p.startsWith("no"))
	+ return false;
	+ if (p.equals("0"))
	+ return false;
	+ if (p.equals("false"))
	+ return false;
	+ if (p.startsWith("dis"))
	+ return false;
	+ return true;
	+ }

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/CommandSegment.java b/DeconvolutionLab2/src/deconvolution/CommandSegment.java
	index 4738201..f261cf8 100644
	--- a/DeconvolutionLab2/src/deconvolution/CommandSegment.java
	+++ b/DeconvolutionLab2/src/deconvolution/CommandSegment.java
	@@ -1,17 +1,48 @@
	+/*
	+ * 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;

	public class CommandSegment implements Comparable<CommandSegment> {
	public String keyword;
	public int index = 0;

	public CommandSegment(String keyword, int index) {
	this.keyword = keyword;
	this.index = index;
	}

	@Override
	public int compareTo(CommandSegment o) {
	return index > o.index ? 1 : -1;
	}

	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/deconvolution/Deconvolution.java b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	index 35cce6f..d6076c5 100644
	--- a/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	+++ b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
	@@ -1,595 +1,393 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution;

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

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

	+/**
	+ * This class is the main class to run deconvolution with or without user interface.
	+ *
	+ * All the parameters are given in the command line (String variable command).
	+ *
	+ * @author Daniel Sage
	+ *
	+ */
	public class Deconvolution implements Runnable {

	public enum Finish {
	DIE, ALIVE, KILL
	};

	- public AbstractAlgorithm algo = null;
	-
	- private String path;
	- public double norm = 1.0;
	- public Padding pad = new Padding();
	- public Apodization apo = new Apodization();
	- private OutputCollection outs;
	- private Verbose verbose = Verbose.Log;
	- private AbstractFFTLibrary fft;
	- private int flagMonitor = 3;
	- private int flagStats = 0;
	- private boolean flagDisplay = true;
	- private boolean flagMultithreading = true;
	- private boolean flagSystem = true;
	-
	- public Monitors monitors = new Monitors();
	-
	+ private AbstractAlgorithm algo = null;
	+ private Controller controller = new Controller();
	private String command = "";
	- private boolean live = false;
	-
	private Features report = new Features();
	-
	private String name = "";
	-
	- private ArrayList<DeconvolutionListener> listeners = new ArrayList<DeconvolutionListener>();
	public RealSignal image;
	public RealSignal psf;
	private RealSignal deconvolvedImage;
	-
	private Finish finish = Finish.DIE;
	private DeconvolutionDialog dialog;

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

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

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

	- /**
	- * This method runs the deconvolution without graphical user interface.
	- *
	- * @param exit
	- * System.exit call is true
	- */
	+ public RealSignal deconvolve() {
	+ return deconvolve(image, psf);
	+ }
	+
	public RealSignal deconvolve(RealSignal image, RealSignal psf) {
	this.image = image;
	this.psf = psf;
	- runDeconvolve();
	- return deconvolvedImage;
	- }
	+ for(AbstractMonitor monitor : controller.getMonitors())
	+ if (monitor instanceof TableMonitor)
	+ Lab.setVisible(((TableMonitor)monitor).getPanel(), "Monitor of " + name, 10, 10);

	- public RealSignal deconvolve() {
	- this.image = null;
	- this.psf = null;
	- runDeconvolve();
	- return deconvolvedImage;
	- }
	-
	- /**
	- * This method runs the deconvolution without graphical user interface.
	- *
	- * @param exit
	- * System.exit call is true
	- */
	- private void runDeconvolve() {
	- if ((flagMonitor & 2) == 2) {
	- TableMonitor tableMonitor = new TableMonitor(name , Constants.widthGUI, 240);
	- monitors.add(tableMonitor);
	- Lab.setVisible(tableMonitor.getPanel(), "Monitor of " + name, 10, 10);
	- }
	-
	- if ((flagMonitor & 1) == 1)
	- monitors.add(new ConsoleMonitor());
	-
	- if ((flagStats & 1) == 1) {
	- Lab.setVisible(tableStats.getPanel(), "Stats of " + name, 50, 50);
	- }
	-
	- if (fft == null) {
	+ if (controller.getFFT() == null) {
	run();
	- return;
	+ return deconvolvedImage;
	}
	-
	- if (!fft.isMultithreadable()) {
	+
	+ if (!controller.getFFT().isMultithreadable()) {
	run();
	- return;
	+ return deconvolvedImage;
	}

	- if (flagMultithreading) {
	+ if (controller.isMultithreading()) {
	Thread thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}
	else {
	run();
	- }
	-
	+ }
	+ return deconvolvedImage;
	}

	/**
	* This method runs the deconvolution with a graphical user interface.
	- *
	- * @param job
	- * Name of the job of deconvolution
	*/
	public void launch() {
	- monitors = new Monitors();
	TableMonitor tableMonitor = null;
	- if ((flagMonitor & 2) == 2) {
	- tableMonitor = new TableMonitor(name , Constants.widthGUI, 240);
	- monitors.add(tableMonitor);
	- }
	- if ((flagMonitor & 1) == 1)
	- monitors.add(new ConsoleMonitor());
	- if (flagStats == 0) {
	- tableStats = null;
	- }
	-
	- dialog = new DeconvolutionDialog(DeconvolutionDialog.Module.ALL, this, tableMonitor, tableStats);
	- monitors.add(new StatusMonitor(dialog.getProgressBar()));
	+ for(AbstractMonitor monitor : controller.getMonitors())
	+ if (monitor instanceof TableMonitor)
	+ tableMonitor = (TableMonitor)monitor;
	+
	+ dialog = new DeconvolutionDialog(DeconvolutionDialog.Module.ALL, this, tableMonitor, controller.getStats());
	+ controller.getMonitors().add(new StatusMonitor(dialog.getProgressBar()));

	Lab.setVisible(dialog, false);
	}

	@Override
	public void run() {
	double chrono = System.nanoTime();
	-
	- if (flagSystem)
	+ Monitors monitors = controller.getMonitors();
	+
	+ if (controller.isSystem())
	SystemInfo.activate();

	- for (DeconvolutionListener listener : listeners)
	- listener.started();
	-
	- live = true;
	- if (monitors != null)
	- monitors.setVerbose(verbose);
	+ report.add("Path", controller.toStringPath());

	- report.add("Path", checkPath(path));
	- monitors.log("Path: " + checkPath(path));
	-
	if (image == null)
	image = openImage();

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

	psf = openPSF();

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

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

	- Controller controller = algo.getController();
	- if (controller == null) {
	- monitors.error("Controller: not valid");
	- if (finish == Finish.KILL)
	- System.exit(-104);
	- return;
	- }
	-
	- if (flagStats > 0)
	- controller.setTableStats(tableStats);
	-
	- report.add("FFT", fft.getLibraryName());
	-
	- if (outs != null) {
	- outs.setPath(path);
	- controller.setOutputs(outs);
	- }
	-
	- monitors.log("Algorithm: " + algo.getName());
	+ report.add("FFT", controller.getFFT().getName());
	report.add("Algorithm", algo.getName());
	- algo.setController(controller);
	-
	- algo.setFFT(fft);
	- algo.setMonitors(monitors);
	-
	- deconvolvedImage = algo.run(image, psf, pad, apo, norm);

	- live = false;
	- for (DeconvolutionListener listener : listeners)
	- listener.finish();
	+ algo.setController(controller);
	+ deconvolvedImage = algo.run(image, psf, controller.getStats());

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

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

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

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

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

	-
	/**
	* This methods make a recap of the deconvolution. Useful before starting
	* the processing.
	*
	* @return list of messages to print
	*/
	public Features recap() {
	Features features = new Features();
	Token image = Command.extract(command, "-image");
	features.add("Image", image == null ? "keyword -image not found" : image.parameters);
	-
	+ double norm = controller.getNormalizationPSF();
	String normf = (norm < 0 ? " (no normalization)" : " (normalization to " + norm + ")");
	Token psf = Command.extract(command, "-psf");
	features.add("PSF", psf == null ? "keyword -psf not found" : psf.parameters + " norm:" + normf);

	if (algo == null) {
	features.add("Algorithm", "not valid>");
	}
	else {
	Controller controller = algo.getController();
	features.add("Algorithm", algo.toString());
	features.add("Stopping Criteria", controller.getStoppingCriteriaAsString(algo));
	features.add("Reference", controller.getReference());
	features.add("Constraint", controller.getConstraintAsString());
	- features.add("Padding", pad.toString());
	- features.add("Apodization", apo.toString());
	- features.add("FFT", fft == null ? "null" : fft.getLibraryName());
	+ features.add("Padding", controller.getPadding().toString());
	+ features.add("Apodization", controller.getApodization().toString());
	+ features.add("FFT", controller.getFFT() == null ? "null" : controller.getFFT().getName());
	}
	- features.add("Path", path);
	-
	- String monitor = "";
	- if (flagMonitor == 0)
	- monitor = "no ";
	- if (flagMonitor == 1)
	- monitor = "console (" + verbose.name().toLowerCase() + ")";
	- if (flagMonitor == 2)
	- monitor = "table (" + verbose.name().toLowerCase() + ")";
	- if (flagMonitor == 3)
	- monitor = "console table (" + verbose.name().toLowerCase() + ")";
	- String stats = "";
	- if (flagStats == 0)
	- stats = "no ";
	- if (flagStats == 1)
	- stats = "show ";
	- if (flagStats == 2)
	- stats = "save ";
	- if (flagStats == 3)
	- stats = "show save";
	- String running = "";
	- running += "multithreading: " + (flagMultithreading ? "on " : "off ");
	- running += " display: " + (flagDisplay ? "on " : "off ");
	- running += " system: " + (flagSystem ? "shown" : "hidden ");
	-
	- features.add("Monitor", monitor);
	- features.add("Stats", stats);
	- features.add("Running", running);
	- if (outs == null)
	- features.add("Output", "not valid");
	- else
	- for (Output out : outs)
	- features.add("Output " + out.getName(), out.toString());
	+ features.add("Path", controller.getPath());
	+
	+ features.add("Monitor", controller.toStringMonitor());
	+ if (controller.getStats() != null)
	+ features.add("Stats", controller.getStats().toStringStats());
	+ features.add("Running", controller.toStringRunning());
	+
	+ for (Output out : controller.getOuts())
	+ features.add("Output " + out.getName(), out.toString());
	return features;
	}

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

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

	- public String checkPath(String path) {
	- File dir = new File(path);
	- if (dir.exists()) {
	- if (dir.isDirectory()) {
	- if (dir.canWrite())
	- return path + " (writable)";
	- else
	- return path + " (non-writable)";
	- }
	- else {
	- return path + " (non-directory)";
	- }
	- }
	- else {
	- return path + " (not-valid)";
	- }
	- }
	-
	public RealSignal openImage() {
	Token token = Command.extract(command, "-image");
	if (token == null)
	return null;
	if (token.parameters.startsWith(">>>"))
	return null;
	String arg = token.option.trim();
	String cmd = token.parameters.substring(arg.length(), token.parameters.length()).trim();
	- image = createRealSignal(monitors, arg, cmd, path);
	+ image = createRealSignal(controller.getMonitors(), arg, cmd, controller.getPath());
	return image;
	}

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

	private static RealSignal createRealSignal(Monitors monitors, String arg, String cmd, String path) {
	RealSignal signal = null;
	if (arg.equalsIgnoreCase("synthetic")) {
	signal = Lab.createSynthetic(monitors, cmd);
	}

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

	- public void addDeconvolutionListener(DeconvolutionListener listener) {
	- listeners.add(listener);
	- }
	-
	- public OutputCollection getOuts() {
	- return outs;
	- }
	-
	- public void setAlgorithm(AbstractAlgorithm algo, Controller controller) {
	+ public void setAlgorithm(AbstractAlgorithm algo) {
	this.algo = algo;
	- if (algo != null && controller != null) {
	- algo.setController(controller);
	- }
	}

	- public AbstractAlgorithm getAlgo() {
	+ public AbstractAlgorithm getAlgorithm() {
	return algo;
	}
	-
	- public void setPath(String path) {
	- this.path = path;
	- }
	-
	- public String getPath() {
	- return path;
	- }
	-
	- public void setNormalization(double norm) {
	- this.norm = norm;
	+
	+ public void setController(Controller controller) {
	+ this.controller = controller;
	}

	- public void setPadding(Padding pad) {
	- this.pad = pad;
	- }
	-
	- public Padding getPadding() {
	- return pad;
	+ public Controller getController() {
	+ return controller;
	}

	public RealSignal getOutput() {
	return deconvolvedImage;
	}

	public RealSignal getImage() {
	return image;
	}

	public RealSignal getPSF() {
	return psf;
	}

	public Features getDeconvolutionReports() {
	return report;
	}

	public String getName() {
	return name;
	}
	-
	- public void setApodization(Apodization apo) {
	- this.apo = apo;
	- }

	- public Apodization getApodization() {
	- return apo;
	- }
	-
	- public void setOutput(OutputCollection outs) {
	- this.outs = outs;
	- }
	-
	- public void setVerbose(Verbose verbose) {
	- this.verbose = verbose;
	- }
	-
	- public void setFFT(AbstractFFTLibrary fft) {
	- this.fft = fft;
	- }
	-
	- public void setMonitor(int flagMonitor) {
	- this.flagMonitor = flagMonitor;
	- }
	-
	- public void setStats(int flagStats) {
	- this.flagStats = flagStats;
	- }
	-
	- public void setFlags(boolean flagDisplay, boolean flagMultithreading, boolean flagSystem) {
	- this.flagDisplay = flagDisplay;
	- this.flagMultithreading = flagMultithreading;
	- this.flagSystem = flagSystem;
	+ public Monitors getMonitors() {
	+ return controller.getMonitors();
	}

	public String getCommand() {
	return command;
	}

	-
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java b/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
	index c99c3d4..86340c8 100644
	--- a/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
	+++ b/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
	@@ -1,379 +1,374 @@
	/*
	* 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.awt.BorderLayout;
	import java.awt.CardLayout;
	import java.awt.Dimension;
	import java.awt.FlowLayout;
	import java.awt.GridLayout;
	import java.awt.Point;
	import java.awt.Rectangle;
	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.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.JToolBar;

	import bilib.component.BorderToggledButton;
	import bilib.component.PanelImage;
	-import deconvolution.modules.AlgorithmDModule;
	-import deconvolution.modules.ImageDModule;
	-import deconvolution.modules.PSFDModule;
	-import deconvolution.modules.RecapDModule;
	-import deconvolution.modules.ReportDModule;
	+import deconvolution.capsule.AlgorithmCapsule;
	+import deconvolution.capsule.ImageCapsule;
	+import deconvolution.capsule.PSFCapsule;
	+import deconvolution.capsule.RecapCapsule;
	+import deconvolution.capsule.ReportCapsule;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Lab;
	-import deconvolutionlab.TableStats;
	import deconvolutionlab.monitor.StatusMonitor;
	import deconvolutionlab.monitor.TableMonitor;

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

	public enum State {
	NOTDEFINED, READY, RUN, FINISH
	};

	public enum Module {
	ALL, RECAP, IMAGE, PSF, ALGO
	};

	private JButton bnStart = new JButton("Run");
	private JButton bnStop = new JButton("Stop");
	private JButton bnReset = new JButton("Reset");
	private JButton bnHelp = new JButton("Help");
	private JButton bnQuit = new JButton("Quit");

	private BorderToggledButton bnRecap = new BorderToggledButton("Recap");
	private BorderToggledButton bnImage = new BorderToggledButton("Image");
	private BorderToggledButton bnPSF = new BorderToggledButton("PSF");
	private BorderToggledButton bnAlgo = new BorderToggledButton("Algorithm");
	private BorderToggledButton bnReport = new BorderToggledButton("Report");
	private BorderToggledButton bnMonitor = new BorderToggledButton("Monitor");
	private BorderToggledButton bnStats = new BorderToggledButton("Stats");

	private Thread thread = null;

	private Deconvolution deconvolution;
	private JProgressBar progress = new JProgressBar();

	public static Point location = new Point(0, 0);

	private JPanel cards = new JPanel(new CardLayout());

	private boolean flagMonitor = false;
	private boolean flagStats = false;

	- private ImageDModule image;
	- private PSFDModule psf;
	- private RecapDModule recap;
	- private AlgorithmDModule algorithm;
	- private ReportDModule report;
	+ private ImageCapsule image;
	+ private PSFCapsule psf;
	+ private RecapCapsule recap;
	+ private AlgorithmCapsule algorithm;
	+ private ReportCapsule report;

	- private TableStats tableStats;
	private TableMonitor tableMonitor;

	- public DeconvolutionDialog(Module module, Deconvolution deconvolution, TableMonitor tableMonitor, TableStats tableStats) {
	+ public DeconvolutionDialog(Module module, Deconvolution deconvolution, TableMonitor tableMonitor, Stats stats) {
	super(new JFrame(), deconvolution.getName());

	this.deconvolution = deconvolution;
	this.tableMonitor = tableMonitor;
	- this.tableStats = tableStats;

	- image = new ImageDModule(deconvolution);
	- psf = new PSFDModule(deconvolution);
	- recap = new RecapDModule(deconvolution);
	- algorithm = new AlgorithmDModule(deconvolution);
	- report = new ReportDModule(deconvolution);
	+ image = new ImageCapsule(deconvolution);
	+ psf = new PSFCapsule(deconvolution);
	+ recap = new RecapCapsule(deconvolution);
	+ algorithm = new AlgorithmCapsule(deconvolution);
	+ report = new ReportCapsule(deconvolution);

	// Panel status bar on bottom
	progress.setAlignmentX(JLabel.CENTER_ALIGNMENT);
	progress.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(progress, BorderLayout.CENTER);
	statusBar.add(bnQuit, BorderLayout.EAST);

	// Panel bottom
	JPanel bottom = new JPanel();
	bottom.setLayout(new BoxLayout(bottom, BoxLayout.PAGE_AXIS));

	// Panel buttons
	if (module == Module.ALL) {
	PanelImage buttons = new PanelImage("celegans.jpg");
	buttons.setLayout(new FlowLayout());
	buttons.setBorder(BorderFactory.createEtchedBorder());
	buttons.add(bnReset);
	buttons.add(bnStop);
	buttons.add(bnStart);
	bottom.add(buttons);
	}
	bottom.add(statusBar);

	// Panel Image
	cards.add(recap.getName(), recap.getPane());
	cards.add(image.getName(), image.getPane());
	cards.add(psf.getName(), psf.getPane());
	cards.add(algorithm.getName(), algorithm.getPane());
	cards.add(report.getName(), report.getPane());
	if (tableMonitor != null)
	cards.add("Monitor", tableMonitor.getPanel());
	- if (tableStats != null)
	- cards.add("Stats", tableStats.getPanel());
	+ if (stats != null)
	+ cards.add("Stats", stats.getPanel());

	// Panel Main
	JPanel panel = new JPanel();
	panel.setLayout(new BorderLayout());
	panel.add(cards, BorderLayout.CENTER);
	panel.add(bottom, BorderLayout.SOUTH);

	// Panel tool with all buttons
	if (module == Module.ALL) {
	JToolBar tool = new JToolBar();
	tool.setFloatable(false);
	tool.setLayout(new GridLayout(1, 6));
	tool.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 0));
	tool.add(bnRecap);
	tool.add(bnImage);
	tool.add(bnPSF);
	tool.add(bnAlgo);
	if (tableMonitor != null)
	tool.add(bnMonitor);
	- if (tableStats != null)
	+ if (stats != null)
	tool.add(bnStats);
	tool.add(bnReport);
	panel.add(tool, BorderLayout.NORTH);
	}

	add(panel);
	bnReset.addActionListener(this);
	bnQuit.addActionListener(this);
	bnStart.addActionListener(this);
	bnStop.addActionListener(this);
	bnHelp.addActionListener(this);

	bnImage.addActionListener(this);
	bnPSF.addActionListener(this);
	bnAlgo.addActionListener(this);
	bnRecap.addActionListener(this);
	if (tableMonitor != null)
	bnMonitor.addActionListener(this);
	- if (tableStats != null)
	+ if (stats != null)
	bnStats.addActionListener(this);
	bnReport.addActionListener(this);

	this.addWindowListener(this);
	setMinimumSize(new Dimension(Constants.widthGUI, 400));
	setPreferredSize(new Dimension(Constants.widthGUI, 400));
	pack();
	Config.registerFrame("DeconvolutionLab", "DeconvolutionDialog", this);

	Rectangle rect = Config.getDialog("DeconvolutionLab.DeconvolutionDialog");
	if (rect.x > 0 && rect.y > 0)
	setLocation(rect.x, rect.y);

	bnStop.setEnabled(false);

	if (module == Module.ALL) {
	toggle(bnRecap);
	recap.update();
	}
	if (module == Module.IMAGE) {
	toggle(bnImage);
	- deconvolution.monitors.add(new StatusMonitor(getProgressBar()));
	+ deconvolution.getMonitors().add(new StatusMonitor(getProgressBar()));
	image.update();
	}
	if (module == Module.PSF) {
	toggle(bnPSF);
	- deconvolution.monitors.add(new StatusMonitor(getProgressBar()));
	+ deconvolution.getMonitors().add(new StatusMonitor(getProgressBar()));
	psf.update();
	}
	if (module == Module.ALGO) {
	toggle(bnAlgo);
	- deconvolution.monitors.add(new StatusMonitor(getProgressBar()));
	+ deconvolution.getMonitors().add(new StatusMonitor(getProgressBar()));
	algorithm.update();
	}
	if (module == Module.RECAP) {
	toggle(bnRecap);
	recap.update();
	}
	}

	@Override
	public void actionPerformed(ActionEvent e) {

	if (e.getSource() == bnStart) {
	if (flagMonitor)
	toggle(bnMonitor);
	else if (flagStats)
	toggle(bnStats);

	if (thread == null) {
	thread = new Thread(this);
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	}
	}
	else if (e.getSource() == bnStop) {
	toggle(bnReport);
	if (deconvolution != null)
	deconvolution.abort();
	}
	else if (e.getSource() == bnImage) {
	toggle(bnImage);
	image.update();
	}
	else if (e.getSource() == bnPSF) {
	toggle(bnPSF);
	psf.update();
	}
	else if (e.getSource() == bnAlgo) {
	toggle(bnAlgo);
	algorithm.update();
	}
	else if (e.getSource() == bnRecap) {
	toggle(bnRecap);
	recap.update();
	}
	else if (e.getSource() == bnReport) {
	toggle(bnReport);
	report.update();
	}
	else if (e.getSource() == bnReset) {
	toggle(bnRecap);
	if (tableMonitor != null)
	tableMonitor.clear();
	- if (tableStats != null)
	- tableStats.clear();

	bnStart.setEnabled(true);
	}
	else if (e.getSource() == bnQuit) {
	deconvolution.close();
	deconvolution = null;
	dispose();
	}
	else if (e.getSource() == bnHelp)
	Lab.help();
	else if (e.getSource() == bnMonitor)
	toggle(bnMonitor);
	else if (e.getSource() == bnStats)
	toggle(bnStats);
	}

	@Override
	public void run() {
	bnRecap.setEnabled(false);
	bnImage.setEnabled(false);
	bnPSF.setEnabled(false);
	bnAlgo.setEnabled(false);
	bnStart.setEnabled(false);
	bnStop.setEnabled(true);

	deconvolution.setCommand(recap.getCommand());

	deconvolution.run();
	toggle(bnReport);

	bnStop.setEnabled(false);
	report.update();
	bnRecap.setEnabled(true);
	bnAlgo.setEnabled(true);
	bnPSF.setEnabled(true);
	bnImage.setEnabled(true);
	thread = null;
	}

	public static void setLocationLaunch(Point l) {
	location = l;
	}

	private void toggle(BorderToggledButton bn) {
	((CardLayout) (cards.getLayout())).show(cards, bn.getText());
	bnRecap.setSelected(false);
	bnImage.setSelected(false);
	bnPSF.setSelected(false);
	bnAlgo.setSelected(false);
	bnMonitor.setSelected(false);
	bnStats.setSelected(false);
	bnReport.setSelected(false);
	bn.setSelected(true);
	}

	@Override
	public void windowOpened(WindowEvent e) {
	}

	@Override
	public void windowClosing(WindowEvent e) {
	deconvolution.close();
	deconvolution = null;
	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) {
	}

	public JProgressBar getProgressBar() {
	return progress;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/DeconvolutionListener.java b/DeconvolutionLab2/src/deconvolution/DeconvolutionListener.java
	deleted file mode 100644
	index fe4542b..0000000
	--- a/DeconvolutionLab2/src/deconvolution/DeconvolutionListener.java
	+++ /dev/null
	@@ -1,7 +0,0 @@
	-package deconvolution;
	-
	-public interface DeconvolutionListener {
	-
	- public abstract void started();
	- public abstract void finish();
	-}
	diff --git a/DeconvolutionLab2/src/deconvolution/Features.java b/DeconvolutionLab2/src/deconvolution/Features.java
	index 23f2a0c..ab814dd 100644
	--- a/DeconvolutionLab2/src/deconvolution/Features.java
	+++ b/DeconvolutionLab2/src/deconvolution/Features.java
	@@ -1,16 +1,47 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution;

	import java.util.ArrayList;

	public class Features extends ArrayList<String[]>{

	public Features() {
	super();
	}


	public void add(String feature, String value) {
	add(new String[] {feature, value});
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/RegularizationPanel.java b/DeconvolutionLab2/src/deconvolution/RegularizationPanel.java
	index d1f116d..ce04632 100644
	--- a/DeconvolutionLab2/src/deconvolution/RegularizationPanel.java
	+++ b/DeconvolutionLab2/src/deconvolution/RegularizationPanel.java
	@@ -1,83 +1,114 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	package deconvolution;

	import java.awt.BorderLayout;
	import java.awt.Dimension;
	import java.util.Hashtable;

	import javax.swing.JLabel;
	import javax.swing.JPanel;
	import javax.swing.JSlider;
	import javax.swing.JTextField;

	import bilib.tools.NumFormat;

	public class RegularizationPanel extends JPanel {

	private JSlider slider = new JSlider();
	private JTextField txt = new JTextField(10);
	private double base = Math.pow(10, 1. / 3.0);
	private double logbase = Math.log(base);

	public RegularizationPanel(double value) {
	setLayout(new BorderLayout());
	slider.setMinimum(-54);
	slider.setMaximum(30);
	slider.setPreferredSize(new Dimension(200, 40));
	int p = (int) Math.round(Math.log(Math.abs(value)) / logbase);
	slider.setValue(p);

	Hashtable<Integer, JLabel> labels = new Hashtable<Integer, JLabel>();
	JLabel lbl0 = new JLabel("Off");
	JLabel lbl1 = new JLabel("Low");
	JLabel lbl2 = new JLabel("High");
	JLabel lbl4 = new JLabel("1E-6");
	JLabel lbl5 = new JLabel("1.0");
	java.awt.Font font = lbl1.getFont();
	java.awt.Font small = new java.awt.Font(font.getFamily(), font.getStyle(), font.getSize() - 3);
	lbl0.setFont(small);
	lbl1.setFont(small);
	lbl2.setFont(small);
	lbl4.setFont(small);
	lbl5.setFont(small);
	labels.put(-54, lbl0);
	labels.put(-36, lbl1);
	labels.put(-18, lbl4);
	labels.put(0, lbl5);
	labels.put(27, lbl2);
	slider.setMinorTickSpacing(3);
	// js.setSnapToTicks(true);
	slider.setPaintTicks(true);
	slider.setPaintLabels(true);
	slider.setMajorTickSpacing(9);
	slider.setLabelTable(labels);
	add(new JLabel("<html>Reg. λ</html>"), BorderLayout.WEST);
	add(slider, BorderLayout.CENTER);
	add(txt, BorderLayout.EAST);
	}

	public JSlider getSlider() {
	return slider;
	}

	public JTextField getText() {
	return txt;
	}

	public void updateFromSlider() {
	double d = Math.pow(base, slider.getValue());
	d = Math.min(d, Math.pow(base, slider.getMaximum()));
	d = Math.max(d, Math.pow(base, slider.getMinimum()));
	txt.setText(NumFormat.nice(d));
	}

	public void updateFromText() {
	String typed = txt.getText();
	double value = NumFormat.parseNumber(typed, 1);
	int p = (int) Math.round(Math.log(Math.abs(value)) / logbase);
	slider.setValue(p);
	}

	public double getValue() {
	return Math.pow(base, slider.getValue());
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/Stats.java b/DeconvolutionLab2/src/deconvolution/Stats.java
	new file mode 100644
	index 0000000..a753b08
	--- /dev/null
	+++ b/DeconvolutionLab2/src/deconvolution/Stats.java
	@@ -0,0 +1,159 @@
	+/*
	+ * 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.awt.BorderLayout;
	+import java.awt.Dimension;
	+import java.io.File;
	+import java.util.ArrayList;
	+
	+import javax.swing.BorderFactory;
	+import javax.swing.JFrame;
	+import javax.swing.JPanel;
	+import javax.swing.JScrollPane;
	+
	+import bilib.table.CustomizedColumn;
	+import bilib.table.CustomizedTable;
	+import bilib.tools.NumFormat;
	+import deconvolutionlab.Constants;
	+import deconvolutionlab.Lab;
	+import deconvolutionlab.monitor.Monitors;
	+import deconvolutionlab.system.SystemUsage;
	+import signal.RealSignal;
	+import signal.SignalCollector;
	+
	+public class Stats {
	+
	+ public enum Mode {NO, SHOW, SAVE, SHOWSAVE};
	+
	+ private CustomizedTable table;
	+ private float[] statsInput;
	+ private Mode mode;
	+
	+ public Stats(Mode mode) {
	+ this.mode = mode;
	+ ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	+ columns.add(new CustomizedColumn("Iterations", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Mean", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Minimum", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Maximum", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Stdev", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Energy", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Time", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Memory", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Signal", String.class, 100, false));
	+ columns.add(new CustomizedColumn("PSNR", String.class, 100, false));
	+ columns.add(new CustomizedColumn("SNR", String.class, 100, false));
	+ columns.add(new CustomizedColumn("Residu", String.class, 100, false));
	+ table = new CustomizedTable(columns, true);
	+ }
	+
	+ public void show() {
	+ if (mode == Mode.SHOW \|\| mode == Mode.SHOWSAVE) {
	+ JFrame frame = new JFrame("Stats");
	+ frame.getContentPane().add(getPanel());
	+ frame.pack();
	+ Lab.setVisible(frame);
	+ }
	+ }
	+
	+ public void save(Monitors monitors, String path) {
	+ if (mode == Mode.SAVE \|\| mode == Mode.SHOWSAVE) {
	+ String filename = path + File.separator + "stats.csv";
	+ monitors.log("Stats save " + filename);
	+ table.saveCSV(filename);
	+ }
	+
	+ }
	+
	+ public void addInput(RealSignal x) {
	+ statsInput = x.getStats();
	+ table.append(compute(x, 0, "", "", "", ""));
	+ }
	+
	+ public void add(RealSignal x, int iterations) {
	+ table.append(compute(x, iterations, "", "", "", ""));
	+ }
	+
	+ public void add(RealSignal x, int iterations, String time, String psnr, String snr, String residu) {
	+ table.append(compute(x, iterations, time, psnr, snr, residu));
	+ }
	+
	+ public String[] compute(RealSignal x, int iterations, String time, String psnr, String snr, String residu) {
	+ float params[] = null;
	+ if (x != null)
	+ params = x.getStats();
	+ String[] row = new String[12];
	+ row[0] = "" + iterations;
	+ row[1] = (params == null ? "-" : "" + params[0]);
	+ row[2] = (params == null ? "-" : "" + params[1]);
	+ row[3] = (params == null ? "-" : "" + params[2]);
	+ row[4] = (params == null ? "-" : "" + params[3]);
	+ row[5] = (params == null ? "-" : "" + params[5]);
	+ row[6] = time;
	+ row[7] = NumFormat.bytes(SystemUsage.getHeapUsed());
	+ row[8] = SignalCollector.sumarize();
	+ row[9] = psnr;
	+ row[10] = snr;
	+ row[11] = residu;
	+
	+ return row;
	+ }
	+
	+ public JPanel getPanel() {
	+ JScrollPane scroll = new JScrollPane(table);
	+ scroll.setPreferredSize(new Dimension(Constants.widthGUI, 400));
	+ JPanel panel = new JPanel(new BorderLayout());
	+ panel = new JPanel(new BorderLayout());
	+ panel.add(scroll);
	+ panel.setBorder(BorderFactory.createEtchedBorder());
	+ return panel;
	+ }
	+
	+ public String toStringStats() {
	+ if (mode == Mode.SHOW)
	+ return "show";
	+ if (mode == Mode.SAVE)
	+ return "save";
	+ if (mode == Mode.SHOWSAVE)
	+ return "show and save";
	+ return "no";
	+ }
	+
	+ public Mode getMode() {
	+ return mode;
	+ }
	+ public float[] getStatsInput() {
	+ return statsInput;
	+ }
	+
	+}
	diff --git a/DeconvolutionLab2/src/deconvolution/Token.java b/DeconvolutionLab2/src/deconvolution/Token.java
	index c556f42..3b1cc05 100644
	--- a/DeconvolutionLab2/src/deconvolution/Token.java
	+++ b/DeconvolutionLab2/src/deconvolution/Token.java
	@@ -1,53 +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 deconvolution;
	+/*
	+ * 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;
	+

	public class Token {

	public String keyword;
	public String parameters = "?";
	public String option = "?";

	public Token(String keyword, String command, int begin, int end) {
	this.keyword = keyword;
	- this.parameters = command.substring(begin, end).trim();
	- String arg[] = parameters.split(" ");
	- option = arg.length >= 1 ? arg[0].trim() : "";
	+ try {
	+ this.parameters = command.substring(begin, end).trim();
	+ String arg[] = parameters.split(" ");
	+ option = arg.length >= 1 ? arg[0].trim() : "";
	+ }
	+ catch(Exception ex) {
	+ option = "";
	+ }
	}

	@Override
	public String toString() {
	return keyword + " [" + option + "]" + parameters;
	}
	-
	-
	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	index ebafedf..b24857d 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
	@@ -1,269 +1,398 @@
	/*
	* 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;
	import java.util.concurrent.Callable;
	import java.util.concurrent.ExecutionException;
	import java.util.concurrent.ExecutorService;
	import java.util.concurrent.Executors;
	import java.util.concurrent.Future;

	import bilib.tools.NumFormat;
	+import deconvolution.Stats;
	+import deconvolutionlab.Output;
	import deconvolutionlab.monitor.Monitors;
	+import deconvolutionlab.monitor.Verbose;
	import fft.AbstractFFT;
	-import fft.AbstractFFTLibrary;
	import fft.FFT;
	-import signal.Operations;
	+import signal.Constraint;
	import signal.RealSignal;
	import signal.SignalCollector;
	import signal.apodization.Apodization;
	import signal.padding.Padding;

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

	/** y is the input signal of the deconvolution. */
	protected RealSignal y;

	/** h is the PSF signal for the deconvolution. */
	protected RealSignal h;

	- /**
	- * The controller takes the control of the algorithm, in particular to do
	- * some operations at the starting, at every iteration and at the end.
	- */
	- protected Controller controller;
	-
	- /** This is the FFT used. */
	- protected AbstractFFT fft ;
	-
	- protected Monitors monitors;
	- protected AbstractFFTLibrary fftlib;
	protected boolean threaded;

	/** Optimized implementation in term of memory footprint */
	protected boolean optimizedMemoryFootprint;

	+ protected int iterMax = 0;
	+
	+ protected AbstractFFT fft;
	+ protected Controller controller;
	+
	public AbstractAlgorithm() {
	- this.controller = new Controller();
	- monitors = Monitors.createDefaultMonitor();
	- fftlib = FFT.getFastestFFT();
	+ setController(new Controller());
	optimizedMemoryFootprint = true;
	threaded = true;
	+ fft = FFT.getFastestFFT().getDefaultFFT();
	+ }
	+
	+ public AbstractAlgorithm(Controller controller) {
	+ this.controller = controller;
	+ optimizedMemoryFootprint = true;
	+ threaded = true;
	+ fft = FFT.getFastestFFT().getDefaultFFT();
	}

	public void setOptimizedMemoryFootprint(boolean optimizedMemoryFootprint) {
	this.optimizedMemoryFootprint = optimizedMemoryFootprint;
	}

	public abstract String getName();
	public abstract String[] getShortnames();
	-
	public abstract double getMemoryFootprintRatio();
	-
	public abstract int getComplexityNumberofFFT();
	-
	public abstract boolean isRegularized();
	-
	public abstract boolean isStepControllable();
	-
	public abstract boolean isIterative();
	-
	public abstract boolean isWaveletsBased();
	-
	public abstract void setParameters(double[] params);
	-
	public abstract double getRegularizationFactor();
	-
	public abstract double getStepFactor();
	-
	public abstract double[] getParameters();
	-
	public abstract double[] getDefaultParameters();

	public RealSignal run(RealSignal image, RealSignal psf) {
	- return run(image, psf, new Padding(), new Apodization(), 1);
	+ return run(image, psf, new Stats(Stats.Mode.NO));
	}

	- public RealSignal run(RealSignal image, RealSignal psf, Padding pad, Apodization apo) {
	- return run(image, psf, pad, apo, 1);
	- }
	-
	- public RealSignal run(RealSignal image, RealSignal psf, Padding pad, Apodization apo, double norm) {
	+ public RealSignal run(RealSignal image, RealSignal psf, Stats stats) {
	+ Padding pad = controller.getPadding();
	+ Apodization apo = controller.getApodization();
	+ double norm = controller.getNormalizationPSF();
	+
	+ fft = controller.getFFT();
	+ controller.setIterationsMax(iterMax);

	if (image == null)
	return null;
	+
	if (psf == null)
	return null;
	-
	- if (fftlib != null)
	- fft = FFT.createFFT(monitors, fftlib, image.nx, image.ny, image.nz);
	- else
	- fft = FFT.createDefaultFFT(monitors, image.nx, image.ny, image.nz);
	- controller.setFFT(fft);
	-
	+
	+ // Prepare the controller and the outputs
	+
	+ Monitors monitors = controller.getMonitors();
	+ monitors.setVerbose(controller.getVerbose());
	+ monitors.log("Path: " + controller.toStringPath());
	+ monitors.log("Algorithm: " + getName());
	+
	+ // Prepare the signal and the PSF
	y = pad.pad(monitors, image);
	y.setName("y");
	apo.apodize(monitors, y);
	monitors.log("Input: " + y.dimAsString());
	-
	h = psf.changeSizeAs(y);
	h.setName("h");
	h.normalize(norm);
	monitors.log("PSF: " + h.dimAsString() + " normalized " + (norm <= 0 ? "no" : norm));

	- String iterations = (isIterative() ? controller.getIterationMax() + " iterations" : "direct");
	+ String iterations = (isIterative() ? iterMax + " iterations" : "direct");
	+
	+ controller.setIterationsMax(iterMax);
	+
	monitors.log(getShortnames()[0] + " is starting (" + iterations + ")");
	controller.setMonitors(monitors);
	- controller.start(y);
	-
	+
	+ controller.start(y, stats);
	h.circular();
	- if (fft == null)
	- fft = FFT.createDefaultFFT(monitors, y.nx, y.ny, y.nz);
	- else
	- fft.init(monitors, y.nx, y.ny, y.nz);
	+
	+ // FFT
	+ fft.init(monitors, y.nx, y.ny, y.nz);
	+ controller.setFFT(fft);
	+
	monitors.log(getShortnames()[0] + " data ready");

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

	try {
	if (threaded == true) {
	ExecutorService pool = Executors.newSingleThreadExecutor();
	Future<RealSignal> future = pool.submit(this);
	x = future.get();
	}
	else {
	x = call();
	}
	}
	catch (InterruptedException ex) {
	ex.printStackTrace();
	x = y.duplicate();
	}
	catch (ExecutionException ex) {
	ex.printStackTrace();
	x = y.duplicate();
	}
	catch (Exception e) {
	e.printStackTrace();
	x = y.duplicate();
	}
	- x.setName("x");
	- controller.finish(x);
	- monitors.log(getName() + " is finished");
	SignalCollector.free(y);
	SignalCollector.free(h);
	-
	+ x.setName("x");
	RealSignal result = pad.crop(monitors, x);
	+
	+ controller.finish(result);
	+ monitors.log(getName() + " is finished");
	+
	SignalCollector.free(x);
	result.setName("Output of " + this.getShortnames()[0]);
	return result;
	}

	- public Monitors getMonitors() {
	- return monitors;
	- }
	-
	- public void setMonitors(Monitors monitors) {
	- this.monitors = monitors;
	- }
	-
	- public AbstractFFT getFFT() {
	- return fft;
	- }
	-
	- public void setFFT(AbstractFFT fft) {
	- this.fft = fft;
	- }
	-
	- public void setFFT(AbstractFFTLibrary fftlib) {
	- this.fftlib = fftlib;
	+ public void setController(Controller controller) {
	+ this.controller = controller;
	}

	public Controller getController() {
	return controller;
	}

	- public void setController(Controller controller) {
	- this.controller = controller;
	+ public int getIterationsMax() {
	+ return iterMax;
	}

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

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

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

	public void setWavelets(String waveletsName) {
	}

	@Override
	public String toString() {
	String s = "";
	s += getName();
	- s += (isIterative() ? ", " + controller.getIterationMax() + " iterations" : " (direct)");
	+ s += (isIterative() ? ", " + iterMax + " iterations" : " (direct)");
	s += (isRegularized() ? ", &lambda=" + NumFormat.nice(getRegularizationFactor()) : "");
	s += (isStepControllable() ? ", &gamma=" + NumFormat.nice(getStepFactor()) : "");
	return s;
	}

	public String getParametersAsString() {
	double p[] = getParameters();
	String param = "";
	for (int i = 0; i < p.length; i++)
	if (i == p.length - 1)
	param += p[i];
	else
	param += p[i] + ", ";
	return param;
	}
	+
	+
	+ public AbstractFFT getFFT() {
	+ return controller.getFFT();
	+ }
	+
	+ public void setFFT(AbstractFFT fft) {
	+ this.fft = fft;
	+ controller.setFFT(fft);
	+ }
	+
	+ public String getPath() {
	+ return controller.getPath();
	+ }
	+
	+ public void setPath(String path) {
	+ controller.setPath(path);
	+ }
	+
	+ public boolean isSystem() {
	+ return controller.isSystem();
	+ }
	+
	+ public void setSystem(boolean system) {
	+ controller.setSystem(system);
	+ }
	+
	+ public boolean isMultithreading() {
	+ return controller.isMultithreading();
	+ }
	+
	+ public void setMultithreading(boolean multithreading) {
	+ controller.setMultithreading(multithreading);
	+ }
	+
	+ public boolean isDisplayFinal() {
	+ return controller.isDisplayFinal();
	+ }
	+
	+ public void setDisplayFinal(boolean displayFinal) {
	+ controller.setDisplayFinal(displayFinal);
	+ }
	+
	+ public double getNormalizationPSF() {
	+ return controller.getNormalizationPSF();
	+ }
	+
	+ public void setNormalizationPSF(double normalizationPSF) {
	+ controller.setNormalizationPSF(normalizationPSF);
	+ }
	+
	+ public double getEpsilon() {
	+ return controller.getEpsilon();
	+ }
	+
	+ public void setEpsilon(double epsilon) {
	+ controller.setEpsilon(epsilon);
	+ }
	+
	+ public Padding getPadding() {
	+ return controller.getPadding();
	+ }
	+
	+ public void setPadding(Padding padding) {
	+ controller.setPadding(padding);
	+ }
	+
	+ public Apodization getApodization() {
	+ return controller.getApodization();
	+ }
	+
	+ public void setApodization(Apodization apodization) {
	+ controller.setApodization(apodization);
	+ }
	+
	+ public Monitors getMonitors() {
	+ return controller.getMonitors();
	+ }
	+
	+ public void setMonitors(Monitors monitors) {
	+ controller.setMonitors(monitors);
	+ }
	+
	+ public Verbose getVerbose() {
	+ return controller.getVerbose();
	+ }
	+
	+ public void setVerbose(Verbose verbose) {
	+ controller.setVerbose(verbose);
	+ }
	+
	+ public Constraint.Mode getConstraint() {
	+ return controller.getConstraint();
	+ }
	+
	+ public void setConstraint(Constraint.Mode constraint) {
	+ controller.setConstraint(constraint);
	+ }
	+
	+ public Stats getStats() {
	+ return controller.getStats();
	+ }
	+
	+ public void setStats(Stats stats) {
	+ controller.setStats(stats);
	+ }
	+
	+ public double getResiduMin() {
	+ return controller.getResiduMin();
	+ }
	+
	+ public void setResiduMin(double residuMin) {
	+ controller.setResiduMin(residuMin);
	+ }
	+
	+ public double getTimeLimit() {
	+ return controller.getTimeLimit();
	+ }
	+
	+ public void setTimeLimit(double timeLimit) {
	+ controller.setTimeLimit(timeLimit);
	+ }
	+
	+ public String getReference() {
	+ return controller.getReference();
	+ }
	+
	+ public void setReference(String reference) {
	+ controller.setReference(reference);
	+ }
	+
	+ public ArrayList<Output> getOuts() {
	+ return controller.getOuts();
	+ }
	+
	+ public void setOuts(ArrayList<Output> outs) {
	+ controller.setOuts(outs);
	+ }
	+
	+ public void addOutput(Output out) {
	+ controller.addOutput(out);
	+ }
	+
	+
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java b/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	index e1bc26b..5701561 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
	@@ -1,353 +1,638 @@
	/*
	* 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.io.File;
	+import java.util.ArrayList;
	import java.util.Timer;
	import java.util.TimerTask;

	import bilib.tools.NumFormat;
	import deconvolution.Deconvolution;
	-import deconvolutionlab.OutputCollection;
	-import deconvolutionlab.TableStats;
	+import deconvolution.Stats;
	+import deconvolutionlab.Constants;
	+import deconvolutionlab.Output;
	+import deconvolutionlab.monitor.AbstractMonitor;
	+import deconvolutionlab.monitor.ConsoleMonitor;
	import deconvolutionlab.monitor.Monitors;
	+import deconvolutionlab.monitor.TableMonitor;
	+import deconvolutionlab.monitor.Verbose;
	import deconvolutionlab.system.SystemUsage;
	import fft.AbstractFFT;
	import fft.FFT;
	import signal.Assessment;
	import signal.ComplexSignal;
	import signal.Constraint;
	import signal.RealSignal;
	-import signal.SignalCollector;
	+import signal.apodization.Apodization;
	+import signal.padding.Padding;

	/**
	- * This is an important class to manage all the common task
	- * of the algorithm.
	- * The method start() is called before at the starting of the
	- * algorithm.
	- * The method ends() is called at the end of every iterations
	- * for the iterative algorithm. It returns true if one the
	- * stopping criteria is true.
	- * The method finish() is called when the algorithm is completely
	- * terminated.
	+ * This is an important class to manage all the common task of the algorithm.
	+ * The method start() is called before at the starting of the algorithm. The
	+ * method ends() is called at the end of every iterations for the iterative
	+ * algorithm. It returns true if one the stopping criteria is true. The method
	+ * finish() is called when the algorithm is completely terminated.
	*
	- * @author sage
	+ * @author Daniel Sage
	*
	*/
	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 abort = false;
	-
	- 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 path;
	+ private boolean system;
	+ private boolean multithreading;
	+ private boolean displayFinal;
	+ private double normalizationPSF;
	+ private double epsilon;
	+
	+ private Padding padding;
	+ private Apodization apodization;
	+ private ArrayList<Output> outs;
	+ private Stats stats;
	+ private Constraint.Mode constraintMode;
	+ private double residuMin;
	+ private double timeLimit;
	+ private String reference;
	+ private Monitors monitors;
	+ private Verbose verbose;
	+ private AbstractFFT fft;
	+
	+ private int iterationsMax = 100;
	+
	+ private boolean doResidu = false;
	+ private boolean doTime = false;
	+ private boolean doReference = false;
	+ private boolean doConstraint = false;
	+ private boolean abort = false;
	+
	+ 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 RealSignal refImage;
	private RealSignal prevImage;
	private RealSignal x;
	-
	- private Timer timer;
	- private AbstractFFT fft;
	-
	- private TableStats tableStats;
	- private float[] statsInput;

	- private Monitors monitors = new Monitors();
	+ private Timer timer;

	public Controller() {
	- constraint = Constraint.Mode.NO;
	doResidu = false;
	doTime = false;
	doReference = false;
	doConstraint = false;
	- }
	-
	- public void setTableStats(TableStats tableStats) {
	- this.tableStats = tableStats;
	- }
	-
	- public void setMonitors(Monitors monitors) {
	- this.monitors = monitors;
	+ timeStarting = System.nanoTime();
	+
	+ setPath(System.getProperty("user.dir"));
	+ setSystem(true);
	+ setMultithreading(true);
	+ setDisplayFinal(true);
	+ setFFT(FFT.getFastestFFT().getDefaultFFT());
	+ setNormalizationPSF(1);
	+ setEpsilon(1e-6);
	+ setPadding(new Padding());
	+ setApodization(new Apodization());
	+
	+ monitors = new Monitors();
	+ monitors.add(new ConsoleMonitor());
	+ monitors.add(new TableMonitor("Monitor", Constants.widthGUI, 240));
	+
	+ setVerbose(Verbose.Log);
	+ setStats(new Stats(Stats.Mode.NO));
	+ setConstraint(Constraint.Mode.NO);
	+ setResiduMin(-1);
	+ setTimeLimit(-1);
	+ setReference("");
	+ setOuts(new ArrayList<Output>());
	}

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

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

	- public int getIterationMax() {
	- return iterationsMax;
	- }
	-
	- public void setIterationMax(int iterationsMax) {
	+ public void setIterationsMax(int iterationsMax) {
	this.iterationsMax = iterationsMax;
	}

	- public void setTimeStop(double timeMax) {
	- this.doTime = true;
	- this.timeMax = timeMax * 1e9;
	- }
	-
	- public void setResiduStop(double residuMin) {
	- this.doResidu = true;
	- this.residuMin = residuMin;
	- }
	-
	- public void setReference(String referenceName) {
	- this.doReference = true;
	- this.referenceName = referenceName;
	- }
	-
	- public void setConstraint(Constraint.Mode constraint) {
	- this.doConstraint = true;
	- this.constraint = constraint;
	- }
	-
	- public void setOutputs(OutputCollection outs) {
	- this.outs = outs;
	- }
	-
	public boolean needSpatialComputation() {
	return doConstraint \|\| doResidu \|\| doReference;
	}
	-
	- public void start(RealSignal x) {
	+
	+ /**
	+ * Call one time at the beginning of the algorithms
	+ *
	+ * @param x
	+ * the input signal
	+ */
	+ public void start(RealSignal x, Stats stats) {
	this.x = x;
	- statsInput = x.getStats();
	- if (tableStats != null)
	- tableStats.nextStats(monitors, stats());
	+ this.stats = stats;
	+
	+ stats.show();
	+ stats.addInput(x);
	+
	iterations = 0;
	timer = new Timer();
	timer.schedule(new Updater(), 0, 100);
	timeStarting = System.nanoTime();
	memoryStarting = SystemUsage.getHeapUsed();

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

	if (doReference) {
	- refImage = new Deconvolution("Reference", "-image file " + referenceName).openImage();
	+ refImage = new Deconvolution("Reference", "-image file " + reference).openImage();
	if (refImage == null)
	- monitors.error("Impossible to load the reference image " + referenceName);
	+ monitors.error("Impossible to load the reference image " + reference);
	else
	monitors.log("Reference image loaded");
	}
	+ for (Output out : outs)
	+ out.executeStarting(monitors, x, this);

	- if (outs != null)
	- outs.executeStarting(monitors, x, this);
	this.prevImage = x;
	}

	public boolean ends(ComplexSignal X) {
	- boolean out = outs == null ? false : outs.hasShow(iterations);
	+
	+ boolean out = false;
	+ for (Output output : outs)
	+ out = out \| output.is(iterations);

	if (doConstraint \|\| doResidu \|\| doReference \|\| out) {
	if (fft == null)
	fft = FFT.createDefaultFFT(monitors, X.nx, X.ny, X.nz);
	x = fft.inverse(X, x);
	return ends(x);
	}

	return ends((RealSignal) null);
	}

	public boolean ends(RealSignal x) {
	this.x = x;

	if (doConstraint \|\| doResidu \|\| doReference)
	compute(iterations, x, doConstraint, doResidu, doReference);

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

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

	- if (tableStats != null)
	- tableStats.nextStats(monitors, stats());
	-
	+ addStats();
	+
	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);
	+ monitors.log(prefix + "time " + timeElapsed + " > " + timeLimit);
	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 (tableStats != null)
	- tableStats.lastStats(monitors, stats());
	-
	- if (outs != null)
	- outs.executeFinal(monitors, x, this);
	+ addStats();
	+ stats.save(monitors, path);
	+
	+ for (Output out : outs)
	+ out.executeFinal(monitors, x, this);

	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 (con && constraintMode != null)
	+ new Constraint(monitors).apply(x, constraintMode);

	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() {
	- if (tableStats == null)
	- return null;
	- float params[] = null;
	- if (x != null)
	- params = x.getStats();
	- String[] row = new String[12];
	- row[0] = "" + iterations;
	- row[1] = (params == null ? "-" : "" + params[0]);
	- row[2] = (params == null ? "-" : "" + params[1]);
	- row[3] = (params == null ? "-" : "" + params[2]);
	- row[4] = (params == null ? "-" : "" + params[3]);
	- row[5] = (params == null ? "-" : "" + params[5]);
	- row[6] = NumFormat.seconds(getTimeNano());
	- row[7] = NumFormat.bytes(SystemUsage.getHeapUsed());
	- row[8] = SignalCollector.sumarize();
	- row[9] = doReference ? NumFormat.nice(psnr) : "n/a";
	- row[10] = doReference ? NumFormat.nice(snr) : "n/a";
	- row[11] = doResidu ? NumFormat.nice(residu) : "n/a";
	- return row;
	+ private void addStats() {
	+ String pnsrText = doReference ? NumFormat.nice(psnr) : "n/a";
	+ String snrText = doReference ? NumFormat.nice(snr) : "n/a";
	+ String residuText = doResidu ? NumFormat.nice(residu) : "n/a";
	+
	+ stats.add(x, iterations, NumFormat.seconds(getTimeNano()), pnsrText, snrText, residuText);
	}

	public double getTimeNano() {
	return (System.nanoTime() - timeStarting);
	}
	-
	- public Constraint.Mode getConstraint() {
	- return constraint;
	- }
	-
	- public String getReference() {
	- return doReference ? referenceName : "no ground-truth";
	+
	+ public double getTimeSecond() {
	+ return (System.nanoTime() - timeStarting) * 1e-9;
	}

	public String getConstraintAsString() {
	if (!doConstraint)
	return "no";
	- if (constraint == null)
	+ if (constraintMode == null)
	return "null";
	- return constraint.name().toLowerCase();
	+ return constraintMode.name().toLowerCase();
	}

	public String getStoppingCriteriaAsString(AbstractAlgorithm algo) {
	- String stop = algo.isIterative() ? "iterations limit=" + getIterationMax() + ", " : "direct, ";
	- stop += doTime ? ", time limit=" + NumFormat.nice(timeMax * 1e-9) : " no time limit" + ", ";
	+ String stop = algo.isIterative() ? "iterations limit=" + algo.getIterationsMax() + ", " : "direct, ";
	+ stop += doTime ? ", time limit=" + NumFormat.nice(timeLimit * 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());
	}

	+ public AbstractFFT getFFT() {
	+ return fft;
	+ }
	+
	+ /**
	+ * @return the path
	+ */
	+ public String getPath() {
	+ return path;
	+ }
	+
	+ /**
	+ * @param path
	+ * the path to set
	+ */
	+ public void setPath(String path) {
	+ this.path = path;
	+ }
	+
	+ /**
	+ * @return the system
	+ */
	+ public boolean isSystem() {
	+ return system;
	+ }
	+
	+ /**
	+ * @param system
	+ * the system to set
	+ */
	+ public void setSystem(boolean system) {
	+ this.system = system;
	+ }
	+
	+ /**
	+ * @return the multithreading
	+ */
	+ public boolean isMultithreading() {
	+ return multithreading;
	+ }
	+
	+ /**
	+ * @param multithreading
	+ * the multithreading to set
	+ */
	+ public void setMultithreading(boolean multithreading) {
	+ this.multithreading = multithreading;
	+ }
	+
	+ /**
	+ * @return the displayFinal
	+ */
	+ public boolean isDisplayFinal() {
	+ return displayFinal;
	+ }
	+
	+ /**
	+ * @param displayFinal
	+ * the displayFinal to set
	+ */
	+ public void setDisplayFinal(boolean displayFinal) {
	+ this.displayFinal = displayFinal;
	+ }
	+
	+ /**
	+ * @return the normalizationPSF
	+ */
	+ public double getNormalizationPSF() {
	+ return normalizationPSF;
	+ }
	+
	+ /**
	+ * @param normalizationPSF
	+ * the normalizationPSF to set
	+ */
	+ public void setNormalizationPSF(double normalizationPSF) {
	+ this.normalizationPSF = normalizationPSF;
	+ }
	+
	+ /**
	+ * @return the epsilon
	+ */
	+ public double getEpsilon() {
	+ return epsilon;
	+ }
	+
	+ /**
	+ * @param epsilon
	+ * the epsilon to set
	+ */
	+ public void setEpsilon(double epsilon) {
	+ this.epsilon = epsilon;
	+ }
	+
	+ /**
	+ * @return the padding
	+ */
	+ public Padding getPadding() {
	+ return padding;
	+ }
	+
	+ /**
	+ * @param padding
	+ * the padding to set
	+ */
	+ public void setPadding(Padding padding) {
	+ this.padding = padding;
	+ }
	+
	+ /**
	+ * @return the apodization
	+ */
	+ public Apodization getApodization() {
	+ return apodization;
	+ }
	+
	+ /**
	+ * @param apodization
	+ * the apodization to set
	+ */
	+ public void setApodization(Apodization apodization) {
	+ this.apodization = apodization;
	+ }
	+
	+ /**
	+ * @return the monitors
	+ */
	+ public Monitors getMonitors() {
	+ return monitors;
	+ }
	+
	+ /**
	+ * @param monitors
	+ * the monitors to set
	+ */
	+ public void setMonitors(Monitors monitors) {
	+ this.monitors = monitors;
	+ }
	+
	+ /**
	+ * @return the verbose
	+ */
	+ public Verbose getVerbose() {
	+ return verbose;
	+ }
	+
	+ /**
	+ * @param verbose
	+ * the verbose to set
	+ */
	+ public void setVerbose(Verbose verbose) {
	+ this.verbose = verbose;
	+ }
	+
	+ public Constraint.Mode getConstraint() {
	+ return constraintMode;
	+ }
	+
	+ public void setConstraint(Constraint.Mode constraintMode) {
	+ doConstraint = constraintMode != Constraint.Mode.NO;
	+ this.constraintMode = constraintMode;
	+ }
	+
	+ /**
	+ * @return the stats
	+ */
	+ public Stats getStats() {
	+ return stats;
	+ }
	+
	+ /**
	+ * @param stats
	+ * the stats to set
	+ */
	+ public void setStats(Stats stats) {
	+ this.stats = stats;
	+ }
	+
	+ /**
	+ * @return the residuMin
	+ */
	+ public double getResiduMin() {
	+ return residuMin;
	+ }
	+
	+ /**
	+ * @param residuMin
	+ * the residuMin to set
	+ */
	+ public void setResiduMin(double residuMin) {
	+ doResidu = residuMin > 0;
	+ this.residuMin = residuMin;
	+ }
	+
	+ /**
	+ * @return the timeLimit
	+ */
	+ public double getTimeLimit() {
	+ return timeLimit;
	+ }
	+
	+ /**
	+ * @param timeLimit
	+ * the timeLimit to set
	+ */
	+ public void setTimeLimit(double timeLimit) {
	+ doTime = timeLimit > 0;
	+ this.timeLimit = timeLimit;
	+ }
	+
	+ /**
	+ * @return the reference
	+ */
	+ public String getReference() {
	+ return reference;
	+ }
	+
	+ /**
	+ * @param reference
	+ * the reference to set
	+ */
	+ public void setReference(String reference) {
	+ doReference = false;
	+ if (reference == null)
	+ return;
	+ if (reference.equals(""))
	+ return;
	+ doReference = true;
	+ this.reference = reference;
	+ }
	+
	+ /**
	+ * @return the outs
	+ */
	+ public ArrayList<Output> getOuts() {
	+ return outs;
	+ }
	+
	+ /**
	+ * @param outs
	+ * the outs to set
	+ */
	+ public void setOuts(ArrayList<Output> outs) {
	+ this.outs = outs;
	+ }
	+
	+ public void addOutput(Output out) {
	+ this.outs.add(out);
	+ }
	+
	+ public String toStringMonitor() {
	+ String s = "[" + verbose.name().toLowerCase() + "] ";
	+ for (AbstractMonitor monitor : monitors) {
	+ s += "" + monitor.getName() + " ";
	+ }
	+ return s;
	+ }
	+
	+ /**
	+ * @return the stats
	+ */
	+ public Stats.Mode getStatsMode() {
	+ return stats.getMode();
	+ }
	+
	+ /**
	+ * @param stats
	+ * the stats to set
	+ */
	+ public void setStatsMode(Stats.Mode mode) {
	+ this.stats = new Stats(mode);
	+ }
	+
	+ public String toStringRunning() {
	+ String s = "";
	+ s += "system " + (system ? "shown" : "hidden ");
	+ s += ", multithreading " + (multithreading ? "on" : "off ");
	+ s += ", display final " + (displayFinal ? "on " : "off ");
	+ return s;
	+ }
	+
	+ public String toStringPath() {
	+ 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)";
	+ }
	+ }
	+
	private class Updater extends TimerTask {
	@Override
	public void run() {
	update();
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java b/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	index 2454d9f..bbb5e4b 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/FISTA.java
	@@ -1,188 +1,188 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class FISTA extends AbstractAlgorithm implements Callable<RealSignal> {

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

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

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

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

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

	@Override
	public String getName() {
	return "Fast Iterative Shrinkage-Thresholding";
	}

	@Override
	public String[] getShortnames() {
	return new String[] {"FISTA"};
	}

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

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

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

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

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

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

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

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

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

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

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

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

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java b/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	index 1f051ab..0e13a33 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ICTM.java
	@@ -1,153 +1,153 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class ICTM extends AbstractAlgorithm implements Callable<RealSignal> {

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

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

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

	@Override
	public String getName() {
	return "Iterative Contraint Tikhonov-Miller";
	}

	@Override
	public String[] getShortnames() {
	return new String[] {"ICTM"};
	}

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

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

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

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

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

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

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

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

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

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

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java b/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	index e041133..a81998b 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/ISTA.java
	@@ -1,180 +1,180 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class ISTA extends AbstractAlgorithm implements Callable<RealSignal> {

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

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

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

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

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

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

	@Override
	public String getName() {
	return "Iterative Shrinkage-Thresholding";
	}

	@Override
	public String[] getShortnames() {
	return new String[] {"ISTA"};
	}


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

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

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

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

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

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

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

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

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

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

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

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java b/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	index 9592e83..b737e30 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Landweber.java
	@@ -1,147 +1,147 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class Landweber extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

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

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

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

	@Override
	public String[] getShortnames() {
	return new String[] {"LW", "LLS"};
	}

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

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

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

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

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

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

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

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

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	index 1110ba6..90fcda7 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/LandweberPositivity.java
	@@ -1,149 +1,149 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class LandweberPositivity extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

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

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

	@Override
	public String getName() {
	return "Non-Negative Least-Square";
	}

	@Override
	public String[] getShortnames() {
	return new String[] {"NNLS", "LW+"};
	}

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

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

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

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

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

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

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

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

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	index bf806d6..4dcd0e8 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/NonStabilizedDivision.java
	@@ -1,123 +1,123 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class NonStabilizedDivision extends AbstractAlgorithm implements Callable<RealSignal> {

	public NonStabilizedDivision() {
	super();
	}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	index 3d149e8..4a25f4b 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucy.java
	@@ -1,141 +1,141 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class RichardsonLucy extends AbstractAlgorithm implements Callable<RealSignal> {

	public RichardsonLucy(int iter) {
	super();
	- controller.setIterationMax(iter);
	+ this.iterMax = iterMax;
	}

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

	@Override
	public String getName() {
	return "Richardson-Lucy";
	}

	@Override
	public String[] getShortnames() {
	return new String[] {"RL"};
	}

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

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

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

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

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

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

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

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

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

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

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

	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTV.java b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTV.java
	index 479af1c..18e9e25 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTV.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/RichardsonLucyTV.java
	@@ -1,235 +1,235 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class RichardsonLucyTV extends AbstractAlgorithm implements Callable<RealSignal> {

	private double lambda = 0.1;

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

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

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

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

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

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

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

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

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

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

	@Override
	public String getName() {
	return "Richardson-Lucy Total Variation";
	}

	@Override
	public String[] getShortnames() {
	return new String[] {"RLTV"};
	}

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

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

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

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

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

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

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

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

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

	@Override
	public double getStepFactor() {
	return 0.0;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/StarkParker.java b/DeconvolutionLab2/src/deconvolution/algorithm/StarkParker.java
	index 794d5c2..eaa4476 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/StarkParker.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/StarkParker.java
	@@ -1,148 +1,148 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class StarkParker extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

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

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

	@Override
	public String getName() {
	return "Bounded-Variable Least Squares";
	}

	@Override
	public String[] getShortnames() {
	return new String[] {"BVLS", "SP"};
	}

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

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

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

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

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

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

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

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

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMiller.java b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMiller.java
	index 350c3e2..ab67126 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMiller.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/TikhonovMiller.java
	@@ -1,151 +1,151 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class TikhonovMiller extends AbstractAlgorithm implements Callable<RealSignal> {

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

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

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

	return x;
	}

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

	@Override
	public String getName() {
	return "Tikhonov-Miller";
	}

	@Override
	public String[] getShortnames() {
	return new String[] {"TM"};
	}

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

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

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

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

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

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

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

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

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

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/VanCittert.java b/DeconvolutionLab2/src/deconvolution/algorithm/VanCittert.java
	index 11c33fa..7dfccbc 100644
	--- a/DeconvolutionLab2/src/deconvolution/algorithm/VanCittert.java
	+++ b/DeconvolutionLab2/src/deconvolution/algorithm/VanCittert.java
	@@ -1,145 +1,145 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package deconvolution.algorithm;

	import java.util.concurrent.Callable;

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

	public class VanCittert extends AbstractAlgorithm implements Callable<RealSignal> {

	private double gamma = 1.0;

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

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

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

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

	@Override
	public String[] getShortnames() {
	return new String[] {"VC"};
	}

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

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

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

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

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

	@Override
	public void setParameters(double[] params) {
	if (params == null)
	return;
	if (params.length > 0)
	- controller.setIterationMax((int)Math.round(params[0]));
	+ iterMax = (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[] {iterMax, gamma};
	}
	@Override
	public double getRegularizationFactor() {
	return 0.0;
	}

	@Override
	public double getStepFactor() {
	return gamma;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/capsule/AbstractCapsule.java b/DeconvolutionLab2/src/deconvolution/capsule/AbstractCapsule.java
	new file mode 100644
	index 0000000..aab8f59
	--- /dev/null
	+++ b/DeconvolutionLab2/src/deconvolution/capsule/AbstractCapsule.java
	@@ -0,0 +1,117 @@
	+/*
	+ * 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.capsule;
	+
	+import java.util.Timer;
	+import java.util.TimerTask;
	+
	+import javax.swing.JFrame;
	+import javax.swing.JSplitPane;
	+
	+import deconvolution.Deconvolution;
	+import deconvolutionlab.Lab;
	+import deconvolutionlab.monitor.Monitors;
	+
	+public abstract class AbstractCapsule {
	+
	+ protected Deconvolution deconvolution;
	+ protected JSplitPane split;
	+ private AsynchronousTimer signalTimer;
	+ private Timer timer = new Timer();
	+ private int count = 0;
	+ private Monitors monitors;
	+ private String message = "";
	+
	+ public AbstractCapsule(Deconvolution deconvolution) {
	+ this.deconvolution = deconvolution;
	+ this.monitors = deconvolution.getMonitors();
	+ }
	+
	+ public JSplitPane getPane() {
	+ return split;
	+ }
	+
	+ public void show(String name) {
	+ JFrame frame = new JFrame(name);
	+ update();
	+ frame.getContentPane().add(split);
	+ frame.pack();
	+ Lab.setVisible(frame);
	+ }
	+
	+ public abstract void update();
	+
	+ public abstract String getName();
	+
	+ public void stopAsynchronousTimer() {
	+ if (monitors != null)
	+ monitors.progress(message, 100);
	+ if (signalTimer != null) {
	+ signalTimer.cancel();
	+ signalTimer = null;
	+ }
	+ }
	+
	+ public void startAsynchronousTimer(String message, long refreshTime) {
	+ if (signalTimer != null) {
	+ signalTimer.cancel();
	+ signalTimer = null;
	+ }
	+ this.message = message;
	+ signalTimer = new AsynchronousTimer(message);
	+ timer.schedule(signalTimer, 0, refreshTime);
	+ }
	+
	+ public void signal(String message) {
	+ if (monitors != null)
	+ monitors.progress(message, count += 2);
	+ }
	+
	+ private class AsynchronousTimer extends TimerTask {
	+ private String message;
	+
	+ public AsynchronousTimer(String message) {
	+ this.message = message;
	+ }
	+
	+ @Override
	+ public void run() {
	+ signal(message);
	+ }
	+ }
	+
	+ @Override
	+ public void finalize() {
	+ stopAsynchronousTimer();
	+ }
	+
	+}
	diff --git a/DeconvolutionLab2/src/deconvolution/modules/AlgorithmDModule.java b/DeconvolutionLab2/src/deconvolution/capsule/AlgorithmCapsule.java
	similarity index 67%
	rename from DeconvolutionLab2/src/deconvolution/modules/AlgorithmDModule.java
	rename to DeconvolutionLab2/src/deconvolution/capsule/AlgorithmCapsule.java
	index 0415057..60af01a 100644
	--- a/DeconvolutionLab2/src/deconvolution/modules/AlgorithmDModule.java
	+++ b/DeconvolutionLab2/src/deconvolution/capsule/AlgorithmCapsule.java
	@@ -1,153 +1,183 @@
	-package deconvolution.modules;
	+/*
	+ * 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.capsule;

	import javax.swing.JSplitPane;

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

	-public class AlgorithmDModule extends AbstractDModule implements Runnable {
	+/**
	+ * This class is a information module for the algorithm.
	+ *
	+ * @author Daniel Sage
	+ *
	+ */
	+public class AlgorithmCapsule extends AbstractCapsule implements Runnable {

	private CustomizedTable table;
	private HTMLPane doc;

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

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

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

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

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

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

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

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

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

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

	- Controller controller = deconvolution.algo.getController();
	- if (controller == null) {
	- features.add("Controller", "No valid controller");
	- return;
	- }
	-
	startAsynchronousTimer("Run FFT", 200);
	- deconvolution.algo.setController(controller);
	+
	AbstractFFT f = FFT.getFastestFFT().getDefaultFFT();
	double Q = Math.sqrt(2);
	if (deconvolution.image != null) {
	int mx = deconvolution.image.nx;
	int my = deconvolution.image.ny;
	int mz = deconvolution.image.nz;

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

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

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

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

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

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

	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/deconvolution/modules/ImageDModule.java b/DeconvolutionLab2/src/deconvolution/capsule/ImageCapsule.java
	similarity index 51%
	rename from DeconvolutionLab2/src/deconvolution/modules/ImageDModule.java
	rename to DeconvolutionLab2/src/deconvolution/capsule/ImageCapsule.java
	index a1832ee..6091f29 100644
	--- a/DeconvolutionLab2/src/deconvolution/modules/ImageDModule.java
	+++ b/DeconvolutionLab2/src/deconvolution/capsule/ImageCapsule.java
	@@ -1,109 +1,151 @@
	-package deconvolution.modules;
	+/*
	+ * 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.capsule;

	import java.awt.Dimension;

	import javax.swing.JSplitPane;

	import bilib.component.PanelImage;
	import bilib.table.CustomizedTable;
	import bilib.tools.NumFormat;
	import deconvolution.Deconvolution;
	import deconvolution.Features;
	import signal.RealSignal;
	import signal.SignalCollector;
	+import signal.apodization.Apodization;
	+import signal.padding.Padding;

	-public class ImageDModule extends AbstractDModule implements Runnable {
	+/**
	+ * This class is a information module for the image source.
	+ *
	+ * @author Daniel Sage
	+ *
	+ */
	+public class ImageCapsule extends AbstractCapsule implements Runnable {

	private PanelImage pnImage;
	private CustomizedTable table;

	- public ImageDModule(Deconvolution deconvolution) {
	+ public ImageCapsule(Deconvolution deconvolution) {
	super(deconvolution);
	pnImage = new PanelImage();
	table = new CustomizedTable(new String[] { "Features", "Values" }, false);
	pnImage.setPreferredSize(new Dimension(300, 300));
	split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, table.getPane(300, 300), pnImage);
	}

	public void update() {
	split.setDividerLocation(300);
	if (pnImage == null)
	return;
	if (table == null)
	return;

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

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

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

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

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

	- if (deconvolution.pad == null) {
	+ if (deconvolution.getController().getPadding() == null) {
	features.add("Padding", "No valid padding");
	return;
	}

	- if (deconvolution.apo == null) {
	+ if (deconvolution.getController().getApodization() == null) {
	features.add("Apodization", "No valid apodization");
	return;
	}

	startAsynchronousTimer("Preprocessing image", 200);

	float stati[] = deconvolution.image.getStats();
	int sizi = deconvolution.image.nx * deconvolution.image.ny * deconvolution.image.nz;
	float totali = stati[0] * sizi;
	features.add("<html><b>Orignal Image</b></html>", "");
	features.add("Size", deconvolution.image.dimAsString() + " " + NumFormat.bytes(sizi*4));
	features.add("Mean (stdev)", NumFormat.nice(stati[0]) + " (" + NumFormat.nice(stati[3]) + ")");
	- features.add("Min ... Max", NumFormat.nice(stati[1]) + " ... " + NumFormat.nice(stati[2]));
	- features.add("Energy (int)", NumFormat.nice(stati[5]) + " (" + NumFormat.nice(totali) + ")");
	+ features.add("Extrema (min, max)", NumFormat.nice(stati[1]) + ", " + NumFormat.nice(stati[2]));
	+ features.add("Energy (integral)", NumFormat.nice(stati[5]) + " (" + NumFormat.nice(totali) + ")");
	table.removeRows();
	for (String[] feature : features)
	table.append(feature);
	-
	- RealSignal signal = deconvolution.pad.pad(deconvolution.monitors, deconvolution.image);
	- deconvolution.apo.apodize(deconvolution.monitors, signal);
	+ Padding pad = deconvolution.getController().getPadding();
	+ Apodization apo = deconvolution.getController().getApodization();
	+ RealSignal signal = pad.pad(deconvolution.getMonitors(), deconvolution.image);
	+ apo.apodize(deconvolution.getMonitors(), signal);
	float stats[] = signal.getStats();
	int sizs = signal.nx * signal.ny * signal.nz;
	float totals = stats[0] * sizs;

	+ double incpad = (double)((sizs-sizi)/sizi*100.0);
	features.add("<html><b>Working Image</b></html>", "");
	features.add("Size", signal.dimAsString() + " " + NumFormat.bytes(sizs*4));
	features.add("Mean (stdev)", NumFormat.nice(stats[0]) + " (" + NumFormat.nice(stats[3]) + ")");
	- features.add("Min Max", NumFormat.nice(stats[1]) + " " + NumFormat.nice(stats[2]));
	- features.add("Energy (int)", NumFormat.nice(stats[5]) + " (" + NumFormat.nice(totals) + ")");
	+ features.add("Extrema (min, max)", NumFormat.nice(stats[1]) + ", " + NumFormat.nice(stats[2]));
	+ features.add("Energy (integral)", NumFormat.nice(stats[5]) + " (" + NumFormat.nice(totals) + ")");
	+
	features.add("<html><b>Information</b></html>", "");
	- features.add("Size Increase ", NumFormat.nice((double)(sizs-sizi)/sizi*100.0));
	- features.add("Energy Lost", NumFormat.nice((stats[5]-stati[5])/stati[5]*100));
	+ features.add("Size increase (pad.)", NumFormat.nice(incpad) + "%");
	+ features.add("Energy lost (apo.)", NumFormat.nice((stats[5]-stati[5])/stati[5]*100));
	SignalCollector.free(signal);
	table.removeRows();
	for (String[] feature : features)
	table.append(feature);

	pnImage.setImage(deconvolution.image.preview());
	stopAsynchronousTimer();

	}
	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/deconvolution/modules/PSFDModule.java b/DeconvolutionLab2/src/deconvolution/capsule/PSFCapsule.java
	similarity index 53%
	rename from DeconvolutionLab2/src/deconvolution/modules/PSFDModule.java
	rename to DeconvolutionLab2/src/deconvolution/capsule/PSFCapsule.java
	index 1e3d408..0d38cb1 100644
	--- a/DeconvolutionLab2/src/deconvolution/modules/PSFDModule.java
	+++ b/DeconvolutionLab2/src/deconvolution/capsule/PSFCapsule.java
	@@ -1,118 +1,157 @@
	-package deconvolution.modules;
	+/*
	+ * 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.capsule;

	import java.awt.Dimension;

	import javax.swing.JSplitPane;

	import bilib.component.PanelImage;
	import bilib.table.CustomizedTable;
	import bilib.tools.NumFormat;
	import deconvolution.Deconvolution;
	import deconvolution.Features;
	import signal.RealSignal;
	import signal.SignalCollector;

	-public class PSFDModule extends AbstractDModule implements Runnable {
	+/**
	+ * This class is a information module for the PSF source.
	+ *
	+ * @author Daniel Sage
	+ *
	+ */
	+public class PSFCapsule extends AbstractCapsule implements Runnable {

	private PanelImage pnImage;
	private CustomizedTable table;

	- public PSFDModule(Deconvolution deconvolution) {
	+ public PSFCapsule(Deconvolution deconvolution) {
	super(deconvolution);
	pnImage = new PanelImage();
	table = new CustomizedTable(new String[] { "Features", "Values" }, false);
	pnImage.setPreferredSize(new Dimension(300, 300));
	split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, table.getPane(300, 300), pnImage);
	}

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

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

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

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

	- if (deconvolution.image == null) {
	- features.add("Image", "No valid input image");
	- return;
	- }
	-
	- if (deconvolution.pad == null) {
	+ if (deconvolution.getController().getPadding() == null) {
	features.add("Padding", "No valid padding");
	return;
	}

	- if (deconvolution.apo == null) {
	+ if (deconvolution.getController().getApodization() == null) {
	features.add("Apodization", "No valid apodization");
	return;
	}

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

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

	startAsynchronousTimer("Preprocessing PSF", 200);

	float stati[] = deconvolution.psf.getStats();
	int sizi = deconvolution.psf.nx * deconvolution.psf.ny * deconvolution.psf.nz;
	float totali = stati[0] * sizi;
	features.add("<html><b>Orignal PSF</b></html>", "");
	features.add("Size", deconvolution.psf.dimAsString() + " " + NumFormat.bytes(sizi * 4));
	features.add("Mean (stdev)", NumFormat.nice(stati[0]) + " (" + NumFormat.nice(stati[3]) + ")");
	- features.add("Min ... Max", NumFormat.nice(stati[1]) + " ... " + NumFormat.nice(stati[2]));
	- features.add("Energy (int)", NumFormat.nice(stati[5]) + " (" + NumFormat.nice(totali) + ")");
	+ features.add("Extrema (min, max)", NumFormat.nice(stati[1]) + ", " + NumFormat.nice(stati[2]));
	+ features.add("Energy (integral)", NumFormat.nice(stati[5]) + " (" + NumFormat.nice(totali) + ")");
	table.removeRows();
	for (String[] feature : features)
	table.append(feature);

	- RealSignal h = deconvolution.psf.changeSizeAs(deconvolution.image);
	- h.normalize(deconvolution.norm);
	+ RealSignal h;
	+ if (deconvolution.image == null) {
	+ features.add("Image", "No valid input image to resize");
	+ h = deconvolution.psf.duplicate();
	+ }
	+ else
	+ h = deconvolution.psf.changeSizeAs(deconvolution.image);
	+ h.normalize(deconvolution.getController().getNormalizationPSF());
	float stats[] = h.getStats();
	int sizs = h.nx * h.ny * h.nz;
	float totals = stats[0] * sizs;
	+ double incpad = (double)((sizs-sizi)/sizi*100.0);
	features.add("<html><b>Working PSF</b></html>", "");
	features.add("Size", h.dimAsString() + " " + NumFormat.bytes(sizs * 4));
	features.add("Mean (stdev)", NumFormat.nice(stats[0]) + " (" + NumFormat.nice(stats[3]) + ")");
	- features.add("Min Max", NumFormat.nice(stats[1]) + " " + NumFormat.nice(stats[2]));
	- features.add("Energy (int)", NumFormat.nice(stats[5]) + " (" + NumFormat.nice(totals) + ")");
	+ features.add("Extrema (min, max)", NumFormat.nice(stats[1]) + ", " + NumFormat.nice(stats[2]));
	+ features.add("Energy (integral)", NumFormat.nice(stats[5]) + " (" + NumFormat.nice(totals) + ")");
	features.add("<html><b>Information</b></html>", "");
	- features.add("Size Increase ", NumFormat.nice((double) (sizs - sizi) / sizi * 100.0));
	- features.add("Energy Lost", NumFormat.nice((stats[5] - stati[5]) / stati[5] * 100));
	+ features.add("Size increase (image)", NumFormat.nice(incpad) + "%");
	+ features.add("Energy lost", NumFormat.nice((stats[5] - stati[5]) / stati[5] * 100));
	SignalCollector.free(h);
	table.removeRows();
	for (String[] feature : features)
	table.append(feature);

	pnImage.setImage(deconvolution.psf.preview());
	stopAsynchronousTimer();
	}

	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/deconvolution/modules/RecapDModule.java b/DeconvolutionLab2/src/deconvolution/capsule/RecapCapsule.java
	similarity index 50%
	rename from DeconvolutionLab2/src/deconvolution/modules/RecapDModule.java
	rename to DeconvolutionLab2/src/deconvolution/capsule/RecapCapsule.java
	index cb0f5c0..27e247f 100644
	--- a/DeconvolutionLab2/src/deconvolution/modules/RecapDModule.java
	+++ b/DeconvolutionLab2/src/deconvolution/capsule/RecapCapsule.java
	@@ -1,74 +1,111 @@
	-package deconvolution.modules;
	+/*
	+ * 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.capsule;

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

	import javax.swing.JSplitPane;
	import javax.swing.text.BadLocationException;

	import bilib.component.HTMLPane;
	import bilib.table.CustomizedTable;
	import deconvolution.Deconvolution;

	-public class RecapDModule extends AbstractDModule implements KeyListener {
	+/**
	+ * This class is a information module for a recapitulation of the command line.
	+ *
	+ * @author Daniel Sage
	+ *
	+ */
	+public class RecapCapsule extends AbstractCapsule implements KeyListener {

	private HTMLPane pnCommand;
	private CustomizedTable table;

	- public RecapDModule(Deconvolution deconvolution) {
	+ public RecapCapsule(Deconvolution deconvolution) {
	super(deconvolution);
	// Panel command
	pnCommand = new HTMLPane("Monaco", "#10FF10", "100020", 100, 100);
	pnCommand.append("p", deconvolution.getCommand());
	pnCommand.setEditable(true);
	pnCommand.addKeyListener(this);
	table = new CustomizedTable(new String[] { "Features", "Values" }, false);
	split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, table.getPane(200, 200), pnCommand.getPane());
	}

	public void update() {
	if (table == null)
	return;
	table.removeRows();
	for (String[] feature : deconvolution.recap())
	table.append(feature);

	split.setDividerLocation(0.5);
	split.repaint();
	}

	public String getCommand() {
	return pnCommand.getText();
	}

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

	@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 = pnCommand.getDocument().getText(0, len);
	deconvolution.setCommand(command);
	table.removeRows();
	for (String[] feature : deconvolution.recap())
	table.append(feature);
	}
	catch (BadLocationException e1) {
	e1.printStackTrace();
	}
	}



	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/signal/factory/Astigmatism.java b/DeconvolutionLab2/src/deconvolution/capsule/ReportCapsule.java
	similarity index 50%
	copy from DeconvolutionLab2/src/signal/factory/Astigmatism.java
	copy to DeconvolutionLab2/src/deconvolution/capsule/ReportCapsule.java
	index 36017a6..7337fe3 100644
	--- a/DeconvolutionLab2/src/signal/factory/Astigmatism.java
	+++ b/DeconvolutionLab2/src/deconvolution/capsule/ReportCapsule.java
	@@ -1,90 +1,87 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	-package signal.factory;
	+package deconvolution.capsule;

	-import signal.RealSignal;
	+import java.awt.Dimension;

	-public class Astigmatism extends SignalFactory {
	+import javax.swing.JSplitPane;

	- private double fwhm = 3.0;
	- private double factor = 0.20;
	-
	- public Astigmatism(double fwhm, double factor) {
	- super(new double[] {fwhm, factor});
	- }
	-
	- @Override
	- public String getName() {
	- return "Astigmatism";
	- }
	-
	- @Override
	- public String[] getParametersName() {
	- return new String[] {"FWHM at focus plane", "Astigmatism factor"};
	- }
	+import bilib.component.PanelImage;
	+import bilib.table.CustomizedTable;
	+import deconvolution.Deconvolution;
	+import signal.RealSignal;

	- @Override
	- public void setParameters(double[] parameters) {
	- if (parameters.length >= 1)
	- this.fwhm = parameters[0];
	- if (parameters.length >= 2)
	- this.fwhm = parameters[1];
	- }
	+/**
	+ * This class is a information module for report the output.
	+ *
	+ * @author Daniel Sage
	+ *
	+ */
	+public class ReportCapsule extends AbstractCapsule {

	- @Override
	- public double[] getParameters() {
	- return new double[] {fwhm, factor};
	+ private PanelImage pnImage;
	+ private CustomizedTable table;
	+
	+ public ReportCapsule(Deconvolution deconvolution) {
	+ super(deconvolution);
	+ pnImage = new PanelImage();
	+ table = new CustomizedTable(new String[] { "Output", "Values" }, false);
	+ pnImage.setPreferredSize(new Dimension(300, 300));
	+ split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, table.getPane(300, 300), pnImage);
	}

	- @Override
	- public void fill(RealSignal signal) {
	- double A = (amplitude-background);
	- double sigma = 0.8493218 * fwhm; // 1/sqrt(-2*log(0.5))
	- for(int z=0; z<nz; z++) {
	- double dx = (zc-z) * factor + 1;
	- double dy = 1/dx;
	- if (z-zc > 0) {
	- dy = (z-zc) * factor + 1;
	- dx = 1.0 / dy;
	- }
	- double kx = 1.0 / (dx * dx * sigma * sigma * 2.0);
	- double ky = 1.0 / (dy * dy * sigma * sigma * 2.0);
	- for(int x=0; x<nx; x++)
	- for(int y=0; y<ny; y++) {
	- double r2 = kx(x-xc)(x-xc) + ky(y-yc)(y-yc);
	- signal.data[z][x+nxy] = (float)(A Math.exp(-r2) + background);
	- }
	+ public void update() {
	+ split.setDividerLocation(300);
	+ if (pnImage == null)
	+ return;
	+ if (table == null)
	+ return;
	+ table.removeRows();
	+
	+ for (String[] feature : deconvolution.getDeconvolutionReports())
	+ table.append(feature);
	+ RealSignal image = deconvolution.getOutput();
	+ if (image == null) {
	+ table.append(new String[] {"ERROR", "No open output"});
	+ return;
	}
	+ pnImage.setImage(image.preview());
	+ for (String[] feature : deconvolution.checkOutput())
	+ table.append(feature);
	+ split.setDividerLocation(300);
	}

	-
	+ @Override
	+ public String getName() {
	+ return "Report";
	+ }
	}
	diff --git a/DeconvolutionLab2/src/deconvolution/modules/AbstractDModule.java b/DeconvolutionLab2/src/deconvolution/modules/AbstractDModule.java
	deleted file mode 100644
	index 35eb768..0000000
	--- a/DeconvolutionLab2/src/deconvolution/modules/AbstractDModule.java
	+++ /dev/null
	@@ -1,84 +0,0 @@
	-package deconvolution.modules;
	-
	-import java.util.Timer;
	-import java.util.TimerTask;
	-
	-import javax.swing.JFrame;
	-import javax.swing.JSplitPane;
	-
	-import deconvolution.Deconvolution;
	-import deconvolutionlab.Lab;
	-import deconvolutionlab.monitor.Monitors;
	-
	-public abstract class AbstractDModule {
	-
	- protected Deconvolution deconvolution;
	- protected JSplitPane split;
	- private AsynchronousTimer signalTimer;
	- private Timer timer = new Timer();
	- private int count = 0;
	-
	- private Monitors monitors;
	- private String message = "";
	-
	- public AbstractDModule(Deconvolution deconvolution) {
	- this.deconvolution = deconvolution;
	- this.monitors = deconvolution.monitors;
	- }
	-
	- public JSplitPane getPane() {
	- return split;
	- }
	-
	- public void show(String name) {
	- JFrame frame = new JFrame(name);
	- update();
	- frame.getContentPane().add(split);
	- frame.pack();
	- Lab.setVisible(frame);
	- }
	-
	- public abstract void update();
	- public abstract String getName();
	-
	- public void stopAsynchronousTimer() {
	- if (monitors != null)
	- monitors.progress(message, 100);
	- if (signalTimer != null) {
	- signalTimer.cancel();
	- signalTimer = null;
	- }
	- }
	-
	- public void startAsynchronousTimer(String message, long refreshTime) {
	- if (signalTimer != null) {
	- signalTimer.cancel();
	- signalTimer = null;
	- }
	- this.message = message;
	- signalTimer = new AsynchronousTimer(message);
	- timer.schedule(signalTimer, 0, refreshTime);
	- }
	-
	- public void signal(String message) {
	- if (monitors != null)
	- monitors.progress(message, count+=2);
	- }
	-
	- private class AsynchronousTimer extends TimerTask {
	- private String message;
	- public AsynchronousTimer(String message) {
	- this.message = message;
	- }
	- @Override
	- public void run() {
	- signal(message);
	- }
	- }
	-
	- @Override
	- public void finalize() {
	- stopAsynchronousTimer();
	- }
	-
	-}
	diff --git a/DeconvolutionLab2/src/deconvolution/modules/ReportDModule.java b/DeconvolutionLab2/src/deconvolution/modules/ReportDModule.java
	deleted file mode 100644
	index 2a38463..0000000
	--- a/DeconvolutionLab2/src/deconvolution/modules/ReportDModule.java
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-package deconvolution.modules;
	-
	-import java.awt.Dimension;
	-import java.awt.image.BufferedImage;
	-
	-import javax.swing.JSplitPane;
	-
	-import bilib.component.PanelImage;
	-import bilib.table.CustomizedTable;
	-import deconvolution.Deconvolution;
	-import signal.RealSignal;
	-
	-public class ReportDModule extends AbstractDModule {
	-
	- private PanelImage pnImage;
	- private CustomizedTable table;
	-
	- public ReportDModule(Deconvolution deconvolution) {
	- super(deconvolution);
	- pnImage = new PanelImage();
	- table = new CustomizedTable(new String[] { "Output", "Values" }, false);
	- pnImage.setPreferredSize(new Dimension(300, 300));
	- split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, table.getPane(300, 300), pnImage);
	- }
	-
	- public void update() {
	- split.setDividerLocation(300);
	- if (pnImage == null)
	- return;
	- if (table == null)
	- return;
	- table.removeRows();
	-
	- for (String[] feature : deconvolution.getDeconvolutionReports())
	- table.append(feature);
	- RealSignal image = deconvolution.getOutput();
	- if (image == null) {
	- table.append(new String[] {"ERROR", "No open output"});
	- return;
	- }
	- pnImage.setImage(image.preview());
	- for (String[] feature : deconvolution.checkOutput())
	- table.append(feature);
	- split.setDividerLocation(300);
	- }
	-
	- @Override
	- public String getName() {
	- return "Report";
	- }
	-}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/LabPanel.java b/DeconvolutionLab2/src/deconvolutionlab/LabPanel.java
	index 3568db5..6e768b9 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/LabPanel.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/LabPanel.java
	@@ -1,293 +1,297 @@
	/*
	* 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.BorderLayout;
	import java.awt.Dimension;
	import java.awt.GridLayout;
	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.BorderFactory;
	import javax.swing.JButton;
	import javax.swing.JPanel;
	import javax.swing.JTabbedPane;
	import javax.swing.border.Border;
	import javax.swing.event.ChangeEvent;
	import javax.swing.event.ChangeListener;

	import bilib.component.PanelImage;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.dialog.BatchDialog;
	-import deconvolutionlab.modules.AboutModule;
	-import deconvolutionlab.modules.AbstractModule;
	-import deconvolutionlab.modules.AlgorithmModule;
	-import deconvolutionlab.modules.BatchModule;
	-import deconvolutionlab.modules.BorderModule;
	-import deconvolutionlab.modules.CommandModule;
	-import deconvolutionlab.modules.ConfigModule;
	-import deconvolutionlab.modules.ControllerModule;
	-import deconvolutionlab.modules.FFTModule;
	-import deconvolutionlab.modules.GroupedModulePanel;
	-import deconvolutionlab.modules.ImageModule;
	-import deconvolutionlab.modules.LanguageModule;
	-import deconvolutionlab.modules.LicenceModule;
	-import deconvolutionlab.modules.OutputModule;
	-import deconvolutionlab.modules.PSFModule;
	-import deconvolutionlab.modules.RunningModule;
	+import deconvolutionlab.module.AboutModule;
	+import deconvolutionlab.module.AbstractModule;
	+import deconvolutionlab.module.AlgorithmModule;
	+import deconvolutionlab.module.BatchModule;
	+import deconvolutionlab.module.BorderModule;
	+import deconvolutionlab.module.CommandModule;
	+import deconvolutionlab.module.ComputationModule;
	+import deconvolutionlab.module.ConfigModule;
	+import deconvolutionlab.module.ControllerModule;
	+import deconvolutionlab.module.DirectoryModule;
	+import deconvolutionlab.module.GroupedModulePanel;
	+import deconvolutionlab.module.ImageModule;
	+import deconvolutionlab.module.LanguageModule;
	+import deconvolutionlab.module.LicenceModule;
	+import deconvolutionlab.module.OutputModule;
	+import deconvolutionlab.module.PSFModule;
	+import deconvolutionlab.module.RunningModule;
	import deconvolutionlab.system.SystemInfo;

	public class LabPanel extends JPanel implements ActionListener, ChangeListener {

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

	private ImageModule image;
	private PSFModule psf;
	private AlgorithmModule algo;
	private AboutModule about;
	private LicenceModule licence;
	private OutputModule output;
	- private FFTModule fourier;
	+ private ComputationModule computation;
	private BorderModule border;
	private ConfigModule config;
	private BatchModule batch;
	private LanguageModule language;
	private CommandModule command;
	private RunningModule running;
	+ private DirectoryModule directory;

	private ControllerModule controller;

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

	public LabPanel(JButton bnClose) {
	this.bnClose = bnClose;
	image = new ImageModule(false);
	psf = new PSFModule(false);
	algo = new AlgorithmModule(true);
	output = new OutputModule(true);
	- fourier = new FFTModule(false);
	+ computation = new ComputationModule(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();
	running = new RunningModule(false);
	- modules = new AbstractModule[] { image, psf, algo, output, controller, border, fourier, batch, running };
	+ directory = new DirectoryModule(false);
	+
	+ modules = new AbstractModule[] { image, psf, algo, output, controller, border, computation, batch, directory };
	Command.active(modules, command);
	Command.command();

	panelDeconv = new GroupedModulePanel(buildDeconvolutionPanel(), this);
	panelAdvanc = new GroupedModulePanel(buildAdvancedPanel(), this);
	panelScript = new GroupedModulePanel(buildProgrammingPanel(), this);
	panelAbout = new GroupedModulePanel(buildAboutPanel(), this);
	Border border = BorderFactory.createEmptyBorder(5, 5, 5, 5);
	PanelImage bottom = new PanelImage("celegans.jpg");
	bottom.setBorder(border);

	bottom.setLayout(new GridLayout(1, 6));
	bottom.setBorder(border);

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

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

	setLayout(new BorderLayout());
	add(tab, BorderLayout.CENTER);
	add(bottom, BorderLayout.SOUTH);

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

	((GroupedModulePanel) tab.getSelectedComponent()).organize();
	setMinimumSize(new Dimension(500, 500));

	Config.load();
	running.init();
	//sizeModule();
	Command.command();
	running.update();
	image.update();
	psf.update();
	output.update();
	}

	@Override
	public void actionPerformed(ActionEvent e) {

	if (e.getSource() == bnHelp)
	Lab.help();
	else if (e.getSource() == bnClose)
	Config.store();
	else if (e.getSource() == bnSystem)
	SystemInfo.activate();
	else if (e.getSource() == bnBatch) {
	tab.setSelectedIndex(2);
	batch.expand();
	sizeModule();
	BatchDialog dlg = new BatchDialog(batch);
	Lab.setVisible(dlg, true);
	}

	else if (e.getSource() == bnLaunch) {
	String job = language.getJobName() + " " + new SimpleDateFormat("yyyy-MM-dd-HH-mm-ss").format(new Date());
	Deconvolution d = new Deconvolution(job, Command.command(), Deconvolution.Finish.ALIVE);
	d.launch();
	}
	else if (e.getSource() == bnRun) {
	String job = language.getJobName() + " " + new SimpleDateFormat("yyyy-MM-dd-HH-mm-ss").format(new Date());
	Deconvolution d = new Deconvolution(job, Command.command());
	d.deconvolve();
	}
	}

	@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(running);
	+ list.add(directory);
	return list;
	}

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

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

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

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

	Lab.close();
	}

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

	private void sizePanel(GroupedModulePanel panel) {
	Dimension dim = getSize();
	int hpc = 70;
	int npc = hpc * panel.getModules().size();
	Dimension small = new Dimension(dim.width, hpc);
	Dimension large = new Dimension(dim.width, dim.height - npc);
	setMinimumSize(new Dimension(Constants.widthGUI, 4*hpc));
	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/Output.java b/DeconvolutionLab2/src/deconvolutionlab/Output.java
	index 05d9042..eb6a621 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/Output.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/Output.java
	@@ -1,370 +1,368 @@
	/*
	* 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 bilib.tools.NumFormat;
	import deconvolution.algorithm.Controller;
	import deconvolutionlab.Imager.ContainerImage;
	import deconvolutionlab.monitor.Monitors;
	import signal.Constraint;
	import signal.RealSignal;

	public class Output {

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

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

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

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

	- private View view = View.STACK;
	- private Imager.Type type = Imager.Type.FLOAT;
	- private Dynamic dynamic = Dynamic.INTACT;
	+ private View view = View.STACK;
	+ private Imager.Type type = Imager.Type.FLOAT;
	+ private Dynamic dynamic = Dynamic.INTACT;

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

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

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

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

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

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

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

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

	public View getView() {
	return view;
	}

	public String getName() {
	return name;
	}

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

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

	public String[] getAsString() {
	String t = (type == Imager.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, "\u232B" };
	}

	public void executeStarting(Monitors monitors, RealSignal signal, Controller controller) {
	+ if (signal == null)
	+ return;
	execute(monitors, signal, controller, true, false, false, 0);
	}

	public void executeFinal(Monitors monitors, RealSignal signal, Controller controller) {
	+ if (signal == null)
	+ return;
	execute(monitors, signal, controller, false, false, true, 0);
	}

	public void executeIterative(Monitors monitors, RealSignal signal, Controller controller, int iter) {
	- execute(monitors, signal, controller, false, true, false, iter);
	- }
	-
	- public void execute(Monitors monitors, RealSignal signal, Controller controller, boolean start, boolean live, boolean finish, int iter) {
	if (signal == null)
	return;
	+ execute(monitors, signal, controller, false, true, false, iter);
	+ }

	+ private void execute(Monitors monitors, RealSignal signal, Controller controller, boolean start, boolean live, boolean finish, int iter) {
	String title = name;
	if (live)
	if (!is(iter))
	return;

	if (controller != null && live) {
	if (controller.getIterations() > 0) {
	title += "@" + controller.getIterations();
	}
	}
	RealSignal x = null;
	Constraint constraint = new Constraint(monitors);

	switch (dynamic) {
	case RESCALED:
	x = signal.duplicate();
	constraint.rescaled(x, 0, 255);
	break;
	case CLIPPED:
	x = signal.duplicate();
	- float[] stats = controller.getStatsInput();
	+ float[] stats = controller.getStats().getStatsInput();
	if (stats != null)
	constraint.clipped(x, stats[1], stats[2]);
	break;
	case NORMALIZED:
	x = signal.duplicate();
	- float[] stats1 = controller.getStatsInput();
	+ float[] stats1 = controller.getStats().getStatsInput();
	if (stats1 != null)
	constraint.normalized(x, stats1[0], stats1[3]);
	break;
	default:
	x = signal;
	}
	- String filename = path + File.separator + title + ".tif";
	+ String filename = controller.getPath() + File.separator + title + ".tif";

	switch (view) {
	case STACK:
	if (show && !live)
	Lab.show(monitors, x, title, type, (center ? x.nz / 2 : pz));
	if (save && !live)
	Lab.save(monitors, x, filename, type);
	break;
	case SERIES:
	for (int k = 0; k < x.nz; k++) {
	RealSignal slice = x.getSlice(k);
	if (show && !live)
	Lab.show(monitors, slice, title, type);
	if (save && !live)
	Lab.save(monitors, slice, filename, type);
	}
	break;
	case ORTHO:
	if (!start)
	orthoview(monitors, x, title, filename, live);
	break;
	case FIGURE:
	if (!start)
	figure(monitors, x, title, filename, live);
	break;
	case MIP:
	if (!start)
	mip(monitors, x, title, filename, live);
	break;
	case PLANAR:
	if (!start)
	planar(monitors, x, title, filename, live);
	break;
	default:
	break;
	}
	}

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

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

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

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

	@Override
	public String toString() {
	String t = type.name().toLowerCase();
	String v = view.name().toLowerCase();
	String d = dynamic.name().toLowerCase();
	String f = frequency > 0 ? " every " + frequency + " iterations" : "";
	String k = (center ? "" : " keypoint = (" + px + "," + py + "," + pz + ")");
	return v + " " + name + " format = (" + d + ", " + t + ") " + k + f;
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java b/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java
	deleted file mode 100644
	index db2b6d3..0000000
	--- a/DeconvolutionLab2/src/deconvolutionlab/OutputCollection.java
	+++ /dev/null
	@@ -1,83 +0,0 @@
	-/*
	- * DeconvolutionLab2
	- *
	- * Conditions of use: You are free to use this software for research or
	- * educational purposes. In addition, we expect you to include adequate
	- * citations and acknowledgments whenever you present or publish results that
	- * are based on it.
	- *
	- * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	- * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	- * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	- */
	-
	-/*
	- * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	- *
	- * This file is part of DeconvolutionLab2 (DL2).
	- *
	- * DL2 is free software: you can redistribute it and/or modify it under the
	- * terms of the GNU General Public License as published by the Free Software
	- * Foundation, either version 3 of the License, or (at your option) any later
	- * version.
	- *
	- * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	- * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	- *
	- * You should have received a copy of the GNU General Public License along with
	- * DL2. If not, see <http://www.gnu.org/licenses/>.
	- */
	-
	-package deconvolutionlab;
	-
	-import java.util.ArrayList;
	-
	-import deconvolution.algorithm.Controller;
	-import deconvolutionlab.monitor.Monitors;
	-import signal.RealSignal;
	-
	-public class OutputCollection extends ArrayList<Output> {
	-
	- public void setPath(String path) {
	- for (Output out : this)
	- out.setPath(path);
	- }
	-
	- public boolean hasShow(int iterations) {
	- boolean flag = false;
	- for (Output out : this)
	- flag = flag \| out.is(iterations);
	- return flag;
	- }
	-
	- public void executeStarting(Monitors monitors, RealSignal signal, Controller controller) {
	- for (Output out : this)
	- if (out != null)
	- out.executeStarting(monitors, signal, controller);
	- }
	-
	- public void executeFinal(Monitors monitors, RealSignal signal, Controller controller) {
	- for (Output out : this)
	- if (out != null)
	- out.executeFinal(monitors, signal, controller);
	- }
	-
	- public void executeIterative(Monitors monitors, RealSignal signal, Controller controller, int iter) {
	- for (Output out : this)
	- if (out != null)
	- out.executeIterative(monitors, signal, controller, iter);
	- }
	-
	- public ArrayList<String> getInformation() {
	- ArrayList<String> lines = new ArrayList<String>();
	- for (Output out : this) {
	- if (out == null)
	- lines.add("ERR>" + this.size());
	- else
	- lines.add("" + out.toString());
	- }
	- return lines;
	- }
	-
	-}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/TableStats.java b/DeconvolutionLab2/src/deconvolutionlab/TableStats.java
	deleted file mode 100644
	index 028285f..0000000
	--- a/DeconvolutionLab2/src/deconvolutionlab/TableStats.java
	+++ /dev/null
	@@ -1,88 +0,0 @@
	-package deconvolutionlab;
	-
	-import java.awt.BorderLayout;
	-import java.awt.Dimension;
	-import java.io.File;
	-import java.util.ArrayList;
	-
	-import javax.swing.BorderFactory;
	-import javax.swing.JPanel;
	-import javax.swing.JScrollPane;
	-import javax.swing.table.DefaultTableModel;
	-
	-import bilib.table.CustomizedColumn;
	-import bilib.table.CustomizedTable;
	-import deconvolutionlab.monitor.Monitors;
	-
	-public class TableStats {
	-
	- private JPanel panel;
	- private CustomizedTable table;
	- private String name;
	- private boolean save;
	- private String path;
	-
	- public TableStats(String name, int width, int height, String path, boolean save) {
	- this.name = name;
	- this.save = save;
	- this.path = path;
	- ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	- columns.add(new CustomizedColumn("Iterations", String.class, 100, false));
	- columns.add(new CustomizedColumn("Mean", String.class, 100, false));
	- columns.add(new CustomizedColumn("Minimum", String.class, 100, false));
	- columns.add(new CustomizedColumn("Maximum", String.class, 100, false));
	- columns.add(new CustomizedColumn("Stdev", String.class, 100, false));
	- columns.add(new CustomizedColumn("Energy", String.class, 100, false));
	- columns.add(new CustomizedColumn("Time", String.class, 100, false));
	- columns.add(new CustomizedColumn("Memory", String.class, 100, false));
	- columns.add(new CustomizedColumn("Signal", String.class, 100, false));
	- columns.add(new CustomizedColumn("PSNR", String.class, 100, false));
	- columns.add(new CustomizedColumn("SNR", String.class, 100, false));
	- columns.add(new CustomizedColumn("Residu", String.class, 100, false));
	- table = new CustomizedTable(columns, true);
	-
	- JScrollPane scroll = new JScrollPane(table);
	- scroll.setPreferredSize(new Dimension(width, height));
	- JPanel main = new JPanel(new BorderLayout());
	-
	- main.add(scroll, BorderLayout.CENTER);
	- panel = new JPanel(new BorderLayout());
	- panel.add(main);
	- panel.setBorder(BorderFactory.createEtchedBorder());
	- }
	-
	- public String getName() {
	- return name;
	- }
	-
	- public void clear() {
	- DefaultTableModel model = (DefaultTableModel) table.getModel();
	- model.setRowCount(0);
	- }
	-
	- public void nextStats(Monitors monitors, String[] stats) {
	- if (table == null)
	- return;
	- if (stats == null)
	- return;
	- table.append(stats);
	- monitors.log("Stats ");
	- }
	-
	- public void lastStats(Monitors monitors, String[] stats) {
	- if (stats == null)
	- return;
	- if (table == null)
	- return;
	- if (save) {
	- String filename = path + File.separator + name + ".csv";
	- monitors.log("Stats save " + filename);
	- table.saveCSV(filename);
	- }
	- }
	-
	- public JPanel getPanel() {
	- return panel;
	- }
	-
	-}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/dialog/BatchDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/BatchDialog.java
	index f6ffa22..3104f9a 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/BatchDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/BatchDialog.java
	@@ -1,152 +1,152 @@
	/*
	* 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.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 bilib.component.GridPanel;
	import bilib.component.HTMLPane;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Constants;
	-import deconvolutionlab.modules.BatchModule;
	+import deconvolutionlab.module.BatchModule;

	public class BatchDialog extends JDialog implements ActionListener, WindowListener {

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

	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(txt.getText(), Command.command());
	pnCommand = new HTMLPane("Monaco", Constants.widthGUI, 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();
	addWindowListener(this);
	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/SyntheticDialog.java b/DeconvolutionLab2/src/deconvolutionlab/dialog/SyntheticDialog.java
	index 78011ef..6a95ed2 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/dialog/SyntheticDialog.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/dialog/SyntheticDialog.java
	@@ -1,311 +1,336 @@
	/*
	* 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.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 bilib.component.GridPanel;
	import bilib.component.SpinnerRangeDouble;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.Monitors;
	import ij.gui.GUI;
	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 SpinnerRangeDouble spnIntensity = new SpinnerRangeDouble(255, -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 SpinnerRangeDouble spnParameter4 = 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 JLabel lbl4 = new JLabel("Parameters 4 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 pnParams = new GridPanel("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);
	+ pnParams.place(11, 0, lbl4);
	+ pnParams.place(11, 1, spnParameter4);

	- GridPanel pnSize = new GridPanel("Dimension", 3);
	+ GridPanel pnSize = new GridPanel("size", 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);
	+ GridPanel pnIntensity = new GridPanel("intensity", 3);
	+ pnIntensity.place(1, 0, "Signal Intensity");
	+ pnIntensity.place(1, 1, spnIntensity);
	+
	+ 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);
	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(1, 0, 3, 1, pnParams);
	+ pn.place(2, 0, 3, 1, pnSize);
	+ pn.place(3, 0, 3, 1, pnIntensity);
	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());
	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]);
	}
	+ if (labels.length >= 4) {
	+ lbl4.setVisible(true);
	+ lbl4.setText(labels[3]);
	+ }
	+
	double params[] = factory.getParameters();
	spnParameter1.setVisible(false);
	spnParameter2.setVisible(false);
	spnParameter3.setVisible(false);
	+ spnParameter4.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]);
	}
	+ if (params.length >= 4) {
	+ spnParameter4.setVisible(true);
	+ spnParameter4.set(params[3]);
	+ }
	pack();
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	if (e.getSource() == bnShow) {
	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());
	+ factory.intensity(spnIntensity.get());
	+ factory.center(spnCenterX.get(), spnCenterY.get(), spnCenterZ.get());
	+ RealSignal signal = factory.generate(spnWidth.get(), spnHeight.get(), spnSlices.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();
	- command = shape + " " + spnSignal.get() + " " + spnBackground.get() + " ";
	+ command = shape + " ";
	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();
	+ if (n >= 4)
	+ command += " " + spnParameter4.get();
	command += " ";
	}
	- command += " size " + nx + " " + ny + " " + nz + " ";
	+ command += " size " + nx + " " + ny + " " + nz + " intensity " + + spnIntensity.get() + " ";
	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 + " ";
	}
	dispose();
	cancel = false;
	}
	}

	+ /**
	+ * Set the command line parameters to the components of the user interface
	+ *
	+ * @param name String containing the name of shape
	+ * @param parameters String containing all the parameters plus the optional keywords: size, intensity, center
	+ */
	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)
	- spnParameter1.set(params[2]);
	- if (np >= 2 && params.length > 3 + np)
	- spnParameter2.set(params[3]);
	- if (np >= 3 && params.length > 4 + np)
	- spnParameter3.set(params[4]);
	-
	+ double params[] = NumFormat.parseNumbers(parameters);
	+ if (np >= 1 && params.length >= 1)
	+ spnParameter1.set(params[0]);
	+ if (np >= 2 && params.length >= 2)
	+ spnParameter2.set(params[1]);
	+ if (np >= 3 && params.length >= 3)
	+ spnParameter3.set(params[2]);
	+ if (np >= 4 && params.length >= 4)
	+ spnParameter4.set(params[3]);
	+
	+ double size[] = NumFormat.parseNumbersAfter("size", parameters);
	+ if (size.length > 0)
	+ spnWidth.set((int) size[0]);
	+ if (size.length > 1)
	+ spnHeight.set((int) size[1]);
	+ if (size.length > 2)
	+ spnSlices.set((int) size[2]);
	+
	+ double intensity[] = NumFormat.parseNumbersAfter("intensity", parameters);
	+ if (intensity.length > 0)
	+ spnIntensity.set(intensity[0]);
	+
	+ double center[] = NumFormat.parseNumbersAfter("center", parameters);
	+ if (center.length > 0)
	+ spnCenterX.set(center[0]);
	+ if (center.length > 1)
	+ spnCenterY.set(center[1]);
	+ if (center.length > 2)
	+ spnCenterZ.set(center[2]);
	}

	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/module/AboutModule.java
	similarity index 88%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/AboutModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/AboutModule.java
	index 8ce410b..ad2c0f1 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AboutModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/AboutModule.java
	@@ -1,78 +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 deconvolutionlab.modules;
	+package deconvolutionlab.module;

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

	import javax.swing.JPanel;

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

	public class AboutModule extends AbstractModule {

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

	@Override
	public String getCommand() {
	+ setSynopsis("DeconvolutionLab2 " + Constants.version);
	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);
	+ setSynopsis("DeconvolutionLab2 " + Constants.version);
	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/module/AbstractModule.java
	similarity index 92%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/AbstractModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/AbstractModule.java
	index baf3073..a75fa58 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AbstractModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/AbstractModule.java
	@@ -1,233 +1,231 @@
	/*
	* 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;
	+package deconvolutionlab.module;

	import java.awt.BorderLayout;
	import java.awt.CardLayout;
	import java.awt.Dimension;
	import java.awt.Font;
	import java.awt.Insets;
	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();
	+ protected JButton bnTitle = new JButton("");
	+ protected JButton bnSynopsis = new JButton("");
	+ protected JButton bnAction1 = new JButton();
	+ protected JButton bnAction2 = new JButton();
	+ protected JButton bnExpand = new JButton("\u25BA");
	private JLabel lblCommand;
	-
	- private JButton bnExpand;
	- private CardLayout card = new CardLayout();
	- private JPanel space = new JPanel(card);
	- private boolean expanded = false;
	+ protected 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;

	- private int heightButton = 22;
	-
	+ private int heightButton = 22;
	+
	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.setText("<html><b>" + name + "</b></html>");
	bnTitle.setHorizontalAlignment(SwingConstants.LEFT);
	bnTitle.setPreferredSize(new Dimension(150, heightButton));
	bnTitle.setMaximumSize(new Dimension(250, heightButton));
	bnTitle.setMinimumSize(new Dimension(120, heightButton));
	bnTitle.setMargin(new Insets(1, 1, 1, 1));
	bnTitle.addActionListener(this);

	- bnSynopsis = new JButton("");
	bnSynopsis.setHorizontalAlignment(SwingConstants.LEFT);
	bnSynopsis.setPreferredSize(new Dimension(200, heightButton));
	bnSynopsis.setMargin(new Insets(1, 1, 1, 1));
	bnSynopsis.addActionListener(this);

	- bnExpand = new JButton("\u25BA");
	Font font = bnExpand.getFont();
	bnExpand.setFont(new Font(font.getFamily(), font.getStyle(), font.getSize()-3));
	bnExpand.setPreferredSize(new Dimension(40, heightButton));
	bnExpand.setMaximumSize(new Dimension(40, heightButton));
	bnExpand.setMinimumSize(new Dimension(40, heightButton));
	bnExpand.setMargin(new Insets(1, 1, 1, 1));
	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(70, heightButton));
	bnAction1.setMargin(new Insets(1, 1, 1, 1));
	if (toola == null)
	toola = new JPanel(new BorderLayout());
	toola.add(bnAction1, BorderLayout.WEST);
	}
	if (!action2.equals("")) {
	bnAction2.setText(action2);
	bnAction2.setPreferredSize(new Dimension(70, heightButton));
	bnAction2.setMargin(new Insets(1, 1, 1, 1));
	if (toola == null)
	toola = new JPanel(new BorderLayout());
	toola.add(bnAction2, BorderLayout.EAST);
	}

	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, 32));
	panel.add(lblCommand, BorderLayout.NORTH);
	lblCommand.setMinimumSize(new Dimension(500, 36));
	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/module/AlgorithmModule.java
	similarity index 88%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/AlgorithmModule.java
	index 62230dc..70a6d4e 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/AlgorithmModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/AlgorithmModule.java
	@@ -1,155 +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 deconvolutionlab.modules;
	+package deconvolutionlab.module;

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

	public class AlgorithmModule extends AbstractModule implements ActionListener, ChangeListener {

	private JComboBox<String> cmb;
	private HTMLPane doc;
	private JPanel cards;
	-
	+ private JLabel shortname;
	+
	public AlgorithmModule(boolean expanded) {
	super("Algorithm", "-algorithm", "", "Check", expanded);
	ArrayList<AbstractAlgorithmPanel> deconv = Algorithm.getAvailableAlgorithms();
	for (AbstractAlgorithmPanel panel : deconv)
	cmb.addItem(panel.getName());
	cmb.addActionListener(this);
	}

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

	@Override
	public JPanel buildExpandedPanel() {
	+ shortname = new JLabel("-------");
	+ Border bl1 = BorderFactory.createEtchedBorder();
	+ Border bl2 = BorderFactory.createEmptyBorder(0, 10, 0, 10);
	+ shortname.setBorder(BorderFactory.createCompoundBorder(bl1, bl2));
	cmb = new JComboBox<String>();
	JPanel pnc = new JPanel();
	pnc.add(cmb);
	doc = new HTMLPane(100, 1000);
	cards = new JPanel(new CardLayout());
	ArrayList<AbstractAlgorithmPanel> panels = Algorithm.getAvailableAlgorithms();

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

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

	- control.add(cmb);
	+ control.add(top);
	control.add(cards);

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

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

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == cmb) {
	doc.clear();
	String name = (String) cmb.getSelectedItem();
	AbstractAlgorithmPanel algo = Algorithm.getPanel(name);
	doc.append(algo.getDocumentation());
	CardLayout cl = (CardLayout) (cards.getLayout());
	cl.show(cards, name);
	+ String s = "<html><b><p style =\"font-family:georgia\">";
	+ for(int i=0; i<algo.getShortnames().length; i++)
	+ s += (i==0 ? "" : " \| ") + algo.getShortnames()[i] ;
	+ shortname.setText(s + "</b></html>");
	}
	if (e.getSource() == getAction2Button()) {
	Deconvolution deconvolution = new Deconvolution("Check Algorithm", Command.command());
	DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.ALGO, deconvolution, null, null);
	Lab.setVisible(d, false);
	}
	setSynopsis((String) cmb.getSelectedItem());
	setCommand(getCommand());
	Command.command();
	}

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

	@Override
	public void close() {
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/BatchModule.java
	similarity index 99%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/BatchModule.java
	index db5dbd8..47cfaab 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/BatchModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/BatchModule.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 deconvolutionlab.modules;
	+package deconvolutionlab.module;

	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 bilib.table.CustomizedColumn;
	import bilib.table.CustomizedTable;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Constants;

	public class BatchModule extends AbstractModule implements MouseListener, ActionListener {

	private CustomizedTable table;
	private JButton bnRun;
	private JButton bnLaunch;

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

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

	@Override
	public JPanel buildExpandedPanel() {

	bnRun = new JButton("Run Jobs");
	bnLaunch = new JButton("Launch 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, 2));
	pn.setFloatable(false);
	pn.add(bnRun);
	pn.add(bnLaunch);

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

	bnRun.addActionListener(this);
	bnLaunch.addActionListener(this);
	return panel;
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnRun) {
	if (table.getSelectedRows().length == 0)
	table.setColumnSelectionInterval(0, table.getRowCount());
	int rows[] = table.getSelectedRows();
	for (int row : rows)
	new Deconvolution("Batch" + table.getCell(row, 0), table.getCell(row, 1)).deconvolve();
	}
	else if (e.getSource() == bnLaunch) {
	if (table.getSelectedRows().length == 0)
	table.setColumnSelectionInterval(0, table.getRowCount());
	int rows[] = table.getSelectedRows();
	for (int row : rows)
	new Deconvolution("Batch " + table.getCell(row, 0), table.getCell(row, 1)).launch();
	}
	}

	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/module/BorderModule.java
	similarity index 97%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/BorderModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/BorderModule.java
	index eb49308..6d97e0a 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/BorderModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/BorderModule.java
	@@ -1,243 +1,243 @@
	/*
	* 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;
	+package deconvolutionlab.module;

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

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

	import bilib.component.GridPanel;
	import bilib.component.SpinnerRangeInteger;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolutionlab.Config;
	import deconvolutionlab.monitor.Monitors;
	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;

	public class BorderModule extends AbstractModule implements ActionListener, ChangeListener {

	private JComboBox<String> cmbPadXY;
	private JComboBox<String> cmbPadZ;
	private JComboBox<String> cmbApoXY;
	private JComboBox<String> cmbApoZ;
	private SpinnerRangeInteger spnExtensionXY;
	private SpinnerRangeInteger spnExtensionZ;
	private JLabel lblPad;
	private JLabel lblApo;

	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() + " ";
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {
	lblPad = new JLabel("Information on padding size");
	lblPad.setBorder(BorderFactory.createEtchedBorder());
	lblApo = new JLabel("Information on apodization energy");
	lblApo.setBorder(BorderFactory.createEtchedBorder());
	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);

	- GridPanel pnBorder = new GridPanel(false, 3);
	+ GridPanel pnBorder = new GridPanel(false, 2);
	pnBorder.place(0, 1, "Lateral (XY)");
	pnBorder.place(0, 2, "Axial (Z)");
	pnBorder.place(2, 0, "Apodization");
	pnBorder.place(2, 1, cmbApoXY);
	pnBorder.place(2, 2, cmbApoZ);

	pnBorder.place(3, 0, "Padding Extension");
	pnBorder.place(3, 1, spnExtensionXY);
	pnBorder.place(3, 2, spnExtensionZ);

	pnBorder.place(4, 0, "Padding Constraint");
	pnBorder.place(4, 1, cmbPadXY);
	pnBorder.place(4, 2, cmbPadZ);
	pnBorder.place(5, 0, 3, 1, lblPad);
	pnBorder.place(6, 0, 3, 1, lblApo);

	JScrollPane scroll = new JScrollPane(pnBorder);
	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.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");
	spnExtensionXY.addChangeListener(this);
	spnExtensionZ.addChangeListener(this);
	cmbPadXY.addActionListener(this);
	cmbPadZ.addActionListener(this);
	cmbApoXY.addActionListener(this);
	cmbApoZ.addActionListener(this);

	getAction1Button().addActionListener(this);
	getAction2Button().addActionListener(this);
	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) {
	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);
	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);
	Deconvolution d = new Deconvolution("CheckImage", Command.command());
	- Apodization apo = d.getApodization();
	+ Apodization apo = d.getController().getApodization();
	if (apo == null) {
	lblApo.setText("Error in Apodization");
	return;
	}
	- Padding pad = d.getPadding();
	+ Padding pad = d.getController().getPadding();
	if (pad == null) {
	lblPad.setText("Error in Padding");
	return;
	}
	RealSignal x = d.openImage();
	if (x == null) {
	lblPad.setText("Error in input image");
	lblApo.setText("Error in input image");
	return;
	}
	Monitors m = Monitors.createDefaultMonitor();
	RealSignal y = pad.pad(m, x);
	apo.apodize(m, y);
	lblPad.setText(x.dimAsString() + " > " + y.dimAsString());
	lblApo.setText(NumFormat.nice(x.getStats()[5]) + " > " + NumFormat.nice(y.getStats()[5]));
	getAction1Button().setEnabled(true);
	getAction2Button().setEnabled(true);
	}
	});
	thread.setPriority(Thread.MIN_PRIORITY);
	thread.start();
	return;
	}
	update();
	}

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


	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/CommandModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/CommandModule.java
	similarity index 97%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/CommandModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/CommandModule.java
	index 3eb9faf..abc1941 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/CommandModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/CommandModule.java
	@@ -1,92 +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 deconvolutionlab.modules;
	+package deconvolutionlab.module;

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

	import javax.swing.JPanel;

	import bilib.component.HTMLPane;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolution.DeconvolutionDialog;
	import deconvolutionlab.Lab;

	public class CommandModule extends AbstractModule {

	private HTMLPane window;

	public CommandModule() {
	super("Command", "", "", "Check", true);
	}

	public HTMLPane getPane() {
	return window;
	}

	@Override
	public JPanel buildExpandedPanel() {
	window = new HTMLPane("Monaco", 100, 100);
	JPanel panel = new JPanel(new BorderLayout());
	panel.add(window.getPane(), BorderLayout.CENTER);
	getAction2Button().setToolTipText("Human readable of the command line");
	getAction2Button().addActionListener(this);
	return panel;
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == getAction2Button()) {
	Deconvolution deconvolution = new Deconvolution("Check Command", Command.command());
	DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.RECAP, deconvolution, null, null);
	Lab.setVisible(d, false);
	}
	}

	@Override
	public void close() {
	}

	@Override
	public void setCommand(String command) {
	window.clear();
	window.append("p", command);
	}

	@Override
	public String getCommand() {
	- return "";
	+ return window.getText();
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/ComputationModule.java
	similarity index 66%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/ComputationModule.java
	index fb27b6b..0e6ff1b 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/FFTModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/ComputationModule.java
	@@ -1,170 +1,186 @@
	/*
	* 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;
	+package deconvolutionlab.module;

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

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

	import bilib.component.GridPanel;
	import bilib.tools.NumFormat;
	import deconvolution.Command;
	import deconvolution.algorithm.Algorithm;
	import deconvolutionlab.Config;
	import fft.FFT;

	-public class FFTModule extends AbstractModule implements ActionListener, ChangeListener {
	+public class ComputationModule extends AbstractModule implements ActionListener, ChangeListener {

	private JComboBox<String> cmbFFT;
	- private JComboBox<String> cmbType;
	- private JComboBox<String> cmbSep;
	+ private JComboBox<String> cmbMultithreading;
	+ private JComboBox<String> cmbSystem;
	+ private JComboBox<String> cmbDisplayFinal;
	private JComboBox<String> cmbEpsilon;
	private JComboBox<String> cmbNormalization;
	boolean init = false;

	- public FFTModule(boolean expanded) {
	- super("Computation", "", "", "Default", expanded);
	+ public ComputationModule(boolean expanded) {
	+ super("Computation", "", "Default", "", expanded);
	}

	@Override
	public String getCommand() {
	String cmd = "";
	if (cmbNormalization.getSelectedIndex() != 0)
	cmd += " -norm " + NumFormat.parseNumber((String)cmbNormalization.getSelectedItem(), 1);
	- if (cmbFFT.getSelectedIndex() != 0) {
	+ if (cmbSystem.getSelectedIndex() != 0)
	+ cmd += " -system no";
	+ if (cmbMultithreading.getSelectedIndex() != 0)
	+ cmd += " -multithreading no";
	+ if (cmbDisplayFinal.getSelectedIndex() != 0)
	+ cmd += " -display no";
	+ if (cmbFFT.getSelectedIndex() != 0)
	cmd += " -fft " + FFT.getLibraryByName((String) cmbFFT.getSelectedItem()).getLibraryName();
	- }
	if (cmbEpsilon.getSelectedIndex() != 6)
	cmd += " -epsilon " + (String) cmbEpsilon.getSelectedItem();
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {
	cmbFFT = new JComboBox<String>(FFT.getLibrariesAsArray());
	- cmbType = new JComboBox<String>(new String[] { "float" });
	- cmbSep = new JComboBox<String>(new String[] { "XYZ" });
	+ cmbSystem = new JComboBox<String>(new String[] { "yes", "no" });
	+ cmbMultithreading = new JComboBox<String>(new String[] { "yes", "no" });
	+ cmbDisplayFinal = new JComboBox<String>(new String[] { "yes", "no" });
	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");
	cmbNormalization = new JComboBox<String>(new String[] { "1", "10", "1000", "1E+6", "1E+9", "no" });

	cmbNormalization.addActionListener(this);
	cmbNormalization.setSelectedIndex(0);
	cmbNormalization.removeActionListener(this);

	- GridPanel pnNumeric = new GridPanel(false, 3);
	- pnNumeric.place(1, 0, "PSF Normalization");
	+ GridPanel pnNumeric = new GridPanel(false, 2);
	+ pnNumeric.place(1, 0, "norm");
	pnNumeric.place(1, 1, cmbNormalization);
	- pnNumeric.place(1, 2, "1, recommended");
	- pnNumeric.place(3, 0, new JLabel("FFT Library"));
	+ pnNumeric.place(1, 2, "PSF normalization (def:1)");
	+ pnNumeric.place(3, 0, new JLabel("fft"));
	pnNumeric.place(3, 1, cmbFFT);
	- pnNumeric.place(3, 2, new JLabel("Fourier"));
	- pnNumeric.place(6, 0, new JLabel("FFT Processing"));
	- pnNumeric.place(6, 1, cmbSep);
	- pnNumeric.place(6, 2, new JLabel("Dimension Ordering"));
	+ pnNumeric.place(3, 2, new JLabel("FFT library (Fourier)"));
	+ pnNumeric.place(6, 0, new JLabel("system"));
	+ pnNumeric.place(6, 1, cmbSystem);
	+ pnNumeric.place(6, 2, new JLabel("Show the system panel"));

	- pnNumeric.place(7, 0, new JLabel("Machine Epsilon"));
	- pnNumeric.place(7, 1, cmbEpsilon);
	- pnNumeric.place(7, 2, new JLabel("<html>ε</html>"));
	-
	- pnNumeric.place(8, 0, new JLabel("Data Type"));
	- pnNumeric.place(8, 1, cmbType);
	- pnNumeric.place(8, 2, new JLabel("(Only float)"));
	+ pnNumeric.place(7, 0, new JLabel("display"));
	+ pnNumeric.place(7, 1, cmbDisplayFinal);
	+ pnNumeric.place(7, 2, new JLabel("Display the final output"));
	+
	+ pnNumeric.place(8, 0, new JLabel("multithreading"));
	+ pnNumeric.place(8, 1, cmbMultithreading);
	+ pnNumeric.place(8, 2, new JLabel("Activate multithreading"));
	+
	+ pnNumeric.place(9, 0, new JLabel("epsilon"));
	+ pnNumeric.place(9, 1, cmbEpsilon);
	+ pnNumeric.place(9, 2, new JLabel("<html>Machine Epsilon ε</html>"));

	JScrollPane scroll = new JScrollPane(pnNumeric);
	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.CENTER);

	Config.register(getName(), "normalization", cmbNormalization, cmbNormalization.getItemAt(0));
	Config.register(getName(), "fft", cmbFFT, Algorithm.getDefaultAlgorithm());
	- Config.register(getName(), "dim", cmbSep, "XYZ");
	+ Config.register(getName(), "system", cmbSystem, cmbSystem.getItemAt(0));
	+ Config.register(getName(), "display", cmbDisplayFinal, cmbDisplayFinal.getItemAt(0));
	+ Config.register(getName(), "multithreading", cmbMultithreading, cmbMultithreading.getItemAt(0));
	Config.register(getName(), "epsilon", cmbEpsilon, "1E-6");

	cmbFFT.addActionListener(this);
	- cmbType.addActionListener(this);
	- cmbSep.addActionListener(this);
	+ cmbSystem.addActionListener(this);
	+ cmbDisplayFinal.addActionListener(this);
	+ cmbMultithreading.addActionListener(this);
	cmbEpsilon.addActionListener(this);
	cmbNormalization.addActionListener(this);
	getAction1Button().addActionListener(this);
	init = true;
	return panel;
	}

	private void update() {
	setCommand(getCommand());
	if (init)
	setSynopsis("Norm " + cmbNormalization.getSelectedItem() + " " + FFT.getLibraryByName((String) cmbFFT.getSelectedItem()).getLibraryName());
	Command.command();
	}

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

	@Override
	public void actionPerformed(ActionEvent e) {
	-System.out.println("" + e);
	super.actionPerformed(e);
	+System.out.println("" + e);
	if (e.getSource() == getAction1Button()) {
	cmbFFT.setSelectedIndex(0);
	- cmbSep.setSelectedIndex(0);
	- cmbType.setSelectedIndex(0);
	+ cmbMultithreading.setSelectedIndex(0);
	+ cmbDisplayFinal.setSelectedIndex(0);
	+ cmbSystem.setSelectedIndex(0);
	cmbEpsilon.setSelectedIndex(0);
	cmbNormalization.setSelectedIndex(0);
	}
	update();
	}

	@Override
	public void close() {
	getAction1Button().removeActionListener(this);
	cmbFFT.removeActionListener(this);
	- cmbSep.removeActionListener(this);
	- cmbType.removeActionListener(this);
	+ cmbMultithreading.removeActionListener(this);
	+ cmbDisplayFinal.removeActionListener(this);
	+ cmbSystem.removeActionListener(this);
	cmbEpsilon.removeActionListener(this);
	cmbNormalization.removeActionListener(this);
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/ConfigModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/ConfigModule.java
	similarity index 96%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/ConfigModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/ConfigModule.java
	index 483370d..64a71fe 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/ConfigModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/ConfigModule.java
	@@ -1,124 +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 deconvolutionlab.modules;
	+package deconvolutionlab.module;

	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 bilib.table.CustomizedColumn;
	import bilib.table.CustomizedTable;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	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() {
	+ setSynopsis(new File(Config.getFilename()).getName());
	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);
	+ setSynopsis(new File(Config.getFilename()).getName());
	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/module/ControllerModule.java
	similarity index 70%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/ControllerModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/ControllerModule.java
	index 74716db..e66b396 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/ControllerModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/ControllerModule.java
	@@ -1,244 +1,266 @@
	/*
	* 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;
	+package deconvolutionlab.module;

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

	import bilib.component.GridPanel;
	import bilib.tools.Files;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	import signal.Constraint;

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

	private JButton bnBrowse;

	private JTextField txtReference;
	private JTextField txtResidu;
	private JTextField txtTime;
	private JTextField txtIterations;

	private JComboBox<String> cmbConstraint;
	+ private JComboBox<String> cmbStats;
	+ private JComboBox<String> cmbMonitor;
	+ private JComboBox<String> cmbVerbose;

	private JCheckBox chkResidu;
	private JCheckBox chkReference;
	- private JCheckBox chkConstraint;
	private JCheckBox chkTime;
	- private JCheckBox chkItermax;

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

	@Override
	public String getCommand() {
	String cmd = "";
	- if (chkConstraint.isSelected())
	+ if (cmbMonitor.getSelectedIndex() != 0)
	+ cmd += "-monitor " + cmbMonitor.getSelectedItem() + " ";
	+ if (cmbVerbose.getSelectedIndex() != 0)
	+ cmd += "-verbose " + cmbVerbose.getSelectedItem() + " ";
	+ if (cmbStats.getSelectedIndex() != 0)
	+ cmd += "-stats " + cmbStats.getSelectedItem() + " ";
	+ if (cmbConstraint.getSelectedIndex() != 0)
	cmd += "-constraint " + cmbConstraint.getSelectedItem() + " ";
	if (chkReference.isSelected())
	cmd += "-reference " + txtReference.getText() + " ";
	if (chkResidu.isSelected())
	cmd += "-residu " + txtResidu.getText() + " ";
	if (chkTime.isSelected())
	cmd += "-time " + txtTime.getText() + " ";
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {

	- chkTime = new JCheckBox("Time Limitation (s)");
	- chkItermax = new JCheckBox("Early Stopping");
	- chkConstraint = new JCheckBox("Constraint");
	- chkResidu = new JCheckBox("Residu Minimun");
	- chkReference = new JCheckBox("Reference");
	+ chkTime = new JCheckBox("");
	+ chkResidu = new JCheckBox("");
	+ chkReference = new JCheckBox("");

	bnBrowse = new JButton("Browse");
	txtReference = new JTextField("");
	txtResidu = new JTextField("0.01");
	txtTime = new JTextField("3600");
	txtIterations = new JTextField("Iteration max (mandatory)");
	txtIterations.setEditable(false);

	+ cmbMonitor = new JComboBox<String>(new String[] {"console table", "console", "table", "no" });
	+ cmbVerbose = new JComboBox<String>(new String[] {"log", "quiet", "mute", "prolix" });
	cmbConstraint = new JComboBox<String>(Constraint.getContraintsAsArray());
	+ cmbStats = new JComboBox<String>(new String[] {"no", "show", "show + save", "save"});
	txtReference.setPreferredSize(new Dimension(200, 20));

	- GridPanel pn = new GridPanel(true);
	-
	- pn.place(0, 0, chkItermax);
	- pn.place(0, 1, txtIterations);
	- pn.place(1, 0, chkResidu);
	- pn.place(1, 1, txtResidu);
	- pn.place(4, 0, chkConstraint);
	- pn.place(4, 1, cmbConstraint);
	- pn.place(5, 0, chkTime);
	- pn.place(5, 1, txtTime);
	- pn.place(7, 0, chkReference);
	- pn.place(7, 1, txtReference);
	- pn.place(8, 0, "Ground-truth file");
	- pn.place(8, 1, bnBrowse);
	+ GridPanel pn = new GridPanel(true, 2);
	+
	+ pn.place(0, 0, "monitor");
	+ pn.place(0, 2, cmbMonitor);
	+ pn.place(0, 3, "Monitoring message");
	+
	+ pn.place(1, 0, "verbose");
	+ pn.place(1, 2, cmbVerbose);
	+ pn.place(1, 3, "");
	+
	+ pn.place(3, 0, "stats");
	+ pn.place(3, 2, cmbStats);
	+ pn.place(3, 3, "Signal's statistics");
	+
	+ pn.place(4, 0, "constraint");
	+ pn.place(4, 2, cmbConstraint);
	+ pn.place(4, 3, "Additional constraint");
	+
	+ pn.place(5, 0, "residu");
	+ pn.place(5, 1, chkResidu);
	+ pn.place(5, 2, txtResidu);
	+ pn.place(5, 3, "Additional stopping criteria");
	+
	+ pn.place(6, 0, "time");
	+ pn.place(6, 1, chkTime);
	+ pn.place(6, 2, txtTime);
	+ pn.place(6, 3, "Additional stopping criteria");
	+
	+ pn.place(7, 0, "reference");
	+ pn.place(7, 1, chkReference);
	+ pn.place(7, 2, 2, 1, txtReference);
	+ pn.place(8, 2, bnBrowse);
	+ pn.place(8, 3, 1, 1, "Ground-truth file");

	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.CENTER);

	Config.register(getName(), "residu.enable", chkResidu, false);
	Config.register(getName(), "reference.enable", chkReference, false);
	- Config.register(getName(), "constraint.enable", chkConstraint, false);
	Config.register(getName(), "time.enable", chkTime, false);
	- Config.register(getName(), "itmax.enable", chkItermax, true);

	Config.register(getName(), "reference.value", txtReference, "");
	Config.register(getName(), "residu.value", txtResidu, "0.01");
	Config.register(getName(), "time.value", txtTime, "3600");
	- Config.register(getName(), "constraint.value", cmbConstraint, "No");
	+ Config.register(getName(), "constraint", cmbConstraint, cmbConstraint.getItemAt(0));
	+ Config.register(getName(), "stats", cmbStats, cmbStats.getItemAt(0));
	+ Config.register(getName(), "monitor", cmbMonitor, cmbMonitor.getItemAt(0));
	+ Config.register(getName(), "verbose", cmbVerbose, cmbVerbose.getItemAt(0));

	- chkItermax.setSelected(true);
	-
	bnBrowse.addActionListener(this);
	chkResidu.addChangeListener(this);
	chkReference.addChangeListener(this);
	- chkConstraint.addChangeListener(this);
	chkTime.addChangeListener(this);
	- chkItermax.addChangeListener(this);

	txtResidu.addKeyListener(this);
	txtReference.addKeyListener(this);
	txtTime.addKeyListener(this);
	cmbConstraint.addActionListener(this);
	+ cmbMonitor.addActionListener(this);
	+ cmbVerbose.addActionListener(this);
	getAction1Button().addActionListener(this);

	return panel;
	}

	private void update() {
	- chkItermax.setSelected(true);
	+
	setCommand(getCommand());
	int count = 0;
	count += (chkResidu.isSelected() ? 1 : 0);
	- count += (chkConstraint.isSelected() ? 1 : 0);
	count += (chkTime.isSelected() ? 1 : 0);
	- count += (chkItermax.isSelected() ? 1 : 0);
	- setSynopsis("" + count + " stopping criteria");
	+ count += (chkReference.isSelected() ? 1 : 0);
	+ setSynopsis("" + count + " controls");
	+
	Command.command();
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnBrowse) {
	File file = Files.browseFile(Command.getPath());
	if (file != null)
	txtReference.setText(file.getAbsolutePath());
	}
	if (e.getSource() == getAction1Button()) {
	chkResidu.removeChangeListener(this);
	chkReference.removeChangeListener(this);
	- chkConstraint.removeChangeListener(this);
	chkTime.removeChangeListener(this);
	- chkItermax.removeChangeListener(this);

	chkResidu.setSelected(false);
	chkReference.setSelected(false);
	- chkConstraint.setSelected(false);
	chkTime.setSelected(false);
	- chkItermax.setSelected(true);

	txtReference.setText("");
	txtResidu.setText("0.01");
	txtTime.setText("3600");
	cmbConstraint.setSelectedIndex(0);
	-
	+ cmbStats.setSelectedIndex(0);
	+ cmbMonitor.setSelectedIndex(0);
	+ cmbVerbose.setSelectedIndex(0);

	chkResidu.addChangeListener(this);
	chkReference.addChangeListener(this);
	- chkConstraint.addChangeListener(this);
	chkTime.addChangeListener(this);
	- chkItermax.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);
	- chkItermax.removeChangeListener(this);
	+ cmbVerbose.removeActionListener(this);
	+ cmbMonitor.removeActionListener(this);
	+ cmbConstraint.removeActionListener(this);
	chkTime.removeChangeListener(this);
	getAction1Button().removeChangeListener(this);
	}


	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/WatcherModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/DirectoryModule.java
	similarity index 61%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/WatcherModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/DirectoryModule.java
	index 0f5168e..3ab5d1a 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/WatcherModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/DirectoryModule.java
	@@ -1,186 +1,207 @@
	/*
	* 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;
	-
	+package deconvolutionlab.module;
	+
	+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.KeyEvent;
	import java.awt.event.KeyListener;
	import java.io.File;
	+import java.io.IOException;
	+import java.util.List;

	import javax.swing.BoxLayout;
	import javax.swing.JButton;
	import javax.swing.JComboBox;
	import javax.swing.JPanel;
	import javax.swing.JTextField;

	import bilib.component.GridPanel;
	import bilib.tools.Files;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	+import deconvolutionlab.module.ImageModule.LocalDropTarget;

	-public class WatcherModule extends AbstractModule implements ActionListener, KeyListener {
	+public class DirectoryModule extends AbstractModule implements ActionListener, KeyListener {

	- private JComboBox<String> cmbVerbose;
	- private JComboBox<String> cmbMonitor;
	- private JComboBox<String> cmbDisplay;
	- private JComboBox<String> cmbMultithreading;
	private JComboBox<String> cmbPath;
	private JTextField txtPath;
	private JButton bnBrowse;

	- public WatcherModule(boolean expanded) {
	- super("Path & Watcher", "", "Default", "", expanded);
	+ public DirectoryModule(boolean expanded) {
	+ super("Path", "", "Default", "", expanded);
	}

	@Override
	public String getCommand() {
	String cmd = "";
	if (cmbPath.getSelectedIndex() != 0)
	cmd += " -path " + txtPath.getText();
	- if (cmbMultithreading.getSelectedIndex() != 0)
	- cmd += " -" + (String)cmbMultithreading.getSelectedItem();
	- if (cmbDisplay.getSelectedIndex() != 0)
	- cmd += " -" + (String)cmbDisplay.getSelectedItem();
	- if (cmbMonitor.getSelectedIndex() != 0)
	- cmd += " -" + (String)cmbMonitor.getSelectedItem();
	- if (cmbVerbose.getSelectedIndex() != 0)
	- cmd += " -" + (String)cmbVerbose.getSelectedItem();
	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {

	- cmbVerbose = new JComboBox<String>(new String[] { "verbose log ", "verbose quiet ", "verbose prolix", "verbose mute" });
	- cmbDisplay = new JComboBox<String>(new String[] { "display final", "display no"});
	- cmbMonitor = new JComboBox<String>(new String[] { "monitor full", "monitor console", "monitor none"});
	- cmbMultithreading = new JComboBox<String>(new String[] { "multithreading enabled", "multithreading disabled"});
	cmbPath = new JComboBox<String>(new String[] { "Current", "Specify"});
	- txtPath = new JTextField("", 30);
	+ txtPath = new JTextField("", 35);
	bnBrowse = new JButton("Browse");

	GridPanel pn1 = new GridPanel(true, 3);
	- pn1.place(0, 0, 2, 1, "Working directory");
	+ pn1.place(0, 0, 3, 1, "Working directory");
	pn1.place(1, 0, cmbPath);
	pn1.place(1, 1, bnBrowse);
	- pn1.place(2, 0, 2, 1, txtPath);
	+ pn1.place(2, 0, 3, 1, txtPath);

	- GridPanel pn2 = new GridPanel(true, 3);
	- pn2.place(2, 0, cmbVerbose);
	- pn2.place(2, 1, cmbMonitor);
	- pn2.place(3, 0, cmbDisplay);
	- pn2.place(3, 1, cmbMultithreading);
	-
	JPanel panel = new JPanel();
	panel.setLayout(new BoxLayout(panel, BoxLayout.PAGE_AXIS));
	panel.add(pn1);
	- panel.add(pn2);
	String dir = System.getProperty("user.dir");
	-
	- Config.register(getName(), "verbose", cmbVerbose, cmbVerbose.getItemAt(0));
	- Config.register(getName(), "monitor", cmbMonitor, cmbMonitor.getItemAt(0));
	- Config.register(getName(), "display", cmbDisplay, cmbDisplay.getItemAt(0));
	- Config.register(getName(), "multithreading", cmbMultithreading, cmbMultithreading.getItemAt(0));
	Config.register(getName(), "current", cmbPath, cmbPath.getItemAt(0));
	Config.register(getName(), "path", txtPath, dir);
	-
	+
	+ // Add drop area
	+ pn1.setDropTarget(new LocalDropTarget());
	+ txtPath.setDropTarget(new LocalDropTarget());
	+ getCollapsedPanel().setDropTarget(new LocalDropTarget());
	+ bnTitle.setDropTarget(new LocalDropTarget());
	+ bnSynopsis.setDropTarget(new LocalDropTarget());
	+ bnExpand.setDropTarget(new LocalDropTarget());
	+
	cmbPath.addActionListener(this);
	txtPath.addKeyListener(this);
	- cmbVerbose.addActionListener(this);
	- cmbDisplay.addActionListener(this);
	- cmbMultithreading.addActionListener(this);
	- cmbMonitor.addActionListener(this);
	bnBrowse.addActionListener(this);
	+ getAction1Button().addActionListener(this);
	return panel;
	}

	private void update() {
	-
	setCommand(getCommand());
	if (cmbPath.getSelectedIndex() == 0) {
	txtPath.setText(System.getProperty("user.dir"));
	txtPath.setEnabled(false);
	bnBrowse.setEnabled(false);
	}
	else {
	txtPath.setEnabled(true);
	bnBrowse.setEnabled(true);
	}
	- setSynopsis(txtPath.getText());
	+ setSynopsis(new File(txtPath.getText()).getName());
	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());
	}
	}
	else if (e.getSource() == cmbPath) {
	if (cmbPath.getSelectedIndex() == 0) {
	File f = new File(System.getProperty("user.dir"));
	txtPath.setText(f.getAbsolutePath());
	}
	}
	+ else if (e.getSource() == getAction1Button()) {
	+ txtPath.setText(System.getProperty("user.dir"));
	+ txtPath.setEnabled(false);
	+ bnBrowse.setEnabled(false);
	+ }
	update();
	}

	@Override
	public void close() {
	- cmbVerbose.removeActionListener(this);
	- cmbDisplay.removeActionListener(this);
	- cmbMultithreading.removeActionListener(this);
	- cmbMonitor.removeActionListener(this);
	cmbPath.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();
	}

	+ 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) {
	+ cmbPath.setSelectedIndex(1);
	+ bnBrowse.setEnabled(true);
	+ txtPath.setEnabled(true);
	+ if (file.isDirectory())
	+ txtPath.setText(file.getAbsolutePath());
	+ else
	+ txtPath.setText(file.getParent());
	+ update();
	+ }
	+ }
	+ catch (UnsupportedFlavorException ex) {
	+ ex.printStackTrace();
	+ }
	+ catch (IOException ex) {
	+ ex.printStackTrace();
	+ }
	+ }
	+ }
	+ e.dropComplete(true);
	+ super.drop(e);
	+ }
	+ }
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/GroupedModulePanel.java b/DeconvolutionLab2/src/deconvolutionlab/module/GroupedModulePanel.java
	similarity index 98%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/GroupedModulePanel.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/GroupedModulePanel.java
	index 8fec2b5..c483500 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/GroupedModulePanel.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/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;
	+package deconvolutionlab.module;

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

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

	import deconvolutionlab.LabPanel;

	public class GroupedModulePanel extends JPanel {
	private ArrayList<AbstractModule> modules;
	private LabPanel parent;
	private Dimension min;

	public GroupedModulePanel(ArrayList<AbstractModule> modules, LabPanel 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/module/ImageModule.java
	similarity index 92%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/ImageModule.java
	index 1e9e5b0..0e11e00 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/ImageModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/ImageModule.java
	@@ -1,353 +1,362 @@
	/*
	* 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;
	+package deconvolutionlab.module;

	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 bilib.table.CustomizedColumn;
	import bilib.table.CustomizedTable;
	import bilib.tools.Files;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolution.DeconvolutionDialog;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Imager;
	import deconvolutionlab.Lab;
	import deconvolutionlab.dialog.PatternDialog;
	import deconvolutionlab.dialog.SyntheticDialog;
	import deconvolutionlab.monitor.Monitors;
	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", (Lab.getPlatform() == Imager.Platform.IMAGEJ ? "Active" : ""), "Check", 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, 4));
	pn.setFloatable(false);
	pn.add(bnFile);
	pn.add(bnDirectory);
	pn.add(bnSynthetic);
	if (Lab.getPlatform() == Imager.Platform.IMAGEJ)
	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);

	+ // Add drop area
	table.setDropTarget(new LocalDropTarget());
	getCollapsedPanel().setDropTarget(new LocalDropTarget());
	-
	+ bnTitle.setDropTarget(new LocalDropTarget());
	+ bnSynopsis.setDropTarget(new LocalDropTarget());
	+ bnExpand.setDropTarget(new LocalDropTarget());
	+
	bnFile.addActionListener(this);
	bnDirectory.addActionListener(this);
	bnSynthetic.addActionListener(this);
	bnPlatform.addActionListener(this);
	getAction1Button().addActionListener(this);
	getAction2Button().addActionListener(this);

	+ bnFile.setToolTipText("Add a new source read from a single file (3D z-stack)");
	+ bnDirectory.setToolTipText("Add a new source read from the 2D images from a directory");
	+ bnSynthetic.setToolTipText("Add a new source artificially created");
	+ bnPlatform.setToolTipText("Add a new source from a list of images of the platform");
	getAction2Button().setToolTipText("Click to have a preview, Shift-click or Ctrl-click to show the complete stack");
	- getAction1Button().setToolTipText("Select the active window");
	+ getAction1Button().setToolTipText("Select the active window from the running platform");

	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 {
	setSynopsis("");
	setCommand("Drag your image file, here");
	}
	getAction2Button().setEnabled(table.getRowCount() > 0);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnFile)
	file(Command.getPath());
	else if (e.getSource() == bnDirectory)
	dir(Command.getPath());
	else if (e.getSource() == bnSynthetic)
	synthetic(false);
	else if (e.getSource() == bnPlatform)
	platform();
	else if (e.getSource() == getAction1Button()) {
	int row = -1;
	for(int i=0; i<table.getRowCount(); i++) {
	if (table.getCell(i, 0).equalsIgnoreCase("active"))
	if (table.getCell(i, 1).equalsIgnoreCase("platform"))
	if (table.getCell(i, 2).equalsIgnoreCase("active"))
	row = i;
	}
	if (row < 0)
	table.insert(new String[] { "active", "platform", "active", "\u232B" });
	else
	table.setRowSelectionInterval(row, row);
	}
	else if (e.getSource() == getAction2Button()) {
	boolean s = (e.getModifiers() & ActionEvent.SHIFT_MASK) == ActionEvent.SHIFT_MASK;
	boolean c = (e.getModifiers() & ActionEvent.CTRL_MASK) == ActionEvent.CTRL_MASK;
	display(s \| c);
	}
	-
	update();
	}

	public void platform() {
	String name = Lab.getActiveImage();
	if (name != "")
	table.insert(new String[] { name, "platform", name, "\u232B" });
	}

	private void file(String path) {
	File file = Files.browseFile(path);
	if (file == null)
	return;
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "\u232B" });
	}

	private void dir(String path) {
	File file = Files.browseDirectory(path);
	if (file == null)
	return;
	PatternDialog dlg = new PatternDialog(file);
	Lab.setVisible(dlg, true);

	if (dlg.wasCancel())
	return;
	table.insert(new String[] { dlg.getDirName(), "directory", dlg.getCommand(), "\u232B" });
	}

	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.setParameters(table.getCell(row, 0), table.getCell(row, 2));
	}
	}
	Lab.setVisible(dlg, 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(), "\u232B" });
	}

	private void edit() {
	int row = table.getSelectedRow();
	-
	if (row < 0)
	return;
	String name = table.getCell(row, 0).trim();
	for (SignalFactory factory : SignalFactory.getAll()) {
	- if (name.equals(factory.getName().trim()))
	+ System.out.println(">>edit>> " + name + " == " + factory.getName().trim());
	+
	+ if (name.equals(factory.getName().trim())) {
	synthetic(true);
	- return;
	+ return;
	+ }
	}
	String filename = table.getCell(row, 1).trim();
	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(boolean stack) {
	int row = table.getSelectedRow();
	if (row < 0)
	return;
	Deconvolution deconvolution = new Deconvolution("Check Image", Command.command());
	deconvolution.openImage();
	if (stack) {
	RealSignal x = deconvolution.getImage();
	if (x != null)
	Lab.show(Monitors.createDefaultMonitor(), x, table.getCell(row, 0));
	}
	else {
	DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.IMAGE, deconvolution, null, null);
	Lab.setVisible(d, false);
	}
	}
	-
	+
	@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.insert(new String[] { file.getName(), "directory", file.getAbsolutePath(), "\u232B" });
	table.setRowSelectionInterval(0, 0);
	update();
	}
	if (file.isFile()) {
	- table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	+ table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "\u232B" });
	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/module/LanguageModule.java
	similarity index 99%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/LanguageModule.java
	index b6eca9e..5227327 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/LanguageModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/LanguageModule.java
	@@ -1,251 +1,251 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	-package deconvolutionlab.modules;
	+package deconvolutionlab.module;

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

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

	import bilib.component.HTMLPane;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolution.Token;
	import deconvolution.algorithm.AbstractAlgorithm;
	import deconvolutionlab.Config;

	public class LanguageModule extends AbstractModule implements ActionListener {

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

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

	public String getJobName() {
	if (txt != null)
	return txt.getText();
	return "";
	}
	@Override
	public JPanel buildExpandedPanel() {
	language = new HTMLPane("Monaco", 100, 100);
	cmb = new JComboBox<String>(new String[] { "Command line", "ImageJ Macro", "Java", "Matlab" });
	gui = new JComboBox<String>(new String[] { "Run (Headless)", "Launch (with control panel)" });
	txt = new JTextField("Job", 8);
	JPanel pn = new JPanel(new BorderLayout());
	pn.add(cmb, BorderLayout.WEST);
	pn.add(txt, BorderLayout.CENTER);
	pn.add(gui, BorderLayout.EAST);

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

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

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

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

	@Override
	public void close() {
	}

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

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

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

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

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


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

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

	return option + cmd;
	}


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

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

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

	code += p1("");

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

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

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

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

	private String p2(String content) {
	return "<p style=\"padding-left:20px\">" + content + "</p>";
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/LicenceModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/LicenceModule.java
	similarity index 90%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/LicenceModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/LicenceModule.java
	index 1052d7f..122e3c7 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/LicenceModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/LicenceModule.java
	@@ -1,88 +1,81 @@
	/*
	* 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;
	+package deconvolutionlab.module;

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

	import javax.swing.JPanel;

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

	public class LicenceModule extends AbstractModule {

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

	@Override
	public String getCommand() {
	+ setSynopsis("GNU General Public License");
	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);
	+ setSynopsis("GNU General Public License");
	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/OutputModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/OutputModule.java
	similarity index 99%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/OutputModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/OutputModule.java
	index 105dd9c..01bf3fe 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/OutputModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/OutputModule.java
	@@ -1,236 +1,236 @@
	/*
	* 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;
	+package deconvolutionlab.module;

	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 bilib.table.CustomizedColumn;
	import bilib.table.CustomizedTable;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Lab;
	import deconvolutionlab.Output;
	import deconvolutionlab.Output.View;
	import deconvolutionlab.dialog.OutputDialog;

	public class OutputModule extends AbstractModule implements ActionListener, MouseListener {

	private CustomizedTable table;
	private JButton bnStack;
	private JButton bnSeries;
	private JButton bnMIP;
	private JButton bnOrtho;
	private JButton bnPlanar;
	private JButton bnFigure;

	public OutputModule(boolean expanded) {
	super("Output", "", "", "Default", expanded);
	}

	@Override
	public String getCommand() {
	String cmd = " ";
	if (table == null)
	return cmd;
	for (int i = 0; i < table.getRowCount(); i++) {
	String[] values = new String[table.getColumnCount()];
	for(int c=0; c<table.getColumnCount(); c++)
	values[c] = table.getCell(i, c) == null ? "" : table.getCell(i, c).trim();
	cmd += " -out " + values[0] + " " + values[1] + " " + values[2] + " " + values[3] + " " + values[4];
	if (values[5].equals(""))
	cmd += " noshow";
	if (values[6].equals(""))
	cmd += " nosave";
	}
	return cmd;
	}

	public void update() {
	setCommand(getCommand());
	setSynopsis(table.getRowCount() + " output" + (table.getRowCount() > 1 ? "s" : ""));
	Command.command();
	getAction1Button().setEnabled(table.getRowCount() > 0);
	}

	@Override
	public JPanel buildExpandedPanel() {

	String[] dynamics = { "intact", "rescaled", "normalized", "clipped" };
	String[] types = { "float", "short", "byte" };

	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Mode", String.class, 80, false));
	columns.add(new CustomizedColumn("Name", String.class, Constants.widthGUI, true));
	columns.add(new CustomizedColumn("Dynamic", String.class, 100, dynamics, "Select the dynamic range"));
	columns.add(new CustomizedColumn("Type", String.class, 100, types, "Select the type"));
	columns.add(new CustomizedColumn("Keypoint", String.class, 120, false));
	columns.add(new CustomizedColumn("Show", String.class, 50, false));
	columns.add(new CustomizedColumn("Save", String.class, 50, false));
	columns.add(new CustomizedColumn("Del", String.class, 30, "\u232B", "Delete this image source"));
	table = new CustomizedTable(columns, true);
	table.getColumnModel().getColumn(5).setMaxWidth(50);
	table.getColumnModel().getColumn(6).setMaxWidth(50);
	table.getColumnModel().getColumn(7).setMaxWidth(30);
	table.getColumnModel().getColumn(0).setMaxWidth(100);
	table.getColumnModel().getColumn(2).setMaxWidth(100);
	table.getColumnModel().getColumn(3).setMaxWidth(100);

	table.addMouseListener(this);
	bnStack = new JButton("\u2295 stack");
	bnSeries = new JButton("\u2295 series");
	bnMIP = new JButton("\u2295 mip");
	bnOrtho = new JButton("\u2295 ortho");
	bnPlanar = new JButton("\u2295 planar");
	bnFigure = new JButton("\u2295 figure");

	JToolBar pn = new JToolBar("Controls Image");
	pn.setBorder(BorderFactory.createEmptyBorder());
	pn.setLayout(new GridLayout(1, 6));
	pn.setFloatable(false);
	pn.add(bnStack);
	pn.add(bnSeries);
	pn.add(bnMIP);
	pn.add(bnOrtho);
	pn.add(bnPlanar);
	pn.add(bnFigure);

	JToolBar tool = new JToolBar("Path");
	tool.setBorder(BorderFactory.createEmptyBorder());
	tool.setLayout(new BorderLayout());
	tool.setFloatable(false);
	JPanel panel = new JPanel();
	panel.setBorder(BorderFactory.createEtchedBorder());
	panel.setLayout(new BorderLayout());
	panel.add(tool, BorderLayout.NORTH);
	panel.add(pn, BorderLayout.SOUTH);
	panel.add(table.getMinimumPane(100, 100), BorderLayout.CENTER);

	bnStack.addActionListener(this);
	bnSeries.addActionListener(this);
	bnMIP.addActionListener(this);
	bnOrtho.addActionListener(this);
	bnPlanar.addActionListener(this);
	bnFigure.addActionListener(this);
	getAction1Button().addActionListener(this);
	Config.registerTable(getName(), "output", table);

	return panel;
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	View view = null;
	if (e.getSource() == bnStack)
	view = View.STACK;
	else if (e.getSource() == bnSeries)
	view = View.SERIES;
	else if (e.getSource() == bnMIP)
	view = View.MIP;
	else if (e.getSource() == bnOrtho)
	view = View.ORTHO;
	else if (e.getSource() == bnPlanar)
	view = View.PLANAR;
	else if (e.getSource() == bnFigure)
	view = View.FIGURE;

	if (view != null) {
	OutputDialog dlg = new OutputDialog(view);
	Lab.setVisible(dlg, true);
	if (dlg.wasCancel())
	return;

	Output out = dlg.getOut();
	if (out != null)
	table.insert(out.getAsString());

	//Lab.setVisible(new OutputPanel(view), "panel", 30, 30);
	update();
	}

	if (e.getSource() == getAction1Button()) {
	table.removeRows();
	}
	}

	@Override
	public void mouseClicked(MouseEvent e) {
	int row = table.getSelectedRow();
	if (table.getSelectedColumn() == 7) {
	table.removeRow(row);
	if (table.getRowCount() > 0)
	table.setRowSelectionInterval(0, 0);
	}
	update();
	Command.command();
	}

	@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() {
	bnStack.removeActionListener(this);
	bnSeries.removeActionListener(this);
	bnMIP.removeActionListener(this);
	bnOrtho.removeActionListener(this);
	bnPlanar.removeActionListener(this);
	bnFigure.removeActionListener(this);
	getAction1Button().removeActionListener(this);
	getAction2Button().removeActionListener(this);
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/PSFModule.java
	similarity index 92%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/PSFModule.java
	index 43d9f18..3019f59 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/PSFModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/PSFModule.java
	@@ -1,341 +1,350 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	-package deconvolutionlab.modules;
	+package deconvolutionlab.module;

	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 bilib.table.CustomizedColumn;
	import bilib.table.CustomizedTable;
	import bilib.tools.Files;
	import deconvolution.Command;
	import deconvolution.Deconvolution;
	import deconvolution.DeconvolutionDialog;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import deconvolutionlab.Imager;
	import deconvolutionlab.Lab;
	import deconvolutionlab.dialog.PatternDialog;
	import deconvolutionlab.dialog.SyntheticDialog;
	import deconvolutionlab.monitor.Monitors;
	import signal.RealSignal;
	import signal.factory.SignalFactory;

	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", "", "Check", 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);
	if (Lab.getPlatform() == Imager.Platform.IMAGEJ)
	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);

	+ // Add drop area
	table.setDropTarget(new LocalDropTarget());
	getCollapsedPanel().setDropTarget(new LocalDropTarget());
	+ bnTitle.setDropTarget(new LocalDropTarget());
	+ bnSynopsis.setDropTarget(new LocalDropTarget());
	+ bnExpand.setDropTarget(new LocalDropTarget());

	bnFile.addActionListener(this);
	bnDirectory.addActionListener(this);
	bnSynthetic.addActionListener(this);
	- if (Lab.getPlatform() == Imager.Platform.IMAGEJ)
	- bnPlatform.addActionListener(this);
	+ bnPlatform.addActionListener(this);
	getAction1Button().addActionListener(this);
	getAction2Button().addActionListener(this);
	- getAction2Button().setToolTipText("Click to have a preview, Shift-click or Ctrl-click to show the complete stack");
	+
	+ bnFile.setToolTipText("Add a new source read from a single file (3D z-stack)");
	+ bnDirectory.setToolTipText("Add a new source read from the 2D images from a directory");
	+ bnSynthetic.setToolTipText("Add a new source artificially created");
	+ bnPlatform.setToolTipText("Add a new source from a list of images of the platform");
	+getAction2Button().setToolTipText("Click to have a preview, Shift-click or Ctrl-click to show the complete stack");
	getAction1Button().setToolTipText("Select the active window");

	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("");
	setCommand("Drag your image file, here");
	}
	getAction2Button().setEnabled(table.getRowCount() > 0);
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == bnFile)
	file(Command.getPath());
	else if (e.getSource() == bnDirectory)
	dir(Command.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()) {
	boolean s = (e.getModifiers() & ActionEvent.SHIFT_MASK) == ActionEvent.SHIFT_MASK;
	boolean c = (e.getModifiers() & ActionEvent.CTRL_MASK) == ActionEvent.CTRL_MASK;
	display(s \| c);
	}
	update();
	}

	public void platform() {
	String name = Lab.getActiveImage();
	if (name != "")
	table.insert(new String[] {name, "platform", name, "\u232B" });
	}

	private void file(String path) {
	File file = Files.browseFile(path);
	if (file == null)
	return;
	table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "\u232B" });
	}

	private void dir(String path) {
	File file = Files.browseDirectory(path);
	if (file == null)
	return;
	PatternDialog dlg = new PatternDialog(file);
	Lab.setVisible(dlg, true);
	if (dlg.wasCancel())
	return;
	table.insert(new String[] { dlg.getDirName(), "directory", dlg.getCommand(), "\u232B" });
	}

	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.setParameters(table.getCell(row, 0), table.getCell(row, 2));
	}
	}
	Lab.setVisible(dlg, 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();
	for(SignalFactory factory : SignalFactory.getAll()) {
	- if (name.equals(factory.getName().trim()))
	+ if (name.equals(factory.getName().trim())) {
	synthetic(true);
	return;
	+ }
	}
	String filename = table.getCell(row, 1).trim();
	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(boolean stack) {
	int row = table.getSelectedRow();
	if (row < 0)
	return;
	Deconvolution deconvolution = new Deconvolution("Check PSF", Command.command());
	deconvolution.openPSF();
	if (stack) {
	RealSignal x = deconvolution.getPSF();
	if (x != null)
	Lab.show(Monitors.createDefaultMonitor(), x, table.getCell(row, 0));
	}
	else {
	DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.PSF, deconvolution, null, null);
	Lab.setVisible(d, false);
	}
	}

	@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.insert(new String[] { file.getName(), "directory", file.getAbsolutePath(), "\u232B" });
	table.setRowSelectionInterval(0, 0);
	update();
	}
	if (file.isFile()) {
	- table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "" });
	+ table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "\u232B" });
	update();
	}
	}
	}
	catch (UnsupportedFlavorException ex) {
	ex.printStackTrace();
	}
	catch (IOException ex) {
	ex.printStackTrace();
	}
	}
	}
	e.dropComplete(true);
	super.drop(e);
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/PreferencesModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/PreferencesModule.java
	similarity index 98%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/PreferencesModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/PreferencesModule.java
	index 7537dd6..56419f5 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/PreferencesModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/PreferencesModule.java
	@@ -1,73 +1,73 @@
	/*
	* 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;
	+package deconvolutionlab.module;

	import java.awt.BorderLayout;

	import javax.swing.JPanel;

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

	public class PreferencesModule extends AbstractModule {

	private SpinnerRangeInteger spnMaxItems;

	public PreferencesModule(boolean expanded) {
	super("Preferences", "", "", "", expanded);
	}

	@Override
	public String getCommand() {
	return "NO";
	}

	@Override
	public JPanel buildExpandedPanel() {
	spnMaxItems = new SpinnerRangeInteger(50, 1, 1000, 1);
	JPanel panel = new JPanel(new BorderLayout());
	GridPanel pn = new GridPanel(true);
	pn.place(3, 0, "Maximum number of items in table");
	pn.place(3, 1, spnMaxItems);

	panel.add(pn, BorderLayout.NORTH);

	Config.register(getName(), "maximum-items", spnMaxItems, 50);
	return panel;
	}

	@Override
	public void close() {
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/modules/RunningModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/RunningModule.java
	similarity index 70%
	rename from DeconvolutionLab2/src/deconvolutionlab/modules/RunningModule.java
	rename to DeconvolutionLab2/src/deconvolutionlab/module/RunningModule.java
	index 89baf47..4ce133a 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/modules/RunningModule.java
	+++ b/DeconvolutionLab2/src/deconvolutionlab/module/RunningModule.java
	@@ -1,264 +1,216 @@
	/*
	* 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;
	+package deconvolutionlab.module;

	import java.awt.BorderLayout;
	import java.awt.event.ActionEvent;
	import java.awt.event.MouseEvent;
	import java.awt.event.MouseListener;
	import java.io.File;
	import java.util.ArrayList;

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

	import bilib.table.CustomizedColumn;
	import bilib.table.CustomizedTable;
	import bilib.tools.Files;
	import deconvolution.Command;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;

	public class RunningModule extends AbstractModule implements MouseListener {

	private CustomizedTable table;

	private String[] valuesMonitor;
	private String[] valuesVerbose;
	- private String[] valuesSystem;
	- private String[] valuesMultithreading;
	- private String[] valuesDisplay;
	- private String[] valuesStats;
	private String[] valuesPath;

	private JTextField txtMonitor;
	private JTextField txtVerbose;
	- private JTextField txtSystem;
	- private JTextField txtMultithreading;
	- private JTextField txtDisplay;
	- private JTextField txtStats;
	private JTextField txtPath;
	private JTextField txtDirectory;

	public RunningModule(boolean expanded) {
	super("Running", "", "Default", "Browse", expanded);
	}

	@Override
	public String getCommand() {
	String cmd = "";
	String p = txtPath.getText();
	if (!p.equalsIgnoreCase(valuesPath[0]))
	cmd += " -path " + txtDirectory.getText().toLowerCase();
	if (!txtMonitor.getText().equalsIgnoreCase(valuesMonitor[0]))
	cmd += " -monitor " + txtMonitor.getText().toLowerCase();
	if (!txtVerbose.getText().equalsIgnoreCase(valuesVerbose[0]))
	cmd += " -verbose " + txtVerbose.getText().toLowerCase();
	- if (!txtSystem.getText().equalsIgnoreCase(valuesSystem[0]))
	- cmd += " -system " + txtSystem.getText().toLowerCase();
	- if (!txtDisplay.getText().equalsIgnoreCase(valuesDisplay[0]))
	- cmd += " -display " + txtDisplay.getText().toLowerCase();
	- if (!txtStats.getText().equalsIgnoreCase(valuesStats[0]))
	- cmd += " -stats " + txtStats.getText().toLowerCase();
	- if (!txtMultithreading.getText().equalsIgnoreCase(valuesMultithreading[0]))
	- cmd += " -multithreading " + txtMultithreading.getText().toLowerCase();

	return cmd;
	}

	@Override
	public JPanel buildExpandedPanel() {

	valuesPath = new String[] { "current", "specify" };
	valuesMonitor = new String[] { "console table", "console", "table", "no" };
	- valuesStats = new String[] { "no", "show", "save", "show save" };
	valuesVerbose = new String[] { "log", "quiet", "mute", "prolix" };
	- valuesSystem = new String[] { "yes", "no" };
	- valuesMultithreading = new String[] { "yes", "no" };
	- valuesDisplay = new String[] { "yes", "no" };

	txtDirectory = new JTextField(System.getProperty("user.dir"));
	txtPath = new JTextField(valuesPath[0]);
	txtMonitor = new JTextField(valuesMonitor[0]);
	- txtStats = new JTextField(valuesStats[0]);
	txtVerbose = new JTextField(valuesVerbose[0]);
	- txtSystem = new JTextField(valuesSystem[0]);
	- txtMultithreading = new JTextField(valuesMultithreading[0]);
	- txtDisplay = new JTextField(valuesDisplay[0]);

	ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
	columns.add(new CustomizedColumn("Settings", String.class, 150, false));
	columns.add(new CustomizedColumn("State", String.class, 100, false));
	columns.add(new CustomizedColumn("Information", String.class, Constants.widthGUI - 250, true));
	columns.add(new CustomizedColumn("", String.class, 100, "Change", "Change this setting"));
	table = new CustomizedTable(columns, false);

	table.getColumnModel().getColumn(3).setMaxWidth(140);
	table.getColumnModel().getColumn(3).setMaxWidth(140);

	JPanel panel = new JPanel(new BorderLayout());
	panel.add(table.getPane(100, 100), BorderLayout.CENTER);

	Config.register(getName(), "Path", txtPath, valuesPath[0]);
	Config.register(getName(), "Monitor", txtMonitor, valuesMonitor[0]);
	- Config.register(getName(), "Stats", txtStats, valuesStats[0]);
	Config.register(getName(), "Verbose", txtVerbose, valuesVerbose[0]);
	- Config.register(getName(), "System", txtSystem, valuesSystem[0]);
	- Config.register(getName(), "Multithreading", txtMultithreading, valuesMultithreading[0]);
	- Config.register(getName(), "Display", txtDisplay, valuesDisplay[0]);
	Config.register(getName(), "Directory", txtDirectory, System.getProperty("user.dir"));

	getAction1Button().addActionListener(this);
	getAction2Button().addActionListener(this);

	table.addMouseListener(this);

	return panel;
	}

	public void init() {
	table.append(new String[] { "Path", txtPath.getText(), txtDirectory.getText(), "Change" });
	table.append(new String[] { "Monitor", txtMonitor.getText(), "Monitor in table and in console", "Change" });
	- table.append(new String[] { "Stats", txtStats.getText(), "Compute stats (slow down)", "Change" });
	table.append(new String[] { "Verbose", txtVerbose.getText(), "Level of messages in monitor", "Change" });
	- table.append(new String[] { "System", txtSystem.getText(), "Open the system window", "Change" });
	- table.append(new String[] { "Multithreading", txtMultithreading.getText(), "Activation of the multithreading", "Change" });
	- table.append(new String[] { "Display", txtDisplay.getText(), "Display result at the end", "Change" });
	update();
	}

	public void update() {
	setCommand(getCommand());
	setSynopsis(txtDirectory.getText());
	Command.command();
	}

	@Override
	public void actionPerformed(ActionEvent e) {
	super.actionPerformed(e);
	if (e.getSource() == getAction1Button()) {
	for (int row = 0; row < table.getRowCount(); row++) {
	if (table.getCell(row, 0).equalsIgnoreCase("path")) {
	setDefault(row, valuesPath, txtPath);
	txtDirectory.setText(System.getProperty("user.dir"));
	table.setCell(0, 2, System.getProperty("user.dir"));
	}
	if (table.getCell(row, 0).equalsIgnoreCase("monitor"))
	setDefault(row, valuesMonitor, txtMonitor);
	- if (table.getCell(row, 0).equalsIgnoreCase("stats"))
	- setDefault(row, valuesStats, txtStats);
	if (table.getCell(row, 0).equalsIgnoreCase("verbose"))
	setDefault(row, valuesVerbose, txtVerbose);
	- if (table.getCell(row, 0).equalsIgnoreCase("system"))
	- setDefault(row, valuesSystem, txtSystem);
	- if (table.getCell(row, 0).equalsIgnoreCase("multithreading"))
	- setDefault(row, valuesMultithreading, txtMultithreading);
	- if (table.getCell(row, 0).equalsIgnoreCase("display"))
	- setDefault(row, valuesDisplay, txtDisplay);
	}
	}
	if (e.getSource() == getAction2Button()) {
	File f = Files.browseDirectory(txtPath.getText());
	if (f != null) {
	txtDirectory.setText(f.getAbsolutePath());
	txtPath.setText(valuesPath[1]);
	table.setCell(0, 1, txtPath.getText());
	table.setCell(0, 2, txtDirectory.getText());
	}
	}
	update();
	}

	@Override
	public void close() {
	}

	@Override
	public void mouseClicked(MouseEvent e) {
	int row = table.getSelectedRow();
	if (table.getSelectedColumn() == 3) {
	if (table.getCell(row, 0).equalsIgnoreCase("path")) {
	toggle(row, valuesPath, txtPath);
	txtDirectory.setText(System.getProperty("user.dir"));
	table.setCell(0, 2, System.getProperty("user.dir"));
	}
	if (table.getCell(row, 0).equalsIgnoreCase("monitor"))
	toggle(row, valuesMonitor, txtMonitor);
	- if (table.getCell(row, 0).equalsIgnoreCase("stats"))
	- toggle(row, valuesStats, txtStats);
	if (table.getCell(row, 0).equalsIgnoreCase("verbose"))
	toggle(row, valuesVerbose, txtVerbose);
	- if (table.getCell(row, 0).equalsIgnoreCase("system"))
	- toggle(row, valuesSystem, txtSystem);
	- if (table.getCell(row, 0).equalsIgnoreCase("multithreading"))
	- toggle(row, valuesMultithreading, txtMultithreading);
	- if (table.getCell(row, 0).equalsIgnoreCase("display"))
	- toggle(row, valuesDisplay, txtDisplay);
	}
	update();
	Command.command();
	}

	@Override
	public void mousePressed(MouseEvent e) {
	}

	@Override
	public void mouseReleased(MouseEvent e) {
	}

	@Override
	public void mouseEntered(MouseEvent e) {
	}

	@Override
	public void mouseExited(MouseEvent e) {
	}

	private void toggle(int row, String values[], JTextField txt) {
	for (int i = 0; i < values.length; i++) {
	if (table.getCell(row, 1).equalsIgnoreCase(values[i])) {
	int k = i == values.length - 1 ? 0 : i + 1;
	table.setCell(row, 1, values[k]);
	txt.setText(values[k]);
	return;
	}
	}
	setDefault(row, values, txt);
	}

	private void setDefault(int row, String values[], JTextField txt) {
	table.setCell(row, 1, values[0]);
	txt.setText(values[0]);
	}

	}
	diff --git a/DeconvolutionLab2/src/fft/AbstractFFT.java b/DeconvolutionLab2/src/fft/AbstractFFT.java
	index 271bdb7..90d3819 100644
	--- a/DeconvolutionLab2/src/fft/AbstractFFT.java
	+++ b/DeconvolutionLab2/src/fft/AbstractFFT.java
	@@ -1,101 +1,102 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package fft;

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

	public abstract class AbstractFFT {

	protected int nx = 2;
	protected int ny = 2;
	protected int nz = 2;
	protected Separability sep;

	public AbstractFFT(Separability sep) {
	this.sep = sep;
	}

	public Separability getSeparability() {
	return sep;
	}

	public void init(Monitors monitors, int nx, int ny, int nz) {
	this.nx = nx;
	this.ny = ny;
	this.nz = nz;
	monitors.log(getName() + " initialized for [" + nx + "x" + ny + "x" + nz + "]");
	}

	public abstract void transformInternal(RealSignal xInput, ComplexSignal XAllocated);
	public abstract void inverseInternal(ComplexSignal XInput, RealSignal xAllocated);

	public ComplexSignal transform(RealSignal x, ComplexSignal XAllocated) {
	if (XAllocated == null)
	XAllocated = new ComplexSignal("fft(" + x.name + ")", nx, ny, nz);
	transformInternal(x, XAllocated);
	return XAllocated;
	}

	public ComplexSignal transform(RealSignal x) {
	ComplexSignal X = new ComplexSignal("fft(" + x.name + ")", nx, ny, nz);
	transformInternal(x, X);
	return X;
	}

	public RealSignal inverse(ComplexSignal X, RealSignal xAllocated) {
	if (xAllocated == null)
	xAllocated = new RealSignal("ifft(" + X.name + ")", nx, ny, nz);
	inverseInternal(X, xAllocated);
	return xAllocated;
	}
	public RealSignal inverse(ComplexSignal X) {
	RealSignal x = new RealSignal("ifft(" + X.name + ")", nx, ny, nz);
	inverseInternal(X, x);
	return x;
	}

	public abstract String getName();
	+ public abstract boolean isMultithreadable();

	public int getSizeX() {
	return nx;
	}

	public int getSizeY() {
	return ny;
	}

	public int getSizeZ() {
	return nz;
	}
	}
	diff --git a/DeconvolutionLab2/src/fft/AbstractFFTLibrary.java b/DeconvolutionLab2/src/fft/AbstractFFTLibrary.java
	index 60355ba..f1673ca 100644
	--- a/DeconvolutionLab2/src/fft/AbstractFFTLibrary.java
	+++ b/DeconvolutionLab2/src/fft/AbstractFFTLibrary.java
	@@ -1,57 +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 fft;

	import java.util.ArrayList;

	public abstract class AbstractFFTLibrary {

	protected boolean installed = false;
	protected ArrayList<AbstractFFT> ffts = new ArrayList<AbstractFFT>();

	public abstract AbstractFFT getDefaultFFT();

	public abstract String getLibraryName();
	public abstract String getCredit();
	public abstract String getLicence();
	- public abstract boolean isMultithreadable();
	public abstract String getLocation();

	public boolean isInstalled() {
	return installed;
	}


	public ArrayList<AbstractFFT> getFFTs() {
	return ffts;
	}
	}
	diff --git a/DeconvolutionLab2/src/fft/FFTPanel.java b/DeconvolutionLab2/src/fft/FFTPanel.java
	index 377962d..7fdeb14 100644
	--- a/DeconvolutionLab2/src/fft/FFTPanel.java
	+++ b/DeconvolutionLab2/src/fft/FFTPanel.java
	@@ -1,86 +1,86 @@
	package fft;

	import java.awt.BorderLayout;
	import java.awt.FlowLayout;
	import java.awt.event.MouseEvent;
	import java.awt.event.MouseListener;
	import java.util.ArrayList;

	import javax.swing.JComboBox;
	import javax.swing.JLabel;
	import javax.swing.JPanel;
	import javax.swing.JSplitPane;

	import bilib.component.HTMLPane;
	import bilib.table.CustomizedColumn;
	import bilib.table.CustomizedTable;
	import bilib.tools.NumFormat;
	import deconvolutionlab.Config;
	import deconvolutionlab.Constants;
	import signal.Operations;

	public class FFTPanel extends JPanel implements MouseListener {

	private HTMLPane info;
	private CustomizedTable table;
	private ArrayList<AbstractFFTLibrary> libs;

	public FFTPanel(int w, int h) {
	super(new BorderLayout());
	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("Multithreadable", String.class, 120, false));
	columns.add(new CustomizedColumn("Location", String.class, Constants.widthGUI, false));
	table = new CustomizedTable(columns, true);
	table.setRowSelectionAllowed(true);
	table.addMouseListener(this);
	libs = FFT.getRegisteredLibraries();
	for (AbstractFFTLibrary lib : libs) {
	String name = lib.getLibraryName();
	String installed = lib.isInstalled() ? "Yes" : "No";
	- String multit = lib.isMultithreadable() ? "Yes" : "No";
	+ String multit = lib.getDefaultFFT().isMultithreadable() ? "Yes" : "No";
	String location = lib.getLocation();
	table.append(new String[] { name, installed, multit, location });
	}
	info = new HTMLPane(w, h-100);

	JSplitPane split = new JSplitPane(JSplitPane.VERTICAL_SPLIT, table.getPane(w, 100), info.getPane());
	split.setDividerLocation(0.5);
	add(split, BorderLayout.CENTER);
	table.setRowSelectionInterval(0, 0);
	info.clear();
	info.append("p", libs.get(0).getLicence());
	}

	@Override
	public void mouseClicked(MouseEvent e) {
	int i = table.getSelectedRow();
	if (i<0)
	return;
	if (i>=libs.size())
	return;
	info.clear();
	info.append("p", libs.get(i).getLicence());
	}

	@Override
	public void mousePressed(MouseEvent e) {
	}

	@Override
	public void mouseReleased(MouseEvent e) {
	}

	@Override
	public void mouseEntered(MouseEvent e) {
	// TODO Auto-generated method stub

	}

	@Override
	public void mouseExited(MouseEvent e) {
	// TODO Auto-generated method stub

	}
	}
	diff --git a/DeconvolutionLab2/src/fft/academic/Academic.java b/DeconvolutionLab2/src/fft/academic/Academic.java
	index 66a090c..1f50501 100644
	--- a/DeconvolutionLab2/src/fft/academic/Academic.java
	+++ b/DeconvolutionLab2/src/fft/academic/Academic.java
	@@ -1,74 +1,80 @@
	/*
	* 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.academic;

	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.Separability;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class Academic extends AbstractFFT {

	private AcademicFFT fftXYZ;

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

	@Override
	public void init(Monitors monitors, int nx, int ny, int nz) {
	super.init(monitors, nx, ny, nz);
	fftXYZ = new AcademicFFT(nx, ny, nz, 0, 0, 0);
	}

	@Override
	public void transformInternal(RealSignal x, ComplexSignal X) {
	float imag[] = new float[nx * ny * nz];
	float real[] = x.getXYZ();
	fftXYZ.directTransform(real, imag, null, null, AcademicFFT.InputDataType.REALINPUT);
	X.setXYZ(real, imag);
	}

	@Override
	public void inverseInternal(ComplexSignal X, RealSignal x) {
	float real[] = X.getRealXYZ();
	float imag[] = X.getImagXYZ();
	fftXYZ.inverseTransform(real, imag, null, null);
	x.setXYZ(real);
	}

	@Override
	public String getName() {
	return "AcademicFFT";
	}
	+
	+ @Override
	+ public boolean isMultithreadable() {
	+ return false;
	+ }
	+
	}
	diff --git a/DeconvolutionLab2/src/fft/academic/AcademicFFT_XYZ.java b/DeconvolutionLab2/src/fft/academic/AcademicFFT_XYZ.java
	index 950a230..8ca6d97 100644
	--- a/DeconvolutionLab2/src/fft/academic/AcademicFFT_XYZ.java
	+++ b/DeconvolutionLab2/src/fft/academic/AcademicFFT_XYZ.java
	@@ -1,105 +1,112 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package fft.academic;

	/*
	* 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/>.
	*/

	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.Separability;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class AcademicFFT_XYZ extends AbstractFFT {

	private AcademicFFT fftXYZ;

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

	@Override
	public void init(Monitors monitors, int nx, int ny, int nz) {
	super.init(monitors, nx, ny, nz);
	fftXYZ = new AcademicFFT(nx, ny, nz, 0, 0, 0);
	}

	@Override
	public void transformInternal(RealSignal x, ComplexSignal X) {
	float imag[] = new float[nx * ny * nz];
	float real[] = x.getXYZ();
	fftXYZ.directTransform(real, imag, null, null, AcademicFFT.InputDataType.REALINPUT);
	X.setXYZ(real, imag);
	}

	@Override
	public void inverseInternal(ComplexSignal X, RealSignal x) {
	float real[] = X.getRealXYZ();
	float imag[] = X.getImagXYZ();
	fftXYZ.inverseTransform(real, imag, null, null);
	x.setXYZ(real);
	}

	@Override
	public String getName() {
	return "AcademicFFT XYZ";
	}
	+
	+
	+ @Override
	+ public boolean isMultithreadable() {
	+ return false;
	+ }
	+
	}
	diff --git a/DeconvolutionLab2/src/fft/academic/AcademicFFT_XY_Z.java b/DeconvolutionLab2/src/fft/academic/AcademicFFT_XY_Z.java
	index 1435d3d..301ca63 100644
	--- a/DeconvolutionLab2/src/fft/academic/AcademicFFT_XY_Z.java
	+++ b/DeconvolutionLab2/src/fft/academic/AcademicFFT_XY_Z.java
	@@ -1,99 +1,105 @@
	/*
	* 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.academic;

	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.Separability;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class AcademicFFT_XY_Z extends AbstractFFT {

	private AcademicFFT fftXY;
	private AcademicFFT fftZ;

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

	@Override
	public void init(Monitors monitors, int nx, int ny, int nz) {
	super.init(monitors, nx, ny, nz);
	fftXY = new AcademicFFT(nx, ny, 0, 0);
	fftZ = new AcademicFFT(nz, 0);
	}

	@Override
	public void transformInternal(RealSignal x, ComplexSignal X) {
	for (int k = 0; k < nz; k++) {
	float real[] = new float[nx * ny];
	float imag[] = new float[nx * ny];
	System.arraycopy(x.data[k], 0, real, 0, nx * ny);
	fftXY.directTransform(real, imag, null, null, AcademicFFT.InputDataType.REALINPUT);
	X.setRealXY(k, real);
	X.setImagXY(k, imag);
	}

	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	float real[] = X.getRealZ(i, j);
	float imag[] = X.getImagZ(i, j);
	fftZ.directTransform(real, imag, null, null, AcademicFFT.InputDataType.COMPLEXINPUT);
	X.setRealZ(i, j, real);
	X.setImagZ(i, j, imag);
	}
	}

	@Override
	public void inverseInternal(ComplexSignal X, RealSignal x) {
	for (int k = 0; k < nz; k++) {
	float real[] = X.getRealXY(k);
	float imag[] = X.getImagXY(k);
	fftXY.inverseTransform(real, imag, null, null);
	X.setRealXY(k, real);
	X.setImagXY(k, imag);
	}
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	float real[] = X.getRealZ(i, j);
	float imag[] = X.getImagZ(i, j);
	fftZ.inverseTransform(real, imag, null, null);
	x.setZ(i, j, real);
	}
	}

	@Override
	public String getName() {
	return "AcademicFFT XY and Z";
	}
	+
	+ @Override
	+ public boolean isMultithreadable() {
	+ return false;
	+ }
	+
	}
	diff --git a/DeconvolutionLab2/src/fft/academic/AcademicLibrary.java b/DeconvolutionLab2/src/fft/academic/AcademicLibrary.java
	index 7134c58..861a5e0 100644
	--- a/DeconvolutionLab2/src/fft/academic/AcademicLibrary.java
	+++ b/DeconvolutionLab2/src/fft/academic/AcademicLibrary.java
	@@ -1,82 +1,77 @@
	/*
	* 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.academic;

	import fft.AbstractFFT;
	import fft.AbstractFFTLibrary;

	public class AcademicLibrary extends AbstractFFTLibrary {

	public AcademicLibrary() {
	installed = true;
	if (installed) {
	ffts.add(new Academic());
	ffts.add(new AcademicFFT_XYZ());
	ffts.add(new AcademicFFT_XY_Z());
	}
	}

	@Override
	public String getLocation() {
	return AcademicLibrary.class.getCanonicalName();
	}
	-
	- @Override
	- public boolean isMultithreadable() {
	- return false;
	- }

	@Override
	public String getCredit() {
	return "http://bigwww.epfl.ch/thevenaz/academicFFT/ (P. Thévenaz)";
	}

	@Override
	public String getLicence() {
	String licence = "<h1>AcademicFFT of Philippe Thévenaz, EPFL.</h1>";
	licence += "<p>EPFL makes no warranties of any kind on this software and ";
	licence += "shall in no event be liable for damages of any kind in ";
	licence += "connection with the use and exploitation of this technology.</p>";
	return licence;
	}

	@Override
	public String getLibraryName() {
	return "Academic";
	}

	@Override
	public AbstractFFT getDefaultFFT() {
	return new Academic();
	}

	}
	diff --git a/DeconvolutionLab2/src/fft/fftw/FFTW3D.java b/DeconvolutionLab2/src/fft/fftw/FFTW3D.java
	index 4950293..afb2c8d 100644
	--- a/DeconvolutionLab2/src/fft/fftw/FFTW3D.java
	+++ b/DeconvolutionLab2/src/fft/fftw/FFTW3D.java
	@@ -1,77 +1,83 @@
	/*
	* 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.fftw;

	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.Separability;
	import jfftw.complex.nd.Plan;
	import signal.ComplexSignal;
	import signal.RealSignal;

	public class FFTW3D extends AbstractFFT {

	private Plan planForwardFFTW = null;
	private Plan planBackwardFFTW = null;

	public FFTW3D() {
	super(Separability.XYZ);
	}

	@Override
	public void init(Monitors monitors, int nx, int ny, int nz) {
	super.init(monitors, nx, ny, nz);
	int dim[] = new int[] {nz, ny, nx};
	planForwardFFTW = new Plan(dim, Plan.FORWARD, Plan.ESTIMATE \| Plan.IN_PLACE \| Plan.USE_WISDOM);
	planBackwardFFTW = new Plan(dim, Plan.BACKWARD, Plan.ESTIMATE \| Plan.IN_PLACE \| Plan.USE_WISDOM);
	}

	@Override
	public void transformInternal(RealSignal x, ComplexSignal X) {
	float interleave[] = x.getInterleaveXYZAtReal();
	planForwardFFTW.transform(interleave);
	X.setInterleaveXYZ(interleave);
	}

	@Override
	public void inverseInternal(ComplexSignal X, RealSignal x) {
	float[] interleave = X.getInterleaveXYZ();
	planBackwardFFTW.transform(interleave);
	x.setInterleaveXYZAtReal(interleave);
	x.multiply(1.0/(nxnynz));
	}

	@Override
	public String getName() {
	return "FFTW2";
	}
	+
	+ @Override
	+ public boolean isMultithreadable() {
	+ return true;
	+ }
	+
	}
	diff --git a/DeconvolutionLab2/src/fft/fftw/FFTWLibrary.java b/DeconvolutionLab2/src/fft/fftw/FFTWLibrary.java
	index a8e2eb8..b0ceaa2 100644
	--- a/DeconvolutionLab2/src/fft/fftw/FFTWLibrary.java
	+++ b/DeconvolutionLab2/src/fft/fftw/FFTWLibrary.java
	@@ -1,206 +1,200 @@
	/*
	* 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.fftw;

	import java.io.File;
	import java.security.CodeSource;

	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.AbstractFFTLibrary;
	import jfftw.complex.nd.Plan;

	public class FFTWLibrary extends AbstractFFTLibrary {

	private String location;
	public FFTWLibrary(Monitors monitors) {

	String path = "";
	boolean found = false;
	if (!found) {
	try {
	CodeSource code = FFTWLibrary.class.getProtectionDomain().getCodeSource();
	File file = new File(code.getLocation().toURI().getPath());
	path = file.getParentFile().getPath() + File.separator + "FFTW" + File.separator;
	found = existsWidsom(monitors, path);
	location = path;
	}
	catch (Exception ex) {
	monitors.log("FFTW Widsom not found in : " + path);
	location = "Not found in " + path;
	found = false;
	}
	}

	if (!found) {
	try {
	CodeSource code = FFTWLibrary.class.getProtectionDomain().getCodeSource();
	File file = new File(code.getLocation().toURI().getPath());
	path = file.getParentFile().getPath() + File.separator;
	found = existsWidsom(monitors, path);
	location = path;
	}
	catch (Exception ex) {
	monitors.log("FFTW Widsom not found in : " + path);
	location = "Not found in " + path;
	found = false;
	}
	}

	if (!found) {
	try {
	path = System.getProperty("user.home") + File.separator + "FFTW" + File.separator;
	found = existsWidsom(monitors, path);
	location = path;
	}
	catch (Exception ex) {
	monitors.log("FFTW Widsom not found in : " + path);
	location = "Not found in " + path;
	found = false;
	}
	}

	if (!found) {
	try {
	path = System.getProperty("user.home") + File.separator;
	found = existsWidsom(monitors, path);
	location = path;
	}
	catch (Exception ex) {
	monitors.log("FFTW Widsom not found in : " + path);
	location = "Not found in " + path;
	found = false;
	}
	}

	if (!found)
	return;

	loadLibraries(monitors, path);

	try {
	new Plan(new int[] { 20, 20, 20 }, Plan.FORWARD, Plan.ESTIMATE \| Plan.IN_PLACE \| Plan.USE_WISDOM);
	ffts.add(new FFTW3D());
	installed = true;
	}
	catch (UnsatisfiedLinkError ex) {
	ex.printStackTrace();
	installed = false;
	}

	}

	@Override
	public String getLocation() {
	return location;
	}

	- @Override
	- public boolean isMultithreadable() {
	- return true;
	- }
	-
	@Override
	public String getCredit() {
	return "http://www.fftw.org (FFTW Version 2)";
	}

	@Override
	public String getLibraryName() {
	return "FFTW2";
	}

	@Override
	public String getLicence() {
	return "<h1>FFTW Version 2, " + "<p>http://www.fftw.org" + "<p>FFTW 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 2 of the License, or " + "(at your option) any later version.";
	}

	private static void loadLibraries(Monitors monitors, String path) {
	try {
	String osname = System.getProperty("os.name");

	if (osname.startsWith("Linux")) {
	String osarch = System.getProperty("os.arch");
	if (osarch.contains("64")) {
	System.load(path + "libFFTWJNI64.so");
	monitors.log("Loading library FFTW for " + osarch + " " + osname + " " + path + "libFFTWJNI64.so");
	}
	else {
	System.load(path + "libFFTWJNI32.so");
	monitors.log("Loading library FFTW for " + osarch + " " + osname + " " + path + "libFFTWJNI32.so");
	}
	}
	else if (osname.startsWith("Windows")) {
	String osarch = System.getProperty("os.arch");
	if (osarch.contains("64")) {
	System.load(path + "FFTWJNIWin64.dll");
	monitors.log("Loading library FFTW for " + osarch + " " + osname + " " + path + "FFTWJNIWin64.dll");
	}
	else {
	System.load(path + "FFTWJNIWin32.dll");
	monitors.log("Loading library FFTW for " + osarch + " " + osname + " " + path + "FFTWJNIWin32.dll");
	}
	}
	else if (osname.startsWith("Mac")) {
	System.load(path + "libFFTWJNIMac.jnilib");
	monitors.log("Loading library FFTW for " + osname + " " + path + "libFFTWJNIMac.jnilib");
	}
	else {
	monitors.log("FFTW is not provided for the architecture : " + osname);
	}

	}
	catch (Exception ex) {
	monitors.log("FFTW not found in : " + path);
	}
	}

	private static boolean existsWidsom(Monitors monitors, String path) {
	boolean found = false;
	if (new File(path + "Wisdom").exists()) {
	monitors.log("FFTW found in : " + path);
	found = true;
	}
	else {
	monitors.log("FFTW Widsom not found in : " + path);
	found = false;
	}
	return found;
	}

	@Override
	public AbstractFFT getDefaultFFT() {
	return new FFTW3D();
	}
	-
	}
	diff --git a/DeconvolutionLab2/src/fft/jtransforms/JTransforms.java b/DeconvolutionLab2/src/fft/jtransforms/JTransforms.java
	index ff5719b..039d8d6 100644
	--- a/DeconvolutionLab2/src/fft/jtransforms/JTransforms.java
	+++ b/DeconvolutionLab2/src/fft/jtransforms/JTransforms.java
	@@ -1,89 +1,95 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package fft.jtransforms;

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

	public class JTransforms extends AbstractFFT {

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

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

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

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

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

	@Override
	public String getName() {
	return "JTransforms";
	}
	+
	+ @Override
	+ public boolean isMultithreadable() {
	+ return true;
	+ }
	+
	}
	diff --git a/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XYZ.java b/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XYZ.java
	index da8d8c6..2358533 100644
	--- a/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XYZ.java
	+++ b/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XYZ.java
	@@ -1,89 +1,95 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package fft.jtransforms;

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

	public class JTransformsFFT_XYZ extends AbstractFFT {

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

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

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

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

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

	@Override
	public String getName() {
	return "JTransforms XYZ";
	}
	+
	+ @Override
	+ public boolean isMultithreadable() {
	+ return true;
	+ }
	+
	}
	diff --git a/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XY_Z.java b/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XY_Z.java
	index 5f02651..b6c6f09 100644
	--- a/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XY_Z.java
	+++ b/DeconvolutionLab2/src/fft/jtransforms/JTransformsFFT_XY_Z.java
	@@ -1,102 +1,108 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package fft.jtransforms;

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

	public class JTransformsFFT_XY_Z extends AbstractFFT {

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

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

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

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

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

	@Override
	public String getName() {
	return "JTransforms XY_Z";
	}
	+
	+ @Override
	+ public boolean isMultithreadable() {
	+ return true;
	+ }
	+
	}
	diff --git a/DeconvolutionLab2/src/fft/jtransforms/JTransformsLibrary.java b/DeconvolutionLab2/src/fft/jtransforms/JTransformsLibrary.java
	index 33ec577..50ca6b3 100644
	--- a/DeconvolutionLab2/src/fft/jtransforms/JTransformsLibrary.java
	+++ b/DeconvolutionLab2/src/fft/jtransforms/JTransformsLibrary.java
	@@ -1,87 +1,82 @@
	/*
	* 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.AbstractFFT;
	import fft.AbstractFFTLibrary;

	public class JTransformsLibrary extends AbstractFFTLibrary {

	public JTransformsLibrary() {
	System.out.println("JTransformsLibrary");
	try {
	Class.forName("org.jtransforms.fft.FloatFFT_3D");
	Class.forName("org.jtransforms.fft.FloatFFT_1D");
	Class.forName("org.jtransforms.fft.FloatFFT_2D");
	installed = true;
	}
	catch (ClassNotFoundException ex) {
	System.out.println("" + 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</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.";
	}

	@Override
	public AbstractFFT getDefaultFFT() {
	return new JTransforms();
	}
	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/splash/ImageLoader.java b/DeconvolutionLab2/src/resources/ImageLoader.java
	similarity index 82%
	rename from DeconvolutionLab2/src/deconvolutionlab/splash/ImageLoader.java
	rename to DeconvolutionLab2/src/resources/ImageLoader.java
	index 53f3827..b104ecc 100644
	--- a/DeconvolutionLab2/src/deconvolutionlab/splash/ImageLoader.java
	+++ b/DeconvolutionLab2/src/resources/ImageLoader.java
	@@ -1,50 +1,48 @@
	/*
	- * DeconvolutionLab2
	+ * bilib --- Java Bioimaging Library ---
	+ *
	+ * Author: Daniel Sage, Biomedical Imaging Group, EPFL, Lausanne, Switzerland
	*
	* 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.splash;
	+package resources;

	import java.awt.Image;
	import java.net.URL;

	import javax.swing.ImageIcon;

	public class ImageLoader {

	public static Image get(String filename) {
	URL url = ImageLoader.class.getResource(filename);
	if (url != null) {
	ImageIcon img = new ImageIcon(url, "") ;
	return img.getImage();
	}
	return null;
	}

	}
	diff --git a/DeconvolutionLab2/src/deconvolutionlab/splash/celegans.jpg b/DeconvolutionLab2/src/resources/celegans.jpg
	similarity index 100%
	rename from DeconvolutionLab2/src/deconvolutionlab/splash/celegans.jpg
	rename to DeconvolutionLab2/src/resources/celegans.jpg
	diff --git a/DeconvolutionLab2/src/signal/RealSignal.java b/DeconvolutionLab2/src/signal/RealSignal.java
	index 44351d4..1af1ba2 100644
	--- a/DeconvolutionLab2/src/signal/RealSignal.java
	+++ b/DeconvolutionLab2/src/signal/RealSignal.java
	@@ -1,706 +1,732 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal;

	import java.awt.image.BufferedImage;

	import deconvolutionlab.monitor.Monitors;

	public class RealSignal extends Signal implements SignalListener {

	private BufferedImage preview;

	public RealSignal(String name, int nx, int ny, int nz) {
	super(name, nx, ny, nz);
	this.data = new float[nz][];
	int step = Math.max(1, nz / SignalCollector.NOTIFICATION_RATE);
	notify(name, 0);
	for (int k = 0; k < nz; k++) {
	data[k] = new float[nx * ny];
	if (k % step == 0)
	notify(name, k * 100.0 / nz);
	}
	notify(name, 100);
	SignalCollector.alloc(this);//name, nx, ny, ny, false);
	}

	@Override
	public void notify(String name, double progress) {
	SignalCollector.setProgress(progress);
	}

	public void copy(RealSignal source) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = source.data[k][i];
	}
	}

	public void setSignal(RealSignal signal) {
	int sx = signal.nx;
	int mx = Math.min(nx, signal.nx);
	int my = Math.min(ny, signal.ny);
	int mz = Math.min(nz, signal.nz);
	for (int i = 0; i < mx; i++)
	for (int j = 0; j < my; j++)
	for (int k = 0; k < mz; k++)
	data[k][i + nx * j] = signal.data[k][i + sx * j];
	}

	public void getSignal(RealSignal signal) {
	int sx = signal.nx;
	int mx = Math.min(nx, signal.nx);
	int my = Math.min(ny, signal.ny);
	int mz = Math.min(nz, signal.nz);
	for (int i = 0; i < mx; i++)
	for (int j = 0; j < my; j++)
	for (int k = 0; k < mz; k++)
	signal.data[k][i + sx * j] = data[k][i + nx * j];
	}

	/**
	* Applies a soft threshold (in-place processing)
	*
	* @param inferiorLimit
	* @param superiorLimit
	* @return the instance of the calling object
	*/
	public RealSignal thresholdSoft(float inferiorLimit, float superiorLimit) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	if (data[k][i] <= inferiorLimit)
	data[k][i] += inferiorLimit;
	else if (data[k][i] >= superiorLimit)
	data[k][i] -= superiorLimit;
	else
	data[k][i] = 0f;
	}
	return this;
	}

	/**
	* Multiplies by a signal pixelwise (in-place processing)
	*
	* @param factor
	* @return the instance of the calling object
	*/
	public RealSignal times(RealSignal factor) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] *= factor.data[k][i];
	}
	return this;
	}

	/**
	* Multiplies by a scalar factor (in-place processing)
	*
	* @param factor
	* @return the instance of the calling object
	*/
	public RealSignal times(float factor) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] *= factor;
	}
	return this;
	}

	/**
	* Adds a signal pixelwise (in-place processing)
	*
	* @param factor
	* @return the instance of the calling object
	*/
	public RealSignal plus(RealSignal factor) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] += factor.data[k][i];
	}
	return this;
	}

	/**
	* Subtracts by a signal pixelwise (in-place processing)
	*
	* @param factor
	* @return the instance of the calling object
	*/
	public RealSignal minus(RealSignal factor) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] -= factor.data[k][i];
	}
	return this;
	}

	/**
	* Adds a scalar term (in-place processing)
	*
	* @param term
	* @return the instance of the calling object
	*/
	public RealSignal plus(float term) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] += term;
	}
	return this;
	}

	+ /**
	+ * Subtracts a scalar term (in-place processing)
	+ *
	+ * @param term
	+ * @return the instance of the calling object
	+ */
	+ public RealSignal minus(float term) {
	+ int nxy = nx * ny;
	+ for (int k = 0; k < nz; k++)
	+ for (int i = 0; i < nxy; i++) {
	+ data[k][i] -= term;
	+ }
	+ return this;
	+ }
	+
	/**
	* Takes the maximum (in-place processing)
	*
	* @param factor
	* @return the instance of the calling object
	*/
	public RealSignal max(RealSignal factor) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = Math.max(data[k][i], factor.data[k][i]);
	}
	return this;
	}

	/**
	* Takes the minimum (in-place processing)
	*
	* @param factor
	* @return the instance of the calling object
	*/
	public RealSignal min(RealSignal factor) {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = Math.min(data[k][i], factor.data[k][i]);
	}
	return this;
	}

	public double[][][] get3DArrayAsDouble() {
	double[][][] ar = new double[nx][ny][nz];
	for (int k = 0; k < nz; k++) {
	float[] s = data[k];
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	ar[i][j][k] = s[i + j * nx];
	}
	}
	return ar;
	}

	public void set3DArrayAsDouble(double[][][] real) {
	for (int k = 0; k < nz; k++) {
	float[] s = data[k];
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	s[i + j * nx] = (float) real[i][j][k];
	}
	}
	}

	public RealSignal duplicate() {
	RealSignal out = new RealSignal("copy(" + name + ")", nx, ny, nz);
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	System.arraycopy(data[k], 0, out.data[k], 0, nxy);
	return out;
	}

	public float getEnergy() {
	int nxy = nx * ny;
	float energy = 0.f;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++)
	energy += data[k][i];
	return energy;
	}

	public float[] getStats() {
	int nxy = nx * ny;
	float min = Float.MAX_VALUE;
	float max = -Float.MAX_VALUE;
	double norm1 = 0.0;
	double norm2 = 0.0;
	double mean = 0.0;

	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	float v = data[k][i];
	max = Math.max(max, v);
	min = Math.min(min, v);
	mean += v;
	norm1 += (v > 0 ? v : -v);
	norm2 += v * v;
	}
	mean = mean / (nz * nxy);
	norm1 = norm1 / (nz * nxy);
	norm2 = Math.sqrt(norm2 / (nz * nxy));
	double stdev = 0.0;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	stdev += (data[k][i] - mean) * (data[k][i] - mean);
	}
	stdev = Math.sqrt(stdev / (nz * nxy));
	return new float[] { (float) mean, min, max, (float) stdev, (float) norm1, (float) norm2 };
	}

	public float[] getExtrema() {
	int nxy = nx * ny;
	float min = Float.MAX_VALUE;
	float max = -Float.MAX_VALUE;

	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	float v = data[k][i];
	max = Math.max(max, v);
	min = Math.min(min, v);
	}
	return new float[] { min, max };
	}

	public RealSignal normalize(double to) {
	if (to == 0)
	return this;
	int nxy = nx * ny;
	float sum = 0f;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++)
	sum += data[k][i];
	if (sum != 0f) {
	double r = to / sum;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++)
	data[k][i] *= r;
	}
	return this;
	}

	public void setSlice(int z, RealSignal slice) {
	int mx = slice.nx;
	int my = slice.ny;
	for (int j = 0; j < Math.min(ny, my); j++)
	for (int i = 0; i < Math.min(nx, mx); i++)
	data[z][i + nx * j] = slice.data[0][i + mx * j];
	}

	public RealSignal getSlice(int z) {
	RealSignal slice = new RealSignal(name + "_z=" + z, nx, ny, 1);
	for (int j = 0; j < nx * ny; j++)
	slice.data[0][j] = data[z][j];
	return slice;
	}

	public void multiply(double factor) {
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nx * ny; i++)
	data[k][i] *= factor;
	}

	public float[] getInterleaveXYZAtReal() {
	float[] interleave = new float[2 * nz * nx * ny];
	for (int k = 0; k < nz; k++)
	for (int j = 0; j < ny; j++)
	for (int i = 0; i < nx; i++)
	interleave[2 * (k * nx * ny + j * nx + i)] = data[k][i + j * nx];
	return interleave;
	}

	public void setInterleaveXYZAtReal(float[] interleave) {
	for (int k = 0; k < nz; k++)
	for (int j = 0; j < ny; j++)
	for (int i = 0; i < nx; i++)
	data[k][i + nx * j] = interleave[(k * nx * ny + j * nx + i) * 2];
	}

	public float[] getInterleaveXYAtReal(int k) {
	float real[] = new float[nx * ny * 2];
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	int index = i + j * nx;
	real[2 * index] = data[k][index];
	}
	return real;
	}

	public void setInterleaveXYAtReal(int k, float real[]) {
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	int index = i + j * nx;
	data[k][index] = real[2 * index];
	}
	}

	public float[] getXYZ() {
	int nxy = nx * ny;
	float[] d = new float[nz * nx * ny];
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++)
	d[k * nxy + i] = data[k][i];
	return d;
	}

	public void setXYZ(float[] data) {
	if (nx * ny * nz != data.length)
	return;
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++)
	this.data[k][i] = data[k * nxy + i];
	}

	public float[] getXY(int k) {
	return data[k];
	}

	public void setXY(int k, float slice[]) {
	data[k] = slice;
	}

	public float[] getX(int j, int k) {
	float line[] = new float[nx];
	for (int i = 0; i < nx; i++)
	line[i] = data[k][i + j * nx];
	return line;
	}

	public float[] getZ(int i, int j) {
	float line[] = new float[nz];
	int index = i + j * nx;
	for (int k = 0; k < nz; k++)
	line[k] = data[k][index];
	return line;
	}

	public float[] getY(int i, int k) {
	float line[] = new float[ny];
	for (int j = 0; j < ny; j++)
	line[j] = data[k][i + j * nx];
	return line;
	}

	public void setX(int j, int k, float line[]) {
	for (int i = 0; i < nx; i++)
	data[k][i + j * nx] = line[i];
	}

	public void setY(int i, int k, float line[]) {
	for (int j = 0; j < ny; j++)
	data[k][i + j * nx] = line[j];
	}

	public void setZ(int i, int j, float line[]) {
	int index = i + j * nx;
	for (int k = 0; k < nz; k++)
	data[k][index] = line[k];
	}

	public void clip(float min, float max) {
	for (int k = 0; k < nz; k++)
	for (int j = 0; j < ny * nx; j++)
	if (data[k][j] < min)
	data[k][j] = min;
	else if (data[k][j] > max)
	data[k][j] = max;
	}

	public void fill(float constant) {
	for (int k = 0; k < nz; k++)
	for (int j = 0; j < ny * nx; j++)
	data[k][j] = constant;
	}

	public RealSignal changeSizeAs(RealSignal model) {
	return size(model.nx, model.ny, model.nz);
	}

	public RealSignal size(int mx, int my, int mz) {
	String n = "resize(" + name + ")";

	int ox = (mx - nx) / 2;
	int oy = (my - ny) / 2;
	int oz = (mz - nz) / 2;
	RealSignal signal = new RealSignal(n, mx, my, mz);
	int vx = Math.min(nx, mx);
	int vy = Math.min(ny, my);
	int vz = Math.min(nz, mz);
	for (int k = 0; k < vz; k++)
	for (int j = 0; j < vy; j++)
	for (int i = 0; i < vx; i++) {
	int pi = ox >= 0 ? i + ox : i;
	int qi = ox >= 0 ? i : i - ox;
	int pj = oy >= 0 ? j + oy : j;
	int qj = oy >= 0 ? j : j - oy;
	int pk = oz >= 0 ? k + oz : k;
	int qk = oz >= 0 ? k : k - oz;
	signal.data[pk][pi + pj * mx] = data[qk][qi + qj * nx];
	}
	return signal;
	}

	public RealSignal createOrthoview() {
	return createOrthoview(nx / 2, ny / 2, nz / 2);
	}

	public RealSignal createOrthoview(int hx, int hy, int hz) {
	String n = "ortho(" + name + ")";

	int vx = nx + nz;
	int vy = ny + nz;
	RealSignal view = new RealSignal(n, vx, vy, 1);
	hx = Math.min(nx - 1, Math.max(0, hx));
	hy = Math.min(ny - 1, Math.max(0, hy));
	hz = Math.min(nz - 1, Math.max(0, hz));
	for (int x = 0; x < nx; x++)
	for (int y = 0; y < ny; y++)
	view.data[0][x + vx * y] = data[hz][x + nx * y];

	for (int z = 0; z < nz; z++)
	for (int y = 0; y < ny; y++)
	view.data[0][nx + z + vx * y] = data[z][hx + nx * y];

	for (int z = 0; z < nz; z++)
	for (int x = 0; x < nx; x++)
	view.data[0][x + vx * (ny + z)] = data[z][x + nx * hy];
	return view;
	}

	public RealSignal createFigure(int hx, int hy, int hz) {
	String n = "figure(" + name + ")";
	int vx = nx + nz + 4;
	int vy = ny + 2;
	float max = this.getExtrema()[1];
	RealSignal view = new RealSignal(n, vx, vy, 1);
	for (int i = 0; i < vx * vy; i++)
	view.data[0][i] = max;

	hx = Math.min(nx - 1, Math.max(0, hx));
	hy = Math.min(ny - 1, Math.max(0, hy));
	hz = Math.min(nz - 1, Math.max(0, hz));
	for (int x = 0; x < nx; x++)
	for (int y = 0; y < ny; y++)
	view.data[0][x + 1 + vx * (y + 1)] = data[hz][x + nx * y];

	for (int z = 0; z < nz; z++)
	for (int y = 0; y < ny; y++)
	view.data[0][nx + 3 + z + vx * (y + 1)] = data[z][hx + nx * y];

	return view;
	}

	public RealSignal createMIP() {
	String n = "mip(" + name + ")";

	- int vx = nx + nz + 1;
	- int vy = ny + nz + 1;
	+ int vx = nx + nz;
	+ int vy = ny + nz;
	RealSignal view = new RealSignal(n, vx, vy, 1);

	for (int x = 0; x < nx; x++)
	for (int y = 0; y < ny; y++)
	for (int k = 0; k < nz; k++) {
	int index = x + vx * y;
	view.data[0][index] = Math.max(view.data[0][index], data[k][x + nx * y]);
	}

	for (int z = 0; z < nz; z++)
	for (int y = 0; y < ny; y++)
	for (int x = 0; x < nx; x++) {
	- int index = nx + 1 + z + vx * y;
	+ int index = nx + z + vx * y;
	view.data[0][index] = Math.max(view.data[0][index], data[z][x + nx * y]);
	}

	for (int z = 0; z < nz; z++)
	for (int x = 0; x < nx; x++)
	for (int y = 0; y < ny; y++) {
	- int index = x + vx * (ny + 1 + z);
	+ int index = x + vx * (ny + z);
	view.data[0][index] = Math.max(view.data[0][index], data[z][x + nx * y]);
	}
	return view;
	}

	public RealSignal createMontage() {
	String n = "planar(" + name + ")";
	int nr = (int) Math.sqrt(nz);
	int nc = (int) Math.ceil(nz / nr) + 1;
	int w = nx * nr;
	int h = ny * nc;
	RealSignal view = new RealSignal(n, w, h, 1);
	for (int k = 0; k < nz; k++) {
	int col = k % nr;
	int row = k / nr;
	int offx = col * nx;
	int offy = row * ny;
	for (int x = 0; x < nx; x++)
	for (int y = 0; y < ny; y++)
	view.data[0][x + offx + w * (y + offy)] = data[k][x + nx * y];
	}
	return view;
	}

	public RealSignal circular() {
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++)
	setZ(i, j, rotate(getZ(i, j)));
	for (int i = 0; i < nx; i++)
	for (int k = 0; k < nz; k++)
	setY(i, k, rotate(getY(i, k)));
	for (int j = 0; j < ny; j++)
	for (int k = 0; k < nz; k++)
	setX(j, k, rotate(getX(j, k)));
	return this;
	}

	public RealSignal rescale(Monitors monitors) {
	new Constraint(monitors).rescaled(this, 0, 255);
	return this;
	}

	public float[] rotate(float[] buffer) {
	int len = buffer.length;
	if (len <= 1)
	return buffer;
	int count = 0;
	int offset = 0;
	int start = len / 2;
	while (count < len) {
	int index = offset;
	float tmp = buffer[index];
	int index2 = (start + index) % len;
	while (index2 != offset) {
	buffer[index] = buffer[index2];
	count++;
	index = index2;
	index2 = (start + index) % len;
	}
	buffer[index] = tmp;
	count++;
	offset++;
	}
	return buffer;
	}

	@Override
	public String toString() {
	return "Real Signal [" + nx + ", " + ny + ", " + nz + "]";
	}

	public BufferedImage preview() {
	if (preview != null)
	return preview;
	int nxy = nx*ny;
	float[] pixels = new float[nx*ny];
	for (int i = 0; i < nxy; i++)
	for (int k = 0; k < nz; k++) {
	pixels[i] = Math.max(pixels[i], data[k][i]);
	}
	float max = -Float.MAX_VALUE;
	float min = Float.MAX_VALUE;
	for (int i = 0; i < nxy; i++) {
	if (pixels[i] > max)
	max = pixels[i];
	if (pixels[i] < min)
	min = pixels[i];
	}
	float a = 255f / Math.max(max-min, (float)Operations.epsilon);
	preview = new BufferedImage(nx, ny, BufferedImage.TYPE_INT_ARGB);
	int alpha = (255 << 24);
	for (int i = 0; i < nx; i++)
	for (int j = 0; j < ny; j++) {
	int v = (int)(a(pixels[i+jnx] - min));
	preview.setRGB(i, j, alpha \| (v << 16) \| (v << 8) \| v);
	}
	return preview;
	}

	public RealSignal log10() {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = (float)Math.log10(data[k][i]);
	}
	return this;
	}

	public RealSignal log() {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = (float)Math.log(data[k][i]);
	}
	return this;
	}

	public RealSignal exp() {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = (float)Math.exp(data[k][i]);
	}
	return this;
	}

	public RealSignal abs() {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = (float)Math.abs(data[k][i]);
	}
	return this;
	}

	public RealSignal sqrt() {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = (float)Math.sqrt(data[k][i]);
	}
	return this;
	}

	public RealSignal sqr() {
	int nxy = nx * ny;
	for (int k = 0; k < nz; k++)
	for (int i = 0; i < nxy; i++) {
	data[k][i] = (float)(data[k][i]*data[k][i]);
	}
	return this;
	}

	+ public RealSignal rescale(double min, double max) {
	+ int nxy = nx * ny;
	+ float minf = (float)min;
	+ float stats[] = getStats();
	+ float a = ((float)max-minf) / (stats[2] - stats[1]);
	+ for(int k=0; k<nz; k++)
	+ for(int i=0; i<nxy; i++) {
	+ data[k][i] = a*(data[k][i] - stats[1]) + minf;
	+ }
	+ return this;
	+ }
	}
	diff --git a/DeconvolutionLab2/src/signal/apodization/Apodization.java b/DeconvolutionLab2/src/signal/apodization/Apodization.java
	index 1378a5e..20c0cd9 100644
	--- a/DeconvolutionLab2/src/signal/apodization/Apodization.java
	+++ b/DeconvolutionLab2/src/signal/apodization/Apodization.java
	@@ -1,160 +1,161 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.apodization;

	import java.util.ArrayList;

	+import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.Monitors;
	+import signal.Operations;
	import signal.RealSignal;
	-import signal.factory.Constant;

	public class Apodization {

	private AbstractApodization apoX = getDefault();
	private AbstractApodization apoY = getDefault();
	private AbstractApodization apoZ = getDefault();

	public Apodization() {
	apoX = new UniformApodization();
	apoY = new UniformApodization();
	apoZ = new UniformApodization();
	}

	public Apodization(AbstractApodization apoX, AbstractApodization apoY, AbstractApodization apoZ) {
	this.apoX = apoX;
	this.apoY = apoY;
	this.apoZ = apoZ;
	}

	public Apodization(String nameX, String nameY, String nameZ) {
	for(AbstractApodization apo : getApodizations()) {
	if (apo.getName().equals(nameX))
	apoX = apo;
	if (apo.getName().equals(nameY))
	apoY = apo;
	if (apo.getName().equals(nameZ))
	apoZ = apo;
	if (apo.getShortname().equals(nameX))
	apoX = apo;
	if (apo.getShortname().equals(nameY))
	apoY = apo;
	if (apo.getShortname().equals(nameZ))
	apoZ = apo;
	}
	}

	public static ArrayList<AbstractApodization> getApodizations() {
	ArrayList<AbstractApodization> apos = new ArrayList<AbstractApodization>();
	apos.add(new UniformApodization());
	apos.add(new HammingApodization());
	apos.add(new HannApodization());
	apos.add(new RaisedCosineApodization(1));
	apos.add(new TukeyApodization(0.5));
	apos.add(new WelchApodization());
	return apos;
	}

	public static ArrayList<String> getApodizationsName() {
	ArrayList<AbstractApodization> apos = getApodizations();
	ArrayList<String> names = new ArrayList<String>();
	for(AbstractApodization apo : apos)
	names.add(apo.getName());
	return names;
	}

	public static String[] getApodizationsAsArray() {
	ArrayList<AbstractApodization> apos = getApodizations();
	String names[] = new String[apos.size()];
	for(int i=0; i<apos.size(); i++)
	names[i] = apos.get(i).getName();
	return names;
	}

	public static AbstractApodization getByName(String name) {
	ArrayList<AbstractApodization> apos = getApodizations();
	for(AbstractApodization apo : apos)
	if (name.equals(apo.getName()))
	return apo;
	return getDefault();
	}

	public static AbstractApodization getByShortname(String name) {
	ArrayList<AbstractApodization> apos = getApodizations();
	for(AbstractApodization apo : apos)
	if (name.equals(apo.getShortname()))
	return apo;
	return getDefault();
	}

	public static AbstractApodization getDefault() {
	return new UniformApodization();
	}

	public void apodize(Monitors monitors, RealSignal signal) {
	if (apoX instanceof UniformApodization &&
	apoY instanceof UniformApodization &&
	apoZ instanceof UniformApodization) {
	return;
	}
	if (monitors != null)
	monitors.log("Apodization (" + apoX.getName() + ", " + apoY.getName() + ", " + apoZ.getName() + ")");
	signal.setName("apo(" + signal.name + ")");
	for(int i=0; i<signal.nx; i++) {
	double cx = apoX.apodize(i, signal.nx);
	for(int j=0; j<signal.ny; j++) {
	double cy = apoY.apodize(j, signal.ny);
	int index = i + signal.nx*j;
	for(int k=0; k<signal.nz; k++) {
	double cz = apoZ.apodize(k, signal.nz);
	signal.data[k][index] = (float)(cx * cy * cz * signal.data[k][index]);
	}
	}
	}
	}

	@Override
	public String toString() {
	String s = "";
	s += "lateral (XY)";
	if (apoX instanceof UniformApodization)
	s += " keep unchanged";
	else
	s+= " " + apoX.getName();
	s += ", axial (Z)";
	if (apoZ instanceof UniformApodization)
	s += " keep unchanged";
	else
	s+= " " + apoZ.getName();

	return s;
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Defocus.java b/DeconvolutionLab2/src/signal/factory/Airy.java
	similarity index 53%
	copy from DeconvolutionLab2/src/signal/factory/Defocus.java
	copy to DeconvolutionLab2/src/signal/factory/Airy.java
	index 14fc015..4eef21a 100644
	--- a/DeconvolutionLab2/src/signal/factory/Defocus.java
	+++ b/DeconvolutionLab2/src/signal/factory/Airy.java
	@@ -1,99 +1,96 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	+import bilib.tools.Bessel;
	import signal.RealSignal;

	-public class Defocus extends SignalFactory {
	+public class Airy extends SignalFactory {

	- private double fwhm = 3.0;
	- private double low2fwhm = 10;
	- private double up2fwhm = 10;
	+ private double pupil = 5;
	+ private double lambda = 1;
	+ private double distanceAxial = 0.5;
	+ private double attenuationFactor = 3;

	- public Defocus(double fwhm, double low2fwhm, double up2fwhm) {
	- super(new double[] {fwhm, low2fwhm, up2fwhm});
	+ public Airy(double pupil, double lambda, double distanceAxial, double attenuationFactor) {
	+ super(new double[] {pupil, lambda, distanceAxial, attenuationFactor});
	+ setParameters(new double[] {pupil, lambda, distanceAxial, attenuationFactor});
	}

	@Override
	public String getName() {
	- return "Defocus";
	+ return "Airy";
	}
	-
	+
	@Override
	public String[] getParametersName() {
	- return new String[] {"FWHM at focus plane", "-Delta Z (2xFWHM)", "+Delta Z (2xFWHM)"};
	- }
	+ return new String[] { "Pupil (normalized unit)", "Wavelength (normalized unit)", "Axial distance (normalized unit)", "Attenuation Factor" };
	+ }

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	- this.fwhm = parameters[0];
	+ this.pupil = parameters[0];
	if (parameters.length >= 2)
	- this.low2fwhm = parameters[1];
	+ this.lambda = parameters[1];
	if (parameters.length >= 3)
	- this.up2fwhm = parameters[2];
	+ this.distanceAxial = parameters[2];
	+ if (parameters.length >= 4)
	+ this.attenuationFactor = parameters[3];
	+
	}

	@Override
	public double[] getParameters() {
	- return new double[] {fwhm, low2fwhm, up2fwhm};
	+ return new double[] {pupil, lambda, distanceAxial, attenuationFactor};
	}
	-
	+
	@Override
	public void fill(RealSignal signal) {
	- double sigma = 2.0 * Math.sqrt(2.0 * Math.log(2.0));
	- double zup = zc - low2fwhm;
	- double zlw = zc + up2fwhm;
	- double Q = 2.0*Math.PI;
	-
	- double A0 = (amplitude-background) * (sigma * sigma * Q);
	- double aup = 2.0 / ((zup-zc)*(zup-zc));
	- double alw = 2.0 / ((zlw-zc)*(zlw-zc));
	- for(int z=0; z<nz; z++) {
	- double sigmaZ = sigma;
	- if (z > zc)
	- sigmaZ += sigma * aup * (z-zc)*(z-zc);
	- else
	- sigmaZ += sigma * alw * (z-zc)*(z-zc);
	-
	- double K = 1.0 / (2.0sigmaZsigmaZ);
	- double A = A0 / (sigmaZ * sigmaZ * 2);
	- for(int x=0; x<nx; x++)
	- for(int y=0; y<ny; y++) {
	- double r2 = (x-xc)(x-xc) + (y-yc)(y-yc);
	- signal.data[z][x+nxy] = (float)(A Math.exp(-K*r2) + background);
	+ int xsize = nx / 2;
	+ int ysize = ny / 2;
	+ double d = Math.max(0.01, distanceAxial);
	+ double diag = Math.sqrt(xsizexsize + ysizeysize);
	+ double b = 2.0 * Math.PI * pupil / lambda;
	+ double epsilon = 0.01 / diag;
	+ for(int i=0; i<nx; i++)
	+ for(int j=0; j<ny; j++) {
	+ double r = Math.max(epsilon, Math.sqrt((i-xc)(i-xc)+(j-yc)(j-yc)) / diag);
	+ for(int k=0; k<nz; k++) {
	+ double dz = Math.abs(k-zc)/nz;
	+ double z1 = d + dz;
	+ double jc = Bessel.J1(r * b / z1) / r;
	+ signal.data[k][i+jnx] = (float)(jcjc* Math.exp(-dz*attenuationFactor));
	}
	}
	}
	-
	-
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Astigmatism.java b/DeconvolutionLab2/src/signal/factory/Astigmatism.java
	index 36017a6..674eb7f 100644
	--- a/DeconvolutionLab2/src/signal/factory/Astigmatism.java
	+++ b/DeconvolutionLab2/src/signal/factory/Astigmatism.java
	@@ -1,90 +1,95 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import signal.RealSignal;

	public class Astigmatism extends SignalFactory {

	- private double fwhm = 3.0;
	- private double factor = 0.20;
	+ private double fwhm = 5.0;
	+ private double factor = 1;

	public Astigmatism(double fwhm, double factor) {
	super(new double[] {fwhm, factor});
	+ setParameters(new double[] {fwhm, factor});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"FWHM at focus plane", "Astigmatism factor"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.fwhm = parameters[0];
	if (parameters.length >= 2)
	- this.fwhm = parameters[1];
	+ this.factor = parameters[1];
	}

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

	@Override
	public void fill(RealSignal signal) {
	- double A = (amplitude-background);
	double sigma = 0.8493218 * fwhm; // 1/sqrt(-2*log(0.5))
	+ factor = 1;
	for(int z=0; z<nz; z++) {
	- double dx = (zc-z) * factor + 1;
	- double dy = 1/dx;
	- if (z-zc > 0) {
	- dy = (z-zc) * factor + 1;
	+ double dx = 1.0;
	+ double dy = 1.0;
	+ if (z>zc) {
	+ dy = (1.0-factor*(z-zc)/(double)nz);
	dx = 1.0 / dy;
	}
	+ if (z<zc) {
	+ dx = (1.0-factor*(zc-z)/(double)nz);
	+ dy = 1.0 / dx;
	+ }
	double kx = 1.0 / (dx * dx * sigma * sigma * 2.0);
	double ky = 1.0 / (dy * dy * sigma * sigma * 2.0);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++) {
	double r2 = kx(x-xc)(x-xc) + ky(y-yc)(y-yc);
	- signal.data[z][x+nxy] = (float)(A Math.exp(-r2) + background);
	+ signal.data[z][x+nxy] = (float)(amplitude Math.exp(-r2));
	}
	}
	}


	}
	diff --git a/DeconvolutionLab2/src/signal/factory/AxialDiffractionSimulation.java b/DeconvolutionLab2/src/signal/factory/AxialDiffractionSimulation.java
	new file mode 100644
	index 0000000..db3459f
	--- /dev/null
	+++ b/DeconvolutionLab2/src/signal/factory/AxialDiffractionSimulation.java
	@@ -0,0 +1,116 @@
	+/*
	+ * DeconvolutionLab2
	+ *
	+ * Conditions of use: You are free to use this software for research or
	+ * educational purposes. In addition, we expect you to include adequate
	+ * citations and acknowledgments whenever you present or publish results that
	+ * are based on it.
	+ *
	+ * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	+ * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	+ * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	+ */
	+
	+/*
	+ * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	+ *
	+ * This file is part of DeconvolutionLab2 (DL2).
	+ *
	+ * DL2 is free software: you can redistribute it and/or modify it under the
	+ * terms of the GNU General Public License as published by the Free Software
	+ * Foundation, either version 3 of the License, or (at your option) any later
	+ * version.
	+ *
	+ * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	+ *
	+ * You should have received a copy of the GNU General Public License along with
	+ * DL2. If not, see <http://www.gnu.org/licenses/>.
	+ */
	+
	+package signal.factory;
	+
	+import deconvolutionlab.monitor.Monitors;
	+import fft.AbstractFFT;
	+import fft.FFT;
	+import signal.ComplexSignal;
	+import signal.RealSignal;
	+import signal.factory.complex.ComplexSignalFactory;
	+
	+public class AxialDiffractionSimulation extends SignalFactory {
	+
	+ private double pupil = 10;
	+ private double defocusFactor = 10;
	+ private double waveNumberAxial = 2;
	+
	+ public AxialDiffractionSimulation(double pupil, double defocusFactor, double waveNumberAxial) {
	+ super(new double[] {pupil, defocusFactor, waveNumberAxial});
	+ setParameters(new double[] {pupil, defocusFactor, waveNumberAxial});
	+ }
	+
	+ @Override
	+ public String getName() {
	+ return "Axial Diffraction Simulation";
	+ }
	+
	+ @Override
	+ public String[] getParametersName() {
	+ return new String[] { "Pupil Size", "Defocus Factor", "Wave Number (Axial)" };
	+ }
	+
	+ @Override
	+ public void setParameters(double[] parameters) {
	+ if (parameters.length >= 1)
	+ this.pupil = parameters[0];
	+ if (parameters.length >= 2)
	+ this.defocusFactor = parameters[1];
	+ if (parameters.length >= 3)
	+ this.waveNumberAxial = parameters[2];
	+
	+ }
	+
	+ @Override
	+ public double[] getParameters() {
	+ return new double[] {pupil, defocusFactor, waveNumberAxial};
	+ }
	+
	+ @Override
	+ public void fill(RealSignal signal) {
	+ AbstractFFT fft = FFT.getFastestFFT().getDefaultFFT();
	+ fft.init(Monitors.createDefaultMonitor(), nx, ny, 1);
	+
	+ double defocusTop = 2.0Math.PI / (defocusFactorpupil);
	+ double defocusCen = 2.0*Math.PI / pupil;
	+ int xsize = nx / 2;
	+ int ysize = ny / 2;
	+ int zsize = nz / 2;
	+
	+ double diag = Math.sqrt(xsizexsize + ysizeysize);
	+ double wx, wy, wz;
	+ for (int z = 0; z <= zsize; z++) {
	+ float[][][] real = new float[xsize + 1][ysize + 1][1];
	+ float[][][] imag = new float[xsize + 1][ysize + 1][1];
	+ wz = waveNumberAxial(zsize-z)2.0*Math.PI / zsize;
	+ double cosz = Math.cos(wz);
	+ double sinz = Math.sin(wz);
	+ double fcz = z * Math.abs(defocusTop-defocusCen) / zsize + defocusCen;
	+ double fcz2 = fcz*fcz;
	+ for (int y = 0; y <= ysize; y++)
	+ for (int x = 0; x <= xsize; x++) {
	+ wx = x * x;
	+ wy = y * y;
	+ double g = (wy + wx) / diag;
	+ if (g < fcz2) {
	+ real[x][y][0] = (float) (g * cosz);
	+ imag[x][y][0] = (float) (g * sinz);
	+ }
	+ }
	+ ComplexSignal c = ComplexSignalFactory.createHermitian(""+z, nx, ny, 1, real, imag);
	+ RealSignal pz = fft.inverse(c).circular();
	+ signal.setXY(z, pz.getXY(0));
	+ signal.setXY(nz-1-z, pz.duplicate().getXY(0));
	+ }
	+ signal.rescale(0, amplitude);
	+ }
	+}
	diff --git a/DeconvolutionLab2/src/signal/factory/Constant.java b/DeconvolutionLab2/src/signal/factory/Constant.java
	index de0367f..30d09fe 100644
	--- a/DeconvolutionLab2/src/signal/factory/Constant.java
	+++ b/DeconvolutionLab2/src/signal/factory/Constant.java
	@@ -1,70 +1,70 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import signal.RealSignal;

	public class Constant extends SignalFactory {

	public Constant() {
	super(new double[] {});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {};
	}

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

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

	@Override
	public void fill(RealSignal signal) {
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++)
	for(int z=0; z<nz; z++) {
	- signal.data[z][x+nx*y] = (float)(amplitude + background);
	+ signal.data[z][x+nx*y] = (float)(amplitude);
	}
	}

	}
	\ No newline at end of file
	diff --git a/DeconvolutionLab2/src/signal/factory/Cross.java b/DeconvolutionLab2/src/signal/factory/Cross.java
	index d8d5d92..1a7b8fc 100644
	--- a/DeconvolutionLab2/src/signal/factory/Cross.java
	+++ b/DeconvolutionLab2/src/signal/factory/Cross.java
	@@ -1,111 +1,112 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import signal.RealSignal;

	public class Cross extends SignalFactory {

	private double thickness = 1.0;
	private double slope = 1.0;
	private double lengthPercentage = 30.0;

	public Cross(double thickness, double slope, double lengthPercentage) {
	super(new double[] {thickness, slope, lengthPercentage});
	+ setParameters(new double[] {thickness, slope, lengthPercentage});
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.thickness = parameters[0];
	if (parameters.length >= 2)
	this.slope = parameters[1];
	if (parameters.length >= 3)
	this.lengthPercentage = parameters[2];
	}

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

	@Override
	public double[] getParameters() {
	return new double[] { thickness, slope, lengthPercentage };
	}

	@Override
	public String[] getParametersName() {
	return new String[] { "Thickness", "Sigmoid Curve Slope", "Length (percentage)" };
	}

	@Override
	public void fill(RealSignal signal) {
	double length = lengthPercentage * 0.01 * 0.5;
	- double A = (amplitude - background);
	int x1 = (int) Math.round(xc - nx * length);
	int x2 = (int) Math.round(xc + nx * length);
	int y1 = (int) Math.round(yc - ny * length);
	int y2 = (int) Math.round(yc + ny * length);
	int z1 = (int) Math.round(zc - nz * length);
	int z2 = (int) Math.round(zc + nz * length);
	for (int z = 0; z < nz; z++) {
	for (int x = 0; x < nx; x++)
	for (int y = 0; y < ny; y++) {
	double px = (x - xc) * (x - xc);
	double py = (y - yc) * (y - yc);
	double pz = (z - zc) * (z - zc);

	double dx = Double.MAX_VALUE;
	for (int i = x1; i < x2; i++)
	dx = Math.min(dx, (i - x) * (i - x) + py + pz);
	dx = Math.sqrt(dx) - thickness;
	double ax = (1.0 - 1.0 / (1.0 + Math.exp(-dx / slope)));

	double dy = Double.MAX_VALUE;
	for (int j = y1; j < y2; j++)
	dy = Math.min(dy, px + (j - y) * (j - y) + pz);
	dy = Math.sqrt(dy) - thickness;
	double ay = (1.0 - 1.0 / (1.0 + Math.exp(-dy / slope)));

	double dz = Double.MAX_VALUE;
	for (int k = z1; k < z2; k++)
	dz = Math.min(dz, px + py + (k - z) * (k - z));
	dz = Math.sqrt(dz) - thickness;
	double az = (1.0 - 1.0 / (1.0 + Math.exp(-dz / slope)));

	- signal.data[z][x + nx * y] = (float) (A * Math.max(Math.max(ax, ay), az) + background);
	+ signal.data[z][x + nx * y] = (float) (Math.max(Math.max(ax, ay), az));
	}
	}
	+ signal.rescale(0, amplitude);
	}

	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Cube.java b/DeconvolutionLab2/src/signal/factory/Cube.java
	index 1af4c5a..95c6712 100644
	--- a/DeconvolutionLab2/src/signal/factory/Cube.java
	+++ b/DeconvolutionLab2/src/signal/factory/Cube.java
	@@ -1,85 +1,84 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import signal.RealSignal;

	public class Cube extends SignalFactory {

	private double side = 10;
	private double slope = 1;

	public Cube(double side, double slope) {
	super(new double[] {side, slope});
	setParameters(new double[] {side, slope});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"Side", "Sigmoid Curve Slope"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.side = parameters[0];
	if (parameters.length >= 2)
	this.slope = parameters[1];
	}

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

	@Override
	public void fill(RealSignal signal) {
	- double A = (amplitude-background);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++)
	for(int z=0; z<nz; z++) {
	double dx = Math.sqrt((x-xc)*(x-xc)) - side;
	double dy = Math.sqrt((y-yc)*(y-yc)) - side;
	double dz = Math.sqrt((z-zc)*(z-zc)) - side;
	double rx = 1.0- 1.0 / (1.0 + Math.exp(-dx/slope));
	double ry = 1.0- 1.0 / (1.0 + Math.exp(-dy/slope));
	double rz = 1.0- 1.0 / (1.0 + Math.exp(-dz/slope));
	- signal.data[z][x+nxy] = (float)(A (rx ry rz) + background);
	+ signal.data[z][x+nxy] = (float)(amplitude (rx ry rz));
	}

	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/GridSpots.java b/DeconvolutionLab2/src/signal/factory/CubeSphericalBeads.java
	similarity index 68%
	rename from DeconvolutionLab2/src/signal/factory/GridSpots.java
	rename to DeconvolutionLab2/src/signal/factory/CubeSphericalBeads.java
	index c8ab88c..4214275 100644
	--- a/DeconvolutionLab2/src/signal/factory/GridSpots.java
	+++ b/DeconvolutionLab2/src/signal/factory/CubeSphericalBeads.java
	@@ -1,116 +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 signal.factory;

	import signal.RealSignal;

	-public class GridSpots extends SignalFactory {
	+public class CubeSphericalBeads extends SignalFactory {

	private double radius = 3.0;
	- private double slope = 1;
	- private double spacing = 10.0;
	+ private double slope = 0.5;
	+ private double spacing = 8.0;
	+ private double border = 8.0;

	- public GridSpots(double radius, double slope, double spacing) {
	- super(new double[] {radius, spacing});
	+ public CubeSphericalBeads(double side, double slope, double spacing, double border) {
	+ super(new double[] { side, slope, spacing, border });
	+ setParameters(new double[] { side, slope, spacing, border });
	}

	@Override
	public String getName() {
	- return "GridSpots";
	+ return "Cube of Spherical Beads";
	}

	@Override
	public String[] getParametersName() {
	- return new String[] { "Radius", "Sigmoid Curve Slope", "Spacing" };
	+ return new String[] { "Radius", "Sigmoid Curve Slope", "Spacing", "Border" };
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.radius = parameters[0];
	if (parameters.length >= 2)
	this.slope = parameters[1];
	if (parameters.length >= 3)
	this.spacing = parameters[2];
	+ if (parameters.length >= 4)
	+ this.border = parameters[3];
	}

	@Override
	public double[] getParameters() {
	- return new double[] { radius, slope, spacing };
	+ return new double[] { radius, slope, spacing, border };
	}

	@Override
	- public void fill(RealSignal signal) {
	- float b = (float) background;
	- for (int x = 0; x < nx; x++)
	- for (int y = 0; y < ny; y++)
	- for (int z = 0; z < nz; z++)
	- signal.data[z][x + nx * y] = b;
	-
	- int nc = (int) ((nx - spacing) / spacing);
	-
	- int nr = (int) ((2 * (ny - spacing)) / spacing);
	- double deltaY = spacing / nr;
	- int np = (int) ((2 * (nz - spacing)) / spacing);
	- double deltaZ = spacing / np;
	- double y = 0;
	- double z = 0;
	- for (int j = 0; j < nr; j++) {
	- y += (spacing - j * deltaY);
	- z = 0;
	- for (int k = 0; k < np; k++) {
	- z += (spacing - k * deltaZ);
	- for (int i = 0; i < nc; i++) {
	- double x = spacing + i * spacing;
	- double A = amplitude- background; //i*(amplitude-background) / (nc+1);
	- spot(signal, x, y, z, A);
	+ public void fill(RealSignal signal) {
	+ double dimx = (nx - 2.0 * border);
	+ double dimy = (ny - 2.0 * border);
	+ double dimz = (nz - 2.0 * border);
	+ int mx = (int) (dimx / spacing) - 1;
	+ int my = (int) (dimy / spacing) - 1;
	+ int mz = (int) (dimz / spacing) - 1;
	+ double stepx = dimx / mx;
	+ float stepa = (float) (0.5 * amplitude / mx);
	+ double x = border;
	+ for (int i = 0; i < mx; i++) {
	+ for (int j = 0; j < my; j++) {
	+ double y = border + (dimy) * Math.sin(j * 0.5 * Math.PI / my);
	+ for (int k = 0; k < mz; k++) {
	+ double z = border + (dimz) * Math.sin(k * 0.5 * Math.PI / mz);
	+ spot(signal, x, y, z, amplitude - i * stepa);
	}
	}
	+ x += stepx;
	}
	}

	private void spot(RealSignal signal, double xc, double yc, double zc, double A) {
	int x1 = (int) Math.max(0, Math.round(xc - radius - 3 * slope));
	int x2 = (int) Math.min(nx - 1, Math.round(xc + radius + 3 * slope));
	int y1 = (int) Math.max(0, Math.round(yc - radius - 3 * slope));
	int y2 = (int) Math.min(ny - 1, Math.round(yc + radius + 3 * slope));
	int z1 = (int) Math.max(0, Math.round(zc - radius - 3 * slope));
	int z2 = (int) Math.min(nz - 1, Math.round(zc + radius + 3 * slope));
	for (int x = x1; x <= x2; x++)
	for (int y = y1; y <= y2; y++)
	for (int z = z1; z <= z2; z++) {
	double dr = Math.sqrt((x - xc) * (x - xc) + (y - yc) * (y - yc) + (z - zc) * (z - zc)) - radius;
	signal.data[z][x + nx * y] = Math.max(signal.data[z][x + nx * y], (float) (A - A / (1.0 + Math.exp(-dr / slope))));
	}
	}

	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Defocus.java b/DeconvolutionLab2/src/signal/factory/Defocus.java
	index 14fc015..c3ba9d8 100644
	--- a/DeconvolutionLab2/src/signal/factory/Defocus.java
	+++ b/DeconvolutionLab2/src/signal/factory/Defocus.java
	@@ -1,99 +1,98 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import signal.RealSignal;

	public class Defocus extends SignalFactory {

	private double fwhm = 3.0;
	private double low2fwhm = 10;
	private double up2fwhm = 10;

	public Defocus(double fwhm, double low2fwhm, double up2fwhm) {
	super(new double[] {fwhm, low2fwhm, up2fwhm});
	+ setParameters(new double[] { fwhm, low2fwhm, up2fwhm });
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"FWHM at focus plane", "-Delta Z (2xFWHM)", "+Delta Z (2xFWHM)"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.fwhm = parameters[0];
	if (parameters.length >= 2)
	this.low2fwhm = parameters[1];
	if (parameters.length >= 3)
	this.up2fwhm = parameters[2];
	}

	@Override
	public double[] getParameters() {
	return new double[] {fwhm, low2fwhm, up2fwhm};
	}

	@Override
	public void fill(RealSignal signal) {
	- double sigma = 2.0 * Math.sqrt(2.0 * Math.log(2.0));
	+ double sigma = fwhm;
	double zup = zc - low2fwhm;
	double zlw = zc + up2fwhm;
	double Q = 2.0*Math.PI;

	- double A0 = (amplitude-background) * (sigma * sigma * Q);
	+ double A0 = (sigma * sigma * Q);
	double aup = 2.0 / ((zup-zc)*(zup-zc));
	double alw = 2.0 / ((zlw-zc)*(zlw-zc));
	for(int z=0; z<nz; z++) {
	double sigmaZ = sigma;
	if (z > zc)
	sigmaZ += sigma * aup * (z-zc)*(z-zc);
	else
	sigmaZ += sigma * alw * (z-zc)*(z-zc);

	double K = 1.0 / (2.0sigmaZsigmaZ);
	double A = A0 / (sigmaZ * sigmaZ * 2);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++) {
	double r2 = (x-xc)(x-xc) + (y-yc)(y-yc);
	- signal.data[z][x+nxy] = (float)(A Math.exp(-K*r2) + background);
	+ signal.data[z][x+nxy] = (float)(amplitude Math.exp(-K*r2));
	}
	}
	}
	-
	-
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/AirySimulated.java b/DeconvolutionLab2/src/signal/factory/DirectionalDerivative.java
	similarity index 74%
	copy from DeconvolutionLab2/src/signal/factory/AirySimulated.java
	copy to DeconvolutionLab2/src/signal/factory/DirectionalDerivative.java
	index 644d04a..ef6e451 100644
	--- a/DeconvolutionLab2/src/signal/factory/AirySimulated.java
	+++ b/DeconvolutionLab2/src/signal/factory/DirectionalDerivative.java
	@@ -1,80 +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 signal.factory;

	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.FFT;
	import signal.ComplexSignal;
	import signal.RealSignal;
	import signal.factory.complex.ComplexSignalFactory;

	-public class AirySimulated extends SignalFactory {
	+public class DirectionalDerivative extends SignalFactory {

	- private double mu = 1.0;
	+ private double vx = 1.0;
	+ private double vy = 1.0;
	+ private double vz = 0.0;

	- public AirySimulated(double mu) {
	- super(new double[] {mu});
	+ public DirectionalDerivative(double vx, double vy, double vz) {
	+ super(new double[] {vx, vy, vz});
	+ setParameters(new double[] {vx, vy, vz});
	}

	@Override
	public String getName() {
	- return "AirySimulated";
	+ return "Directional Derivative";
	}

	@Override
	public String[] getParametersName() {
	- return new String[] {"Parameter (mu)"};
	+ return new String[] {"Direction in X", "Direction in Y", "Direction in Z"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	- this.mu = parameters[0];
	+ this.vx = parameters[0];
	+ if (parameters.length >= 2)
	+ this.vy = parameters[1];
	+ if (parameters.length >= 3)
	+ this.vz = parameters[2];
	}

	@Override
	public double[] getParameters() {
	- return new double[] {mu};
	+ return new double[] {vx, vy, vz};
	}

	@Override
	public void fill(RealSignal signal) {
	AbstractFFT fft = FFT.createDefaultFFT(Monitors.createDefaultMonitor(), nx, ny, nz);
	- ComplexSignal C = ComplexSignalFactory.airySimulated(nx, ny, nz, mu);
	+ ComplexSignal C = ComplexSignalFactory.directionalDerivative(nx, ny, nz, vx, vy, vz);
	RealSignal s = fft.inverse(C).circular().times((float)amplitude);
	- s.times(s);
	signal.copy(s);
	}


	}
	diff --git a/DeconvolutionLab2/src/signal/factory/MotionBlur.java b/DeconvolutionLab2/src/signal/factory/DirectionalMotionBlur.java
	similarity index 58%
	rename from DeconvolutionLab2/src/signal/factory/MotionBlur.java
	rename to DeconvolutionLab2/src/signal/factory/DirectionalMotionBlur.java
	index 61042fa..1d64521 100644
	--- a/DeconvolutionLab2/src/signal/factory/MotionBlur.java
	+++ b/DeconvolutionLab2/src/signal/factory/DirectionalMotionBlur.java
	@@ -1,93 +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 signal.factory;

	-import signal.Operations;
	import signal.RealSignal;
	-import signal.Signal;

	-public class MotionBlur extends SignalFactory {
	+public class DirectionalMotionBlur extends SignalFactory {

	private double sigma = 3.0;
	private double direction = 30.0;
	- private double elongation = 3.0;
	+ private double elongation = 30.0;

	- public MotionBlur(double sigma, double direction, double elongation) {
	+ public DirectionalMotionBlur(double sigma, double direction, double elongation) {
	super(new double[] { sigma, direction, elongation });
	+ setParameters(new double[] { sigma, direction, elongation });
	}

	@Override
	public String getName() {
	- return "MotionBlur";
	+ return "Direction Motion Blur";
	}

	@Override
	public String[] getParametersName() {
	- return new String[] { "Sigma", "Direction", "Elongation" };
	+ return new String[] { "Sigma", "Lateral Direction (Degree)", "Elongation" };
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.sigma = parameters[0];
	if (parameters.length >= 2)
	this.direction = parameters[1];
	if (parameters.length >= 3)
	this.elongation = parameters[2];
	}

	@Override
	public double[] getParameters() {
	return new double[] { sigma, direction, elongation };
	}

	@Override
	public void fill(RealSignal signal) {
	- double K1 = 0.5 / (sigma * sigma);
	- double K2 = 0.5 / (sigma * sigma * elongation * elongation);
	+
	double cosa = Math.cos(Math.toRadians(direction));
	double sina = Math.sin(Math.toRadians(direction));
	- for (int x = 0; x < nx; x++)
	- for (int y = 0; y < ny; y++) {
	- double dx = (x - xc);
	- double dy = (y - yc);
	-
	- double M = (dx * cosa + dy * sina) / Math.max(dx * dx + dy * dy, Operations.epsilon);
	- M = (1.0 - 1.0 / (1.0 + Math.exp(-M / elongation)));

	- double r2 = (x - xc) * (x - xc) + (y - yc) * (y - yc);
	- for (int z = 0; z < nz; z++) {
	- signal.data[z][x + nx * y] = (float) ((amplitude - background) * M * Math.exp(0) + background);
	+ double xe = elongation * cosa + xc;
	+ double ye = elongation * sina + yc;
	+ double dx = (xe - xc) / elongation;
	+ double dy = (ye - yc) / elongation;
	+ for(int k=0; k<elongation; k++) {
	+ double x = xc + k*dx;
	+ double y = yc + k*dy;
	+ spot(signal, x, y, amplitude);
	+ }
	+ }
	+
	+ private void spot(RealSignal signal, double xc, double yc, double A) {
	+ double slope = 1;
	+ int x1 = (int) Math.max(0, Math.round(xc - sigma - 3 * slope));
	+ int x2 = (int) Math.min(nx - 1, Math.round(xc + sigma + 3 * slope));
	+ int y1 = (int) Math.max(0, Math.round(yc - sigma - 3 * slope));
	+ int y2 = (int) Math.min(ny - 1, Math.round(yc + sigma + 3 * slope));
	+ int z1 = (int) Math.max(0, Math.round(zc - sigma - 3 * slope));
	+ int z2 = (int) Math.min(nz - 1, Math.round(zc + sigma + 3 * slope));
	+ for (int x = x1; x <= x2; x++)
	+ for (int y = y1; y <= y2; y++) {
	+ double dr = Math.sqrt((x - xc) * (x - xc) + (y - yc) * (y - yc)) - sigma;
	+ float v = (float) (A - A / (1.0 + Math.exp(-dr / slope)));
	+ for (int z = z1; z <= z2; z++) {
	+ signal.data[z][x + nx * y] = Math.max(signal.data[z][x + nx * y], v);
	}
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/DoG.java b/DeconvolutionLab2/src/signal/factory/DoG.java
	index 74dc3ce..dee4526 100644
	--- a/DeconvolutionLab2/src/signal/factory/DoG.java
	+++ b/DeconvolutionLab2/src/signal/factory/DoG.java
	@@ -1,80 +1,81 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import signal.RealSignal;

	public class DoG extends SignalFactory {

	private double sigma1 = 3.0;
	private double sigma2 = 4.0;

	public DoG(double sigma1, double sigma2) {
	super(new double[] {sigma1, sigma2});
	+ setParameters(new double[] {sigma1, sigma2});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"Sigma 1", "Sigma 2"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.sigma1 = parameters[0];
	if (parameters.length >= 2)
	this.sigma2 = parameters[1];
	}

	@Override
	public double[] getParameters() {
	return new double[] {sigma1, sigma2};
	}

	@Override
	public void fill(RealSignal signal) {
	double K1 = 0.5 / (sigma1*sigma1);
	double K2 = 0.5 / (sigma2*sigma2);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++)
	for(int z=0; z<nz; z++) {
	double r2 = (x-xc)(x-xc) + (y-yc)(y-yc) + (z-zc)*(z-zc);
	double v = Math.exp(-K2r2) - Math.exp(-K1r2);
	- signal.data[z][x+nxy] = (float)((amplitude-background) v + background);
	+ signal.data[z][x+nxy] = (float)(amplitude v);
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/DoubleHelix.java b/DeconvolutionLab2/src/signal/factory/DoubleConeWave.java
	similarity index 52%
	copy from DeconvolutionLab2/src/signal/factory/DoubleHelix.java
	copy to DeconvolutionLab2/src/signal/factory/DoubleConeWave.java
	index b40c050..0f5ad20 100644
	--- a/DeconvolutionLab2/src/signal/factory/DoubleHelix.java
	+++ b/DeconvolutionLab2/src/signal/factory/DoubleConeWave.java
	@@ -1,92 +1,95 @@
	-package signal.factory;
	-
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	+package signal.factory;
	+
	import signal.RealSignal;

	-public class DoubleHelix extends SignalFactory {
	+public class DoubleConeWave extends SignalFactory {

	- private double fwhm = 3.0;
	- private double dist = 10;
	- private double delta = 10;
	+ private double aperture = 60;
	+ private double periodTopZ = 5;
	+ private double periodCenterZ = 15;
	+ private double attenuation = 10;

	- public DoubleHelix(double fwhm, double dist, double delta) {
	- super(new double[] {fwhm, dist, delta});
	+ public DoubleConeWave(double aperture, double periodTopZ, double periodCenterZ, double attenuation) {
	+ super(new double[] {aperture, periodTopZ, periodCenterZ, attenuation});
	+ setParameters(new double[] {aperture, periodTopZ, periodCenterZ, attenuation});
	}

	@Override
	public String getName() {
	- return "Double-Helix";
	+ return "Double Cone Wave";
	}
	-
	+
	@Override
	public String[] getParametersName() {
	- return new String[] {"FWHM at focus plane", "Distance", "Delta Z (rotation PI)"};
	- }
	+ return new String[] { "Aperture", "Period TopZ", "Period CenterZ", "Attenuation" };
	+ }

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	- this.fwhm = parameters[0];
	+ this.aperture = parameters[0];
	if (parameters.length >= 2)
	- this.dist = parameters[1];
	+ this.periodTopZ = parameters[1];
	if (parameters.length >= 3)
	- this.delta = parameters[2];
	+ this.periodCenterZ = parameters[2];
	+ if (parameters.length >= 4)
	+ this.attenuation = parameters[3];
	}

	@Override
	public double[] getParameters() {
	- return new double[] {fwhm, dist, delta};
	+ return new double[] {aperture, periodTopZ, periodCenterZ, attenuation};
	}
	-
	+
	@Override
	public void fill(RealSignal signal) {
	- double K = 0.5 / (fwhm*fwhm);
	- double A = (amplitude-background);
	- double T = Math.PI/(delta*2.0);
	- for(int z=0; z<nz; z++) {
	- double cosa = Math.cos((z-zc)*T);
	- double sina = Math.sin((z-zc)*T);
	- for(int x=0; x<nx; x++)
	- for(int y=0; y<ny; y++) {
	- double u = (x-xc) * cosa + (y-yc) * sina;
	- double v = -(x-xc) * sina + (y-yc) * cosa;
	- double u1 = (u - dist * 0.5);
	- double u2 = (u + dist * 0.5);
	- double p = Math.exp(-((u1 * u1 + v * v) * K)) + Math.exp(-((u2 * u2 + v * v) * K));
	- signal.data[z][x+nxy] = (float)(A p + background);
	+ double apernorm = (2.0*aperture)/(nx+ny);
	+ double diag = Math.sqrt(nxnx+nyny+nz*nz);
	+ double step = (periodCenterZ-periodTopZ)/nz;
	+ for(int i=0; i<nx; i++)
	+ for(int j=0; j<ny; j++) {
	+ double r = Math.sqrt((i-xc)(i-xc)+(j-yc)(j-yc));
	+ for(int k=0; k<nz; k++) {
	+ double z = Math.abs(k-zc);
	+ double p = Math.sqrt(rr + zz)/diag;
	+ double period = Math.max(1, periodCenterZ-step*z);
	+ double sz = apernormz + period0.25;
	+ double s = 1.0 / (1.0+Math.exp(-(r+sz))) - 1.0 / (1.0+Math.exp(-(r-sz)));
	+ double q = Math.cos(2.0Math.PI(r-apernorm*z)/period);
	+ double g = (attenuation*p+1);
	+ signal.data[k][i+jnx] = (float)(amplitude s * q * q / g);
	}
	}
	}
	-
	-
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/DoubleHelix.java b/DeconvolutionLab2/src/signal/factory/DoubleHelix.java
	index b40c050..8720576 100644
	--- a/DeconvolutionLab2/src/signal/factory/DoubleHelix.java
	+++ b/DeconvolutionLab2/src/signal/factory/DoubleHelix.java
	@@ -1,92 +1,92 @@
	package signal.factory;

	/*
	* 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/>.
	*/

	import signal.RealSignal;

	public class DoubleHelix extends SignalFactory {

	private double fwhm = 3.0;
	- private double dist = 10;
	+ private double dist = 30;
	private double delta = 10;

	public DoubleHelix(double fwhm, double dist, double delta) {
	super(new double[] {fwhm, dist, delta});
	+ setParameters(new double[] {fwhm, dist, delta});
	}

	@Override
	public String getName() {
	return "Double-Helix";
	}

	@Override
	public String[] getParametersName() {
	return new String[] {"FWHM at focus plane", "Distance", "Delta Z (rotation PI)"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.fwhm = parameters[0];
	if (parameters.length >= 2)
	this.dist = parameters[1];
	if (parameters.length >= 3)
	this.delta = parameters[2];
	}

	@Override
	public double[] getParameters() {
	return new double[] {fwhm, dist, delta};
	}

	@Override
	public void fill(RealSignal signal) {
	double K = 0.5 / (fwhm*fwhm);
	- double A = (amplitude-background);
	double T = Math.PI/(delta*2.0);
	for(int z=0; z<nz; z++) {
	double cosa = Math.cos((z-zc)*T);
	double sina = Math.sin((z-zc)*T);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++) {
	double u = (x-xc) * cosa + (y-yc) * sina;
	double v = -(x-xc) * sina + (y-yc) * cosa;
	double u1 = (u - dist * 0.5);
	double u2 = (u + dist * 0.5);
	double p = Math.exp(-((u1 * u1 + v * v) * K)) + Math.exp(-((u2 * u2 + v * v) * K));
	- signal.data[z][x+nxy] = (float)(A p + background);
	+ signal.data[z][x+nxy] = (float)(amplitude p);
	}
	}
	}


	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Gaussian.java b/DeconvolutionLab2/src/signal/factory/Gaussian.java
	index f4bfc01..95496f6 100644
	--- a/DeconvolutionLab2/src/signal/factory/Gaussian.java
	+++ b/DeconvolutionLab2/src/signal/factory/Gaussian.java
	@@ -1,85 +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 signal.factory;

	import signal.RealSignal;

	public class Gaussian extends SignalFactory {

	private double sigmaX = 3.0;
	private double sigmaY = 3.0;
	private double sigmaZ = 3.0;

	public Gaussian(double sigmaX, double sigmaY, double sigmaZ) {
	super(new double[] {sigmaX, sigmaY, sigmaZ});
	+ setParameters(new double[] {sigmaX, sigmaY, sigmaZ});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"Sigma X", "Sigma Y", "Sigma Z"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.sigmaX = parameters[0];
	if (parameters.length >= 2)
	this.sigmaY = parameters[1];
	if (parameters.length >= 3)
	this.sigmaZ = parameters[2];
	}

	@Override
	public double[] getParameters() {
	return new double[] {sigmaX, sigmaY, sigmaZ};
	}

	@Override
	public void fill(RealSignal signal) {
	double KX = 0.5 / (sigmaX*sigmaX);
	double KY = 0.5 / (sigmaY*sigmaY);
	double KZ = 0.5 / (sigmaZ*sigmaZ);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++)
	for(int z=0; z<nz; z++) {
	double r2 = KX(x-xc)(x-xc) + KY(y-yc)(y-yc) + KZ(z-zc)(z-zc);
	- signal.data[z][x+nxy] = (float)((amplitude-background) Math.exp(-r2) + background);
	+ signal.data[z][x+nxy] = (float)(amplitude Math.exp(-r2));
	}
	}


	}
	diff --git a/DeconvolutionLab2/src/signal/factory/GridGroupedSpots.java b/DeconvolutionLab2/src/signal/factory/GridGroupedSpots.java
	deleted file mode 100644
	index 4038774..0000000
	--- a/DeconvolutionLab2/src/signal/factory/GridGroupedSpots.java
	+++ /dev/null
	@@ -1,123 +0,0 @@
	-/*
	- * DeconvolutionLab2
	- *
	- * Conditions of use: You are free to use this software for research or
	- * educational purposes. In addition, we expect you to include adequate
	- * citations and acknowledgments whenever you present or publish results that
	- * are based on it.
	- *
	- * Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	- * Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	- * R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	- */
	-
	-/*
	- * Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
	- *
	- * This file is part of DeconvolutionLab2 (DL2).
	- *
	- * DL2 is free software: you can redistribute it and/or modify it under the
	- * terms of the GNU General Public License as published by the Free Software
	- * Foundation, either version 3 of the License, or (at your option) any later
	- * version.
	- *
	- * DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
	- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	- * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	- *
	- * You should have received a copy of the GNU General Public License along with
	- * DL2. If not, see <http://www.gnu.org/licenses/>.
	- */
	-
	-package signal.factory;
	-
	-import signal.RealSignal;
	-
	-public class GridGroupedSpots extends SignalFactory {
	-
	- private double radius = 3.0;
	- private double slope = 1;
	- private double largest = 10;
	- private double spacing = 10.0;
	-
	- public GridGroupedSpots(double side, double slope, double largest, double spacing) {
	- super(new double[] {side, slope, largest, spacing});
	- }
	-
	- @Override
	- public String getName() {
	- return "GridGroupedSpots";
	- }
	-
	- @Override
	- public String[] getParametersName() {
	- return new String[] {"Radius", "Sigmoid Curve Slope", "LargestDistance", "Spacing"};
	- }
	-
	- @Override
	- public void setParameters(double[] parameters) {
	- if (parameters.length >= 1)
	- this.radius = parameters[0];
	- if (parameters.length >= 2)
	- this.slope = parameters[1];
	- if (parameters.length >= 3)
	- this.largest = parameters[2];
	- if (parameters.length >= 4)
	- this.spacing = parameters[3];
	- }
	-
	- @Override
	- public double[] getParameters() {
	- return new double[] {radius, slope, largest, spacing};
	- }
	-
	- @Override
	- public void fill(RealSignal signal) {
	- float b = (float)background;
	- for(int x=0; x<nx; x++)
	- for(int y=0; y<ny; y++)
	- for(int z=0; z<nz; z++)
	- signal.data[z][x+nx*y] = b;
	-
	- int nc = (int)( (nx-spacing) / spacing);
	- int nr = (int)( (ny-spacing) / spacing);
	- int np = (int)( (nz-spacing) / spacing);
	-
	- for(int i=0; i<nc; i++)
	- for(int j=0; j<nr; j++)
	- for(int k=0; k<np; k++) {
	- double x = spacing + i*spacing;
	- double y = spacing + j*spacing;
	- double z = spacing + k*spacing;
	- double dist = largest - j*largest / (nr-1);
	- double distk = largest - k*largest / (np-1);
	- double A = amplitude - i*(amplitude-background) / (nc+1);
	- spot(signal, x, y, z, A);
	- spot(signal, x+dist, y, z, A);
	- spot(signal, x, y+dist, z, A);
	- spot(signal, x+dist, y+dist, z, A);
	-
	- spot(signal, x, y, z+distk, A);
	- spot(signal, x+dist, y, z+distk, A);
	- spot(signal, x, y+dist, z+distk, A);
	- spot(signal, x+dist, y+dist, z+distk, A);
	- }
	- }
	-
	- private void spot(RealSignal signal, double xc, double yc, double zc, double A) {
	- int x1 = (int)Math.max(0, Math.round(xc-radius-3*slope));
	- int x2 = (int)Math.min(nx-1, Math.round(xc+radius+3*slope));
	- int y1 = (int)Math.max(0, Math.round(yc-radius-3*slope));
	- int y2 = (int)Math.min(ny-1, Math.round(yc+radius+3*slope));
	- int z1 = (int)Math.max(0, Math.round(zc-radius-3*slope));
	- int z2 = (int)Math.min(nz-1, Math.round(zc+radius+3*slope));
	- for(int x=x1; x<=x2; x++)
	- for(int y=y1; y<=y2; y++)
	- for(int z=z1; z<=z2; z++) {
	- double dr = Math.sqrt((x-xc)(x-xc) + (y-yc)(y-yc) + (z-zc)*(z-zc)) - radius;
	- signal.data[z][x+nxy] = Math.max(signal.data[z][x+nxy], (float)(A - A / (1.0 + Math.exp(-dr/slope))));
	- }
	- }
	-
	-
	-}
	diff --git a/DeconvolutionLab2/src/signal/factory/Impulse.java b/DeconvolutionLab2/src/signal/factory/Impulse.java
	index ec60144..2356025 100644
	--- a/DeconvolutionLab2/src/signal/factory/Impulse.java
	+++ b/DeconvolutionLab2/src/signal/factory/Impulse.java
	@@ -1,70 +1,64 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import signal.RealSignal;

	public class Impulse extends SignalFactory {

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

	@Override
	public String[] getParametersName() {
	return new String[] {};
	}

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

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

	@Override
	public void fill(RealSignal signal) {
	- for(int x=0; x<nx; x++)
	- for(int y=0; y<ny; y++)
	- for(int z=0; z<nz; z++) {
	- signal.data[z][x+nx*y] = (float)(background);
	- }
	int i = (int)(xc);
	int j = (int)(yc);
	int k = (int)(zc);
	-
	signal.data[k][i+nx*j] += (float)(amplitude);
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/AirySimulated.java b/DeconvolutionLab2/src/signal/factory/Laplacian.java
	similarity index 83%
	rename from DeconvolutionLab2/src/signal/factory/AirySimulated.java
	rename to DeconvolutionLab2/src/signal/factory/Laplacian.java
	index 644d04a..1b326e3 100644
	--- a/DeconvolutionLab2/src/signal/factory/AirySimulated.java
	+++ b/DeconvolutionLab2/src/signal/factory/Laplacian.java
	@@ -1,80 +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 signal.factory;

	+import deconvolutionlab.Lab;
	import deconvolutionlab.monitor.Monitors;
	import fft.AbstractFFT;
	import fft.FFT;
	import signal.ComplexSignal;
	import signal.RealSignal;
	import signal.factory.complex.ComplexSignalFactory;

	-public class AirySimulated extends SignalFactory {
	+public class Laplacian extends SignalFactory {

	- private double mu = 1.0;
	-
	- public AirySimulated(double mu) {
	- super(new double[] {mu});
	+ public Laplacian() {
	+ super(new double[] {});
	}

	@Override
	public String getName() {
	- return "AirySimulated";
	+ return "Laplacian";
	}

	@Override
	public String[] getParametersName() {
	- return new String[] {"Parameter (mu)"};
	+ return new String[] {};
	}

	@Override
	public void setParameters(double[] parameters) {
	- if (parameters.length >= 1)
	- this.mu = parameters[0];
	}

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

	@Override
	public void fill(RealSignal signal) {
	AbstractFFT fft = FFT.createDefaultFFT(Monitors.createDefaultMonitor(), nx, ny, nz);
	- ComplexSignal C = ComplexSignalFactory.airySimulated(nx, ny, nz, mu);
	+ ComplexSignal C = ComplexSignalFactory.laplacian(nx, ny, nz);
	RealSignal s = fft.inverse(C).circular().times((float)amplitude);
	- s.times(s);
	signal.copy(s);
	}
	-
	-
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Ramp.java b/DeconvolutionLab2/src/signal/factory/Ramp.java
	index 0607dd4..0298091 100644
	--- a/DeconvolutionLab2/src/signal/factory/Ramp.java
	+++ b/DeconvolutionLab2/src/signal/factory/Ramp.java
	@@ -1,89 +1,90 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import signal.RealSignal;

	public class Ramp extends SignalFactory {

	private double orientationX = 1;
	- private double orientationY = 0;
	- private double orientationZ = 0;
	+ private double orientationY = 1;
	+ private double orientationZ = 1;

	public Ramp(double orientationX, double orientationY, double orientationZ) {
	super(new double[] {orientationX, orientationY, orientationZ});
	+ setParameters(new double[] {orientationX, orientationY, orientationZ});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"Orientation X", "Orientation Y", "Orientation Z"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.orientationX = parameters[0];
	if (parameters.length >= 2)
	this.orientationY = parameters[1];
	if (parameters.length >= 3)
	this.orientationZ = parameters[1];
	}

	@Override
	public double[] getParameters() {
	return new double[] {orientationX, orientationY, orientationZ};
	}

	@Override
	public void fill(RealSignal signal) {
	- double A = (amplitude-background);
	double ox = orientationX;
	double oy = orientationY;
	double oz = orientationZ;
	- double diag = Math.sqrt(nxnx + nyny + nz*nz);
	- double len = Math.sqrt(oxox + oyoy + oz*oz);
	+ double mx = 1 / (3.0*nx);
	+ double my = 1 / (3.0*ny);
	+ double mz = 1 / (3.0*nz);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++)
	for(int z=0; z<nz; z++) {
	- double dx = (xc-x);
	- double dy = (yc-y);
	- double dz = (zc-z);
	- double r = (dxox + dyoy + dzoz) / (diag len);
	- signal.data[z][x+nxy] = (float)(A r + background);
	+ double dx = (xc-x) * mx;
	+ double dy = (yc-y) * my;
	+ double dz = (zc-z) * mz;
	+ signal.data[z][x+nxy] = (float)(dxox + dyoy + dzoz);
	}
	+ signal.rescale(0, amplitude);
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/RandomLines.java b/DeconvolutionLab2/src/signal/factory/RandomLines.java
	index 36385b6..05b03ec 100644
	--- a/DeconvolutionLab2/src/signal/factory/RandomLines.java
	+++ b/DeconvolutionLab2/src/signal/factory/RandomLines.java
	@@ -1,108 +1,107 @@
	package signal.factory;

	import java.util.Random;

	/*
	* 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/>.
	*/

	import signal.RealSignal;

	public class RandomLines extends SignalFactory {

	- private double number = 3.0;
	+ private double number = 100.0;

	public RandomLines(double number) {
	super(new double[] {number});
	+ setParameters(new double[] {number});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] { "Number of lines" };
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1) this.number = parameters[0];
	}

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

	@Override
	public void fill(RealSignal signal) {
	Random rand = new Random(12345);
	- float A = (float)(amplitude - background);
	- signal.fill((float) (background));
	double Q = Math.sqrt(3)*1.5;
	for (int index = 0; index < number; index++) {
	double x1 = -rand.nextDouble() * nx;
	double x2 = nx + rand.nextDouble() * nx;
	double y1 = (-0.1 + rand.nextDouble() * 1.2) * ny;
	double y2 = (-0.1 + rand.nextDouble() * 1.2) * ny;
	double z1 = (-0.1 + rand.nextDouble() * 1.2) * nz;
	double z2 = (-0.1 + rand.nextDouble() * 1.2) * nz;
	double d = (x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) + (z1 - z2) * (z1 - z2);
	d = Math.sqrt(d);
	int n = (int) (d / 0.3);
	double dx = (x2 - x1) / d;
	double dy = (y2 - y1) / d;
	double dz = (z2 - z1) / d;
	for (int s = 0; s < n; s++) {
	double x = x1 + s * dx;
	int i = (int) Math.round(x);
	if (i >= 1 && i < nx-1) {
	double y = y1 + s * dy;
	int j = (int) Math.round(y);
	if (j >= 1 && j < ny-1) {
	double z = z1 + s * dz;
	int k = (int) Math.round(z);
	if (k >= 1 && k < nz-1) {
	- //for(int ii=i-1; ii<=i+1; ii++)
	- //for(int jj=j-1; jj<=j+1; jj++)
	- //for(int kk=k-1; kk<=k+1; kk++) {
	- double p = Q - Math.sqrt((x - i) * (x - i) + (y - j) * (y - j) + (z - k) * (z - k));
	- signal.data[k][i + nx * j] = Math.max(signal.data[k][i + nx * j], (float)(p*A));
	- //}
	+ for(int ii=i-1; ii<=i+1; ii++)
	+ for(int jj=j-1; jj<=j+1; jj++)
	+ for(int kk=k-1; kk<=k+1; kk++) {
	+ double p = 1.0 - Math.sqrt((x - i) * (x - i) + (y - j) * (y - j) + (z - k) * (z - k))/Q;
	+ signal.data[k][i + nx * j] = Math.max(signal.data[k][i + nx * j], (float)(p*amplitude));
	+ }
	}
	}
	}
	}
	}
	}

	}
	diff --git a/DeconvolutionLab2/src/signal/factory/SignalFactory.java b/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	index ee1f9d3..cb5d407 100644
	--- a/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	+++ b/DeconvolutionLab2/src/signal/factory/SignalFactory.java
	@@ -1,244 +1,274 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory;

	import java.util.ArrayList;

	import javax.swing.SwingWorker;

	+import bilib.tools.NumFormat;
	import deconvolution.Command;
	import signal.RealSignal;

	public abstract class SignalFactory {

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

	public SignalFactory() {
	}

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

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

	public static RealSignal createFromCommand(String cmd) {
	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;
	+ double parameters[] = new double[np];
	+ if (np >= 1 && params.length >= 1)
	+ parameters[0] = params[0];
	+ if (np >= 2 && params.length >= 2)
	+ parameters[1] = params[1];
	+ if (np >= 3 && params.length >= 3)
	+ parameters[2] = params[2];
	+ if (np >= 4 && params.length >= 4)
	+ parameters[3] = params[3];
	+
	+ double size[] = NumFormat.parseNumbersAfter("size", cmd);
	+ int nx = 128;
	+ int ny = 128;
	+ int nz = 32;
	+ if (size.length > 0)
	+ nx = (int) size[0];
	+ if (size.length > 1)
	+ ny = (int) size[1];
	+ if (size.length > 2)
	+ nz = (int) size[2];
	+
	+ double intensity[] = NumFormat.parseNumbersAfter("intensity", cmd);
	+ double amplitude = 255;
	+ if (intensity.length > 0)
	+ amplitude = intensity[0];
	+
	+ double center[] = NumFormat.parseNumbersAfter("center", cmd);
	+ double cx = 0.5;
	+ double cy = 0.5;
	+ double cz = 0.5;
	+ if (center.length > 0)
	+ cx = center[0];
	+ if (center.length > 1)
	+ cy = center[1];
	+ if (center.length > 2)
	+ cz = center[2];
	+
	+ factory.intensity(amplitude);
	+ factory.setParameters(parameters);
	factory = factory.center(cx, cy, cz);
	return factory.generate(nx, ny, nz);
	}
	}
	return null;

	}

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

	public static ArrayList<SignalFactory> getAll() {
	ArrayList<SignalFactory> list = new ArrayList<SignalFactory>();
	- list.add(new AirySimulated(1));
	- list.add(new Astigmatism(3, 0.2));
	+ list.add(new Airy(5, 1, 0.5, 3));
	+ list.add(new Astigmatism(5, 1));
	+ list.add(new AxialDiffractionSimulation(10, 10, 2));
	list.add(new Constant());
	list.add(new Cross(1, 1, 30));
	list.add(new Cube(10 ,1));
	+ list.add(new CubeSphericalBeads(3, 0.5, 8, 16));
	list.add(new Defocus(3, 10, 10));
	+ list.add(new DirectionalDerivative(1, 1, 0));
	+ list.add(new DirectionalMotionBlur(3, 30, 3));
	list.add(new DoG(3, 4));
	- list.add(new DoubleHelix(3, 10, 10));
	+ list.add(new DoubleConeWave(60, 5, 15, 10));
	+ list.add(new DoubleHelix(3, 30, 10));
	list.add(new Gaussian(3, 3, 3));
	- list.add(new GridSpots(3, 1, 10));
	list.add(new Impulse());
	- //list.add(new MotionBlur(3, 30, 3));
	- list.add(new Ramp(1, 0, 0));
	- list.add(new RandomLines(3));
	+ list.add(new Laplacian());
	+ list.add(new Ramp(1, 1, 1));
	+ list.add(new RandomLines(100));
	list.add(new Sinc(3, 3, 3));
	list.add(new Sphere(10, 1));
	- list.add(new Torus(10));
	+ list.add(new Torus(30));
	return list;
	}

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

	public static ArrayList<SignalFactory> getPSF() {
	ArrayList<SignalFactory> list = new ArrayList<SignalFactory>();
	- list.add(new AirySimulated(1));
	- list.add(new Astigmatism(3, 0.2));
	- list.add(new Cross(3, 1, 10));
	- list.add(new Cube(10, 1));
	+ list.add(new Airy(5, 1, 0.5, 3));
	+ list.add(new Astigmatism(5, 1));
	+ list.add(new AxialDiffractionSimulation(10, 10, 2));
	+ list.add(new Cross(1, 1, 30));
	+ list.add(new CubeSphericalBeads(3, 0.5, 8, 16));
	list.add(new Defocus(3, 10, 10));
	+ list.add(new DirectionalDerivative(1, 1, 0));
	+ list.add(new DirectionalMotionBlur(3, 30, 3));
	list.add(new DoG(3, 4));
	- list.add(new DoubleHelix(3, 10, 10));
	+ list.add(new DoubleConeWave(60, 5, 15, 10));
	+ list.add(new DoubleHelix(3, 30, 10));
	list.add(new Gaussian(3, 3, 3));
	- //list.add(new MotionBlur(3, 30, 3));
	list.add(new Impulse());
	- list.add(new Sinc(3, 3, 3));
	+ list.add(new Laplacian());
	+ list.add(new Sinc(3, 3, 3));
	list.add(new Sphere(10, 1));
	- list.add(new RandomLines(3));
	- list.add(new Torus(10));
	return list;
	}

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

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

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

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

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

	return signal;
	}

	public abstract String getName();

	public abstract void setParameters(double[] parameters);

	public abstract double[] getParameters();

	public abstract String[] getParametersName();

	public abstract void fill(RealSignal signal);

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

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

	protected void done() {
	done = true;
	}

	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Sinc.java b/DeconvolutionLab2/src/signal/factory/Sinc.java
	index 7adf5f8..e60ea6c 100644
	--- a/DeconvolutionLab2/src/signal/factory/Sinc.java
	+++ b/DeconvolutionLab2/src/signal/factory/Sinc.java
	@@ -1,91 +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 signal.factory;

	-import deconvolutionlab.Lab;
	import signal.Operations;
	import signal.RealSignal;

	public class Sinc extends SignalFactory {

	private double periodX = 3.0;
	private double periodY = 3.0;
	private double periodZ = 3.0;

	public Sinc(double periodX, double periodY, double periodZ) {
	super(new double[] {periodX, periodY, periodZ});
	+ setParameters(new double[] {periodX, periodY, periodZ});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"Period X", "Period Y", "Period Z"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.periodX = parameters[0];
	if (parameters.length >= 2)
	this.periodY = parameters[1];
	if (parameters.length >= 3)
	this.periodZ = parameters[2];
	}

	@Override
	public double[] getParameters() {
	return new double[] {periodX, periodY, periodZ};
	}

	@Override
	public void fill(RealSignal signal) {
	double KX = 1. / (periodX*periodX);
	double KY = 1. / (periodY*periodY);
	double KZ = 1. / (periodZ*periodZ);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++)
	for(int z=0; z<nz; z++) {

	double r = Math.sqrt(KX(x-xc)(x-xc) + KY(y-yc)(y-yc) + KZ(z-zc)(z-zc));
	double v = 1.0;
	if (r > Operations.epsilon)
	v = Math.sin(r) / r;
	- signal.data[z][x+nxy] = (float)((amplitude-background) v + background);
	+ signal.data[z][x+nx*y] = (float)(v);
	}
	+ signal.rescale(0, amplitude);
	}


	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Sphere.java b/DeconvolutionLab2/src/signal/factory/Sphere.java
	index d1f4c8e..720f974 100644
	--- a/DeconvolutionLab2/src/signal/factory/Sphere.java
	+++ b/DeconvolutionLab2/src/signal/factory/Sphere.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 signal.factory;

	import signal.RealSignal;

	public class Sphere extends SignalFactory {

	private double radius = 10;
	private double slope = 1;

	public Sphere(double radius, double slope) {
	super(new double[] {radius, slope});
	+ setParameters(new double[] {radius, slope});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"Radius", "Sigmoid Curve Slope"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.radius = parameters[0];
	if (parameters.length >= 2)
	this.slope = parameters[1];
	}

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

	@Override
	public void fill(RealSignal signal) {
	- double A = (amplitude-background);
	for(int x=0; x<nx; x++)
	for(int y=0; y<ny; y++)
	for(int z=0; z<nz; z++) {
	double dr = Math.sqrt((x-xc)(x-xc) + (y-yc)(y-yc) + (z-zc)*(z-zc)) - radius;
	- signal.data[z][x+nxy] = (float)(A (1.0- 1.0 / (1.0 + Math.exp(-dr/slope))) + background);
	+ signal.data[z][x+nxy] = (float)(amplitude (1.0- 1.0 / (1.0 + Math.exp(-dr/slope))));
	}
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/Torus.java b/DeconvolutionLab2/src/signal/factory/Torus.java
	index 13e2a83..4ee7371 100644
	--- a/DeconvolutionLab2/src/signal/factory/Torus.java
	+++ b/DeconvolutionLab2/src/signal/factory/Torus.java
	@@ -1,92 +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 signal.factory;

	import signal.RealSignal;

	public class Torus extends SignalFactory {

	private double radius = 10.0;

	public Torus(double radius) {
	super(new double[] {radius});
	+ setParameters(new double[] {radius});
	}

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

	@Override
	public String[] getParametersName() {
	return new String[] {"Radius"};
	}

	@Override
	public void setParameters(double[] parameters) {
	if (parameters.length >= 1)
	this.radius = parameters[0];
	}

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

	@Override
	public void fill(RealSignal signal) {
	- float A = (float)(amplitude-background);
	- float B = (float)(background);
	double thick = radius * 0.2;
	double thick2 = thick * thick;
	- double hx = nx * 0.5;
	- double hy = ny * 0.5;
	- double hz = nz * 0.5;
	- for(int i=0; i<nx; i++)
	+ for(int i=0; i<nx; i++)
	for(int j=0; j<ny; j++) {
	- double dxy = Math.abs(radius - dist(i, j, hx, hy));
	+ double dxy = Math.abs(radius - dist(i, j, xc, yc));
	if (dxy < thick) {
	for(int k=0; k<nz; k++) {
	- double dz = k - hz;
	+ double dz = k - zc;
	if (dxydxy + dzdz < thick2)
	- signal.data[k][i+j*nx] = A;
	- else
	- signal.data[k][i+j*nx] = B;
	+ signal.data[k][i+jnx] = (float)(amplitude (1.0-(dxydxy + dzdz)/thick2));
	}
	}
	}
	}

	private static double dist(double x1, double y1, double x2, double y2) {
	return Math.sqrt((x1-x2)(x1-x2) + (y1-y2)(y1-y2));
	}
	}
	diff --git a/DeconvolutionLab2/src/signal/factory/complex/ComplexSignalFactory.java b/DeconvolutionLab2/src/signal/factory/complex/ComplexSignalFactory.java
	index 00ef89e..a17d6c1 100644
	--- a/DeconvolutionLab2/src/signal/factory/complex/ComplexSignalFactory.java
	+++ b/DeconvolutionLab2/src/signal/factory/complex/ComplexSignalFactory.java
	@@ -1,151 +1,222 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.factory.complex;

	import signal.ComplexSignal;

	public class ComplexSignalFactory {

	public static ComplexSignal gaussian(int nx, int ny, int nz, double sigma) {
	double K = sigma * sigma / 2.0;
	int xsize = nx / 2;
	int ysize = ny / 2;
	int zsize = nz / 2;
	float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
	double wx, wy, wz, wr;
	for (int z = 0; z <= zsize; z++)
	for (int y = 0; y <= ysize; y++)
	for (int x = 0; x <= xsize; x++) {
	wx = Math.PI * x / xsize;
	wy = Math.PI * y / ysize;
	wz = Math.PI * z / ysize;
	wr = Math.sqrt(wx * wx + wy * wy + wz * wz);
	function[x][y][z] = (float) Math.exp(-wr * wr * K);
	}
	return createHermitian("Gaussian", nx, ny, nz, function);
	}

	public static ComplexSignal identity(int nx, int ny, int nz) {
	int xsize = nx / 2;
	int ysize = ny / 2;
	int zsize = nz / 2;
	float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
	for (int z = 0; z <= zsize; z++)
	for (int y = 0; y <= ysize; y++)
	for (int x = 0; x <= xsize; x++)
	function[x][y][z] = 1.0f;
	return createHermitian("Identity", nx, ny, nz, function);
	}

	public static ComplexSignal laplacian(int nx, int ny, int nz) {
	int xsize = nx / 2;
	int ysize = ny / 2;
	int zsize = nz / 2;
	float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
	double wx, wy, wz;
	for (int z = 0; z <= zsize; z++)
	for (int y = 0; y <= ysize; y++)
	for (int x = 0; x <= xsize; x++) {
	wx = Math.PI * x / xsize;
	wy = Math.PI * y / ysize;
	- wz = Math.PI * z / ysize;
	+ wz = Math.PI * z / zsize;
	function[x][y][z] = (float) ((wx * wx + wy * wy + wz * wz));
	}
	return createHermitian("Laplacian", nx, ny, nz, function);
	}
	+
	+ public static ComplexSignal directionalDerivative(int nx, int ny, int nz, double vx, double vy, double vz) {
	+ int xsize = nx / 2;
	+ int ysize = ny / 2;
	+ int zsize = nz / 2;
	+ float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
	+ double wx, wy, wz;
	+ for (int z = 0; z <= zsize; z++)
	+ for (int y = 0; y <= ysize; y++)
	+ for (int x = 0; x <= xsize; x++) {
	+ wx = Math.PI * x / xsize;
	+ wy = Math.PI * y / ysize;
	+ wz = Math.PI * z / zsize;
	+ function[x][y][z] = (float) ((wx * vx + vy * wy + vz * wz));
	+ }
	+ return createHermitian("Directional Derivative", nx, ny, nz, function);
	+ }

	- public static ComplexSignal airySimulated(int nx, int ny, int nz, double mu) {
	+ public static ComplexSignal rings(int nx, int ny, int nz, double mu) {
	int xsize = nx / 2;
	int ysize = ny / 2;
	int zsize = nz / 2;
	double K = ysize/2;
	float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
	double wx, wy, wz, wr;
	for (int z = 0; z <= zsize; z++)
	for (int y = 0; y <= ysize; y++)
	for (int x = 0; x <= xsize; x++) {
	wx = Math.PI * x / xsize;
	wy = Math.PI * y / ysize;
	wz = Math.PI * z / ysize;
	wr = Math.sqrt(wx * wx + wy * wy + wz*wz);
	function[x][y][z] =
	(float) (1.0 - 1.0 / (1.0 + Math.exp(-K * (wr - mu)))
	+ 1.0 / (1.0 + Math.exp(-K * (wr - 0.6 * mu)))
	- 1.0 / (1.0 + Math.exp(-K * (wr - 0.4 * mu))));
	}
	return createHermitian("Airy", nx, ny, nz, function);
	}

	+ public static ComplexSignal createHermitian(String name, int nx, int ny, int nz, float[][][] firstQuadrantReal, float[][][] firstQuadrantImag) {
	+ ComplexSignal signal = new ComplexSignal(name, nx, ny, nz);
	+ int xsize = firstQuadrantReal.length - 1;
	+ int ysize = firstQuadrantReal[0].length - 1;
	+ int zsize = firstQuadrantReal[0][0].length - 1;
	+ if (xsize >= 1 && ysize >= 1 && zsize >= 1) {
	+ for (int z = 0; z <= zsize; z++)
	+ for (int y = 0; y <= ysize; y++)
	+ for (int x = 0; x <= xsize; x++) {
	+ signal.data[z][2 * (x + nx * y)] = firstQuadrantReal[x][y][z];
	+ signal.data[z][2 * (x + nx * y)+1] = firstQuadrantImag[x][y][z];
	+ }
	+ for (int z = 0; z < zsize; z++)
	+ for (int y = 0; y < ysize; y++)
	+ for (int x = 0; x < xsize; x++) {
	+ int a = nx - 1 - x;
	+ int b = nx * (ny - 1 - y);
	+ signal.data[z][2 * (a + nx * y)] = firstQuadrantReal[x + 1][y][z];
	+ signal.data[z][2 * (a + b)] = firstQuadrantReal[x + 1][y + 1][z];
	+ signal.data[z][2 * (x + b)] = firstQuadrantReal[x][y + 1][z];
	+ signal.data[z][1 + 2 * (a + nx * y)] = firstQuadrantImag[x + 1][y][z];
	+ signal.data[z][1 + 2 * (a + b)] = firstQuadrantImag[x + 1][y + 1][z];
	+ signal.data[z][1 + 2 * (x + b)] = firstQuadrantImag[x][y + 1][z];
	+ int c = nz - 1 - z;
	+ signal.data[c][2 * (x + nx * y)] = firstQuadrantReal[x][y][z + 1];
	+ signal.data[c][2 * (a + nx * y)] = firstQuadrantReal[x + 1][y][z + 1];
	+ signal.data[c][2 * (a + b)] = firstQuadrantReal[x + 1][y + 1][z + 1];
	+ signal.data[c][2 * (x + b)] = firstQuadrantReal[x][y + 1][z + 1];
	+ signal.data[c][1 + 2 * (x + nx * y)] = firstQuadrantImag[x][y][z + 1];
	+ signal.data[c][1 + 2 * (a + nx * y)] = firstQuadrantImag[x + 1][y][z + 1];
	+ signal.data[c][1 + 2 * (a + b)] = firstQuadrantImag[x + 1][y + 1][z + 1];
	+ signal.data[c][1 + 2 * (x + b)] = firstQuadrantImag[x][y + 1][z + 1];
	+ }
	+ }
	+ if (zsize == 0) {
	+ for (int y = 0; y <= ysize; y++)
	+ for (int x = 0; x <= xsize; x++) {
	+ signal.data[0][2 * (x + nx * y)] = firstQuadrantReal[x][y][0];
	+ signal.data[0][1 + 2 * (x + nx * y)] = firstQuadrantImag[x][y][0];
	+ }
	+ for (int y = 0; y < ysize; y++)
	+ for (int x = 0; x < xsize; x++) {
	+ int a = nx - 1 - x;
	+ int b = nx * (ny - 1 - y);
	+ signal.data[0][2 * (a + nx * y)] = firstQuadrantReal[x + 1][y][0];
	+ signal.data[0][2 * (a + b)] = firstQuadrantReal[x + 1][y + 1][0];
	+ signal.data[0][2 * (x + b)] = firstQuadrantReal[x][y + 1][0];
	+ signal.data[0][1 + 2 * (a + nx * y)] = firstQuadrantImag[x + 1][y][0];
	+ signal.data[0][1 + 2 * (a + b)] = firstQuadrantImag[x + 1][y + 1][0];
	+ signal.data[0][1 + 2 * (x + b)] = firstQuadrantImag[x][y + 1][0];
	+ }
	+ }
	+ return signal;
	+ }
	+
	public static ComplexSignal createHermitian(String name, int nx, int ny, int nz, float[][][] firstQuadrant) {
	ComplexSignal signal = new ComplexSignal(name, nx, ny, nz);
	int xsize = firstQuadrant.length - 1;
	int ysize = firstQuadrant[0].length - 1;
	int zsize = firstQuadrant[0][0].length - 1;
	if (xsize >= 1 && ysize >= 1 && zsize >= 1) {
	for (int z = 0; z <= zsize; z++)
	for (int y = 0; y <= ysize; y++)
	for (int x = 0; x <= xsize; x++) {
	signal.data[z][2 * (x + nx * y)] = firstQuadrant[x][y][z];
	}
	for (int z = 0; z < zsize; z++)
	for (int y = 0; y < ysize; y++)
	for (int x = 0; x < xsize; x++) {
	int a = nx - 1 - x;
	int b = nx * (ny - 1 - y);
	signal.data[z][2 * (a + nx * y)] = firstQuadrant[x + 1][y][z];
	signal.data[z][2 * (a + b)] = firstQuadrant[x + 1][y + 1][z];
	signal.data[z][2 * (x + b)] = firstQuadrant[x][y + 1][z];
	int c = nz - 1 - z;
	signal.data[c][2 * (x + nx * y)] = firstQuadrant[x][y][z + 1];
	signal.data[c][2 * (a + nx * y)] = firstQuadrant[x + 1][y][z + 1];
	signal.data[c][2 * (a + b)] = firstQuadrant[x + 1][y + 1][z + 1];
	signal.data[c][2 * (x + b)] = firstQuadrant[x][y + 1][z + 1];
	}
	}
	if (zsize == 0) {
	for (int y = 0; y <= ysize; y++)
	for (int x = 0; x <= xsize; x++) {
	signal.data[0][2 * (x + nx * y)] = firstQuadrant[x][y][0];
	}
	for (int y = 0; y < ysize; y++)
	for (int x = 0; x < xsize; x++) {
	int a = nx - 1 - x;
	int b = nx * (ny - 1 - y);
	signal.data[0][2 * (a + nx * y)] = firstQuadrant[x + 1][y][0];
	signal.data[0][2 * (a + b)] = firstQuadrant[x + 1][y + 1][0];
	signal.data[0][2 * (x + b)] = firstQuadrant[x][y + 1][0];
	}
	}
	return signal;
	}
	-
	}
	diff --git a/DeconvolutionLab2/src/signal/padding/Padding.java b/DeconvolutionLab2/src/signal/padding/Padding.java
	index 57f2102..32ad103 100644
	--- a/DeconvolutionLab2/src/signal/padding/Padding.java
	+++ b/DeconvolutionLab2/src/signal/padding/Padding.java
	@@ -1,253 +1,252 @@
	/*
	* DeconvolutionLab2
	*
	* Conditions of use: You are free to use this software for research or
	* educational purposes. In addition, we expect you to include adequate
	* citations and acknowledgments whenever you present or publish results that
	* are based on it.
	*
	* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
	* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
	* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
	*/

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

	package signal.padding;

	import java.util.ArrayList;

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

	public class Padding {

	private AbstractPadding padX = getDefault();
	private AbstractPadding padY = getDefault();
	private AbstractPadding padZ = getDefault();

	private int minExtensionX = 0;
	private int minExtensionY = 0;
	private int minExtensionZ = 0;

	private int nx = -1;
	private int ny = -1;
	private int nz = -1;

	public Padding() {
	padX = new NoPadding();
	padY = new NoPadding();
	padZ = new NoPadding();
	this.minExtensionX = 0;
	this.minExtensionY = 0;
	this.minExtensionZ = 0;
	}

	public Padding(int minExtensionX, int minExtensionY, int minExtensionZ) {
	padX = new NoPadding();
	padY = new NoPadding();
	padZ = new NoPadding();
	this.minExtensionX = minExtensionX;
	this.minExtensionY = minExtensionY;
	this.minExtensionZ = minExtensionZ;
	}

	public Padding(AbstractPadding padX, AbstractPadding padY, AbstractPadding padZ, int minExtensionX, int minExtensionY, int minExtensionZ) {
	this.padX = padX;
	this.padY = padY;
	this.padZ = padZ;
	this.minExtensionX = minExtensionX;
	this.minExtensionY = minExtensionY;
	this.minExtensionZ = minExtensionZ;
	}

	public Padding(AbstractPadding pad, int extension) {
	this.padX = pad;
	this.padY = pad;
	this.padZ = pad;
	this.minExtensionX = extension;
	this.minExtensionY = extension;
	this.minExtensionZ = extension;
	}

	public Padding(String nameX, String nameY, String nameZ, int minExtensionX, int minExtensionY, int minExtensionZ) {
	for(AbstractPadding pad : getPaddings()) {
	if (pad.getName().equals(nameX))
	padX = pad;
	if (pad.getName().equals(nameY))
	padY = pad;
	if (pad.getName().equals(nameZ))
	padZ = pad;
	if (pad.getShortname().equals(nameX))
	padX = pad;
	if (pad.getShortname().equals(nameY))
	padY = pad;
	if (pad.getShortname().equals(nameZ))
	padZ = pad;
	this.minExtensionX = minExtensionX;
	this.minExtensionY = minExtensionY;
	this.minExtensionZ = minExtensionZ;
	}
	}

	public static ArrayList<AbstractPadding> getPaddings() {
	ArrayList<AbstractPadding> pads = new ArrayList<AbstractPadding>();
	pads.add(new NoPadding());
	pads.add(new Multiple2Padding());
	pads.add(new Power2Padding());
	pads.add(new Multiple23Padding());
	pads.add(new Multiple235Padding());
	return pads;
	}

	public static ArrayList<String> getPaddingsName() {
	ArrayList<AbstractPadding> pads = getPaddings();
	ArrayList<String> names = new ArrayList<String>();
	for(AbstractPadding pad : pads)
	names.add(pad.getName());
	return names;
	}

	public static String[] getPaddingsAsArray() {
	ArrayList<AbstractPadding> pads = getPaddings();
	String names[] = new String[pads.size()];
	for(int i=0; i<pads.size(); i++)
	names[i] = pads.get(i).getName();
	return names;
	}

	public static AbstractPadding getByName(String name) {
	ArrayList<AbstractPadding> pads = getPaddings();
	for(AbstractPadding pad : pads)
	if (name.equals(pad.getName()))
	return pad;
	return getDefault();
	}

	public static AbstractPadding getByShortname(String name) {
	ArrayList<AbstractPadding> pads = getPaddings();
	for(AbstractPadding pad : pads)
	if (name.equals(pad.getShortname()))
	return pad;
	return getDefault();
	}


	public static AbstractPadding getDefault() {
	return new NoPadding();
	}

	public int[] pad(int nx, int ny, int nz) {
	return new int[] { padX.padding(nx+minExtensionX), padY.padding(ny+minExtensionY), padZ.padding(nz+minExtensionZ)};
	}

	public RealSignal pad(Monitors monitors, RealSignal input) {
	if (padX instanceof NoPadding && padY instanceof NoPadding &&
	padZ instanceof NoPadding && (minExtensionX + minExtensionY + minExtensionZ == 0)) {
	nx = ny = nz = -1;
	return input.duplicate();
	}
	nx = input.nx;
	ny = input.ny;
	nz = input.nz;

	int lx = padX.padding(nx+minExtensionX);
	int ly = padY.padding(ny+minExtensionY);
	int lz = padZ.padding(nz+minExtensionZ);
	monitors.log("Padding to (" + lx + ", " + ly + ", " + lz + ")");
	if (lx == nx)
	if (ly == ny)
	if (lz == nz)
	return input.duplicate();

	int ox = (lx - nx) / 2;
	int oy = (ly - ny) / 2;
	int oz = (lz - nz) / 2;
	String name = "pad(" + input.name + ")";
	RealSignal large = new RealSignal(name, lx, ly, lz);
	for(int k=0; k<nz; k++) {
	float in[] = input.data[k];
	float lpix[] = large.data[k+oz];
	for(int i=0; i<nx; i++)
	for(int j=0; j<ny; j++)
	lpix[(i+ox) + lx(j+oy)] = in[i + nxj];
	}
	return large;
	}

	public RealSignal crop(Monitors monitors, RealSignal large) {
	if (nx == -1 \|\| ny == -1 \|\| nz == -1) {
	return large.duplicate();
	}
	int lx = large.nx;
	int ly = large.ny;
	int lz = large.nz;
	int ox = (lx - nx) / 2;
	int oy = (ly - ny) / 2;
	int oz = (lz - nz) / 2;

	if (lx == nx)
	if (ly == ny)
	if (lz == nz)
	return large;

	String name = " crop( " + large.name + ")";

	RealSignal output = new RealSignal(name, nx, ny, nz);
	monitors.log("Cropping to (" + nx + ", " + ny + ", " + nz + ")");

	for(int k=0; k<nz; k++) {
	float lpix[] = large.data[k+oz];
	float out[] = output.data[k];
	for(int i=0; i<nx; i++)
	for(int j=0; j<ny; j++)
	out[i + nxj] = lpix[(i+ox) + lx(j+oy)];
	}
	return output;
	}

	@Override
	public String toString() {
	String s = "";
	s += "lateral (XY)";
	if (padX instanceof NoPadding) {
	if (minExtensionX == 0)
	s += " no padding";
	else
	s += " extension of " + minExtensionX;
	}
	else {
	s += " enforced to " + padX.getName();
	}

	s += ", axial (Z)";
	if (padZ instanceof NoPadding) {
	if (minExtensionZ == 0)
	s += " no padding";
	else
	s += " extension of " + minExtensionZ;
	}
	else {
	s += " enforced to " + padZ.getName();
	}

	return s;
	}
	}

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